Multiple sequence alignment - TraesCS1B01G145000

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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 TraesCS1B01G145000 chr1B 100.000 2531 0 0 1 2531 198485343 198487873 0.000000e+00 4674.0
1 TraesCS1B01G145000 chr1D 92.100 1848 84 23 710 2531 140056170 140054359 0.000000e+00 2547.0
2 TraesCS1B01G145000 chr1D 89.414 444 36 4 267 707 140056654 140056219 1.320000e-152 549.0
3 TraesCS1B01G145000 chr1A 96.091 793 26 4 770 1560 150860402 150861191 0.000000e+00 1288.0
4 TraesCS1B01G145000 chr1A 85.251 678 92 4 45 718 150797523 150798196 0.000000e+00 691.0
5 TraesCS1B01G145000 chr1A 94.643 280 12 1 2064 2343 150862581 150862857 5.000000e-117 431.0
6 TraesCS1B01G145000 chr1A 85.494 324 17 9 1658 1980 150861951 150862245 6.800000e-81 311.0
7 TraesCS1B01G145000 chr3D 85.714 98 14 0 1271 1368 104293043 104292946 1.240000e-18 104.0
8 TraesCS1B01G145000 chr3D 97.619 42 1 0 1 42 361169101 361169142 3.490000e-09 73.1
9 TraesCS1B01G145000 chr3D 97.619 42 1 0 1 42 361172901 361172942 3.490000e-09 73.1
10 TraesCS1B01G145000 chr3D 97.619 42 1 0 1 42 361176703 361176744 3.490000e-09 73.1
11 TraesCS1B01G145000 chr3B 75.207 242 42 15 1271 1500 155418923 155418688 5.760000e-17 99.0
12 TraesCS1B01G145000 chr7A 85.714 91 9 2 291 378 647934574 647934663 2.680000e-15 93.5
13 TraesCS1B01G145000 chr7A 100.000 43 0 0 1 43 672362459 672362417 2.090000e-11 80.5
14 TraesCS1B01G145000 chr7A 100.000 43 0 0 1 43 672389684 672389642 2.090000e-11 80.5
15 TraesCS1B01G145000 chr2A 88.158 76 4 3 291 362 665843274 665843348 4.490000e-13 86.1
16 TraesCS1B01G145000 chr2A 97.727 44 1 0 1 44 114340849 114340892 2.700000e-10 76.8
17 TraesCS1B01G145000 chr2A 82.895 76 8 4 291 362 665990290 665990364 2.100000e-06 63.9
18 TraesCS1B01G145000 chr6D 100.000 42 0 0 1 42 36251210 36251169 7.510000e-11 78.7
19 TraesCS1B01G145000 chr4D 73.853 218 48 7 289 500 25210203 25210417 7.510000e-11 78.7
20 TraesCS1B01G145000 chr4A 74.146 205 46 7 289 488 578215796 578215998 7.510000e-11 78.7
21 TraesCS1B01G145000 chr7B 97.674 43 1 0 1 43 656532874 656532916 9.710000e-10 75.0
22 TraesCS1B01G145000 chr7B 97.674 43 1 0 1 43 666603565 666603523 9.710000e-10 75.0
23 TraesCS1B01G145000 chr2B 81.319 91 13 2 291 378 613037577 613037666 1.260000e-08 71.3
24 TraesCS1B01G145000 chr4B 85.000 60 6 1 292 348 234183420 234183361 9.780000e-05 58.4


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 TraesCS1B01G145000 chr1B 198485343 198487873 2530 False 4674.000000 4674 100.000 1 2531 1 chr1B.!!$F1 2530
1 TraesCS1B01G145000 chr1D 140054359 140056654 2295 True 1548.000000 2547 90.757 267 2531 2 chr1D.!!$R1 2264
2 TraesCS1B01G145000 chr1A 150797523 150798196 673 False 691.000000 691 85.251 45 718 1 chr1A.!!$F1 673
3 TraesCS1B01G145000 chr1A 150860402 150862857 2455 False 676.666667 1288 92.076 770 2343 3 chr1A.!!$F2 1573

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
169 170 0.035881 AGACCATGCCATGCCTATCG 59.964 55.0 0.0 0.0 0.0 2.92 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1556 1611 1.557371 GCTAGTCCTTCCCTTCAAGCT 59.443 52.381 0.0 0.0 0.0 3.74 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
18 19 2.240510 ACTTTGAGCCCACCCTTCA 58.759 52.632 0.00 0.00 0.00 3.02
19 20 0.779997 ACTTTGAGCCCACCCTTCAT 59.220 50.000 0.00 0.00 0.00 2.57
20 21 1.147817 ACTTTGAGCCCACCCTTCATT 59.852 47.619 0.00 0.00 0.00 2.57
21 22 2.250924 CTTTGAGCCCACCCTTCATTT 58.749 47.619 0.00 0.00 0.00 2.32
22 23 2.397044 TTGAGCCCACCCTTCATTTT 57.603 45.000 0.00 0.00 0.00 1.82
23 24 1.923356 TGAGCCCACCCTTCATTTTC 58.077 50.000 0.00 0.00 0.00 2.29
24 25 1.428912 TGAGCCCACCCTTCATTTTCT 59.571 47.619 0.00 0.00 0.00 2.52
25 26 2.158325 TGAGCCCACCCTTCATTTTCTT 60.158 45.455 0.00 0.00 0.00 2.52
26 27 2.899900 GAGCCCACCCTTCATTTTCTTT 59.100 45.455 0.00 0.00 0.00 2.52
27 28 2.899900 AGCCCACCCTTCATTTTCTTTC 59.100 45.455 0.00 0.00 0.00 2.62
28 29 2.899900 GCCCACCCTTCATTTTCTTTCT 59.100 45.455 0.00 0.00 0.00 2.52
29 30 4.086457 GCCCACCCTTCATTTTCTTTCTA 58.914 43.478 0.00 0.00 0.00 2.10
30 31 4.158579 GCCCACCCTTCATTTTCTTTCTAG 59.841 45.833 0.00 0.00 0.00 2.43
31 32 5.570320 CCCACCCTTCATTTTCTTTCTAGA 58.430 41.667 0.00 0.00 0.00 2.43
32 33 6.190587 CCCACCCTTCATTTTCTTTCTAGAT 58.809 40.000 0.00 0.00 0.00 1.98
33 34 6.665248 CCCACCCTTCATTTTCTTTCTAGATT 59.335 38.462 0.00 0.00 0.00 2.40
34 35 7.148000 CCCACCCTTCATTTTCTTTCTAGATTC 60.148 40.741 0.00 0.00 0.00 2.52
35 36 7.414540 CCACCCTTCATTTTCTTTCTAGATTCG 60.415 40.741 0.00 0.00 0.00 3.34
36 37 6.094186 ACCCTTCATTTTCTTTCTAGATTCGC 59.906 38.462 0.00 0.00 0.00 4.70
37 38 6.458888 CCCTTCATTTTCTTTCTAGATTCGCC 60.459 42.308 0.00 0.00 0.00 5.54
38 39 6.094048 CCTTCATTTTCTTTCTAGATTCGCCA 59.906 38.462 0.00 0.00 0.00 5.69
39 40 6.422776 TCATTTTCTTTCTAGATTCGCCAC 57.577 37.500 0.00 0.00 0.00 5.01
40 41 6.173339 TCATTTTCTTTCTAGATTCGCCACT 58.827 36.000 0.00 0.00 0.00 4.00
41 42 5.862924 TTTTCTTTCTAGATTCGCCACTG 57.137 39.130 0.00 0.00 0.00 3.66
42 43 3.526931 TCTTTCTAGATTCGCCACTGG 57.473 47.619 0.00 0.00 0.00 4.00
43 44 1.936547 CTTTCTAGATTCGCCACTGGC 59.063 52.381 10.35 10.35 46.75 4.85
53 54 3.625897 CCACTGGCGGAGGTGTCA 61.626 66.667 0.00 0.00 0.00 3.58
54 55 2.357517 CACTGGCGGAGGTGTCAC 60.358 66.667 0.00 0.00 0.00 3.67
55 56 2.842462 ACTGGCGGAGGTGTCACA 60.842 61.111 5.12 0.00 0.00 3.58
62 63 1.956170 GGAGGTGTCACACGCACAG 60.956 63.158 0.73 0.00 38.51 3.66
71 72 1.101049 CACACGCACAGGAAAAGGGT 61.101 55.000 0.00 0.00 0.00 4.34
72 73 0.395173 ACACGCACAGGAAAAGGGTT 60.395 50.000 0.00 0.00 0.00 4.11
138 139 3.380479 TCTCCTTGTGTTAGGTTGTCG 57.620 47.619 0.00 0.00 36.63 4.35
139 140 1.798813 CTCCTTGTGTTAGGTTGTCGC 59.201 52.381 0.00 0.00 36.63 5.19
147 148 3.869473 TAGGTTGTCGCGCACCACC 62.869 63.158 19.94 18.93 40.58 4.61
167 168 3.739703 CAGACCATGCCATGCCTAT 57.260 52.632 0.00 0.00 0.00 2.57
169 170 0.035881 AGACCATGCCATGCCTATCG 59.964 55.000 0.00 0.00 0.00 2.92
175 176 2.033141 CCATGCCTATCGCCAGGG 59.967 66.667 4.54 0.00 36.10 4.45
191 192 4.078516 GGCCGCCGTTGTAGACCT 62.079 66.667 0.00 0.00 0.00 3.85
192 193 2.713967 GGCCGCCGTTGTAGACCTA 61.714 63.158 0.00 0.00 0.00 3.08
203 204 5.184711 CGTTGTAGACCTAGGAGTAGTCTT 58.815 45.833 17.98 0.00 0.00 3.01
207 208 1.598601 GACCTAGGAGTAGTCTTCGCG 59.401 57.143 17.98 0.00 0.00 5.87
230 231 4.589675 GGGCCGTTGGTGGGACAA 62.590 66.667 0.00 0.00 44.16 3.18
234 235 2.038269 CCGTTGGTGGGACAATCCG 61.038 63.158 0.00 0.00 44.16 4.18
265 266 1.250328 TGCCAGGATGCTTGTTTCTG 58.750 50.000 0.00 0.00 31.97 3.02
270 271 3.094572 CAGGATGCTTGTTTCTGGGAAT 58.905 45.455 0.00 0.00 0.00 3.01
283 284 2.376518 TCTGGGAATGTGAGGCTTTCTT 59.623 45.455 0.00 0.00 33.34 2.52
365 369 0.874390 GCCAGTGAATGTCTTCGCAA 59.126 50.000 0.00 0.00 43.03 4.85
369 373 3.730715 CCAGTGAATGTCTTCGCAAAAAC 59.269 43.478 0.00 0.00 43.03 2.43
405 409 5.654650 AGGTTAAGTCTCGATGAAGATCTGT 59.345 40.000 0.00 0.00 0.00 3.41
416 420 5.619981 CGATGAAGATCTGTATACCATCGCA 60.620 44.000 18.70 14.28 43.03 5.10
453 457 2.832129 GTGTGGTATGGACTCCTTCTGA 59.168 50.000 0.00 0.00 0.00 3.27
473 477 3.255642 TGAATTTTGTAGTCAGCCAAGGC 59.744 43.478 2.02 2.02 42.33 4.35
474 478 2.356665 TTTTGTAGTCAGCCAAGGCA 57.643 45.000 14.40 0.00 44.88 4.75
477 481 0.692476 TGTAGTCAGCCAAGGCATGT 59.308 50.000 14.40 0.00 44.88 3.21
488 492 2.619849 CCAAGGCATGTCATCCTCAAGT 60.620 50.000 0.00 0.00 0.00 3.16
584 588 4.623932 ACATGTCACCTTAGAAGAAGCA 57.376 40.909 0.00 0.00 0.00 3.91
598 602 2.097825 AGAAGCATGGGTGAGCATTTC 58.902 47.619 0.00 0.00 0.00 2.17
600 604 1.760192 AGCATGGGTGAGCATTTCTC 58.240 50.000 0.00 0.00 42.23 2.87
601 605 1.284198 AGCATGGGTGAGCATTTCTCT 59.716 47.619 0.00 0.00 42.38 3.10
614 618 3.426695 GCATTTCTCTGGATTGGTTGACG 60.427 47.826 0.00 0.00 0.00 4.35
646 650 1.679977 CAAGACCACCATGGCCCAG 60.680 63.158 13.04 0.00 42.67 4.45
653 657 1.690633 ACCATGGCCCAGACTCGAT 60.691 57.895 13.04 0.00 0.00 3.59
654 658 1.227764 CCATGGCCCAGACTCGATG 60.228 63.158 0.00 0.00 0.00 3.84
656 660 0.812811 CATGGCCCAGACTCGATGTG 60.813 60.000 0.00 0.00 0.00 3.21
718 769 2.819595 CCCTCATGCAACGGACGG 60.820 66.667 0.00 0.00 0.00 4.79
738 789 3.896317 GTGGAAGACACTCTCGCTT 57.104 52.632 0.00 0.00 46.72 4.68
747 798 0.243365 CACTCTCGCTTGCAGAGACT 59.757 55.000 20.38 8.72 40.02 3.24
854 906 3.068732 TGACATTCTATCTCTTCCCGCAG 59.931 47.826 0.00 0.00 0.00 5.18
955 1010 2.010670 CGAGTCAAACGCAACCACA 58.989 52.632 0.00 0.00 0.00 4.17
971 1026 2.337532 CAGCACAAGCACAAGGCC 59.662 61.111 0.00 0.00 46.50 5.19
973 1028 1.757731 AGCACAAGCACAAGGCCAA 60.758 52.632 5.01 0.00 46.50 4.52
974 1029 1.143620 GCACAAGCACAAGGCCAAA 59.856 52.632 5.01 0.00 46.50 3.28
975 1030 0.461693 GCACAAGCACAAGGCCAAAA 60.462 50.000 5.01 0.00 46.50 2.44
1030 1085 0.246086 GACACAGGAGTCTGAGCAGG 59.754 60.000 0.00 0.00 43.49 4.85
1143 1198 4.099170 CTCTCCGGCGTCGACGTT 62.099 66.667 35.48 0.00 42.22 3.99
1392 1447 0.178973 TGGTTGTCGAGGAGGAGACA 60.179 55.000 0.00 0.00 44.57 3.41
1573 1628 0.037447 GCAGCTTGAAGGGAAGGACT 59.963 55.000 0.00 0.00 0.00 3.85
1600 1655 8.610035 AGCGTAACAAAAGCTAATAAGTAATCC 58.390 33.333 0.00 0.00 41.48 3.01
1652 1711 3.969117 TTTGCTGTAGTCTGTTGCTTG 57.031 42.857 0.00 0.00 0.00 4.01
1656 1715 1.227999 TGTAGTCTGTTGCTTGCCGC 61.228 55.000 0.00 0.00 39.77 6.53
1690 2441 7.753659 TCTATTATGATTAGCGTCAGAGTAGC 58.246 38.462 8.18 0.00 32.77 3.58
1691 2442 6.582677 ATTATGATTAGCGTCAGAGTAGCT 57.417 37.500 0.00 0.00 44.24 3.32
1706 2457 2.359230 GCTGCTCGCTTCCCAGTT 60.359 61.111 0.00 0.00 35.14 3.16
1724 2475 7.546358 TCCCAGTTTGCAATGAATAAATGTAG 58.454 34.615 0.00 0.00 0.00 2.74
1752 2503 6.561737 ACGTATGAGGTCTATACATGTCTG 57.438 41.667 0.00 0.00 31.94 3.51
1760 2511 5.772672 AGGTCTATACATGTCTGTCCATCTC 59.227 44.000 0.00 0.00 36.79 2.75
1773 2524 5.070446 TCTGTCCATCTCTGTGTTTAGTGTT 59.930 40.000 0.00 0.00 0.00 3.32
1774 2525 6.266786 TCTGTCCATCTCTGTGTTTAGTGTTA 59.733 38.462 0.00 0.00 0.00 2.41
1775 2526 6.455647 TGTCCATCTCTGTGTTTAGTGTTAG 58.544 40.000 0.00 0.00 0.00 2.34
1776 2527 6.041637 TGTCCATCTCTGTGTTTAGTGTTAGT 59.958 38.462 0.00 0.00 0.00 2.24
1777 2528 7.231925 TGTCCATCTCTGTGTTTAGTGTTAGTA 59.768 37.037 0.00 0.00 0.00 1.82
1778 2529 7.541437 GTCCATCTCTGTGTTTAGTGTTAGTAC 59.459 40.741 0.00 0.00 0.00 2.73
1779 2530 7.450634 TCCATCTCTGTGTTTAGTGTTAGTACT 59.549 37.037 0.00 0.00 34.71 2.73
1780 2531 8.088981 CCATCTCTGTGTTTAGTGTTAGTACTT 58.911 37.037 0.00 0.00 32.19 2.24
1783 2534 9.347240 TCTCTGTGTTTAGTGTTAGTACTTAGT 57.653 33.333 0.00 0.00 32.19 2.24
1907 2658 1.593196 CGTGCCTCTTTTTCCTCACA 58.407 50.000 0.00 0.00 0.00 3.58
1951 2702 2.826128 TGGACACTAGTGCTCGATTCTT 59.174 45.455 22.90 0.00 36.96 2.52
1985 2736 6.475504 TGTGTAAGGTCATGTTTCATCTCAT 58.524 36.000 0.00 0.00 0.00 2.90
2026 2777 5.103728 TCTCTCTCTCTCTCTCTCTCTCTCT 60.104 48.000 0.00 0.00 0.00 3.10
2027 2778 5.136828 TCTCTCTCTCTCTCTCTCTCTCTC 58.863 50.000 0.00 0.00 0.00 3.20
2058 2809 5.103728 TCTCTCTCTCTCTCTCTCTCTCTCT 60.104 48.000 0.00 0.00 0.00 3.10
2062 3065 5.103728 TCTCTCTCTCTCTCTCTCTCTCTCT 60.104 48.000 0.00 0.00 0.00 3.10
2065 3068 5.136828 TCTCTCTCTCTCTCTCTCTCTCTC 58.863 50.000 0.00 0.00 0.00 3.20
2148 3153 1.265095 CAGATGTGCATATGTTCCGCC 59.735 52.381 0.00 0.00 0.00 6.13
2198 3203 8.885494 AATCCAAAACTTTCGAATCAAATGAA 57.115 26.923 0.00 0.00 0.00 2.57
2234 3239 5.674933 AAGGAGAAACGTTCAACAAGATC 57.325 39.130 0.00 0.00 0.00 2.75
2275 3280 5.473066 AGCAACCATAGAAAACATTTGCT 57.527 34.783 0.16 0.16 42.50 3.91
2276 3281 5.857268 AGCAACCATAGAAAACATTTGCTT 58.143 33.333 0.16 0.00 44.34 3.91
2277 3282 6.290605 AGCAACCATAGAAAACATTTGCTTT 58.709 32.000 0.16 0.00 44.34 3.51
2346 3366 2.270923 TCTGCTACTTTATGCGTGCAG 58.729 47.619 7.22 7.22 46.21 4.41
2355 3375 4.156556 ACTTTATGCGTGCAGAATGTTCAT 59.843 37.500 13.02 0.00 39.31 2.57
2358 3378 4.906065 ATGCGTGCAGAATGTTCATAAT 57.094 36.364 0.00 0.00 39.31 1.28
2359 3379 7.489574 TTATGCGTGCAGAATGTTCATAATA 57.510 32.000 0.00 0.00 39.31 0.98
2412 3432 1.216710 CTGAACTCCCTCTCACCGC 59.783 63.158 0.00 0.00 0.00 5.68
2414 3434 1.079750 GAACTCCCTCTCACCGCAC 60.080 63.158 0.00 0.00 0.00 5.34
2422 3442 3.775654 CTCACCGCACCTCCCCTC 61.776 72.222 0.00 0.00 0.00 4.30
2488 3508 2.666190 CCACCATAGCGCCATCCG 60.666 66.667 2.29 0.00 40.75 4.18
2489 3509 2.108976 CACCATAGCGCCATCCGT 59.891 61.111 2.29 0.00 39.71 4.69
2490 3510 1.956170 CACCATAGCGCCATCCGTC 60.956 63.158 2.29 0.00 39.71 4.79
2491 3511 2.357517 CCATAGCGCCATCCGTCC 60.358 66.667 2.29 0.00 39.71 4.79
2492 3512 2.357517 CATAGCGCCATCCGTCCC 60.358 66.667 2.29 0.00 39.71 4.46
2493 3513 3.626924 ATAGCGCCATCCGTCCCC 61.627 66.667 2.29 0.00 39.71 4.81
2497 3517 4.626081 CGCCATCCGTCCCCATCC 62.626 72.222 0.00 0.00 0.00 3.51
2498 3518 4.271016 GCCATCCGTCCCCATCCC 62.271 72.222 0.00 0.00 0.00 3.85
2505 3525 2.372688 GTCCCCATCCCTCCTCCA 59.627 66.667 0.00 0.00 0.00 3.86
2528 3548 1.305201 TCTCCTGCGGTTTTTGTGAC 58.695 50.000 0.00 0.00 0.00 3.67
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 0.779997 ATGAAGGGTGGGCTCAAAGT 59.220 50.000 0.00 0.00 0.00 2.66
1 2 1.928868 AATGAAGGGTGGGCTCAAAG 58.071 50.000 0.00 0.00 0.00 2.77
2 3 2.397044 AAATGAAGGGTGGGCTCAAA 57.603 45.000 0.00 0.00 0.00 2.69
3 4 2.158325 AGAAAATGAAGGGTGGGCTCAA 60.158 45.455 0.00 0.00 0.00 3.02
4 5 1.428912 AGAAAATGAAGGGTGGGCTCA 59.571 47.619 0.00 0.00 0.00 4.26
5 6 2.222227 AGAAAATGAAGGGTGGGCTC 57.778 50.000 0.00 0.00 0.00 4.70
6 7 2.702270 AAGAAAATGAAGGGTGGGCT 57.298 45.000 0.00 0.00 0.00 5.19
9 10 7.414540 CGAATCTAGAAAGAAAATGAAGGGTGG 60.415 40.741 0.00 0.00 34.73 4.61
11 12 6.094186 GCGAATCTAGAAAGAAAATGAAGGGT 59.906 38.462 0.00 0.00 34.73 4.34
12 13 6.458888 GGCGAATCTAGAAAGAAAATGAAGGG 60.459 42.308 0.00 0.00 34.73 3.95
13 14 6.094048 TGGCGAATCTAGAAAGAAAATGAAGG 59.906 38.462 0.00 0.00 34.73 3.46
14 15 6.963805 GTGGCGAATCTAGAAAGAAAATGAAG 59.036 38.462 0.00 0.00 34.73 3.02
15 16 6.655003 AGTGGCGAATCTAGAAAGAAAATGAA 59.345 34.615 0.00 0.00 34.73 2.57
16 17 6.092670 CAGTGGCGAATCTAGAAAGAAAATGA 59.907 38.462 0.00 0.00 34.73 2.57
17 18 6.253746 CAGTGGCGAATCTAGAAAGAAAATG 58.746 40.000 0.00 0.00 34.73 2.32
18 19 5.355350 CCAGTGGCGAATCTAGAAAGAAAAT 59.645 40.000 0.00 0.00 34.73 1.82
19 20 4.695455 CCAGTGGCGAATCTAGAAAGAAAA 59.305 41.667 0.00 0.00 34.73 2.29
20 21 4.253685 CCAGTGGCGAATCTAGAAAGAAA 58.746 43.478 0.00 0.00 34.73 2.52
21 22 3.861840 CCAGTGGCGAATCTAGAAAGAA 58.138 45.455 0.00 0.00 34.73 2.52
22 23 2.418746 GCCAGTGGCGAATCTAGAAAGA 60.419 50.000 20.55 0.00 39.62 2.52
23 24 1.936547 GCCAGTGGCGAATCTAGAAAG 59.063 52.381 20.55 0.00 39.62 2.62
24 25 2.024176 GCCAGTGGCGAATCTAGAAA 57.976 50.000 20.55 0.00 39.62 2.52
25 26 3.760693 GCCAGTGGCGAATCTAGAA 57.239 52.632 20.55 0.00 39.62 2.10
36 37 3.625897 TGACACCTCCGCCAGTGG 61.626 66.667 4.20 4.20 38.34 4.00
37 38 2.357517 GTGACACCTCCGCCAGTG 60.358 66.667 0.00 0.00 39.93 3.66
38 39 2.842462 TGTGACACCTCCGCCAGT 60.842 61.111 2.45 0.00 0.00 4.00
39 40 2.357517 GTGTGACACCTCCGCCAG 60.358 66.667 3.92 0.00 0.00 4.85
40 41 4.293648 CGTGTGACACCTCCGCCA 62.294 66.667 10.52 0.00 0.00 5.69
42 43 4.961511 TGCGTGTGACACCTCCGC 62.962 66.667 20.72 20.72 44.27 5.54
43 44 3.036084 GTGCGTGTGACACCTCCG 61.036 66.667 10.52 0.00 31.67 4.63
44 45 1.956170 CTGTGCGTGTGACACCTCC 60.956 63.158 10.52 0.00 37.22 4.30
45 46 1.956170 CCTGTGCGTGTGACACCTC 60.956 63.158 10.52 2.94 37.22 3.85
46 47 1.966901 TTCCTGTGCGTGTGACACCT 61.967 55.000 10.52 0.00 37.22 4.00
47 48 1.092921 TTTCCTGTGCGTGTGACACC 61.093 55.000 10.52 3.75 37.22 4.16
48 49 0.730265 TTTTCCTGTGCGTGTGACAC 59.270 50.000 5.47 5.47 38.55 3.67
49 50 1.013596 CTTTTCCTGTGCGTGTGACA 58.986 50.000 0.00 0.00 0.00 3.58
50 51 0.307760 CCTTTTCCTGTGCGTGTGAC 59.692 55.000 0.00 0.00 0.00 3.67
51 52 0.817634 CCCTTTTCCTGTGCGTGTGA 60.818 55.000 0.00 0.00 0.00 3.58
52 53 1.101049 ACCCTTTTCCTGTGCGTGTG 61.101 55.000 0.00 0.00 0.00 3.82
53 54 0.395173 AACCCTTTTCCTGTGCGTGT 60.395 50.000 0.00 0.00 0.00 4.49
54 55 0.030638 CAACCCTTTTCCTGTGCGTG 59.969 55.000 0.00 0.00 0.00 5.34
55 56 1.106944 CCAACCCTTTTCCTGTGCGT 61.107 55.000 0.00 0.00 0.00 5.24
62 63 3.660501 GTGATTCACCAACCCTTTTCC 57.339 47.619 5.44 0.00 0.00 3.13
109 110 0.536006 ACACAAGGAGAAGCTGCCAC 60.536 55.000 0.00 0.00 0.00 5.01
151 152 1.580845 GCGATAGGCATGGCATGGTC 61.581 60.000 27.48 12.58 42.87 4.02
175 176 1.226888 CTAGGTCTACAACGGCGGC 60.227 63.158 13.24 0.00 0.00 6.53
178 179 1.472188 ACTCCTAGGTCTACAACGGC 58.528 55.000 9.08 0.00 0.00 5.68
182 183 5.426504 CGAAGACTACTCCTAGGTCTACAA 58.573 45.833 9.08 0.00 39.09 2.41
191 192 0.543277 TCCCGCGAAGACTACTCCTA 59.457 55.000 8.23 0.00 0.00 2.94
192 193 0.323178 TTCCCGCGAAGACTACTCCT 60.323 55.000 8.23 0.00 0.00 3.69
244 245 1.615392 AGAAACAAGCATCCTGGCAAC 59.385 47.619 0.00 0.00 35.83 4.17
265 266 3.306294 CCAAAAGAAAGCCTCACATTCCC 60.306 47.826 0.00 0.00 0.00 3.97
270 271 5.385198 AGATTACCAAAAGAAAGCCTCACA 58.615 37.500 0.00 0.00 0.00 3.58
283 284 3.838565 TGTCAAGGCCAAGATTACCAAA 58.161 40.909 5.01 0.00 0.00 3.28
354 358 5.700832 TGATGTAGAGTTTTTGCGAAGACAT 59.299 36.000 9.84 3.85 0.00 3.06
365 369 8.598041 AGACTTAACCTCATGATGTAGAGTTTT 58.402 33.333 15.49 8.54 0.00 2.43
369 373 6.261158 TCGAGACTTAACCTCATGATGTAGAG 59.739 42.308 3.91 7.81 0.00 2.43
405 409 1.964933 TCCCGACAATGCGATGGTATA 59.035 47.619 0.00 0.00 0.00 1.47
416 420 2.683933 ACTCCGCCTCCCGACAAT 60.684 61.111 0.00 0.00 40.02 2.71
453 457 3.230134 TGCCTTGGCTGACTACAAAATT 58.770 40.909 13.18 0.00 0.00 1.82
473 477 3.504906 ACAAGCAACTTGAGGATGACATG 59.495 43.478 13.94 0.00 43.42 3.21
474 478 3.755378 GACAAGCAACTTGAGGATGACAT 59.245 43.478 13.94 0.00 43.42 3.06
477 481 3.405831 CTGACAAGCAACTTGAGGATGA 58.594 45.455 13.94 0.00 43.42 2.92
584 588 1.918262 TCCAGAGAAATGCTCACCCAT 59.082 47.619 0.00 0.00 46.45 4.00
598 602 0.321564 TGGCGTCAACCAATCCAGAG 60.322 55.000 0.00 0.00 36.55 3.35
600 604 0.734889 GATGGCGTCAACCAATCCAG 59.265 55.000 0.00 0.00 44.65 3.86
601 605 0.679640 GGATGGCGTCAACCAATCCA 60.680 55.000 11.96 0.00 44.65 3.41
614 618 1.153168 TCTTGCTTAGCGGGATGGC 60.153 57.895 0.00 0.00 0.00 4.40
646 650 1.153823 CCCACGGACACATCGAGTC 60.154 63.158 0.00 0.00 35.29 3.36
702 707 3.499737 GCCGTCCGTTGCATGAGG 61.500 66.667 0.00 0.00 0.00 3.86
747 798 1.681327 GAGTACCCGTCTCCTGGCA 60.681 63.158 0.00 0.00 0.00 4.92
768 819 1.438651 CACACGGTGTGGACATTAGG 58.561 55.000 29.07 4.38 44.27 2.69
864 916 1.836166 CTGGTGGAGATGGACATGTCT 59.164 52.381 24.50 6.55 32.31 3.41
955 1010 1.329171 TTTGGCCTTGTGCTTGTGCT 61.329 50.000 3.32 0.00 40.92 4.40
971 1026 1.135689 GGCTCGTGTATGCACCTTTTG 60.136 52.381 8.45 0.00 42.39 2.44
973 1028 1.019278 CGGCTCGTGTATGCACCTTT 61.019 55.000 8.45 0.00 42.39 3.11
974 1029 1.447838 CGGCTCGTGTATGCACCTT 60.448 57.895 8.45 0.00 42.39 3.50
975 1030 1.676678 ATCGGCTCGTGTATGCACCT 61.677 55.000 8.45 0.00 42.39 4.00
1215 1270 3.273654 TGGTCCTCCTCTCCCGGT 61.274 66.667 0.00 0.00 34.23 5.28
1556 1611 1.557371 GCTAGTCCTTCCCTTCAAGCT 59.443 52.381 0.00 0.00 0.00 3.74
1599 1654 6.519679 TTCCATCTTTGTTTCATCTCATGG 57.480 37.500 0.00 0.00 0.00 3.66
1600 1655 7.491372 CCATTTCCATCTTTGTTTCATCTCATG 59.509 37.037 0.00 0.00 0.00 3.07
1613 1672 7.093201 ACAGCAAATACATCCATTTCCATCTTT 60.093 33.333 0.00 0.00 0.00 2.52
1690 2441 1.871772 CAAACTGGGAAGCGAGCAG 59.128 57.895 0.00 0.00 0.00 4.24
1691 2442 2.260869 GCAAACTGGGAAGCGAGCA 61.261 57.895 0.00 0.00 0.00 4.26
1706 2457 9.373603 ACGTACTACTACATTTATTCATTGCAA 57.626 29.630 0.00 0.00 0.00 4.08
1724 2475 8.545229 ACATGTATAGACCTCATACGTACTAC 57.455 38.462 0.00 0.00 32.55 2.73
1733 2484 5.458595 TGGACAGACATGTATAGACCTCAT 58.541 41.667 0.00 0.00 40.68 2.90
1737 2488 5.772672 AGAGATGGACAGACATGTATAGACC 59.227 44.000 0.00 2.31 40.68 3.85
1752 2503 6.456501 ACTAACACTAAACACAGAGATGGAC 58.543 40.000 0.00 0.00 0.00 4.02
1784 2535 9.275398 TGTTTATCGGAATTGTAGTTTTGTACT 57.725 29.630 0.00 0.00 41.04 2.73
1907 2658 3.753272 GTGAGGCAGTGACAAACATACAT 59.247 43.478 0.00 0.00 0.00 2.29
1951 2702 6.119536 ACATGACCTTACACAAAGAGTTGAA 58.880 36.000 0.00 0.00 37.38 2.69
1985 2736 1.998315 GAGAGTCGTACACTACTCGCA 59.002 52.381 14.64 0.00 45.47 5.10
2026 2777 5.103728 AGAGAGAGAGAGAGAGAGAGAGAGA 60.104 48.000 0.00 0.00 0.00 3.10
2027 2778 5.139727 AGAGAGAGAGAGAGAGAGAGAGAG 58.860 50.000 0.00 0.00 0.00 3.20
2058 2809 4.600692 TCCACGAAATGTTTGAGAGAGA 57.399 40.909 0.00 0.00 0.00 3.10
2062 3065 3.081061 CCCATCCACGAAATGTTTGAGA 58.919 45.455 0.00 0.00 0.00 3.27
2065 3068 2.164219 CTCCCCATCCACGAAATGTTTG 59.836 50.000 0.00 0.00 0.00 2.93
2148 3153 4.696479 ACAAAGGATAGATAGTGGCCTG 57.304 45.455 3.32 0.00 0.00 4.85
2198 3203 0.109342 CTCCTTTGTGGACCTGCACT 59.891 55.000 0.00 0.00 40.56 4.40
2234 3239 5.407407 TGCTAAGGAAAGTAGAGGAACAG 57.593 43.478 0.00 0.00 0.00 3.16
2380 3400 6.651086 AGGGAGTTCAGGTTTTAATACTAGC 58.349 40.000 0.00 0.00 0.00 3.42
2392 3412 0.900647 CGGTGAGAGGGAGTTCAGGT 60.901 60.000 0.00 0.00 0.00 4.00
2396 3416 1.079750 GTGCGGTGAGAGGGAGTTC 60.080 63.158 0.00 0.00 0.00 3.01
2476 3496 3.626924 GGGGACGGATGGCGCTAT 61.627 66.667 5.72 5.72 0.00 2.97
2488 3508 0.699231 AATGGAGGAGGGATGGGGAC 60.699 60.000 0.00 0.00 0.00 4.46
2489 3509 0.047802 AAATGGAGGAGGGATGGGGA 59.952 55.000 0.00 0.00 0.00 4.81
2490 3510 0.936691 AAAATGGAGGAGGGATGGGG 59.063 55.000 0.00 0.00 0.00 4.96
2491 3511 1.855599 AGAAAATGGAGGAGGGATGGG 59.144 52.381 0.00 0.00 0.00 4.00
2492 3512 2.158549 GGAGAAAATGGAGGAGGGATGG 60.159 54.545 0.00 0.00 0.00 3.51
2493 3513 2.782341 AGGAGAAAATGGAGGAGGGATG 59.218 50.000 0.00 0.00 0.00 3.51
2494 3514 2.782341 CAGGAGAAAATGGAGGAGGGAT 59.218 50.000 0.00 0.00 0.00 3.85
2495 3515 2.200081 CAGGAGAAAATGGAGGAGGGA 58.800 52.381 0.00 0.00 0.00 4.20
2496 3516 1.409381 GCAGGAGAAAATGGAGGAGGG 60.409 57.143 0.00 0.00 0.00 4.30
2497 3517 1.745141 CGCAGGAGAAAATGGAGGAGG 60.745 57.143 0.00 0.00 0.00 4.30
2498 3518 1.661341 CGCAGGAGAAAATGGAGGAG 58.339 55.000 0.00 0.00 0.00 3.69


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

AutoCloner maintained by Alex Coulton.