Multiple sequence alignment - TraesCS1D01G208600

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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 TraesCS1D01G208600 chr1D 100.000 5270 0 0 1 5270 294738019 294743288 0.000000e+00 9732.0
1 TraesCS1D01G208600 chr1B 93.258 2210 95 15 1399 3568 396357629 396359824 0.000000e+00 3206.0
2 TraesCS1D01G208600 chr1B 97.440 1211 27 4 177 1385 396356437 396357645 0.000000e+00 2061.0
3 TraesCS1D01G208600 chr1B 93.182 1012 44 13 3687 4679 396359877 396360882 0.000000e+00 1463.0
4 TraesCS1D01G208600 chr1B 94.467 488 20 3 4784 5270 396361204 396361685 0.000000e+00 745.0
5 TraesCS1D01G208600 chr1B 100.000 92 0 0 3592 3683 619191595 619191504 2.520000e-38 171.0
6 TraesCS1D01G208600 chr1B 98.039 51 1 0 1 51 396356273 396356323 7.270000e-14 89.8
7 TraesCS1D01G208600 chr1A 97.053 1595 28 10 3683 5270 367873468 367875050 0.000000e+00 2667.0
8 TraesCS1D01G208600 chr1A 96.279 1317 35 9 80 1385 367869876 367871189 0.000000e+00 2148.0
9 TraesCS1D01G208600 chr1A 96.060 1142 28 7 2466 3592 367872330 367873469 0.000000e+00 1844.0
10 TraesCS1D01G208600 chr1A 94.972 1074 41 4 1399 2468 367871173 367872237 0.000000e+00 1672.0
11 TraesCS1D01G208600 chr1A 94.681 94 4 1 1 93 367852662 367852755 1.530000e-30 145.0
12 TraesCS1D01G208600 chr6D 100.000 92 0 0 3592 3683 458924625 458924534 2.520000e-38 171.0
13 TraesCS1D01G208600 chr3B 100.000 92 0 0 3592 3683 92292998 92292907 2.520000e-38 171.0
14 TraesCS1D01G208600 chr2B 100.000 92 0 0 3592 3683 234537421 234537330 2.520000e-38 171.0
15 TraesCS1D01G208600 chrUn 98.913 92 1 0 3592 3683 399313446 399313355 1.170000e-36 165.0
16 TraesCS1D01G208600 chr4D 98.913 92 1 0 3592 3683 123445243 123445152 1.170000e-36 165.0
17 TraesCS1D01G208600 chr4D 98.913 92 1 0 3592 3683 281307687 281307778 1.170000e-36 165.0
18 TraesCS1D01G208600 chr4A 98.913 92 1 0 3592 3683 67523235 67523326 1.170000e-36 165.0
19 TraesCS1D01G208600 chr3D 98.913 92 1 0 3592 3683 501834644 501834553 1.170000e-36 165.0


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 TraesCS1D01G208600 chr1D 294738019 294743288 5269 False 9732.00 9732 100.0000 1 5270 1 chr1D.!!$F1 5269
1 TraesCS1D01G208600 chr1B 396356273 396361685 5412 False 1512.96 3206 95.2772 1 5270 5 chr1B.!!$F1 5269
2 TraesCS1D01G208600 chr1A 367869876 367875050 5174 False 2082.75 2667 96.0910 80 5270 4 chr1A.!!$F2 5190

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
474 512 0.385348 CTGATCTGCTCGTCGATCGG 60.385 60.000 16.41 0.00 39.05 4.18 F
1007 1055 1.277557 GCGGAGATGAGGGATGCTATT 59.722 52.381 0.00 0.00 0.00 1.73 F
1568 1620 1.067142 GCCTGCATTGCATGGGATATG 60.067 52.381 18.37 2.72 38.13 1.78 F
2077 2129 1.340017 GGAGAGGTTGTGGCTATGCAA 60.340 52.381 0.00 0.00 0.00 4.08 F
2322 2374 1.402325 GCGTTTAAATGCTGTGTCCCC 60.402 52.381 22.42 0.00 37.92 4.81 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1461 1509 2.009774 CAGGTCTAGCAATGGGAAACG 58.990 52.381 0.00 0.00 0.00 3.60 R
2577 2724 3.574354 TGCACATGGCCATATTGTAGA 57.426 42.857 20.30 0.86 43.89 2.59 R
3315 3470 0.738389 AAACACCAACAACTGCGGAG 59.262 50.000 0.85 0.85 0.00 4.63 R
3584 3784 2.392662 TCATCGAGAATGGAGGAGCTT 58.607 47.619 0.00 0.00 35.94 3.74 R
4321 4536 1.302351 GTGGCTGCTGCTCTTGTCT 60.302 57.895 15.64 0.00 39.59 3.41 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
66 67 7.618502 AACTCAAAACACAGTATACACAACA 57.381 32.000 5.50 0.00 0.00 3.33
67 68 7.011828 ACTCAAAACACAGTATACACAACAC 57.988 36.000 5.50 0.00 0.00 3.32
68 69 6.596106 ACTCAAAACACAGTATACACAACACA 59.404 34.615 5.50 0.00 0.00 3.72
69 70 7.282224 ACTCAAAACACAGTATACACAACACAT 59.718 33.333 5.50 0.00 0.00 3.21
70 71 7.413644 TCAAAACACAGTATACACAACACATG 58.586 34.615 5.50 0.00 0.00 3.21
71 72 7.281100 TCAAAACACAGTATACACAACACATGA 59.719 33.333 5.50 0.00 0.00 3.07
72 73 7.744087 AAACACAGTATACACAACACATGAT 57.256 32.000 5.50 0.00 0.00 2.45
113 114 3.758023 TGAACAAGTGCCCACATGAATAG 59.242 43.478 10.23 0.00 34.46 1.73
120 121 6.352016 AGTGCCCACATGAATAGAGTATAG 57.648 41.667 0.00 0.00 0.00 1.31
158 159 1.068748 GGTGATCGTCAGTGTGTACGT 60.069 52.381 0.00 0.00 39.99 3.57
228 266 5.767816 AAAGCCTTTTTCTTCGTGTGTAT 57.232 34.783 0.00 0.00 0.00 2.29
243 281 4.870426 CGTGTGTATGATAAGAAAGGCAGT 59.130 41.667 0.00 0.00 0.00 4.40
421 459 4.262249 GCTAGTCCTCTCTCTCTCTCTCTC 60.262 54.167 0.00 0.00 0.00 3.20
422 460 4.000928 AGTCCTCTCTCTCTCTCTCTCT 57.999 50.000 0.00 0.00 0.00 3.10
474 512 0.385348 CTGATCTGCTCGTCGATCGG 60.385 60.000 16.41 0.00 39.05 4.18
729 770 2.825264 GGCTCGGCAGGAAGCTAT 59.175 61.111 0.00 0.00 44.79 2.97
792 834 2.415491 CCTCGTCTTCAATGCGTGTAGA 60.415 50.000 0.00 0.00 31.72 2.59
799 841 1.616374 TCAATGCGTGTAGAGTGTGGA 59.384 47.619 0.00 0.00 0.00 4.02
800 842 2.233676 TCAATGCGTGTAGAGTGTGGAT 59.766 45.455 0.00 0.00 0.00 3.41
1007 1055 1.277557 GCGGAGATGAGGGATGCTATT 59.722 52.381 0.00 0.00 0.00 1.73
1012 1060 4.774726 GGAGATGAGGGATGCTATTGTCTA 59.225 45.833 0.00 0.00 0.00 2.59
1371 1419 5.408909 GGCTCTCCTGTTGTAGAACTTAAAC 59.591 44.000 4.21 0.00 32.79 2.01
1372 1420 6.224584 GCTCTCCTGTTGTAGAACTTAAACT 58.775 40.000 4.21 0.00 32.79 2.66
1373 1421 7.376615 GCTCTCCTGTTGTAGAACTTAAACTA 58.623 38.462 4.21 0.00 32.79 2.24
1374 1422 7.542824 GCTCTCCTGTTGTAGAACTTAAACTAG 59.457 40.741 4.21 0.00 32.79 2.57
1375 1423 8.701908 TCTCCTGTTGTAGAACTTAAACTAGA 57.298 34.615 4.21 0.00 32.79 2.43
1376 1424 9.139734 TCTCCTGTTGTAGAACTTAAACTAGAA 57.860 33.333 4.21 0.00 32.79 2.10
1377 1425 9.760077 CTCCTGTTGTAGAACTTAAACTAGAAA 57.240 33.333 4.21 0.00 32.79 2.52
1378 1426 9.760077 TCCTGTTGTAGAACTTAAACTAGAAAG 57.240 33.333 4.21 0.00 32.79 2.62
1379 1427 8.989980 CCTGTTGTAGAACTTAAACTAGAAAGG 58.010 37.037 4.21 0.00 32.79 3.11
1380 1428 9.760077 CTGTTGTAGAACTTAAACTAGAAAGGA 57.240 33.333 4.21 0.00 32.79 3.36
1388 1436 9.894783 GAACTTAAACTAGAAAGGATTTTCACC 57.105 33.333 0.00 0.00 44.14 4.02
1389 1437 8.405418 ACTTAAACTAGAAAGGATTTTCACCC 57.595 34.615 0.00 0.00 44.14 4.61
1390 1438 5.959618 AAACTAGAAAGGATTTTCACCCG 57.040 39.130 0.00 0.00 44.14 5.28
1391 1439 3.344515 ACTAGAAAGGATTTTCACCCGC 58.655 45.455 0.00 0.00 44.14 6.13
1392 1440 2.286365 AGAAAGGATTTTCACCCGCA 57.714 45.000 3.21 0.00 44.14 5.69
1393 1441 2.593026 AGAAAGGATTTTCACCCGCAA 58.407 42.857 3.21 0.00 44.14 4.85
1394 1442 2.962421 AGAAAGGATTTTCACCCGCAAA 59.038 40.909 3.21 0.00 44.14 3.68
1395 1443 3.386402 AGAAAGGATTTTCACCCGCAAAA 59.614 39.130 3.21 0.00 44.14 2.44
1396 1444 3.828875 AAGGATTTTCACCCGCAAAAA 57.171 38.095 0.00 0.00 0.00 1.94
1432 1480 7.396540 AGGATTTTACATCAAATGTCAGTCC 57.603 36.000 0.00 1.74 43.67 3.85
1455 1503 5.278709 CCAGCTATGCTATACGATCCATAGG 60.279 48.000 13.14 0.00 36.40 2.57
1461 1509 6.694877 TGCTATACGATCCATAGGTGTATC 57.305 41.667 9.80 0.00 0.00 2.24
1492 1540 1.719600 CTAGACCTGCAAGTGTCTGC 58.280 55.000 18.49 0.00 42.08 4.26
1568 1620 1.067142 GCCTGCATTGCATGGGATATG 60.067 52.381 18.37 2.72 38.13 1.78
1615 1667 4.771360 ACAAACAAGCGCAATTTAAATGC 58.229 34.783 11.47 6.95 40.41 3.56
1632 1684 4.389890 AATGCTGTTTTGTTCAGAGCAA 57.610 36.364 0.00 0.00 35.20 3.91
1634 1686 3.968649 TGCTGTTTTGTTCAGAGCAATC 58.031 40.909 0.00 0.00 35.20 2.67
1635 1687 3.380954 TGCTGTTTTGTTCAGAGCAATCA 59.619 39.130 0.00 3.48 35.20 2.57
1679 1731 8.889717 TCGATCCTTGGTTGATTTATTTTACTC 58.110 33.333 0.00 0.00 0.00 2.59
1680 1732 8.129211 CGATCCTTGGTTGATTTATTTTACTCC 58.871 37.037 0.00 0.00 0.00 3.85
1681 1733 8.893563 ATCCTTGGTTGATTTATTTTACTCCA 57.106 30.769 0.00 0.00 0.00 3.86
1682 1734 8.713708 TCCTTGGTTGATTTATTTTACTCCAA 57.286 30.769 0.00 0.00 0.00 3.53
1683 1735 9.148879 TCCTTGGTTGATTTATTTTACTCCAAA 57.851 29.630 0.00 0.00 33.13 3.28
1684 1736 9.771534 CCTTGGTTGATTTATTTTACTCCAAAA 57.228 29.630 0.00 0.00 40.34 2.44
1758 1810 3.009301 AGTGTCGTTTACTCACCTTCG 57.991 47.619 0.00 0.00 33.21 3.79
1951 2003 1.748879 GGTGAGGCCGCAATTAGCA 60.749 57.895 12.05 0.00 46.13 3.49
2077 2129 1.340017 GGAGAGGTTGTGGCTATGCAA 60.340 52.381 0.00 0.00 0.00 4.08
2322 2374 1.402325 GCGTTTAAATGCTGTGTCCCC 60.402 52.381 22.42 0.00 37.92 4.81
2388 2440 8.276325 GGCAAATTCTCAGTTATCAACTATACG 58.724 37.037 0.00 0.00 40.46 3.06
2545 2692 9.485591 CGATCCCGCAAATAAATTATTATGTAC 57.514 33.333 0.00 0.00 32.06 2.90
2589 2744 7.332926 CAGATATGAGGTGTTCTACAATATGGC 59.667 40.741 0.00 0.00 0.00 4.40
3215 3370 7.659799 ACATGTAACAGTTCTGCAAGTACATAA 59.340 33.333 0.00 0.00 36.61 1.90
3301 3456 5.105917 CCGACTTAAATGGCACCAAGTTATT 60.106 40.000 10.45 0.00 31.57 1.40
3315 3470 6.586082 CACCAAGTTATTGATTTTGTAGCACC 59.414 38.462 0.00 0.00 38.83 5.01
3569 3769 8.638873 TCGCTTATTGAGGAGATATTTTGTAGA 58.361 33.333 0.00 0.00 0.00 2.59
3590 3790 9.601217 TGTAGAAGTTATTATCTTCAAAGCTCC 57.399 33.333 14.11 0.00 42.35 4.70
3591 3791 9.825109 GTAGAAGTTATTATCTTCAAAGCTCCT 57.175 33.333 14.11 0.00 42.35 3.69
3592 3792 8.956533 AGAAGTTATTATCTTCAAAGCTCCTC 57.043 34.615 14.11 0.00 42.35 3.71
3594 3794 7.200434 AGTTATTATCTTCAAAGCTCCTCCA 57.800 36.000 0.00 0.00 0.00 3.86
3596 3796 8.277918 AGTTATTATCTTCAAAGCTCCTCCATT 58.722 33.333 0.00 0.00 0.00 3.16
3599 3799 4.213564 TCTTCAAAGCTCCTCCATTCTC 57.786 45.455 0.00 0.00 0.00 2.87
3600 3800 2.680312 TCAAAGCTCCTCCATTCTCG 57.320 50.000 0.00 0.00 0.00 4.04
3601 3801 2.179427 TCAAAGCTCCTCCATTCTCGA 58.821 47.619 0.00 0.00 0.00 4.04
3602 3802 2.768527 TCAAAGCTCCTCCATTCTCGAT 59.231 45.455 0.00 0.00 0.00 3.59
3603 3803 2.871022 CAAAGCTCCTCCATTCTCGATG 59.129 50.000 0.00 0.00 35.42 3.84
3604 3804 2.079170 AGCTCCTCCATTCTCGATGA 57.921 50.000 0.00 0.00 38.03 2.92
3606 3806 2.299582 AGCTCCTCCATTCTCGATGATG 59.700 50.000 0.00 0.00 38.03 3.07
3607 3807 2.298446 GCTCCTCCATTCTCGATGATGA 59.702 50.000 9.11 0.00 38.03 2.92
3608 3808 3.244009 GCTCCTCCATTCTCGATGATGAA 60.244 47.826 9.11 0.00 38.03 2.57
3609 3809 4.563168 GCTCCTCCATTCTCGATGATGAAT 60.563 45.833 9.11 1.48 38.03 2.57
3610 3810 5.144692 TCCTCCATTCTCGATGATGAATC 57.855 43.478 9.11 0.00 38.03 2.52
3626 3826 9.583765 GATGATGAATCGATTTGATAGATCAGA 57.416 33.333 12.81 0.00 37.83 3.27
3656 3856 9.348476 TGTTATTCCAAATATTGATCCGATTCA 57.652 29.630 0.00 0.00 0.00 2.57
3657 3857 9.831737 GTTATTCCAAATATTGATCCGATTCAG 57.168 33.333 0.00 0.00 0.00 3.02
3658 3858 9.573166 TTATTCCAAATATTGATCCGATTCAGT 57.427 29.630 0.00 0.00 0.00 3.41
3660 3860 9.745018 ATTCCAAATATTGATCCGATTCAGTAT 57.255 29.630 0.00 0.00 31.94 2.12
3661 3861 8.777865 TCCAAATATTGATCCGATTCAGTATC 57.222 34.615 0.00 0.00 30.05 2.24
3662 3862 8.374743 TCCAAATATTGATCCGATTCAGTATCA 58.625 33.333 0.00 0.00 30.05 2.15
3663 3863 9.170734 CCAAATATTGATCCGATTCAGTATCAT 57.829 33.333 0.00 0.00 30.05 2.45
3665 3865 9.948964 AAATATTGATCCGATTCAGTATCATCA 57.051 29.630 0.00 0.00 30.05 3.07
3666 3866 9.597170 AATATTGATCCGATTCAGTATCATCAG 57.403 33.333 0.00 0.00 31.23 2.90
3667 3867 6.655078 TTGATCCGATTCAGTATCATCAGA 57.345 37.500 0.00 0.00 31.23 3.27
3668 3868 6.655078 TGATCCGATTCAGTATCATCAGAA 57.345 37.500 0.00 0.00 32.45 3.02
3669 3869 7.237209 TGATCCGATTCAGTATCATCAGAAT 57.763 36.000 0.00 0.00 33.70 2.40
3670 3870 7.095270 TGATCCGATTCAGTATCATCAGAATG 58.905 38.462 0.00 0.00 31.35 2.67
3734 3935 5.818336 AGATCTCTTCAACATCTGCATTCTG 59.182 40.000 0.00 0.00 0.00 3.02
3807 4008 3.009033 TCACACCTTTCCTGAACTATGGG 59.991 47.826 0.00 0.00 0.00 4.00
3908 4109 6.378745 TGTAGTAGGACCCAGCTTCATTATA 58.621 40.000 0.00 0.00 0.00 0.98
3973 4174 7.390440 TGTTCCTTCATTCATTTCGTAGAACAT 59.610 33.333 0.00 0.00 45.90 2.71
4314 4529 2.558359 ACGAAGGCCAGAAAAGAAATGG 59.442 45.455 5.01 0.00 37.15 3.16
4321 4536 4.524328 GGCCAGAAAAGAAATGGAGAAGAA 59.476 41.667 0.00 0.00 36.09 2.52
4322 4537 5.336293 GGCCAGAAAAGAAATGGAGAAGAAG 60.336 44.000 0.00 0.00 36.09 2.85
4324 4539 6.569418 GCCAGAAAAGAAATGGAGAAGAAGAC 60.569 42.308 0.00 0.00 36.09 3.01
4552 4769 2.141517 CATCTCAAGGCTGGCTAATCG 58.858 52.381 3.41 0.00 0.00 3.34
4613 4830 2.858941 CTGAGCTCTGATCAACACGATG 59.141 50.000 16.19 0.00 33.17 3.84
4684 4907 2.557317 ACGGTTCTTGTCACATCGTTT 58.443 42.857 0.00 0.00 0.00 3.60
4866 5306 8.198778 TCTACTACTACAAAACATGAACACACA 58.801 33.333 0.00 0.00 0.00 3.72
4867 5307 7.801716 ACTACTACAAAACATGAACACACAT 57.198 32.000 0.00 0.00 0.00 3.21
4925 5365 1.362224 TTGAGGGCTTGCTCCTTACT 58.638 50.000 4.60 0.00 34.21 2.24
4947 5387 2.290323 GGAGGCCAGAGAAGCAAAAGTA 60.290 50.000 5.01 0.00 0.00 2.24
5016 5457 0.758734 CACTGTGAGTTCAGGGACCA 59.241 55.000 0.32 0.00 40.91 4.02
5025 5466 2.031870 GTTCAGGGACCAAGCAACTTT 58.968 47.619 0.00 0.00 0.00 2.66
5052 5493 1.461897 CAGGCGTACCCTAACAAAACG 59.538 52.381 2.94 0.00 44.09 3.60
5067 5508 3.623960 ACAAAACGACGGAGATCACAAAA 59.376 39.130 0.00 0.00 0.00 2.44
5117 5558 1.891150 CCAAAAGAAGCTGCCATCTGT 59.109 47.619 6.35 0.00 0.00 3.41
5130 5571 5.732528 GCTGCCATCTGTGATGTCATAAAAG 60.733 44.000 6.78 0.00 0.00 2.27
5205 5646 1.148310 CGAAAGACGCAATGGTCAGT 58.852 50.000 5.04 0.00 39.42 3.41
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
51 52 7.391016 CGTAATCATGTGTTGTGTATACTGTG 58.609 38.462 4.17 0.00 0.00 3.66
52 53 6.533723 CCGTAATCATGTGTTGTGTATACTGT 59.466 38.462 4.17 0.00 0.00 3.55
53 54 6.509517 GCCGTAATCATGTGTTGTGTATACTG 60.510 42.308 4.17 0.00 0.00 2.74
54 55 5.522460 GCCGTAATCATGTGTTGTGTATACT 59.478 40.000 4.17 0.00 0.00 2.12
55 56 5.292345 TGCCGTAATCATGTGTTGTGTATAC 59.708 40.000 0.00 0.00 0.00 1.47
56 57 5.420409 TGCCGTAATCATGTGTTGTGTATA 58.580 37.500 0.00 0.00 0.00 1.47
57 58 4.257731 TGCCGTAATCATGTGTTGTGTAT 58.742 39.130 0.00 0.00 0.00 2.29
58 59 3.665190 TGCCGTAATCATGTGTTGTGTA 58.335 40.909 0.00 0.00 0.00 2.90
59 60 2.499197 TGCCGTAATCATGTGTTGTGT 58.501 42.857 0.00 0.00 0.00 3.72
60 61 3.550950 TTGCCGTAATCATGTGTTGTG 57.449 42.857 0.00 0.00 0.00 3.33
61 62 4.576216 TTTTGCCGTAATCATGTGTTGT 57.424 36.364 0.00 0.00 0.00 3.32
62 63 5.159925 TGATTTTGCCGTAATCATGTGTTG 58.840 37.500 0.00 0.00 37.15 3.33
63 64 5.384063 TGATTTTGCCGTAATCATGTGTT 57.616 34.783 0.00 0.00 37.15 3.32
64 65 5.581126 ATGATTTTGCCGTAATCATGTGT 57.419 34.783 13.86 0.00 45.95 3.72
65 66 6.890663 AAATGATTTTGCCGTAATCATGTG 57.109 33.333 14.83 0.00 46.61 3.21
66 67 7.903995 AAAAATGATTTTGCCGTAATCATGT 57.096 28.000 14.83 9.37 46.61 3.21
92 93 4.009675 TCTATTCATGTGGGCACTTGTTC 58.990 43.478 0.00 0.00 37.62 3.18
97 98 5.247110 CCTATACTCTATTCATGTGGGCACT 59.753 44.000 0.00 0.00 0.00 4.40
105 106 6.151312 ACGCAGGTACCTATACTCTATTCATG 59.849 42.308 15.80 0.00 0.00 3.07
113 114 4.382345 ACAAACGCAGGTACCTATACTC 57.618 45.455 15.80 0.84 0.00 2.59
120 121 1.274447 ACCTCTACAAACGCAGGTACC 59.726 52.381 2.73 2.73 37.50 3.34
158 159 5.855925 GCATGATACAAATCAAACGTTCACA 59.144 36.000 0.00 0.00 45.12 3.58
209 246 4.742438 TCATACACACGAAGAAAAAGGC 57.258 40.909 0.00 0.00 0.00 4.35
228 266 5.745312 TTCTCTGACTGCCTTTCTTATCA 57.255 39.130 0.00 0.00 0.00 2.15
243 281 3.260269 TCTCTCCCCTGTTTTCTCTGA 57.740 47.619 0.00 0.00 0.00 3.27
729 770 4.453480 ACTCACCTTTTTCTTGGATGGA 57.547 40.909 0.00 0.00 0.00 3.41
792 834 0.396435 TCGCCAAGAACATCCACACT 59.604 50.000 0.00 0.00 0.00 3.55
799 841 1.139853 GGGAGAGATCGCCAAGAACAT 59.860 52.381 4.95 0.00 37.57 2.71
800 842 0.537188 GGGAGAGATCGCCAAGAACA 59.463 55.000 4.95 0.00 37.57 3.18
1007 1055 4.788679 TCTCAGGTAATCCATCGTAGACA 58.211 43.478 0.00 0.00 42.51 3.41
1012 1060 4.502259 GCAAGATCTCAGGTAATCCATCGT 60.502 45.833 0.00 0.00 35.89 3.73
1371 1419 3.343617 TGCGGGTGAAAATCCTTTCTAG 58.656 45.455 0.00 0.00 41.41 2.43
1372 1420 3.426787 TGCGGGTGAAAATCCTTTCTA 57.573 42.857 0.00 0.00 41.41 2.10
1373 1421 2.286365 TGCGGGTGAAAATCCTTTCT 57.714 45.000 0.00 0.00 41.41 2.52
1374 1422 3.378911 TTTGCGGGTGAAAATCCTTTC 57.621 42.857 0.00 0.00 41.25 2.62
1375 1423 3.828875 TTTTGCGGGTGAAAATCCTTT 57.171 38.095 0.00 0.00 0.00 3.11
1376 1424 3.828875 TTTTTGCGGGTGAAAATCCTT 57.171 38.095 0.00 0.00 0.00 3.36
1400 1448 9.533831 ACATTTGATGTAAAATCCTTTCTAGGT 57.466 29.630 0.00 0.00 42.78 3.08
1432 1480 5.300539 ACCTATGGATCGTATAGCATAGCTG 59.699 44.000 0.00 0.00 40.10 4.24
1455 1503 4.270325 GTCTAGCAATGGGAAACGATACAC 59.730 45.833 0.00 0.00 0.00 2.90
1461 1509 2.009774 CAGGTCTAGCAATGGGAAACG 58.990 52.381 0.00 0.00 0.00 3.60
1568 1620 9.786105 GTTCTCTGTATTACTACAAGTAGAACC 57.214 37.037 19.43 10.37 40.76 3.62
1615 1667 4.037208 AGGTGATTGCTCTGAACAAAACAG 59.963 41.667 0.00 0.00 36.80 3.16
1679 1731 6.697019 CGCTTCCATTATATTTGGACTTTTGG 59.303 38.462 6.59 0.00 42.88 3.28
1680 1732 6.198966 GCGCTTCCATTATATTTGGACTTTTG 59.801 38.462 0.00 0.00 42.88 2.44
1681 1733 6.127479 TGCGCTTCCATTATATTTGGACTTTT 60.127 34.615 9.73 0.00 42.88 2.27
1682 1734 5.359576 TGCGCTTCCATTATATTTGGACTTT 59.640 36.000 9.73 0.00 42.88 2.66
1683 1735 4.887071 TGCGCTTCCATTATATTTGGACTT 59.113 37.500 9.73 0.00 42.88 3.01
1684 1736 4.460263 TGCGCTTCCATTATATTTGGACT 58.540 39.130 9.73 0.00 42.88 3.85
1685 1737 4.829064 TGCGCTTCCATTATATTTGGAC 57.171 40.909 9.73 0.00 42.88 4.02
1691 1743 8.575589 TCAACAATAAATGCGCTTCCATTATAT 58.424 29.630 9.73 0.00 34.50 0.86
1704 1756 7.364522 TCACTCTACAGTCAACAATAAATGC 57.635 36.000 0.00 0.00 0.00 3.56
1789 1841 3.879892 GTGAGGGAACTAATGGAGATTGC 59.120 47.826 0.00 0.00 44.43 3.56
1852 1904 4.333649 CGAATTACTTCCACTGACATGCAT 59.666 41.667 0.00 0.00 0.00 3.96
2077 2129 4.212143 TGCATTATGTTCTGCTGAGAGT 57.788 40.909 0.00 0.00 39.16 3.24
2322 2374 5.571741 CAGCAACAATTCTAACAGAAGCATG 59.428 40.000 0.00 0.00 37.69 4.06
2388 2440 5.959618 AAATAGCCAACAAGAACACCTAC 57.040 39.130 0.00 0.00 0.00 3.18
2445 2497 9.968870 CTAATACCTAATTACAAGACTCAGACC 57.031 37.037 0.00 0.00 0.00 3.85
2449 2501 8.313944 TGGCTAATACCTAATTACAAGACTCA 57.686 34.615 0.00 0.00 0.00 3.41
2577 2724 3.574354 TGCACATGGCCATATTGTAGA 57.426 42.857 20.30 0.86 43.89 2.59
2589 2744 5.533528 TGATTCATCTAGGAAATGCACATGG 59.466 40.000 0.00 0.00 0.00 3.66
2986 3141 4.580580 AGCTTTCAAAGAACCCAGTAACAG 59.419 41.667 0.00 0.00 0.00 3.16
3170 3325 7.404139 ACATGTTAACAGAACTTAGAACGAC 57.596 36.000 14.65 0.00 0.00 4.34
3237 3392 6.590357 CAGGCGAACAAAATCTAATATACCG 58.410 40.000 0.00 0.00 0.00 4.02
3301 3456 1.271108 TGCGGAGGTGCTACAAAATCA 60.271 47.619 0.00 0.00 35.36 2.57
3315 3470 0.738389 AAACACCAACAACTGCGGAG 59.262 50.000 0.85 0.85 0.00 4.63
3462 3623 6.828273 TGACATGAAAAGGGGACATACATAAG 59.172 38.462 0.00 0.00 0.00 1.73
3569 3769 7.633789 TGGAGGAGCTTTGAAGATAATAACTT 58.366 34.615 0.00 0.00 0.00 2.66
3576 3776 5.452496 CGAGAATGGAGGAGCTTTGAAGATA 60.452 44.000 0.00 0.00 0.00 1.98
3584 3784 2.392662 TCATCGAGAATGGAGGAGCTT 58.607 47.619 0.00 0.00 35.94 3.74
3599 3799 8.403606 TGATCTATCAAATCGATTCATCATCG 57.596 34.615 11.83 0.00 44.03 3.84
3600 3800 9.583765 TCTGATCTATCAAATCGATTCATCATC 57.416 33.333 11.83 11.32 36.18 2.92
3630 3830 9.348476 TGAATCGGATCAATATTTGGAATAACA 57.652 29.630 0.00 0.00 0.00 2.41
3631 3831 9.831737 CTGAATCGGATCAATATTTGGAATAAC 57.168 33.333 0.00 0.00 0.00 1.89
3632 3832 9.573166 ACTGAATCGGATCAATATTTGGAATAA 57.427 29.630 0.00 0.00 0.00 1.40
3634 3834 9.745018 ATACTGAATCGGATCAATATTTGGAAT 57.255 29.630 0.00 0.00 0.00 3.01
3635 3835 9.219603 GATACTGAATCGGATCAATATTTGGAA 57.780 33.333 0.00 0.00 0.00 3.53
3636 3836 8.374743 TGATACTGAATCGGATCAATATTTGGA 58.625 33.333 0.00 0.00 37.42 3.53
3637 3837 8.552083 TGATACTGAATCGGATCAATATTTGG 57.448 34.615 0.00 0.00 37.42 3.28
3639 3839 9.948964 TGATGATACTGAATCGGATCAATATTT 57.051 29.630 0.00 0.00 37.42 1.40
3640 3840 9.597170 CTGATGATACTGAATCGGATCAATATT 57.403 33.333 0.00 0.00 37.42 1.28
3641 3841 8.975295 TCTGATGATACTGAATCGGATCAATAT 58.025 33.333 0.00 0.00 37.42 1.28
3642 3842 8.353423 TCTGATGATACTGAATCGGATCAATA 57.647 34.615 0.00 0.00 37.42 1.90
3643 3843 7.237209 TCTGATGATACTGAATCGGATCAAT 57.763 36.000 0.00 0.00 37.42 2.57
3644 3844 6.655078 TCTGATGATACTGAATCGGATCAA 57.345 37.500 0.00 0.00 37.42 2.57
3645 3845 6.655078 TTCTGATGATACTGAATCGGATCA 57.345 37.500 0.00 0.00 37.87 2.92
3646 3846 7.275341 GTCATTCTGATGATACTGAATCGGATC 59.725 40.741 0.00 0.00 43.76 3.36
3647 3847 7.095910 GTCATTCTGATGATACTGAATCGGAT 58.904 38.462 0.00 0.00 43.76 4.18
3648 3848 6.040842 TGTCATTCTGATGATACTGAATCGGA 59.959 38.462 0.00 0.00 43.76 4.55
3649 3849 6.218746 TGTCATTCTGATGATACTGAATCGG 58.781 40.000 0.00 0.00 43.76 4.18
3650 3850 7.704789 TTGTCATTCTGATGATACTGAATCG 57.295 36.000 0.00 0.00 43.76 3.34
3651 3851 9.932699 CTTTTGTCATTCTGATGATACTGAATC 57.067 33.333 0.00 0.00 43.76 2.52
3652 3852 8.404000 GCTTTTGTCATTCTGATGATACTGAAT 58.596 33.333 0.00 0.00 43.76 2.57
3653 3853 7.609146 AGCTTTTGTCATTCTGATGATACTGAA 59.391 33.333 0.00 0.00 43.76 3.02
3654 3854 7.065443 CAGCTTTTGTCATTCTGATGATACTGA 59.935 37.037 0.00 0.00 43.76 3.41
3655 3855 7.065443 TCAGCTTTTGTCATTCTGATGATACTG 59.935 37.037 0.00 0.00 43.76 2.74
3656 3856 7.065563 GTCAGCTTTTGTCATTCTGATGATACT 59.934 37.037 0.00 0.00 43.76 2.12
3657 3857 7.065563 AGTCAGCTTTTGTCATTCTGATGATAC 59.934 37.037 0.00 0.00 43.76 2.24
3658 3858 7.108194 AGTCAGCTTTTGTCATTCTGATGATA 58.892 34.615 0.00 0.00 43.76 2.15
3659 3859 5.944599 AGTCAGCTTTTGTCATTCTGATGAT 59.055 36.000 0.00 0.00 43.76 2.45
3660 3860 5.311265 AGTCAGCTTTTGTCATTCTGATGA 58.689 37.500 0.00 0.00 39.92 2.92
3661 3861 5.624344 AGTCAGCTTTTGTCATTCTGATG 57.376 39.130 0.00 0.00 36.37 3.07
3662 3862 5.533903 ACAAGTCAGCTTTTGTCATTCTGAT 59.466 36.000 2.93 0.00 36.37 2.90
3663 3863 4.883585 ACAAGTCAGCTTTTGTCATTCTGA 59.116 37.500 2.93 0.00 32.32 3.27
3664 3864 5.179045 ACAAGTCAGCTTTTGTCATTCTG 57.821 39.130 2.93 0.00 32.32 3.02
3665 3865 5.841957 AACAAGTCAGCTTTTGTCATTCT 57.158 34.783 8.09 0.00 36.56 2.40
3666 3866 6.892310 AAAACAAGTCAGCTTTTGTCATTC 57.108 33.333 8.09 0.00 36.56 2.67
3734 3935 3.306166 GCTCATTCACAATGCTTCAATGC 59.694 43.478 0.00 0.00 38.77 3.56
3807 4008 2.568623 AGTTGGTGAGGTGACAATCC 57.431 50.000 0.00 0.00 0.00 3.01
4314 4529 2.995258 CTGCTGCTCTTGTCTTCTTCTC 59.005 50.000 0.00 0.00 0.00 2.87
4321 4536 1.302351 GTGGCTGCTGCTCTTGTCT 60.302 57.895 15.64 0.00 39.59 3.41
4322 4537 2.675056 CGTGGCTGCTGCTCTTGTC 61.675 63.158 15.64 0.00 39.59 3.18
4324 4539 3.429141 CCGTGGCTGCTGCTCTTG 61.429 66.667 15.64 3.48 39.59 3.02
4552 4769 0.804989 GCAACCTGCTACATGTCCAC 59.195 55.000 0.00 0.00 40.96 4.02
4613 4830 5.344128 ACATGTCAACAGAATAACGTCGTAC 59.656 40.000 0.00 0.00 0.00 3.67
4617 4834 5.176774 TGTGACATGTCAACAGAATAACGTC 59.823 40.000 29.42 12.86 41.85 4.34
4658 4881 4.387559 CGATGTGACAAGAACCGTTCAATA 59.612 41.667 13.69 0.00 0.00 1.90
4659 4882 3.186409 CGATGTGACAAGAACCGTTCAAT 59.814 43.478 13.69 0.00 0.00 2.57
4684 4907 4.088634 AGGTTTATCATGCTTGCTTTCCA 58.911 39.130 0.00 0.00 0.00 3.53
4866 5306 5.098663 TGTTGGGTTAGGGAGAAACTCTAT 58.901 41.667 0.00 0.00 30.99 1.98
4867 5307 4.495565 TGTTGGGTTAGGGAGAAACTCTA 58.504 43.478 0.00 0.00 0.00 2.43
4907 5347 0.615331 CAGTAAGGAGCAAGCCCTCA 59.385 55.000 3.15 0.00 33.47 3.86
4925 5365 0.478072 TTTTGCTTCTCTGGCCTCCA 59.522 50.000 3.32 0.00 0.00 3.86
4947 5387 4.346730 TCATCATTCTGAAGGTGGCAAAT 58.653 39.130 1.70 0.00 0.00 2.32
5016 5457 1.138859 GCCTGGTGGAAAAAGTTGCTT 59.861 47.619 0.00 0.00 34.57 3.91
5025 5466 0.544833 TAGGGTACGCCTGGTGGAAA 60.545 55.000 12.58 0.00 34.57 3.13
5052 5493 1.464997 GGCTGTTTTGTGATCTCCGTC 59.535 52.381 0.00 0.00 0.00 4.79
5067 5508 0.818296 GAGGTACATCGTCAGGCTGT 59.182 55.000 15.27 0.00 0.00 4.40
5117 5558 4.598022 TCCATGCCACTTTTATGACATCA 58.402 39.130 0.00 0.00 0.00 3.07
5130 5571 1.534595 GCGATGAACATTCCATGCCAC 60.535 52.381 0.00 0.00 0.00 5.01
5205 5646 4.623932 ACTGATCCAACTTCAGCTTACA 57.376 40.909 0.78 0.00 43.57 2.41


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

AutoCloner maintained by Alex Coulton.