Multiple sequence alignment - TraesCS4A01G355800

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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 TraesCS4A01G355800 chr4A 100.000 3652 0 0 1 3652 629479980 629476329 0 6745
1 TraesCS4A01G355800 chr5B 93.932 3016 115 28 668 3652 680601108 680604086 0 4494
2 TraesCS4A01G355800 chr5D 92.470 2696 106 41 12 2658 539021534 539024181 0 3764
3 TraesCS4A01G355800 chr5D 93.485 967 37 7 2688 3652 539024256 539025198 0 1413
4 TraesCS4A01G355800 chr2D 92.276 1696 86 19 1040 2720 68584080 68582415 0 2364
5 TraesCS4A01G355800 chr2D 92.080 1692 89 20 1044 2720 68621227 68619566 0 2340
6 TraesCS4A01G355800 chr2D 92.007 1689 99 15 1044 2720 68561918 68560254 0 2338


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 TraesCS4A01G355800 chr4A 629476329 629479980 3651 True 6745.0 6745 100.0000 1 3652 1 chr4A.!!$R1 3651
1 TraesCS4A01G355800 chr5B 680601108 680604086 2978 False 4494.0 4494 93.9320 668 3652 1 chr5B.!!$F1 2984
2 TraesCS4A01G355800 chr5D 539021534 539025198 3664 False 2588.5 3764 92.9775 12 3652 2 chr5D.!!$F1 3640
3 TraesCS4A01G355800 chr2D 68582415 68584080 1665 True 2364.0 2364 92.2760 1040 2720 1 chr2D.!!$R2 1680
4 TraesCS4A01G355800 chr2D 68619566 68621227 1661 True 2340.0 2340 92.0800 1044 2720 1 chr2D.!!$R3 1676
5 TraesCS4A01G355800 chr2D 68560254 68561918 1664 True 2338.0 2338 92.0070 1044 2720 1 chr2D.!!$R1 1676

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
968 986 0.02970 TGGCGATGGTGATACGTACG 59.970 55.000 15.01 15.01 0.00 3.67 F
1791 1818 1.21671 GGACTTCCTCCAGACGCTG 59.783 63.158 0.52 0.52 39.21 5.18 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1977 2004 1.994507 CTCCTCCCTCAGCTTGGCT 60.995 63.158 0.0 0.0 40.77 4.75 R
3261 3384 0.472471 GGTCACTGGAGTTTGTCCCA 59.528 55.000 0.0 0.0 46.31 4.37 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
20 21 4.007644 CACCGCCAGAGCCTCACA 62.008 66.667 0.00 0.00 34.57 3.58
25 26 1.670406 GCCAGAGCCTCACACACTG 60.670 63.158 0.00 0.00 0.00 3.66
37 38 1.973281 CACACTGCCACCCCATGTC 60.973 63.158 0.00 0.00 0.00 3.06
40 41 1.847506 ACTGCCACCCCATGTCTCA 60.848 57.895 0.00 0.00 0.00 3.27
41 42 1.210204 ACTGCCACCCCATGTCTCAT 61.210 55.000 0.00 0.00 0.00 2.90
60 61 3.338250 CTACCCAGGCAAGCCCCA 61.338 66.667 7.62 0.00 36.58 4.96
61 62 3.645268 CTACCCAGGCAAGCCCCAC 62.645 68.421 7.62 0.00 36.58 4.61
92 94 2.027751 GAGTCTGCCCGTATCGCC 59.972 66.667 0.00 0.00 0.00 5.54
100 102 1.953017 CCCGTATCGCCTGAGAGAG 59.047 63.158 0.00 0.00 0.00 3.20
104 106 1.003331 CGTATCGCCTGAGAGAGTCAC 60.003 57.143 0.00 0.00 0.00 3.67
111 113 2.098680 GAGAGAGTCACCGACGCG 59.901 66.667 3.53 3.53 37.43 6.01
114 116 2.962827 GAGAGTCACCGACGCGTCA 61.963 63.158 35.71 16.32 37.43 4.35
115 117 2.050714 GAGTCACCGACGCGTCAA 60.051 61.111 35.71 17.00 37.67 3.18
120 122 3.335534 ACCGACGCGTCAAACAGC 61.336 61.111 35.71 10.89 0.00 4.40
128 130 1.660575 CGTCAAACAGCCGTCTCGT 60.661 57.895 0.00 0.00 0.00 4.18
169 187 0.108186 TAGCATCGCAACCCTGACAG 60.108 55.000 0.00 0.00 0.00 3.51
170 188 1.672356 GCATCGCAACCCTGACAGT 60.672 57.895 0.93 0.00 0.00 3.55
175 193 1.367840 GCAACCCTGACAGTCGACT 59.632 57.895 13.58 13.58 0.00 4.18
208 226 2.514013 CGTCGCCGTTGACATAGGC 61.514 63.158 10.66 10.66 46.88 3.93
238 256 4.771127 GACAACACCTTCTGGCGA 57.229 55.556 0.00 0.00 36.63 5.54
240 258 0.249911 GACAACACCTTCTGGCGACT 60.250 55.000 0.00 0.00 36.63 4.18
241 259 0.532862 ACAACACCTTCTGGCGACTG 60.533 55.000 0.00 0.00 36.63 3.51
242 260 0.249868 CAACACCTTCTGGCGACTGA 60.250 55.000 0.00 0.00 36.63 3.41
244 262 1.079543 CACCTTCTGGCGACTGAGG 60.080 63.158 10.64 10.64 39.62 3.86
245 263 1.534235 ACCTTCTGGCGACTGAGGT 60.534 57.895 11.67 11.67 39.62 3.85
246 264 1.079543 CCTTCTGGCGACTGAGGTG 60.080 63.158 6.53 0.00 39.62 4.00
247 265 1.079543 CTTCTGGCGACTGAGGTGG 60.080 63.158 0.00 0.00 39.62 4.61
248 266 1.533033 TTCTGGCGACTGAGGTGGA 60.533 57.895 0.00 0.00 39.62 4.02
249 267 1.536073 TTCTGGCGACTGAGGTGGAG 61.536 60.000 0.00 0.00 39.62 3.86
250 268 1.979155 CTGGCGACTGAGGTGGAGA 60.979 63.158 0.00 0.00 0.00 3.71
251 269 1.943116 CTGGCGACTGAGGTGGAGAG 61.943 65.000 0.00 0.00 0.00 3.20
252 270 2.716017 GGCGACTGAGGTGGAGAGG 61.716 68.421 0.00 0.00 0.00 3.69
253 271 2.716017 GCGACTGAGGTGGAGAGGG 61.716 68.421 0.00 0.00 0.00 4.30
254 272 2.055042 CGACTGAGGTGGAGAGGGG 61.055 68.421 0.00 0.00 0.00 4.79
255 273 1.687493 GACTGAGGTGGAGAGGGGG 60.687 68.421 0.00 0.00 0.00 5.40
256 274 2.169590 GACTGAGGTGGAGAGGGGGA 62.170 65.000 0.00 0.00 0.00 4.81
257 275 1.382420 CTGAGGTGGAGAGGGGGAG 60.382 68.421 0.00 0.00 0.00 4.30
258 276 2.041405 GAGGTGGAGAGGGGGAGG 60.041 72.222 0.00 0.00 0.00 4.30
263 281 3.695825 GGAGAGGGGGAGGGGTGA 61.696 72.222 0.00 0.00 0.00 4.02
273 291 1.229529 GAGGGGTGAAGGAGGTGGA 60.230 63.158 0.00 0.00 0.00 4.02
283 301 0.119155 AGGAGGTGGAGGATTGTCCA 59.881 55.000 0.00 0.00 44.82 4.02
291 309 0.247736 GAGGATTGTCCAGCTGTCGT 59.752 55.000 13.81 4.52 39.61 4.34
299 317 4.641645 CAGCTGTCGTGGGGGCAA 62.642 66.667 5.25 0.00 0.00 4.52
301 319 4.947147 GCTGTCGTGGGGGCAACA 62.947 66.667 0.00 0.00 39.74 3.33
322 340 3.559655 CACGAACAAGATGAAGGTGTCAA 59.440 43.478 0.00 0.00 40.50 3.18
323 341 3.560068 ACGAACAAGATGAAGGTGTCAAC 59.440 43.478 0.00 0.00 40.50 3.18
336 354 1.993370 GTGTCAACTCGTCAGCCATAC 59.007 52.381 0.00 0.00 0.00 2.39
341 359 0.966179 ACTCGTCAGCCATACACACA 59.034 50.000 0.00 0.00 0.00 3.72
361 379 2.419673 CACATTCATGCAACGGCTAAGA 59.580 45.455 0.00 0.00 41.91 2.10
372 390 4.442706 CAACGGCTAAGATACAACCATCT 58.557 43.478 0.00 0.00 36.83 2.90
373 391 5.597806 CAACGGCTAAGATACAACCATCTA 58.402 41.667 0.00 0.00 34.08 1.98
392 410 7.993183 ACCATCTAGTTAACCATTCAACCATAG 59.007 37.037 0.88 0.00 0.00 2.23
394 412 6.354130 TCTAGTTAACCATTCAACCATAGGC 58.646 40.000 0.88 0.00 0.00 3.93
470 488 4.516365 AGGTACCTGTGAGTAGAAAACG 57.484 45.455 15.42 0.00 0.00 3.60
523 541 5.499139 AGAATAATACGTTTGTGGGCATG 57.501 39.130 0.00 0.00 0.00 4.06
524 542 4.947388 AGAATAATACGTTTGTGGGCATGT 59.053 37.500 0.00 0.00 0.00 3.21
525 543 4.893424 ATAATACGTTTGTGGGCATGTC 57.107 40.909 0.00 0.00 0.00 3.06
526 544 2.192664 ATACGTTTGTGGGCATGTCA 57.807 45.000 0.00 0.00 0.00 3.58
527 545 2.192664 TACGTTTGTGGGCATGTCAT 57.807 45.000 0.00 0.00 0.00 3.06
528 546 2.192664 ACGTTTGTGGGCATGTCATA 57.807 45.000 0.00 0.00 0.00 2.15
529 547 2.083774 ACGTTTGTGGGCATGTCATAG 58.916 47.619 0.00 0.00 0.00 2.23
530 548 2.083774 CGTTTGTGGGCATGTCATAGT 58.916 47.619 0.00 0.00 0.00 2.12
531 549 2.487762 CGTTTGTGGGCATGTCATAGTT 59.512 45.455 0.00 0.00 0.00 2.24
532 550 3.670359 CGTTTGTGGGCATGTCATAGTTG 60.670 47.826 0.00 0.00 0.00 3.16
557 575 3.010420 GTCCTTATCAAAGCCTGTCCAC 58.990 50.000 0.00 0.00 0.00 4.02
615 633 3.434319 CACATGGCCGGCACACTC 61.434 66.667 30.85 11.16 0.00 3.51
616 634 3.640407 ACATGGCCGGCACACTCT 61.640 61.111 30.85 6.23 0.00 3.24
623 641 0.320421 GCCGGCACACTCTTCTACAA 60.320 55.000 24.80 0.00 0.00 2.41
638 656 8.204836 ACTCTTCTACAAGTCACACAAATACTT 58.795 33.333 0.00 0.00 33.82 2.24
639 657 8.589335 TCTTCTACAAGTCACACAAATACTTC 57.411 34.615 0.00 0.00 31.21 3.01
641 659 8.958119 TTCTACAAGTCACACAAATACTTCTT 57.042 30.769 0.00 0.00 31.21 2.52
642 660 8.958119 TCTACAAGTCACACAAATACTTCTTT 57.042 30.769 0.00 0.00 31.21 2.52
643 661 8.826710 TCTACAAGTCACACAAATACTTCTTTG 58.173 33.333 0.00 0.00 41.02 2.77
644 662 6.795399 ACAAGTCACACAAATACTTCTTTGG 58.205 36.000 2.08 0.00 39.83 3.28
645 663 6.377146 ACAAGTCACACAAATACTTCTTTGGT 59.623 34.615 2.08 0.00 39.83 3.67
649 667 7.759433 AGTCACACAAATACTTCTTTGGTTTTG 59.241 33.333 2.08 0.00 39.83 2.44
655 673 2.039418 ACTTCTTTGGTTTTGGGAGCC 58.961 47.619 0.00 0.00 0.00 4.70
662 680 3.436577 TGGTTTTGGGAGCCGTTATAA 57.563 42.857 0.00 0.00 0.00 0.98
754 772 4.551603 GCTAAAGCAGAGCACGTAATCATG 60.552 45.833 0.00 0.00 39.84 3.07
930 948 3.260740 GCATCAGAGGACAAGAGACAAG 58.739 50.000 0.00 0.00 0.00 3.16
968 986 0.029700 TGGCGATGGTGATACGTACG 59.970 55.000 15.01 15.01 0.00 3.67
1019 1037 2.123726 GGCGGCCATCTTGGGAAT 60.124 61.111 15.62 0.00 38.19 3.01
1087 1105 3.612247 CTGTTCTGGCTCCGGGTGG 62.612 68.421 0.00 0.00 0.00 4.61
1736 1763 1.955495 ATGTACGCCATGCTGGACGA 61.955 55.000 18.14 4.80 40.96 4.20
1791 1818 1.216710 GGACTTCCTCCAGACGCTG 59.783 63.158 0.52 0.52 39.21 5.18
1977 2004 2.693762 CGAGAACCCCGACGTGCTA 61.694 63.158 0.00 0.00 0.00 3.49
2202 2229 1.372623 GTCGGTGAACCTGGACGTC 60.373 63.158 7.13 7.13 0.00 4.34
2268 2295 1.763968 TCGACCCAGACAGATTCGAT 58.236 50.000 0.00 0.00 33.95 3.59
2292 2331 3.181454 TGCGTCTCCTTTCTTTCTTCCTT 60.181 43.478 0.00 0.00 0.00 3.36
2441 2482 2.193532 TCGCCAAGCTCGAGATCTT 58.806 52.632 18.75 8.12 0.00 2.40
2489 2541 2.807045 CGAGTGAGTCGCTGTGCC 60.807 66.667 11.81 0.00 43.03 5.01
2490 2542 2.433318 GAGTGAGTCGCTGTGCCC 60.433 66.667 11.81 0.00 0.00 5.36
2491 2543 3.941657 GAGTGAGTCGCTGTGCCCC 62.942 68.421 11.81 0.00 0.00 5.80
2661 2737 2.935481 TCCCCTGAACCCCAGCTG 60.935 66.667 6.78 6.78 41.57 4.24
2662 2738 3.260100 CCCCTGAACCCCAGCTGT 61.260 66.667 13.81 0.00 41.57 4.40
2767 2888 1.210234 TGTCATCGGCATGGTCAGATT 59.790 47.619 0.00 0.00 0.00 2.40
2768 2889 2.433970 TGTCATCGGCATGGTCAGATTA 59.566 45.455 0.00 0.00 0.00 1.75
2778 2899 6.058183 GGCATGGTCAGATTATATGGTATCC 58.942 44.000 0.00 0.00 0.00 2.59
2851 2972 2.895404 AGCAAGTGAAACCAGCAATCAT 59.105 40.909 0.00 0.00 39.29 2.45
2881 3002 9.161629 TCTTAGTACAACAATTCCATACACATG 57.838 33.333 0.00 0.00 0.00 3.21
2883 3004 7.377766 AGTACAACAATTCCATACACATGAC 57.622 36.000 0.00 0.00 33.67 3.06
2947 3069 8.911247 AAGTGAACAAAACATTCTTTAGACAC 57.089 30.769 0.00 0.00 0.00 3.67
2948 3070 7.480810 AGTGAACAAAACATTCTTTAGACACC 58.519 34.615 0.00 0.00 0.00 4.16
2984 3107 4.605640 ACTTGCAATGCCATGTAAACTT 57.394 36.364 1.53 0.00 0.00 2.66
3118 3241 1.406898 GCCAAAGAAGAATAGCCAGGC 59.593 52.381 1.84 1.84 0.00 4.85
3119 3242 2.726821 CCAAAGAAGAATAGCCAGGCA 58.273 47.619 15.80 0.00 0.00 4.75
3120 3243 2.686915 CCAAAGAAGAATAGCCAGGCAG 59.313 50.000 15.80 0.00 0.00 4.85
3133 3256 1.297664 CAGGCAGAGCTCAGCATTAC 58.702 55.000 29.30 14.05 0.00 1.89
3187 3310 2.735663 CAATGATGCATCTCTAGCGACC 59.264 50.000 26.32 0.00 33.85 4.79
3261 3384 1.003718 GTAGCAAGGCCGACCAACT 60.004 57.895 0.00 0.00 39.06 3.16
3286 3409 2.368875 ACAAACTCCAGTGACCAGGTAG 59.631 50.000 0.00 0.00 0.00 3.18
3296 3419 0.741221 GACCAGGTAGCAAAGCCGAG 60.741 60.000 0.00 0.00 0.00 4.63
3601 3724 1.216990 GATGATTGTCACCTCCCCCT 58.783 55.000 0.00 0.00 0.00 4.79
3617 3740 2.298729 CCCCCTTTTTCTTGCGATGAAA 59.701 45.455 0.00 0.00 0.00 2.69
3636 3759 7.737311 CGATGAAATTTTCAAGCAAAGTTTAGC 59.263 33.333 15.34 0.00 43.95 3.09
3638 3761 7.908230 TGAAATTTTCAAGCAAAGTTTAGCTG 58.092 30.769 9.36 7.66 41.70 4.24
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 2.202987 GAGGCTCTGGCGGTGATG 60.203 66.667 7.40 0.00 39.81 3.07
1 2 2.685017 TGAGGCTCTGGCGGTGAT 60.685 61.111 16.72 0.00 39.81 3.06
2 3 3.695606 GTGAGGCTCTGGCGGTGA 61.696 66.667 16.72 0.00 39.81 4.02
3 4 4.007644 TGTGAGGCTCTGGCGGTG 62.008 66.667 16.72 0.00 39.81 4.94
5 6 4.007644 TGTGTGAGGCTCTGGCGG 62.008 66.667 16.72 0.00 39.81 6.13
6 7 2.740055 GTGTGTGAGGCTCTGGCG 60.740 66.667 16.72 0.00 39.81 5.69
7 8 1.670406 CAGTGTGTGAGGCTCTGGC 60.670 63.158 16.72 6.70 37.82 4.85
8 9 1.670406 GCAGTGTGTGAGGCTCTGG 60.670 63.158 16.72 0.00 0.00 3.86
9 10 1.670406 GGCAGTGTGTGAGGCTCTG 60.670 63.158 16.72 5.43 0.00 3.35
10 11 2.142761 TGGCAGTGTGTGAGGCTCT 61.143 57.895 16.72 0.00 0.00 4.09
20 21 2.129555 GAGACATGGGGTGGCAGTGT 62.130 60.000 0.00 0.00 38.81 3.55
25 26 1.152881 GGATGAGACATGGGGTGGC 60.153 63.158 0.00 0.00 35.41 5.01
60 61 1.129058 GACTCCCCGTTCCATATGGT 58.871 55.000 21.28 0.00 36.34 3.55
61 62 1.070758 CAGACTCCCCGTTCCATATGG 59.929 57.143 16.25 16.25 0.00 2.74
63 64 0.759346 GCAGACTCCCCGTTCCATAT 59.241 55.000 0.00 0.00 0.00 1.78
92 94 1.135731 GCGTCGGTGACTCTCTCAG 59.864 63.158 0.00 0.00 0.00 3.35
100 102 2.142418 CTGTTTGACGCGTCGGTGAC 62.142 60.000 31.88 25.08 0.00 3.67
104 106 4.072088 GGCTGTTTGACGCGTCGG 62.072 66.667 31.88 16.67 0.00 4.79
111 113 1.058404 GTACGAGACGGCTGTTTGAC 58.942 55.000 0.00 0.00 0.00 3.18
195 213 1.883084 GCTCGGCCTATGTCAACGG 60.883 63.158 0.00 0.00 0.00 4.44
238 256 2.174876 CTCCCCCTCTCCACCTCAGT 62.175 65.000 0.00 0.00 0.00 3.41
240 258 2.780693 CTCCCCCTCTCCACCTCA 59.219 66.667 0.00 0.00 0.00 3.86
241 259 2.041405 CCTCCCCCTCTCCACCTC 60.041 72.222 0.00 0.00 0.00 3.85
242 260 3.700350 CCCTCCCCCTCTCCACCT 61.700 72.222 0.00 0.00 0.00 4.00
244 262 4.026357 ACCCCTCCCCCTCTCCAC 62.026 72.222 0.00 0.00 0.00 4.02
245 263 4.024984 CACCCCTCCCCCTCTCCA 62.025 72.222 0.00 0.00 0.00 3.86
246 264 3.268647 TTCACCCCTCCCCCTCTCC 62.269 68.421 0.00 0.00 0.00 3.71
247 265 1.690985 CTTCACCCCTCCCCCTCTC 60.691 68.421 0.00 0.00 0.00 3.20
248 266 2.456840 CTTCACCCCTCCCCCTCT 59.543 66.667 0.00 0.00 0.00 3.69
249 267 2.692741 CCTTCACCCCTCCCCCTC 60.693 72.222 0.00 0.00 0.00 4.30
250 268 3.216371 TCCTTCACCCCTCCCCCT 61.216 66.667 0.00 0.00 0.00 4.79
251 269 2.692741 CTCCTTCACCCCTCCCCC 60.693 72.222 0.00 0.00 0.00 5.40
252 270 2.692741 CCTCCTTCACCCCTCCCC 60.693 72.222 0.00 0.00 0.00 4.81
253 271 2.125225 ACCTCCTTCACCCCTCCC 59.875 66.667 0.00 0.00 0.00 4.30
254 272 2.301738 CCACCTCCTTCACCCCTCC 61.302 68.421 0.00 0.00 0.00 4.30
255 273 1.229529 TCCACCTCCTTCACCCCTC 60.230 63.158 0.00 0.00 0.00 4.30
256 274 1.229658 CTCCACCTCCTTCACCCCT 60.230 63.158 0.00 0.00 0.00 4.79
257 275 2.301738 CCTCCACCTCCTTCACCCC 61.302 68.421 0.00 0.00 0.00 4.95
258 276 0.621862 ATCCTCCACCTCCTTCACCC 60.622 60.000 0.00 0.00 0.00 4.61
263 281 1.290134 GGACAATCCTCCACCTCCTT 58.710 55.000 0.00 0.00 32.53 3.36
273 291 0.036952 CACGACAGCTGGACAATCCT 60.037 55.000 19.93 0.00 37.46 3.24
283 301 4.643387 GTTGCCCCCACGACAGCT 62.643 66.667 0.00 0.00 0.00 4.24
291 309 1.826054 CTTGTTCGTGTTGCCCCCA 60.826 57.895 0.00 0.00 0.00 4.96
299 317 3.131396 GACACCTTCATCTTGTTCGTGT 58.869 45.455 0.00 0.00 35.78 4.49
301 319 3.469008 TGACACCTTCATCTTGTTCGT 57.531 42.857 0.00 0.00 0.00 3.85
322 340 0.966179 TGTGTGTATGGCTGACGAGT 59.034 50.000 0.00 0.00 0.00 4.18
323 341 1.336795 TGTGTGTGTATGGCTGACGAG 60.337 52.381 0.00 0.00 0.00 4.18
336 354 1.688793 CCGTTGCATGAATGTGTGTG 58.311 50.000 0.00 0.00 0.00 3.82
341 359 2.710377 TCTTAGCCGTTGCATGAATGT 58.290 42.857 0.00 0.00 41.13 2.71
361 379 9.174166 GTTGAATGGTTAACTAGATGGTTGTAT 57.826 33.333 5.42 0.00 0.00 2.29
372 390 6.119536 CAGCCTATGGTTGAATGGTTAACTA 58.880 40.000 5.42 0.00 35.94 2.24
373 391 4.949856 CAGCCTATGGTTGAATGGTTAACT 59.050 41.667 5.42 0.00 35.94 2.24
392 410 0.674895 ATGAAGCGTGAGAACCAGCC 60.675 55.000 0.00 0.00 0.00 4.85
394 412 2.084610 TGATGAAGCGTGAGAACCAG 57.915 50.000 0.00 0.00 0.00 4.00
531 549 5.163301 GGACAGGCTTTGATAAGGACTATCA 60.163 44.000 0.00 0.00 43.88 2.15
532 550 5.163301 TGGACAGGCTTTGATAAGGACTATC 60.163 44.000 0.00 0.00 37.51 2.08
557 575 1.498865 AACTTGTGCCACGAAGCTCG 61.499 55.000 6.86 4.36 46.93 5.03
614 632 8.421784 AGAAGTATTTGTGTGACTTGTAGAAGA 58.578 33.333 6.63 0.00 33.61 2.87
615 633 8.594881 AGAAGTATTTGTGTGACTTGTAGAAG 57.405 34.615 0.00 0.00 33.61 2.85
616 634 8.958119 AAGAAGTATTTGTGTGACTTGTAGAA 57.042 30.769 0.00 0.00 33.61 2.10
623 641 7.404671 AAACCAAAGAAGTATTTGTGTGACT 57.595 32.000 0.00 0.00 38.28 3.41
638 656 0.106419 ACGGCTCCCAAAACCAAAGA 60.106 50.000 0.00 0.00 0.00 2.52
639 657 0.750249 AACGGCTCCCAAAACCAAAG 59.250 50.000 0.00 0.00 0.00 2.77
641 659 2.296073 ATAACGGCTCCCAAAACCAA 57.704 45.000 0.00 0.00 0.00 3.67
642 660 3.083293 GTTATAACGGCTCCCAAAACCA 58.917 45.455 0.00 0.00 0.00 3.67
643 661 3.083293 TGTTATAACGGCTCCCAAAACC 58.917 45.455 10.92 0.00 0.00 3.27
644 662 4.216902 AGTTGTTATAACGGCTCCCAAAAC 59.783 41.667 10.92 6.39 0.00 2.43
645 663 4.400120 AGTTGTTATAACGGCTCCCAAAA 58.600 39.130 10.92 0.00 0.00 2.44
649 667 3.870274 AGAAGTTGTTATAACGGCTCCC 58.130 45.455 10.92 7.11 0.00 4.30
773 791 8.950007 TGGTTGTCCTTTTTCCTTTAGATTAT 57.050 30.769 0.00 0.00 34.23 1.28
968 986 2.345876 GAGAGAAAGCTTGACAGAGCC 58.654 52.381 0.00 0.00 43.74 4.70
1296 1314 1.684386 CGGAGAGCAGGATCTTGGCT 61.684 60.000 6.99 6.49 41.35 4.75
1977 2004 1.994507 CTCCTCCCTCAGCTTGGCT 60.995 63.158 0.00 0.00 40.77 4.75
2268 2295 2.910688 AGAAAGAAAGGAGACGCACA 57.089 45.000 0.00 0.00 0.00 4.57
2412 2453 4.161295 TTGGCGAGGCTCATCCCG 62.161 66.667 15.95 1.27 34.51 5.14
2441 2482 3.998672 GGTGGTGGGCGAAGACGA 61.999 66.667 0.00 0.00 42.66 4.20
2661 2737 2.435059 GCTGGGGTCAGAGCGAAC 60.435 66.667 0.00 0.00 43.49 3.95
2662 2738 2.604686 AGCTGGGGTCAGAGCGAA 60.605 61.111 0.00 0.00 43.49 4.70
2767 2888 6.562228 ACAAGTAGCCTCAGGATACCATATA 58.438 40.000 15.86 0.00 44.67 0.86
2768 2889 5.407049 ACAAGTAGCCTCAGGATACCATAT 58.593 41.667 15.86 0.00 44.67 1.78
2778 2899 5.986135 GTCCATACAATACAAGTAGCCTCAG 59.014 44.000 0.00 0.00 0.00 3.35
2874 2995 4.270245 TGAGCTGTTCATGTCATGTGTA 57.730 40.909 12.54 0.08 0.00 2.90
2946 3068 4.081420 TGCAAGTTTTACATGTTTGGTGGT 60.081 37.500 2.30 0.00 0.00 4.16
2947 3069 4.437239 TGCAAGTTTTACATGTTTGGTGG 58.563 39.130 2.30 0.00 0.00 4.61
2948 3070 6.420588 CATTGCAAGTTTTACATGTTTGGTG 58.579 36.000 2.30 0.00 0.00 4.17
3119 3242 3.493002 GCATCAGAGTAATGCTGAGCTCT 60.493 47.826 16.19 0.00 44.75 4.09
3120 3243 2.801679 GCATCAGAGTAATGCTGAGCTC 59.198 50.000 6.82 6.82 44.75 4.09
3133 3256 2.798804 CGAGAGATGCGCATCAGAG 58.201 57.895 42.35 28.75 40.22 3.35
3187 3310 1.771073 TTCGTTGAGCTGTGCCGTTG 61.771 55.000 0.00 0.00 0.00 4.10
3261 3384 0.472471 GGTCACTGGAGTTTGTCCCA 59.528 55.000 0.00 0.00 46.31 4.37
3286 3409 2.429739 GCTGTTGCTCGGCTTTGC 60.430 61.111 6.14 0.00 44.39 3.68
3296 3419 4.283403 TGCCTTTGCCGCTGTTGC 62.283 61.111 0.00 0.00 36.33 4.17
3347 3470 0.645496 TAGCCATTGGAGGTCCCCTA 59.355 55.000 6.95 0.00 31.76 3.53
3519 3642 4.816385 TGCTCTGTTTTCGAGATTGAGTTT 59.184 37.500 0.00 0.00 0.00 2.66
3531 3654 7.752686 GGTAATCTCTTTCAATGCTCTGTTTTC 59.247 37.037 0.00 0.00 0.00 2.29
3617 3740 5.985530 GGTCAGCTAAACTTTGCTTGAAAAT 59.014 36.000 0.00 0.00 37.15 1.82


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

AutoCloner maintained by Alex Coulton.