Multiple sequence alignment - TraesCS3D01G464300

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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 TraesCS3D01G464300 chr3D 100.000 2891 0 0 1387 4277 568088891 568086001 0.000000e+00 5339.0
1 TraesCS3D01G464300 chr3D 100.000 1158 0 0 1 1158 568090277 568089120 0.000000e+00 2139.0
2 TraesCS3D01G464300 chr3D 86.646 1273 160 9 2070 3338 570146363 570145097 0.000000e+00 1400.0
3 TraesCS3D01G464300 chr3D 84.694 98 14 1 982 1078 570146613 570146516 3.520000e-16 97.1
4 TraesCS3D01G464300 chr3A 95.282 2077 85 10 1391 3462 702490780 702492848 0.000000e+00 3280.0
5 TraesCS3D01G464300 chr3A 92.893 999 46 10 176 1155 702489779 702490771 0.000000e+00 1428.0
6 TraesCS3D01G464300 chr3A 87.469 407 38 2 3616 4022 702493075 702493468 1.400000e-124 457.0
7 TraesCS3D01G464300 chr3A 96.842 190 6 0 3 192 702489215 702489404 6.900000e-83 318.0
8 TraesCS3D01G464300 chr3A 95.161 124 6 0 3498 3621 702492836 702492959 3.370000e-46 196.0
9 TraesCS3D01G464300 chr3B 93.976 2075 106 6 1391 3464 756588481 756590537 0.000000e+00 3121.0
10 TraesCS3D01G464300 chr3B 94.062 1903 94 6 1563 3464 756602037 756603921 0.000000e+00 2870.0
11 TraesCS3D01G464300 chr3B 92.113 989 36 25 176 1158 756600660 756601612 0.000000e+00 1356.0
12 TraesCS3D01G464300 chr3B 92.012 989 37 25 176 1158 756587522 756588474 0.000000e+00 1351.0
13 TraesCS3D01G464300 chr3B 85.703 1266 172 7 2070 3331 756823936 756822676 0.000000e+00 1327.0
14 TraesCS3D01G464300 chr3B 85.624 1266 172 8 2070 3331 756708804 756707545 0.000000e+00 1321.0
15 TraesCS3D01G464300 chr3B 84.424 764 114 4 2571 3331 756743826 756743065 0.000000e+00 747.0
16 TraesCS3D01G464300 chr3B 92.398 171 13 0 1391 1561 756601619 756601789 1.190000e-60 244.0
17 TraesCS3D01G464300 chr3B 93.590 156 10 0 37 192 756586929 756587084 2.570000e-57 233.0
18 TraesCS3D01G464300 chr3B 93.590 156 10 0 37 192 756600067 756600222 2.570000e-57 233.0
19 TraesCS3D01G464300 chr3B 94.915 59 3 0 1391 1449 756588397 756588455 4.550000e-15 93.5
20 TraesCS3D01G464300 chr3B 94.915 59 3 0 1391 1449 756601535 756601593 4.550000e-15 93.5
21 TraesCS3D01G464300 chr3B 83.505 97 14 2 997 1092 756686831 756686736 5.890000e-14 89.8
22 TraesCS3D01G464300 chr3B 91.525 59 5 0 3913 3971 584739008 584738950 9.860000e-12 82.4
23 TraesCS3D01G464300 chrUn 95.645 1883 77 5 1583 3464 264011142 264009264 0.000000e+00 3018.0
24 TraesCS3D01G464300 chrUn 95.645 1883 77 5 1583 3464 294197616 294195738 0.000000e+00 3018.0
25 TraesCS3D01G464300 chrUn 95.708 466 17 3 691 1155 264013222 264012759 0.000000e+00 747.0
26 TraesCS3D01G464300 chrUn 92.698 493 26 6 176 664 264013706 264013220 0.000000e+00 702.0
27 TraesCS3D01G464300 chrUn 90.995 211 11 4 1388 1598 264012716 264012514 1.170000e-70 278.0
28 TraesCS3D01G464300 chrUn 90.476 168 12 3 29 192 264014254 264014087 7.200000e-53 219.0
29 TraesCS3D01G464300 chrUn 97.590 83 1 1 3501 3582 264009275 264009193 1.600000e-29 141.0
30 TraesCS3D01G464300 chrUn 97.590 83 1 1 3501 3582 294195749 294195667 1.600000e-29 141.0
31 TraesCS3D01G464300 chr1A 82.855 1289 185 20 2027 3306 14109448 14108187 0.000000e+00 1123.0
32 TraesCS3D01G464300 chr1A 87.500 48 6 0 3619 3666 572223242 572223289 5.970000e-04 56.5
33 TraesCS3D01G464300 chr4A 92.632 665 38 6 3616 4277 692827302 692827958 0.000000e+00 946.0
34 TraesCS3D01G464300 chr2B 92.632 665 38 6 3616 4277 360281161 360281817 0.000000e+00 946.0
35 TraesCS3D01G464300 chr1B 95.708 466 17 3 691 1155 333605078 333604615 0.000000e+00 747.0
36 TraesCS3D01G464300 chr1B 92.698 493 26 6 176 664 333605562 333605076 0.000000e+00 702.0
37 TraesCS3D01G464300 chr1B 90.995 211 11 4 1388 1598 333604572 333604370 1.170000e-70 278.0
38 TraesCS3D01G464300 chr1B 90.476 168 12 3 29 192 333606110 333605943 7.200000e-53 219.0


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 TraesCS3D01G464300 chr3D 568086001 568090277 4276 True 3739.000000 5339 100.00000 1 4277 2 chr3D.!!$R1 4276
1 TraesCS3D01G464300 chr3D 570145097 570146613 1516 True 748.550000 1400 85.67000 982 3338 2 chr3D.!!$R2 2356
2 TraesCS3D01G464300 chr3A 702489215 702493468 4253 False 1135.800000 3280 93.52940 3 4022 5 chr3A.!!$F1 4019
3 TraesCS3D01G464300 chr3B 756822676 756823936 1260 True 1327.000000 1327 85.70300 2070 3331 1 chr3B.!!$R5 1261
4 TraesCS3D01G464300 chr3B 756707545 756708804 1259 True 1321.000000 1321 85.62400 2070 3331 1 chr3B.!!$R3 1261
5 TraesCS3D01G464300 chr3B 756586929 756590537 3608 False 1199.625000 3121 93.62325 37 3464 4 chr3B.!!$F1 3427
6 TraesCS3D01G464300 chr3B 756600067 756603921 3854 False 959.300000 2870 93.41560 37 3464 5 chr3B.!!$F2 3427
7 TraesCS3D01G464300 chr3B 756743065 756743826 761 True 747.000000 747 84.42400 2571 3331 1 chr3B.!!$R4 760
8 TraesCS3D01G464300 chrUn 294195667 294197616 1949 True 1579.500000 3018 96.61750 1583 3582 2 chrUn.!!$R2 1999
9 TraesCS3D01G464300 chrUn 264009193 264014254 5061 True 850.833333 3018 93.85200 29 3582 6 chrUn.!!$R1 3553
10 TraesCS3D01G464300 chr1A 14108187 14109448 1261 True 1123.000000 1123 82.85500 2027 3306 1 chr1A.!!$R1 1279
11 TraesCS3D01G464300 chr4A 692827302 692827958 656 False 946.000000 946 92.63200 3616 4277 1 chr4A.!!$F1 661
12 TraesCS3D01G464300 chr2B 360281161 360281817 656 False 946.000000 946 92.63200 3616 4277 1 chr2B.!!$F1 661
13 TraesCS3D01G464300 chr1B 333604370 333606110 1740 True 486.500000 747 92.46925 29 1598 4 chr1B.!!$R1 1569

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
194 199 0.176680 ATCTGGAACGAGCGCAAGAT 59.823 50.0 11.47 3.24 43.02 2.40 F
514 994 0.389296 TGGTTGAGTATGCCGTGACG 60.389 55.0 0.00 0.00 0.00 4.35 F
515 995 0.389426 GGTTGAGTATGCCGTGACGT 60.389 55.0 3.64 0.00 0.00 4.34 F
681 1165 0.670162 CCTTGGAAGGTGCAGTTGTG 59.330 55.0 0.00 0.00 41.41 3.33 F
1865 4039 0.739462 CGATTGTGTTGGGCGAGCTA 60.739 55.0 0.00 0.00 0.00 3.32 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1970 4145 0.107312 AAGGCTGCTAGGCACATCAG 60.107 55.000 11.23 0.0 44.19 2.90 R
2294 4473 0.623723 ATATTTCCGGTGGTGGCTGT 59.376 50.000 0.00 0.0 0.00 4.40 R
2314 4493 3.327757 AGGAAGGTCATTGAGTAGCACAA 59.672 43.478 0.00 0.0 0.00 3.33 R
2819 5003 0.593263 GTACCTCCGCGACCATTACG 60.593 60.000 8.23 0.0 0.00 3.18 R
3898 6207 0.100503 GGTCAATTATGGCGTGGTGC 59.899 55.000 0.00 0.0 45.38 5.01 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
44 45 5.514274 CTTTCACTAAGGAAGTTTGGCAA 57.486 39.130 0.00 0.00 35.76 4.52
54 55 0.475906 AGTTTGGCAACTCAGAGGCT 59.524 50.000 0.00 0.00 39.15 4.58
112 113 0.331616 CCGGGACCATTTCTCCCTTT 59.668 55.000 0.00 0.00 45.00 3.11
156 157 4.034742 GTCTTAAGGACAAAAGTTGCGTCA 59.965 41.667 1.85 0.00 43.94 4.35
192 197 1.524355 CATATCTGGAACGAGCGCAAG 59.476 52.381 11.47 5.17 43.44 4.01
194 199 0.176680 ATCTGGAACGAGCGCAAGAT 59.823 50.000 11.47 3.24 43.02 2.40
196 201 1.202302 TCTGGAACGAGCGCAAGATAG 60.202 52.381 11.47 0.00 43.02 2.08
197 202 0.815095 TGGAACGAGCGCAAGATAGA 59.185 50.000 11.47 0.00 43.02 1.98
204 682 3.914966 ACGAGCGCAAGATAGATTTATCG 59.085 43.478 11.47 7.80 40.53 2.92
213 691 9.517361 CGCAAGATAGATTTATCGTATCAAAAC 57.483 33.333 0.00 0.00 40.53 2.43
409 889 6.707440 TCTAAAAATTGTGGTCTTCAGCAA 57.293 33.333 0.00 0.00 0.00 3.91
510 990 1.346395 TGACTTGGTTGAGTATGCCGT 59.654 47.619 0.00 0.00 0.00 5.68
511 991 1.732259 GACTTGGTTGAGTATGCCGTG 59.268 52.381 0.00 0.00 0.00 4.94
512 992 1.346395 ACTTGGTTGAGTATGCCGTGA 59.654 47.619 0.00 0.00 0.00 4.35
513 993 1.732259 CTTGGTTGAGTATGCCGTGAC 59.268 52.381 0.00 0.00 0.00 3.67
514 994 0.389296 TGGTTGAGTATGCCGTGACG 60.389 55.000 0.00 0.00 0.00 4.35
515 995 0.389426 GGTTGAGTATGCCGTGACGT 60.389 55.000 3.64 0.00 0.00 4.34
527 1007 2.727777 CCGTGACGTCGACATATGAAT 58.272 47.619 17.16 0.00 0.00 2.57
667 1151 4.574013 GCATGACTTGTTATCTCTCCTTGG 59.426 45.833 0.00 0.00 0.00 3.61
670 1154 6.042638 TGACTTGTTATCTCTCCTTGGAAG 57.957 41.667 0.00 0.00 0.00 3.46
676 1160 0.979665 TCTCTCCTTGGAAGGTGCAG 59.020 55.000 5.33 3.81 46.54 4.41
681 1165 0.670162 CCTTGGAAGGTGCAGTTGTG 59.330 55.000 0.00 0.00 41.41 3.33
866 1350 2.034048 TTGTCAGCACCGTACCAGCA 62.034 55.000 2.30 0.00 0.00 4.41
902 1386 4.948004 GGTCCCAGGAAAACGAGATATTTT 59.052 41.667 0.00 0.00 31.96 1.82
1099 1596 9.771534 AGGTAGTATCTTATCTTTTCATTGAGC 57.228 33.333 0.00 0.00 0.00 4.26
1103 1609 8.421784 AGTATCTTATCTTTTCATTGAGCGGTA 58.578 33.333 0.00 0.00 0.00 4.02
1130 1636 5.782893 TGACCTTTTATTTGACACTTGGG 57.217 39.130 0.00 0.00 0.00 4.12
1438 1980 9.897744 TTTCTATGAGCTTTTATTTGACACTTG 57.102 29.630 0.00 0.00 0.00 3.16
1440 1982 6.655078 ATGAGCTTTTATTTGACACTTGGT 57.345 33.333 0.00 0.00 0.00 3.67
1450 1992 6.735678 ATTTGACACTTGGTTTCCAAAAAC 57.264 33.333 2.85 0.00 43.44 2.43
1501 2043 4.526262 AGAGCCGATAGAGCAATGTTAGAT 59.474 41.667 0.00 0.00 39.76 1.98
1548 2090 8.547967 TTTGTTAAATGCTTGGTTGTTTGTAA 57.452 26.923 0.00 0.00 0.00 2.41
1599 3773 2.303175 GATACTGGCTCTCTCCTTCGT 58.697 52.381 0.00 0.00 0.00 3.85
1616 3790 3.510388 TCGTTCTCTGCATCCTAAGTG 57.490 47.619 0.00 0.00 0.00 3.16
1642 3816 9.399403 GAATTAAACAACATGAAAGGAGAAGAC 57.601 33.333 0.00 0.00 0.00 3.01
1643 3817 5.424121 AAACAACATGAAAGGAGAAGACG 57.576 39.130 0.00 0.00 0.00 4.18
1701 3875 8.194769 TGATAGTATTAACGTGCTCATGAAGAA 58.805 33.333 0.00 0.00 0.00 2.52
1755 3929 4.094442 GGACACTGCGGGTAAAAAGAATAG 59.906 45.833 0.00 0.00 0.00 1.73
1809 3983 5.415221 AGGCTTTCGTCAACAAATCAAAAA 58.585 33.333 0.00 0.00 0.00 1.94
1865 4039 0.739462 CGATTGTGTTGGGCGAGCTA 60.739 55.000 0.00 0.00 0.00 3.32
2054 4229 7.095649 GCGTATGAGCTAATTAACACATCATGA 60.096 37.037 0.00 0.00 0.00 3.07
2055 4230 8.217115 CGTATGAGCTAATTAACACATCATGAC 58.783 37.037 0.00 0.00 0.00 3.06
2240 4419 1.988107 TCCTCTGGTCCAAATGCTCTT 59.012 47.619 0.00 0.00 0.00 2.85
2282 4461 1.941377 ATGCCATCCACAACCATTGT 58.059 45.000 0.00 0.00 46.75 2.71
2294 4473 5.067153 CCACAACCATTGTCTTCAGTTACAA 59.933 40.000 0.00 0.00 43.23 2.41
2314 4493 1.005450 ACAGCCACCACCGGAAATATT 59.995 47.619 9.46 0.00 0.00 1.28
2819 5003 5.468409 GGGAATTGTAGCTCAGATTCTAAGC 59.532 44.000 0.03 0.03 36.27 3.09
2868 5054 5.277857 TGCCCTTTTCTAGTATAGCAGAC 57.722 43.478 0.00 0.00 38.99 3.51
2902 5088 6.750039 GCAATTGTATGTGCGGTTATTTTACT 59.250 34.615 7.40 0.00 0.00 2.24
2904 5090 8.582930 CAATTGTATGTGCGGTTATTTTACTTG 58.417 33.333 0.00 0.00 0.00 3.16
2926 5112 4.135306 GCCAATCTCATGACATGTCTGAT 58.865 43.478 25.55 18.72 0.00 2.90
3029 5215 4.536295 TCAAAGAAGAGGGGTCCTTTTT 57.464 40.909 0.00 0.00 31.76 1.94
3165 5351 5.009410 GCATTTTGGAGAGGTTATGGATGAG 59.991 44.000 0.00 0.00 0.00 2.90
3265 5451 2.104792 GCTATGCTGGTTGTATCCCTCA 59.895 50.000 0.00 0.00 0.00 3.86
3396 5583 8.389779 TGTTGTCTATGTAACATTGTGTGATT 57.610 30.769 0.00 0.00 32.30 2.57
3410 5597 4.009002 TGTGTGATTGATGTATGGTGTGG 58.991 43.478 0.00 0.00 0.00 4.17
3411 5598 3.378112 GTGTGATTGATGTATGGTGTGGG 59.622 47.826 0.00 0.00 0.00 4.61
3420 5607 3.439154 TGTATGGTGTGGGCAAATTCAT 58.561 40.909 0.00 0.00 0.00 2.57
3452 5639 8.729756 CATTTGTGTCATGTATCTGTTTTAGGA 58.270 33.333 0.00 0.00 0.00 2.94
3453 5640 8.684386 TTTGTGTCATGTATCTGTTTTAGGAA 57.316 30.769 0.00 0.00 0.00 3.36
3454 5641 7.905604 TGTGTCATGTATCTGTTTTAGGAAG 57.094 36.000 0.00 0.00 0.00 3.46
3455 5642 7.676004 TGTGTCATGTATCTGTTTTAGGAAGA 58.324 34.615 0.00 0.00 0.00 2.87
3456 5643 8.321353 TGTGTCATGTATCTGTTTTAGGAAGAT 58.679 33.333 0.00 0.00 34.99 2.40
3457 5644 8.821894 GTGTCATGTATCTGTTTTAGGAAGATC 58.178 37.037 0.00 0.00 32.92 2.75
3458 5645 8.762645 TGTCATGTATCTGTTTTAGGAAGATCT 58.237 33.333 0.00 0.00 32.92 2.75
3459 5646 9.039870 GTCATGTATCTGTTTTAGGAAGATCTG 57.960 37.037 0.00 0.00 32.92 2.90
3460 5647 7.712639 TCATGTATCTGTTTTAGGAAGATCTGC 59.287 37.037 0.00 0.00 32.92 4.26
3461 5648 6.946340 TGTATCTGTTTTAGGAAGATCTGCA 58.054 36.000 2.29 0.00 32.92 4.41
3462 5649 7.568349 TGTATCTGTTTTAGGAAGATCTGCAT 58.432 34.615 2.29 0.00 32.92 3.96
3463 5650 8.049117 TGTATCTGTTTTAGGAAGATCTGCATT 58.951 33.333 2.29 0.00 32.92 3.56
3464 5651 7.951347 ATCTGTTTTAGGAAGATCTGCATTT 57.049 32.000 2.29 0.00 0.00 2.32
3465 5652 7.765695 TCTGTTTTAGGAAGATCTGCATTTT 57.234 32.000 2.29 0.00 0.00 1.82
3466 5653 8.181904 TCTGTTTTAGGAAGATCTGCATTTTT 57.818 30.769 2.29 0.00 0.00 1.94
3490 5677 6.852858 TTTTTGCGAGGGAAAATTTTTAGG 57.147 33.333 4.63 0.00 0.00 2.69
3491 5678 5.793030 TTTGCGAGGGAAAATTTTTAGGA 57.207 34.783 4.63 0.00 0.00 2.94
3492 5679 5.793030 TTGCGAGGGAAAATTTTTAGGAA 57.207 34.783 4.63 0.85 0.00 3.36
3493 5680 5.793030 TGCGAGGGAAAATTTTTAGGAAA 57.207 34.783 4.63 0.00 0.00 3.13
3494 5681 5.778862 TGCGAGGGAAAATTTTTAGGAAAG 58.221 37.500 4.63 0.00 0.00 2.62
3495 5682 5.536916 TGCGAGGGAAAATTTTTAGGAAAGA 59.463 36.000 4.63 0.00 0.00 2.52
3496 5683 6.041069 TGCGAGGGAAAATTTTTAGGAAAGAA 59.959 34.615 4.63 0.00 0.00 2.52
3497 5684 6.926826 GCGAGGGAAAATTTTTAGGAAAGAAA 59.073 34.615 4.63 0.00 0.00 2.52
3498 5685 7.116376 GCGAGGGAAAATTTTTAGGAAAGAAAG 59.884 37.037 4.63 0.00 0.00 2.62
3499 5686 8.357402 CGAGGGAAAATTTTTAGGAAAGAAAGA 58.643 33.333 4.63 0.00 0.00 2.52
3598 5785 8.537016 TCCCTATGTATTTACTTATTGGATCGG 58.463 37.037 0.00 0.00 0.00 4.18
3695 6002 8.568794 GGGCACATTTTTCTATAGATTTAGTCC 58.431 37.037 2.58 0.00 0.00 3.85
3765 6072 4.337555 GGAGGTAGTACTTGCTAACGATCA 59.662 45.833 0.00 0.00 34.06 2.92
3770 6077 5.511088 AGTACTTGCTAACGATCAAAACG 57.489 39.130 0.00 0.00 0.00 3.60
3857 6164 3.781307 CCGGTTCGCATCCTCCCA 61.781 66.667 0.00 0.00 0.00 4.37
3878 6185 1.602377 CCACGTCCCTTCACTGTTTTC 59.398 52.381 0.00 0.00 0.00 2.29
3881 6190 3.377172 CACGTCCCTTCACTGTTTTCTTT 59.623 43.478 0.00 0.00 0.00 2.52
3887 6196 4.760204 CCCTTCACTGTTTTCTTTATCGGT 59.240 41.667 0.00 0.00 0.00 4.69
3890 6199 4.873817 TCACTGTTTTCTTTATCGGTCGA 58.126 39.130 0.00 0.00 0.00 4.20
3950 6259 1.290203 ACGCCGCTCAATCACATTAG 58.710 50.000 0.00 0.00 0.00 1.73
3953 6262 2.863740 CGCCGCTCAATCACATTAGTTA 59.136 45.455 0.00 0.00 0.00 2.24
4036 6345 4.870363 ACGTACTTTACTTTCCTTACGCA 58.130 39.130 0.00 0.00 36.61 5.24
4043 6352 7.527457 ACTTTACTTTCCTTACGCATCAAATC 58.473 34.615 0.00 0.00 0.00 2.17
4138 6447 3.678072 ACATTTGATTGTGTACCGTCTCG 59.322 43.478 0.00 0.00 0.00 4.04
4193 6503 7.536964 GTGTTTTTGAATGTTTGGAGTTTTTGG 59.463 33.333 0.00 0.00 0.00 3.28
4214 6524 1.512926 AACGCAATTCGCTTGTCTCT 58.487 45.000 0.00 0.00 43.23 3.10
4215 6525 1.512926 ACGCAATTCGCTTGTCTCTT 58.487 45.000 0.00 0.00 43.23 2.85
4216 6526 1.873591 ACGCAATTCGCTTGTCTCTTT 59.126 42.857 0.00 0.00 43.23 2.52
4239 6549 2.708051 TCTCTCTTCGACTTAGCCGAA 58.292 47.619 3.09 3.09 42.79 4.30
4259 6569 1.612463 AGAAGACAAGCTACGGACGTT 59.388 47.619 1.57 0.00 0.00 3.99
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
1 2 0.944386 ACACACGTTGAACAGATGCC 59.056 50.000 0.00 0.00 0.00 4.40
44 45 0.392729 GATGCTTGCAGCCTCTGAGT 60.393 55.000 3.66 0.00 41.51 3.41
112 113 3.699038 ACAGGAAACAAAGCAGTAAAGCA 59.301 39.130 0.00 0.00 36.85 3.91
156 157 4.874396 CAGATATGCCAAGCGACATATGAT 59.126 41.667 10.38 0.00 39.10 2.45
194 199 9.249457 CTCTGCAGTTTTGATACGATAAATCTA 57.751 33.333 14.67 0.00 0.00 1.98
196 201 7.910304 ACTCTGCAGTTTTGATACGATAAATC 58.090 34.615 14.67 0.00 0.00 2.17
197 202 7.549134 TGACTCTGCAGTTTTGATACGATAAAT 59.451 33.333 14.67 0.00 30.63 1.40
213 691 7.814642 AGAAATAATTCAAACTGACTCTGCAG 58.185 34.615 7.63 7.63 38.67 4.41
251 729 3.958147 TCTCAAGTGACACACCACTAAGA 59.042 43.478 8.59 0.00 45.82 2.10
434 914 0.107993 CTCGACAGGCACATCCATGT 60.108 55.000 0.00 0.00 42.84 3.21
468 948 4.463891 CACCTTCACCAAAATAGAGGCAAT 59.536 41.667 0.00 0.00 0.00 3.56
510 990 7.540745 CCATGTATAATTCATATGTCGACGTCA 59.459 37.037 14.83 2.18 0.00 4.35
511 991 7.753580 TCCATGTATAATTCATATGTCGACGTC 59.246 37.037 14.83 5.18 0.00 4.34
512 992 7.599171 TCCATGTATAATTCATATGTCGACGT 58.401 34.615 15.78 15.78 0.00 4.34
513 993 8.534778 CATCCATGTATAATTCATATGTCGACG 58.465 37.037 11.62 0.00 0.00 5.12
514 994 9.371136 ACATCCATGTATAATTCATATGTCGAC 57.629 33.333 9.11 9.11 39.68 4.20
515 995 9.586435 GACATCCATGTATAATTCATATGTCGA 57.414 33.333 1.90 0.00 41.95 4.20
667 1151 2.050985 GCGCACAACTGCACCTTC 60.051 61.111 0.30 0.00 44.50 3.46
670 1154 3.542629 GAAGGCGCACAACTGCACC 62.543 63.158 10.83 0.00 44.86 5.01
676 1160 2.485795 TTGGGTGAAGGCGCACAAC 61.486 57.895 10.83 8.94 42.61 3.32
681 1165 1.312371 TTGCTATTGGGTGAAGGCGC 61.312 55.000 0.00 0.00 0.00 6.53
684 1168 2.514458 ACCTTGCTATTGGGTGAAGG 57.486 50.000 0.00 0.00 39.35 3.46
689 1173 3.622455 GCAGAGTAACCTTGCTATTGGGT 60.622 47.826 0.00 0.00 34.47 4.51
902 1386 9.234827 TGTAGTACTAACAATGAAGTAGCACTA 57.765 33.333 3.61 0.00 0.00 2.74
1099 1596 8.548721 GTGTCAAATAAAAGGTCATAGATACCG 58.451 37.037 0.00 0.00 42.15 4.02
1103 1609 8.960591 CCAAGTGTCAAATAAAAGGTCATAGAT 58.039 33.333 0.00 0.00 0.00 1.98
1130 1636 3.146847 ACTGGATCTTCGGTTTTGGAAC 58.853 45.455 0.00 0.00 34.96 3.62
1438 1980 8.017373 GGTAATACTAGTTCGTTTTTGGAAACC 58.983 37.037 0.00 0.00 41.66 3.27
1440 1982 7.440856 ACGGTAATACTAGTTCGTTTTTGGAAA 59.559 33.333 0.00 0.00 0.00 3.13
1450 1992 7.512579 CGTTGAAATCACGGTAATACTAGTTCG 60.513 40.741 0.00 0.91 0.00 3.95
1510 2052 8.782137 AGCATTTAACAAATTATATCCACCCT 57.218 30.769 0.00 0.00 0.00 4.34
1543 2085 4.260866 GCAACGAGCTACAAAAGGTTACAA 60.261 41.667 0.00 0.00 41.15 2.41
1548 2090 0.865769 CGCAACGAGCTACAAAAGGT 59.134 50.000 0.00 0.00 42.61 3.50
1567 2355 6.042208 AGAGAGCCAGTATCCCAGTAATAAAC 59.958 42.308 0.00 0.00 0.00 2.01
1599 3773 7.882791 TGTTTAATTCACTTAGGATGCAGAGAA 59.117 33.333 0.00 0.00 0.00 2.87
1616 3790 9.399403 GTCTTCTCCTTTCATGTTGTTTAATTC 57.601 33.333 0.00 0.00 0.00 2.17
1701 3875 9.280174 TCTCCAAAGTACTTTTCAACGAATTAT 57.720 29.630 18.25 0.00 0.00 1.28
1755 3929 1.135286 GCACATCACTTTTAGGCTGCC 60.135 52.381 11.65 11.65 0.00 4.85
1846 4020 0.739462 TAGCTCGCCCAACACAATCG 60.739 55.000 0.00 0.00 0.00 3.34
1865 4039 4.747108 GTGTAGCGATGCAGAACATTATCT 59.253 41.667 0.00 0.00 39.84 1.98
1970 4145 0.107312 AAGGCTGCTAGGCACATCAG 60.107 55.000 11.23 0.00 44.19 2.90
2049 4224 9.453572 AGTCTAATATTTTTGCTCAAGTCATGA 57.546 29.630 0.00 0.00 36.38 3.07
2079 4258 8.405531 CAATCAAGTTGTAGTCCTTCAGAAAAA 58.594 33.333 2.11 0.00 33.01 1.94
2240 4419 1.218047 GGCAGTCGATACCAGTGCA 59.782 57.895 3.62 0.00 41.32 4.57
2282 4461 2.171659 TGGTGGCTGTTGTAACTGAAGA 59.828 45.455 5.91 0.00 0.00 2.87
2294 4473 0.623723 ATATTTCCGGTGGTGGCTGT 59.376 50.000 0.00 0.00 0.00 4.40
2314 4493 3.327757 AGGAAGGTCATTGAGTAGCACAA 59.672 43.478 0.00 0.00 0.00 3.33
2819 5003 0.593263 GTACCTCCGCGACCATTACG 60.593 60.000 8.23 0.00 0.00 3.18
2868 5054 6.073058 ACCGCACATACAATTGCAATAGATAG 60.073 38.462 13.39 6.00 38.76 2.08
2902 5088 3.692593 CAGACATGTCATGAGATTGGCAA 59.307 43.478 27.02 0.68 34.38 4.52
2904 5090 3.538591 TCAGACATGTCATGAGATTGGC 58.461 45.455 27.02 1.61 0.00 4.52
2926 5112 1.621317 TGCTTTGTCGATCACACCCTA 59.379 47.619 0.00 0.00 33.41 3.53
2988 5174 4.883759 TGATGATCTCCCTTACCTCTTCA 58.116 43.478 0.00 0.00 0.00 3.02
3029 5215 1.134699 GGACACGCATCTCCTTGATCA 60.135 52.381 0.00 0.00 32.05 2.92
3165 5351 2.281484 TCTGCCGCCCTCACAAAC 60.281 61.111 0.00 0.00 0.00 2.93
3265 5451 1.745141 GCCTCATCTTCATGCCTTCGT 60.745 52.381 0.00 0.00 0.00 3.85
3396 5583 2.593925 TTTGCCCACACCATACATCA 57.406 45.000 0.00 0.00 0.00 3.07
3467 5654 6.583562 TCCTAAAAATTTTCCCTCGCAAAAA 58.416 32.000 3.41 0.00 0.00 1.94
3468 5655 6.163135 TCCTAAAAATTTTCCCTCGCAAAA 57.837 33.333 3.41 0.00 0.00 2.44
3469 5656 5.793030 TCCTAAAAATTTTCCCTCGCAAA 57.207 34.783 3.41 0.00 0.00 3.68
3470 5657 5.793030 TTCCTAAAAATTTTCCCTCGCAA 57.207 34.783 3.41 0.00 0.00 4.85
3471 5658 5.536916 TCTTTCCTAAAAATTTTCCCTCGCA 59.463 36.000 3.41 0.00 0.00 5.10
3472 5659 6.020971 TCTTTCCTAAAAATTTTCCCTCGC 57.979 37.500 3.41 0.00 0.00 5.03
3473 5660 8.357402 TCTTTCTTTCCTAAAAATTTTCCCTCG 58.643 33.333 3.41 0.00 0.00 4.63
3482 5669 9.920133 GCAGATCTTTCTTTCTTTCCTAAAAAT 57.080 29.630 0.00 0.00 0.00 1.82
3483 5670 8.912988 TGCAGATCTTTCTTTCTTTCCTAAAAA 58.087 29.630 0.00 0.00 0.00 1.94
3484 5671 8.463930 TGCAGATCTTTCTTTCTTTCCTAAAA 57.536 30.769 0.00 0.00 0.00 1.52
3485 5672 8.641498 ATGCAGATCTTTCTTTCTTTCCTAAA 57.359 30.769 0.00 0.00 0.00 1.85
3486 5673 8.517878 CAATGCAGATCTTTCTTTCTTTCCTAA 58.482 33.333 0.00 0.00 0.00 2.69
3487 5674 7.884877 TCAATGCAGATCTTTCTTTCTTTCCTA 59.115 33.333 0.00 0.00 0.00 2.94
3488 5675 6.718454 TCAATGCAGATCTTTCTTTCTTTCCT 59.282 34.615 0.00 0.00 0.00 3.36
3489 5676 6.917533 TCAATGCAGATCTTTCTTTCTTTCC 58.082 36.000 0.00 0.00 0.00 3.13
3490 5677 7.814642 TCTCAATGCAGATCTTTCTTTCTTTC 58.185 34.615 0.00 0.00 0.00 2.62
3491 5678 7.447853 ACTCTCAATGCAGATCTTTCTTTCTTT 59.552 33.333 0.00 0.00 0.00 2.52
3492 5679 6.941436 ACTCTCAATGCAGATCTTTCTTTCTT 59.059 34.615 0.00 0.00 0.00 2.52
3493 5680 6.474630 ACTCTCAATGCAGATCTTTCTTTCT 58.525 36.000 0.00 0.00 0.00 2.52
3494 5681 6.740411 ACTCTCAATGCAGATCTTTCTTTC 57.260 37.500 0.00 0.00 0.00 2.62
3495 5682 8.627208 TTTACTCTCAATGCAGATCTTTCTTT 57.373 30.769 0.00 0.00 0.00 2.52
3496 5683 7.336427 CCTTTACTCTCAATGCAGATCTTTCTT 59.664 37.037 0.00 0.00 0.00 2.52
3497 5684 6.822676 CCTTTACTCTCAATGCAGATCTTTCT 59.177 38.462 0.00 0.00 0.00 2.52
3498 5685 6.820656 TCCTTTACTCTCAATGCAGATCTTTC 59.179 38.462 0.00 0.00 0.00 2.62
3499 5686 6.715280 TCCTTTACTCTCAATGCAGATCTTT 58.285 36.000 0.00 0.00 0.00 2.52
3534 5721 3.674955 GCGGTGGGTTCAACATTTATTCC 60.675 47.826 0.00 0.00 0.00 3.01
3707 6014 7.881775 AGTTCAAGTTTGTCCTAAGTCAAAT 57.118 32.000 0.00 0.00 34.35 2.32
3797 6104 3.555518 CAGGAAAAGAAACGCTGCTTAC 58.444 45.455 0.00 0.00 0.00 2.34
3802 6109 0.667993 TGGCAGGAAAAGAAACGCTG 59.332 50.000 0.00 0.00 0.00 5.18
3847 6154 2.125106 GACGTGGTGGGAGGATGC 60.125 66.667 0.00 0.00 0.00 3.91
3857 6164 0.544697 AAACAGTGAAGGGACGTGGT 59.455 50.000 0.00 0.00 0.00 4.16
3898 6207 0.100503 GGTCAATTATGGCGTGGTGC 59.899 55.000 0.00 0.00 45.38 5.01
3968 6277 4.020485 GGTAAGGTGGAGTTGATGTAGTGT 60.020 45.833 0.00 0.00 0.00 3.55
4027 6336 7.581213 AAATTATGGATTTGATGCGTAAGGA 57.419 32.000 1.65 0.00 38.24 3.36
4034 6343 7.644490 TGGTACGTAAATTATGGATTTGATGC 58.356 34.615 0.00 0.00 38.40 3.91
4036 6345 8.296713 GCATGGTACGTAAATTATGGATTTGAT 58.703 33.333 0.00 0.00 38.40 2.57
4043 6352 6.017523 TGTCATGCATGGTACGTAAATTATGG 60.018 38.462 25.97 0.00 0.00 2.74
4115 6424 4.860352 CGAGACGGTACACAATCAAATGTA 59.140 41.667 0.00 0.00 30.84 2.29
4148 6457 2.094894 CACAGGCATTTAAGCGACTCAG 59.905 50.000 0.00 0.00 34.64 3.35
4154 6463 4.047822 TCAAAAACACAGGCATTTAAGCG 58.952 39.130 0.00 0.00 34.64 4.68
4162 6471 3.937706 CCAAACATTCAAAAACACAGGCA 59.062 39.130 0.00 0.00 0.00 4.75
4214 6524 4.379603 CGGCTAAGTCGAAGAGAGAAGAAA 60.380 45.833 0.00 0.00 36.95 2.52
4215 6525 3.127203 CGGCTAAGTCGAAGAGAGAAGAA 59.873 47.826 0.00 0.00 36.95 2.52
4216 6526 2.678836 CGGCTAAGTCGAAGAGAGAAGA 59.321 50.000 0.00 0.00 36.95 2.87
4239 6549 1.245732 ACGTCCGTAGCTTGTCTTCT 58.754 50.000 0.00 0.00 0.00 2.85


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

AutoCloner maintained by Alex Coulton.