Multiple sequence alignment - TraesCS6A01G198000

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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 TraesCS6A01G198000 chr6A 100.000 6350 0 0 1 6350 301094458 301088109 0.000000e+00 11727.0
1 TraesCS6A01G198000 chr6A 95.701 535 23 0 1 535 23358604 23359138 0.000000e+00 861.0
2 TraesCS6A01G198000 chr6A 76.636 107 23 2 2563 2668 301091791 301091896 2.470000e-04 58.4
3 TraesCS6A01G198000 chr6B 96.806 3100 77 11 2928 6016 361581365 361584453 0.000000e+00 5156.0
4 TraesCS6A01G198000 chr6B 96.976 2381 49 7 543 2922 361578574 361580932 0.000000e+00 3976.0
5 TraesCS6A01G198000 chr6B 88.889 45 3 2 2640 2682 361580605 361580561 3.000000e-03 54.7
6 TraesCS6A01G198000 chr6B 100.000 28 0 0 2564 2591 361580682 361580655 1.200000e-02 52.8
7 TraesCS6A01G198000 chr6D 97.644 2207 38 7 524 2728 191648057 191650251 0.000000e+00 3775.0
8 TraesCS6A01G198000 chr6D 95.158 2210 64 23 4152 6348 191651497 191653676 0.000000e+00 3448.0
9 TraesCS6A01G198000 chr6D 96.936 1175 16 7 2992 4154 191650250 191651416 0.000000e+00 1953.0
10 TraesCS6A01G198000 chr6D 88.106 227 25 2 6123 6347 162645938 162645712 1.050000e-67 268.0
11 TraesCS6A01G198000 chr6D 100.000 37 0 0 1407 1443 57825672 57825636 1.140000e-07 69.4
12 TraesCS6A01G198000 chr6D 89.796 49 4 1 1443 1490 391046420 391046372 1.910000e-05 62.1
13 TraesCS6A01G198000 chr6D 100.000 29 0 0 2640 2668 191650114 191650086 3.000000e-03 54.7
14 TraesCS6A01G198000 chr1A 96.679 542 16 1 1 540 585985927 585985386 0.000000e+00 900.0
15 TraesCS6A01G198000 chr1A 96.078 51 2 0 1421 1471 342432361 342432311 4.080000e-12 84.2
16 TraesCS6A01G198000 chr7A 96.097 538 18 2 1 536 510161560 510162096 0.000000e+00 874.0
17 TraesCS6A01G198000 chr7A 90.909 99 6 2 5914 6012 452650601 452650506 5.170000e-26 130.0
18 TraesCS6A01G198000 chr3D 95.564 541 22 1 1 539 47339412 47338872 0.000000e+00 865.0
19 TraesCS6A01G198000 chr3D 95.717 537 20 2 5 539 335200185 335200720 0.000000e+00 861.0
20 TraesCS6A01G198000 chr3D 88.789 223 24 1 6125 6346 215016402 215016624 8.110000e-69 272.0
21 TraesCS6A01G198000 chr3D 83.333 108 7 4 1393 1489 463716972 463716865 8.770000e-14 89.8
22 TraesCS6A01G198000 chr5A 95.547 539 21 2 1 536 103567310 103566772 0.000000e+00 859.0
23 TraesCS6A01G198000 chr5A 95.531 537 21 3 1 536 457518286 457518820 0.000000e+00 856.0
24 TraesCS6A01G198000 chr5A 90.816 98 7 2 5919 6014 607195228 607195131 5.170000e-26 130.0
25 TraesCS6A01G198000 chr5A 82.243 107 8 4 1394 1489 410504852 410504958 1.470000e-11 82.4
26 TraesCS6A01G198000 chr5A 100.000 34 0 0 6014 6047 689703785 689703752 5.310000e-06 63.9
27 TraesCS6A01G198000 chr5A 100.000 28 0 0 5763 5790 141071946 141071919 1.200000e-02 52.8
28 TraesCS6A01G198000 chr5D 95.693 534 21 1 5 536 445036811 445036278 0.000000e+00 857.0
29 TraesCS6A01G198000 chr5D 90.265 226 20 2 6122 6345 102009558 102009333 1.730000e-75 294.0
30 TraesCS6A01G198000 chr5D 88.571 105 9 3 5914 6016 442891688 442891585 2.400000e-24 124.0
31 TraesCS6A01G198000 chr5D 85.470 117 14 3 5902 6016 354507056 354506941 1.120000e-22 119.0
32 TraesCS6A01G198000 chr3A 95.353 538 23 1 1 536 718079695 718080232 0.000000e+00 854.0
33 TraesCS6A01G198000 chr1D 89.868 227 21 2 6123 6347 155622467 155622241 2.240000e-74 291.0
34 TraesCS6A01G198000 chr1D 88.496 226 25 1 6123 6347 177421598 177421823 8.110000e-69 272.0
35 TraesCS6A01G198000 chr1D 88.158 228 25 2 6122 6347 95437518 95437291 2.920000e-68 270.0
36 TraesCS6A01G198000 chr2A 89.035 228 23 2 6123 6348 304778442 304778215 1.350000e-71 281.0
37 TraesCS6A01G198000 chr2A 91.489 47 3 1 1444 1489 632934444 632934398 5.310000e-06 63.9
38 TraesCS6A01G198000 chr4D 88.106 227 26 1 6123 6348 338158762 338158536 1.050000e-67 268.0
39 TraesCS6A01G198000 chr4D 89.320 103 9 2 5914 6014 105123850 105123952 1.860000e-25 128.0
40 TraesCS6A01G198000 chr4D 95.000 40 1 1 1443 1481 367162387 367162426 1.910000e-05 62.1
41 TraesCS6A01G198000 chr4B 86.667 120 10 5 5902 6016 235376191 235376073 1.860000e-25 128.0
42 TraesCS6A01G198000 chr4B 97.222 36 1 0 6014 6049 235376102 235376067 1.910000e-05 62.1
43 TraesCS6A01G198000 chr5B 88.462 104 10 2 5913 6014 598047571 598047468 2.400000e-24 124.0
44 TraesCS6A01G198000 chr5B 93.182 44 3 0 1394 1437 650559918 650559875 1.480000e-06 65.8
45 TraesCS6A01G198000 chr5B 79.208 101 10 2 1394 1483 257334195 257334295 6.880000e-05 60.2
46 TraesCS6A01G198000 chr3B 81.034 116 9 4 1387 1489 581965978 581966093 5.280000e-11 80.5
47 TraesCS6A01G198000 chr4A 81.553 103 8 2 1393 1484 576605175 576605073 2.460000e-09 75.0
48 TraesCS6A01G198000 chr4A 95.455 44 2 0 6014 6057 668107466 668107509 3.180000e-08 71.3
49 TraesCS6A01G198000 chr4A 86.154 65 8 1 1380 1443 82739113 82739177 1.140000e-07 69.4
50 TraesCS6A01G198000 chr2B 100.000 34 0 0 6014 6047 556558965 556558932 5.310000e-06 63.9
51 TraesCS6A01G198000 chr2B 89.796 49 4 1 1443 1490 412549378 412549330 1.910000e-05 62.1
52 TraesCS6A01G198000 chr2B 97.222 36 1 0 6014 6049 556598386 556598351 1.910000e-05 62.1
53 TraesCS6A01G198000 chr2D 97.222 36 1 0 6014 6049 403330598 403330633 1.910000e-05 62.1
54 TraesCS6A01G198000 chr1B 97.222 36 1 0 6014 6049 12975017 12975052 1.910000e-05 62.1
55 TraesCS6A01G198000 chr7D 100.000 32 0 0 6014 6045 53482366 53482397 6.880000e-05 60.2


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 TraesCS6A01G198000 chr6A 301088109 301094458 6349 True 11727.000000 11727 100.000000 1 6350 1 chr6A.!!$R1 6349
1 TraesCS6A01G198000 chr6A 23358604 23359138 534 False 861.000000 861 95.701000 1 535 1 chr6A.!!$F1 534
2 TraesCS6A01G198000 chr6B 361578574 361584453 5879 False 4566.000000 5156 96.891000 543 6016 2 chr6B.!!$F1 5473
3 TraesCS6A01G198000 chr6D 191648057 191653676 5619 False 3058.666667 3775 96.579333 524 6348 3 chr6D.!!$F1 5824
4 TraesCS6A01G198000 chr1A 585985386 585985927 541 True 900.000000 900 96.679000 1 540 1 chr1A.!!$R2 539
5 TraesCS6A01G198000 chr7A 510161560 510162096 536 False 874.000000 874 96.097000 1 536 1 chr7A.!!$F1 535
6 TraesCS6A01G198000 chr3D 47338872 47339412 540 True 865.000000 865 95.564000 1 539 1 chr3D.!!$R1 538
7 TraesCS6A01G198000 chr3D 335200185 335200720 535 False 861.000000 861 95.717000 5 539 1 chr3D.!!$F2 534
8 TraesCS6A01G198000 chr5A 103566772 103567310 538 True 859.000000 859 95.547000 1 536 1 chr5A.!!$R1 535
9 TraesCS6A01G198000 chr5A 457518286 457518820 534 False 856.000000 856 95.531000 1 536 1 chr5A.!!$F2 535
10 TraesCS6A01G198000 chr5D 445036278 445036811 533 True 857.000000 857 95.693000 5 536 1 chr5D.!!$R4 531
11 TraesCS6A01G198000 chr3A 718079695 718080232 537 False 854.000000 854 95.353000 1 536 1 chr3A.!!$F1 535

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
86 87 1.891150 AGGCAGCTCAATTGAAACTGG 59.109 47.619 27.11 12.01 32.17 4.00 F
1045 1051 0.606604 GAGGGAGCGGTGAGTTTGTA 59.393 55.000 0.00 0.00 0.00 2.41 F
2812 2820 0.517316 CTCCGTGGCTTAAGCAACAC 59.483 55.000 29.79 24.90 45.13 3.32 F
3626 4064 1.119684 TCGCACATGCTATACCTGGT 58.880 50.000 4.05 4.05 39.32 4.00 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1929 1935 1.066143 CGTTATTCAGGGTGTCAGGCT 60.066 52.381 0.0 0.0 0.00 4.58 R
2933 2941 2.559668 CAAGGTGCTTCACATGGACAAT 59.440 45.455 0.0 0.0 35.86 2.71 R
3679 4117 2.224744 TGCCCTGTCTAGAAATTGCACA 60.225 45.455 0.0 0.0 0.00 4.57 R
5610 6139 1.613925 TGGGACGAAGAGAGTGTCAAG 59.386 52.381 0.0 0.0 34.32 3.02 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 2.754658 GGAGAGGGACGCGAGGAA 60.755 66.667 15.93 0.00 0.00 3.36
86 87 1.891150 AGGCAGCTCAATTGAAACTGG 59.109 47.619 27.11 12.01 32.17 4.00
100 101 4.776349 TGAAACTGGAGCTACAAGAAACA 58.224 39.130 0.00 0.00 0.00 2.83
373 378 2.333938 CGTCCGTCTTGTGTCCGT 59.666 61.111 0.00 0.00 0.00 4.69
540 545 3.441572 CCCAATTGGAGTTGCTCTTAGTG 59.558 47.826 26.60 0.00 37.39 2.74
541 546 3.441572 CCAATTGGAGTTGCTCTTAGTGG 59.558 47.826 20.50 0.00 37.39 4.00
683 689 2.444624 CGGTCATTGACTCACCGCG 61.445 63.158 16.02 0.00 46.08 6.46
1045 1051 0.606604 GAGGGAGCGGTGAGTTTGTA 59.393 55.000 0.00 0.00 0.00 2.41
1096 1102 3.341823 CATCTCTGTTGGCACTTAGCTT 58.658 45.455 0.00 0.00 44.79 3.74
1256 1262 3.626217 CGCAGGGATAGGAAAAACTTACC 59.374 47.826 0.00 0.00 0.00 2.85
1419 1425 4.166144 CCCCTCTGTCCCATATTAGTTGTT 59.834 45.833 0.00 0.00 0.00 2.83
1769 1775 6.606796 TGGAATTTAGCAGAATGATTGCCTTA 59.393 34.615 0.00 0.00 42.48 2.69
2256 2262 1.416401 ACCCACCAACAGTGTGTCTAG 59.584 52.381 0.00 0.00 45.74 2.43
2544 2551 5.777732 TGGGAAACATAGGTAACATGCTTTT 59.222 36.000 0.00 0.00 41.41 2.27
2556 2563 2.288458 ACATGCTTTTGTGCAATGCAAC 59.712 40.909 10.44 5.14 45.80 4.17
2602 2609 6.097839 TGCTGTATTCCGAATTCTTAGGTAGT 59.902 38.462 3.52 0.00 0.00 2.73
2763 2771 9.698309 ATCACTTCTATATTGATTTGTACTCCG 57.302 33.333 0.00 0.00 0.00 4.63
2811 2819 0.605319 CCTCCGTGGCTTAAGCAACA 60.605 55.000 29.79 17.23 45.13 3.33
2812 2820 0.517316 CTCCGTGGCTTAAGCAACAC 59.483 55.000 29.79 24.90 45.13 3.32
2987 3420 6.183360 TGTCATACGGTTCTATCTGTACACAG 60.183 42.308 2.84 2.84 45.08 3.66
3071 3508 7.938140 AACAGATAAAACAGCCAAGCTAATA 57.062 32.000 0.00 0.00 36.40 0.98
3152 3589 6.319658 ACGATCATAAGCTCACATTCCAAATT 59.680 34.615 0.00 0.00 0.00 1.82
3231 3668 2.680339 GCCTATCTCCTTCTGTTTGCAC 59.320 50.000 0.00 0.00 0.00 4.57
3328 3765 9.369904 TGGTTTATATTACGTTTCTCTGTTACC 57.630 33.333 0.00 0.00 0.00 2.85
3329 3766 8.534778 GGTTTATATTACGTTTCTCTGTTACCG 58.465 37.037 0.00 0.00 0.00 4.02
3331 3768 9.853555 TTTATATTACGTTTCTCTGTTACCGAA 57.146 29.630 0.00 0.00 0.00 4.30
3333 3770 8.761575 ATATTACGTTTCTCTGTTACCGAAAA 57.238 30.769 0.00 0.00 0.00 2.29
3334 3771 6.900568 TTACGTTTCTCTGTTACCGAAAAA 57.099 33.333 0.00 0.00 0.00 1.94
3335 3772 5.399604 ACGTTTCTCTGTTACCGAAAAAG 57.600 39.130 0.00 0.00 0.00 2.27
3336 3773 4.271776 ACGTTTCTCTGTTACCGAAAAAGG 59.728 41.667 0.00 0.00 37.30 3.11
3337 3774 4.534168 GTTTCTCTGTTACCGAAAAAGGC 58.466 43.478 0.00 0.00 33.69 4.35
3338 3775 3.764237 TCTCTGTTACCGAAAAAGGCT 57.236 42.857 0.00 0.00 33.69 4.58
3339 3776 4.081322 TCTCTGTTACCGAAAAAGGCTT 57.919 40.909 0.00 0.00 33.69 4.35
3340 3777 4.457466 TCTCTGTTACCGAAAAAGGCTTT 58.543 39.130 6.68 6.68 33.69 3.51
3341 3778 4.514066 TCTCTGTTACCGAAAAAGGCTTTC 59.486 41.667 13.76 0.41 33.69 2.62
3545 3983 9.706846 CTGACAAACAAATTTTGATTTTCCTTC 57.293 29.630 15.81 4.43 33.83 3.46
3564 4002 1.757118 TCCAGGAAGATAAGGTGCTCG 59.243 52.381 0.00 0.00 0.00 5.03
3626 4064 1.119684 TCGCACATGCTATACCTGGT 58.880 50.000 4.05 4.05 39.32 4.00
3668 4106 5.513849 CCGACAAAGGTAAAACAAAGTGTTC 59.486 40.000 0.00 0.00 40.14 3.18
3679 4117 3.551846 ACAAAGTGTTCGGTTGATTCCT 58.448 40.909 0.00 0.00 0.00 3.36
3837 4283 6.651225 GGTGACTTGTTTATTCTTCAGTAGCT 59.349 38.462 0.00 0.00 0.00 3.32
4237 4766 1.001974 ACTTGTGCTATCACCGCTTGA 59.998 47.619 0.00 0.00 42.46 3.02
4238 4767 2.076100 CTTGTGCTATCACCGCTTGAA 58.924 47.619 0.00 0.00 42.46 2.69
4239 4768 2.177394 TGTGCTATCACCGCTTGAAA 57.823 45.000 0.00 0.00 42.46 2.69
4254 4783 5.281727 CGCTTGAAAATAAATAAGGGCTCC 58.718 41.667 0.00 0.00 0.00 4.70
4290 4819 2.561733 TTAGATTCTGTCAGACGGCG 57.438 50.000 4.80 4.80 0.00 6.46
4764 5293 3.005554 CCTGTCAGGCACACAGAATAAG 58.994 50.000 15.35 0.00 43.54 1.73
4815 5344 7.531280 AGTTTCTGATATTCTGAATGACACG 57.469 36.000 13.01 7.20 34.93 4.49
4913 5442 6.054860 AGTAGGTGAAAATGCTGATGTACT 57.945 37.500 0.00 0.00 0.00 2.73
5059 5588 3.744660 GTGGAACTCAAGTCATCCAGTT 58.255 45.455 4.21 0.00 42.35 3.16
5262 5791 6.482641 CCTCAGATCCATGTTCATTAGAGTTG 59.517 42.308 0.00 0.00 0.00 3.16
5378 5907 6.888105 AGGAAAGTGACAATGACCAAAATTT 58.112 32.000 0.00 0.00 0.00 1.82
5448 5977 4.011023 ACTCACTGTTACTGCTATCGTCT 58.989 43.478 0.00 0.00 0.00 4.18
5610 6139 9.850628 TTCGACCTATAATATAGTGTACATTGC 57.149 33.333 0.00 0.00 0.00 3.56
5645 6174 3.057104 TCGTCCCATAACAGTGTACAGTG 60.057 47.826 25.82 25.82 37.75 3.66
5650 6179 4.454504 CCCATAACAGTGTACAGTGGTTTC 59.545 45.833 29.50 2.59 36.10 2.78
5859 6393 6.498304 AGGATATTTAGTTTGATTTGCGCAG 58.502 36.000 11.31 0.00 0.00 5.18
5948 6483 7.171337 GTGGCAATAAACACATGTTTTCTTCAT 59.829 33.333 14.78 0.25 45.07 2.57
5983 6520 7.284034 ACATTTGTAAAATCCATTTTTGGCACA 59.716 29.630 2.68 0.00 40.24 4.57
5990 6527 1.606224 CCATTTTTGGCACACAGGAGC 60.606 52.381 0.00 0.00 39.29 4.70
6016 6553 3.205784 CTCCCTAGAGCCAAAATGGAG 57.794 52.381 0.00 0.00 40.96 3.86
6017 6554 1.212935 TCCCTAGAGCCAAAATGGAGC 59.787 52.381 0.00 0.00 40.96 4.70
6018 6555 1.064463 CCCTAGAGCCAAAATGGAGCA 60.064 52.381 0.00 0.00 40.96 4.26
6019 6556 2.423947 CCCTAGAGCCAAAATGGAGCAT 60.424 50.000 0.00 0.00 40.96 3.79
6020 6557 2.621998 CCTAGAGCCAAAATGGAGCATG 59.378 50.000 0.00 0.00 40.96 4.06
6021 6558 2.226962 AGAGCCAAAATGGAGCATGT 57.773 45.000 0.00 0.00 40.96 3.21
6022 6559 1.822990 AGAGCCAAAATGGAGCATGTG 59.177 47.619 0.00 0.00 40.96 3.21
6070 6608 5.049828 CGTGCCAGTGATTCTTATGTATCA 58.950 41.667 0.00 0.00 0.00 2.15
6118 6656 2.397044 AATCAAAACCTGGGGAGCAA 57.603 45.000 0.00 0.00 0.00 3.91
6126 6664 0.251297 CCTGGGGAGCAACATTGTCA 60.251 55.000 0.00 0.00 0.00 3.58
6129 6667 1.075212 TGGGGAGCAACATTGTCATGA 59.925 47.619 0.00 0.00 34.11 3.07
6131 6669 2.618816 GGGGAGCAACATTGTCATGAGA 60.619 50.000 0.00 0.00 34.11 3.27
6211 6751 1.217882 CACAAAGAGCGGAGAACGTT 58.782 50.000 0.00 0.00 46.52 3.99
6246 6786 4.336433 CAGAGATCACACGGGCAATTTTAT 59.664 41.667 0.00 0.00 0.00 1.40
6254 6794 3.056179 CACGGGCAATTTTATCCAGGTTT 60.056 43.478 0.00 0.00 0.00 3.27
6255 6795 3.056179 ACGGGCAATTTTATCCAGGTTTG 60.056 43.478 0.00 0.00 0.00 2.93
6258 6798 3.263170 GGCAATTTTATCCAGGTTTGGGT 59.737 43.478 0.00 0.00 45.10 4.51
6259 6799 4.503910 GCAATTTTATCCAGGTTTGGGTC 58.496 43.478 0.00 0.00 45.10 4.46
6269 6809 4.077184 TTTGGGTCGCCGCGAGAT 62.077 61.111 17.42 0.00 36.23 2.75
6284 6824 3.181489 CGCGAGATGTAAAACCCTACTCT 60.181 47.826 0.00 0.00 0.00 3.24
6305 6856 1.327303 GCTTTGGTGGATTGTGGTGA 58.673 50.000 0.00 0.00 0.00 4.02
6338 6889 0.981277 TAGCCTGGTAGGGTTGCCTC 60.981 60.000 4.75 0.00 45.25 4.70
6339 6890 2.584608 CCTGGTAGGGTTGCCTCG 59.415 66.667 0.00 0.00 0.00 4.63
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
86 87 2.973945 ACCCGATGTTTCTTGTAGCTC 58.026 47.619 0.00 0.00 0.00 4.09
100 101 1.702957 TCTTCAAAGTCCCAACCCGAT 59.297 47.619 0.00 0.00 0.00 4.18
514 519 1.551883 GAGCAACTCCAATTGGGCAAT 59.448 47.619 24.29 4.89 36.21 3.56
521 526 4.640771 TCCACTAAGAGCAACTCCAATT 57.359 40.909 0.00 0.00 0.00 2.32
625 631 4.397417 GGCTGTTTCTATGTGAGCATTTCT 59.603 41.667 0.00 0.00 36.58 2.52
668 674 0.948623 CAACCGCGGTGAGTCAATGA 60.949 55.000 34.95 0.00 0.00 2.57
1045 1051 1.219935 GTAACACGGGGCGGAGATT 59.780 57.895 0.00 0.00 0.00 2.40
1096 1102 3.454719 TCTCCAATCCAAATCAAGGCA 57.545 42.857 0.00 0.00 0.00 4.75
1256 1262 8.040727 TGTAGGAATTCCGGATACATGATATTG 58.959 37.037 18.82 0.00 42.08 1.90
1419 1425 4.497507 CGTCTAGATACATCCGTTTGAGCA 60.498 45.833 0.00 0.00 0.00 4.26
1723 1729 4.063689 CAGATATAGTTGGCTTGAGGCTG 58.936 47.826 6.13 0.00 41.69 4.85
1769 1775 6.214005 ACCAATTGTTTCCCATGATCTTCAAT 59.786 34.615 4.43 0.00 0.00 2.57
1929 1935 1.066143 CGTTATTCAGGGTGTCAGGCT 60.066 52.381 0.00 0.00 0.00 4.58
2256 2262 5.491982 ACATTTTGGTACAGAGATCTCCAC 58.508 41.667 19.30 13.93 42.39 4.02
2384 2390 6.006449 AGCTAACTGACCACTCAAATTGATT 58.994 36.000 0.00 0.00 0.00 2.57
2544 2551 5.388408 TCATAATGAAGTTGCATTGCACA 57.612 34.783 11.66 6.48 38.71 4.57
2556 2563 4.522022 GCATCCTCCCCTTTCATAATGAAG 59.478 45.833 0.00 0.00 37.70 3.02
2733 2741 9.056005 GTACAAATCAATATAGAAGTGATGCCA 57.944 33.333 0.00 0.00 32.38 4.92
2811 2819 7.716998 GGATAGACATGTGGAATAATTGACTGT 59.283 37.037 1.15 0.00 0.00 3.55
2812 2820 7.935755 AGGATAGACATGTGGAATAATTGACTG 59.064 37.037 1.15 0.00 0.00 3.51
2925 2933 9.618890 GGTGCTTCACATGGACAATATATATAT 57.381 33.333 0.00 0.00 35.86 0.86
2926 2934 8.825774 AGGTGCTTCACATGGACAATATATATA 58.174 33.333 0.00 0.00 35.86 0.86
2927 2935 7.693132 AGGTGCTTCACATGGACAATATATAT 58.307 34.615 0.00 0.00 35.86 0.86
2929 2937 5.945310 AGGTGCTTCACATGGACAATATAT 58.055 37.500 0.00 0.00 35.86 0.86
2930 2938 5.372343 AGGTGCTTCACATGGACAATATA 57.628 39.130 0.00 0.00 35.86 0.86
2931 2939 4.240881 AGGTGCTTCACATGGACAATAT 57.759 40.909 0.00 0.00 35.86 1.28
2932 2940 3.719268 AGGTGCTTCACATGGACAATA 57.281 42.857 0.00 0.00 35.86 1.90
2933 2941 2.559668 CAAGGTGCTTCACATGGACAAT 59.440 45.455 0.00 0.00 35.86 2.71
2987 3420 5.466728 ACGCATGACACATGGATACTATTTC 59.533 40.000 12.56 0.00 37.61 2.17
3071 3508 8.787852 GGAATGAGTCAAAGAAACAAGTCTAAT 58.212 33.333 0.00 0.00 0.00 1.73
3152 3589 2.204889 ACCCGTAGTCCCAACCCA 59.795 61.111 0.00 0.00 0.00 4.51
3231 3668 5.755375 CAGCAGTACAAATGGTAGTCATAGG 59.245 44.000 0.00 0.00 33.26 2.57
3329 3766 3.315470 AGTTGTCCTCGAAAGCCTTTTTC 59.685 43.478 0.00 0.00 0.00 2.29
3331 3768 2.932261 AGTTGTCCTCGAAAGCCTTTT 58.068 42.857 0.00 0.00 0.00 2.27
3333 3770 2.618709 CAAAGTTGTCCTCGAAAGCCTT 59.381 45.455 0.00 0.00 0.00 4.35
3334 3771 2.222027 CAAAGTTGTCCTCGAAAGCCT 58.778 47.619 0.00 0.00 0.00 4.58
3335 3772 1.335051 GCAAAGTTGTCCTCGAAAGCC 60.335 52.381 0.00 0.00 0.00 4.35
3336 3773 1.333619 TGCAAAGTTGTCCTCGAAAGC 59.666 47.619 0.00 0.00 0.00 3.51
3337 3774 3.312421 TCTTGCAAAGTTGTCCTCGAAAG 59.688 43.478 0.00 0.00 46.34 2.62
3338 3775 3.275143 TCTTGCAAAGTTGTCCTCGAAA 58.725 40.909 0.00 0.00 46.34 3.46
3339 3776 2.912771 TCTTGCAAAGTTGTCCTCGAA 58.087 42.857 0.00 0.00 46.34 3.71
3340 3777 2.613026 TCTTGCAAAGTTGTCCTCGA 57.387 45.000 0.00 0.00 46.34 4.04
3341 3778 3.250762 TCATTCTTGCAAAGTTGTCCTCG 59.749 43.478 0.00 0.00 46.34 4.63
3545 3983 1.808133 GCGAGCACCTTATCTTCCTGG 60.808 57.143 0.00 0.00 0.00 4.45
3564 4002 4.628333 CCCATGTTTGTTGATCATTTGAGC 59.372 41.667 0.00 0.00 0.00 4.26
3626 4064 2.965147 GCATTGCGGTGCACTTCGA 61.965 57.895 17.98 8.92 44.43 3.71
3668 4106 3.057315 AGAAATTGCACAGGAATCAACCG 60.057 43.478 0.00 0.00 34.73 4.44
3679 4117 2.224744 TGCCCTGTCTAGAAATTGCACA 60.225 45.455 0.00 0.00 0.00 4.57
3837 4283 4.777896 AGAGGTAGGCTAACAGACAATGAA 59.222 41.667 12.94 0.00 0.00 2.57
4237 4766 7.017155 ACAAACCTTGGAGCCCTTATTTATTTT 59.983 33.333 0.00 0.00 34.12 1.82
4238 4767 6.500400 ACAAACCTTGGAGCCCTTATTTATTT 59.500 34.615 0.00 0.00 34.12 1.40
4239 4768 6.022958 ACAAACCTTGGAGCCCTTATTTATT 58.977 36.000 0.00 0.00 34.12 1.40
4290 4819 4.217550 TGAAGTAATAAAGTTGCTGGGCAC 59.782 41.667 0.00 0.00 38.71 5.01
4539 5068 6.935771 TGGAAAGAATTAAATGCAACAGCAAT 59.064 30.769 0.00 0.00 42.37 3.56
4561 5090 8.888836 AATGCATCCTGAATTATTATGATGGA 57.111 30.769 0.00 8.97 35.52 3.41
4764 5293 5.104318 AGTCCCCTTCAGAATATCCAAACTC 60.104 44.000 0.00 0.00 0.00 3.01
4815 5344 3.662247 TTTCTCTCAGACGAACCTTCC 57.338 47.619 0.00 0.00 0.00 3.46
4913 5442 2.270434 ATCTGCACTTTCTCCCCCTA 57.730 50.000 0.00 0.00 0.00 3.53
5059 5588 7.633789 AGAGGCCTTTGAGAATTTACTTCATA 58.366 34.615 6.77 0.00 36.24 2.15
5211 5740 2.350522 GCAGAATGAACATCACTCGGT 58.649 47.619 0.00 0.00 39.69 4.69
5214 5743 1.667724 CCCGCAGAATGAACATCACTC 59.332 52.381 0.00 0.00 39.69 3.51
5262 5791 9.160496 GACATTTCCATAAGATCTGATATGTCC 57.840 37.037 21.24 11.50 38.82 4.02
5378 5907 9.605275 CAAAAGAGTGAATATATCTGAGGTTGA 57.395 33.333 0.00 0.00 0.00 3.18
5610 6139 1.613925 TGGGACGAAGAGAGTGTCAAG 59.386 52.381 0.00 0.00 34.32 3.02
5615 6144 3.193691 ACTGTTATGGGACGAAGAGAGTG 59.806 47.826 0.00 0.00 0.00 3.51
5645 6174 5.167845 TGAAACTTCACTTTTGCAGAAACC 58.832 37.500 0.00 0.00 31.01 3.27
5859 6393 6.560711 AGAATGCCAACATATAAAACCGAAC 58.439 36.000 0.00 0.00 34.62 3.95
5916 6451 1.959985 TGTGTTTATTGCCACACCCAG 59.040 47.619 0.20 0.00 42.33 4.45
5955 6492 7.500227 TGCCAAAAATGGATTTTACAAATGTCA 59.500 29.630 0.00 0.00 39.20 3.58
5996 6533 2.747799 GCTCCATTTTGGCTCTAGGGAG 60.748 54.545 0.00 0.00 42.54 4.30
5997 6534 1.212935 GCTCCATTTTGGCTCTAGGGA 59.787 52.381 0.00 0.00 37.47 4.20
5998 6535 1.064463 TGCTCCATTTTGGCTCTAGGG 60.064 52.381 0.00 0.00 37.47 3.53
5999 6536 2.425143 TGCTCCATTTTGGCTCTAGG 57.575 50.000 0.00 0.00 37.47 3.02
6000 6537 3.066342 CACATGCTCCATTTTGGCTCTAG 59.934 47.826 0.00 0.00 37.47 2.43
6001 6538 3.018856 CACATGCTCCATTTTGGCTCTA 58.981 45.455 0.00 0.00 37.47 2.43
6002 6539 1.822990 CACATGCTCCATTTTGGCTCT 59.177 47.619 0.00 0.00 37.47 4.09
6003 6540 1.738030 GCACATGCTCCATTTTGGCTC 60.738 52.381 0.00 0.00 37.47 4.70
6004 6541 0.248289 GCACATGCTCCATTTTGGCT 59.752 50.000 0.00 0.00 37.47 4.75
6005 6542 2.758497 GCACATGCTCCATTTTGGC 58.242 52.632 0.00 0.00 37.47 4.52
6070 6608 8.659925 TTTTCATGTTTTGTCTTAATGTGCAT 57.340 26.923 0.00 0.00 0.00 3.96
6099 6637 1.970640 GTTGCTCCCCAGGTTTTGATT 59.029 47.619 0.00 0.00 0.00 2.57
6100 6638 1.133199 TGTTGCTCCCCAGGTTTTGAT 60.133 47.619 0.00 0.00 0.00 2.57
6101 6639 0.260230 TGTTGCTCCCCAGGTTTTGA 59.740 50.000 0.00 0.00 0.00 2.69
6102 6640 1.341080 ATGTTGCTCCCCAGGTTTTG 58.659 50.000 0.00 0.00 0.00 2.44
6103 6641 1.693606 CAATGTTGCTCCCCAGGTTTT 59.306 47.619 0.00 0.00 0.00 2.43
6118 6656 4.410099 ACCATGGTTTCTCATGACAATGT 58.590 39.130 13.00 0.00 45.30 2.71
6126 6664 4.385643 CCCATAGTGACCATGGTTTCTCAT 60.386 45.833 20.85 6.48 41.26 2.90
6129 6667 2.242196 CCCCATAGTGACCATGGTTTCT 59.758 50.000 20.85 20.89 41.26 2.52
6131 6669 1.341976 GCCCCATAGTGACCATGGTTT 60.342 52.381 20.85 10.62 41.26 3.27
6211 6751 3.286915 ATCTCTGTCGTGCTGCGCA 62.287 57.895 10.98 10.98 41.07 6.09
6227 6767 3.380004 TGGATAAAATTGCCCGTGTGATC 59.620 43.478 0.00 0.00 0.00 2.92
6246 6786 4.323477 CGGCGACCCAAACCTGGA 62.323 66.667 0.00 0.00 46.92 3.86
6255 6795 2.894240 TTTACATCTCGCGGCGACCC 62.894 60.000 22.69 0.00 0.00 4.46
6258 6798 1.079875 GGTTTTACATCTCGCGGCGA 61.080 55.000 24.84 24.84 0.00 5.54
6259 6799 1.347221 GGTTTTACATCTCGCGGCG 59.653 57.895 17.70 17.70 0.00 6.46
6268 6808 5.476945 CCAAAGCAAGAGTAGGGTTTTACAT 59.523 40.000 0.00 0.00 32.89 2.29
6269 6809 4.825085 CCAAAGCAAGAGTAGGGTTTTACA 59.175 41.667 0.00 0.00 32.89 2.41
6284 6824 1.411977 CACCACAATCCACCAAAGCAA 59.588 47.619 0.00 0.00 0.00 3.91
6305 6856 0.602905 AGGCTAGAGCGTTGCGTTTT 60.603 50.000 0.00 0.00 43.26 2.43


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

AutoCloner maintained by Alex Coulton.