Multiple sequence alignment - TraesCS3A01G490200

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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 TraesCS3A01G490200 chr3A 100.000 2309 0 0 1 2309 717900964 717903272 0.000000e+00 4265
1 TraesCS3A01G490200 chr3A 82.566 1216 184 22 245 1448 717852389 717851190 0.000000e+00 1046
2 TraesCS3A01G490200 chr3A 77.163 289 59 5 475 761 686725181 686724898 6.600000e-36 161
3 TraesCS3A01G490200 chr3B 90.030 2006 163 24 188 2169 786139066 786141058 0.000000e+00 2562
4 TraesCS3A01G490200 chr3B 83.251 1218 176 22 245 1448 785693285 785692082 0.000000e+00 1094
5 TraesCS3A01G490200 chr3B 94.805 154 7 1 2157 2309 786141071 786141224 2.960000e-59 239
6 TraesCS3A01G490200 chr3B 74.860 537 120 11 308 838 728810640 728810113 1.780000e-56 230
7 TraesCS3A01G490200 chr3D 85.580 638 92 0 207 844 587948098 587947461 0.000000e+00 669
8 TraesCS3A01G490200 chr3D 81.685 546 87 8 844 1380 587947380 587946839 2.110000e-120 442
9 TraesCS3A01G490200 chr3D 86.000 300 38 2 268 566 591709644 591709940 3.700000e-83 318
10 TraesCS3A01G490200 chr3D 92.746 193 13 1 1 192 388514960 388515152 6.280000e-71 278
11 TraesCS3A01G490200 chr3D 74.855 517 116 10 327 838 549373304 549372797 2.990000e-54 222
12 TraesCS3A01G490200 chr3D 79.310 261 29 13 2051 2309 588019274 588019511 2.370000e-35 159
13 TraesCS3A01G490200 chr5A 77.099 1048 197 27 209 1237 69999468 70000491 1.200000e-157 566
14 TraesCS3A01G490200 chr5A 95.312 192 6 2 1 190 446425956 446426146 3.730000e-78 302
15 TraesCS3A01G490200 chr5D 81.784 538 90 7 301 834 74735040 74735573 5.850000e-121 444
16 TraesCS3A01G490200 chr5D 76.481 574 124 9 266 835 559960281 559959715 3.730000e-78 302
17 TraesCS3A01G490200 chr5D 93.814 194 8 3 1 192 424820148 424820339 2.900000e-74 289
18 TraesCS3A01G490200 chr5D 83.721 129 21 0 963 1091 495548743 495548615 3.120000e-24 122
19 TraesCS3A01G490200 chr5D 76.500 200 44 1 942 1141 555065284 555065480 3.140000e-19 106
20 TraesCS3A01G490200 chr5D 79.856 139 28 0 942 1080 555558587 555558725 4.060000e-18 102
21 TraesCS3A01G490200 chrUn 79.565 460 86 6 300 758 287474429 287474881 2.860000e-84 322
22 TraesCS3A01G490200 chrUn 79.318 469 89 6 300 767 296159290 296158829 2.860000e-84 322
23 TraesCS3A01G490200 chr4A 77.932 503 102 7 265 764 604209584 604209088 2.880000e-79 305
24 TraesCS3A01G490200 chr4D 93.814 194 10 1 1 192 451681145 451681338 8.070000e-75 291
25 TraesCS3A01G490200 chr1D 93.750 192 10 1 1 190 236090273 236090082 1.040000e-73 287
26 TraesCS3A01G490200 chr2A 92.821 195 10 2 1 193 588428739 588428547 1.750000e-71 279
27 TraesCS3A01G490200 chr1A 93.229 192 10 2 1 190 544589153 544588963 1.750000e-71 279
28 TraesCS3A01G490200 chr7D 92.746 193 11 2 2 192 599718341 599718150 2.260000e-70 276
29 TraesCS3A01G490200 chr7A 92.708 192 12 1 1 190 667481244 667481053 2.260000e-70 276
30 TraesCS3A01G490200 chr5B 73.372 860 176 38 266 1091 695694398 695693558 1.050000e-68 270
31 TraesCS3A01G490200 chr5B 82.171 129 23 0 963 1091 695811308 695811180 6.740000e-21 111


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 TraesCS3A01G490200 chr3A 717900964 717903272 2308 False 4265.0 4265 100.0000 1 2309 1 chr3A.!!$F1 2308
1 TraesCS3A01G490200 chr3A 717851190 717852389 1199 True 1046.0 1046 82.5660 245 1448 1 chr3A.!!$R2 1203
2 TraesCS3A01G490200 chr3B 786139066 786141224 2158 False 1400.5 2562 92.4175 188 2309 2 chr3B.!!$F1 2121
3 TraesCS3A01G490200 chr3B 785692082 785693285 1203 True 1094.0 1094 83.2510 245 1448 1 chr3B.!!$R2 1203
4 TraesCS3A01G490200 chr3B 728810113 728810640 527 True 230.0 230 74.8600 308 838 1 chr3B.!!$R1 530
5 TraesCS3A01G490200 chr3D 587946839 587948098 1259 True 555.5 669 83.6325 207 1380 2 chr3D.!!$R2 1173
6 TraesCS3A01G490200 chr3D 549372797 549373304 507 True 222.0 222 74.8550 327 838 1 chr3D.!!$R1 511
7 TraesCS3A01G490200 chr5A 69999468 70000491 1023 False 566.0 566 77.0990 209 1237 1 chr5A.!!$F1 1028
8 TraesCS3A01G490200 chr5D 74735040 74735573 533 False 444.0 444 81.7840 301 834 1 chr5D.!!$F1 533
9 TraesCS3A01G490200 chr5D 559959715 559960281 566 True 302.0 302 76.4810 266 835 1 chr5D.!!$R2 569
10 TraesCS3A01G490200 chr5B 695693558 695694398 840 True 270.0 270 73.3720 266 1091 1 chr5B.!!$R1 825

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
603 604 0.319555 GGGCGAAAGACTTTTTGGGC 60.32 55.0 1.12 7.15 40.87 5.36 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1722 1868 0.039527 GCCGAATTGGTTGCGAAGTT 60.04 50.0 0.0 0.0 41.21 2.66 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
47 48 4.173659 GCGCGCGCTGTATTTTAG 57.826 55.556 44.38 11.16 38.26 1.85
48 49 1.998772 GCGCGCGCTGTATTTTAGC 60.999 57.895 44.38 17.67 38.26 3.09
53 54 4.589967 GCTGTATTTTAGCGCGGC 57.410 55.556 8.83 0.00 0.00 6.53
54 55 1.010013 GCTGTATTTTAGCGCGGCC 60.010 57.895 8.83 0.00 0.00 6.13
55 56 1.275657 CTGTATTTTAGCGCGGCCG 59.724 57.895 24.05 24.05 37.57 6.13
82 83 2.276368 CGCGCGCGCTCAATTTTA 60.276 55.556 45.97 0.00 39.32 1.52
83 84 1.861284 CGCGCGCGCTCAATTTTAA 60.861 52.632 45.97 0.00 39.32 1.52
84 85 1.618699 GCGCGCGCTCAATTTTAAC 59.381 52.632 44.38 13.88 38.26 2.01
85 86 1.893666 CGCGCGCTCAATTTTAACG 59.106 52.632 30.48 4.48 0.00 3.18
86 87 0.787908 CGCGCGCTCAATTTTAACGT 60.788 50.000 30.48 0.00 0.00 3.99
87 88 0.628289 GCGCGCTCAATTTTAACGTG 59.372 50.000 26.67 0.00 37.31 4.49
88 89 1.945207 CGCGCTCAATTTTAACGTGT 58.055 45.000 5.56 0.00 0.00 4.49
89 90 1.896193 CGCGCTCAATTTTAACGTGTC 59.104 47.619 5.56 0.00 0.00 3.67
90 91 2.411031 CGCGCTCAATTTTAACGTGTCT 60.411 45.455 5.56 0.00 0.00 3.41
91 92 2.902484 GCGCTCAATTTTAACGTGTCTG 59.098 45.455 0.00 0.00 0.00 3.51
92 93 2.902484 CGCTCAATTTTAACGTGTCTGC 59.098 45.455 0.00 0.00 0.00 4.26
93 94 3.363970 CGCTCAATTTTAACGTGTCTGCT 60.364 43.478 0.00 0.00 0.00 4.24
94 95 3.908382 GCTCAATTTTAACGTGTCTGCTG 59.092 43.478 0.00 0.00 0.00 4.41
95 96 4.466828 CTCAATTTTAACGTGTCTGCTGG 58.533 43.478 0.00 0.00 0.00 4.85
96 97 4.130857 TCAATTTTAACGTGTCTGCTGGA 58.869 39.130 0.00 0.00 0.00 3.86
97 98 4.213270 TCAATTTTAACGTGTCTGCTGGAG 59.787 41.667 0.00 0.00 0.00 3.86
98 99 1.508632 TTTAACGTGTCTGCTGGAGC 58.491 50.000 0.00 0.00 42.50 4.70
99 100 0.320421 TTAACGTGTCTGCTGGAGCC 60.320 55.000 0.00 0.00 41.18 4.70
100 101 1.468506 TAACGTGTCTGCTGGAGCCA 61.469 55.000 0.00 0.00 41.18 4.75
101 102 2.740055 CGTGTCTGCTGGAGCCAC 60.740 66.667 0.00 0.00 41.18 5.01
102 103 2.359230 GTGTCTGCTGGAGCCACC 60.359 66.667 0.00 0.00 41.18 4.61
103 104 4.007644 TGTCTGCTGGAGCCACCG 62.008 66.667 0.00 0.00 42.61 4.94
130 131 2.251371 GCGTCAAACCAGGCGAAC 59.749 61.111 0.00 0.00 0.00 3.95
131 132 2.549282 CGTCAAACCAGGCGAACG 59.451 61.111 0.00 0.00 0.00 3.95
132 133 2.943653 GTCAAACCAGGCGAACGG 59.056 61.111 0.00 0.00 0.00 4.44
133 134 2.975799 TCAAACCAGGCGAACGGC 60.976 61.111 12.58 12.58 42.51 5.68
134 135 3.283684 CAAACCAGGCGAACGGCA 61.284 61.111 21.28 0.00 46.16 5.69
135 136 3.284449 AAACCAGGCGAACGGCAC 61.284 61.111 21.28 0.00 46.16 5.01
149 150 2.255252 GCACGCGGCAAATGACTT 59.745 55.556 12.47 0.00 43.97 3.01
150 151 1.371635 GCACGCGGCAAATGACTTT 60.372 52.632 12.47 0.00 43.97 2.66
151 152 0.939106 GCACGCGGCAAATGACTTTT 60.939 50.000 12.47 0.00 43.97 2.27
152 153 1.486439 CACGCGGCAAATGACTTTTT 58.514 45.000 12.47 0.00 0.00 1.94
182 183 4.389576 GTTGCGCGGCTGTTGGAG 62.390 66.667 8.83 0.00 0.00 3.86
183 184 4.617520 TTGCGCGGCTGTTGGAGA 62.618 61.111 8.83 0.00 0.00 3.71
184 185 3.899981 TTGCGCGGCTGTTGGAGAT 62.900 57.895 8.83 0.00 0.00 2.75
185 186 3.869272 GCGCGGCTGTTGGAGATG 61.869 66.667 8.83 0.00 0.00 2.90
186 187 3.869272 CGCGGCTGTTGGAGATGC 61.869 66.667 0.00 0.00 0.00 3.91
221 222 6.039270 ACCAATCGATGAGAAACAAACTCAAA 59.961 34.615 0.00 0.00 45.44 2.69
259 260 9.002592 CAAAGCGTTTGATGATCTGACAGATCT 62.003 40.741 34.38 24.08 45.24 2.75
278 279 5.543405 AGATCTAGCAAGCCATCAGATAGTT 59.457 40.000 0.00 0.00 0.00 2.24
297 298 3.117663 AGTTTCCCACCTTGAGCTTGTTA 60.118 43.478 0.00 0.00 0.00 2.41
344 345 1.747444 ACTTGTTGGGATCTGGAGGT 58.253 50.000 0.00 0.00 0.00 3.85
383 384 1.508632 GACAACTGAGCAGCGGTTTA 58.491 50.000 1.49 0.00 43.52 2.01
500 501 5.871396 ACCTGATACGGATAATCAACACT 57.129 39.130 0.00 0.00 33.13 3.55
511 512 7.442969 ACGGATAATCAACACTTGTTCTAACAA 59.557 33.333 7.95 7.95 45.88 2.83
558 559 5.182950 CAGTACATGTCCAATGGCAACTTAA 59.817 40.000 0.00 0.00 37.61 1.85
595 596 1.073199 CACAAGGGGGCGAAAGACT 59.927 57.895 0.00 0.00 40.87 3.24
596 597 0.537371 CACAAGGGGGCGAAAGACTT 60.537 55.000 0.00 0.00 40.87 3.01
603 604 0.319555 GGGCGAAAGACTTTTTGGGC 60.320 55.000 1.12 7.15 40.87 5.36
768 769 5.627499 TTTTGGCATTGCAAGACTACTAG 57.373 39.130 11.39 0.00 0.00 2.57
771 772 4.905429 TGGCATTGCAAGACTACTAGAAA 58.095 39.130 11.39 0.00 0.00 2.52
772 773 5.500234 TGGCATTGCAAGACTACTAGAAAT 58.500 37.500 11.39 0.00 0.00 2.17
794 795 8.531622 AAATTGATGATAGCTCTGTATTCTCG 57.468 34.615 0.00 0.00 0.00 4.04
824 825 1.984020 TGGCACAACCGGCTACATA 59.016 52.632 0.00 0.00 43.94 2.29
845 938 8.688747 ACATATCACCAGGTACTTAGTACTAC 57.311 38.462 20.15 6.59 38.85 2.73
847 940 8.784994 CATATCACCAGGTACTTAGTACTACTG 58.215 40.741 20.15 18.12 38.85 2.74
851 944 6.827251 CACCAGGTACTTAGTACTACTGATCA 59.173 42.308 21.84 0.00 38.85 2.92
852 945 7.502895 CACCAGGTACTTAGTACTACTGATCAT 59.497 40.741 21.84 8.53 38.85 2.45
853 946 7.720515 ACCAGGTACTTAGTACTACTGATCATC 59.279 40.741 21.84 5.56 38.85 2.92
869 962 5.354767 TGATCATCTTGCTCAGTGTATCAC 58.645 41.667 0.00 0.00 34.10 3.06
870 963 4.128925 TCATCTTGCTCAGTGTATCACC 57.871 45.455 0.00 0.00 34.49 4.02
888 984 3.949113 TCACCTTTTGTTAAGCCGTCTTT 59.051 39.130 0.00 0.00 33.85 2.52
907 1023 7.234384 CGTCTTTACTGTTATTGACCAATCAC 58.766 38.462 0.00 0.00 33.38 3.06
908 1024 7.095397 CGTCTTTACTGTTATTGACCAATCACA 60.095 37.037 8.80 8.80 34.75 3.58
915 1031 8.084073 ACTGTTATTGACCAATCACATTGAAAG 58.916 33.333 9.38 2.01 42.83 2.62
961 1083 1.618837 CAGAGTATGGGTCGTATGGGG 59.381 57.143 0.00 0.00 0.00 4.96
994 1116 3.660501 AGAGCGATGTGTTCAGTTACA 57.339 42.857 0.00 0.00 0.00 2.41
1145 1279 1.002366 CTACTGCAATGCTCCGACAC 58.998 55.000 6.82 0.00 0.00 3.67
1177 1311 4.465632 TTTCTTGCGCCAATACTAGAGA 57.534 40.909 4.18 0.00 0.00 3.10
1317 1451 1.965930 GTCACAGTGATTGGCCGCA 60.966 57.895 6.51 0.00 0.00 5.69
1371 1509 6.405842 GGAGAAAGAAAAAGAAAAGGTGAGCA 60.406 38.462 0.00 0.00 0.00 4.26
1400 1538 7.906199 ATATCTGGATATACTTGGTAGCCTC 57.094 40.000 1.67 0.00 32.55 4.70
1403 1541 6.143915 TCTGGATATACTTGGTAGCCTCTTT 58.856 40.000 0.00 0.00 0.00 2.52
1406 1544 7.054124 TGGATATACTTGGTAGCCTCTTTTTG 58.946 38.462 0.00 0.00 0.00 2.44
1418 1556 5.976458 AGCCTCTTTTTGTTTTGTTCATCA 58.024 33.333 0.00 0.00 0.00 3.07
1437 1576 2.230508 TCAGAACGATTTGCTACCGACT 59.769 45.455 0.00 0.00 0.00 4.18
1451 1590 2.427506 ACCGACTTTGGAGCTGAAATC 58.572 47.619 0.00 0.00 0.00 2.17
1453 1592 2.675348 CCGACTTTGGAGCTGAAATCTC 59.325 50.000 0.00 0.00 0.00 2.75
1455 1594 3.370366 CGACTTTGGAGCTGAAATCTCTG 59.630 47.826 0.00 0.00 0.00 3.35
1500 1646 9.868277 TTTTTGTTTCATTTCTGAGTGTATTGT 57.132 25.926 0.00 0.00 31.68 2.71
1579 1725 7.328277 ACTTGCACACTTACTATTGTTTTGA 57.672 32.000 0.00 0.00 0.00 2.69
1587 1733 7.936847 ACACTTACTATTGTTTTGAGGACATGA 59.063 33.333 0.00 0.00 0.00 3.07
1722 1868 6.191657 ACTTCAATCCATATCATGCTACCA 57.808 37.500 0.00 0.00 0.00 3.25
1734 1880 0.179043 TGCTACCAACTTCGCAACCA 60.179 50.000 0.00 0.00 0.00 3.67
1741 1887 0.039527 AACTTCGCAACCAATTCGGC 60.040 50.000 0.00 0.00 39.03 5.54
1742 1888 1.169661 ACTTCGCAACCAATTCGGCA 61.170 50.000 0.00 0.00 39.03 5.69
1770 1916 0.178967 TTTGCTTCAGGGCCACATGA 60.179 50.000 6.18 2.17 0.00 3.07
1782 1928 0.109643 CCACATGACATGCACAACCG 60.110 55.000 15.49 0.00 0.00 4.44
1799 1945 6.265577 CACAACCGTTCTTGAGAAAGAAAAT 58.734 36.000 8.02 0.00 40.15 1.82
1800 1946 6.197096 CACAACCGTTCTTGAGAAAGAAAATG 59.803 38.462 8.02 3.45 40.15 2.32
1801 1947 5.438761 ACCGTTCTTGAGAAAGAAAATGG 57.561 39.130 8.02 7.78 40.15 3.16
1802 1948 5.130350 ACCGTTCTTGAGAAAGAAAATGGA 58.870 37.500 16.20 0.00 40.15 3.41
1805 1951 6.638468 CCGTTCTTGAGAAAGAAAATGGAAAG 59.362 38.462 8.02 0.00 40.15 2.62
1808 1954 8.624776 GTTCTTGAGAAAGAAAATGGAAAGAGA 58.375 33.333 2.63 0.00 40.15 3.10
1809 1955 8.930846 TCTTGAGAAAGAAAATGGAAAGAGAT 57.069 30.769 0.00 0.00 0.00 2.75
1811 1957 8.696043 TTGAGAAAGAAAATGGAAAGAGATGA 57.304 30.769 0.00 0.00 0.00 2.92
1812 1958 8.332996 TGAGAAAGAAAATGGAAAGAGATGAG 57.667 34.615 0.00 0.00 0.00 2.90
1844 1994 0.895530 GGACACAGGCTGTAGCACTA 59.104 55.000 21.59 0.00 44.36 2.74
1845 1995 1.275291 GGACACAGGCTGTAGCACTAA 59.725 52.381 21.59 0.00 44.36 2.24
1846 1996 2.611518 GACACAGGCTGTAGCACTAAG 58.388 52.381 21.59 7.83 44.36 2.18
1847 1997 1.971357 ACACAGGCTGTAGCACTAAGT 59.029 47.619 21.59 8.53 44.36 2.24
1849 1999 2.996621 CACAGGCTGTAGCACTAAGTTC 59.003 50.000 21.59 0.00 44.36 3.01
1850 2000 2.263077 CAGGCTGTAGCACTAAGTTCG 58.737 52.381 6.28 0.00 44.36 3.95
1925 2077 0.093535 CATGTGTGCTTCGTACTGCG 59.906 55.000 0.00 0.00 43.01 5.18
1931 2083 0.856641 TGCTTCGTACTGCGTGAAAC 59.143 50.000 0.00 0.00 42.13 2.78
1958 2110 6.124088 ACACAAAATGTTCACAGAGAAGTC 57.876 37.500 0.00 0.00 38.98 3.01
1964 2116 2.224281 TGTTCACAGAGAAGTCGGCATT 60.224 45.455 0.00 0.00 36.78 3.56
1986 2139 9.130312 GCATTATGTCGATCTAACTAAACCTAG 57.870 37.037 0.00 0.00 0.00 3.02
1999 2152 6.964876 ACTAAACCTAGAAAACAGGGGTAT 57.035 37.500 0.00 0.00 37.51 2.73
2070 2223 7.533426 GGCAGTCATATAAGCCAATATTTCAG 58.467 38.462 0.00 0.00 46.26 3.02
2082 2235 8.121305 AGCCAATATTTCAGTTGTACAATCAA 57.879 30.769 12.26 2.34 0.00 2.57
2106 2259 8.773645 CAAGAAAAATGCCGAGTATATGTCATA 58.226 33.333 0.00 0.00 0.00 2.15
2108 2261 8.939929 AGAAAAATGCCGAGTATATGTCATATG 58.060 33.333 14.54 0.00 0.00 1.78
2126 2280 5.989168 TCATATGGTAGTATGCTGGAAAACG 59.011 40.000 2.13 0.00 33.15 3.60
2130 2284 2.851263 AGTATGCTGGAAAACGGACA 57.149 45.000 0.00 0.00 0.00 4.02
2137 2291 3.243367 TGCTGGAAAACGGACAGAATTTG 60.243 43.478 0.00 0.00 34.21 2.32
2148 2302 2.887152 GACAGAATTTGCAGGACAAGGT 59.113 45.455 0.00 0.00 40.06 3.50
2155 2309 3.719268 TTGCAGGACAAGGTGTATGAT 57.281 42.857 0.00 0.00 33.24 2.45
2180 2359 5.041191 ACCCTCATAATGCTTTACAGAGG 57.959 43.478 22.99 22.99 39.94 3.69
2190 2369 3.075148 GCTTTACAGAGGGGAAAGTGTC 58.925 50.000 1.42 0.00 33.58 3.67
2199 2378 3.104512 AGGGGAAAGTGTCGATGTATCA 58.895 45.455 0.00 0.00 0.00 2.15
2244 2423 7.929941 AACCTTGATTCCTAGAGATGAAAAC 57.070 36.000 0.00 0.00 0.00 2.43
2256 2435 8.077386 CCTAGAGATGAAAACTAACCTCGATAC 58.923 40.741 0.00 0.00 0.00 2.24
2266 2445 9.675464 AAAACTAACCTCGATACCAAATCATTA 57.325 29.630 0.00 0.00 0.00 1.90
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
10 11 4.215965 CGCTAAACAGTGCGTACATTTTT 58.784 39.130 6.38 4.58 46.09 1.94
11 12 3.805823 CGCTAAACAGTGCGTACATTTT 58.194 40.909 6.38 7.04 46.09 1.82
12 13 3.449322 CGCTAAACAGTGCGTACATTT 57.551 42.857 6.38 8.60 46.09 2.32
30 31 1.998772 GCTAAAATACAGCGCGCGC 60.999 57.895 45.10 45.10 42.33 6.86
31 32 4.173659 GCTAAAATACAGCGCGCG 57.826 55.556 28.44 28.44 0.00 6.86
36 37 1.010013 GGCCGCGCTAAAATACAGC 60.010 57.895 5.56 0.00 35.61 4.40
37 38 1.275657 CGGCCGCGCTAAAATACAG 59.724 57.895 14.67 0.00 0.00 2.74
38 39 2.815298 GCGGCCGCGCTAAAATACA 61.815 57.895 37.24 0.00 0.00 2.29
39 40 2.052502 GCGGCCGCGCTAAAATAC 60.053 61.111 37.24 5.14 0.00 1.89
66 67 1.618699 GTTAAAATTGAGCGCGCGC 59.381 52.632 45.10 45.10 42.33 6.86
67 68 0.787908 ACGTTAAAATTGAGCGCGCG 60.788 50.000 28.44 28.44 0.00 6.86
68 69 0.628289 CACGTTAAAATTGAGCGCGC 59.372 50.000 26.66 26.66 0.00 6.86
69 70 1.896193 GACACGTTAAAATTGAGCGCG 59.104 47.619 0.00 0.00 0.00 6.86
70 71 2.902484 CAGACACGTTAAAATTGAGCGC 59.098 45.455 0.00 0.00 0.00 5.92
71 72 2.902484 GCAGACACGTTAAAATTGAGCG 59.098 45.455 0.00 0.00 0.00 5.03
72 73 3.908382 CAGCAGACACGTTAAAATTGAGC 59.092 43.478 0.00 0.00 0.00 4.26
73 74 4.213270 TCCAGCAGACACGTTAAAATTGAG 59.787 41.667 0.00 0.00 0.00 3.02
74 75 4.130857 TCCAGCAGACACGTTAAAATTGA 58.869 39.130 0.00 0.00 0.00 2.57
75 76 4.466828 CTCCAGCAGACACGTTAAAATTG 58.533 43.478 0.00 0.00 0.00 2.32
76 77 3.058224 GCTCCAGCAGACACGTTAAAATT 60.058 43.478 0.00 0.00 41.59 1.82
77 78 2.484264 GCTCCAGCAGACACGTTAAAAT 59.516 45.455 0.00 0.00 41.59 1.82
78 79 1.871039 GCTCCAGCAGACACGTTAAAA 59.129 47.619 0.00 0.00 41.59 1.52
79 80 1.508632 GCTCCAGCAGACACGTTAAA 58.491 50.000 0.00 0.00 41.59 1.52
80 81 0.320421 GGCTCCAGCAGACACGTTAA 60.320 55.000 0.03 0.00 44.36 2.01
81 82 1.292223 GGCTCCAGCAGACACGTTA 59.708 57.895 0.03 0.00 44.36 3.18
82 83 2.031163 GGCTCCAGCAGACACGTT 59.969 61.111 0.03 0.00 44.36 3.99
83 84 3.233980 TGGCTCCAGCAGACACGT 61.234 61.111 0.03 0.00 44.36 4.49
86 87 4.007644 CGGTGGCTCCAGCAGACA 62.008 66.667 17.07 0.00 43.82 3.41
112 113 3.342627 TTCGCCTGGTTTGACGCG 61.343 61.111 3.53 3.53 45.76 6.01
113 114 2.251371 GTTCGCCTGGTTTGACGC 59.749 61.111 0.00 0.00 0.00 5.19
114 115 2.549282 CGTTCGCCTGGTTTGACG 59.451 61.111 0.00 0.00 0.00 4.35
115 116 2.943653 CCGTTCGCCTGGTTTGAC 59.056 61.111 0.00 0.00 0.00 3.18
116 117 2.975799 GCCGTTCGCCTGGTTTGA 60.976 61.111 0.00 0.00 0.00 2.69
117 118 3.283684 TGCCGTTCGCCTGGTTTG 61.284 61.111 0.00 0.00 36.24 2.93
118 119 3.284449 GTGCCGTTCGCCTGGTTT 61.284 61.111 0.00 0.00 36.24 3.27
127 128 4.398598 ATTTGCCGCGTGCCGTTC 62.399 61.111 15.40 0.00 40.16 3.95
128 129 4.698651 CATTTGCCGCGTGCCGTT 62.699 61.111 15.40 0.00 40.16 4.44
131 132 2.747507 AAAGTCATTTGCCGCGTGCC 62.748 55.000 15.40 0.00 40.16 5.01
132 133 0.939106 AAAAGTCATTTGCCGCGTGC 60.939 50.000 4.92 9.16 41.77 5.34
133 134 1.486439 AAAAAGTCATTTGCCGCGTG 58.514 45.000 4.92 0.00 0.00 5.34
134 135 3.957383 AAAAAGTCATTTGCCGCGT 57.043 42.105 4.92 0.00 0.00 6.01
165 166 4.389576 CTCCAACAGCCGCGCAAC 62.390 66.667 8.75 0.00 0.00 4.17
166 167 3.899981 ATCTCCAACAGCCGCGCAA 62.900 57.895 8.75 0.00 0.00 4.85
167 168 4.393155 ATCTCCAACAGCCGCGCA 62.393 61.111 8.75 0.00 0.00 6.09
168 169 3.869272 CATCTCCAACAGCCGCGC 61.869 66.667 0.00 0.00 0.00 6.86
169 170 3.869272 GCATCTCCAACAGCCGCG 61.869 66.667 0.00 0.00 0.00 6.46
170 171 2.437359 AGCATCTCCAACAGCCGC 60.437 61.111 0.00 0.00 0.00 6.53
171 172 3.805267 GAGCATCTCCAACAGCCG 58.195 61.111 0.00 0.00 0.00 5.52
182 183 7.539436 TCATCGATTGGTAGTATAAGAGCATC 58.461 38.462 0.00 0.00 0.00 3.91
183 184 7.394641 TCTCATCGATTGGTAGTATAAGAGCAT 59.605 37.037 0.00 0.00 0.00 3.79
184 185 6.715264 TCTCATCGATTGGTAGTATAAGAGCA 59.285 38.462 0.00 0.00 0.00 4.26
185 186 7.147143 TCTCATCGATTGGTAGTATAAGAGC 57.853 40.000 0.00 0.00 0.00 4.09
186 187 9.400638 GTTTCTCATCGATTGGTAGTATAAGAG 57.599 37.037 0.00 0.00 0.00 2.85
221 222 6.325919 TCAAACGCTTTGATCATACCTTTT 57.674 33.333 0.00 0.00 44.21 2.27
259 260 4.444876 GGGAAACTATCTGATGGCTTGCTA 60.445 45.833 8.16 0.00 0.00 3.49
278 279 3.586470 TTAACAAGCTCAAGGTGGGAA 57.414 42.857 0.00 0.00 0.00 3.97
344 345 5.954757 TGTCCCTTAAATACCTTTCCACAA 58.045 37.500 0.00 0.00 0.00 3.33
383 384 4.892934 TCAAGAACCTTTATTGCAACCACT 59.107 37.500 0.00 0.00 0.00 4.00
500 501 5.179368 CGCTCTGAAATCCTTGTTAGAACAA 59.821 40.000 7.56 7.56 45.88 2.83
511 512 1.072331 ACACCAACGCTCTGAAATCCT 59.928 47.619 0.00 0.00 0.00 3.24
558 559 3.384789 TGTGAGTAGTGAAGCAGTGTCTT 59.615 43.478 0.00 0.00 0.00 3.01
603 604 3.764466 ACCCAGCCTCTCGCGAAG 61.764 66.667 11.33 10.63 44.76 3.79
683 684 1.267806 CTTGGCTTCAAGTCGCAATGT 59.732 47.619 0.00 0.00 42.07 2.71
768 769 8.646356 CGAGAATACAGAGCTATCATCAATTTC 58.354 37.037 0.00 0.00 0.00 2.17
771 772 7.459795 TCGAGAATACAGAGCTATCATCAAT 57.540 36.000 0.00 0.00 0.00 2.57
772 773 6.884280 TCGAGAATACAGAGCTATCATCAA 57.116 37.500 0.00 0.00 0.00 2.57
794 795 2.466846 GTTGTGCCATGCATGCTTATC 58.533 47.619 21.69 9.40 41.91 1.75
815 816 2.891580 AGTACCTGGTGATATGTAGCCG 59.108 50.000 10.23 0.00 0.00 5.52
824 825 6.966751 TCAGTAGTACTAAGTACCTGGTGAT 58.033 40.000 10.23 0.00 39.58 3.06
847 940 4.749099 GGTGATACACTGAGCAAGATGATC 59.251 45.833 0.00 0.00 34.40 2.92
851 944 4.833478 AAGGTGATACACTGAGCAAGAT 57.167 40.909 0.00 0.00 34.40 2.40
852 945 4.623932 AAAGGTGATACACTGAGCAAGA 57.376 40.909 0.00 0.00 34.40 3.02
853 946 4.516698 ACAAAAGGTGATACACTGAGCAAG 59.483 41.667 0.00 0.00 34.40 4.01
869 962 5.008316 ACAGTAAAGACGGCTTAACAAAAGG 59.992 40.000 2.54 0.00 32.98 3.11
870 963 6.056428 ACAGTAAAGACGGCTTAACAAAAG 57.944 37.500 2.54 0.00 32.98 2.27
888 984 8.628630 TTCAATGTGATTGGTCAATAACAGTA 57.371 30.769 16.32 5.05 43.39 2.74
961 1083 1.350193 TCGCTCTTTCGTGATGCTTC 58.650 50.000 0.00 0.00 0.00 3.86
994 1116 4.840716 AGACTTCAAGGAGCATGATTCT 57.159 40.909 0.00 0.00 0.00 2.40
1145 1279 1.685302 CGCAAGAAAACCAATGTCCG 58.315 50.000 0.00 0.00 43.02 4.79
1177 1311 1.999648 TTGGAGCAGAGCAAACCAAT 58.000 45.000 0.00 0.00 35.25 3.16
1380 1518 6.426646 AAAGAGGCTACCAAGTATATCCAG 57.573 41.667 0.00 0.00 0.00 3.86
1387 1525 6.378848 ACAAAACAAAAAGAGGCTACCAAGTA 59.621 34.615 0.00 0.00 0.00 2.24
1418 1556 3.314541 AAGTCGGTAGCAAATCGTTCT 57.685 42.857 0.00 0.00 0.00 3.01
1437 1576 4.090761 ACACAGAGATTTCAGCTCCAAA 57.909 40.909 0.00 0.00 32.82 3.28
1451 1590 4.641094 AGGATACCGACTAAGAACACAGAG 59.359 45.833 0.00 0.00 37.17 3.35
1453 1592 4.985538 AGGATACCGACTAAGAACACAG 57.014 45.455 0.00 0.00 37.17 3.66
1455 1594 6.426025 ACAAAAAGGATACCGACTAAGAACAC 59.574 38.462 0.00 0.00 37.17 3.32
1500 1646 2.965572 GCTGCTGGCATAAAATTGGA 57.034 45.000 0.00 0.00 41.35 3.53
1579 1725 9.388506 CAAAGAAAGTGATACTATTCATGTCCT 57.611 33.333 0.00 0.00 0.00 3.85
1587 1733 7.665559 TGAACCAGCAAAGAAAGTGATACTATT 59.334 33.333 0.00 0.00 0.00 1.73
1630 1776 5.769484 TTTTTACATTTGCCACGGTAAGA 57.231 34.783 0.00 0.00 0.00 2.10
1657 1803 6.983307 ACGATGAGAATTTAGACAAGGAGATG 59.017 38.462 0.00 0.00 0.00 2.90
1658 1804 7.118496 ACGATGAGAATTTAGACAAGGAGAT 57.882 36.000 0.00 0.00 0.00 2.75
1659 1805 6.531503 ACGATGAGAATTTAGACAAGGAGA 57.468 37.500 0.00 0.00 0.00 3.71
1660 1806 8.879342 ATTACGATGAGAATTTAGACAAGGAG 57.121 34.615 0.00 0.00 0.00 3.69
1722 1868 0.039527 GCCGAATTGGTTGCGAAGTT 60.040 50.000 0.00 0.00 41.21 2.66
1770 1916 1.603802 CTCAAGAACGGTTGTGCATGT 59.396 47.619 0.00 0.00 0.00 3.21
1782 1928 8.624776 TCTCTTTCCATTTTCTTTCTCAAGAAC 58.375 33.333 0.00 0.00 46.71 3.01
1808 1954 9.236006 GCCTGTGTCCAAATTATATATTCTCAT 57.764 33.333 0.00 0.00 0.00 2.90
1809 1955 8.439971 AGCCTGTGTCCAAATTATATATTCTCA 58.560 33.333 0.00 0.00 0.00 3.27
1811 1957 8.220559 ACAGCCTGTGTCCAAATTATATATTCT 58.779 33.333 0.00 0.00 31.90 2.40
1812 1958 8.396272 ACAGCCTGTGTCCAAATTATATATTC 57.604 34.615 0.00 0.00 31.90 1.75
1844 1994 6.676950 TGCAAATCATTATGTTGACGAACTT 58.323 32.000 0.00 0.00 32.79 2.66
1845 1995 6.252967 TGCAAATCATTATGTTGACGAACT 57.747 33.333 0.00 0.00 32.79 3.01
1846 1996 6.183359 GGTTGCAAATCATTATGTTGACGAAC 60.183 38.462 0.00 0.00 0.00 3.95
1847 1997 5.861251 GGTTGCAAATCATTATGTTGACGAA 59.139 36.000 0.00 0.00 0.00 3.85
1849 1999 5.159925 TGGTTGCAAATCATTATGTTGACG 58.840 37.500 0.00 0.00 27.25 4.35
1850 2000 6.158598 ACTGGTTGCAAATCATTATGTTGAC 58.841 36.000 0.00 0.00 35.64 3.18
1891 2043 3.690628 CACACATGGCAGAATGATACACA 59.309 43.478 0.00 0.00 39.69 3.72
1896 2048 2.139323 AGCACACATGGCAGAATGAT 57.861 45.000 0.00 0.00 39.69 2.45
1958 2110 6.128902 GGTTTAGTTAGATCGACATAATGCCG 60.129 42.308 0.00 0.00 0.00 5.69
1977 2130 8.087303 ACTATACCCCTGTTTTCTAGGTTTAG 57.913 38.462 0.00 0.00 37.83 1.85
1999 2152 6.660521 TGTTGTCCTCCGTAAGAGATAAACTA 59.339 38.462 0.00 0.00 46.50 2.24
2070 2223 5.918011 TCGGCATTTTTCTTGATTGTACAAC 59.082 36.000 11.22 5.88 0.00 3.32
2082 2235 8.939929 CATATGACATATACTCGGCATTTTTCT 58.060 33.333 7.64 0.00 0.00 2.52
2106 2259 3.199071 TCCGTTTTCCAGCATACTACCAT 59.801 43.478 0.00 0.00 0.00 3.55
2108 2261 2.934553 GTCCGTTTTCCAGCATACTACC 59.065 50.000 0.00 0.00 0.00 3.18
2126 2280 2.229784 CCTTGTCCTGCAAATTCTGTCC 59.770 50.000 0.00 0.00 36.53 4.02
2130 2284 2.949447 ACACCTTGTCCTGCAAATTCT 58.051 42.857 0.00 0.00 36.53 2.40
2137 2291 4.335594 GGTTTATCATACACCTTGTCCTGC 59.664 45.833 0.00 0.00 0.00 4.85
2148 2302 8.995027 AAAGCATTATGAGGGTTTATCATACA 57.005 30.769 0.00 0.00 38.92 2.29
2155 2309 7.054124 CCTCTGTAAAGCATTATGAGGGTTTA 58.946 38.462 18.18 2.85 38.98 2.01
2180 2359 5.007724 GGAAATGATACATCGACACTTTCCC 59.992 44.000 0.00 0.00 36.15 3.97
2190 2369 5.764686 TCCTTTCCATGGAAATGATACATCG 59.235 40.000 34.40 21.03 42.34 3.84
2234 2413 6.570692 TGGTATCGAGGTTAGTTTTCATCTC 58.429 40.000 0.00 0.00 0.00 2.75
2239 2418 7.605410 TGATTTGGTATCGAGGTTAGTTTTC 57.395 36.000 0.00 0.00 0.00 2.29
2244 2423 9.104965 TGTTTAATGATTTGGTATCGAGGTTAG 57.895 33.333 0.00 0.00 0.00 2.34
2256 2435 6.983307 TGTTTGTGGAGTGTTTAATGATTTGG 59.017 34.615 0.00 0.00 0.00 3.28


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

AutoCloner maintained by Alex Coulton.