Multiple sequence alignment - TraesCS4B01G048700

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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 TraesCS4B01G048700 chr4B 100.000 2566 0 0 1 2566 37091973 37089408 0.000000e+00 4739.0
1 TraesCS4B01G048700 chr4B 78.440 218 39 8 1742 1954 653948983 653949197 4.450000e-28 135.0
2 TraesCS4B01G048700 chr4B 93.258 89 5 1 1654 1742 36009462 36009549 2.070000e-26 130.0
3 TraesCS4B01G048700 chr4D 91.401 1349 92 15 406 1742 25165326 25163990 0.000000e+00 1827.0
4 TraesCS4B01G048700 chr4D 93.333 315 20 1 94 407 25166515 25166201 5.000000e-127 464.0
5 TraesCS4B01G048700 chr4D 85.047 214 15 5 1746 1957 102115884 102115686 4.330000e-48 202.0
6 TraesCS4B01G048700 chr4A 89.698 1359 103 23 406 1742 578377441 578378784 0.000000e+00 1700.0
7 TraesCS4B01G048700 chr4A 94.603 315 16 1 93 406 578376959 578377273 1.070000e-133 486.0
8 TraesCS4B01G048700 chr4A 93.333 270 11 2 1746 2014 621660461 621660198 2.390000e-105 392.0
9 TraesCS4B01G048700 chr4A 91.589 214 15 3 1746 1957 674746978 674746766 2.500000e-75 292.0
10 TraesCS4B01G048700 chr4A 93.038 158 3 2 2410 2566 621660191 621660041 9.240000e-55 224.0
11 TraesCS4B01G048700 chr4A 85.276 163 22 1 616 778 387129666 387129506 1.580000e-37 167.0
12 TraesCS4B01G048700 chr4A 92.941 85 5 1 1 84 708776283 708776199 3.470000e-24 122.0
13 TraesCS4B01G048700 chr4A 91.954 87 4 2 1 87 357263716 357263799 4.490000e-23 119.0
14 TraesCS4B01G048700 chr1A 92.613 555 23 4 1746 2288 399489623 399489075 0.000000e+00 782.0
15 TraesCS4B01G048700 chr1A 93.358 271 8 3 2297 2566 399489095 399488834 2.390000e-105 392.0
16 TraesCS4B01G048700 chr5B 92.460 504 9 7 2065 2566 546498830 546499306 0.000000e+00 693.0
17 TraesCS4B01G048700 chr5B 95.851 241 9 1 1749 1988 546498557 546498797 3.100000e-104 388.0
18 TraesCS4B01G048700 chr5B 82.967 182 23 6 2069 2243 493092549 493092729 9.500000e-35 158.0
19 TraesCS4B01G048700 chr5B 80.711 197 35 3 612 807 289162817 289162623 1.590000e-32 150.0
20 TraesCS4B01G048700 chr6A 90.141 213 18 3 1746 1957 100234463 100234673 9.050000e-70 274.0
21 TraesCS4B01G048700 chr6D 86.752 234 21 7 2058 2282 83285508 83285740 4.240000e-63 252.0
22 TraesCS4B01G048700 chr3D 81.935 310 44 10 606 909 313180639 313180336 4.240000e-63 252.0
23 TraesCS4B01G048700 chr3A 80.195 308 51 9 606 909 419333873 419334174 3.320000e-54 222.0
24 TraesCS4B01G048700 chr2D 82.308 260 41 4 632 889 477039942 477039686 1.200000e-53 220.0
25 TraesCS4B01G048700 chr2D 91.954 87 4 3 1 86 44345551 44345467 4.490000e-23 119.0
26 TraesCS4B01G048700 chr1D 80.000 280 41 11 612 884 349567373 349567644 2.610000e-45 193.0
27 TraesCS4B01G048700 chr2B 82.791 215 33 4 1746 1957 732232179 732231966 3.370000e-44 189.0
28 TraesCS4B01G048700 chr2B 85.849 106 8 7 2 104 543317816 543317917 3.490000e-19 106.0
29 TraesCS4B01G048700 chr7B 82.326 215 30 8 1746 1957 673570774 673570565 2.030000e-41 180.0
30 TraesCS4B01G048700 chr5D 80.000 220 41 3 612 830 255577716 255577499 2.640000e-35 159.0
31 TraesCS4B01G048700 chr6B 94.118 85 3 2 1 85 3539866 3539784 7.450000e-26 128.0
32 TraesCS4B01G048700 chr6B 94.118 85 3 2 1 85 3549597 3549515 7.450000e-26 128.0
33 TraesCS4B01G048700 chr6B 93.976 83 5 0 1 83 27968682 27968600 2.680000e-25 126.0
34 TraesCS4B01G048700 chr6B 79.592 98 15 4 163 258 460933715 460933809 5.930000e-07 65.8
35 TraesCS4B01G048700 chr2A 94.118 85 3 2 1 85 17448727 17448645 7.450000e-26 128.0
36 TraesCS4B01G048700 chr2A 94.118 85 3 2 1 85 18058335 18058417 7.450000e-26 128.0


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 TraesCS4B01G048700 chr4B 37089408 37091973 2565 True 4739.0 4739 100.0000 1 2566 1 chr4B.!!$R1 2565
1 TraesCS4B01G048700 chr4D 25163990 25166515 2525 True 1145.5 1827 92.3670 94 1742 2 chr4D.!!$R2 1648
2 TraesCS4B01G048700 chr4A 578376959 578378784 1825 False 1093.0 1700 92.1505 93 1742 2 chr4A.!!$F2 1649
3 TraesCS4B01G048700 chr1A 399488834 399489623 789 True 587.0 782 92.9855 1746 2566 2 chr1A.!!$R1 820
4 TraesCS4B01G048700 chr5B 546498557 546499306 749 False 540.5 693 94.1555 1749 2566 2 chr5B.!!$F2 817

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
811 1690 0.57539 CGCTAAATACCGGAGCAACG 59.425 55.0 9.46 0.0 35.91 4.1 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1802 2702 0.105778 TTGCACACATCACCTCACGA 59.894 50.0 0.0 0.0 0.0 4.35 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
22 23 5.373812 GAGGTGGGAGGATAGATGAAAAA 57.626 43.478 0.00 0.00 0.00 1.94
47 48 3.272043 GCGAAAATTAACCGCGCG 58.728 55.556 25.67 25.67 39.54 6.86
48 49 2.212330 GCGAAAATTAACCGCGCGG 61.212 57.895 44.88 44.88 39.54 6.46
58 59 2.960129 CCGCGCGGACTATTCACC 60.960 66.667 44.86 0.00 37.50 4.02
59 60 2.202690 CGCGCGGACTATTCACCA 60.203 61.111 24.84 0.00 0.00 4.17
60 61 1.807981 CGCGCGGACTATTCACCAA 60.808 57.895 24.84 0.00 0.00 3.67
61 62 1.713830 GCGCGGACTATTCACCAAC 59.286 57.895 8.83 0.00 0.00 3.77
62 63 0.739813 GCGCGGACTATTCACCAACT 60.740 55.000 8.83 0.00 0.00 3.16
63 64 0.999406 CGCGGACTATTCACCAACTG 59.001 55.000 0.00 0.00 0.00 3.16
64 65 0.727398 GCGGACTATTCACCAACTGC 59.273 55.000 0.00 0.00 0.00 4.40
65 66 1.676014 GCGGACTATTCACCAACTGCT 60.676 52.381 0.00 0.00 0.00 4.24
66 67 2.271800 CGGACTATTCACCAACTGCTC 58.728 52.381 0.00 0.00 0.00 4.26
67 68 2.633488 GGACTATTCACCAACTGCTCC 58.367 52.381 0.00 0.00 0.00 4.70
68 69 2.027192 GGACTATTCACCAACTGCTCCA 60.027 50.000 0.00 0.00 0.00 3.86
69 70 3.370953 GGACTATTCACCAACTGCTCCAT 60.371 47.826 0.00 0.00 0.00 3.41
70 71 4.265073 GACTATTCACCAACTGCTCCATT 58.735 43.478 0.00 0.00 0.00 3.16
71 72 5.428253 GACTATTCACCAACTGCTCCATTA 58.572 41.667 0.00 0.00 0.00 1.90
72 73 5.431765 ACTATTCACCAACTGCTCCATTAG 58.568 41.667 0.00 0.00 0.00 1.73
73 74 2.787473 TCACCAACTGCTCCATTAGG 57.213 50.000 0.00 0.00 0.00 2.69
74 75 2.265367 TCACCAACTGCTCCATTAGGA 58.735 47.619 0.00 0.00 43.21 2.94
89 90 6.923670 TCCATTAGGAGTAGAGATACAAGGT 58.076 40.000 0.00 0.00 39.61 3.50
90 91 8.053776 TCCATTAGGAGTAGAGATACAAGGTA 57.946 38.462 0.00 0.00 39.61 3.08
91 92 8.508601 TCCATTAGGAGTAGAGATACAAGGTAA 58.491 37.037 0.00 0.00 39.61 2.85
143 144 0.899019 TAGGAATGGTACTGCACGCA 59.101 50.000 0.00 0.00 0.00 5.24
309 311 8.902540 TTTAATATGAGTAGCATGGTAAGGTG 57.097 34.615 6.12 0.00 37.87 4.00
310 312 6.747414 AATATGAGTAGCATGGTAAGGTGA 57.253 37.500 6.12 0.00 37.87 4.02
375 377 9.081997 GTTGTATGTTGAGAGAATTAGAGTCAG 57.918 37.037 0.00 0.00 0.00 3.51
398 400 4.678287 GCTCATGCATGTTACATGTTATGC 59.322 41.667 25.43 24.09 44.26 3.14
418 1296 0.606944 TGGATCCAAAAACGTCCCCG 60.607 55.000 13.46 0.00 40.83 5.73
425 1303 0.604511 AAAAACGTCCCCGCACTAGG 60.605 55.000 0.00 0.00 37.70 3.02
451 1329 6.259387 GCCAATCAATTCATCCAAAATCTTCC 59.741 38.462 0.00 0.00 0.00 3.46
453 1331 7.279313 CCAATCAATTCATCCAAAATCTTCCAC 59.721 37.037 0.00 0.00 0.00 4.02
503 1381 4.572389 GTCATCTCAAGCACCGAATACAAT 59.428 41.667 0.00 0.00 0.00 2.71
589 1468 5.799827 TCCTAAAGGGATTTTGGTTGTTG 57.200 39.130 0.00 0.00 39.58 3.33
590 1469 5.212745 TCCTAAAGGGATTTTGGTTGTTGT 58.787 37.500 0.00 0.00 39.58 3.32
591 1470 6.374588 TCCTAAAGGGATTTTGGTTGTTGTA 58.625 36.000 0.00 0.00 39.58 2.41
592 1471 7.013834 TCCTAAAGGGATTTTGGTTGTTGTAT 58.986 34.615 0.00 0.00 39.58 2.29
593 1472 8.171400 TCCTAAAGGGATTTTGGTTGTTGTATA 58.829 33.333 0.00 0.00 39.58 1.47
594 1473 8.248253 CCTAAAGGGATTTTGGTTGTTGTATAC 58.752 37.037 0.00 0.00 37.23 1.47
595 1474 7.849322 AAAGGGATTTTGGTTGTTGTATACT 57.151 32.000 4.17 0.00 0.00 2.12
596 1475 8.943594 AAAGGGATTTTGGTTGTTGTATACTA 57.056 30.769 4.17 0.00 0.00 1.82
650 1529 5.345741 CACAATGCAAGTTAATGTTAGGCAC 59.654 40.000 0.00 0.00 32.04 5.01
670 1549 6.262049 AGGCACGATATTAATTGTATTGCACA 59.738 34.615 0.00 0.00 34.51 4.57
803 1682 9.577003 GTTTATCATTTTAGACGCTAAATACCG 57.423 33.333 11.18 0.00 0.00 4.02
811 1690 0.575390 CGCTAAATACCGGAGCAACG 59.425 55.000 9.46 0.00 35.91 4.10
830 1709 2.771943 ACGTGGACCATTGGATAGATGT 59.228 45.455 10.37 0.00 0.00 3.06
859 1738 3.701664 GGGTGGGATTTGTTTGATCTCT 58.298 45.455 0.00 0.00 0.00 3.10
860 1739 4.625324 CGGGTGGGATTTGTTTGATCTCTA 60.625 45.833 0.00 0.00 0.00 2.43
876 1755 7.993821 TGATCTCTATAACTCGCTCTTTTTG 57.006 36.000 0.00 0.00 0.00 2.44
995 1883 7.984002 TTCATGCCAAAAATTATATGACACG 57.016 32.000 0.00 0.00 0.00 4.49
1010 1898 7.925703 ATATGACACGACTTCTATAAAACGG 57.074 36.000 0.00 0.00 0.00 4.44
1011 1899 5.125100 TGACACGACTTCTATAAAACGGT 57.875 39.130 0.00 0.00 0.00 4.83
1053 1942 9.927668 ACACAAATTGGATTAAAAGGAATACTG 57.072 29.630 0.00 0.00 0.00 2.74
1072 1961 0.823356 GGGCAGCTGGAAGACACAAA 60.823 55.000 17.12 0.00 34.07 2.83
1092 1981 8.134895 ACACAAACCATATTCAACAAACTACTG 58.865 33.333 0.00 0.00 0.00 2.74
1126 2015 1.338136 ACAAGGATGAGGGGTAGCCG 61.338 60.000 4.56 0.00 0.00 5.52
1178 2067 1.991121 TAGCCTCAGGTACCGTATGG 58.009 55.000 6.18 8.90 42.84 2.74
1232 2121 8.792830 TGATATGAATAACCTACCTAGTGGTT 57.207 34.615 13.93 13.93 46.05 3.67
1244 2133 8.000127 ACCTACCTAGTGGTTTTTGATGTTTTA 59.000 33.333 0.00 0.00 46.05 1.52
1248 2137 9.143155 ACCTAGTGGTTTTTGATGTTTTAATCT 57.857 29.630 0.00 0.00 46.05 2.40
1306 2195 2.124024 ACGGGATCGACGATGGGA 60.124 61.111 16.49 0.00 40.11 4.37
1318 2207 2.559231 GACGATGGGAGGATCTCTAACC 59.441 54.545 0.00 0.00 35.73 2.85
1331 2220 4.015872 TCTCTAACCGGAACAAATTGCT 57.984 40.909 9.46 0.00 0.00 3.91
1381 2270 6.519382 TGAAATCAAGAGATGCATCGATACT 58.481 36.000 20.67 15.02 33.90 2.12
1399 2288 1.771255 ACTTGCAACTCCTTGTCTCCT 59.229 47.619 0.00 0.00 0.00 3.69
1436 2325 5.399301 CCTGAAATTAGTTGCGTTGACAAAG 59.601 40.000 0.00 0.00 0.00 2.77
1443 2332 3.555956 AGTTGCGTTGACAAAGAGTGTAG 59.444 43.478 5.22 0.00 41.96 2.74
1581 2478 8.899427 TCTCAAAACAATAAATGGCATGAAAA 57.101 26.923 0.00 0.00 0.00 2.29
1623 2520 6.356977 CGAAACATCATGTATAACCAAATCGC 59.643 38.462 0.00 0.00 0.00 4.58
1631 2531 0.812412 TAACCAAATCGCTAGCGGGC 60.812 55.000 34.76 0.00 40.25 6.13
1650 2550 2.551459 GGCTGTTGCTAGCTTATCCATG 59.449 50.000 17.23 0.00 43.22 3.66
1652 2552 3.208594 CTGTTGCTAGCTTATCCATGCA 58.791 45.455 17.23 0.00 0.00 3.96
1686 2586 5.936372 GTGACATACTGGCATACATGATCAT 59.064 40.000 1.18 1.18 37.93 2.45
1695 2595 7.174426 ACTGGCATACATGATCATATCTTTGTG 59.826 37.037 8.15 0.00 31.82 3.33
1696 2596 6.431852 TGGCATACATGATCATATCTTTGTGG 59.568 38.462 8.15 1.58 31.82 4.17
1822 2722 0.235665 CGTGAGGTGATGTGTGCAAC 59.764 55.000 0.00 0.00 37.35 4.17
1877 2778 3.954999 TCGATCGATACACGCAAATACA 58.045 40.909 15.15 0.00 42.26 2.29
1908 2809 2.604079 TTTCGGTGGGGTCGCCTA 60.604 61.111 7.55 0.00 41.26 3.93
1962 2869 0.034767 CAGAGCATGCAGGGAAAGGA 60.035 55.000 21.98 0.00 0.00 3.36
1963 2870 0.034670 AGAGCATGCAGGGAAAGGAC 60.035 55.000 21.98 0.00 0.00 3.85
1964 2871 1.000396 AGCATGCAGGGAAAGGACC 60.000 57.895 21.98 0.00 0.00 4.46
1965 2872 1.304381 GCATGCAGGGAAAGGACCA 60.304 57.895 14.21 0.00 0.00 4.02
1966 2873 1.318158 GCATGCAGGGAAAGGACCAG 61.318 60.000 14.21 0.00 0.00 4.00
1967 2874 0.682209 CATGCAGGGAAAGGACCAGG 60.682 60.000 0.00 0.00 0.00 4.45
2016 2923 0.392595 GGGCCCGACTCTGGTTTTAG 60.393 60.000 5.69 0.00 0.00 1.85
2030 2937 9.063615 ACTCTGGTTTTAGTACTAAAATGGTTG 57.936 33.333 32.67 25.26 44.01 3.77
2031 2938 7.878036 TCTGGTTTTAGTACTAAAATGGTTGC 58.122 34.615 32.67 22.15 44.01 4.17
2038 2945 3.799137 ACTAAAATGGTTGCGTGTACG 57.201 42.857 0.00 0.00 43.27 3.67
2039 2946 3.391965 ACTAAAATGGTTGCGTGTACGA 58.608 40.909 8.82 0.00 43.02 3.43
2053 2960 1.518572 TACGAAGCTTAGGCGCTGC 60.519 57.895 7.64 7.25 44.37 5.25
2115 3033 2.614983 GTTGTCGTGAGGCTTTTTACCA 59.385 45.455 0.00 0.00 36.07 3.25
2177 3095 7.093354 GGTGACTGATGTATGACTATATGTGG 58.907 42.308 0.00 0.00 0.00 4.17
2282 3200 2.645838 ACTGAGTGCACACCATTCTT 57.354 45.000 21.04 0.00 31.92 2.52
2283 3201 2.224606 ACTGAGTGCACACCATTCTTG 58.775 47.619 21.04 6.74 31.92 3.02
2284 3202 2.224606 CTGAGTGCACACCATTCTTGT 58.775 47.619 21.04 0.00 31.92 3.16
2285 3203 2.620115 CTGAGTGCACACCATTCTTGTT 59.380 45.455 21.04 0.00 31.92 2.83
2286 3204 3.023119 TGAGTGCACACCATTCTTGTTT 58.977 40.909 21.04 0.00 31.92 2.83
2287 3205 3.446873 TGAGTGCACACCATTCTTGTTTT 59.553 39.130 21.04 0.00 31.92 2.43
2288 3206 4.044426 GAGTGCACACCATTCTTGTTTTC 58.956 43.478 21.04 0.00 0.00 2.29
2289 3207 3.701040 AGTGCACACCATTCTTGTTTTCT 59.299 39.130 21.04 0.00 0.00 2.52
2290 3208 4.044426 GTGCACACCATTCTTGTTTTCTC 58.956 43.478 13.17 0.00 0.00 2.87
2291 3209 3.698539 TGCACACCATTCTTGTTTTCTCA 59.301 39.130 0.00 0.00 0.00 3.27
2292 3210 4.159321 TGCACACCATTCTTGTTTTCTCAA 59.841 37.500 0.00 0.00 0.00 3.02
2293 3211 5.108517 GCACACCATTCTTGTTTTCTCAAA 58.891 37.500 0.00 0.00 0.00 2.69
2294 3212 5.580297 GCACACCATTCTTGTTTTCTCAAAA 59.420 36.000 0.00 0.00 0.00 2.44
2295 3213 6.091986 GCACACCATTCTTGTTTTCTCAAAAA 59.908 34.615 0.00 0.00 31.13 1.94
2353 3272 3.056313 GCCTGGCTCGGACATTTGC 62.056 63.158 12.43 0.00 0.00 3.68
2394 3313 1.202867 TGCAACATACTGCCTGGTTCA 60.203 47.619 0.00 0.00 41.90 3.18
2418 3337 6.819649 CAGGTATTTGTAAAACCGGATGTCTA 59.180 38.462 9.46 0.00 38.37 2.59
2497 3417 1.451927 GATCAATGGCAGCCGTGGA 60.452 57.895 13.62 13.62 0.00 4.02
2498 3418 1.718757 GATCAATGGCAGCCGTGGAC 61.719 60.000 13.52 4.06 0.00 4.02
2499 3419 3.443045 CAATGGCAGCCGTGGACC 61.443 66.667 7.01 0.00 0.00 4.46
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 5.373812 TTTTTCATCTATCCTCCCACCTC 57.626 43.478 0.00 0.00 0.00 3.85
22 23 3.491639 GCGGTTAATTTTCGCTGGTTTTT 59.508 39.130 10.91 0.00 45.16 1.94
23 24 3.054166 GCGGTTAATTTTCGCTGGTTTT 58.946 40.909 10.91 0.00 45.16 2.43
24 25 2.668250 GCGGTTAATTTTCGCTGGTTT 58.332 42.857 10.91 0.00 45.16 3.27
25 26 1.400500 CGCGGTTAATTTTCGCTGGTT 60.400 47.619 0.00 0.00 46.23 3.67
26 27 0.167251 CGCGGTTAATTTTCGCTGGT 59.833 50.000 0.00 0.00 46.23 4.00
27 28 1.131618 GCGCGGTTAATTTTCGCTGG 61.132 55.000 8.83 4.98 46.23 4.85
28 29 1.452837 CGCGCGGTTAATTTTCGCTG 61.453 55.000 24.84 10.45 46.23 5.18
29 30 1.225908 CGCGCGGTTAATTTTCGCT 60.226 52.632 24.84 0.00 46.23 4.93
30 31 2.212330 CCGCGCGGTTAATTTTCGC 61.212 57.895 39.71 8.90 45.15 4.70
31 32 0.854445 GTCCGCGCGGTTAATTTTCG 60.854 55.000 44.16 18.40 36.47 3.46
32 33 0.445043 AGTCCGCGCGGTTAATTTTC 59.555 50.000 44.16 24.31 36.47 2.29
33 34 1.724429 TAGTCCGCGCGGTTAATTTT 58.276 45.000 44.16 24.87 36.47 1.82
34 35 1.944032 ATAGTCCGCGCGGTTAATTT 58.056 45.000 44.16 26.13 36.47 1.82
35 36 1.862827 GAATAGTCCGCGCGGTTAATT 59.137 47.619 44.16 36.15 36.47 1.40
36 37 1.202440 TGAATAGTCCGCGCGGTTAAT 60.202 47.619 44.16 31.32 36.47 1.40
37 38 0.173029 TGAATAGTCCGCGCGGTTAA 59.827 50.000 44.16 30.62 36.47 2.01
38 39 0.526096 GTGAATAGTCCGCGCGGTTA 60.526 55.000 44.16 35.14 36.47 2.85
39 40 1.808390 GTGAATAGTCCGCGCGGTT 60.808 57.895 44.16 34.29 36.47 4.44
40 41 2.202703 GTGAATAGTCCGCGCGGT 60.203 61.111 44.16 30.82 36.47 5.68
41 42 2.960129 GGTGAATAGTCCGCGCGG 60.960 66.667 42.13 42.13 0.00 6.46
42 43 1.807981 TTGGTGAATAGTCCGCGCG 60.808 57.895 25.67 25.67 0.00 6.86
43 44 0.739813 AGTTGGTGAATAGTCCGCGC 60.740 55.000 0.00 0.00 0.00 6.86
44 45 0.999406 CAGTTGGTGAATAGTCCGCG 59.001 55.000 0.00 0.00 0.00 6.46
45 46 0.727398 GCAGTTGGTGAATAGTCCGC 59.273 55.000 0.00 0.00 0.00 5.54
46 47 2.271800 GAGCAGTTGGTGAATAGTCCG 58.728 52.381 0.00 0.00 0.00 4.79
47 48 2.027192 TGGAGCAGTTGGTGAATAGTCC 60.027 50.000 0.00 0.00 0.00 3.85
48 49 3.334583 TGGAGCAGTTGGTGAATAGTC 57.665 47.619 0.00 0.00 0.00 2.59
49 50 4.307032 AATGGAGCAGTTGGTGAATAGT 57.693 40.909 0.00 0.00 0.00 2.12
50 51 4.818546 CCTAATGGAGCAGTTGGTGAATAG 59.181 45.833 0.00 0.00 34.57 1.73
51 52 4.473196 TCCTAATGGAGCAGTTGGTGAATA 59.527 41.667 0.00 0.00 37.46 1.75
52 53 3.266772 TCCTAATGGAGCAGTTGGTGAAT 59.733 43.478 0.00 0.00 37.46 2.57
53 54 2.642311 TCCTAATGGAGCAGTTGGTGAA 59.358 45.455 0.00 0.00 37.46 3.18
54 55 2.265367 TCCTAATGGAGCAGTTGGTGA 58.735 47.619 0.00 0.00 37.46 4.02
55 56 2.787473 TCCTAATGGAGCAGTTGGTG 57.213 50.000 0.00 0.00 37.46 4.17
65 66 6.923670 ACCTTGTATCTCTACTCCTAATGGA 58.076 40.000 0.00 0.00 40.69 3.41
66 67 8.707796 TTACCTTGTATCTCTACTCCTAATGG 57.292 38.462 0.00 0.00 0.00 3.16
71 72 9.747898 CATCTATTACCTTGTATCTCTACTCCT 57.252 37.037 0.00 0.00 0.00 3.69
72 73 9.523168 ACATCTATTACCTTGTATCTCTACTCC 57.477 37.037 0.00 0.00 0.00 3.85
127 128 2.178474 CAATGCGTGCAGTACCATTC 57.822 50.000 0.00 0.00 31.84 2.67
143 144 2.162681 GCAACCAAGTCCTGTAGCAAT 58.837 47.619 0.00 0.00 0.00 3.56
149 150 3.508845 ATAACTGCAACCAAGTCCTGT 57.491 42.857 0.00 0.00 0.00 4.00
302 304 6.494893 TGCATGTGAAAATACTCACCTTAC 57.505 37.500 0.00 0.00 44.30 2.34
309 311 5.975344 CACCATCATGCATGTGAAAATACTC 59.025 40.000 25.43 0.00 0.00 2.59
310 312 5.419788 ACACCATCATGCATGTGAAAATACT 59.580 36.000 25.43 0.00 0.00 2.12
351 353 7.123397 AGCTGACTCTAATTCTCTCAACATACA 59.877 37.037 0.00 0.00 0.00 2.29
375 377 4.678287 GCATAACATGTAACATGCATGAGC 59.322 41.667 32.75 20.19 44.60 4.26
398 400 1.173913 GGGGACGTTTTTGGATCCAG 58.826 55.000 15.53 5.41 32.45 3.86
418 1296 2.378038 TGAATTGATTGGCCCTAGTGC 58.622 47.619 0.00 0.00 0.00 4.40
425 1303 5.677567 AGATTTTGGATGAATTGATTGGCC 58.322 37.500 0.00 0.00 0.00 5.36
451 1329 4.326504 AAATGGCTTGTCTTTTGGAGTG 57.673 40.909 0.00 0.00 0.00 3.51
453 1331 5.841810 TGTAAAATGGCTTGTCTTTTGGAG 58.158 37.500 0.00 0.00 0.00 3.86
503 1381 6.596309 AAGAGATACTTCACATGTGAGACA 57.404 37.500 26.48 16.22 41.13 3.41
552 1430 8.567198 TCCCTTTAGGATCTCAATGAAGATTA 57.433 34.615 0.00 0.00 40.93 1.75
625 1504 5.010516 TGCCTAACATTAACTTGCATTGTGT 59.989 36.000 0.00 0.00 0.00 3.72
778 1657 8.767085 CCGGTATTTAGCGTCTAAAATGATAAA 58.233 33.333 13.47 0.00 44.83 1.40
780 1659 7.660112 TCCGGTATTTAGCGTCTAAAATGATA 58.340 34.615 13.47 2.85 44.83 2.15
782 1661 5.904941 TCCGGTATTTAGCGTCTAAAATGA 58.095 37.500 13.47 6.13 44.83 2.57
790 1669 1.591619 GTTGCTCCGGTATTTAGCGTC 59.408 52.381 0.00 0.00 44.83 5.19
803 1682 1.586154 CCAATGGTCCACGTTGCTCC 61.586 60.000 0.00 0.00 43.32 4.70
811 1690 3.117888 ACCACATCTATCCAATGGTCCAC 60.118 47.826 0.00 0.00 39.51 4.02
830 1709 0.538516 CAAATCCCACCCGTCAACCA 60.539 55.000 0.00 0.00 0.00 3.67
968 1849 9.149225 GTGTCATATAATTTTTGGCATGAAACA 57.851 29.630 0.00 0.00 33.00 2.83
969 1850 8.320295 CGTGTCATATAATTTTTGGCATGAAAC 58.680 33.333 0.00 0.00 34.66 2.78
973 1854 7.195646 AGTCGTGTCATATAATTTTTGGCATG 58.804 34.615 0.00 0.00 34.17 4.06
985 1873 8.623903 ACCGTTTTATAGAAGTCGTGTCATATA 58.376 33.333 0.00 0.00 0.00 0.86
1053 1942 0.823356 TTTGTGTCTTCCAGCTGCCC 60.823 55.000 8.66 0.00 0.00 5.36
1072 1961 7.148474 CGTTAGCAGTAGTTTGTTGAATATGGT 60.148 37.037 0.00 0.00 0.00 3.55
1092 1981 4.199840 TCCTTGTTCGAAAAACGTTAGC 57.800 40.909 0.00 0.00 43.13 3.09
1126 2015 4.445452 ACAAGACCAACAATGATCATGC 57.555 40.909 9.46 0.00 0.00 4.06
1291 2180 0.900647 ATCCTCCCATCGTCGATCCC 60.901 60.000 4.34 0.00 0.00 3.85
1293 2182 1.470890 GAGATCCTCCCATCGTCGATC 59.529 57.143 4.34 0.00 0.00 3.69
1300 2189 1.896465 CCGGTTAGAGATCCTCCCATC 59.104 57.143 0.00 0.00 0.00 3.51
1302 2191 0.931468 TCCGGTTAGAGATCCTCCCA 59.069 55.000 0.00 0.00 0.00 4.37
1306 2195 5.186198 CAATTTGTTCCGGTTAGAGATCCT 58.814 41.667 0.00 0.00 0.00 3.24
1318 2207 5.174943 GGTTTTGACTAAGCAATTTGTTCCG 59.825 40.000 0.00 0.00 0.00 4.30
1331 2220 4.202631 ACAAGGCATAGGGGTTTTGACTAA 60.203 41.667 0.00 0.00 0.00 2.24
1381 2270 1.490490 ACAGGAGACAAGGAGTTGCAA 59.510 47.619 0.00 0.00 37.14 4.08
1399 2288 1.315981 TTTCAGGTTTGCCGTGCACA 61.316 50.000 18.64 0.00 38.71 4.57
1436 2325 6.000891 TCAACAAAATGTGCATCTACACTC 57.999 37.500 0.00 0.00 41.30 3.51
1443 2332 6.035866 TGTCAAACTTCAACAAAATGTGCATC 59.964 34.615 0.00 0.00 0.00 3.91
1535 2427 2.639065 ACACCGTTGGTATATTGCCAG 58.361 47.619 0.00 0.00 37.31 4.85
1581 2478 5.282510 TGTTTCGTACGCAATTGGATTTTT 58.717 33.333 11.24 0.00 0.00 1.94
1594 2491 6.815672 TGGTTATACATGATGTTTCGTACG 57.184 37.500 9.53 9.53 0.00 3.67
1598 2495 6.356977 GCGATTTGGTTATACATGATGTTTCG 59.643 38.462 2.29 1.24 0.00 3.46
1631 2531 3.208594 TGCATGGATAAGCTAGCAACAG 58.791 45.455 18.83 0.00 0.00 3.16
1640 2540 4.546637 GCGCATGCATGGATAAGC 57.453 55.556 27.34 11.38 42.15 3.09
1650 2550 1.420641 TATGTCACGAGTGCGCATGC 61.421 55.000 15.91 7.91 42.48 4.06
1652 2552 0.173481 AGTATGTCACGAGTGCGCAT 59.827 50.000 15.91 1.95 42.48 4.73
1686 2586 4.642437 TGAAAGCAACACACCACAAAGATA 59.358 37.500 0.00 0.00 0.00 1.98
1742 2642 2.038007 AGGAAGGCCGCTCTCTGA 59.962 61.111 0.00 0.00 39.96 3.27
1743 2643 2.186384 CAGGAAGGCCGCTCTCTG 59.814 66.667 0.00 4.74 39.96 3.35
1744 2644 3.780173 GCAGGAAGGCCGCTCTCT 61.780 66.667 0.00 0.00 39.96 3.10
1802 2702 0.105778 TTGCACACATCACCTCACGA 59.894 50.000 0.00 0.00 0.00 4.35
1822 2722 6.353582 CGCTTTACTTACTTTCACGTTTTCTG 59.646 38.462 0.00 0.00 0.00 3.02
1877 2778 2.585869 CGAAAGCGACGTGTGCTGT 61.586 57.895 12.22 7.19 43.14 4.40
2010 2917 7.134163 ACACGCAACCATTTTAGTACTAAAAC 58.866 34.615 32.75 21.46 44.68 2.43
2016 2923 4.385447 TCGTACACGCAACCATTTTAGTAC 59.615 41.667 0.00 0.00 39.60 2.73
2030 2937 1.740043 CGCCTAAGCTTCGTACACGC 61.740 60.000 0.00 0.00 36.60 5.34
2031 2938 1.740043 GCGCCTAAGCTTCGTACACG 61.740 60.000 0.00 0.87 37.54 4.49
2038 2945 2.467826 CCAGCAGCGCCTAAGCTTC 61.468 63.158 0.00 0.00 46.80 3.86
2039 2946 2.437359 CCAGCAGCGCCTAAGCTT 60.437 61.111 2.29 3.48 46.80 3.74
2053 2960 3.939837 ATGCGAGCGTGGACACCAG 62.940 63.158 0.00 0.00 32.34 4.00
2115 3033 4.119363 ACTGGCGCCTGGATGCAT 62.119 61.111 33.10 11.81 0.00 3.96
2135 3053 1.064946 CCGATGAGCTCCGAGACAC 59.935 63.158 12.15 0.00 0.00 3.67
2292 3210 4.942761 ATGAGAATGGTGTGCACTTTTT 57.057 36.364 19.41 6.50 0.00 1.94
2293 3211 6.594788 AATATGAGAATGGTGTGCACTTTT 57.405 33.333 19.41 6.14 0.00 2.27
2294 3212 6.594788 AAATATGAGAATGGTGTGCACTTT 57.405 33.333 19.41 6.51 0.00 2.66
2295 3213 6.594788 AAAATATGAGAATGGTGTGCACTT 57.405 33.333 19.41 3.21 0.00 3.16
2296 3214 6.594788 AAAAATATGAGAATGGTGTGCACT 57.405 33.333 19.41 0.00 0.00 4.40
2353 3272 4.033358 GCACTGAACAAGTATCCGATTCTG 59.967 45.833 0.00 0.00 36.83 3.02
2394 3313 5.812286 AGACATCCGGTTTTACAAATACCT 58.188 37.500 0.00 0.00 0.00 3.08
2497 3417 2.341101 CGGACAGCTCTACCACGGT 61.341 63.158 0.00 0.00 0.00 4.83
2498 3418 2.490217 CGGACAGCTCTACCACGG 59.510 66.667 0.00 0.00 0.00 4.94
2499 3419 1.994507 CTCCGGACAGCTCTACCACG 61.995 65.000 0.00 0.00 0.00 4.94
2500 3420 0.680280 TCTCCGGACAGCTCTACCAC 60.680 60.000 0.00 0.00 0.00 4.16
2501 3421 0.680280 GTCTCCGGACAGCTCTACCA 60.680 60.000 0.00 0.00 41.75 3.25
2502 3422 0.680280 TGTCTCCGGACAGCTCTACC 60.680 60.000 0.00 0.00 46.19 3.18
2503 3423 2.869636 TGTCTCCGGACAGCTCTAC 58.130 57.895 0.00 0.00 46.19 2.59
2521 3441 1.528292 AAGTTCGTCCTCTGCTCGCT 61.528 55.000 0.00 0.00 0.00 4.93


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

AutoCloner maintained by Alex Coulton.