Multiple sequence alignment - TraesCS4D01G205700

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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 TraesCS4D01G205700 chr4D 100.000 6495 0 0 1 6495 353425462 353418968 0.000000e+00 11995.0
1 TraesCS4D01G205700 chr4D 90.722 388 21 6 6111 6495 194080734 194081109 2.700000e-138 503.0
2 TraesCS4D01G205700 chr4D 81.040 327 34 19 6111 6424 310561219 310560908 1.090000e-57 235.0
3 TraesCS4D01G205700 chr4B 93.235 4952 184 52 1 4840 436892484 436887572 0.000000e+00 7149.0
4 TraesCS4D01G205700 chr4B 95.782 1304 25 10 4790 6077 436887567 436886278 0.000000e+00 2076.0
5 TraesCS4D01G205700 chr4B 85.141 249 22 11 6221 6460 305509994 305510236 2.340000e-59 241.0
6 TraesCS4D01G205700 chr3B 93.325 4165 196 31 1974 6077 671429826 671433969 0.000000e+00 6076.0
7 TraesCS4D01G205700 chr3B 94.026 3415 134 26 2073 5426 671362974 671366379 0.000000e+00 5112.0
8 TraesCS4D01G205700 chr3B 93.126 611 31 3 5469 6077 671366381 671366982 0.000000e+00 885.0
9 TraesCS4D01G205700 chr3B 89.354 263 15 3 1717 1967 671362367 671362628 1.050000e-82 318.0
10 TraesCS4D01G205700 chr3B 85.926 270 16 5 1717 1965 671429184 671429452 1.070000e-67 268.0
11 TraesCS4D01G205700 chr4A 88.953 2435 152 62 2397 4722 111908907 111911333 0.000000e+00 2898.0
12 TraesCS4D01G205700 chr4A 86.652 1843 134 54 1 1784 111906390 111908179 0.000000e+00 1938.0
13 TraesCS4D01G205700 chr4A 93.312 927 36 12 4875 5776 111911771 111912696 0.000000e+00 1345.0
14 TraesCS4D01G205700 chr4A 93.031 287 12 2 5825 6111 111912696 111912974 4.690000e-111 412.0
15 TraesCS4D01G205700 chr4A 94.186 86 5 0 6339 6424 302652518 302652433 1.470000e-26 132.0
16 TraesCS4D01G205700 chr4A 90.323 93 5 4 6244 6334 302652659 302652569 1.140000e-22 119.0
17 TraesCS4D01G205700 chr4A 90.141 71 7 0 4742 4812 111911740 111911810 6.930000e-15 93.5
18 TraesCS4D01G205700 chr4A 91.667 48 4 0 6351 6398 302652576 302652529 4.200000e-07 67.6
19 TraesCS4D01G205700 chr4A 94.444 36 1 1 1968 2003 111908540 111908574 3.000000e-03 54.7
20 TraesCS4D01G205700 chr7D 90.909 396 21 6 6111 6495 412661361 412660970 9.650000e-143 518.0
21 TraesCS4D01G205700 chr5D 86.957 253 23 6 6111 6354 210777370 210777621 6.410000e-70 276.0
22 TraesCS4D01G205700 chr6A 91.837 196 13 2 6111 6304 602225722 602225916 2.980000e-68 270.0
23 TraesCS4D01G205700 chr6A 86.992 123 8 4 6380 6495 602226157 602226278 1.470000e-26 132.0
24 TraesCS4D01G205700 chrUn 91.250 80 5 2 6110 6187 124971274 124971353 2.480000e-19 108.0
25 TraesCS4D01G205700 chr2B 100.000 28 0 0 6204 6231 120181321 120181294 1.200000e-02 52.8
26 TraesCS4D01G205700 chr1B 96.774 31 1 0 6201 6231 113647503 113647533 1.200000e-02 52.8


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 TraesCS4D01G205700 chr4D 353418968 353425462 6494 True 11995.000000 11995 100.000000 1 6495 1 chr4D.!!$R2 6494
1 TraesCS4D01G205700 chr4B 436886278 436892484 6206 True 4612.500000 7149 94.508500 1 6077 2 chr4B.!!$R1 6076
2 TraesCS4D01G205700 chr3B 671429184 671433969 4785 False 3172.000000 6076 89.625500 1717 6077 2 chr3B.!!$F2 4360
3 TraesCS4D01G205700 chr3B 671362367 671366982 4615 False 2105.000000 5112 92.168667 1717 6077 3 chr3B.!!$F1 4360
4 TraesCS4D01G205700 chr4A 111906390 111912974 6584 False 1123.533333 2898 91.088833 1 6111 6 chr4A.!!$F1 6110
5 TraesCS4D01G205700 chr6A 602225722 602226278 556 False 201.000000 270 89.414500 6111 6495 2 chr6A.!!$F1 384

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
742 789 0.182299 GGGAAGGCAAGGATCAGGAG 59.818 60.000 0.00 0.0 0.00 3.69 F
1310 1408 0.107993 CGCACACTGTCTCCATCCAT 60.108 55.000 0.00 0.0 0.00 3.41 F
2872 3636 0.806492 GCACAAGTAGAGGCTACGGC 60.806 60.000 0.00 0.0 37.82 5.68 F
2890 3654 0.308993 GCTTCGTTCAGTTTGCAGCT 59.691 50.000 0.00 0.0 0.00 4.24 F
4048 4873 2.308570 TCATGTGTACTTTGCCCATCCT 59.691 45.455 0.00 0.0 0.00 3.24 F
5117 6346 1.200948 GATTCTTTCGCCAGCTTGCTT 59.799 47.619 8.31 0.0 0.00 3.91 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2337 3064 0.106708 AACTGAAGAGAGCCGCAACA 59.893 50.000 0.00 0.0 0.00 3.33 R
2890 3654 0.108472 CGATGTCTGCTGGCTCTTGA 60.108 55.000 0.00 0.0 0.00 3.02 R
4295 5126 2.371510 TCATCATATTCCCGGTCATGCA 59.628 45.455 0.00 0.0 0.00 3.96 R
4428 5297 4.729227 AGGGACAAACGTGAAACATTTT 57.271 36.364 0.00 0.0 35.74 1.82 R
5386 6621 0.250038 GGAGAGCTTGCACACACTCA 60.250 55.000 12.58 0.0 0.00 3.41 R
6140 7397 0.251165 ACATGGGTTTAGCGTGCCTT 60.251 50.000 0.00 0.0 0.00 4.35 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
117 118 3.995506 CTTGGGGATGTGGGGCGTC 62.996 68.421 0.00 0.00 0.00 5.19
355 356 4.324991 ACGTCTTGTTCCCCGGCC 62.325 66.667 0.00 0.00 0.00 6.13
604 621 1.750778 CGATGGCAGGCTGGTAATTTT 59.249 47.619 17.64 0.00 0.00 1.82
727 774 2.754375 GGGCGAGGAAACTGGGAA 59.246 61.111 0.00 0.00 44.43 3.97
730 777 2.041115 GCGAGGAAACTGGGAAGGC 61.041 63.158 0.00 0.00 44.43 4.35
731 778 1.374947 CGAGGAAACTGGGAAGGCA 59.625 57.895 0.00 0.00 44.43 4.75
736 783 1.272704 GGAAACTGGGAAGGCAAGGAT 60.273 52.381 0.00 0.00 0.00 3.24
737 784 2.095461 GAAACTGGGAAGGCAAGGATC 58.905 52.381 0.00 0.00 0.00 3.36
738 785 1.075601 AACTGGGAAGGCAAGGATCA 58.924 50.000 0.00 0.00 0.00 2.92
739 786 0.622665 ACTGGGAAGGCAAGGATCAG 59.377 55.000 0.00 0.00 0.00 2.90
741 788 0.549902 TGGGAAGGCAAGGATCAGGA 60.550 55.000 0.00 0.00 0.00 3.86
742 789 0.182299 GGGAAGGCAAGGATCAGGAG 59.818 60.000 0.00 0.00 0.00 3.69
743 790 0.915364 GGAAGGCAAGGATCAGGAGT 59.085 55.000 0.00 0.00 0.00 3.85
779 828 4.387343 TCGGGTCGGGTAGGGCTT 62.387 66.667 0.00 0.00 0.00 4.35
892 945 1.134640 GCAAACAAAAACCGACCCCTT 60.135 47.619 0.00 0.00 0.00 3.95
981 1050 3.868985 AATAACGCCCGGCCCGAT 61.869 61.111 17.89 9.72 0.00 4.18
1179 1260 1.411977 CAGGAGGAGCACATCTTCGAT 59.588 52.381 0.00 0.00 34.88 3.59
1188 1269 2.625737 CACATCTTCGATGCCTTCAGT 58.374 47.619 3.88 0.00 0.00 3.41
1310 1408 0.107993 CGCACACTGTCTCCATCCAT 60.108 55.000 0.00 0.00 0.00 3.41
1311 1409 1.661341 GCACACTGTCTCCATCCATC 58.339 55.000 0.00 0.00 0.00 3.51
1312 1410 1.209019 GCACACTGTCTCCATCCATCT 59.791 52.381 0.00 0.00 0.00 2.90
1313 1411 2.432146 GCACACTGTCTCCATCCATCTA 59.568 50.000 0.00 0.00 0.00 1.98
1314 1412 3.070734 GCACACTGTCTCCATCCATCTAT 59.929 47.826 0.00 0.00 0.00 1.98
1315 1413 4.798924 GCACACTGTCTCCATCCATCTATC 60.799 50.000 0.00 0.00 0.00 2.08
1316 1414 4.588106 CACACTGTCTCCATCCATCTATCT 59.412 45.833 0.00 0.00 0.00 1.98
1317 1415 4.832266 ACACTGTCTCCATCCATCTATCTC 59.168 45.833 0.00 0.00 0.00 2.75
1318 1416 5.078949 CACTGTCTCCATCCATCTATCTCT 58.921 45.833 0.00 0.00 0.00 3.10
1319 1417 5.539574 CACTGTCTCCATCCATCTATCTCTT 59.460 44.000 0.00 0.00 0.00 2.85
1320 1418 6.041865 CACTGTCTCCATCCATCTATCTCTTT 59.958 42.308 0.00 0.00 0.00 2.52
1321 1419 6.614906 ACTGTCTCCATCCATCTATCTCTTTT 59.385 38.462 0.00 0.00 0.00 2.27
1322 1420 7.127032 ACTGTCTCCATCCATCTATCTCTTTTT 59.873 37.037 0.00 0.00 0.00 1.94
1357 1455 5.310451 TCCCTTTTCTACAATGTAAGCGTT 58.690 37.500 0.00 0.00 0.00 4.84
1377 1475 4.507756 CGTTTGCTGCTGCTTATGTATCTA 59.492 41.667 17.00 0.00 40.48 1.98
1476 1589 9.009327 TCGATTGCGATTTTATTTCAAGAATTC 57.991 29.630 0.00 0.00 42.51 2.17
1626 1740 9.773328 CTTGTCATACAATTTTCATATCGTTGT 57.227 29.630 0.00 0.00 37.48 3.32
1632 1746 9.716507 ATACAATTTTCATATCGTTGTTGTAGC 57.283 29.630 0.00 0.00 35.20 3.58
1690 1805 3.185297 TGGCAACAGGGGGCATAA 58.815 55.556 0.00 0.00 46.17 1.90
1774 1889 1.629013 TCTTCAGCTTGTATGTCGCG 58.371 50.000 0.00 0.00 0.00 5.87
1793 2068 4.973051 TCGCGCGCAATTTAATTATTGATT 59.027 33.333 32.61 0.00 37.65 2.57
1797 2072 7.354719 CGCGCGCAATTTAATTATTGATTTTTG 60.355 33.333 32.61 2.35 37.65 2.44
1846 2125 3.005261 GTGTGTGTGTGTGAGAGAGAGAT 59.995 47.826 0.00 0.00 0.00 2.75
1847 2126 3.254411 TGTGTGTGTGTGAGAGAGAGATC 59.746 47.826 0.00 0.00 0.00 2.75
1848 2127 3.254411 GTGTGTGTGTGAGAGAGAGATCA 59.746 47.826 0.00 0.00 0.00 2.92
1849 2128 4.082300 GTGTGTGTGTGAGAGAGAGATCAT 60.082 45.833 0.00 0.00 0.00 2.45
1934 2256 6.407202 TCCAAAACTAGAGATTTCACTAGCC 58.593 40.000 10.72 0.00 39.67 3.93
2020 2707 2.220824 CGAATGTGTGTGTGTGTGTAGG 59.779 50.000 0.00 0.00 0.00 3.18
2023 2710 2.104170 TGTGTGTGTGTGTGTAGGAGA 58.896 47.619 0.00 0.00 0.00 3.71
2028 2724 2.158519 TGTGTGTGTGTAGGAGAGAGGA 60.159 50.000 0.00 0.00 0.00 3.71
2113 2815 4.162131 ACCTCCTTTGTGCAAGTTTTGAAT 59.838 37.500 0.00 0.00 0.00 2.57
2114 2816 4.508861 CCTCCTTTGTGCAAGTTTTGAATG 59.491 41.667 0.00 0.00 0.00 2.67
2115 2817 5.083533 TCCTTTGTGCAAGTTTTGAATGT 57.916 34.783 0.00 0.00 0.00 2.71
2116 2818 5.486526 TCCTTTGTGCAAGTTTTGAATGTT 58.513 33.333 0.00 0.00 0.00 2.71
2146 2852 8.961634 TCTAGTAAGATGCATGGTGATATACTC 58.038 37.037 2.46 0.00 0.00 2.59
2157 2863 7.392418 CATGGTGATATACTCTGATGTGGAAT 58.608 38.462 0.00 0.00 0.00 3.01
2263 2982 7.968405 CCTTTGTAGTACATTTCCTTACAATGC 59.032 37.037 3.28 0.00 35.36 3.56
2270 2989 5.232463 ACATTTCCTTACAATGCTTTGCAG 58.768 37.500 11.96 8.33 43.65 4.41
2271 2990 4.935352 TTTCCTTACAATGCTTTGCAGT 57.065 36.364 11.96 0.00 43.65 4.40
2324 3051 6.528537 TGGGAATGTGAATGAATAAGTTGG 57.471 37.500 0.00 0.00 0.00 3.77
2337 3064 7.241042 TGAATAAGTTGGCTACTACTGTCTT 57.759 36.000 1.15 0.00 35.54 3.01
2427 3183 7.807977 ACTTGTCTGCTTTTCTATTTCTTCA 57.192 32.000 0.00 0.00 0.00 3.02
2767 3531 6.919721 TGGTATTAATTGACAGAACTTTGGC 58.080 36.000 0.00 0.00 0.00 4.52
2872 3636 0.806492 GCACAAGTAGAGGCTACGGC 60.806 60.000 0.00 0.00 37.82 5.68
2875 3639 1.477295 ACAAGTAGAGGCTACGGCTTC 59.523 52.381 0.00 0.00 43.65 3.86
2890 3654 0.308993 GCTTCGTTCAGTTTGCAGCT 59.691 50.000 0.00 0.00 0.00 4.24
2944 3708 7.133133 TCTTAACAACTCTTACTTTGAGGGT 57.867 36.000 0.00 0.00 35.98 4.34
3276 4042 7.308891 GGTTTTGGGTTTGTCAGTTTCAAAAAT 60.309 33.333 0.00 0.00 36.71 1.82
3732 4526 2.632377 CGTGATGACAAGGGCATTAGT 58.368 47.619 0.00 0.00 0.00 2.24
3741 4535 6.252995 TGACAAGGGCATTAGTAAAGGATTT 58.747 36.000 0.00 0.00 43.42 2.17
3813 4607 4.283467 AGCATGCGTGGTAATCCTCTATTA 59.717 41.667 13.01 0.00 33.52 0.98
4048 4873 2.308570 TCATGTGTACTTTGCCCATCCT 59.691 45.455 0.00 0.00 0.00 3.24
4239 5065 7.737972 AGTGCAAAAACTTGGTTAAAACTTT 57.262 28.000 0.00 0.00 0.00 2.66
4295 5126 3.810743 GCAGTACAGAAACAACAGGGGAT 60.811 47.826 0.00 0.00 0.00 3.85
4491 5364 7.814587 AGGCTAACAATCTTATTGCAAAGTTTC 59.185 33.333 1.71 0.00 0.00 2.78
4501 5374 9.515020 TCTTATTGCAAAGTTTCTTTTACACTG 57.485 29.630 1.71 0.00 0.00 3.66
4502 5375 8.641499 TTATTGCAAAGTTTCTTTTACACTGG 57.359 30.769 1.71 0.00 0.00 4.00
4889 6117 3.734231 ACATCTTACGTTGTCTTGTGACG 59.266 43.478 0.00 0.00 45.70 4.35
5117 6346 1.200948 GATTCTTTCGCCAGCTTGCTT 59.799 47.619 8.31 0.00 0.00 3.91
5386 6621 6.948309 AGGATACCTTGTCTGCAAAAGTTAAT 59.052 34.615 0.00 0.00 33.73 1.40
5567 6802 4.829872 TTTTTGGGAACTAGATAGCCGA 57.170 40.909 0.00 0.00 0.00 5.54
5612 6848 6.373216 TGAGTTTTTACCGATTGGACTTATGG 59.627 38.462 5.81 0.00 39.21 2.74
6077 7334 4.357142 CCGCTGTGTTGTTACGATACTAT 58.643 43.478 1.40 0.00 0.00 2.12
6078 7335 4.440103 CCGCTGTGTTGTTACGATACTATC 59.560 45.833 1.40 0.00 0.00 2.08
6079 7336 5.271625 CGCTGTGTTGTTACGATACTATCT 58.728 41.667 1.40 0.00 0.00 1.98
6080 7337 5.171516 CGCTGTGTTGTTACGATACTATCTG 59.828 44.000 1.40 0.00 0.00 2.90
6106 7363 5.414789 TCGATTCTCCATGTGGTTTAGAA 57.585 39.130 0.00 1.94 32.39 2.10
6121 7378 7.016858 TGTGGTTTAGAAATAACTAGTGGACCT 59.983 37.037 0.00 0.00 0.00 3.85
6125 7382 9.933723 GTTTAGAAATAACTAGTGGACCTGTTA 57.066 33.333 0.00 0.00 0.00 2.41
6153 7410 4.130857 CGCAAAGGCACGCTAAAC 57.869 55.556 0.00 0.00 41.24 2.01
6194 7453 6.358974 AAAATCCATGGTTTAAGGGTTCAG 57.641 37.500 12.58 0.00 0.00 3.02
6201 7460 5.140106 TGGTTTAAGGGTTCAGGGTTTAA 57.860 39.130 0.00 0.00 0.00 1.52
6203 7462 5.962641 TGGTTTAAGGGTTCAGGGTTTAAAA 59.037 36.000 0.00 0.00 0.00 1.52
6250 7509 9.793259 TTGATAGTATAGAGCCCCATTTAAAAG 57.207 33.333 0.00 0.00 0.00 2.27
6320 7579 3.932545 AAAAGTGTCTTGTTGTGCACA 57.067 38.095 17.42 17.42 34.59 4.57
6321 7580 3.932545 AAAGTGTCTTGTTGTGCACAA 57.067 38.095 27.96 27.96 43.55 3.33
6322 7581 4.454728 AAAGTGTCTTGTTGTGCACAAT 57.545 36.364 33.16 13.56 44.72 2.71
6323 7582 3.425577 AGTGTCTTGTTGTGCACAATG 57.574 42.857 33.16 24.41 44.72 2.82
6324 7583 3.016031 AGTGTCTTGTTGTGCACAATGA 58.984 40.909 33.16 26.00 44.72 2.57
6325 7584 3.065786 AGTGTCTTGTTGTGCACAATGAG 59.934 43.478 33.16 29.25 44.72 2.90
6326 7585 3.065233 GTGTCTTGTTGTGCACAATGAGA 59.935 43.478 33.16 30.69 44.72 3.27
6327 7586 3.884693 TGTCTTGTTGTGCACAATGAGAT 59.115 39.130 32.29 0.00 44.72 2.75
6328 7587 5.049474 GTGTCTTGTTGTGCACAATGAGATA 60.049 40.000 32.29 29.15 44.72 1.98
6329 7588 5.706833 TGTCTTGTTGTGCACAATGAGATAT 59.293 36.000 32.29 0.00 44.72 1.63
6330 7589 6.878389 TGTCTTGTTGTGCACAATGAGATATA 59.122 34.615 32.29 23.89 44.72 0.86
6331 7590 7.553760 TGTCTTGTTGTGCACAATGAGATATAT 59.446 33.333 32.29 0.00 44.72 0.86
6332 7591 9.045223 GTCTTGTTGTGCACAATGAGATATATA 57.955 33.333 32.29 17.67 44.72 0.86
6333 7592 9.783081 TCTTGTTGTGCACAATGAGATATATAT 57.217 29.630 33.16 0.00 44.72 0.86
6335 7594 8.552083 TGTTGTGCACAATGAGATATATATCC 57.448 34.615 33.16 16.16 38.24 2.59
6336 7595 8.156165 TGTTGTGCACAATGAGATATATATCCA 58.844 33.333 33.16 18.41 38.24 3.41
6337 7596 8.446273 GTTGTGCACAATGAGATATATATCCAC 58.554 37.037 33.16 12.53 38.24 4.02
6338 7597 7.678837 TGTGCACAATGAGATATATATCCACA 58.321 34.615 19.28 16.93 33.17 4.17
6339 7598 8.323567 TGTGCACAATGAGATATATATCCACAT 58.676 33.333 19.28 18.33 34.29 3.21
6340 7599 9.170734 GTGCACAATGAGATATATATCCACATT 57.829 33.333 24.51 24.51 38.96 2.71
6341 7600 9.387257 TGCACAATGAGATATATATCCACATTC 57.613 33.333 25.92 20.06 37.72 2.67
6342 7601 9.610705 GCACAATGAGATATATATCCACATTCT 57.389 33.333 25.92 18.91 37.72 2.40
6359 7618 9.787435 TCCACATTCTAATTTGGTGGTATATAC 57.213 33.333 4.14 4.14 46.96 1.47
6360 7619 9.793259 CCACATTCTAATTTGGTGGTATATACT 57.207 33.333 12.54 0.00 43.08 2.12
6373 7632 9.841295 TGGTGGTATATACTCTCATTTAAAACC 57.159 33.333 12.54 4.54 0.00 3.27
6374 7633 9.841295 GGTGGTATATACTCTCATTTAAAACCA 57.159 33.333 12.54 0.00 0.00 3.67
6427 7858 6.909550 AGTAATATTTTTGTCTTGCCCACA 57.090 33.333 0.00 0.00 0.00 4.17
6444 7875 4.036852 GCCCACACTAAGAATTTAGATGCC 59.963 45.833 1.62 0.00 38.88 4.40
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
140 141 2.815647 GCCTCAACGCCTTCCTCG 60.816 66.667 0.00 0.00 0.00 4.63
706 742 2.657237 CAGTTTCCTCGCCCGTCT 59.343 61.111 0.00 0.00 0.00 4.18
727 774 0.908198 GACACTCCTGATCCTTGCCT 59.092 55.000 0.00 0.00 0.00 4.75
741 788 0.251354 TCGGCTACGAGTAGGACACT 59.749 55.000 11.69 0.00 45.59 3.55
742 789 2.772739 TCGGCTACGAGTAGGACAC 58.227 57.895 11.69 0.00 45.59 3.67
1064 1145 4.637489 CCTGATCCTCGCTCGCCG 62.637 72.222 0.00 0.00 38.61 6.46
1212 1293 4.680237 TTGTCGCGGCAGACCCTG 62.680 66.667 15.27 0.00 40.26 4.45
1335 1433 5.622770 AACGCTTACATTGTAGAAAAGGG 57.377 39.130 10.76 10.76 36.50 3.95
1357 1455 5.022282 TGTAGATACATAAGCAGCAGCAA 57.978 39.130 3.17 0.00 45.49 3.91
1377 1475 6.015434 AGCCTAACAGGAAAAATCGAAATTGT 60.015 34.615 0.00 0.00 37.67 2.71
1572 1685 2.987413 TAGCTTGTTCAAACGCCATG 57.013 45.000 0.00 0.00 0.00 3.66
1600 1713 9.773328 ACAACGATATGAAAATTGTATGACAAG 57.227 29.630 0.00 0.00 41.94 3.16
1680 1795 1.064979 CCAAACTACGTTATGCCCCCT 60.065 52.381 0.00 0.00 0.00 4.79
1690 1805 1.944709 GCTGAACAACCCAAACTACGT 59.055 47.619 0.00 0.00 0.00 3.57
1809 2085 5.301551 ACACACACACAAACACAATCCATAT 59.698 36.000 0.00 0.00 0.00 1.78
1889 2211 5.163227 TGGAAGAGATGCTAATTCATGCTCT 60.163 40.000 0.00 0.00 35.00 4.09
1934 2256 6.981722 AGTAAAACATTGTTTCCTGGCTAAG 58.018 36.000 14.80 0.00 0.00 2.18
2020 2707 0.930726 TCTCCCTCCCTTCCTCTCTC 59.069 60.000 0.00 0.00 0.00 3.20
2023 2710 0.933700 CTCTCTCCCTCCCTTCCTCT 59.066 60.000 0.00 0.00 0.00 3.69
2028 2724 2.222271 TGATCTCTCTCTCCCTCCCTT 58.778 52.381 0.00 0.00 0.00 3.95
2116 2818 9.851686 ATATCACCATGCATCTTACTAGAAAAA 57.148 29.630 0.00 0.00 33.20 1.94
2210 2929 2.417924 CGTGCAGGCAAAGTCTCTCTAT 60.418 50.000 0.00 0.00 0.00 1.98
2214 2933 0.679505 TACGTGCAGGCAAAGTCTCT 59.320 50.000 6.26 0.00 0.00 3.10
2270 2989 6.033831 CAGACATTAATTGGAAATTGTGCGAC 59.966 38.462 0.00 0.00 0.00 5.19
2271 2990 6.092092 CAGACATTAATTGGAAATTGTGCGA 58.908 36.000 0.00 0.00 0.00 5.10
2324 3051 1.993370 CCGCAACAAGACAGTAGTAGC 59.007 52.381 0.00 0.00 0.00 3.58
2337 3064 0.106708 AACTGAAGAGAGCCGCAACA 59.893 50.000 0.00 0.00 0.00 3.33
2439 3195 8.314143 ACGAAATCGGTACTAAGAAAATGAAA 57.686 30.769 7.81 0.00 44.95 2.69
2456 3212 5.108405 GGTCATTTGTTGAACAACGAAATCG 60.108 40.000 19.67 13.17 44.95 3.34
2711 3474 8.265055 AGTTAGTACTTACACATGGCAATACAT 58.735 33.333 14.05 0.00 0.00 2.29
2869 3633 0.384725 CTGCAAACTGAACGAAGCCG 60.385 55.000 0.00 0.00 42.50 5.52
2872 3636 1.599071 TGAGCTGCAAACTGAACGAAG 59.401 47.619 1.02 0.00 0.00 3.79
2875 3639 1.599071 TCTTGAGCTGCAAACTGAACG 59.401 47.619 1.02 0.00 35.74 3.95
2890 3654 0.108472 CGATGTCTGCTGGCTCTTGA 60.108 55.000 0.00 0.00 0.00 3.02
3276 4042 1.604604 CTTTCTTGGCACTTTCCGGA 58.395 50.000 0.00 0.00 0.00 5.14
3434 4203 1.172180 TTTTCTGAGCCCTTGCCACG 61.172 55.000 0.00 0.00 38.69 4.94
3741 4535 4.457603 GGTGTGCTGTAACATACAAATCCA 59.542 41.667 0.00 0.00 38.38 3.41
3813 4607 9.855021 GTATAACTATGAGTTGGTGCAAAAATT 57.145 29.630 2.09 0.00 39.11 1.82
3855 4679 9.824534 ATTTCAAACAAAACAAAACATTCTCAC 57.175 25.926 0.00 0.00 0.00 3.51
4048 4873 3.830755 GACCCTGAGGAAAGTGTGTACTA 59.169 47.826 0.00 0.00 34.48 1.82
4212 5038 8.834749 AGTTTTAACCAAGTTTTTGCACTTAA 57.165 26.923 0.00 0.00 35.10 1.85
4213 5039 8.834749 AAGTTTTAACCAAGTTTTTGCACTTA 57.165 26.923 0.00 0.00 35.10 2.24
4295 5126 2.371510 TCATCATATTCCCGGTCATGCA 59.628 45.455 0.00 0.00 0.00 3.96
4428 5297 4.729227 AGGGACAAACGTGAAACATTTT 57.271 36.364 0.00 0.00 35.74 1.82
4439 5308 7.619964 ACCACTATTTAAATAGGGACAAACG 57.380 36.000 30.74 18.58 43.57 3.60
4491 5364 5.209818 TGGTCAGAGTACCAGTGTAAAAG 57.790 43.478 0.00 0.00 44.68 2.27
4501 5374 7.923414 AATGAAAATTAGTGGTCAGAGTACC 57.077 36.000 0.00 0.00 40.19 3.34
4502 5375 9.431887 TGTAATGAAAATTAGTGGTCAGAGTAC 57.568 33.333 0.00 0.00 0.00 2.73
4692 5669 8.733458 GGAACAAGGATATACGGTTTAAAAAGT 58.267 33.333 0.00 0.00 0.00 2.66
4702 5681 8.419442 AGTAACTAAAGGAACAAGGATATACGG 58.581 37.037 0.00 0.00 0.00 4.02
4889 6117 4.889832 CAATCCATGCTAGTGAAGTTCC 57.110 45.455 0.00 0.00 0.00 3.62
5117 6346 2.532465 GATCAGGTGGAGCAGCAGCA 62.532 60.000 3.17 0.00 45.49 4.41
5172 6401 7.233553 AGGAATTACATGATATCTCTCGACCAA 59.766 37.037 0.00 0.00 0.00 3.67
5205 6434 6.493189 AAGAAGCAAAATAAGGGACCAAAA 57.507 33.333 0.00 0.00 0.00 2.44
5386 6621 0.250038 GGAGAGCTTGCACACACTCA 60.250 55.000 12.58 0.00 0.00 3.41
5879 7136 2.223971 ACGACACCAGGTCTACACTTTG 60.224 50.000 0.00 0.00 44.68 2.77
6077 7334 3.118992 CCACATGGAGAATCGAAGACAGA 60.119 47.826 0.00 0.00 36.82 3.41
6078 7335 3.193263 CCACATGGAGAATCGAAGACAG 58.807 50.000 0.00 0.00 36.82 3.51
6079 7336 2.567169 ACCACATGGAGAATCGAAGACA 59.433 45.455 4.53 0.00 37.94 3.41
6080 7337 3.252974 ACCACATGGAGAATCGAAGAC 57.747 47.619 4.53 0.00 37.94 3.01
6106 7363 4.382362 GGCGTAACAGGTCCACTAGTTATT 60.382 45.833 0.00 0.00 30.79 1.40
6140 7397 0.251165 ACATGGGTTTAGCGTGCCTT 60.251 50.000 0.00 0.00 0.00 4.35
6147 7404 1.014352 ATCGCGAACATGGGTTTAGC 58.986 50.000 15.24 0.00 37.36 3.09
6153 7410 2.627863 TTTTTCATCGCGAACATGGG 57.372 45.000 15.24 0.00 31.73 4.00
6310 7569 8.156165 TGGATATATATCTCATTGTGCACAACA 58.844 33.333 33.29 21.38 34.47 3.33
6311 7570 8.446273 GTGGATATATATCTCATTGTGCACAAC 58.554 37.037 33.29 15.69 34.47 3.32
6312 7571 8.156165 TGTGGATATATATCTCATTGTGCACAA 58.844 33.333 32.78 32.78 35.30 3.33
6313 7572 7.678837 TGTGGATATATATCTCATTGTGCACA 58.321 34.615 17.42 17.42 33.28 4.57
6314 7573 8.728337 ATGTGGATATATATCTCATTGTGCAC 57.272 34.615 19.72 10.75 33.28 4.57
6315 7574 9.387257 GAATGTGGATATATATCTCATTGTGCA 57.613 33.333 28.99 17.89 37.35 4.57
6316 7575 9.610705 AGAATGTGGATATATATCTCATTGTGC 57.389 33.333 28.99 21.47 37.35 4.57
6333 7592 9.787435 GTATATACCACCAAATTAGAATGTGGA 57.213 33.333 16.88 0.00 45.08 4.02
6347 7606 9.841295 GGTTTTAAATGAGAGTATATACCACCA 57.159 33.333 9.32 5.39 0.00 4.17
6348 7607 9.841295 TGGTTTTAAATGAGAGTATATACCACC 57.159 33.333 9.32 0.00 0.00 4.61
6356 7615 9.466497 ACATGACATGGTTTTAAATGAGAGTAT 57.534 29.630 19.39 0.00 33.60 2.12
6357 7616 8.862325 ACATGACATGGTTTTAAATGAGAGTA 57.138 30.769 19.39 0.00 33.60 2.59
6358 7617 7.765695 ACATGACATGGTTTTAAATGAGAGT 57.234 32.000 19.39 0.00 33.60 3.24
6359 7618 8.298854 TCAACATGACATGGTTTTAAATGAGAG 58.701 33.333 19.39 0.00 33.60 3.20
6360 7619 8.175925 TCAACATGACATGGTTTTAAATGAGA 57.824 30.769 19.39 0.64 33.60 3.27
6361 7620 8.815141 TTCAACATGACATGGTTTTAAATGAG 57.185 30.769 19.39 0.00 33.60 2.90
6362 7621 9.605275 TTTTCAACATGACATGGTTTTAAATGA 57.395 25.926 19.39 2.07 33.60 2.57
6368 7627 8.991026 CACATATTTTCAACATGACATGGTTTT 58.009 29.630 19.39 2.34 33.60 2.43
6369 7628 8.149647 ACACATATTTTCAACATGACATGGTTT 58.850 29.630 19.39 3.06 33.60 3.27
6370 7629 7.669427 ACACATATTTTCAACATGACATGGTT 58.331 30.769 19.39 8.56 33.60 3.67
6371 7630 7.230849 ACACATATTTTCAACATGACATGGT 57.769 32.000 19.39 10.56 33.60 3.55
6372 7631 9.454585 GATACACATATTTTCAACATGACATGG 57.545 33.333 19.39 3.03 33.60 3.66
6373 7632 9.454585 GGATACACATATTTTCAACATGACATG 57.545 33.333 14.02 14.02 0.00 3.21
6374 7633 9.412460 AGGATACACATATTTTCAACATGACAT 57.588 29.630 0.00 0.00 41.41 3.06
6375 7634 8.806429 AGGATACACATATTTTCAACATGACA 57.194 30.769 0.00 0.00 41.41 3.58
6410 7834 4.892934 TCTTAGTGTGGGCAAGACAAAAAT 59.107 37.500 0.00 0.00 0.00 1.82
6417 7841 6.121776 TCTAAATTCTTAGTGTGGGCAAGA 57.878 37.500 0.00 0.00 36.63 3.02
6420 7844 4.640201 GCATCTAAATTCTTAGTGTGGGCA 59.360 41.667 0.00 0.00 36.63 5.36
6422 7846 5.440610 AGGCATCTAAATTCTTAGTGTGGG 58.559 41.667 0.00 0.00 36.63 4.61


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

AutoCloner maintained by Alex Coulton.