Multiple sequence alignment - TraesCS4D01G308300

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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 TraesCS4D01G308300 chr4D 100.000 4469 0 0 1 4469 476308752 476313220 0.000000e+00 8253.0
1 TraesCS4D01G308300 chr4D 96.503 143 4 1 1479 1621 359125655 359125514 7.470000e-58 235.0
2 TraesCS4D01G308300 chr4D 87.692 65 7 1 603 667 682076 682013 1.720000e-09 75.0
3 TraesCS4D01G308300 chr4B 95.359 1810 54 16 992 2783 600664852 600666649 0.000000e+00 2850.0
4 TraesCS4D01G308300 chr4B 93.905 1247 53 5 3226 4469 600667096 600668322 0.000000e+00 1860.0
5 TraesCS4D01G308300 chr4B 89.706 612 39 8 1 595 600660238 600660842 0.000000e+00 760.0
6 TraesCS4D01G308300 chr4B 84.634 423 48 14 2821 3229 600666646 600667065 5.380000e-109 405.0
7 TraesCS4D01G308300 chr4B 89.068 311 26 4 770 1080 600660937 600661239 3.260000e-101 379.0
8 TraesCS4D01G308300 chr4B 95.855 193 1 4 770 955 600664230 600664422 5.620000e-79 305.0
9 TraesCS4D01G308300 chr4B 89.610 77 7 1 680 755 600660876 600660952 3.680000e-16 97.1
10 TraesCS4D01G308300 chr4B 96.364 55 2 0 681 735 600662685 600662739 1.710000e-14 91.6
11 TraesCS4D01G308300 chr4A 89.058 1910 120 37 2603 4464 683493883 683495751 0.000000e+00 2287.0
12 TraesCS4D01G308300 chr4A 92.695 972 46 15 1647 2601 683492851 683493814 0.000000e+00 1378.0
13 TraesCS4D01G308300 chr4A 90.996 733 35 13 772 1486 683492120 683492839 0.000000e+00 959.0
14 TraesCS4D01G308300 chr4A 88.435 588 46 9 1 575 683490032 683490610 0.000000e+00 689.0
15 TraesCS4D01G308300 chr4A 92.208 77 4 1 681 755 683492057 683492133 1.700000e-19 108.0
16 TraesCS4D01G308300 chr3D 98.529 136 2 0 1486 1621 7607558 7607423 1.610000e-59 241.0
17 TraesCS4D01G308300 chr3D 88.710 62 7 0 603 664 76376675 76376736 4.790000e-10 76.8
18 TraesCS4D01G308300 chr2D 98.529 136 2 0 1486 1621 554128209 554128344 1.610000e-59 241.0
19 TraesCS4D01G308300 chr2D 93.506 154 7 3 1468 1621 425287112 425286962 4.500000e-55 226.0
20 TraesCS4D01G308300 chr2B 95.918 147 6 0 1486 1632 9619373 9619227 5.780000e-59 239.0
21 TraesCS4D01G308300 chr2B 91.667 60 2 3 607 664 703710545 703710603 3.710000e-11 80.5
22 TraesCS4D01G308300 chr2B 90.164 61 4 2 608 667 47635121 47635062 1.330000e-10 78.7
23 TraesCS4D01G308300 chr6D 96.503 143 5 0 1479 1621 206560267 206560409 2.080000e-58 237.0
24 TraesCS4D01G308300 chr1D 94.231 156 7 2 1468 1621 238940400 238940245 2.080000e-58 237.0
25 TraesCS4D01G308300 chr1D 96.000 50 1 1 615 664 365894421 365894469 3.710000e-11 80.5
26 TraesCS4D01G308300 chr5A 96.503 143 3 2 1481 1621 290391690 290391832 7.470000e-58 235.0
27 TraesCS4D01G308300 chr6A 91.525 59 3 2 620 678 144052449 144052505 3.710000e-11 80.5
28 TraesCS4D01G308300 chr6A 88.710 62 5 2 603 664 574818693 574818752 1.720000e-09 75.0
29 TraesCS4D01G308300 chr6B 90.323 62 3 3 604 664 123700628 123700687 1.330000e-10 78.7
30 TraesCS4D01G308300 chr2A 86.364 66 7 2 600 664 362443056 362443120 2.230000e-08 71.3


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 TraesCS4D01G308300 chr4D 476308752 476313220 4468 False 8253.0000 8253 100.000000 1 4469 1 chr4D.!!$F1 4468
1 TraesCS4D01G308300 chr4B 600660238 600668322 8084 False 843.4625 2850 91.812625 1 4469 8 chr4B.!!$F1 4468
2 TraesCS4D01G308300 chr4A 683490032 683495751 5719 False 1084.2000 2287 90.678400 1 4464 5 chr4A.!!$F1 4463

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
229 238 0.036858 AGAACAGCGAGGAGGAAAGC 60.037 55.0 0.00 0.0 0.00 3.51 F
301 315 0.107557 TGCGTGTCTGGATGCATGAT 60.108 50.0 2.46 0.0 31.31 2.45 F
1929 6201 0.179032 TTTTGCAGTTCTCTCCGGCA 60.179 50.0 0.00 0.0 0.00 5.69 F
2309 6594 0.036732 TTGGTGCTCTGGCTACTTGG 59.963 55.0 0.00 0.0 39.59 3.61 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1733 6005 0.890683 GTGATCAAACCTTGCCCTGG 59.109 55.000 0.0 0.0 0.00 4.45 R
1998 6272 6.147164 TCGAGATTCCAACACACAAATAGAAC 59.853 38.462 0.0 0.0 0.00 3.01 R
3234 7665 1.059584 TGGCTTGAGGTGTTCCTGGA 61.060 55.000 0.0 0.0 45.24 3.86 R
4154 8610 0.321671 CCCACAGAGAAGAAGGCGAA 59.678 55.000 0.0 0.0 0.00 4.70 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
68 69 8.788806 TCGTAACAGAAACATTTAATCATTGGT 58.211 29.630 0.00 0.00 0.00 3.67
82 83 6.737254 AATCATTGGTGTTACTTTACTCGG 57.263 37.500 0.00 0.00 0.00 4.63
85 86 3.665745 TGGTGTTACTTTACTCGGGAC 57.334 47.619 0.00 0.00 0.00 4.46
107 108 5.235516 ACGTCAGGAAACGAAGACATATTT 58.764 37.500 3.16 0.00 45.37 1.40
128 129 1.482278 GTCCTCATCGTCATCTTCGC 58.518 55.000 0.00 0.00 0.00 4.70
229 238 0.036858 AGAACAGCGAGGAGGAAAGC 60.037 55.000 0.00 0.00 0.00 3.51
283 297 1.986378 CTACTTTCGCCGTGTCTTCTG 59.014 52.381 0.00 0.00 0.00 3.02
301 315 0.107557 TGCGTGTCTGGATGCATGAT 60.108 50.000 2.46 0.00 31.31 2.45
345 360 6.891624 AGCGCTAATATTCATACAACACATG 58.108 36.000 8.99 0.00 0.00 3.21
380 395 3.585289 TGTGCTAATAGTCACCCCTTTCA 59.415 43.478 10.65 0.00 32.51 2.69
470 492 3.480470 AGTGCCACAACATGCCTATATC 58.520 45.455 0.00 0.00 0.00 1.63
471 493 3.137176 AGTGCCACAACATGCCTATATCT 59.863 43.478 0.00 0.00 0.00 1.98
472 494 4.347876 AGTGCCACAACATGCCTATATCTA 59.652 41.667 0.00 0.00 0.00 1.98
473 495 5.013495 AGTGCCACAACATGCCTATATCTAT 59.987 40.000 0.00 0.00 0.00 1.98
474 496 6.213397 AGTGCCACAACATGCCTATATCTATA 59.787 38.462 0.00 0.00 0.00 1.31
475 497 7.050377 GTGCCACAACATGCCTATATCTATAT 58.950 38.462 0.00 0.00 0.00 0.86
552 578 9.180678 GGAAGTATTTAATCATATTTTGGCACG 57.819 33.333 0.00 0.00 0.00 5.34
602 628 9.725019 ACTGTTATGTAATGTTCATTCAGAAGA 57.275 29.630 12.97 8.22 36.78 2.87
648 674 8.553459 TTCCTCTGTTTCAAAATAGATGACTC 57.447 34.615 6.69 0.00 35.92 3.36
650 676 8.156820 TCCTCTGTTTCAAAATAGATGACTCAA 58.843 33.333 2.91 0.00 35.92 3.02
653 679 9.342308 TCTGTTTCAAAATAGATGACTCAACTT 57.658 29.630 0.00 0.00 32.24 2.66
654 680 9.956720 CTGTTTCAAAATAGATGACTCAACTTT 57.043 29.630 0.00 0.00 29.67 2.66
744 4604 2.612972 GGACATCCACAGAGCGAGAAAA 60.613 50.000 0.00 0.00 35.64 2.29
745 4605 3.067106 GACATCCACAGAGCGAGAAAAA 58.933 45.455 0.00 0.00 0.00 1.94
746 4606 3.679389 ACATCCACAGAGCGAGAAAAAT 58.321 40.909 0.00 0.00 0.00 1.82
747 4607 3.438087 ACATCCACAGAGCGAGAAAAATG 59.562 43.478 0.00 0.00 0.00 2.32
748 4608 3.126001 TCCACAGAGCGAGAAAAATGT 57.874 42.857 0.00 0.00 0.00 2.71
749 4609 4.265904 TCCACAGAGCGAGAAAAATGTA 57.734 40.909 0.00 0.00 0.00 2.29
750 4610 4.832248 TCCACAGAGCGAGAAAAATGTAT 58.168 39.130 0.00 0.00 0.00 2.29
751 4611 5.245531 TCCACAGAGCGAGAAAAATGTATT 58.754 37.500 0.00 0.00 0.00 1.89
752 4612 5.351465 TCCACAGAGCGAGAAAAATGTATTC 59.649 40.000 0.00 0.00 0.00 1.75
753 4613 5.447818 CCACAGAGCGAGAAAAATGTATTCC 60.448 44.000 0.00 0.00 0.00 3.01
754 4614 5.352569 CACAGAGCGAGAAAAATGTATTCCT 59.647 40.000 0.00 0.00 0.00 3.36
755 4615 5.940470 ACAGAGCGAGAAAAATGTATTCCTT 59.060 36.000 0.00 0.00 0.00 3.36
756 4616 6.431234 ACAGAGCGAGAAAAATGTATTCCTTT 59.569 34.615 0.00 0.00 0.00 3.11
757 4617 7.040409 ACAGAGCGAGAAAAATGTATTCCTTTT 60.040 33.333 0.00 0.00 0.00 2.27
758 4618 7.809806 CAGAGCGAGAAAAATGTATTCCTTTTT 59.190 33.333 0.00 0.00 37.29 1.94
823 4683 2.288825 CCTGCGTCTAACAGAAGTCCAA 60.289 50.000 0.00 0.00 37.32 3.53
1226 5495 2.309764 ATTTCGCGTCGCTGCATTCC 62.310 55.000 16.36 0.00 34.15 3.01
1227 5496 3.932580 TTCGCGTCGCTGCATTCCT 62.933 57.895 16.36 0.00 34.15 3.36
1228 5497 3.918220 CGCGTCGCTGCATTCCTC 61.918 66.667 16.36 0.00 34.15 3.71
1261 5530 3.390639 TGATGTTGCTGTCCCCAAATTTT 59.609 39.130 0.00 0.00 0.00 1.82
1309 5579 5.568620 AGGGCGGATAGTGATAGAATTTT 57.431 39.130 0.00 0.00 0.00 1.82
1361 5631 4.094294 CGAATCCAAGCTTACGGAAATTCA 59.906 41.667 9.42 0.00 34.22 2.57
1385 5655 5.896073 AGATAAGGTTATACAGCCTTGCT 57.104 39.130 0.00 0.00 44.38 3.91
1386 5656 6.996180 AGATAAGGTTATACAGCCTTGCTA 57.004 37.500 0.00 0.00 44.38 3.49
1387 5657 6.998802 AGATAAGGTTATACAGCCTTGCTAG 58.001 40.000 0.00 0.00 44.38 3.42
1388 5658 6.782988 AGATAAGGTTATACAGCCTTGCTAGA 59.217 38.462 0.00 0.00 44.38 2.43
1389 5659 5.896073 AAGGTTATACAGCCTTGCTAGAT 57.104 39.130 0.00 0.00 43.19 1.98
1390 5660 6.996180 AAGGTTATACAGCCTTGCTAGATA 57.004 37.500 0.00 0.00 43.19 1.98
1391 5661 6.996180 AGGTTATACAGCCTTGCTAGATAA 57.004 37.500 0.00 0.00 36.40 1.75
1638 5908 1.867363 AACGGAGGGAGTAGATGCTT 58.133 50.000 0.00 0.00 0.00 3.91
1704 5976 8.649973 ACTCTAGTTATTTTCCTCGCATAAAG 57.350 34.615 0.00 0.00 0.00 1.85
1733 6005 2.031944 GTGGCTCACTCGGTTCTTTTTC 60.032 50.000 0.00 0.00 0.00 2.29
1812 6084 1.277557 TGCTGCCAAGGTTTGTTGTTT 59.722 42.857 0.00 0.00 0.00 2.83
1929 6201 0.179032 TTTTGCAGTTCTCTCCGGCA 60.179 50.000 0.00 0.00 0.00 5.69
1998 6272 5.272167 TGATCGTAAGTTTACTTTTGCCG 57.728 39.130 0.00 0.15 37.40 5.69
2309 6594 0.036732 TTGGTGCTCTGGCTACTTGG 59.963 55.000 0.00 0.00 39.59 3.61
2321 6606 2.287608 GGCTACTTGGTTGTTCAACAGC 60.288 50.000 15.89 14.32 32.84 4.40
2360 6646 2.867429 AGCAACGCTGAATTGTTATGC 58.133 42.857 0.00 0.00 37.57 3.14
2446 6733 9.336171 ACAATAATTTGCATTTGGTAAACTGTT 57.664 25.926 0.00 0.00 36.22 3.16
2811 7185 9.212641 GCTATATTCATGTCTAACACATCATGT 57.787 33.333 0.00 0.00 44.60 3.21
2841 7215 2.865119 TCACTCATGCATCTGTGGTT 57.135 45.000 21.38 0.00 0.00 3.67
2861 7235 7.171167 TGTGGTTCTGATTTGCACATTTTATTG 59.829 33.333 0.00 0.00 0.00 1.90
2915 7289 3.531538 AGTGCTCATGGGTAATACGTTG 58.468 45.455 0.00 0.00 0.00 4.10
2994 7372 1.604604 TGTTAGCTCAAACTGCACCC 58.395 50.000 0.00 0.00 0.00 4.61
3003 7381 0.981183 AAACTGCACCCCTATGTCGA 59.019 50.000 0.00 0.00 0.00 4.20
3026 7404 2.772077 ACCGGCACATATGTTGTACA 57.228 45.000 5.37 0.00 36.57 2.90
3060 7440 8.777865 TTTTCTCTGTAATATTCAGTGTCCAG 57.222 34.615 11.96 0.00 34.86 3.86
3061 7441 7.482169 TTCTCTGTAATATTCAGTGTCCAGT 57.518 36.000 11.96 0.00 34.86 4.00
3066 7446 5.483937 TGTAATATTCAGTGTCCAGTGAGGT 59.516 40.000 5.08 2.26 41.33 3.85
3070 7450 2.179427 TCAGTGTCCAGTGAGGTATGG 58.821 52.381 0.68 0.00 35.96 2.74
3091 7471 2.158755 GGTCTATAGCTGGCACATTGGT 60.159 50.000 0.00 0.00 38.20 3.67
3093 7473 4.263068 GGTCTATAGCTGGCACATTGGTAT 60.263 45.833 0.00 2.43 38.20 2.73
3102 7482 3.195182 TGGCACATTGGTATGATGTTTGG 59.805 43.478 0.00 0.00 35.64 3.28
3120 7500 7.784633 TGTTTGGAGATTGGATTTTTGTTTC 57.215 32.000 0.00 0.00 0.00 2.78
3128 7508 8.198807 AGATTGGATTTTTGTTTCTGGAGATT 57.801 30.769 0.00 0.00 0.00 2.40
3141 7523 4.271661 TCTGGAGATTATTTGTGCATGCA 58.728 39.130 18.46 18.46 0.00 3.96
3164 7549 3.376546 CCAAGCTGCTCTTTAGAATCCAC 59.623 47.826 1.00 0.00 31.27 4.02
3194 7579 8.425577 AATACCAATCGACAGTTTATCTCTTG 57.574 34.615 0.00 0.00 0.00 3.02
3199 7584 7.433719 CCAATCGACAGTTTATCTCTTGACTAG 59.566 40.741 0.00 0.00 0.00 2.57
3201 7586 7.450124 TCGACAGTTTATCTCTTGACTAGTT 57.550 36.000 0.00 0.00 0.00 2.24
3203 7588 6.034044 CGACAGTTTATCTCTTGACTAGTTGC 59.966 42.308 0.00 0.00 0.00 4.17
3204 7589 6.759272 ACAGTTTATCTCTTGACTAGTTGCA 58.241 36.000 0.00 0.00 0.00 4.08
3205 7590 7.390027 ACAGTTTATCTCTTGACTAGTTGCAT 58.610 34.615 0.00 0.00 0.00 3.96
3206 7591 7.547370 ACAGTTTATCTCTTGACTAGTTGCATC 59.453 37.037 0.00 0.00 0.00 3.91
3207 7592 7.547019 CAGTTTATCTCTTGACTAGTTGCATCA 59.453 37.037 0.00 0.00 0.00 3.07
3234 7665 6.126863 TCTCATGTGGTTGGTTCTCTTAAT 57.873 37.500 0.00 0.00 0.00 1.40
3252 7683 0.329596 ATCCAGGAACACCTCAAGCC 59.670 55.000 0.00 0.00 30.75 4.35
3253 7684 1.059584 TCCAGGAACACCTCAAGCCA 61.060 55.000 0.00 0.00 30.75 4.75
3375 7806 1.507141 CCTTTGCGCACGAGAAAGGT 61.507 55.000 23.71 0.00 40.56 3.50
3384 7815 0.106149 ACGAGAAAGGTGGCGTTCTT 59.894 50.000 0.00 0.00 34.23 2.52
3438 7869 4.633175 CATCAGATGCTCTAGCTTCATGT 58.367 43.478 17.16 3.04 44.66 3.21
3469 7900 0.324943 GGTGAAGCCCAAGCACTAGA 59.675 55.000 0.00 0.00 43.56 2.43
3471 7902 0.037326 TGAAGCCCAAGCACTAGACG 60.037 55.000 0.00 0.00 43.56 4.18
3474 7905 1.805945 GCCCAAGCACTAGACGACG 60.806 63.158 0.00 0.00 39.53 5.12
3711 8162 5.111989 ACATCTGAGATATGGTTTGTGACG 58.888 41.667 0.00 0.00 0.00 4.35
3725 8176 5.333875 GGTTTGTGACGGTAAGAATGAAGTC 60.334 44.000 0.00 0.00 0.00 3.01
3730 8181 4.020573 TGACGGTAAGAATGAAGTCATGGT 60.021 41.667 0.00 0.00 36.56 3.55
3812 8268 6.477253 TGGTATCTTTACATTGCACTGGTAA 58.523 36.000 9.06 4.66 0.00 2.85
3813 8269 6.597672 TGGTATCTTTACATTGCACTGGTAAG 59.402 38.462 9.06 10.62 0.00 2.34
3814 8270 6.598064 GGTATCTTTACATTGCACTGGTAAGT 59.402 38.462 9.06 5.36 36.98 2.24
3824 8280 3.704566 TGCACTGGTAAGTATCCTACTGG 59.295 47.826 0.00 0.00 39.39 4.00
3843 8299 2.101750 TGGTTGCTCTGAAGTACGAACA 59.898 45.455 0.00 0.00 0.00 3.18
3925 8381 6.939730 TGCGCCTAATAATGAATAATTCAGGA 59.060 34.615 4.18 0.00 43.98 3.86
4144 8600 4.388499 GTGCGTCCCGTCCATGGT 62.388 66.667 12.58 0.00 0.00 3.55
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
2 3 2.297698 TCAAGGTCAACCCTCGACTA 57.702 50.000 0.00 0.00 45.47 2.59
5 6 1.202722 GGTTTCAAGGTCAACCCTCGA 60.203 52.381 0.00 0.00 45.47 4.04
48 49 9.912634 AGTAACACCAATGATTAAATGTTTCTG 57.087 29.630 6.29 0.00 32.76 3.02
68 69 2.884012 TGACGTCCCGAGTAAAGTAACA 59.116 45.455 14.12 0.00 0.00 2.41
82 83 1.269413 TGTCTTCGTTTCCTGACGTCC 60.269 52.381 14.12 0.00 43.23 4.79
85 86 5.445939 CCAAATATGTCTTCGTTTCCTGACG 60.446 44.000 0.00 0.00 44.06 4.35
107 108 1.405463 CGAAGATGACGATGAGGACCA 59.595 52.381 0.00 0.00 0.00 4.02
229 238 9.177304 CACACTAGCAGCATGAAAAATATATTG 57.823 33.333 0.00 0.00 39.69 1.90
283 297 0.306840 CATCATGCATCCAGACACGC 59.693 55.000 0.00 0.00 0.00 5.34
301 315 3.621268 GCTCCATACAAAACGCTATGACA 59.379 43.478 0.00 0.00 0.00 3.58
351 366 7.354312 AGGGGTGACTATTAGCACATTTTTAT 58.646 34.615 15.41 0.00 36.76 1.40
353 368 5.580022 AGGGGTGACTATTAGCACATTTTT 58.420 37.500 15.41 0.83 36.76 1.94
474 496 9.961265 CTTTATTGTCATTCTTACATCATGCAT 57.039 29.630 0.00 0.00 0.00 3.96
475 497 7.916977 GCTTTATTGTCATTCTTACATCATGCA 59.083 33.333 0.00 0.00 0.00 3.96
624 650 7.679783 TGAGTCATCTATTTTGAAACAGAGGA 58.320 34.615 0.00 0.00 0.00 3.71
686 3062 1.916000 GCAACATTTTCAGCTGCGATC 59.084 47.619 9.47 0.00 0.00 3.69
756 4616 8.449251 AATGCATTTTTCTTTGCCTCTAAAAA 57.551 26.923 5.99 0.00 38.08 1.94
757 4617 7.173047 GGAATGCATTTTTCTTTGCCTCTAAAA 59.827 33.333 14.33 0.00 38.08 1.52
758 4618 6.650390 GGAATGCATTTTTCTTTGCCTCTAAA 59.350 34.615 14.33 0.00 38.08 1.85
759 4619 6.014327 AGGAATGCATTTTTCTTTGCCTCTAA 60.014 34.615 14.33 0.00 38.08 2.10
760 4620 5.481473 AGGAATGCATTTTTCTTTGCCTCTA 59.519 36.000 14.33 0.00 38.08 2.43
761 4621 4.285260 AGGAATGCATTTTTCTTTGCCTCT 59.715 37.500 14.33 0.00 38.08 3.69
762 4622 4.390909 CAGGAATGCATTTTTCTTTGCCTC 59.609 41.667 14.33 0.00 38.08 4.70
763 4623 4.040706 TCAGGAATGCATTTTTCTTTGCCT 59.959 37.500 14.33 9.67 38.08 4.75
764 4624 4.152938 GTCAGGAATGCATTTTTCTTTGCC 59.847 41.667 14.33 7.39 38.08 4.52
765 4625 4.992951 AGTCAGGAATGCATTTTTCTTTGC 59.007 37.500 14.33 0.00 39.33 3.68
766 4626 6.462073 CAGTCAGGAATGCATTTTTCTTTG 57.538 37.500 14.33 5.56 0.00 2.77
981 4858 1.801913 CTCCCTGAACGAACTCGCG 60.802 63.158 0.00 0.00 44.43 5.87
1226 5495 6.282167 ACAGCAACATCAGAGAGATAATGAG 58.718 40.000 0.00 0.00 34.43 2.90
1227 5496 6.231258 ACAGCAACATCAGAGAGATAATGA 57.769 37.500 0.00 0.00 34.43 2.57
1228 5497 5.466058 GGACAGCAACATCAGAGAGATAATG 59.534 44.000 0.00 0.00 34.43 1.90
1261 5530 2.365617 AGAGCTGACTCCGAAAACAGAA 59.634 45.455 0.00 0.00 44.65 3.02
1292 5561 7.500559 AGTGCAAGGAAAATTCTATCACTATCC 59.499 37.037 0.00 0.00 31.40 2.59
1309 5579 2.661537 CACGCGTCAGTGCAAGGA 60.662 61.111 9.86 0.00 35.17 3.36
1361 5631 7.560796 AGCAAGGCTGTATAACCTTATCTAT 57.439 36.000 0.00 0.00 44.55 1.98
1638 5908 9.344772 AGTTAGTGAAACCATACAAACACAATA 57.655 29.630 0.00 0.00 39.03 1.90
1704 5976 1.471676 CCGAGTGAGCCACATAAGGAC 60.472 57.143 7.86 0.00 36.74 3.85
1733 6005 0.890683 GTGATCAAACCTTGCCCTGG 59.109 55.000 0.00 0.00 0.00 4.45
1812 6084 7.017551 AGAGAACATATCCCCACAAGCATTATA 59.982 37.037 0.00 0.00 0.00 0.98
1929 6201 7.944729 ATAAGCACACAATAAAACTCTGGAT 57.055 32.000 0.00 0.00 0.00 3.41
1998 6272 6.147164 TCGAGATTCCAACACACAAATAGAAC 59.853 38.462 0.00 0.00 0.00 3.01
2360 6646 4.858692 CAGATTGCCAACCAAGAATTTACG 59.141 41.667 0.00 0.00 36.76 3.18
2394 6680 8.755977 TCCTAACCATACAGTTTTAGGAAGTAG 58.244 37.037 6.49 0.00 44.28 2.57
2446 6733 6.016527 CGCTCAATGGACTACCTACATACTAA 60.017 42.308 0.00 0.00 37.04 2.24
2679 7033 2.543777 AAACACGCACTCAGGTGTAT 57.456 45.000 0.00 0.00 46.01 2.29
2685 7053 1.202177 ACAAGCAAAACACGCACTCAG 60.202 47.619 0.00 0.00 0.00 3.35
2779 7153 8.360390 TGTGTTAGACATGAATATAGCTCGATT 58.640 33.333 0.00 0.00 0.00 3.34
2780 7154 7.886338 TGTGTTAGACATGAATATAGCTCGAT 58.114 34.615 0.00 0.00 0.00 3.59
2811 7185 6.537660 CAGATGCATGAGTGATTCAGTTTCTA 59.462 38.462 2.46 0.00 39.68 2.10
2841 7215 8.358895 TGTTCTCAATAAAATGTGCAAATCAGA 58.641 29.630 0.00 0.00 0.00 3.27
2861 7235 3.207474 ACATTGCAGCGAATTGTTCTC 57.793 42.857 0.00 0.00 0.00 2.87
2931 7305 5.764686 TGTGTCCAGCTAGCCATTAATATTG 59.235 40.000 12.13 0.00 0.00 1.90
2994 7372 2.132762 GTGCCGGTAAATCGACATAGG 58.867 52.381 1.90 0.00 0.00 2.57
3003 7381 5.186942 TGTACAACATATGTGCCGGTAAAT 58.813 37.500 9.63 0.49 43.29 1.40
3026 7404 8.689061 TGAATATTACAGAGAAAAGCAATGCAT 58.311 29.630 8.35 0.00 0.00 3.96
3060 7440 3.511934 CCAGCTATAGACCCATACCTCAC 59.488 52.174 3.21 0.00 0.00 3.51
3061 7441 3.779444 CCAGCTATAGACCCATACCTCA 58.221 50.000 3.21 0.00 0.00 3.86
3066 7446 2.970987 TGTGCCAGCTATAGACCCATA 58.029 47.619 3.21 0.00 0.00 2.74
3070 7450 2.158755 ACCAATGTGCCAGCTATAGACC 60.159 50.000 3.21 0.00 0.00 3.85
3091 7471 8.814931 ACAAAAATCCAATCTCCAAACATCATA 58.185 29.630 0.00 0.00 0.00 2.15
3093 7473 7.065120 ACAAAAATCCAATCTCCAAACATCA 57.935 32.000 0.00 0.00 0.00 3.07
3102 7482 7.219484 TCTCCAGAAACAAAAATCCAATCTC 57.781 36.000 0.00 0.00 0.00 2.75
3120 7500 4.357142 GTGCATGCACAAATAATCTCCAG 58.643 43.478 39.12 0.00 45.53 3.86
3141 7523 3.009473 TGGATTCTAAAGAGCAGCTTGGT 59.991 43.478 0.00 0.00 36.80 3.67
3176 7561 7.633193 ACTAGTCAAGAGATAAACTGTCGAT 57.367 36.000 0.00 0.00 0.00 3.59
3177 7562 7.306213 CAACTAGTCAAGAGATAAACTGTCGA 58.694 38.462 0.00 0.00 0.00 4.20
3194 7579 6.965500 CACATGAGAAAATGATGCAACTAGTC 59.035 38.462 0.00 0.00 0.00 2.59
3199 7584 4.813027 ACCACATGAGAAAATGATGCAAC 58.187 39.130 0.00 0.00 0.00 4.17
3201 7586 4.322123 CCAACCACATGAGAAAATGATGCA 60.322 41.667 0.00 0.00 0.00 3.96
3203 7588 5.395682 ACCAACCACATGAGAAAATGATG 57.604 39.130 0.00 0.00 0.00 3.07
3204 7589 5.776716 AGAACCAACCACATGAGAAAATGAT 59.223 36.000 0.00 0.00 0.00 2.45
3205 7590 5.139727 AGAACCAACCACATGAGAAAATGA 58.860 37.500 0.00 0.00 0.00 2.57
3206 7591 5.242393 AGAGAACCAACCACATGAGAAAATG 59.758 40.000 0.00 0.00 0.00 2.32
3207 7592 5.388654 AGAGAACCAACCACATGAGAAAAT 58.611 37.500 0.00 0.00 0.00 1.82
3234 7665 1.059584 TGGCTTGAGGTGTTCCTGGA 61.060 55.000 0.00 0.00 45.24 3.86
3348 7779 2.110835 TGCGCAAAGGTCAGAGCA 59.889 55.556 8.16 0.00 38.22 4.26
3384 7815 2.754375 GGAAGCGTGAAAGGGGGA 59.246 61.111 0.00 0.00 0.00 4.81
3469 7900 2.414994 TTCTCTCCCTATGACGTCGT 57.585 50.000 15.78 15.78 0.00 4.34
3471 7902 4.200874 TCTCTTTCTCTCCCTATGACGTC 58.799 47.826 9.11 9.11 0.00 4.34
3474 7905 6.068010 TCATCTCTCTTTCTCTCCCTATGAC 58.932 44.000 0.00 0.00 0.00 3.06
3711 8162 4.589908 ACCACCATGACTTCATTCTTACC 58.410 43.478 0.00 0.00 33.61 2.85
3725 8176 4.582869 TCAGAATCTGAAGAACCACCATG 58.417 43.478 10.99 0.00 37.57 3.66
3813 8269 4.160626 ACTTCAGAGCAACCAGTAGGATAC 59.839 45.833 0.00 0.00 43.47 2.24
3814 8270 4.353777 ACTTCAGAGCAACCAGTAGGATA 58.646 43.478 0.00 0.00 38.69 2.59
3824 8280 3.060473 GTGTGTTCGTACTTCAGAGCAAC 60.060 47.826 0.00 0.00 29.82 4.17
3843 8299 1.676014 GCTTCGATTGTAGGCCAGTGT 60.676 52.381 5.01 0.00 0.00 3.55
3906 8362 9.524496 AGCTGCATCCTGAATTATTCATTATTA 57.476 29.630 8.17 0.00 39.30 0.98
3907 8363 8.304596 CAGCTGCATCCTGAATTATTCATTATT 58.695 33.333 8.17 0.00 39.30 1.40
3908 8364 7.577046 GCAGCTGCATCCTGAATTATTCATTAT 60.577 37.037 33.36 2.69 38.94 1.28
3947 8403 4.459089 GGCGAGGTCAGAGTGGCC 62.459 72.222 0.00 0.00 44.07 5.36
3948 8404 4.803426 CGGCGAGGTCAGAGTGGC 62.803 72.222 0.00 0.00 0.00 5.01
4144 8600 3.524648 GAAGGCGAACGGGTGGTCA 62.525 63.158 0.00 0.00 0.00 4.02
4154 8610 0.321671 CCCACAGAGAAGAAGGCGAA 59.678 55.000 0.00 0.00 0.00 4.70
4213 8672 2.606519 CCTGGAGGTCCAACCCGA 60.607 66.667 0.00 0.00 46.97 5.14
4217 8676 1.303643 CAAGGCCTGGAGGTCCAAC 60.304 63.158 5.69 0.00 46.97 3.77
4334 8793 4.747218 GTCTGGGACCTCGAGACT 57.253 61.111 15.71 0.00 44.54 3.24


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

AutoCloner maintained by Alex Coulton.