Multiple sequence alignment - TraesCS6D01G307300

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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 TraesCS6D01G307300 chr6D 100.000 2330 0 0 1 2330 418314137 418311808 0.000000e+00 4303.0
1 TraesCS6D01G307300 chr6D 90.736 421 33 4 970 1385 418530982 418530563 7.270000e-155 556.0
2 TraesCS6D01G307300 chr6D 87.708 480 52 6 976 1451 418524221 418523745 9.410000e-154 553.0
3 TraesCS6D01G307300 chr6D 78.900 673 85 33 471 1100 418463510 418462852 1.000000e-108 403.0
4 TraesCS6D01G307300 chr6B 91.605 2299 130 30 82 2330 630466857 630464572 0.000000e+00 3118.0
5 TraesCS6D01G307300 chr6B 83.537 984 97 34 471 1411 630505545 630504584 0.000000e+00 859.0
6 TraesCS6D01G307300 chr6B 90.465 409 37 2 976 1383 630529582 630529175 2.630000e-149 538.0
7 TraesCS6D01G307300 chr6B 86.946 406 51 2 976 1380 630514592 630514188 2.730000e-124 455.0
8 TraesCS6D01G307300 chr6B 88.158 380 40 3 970 1345 630568740 630568362 4.570000e-122 448.0
9 TraesCS6D01G307300 chr6A 94.654 636 22 6 810 1434 560753830 560753196 0.000000e+00 976.0
10 TraesCS6D01G307300 chr6A 82.739 1037 102 45 471 1449 560817345 560816328 0.000000e+00 852.0
11 TraesCS6D01G307300 chr6A 87.712 708 49 17 82 777 560754514 560753833 0.000000e+00 791.0
12 TraesCS6D01G307300 chr6A 89.549 421 39 3 970 1386 560829438 560829019 1.590000e-146 529.0
13 TraesCS6D01G307300 chr6A 79.288 618 65 22 1496 2066 560753079 560752478 7.860000e-100 374.0
14 TraesCS6D01G307300 chr2D 87.500 264 33 0 2067 2330 643954355 643954618 2.910000e-79 305.0
15 TraesCS6D01G307300 chr2D 96.591 88 2 1 1 87 231429313 231429400 6.710000e-31 145.0
16 TraesCS6D01G307300 chr2D 89.796 49 2 2 1431 1477 643842874 643842827 2.500000e-05 60.2
17 TraesCS6D01G307300 chr5D 86.142 267 34 1 2067 2330 75417433 75417699 3.790000e-73 285.0
18 TraesCS6D01G307300 chr5D 96.552 87 3 0 1 87 278540678 278540764 6.710000e-31 145.0
19 TraesCS6D01G307300 chr5D 89.796 49 4 1 1843 1891 486530749 486530796 6.950000e-06 62.1
20 TraesCS6D01G307300 chr5A 85.985 264 37 0 2067 2330 691036525 691036262 1.360000e-72 283.0
21 TraesCS6D01G307300 chr5A 85.227 264 39 0 2067 2330 364423234 364423497 2.950000e-69 272.0
22 TraesCS6D01G307300 chr2A 85.985 264 35 2 2067 2330 726767948 726767687 4.900000e-72 281.0
23 TraesCS6D01G307300 chr1D 85.036 274 41 0 2057 2330 227115310 227115583 1.760000e-71 279.0
24 TraesCS6D01G307300 chr1D 84.307 274 43 0 2057 2330 226948039 226948312 3.820000e-68 268.0
25 TraesCS6D01G307300 chr3A 85.606 264 38 0 2067 2330 749638560 749638297 6.340000e-71 278.0
26 TraesCS6D01G307300 chr3D 98.795 83 1 0 1 83 193761231 193761313 5.190000e-32 148.0
27 TraesCS6D01G307300 chr3D 97.647 85 2 0 1 85 294225785 294225701 1.870000e-31 147.0
28 TraesCS6D01G307300 chr3D 95.506 89 4 0 1 89 404265222 404265310 2.410000e-30 143.0
29 TraesCS6D01G307300 chr7D 95.556 90 4 0 1 90 129171593 129171504 6.710000e-31 145.0
30 TraesCS6D01G307300 chr7D 96.552 87 3 0 1 87 316826842 316826928 6.710000e-31 145.0
31 TraesCS6D01G307300 chr7D 93.617 94 5 1 2 95 438486705 438486797 3.120000e-29 139.0
32 TraesCS6D01G307300 chr4D 95.455 88 3 1 1 88 158748448 158748534 3.120000e-29 139.0


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 TraesCS6D01G307300 chr6D 418311808 418314137 2329 True 4303.000000 4303 100.000 1 2330 1 chr6D.!!$R1 2329
1 TraesCS6D01G307300 chr6D 418462852 418463510 658 True 403.000000 403 78.900 471 1100 1 chr6D.!!$R2 629
2 TraesCS6D01G307300 chr6B 630464572 630466857 2285 True 3118.000000 3118 91.605 82 2330 1 chr6B.!!$R1 2248
3 TraesCS6D01G307300 chr6B 630504584 630505545 961 True 859.000000 859 83.537 471 1411 1 chr6B.!!$R2 940
4 TraesCS6D01G307300 chr6A 560816328 560817345 1017 True 852.000000 852 82.739 471 1449 1 chr6A.!!$R1 978
5 TraesCS6D01G307300 chr6A 560752478 560754514 2036 True 713.666667 976 87.218 82 2066 3 chr6A.!!$R3 1984

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
793 838 0.037734 CCCAACACCCACCTTCCTAC 59.962 60.0 0.0 0.0 0.0 3.18 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2265 2472 0.53264 CCGGACATGATCGCCAATGA 60.533 55.0 0.0 0.0 0.0 2.57 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
24 25 7.295952 CGAAGGGAATATCATAACACATAGC 57.704 40.000 0.00 0.00 0.00 2.97
25 26 6.313905 CGAAGGGAATATCATAACACATAGCC 59.686 42.308 0.00 0.00 0.00 3.93
26 27 5.734720 AGGGAATATCATAACACATAGCCG 58.265 41.667 0.00 0.00 0.00 5.52
27 28 5.483937 AGGGAATATCATAACACATAGCCGA 59.516 40.000 0.00 0.00 0.00 5.54
28 29 6.013725 AGGGAATATCATAACACATAGCCGAA 60.014 38.462 0.00 0.00 0.00 4.30
29 30 6.653320 GGGAATATCATAACACATAGCCGAAA 59.347 38.462 0.00 0.00 0.00 3.46
30 31 7.174253 GGGAATATCATAACACATAGCCGAAAA 59.826 37.037 0.00 0.00 0.00 2.29
31 32 8.730680 GGAATATCATAACACATAGCCGAAAAT 58.269 33.333 0.00 0.00 0.00 1.82
32 33 9.546909 GAATATCATAACACATAGCCGAAAATG 57.453 33.333 0.00 0.00 0.00 2.32
33 34 5.749596 TCATAACACATAGCCGAAAATGG 57.250 39.130 0.00 0.00 0.00 3.16
34 35 5.189928 TCATAACACATAGCCGAAAATGGT 58.810 37.500 0.00 0.00 0.00 3.55
35 36 6.350103 TCATAACACATAGCCGAAAATGGTA 58.650 36.000 0.00 0.00 0.00 3.25
36 37 6.824196 TCATAACACATAGCCGAAAATGGTAA 59.176 34.615 0.00 0.00 0.00 2.85
37 38 5.560966 AACACATAGCCGAAAATGGTAAG 57.439 39.130 0.00 0.00 0.00 2.34
38 39 4.839121 ACACATAGCCGAAAATGGTAAGA 58.161 39.130 0.00 0.00 0.00 2.10
39 40 4.876107 ACACATAGCCGAAAATGGTAAGAG 59.124 41.667 0.00 0.00 0.00 2.85
40 41 4.876107 CACATAGCCGAAAATGGTAAGAGT 59.124 41.667 0.00 0.00 0.00 3.24
41 42 5.354234 CACATAGCCGAAAATGGTAAGAGTT 59.646 40.000 0.00 0.00 0.00 3.01
42 43 5.354234 ACATAGCCGAAAATGGTAAGAGTTG 59.646 40.000 0.00 0.00 0.00 3.16
43 44 4.015872 AGCCGAAAATGGTAAGAGTTGA 57.984 40.909 0.00 0.00 0.00 3.18
44 45 4.394729 AGCCGAAAATGGTAAGAGTTGAA 58.605 39.130 0.00 0.00 0.00 2.69
45 46 4.455877 AGCCGAAAATGGTAAGAGTTGAAG 59.544 41.667 0.00 0.00 0.00 3.02
46 47 4.215613 GCCGAAAATGGTAAGAGTTGAAGT 59.784 41.667 0.00 0.00 0.00 3.01
47 48 5.278315 GCCGAAAATGGTAAGAGTTGAAGTT 60.278 40.000 0.00 0.00 0.00 2.66
48 49 6.072893 GCCGAAAATGGTAAGAGTTGAAGTTA 60.073 38.462 0.00 0.00 0.00 2.24
49 50 7.295930 CCGAAAATGGTAAGAGTTGAAGTTAC 58.704 38.462 0.00 0.00 0.00 2.50
50 51 7.041644 CCGAAAATGGTAAGAGTTGAAGTTACA 60.042 37.037 0.00 0.00 0.00 2.41
51 52 8.339714 CGAAAATGGTAAGAGTTGAAGTTACAA 58.660 33.333 0.00 0.00 0.00 2.41
57 58 9.226606 TGGTAAGAGTTGAAGTTACAAATATGG 57.773 33.333 0.00 0.00 0.00 2.74
58 59 9.444600 GGTAAGAGTTGAAGTTACAAATATGGA 57.555 33.333 0.00 0.00 0.00 3.41
62 63 9.574516 AGAGTTGAAGTTACAAATATGGAAAGT 57.425 29.630 0.00 0.00 28.98 2.66
70 71 8.889717 AGTTACAAATATGGAAAGTTACATCCG 58.110 33.333 0.00 0.00 38.63 4.18
71 72 6.693315 ACAAATATGGAAAGTTACATCCGG 57.307 37.500 0.00 0.00 38.63 5.14
72 73 5.592688 ACAAATATGGAAAGTTACATCCGGG 59.407 40.000 0.00 0.00 38.63 5.73
73 74 2.729028 ATGGAAAGTTACATCCGGGG 57.271 50.000 0.00 0.00 38.63 5.73
74 75 1.364269 TGGAAAGTTACATCCGGGGT 58.636 50.000 0.00 2.79 38.63 4.95
75 76 1.003812 TGGAAAGTTACATCCGGGGTG 59.996 52.381 5.55 5.55 38.63 4.61
76 77 1.003928 GGAAAGTTACATCCGGGGTGT 59.996 52.381 18.45 18.45 0.00 4.16
77 78 2.553685 GGAAAGTTACATCCGGGGTGTT 60.554 50.000 19.71 0.00 0.00 3.32
78 79 3.307621 GGAAAGTTACATCCGGGGTGTTA 60.308 47.826 19.71 6.65 0.00 2.41
79 80 3.339253 AAGTTACATCCGGGGTGTTAC 57.661 47.619 19.71 19.44 31.30 2.50
80 81 2.259012 AGTTACATCCGGGGTGTTACA 58.741 47.619 26.16 4.90 33.02 2.41
129 137 2.676471 ATTGACGGCAAGTGGGGC 60.676 61.111 10.69 0.00 37.45 5.80
167 175 2.601067 TGGGCGGTGTTCGAGGTA 60.601 61.111 0.00 0.00 42.43 3.08
203 211 0.324460 CGGGGTTCTCTAGTGGAGGT 60.324 60.000 3.39 0.00 42.10 3.85
221 229 1.214424 GGTAGAGAGCAGAGGAGGAGT 59.786 57.143 0.00 0.00 0.00 3.85
310 318 4.642429 ACATGGAGGACAGTTCAAACTAC 58.358 43.478 0.00 0.00 37.08 2.73
374 382 0.553819 AGTCCGGACTATCCAGAGCT 59.446 55.000 35.59 7.66 40.43 4.09
392 400 6.489022 CCAGAGCTCATTGGATGATATTTTCA 59.511 38.462 17.77 0.00 38.85 2.69
421 429 5.337250 CCATTAGATGATATTTCCGGACCGA 60.337 44.000 17.49 0.00 0.00 4.69
431 439 1.559368 TCCGGACCGAACAAATAGGA 58.441 50.000 17.49 0.00 0.00 2.94
481 490 9.023962 TGTCCTAAGTAAATGAAATCTTGCAAT 57.976 29.630 0.00 0.00 0.00 3.56
551 573 6.650807 CAGATAGTAAAACAGTTGCAGAGGAA 59.349 38.462 0.00 0.00 0.00 3.36
659 699 1.512156 AAACCGCAATCGAAACGCCT 61.512 50.000 0.00 0.00 38.10 5.52
793 838 0.037734 CCCAACACCCACCTTCCTAC 59.962 60.000 0.00 0.00 0.00 3.18
794 839 0.768622 CCAACACCCACCTTCCTACA 59.231 55.000 0.00 0.00 0.00 2.74
795 840 1.144093 CCAACACCCACCTTCCTACAA 59.856 52.381 0.00 0.00 0.00 2.41
796 841 2.504367 CAACACCCACCTTCCTACAAG 58.496 52.381 0.00 0.00 0.00 3.16
797 842 1.064825 ACACCCACCTTCCTACAAGG 58.935 55.000 0.00 0.00 43.05 3.61
910 965 7.390027 CAAATCTCTTCTTCTTCCACTCCTAA 58.610 38.462 0.00 0.00 0.00 2.69
946 1018 2.569404 CCAAGAAGTACAGCTCCTCCTT 59.431 50.000 0.00 0.00 0.00 3.36
949 1021 2.180276 GAAGTACAGCTCCTCCTTCCA 58.820 52.381 0.00 0.00 0.00 3.53
951 1023 1.077993 AGTACAGCTCCTCCTTCCACT 59.922 52.381 0.00 0.00 0.00 4.00
954 1026 0.617249 CAGCTCCTCCTTCCACTCCT 60.617 60.000 0.00 0.00 0.00 3.69
1533 1691 8.608844 AGACTTGACAGTAATAAGGACAAAAG 57.391 34.615 0.00 0.00 31.22 2.27
1536 1694 7.284489 ACTTGACAGTAATAAGGACAAAAGCAA 59.716 33.333 0.00 0.00 0.00 3.91
1576 1734 5.128335 AGGGATCCTTTGATTCAAAGCAATC 59.872 40.000 26.74 26.24 46.44 2.67
1622 1780 9.752961 TTTAAATACTTAGGAACCTTTTTGTGC 57.247 29.630 0.00 0.00 0.00 4.57
1728 1887 6.094603 CCATCCACTCAAACCTCTTCATAAAG 59.905 42.308 0.00 0.00 0.00 1.85
2075 2281 9.798994 GATGCATTTTCTATTGAAGTGAATTCT 57.201 29.630 0.00 0.00 38.83 2.40
2088 2294 8.617290 TGAAGTGAATTCTACTTTTTACCCTC 57.383 34.615 18.24 8.69 38.42 4.30
2098 2304 8.710749 TCTACTTTTTACCCTCTAGTTGTACA 57.289 34.615 0.00 0.00 0.00 2.90
2104 2310 7.972832 TTTACCCTCTAGTTGTACATTTGTG 57.027 36.000 0.00 0.00 0.00 3.33
2116 2322 8.726988 AGTTGTACATTTGTGACACATATTACC 58.273 33.333 9.55 1.21 0.00 2.85
2169 2375 8.306680 TCAGATTTTAGAGACTTTAAACACGG 57.693 34.615 0.00 0.00 0.00 4.94
2216 2422 5.734220 GCGTGTTTATGTTAGATAGGACCGA 60.734 44.000 0.00 0.00 0.00 4.69
2223 2429 6.971726 ATGTTAGATAGGACCGACATGTTA 57.028 37.500 0.00 0.00 0.00 2.41
2224 2430 6.140303 TGTTAGATAGGACCGACATGTTAC 57.860 41.667 0.00 0.00 0.00 2.50
2237 2443 4.258935 ACATGTTACGTCAATGATTCGC 57.741 40.909 10.88 0.00 0.00 4.70
2242 2448 5.511571 TGTTACGTCAATGATTCGCAAAAA 58.488 33.333 0.00 0.00 0.00 1.94
2243 2449 5.623264 TGTTACGTCAATGATTCGCAAAAAG 59.377 36.000 0.00 0.00 0.00 2.27
2244 2450 4.223320 ACGTCAATGATTCGCAAAAAGT 57.777 36.364 0.00 0.00 0.00 2.66
2245 2451 4.606961 ACGTCAATGATTCGCAAAAAGTT 58.393 34.783 0.00 0.00 0.00 2.66
2246 2452 4.440758 ACGTCAATGATTCGCAAAAAGTTG 59.559 37.500 0.00 0.00 37.83 3.16
2257 2464 4.789119 TCGCAAAAAGTTGTGTAAAGAACG 59.211 37.500 0.44 0.00 44.17 3.95
2264 2471 0.759959 TGTGTAAAGAACGGAGGGCA 59.240 50.000 0.00 0.00 0.00 5.36
2265 2472 1.349688 TGTGTAAAGAACGGAGGGCAT 59.650 47.619 0.00 0.00 0.00 4.40
2267 2474 1.626321 TGTAAAGAACGGAGGGCATCA 59.374 47.619 0.08 0.00 0.00 3.07
2283 2490 1.196127 CATCATTGGCGATCATGTCCG 59.804 52.381 0.00 0.00 0.00 4.79
2290 2497 0.103208 GCGATCATGTCCGGACTTCT 59.897 55.000 33.39 17.29 0.00 2.85
2295 2502 1.066858 TCATGTCCGGACTTCTCTTGC 60.067 52.381 33.39 6.04 0.00 4.01
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 6.313905 GGCTATGTGTTATGATATTCCCTTCG 59.686 42.308 0.00 0.00 0.00 3.79
3 4 5.483937 TCGGCTATGTGTTATGATATTCCCT 59.516 40.000 0.00 0.00 0.00 4.20
6 7 9.546909 CATTTTCGGCTATGTGTTATGATATTC 57.453 33.333 0.00 0.00 0.00 1.75
7 8 8.514594 CCATTTTCGGCTATGTGTTATGATATT 58.485 33.333 0.00 0.00 0.00 1.28
8 9 7.665559 ACCATTTTCGGCTATGTGTTATGATAT 59.334 33.333 0.00 0.00 0.00 1.63
9 10 6.995686 ACCATTTTCGGCTATGTGTTATGATA 59.004 34.615 0.00 0.00 0.00 2.15
10 11 5.827797 ACCATTTTCGGCTATGTGTTATGAT 59.172 36.000 0.00 0.00 0.00 2.45
11 12 5.189928 ACCATTTTCGGCTATGTGTTATGA 58.810 37.500 0.00 0.00 0.00 2.15
12 13 5.499139 ACCATTTTCGGCTATGTGTTATG 57.501 39.130 0.00 0.00 0.00 1.90
13 14 7.051623 TCTTACCATTTTCGGCTATGTGTTAT 58.948 34.615 0.00 0.00 0.00 1.89
14 15 6.408035 TCTTACCATTTTCGGCTATGTGTTA 58.592 36.000 0.00 0.00 0.00 2.41
15 16 5.250200 TCTTACCATTTTCGGCTATGTGTT 58.750 37.500 0.00 0.00 0.00 3.32
16 17 4.839121 TCTTACCATTTTCGGCTATGTGT 58.161 39.130 0.00 0.00 0.00 3.72
17 18 4.876107 ACTCTTACCATTTTCGGCTATGTG 59.124 41.667 0.00 0.00 0.00 3.21
18 19 5.099042 ACTCTTACCATTTTCGGCTATGT 57.901 39.130 0.00 0.00 0.00 2.29
19 20 5.584649 TCAACTCTTACCATTTTCGGCTATG 59.415 40.000 0.00 0.00 0.00 2.23
20 21 5.741011 TCAACTCTTACCATTTTCGGCTAT 58.259 37.500 0.00 0.00 0.00 2.97
21 22 5.155278 TCAACTCTTACCATTTTCGGCTA 57.845 39.130 0.00 0.00 0.00 3.93
22 23 4.015872 TCAACTCTTACCATTTTCGGCT 57.984 40.909 0.00 0.00 0.00 5.52
23 24 4.215613 ACTTCAACTCTTACCATTTTCGGC 59.784 41.667 0.00 0.00 0.00 5.54
24 25 5.941948 ACTTCAACTCTTACCATTTTCGG 57.058 39.130 0.00 0.00 0.00 4.30
25 26 7.857569 TGTAACTTCAACTCTTACCATTTTCG 58.142 34.615 0.00 0.00 0.00 3.46
31 32 9.226606 CCATATTTGTAACTTCAACTCTTACCA 57.773 33.333 0.00 0.00 0.00 3.25
32 33 9.444600 TCCATATTTGTAACTTCAACTCTTACC 57.555 33.333 0.00 0.00 0.00 2.85
36 37 9.574516 ACTTTCCATATTTGTAACTTCAACTCT 57.425 29.630 0.00 0.00 0.00 3.24
44 45 8.889717 CGGATGTAACTTTCCATATTTGTAACT 58.110 33.333 0.00 0.00 31.99 2.24
45 46 8.126700 CCGGATGTAACTTTCCATATTTGTAAC 58.873 37.037 0.00 0.00 31.99 2.50
46 47 7.283580 CCCGGATGTAACTTTCCATATTTGTAA 59.716 37.037 0.73 0.00 31.99 2.41
47 48 6.768861 CCCGGATGTAACTTTCCATATTTGTA 59.231 38.462 0.73 0.00 31.99 2.41
48 49 5.592688 CCCGGATGTAACTTTCCATATTTGT 59.407 40.000 0.73 0.00 31.99 2.83
49 50 5.009610 CCCCGGATGTAACTTTCCATATTTG 59.990 44.000 0.73 0.00 31.99 2.32
50 51 5.137551 CCCCGGATGTAACTTTCCATATTT 58.862 41.667 0.73 0.00 31.99 1.40
51 52 4.167307 ACCCCGGATGTAACTTTCCATATT 59.833 41.667 0.73 0.00 31.99 1.28
52 53 3.720002 ACCCCGGATGTAACTTTCCATAT 59.280 43.478 0.73 0.00 31.99 1.78
53 54 3.116959 ACCCCGGATGTAACTTTCCATA 58.883 45.455 0.73 0.00 31.99 2.74
54 55 1.920351 ACCCCGGATGTAACTTTCCAT 59.080 47.619 0.73 0.00 31.99 3.41
55 56 1.003812 CACCCCGGATGTAACTTTCCA 59.996 52.381 0.73 0.00 31.99 3.53
56 57 1.003928 ACACCCCGGATGTAACTTTCC 59.996 52.381 0.73 0.00 0.00 3.13
57 58 2.484742 ACACCCCGGATGTAACTTTC 57.515 50.000 0.73 0.00 0.00 2.62
58 59 2.963599 AACACCCCGGATGTAACTTT 57.036 45.000 0.73 0.00 0.00 2.66
59 60 2.638855 TGTAACACCCCGGATGTAACTT 59.361 45.455 0.73 0.00 0.00 2.66
60 61 2.235402 CTGTAACACCCCGGATGTAACT 59.765 50.000 0.73 0.00 0.00 2.24
61 62 2.624636 CTGTAACACCCCGGATGTAAC 58.375 52.381 0.73 0.05 0.00 2.50
62 63 1.555992 CCTGTAACACCCCGGATGTAA 59.444 52.381 0.73 0.00 0.00 2.41
63 64 1.196911 CCTGTAACACCCCGGATGTA 58.803 55.000 0.73 0.00 0.00 2.29
64 65 0.545787 TCCTGTAACACCCCGGATGT 60.546 55.000 0.73 3.79 0.00 3.06
65 66 0.178068 CTCCTGTAACACCCCGGATG 59.822 60.000 0.73 2.98 0.00 3.51
66 67 0.981277 CCTCCTGTAACACCCCGGAT 60.981 60.000 0.73 0.00 0.00 4.18
67 68 1.611261 CCTCCTGTAACACCCCGGA 60.611 63.158 0.73 0.00 0.00 5.14
68 69 2.666098 CCCTCCTGTAACACCCCGG 61.666 68.421 0.00 0.00 0.00 5.73
69 70 1.486145 AACCCTCCTGTAACACCCCG 61.486 60.000 0.00 0.00 0.00 5.73
70 71 0.327259 GAACCCTCCTGTAACACCCC 59.673 60.000 0.00 0.00 0.00 4.95
71 72 1.003233 CAGAACCCTCCTGTAACACCC 59.997 57.143 0.00 0.00 0.00 4.61
72 73 1.003233 CCAGAACCCTCCTGTAACACC 59.997 57.143 0.00 0.00 0.00 4.16
73 74 1.003233 CCCAGAACCCTCCTGTAACAC 59.997 57.143 0.00 0.00 0.00 3.32
74 75 1.358152 CCCAGAACCCTCCTGTAACA 58.642 55.000 0.00 0.00 0.00 2.41
75 76 0.035343 GCCCAGAACCCTCCTGTAAC 60.035 60.000 0.00 0.00 0.00 2.50
76 77 0.474854 TGCCCAGAACCCTCCTGTAA 60.475 55.000 0.00 0.00 0.00 2.41
77 78 0.909610 CTGCCCAGAACCCTCCTGTA 60.910 60.000 0.00 0.00 0.00 2.74
78 79 2.121963 TGCCCAGAACCCTCCTGT 60.122 61.111 0.00 0.00 0.00 4.00
79 80 2.673523 CTGCCCAGAACCCTCCTG 59.326 66.667 0.00 0.00 0.00 3.86
80 81 3.334054 GCTGCCCAGAACCCTCCT 61.334 66.667 0.00 0.00 0.00 3.69
147 155 4.760047 CTCGAACACCGCCCAGGG 62.760 72.222 0.00 0.00 46.96 4.45
185 193 2.244252 TCTACCTCCACTAGAGAACCCC 59.756 54.545 0.00 0.00 46.50 4.95
190 198 3.116174 TGCTCTCTACCTCCACTAGAGA 58.884 50.000 0.00 5.31 46.50 3.10
203 211 1.214175 CCACTCCTCCTCTGCTCTCTA 59.786 57.143 0.00 0.00 0.00 2.43
221 229 3.238497 CCGTCCCACACTCCACCA 61.238 66.667 0.00 0.00 0.00 4.17
294 302 6.272558 AGAAATAGGGTAGTTTGAACTGTCCT 59.727 38.462 17.59 17.59 41.88 3.85
310 318 6.705863 CTCAAATTGAGGGAAGAAATAGGG 57.294 41.667 14.85 0.00 40.71 3.53
374 382 5.771666 GGGCTCTGAAAATATCATCCAATGA 59.228 40.000 0.00 0.00 44.55 2.57
392 400 5.338708 CCGGAAATATCATCTAATGGGCTCT 60.339 44.000 0.00 0.00 0.00 4.09
421 429 2.645797 TCCCCCTTTCGTCCTATTTGTT 59.354 45.455 0.00 0.00 0.00 2.83
431 439 0.542702 TAACGGACTCCCCCTTTCGT 60.543 55.000 0.00 0.00 0.00 3.85
486 495 6.691818 GCGAAGATTTGTAGACGATTCTCTAA 59.308 38.462 0.00 0.00 32.75 2.10
551 573 1.732259 CGAAGCTACGCACAGGATTTT 59.268 47.619 0.00 0.00 0.00 1.82
579 601 3.973206 TTTCCTCTTCCATGCTACGAA 57.027 42.857 0.00 0.00 0.00 3.85
659 699 3.250280 CGTCGGCTACTCTTCTATGCTTA 59.750 47.826 0.00 0.00 0.00 3.09
793 838 1.600023 TTTCACGGGTTGTAGCCTTG 58.400 50.000 0.00 0.00 36.48 3.61
794 839 2.351706 TTTTCACGGGTTGTAGCCTT 57.648 45.000 0.00 0.00 32.48 4.35
795 840 2.351706 TTTTTCACGGGTTGTAGCCT 57.648 45.000 0.00 0.00 32.48 4.58
841 886 2.935201 TGTGCCAATCTGTTGTTTTTGC 59.065 40.909 0.00 0.00 33.36 3.68
868 913 1.411651 TTGGATGGGTGTGTGGACGA 61.412 55.000 0.00 0.00 0.00 4.20
910 965 1.741327 CTTGGCTTTGCTGGTGCTGT 61.741 55.000 0.00 0.00 40.48 4.40
946 1018 0.896940 AACGGCGAAGTAGGAGTGGA 60.897 55.000 16.62 0.00 0.00 4.02
949 1021 0.245813 GGAAACGGCGAAGTAGGAGT 59.754 55.000 16.62 0.00 0.00 3.85
1485 1575 4.282496 ACGGTCTCAAGGAGTAATCATCT 58.718 43.478 0.00 0.00 0.00 2.90
1486 1576 4.657436 ACGGTCTCAAGGAGTAATCATC 57.343 45.455 0.00 0.00 0.00 2.92
1488 1578 4.639310 GTCTACGGTCTCAAGGAGTAATCA 59.361 45.833 0.00 0.00 0.00 2.57
1489 1579 4.883006 AGTCTACGGTCTCAAGGAGTAATC 59.117 45.833 0.00 0.00 0.00 1.75
1533 1691 3.054878 CCTGAAACTGTTTGATGCTTGC 58.945 45.455 11.03 0.00 0.00 4.01
1536 1694 3.228188 TCCCTGAAACTGTTTGATGCT 57.772 42.857 11.03 0.00 0.00 3.79
1576 1734 7.636259 TTAAATCGTCCAAAAATTCTGCAAG 57.364 32.000 0.00 0.00 0.00 4.01
1702 1861 2.040278 TGAAGAGGTTTGAGTGGATGGG 59.960 50.000 0.00 0.00 0.00 4.00
1728 1887 4.382345 AGCATAGGAAAAGCAATGAAGC 57.618 40.909 0.00 0.00 0.00 3.86
2085 2291 5.989168 TGTGTCACAAATGTACAACTAGAGG 59.011 40.000 2.31 0.00 0.00 3.69
2098 2304 7.732222 AAATGGGGTAATATGTGTCACAAAT 57.268 32.000 10.28 1.91 0.00 2.32
2104 2310 6.877611 CCACTAAATGGGGTAATATGTGTC 57.122 41.667 0.00 0.00 45.95 3.67
2153 2359 5.059161 GGTAAACCCGTGTTTAAAGTCTCT 58.941 41.667 4.74 0.00 45.79 3.10
2169 2375 5.332732 GCAAAATGCAAAACTACGGTAAACC 60.333 40.000 0.00 0.00 44.26 3.27
2194 2400 6.567050 TGTCGGTCCTATCTAACATAAACAC 58.433 40.000 0.00 0.00 0.00 3.32
2205 2411 3.285484 ACGTAACATGTCGGTCCTATCT 58.715 45.455 11.16 0.00 0.00 1.98
2216 2422 3.682377 TGCGAATCATTGACGTAACATGT 59.318 39.130 0.00 0.00 0.00 3.21
2223 2429 4.223320 ACTTTTTGCGAATCATTGACGT 57.777 36.364 0.00 0.00 0.00 4.34
2224 2430 4.440758 ACAACTTTTTGCGAATCATTGACG 59.559 37.500 9.95 0.00 36.00 4.35
2237 2443 5.741982 CCTCCGTTCTTTACACAACTTTTTG 59.258 40.000 0.00 0.00 38.83 2.44
2242 2448 2.809299 GCCCTCCGTTCTTTACACAACT 60.809 50.000 0.00 0.00 0.00 3.16
2243 2449 1.534163 GCCCTCCGTTCTTTACACAAC 59.466 52.381 0.00 0.00 0.00 3.32
2244 2450 1.141254 TGCCCTCCGTTCTTTACACAA 59.859 47.619 0.00 0.00 0.00 3.33
2245 2451 0.759959 TGCCCTCCGTTCTTTACACA 59.240 50.000 0.00 0.00 0.00 3.72
2246 2452 2.007608 GATGCCCTCCGTTCTTTACAC 58.992 52.381 0.00 0.00 0.00 2.90
2257 2464 1.228367 ATCGCCAATGATGCCCTCC 60.228 57.895 0.00 0.00 0.00 4.30
2264 2471 1.516161 CGGACATGATCGCCAATGAT 58.484 50.000 0.00 0.00 0.00 2.45
2265 2472 0.532640 CCGGACATGATCGCCAATGA 60.533 55.000 0.00 0.00 0.00 2.57
2267 2474 0.532862 GTCCGGACATGATCGCCAAT 60.533 55.000 29.75 0.00 0.00 3.16
2283 2490 4.187694 CAACAGATAGGCAAGAGAAGTCC 58.812 47.826 0.00 0.00 0.00 3.85
2290 2497 3.054139 AGGAATGCAACAGATAGGCAAGA 60.054 43.478 0.00 0.00 41.43 3.02
2295 2502 3.185246 ACGAGGAATGCAACAGATAGG 57.815 47.619 0.00 0.00 0.00 2.57


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

AutoCloner maintained by Alex Coulton.