Multiple sequence alignment - TraesCS3D01G217400

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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 TraesCS3D01G217400 chr3D 100.000 3229 0 0 1 3229 295146139 295142911 0.000000e+00 5963
1 TraesCS3D01G217400 chr3A 92.801 1792 69 19 4 1784 392804944 392803202 0.000000e+00 2540
2 TraesCS3D01G217400 chr3A 95.899 1463 46 6 1769 3229 392803059 392801609 0.000000e+00 2357
3 TraesCS3D01G217400 chr3B 92.529 1111 40 9 671 1769 389264809 389263730 0.000000e+00 1552
4 TraesCS3D01G217400 chr3B 95.254 885 26 7 1769 2651 389263610 389262740 0.000000e+00 1387
5 TraesCS3D01G217400 chr3B 97.826 598 13 0 2630 3227 389262692 389262095 0.000000e+00 1033
6 TraesCS3D01G217400 chr3B 88.804 393 38 3 3 390 389290488 389290097 8.100000e-131 477
7 TraesCS3D01G217400 chr3B 94.096 271 15 1 383 653 389266408 389266139 8.340000e-111 411


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 TraesCS3D01G217400 chr3D 295142911 295146139 3228 True 5963.00 5963 100.00000 1 3229 1 chr3D.!!$R1 3228
1 TraesCS3D01G217400 chr3A 392801609 392804944 3335 True 2448.50 2540 94.35000 4 3229 2 chr3A.!!$R1 3225
2 TraesCS3D01G217400 chr3B 389262095 389266408 4313 True 1095.75 1552 94.92625 383 3227 4 chr3B.!!$R2 2844

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
54 56 0.322098 CCCGCCAGGTGTTGTTATGA 60.322 55.0 0.0 0.0 35.12 2.15 F
649 651 0.329261 TGGGGCAACTCTTCTGATGG 59.671 55.0 0.0 0.0 38.64 3.51 F
650 652 0.620556 GGGGCAACTCTTCTGATGGA 59.379 55.0 0.0 0.0 0.00 3.41 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1825 3389 0.469144 GGGGGCAAGGTCAGTTTTCA 60.469 55.000 0.00 0.0 0.00 2.69 R
1832 3396 1.076549 GTTCATGGGGGCAAGGTCA 59.923 57.895 0.00 0.0 0.00 4.02 R
2393 3958 2.825532 TCGCATATGCTATCCTGCAGTA 59.174 45.455 24.56 0.0 46.71 2.74 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
29 30 4.588951 TCTGGCTATATCGGTGTCTTCATT 59.411 41.667 0.00 0.00 0.00 2.57
32 33 4.865365 GGCTATATCGGTGTCTTCATTAGC 59.135 45.833 0.00 0.00 0.00 3.09
54 56 0.322098 CCCGCCAGGTGTTGTTATGA 60.322 55.000 0.00 0.00 35.12 2.15
78 80 1.616374 ACCTTTTAAACCCATGGTGCG 59.384 47.619 11.73 0.00 35.34 5.34
96 98 2.236146 TGCGTTGGATTCCACTATCTGT 59.764 45.455 4.45 0.00 30.78 3.41
105 107 3.543680 TCCACTATCTGTAGGCTTTGC 57.456 47.619 0.00 0.00 31.96 3.68
107 109 3.263170 TCCACTATCTGTAGGCTTTGCAA 59.737 43.478 0.00 0.00 31.96 4.08
108 110 4.009675 CCACTATCTGTAGGCTTTGCAAA 58.990 43.478 12.14 12.14 31.96 3.68
109 111 4.458989 CCACTATCTGTAGGCTTTGCAAAA 59.541 41.667 13.84 0.00 31.96 2.44
110 112 5.048083 CCACTATCTGTAGGCTTTGCAAAAA 60.048 40.000 13.84 0.00 31.96 1.94
111 113 6.350445 CCACTATCTGTAGGCTTTGCAAAAAT 60.350 38.462 13.84 4.62 31.96 1.82
112 114 7.092716 CACTATCTGTAGGCTTTGCAAAAATT 58.907 34.615 13.84 3.96 31.96 1.82
126 128 5.160641 TGCAAAAATTAAAGTCGATGGAGC 58.839 37.500 0.00 0.00 0.00 4.70
163 165 8.418662 ACTACCAACATGAGATTTATTAGCGTA 58.581 33.333 0.00 0.00 0.00 4.42
169 171 6.201044 ACATGAGATTTATTAGCGTAGTGTGC 59.799 38.462 0.00 0.00 0.00 4.57
218 220 5.049129 AGTTCTTCGGCAATTTCTTTCTCTG 60.049 40.000 0.00 0.00 0.00 3.35
235 237 5.085275 TCTCTGGTATGATTGATCCTCCT 57.915 43.478 0.00 0.00 0.00 3.69
242 244 6.214208 TGGTATGATTGATCCTCCTATCCTTG 59.786 42.308 0.00 0.00 0.00 3.61
262 264 4.904466 GCATTGGCTTGCCAAGAG 57.096 55.556 27.60 22.89 36.60 2.85
279 281 1.414527 GAGGCGCTCGTTGTAGCTTC 61.415 60.000 7.64 0.00 40.49 3.86
289 291 6.198403 CGCTCGTTGTAGCTTCAGATTTAATA 59.802 38.462 0.00 0.00 40.49 0.98
294 296 7.254455 CGTTGTAGCTTCAGATTTAATACAGGG 60.254 40.741 0.00 0.00 0.00 4.45
297 299 5.128919 AGCTTCAGATTTAATACAGGGCAG 58.871 41.667 0.00 0.00 0.00 4.85
298 300 4.276926 GCTTCAGATTTAATACAGGGCAGG 59.723 45.833 0.00 0.00 0.00 4.85
300 302 5.912149 TCAGATTTAATACAGGGCAGGAT 57.088 39.130 0.00 0.00 0.00 3.24
301 303 7.387265 TTCAGATTTAATACAGGGCAGGATA 57.613 36.000 0.00 0.00 0.00 2.59
302 304 7.387265 TCAGATTTAATACAGGGCAGGATAA 57.613 36.000 0.00 0.00 0.00 1.75
303 305 7.988937 TCAGATTTAATACAGGGCAGGATAAT 58.011 34.615 0.00 0.00 0.00 1.28
304 306 8.103305 TCAGATTTAATACAGGGCAGGATAATC 58.897 37.037 0.00 0.00 0.00 1.75
305 307 7.884877 CAGATTTAATACAGGGCAGGATAATCA 59.115 37.037 0.00 0.00 0.00 2.57
306 308 7.885399 AGATTTAATACAGGGCAGGATAATCAC 59.115 37.037 0.00 0.00 0.00 3.06
307 309 6.508030 TTAATACAGGGCAGGATAATCACA 57.492 37.500 0.00 0.00 0.00 3.58
308 310 4.630644 ATACAGGGCAGGATAATCACAG 57.369 45.455 0.00 0.00 0.00 3.66
309 311 1.133976 ACAGGGCAGGATAATCACAGC 60.134 52.381 0.00 0.00 0.00 4.40
310 312 0.475906 AGGGCAGGATAATCACAGCC 59.524 55.000 0.00 0.00 41.29 4.85
311 313 0.886490 GGGCAGGATAATCACAGCCG 60.886 60.000 0.00 0.00 42.89 5.52
314 316 1.069765 AGGATAATCACAGCCGCCG 59.930 57.895 0.00 0.00 0.00 6.46
332 334 1.263217 CCGTATTGCAAGGGCGTTATC 59.737 52.381 4.94 0.00 45.35 1.75
338 340 1.202639 TGCAAGGGCGTTATCGATGAT 60.203 47.619 8.54 0.00 45.35 2.45
354 356 3.627123 CGATGATATCAACAAGGGCACAA 59.373 43.478 9.99 0.00 0.00 3.33
358 360 1.915141 ATCAACAAGGGCACAAGAGG 58.085 50.000 0.00 0.00 0.00 3.69
368 370 1.673168 GCACAAGAGGAAGCTATGGG 58.327 55.000 0.00 0.00 0.00 4.00
379 381 5.738909 AGGAAGCTATGGGAATATCATTCG 58.261 41.667 0.00 0.00 0.00 3.34
413 415 4.781570 GCCTCTAATCTTCGGGCC 57.218 61.111 0.00 0.00 37.12 5.80
432 434 4.526970 GGCCTGTATCTTCATCCTTGAAA 58.473 43.478 0.00 0.00 41.22 2.69
492 494 7.527084 AAGCATGATCTACGTCTTTCTAAAC 57.473 36.000 0.00 0.00 0.00 2.01
502 504 0.515564 CTTTCTAAACGGTGCCACGG 59.484 55.000 0.27 0.27 38.39 4.94
631 633 8.576442 AGGTGTAAACTTGGACAAAATTCTATG 58.424 33.333 0.00 0.00 0.00 2.23
636 638 3.464720 TGGACAAAATTCTATGGGGCA 57.535 42.857 0.00 0.00 0.00 5.36
637 639 3.784178 TGGACAAAATTCTATGGGGCAA 58.216 40.909 0.00 0.00 0.00 4.52
638 640 3.513515 TGGACAAAATTCTATGGGGCAAC 59.486 43.478 0.00 0.00 0.00 4.17
639 641 3.769300 GGACAAAATTCTATGGGGCAACT 59.231 43.478 0.00 0.00 0.00 3.16
640 642 4.142160 GGACAAAATTCTATGGGGCAACTC 60.142 45.833 0.00 0.00 37.88 3.01
641 643 4.677182 ACAAAATTCTATGGGGCAACTCT 58.323 39.130 0.00 0.00 38.64 3.24
642 644 5.086621 ACAAAATTCTATGGGGCAACTCTT 58.913 37.500 0.00 0.00 38.64 2.85
643 645 5.185828 ACAAAATTCTATGGGGCAACTCTTC 59.814 40.000 0.00 0.00 38.64 2.87
644 646 4.870021 AATTCTATGGGGCAACTCTTCT 57.130 40.909 0.00 0.00 38.64 2.85
645 647 3.634397 TTCTATGGGGCAACTCTTCTG 57.366 47.619 0.00 0.00 38.64 3.02
646 648 2.832838 TCTATGGGGCAACTCTTCTGA 58.167 47.619 0.00 0.00 38.64 3.27
647 649 3.387962 TCTATGGGGCAACTCTTCTGAT 58.612 45.455 0.00 0.00 38.64 2.90
648 650 2.431954 ATGGGGCAACTCTTCTGATG 57.568 50.000 0.00 0.00 38.64 3.07
649 651 0.329261 TGGGGCAACTCTTCTGATGG 59.671 55.000 0.00 0.00 38.64 3.51
650 652 0.620556 GGGGCAACTCTTCTGATGGA 59.379 55.000 0.00 0.00 0.00 3.41
651 653 1.004745 GGGGCAACTCTTCTGATGGAA 59.995 52.381 0.00 0.00 0.00 3.53
652 654 2.357569 GGGGCAACTCTTCTGATGGAAT 60.358 50.000 0.00 0.00 33.01 3.01
653 655 3.117888 GGGGCAACTCTTCTGATGGAATA 60.118 47.826 0.00 0.00 33.01 1.75
695 2027 7.373778 ACTAATAAACTTTTCGATGGACCAC 57.626 36.000 0.00 0.00 0.00 4.16
701 2033 4.070009 ACTTTTCGATGGACCACCTTTAC 58.930 43.478 0.00 0.00 37.04 2.01
715 2047 3.813166 CACCTTTACCGTGATGACAAAGT 59.187 43.478 0.00 0.00 32.77 2.66
760 2092 3.312828 GCAGCCAATCGAGTATAGACAG 58.687 50.000 0.00 0.00 0.00 3.51
816 2148 4.963276 TGGAAACACAAACACAAGAGAG 57.037 40.909 0.00 0.00 33.40 3.20
817 2149 4.584874 TGGAAACACAAACACAAGAGAGA 58.415 39.130 0.00 0.00 33.40 3.10
893 2231 3.747193 CTGTGGCTGCTATAAAAACACG 58.253 45.455 0.00 0.00 0.00 4.49
911 2249 3.125573 CCGAGAGTCCGAGACGCA 61.126 66.667 9.60 0.00 37.67 5.24
953 2291 1.432251 CACGCCGGAGTCTCGTATT 59.568 57.895 8.30 0.00 34.81 1.89
968 2306 1.435577 GTATTGCAAACGTCGGAGGT 58.564 50.000 1.71 0.00 0.00 3.85
1228 2574 2.759973 CGGCTGAGTGAGGCCCTA 60.760 66.667 0.00 0.00 44.66 3.53
1311 2663 4.074526 GAGTGCCTCAGGAGCGCA 62.075 66.667 11.47 7.93 43.21 6.09
1456 2810 2.047560 GGTGGTAGGTGTGCGTCC 60.048 66.667 0.00 0.00 0.00 4.79
1598 2952 0.641601 AAGGGAGGCTCAGGATCTCT 59.358 55.000 17.69 0.00 0.00 3.10
1764 3118 9.736023 AAAAGAAACAATTTATGTCACTCAGTC 57.264 29.630 0.00 0.00 42.99 3.51
1780 3343 8.753497 TCACTCAGTCTATATAGTGATGTGTT 57.247 34.615 18.95 7.26 42.46 3.32
1805 3369 6.048732 TGAAACCTCAGTGCATTACTCATA 57.951 37.500 0.00 0.00 37.60 2.15
1818 3382 6.658816 TGCATTACTCATATGAAAAGTGGTGT 59.341 34.615 6.90 1.31 0.00 4.16
1819 3383 6.968904 GCATTACTCATATGAAAAGTGGTGTG 59.031 38.462 6.90 5.45 0.00 3.82
1820 3384 6.494893 TTACTCATATGAAAAGTGGTGTGC 57.505 37.500 6.90 0.00 0.00 4.57
1821 3385 4.397420 ACTCATATGAAAAGTGGTGTGCA 58.603 39.130 6.90 0.00 0.00 4.57
1822 3386 4.216257 ACTCATATGAAAAGTGGTGTGCAC 59.784 41.667 10.75 10.75 0.00 4.57
1823 3387 4.140536 TCATATGAAAAGTGGTGTGCACA 58.859 39.130 17.42 17.42 0.00 4.57
1824 3388 4.582240 TCATATGAAAAGTGGTGTGCACAA 59.418 37.500 23.59 3.57 0.00 3.33
1825 3389 5.243507 TCATATGAAAAGTGGTGTGCACAAT 59.756 36.000 23.59 10.57 0.00 2.71
1826 3390 3.162202 TGAAAAGTGGTGTGCACAATG 57.838 42.857 23.59 0.00 0.00 2.82
1832 3396 2.760092 AGTGGTGTGCACAATGAAAACT 59.240 40.909 23.59 15.02 0.00 2.66
1854 3419 1.645919 ACCTTGCCCCCATGAACTAAT 59.354 47.619 0.00 0.00 0.00 1.73
1856 3421 3.106827 CCTTGCCCCCATGAACTAATTT 58.893 45.455 0.00 0.00 0.00 1.82
1908 3473 1.827969 AGAGGATTCAAGGGACAGACG 59.172 52.381 0.00 0.00 0.00 4.18
2141 3706 0.883153 TGATCACCTTGCATGCACAC 59.117 50.000 22.58 7.34 0.00 3.82
2166 3731 3.772387 TCCCAATTGGACTACAAATGCA 58.228 40.909 26.60 0.00 43.46 3.96
2192 3757 3.126831 GAGCAATCCAGTATCAACGGAG 58.873 50.000 0.00 0.00 33.72 4.63
2290 3855 1.811965 TGACCATTTTCACATGCCTCG 59.188 47.619 0.00 0.00 0.00 4.63
2393 3958 2.487934 GCACATTGCGTCTCCTATCAT 58.512 47.619 0.00 0.00 31.71 2.45
2474 4039 2.026905 GCAAGTTCAGGGACCCAACAA 61.027 52.381 14.60 0.00 0.00 2.83
2684 4317 0.897401 TGGTGGCATTTCGGATTGCA 60.897 50.000 12.39 0.00 40.66 4.08
2708 4341 3.602390 ACAGAATGCACGTTGTAACAC 57.398 42.857 0.00 0.00 42.53 3.32
2935 4568 2.582728 ATCTTTCTGCTGCTCTCTCG 57.417 50.000 0.00 0.00 0.00 4.04
2944 4577 0.746063 CTGCTCTCTCGGCAATCTCT 59.254 55.000 0.00 0.00 39.30 3.10
2998 4631 4.420206 TCGTCCTCCATATGGATGAATCT 58.580 43.478 25.84 0.00 44.05 2.40
3018 4651 3.911894 TCTGGGATCAATGGCATCTGATA 59.088 43.478 18.60 8.31 32.40 2.15
3097 4730 0.250038 CATAGTGCTCCATCGTGGGG 60.250 60.000 4.52 2.37 42.32 4.96
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 4.152647 ACACCGATATAGCCAGATCAGAA 58.847 43.478 0.00 0.00 0.00 3.02
1 2 3.759086 GACACCGATATAGCCAGATCAGA 59.241 47.826 0.00 0.00 0.00 3.27
2 3 3.761218 AGACACCGATATAGCCAGATCAG 59.239 47.826 0.00 0.00 0.00 2.90
37 38 2.355197 TCATCATAACAACACCTGGCG 58.645 47.619 0.00 0.00 0.00 5.69
54 56 4.262851 GCACCATGGGTTTAAAAGGTTCAT 60.263 41.667 18.09 0.00 31.02 2.57
78 80 4.101741 AGCCTACAGATAGTGGAATCCAAC 59.898 45.833 2.31 0.00 34.18 3.77
96 98 6.740110 TCGACTTTAATTTTTGCAAAGCCTA 58.260 32.000 12.41 2.36 33.50 3.93
105 107 6.306356 CACTGCTCCATCGACTTTAATTTTTG 59.694 38.462 0.00 0.00 0.00 2.44
107 109 5.106157 CCACTGCTCCATCGACTTTAATTTT 60.106 40.000 0.00 0.00 0.00 1.82
108 110 4.396166 CCACTGCTCCATCGACTTTAATTT 59.604 41.667 0.00 0.00 0.00 1.82
109 111 3.941483 CCACTGCTCCATCGACTTTAATT 59.059 43.478 0.00 0.00 0.00 1.40
110 112 3.535561 CCACTGCTCCATCGACTTTAAT 58.464 45.455 0.00 0.00 0.00 1.40
111 113 2.935238 GCCACTGCTCCATCGACTTTAA 60.935 50.000 0.00 0.00 33.53 1.52
112 114 1.405526 GCCACTGCTCCATCGACTTTA 60.406 52.381 0.00 0.00 33.53 1.85
163 165 4.042187 ACTCCCTCTAAATTTCTGCACACT 59.958 41.667 0.00 0.00 0.00 3.55
169 171 7.786030 TGAGATACACTCCCTCTAAATTTCTG 58.214 38.462 0.00 0.00 44.34 3.02
218 220 6.441924 TCAAGGATAGGAGGATCAATCATACC 59.558 42.308 0.00 0.00 36.25 2.73
258 260 1.446272 GCTACAACGAGCGCCTCTT 60.446 57.895 2.29 0.00 31.57 2.85
270 272 6.542370 GCCCTGTATTAAATCTGAAGCTACAA 59.458 38.462 0.00 0.00 0.00 2.41
272 274 6.055588 TGCCCTGTATTAAATCTGAAGCTAC 58.944 40.000 0.00 0.00 0.00 3.58
279 281 7.884877 TGATTATCCTGCCCTGTATTAAATCTG 59.115 37.037 0.00 0.00 0.00 2.90
289 291 1.133976 GCTGTGATTATCCTGCCCTGT 60.134 52.381 0.00 0.00 0.00 4.00
294 296 1.510480 GGCGGCTGTGATTATCCTGC 61.510 60.000 0.00 0.00 0.00 4.85
297 299 0.032952 TACGGCGGCTGTGATTATCC 59.967 55.000 24.15 0.00 0.00 2.59
298 300 2.080286 ATACGGCGGCTGTGATTATC 57.920 50.000 24.15 0.00 0.00 1.75
300 302 1.577468 CAATACGGCGGCTGTGATTA 58.423 50.000 24.15 4.56 0.00 1.75
301 303 1.714899 GCAATACGGCGGCTGTGATT 61.715 55.000 24.15 15.43 0.00 2.57
302 304 2.180204 GCAATACGGCGGCTGTGAT 61.180 57.895 24.15 9.90 0.00 3.06
303 305 2.817834 GCAATACGGCGGCTGTGA 60.818 61.111 24.15 8.89 0.00 3.58
304 306 2.582202 CTTGCAATACGGCGGCTGTG 62.582 60.000 24.15 9.03 36.28 3.66
305 307 2.359354 TTGCAATACGGCGGCTGT 60.359 55.556 19.67 19.67 36.28 4.40
306 308 2.404789 CTTGCAATACGGCGGCTG 59.595 61.111 13.24 7.39 36.28 4.85
307 309 2.824041 CCTTGCAATACGGCGGCT 60.824 61.111 13.24 0.00 36.28 5.52
308 310 3.887868 CCCTTGCAATACGGCGGC 61.888 66.667 13.24 5.21 36.28 6.53
309 311 3.887868 GCCCTTGCAATACGGCGG 61.888 66.667 13.24 5.09 37.47 6.13
311 313 1.370587 TAACGCCCTTGCAATACGGC 61.371 55.000 17.96 17.96 37.32 5.68
314 316 2.206750 TCGATAACGCCCTTGCAATAC 58.793 47.619 0.00 0.00 39.58 1.89
332 334 3.205338 TGTGCCCTTGTTGATATCATCG 58.795 45.455 6.17 0.00 0.00 3.84
338 340 2.642311 TCCTCTTGTGCCCTTGTTGATA 59.358 45.455 0.00 0.00 0.00 2.15
354 356 6.351711 CGAATGATATTCCCATAGCTTCCTCT 60.352 42.308 0.00 0.00 0.00 3.69
358 360 4.033358 CGCGAATGATATTCCCATAGCTTC 59.967 45.833 0.00 0.00 0.00 3.86
368 370 6.074088 ACAAACTGATCTCGCGAATGATATTC 60.074 38.462 11.33 0.36 0.00 1.75
379 381 1.696832 GGCCGACAAACTGATCTCGC 61.697 60.000 0.00 0.00 0.00 5.03
432 434 4.103153 TGCCTTGATATCGGATTTTCTCCT 59.897 41.667 0.00 0.00 42.47 3.69
631 633 0.620556 TCCATCAGAAGAGTTGCCCC 59.379 55.000 0.00 0.00 0.00 5.80
636 638 8.601546 AGAAGAGTTTATTCCATCAGAAGAGTT 58.398 33.333 0.00 0.00 38.07 3.01
637 639 8.040132 CAGAAGAGTTTATTCCATCAGAAGAGT 58.960 37.037 0.00 0.00 38.07 3.24
638 640 8.256605 TCAGAAGAGTTTATTCCATCAGAAGAG 58.743 37.037 0.00 0.00 38.07 2.85
639 641 8.138928 TCAGAAGAGTTTATTCCATCAGAAGA 57.861 34.615 0.00 0.00 38.07 2.87
640 642 8.828644 CATCAGAAGAGTTTATTCCATCAGAAG 58.171 37.037 0.00 0.00 38.07 2.85
641 643 7.772292 CCATCAGAAGAGTTTATTCCATCAGAA 59.228 37.037 0.00 0.00 39.32 3.02
642 644 7.126268 TCCATCAGAAGAGTTTATTCCATCAGA 59.874 37.037 0.00 0.00 0.00 3.27
643 645 7.278135 TCCATCAGAAGAGTTTATTCCATCAG 58.722 38.462 0.00 0.00 0.00 2.90
644 646 7.199167 TCCATCAGAAGAGTTTATTCCATCA 57.801 36.000 0.00 0.00 0.00 3.07
645 647 8.688747 ATTCCATCAGAAGAGTTTATTCCATC 57.311 34.615 0.00 0.00 38.07 3.51
646 648 9.566432 GTATTCCATCAGAAGAGTTTATTCCAT 57.434 33.333 0.00 0.00 38.07 3.41
647 649 8.772250 AGTATTCCATCAGAAGAGTTTATTCCA 58.228 33.333 0.00 0.00 38.07 3.53
684 2016 0.533491 CGGTAAAGGTGGTCCATCGA 59.467 55.000 0.00 0.00 35.89 3.59
690 2022 2.289195 TGTCATCACGGTAAAGGTGGTC 60.289 50.000 0.00 0.00 36.09 4.02
695 2027 4.390909 GGTACTTTGTCATCACGGTAAAGG 59.609 45.833 0.00 0.00 33.77 3.11
701 2033 2.095853 GCATGGTACTTTGTCATCACGG 59.904 50.000 0.00 0.00 0.00 4.94
715 2047 1.312371 GCCTTCGCCTTTGCATGGTA 61.312 55.000 7.89 0.00 37.32 3.25
760 2092 0.928229 CTTCGCCGTACCATAACTGC 59.072 55.000 0.00 0.00 0.00 4.40
815 2147 0.034059 CGCCACTTGTGACCTCTTCT 59.966 55.000 1.89 0.00 0.00 2.85
816 2148 0.951040 CCGCCACTTGTGACCTCTTC 60.951 60.000 1.89 0.00 0.00 2.87
817 2149 1.071471 CCGCCACTTGTGACCTCTT 59.929 57.895 1.89 0.00 0.00 2.85
893 2231 4.539881 GCGTCTCGGACTCTCGGC 62.540 72.222 3.15 0.00 0.00 5.54
911 2249 2.175202 TCTGTTTGTTTGTTGGTGGCT 58.825 42.857 0.00 0.00 0.00 4.75
953 2291 1.180456 TCCTACCTCCGACGTTTGCA 61.180 55.000 0.00 0.00 0.00 4.08
968 2306 3.766691 GGCGGACGGTGCTTCCTA 61.767 66.667 0.00 0.00 0.00 2.94
1034 2372 2.038690 TCGAAGTCGAACAGCACCT 58.961 52.632 0.00 0.00 46.30 4.00
1226 2572 4.406972 TCATCCTGTCCTGGAAGACATTAG 59.593 45.833 0.00 0.00 45.39 1.73
1228 2574 3.184628 TCATCCTGTCCTGGAAGACATT 58.815 45.455 0.00 0.00 45.39 2.71
1456 2810 1.888512 CCACCTTCAAATCACACCTGG 59.111 52.381 0.00 0.00 0.00 4.45
1598 2952 0.973496 TCGTGGGATCATGGAACGGA 60.973 55.000 0.00 0.00 35.08 4.69
1764 3118 9.469807 GAGGTTTCAGAACACATCACTATATAG 57.530 37.037 8.27 8.27 37.51 1.31
1805 3369 3.384146 TCATTGTGCACACCACTTTTCAT 59.616 39.130 21.56 3.80 44.92 2.57
1818 3382 3.737663 GCAAGGTCAGTTTTCATTGTGCA 60.738 43.478 0.00 0.00 0.00 4.57
1819 3383 2.796593 GCAAGGTCAGTTTTCATTGTGC 59.203 45.455 0.00 0.00 0.00 4.57
1820 3384 3.383761 GGCAAGGTCAGTTTTCATTGTG 58.616 45.455 0.00 0.00 0.00 3.33
1821 3385 2.365293 GGGCAAGGTCAGTTTTCATTGT 59.635 45.455 0.00 0.00 0.00 2.71
1822 3386 2.289010 GGGGCAAGGTCAGTTTTCATTG 60.289 50.000 0.00 0.00 0.00 2.82
1823 3387 1.970640 GGGGCAAGGTCAGTTTTCATT 59.029 47.619 0.00 0.00 0.00 2.57
1824 3388 1.632589 GGGGCAAGGTCAGTTTTCAT 58.367 50.000 0.00 0.00 0.00 2.57
1825 3389 0.469144 GGGGGCAAGGTCAGTTTTCA 60.469 55.000 0.00 0.00 0.00 2.69
1826 3390 0.469144 TGGGGGCAAGGTCAGTTTTC 60.469 55.000 0.00 0.00 0.00 2.29
1832 3396 1.076549 GTTCATGGGGGCAAGGTCA 59.923 57.895 0.00 0.00 0.00 4.02
2166 3731 4.333649 CGTTGATACTGGATTGCTCATGTT 59.666 41.667 0.00 0.00 0.00 2.71
2307 3872 8.956446 TCATATACTAGGATGAATTCTGACCA 57.044 34.615 7.05 0.00 0.00 4.02
2387 3952 6.645827 GCATATGCTATCCTGCAGTATGATAG 59.354 42.308 23.63 23.63 46.71 2.08
2393 3958 2.825532 TCGCATATGCTATCCTGCAGTA 59.174 45.455 24.56 0.00 46.71 2.74
2572 4137 6.403309 GGCTGATACAAAGTGCTAAGGTAAAC 60.403 42.308 0.00 0.00 0.00 2.01
2677 4310 1.820519 TGCATTCTGTTCCTGCAATCC 59.179 47.619 0.00 0.00 42.53 3.01
2684 4317 1.967319 ACAACGTGCATTCTGTTCCT 58.033 45.000 0.00 0.00 0.00 3.36
2935 4568 8.270744 AGGATACATGGAAATATAGAGATTGCC 58.729 37.037 0.00 0.00 35.27 4.52
2944 4577 6.782986 AGCTTGCAGGATACATGGAAATATA 58.217 36.000 0.00 0.00 41.41 0.86
2998 4631 3.911894 TCTATCAGATGCCATTGATCCCA 59.088 43.478 5.88 0.00 35.72 4.37
3018 4651 4.605640 GCTGAGGCTGAATCTCTTATCT 57.394 45.455 0.00 0.00 35.22 1.98
3094 4727 4.906060 AGTAGTGTCTATGGAATTACCCCC 59.094 45.833 0.00 0.00 38.00 5.40
3097 4730 6.183360 TGCTGAGTAGTGTCTATGGAATTACC 60.183 42.308 0.00 0.00 39.54 2.85


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

AutoCloner maintained by Alex Coulton.