Multiple sequence alignment - TraesCS1B01G145800

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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 TraesCS1B01G145800 chr1B 100.000 3727 0 0 1 3727 200297274 200301000 0.000000e+00 6883.0
1 TraesCS1B01G145800 chr1A 95.370 2311 71 23 556 2845 153337122 153339417 0.000000e+00 3642.0
2 TraesCS1B01G145800 chr1A 96.868 894 13 9 2836 3727 153339442 153340322 0.000000e+00 1482.0
3 TraesCS1B01G145800 chr1A 87.770 417 50 1 45 460 153332793 153333209 1.560000e-133 486.0
4 TraesCS1B01G145800 chr1A 90.435 115 8 3 450 564 153333525 153333636 8.340000e-32 148.0
5 TraesCS1B01G145800 chr1A 86.408 103 13 1 61 163 570257616 570257717 1.090000e-20 111.0
6 TraesCS1B01G145800 chr1A 89.655 58 1 1 2053 2110 94623199 94623147 6.680000e-08 69.4
7 TraesCS1B01G145800 chr1D 97.140 1888 42 4 507 2386 138785117 138783234 0.000000e+00 3177.0
8 TraesCS1B01G145800 chr1D 96.125 1342 24 10 2368 3705 138783222 138781905 0.000000e+00 2165.0
9 TraesCS1B01G145800 chr1D 96.610 59 2 0 1995 2053 254402434 254402492 8.520000e-17 99.0
10 TraesCS1B01G145800 chr5D 83.813 278 31 7 247 515 370941807 370942079 6.180000e-63 252.0
11 TraesCS1B01G145800 chr5D 91.089 101 7 2 246 346 375285417 375285319 6.490000e-28 135.0
12 TraesCS1B01G145800 chr5D 96.610 59 2 0 1995 2053 6184614 6184556 8.520000e-17 99.0
13 TraesCS1B01G145800 chr5D 96.610 59 2 0 1995 2053 483807258 483807200 8.520000e-17 99.0
14 TraesCS1B01G145800 chr5D 96.610 59 2 0 1995 2053 503283626 503283684 8.520000e-17 99.0
15 TraesCS1B01G145800 chr4D 83.648 159 25 1 62 220 226541639 226541482 8.340000e-32 148.0
16 TraesCS1B01G145800 chr4D 78.667 225 36 9 9 224 686842 686621 5.020000e-29 139.0
17 TraesCS1B01G145800 chr4D 89.655 58 1 1 2053 2110 123678779 123678727 6.680000e-08 69.4
18 TraesCS1B01G145800 chr4A 93.103 87 4 2 1857 1943 521300853 521300937 3.910000e-25 126.0
19 TraesCS1B01G145800 chr4A 79.661 118 17 3 102 219 628470911 628470801 1.110000e-10 78.7
20 TraesCS1B01G145800 chr4A 89.655 58 1 1 2053 2110 246690936 246690884 6.680000e-08 69.4
21 TraesCS1B01G145800 chr7A 88.119 101 12 0 246 346 686928933 686929033 1.820000e-23 121.0
22 TraesCS1B01G145800 chr7A 96.774 62 2 0 2108 2169 575311308 575311247 1.830000e-18 104.0
23 TraesCS1B01G145800 chr7A 100.000 30 0 0 195 224 90485926 90485955 5.200000e-04 56.5
24 TraesCS1B01G145800 chr3B 88.350 103 7 5 246 346 549425530 549425629 6.540000e-23 119.0
25 TraesCS1B01G145800 chr3B 96.774 62 2 0 2108 2169 822040407 822040346 1.830000e-18 104.0
26 TraesCS1B01G145800 chr3B 96.774 62 2 0 2108 2169 822068497 822068436 1.830000e-18 104.0
27 TraesCS1B01G145800 chr3B 79.675 123 21 3 68 187 188178910 188179031 6.630000e-13 86.1
28 TraesCS1B01G145800 chr3B 94.340 53 2 1 2053 2105 581959219 581959270 3.090000e-11 80.5
29 TraesCS1B01G145800 chr2D 75.502 249 51 8 3 242 511445042 511444795 3.040000e-21 113.0
30 TraesCS1B01G145800 chr3A 96.774 62 2 0 2108 2169 671093559 671093620 1.830000e-18 104.0
31 TraesCS1B01G145800 chr3A 94.828 58 3 0 2053 2110 585018029 585017972 1.430000e-14 91.6
32 TraesCS1B01G145800 chr5B 81.890 127 17 4 8 128 32652354 32652480 6.590000e-18 102.0
33 TraesCS1B01G145800 chr5B 92.308 39 3 0 186 224 8022293 8022255 5.200000e-04 56.5
34 TraesCS1B01G145800 chr6D 96.667 60 2 0 1994 2053 429819876 429819935 2.370000e-17 100.0
35 TraesCS1B01G145800 chr6D 96.610 59 2 0 1995 2053 45515243 45515185 8.520000e-17 99.0
36 TraesCS1B01G145800 chrUn 96.610 59 2 0 1995 2053 458727174 458727232 8.520000e-17 99.0
37 TraesCS1B01G145800 chr3D 96.226 53 1 1 2053 2105 444053635 444053686 6.630000e-13 86.1
38 TraesCS1B01G145800 chr6B 79.661 118 9 11 22 128 560202932 560203045 1.860000e-08 71.3
39 TraesCS1B01G145800 chr5A 89.655 58 1 1 2053 2110 492872025 492871973 6.680000e-08 69.4
40 TraesCS1B01G145800 chr6A 100.000 31 0 0 184 214 449401817 449401847 1.450000e-04 58.4
41 TraesCS1B01G145800 chr2A 80.556 72 14 0 150 221 56944361 56944290 5.200000e-04 56.5


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 TraesCS1B01G145800 chr1B 200297274 200301000 3726 False 6883.0 6883 100.00000 1 3727 1 chr1B.!!$F1 3726
1 TraesCS1B01G145800 chr1A 153332793 153340322 7529 False 1439.5 3642 92.61075 45 3727 4 chr1A.!!$F2 3682
2 TraesCS1B01G145800 chr1D 138781905 138785117 3212 True 2671.0 3177 96.63250 507 3705 2 chr1D.!!$R1 3198

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
45 46 0.038159 GACCAACACTCTGAGGGACG 60.038 60.0 15.05 3.66 0.00 4.79 F
230 231 0.179129 GCCGAATTTGTCATGCCTGG 60.179 55.0 0.00 0.00 0.00 4.45 F
927 4757 0.889186 GGCGGAGAAAAAGACAGCCA 60.889 55.0 0.00 0.00 42.56 4.75 F
1702 5539 0.438830 GTTCGTGCTTTCACTAGCCG 59.561 55.0 0.00 0.00 40.99 5.52 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1385 5222 0.258774 CCCGGGAGATTTGGGTCATT 59.741 55.000 18.48 0.00 38.18 2.57 R
1418 5255 1.897398 AACAGTCCGCGCGATGAAAC 61.897 55.000 34.63 19.67 0.00 2.78 R
2600 6488 1.202758 TCATCCTTTGTGTTGCCGTCT 60.203 47.619 0.00 0.00 0.00 4.18 R
3701 7625 3.119245 CCCTTGGAGATGCTCACAATTTG 60.119 47.826 0.00 0.00 31.08 2.32 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
17 18 4.943822 GGCCTGCTCTACCTTGTC 57.056 61.111 0.00 0.00 0.00 3.18
18 19 1.153549 GGCCTGCTCTACCTTGTCG 60.154 63.158 0.00 0.00 0.00 4.35
19 20 1.153549 GCCTGCTCTACCTTGTCGG 60.154 63.158 0.00 0.00 39.35 4.79
27 28 4.288234 ACCTTGTCGGTGACTGGA 57.712 55.556 13.50 0.00 46.80 3.86
28 29 1.746517 ACCTTGTCGGTGACTGGAC 59.253 57.895 13.50 0.00 46.80 4.02
29 30 1.004918 CCTTGTCGGTGACTGGACC 60.005 63.158 5.22 0.00 33.15 4.46
30 31 1.745890 CTTGTCGGTGACTGGACCA 59.254 57.895 0.00 0.00 35.50 4.02
31 32 0.105964 CTTGTCGGTGACTGGACCAA 59.894 55.000 0.00 0.13 35.50 3.67
32 33 0.179067 TTGTCGGTGACTGGACCAAC 60.179 55.000 0.00 0.00 35.50 3.77
33 34 1.331399 TGTCGGTGACTGGACCAACA 61.331 55.000 0.00 0.00 35.50 3.33
34 35 0.878961 GTCGGTGACTGGACCAACAC 60.879 60.000 17.89 17.89 35.50 3.32
35 36 1.046472 TCGGTGACTGGACCAACACT 61.046 55.000 22.38 0.00 35.50 3.55
36 37 0.600255 CGGTGACTGGACCAACACTC 60.600 60.000 22.38 15.09 35.50 3.51
37 38 0.759346 GGTGACTGGACCAACACTCT 59.241 55.000 22.38 0.00 35.88 3.24
38 39 1.541233 GGTGACTGGACCAACACTCTG 60.541 57.143 22.38 2.99 35.88 3.35
39 40 1.412710 GTGACTGGACCAACACTCTGA 59.587 52.381 18.50 0.00 0.00 3.27
40 41 1.688735 TGACTGGACCAACACTCTGAG 59.311 52.381 2.45 2.45 0.00 3.35
41 42 1.001406 GACTGGACCAACACTCTGAGG 59.999 57.143 9.85 0.76 0.00 3.86
42 43 0.322975 CTGGACCAACACTCTGAGGG 59.677 60.000 5.13 5.13 0.00 4.30
43 44 0.105194 TGGACCAACACTCTGAGGGA 60.105 55.000 15.05 0.00 0.00 4.20
44 45 0.321996 GGACCAACACTCTGAGGGAC 59.678 60.000 15.05 2.94 0.00 4.46
45 46 0.038159 GACCAACACTCTGAGGGACG 60.038 60.000 15.05 3.66 0.00 4.79
46 47 1.374758 CCAACACTCTGAGGGACGC 60.375 63.158 15.05 0.00 0.00 5.19
47 48 1.367471 CAACACTCTGAGGGACGCA 59.633 57.895 15.05 0.00 36.25 5.24
99 100 1.596727 GCTCCACTCAAAGATCGATGC 59.403 52.381 0.54 0.00 0.00 3.91
100 101 2.741228 GCTCCACTCAAAGATCGATGCT 60.741 50.000 0.54 0.00 0.00 3.79
139 140 5.825532 TGGATTTGAGGTATCCAAATGTGA 58.174 37.500 5.91 0.00 46.46 3.58
143 144 8.912988 GGATTTGAGGTATCCAAATGTGAAATA 58.087 33.333 5.91 0.00 42.35 1.40
145 146 7.639113 TTGAGGTATCCAAATGTGAAATACC 57.361 36.000 14.95 14.95 40.35 2.73
164 165 3.739167 TTTTTGAGGCGTGACCGG 58.261 55.556 0.00 0.00 46.52 5.28
221 222 1.550072 CATTTGAGGGGCCGAATTTGT 59.450 47.619 0.00 0.00 0.00 2.83
224 225 0.331278 TGAGGGGCCGAATTTGTCAT 59.669 50.000 0.00 0.00 0.00 3.06
226 227 1.141665 GGGGCCGAATTTGTCATGC 59.858 57.895 0.00 0.00 0.00 4.06
227 228 1.141665 GGGCCGAATTTGTCATGCC 59.858 57.895 0.00 2.83 41.19 4.40
230 231 0.179129 GCCGAATTTGTCATGCCTGG 60.179 55.000 0.00 0.00 0.00 4.45
232 233 2.364632 CCGAATTTGTCATGCCTGGTA 58.635 47.619 0.00 0.00 0.00 3.25
233 234 2.752354 CCGAATTTGTCATGCCTGGTAA 59.248 45.455 0.00 0.00 0.00 2.85
236 237 5.241506 CCGAATTTGTCATGCCTGGTAATAT 59.758 40.000 0.00 0.00 0.00 1.28
242 243 5.879763 TGTCATGCCTGGTAATATATGCTT 58.120 37.500 0.00 0.00 0.00 3.91
261 262 1.803334 TTTATCGCAACAACGGCTCT 58.197 45.000 0.00 0.00 0.00 4.09
262 263 1.075542 TTATCGCAACAACGGCTCTG 58.924 50.000 0.00 0.00 0.00 3.35
293 295 5.105567 TCTAGATCCTTGAGAGAAGTCGT 57.894 43.478 0.00 0.00 0.00 4.34
294 296 5.120399 TCTAGATCCTTGAGAGAAGTCGTC 58.880 45.833 0.00 0.00 0.00 4.20
310 312 1.739049 GTCTCTCATGCTCCTCCCG 59.261 63.158 0.00 0.00 0.00 5.14
325 327 3.878519 CCGAGCTCCCGTCGAGTC 61.879 72.222 8.47 0.00 41.10 3.36
353 355 2.639286 CCGCGCTGCTTTGAGTTT 59.361 55.556 5.56 0.00 0.00 2.66
356 358 1.654220 GCGCTGCTTTGAGTTTCCA 59.346 52.632 0.00 0.00 0.00 3.53
358 360 1.730446 GCGCTGCTTTGAGTTTCCATC 60.730 52.381 0.00 0.00 0.00 3.51
384 386 2.506061 CGCCTCCCTATGCTGCTCT 61.506 63.158 0.00 0.00 0.00 4.09
389 391 2.591923 CTCCCTATGCTGCTCTGACTA 58.408 52.381 0.00 0.00 0.00 2.59
419 421 1.227002 GCTCGCCACCTACTAGCAC 60.227 63.158 0.00 0.00 33.38 4.40
448 450 2.880719 CTTCTCTGGAGAGCCGCACG 62.881 65.000 0.00 0.00 41.80 5.34
486 814 1.674057 CAAAGTGACCGAGCTCCCT 59.326 57.895 8.47 0.00 0.00 4.20
523 851 1.268352 GCCCATGTTACTTTGAACGCA 59.732 47.619 0.00 0.00 31.59 5.24
651 4481 2.695585 TGTAAATGCCTTTTGGGGGTT 58.304 42.857 0.00 0.00 40.82 4.11
714 4544 1.069378 GTCGCCACCGTCGTTCTAAG 61.069 60.000 0.00 0.00 35.54 2.18
927 4757 0.889186 GGCGGAGAAAAAGACAGCCA 60.889 55.000 0.00 0.00 42.56 4.75
1202 5038 1.290134 GTGAGACCCCCATCCTTTCT 58.710 55.000 0.00 0.00 0.00 2.52
1248 5084 1.937223 TGTACCTTTCACTGTTGCGTG 59.063 47.619 0.00 0.00 36.25 5.34
1384 5221 7.518161 TGACGTGTTTGTGATAGAATTCAATC 58.482 34.615 8.44 0.00 0.00 2.67
1385 5222 7.172361 TGACGTGTTTGTGATAGAATTCAATCA 59.828 33.333 8.44 0.00 0.00 2.57
1386 5223 7.870826 ACGTGTTTGTGATAGAATTCAATCAA 58.129 30.769 8.44 3.32 34.06 2.57
1387 5224 8.514594 ACGTGTTTGTGATAGAATTCAATCAAT 58.485 29.630 8.44 0.00 34.06 2.57
1388 5225 8.791605 CGTGTTTGTGATAGAATTCAATCAATG 58.208 33.333 8.44 0.00 34.06 2.82
1389 5226 9.844790 GTGTTTGTGATAGAATTCAATCAATGA 57.155 29.630 8.44 0.00 34.06 2.57
1418 5255 1.004080 CCGGGCAGATGGATAGCTG 60.004 63.158 0.00 0.00 43.10 4.24
1658 5495 4.764172 AGCATATCCTCAGTGTCAAGTTC 58.236 43.478 0.00 0.00 0.00 3.01
1702 5539 0.438830 GTTCGTGCTTTCACTAGCCG 59.561 55.000 0.00 0.00 40.99 5.52
1711 5548 1.144969 TTCACTAGCCGTTTCTTGCG 58.855 50.000 0.00 0.00 0.00 4.85
2102 5959 7.112779 AGTACCGATTGGATCAAGAAGAAAAT 58.887 34.615 5.81 0.00 39.21 1.82
2140 5997 2.676342 GTCTTGGAAACTGTTGTGACGT 59.324 45.455 0.00 0.00 0.00 4.34
2165 6022 2.845795 ACGAAGGTCACCGGGGTT 60.846 61.111 2.12 0.00 0.00 4.11
2255 6112 6.850555 GCATTTAGCTTTTGAAGAGATCACT 58.149 36.000 0.00 0.00 37.85 3.41
2292 6149 9.260002 CTGCAGTTTTACAAAATCAGGTATTTT 57.740 29.630 5.25 0.00 46.48 1.82
2421 6309 5.976458 TGAACCTTGCAAGAAGTTGAAAAT 58.024 33.333 28.05 1.79 35.46 1.82
2422 6310 7.106439 TGAACCTTGCAAGAAGTTGAAAATA 57.894 32.000 28.05 3.85 35.46 1.40
2457 6345 0.679002 GGACATGCCTGCACTGATGT 60.679 55.000 0.00 0.00 0.00 3.06
2600 6488 0.888736 CCTTCGTGGTTGATGTGCCA 60.889 55.000 0.00 0.00 0.00 4.92
2660 6548 1.238439 CCGTGATCAAGTGCAACCTT 58.762 50.000 7.88 0.00 37.80 3.50
2755 6643 0.605319 GGGCACGGACTTGTGAATCA 60.605 55.000 0.00 0.00 42.55 2.57
2878 6800 9.517609 GTAAGGATTAGTATGTAGACTTGTGTG 57.482 37.037 0.00 0.00 0.00 3.82
2890 6812 5.277857 AGACTTGTGTGCTTGTACTAGTT 57.722 39.130 0.00 0.00 34.04 2.24
3028 6950 5.762218 GCATTTGAGACAACTAGATGCCTAT 59.238 40.000 0.00 0.00 33.61 2.57
3030 6952 7.519649 GCATTTGAGACAACTAGATGCCTATTC 60.520 40.741 0.00 0.00 33.61 1.75
3034 6956 7.063593 TGAGACAACTAGATGCCTATTCTACT 58.936 38.462 0.00 0.00 0.00 2.57
3035 6957 8.218488 TGAGACAACTAGATGCCTATTCTACTA 58.782 37.037 0.00 0.00 0.00 1.82
3036 6958 8.398878 AGACAACTAGATGCCTATTCTACTAC 57.601 38.462 0.00 0.00 0.00 2.73
3037 6959 8.221944 AGACAACTAGATGCCTATTCTACTACT 58.778 37.037 0.00 0.00 0.00 2.57
3038 6960 8.172352 ACAACTAGATGCCTATTCTACTACTG 57.828 38.462 0.00 0.00 0.00 2.74
3164 7086 6.042777 TCGCTGTTATTGAGATGGAAGTAAG 58.957 40.000 0.00 0.00 0.00 2.34
3199 7123 2.490903 TCTAGCACCGTAGTCAAAGGAC 59.509 50.000 0.00 0.00 44.66 3.85
3261 7185 3.898741 GGGTTCTTGGGGTTGTAATTGAA 59.101 43.478 0.00 0.00 0.00 2.69
3468 7392 5.181811 TCGTCGTTCTAATCCTCTTGTTGTA 59.818 40.000 0.00 0.00 0.00 2.41
3469 7393 5.285607 CGTCGTTCTAATCCTCTTGTTGTAC 59.714 44.000 0.00 0.00 0.00 2.90
3551 7475 6.558488 AGAAGCTCCTGAAATGACTTCTAT 57.442 37.500 0.00 0.00 41.40 1.98
3553 7477 7.725251 AGAAGCTCCTGAAATGACTTCTATAG 58.275 38.462 0.00 0.00 41.40 1.31
3555 7479 7.667575 AGCTCCTGAAATGACTTCTATAGAA 57.332 36.000 14.42 14.42 34.86 2.10
3557 7481 8.203485 AGCTCCTGAAATGACTTCTATAGAAAG 58.797 37.037 15.85 12.03 34.86 2.62
3558 7482 7.440856 GCTCCTGAAATGACTTCTATAGAAAGG 59.559 40.741 15.85 15.48 34.86 3.11
3560 7484 9.046846 TCCTGAAATGACTTCTATAGAAAGGAA 57.953 33.333 19.23 7.28 34.86 3.36
3701 7625 8.112449 CAGTTTTGCAAGAAAAAGATCTTCAAC 58.888 33.333 8.78 3.25 37.56 3.18
3723 7647 2.431954 ATTGTGAGCATCTCCAAGGG 57.568 50.000 0.00 0.00 34.92 3.95
3724 7648 1.067295 TTGTGAGCATCTCCAAGGGT 58.933 50.000 0.00 0.00 34.92 4.34
3725 7649 0.615331 TGTGAGCATCTCCAAGGGTC 59.385 55.000 0.00 0.00 34.92 4.46
3726 7650 0.908198 GTGAGCATCTCCAAGGGTCT 59.092 55.000 0.00 0.00 34.92 3.85
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 1.153549 CGACAAGGTAGAGCAGGCC 60.154 63.158 0.00 0.00 0.00 5.19
12 13 0.105964 TTGGTCCAGTCACCGACAAG 59.894 55.000 0.00 0.00 39.62 3.16
13 14 0.179067 GTTGGTCCAGTCACCGACAA 60.179 55.000 5.29 0.00 46.70 3.18
14 15 1.444250 GTTGGTCCAGTCACCGACA 59.556 57.895 5.29 0.00 46.70 4.35
15 16 4.355925 GTTGGTCCAGTCACCGAC 57.644 61.111 0.00 0.00 42.52 4.79
16 17 1.046472 AGTGTTGGTCCAGTCACCGA 61.046 55.000 19.15 0.00 39.62 4.69
17 18 0.600255 GAGTGTTGGTCCAGTCACCG 60.600 60.000 19.15 0.00 39.62 4.94
18 19 0.759346 AGAGTGTTGGTCCAGTCACC 59.241 55.000 19.15 13.39 37.27 4.02
19 20 1.412710 TCAGAGTGTTGGTCCAGTCAC 59.587 52.381 16.60 16.60 37.27 3.67
20 21 1.688735 CTCAGAGTGTTGGTCCAGTCA 59.311 52.381 0.00 0.00 37.27 3.41
21 22 1.001406 CCTCAGAGTGTTGGTCCAGTC 59.999 57.143 0.00 0.00 35.44 3.51
22 23 1.051812 CCTCAGAGTGTTGGTCCAGT 58.948 55.000 0.00 0.00 0.00 4.00
23 24 0.322975 CCCTCAGAGTGTTGGTCCAG 59.677 60.000 0.00 0.00 0.00 3.86
24 25 0.105194 TCCCTCAGAGTGTTGGTCCA 60.105 55.000 0.00 0.00 0.00 4.02
25 26 0.321996 GTCCCTCAGAGTGTTGGTCC 59.678 60.000 0.00 0.00 0.00 4.46
26 27 0.038159 CGTCCCTCAGAGTGTTGGTC 60.038 60.000 0.00 0.00 0.00 4.02
27 28 2.050269 CGTCCCTCAGAGTGTTGGT 58.950 57.895 0.00 0.00 0.00 3.67
28 29 1.374758 GCGTCCCTCAGAGTGTTGG 60.375 63.158 0.00 0.00 0.00 3.77
29 30 0.668706 CTGCGTCCCTCAGAGTGTTG 60.669 60.000 0.00 0.00 33.54 3.33
30 31 1.668294 CTGCGTCCCTCAGAGTGTT 59.332 57.895 0.00 0.00 33.54 3.32
31 32 2.936912 GCTGCGTCCCTCAGAGTGT 61.937 63.158 0.00 0.00 33.54 3.55
32 33 2.125753 GCTGCGTCCCTCAGAGTG 60.126 66.667 0.00 0.00 33.54 3.51
33 34 3.386237 GGCTGCGTCCCTCAGAGT 61.386 66.667 0.00 0.00 33.54 3.24
34 35 4.504916 CGGCTGCGTCCCTCAGAG 62.505 72.222 0.00 0.00 33.54 3.35
67 68 1.737008 GTGGAGCTTCGTCCGGTTC 60.737 63.158 0.00 0.00 39.81 3.62
99 100 9.888878 CTCAAATCCATACTATTACATGCAAAG 57.111 33.333 0.00 0.00 0.00 2.77
100 101 8.849168 CCTCAAATCCATACTATTACATGCAAA 58.151 33.333 0.00 0.00 0.00 3.68
212 213 1.176527 ACCAGGCATGACAAATTCGG 58.823 50.000 0.00 0.00 0.00 4.30
215 216 7.452501 AGCATATATTACCAGGCATGACAAATT 59.547 33.333 0.00 0.00 0.00 1.82
221 222 9.177608 GATAAAAGCATATATTACCAGGCATGA 57.822 33.333 0.00 0.00 0.00 3.07
224 225 6.093495 GCGATAAAAGCATATATTACCAGGCA 59.907 38.462 0.00 0.00 34.19 4.75
226 227 7.609760 TGCGATAAAAGCATATATTACCAGG 57.390 36.000 0.00 0.00 40.01 4.45
227 228 8.503196 TGTTGCGATAAAAGCATATATTACCAG 58.497 33.333 0.00 0.00 44.74 4.00
230 231 8.827599 CGTTGTTGCGATAAAAGCATATATTAC 58.172 33.333 0.00 0.00 44.74 1.89
232 233 6.855914 CCGTTGTTGCGATAAAAGCATATATT 59.144 34.615 0.00 0.00 44.74 1.28
233 234 6.370593 CCGTTGTTGCGATAAAAGCATATAT 58.629 36.000 0.00 0.00 44.74 0.86
236 237 3.729462 GCCGTTGTTGCGATAAAAGCATA 60.729 43.478 0.00 0.00 44.74 3.14
242 243 1.463056 CAGAGCCGTTGTTGCGATAAA 59.537 47.619 0.00 0.00 0.00 1.40
293 295 0.467106 CTCGGGAGGAGCATGAGAGA 60.467 60.000 0.00 0.00 35.63 3.10
294 296 2.040330 CTCGGGAGGAGCATGAGAG 58.960 63.158 0.00 0.00 35.63 3.20
347 349 1.808411 GGCAACTCGATGGAAACTCA 58.192 50.000 0.00 0.00 0.00 3.41
353 355 3.371097 GAGGCGGCAACTCGATGGA 62.371 63.158 13.08 0.00 0.00 3.41
356 358 4.162690 GGGAGGCGGCAACTCGAT 62.163 66.667 13.08 0.00 35.82 3.59
358 360 2.797278 ATAGGGAGGCGGCAACTCG 61.797 63.158 13.08 0.00 35.82 4.18
381 383 2.490217 CGGTGGCGGTAGTCAGAG 59.510 66.667 0.00 0.00 29.49 3.35
384 386 3.687102 CACCGGTGGCGGTAGTCA 61.687 66.667 27.57 0.00 40.77 3.41
404 406 2.582498 GCGTGCTAGTAGGTGGCG 60.582 66.667 0.00 0.00 34.70 5.69
410 412 1.011019 CTCGTCGGCGTGCTAGTAG 60.011 63.158 10.18 0.00 39.49 2.57
411 413 3.095911 CTCGTCGGCGTGCTAGTA 58.904 61.111 10.18 0.00 39.49 1.82
419 421 2.578178 CAGAGAAGCTCGTCGGCG 60.578 66.667 1.15 1.15 35.36 6.46
426 428 1.437160 CGGCTCTCCAGAGAAGCTC 59.563 63.158 7.84 0.00 44.74 4.09
470 798 2.344203 CGAGGGAGCTCGGTCACTT 61.344 63.158 7.83 0.00 42.51 3.16
486 814 1.595993 GGCAGGTGACAGCTAGACGA 61.596 60.000 6.88 0.00 43.36 4.20
491 819 1.200760 ACATGGGCAGGTGACAGCTA 61.201 55.000 6.88 0.00 43.36 3.32
523 851 1.956477 GGCGGATAATCATGGTTGCTT 59.044 47.619 0.08 0.00 0.00 3.91
569 4391 4.887655 TCTCTTCAAAACTTTGAGGTTCCC 59.112 41.667 12.39 0.00 46.68 3.97
581 4403 2.155279 GGACAGGGCTCTCTTCAAAAC 58.845 52.381 0.00 0.00 0.00 2.43
591 4413 0.107654 ATAAACAGCGGACAGGGCTC 60.108 55.000 0.00 0.00 39.08 4.70
651 4481 6.119536 AGGCAAAAATATCTTCGGTCATGTA 58.880 36.000 0.00 0.00 0.00 2.29
714 4544 2.673368 CCATGGACTAGAGCGTTGTTTC 59.327 50.000 5.56 0.00 0.00 2.78
1248 5084 2.554032 CGGCATCAGAATCCATTAACCC 59.446 50.000 0.00 0.00 0.00 4.11
1384 5221 1.392589 CCGGGAGATTTGGGTCATTG 58.607 55.000 0.00 0.00 0.00 2.82
1385 5222 0.258774 CCCGGGAGATTTGGGTCATT 59.741 55.000 18.48 0.00 38.18 2.57
1386 5223 1.922821 CCCGGGAGATTTGGGTCAT 59.077 57.895 18.48 0.00 38.18 3.06
1387 5224 2.978946 GCCCGGGAGATTTGGGTCA 61.979 63.158 29.31 0.00 45.19 4.02
1388 5225 2.124278 GCCCGGGAGATTTGGGTC 60.124 66.667 29.31 0.00 45.19 4.46
1389 5226 2.938798 TGCCCGGGAGATTTGGGT 60.939 61.111 29.31 0.00 45.19 4.51
1418 5255 1.897398 AACAGTCCGCGCGATGAAAC 61.897 55.000 34.63 19.67 0.00 2.78
1658 5495 2.885644 CGGTGATCGCCTCCAACG 60.886 66.667 22.59 4.91 37.14 4.10
1702 5539 5.862860 ACTAGTAAGAAGTAGCGCAAGAAAC 59.137 40.000 11.47 0.00 41.00 2.78
1711 5548 6.201234 GCATTTAGGCACTAGTAAGAAGTAGC 59.799 42.308 0.00 0.00 44.25 3.58
2007 5863 2.435938 TGAGGGGTTTGCGATCGC 60.436 61.111 32.48 32.48 42.35 4.58
2255 6112 2.638480 AAACTGCAGGACAAGCACTA 57.362 45.000 19.93 0.00 37.02 2.74
2292 6149 1.422402 GTGTTCCTTCCTTGGTGGGTA 59.578 52.381 0.00 0.00 36.20 3.69
2299 6156 2.185004 ATGACCGTGTTCCTTCCTTG 57.815 50.000 0.00 0.00 0.00 3.61
2369 6226 6.991938 ACAGTAAAACCACATGCACATAATT 58.008 32.000 0.00 0.00 0.00 1.40
2372 6229 7.109501 AGATACAGTAAAACCACATGCACATA 58.890 34.615 0.00 0.00 0.00 2.29
2421 6309 7.178274 AGGCATGTCCATCAACAAAAACTTATA 59.822 33.333 8.58 0.00 37.29 0.98
2422 6310 6.014327 AGGCATGTCCATCAACAAAAACTTAT 60.014 34.615 8.58 0.00 37.29 1.73
2457 6345 7.765695 ATGGATCAAACAGAAGCTTAAAGAA 57.234 32.000 0.00 0.00 0.00 2.52
2600 6488 1.202758 TCATCCTTTGTGTTGCCGTCT 60.203 47.619 0.00 0.00 0.00 4.18
2755 6643 7.458409 TTGAAGCTTCTTTCTTATTCATGCT 57.542 32.000 26.09 0.00 0.00 3.79
2878 6800 4.268884 GCATCACTAGCAACTAGTACAAGC 59.731 45.833 6.94 6.08 44.37 4.01
2890 6812 6.183360 TGCTAAGATCTAAAGCATCACTAGCA 60.183 38.462 22.45 17.37 41.15 3.49
3034 6956 8.544622 TGGAATGTTATCCAAGAACATACAGTA 58.455 33.333 1.70 0.00 46.36 2.74
3035 6957 7.402054 TGGAATGTTATCCAAGAACATACAGT 58.598 34.615 1.70 0.00 46.36 3.55
3036 6958 7.864108 TGGAATGTTATCCAAGAACATACAG 57.136 36.000 1.70 0.00 46.36 2.74
3164 7086 6.456501 ACGGTGCTAGAGATAAATTATCCAC 58.543 40.000 9.21 9.32 35.79 4.02
3199 7123 3.997021 GCTGAAACGGATATACCCTCATG 59.003 47.826 0.00 0.00 34.64 3.07
3261 7185 7.232127 ACTCAGACATTTTTCTCACCAATCATT 59.768 33.333 0.00 0.00 0.00 2.57
3701 7625 3.119245 CCCTTGGAGATGCTCACAATTTG 60.119 47.826 0.00 0.00 31.08 2.32


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

AutoCloner maintained by Alex Coulton.