Multiple sequence alignment - TraesCS6A01G337600

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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 TraesCS6A01G337600 chr6A 100.000 3009 0 0 1 3009 571681977 571684985 0.000000e+00 5557.0
1 TraesCS6A01G337600 chr6D 95.923 1962 75 2 75 2036 426982946 426984902 0.000000e+00 3175.0
2 TraesCS6A01G337600 chr6D 92.463 544 17 8 2487 3006 426985782 426986325 0.000000e+00 756.0
3 TraesCS6A01G337600 chr6D 89.964 279 23 2 2036 2310 426984946 426985223 3.690000e-94 355.0
4 TraesCS6A01G337600 chr6D 87.622 307 23 11 2314 2610 426985305 426985606 2.870000e-90 342.0
5 TraesCS6A01G337600 chr6B 92.949 1475 50 19 572 2039 642723693 642725120 0.000000e+00 2098.0
6 TraesCS6A01G337600 chr6B 81.790 637 63 19 575 1204 642466357 642466947 4.510000e-133 484.0
7 TraesCS6A01G337600 chr6B 84.187 449 49 12 148 578 642717631 642718075 1.670000e-112 416.0
8 TraesCS6A01G337600 chr6B 89.226 297 32 0 2595 2891 642726080 642726376 3.660000e-99 372.0
9 TraesCS6A01G337600 chr6B 90.182 275 26 1 2036 2310 642725158 642725431 1.030000e-94 357.0
10 TraesCS6A01G337600 chr6B 92.347 196 6 8 2314 2507 642725522 642725710 1.370000e-68 270.0
11 TraesCS6A01G337600 chr6B 96.117 103 2 2 2509 2610 642725837 642725938 1.860000e-37 167.0
12 TraesCS6A01G337600 chr2B 83.817 241 38 1 1634 1873 649479852 649479612 8.390000e-56 228.0
13 TraesCS6A01G337600 chr2B 82.540 189 29 4 1625 1811 649975427 649975613 2.400000e-36 163.0
14 TraesCS6A01G337600 chr2A 82.988 241 40 1 1634 1873 686704003 686703763 1.820000e-52 217.0
15 TraesCS6A01G337600 chr2A 87.166 187 24 0 1442 1628 686777763 686777577 2.350000e-51 213.0
16 TraesCS6A01G337600 chr2A 88.050 159 19 0 1453 1611 686797568 686797726 3.960000e-44 189.0
17 TraesCS6A01G337600 chr2A 82.540 189 29 4 1625 1811 686823645 686823831 2.400000e-36 163.0
18 TraesCS6A01G337600 chr2D 82.258 248 42 2 1634 1880 543846897 543846651 2.350000e-51 213.0
19 TraesCS6A01G337600 chr2D 87.166 187 24 0 1442 1628 544171159 544170973 2.350000e-51 213.0
20 TraesCS6A01G337600 chr2D 84.211 171 23 4 1625 1793 544583444 544583612 2.400000e-36 163.0
21 TraesCS6A01G337600 chr7B 85.549 173 23 2 1455 1626 580885295 580885124 2.380000e-41 180.0
22 TraesCS6A01G337600 chr7A 85.549 173 23 2 1455 1626 619576283 619576112 2.380000e-41 180.0
23 TraesCS6A01G337600 chr7D 84.971 173 24 2 1455 1626 538140455 538140284 1.110000e-39 174.0
24 TraesCS6A01G337600 chr7D 84.971 173 24 2 1455 1626 538662456 538662627 1.110000e-39 174.0
25 TraesCS6A01G337600 chr1B 80.488 123 19 4 400 519 335554679 335554799 4.130000e-14 89.8


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 TraesCS6A01G337600 chr6A 571681977 571684985 3008 False 5557.0 5557 100.0000 1 3009 1 chr6A.!!$F1 3008
1 TraesCS6A01G337600 chr6D 426982946 426986325 3379 False 1157.0 3175 91.4930 75 3006 4 chr6D.!!$F1 2931
2 TraesCS6A01G337600 chr6B 642723693 642726376 2683 False 652.8 2098 92.1642 572 2891 5 chr6B.!!$F3 2319
3 TraesCS6A01G337600 chr6B 642466357 642466947 590 False 484.0 484 81.7900 575 1204 1 chr6B.!!$F1 629

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
941 954 0.10412 TTGATCGTATGGAGGGCACG 59.896 55.0 0.0 0.0 37.03 5.34 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2899 3510 0.250727 TGGGCTAAACAGTGTGCTCC 60.251 55.0 0.0 0.92 0.0 4.7 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
21 22 3.810373 CTCTGTTAACGTTCATTGTGCC 58.190 45.455 2.82 0.00 0.00 5.01
22 23 3.472652 TCTGTTAACGTTCATTGTGCCT 58.527 40.909 2.82 0.00 0.00 4.75
23 24 3.496884 TCTGTTAACGTTCATTGTGCCTC 59.503 43.478 2.82 0.00 0.00 4.70
24 25 3.206964 TGTTAACGTTCATTGTGCCTCA 58.793 40.909 2.82 0.00 0.00 3.86
25 26 3.628032 TGTTAACGTTCATTGTGCCTCAA 59.372 39.130 2.82 0.00 40.53 3.02
26 27 4.277174 TGTTAACGTTCATTGTGCCTCAAT 59.723 37.500 2.82 0.00 46.32 2.57
27 28 3.559238 AACGTTCATTGTGCCTCAATC 57.441 42.857 0.00 0.00 43.93 2.67
28 29 1.464608 ACGTTCATTGTGCCTCAATCG 59.535 47.619 1.97 5.81 43.93 3.34
29 30 1.791555 CGTTCATTGTGCCTCAATCGC 60.792 52.381 1.97 0.00 43.93 4.58
30 31 1.199789 GTTCATTGTGCCTCAATCGCA 59.800 47.619 1.97 0.00 43.93 5.10
37 38 2.579207 TGCCTCAATCGCACTAGTAC 57.421 50.000 0.00 0.00 0.00 2.73
38 39 1.136305 TGCCTCAATCGCACTAGTACC 59.864 52.381 0.00 0.00 0.00 3.34
39 40 1.409427 GCCTCAATCGCACTAGTACCT 59.591 52.381 0.00 0.00 0.00 3.08
40 41 2.159085 GCCTCAATCGCACTAGTACCTT 60.159 50.000 0.00 0.00 0.00 3.50
41 42 3.707793 CCTCAATCGCACTAGTACCTTC 58.292 50.000 0.00 0.00 0.00 3.46
42 43 3.364062 CTCAATCGCACTAGTACCTTCG 58.636 50.000 0.00 0.00 0.00 3.79
43 44 2.751259 TCAATCGCACTAGTACCTTCGT 59.249 45.455 0.00 0.00 0.00 3.85
44 45 3.940852 TCAATCGCACTAGTACCTTCGTA 59.059 43.478 0.00 0.00 0.00 3.43
45 46 4.395854 TCAATCGCACTAGTACCTTCGTAA 59.604 41.667 0.00 0.00 0.00 3.18
46 47 5.066893 TCAATCGCACTAGTACCTTCGTAAT 59.933 40.000 0.00 0.00 0.00 1.89
47 48 4.282950 TCGCACTAGTACCTTCGTAATG 57.717 45.455 0.00 0.00 0.00 1.90
48 49 3.691118 TCGCACTAGTACCTTCGTAATGT 59.309 43.478 0.00 0.00 0.00 2.71
49 50 4.156556 TCGCACTAGTACCTTCGTAATGTT 59.843 41.667 0.00 0.00 0.00 2.71
50 51 5.353956 TCGCACTAGTACCTTCGTAATGTTA 59.646 40.000 0.00 0.00 0.00 2.41
51 52 5.680229 CGCACTAGTACCTTCGTAATGTTAG 59.320 44.000 0.00 0.00 0.00 2.34
52 53 5.975939 GCACTAGTACCTTCGTAATGTTAGG 59.024 44.000 0.00 0.00 0.00 2.69
53 54 6.501781 CACTAGTACCTTCGTAATGTTAGGG 58.498 44.000 0.00 0.00 31.91 3.53
54 55 4.397481 AGTACCTTCGTAATGTTAGGGC 57.603 45.455 0.00 0.00 31.91 5.19
55 56 2.704464 ACCTTCGTAATGTTAGGGCC 57.296 50.000 0.00 0.00 31.91 5.80
56 57 1.134610 ACCTTCGTAATGTTAGGGCCG 60.135 52.381 0.00 0.00 31.91 6.13
57 58 1.578583 CTTCGTAATGTTAGGGCCGG 58.421 55.000 0.00 0.00 0.00 6.13
58 59 0.462403 TTCGTAATGTTAGGGCCGGC 60.462 55.000 21.18 21.18 0.00 6.13
59 60 1.890510 CGTAATGTTAGGGCCGGCC 60.891 63.158 38.57 38.57 0.00 6.13
79 80 3.434319 GCCTGTGTCGTGCCCATG 61.434 66.667 0.00 0.00 0.00 3.66
98 99 1.009829 GTGGCGAGTCATTGTCATCC 58.990 55.000 0.00 0.00 0.00 3.51
100 101 1.293924 GGCGAGTCATTGTCATCCTG 58.706 55.000 0.00 0.00 0.00 3.86
107 108 3.053842 AGTCATTGTCATCCTGCCAGAAT 60.054 43.478 0.00 0.00 0.00 2.40
164 165 0.241749 TCGACGCCGACAACATAAGT 59.758 50.000 0.00 0.00 40.30 2.24
171 172 2.939640 GCCGACAACATAAGTCACCCAT 60.940 50.000 0.00 0.00 35.77 4.00
179 180 5.573380 ACATAAGTCACCCATGCATATCT 57.427 39.130 0.00 0.00 0.00 1.98
191 192 6.491403 ACCCATGCATATCTTTTATCCACTTC 59.509 38.462 0.00 0.00 0.00 3.01
227 228 1.599047 CTGGCCGTCCTTGTCATCT 59.401 57.895 0.00 0.00 0.00 2.90
329 330 4.754372 TGTCAATGACAATGTCTTCTGC 57.246 40.909 14.37 3.37 39.78 4.26
354 355 0.177604 CTCCCTCTGTCTGGTGATGC 59.822 60.000 0.00 0.00 0.00 3.91
367 368 0.663269 GTGATGCGACGACACAGTCA 60.663 55.000 0.00 0.00 40.98 3.41
374 375 2.740055 CGACACAGTCAGCCTGCC 60.740 66.667 0.00 0.00 45.68 4.85
514 515 0.105964 ACTGCTACACTGCCGTTTGA 59.894 50.000 0.00 0.00 0.00 2.69
530 531 4.204168 CCGTTTGATTTTGACTGAACGTTG 59.796 41.667 5.00 0.00 38.43 4.10
641 642 1.407712 GGCGCATTGGAAGGTAGGTTA 60.408 52.381 10.83 0.00 0.00 2.85
642 643 1.669265 GCGCATTGGAAGGTAGGTTAC 59.331 52.381 0.30 0.00 0.00 2.50
704 714 1.888512 CGGGAGGCCATGGAAATAATG 59.111 52.381 18.40 0.00 0.00 1.90
718 728 5.044476 TGGAAATAATGAAGCTCCCTGGTAA 60.044 40.000 0.00 0.00 0.00 2.85
763 773 6.142498 TCATCCAATAACAAGCCCCAAATAT 58.858 36.000 0.00 0.00 0.00 1.28
764 774 6.614906 TCATCCAATAACAAGCCCCAAATATT 59.385 34.615 0.00 0.00 0.00 1.28
782 792 0.672889 TTGCAAATTGAGCGAGCCAA 59.327 45.000 0.00 0.00 33.85 4.52
785 795 0.883833 CAAATTGAGCGAGCCAACCT 59.116 50.000 0.00 0.00 0.00 3.50
889 902 3.388024 CCTTCCCCGTTTCATCATCTCTA 59.612 47.826 0.00 0.00 0.00 2.43
941 954 0.104120 TTGATCGTATGGAGGGCACG 59.896 55.000 0.00 0.00 37.03 5.34
999 1015 3.056107 TCGTGTCAATTAGTTAGCCAGCT 60.056 43.478 0.00 0.00 0.00 4.24
1045 1061 1.619827 CTTGTTGGCATTCCATGGTGT 59.380 47.619 12.58 0.00 43.05 4.16
1060 1076 1.367102 GTGTTGGTGGCCATGTTGG 59.633 57.895 9.72 0.00 41.55 3.77
1072 1088 1.228124 ATGTTGGTGGTGGTGGTCG 60.228 57.895 0.00 0.00 0.00 4.79
1299 1315 4.367023 GGCACGGTCACCACGCTA 62.367 66.667 4.52 0.00 34.00 4.26
1326 1342 1.227468 TCCGTCGATCGATCTCCGT 60.227 57.895 22.50 0.00 42.86 4.69
1381 1397 4.397832 ACCGTGCCCCGCGTTTAT 62.398 61.111 4.92 0.00 35.46 1.40
1382 1398 3.569690 CCGTGCCCCGCGTTTATC 61.570 66.667 4.92 0.00 35.46 1.75
1384 1400 2.437002 GTGCCCCGCGTTTATCCA 60.437 61.111 4.92 0.00 0.00 3.41
1389 1405 1.358759 CCCGCGTTTATCCATTGGC 59.641 57.895 4.92 0.00 0.00 4.52
1396 1412 1.133407 GTTTATCCATTGGCGGCGAAA 59.867 47.619 12.98 4.12 0.00 3.46
1408 1424 3.880490 TGGCGGCGAAATATTAAGAATGT 59.120 39.130 12.98 0.00 0.00 2.71
1415 1431 5.790495 GCGAAATATTAAGAATGTGATCGGC 59.210 40.000 0.00 0.00 0.00 5.54
1450 1466 3.771160 GAGGACGTGCCGTGGGAT 61.771 66.667 2.38 0.00 41.37 3.85
1489 1505 1.671379 GGAGTTCCTGGGCAACGTC 60.671 63.158 0.00 0.00 37.60 4.34
1997 2013 2.830370 GGCTCCCCAAGGAATGCG 60.830 66.667 0.00 0.00 43.40 4.73
1998 2014 2.044946 GCTCCCCAAGGAATGCGT 60.045 61.111 0.00 0.00 43.40 5.24
2020 2036 3.932710 TCGTGGAGTAGTTGCATGATTTC 59.067 43.478 0.00 0.00 38.12 2.17
2139 2207 8.421002 AGAATTACATAAGTGCCACAAAAGTTT 58.579 29.630 0.00 0.00 0.00 2.66
2167 2235 3.131396 CTGCGTTGGTCTTGAAGTAGTT 58.869 45.455 0.00 0.00 0.00 2.24
2169 2237 4.695396 TGCGTTGGTCTTGAAGTAGTTAA 58.305 39.130 0.00 0.00 0.00 2.01
2180 2248 8.002665 GTCTTGAAGTAGTTAAAGCAAGTAACG 58.997 37.037 2.76 0.00 36.71 3.18
2204 2272 5.790495 GCAGACGATCAACAATTTAACTGAC 59.210 40.000 0.00 0.00 0.00 3.51
2212 2280 5.534654 TCAACAATTTAACTGACCCCTCTTG 59.465 40.000 0.00 0.00 0.00 3.02
2219 2287 0.906756 CTGACCCCTCTTGAGCTGGA 60.907 60.000 0.00 0.00 0.00 3.86
2264 2332 9.950496 GAATGATCCTGGTGTAAATATGAGTAT 57.050 33.333 0.00 0.00 0.00 2.12
2280 2348 6.579666 ATGAGTATTGCTTGTTGTGAACAT 57.420 33.333 0.00 0.00 41.79 2.71
2284 2352 3.883830 TTGCTTGTTGTGAACATGGTT 57.116 38.095 0.00 0.00 41.79 3.67
2291 2359 4.663166 TGTTGTGAACATGGTTTTGTACG 58.337 39.130 0.00 0.00 36.25 3.67
2310 2378 9.649024 TTTGTACGTTTAACTTAAAAAGGATCG 57.351 29.630 0.00 0.00 0.00 3.69
2410 2570 8.712363 CAATACTAGACATACACAATATGCCAC 58.288 37.037 0.00 0.00 0.00 5.01
2465 2628 3.768215 AGGGTACTTCTACCTAACTGCAC 59.232 47.826 0.00 0.00 42.22 4.57
2507 2670 9.525409 CTTCCAAAATTATCAGATCCATTTGAC 57.475 33.333 12.82 0.00 0.00 3.18
2603 3069 1.542915 ACTGCAACTAATGGCAAGCTG 59.457 47.619 0.00 0.00 39.93 4.24
2845 3432 2.328099 GCCAGCGACAACCAAGGAG 61.328 63.158 0.00 0.00 0.00 3.69
2885 3472 7.790027 TGATCAACCAAGGAATTTTCTTTTGA 58.210 30.769 6.91 6.91 30.47 2.69
2899 3510 6.726035 TTTCTTTTGAAAATGACGTTAGCG 57.274 33.333 0.00 0.00 44.51 4.26
2930 3541 3.761752 TGTTTAGCCCAAATAGGAAGCAC 59.238 43.478 0.00 0.00 41.22 4.40
3006 3617 2.206576 AATTCAGTTCCAGCCAGTCC 57.793 50.000 0.00 0.00 0.00 3.85
3007 3618 1.366319 ATTCAGTTCCAGCCAGTCCT 58.634 50.000 0.00 0.00 0.00 3.85
3008 3619 0.397941 TTCAGTTCCAGCCAGTCCTG 59.602 55.000 0.00 0.00 0.00 3.86
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 3.498397 AGGCACAATGAACGTTAACAGAG 59.502 43.478 0.00 0.00 0.00 3.35
1 2 3.472652 AGGCACAATGAACGTTAACAGA 58.527 40.909 0.00 0.00 0.00 3.41
2 3 3.249799 TGAGGCACAATGAACGTTAACAG 59.750 43.478 0.00 1.29 0.00 3.16
3 4 3.206964 TGAGGCACAATGAACGTTAACA 58.793 40.909 0.00 0.00 0.00 2.41
4 5 3.889196 TGAGGCACAATGAACGTTAAC 57.111 42.857 0.00 0.00 0.00 2.01
18 19 1.136305 GGTACTAGTGCGATTGAGGCA 59.864 52.381 5.39 0.00 38.25 4.75
19 20 1.409427 AGGTACTAGTGCGATTGAGGC 59.591 52.381 5.39 0.00 36.02 4.70
20 21 3.707793 GAAGGTACTAGTGCGATTGAGG 58.292 50.000 5.39 0.00 38.49 3.86
21 22 3.181499 ACGAAGGTACTAGTGCGATTGAG 60.181 47.826 5.39 2.63 38.49 3.02
22 23 2.751259 ACGAAGGTACTAGTGCGATTGA 59.249 45.455 5.39 0.00 38.49 2.57
23 24 3.146618 ACGAAGGTACTAGTGCGATTG 57.853 47.619 5.39 3.17 38.49 2.67
24 25 4.970662 TTACGAAGGTACTAGTGCGATT 57.029 40.909 5.39 2.59 38.49 3.34
25 26 4.337555 ACATTACGAAGGTACTAGTGCGAT 59.662 41.667 5.39 0.00 38.49 4.58
26 27 3.691118 ACATTACGAAGGTACTAGTGCGA 59.309 43.478 5.39 0.00 38.49 5.10
27 28 4.025015 ACATTACGAAGGTACTAGTGCG 57.975 45.455 5.39 4.20 38.49 5.34
28 29 5.975939 CCTAACATTACGAAGGTACTAGTGC 59.024 44.000 5.39 3.50 38.49 4.40
29 30 6.501781 CCCTAACATTACGAAGGTACTAGTG 58.498 44.000 5.39 0.00 38.49 2.74
30 31 5.068329 GCCCTAACATTACGAAGGTACTAGT 59.932 44.000 0.00 0.00 38.49 2.57
31 32 5.508657 GGCCCTAACATTACGAAGGTACTAG 60.509 48.000 0.00 0.00 38.49 2.57
32 33 4.342092 GGCCCTAACATTACGAAGGTACTA 59.658 45.833 0.00 0.00 38.49 1.82
34 35 3.461061 GGCCCTAACATTACGAAGGTAC 58.539 50.000 0.00 0.00 0.00 3.34
35 36 2.101249 CGGCCCTAACATTACGAAGGTA 59.899 50.000 0.00 0.00 0.00 3.08
36 37 1.134610 CGGCCCTAACATTACGAAGGT 60.135 52.381 0.00 0.00 0.00 3.50
37 38 1.578583 CGGCCCTAACATTACGAAGG 58.421 55.000 0.00 0.00 0.00 3.46
38 39 1.578583 CCGGCCCTAACATTACGAAG 58.421 55.000 0.00 0.00 0.00 3.79
39 40 0.462403 GCCGGCCCTAACATTACGAA 60.462 55.000 18.11 0.00 0.00 3.85
40 41 1.144496 GCCGGCCCTAACATTACGA 59.856 57.895 18.11 0.00 0.00 3.43
41 42 1.890510 GGCCGGCCCTAACATTACG 60.891 63.158 36.64 0.00 0.00 3.18
42 43 4.152644 GGCCGGCCCTAACATTAC 57.847 61.111 36.64 5.01 0.00 1.89
60 61 3.907260 ATGGGCACGACACAGGCAG 62.907 63.158 0.00 0.00 0.00 4.85
61 62 3.952508 ATGGGCACGACACAGGCA 61.953 61.111 0.00 0.00 0.00 4.75
62 63 3.434319 CATGGGCACGACACAGGC 61.434 66.667 0.00 0.00 0.00 4.85
63 64 2.032528 ACATGGGCACGACACAGG 59.967 61.111 0.00 0.00 0.00 4.00
64 65 2.327343 CCACATGGGCACGACACAG 61.327 63.158 0.00 0.00 0.00 3.66
65 66 2.281414 CCACATGGGCACGACACA 60.281 61.111 0.00 0.00 0.00 3.72
79 80 1.009829 GGATGACAATGACTCGCCAC 58.990 55.000 0.00 0.00 0.00 5.01
107 108 4.458829 ATGACTCTCCCGGGCGGA 62.459 66.667 18.49 15.62 38.83 5.54
154 155 3.153369 TGCATGGGTGACTTATGTTGT 57.847 42.857 0.00 0.00 0.00 3.32
164 165 5.769662 GTGGATAAAAGATATGCATGGGTGA 59.230 40.000 10.16 0.00 0.00 4.02
171 172 7.975616 GCAAAAGAAGTGGATAAAAGATATGCA 59.024 33.333 0.00 0.00 0.00 3.96
179 180 6.097554 TGGACAAGCAAAAGAAGTGGATAAAA 59.902 34.615 0.00 0.00 0.00 1.52
227 228 1.848388 ACCATGCTCATCCTCCATGAA 59.152 47.619 0.00 0.00 41.25 2.57
294 295 3.619929 TCATTGACATCAACATCGAGCAG 59.380 43.478 0.00 0.00 38.86 4.24
329 330 1.595882 CAGACAGAGGGAGGTGCTG 59.404 63.158 0.00 0.00 35.81 4.41
354 355 1.730902 CAGGCTGACTGTGTCGTCG 60.731 63.158 9.42 0.00 42.42 5.12
367 368 4.292178 GATCGCGCTAGGCAGGCT 62.292 66.667 5.56 0.38 43.84 4.58
374 375 2.727647 GCCACTCGATCGCGCTAG 60.728 66.667 11.09 5.02 37.46 3.42
481 482 1.525077 GCAGTGTTGACCCGACCAA 60.525 57.895 0.00 0.00 0.00 3.67
514 515 2.598907 CGACGCAACGTTCAGTCAAAAT 60.599 45.455 23.82 0.00 41.37 1.82
641 642 1.836999 TACCTTCATGCCACCTGCGT 61.837 55.000 0.00 0.00 45.60 5.24
642 643 1.078497 TACCTTCATGCCACCTGCG 60.078 57.895 0.00 0.00 45.60 5.18
704 714 2.170607 TGCATACTTACCAGGGAGCTTC 59.829 50.000 0.00 0.00 0.00 3.86
740 750 4.758773 ATTTGGGGCTTGTTATTGGATG 57.241 40.909 0.00 0.00 0.00 3.51
763 773 0.672889 TTGGCTCGCTCAATTTGCAA 59.327 45.000 0.00 0.00 0.00 4.08
764 774 0.039256 GTTGGCTCGCTCAATTTGCA 60.039 50.000 0.00 0.00 0.00 4.08
782 792 5.431731 TGTTAGGATCCATGGAATGTTAGGT 59.568 40.000 20.67 0.00 44.81 3.08
785 795 5.769662 GCATGTTAGGATCCATGGAATGTTA 59.230 40.000 20.67 6.53 44.81 2.41
914 927 4.993584 CCCTCCATACGATCAAGATTTGAG 59.006 45.833 0.00 0.00 43.98 3.02
941 954 3.035363 CCTTCTTCTTCTACCTCCTCCC 58.965 54.545 0.00 0.00 0.00 4.30
950 963 5.024803 TCCCTTCCTTCCTTCTTCTTCTA 57.975 43.478 0.00 0.00 0.00 2.10
999 1015 2.507547 GGCAACGACGACGCCATA 60.508 61.111 21.79 0.00 45.52 2.74
1045 1061 1.836158 CCACCAACATGGCCACCAA 60.836 57.895 8.16 0.00 42.67 3.67
1060 1076 1.375523 GATCCACGACCACCACCAC 60.376 63.158 0.00 0.00 0.00 4.16
1072 1088 1.177256 GCCATGGCCATCTGATCCAC 61.177 60.000 27.24 0.00 31.94 4.02
1104 1120 0.592500 CCCACACGATCTCGATGTCG 60.593 60.000 15.40 15.40 43.02 4.35
1337 1353 1.447317 CCCTGACATGGCGTATTGGC 61.447 60.000 0.00 0.00 45.12 4.52
1340 1356 4.559502 GCCCTGACATGGCGTATT 57.440 55.556 5.96 0.00 39.48 1.89
1381 1397 1.686355 AATATTTCGCCGCCAATGGA 58.314 45.000 2.05 0.00 0.00 3.41
1382 1398 3.252215 TCTTAATATTTCGCCGCCAATGG 59.748 43.478 0.00 0.00 0.00 3.16
1384 1400 5.009610 ACATTCTTAATATTTCGCCGCCAAT 59.990 36.000 0.00 0.00 0.00 3.16
1389 1405 6.009474 CGATCACATTCTTAATATTTCGCCG 58.991 40.000 0.00 0.00 0.00 6.46
1396 1412 3.367932 CGCGCCGATCACATTCTTAATAT 59.632 43.478 0.00 0.00 0.00 1.28
1489 1505 4.814294 GTGTAGGGCTCGCCGGTG 62.814 72.222 9.28 9.28 36.85 4.94
1584 1600 1.471676 CGATGGAGTAGGTGTGGAAGC 60.472 57.143 0.00 0.00 0.00 3.86
1789 1805 1.153429 GCGGTAGTGGGCGAAGAAT 60.153 57.895 0.00 0.00 0.00 2.40
1930 1946 3.066760 TGCAGTAGTCGTAGATCATGTGG 59.933 47.826 0.00 0.00 40.67 4.17
1997 2013 2.363788 TCATGCAACTACTCCACGAC 57.636 50.000 0.00 0.00 0.00 4.34
1998 2014 3.610040 AATCATGCAACTACTCCACGA 57.390 42.857 0.00 0.00 0.00 4.35
2117 2185 6.276847 CCAAACTTTTGTGGCACTTATGTAA 58.723 36.000 19.83 0.00 36.45 2.41
2128 2196 2.825205 CAGAAGGCCAAACTTTTGTGG 58.175 47.619 5.01 0.00 36.45 4.17
2139 2207 2.281484 GACCAACGCAGAAGGCCA 60.281 61.111 5.01 0.00 40.31 5.36
2167 2235 3.015934 TCGTCTGCGTTACTTGCTTTA 57.984 42.857 0.00 0.00 39.49 1.85
2169 2237 1.993370 GATCGTCTGCGTTACTTGCTT 59.007 47.619 0.00 0.00 39.49 3.91
2180 2248 5.790495 GTCAGTTAAATTGTTGATCGTCTGC 59.210 40.000 0.00 0.00 0.00 4.26
2204 2272 1.153005 GCATCCAGCTCAAGAGGGG 60.153 63.158 0.00 0.00 41.15 4.79
2219 2287 9.362539 GATCATTCATTTGTTTTCACTTAGCAT 57.637 29.630 0.00 0.00 0.00 3.79
2264 2332 3.883830 AACCATGTTCACAACAAGCAA 57.116 38.095 0.00 0.00 45.86 3.91
2280 2348 9.351570 CCTTTTTAAGTTAAACGTACAAAACCA 57.648 29.630 7.58 0.00 0.00 3.67
2284 2352 9.649024 CGATCCTTTTTAAGTTAAACGTACAAA 57.351 29.630 7.58 0.00 0.00 2.83
2305 2373 9.764363 TGCATATTATCTTTGGTATATCGATCC 57.236 33.333 0.00 0.00 0.00 3.36
2389 2547 7.734924 ATTGTGGCATATTGTGTATGTCTAG 57.265 36.000 0.00 0.00 31.31 2.43
2390 2548 9.791801 AATATTGTGGCATATTGTGTATGTCTA 57.208 29.630 0.00 0.00 31.31 2.59
2392 2550 9.398170 GAAATATTGTGGCATATTGTGTATGTC 57.602 33.333 0.00 0.00 0.00 3.06
2395 2553 7.508636 TGGGAAATATTGTGGCATATTGTGTAT 59.491 33.333 0.00 0.00 0.00 2.29
2396 2554 6.836007 TGGGAAATATTGTGGCATATTGTGTA 59.164 34.615 0.00 0.00 0.00 2.90
2398 2556 6.159299 TGGGAAATATTGTGGCATATTGTG 57.841 37.500 0.00 0.00 0.00 3.33
2399 2557 6.805016 TTGGGAAATATTGTGGCATATTGT 57.195 33.333 0.00 0.00 0.00 2.71
2400 2558 7.227116 CCTTTTGGGAAATATTGTGGCATATTG 59.773 37.037 0.00 0.00 37.23 1.90
2401 2559 7.127032 TCCTTTTGGGAAATATTGTGGCATATT 59.873 33.333 0.00 0.00 41.91 1.28
2402 2560 6.614906 TCCTTTTGGGAAATATTGTGGCATAT 59.385 34.615 0.00 0.00 41.91 1.78
2403 2561 5.960811 TCCTTTTGGGAAATATTGTGGCATA 59.039 36.000 0.00 0.00 41.91 3.14
2405 2563 4.163427 TCCTTTTGGGAAATATTGTGGCA 58.837 39.130 0.00 0.00 41.91 4.92
2406 2564 4.817318 TCCTTTTGGGAAATATTGTGGC 57.183 40.909 0.00 0.00 41.91 5.01
2465 2628 4.345859 TGGAAGTTTAGTGGTACCTGTG 57.654 45.455 14.36 0.00 0.00 3.66
2507 2670 1.379044 GGGAGGATGCTGGTTGGTG 60.379 63.158 0.00 0.00 0.00 4.17
2603 3069 5.747197 CAGATCATGGAAGCTTGTTATTTGC 59.253 40.000 2.10 0.00 0.00 3.68
2608 3074 3.282021 GGCAGATCATGGAAGCTTGTTA 58.718 45.455 2.10 0.00 0.00 2.41
2845 3432 3.921119 TGATCAACAACATTCCACTGC 57.079 42.857 0.00 0.00 0.00 4.40
2885 3472 1.463444 GTGCTCCGCTAACGTCATTTT 59.537 47.619 0.00 0.00 37.70 1.82
2891 3502 1.372997 CAGTGTGCTCCGCTAACGT 60.373 57.895 0.00 0.00 37.70 3.99
2896 3507 0.951040 GCTAAACAGTGTGCTCCGCT 60.951 55.000 0.00 0.00 0.00 5.52
2899 3510 0.250727 TGGGCTAAACAGTGTGCTCC 60.251 55.000 0.00 0.92 0.00 4.70
2930 3541 2.093764 CAGGCTCTACAGAAACCTCAGG 60.094 54.545 0.00 0.00 30.69 3.86


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

AutoCloner maintained by Alex Coulton.