Multiple sequence alignment - TraesCS2A01G415200

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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 TraesCS2A01G415200 chr2A 100.000 2729 0 0 1 2729 672266833 672264105 0.000000e+00 5040
1 TraesCS2A01G415200 chr2A 88.552 297 27 6 1122 1416 672234911 672234620 1.200000e-93 353
2 TraesCS2A01G415200 chr2D 90.215 2790 139 63 6 2727 527273715 527270992 0.000000e+00 3517
3 TraesCS2A01G415200 chr2D 87.205 297 33 4 1123 1416 527004254 527003960 1.570000e-87 333
4 TraesCS2A01G415200 chr2B 90.360 2251 124 45 6 2231 624288414 624286232 0.000000e+00 2868
5 TraesCS2A01G415200 chr2B 87.119 295 31 6 1124 1416 623869995 623869706 7.290000e-86 327
6 TraesCS2A01G415200 chr2B 90.688 247 11 9 2260 2503 624286232 624285995 4.390000e-83 318
7 TraesCS2A01G415200 chr2B 90.000 190 11 3 2545 2727 624285996 624285808 3.510000e-59 239
8 TraesCS2A01G415200 chr6D 88.814 295 30 1 1126 1417 326572772 326573066 2.580000e-95 359
9 TraesCS2A01G415200 chr6A 88.814 295 30 1 1126 1417 465316666 465316960 2.580000e-95 359
10 TraesCS2A01G415200 chr3A 84.462 251 31 7 1170 1416 552641269 552641023 9.760000e-60 241
11 TraesCS2A01G415200 chr3D 83.858 254 33 7 1167 1416 103621541 103621790 4.540000e-58 235


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 TraesCS2A01G415200 chr2A 672264105 672266833 2728 True 5040.000000 5040 100.000000 1 2729 1 chr2A.!!$R2 2728
1 TraesCS2A01G415200 chr2D 527270992 527273715 2723 True 3517.000000 3517 90.215000 6 2727 1 chr2D.!!$R2 2721
2 TraesCS2A01G415200 chr2B 624285808 624288414 2606 True 1141.666667 2868 90.349333 6 2727 3 chr2B.!!$R2 2721

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
606 638 0.028505 GAATGCATGTACCAGCAGCG 59.971 55.0 13.67 0.0 44.94 5.18 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2539 2623 0.322648 GTTGTAGTGGGCCGGTAACT 59.677 55.0 1.9 7.2 0.0 2.24 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 0.764369 TGGAGGGAGAGCCGCATTAT 60.764 55.000 0.00 0.00 33.83 1.28
48 50 3.307762 GGAGGGAGAGCCGCATTATTTAT 60.308 47.826 0.00 0.00 33.83 1.40
51 54 5.246307 AGGGAGAGCCGCATTATTTATAAC 58.754 41.667 0.00 0.00 33.83 1.89
87 94 4.023536 TGAACAAGATAGAAAAACACGGCC 60.024 41.667 0.00 0.00 0.00 6.13
88 95 2.482721 ACAAGATAGAAAAACACGGCCG 59.517 45.455 26.86 26.86 0.00 6.13
136 148 6.222389 ACTTTGCTTTGCTTTGCATTATGTA 58.778 32.000 0.00 0.00 38.76 2.29
143 155 6.683090 TTGCTTTGCATTATGTACGTTTTC 57.317 33.333 0.00 0.00 38.76 2.29
189 201 2.752903 CCCCTCTAACGAACCCATTTTG 59.247 50.000 0.00 0.00 0.00 2.44
195 207 2.270352 ACGAACCCATTTTGCTCTGA 57.730 45.000 0.00 0.00 0.00 3.27
243 255 1.583054 AGTTGACAAGGCACTCGTTC 58.417 50.000 0.00 0.00 38.49 3.95
260 272 5.515626 ACTCGTTCGCATTATTGAACTCTAC 59.484 40.000 3.92 0.00 41.74 2.59
267 279 6.477360 TCGCATTATTGAACTCTACGCATTAA 59.523 34.615 0.00 0.00 0.00 1.40
276 288 9.817809 TTGAACTCTACGCATTAATTAATCTCT 57.182 29.630 7.76 0.00 0.00 3.10
277 289 9.817809 TGAACTCTACGCATTAATTAATCTCTT 57.182 29.630 7.76 0.62 0.00 2.85
328 340 7.148722 GGATCGATCGAAATCTTTTGGATCTAC 60.149 40.741 23.50 0.00 32.70 2.59
331 343 6.129326 CGATCGAAATCTTTTGGATCTACGAG 60.129 42.308 10.26 4.18 36.98 4.18
334 346 5.063438 CGAAATCTTTTGGATCTACGAGCAA 59.937 40.000 0.00 0.00 32.76 3.91
335 347 5.803020 AATCTTTTGGATCTACGAGCAAC 57.197 39.130 0.00 0.00 32.76 4.17
339 351 2.776312 TGGATCTACGAGCAACGATC 57.224 50.000 10.05 3.40 45.77 3.69
340 352 2.021457 TGGATCTACGAGCAACGATCA 58.979 47.619 10.05 0.00 45.77 2.92
341 353 2.223502 TGGATCTACGAGCAACGATCAC 60.224 50.000 10.05 0.20 45.77 3.06
382 394 1.921869 CGAGGCCTATTTGGTGGGGT 61.922 60.000 4.42 0.00 38.35 4.95
383 395 0.395724 GAGGCCTATTTGGTGGGGTG 60.396 60.000 4.42 0.00 38.35 4.61
394 415 1.303282 GTGGGGTGGCTTTAGGGAG 59.697 63.158 0.00 0.00 0.00 4.30
401 426 1.208293 GTGGCTTTAGGGAGAGACAGG 59.792 57.143 0.00 0.00 29.94 4.00
497 522 6.001449 TCCTACCAATGAAAGGGAATACTG 57.999 41.667 1.87 0.00 0.00 2.74
498 523 4.580580 CCTACCAATGAAAGGGAATACTGC 59.419 45.833 0.00 0.00 0.00 4.40
499 524 4.322057 ACCAATGAAAGGGAATACTGCT 57.678 40.909 0.00 0.00 0.00 4.24
541 566 2.022240 TTTGCACAACGGAAAGCCCC 62.022 55.000 0.00 0.00 30.52 5.80
598 630 7.293745 CGAGGAATGATAAAGAATGCATGTAC 58.706 38.462 0.00 0.00 0.00 2.90
604 636 5.297527 TGATAAAGAATGCATGTACCAGCAG 59.702 40.000 13.67 0.00 44.94 4.24
605 637 1.386533 AGAATGCATGTACCAGCAGC 58.613 50.000 13.67 8.97 44.94 5.25
606 638 0.028505 GAATGCATGTACCAGCAGCG 59.971 55.000 13.67 0.00 44.94 5.18
609 641 1.741401 GCATGTACCAGCAGCGTGA 60.741 57.895 0.00 0.00 0.00 4.35
610 642 1.091771 GCATGTACCAGCAGCGTGAT 61.092 55.000 0.00 0.00 0.00 3.06
611 643 0.654160 CATGTACCAGCAGCGTGATG 59.346 55.000 0.00 0.00 32.77 3.07
617 649 4.479993 AGCAGCGTGATGGCCCTC 62.480 66.667 0.00 0.00 0.00 4.30
667 699 2.283727 CGATCGAGAAACAAACGCGTAG 60.284 50.000 14.46 11.59 32.94 3.51
695 727 2.488355 GCAACATGCGCTGATGCT 59.512 55.556 24.14 6.38 46.84 3.79
747 779 1.396996 CATTCACATTTCGTCGGGGAC 59.603 52.381 0.00 0.00 0.00 4.46
756 788 0.178533 TCGTCGGGGACACAAAAACT 59.821 50.000 0.00 0.00 32.09 2.66
769 801 1.600511 AAAAACTAATGCGCCCCCGG 61.601 55.000 4.18 0.00 34.32 5.73
837 869 1.801913 GGCGCGGCGACTATATGAG 60.802 63.158 28.54 0.00 0.00 2.90
868 900 1.332640 CGCATCGCACTCATCATCAAC 60.333 52.381 0.00 0.00 0.00 3.18
890 922 1.450312 CCCAACTCGCTCCATCACC 60.450 63.158 0.00 0.00 0.00 4.02
896 928 1.751924 ACTCGCTCCATCACCTCTAAC 59.248 52.381 0.00 0.00 0.00 2.34
900 932 2.428890 CGCTCCATCACCTCTAACTTCT 59.571 50.000 0.00 0.00 0.00 2.85
901 933 3.632604 CGCTCCATCACCTCTAACTTCTA 59.367 47.826 0.00 0.00 0.00 2.10
902 934 4.279671 CGCTCCATCACCTCTAACTTCTAT 59.720 45.833 0.00 0.00 0.00 1.98
1011 1054 1.590238 GTCGATCAAATGGAGCACGAG 59.410 52.381 0.00 0.00 32.99 4.18
1041 1084 3.626924 GTGCCTCAGGTGTCCGGT 61.627 66.667 0.00 0.00 0.00 5.28
1042 1085 2.118732 TGCCTCAGGTGTCCGGTA 59.881 61.111 0.00 0.00 0.00 4.02
1043 1086 1.534476 TGCCTCAGGTGTCCGGTAA 60.534 57.895 0.00 0.00 0.00 2.85
1046 1089 1.068741 GCCTCAGGTGTCCGGTAATAG 59.931 57.143 0.00 0.00 0.00 1.73
1483 1526 1.970352 GAAGGAGCAGCAGGAGGAGG 61.970 65.000 0.00 0.00 0.00 4.30
1484 1527 4.173924 GGAGCAGCAGGAGGAGGC 62.174 72.222 0.00 0.00 0.00 4.70
1485 1528 4.527583 GAGCAGCAGGAGGAGGCG 62.528 72.222 0.00 0.00 34.54 5.52
1540 1583 2.461110 GCATCGTCGCCGGATTGTT 61.461 57.895 5.05 0.00 33.95 2.83
1541 1584 1.636340 CATCGTCGCCGGATTGTTC 59.364 57.895 5.05 0.00 33.95 3.18
1688 1731 2.202146 GGACGACGTCGACGACAG 60.202 66.667 41.52 30.48 43.02 3.51
1766 1809 2.635338 CGGATGCATGCATGGACG 59.365 61.111 36.73 29.70 36.70 4.79
1786 1829 4.583871 ACGAGATTCTTTTGCTGGATCTT 58.416 39.130 0.00 0.00 0.00 2.40
1787 1830 4.633565 ACGAGATTCTTTTGCTGGATCTTC 59.366 41.667 0.00 0.00 0.00 2.87
1811 1856 5.223382 GTCGATATGCATGCTAGTGTTACT 58.777 41.667 20.33 0.00 0.00 2.24
1814 1859 5.573282 CGATATGCATGCTAGTGTTACTACC 59.427 44.000 20.33 0.00 0.00 3.18
1827 1872 5.645497 AGTGTTACTACCTACTAACCTCGTG 59.355 44.000 0.00 0.00 0.00 4.35
1853 1898 5.463286 TCGACACTAACATCTTCGCTAAAA 58.537 37.500 0.00 0.00 0.00 1.52
1856 1901 6.895040 CGACACTAACATCTTCGCTAAAAATC 59.105 38.462 0.00 0.00 0.00 2.17
1862 1907 3.984018 TCTTCGCTAAAAATCGAACCG 57.016 42.857 0.00 0.00 39.43 4.44
1905 1950 9.423061 ACTTTACAGGTCAAATAAAATTGATGC 57.577 29.630 0.00 0.00 41.09 3.91
1974 2019 3.406764 AGACCTGACTGCAACTTTGATC 58.593 45.455 0.00 0.00 0.00 2.92
1984 2029 2.747446 GCAACTTTGATCTCCCGCTTTA 59.253 45.455 0.00 0.00 0.00 1.85
2003 2049 5.047731 GCTTTAATCTTTTTCCAGCTGAGGT 60.048 40.000 17.39 0.00 0.00 3.85
2023 2069 5.086104 GGTGAGGTTCAGCTTGTAATAGA 57.914 43.478 1.29 0.00 41.34 1.98
2024 2070 5.112686 GGTGAGGTTCAGCTTGTAATAGAG 58.887 45.833 1.29 0.00 41.34 2.43
2025 2071 5.112686 GTGAGGTTCAGCTTGTAATAGAGG 58.887 45.833 0.00 0.00 0.00 3.69
2026 2072 5.023452 TGAGGTTCAGCTTGTAATAGAGGA 58.977 41.667 0.00 0.00 0.00 3.71
2035 2082 7.039293 TCAGCTTGTAATAGAGGAGTACAAACA 60.039 37.037 0.00 0.00 45.29 2.83
2091 2139 2.680974 TTTTGCCCTGCAGCTCGAGT 62.681 55.000 15.13 0.00 40.61 4.18
2126 2185 3.417069 TTTTTCTGGCAGCTAGTAGCA 57.583 42.857 23.77 2.32 45.56 3.49
2127 2186 2.680312 TTTCTGGCAGCTAGTAGCAG 57.320 50.000 23.77 17.01 45.56 4.24
2128 2187 1.561643 TTCTGGCAGCTAGTAGCAGT 58.438 50.000 23.77 1.17 45.56 4.40
2129 2188 1.107114 TCTGGCAGCTAGTAGCAGTC 58.893 55.000 23.77 17.86 45.56 3.51
2163 2222 5.064834 GTGTAAGATCCGTTTTCCCATCTTC 59.935 44.000 0.00 0.00 36.98 2.87
2186 2246 6.969043 TCCATTGGGTGTAAATCAGAGTATT 58.031 36.000 2.09 0.00 34.93 1.89
2246 2316 7.000575 TGCGTGCTGTTCTTACTATTAAATC 57.999 36.000 0.00 0.00 0.00 2.17
2308 2386 3.692576 ACTAGTAGCGTATGAAGCAACG 58.307 45.455 0.00 0.00 41.92 4.10
2320 2400 6.237227 CGTATGAAGCAACGTCTAACAGTAAG 60.237 42.308 0.00 0.00 34.48 2.34
2424 2508 4.634443 GGGGATTATTTTACGATGATCGGG 59.366 45.833 19.82 0.00 45.59 5.14
2466 2550 0.673022 CTTGTCCTCAGGCTGAGCAC 60.673 60.000 34.04 30.96 42.98 4.40
2468 2552 0.251787 TGTCCTCAGGCTGAGCACTA 60.252 55.000 32.33 19.45 42.98 2.74
2509 2593 2.087857 ATTTTGTTGGGCCCTCGGGA 62.088 55.000 25.70 0.00 37.50 5.14
2510 2594 2.706952 TTTTGTTGGGCCCTCGGGAG 62.707 60.000 25.70 0.00 37.50 4.30
2524 2608 0.748450 CGGGAGGGACGTATAAGCAA 59.252 55.000 0.00 0.00 0.00 3.91
2525 2609 1.343465 CGGGAGGGACGTATAAGCAAT 59.657 52.381 0.00 0.00 0.00 3.56
2526 2610 2.224209 CGGGAGGGACGTATAAGCAATT 60.224 50.000 0.00 0.00 0.00 2.32
2527 2611 3.139077 GGGAGGGACGTATAAGCAATTG 58.861 50.000 0.00 0.00 0.00 2.32
2539 2623 3.853831 AAGCAATTGATTGATGCACGA 57.146 38.095 8.40 0.00 42.45 4.35
2561 2645 0.035176 TACCGGCCCACTACAACAAC 59.965 55.000 0.00 0.00 0.00 3.32
2568 2652 3.558321 GGCCCACTACAACAACACTATCA 60.558 47.826 0.00 0.00 0.00 2.15
2669 2760 2.808933 CGGTTGTGGTTGGTGTATGTCT 60.809 50.000 0.00 0.00 0.00 3.41
2727 2821 0.109179 TGCATGTGGGACGTACGTAC 60.109 55.000 22.69 22.69 0.00 3.67
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
27 28 2.262423 AAATAATGCGGCTCTCCCTC 57.738 50.000 0.00 0.00 0.00 4.30
51 54 9.578439 TTCTATCTTGTTCATGATATATCTGCG 57.422 33.333 13.79 2.84 0.00 5.18
70 73 1.677820 CCCGGCCGTGTTTTTCTATCT 60.678 52.381 26.12 0.00 0.00 1.98
99 106 4.830826 AAGCAAAGTAAAGTAAAGCGCT 57.169 36.364 2.64 2.64 0.00 5.92
100 107 4.375005 GCAAAGCAAAGTAAAGTAAAGCGC 60.375 41.667 0.00 0.00 0.00 5.92
101 108 4.976116 AGCAAAGCAAAGTAAAGTAAAGCG 59.024 37.500 0.00 0.00 0.00 4.68
102 109 6.828502 AAGCAAAGCAAAGTAAAGTAAAGC 57.171 33.333 0.00 0.00 0.00 3.51
103 110 7.119360 GCAAAGCAAAGCAAAGTAAAGTAAAG 58.881 34.615 0.00 0.00 0.00 1.85
104 111 6.591834 TGCAAAGCAAAGCAAAGTAAAGTAAA 59.408 30.769 0.00 0.00 37.90 2.01
105 112 6.102663 TGCAAAGCAAAGCAAAGTAAAGTAA 58.897 32.000 0.00 0.00 37.90 2.24
106 113 5.655488 TGCAAAGCAAAGCAAAGTAAAGTA 58.345 33.333 0.00 0.00 37.90 2.24
107 114 4.502962 TGCAAAGCAAAGCAAAGTAAAGT 58.497 34.783 0.00 0.00 37.90 2.66
136 148 6.095300 TGGAATGATATGCATTGAGAAAACGT 59.905 34.615 3.54 0.00 46.90 3.99
143 155 7.813148 GGAAAAGATGGAATGATATGCATTGAG 59.187 37.037 3.54 0.00 46.90 3.02
189 201 1.584175 CAGATGGCAGATGTCAGAGC 58.416 55.000 0.00 0.00 30.80 4.09
243 255 4.715520 ATGCGTAGAGTTCAATAATGCG 57.284 40.909 0.00 0.00 0.00 4.73
281 293 9.862371 CGATCCTGTTCTTGCTTAGTATATATT 57.138 33.333 0.00 0.00 0.00 1.28
282 294 9.244292 TCGATCCTGTTCTTGCTTAGTATATAT 57.756 33.333 0.00 0.00 0.00 0.86
283 295 8.631480 TCGATCCTGTTCTTGCTTAGTATATA 57.369 34.615 0.00 0.00 0.00 0.86
285 297 6.954487 TCGATCCTGTTCTTGCTTAGTATA 57.046 37.500 0.00 0.00 0.00 1.47
287 299 5.505819 CGATCGATCCTGTTCTTGCTTAGTA 60.506 44.000 19.51 0.00 0.00 1.82
288 300 4.688021 GATCGATCCTGTTCTTGCTTAGT 58.312 43.478 14.76 0.00 0.00 2.24
289 301 3.733224 CGATCGATCCTGTTCTTGCTTAG 59.267 47.826 19.51 0.00 0.00 2.18
294 306 5.046529 AGATTTCGATCGATCCTGTTCTTG 58.953 41.667 20.18 3.23 0.00 3.02
298 310 5.065218 CCAAAAGATTTCGATCGATCCTGTT 59.935 40.000 20.18 13.81 0.00 3.16
300 312 4.811024 TCCAAAAGATTTCGATCGATCCTG 59.189 41.667 20.18 11.31 0.00 3.86
301 313 5.023533 TCCAAAAGATTTCGATCGATCCT 57.976 39.130 20.18 12.99 0.00 3.24
302 314 5.698545 AGATCCAAAAGATTTCGATCGATCC 59.301 40.000 20.18 10.89 34.42 3.36
304 316 6.363626 CGTAGATCCAAAAGATTTCGATCGAT 59.636 38.462 20.18 4.47 34.42 3.59
305 317 5.685954 CGTAGATCCAAAAGATTTCGATCGA 59.314 40.000 15.15 15.15 34.42 3.59
306 318 5.685954 TCGTAGATCCAAAAGATTTCGATCG 59.314 40.000 9.36 9.36 34.42 3.69
328 340 0.654160 ATGCATGTGATCGTTGCTCG 59.346 50.000 0.00 0.00 41.41 5.03
331 343 5.760193 TTAAAAATGCATGTGATCGTTGC 57.240 34.783 0.00 7.24 0.00 4.17
334 346 7.701924 CCAAGTATTAAAAATGCATGTGATCGT 59.298 33.333 0.00 0.00 0.00 3.73
335 347 7.306167 GCCAAGTATTAAAAATGCATGTGATCG 60.306 37.037 0.00 0.00 0.00 3.69
339 351 6.454054 CGTGCCAAGTATTAAAAATGCATGTG 60.454 38.462 0.00 0.00 31.62 3.21
340 352 5.576384 CGTGCCAAGTATTAAAAATGCATGT 59.424 36.000 0.00 0.00 31.62 3.21
341 353 5.804473 TCGTGCCAAGTATTAAAAATGCATG 59.196 36.000 0.00 0.00 36.18 4.06
370 382 2.291930 CCTAAAGCCACCCCACCAAATA 60.292 50.000 0.00 0.00 0.00 1.40
382 394 1.573108 CCTGTCTCTCCCTAAAGCCA 58.427 55.000 0.00 0.00 0.00 4.75
383 395 0.179234 GCCTGTCTCTCCCTAAAGCC 59.821 60.000 0.00 0.00 0.00 4.35
394 415 1.375268 GCACCTGTCTGCCTGTCTC 60.375 63.158 0.00 0.00 0.00 3.36
436 461 5.387547 GCGCGAGTAGACTAATGATTAAAGC 60.388 44.000 12.10 0.00 0.00 3.51
497 522 0.378962 TGTGCGTGTTTTGGTGTAGC 59.621 50.000 0.00 0.00 0.00 3.58
498 523 1.398739 TGTGTGCGTGTTTTGGTGTAG 59.601 47.619 0.00 0.00 0.00 2.74
499 524 1.130749 GTGTGTGCGTGTTTTGGTGTA 59.869 47.619 0.00 0.00 0.00 2.90
566 598 4.480115 TCTTTATCATTCCTCGCCTCCTA 58.520 43.478 0.00 0.00 0.00 2.94
567 599 3.309296 TCTTTATCATTCCTCGCCTCCT 58.691 45.455 0.00 0.00 0.00 3.69
568 600 3.753294 TCTTTATCATTCCTCGCCTCC 57.247 47.619 0.00 0.00 0.00 4.30
617 649 1.745320 AATAGCGACTACAGGGCCGG 61.745 60.000 0.79 0.79 0.00 6.13
618 650 0.597637 CAATAGCGACTACAGGGCCG 60.598 60.000 0.00 0.00 0.00 6.13
619 651 0.750850 TCAATAGCGACTACAGGGCC 59.249 55.000 0.00 0.00 0.00 5.80
620 652 1.538419 GGTCAATAGCGACTACAGGGC 60.538 57.143 0.00 0.00 36.12 5.19
690 722 1.659954 CAGGCTACGAGCGAGCATC 60.660 63.158 13.35 0.00 43.62 3.91
691 723 1.949847 AACAGGCTACGAGCGAGCAT 61.950 55.000 13.35 6.28 43.62 3.79
692 724 2.636412 AACAGGCTACGAGCGAGCA 61.636 57.895 13.35 0.00 43.62 4.26
693 725 2.161486 CAACAGGCTACGAGCGAGC 61.161 63.158 0.00 1.56 43.62 5.03
694 726 0.450583 TACAACAGGCTACGAGCGAG 59.549 55.000 0.00 0.00 43.62 5.03
695 727 0.450583 CTACAACAGGCTACGAGCGA 59.549 55.000 0.00 0.00 43.62 4.93
747 779 1.671556 GGGGGCGCATTAGTTTTTGTG 60.672 52.381 10.83 0.00 0.00 3.33
769 801 0.379669 CAATGTGGAAGCAGGATCGC 59.620 55.000 0.00 0.00 0.00 4.58
868 900 1.003355 ATGGAGCGAGTTGGGTGTG 60.003 57.895 0.00 0.00 0.00 3.82
890 922 8.874816 GTTGCTAAACCTTGATAGAAGTTAGAG 58.125 37.037 0.00 0.00 0.00 2.43
896 928 6.317857 GCTTGTTGCTAAACCTTGATAGAAG 58.682 40.000 0.00 0.00 38.95 2.85
1011 1054 1.301677 GAGGCACAACTAGCACCTGC 61.302 60.000 0.00 0.00 42.49 4.85
1023 1066 3.625897 CCGGACACCTGAGGCACA 61.626 66.667 0.00 0.00 0.00 4.57
1454 1497 2.101770 GCTCCTTCGCAGCAATGC 59.898 61.111 0.00 0.00 36.82 3.56
1474 1517 2.581354 CTCAACCGCCTCCTCCTG 59.419 66.667 0.00 0.00 0.00 3.86
1483 1526 2.033194 CCGAAACCTCCTCAACCGC 61.033 63.158 0.00 0.00 0.00 5.68
1484 1527 0.389948 CTCCGAAACCTCCTCAACCG 60.390 60.000 0.00 0.00 0.00 4.44
1485 1528 0.673956 GCTCCGAAACCTCCTCAACC 60.674 60.000 0.00 0.00 0.00 3.77
1527 1570 1.131826 CAACGAACAATCCGGCGAC 59.868 57.895 9.30 0.00 0.00 5.19
1541 1584 1.590238 GTCCTGCATTCTCGATCAACG 59.410 52.381 0.00 0.00 44.09 4.10
1674 1717 1.225422 GAGACTGTCGTCGACGTCG 60.225 63.158 34.40 31.30 44.93 5.12
1688 1731 3.836762 GGTTCCCCGAAGAAGAGAC 57.163 57.895 0.00 0.00 0.00 3.36
1766 1809 4.633565 ACGAAGATCCAGCAAAAGAATCTC 59.366 41.667 0.00 0.00 0.00 2.75
1786 1829 2.293399 ACACTAGCATGCATATCGACGA 59.707 45.455 21.98 0.00 0.00 4.20
1787 1830 2.666026 ACACTAGCATGCATATCGACG 58.334 47.619 21.98 2.04 0.00 5.12
1811 1856 3.134623 TCGATCCACGAGGTTAGTAGGTA 59.865 47.826 0.00 0.00 46.45 3.08
1827 1872 2.789893 GCGAAGATGTTAGTGTCGATCC 59.210 50.000 0.00 0.00 33.63 3.36
1862 1907 9.113876 CCTGTAAAGTGACAAATTAAACGAATC 57.886 33.333 0.00 0.00 0.00 2.52
1974 2019 4.675408 GCTGGAAAAAGATTAAAGCGGGAG 60.675 45.833 0.00 0.00 0.00 4.30
1984 2029 4.077822 CTCACCTCAGCTGGAAAAAGATT 58.922 43.478 15.13 0.00 0.00 2.40
2003 2049 5.023452 TCCTCTATTACAAGCTGAACCTCA 58.977 41.667 0.00 0.00 0.00 3.86
2023 2069 2.158534 TGCACCCATTGTTTGTACTCCT 60.159 45.455 0.00 0.00 0.00 3.69
2024 2070 2.235016 TGCACCCATTGTTTGTACTCC 58.765 47.619 0.00 0.00 0.00 3.85
2025 2071 4.519540 AATGCACCCATTGTTTGTACTC 57.480 40.909 0.00 0.00 40.09 2.59
2026 2072 4.082245 GCTAATGCACCCATTGTTTGTACT 60.082 41.667 0.00 0.00 41.58 2.73
2035 2082 3.808618 GCTAGCTAGCTAATGCACCCATT 60.809 47.826 33.71 0.00 45.62 3.16
2058 2105 1.494824 GCAAAAAGAACTGGCAGCAG 58.505 50.000 15.89 0.00 0.00 4.24
2091 2139 1.150536 AAAAACCCTGCTGCTCGGA 59.849 52.632 11.71 0.00 0.00 4.55
2126 2185 3.728076 TCTTACACGTGCAGAAAGACT 57.272 42.857 17.22 0.00 0.00 3.24
2127 2186 3.368236 GGATCTTACACGTGCAGAAAGAC 59.632 47.826 17.22 12.74 0.00 3.01
2128 2187 3.585862 GGATCTTACACGTGCAGAAAGA 58.414 45.455 17.22 18.48 0.00 2.52
2129 2188 2.345641 CGGATCTTACACGTGCAGAAAG 59.654 50.000 17.22 13.93 0.00 2.62
2163 2222 7.645058 AAATACTCTGATTTACACCCAATGG 57.355 36.000 0.00 0.00 37.80 3.16
2246 2316 0.327591 AGCTGGCCTTTCTTCAGGAG 59.672 55.000 3.32 0.00 35.71 3.69
2308 2386 4.734917 ACATCGTGCTCTTACTGTTAGAC 58.265 43.478 0.00 0.00 0.00 2.59
2320 2400 1.125021 GCGCATACATACATCGTGCTC 59.875 52.381 0.30 0.00 33.82 4.26
2404 2488 4.935808 AGCCCCGATCATCGTAAAATAATC 59.064 41.667 6.25 0.00 38.40 1.75
2424 2508 1.079336 GACAGAACGGTGGGTAGCC 60.079 63.158 3.29 3.29 0.00 3.93
2466 2550 7.210718 TGGGACGAACATACTGTACATATAG 57.789 40.000 0.00 0.00 0.00 1.31
2468 2552 6.665992 ATGGGACGAACATACTGTACATAT 57.334 37.500 0.00 0.00 0.00 1.78
2509 2593 5.680619 TCAATCAATTGCTTATACGTCCCT 58.319 37.500 0.00 0.00 37.68 4.20
2510 2594 6.373779 CATCAATCAATTGCTTATACGTCCC 58.626 40.000 0.00 0.00 37.68 4.46
2511 2595 5.853282 GCATCAATCAATTGCTTATACGTCC 59.147 40.000 0.00 0.00 37.68 4.79
2512 2596 6.358030 GTGCATCAATCAATTGCTTATACGTC 59.642 38.462 0.00 0.00 37.68 4.34
2524 2608 3.309682 CGGTAACTCGTGCATCAATCAAT 59.690 43.478 0.00 0.00 0.00 2.57
2525 2609 2.670905 CGGTAACTCGTGCATCAATCAA 59.329 45.455 0.00 0.00 0.00 2.57
2526 2610 2.267426 CGGTAACTCGTGCATCAATCA 58.733 47.619 0.00 0.00 0.00 2.57
2527 2611 1.593006 CCGGTAACTCGTGCATCAATC 59.407 52.381 0.00 0.00 0.00 2.67
2539 2623 0.322648 GTTGTAGTGGGCCGGTAACT 59.677 55.000 1.90 7.20 0.00 2.24
2669 2760 1.839747 ACTAACCACACCGGCCAGA 60.840 57.895 0.00 0.00 39.03 3.86


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

AutoCloner maintained by Alex Coulton.