Multiple sequence alignment - TraesCS7A01G158300

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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 TraesCS7A01G158300 chr7A 100.000 2352 0 0 352 2703 113370288 113372639 0.000000e+00 4344.0
1 TraesCS7A01G158300 chr7A 92.067 416 31 2 1094 1508 93260967 93260553 3.880000e-163 584.0
2 TraesCS7A01G158300 chr7A 93.162 117 8 0 1932 2048 26547869 26547753 3.580000e-39 172.0
3 TraesCS7A01G158300 chr7A 91.453 117 10 0 1932 2048 307374790 307374674 7.740000e-36 161.0
4 TraesCS7A01G158300 chr7A 89.062 128 7 5 1801 1922 314252341 314252215 4.660000e-33 152.0
5 TraesCS7A01G158300 chr7A 88.281 128 7 6 1802 1922 734198412 734198286 2.170000e-31 147.0
6 TraesCS7A01G158300 chr7A 88.281 128 7 6 1802 1922 734202396 734202270 2.170000e-31 147.0
7 TraesCS7A01G158300 chr7A 100.000 43 0 0 1 43 113369937 113369979 2.230000e-11 80.5
8 TraesCS7A01G158300 chr7D 92.063 1134 73 12 390 1510 108411820 108412949 0.000000e+00 1580.0
9 TraesCS7A01G158300 chr7D 88.738 1101 73 24 701 1758 108085192 108086284 0.000000e+00 1299.0
10 TraesCS7A01G158300 chr7D 90.501 758 59 7 1932 2684 108414010 108414759 0.000000e+00 989.0
11 TraesCS7A01G158300 chr7D 92.048 415 31 2 1095 1508 91699846 91699433 1.390000e-162 582.0
12 TraesCS7A01G158300 chr7D 94.604 278 12 3 1523 1798 108413312 108413588 6.920000e-116 427.0
13 TraesCS7A01G158300 chr7D 100.000 88 0 0 1523 1610 108413218 108413305 2.150000e-36 163.0
14 TraesCS7A01G158300 chr7B 85.650 1331 115 47 444 1736 66978080 66979372 0.000000e+00 1330.0
15 TraesCS7A01G158300 chr7B 85.227 968 88 29 753 1692 67807844 67808784 0.000000e+00 944.0
16 TraesCS7A01G158300 chr7B 92.048 415 31 2 1095 1508 63934977 63935390 1.390000e-162 582.0
17 TraesCS7A01G158300 chr7B 92.920 113 8 0 1936 2048 455019463 455019351 5.990000e-37 165.0
18 TraesCS7A01G158300 chr1B 91.872 406 31 2 1095 1499 434409083 434409487 1.400000e-157 566.0
19 TraesCS7A01G158300 chr1D 91.084 415 35 2 1095 1508 321704951 321704538 6.540000e-156 560.0
20 TraesCS7A01G158300 chr4B 93.162 117 8 0 1932 2048 104440038 104440154 3.580000e-39 172.0
21 TraesCS7A01G158300 chr5B 92.308 117 9 0 1932 2048 212786808 212786924 1.660000e-37 167.0
22 TraesCS7A01G158300 chr5A 91.453 117 10 0 1932 2048 494285394 494285278 7.740000e-36 161.0
23 TraesCS7A01G158300 chr3B 91.453 117 10 0 1932 2048 217156911 217156795 7.740000e-36 161.0
24 TraesCS7A01G158300 chr3B 82.482 137 16 8 2477 2610 547562157 547562026 2.200000e-21 113.0
25 TraesCS7A01G158300 chr2B 91.453 117 10 0 1932 2048 57417517 57417401 7.740000e-36 161.0
26 TraesCS7A01G158300 chr2A 89.062 128 7 6 1801 1922 390406497 390406623 4.660000e-33 152.0
27 TraesCS7A01G158300 chr2A 88.372 129 7 6 1801 1922 427065076 427065203 6.030000e-32 148.0
28 TraesCS7A01G158300 chr2A 80.714 140 17 9 2476 2610 710046880 710047014 1.710000e-17 100.0
29 TraesCS7A01G158300 chr6A 86.301 146 8 9 1801 1935 88860655 88860799 6.030000e-32 148.0
30 TraesCS7A01G158300 chr4A 88.372 129 7 6 1801 1922 448887871 448887744 6.030000e-32 148.0
31 TraesCS7A01G158300 chrUn 88.281 128 7 6 1802 1922 272230554 272230428 2.170000e-31 147.0
32 TraesCS7A01G158300 chrUn 88.281 128 7 6 1802 1922 279336036 279335910 2.170000e-31 147.0


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 TraesCS7A01G158300 chr7A 113369937 113372639 2702 False 2212.25 4344 100.000 1 2703 2 chr7A.!!$F1 2702
1 TraesCS7A01G158300 chr7D 108085192 108086284 1092 False 1299.00 1299 88.738 701 1758 1 chr7D.!!$F1 1057
2 TraesCS7A01G158300 chr7D 108411820 108414759 2939 False 789.75 1580 94.292 390 2684 4 chr7D.!!$F2 2294
3 TraesCS7A01G158300 chr7B 66978080 66979372 1292 False 1330.00 1330 85.650 444 1736 1 chr7B.!!$F2 1292
4 TraesCS7A01G158300 chr7B 67807844 67808784 940 False 944.00 944 85.227 753 1692 1 chr7B.!!$F3 939

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
771 790 0.691078 ACGAGACCCCAGCCATATGT 60.691 55.0 1.24 0.0 0.0 2.29 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1785 2192 0.391228 TTCACCGCTGTAGCAAGACA 59.609 50.0 4.59 0.0 42.21 3.41 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
25 26 6.716934 AGACTAACATATGTGTCCTACCTG 57.283 41.667 18.06 2.73 37.67 4.00
26 27 6.195700 AGACTAACATATGTGTCCTACCTGT 58.804 40.000 18.06 5.21 37.67 4.00
27 28 6.321690 AGACTAACATATGTGTCCTACCTGTC 59.678 42.308 18.06 11.67 37.67 3.51
28 29 5.955959 ACTAACATATGTGTCCTACCTGTCA 59.044 40.000 9.63 0.00 37.67 3.58
29 30 5.344743 AACATATGTGTCCTACCTGTCAG 57.655 43.478 9.63 0.00 37.67 3.51
30 31 4.353777 ACATATGTGTCCTACCTGTCAGT 58.646 43.478 7.78 0.00 31.41 3.41
31 32 4.160439 ACATATGTGTCCTACCTGTCAGTG 59.840 45.833 7.78 0.00 31.41 3.66
32 33 1.338107 TGTGTCCTACCTGTCAGTGG 58.662 55.000 0.00 0.00 0.00 4.00
33 34 1.133294 TGTGTCCTACCTGTCAGTGGA 60.133 52.381 0.00 1.08 0.00 4.02
34 35 2.180276 GTGTCCTACCTGTCAGTGGAT 58.820 52.381 8.93 0.00 0.00 3.41
35 36 2.166664 GTGTCCTACCTGTCAGTGGATC 59.833 54.545 8.93 0.00 0.00 3.36
36 37 2.225267 TGTCCTACCTGTCAGTGGATCA 60.225 50.000 8.93 7.09 0.00 2.92
37 38 2.166664 GTCCTACCTGTCAGTGGATCAC 59.833 54.545 8.93 0.00 34.10 3.06
38 39 2.179427 CCTACCTGTCAGTGGATCACA 58.821 52.381 0.00 0.00 36.74 3.58
368 369 4.504132 GATGAAGCTTCGACGGCT 57.496 55.556 21.11 6.29 42.31 5.52
369 370 2.002127 GATGAAGCTTCGACGGCTG 58.998 57.895 21.11 0.00 40.19 4.85
370 371 2.029904 GATGAAGCTTCGACGGCTGC 62.030 60.000 21.11 10.91 40.19 5.25
371 372 3.491652 GAAGCTTCGACGGCTGCC 61.492 66.667 11.40 9.11 40.19 4.85
372 373 3.941657 GAAGCTTCGACGGCTGCCT 62.942 63.158 17.92 3.54 40.19 4.75
373 374 2.558554 GAAGCTTCGACGGCTGCCTA 62.559 60.000 17.92 0.00 40.19 3.93
374 375 2.837371 AAGCTTCGACGGCTGCCTAC 62.837 60.000 17.92 9.35 40.19 3.18
375 376 2.571757 CTTCGACGGCTGCCTACA 59.428 61.111 17.92 0.00 0.00 2.74
376 377 1.141881 CTTCGACGGCTGCCTACAT 59.858 57.895 17.92 0.00 0.00 2.29
377 378 1.148157 CTTCGACGGCTGCCTACATG 61.148 60.000 17.92 2.80 0.00 3.21
378 379 3.264897 CGACGGCTGCCTACATGC 61.265 66.667 17.92 0.00 0.00 4.06
379 380 3.264897 GACGGCTGCCTACATGCG 61.265 66.667 17.92 3.81 0.00 4.73
380 381 4.838152 ACGGCTGCCTACATGCGG 62.838 66.667 17.92 0.40 40.70 5.69
386 387 4.830765 GCCTACATGCGGCGGTGA 62.831 66.667 9.78 0.00 37.87 4.02
387 388 2.586079 CCTACATGCGGCGGTGAG 60.586 66.667 9.78 5.37 0.00 3.51
399 400 3.142838 GGTGAGCCGGCGGTAGTA 61.143 66.667 28.82 9.02 0.00 1.82
420 421 1.227556 GTAGGCGACGATTGGGCAT 60.228 57.895 0.00 0.00 0.00 4.40
486 487 2.243056 ACGCATTGACGTTGCATGA 58.757 47.368 11.01 0.00 45.75 3.07
750 765 1.535833 ACTGACTCGGTCGATGAACT 58.464 50.000 0.00 0.00 34.95 3.01
771 790 0.691078 ACGAGACCCCAGCCATATGT 60.691 55.000 1.24 0.00 0.00 2.29
779 798 1.676916 CCCAGCCATATGTATCGCCAG 60.677 57.143 1.24 0.00 0.00 4.85
801 820 4.570663 CCGATCCGCACCTCGTCC 62.571 72.222 0.00 0.00 36.19 4.79
1021 1048 1.549170 ACTACAGAATCCGTCGCCTTT 59.451 47.619 0.00 0.00 0.00 3.11
1080 1125 2.112815 CCCAGTTCGAATTCCCGGC 61.113 63.158 0.00 0.00 0.00 6.13
1083 1128 3.872728 GTTCGAATTCCCGGCGGC 61.873 66.667 23.20 5.25 0.00 6.53
1510 1556 2.031163 GGGGAGCGCGCATAGATT 59.969 61.111 35.10 11.72 0.00 2.40
1511 1557 2.320587 GGGGAGCGCGCATAGATTG 61.321 63.158 35.10 0.00 0.00 2.67
1639 2043 5.048364 GGTTGGCTACATTGTTACAATGACA 60.048 40.000 35.44 25.35 0.00 3.58
1646 2050 6.371809 ACATTGTTACAATGACACGTTTCT 57.628 33.333 35.44 13.87 0.00 2.52
1661 2066 9.577110 TGACACGTTTCTTATTTCGTCTATATT 57.423 29.630 3.00 0.00 34.30 1.28
1740 2147 5.821516 TTTCAGCGTTTTGTTCCTTAGAA 57.178 34.783 0.00 0.00 0.00 2.10
1763 2170 0.643820 GATGAAATTTGCTGCTGCGC 59.356 50.000 11.21 0.00 43.34 6.09
1772 2179 2.831366 GCTGCTGCGCTGTATGCAT 61.831 57.895 16.05 3.79 42.32 3.96
1785 2192 3.164268 TGTATGCATTTCTTGTGGCCTT 58.836 40.909 3.54 0.00 0.00 4.35
1786 2193 2.754946 ATGCATTTCTTGTGGCCTTG 57.245 45.000 3.32 0.00 0.00 3.61
1787 2194 1.412079 TGCATTTCTTGTGGCCTTGT 58.588 45.000 3.32 0.00 0.00 3.16
1788 2195 1.340889 TGCATTTCTTGTGGCCTTGTC 59.659 47.619 3.32 0.00 0.00 3.18
1790 2197 2.036346 GCATTTCTTGTGGCCTTGTCTT 59.964 45.455 3.32 0.00 0.00 3.01
1791 2198 3.645884 CATTTCTTGTGGCCTTGTCTTG 58.354 45.455 3.32 0.00 0.00 3.02
1792 2199 1.032014 TTCTTGTGGCCTTGTCTTGC 58.968 50.000 3.32 0.00 0.00 4.01
1798 2205 0.606401 TGGCCTTGTCTTGCTACAGC 60.606 55.000 3.32 0.00 42.50 4.40
1799 2206 1.639298 GGCCTTGTCTTGCTACAGCG 61.639 60.000 0.00 0.00 45.83 5.18
1800 2207 1.639298 GCCTTGTCTTGCTACAGCGG 61.639 60.000 0.00 0.00 45.83 5.52
1802 2209 0.792640 CTTGTCTTGCTACAGCGGTG 59.207 55.000 14.13 14.13 45.83 4.94
1803 2210 0.391228 TTGTCTTGCTACAGCGGTGA 59.609 50.000 23.44 4.04 45.83 4.02
1804 2211 0.391228 TGTCTTGCTACAGCGGTGAA 59.609 50.000 23.44 3.79 45.83 3.18
1805 2212 1.202592 TGTCTTGCTACAGCGGTGAAA 60.203 47.619 23.44 7.93 45.83 2.69
1806 2213 1.871039 GTCTTGCTACAGCGGTGAAAA 59.129 47.619 23.44 8.51 45.83 2.29
1808 2215 3.058224 GTCTTGCTACAGCGGTGAAAATT 60.058 43.478 23.44 0.00 45.83 1.82
1809 2216 4.153475 GTCTTGCTACAGCGGTGAAAATTA 59.847 41.667 23.44 1.35 45.83 1.40
1810 2217 4.757657 TCTTGCTACAGCGGTGAAAATTAA 59.242 37.500 23.44 7.48 45.83 1.40
1811 2218 5.414454 TCTTGCTACAGCGGTGAAAATTAAT 59.586 36.000 23.44 0.00 45.83 1.40
1900 2331 9.750125 AGACTTAATCAAAATTTGACTTTGACC 57.250 29.630 10.91 0.00 43.57 4.02
1901 2332 9.528018 GACTTAATCAAAATTTGACTTTGACCA 57.472 29.630 10.91 0.00 43.57 4.02
1906 2337 9.617523 AATCAAAATTTGACTTTGACCAAATCT 57.382 25.926 10.91 0.00 43.57 2.40
1907 2338 9.617523 ATCAAAATTTGACTTTGACCAAATCTT 57.382 25.926 10.91 0.00 43.57 2.40
1914 2345 9.567776 TTTGACTTTGACCAAATCTTATACAGA 57.432 29.630 0.00 0.00 35.33 3.41
1915 2346 8.547967 TGACTTTGACCAAATCTTATACAGAC 57.452 34.615 0.00 0.00 32.83 3.51
1917 2348 9.871238 GACTTTGACCAAATCTTATACAGACTA 57.129 33.333 0.00 0.00 32.83 2.59
2015 2710 8.359642 GTTTTAGCCTTAATCATATGGATTGCA 58.640 33.333 2.13 0.00 45.70 4.08
2016 2711 8.476064 TTTAGCCTTAATCATATGGATTGCAA 57.524 30.769 0.00 0.00 45.70 4.08
2017 2712 6.585695 AGCCTTAATCATATGGATTGCAAG 57.414 37.500 4.94 3.96 45.70 4.01
2018 2713 6.309357 AGCCTTAATCATATGGATTGCAAGA 58.691 36.000 4.94 0.00 45.70 3.02
2019 2714 6.779049 AGCCTTAATCATATGGATTGCAAGAA 59.221 34.615 4.94 0.00 45.70 2.52
2040 2735 9.025041 CAAGAAAGAAAATTAGGGGATTGTAGT 57.975 33.333 0.00 0.00 0.00 2.73
2048 2743 9.907229 AAAATTAGGGGATTGTAGTTTCTCTAG 57.093 33.333 0.00 0.00 0.00 2.43
2050 2745 4.961585 AGGGGATTGTAGTTTCTCTAGGT 58.038 43.478 0.00 0.00 0.00 3.08
2082 2777 6.038050 GCACAAATTTGGTTGATTTTCTGGAA 59.962 34.615 21.74 0.00 32.59 3.53
2204 2899 4.204573 CAGATCGTGTTAGCTAGCGTAAAC 59.795 45.833 18.17 18.17 0.00 2.01
2272 2967 7.247456 TGGTTACCATAGTTACAATGAGTCA 57.753 36.000 0.00 0.00 0.00 3.41
2325 3021 4.747605 GGCTAAATCGAGAAAGATGAGACC 59.252 45.833 0.00 0.00 0.00 3.85
2357 3053 2.501723 CCTGGCTCCTTAGAGTTTAGCA 59.498 50.000 0.00 0.00 42.59 3.49
2375 3071 2.291043 AACTCTGGGCCGTCGGATT 61.291 57.895 17.49 0.00 0.00 3.01
2376 3072 0.974010 AACTCTGGGCCGTCGGATTA 60.974 55.000 17.49 0.00 0.00 1.75
2380 3076 2.036733 CTCTGGGCCGTCGGATTATTTA 59.963 50.000 17.49 0.00 0.00 1.40
2389 3085 4.509970 CCGTCGGATTATTTACTTGATGCA 59.490 41.667 4.91 0.00 0.00 3.96
2403 3099 0.098728 GATGCAATTTGGACCGTCCG 59.901 55.000 13.02 0.00 40.17 4.79
2408 3104 1.933853 CAATTTGGACCGTCCGATCTC 59.066 52.381 13.02 0.00 40.17 2.75
2411 3107 4.267503 GGACCGTCCGATCTCGCC 62.268 72.222 0.65 0.00 38.18 5.54
2422 3118 2.325393 GATCTCGCCCCCGGACAATT 62.325 60.000 0.73 0.00 34.56 2.32
2426 3122 3.138128 GCCCCCGGACAATTTCGG 61.138 66.667 0.73 5.04 45.29 4.30
2427 3123 2.353573 CCCCCGGACAATTTCGGT 59.646 61.111 0.73 0.00 44.32 4.69
2436 3132 1.997606 GACAATTTCGGTCGTCGGATT 59.002 47.619 0.00 1.26 39.77 3.01
2443 3139 4.433186 TTCGGTCGTCGGATTAAAACTA 57.567 40.909 0.00 0.00 39.77 2.24
2457 3153 5.961396 TTAAAACTAAGGCCGTTGCAATA 57.039 34.783 0.59 0.00 40.13 1.90
2463 3159 1.616159 AGGCCGTTGCAATAAACAGT 58.384 45.000 0.59 0.00 40.13 3.55
2469 3165 1.451651 GTTGCAATAAACAGTGTGCGC 59.548 47.619 0.59 0.00 39.92 6.09
2470 3166 0.665298 TGCAATAAACAGTGTGCGCA 59.335 45.000 5.66 5.66 39.92 6.09
2507 3203 2.110213 TAAATAGCCTGCCCCGCG 59.890 61.111 0.00 0.00 0.00 6.46
2520 3216 4.433877 CCGCGGTGGGCATTTTGG 62.434 66.667 19.50 0.00 43.84 3.28
2528 3224 2.038295 GGTGGGCATTTTGGTCATTTCA 59.962 45.455 0.00 0.00 0.00 2.69
2529 3225 3.307621 GGTGGGCATTTTGGTCATTTCAT 60.308 43.478 0.00 0.00 0.00 2.57
2533 3229 3.125658 GGCATTTTGGTCATTTCATGCAC 59.874 43.478 0.00 0.00 39.04 4.57
2534 3230 3.125658 GCATTTTGGTCATTTCATGCACC 59.874 43.478 0.00 0.00 37.54 5.01
2553 3250 0.877213 CGGGGTATAAAAGGCGACGG 60.877 60.000 0.00 0.00 0.00 4.79
2554 3251 0.178767 GGGGTATAAAAGGCGACGGT 59.821 55.000 0.00 0.00 0.00 4.83
2568 3265 1.332686 CGACGGTTCGTATGGAGATGA 59.667 52.381 0.00 0.00 41.37 2.92
2588 3285 1.456705 CTAGCCGGCTCCTCTCCTT 60.457 63.158 36.73 8.54 0.00 3.36
2596 3293 2.044848 TCCTCTCCTTCTCGCGCT 60.045 61.111 5.56 0.00 0.00 5.92
2700 3400 2.743928 CTGCCACAGTCGCCCTTC 60.744 66.667 0.00 0.00 0.00 3.46
2701 3401 4.329545 TGCCACAGTCGCCCTTCC 62.330 66.667 0.00 0.00 0.00 3.46
2702 3402 4.329545 GCCACAGTCGCCCTTCCA 62.330 66.667 0.00 0.00 0.00 3.53
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 7.837689 ACAGGTAGGACACATATGTTAGTCTTA 59.162 37.037 19.93 15.87 39.95 2.10
1 2 6.668283 ACAGGTAGGACACATATGTTAGTCTT 59.332 38.462 19.93 16.65 39.95 3.01
2 3 6.195700 ACAGGTAGGACACATATGTTAGTCT 58.804 40.000 19.93 12.15 39.95 3.24
3 4 6.096423 TGACAGGTAGGACACATATGTTAGTC 59.904 42.308 14.88 14.88 39.95 2.59
4 5 5.955959 TGACAGGTAGGACACATATGTTAGT 59.044 40.000 5.37 1.61 39.95 2.24
5 6 6.096987 ACTGACAGGTAGGACACATATGTTAG 59.903 42.308 5.37 0.00 39.95 2.34
6 7 5.955959 ACTGACAGGTAGGACACATATGTTA 59.044 40.000 5.37 0.00 39.95 2.41
7 8 4.777896 ACTGACAGGTAGGACACATATGTT 59.222 41.667 5.37 0.00 39.95 2.71
8 9 4.160439 CACTGACAGGTAGGACACATATGT 59.840 45.833 7.51 1.41 43.71 2.29
9 10 4.442052 CCACTGACAGGTAGGACACATATG 60.442 50.000 7.51 0.00 0.00 1.78
10 11 3.706594 CCACTGACAGGTAGGACACATAT 59.293 47.826 7.51 0.00 0.00 1.78
11 12 3.096852 CCACTGACAGGTAGGACACATA 58.903 50.000 7.51 0.00 0.00 2.29
12 13 1.902508 CCACTGACAGGTAGGACACAT 59.097 52.381 7.51 0.00 0.00 3.21
13 14 1.133294 TCCACTGACAGGTAGGACACA 60.133 52.381 7.51 0.00 0.00 3.72
14 15 1.629043 TCCACTGACAGGTAGGACAC 58.371 55.000 7.51 0.00 0.00 3.67
15 16 2.225267 TGATCCACTGACAGGTAGGACA 60.225 50.000 13.64 11.36 0.00 4.02
16 17 2.166664 GTGATCCACTGACAGGTAGGAC 59.833 54.545 13.64 9.57 0.00 3.85
17 18 2.225267 TGTGATCCACTGACAGGTAGGA 60.225 50.000 13.70 13.70 35.11 2.94
18 19 2.093973 GTGTGATCCACTGACAGGTAGG 60.094 54.545 7.51 6.00 41.11 3.18
19 20 2.562738 TGTGTGATCCACTGACAGGTAG 59.437 50.000 7.51 0.00 44.81 3.18
20 21 2.299013 GTGTGTGATCCACTGACAGGTA 59.701 50.000 7.51 0.00 44.81 3.08
21 22 1.070758 GTGTGTGATCCACTGACAGGT 59.929 52.381 7.51 0.00 44.81 4.00
22 23 1.800805 GTGTGTGATCCACTGACAGG 58.199 55.000 7.51 0.00 44.81 4.00
23 24 1.422388 CGTGTGTGATCCACTGACAG 58.578 55.000 13.32 0.00 44.81 3.51
24 25 3.586430 CGTGTGTGATCCACTGACA 57.414 52.632 13.32 0.00 44.81 3.58
351 352 2.002127 CAGCCGTCGAAGCTTCATC 58.998 57.895 25.47 15.78 38.95 2.92
352 353 2.103042 GCAGCCGTCGAAGCTTCAT 61.103 57.895 25.47 1.76 38.95 2.57
353 354 2.738521 GCAGCCGTCGAAGCTTCA 60.739 61.111 25.47 10.50 38.95 3.02
354 355 2.558554 TAGGCAGCCGTCGAAGCTTC 62.559 60.000 16.84 16.84 38.95 3.86
355 356 2.646175 TAGGCAGCCGTCGAAGCTT 61.646 57.895 5.55 0.00 38.95 3.74
356 357 3.068691 TAGGCAGCCGTCGAAGCT 61.069 61.111 5.55 5.41 42.70 3.74
357 358 2.886124 GTAGGCAGCCGTCGAAGC 60.886 66.667 5.55 0.43 0.00 3.86
358 359 1.141881 ATGTAGGCAGCCGTCGAAG 59.858 57.895 5.55 0.00 0.00 3.79
359 360 1.153647 CATGTAGGCAGCCGTCGAA 60.154 57.895 5.55 0.00 0.00 3.71
360 361 2.494445 CATGTAGGCAGCCGTCGA 59.506 61.111 5.55 0.00 0.00 4.20
361 362 3.264897 GCATGTAGGCAGCCGTCG 61.265 66.667 5.55 0.00 0.00 5.12
362 363 3.264897 CGCATGTAGGCAGCCGTC 61.265 66.667 5.55 3.75 0.00 4.79
363 364 4.838152 CCGCATGTAGGCAGCCGT 62.838 66.667 5.55 0.00 0.00 5.68
370 371 2.586079 CTCACCGCCGCATGTAGG 60.586 66.667 5.17 5.17 0.00 3.18
371 372 3.264897 GCTCACCGCCGCATGTAG 61.265 66.667 0.00 0.00 0.00 2.74
382 383 3.142838 TACTACCGCCGGCTCACC 61.143 66.667 26.68 0.00 0.00 4.02
383 384 2.103736 GTACTACCGCCGGCTCAC 59.896 66.667 26.68 8.91 0.00 3.51
384 385 2.361483 TGTACTACCGCCGGCTCA 60.361 61.111 26.68 8.17 0.00 4.26
385 386 1.097547 TACTGTACTACCGCCGGCTC 61.098 60.000 26.68 6.38 0.00 4.70
386 387 1.077501 TACTGTACTACCGCCGGCT 60.078 57.895 26.68 9.55 0.00 5.52
387 388 1.358046 CTACTGTACTACCGCCGGC 59.642 63.158 19.07 19.07 0.00 6.13
388 389 2.028130 CCTACTGTACTACCGCCGG 58.972 63.158 0.00 0.00 0.00 6.13
395 396 2.615447 CCAATCGTCGCCTACTGTACTA 59.385 50.000 0.00 0.00 0.00 1.82
399 400 1.515954 CCCAATCGTCGCCTACTGT 59.484 57.895 0.00 0.00 0.00 3.55
470 471 1.609932 CACTCATGCAACGTCAATGC 58.390 50.000 3.73 3.73 44.08 3.56
473 474 1.960417 TTCCACTCATGCAACGTCAA 58.040 45.000 0.00 0.00 0.00 3.18
514 515 3.587061 TCACCCCTCAAATAGAAGAAGCA 59.413 43.478 0.00 0.00 0.00 3.91
750 765 0.398522 ATATGGCTGGGGTCTCGTGA 60.399 55.000 0.00 0.00 0.00 4.35
771 790 1.461091 GGATCGGTGACCTGGCGATA 61.461 60.000 0.00 0.00 0.00 2.92
779 798 3.718210 GAGGTGCGGATCGGTGACC 62.718 68.421 12.78 12.78 0.00 4.02
801 820 0.877649 CTGATTGGTGCGAGATCCCG 60.878 60.000 0.00 0.00 0.00 5.14
945 967 4.947147 TGACGGGTGTGGGCAAGC 62.947 66.667 0.00 0.00 0.00 4.01
1021 1048 1.133606 GGGTTGGGGAACTTGAAGTGA 60.134 52.381 0.00 0.00 0.00 3.41
1057 1099 1.340114 GGGAATTCGAACTGGGCTTCT 60.340 52.381 0.00 0.00 0.00 2.85
1083 1128 2.851071 GCCATCGGTCTCTCCTCCG 61.851 68.421 0.00 0.00 46.93 4.63
1324 1370 0.037232 GGTCCGTCTTGAAGTCCTGG 60.037 60.000 0.00 0.00 0.00 4.45
1510 1556 1.422531 ACATTGCTTTTCCTTGGGCA 58.577 45.000 0.00 0.00 0.00 5.36
1511 1557 2.825532 TCTACATTGCTTTTCCTTGGGC 59.174 45.455 0.00 0.00 0.00 5.36
1512 1558 3.119352 GCTCTACATTGCTTTTCCTTGGG 60.119 47.826 0.00 0.00 0.00 4.12
1513 1559 3.760684 AGCTCTACATTGCTTTTCCTTGG 59.239 43.478 0.00 0.00 35.86 3.61
1516 1562 4.006319 GACAGCTCTACATTGCTTTTCCT 58.994 43.478 0.00 0.00 37.44 3.36
1517 1563 3.127721 GGACAGCTCTACATTGCTTTTCC 59.872 47.826 0.00 0.00 37.44 3.13
1518 1564 3.181516 CGGACAGCTCTACATTGCTTTTC 60.182 47.826 0.00 0.00 37.44 2.29
1519 1565 2.744202 CGGACAGCTCTACATTGCTTTT 59.256 45.455 0.00 0.00 37.44 2.27
1520 1566 2.289694 ACGGACAGCTCTACATTGCTTT 60.290 45.455 0.00 0.00 37.44 3.51
1521 1567 1.276421 ACGGACAGCTCTACATTGCTT 59.724 47.619 0.00 0.00 37.44 3.91
1522 1568 0.898320 ACGGACAGCTCTACATTGCT 59.102 50.000 0.00 0.00 40.54 3.91
1661 2066 4.128925 TGCATTTTAGCACAAACCAACA 57.871 36.364 0.00 0.00 40.11 3.33
1692 2099 7.921786 TTCAGAATTACTCGGAAACAATGAT 57.078 32.000 0.00 0.00 35.60 2.45
1740 2147 2.353406 GCAGCAGCAAATTTCATCAGGT 60.353 45.455 0.00 0.00 41.58 4.00
1763 2170 2.756760 AGGCCACAAGAAATGCATACAG 59.243 45.455 5.01 0.00 0.00 2.74
1772 2179 1.408702 GCAAGACAAGGCCACAAGAAA 59.591 47.619 5.01 0.00 0.00 2.52
1785 2192 0.391228 TTCACCGCTGTAGCAAGACA 59.609 50.000 4.59 0.00 42.21 3.41
1786 2193 1.508632 TTTCACCGCTGTAGCAAGAC 58.491 50.000 4.59 0.00 42.21 3.01
1787 2194 2.248280 TTTTCACCGCTGTAGCAAGA 57.752 45.000 4.59 0.00 42.21 3.02
1788 2195 3.559238 AATTTTCACCGCTGTAGCAAG 57.441 42.857 4.59 0.00 42.21 4.01
1790 2197 5.637006 AATTAATTTTCACCGCTGTAGCA 57.363 34.783 4.59 0.00 42.21 3.49
1791 2198 6.090129 TGAAATTAATTTTCACCGCTGTAGC 58.910 36.000 14.45 0.00 46.80 3.58
1874 2305 9.750125 GGTCAAAGTCAAATTTTGATTAAGTCT 57.250 29.630 14.54 3.88 43.90 3.24
1875 2306 9.528018 TGGTCAAAGTCAAATTTTGATTAAGTC 57.472 29.630 14.54 1.70 43.90 3.01
1876 2307 9.883142 TTGGTCAAAGTCAAATTTTGATTAAGT 57.117 25.926 14.54 0.00 43.90 2.24
1880 2311 9.617523 AGATTTGGTCAAAGTCAAATTTTGATT 57.382 25.926 14.54 8.12 43.90 2.57
1881 2312 9.617523 AAGATTTGGTCAAAGTCAAATTTTGAT 57.382 25.926 14.54 0.00 43.90 2.57
1888 2319 9.567776 TCTGTATAAGATTTGGTCAAAGTCAAA 57.432 29.630 2.55 0.00 37.29 2.69
1889 2320 8.999431 GTCTGTATAAGATTTGGTCAAAGTCAA 58.001 33.333 2.55 0.00 37.23 3.18
1890 2321 8.375506 AGTCTGTATAAGATTTGGTCAAAGTCA 58.624 33.333 2.55 0.00 37.23 3.41
1921 2352 9.139734 TCATAATCATTACGTACTTCCTAGGTT 57.860 33.333 9.08 0.00 0.00 3.50
1922 2353 8.701908 TCATAATCATTACGTACTTCCTAGGT 57.298 34.615 9.08 0.00 0.00 3.08
1988 2683 8.359642 GCAATCCATATGATTAAGGCTAAAACA 58.640 33.333 3.65 0.00 41.85 2.83
1989 2684 8.359642 TGCAATCCATATGATTAAGGCTAAAAC 58.640 33.333 3.65 0.00 41.85 2.43
2010 2705 6.933514 TCCCCTAATTTTCTTTCTTGCAAT 57.066 33.333 0.00 0.00 0.00 3.56
2015 2710 9.601810 AACTACAATCCCCTAATTTTCTTTCTT 57.398 29.630 0.00 0.00 0.00 2.52
2016 2711 9.601810 AAACTACAATCCCCTAATTTTCTTTCT 57.398 29.630 0.00 0.00 0.00 2.52
2017 2712 9.856488 GAAACTACAATCCCCTAATTTTCTTTC 57.144 33.333 0.00 0.00 0.00 2.62
2018 2713 9.601810 AGAAACTACAATCCCCTAATTTTCTTT 57.398 29.630 0.00 0.00 0.00 2.52
2019 2714 9.244292 GAGAAACTACAATCCCCTAATTTTCTT 57.756 33.333 0.00 0.00 0.00 2.52
2029 2724 4.715297 TCACCTAGAGAAACTACAATCCCC 59.285 45.833 0.00 0.00 0.00 4.81
2040 2735 2.703536 TGTGCAAGGTCACCTAGAGAAA 59.296 45.455 0.00 0.00 36.17 2.52
2048 2743 2.158971 ACCAAATTTGTGCAAGGTCACC 60.159 45.455 16.73 0.00 36.17 4.02
2050 2745 3.196469 TCAACCAAATTTGTGCAAGGTCA 59.804 39.130 16.73 0.00 0.00 4.02
2082 2777 6.671614 TGAAGTGAACGTTATCAAAACTGT 57.328 33.333 0.00 0.00 0.00 3.55
2226 2921 7.149307 ACCAACAAGGATTAATTTTACAACGG 58.851 34.615 0.00 0.00 41.22 4.44
2272 2967 8.216423 ACCAATCATACAGAAGAATAAGCAGAT 58.784 33.333 0.00 0.00 0.00 2.90
2325 3021 2.581354 AGCCAGGTAGCTCGCTTG 59.419 61.111 8.33 0.00 39.48 4.01
2357 3053 0.974010 TAATCCGACGGCCCAGAGTT 60.974 55.000 9.66 0.00 0.00 3.01
2375 3071 6.151985 ACGGTCCAAATTGCATCAAGTAAATA 59.848 34.615 0.00 0.00 0.00 1.40
2376 3072 5.047377 ACGGTCCAAATTGCATCAAGTAAAT 60.047 36.000 0.00 0.00 0.00 1.40
2380 3076 2.228822 GACGGTCCAAATTGCATCAAGT 59.771 45.455 0.00 0.00 0.00 3.16
2389 3085 1.470979 CGAGATCGGACGGTCCAAATT 60.471 52.381 25.80 9.20 35.91 1.82
2403 3099 2.325393 AATTGTCCGGGGGCGAGATC 62.325 60.000 0.00 0.00 0.00 2.75
2408 3104 3.505184 CGAAATTGTCCGGGGGCG 61.505 66.667 0.00 0.00 0.00 6.13
2422 3118 3.302365 AGTTTTAATCCGACGACCGAA 57.698 42.857 0.00 0.00 41.76 4.30
2426 3122 3.308053 GGCCTTAGTTTTAATCCGACGAC 59.692 47.826 0.00 0.00 0.00 4.34
2427 3123 3.524541 GGCCTTAGTTTTAATCCGACGA 58.475 45.455 0.00 0.00 0.00 4.20
2436 3132 5.961396 TTATTGCAACGGCCTTAGTTTTA 57.039 34.783 0.00 0.00 40.13 1.52
2443 3139 1.960689 ACTGTTTATTGCAACGGCCTT 59.039 42.857 0.00 0.00 40.13 4.35
2483 3179 2.235016 GCAGGCTATTTACGCGCGA 61.235 57.895 39.36 15.84 0.00 5.87
2507 3203 2.038295 TGAAATGACCAAAATGCCCACC 59.962 45.455 0.00 0.00 0.00 4.61
2528 3224 1.752788 GCCTTTTATACCCCGGTGCAT 60.753 52.381 0.00 0.00 0.00 3.96
2529 3225 0.394625 GCCTTTTATACCCCGGTGCA 60.395 55.000 0.00 0.00 0.00 4.57
2533 3229 0.877213 CGTCGCCTTTTATACCCCGG 60.877 60.000 0.00 0.00 0.00 5.73
2534 3230 0.877213 CCGTCGCCTTTTATACCCCG 60.877 60.000 0.00 0.00 0.00 5.73
2553 3250 3.305471 GGCTAGGTCATCTCCATACGAAC 60.305 52.174 0.00 0.00 0.00 3.95
2554 3251 2.891580 GGCTAGGTCATCTCCATACGAA 59.108 50.000 0.00 0.00 0.00 3.85
2559 3256 1.476007 GCCGGCTAGGTCATCTCCAT 61.476 60.000 22.15 0.00 43.70 3.41
2564 3261 1.811645 GAGGAGCCGGCTAGGTCATC 61.812 65.000 32.97 20.66 43.70 2.92
2568 3265 2.123640 GAGAGGAGCCGGCTAGGT 60.124 66.667 32.97 17.48 43.70 3.08
2625 3322 0.624795 GGGTTTGGAGGGGGAGAGAT 60.625 60.000 0.00 0.00 0.00 2.75
2631 3328 2.690734 GCCTAGGGTTTGGAGGGGG 61.691 68.421 11.72 0.00 0.00 5.40
2684 3384 4.329545 GGAAGGGCGACTGTGGCA 62.330 66.667 16.54 0.00 35.84 4.92
2685 3385 4.329545 TGGAAGGGCGACTGTGGC 62.330 66.667 6.21 6.21 0.00 5.01


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

AutoCloner maintained by Alex Coulton.