Multiple sequence alignment - TraesCS2B01G484300

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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 TraesCS2B01G484300 chr2B 100.000 3641 0 0 1 3641 681544960 681541320 0.000000e+00 6724.0
1 TraesCS2B01G484300 chr2A 89.462 3644 218 71 1 3533 708190900 708187312 0.000000e+00 4449.0
2 TraesCS2B01G484300 chr2D 90.525 3335 166 78 375 3641 568945637 568942385 0.000000e+00 4270.0
3 TraesCS2B01G484300 chr2D 86.260 262 20 9 10 267 568945906 568945657 1.670000e-68 270.0
4 TraesCS2B01G484300 chr3B 100.000 29 0 0 1768 1796 736658554 736658582 2.000000e-03 54.7
5 TraesCS2B01G484300 chr3A 100.000 29 0 0 1768 1796 690957875 690957903 2.000000e-03 54.7


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 TraesCS2B01G484300 chr2B 681541320 681544960 3640 True 6724 6724 100.0000 1 3641 1 chr2B.!!$R1 3640
1 TraesCS2B01G484300 chr2A 708187312 708190900 3588 True 4449 4449 89.4620 1 3533 1 chr2A.!!$R1 3532
2 TraesCS2B01G484300 chr2D 568942385 568945906 3521 True 2270 4270 88.3925 10 3641 2 chr2D.!!$R1 3631

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
33 38 0.531532 CGAGCCAGGCTTGATCGATT 60.532 55.0 23.37 0.0 42.27 3.34 F
1103 1138 0.329261 TGGTCCCTTCCATGCTCAAG 59.671 55.0 0.00 0.0 31.96 3.02 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1490 1525 1.001641 GGACCCTTCAGCACAGCAT 60.002 57.895 0.0 0.0 0.0 3.79 R
2649 2687 0.377203 GAACGCCGCTAATTTCCTGG 59.623 55.000 0.0 0.0 0.0 4.45 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
33 38 0.531532 CGAGCCAGGCTTGATCGATT 60.532 55.000 23.37 0.00 42.27 3.34
34 39 0.942962 GAGCCAGGCTTGATCGATTG 59.057 55.000 17.46 0.00 39.88 2.67
35 40 0.543277 AGCCAGGCTTGATCGATTGA 59.457 50.000 8.70 0.00 33.89 2.57
46 51 1.810606 ATCGATTGATCCTCGGCGCT 61.811 55.000 7.64 0.00 36.78 5.92
113 122 1.482593 TCTTTCTTCCAGCTCCGGATC 59.517 52.381 3.57 0.00 34.19 3.36
122 131 0.825840 AGCTCCGGATCCAGCTAGTC 60.826 60.000 21.92 5.69 44.45 2.59
128 137 1.394618 GGATCCAGCTAGTCGTCTGT 58.605 55.000 6.95 0.00 0.00 3.41
133 142 2.069273 CCAGCTAGTCGTCTGTTTTGG 58.931 52.381 0.00 0.00 0.00 3.28
134 143 2.069273 CAGCTAGTCGTCTGTTTTGGG 58.931 52.381 0.00 0.00 0.00 4.12
135 144 1.002087 AGCTAGTCGTCTGTTTTGGGG 59.998 52.381 0.00 0.00 0.00 4.96
136 145 1.944430 GCTAGTCGTCTGTTTTGGGGG 60.944 57.143 0.00 0.00 0.00 5.40
191 200 3.160872 AGACGCTGTCTCAGATCGA 57.839 52.632 5.54 0.00 38.71 3.59
267 276 1.970640 GGGGACAAGTTTTCATGGCTT 59.029 47.619 0.00 0.00 0.00 4.35
268 277 2.289010 GGGGACAAGTTTTCATGGCTTG 60.289 50.000 14.18 14.18 43.56 4.01
269 278 2.407090 GGACAAGTTTTCATGGCTTGC 58.593 47.619 15.09 10.38 42.20 4.01
270 279 2.407090 GACAAGTTTTCATGGCTTGCC 58.593 47.619 4.43 4.43 42.20 4.52
271 280 2.036346 GACAAGTTTTCATGGCTTGCCT 59.964 45.455 13.18 0.00 42.20 4.75
272 281 2.435437 ACAAGTTTTCATGGCTTGCCTT 59.565 40.909 13.18 3.61 42.20 4.35
274 283 3.116079 AGTTTTCATGGCTTGCCTTTG 57.884 42.857 13.18 10.35 0.00 2.77
275 284 2.699846 AGTTTTCATGGCTTGCCTTTGA 59.300 40.909 13.18 12.35 0.00 2.69
276 285 3.062042 GTTTTCATGGCTTGCCTTTGAG 58.938 45.455 13.18 0.00 0.00 3.02
277 286 2.291209 TTCATGGCTTGCCTTTGAGA 57.709 45.000 13.18 1.34 0.00 3.27
278 287 2.519771 TCATGGCTTGCCTTTGAGAT 57.480 45.000 13.18 0.00 0.00 2.75
285 294 3.608796 GCTTGCCTTTGAGATTCTCTCT 58.391 45.455 14.54 0.00 43.73 3.10
307 324 5.291128 TCTCTGTTTTTCACGTCAGTTTCTC 59.709 40.000 0.00 0.00 0.00 2.87
317 334 4.452455 CACGTCAGTTTCTCTAGCCAAATT 59.548 41.667 0.00 0.00 0.00 1.82
322 339 4.397417 CAGTTTCTCTAGCCAAATTCAGGG 59.603 45.833 0.00 0.00 0.00 4.45
333 350 3.570550 CCAAATTCAGGGTTTGGTTCGTA 59.429 43.478 8.98 0.00 46.65 3.43
335 352 5.219633 CAAATTCAGGGTTTGGTTCGTAAG 58.780 41.667 0.00 0.00 33.91 2.34
337 354 2.048601 TCAGGGTTTGGTTCGTAAGGA 58.951 47.619 0.00 0.00 38.47 3.36
348 365 4.579270 GTTCGTAAGGACTTTCCGATTG 57.421 45.455 7.15 0.00 44.67 2.67
391 408 5.659440 AACAATATTTCGGGTGCAATTCT 57.341 34.783 0.00 0.00 0.00 2.40
396 413 1.462616 TTCGGGTGCAATTCTCCATG 58.537 50.000 0.00 0.00 0.00 3.66
399 416 1.670811 CGGGTGCAATTCTCCATGTAC 59.329 52.381 0.00 0.00 0.00 2.90
411 428 8.865978 CAATTCTCCATGTACAACAATCAATTG 58.134 33.333 0.00 0.00 43.26 2.32
428 445 0.823356 TTGCCTTTGCTCTGTGTCCC 60.823 55.000 0.00 0.00 38.71 4.46
435 452 0.770499 TGCTCTGTGTCCCAATCCAA 59.230 50.000 0.00 0.00 0.00 3.53
438 455 2.704572 CTCTGTGTCCCAATCCAACTC 58.295 52.381 0.00 0.00 0.00 3.01
464 481 4.447138 TCCGAATGGGTTGGCTTATTAT 57.553 40.909 0.00 0.00 37.00 1.28
500 519 5.827797 TCTTCAACTTTGTGATTAGCTGGTT 59.172 36.000 0.00 0.00 0.00 3.67
501 520 5.689383 TCAACTTTGTGATTAGCTGGTTC 57.311 39.130 0.00 0.00 0.00 3.62
502 521 5.129634 TCAACTTTGTGATTAGCTGGTTCA 58.870 37.500 0.00 0.00 0.00 3.18
503 522 5.239306 TCAACTTTGTGATTAGCTGGTTCAG 59.761 40.000 0.00 0.00 34.12 3.02
528 547 0.666374 GCGGTTGTGTTAGGTGCTTT 59.334 50.000 0.00 0.00 0.00 3.51
551 570 4.780021 TGTTTCTTTCAGAGAGATAGGGCT 59.220 41.667 0.00 0.00 35.37 5.19
575 594 4.801516 GCGTTTACTTGTGACAACCAAATT 59.198 37.500 0.00 0.00 0.00 1.82
586 610 6.538021 TGTGACAACCAAATTTTCCATTTCTG 59.462 34.615 0.00 0.00 0.00 3.02
587 611 5.526846 TGACAACCAAATTTTCCATTTCTGC 59.473 36.000 0.00 0.00 0.00 4.26
674 704 1.324740 TATCTTGCCCGTGCCGTACT 61.325 55.000 0.00 0.00 36.33 2.73
685 715 1.257936 GTGCCGTACTGCGTAATCATG 59.742 52.381 4.75 0.00 39.32 3.07
686 716 0.859232 GCCGTACTGCGTAATCATGG 59.141 55.000 0.00 0.00 39.32 3.66
849 884 7.825681 TGTTCACACCAATAATTGATACTTGG 58.174 34.615 0.00 0.00 43.06 3.61
916 951 8.747471 TGTTTTGGATTCATCTATTGTTGCATA 58.253 29.630 0.00 0.00 0.00 3.14
917 952 9.023967 GTTTTGGATTCATCTATTGTTGCATAC 57.976 33.333 0.00 0.00 0.00 2.39
918 953 8.523915 TTTGGATTCATCTATTGTTGCATACT 57.476 30.769 0.00 0.00 0.00 2.12
919 954 8.523915 TTGGATTCATCTATTGTTGCATACTT 57.476 30.769 0.00 0.00 0.00 2.24
1103 1138 0.329261 TGGTCCCTTCCATGCTCAAG 59.671 55.000 0.00 0.00 31.96 3.02
1105 1140 1.078214 TCCCTTCCATGCTCAAGCG 60.078 57.895 0.00 0.00 45.83 4.68
1132 1167 4.427312 TCCGTTCTTATACGCTTTCTTCC 58.573 43.478 0.00 0.00 40.10 3.46
1133 1168 4.159135 TCCGTTCTTATACGCTTTCTTCCT 59.841 41.667 0.00 0.00 40.10 3.36
1136 1171 6.532657 CCGTTCTTATACGCTTTCTTCCTTTA 59.467 38.462 0.00 0.00 40.10 1.85
1146 1181 8.161699 ACGCTTTCTTCCTTTATTGTTTCTTA 57.838 30.769 0.00 0.00 0.00 2.10
1147 1182 8.626526 ACGCTTTCTTCCTTTATTGTTTCTTAA 58.373 29.630 0.00 0.00 0.00 1.85
1185 1220 9.003658 CATAGTGTGAAGGTCTTTTCTTACAAT 57.996 33.333 0.00 0.00 0.00 2.71
1303 1338 3.482436 ACCACTTCGTCAATGCCTAAAA 58.518 40.909 0.00 0.00 0.00 1.52
1475 1510 4.216902 TCAGACATCAAGCATGAAAACCTG 59.783 41.667 0.00 2.17 39.49 4.00
1490 1525 2.338620 CTGGTCACGCTTGTCGGA 59.661 61.111 0.00 0.00 43.86 4.55
1611 1646 2.535732 GCATTTCTGCTGTTCGTCGATC 60.536 50.000 0.00 0.00 45.32 3.69
1624 1659 1.933853 CGTCGATCCCTTCATTGGTTC 59.066 52.381 0.00 0.00 0.00 3.62
2034 2069 2.036089 AGGTCAAGTGACGAAGAAGTCC 59.964 50.000 5.40 0.00 45.65 3.85
2052 2087 7.232188 AGAAGTCCGACATCTATAGTTATGGA 58.768 38.462 4.45 0.13 0.00 3.41
2166 2204 8.673711 TCTACTTATTTGCAAGCGTTTATTGAT 58.326 29.630 0.00 0.00 0.00 2.57
2199 2237 4.584325 ACAAAATGGTGTCAGTTGCATACT 59.416 37.500 0.00 0.00 37.68 2.12
2224 2262 6.821665 TGAAGCAACTATACCATAAGTTCACC 59.178 38.462 0.00 0.00 33.72 4.02
2229 2267 2.572191 TACCATAAGTTCACCGAGCG 57.428 50.000 0.00 0.00 0.00 5.03
2272 2310 5.358090 TGAATTTGACAAAATCTGCTGCAA 58.642 33.333 15.26 0.00 34.84 4.08
2571 2609 2.430244 CGGTCCAACACGTCGAGG 60.430 66.667 3.03 3.03 0.00 4.63
2589 2627 1.477685 GGTCCTTCTCCACCACGGAA 61.478 60.000 0.00 0.00 45.75 4.30
2595 2633 3.134804 CCTTCTCCACCACGGAAATATCT 59.865 47.826 0.00 0.00 45.75 1.98
2649 2687 4.569966 CAGACATCTGTATGAAGAGTTGGC 59.430 45.833 0.00 0.00 39.44 4.52
2663 2701 0.455815 GTTGGCCAGGAAATTAGCGG 59.544 55.000 5.11 0.00 0.00 5.52
2772 2821 0.035725 CGAGGAGGGGTTGGGTTAAC 60.036 60.000 0.00 0.00 38.60 2.01
2820 2872 6.745116 TGTGTACGATGTAAATATCTGGAGG 58.255 40.000 0.00 0.00 0.00 4.30
2834 2886 2.768527 TCTGGAGGTGGAGATGATCAAC 59.231 50.000 0.00 0.00 0.00 3.18
2840 2892 4.302067 AGGTGGAGATGATCAACATAGGT 58.698 43.478 0.00 0.00 39.56 3.08
2855 2933 7.337938 TCAACATAGGTTCTTGCAAGATATGA 58.662 34.615 34.31 23.72 34.21 2.15
2913 3005 4.184629 GTCAGACTTCAGTGTTCACTGTT 58.815 43.478 25.52 14.99 38.75 3.16
2923 3015 5.928264 TCAGTGTTCACTGTTATGATGACTG 59.072 40.000 25.52 0.00 38.43 3.51
2957 3049 2.061790 GCTGGTCTGGATGGATCCCC 62.062 65.000 9.90 4.51 46.59 4.81
2979 3071 0.322816 TCCTTGAGGCCAAGCATGAC 60.323 55.000 5.01 0.00 46.42 3.06
3001 3093 1.300971 CGAGGAGGCATGGTGTGTTG 61.301 60.000 0.00 0.00 0.00 3.33
3025 3118 4.403752 TGAACAATTTGGAATGGACACACA 59.596 37.500 0.78 0.00 0.00 3.72
3042 3135 4.154737 ACACACATCGACCAAATTCATCTG 59.845 41.667 0.00 0.00 0.00 2.90
3050 3143 4.095334 CGACCAAATTCATCTGCAATCTCA 59.905 41.667 0.00 0.00 0.00 3.27
3213 3359 2.665185 GACGGGCTGAGCGTGTTT 60.665 61.111 0.00 0.00 0.00 2.83
3226 3376 3.531538 AGCGTGTTTGAGAAAGAAGTGA 58.468 40.909 0.00 0.00 0.00 3.41
3248 3398 6.699642 GTGAAGAACGGATCAAAAATTTCCAA 59.300 34.615 0.00 0.00 0.00 3.53
3255 3405 8.620116 ACGGATCAAAAATTTCCAAAAATCAT 57.380 26.923 0.00 0.00 33.93 2.45
3321 3478 4.661125 CGTGAACATGTCAAACCATATGG 58.339 43.478 20.68 20.68 38.23 2.74
3340 3508 2.429930 CCTGTTGAACGGCTCCCA 59.570 61.111 0.00 0.00 0.00 4.37
3360 3528 3.122948 CCATCGTCAACTCGTTAAAGTGG 59.877 47.826 0.00 0.00 0.00 4.00
3401 3579 2.350522 GGATTGCATCGTCAACTCAGT 58.649 47.619 0.00 0.00 0.00 3.41
3415 3593 2.505777 CAGTGAGACAGCGAGCGG 60.506 66.667 0.00 0.00 0.00 5.52
3442 3620 4.397420 ACCAATGCACAAGTCAGTGATTA 58.603 39.130 0.00 0.00 42.05 1.75
3572 3754 3.507233 TCATCAAAAGCGAGGCAGAAAAT 59.493 39.130 0.00 0.00 0.00 1.82
3574 3756 3.900941 TCAAAAGCGAGGCAGAAAATTC 58.099 40.909 0.00 0.00 0.00 2.17
3575 3757 3.317711 TCAAAAGCGAGGCAGAAAATTCA 59.682 39.130 0.00 0.00 0.00 2.57
3629 3811 1.512156 CCCGGGTCAAACTGTTTCGG 61.512 60.000 14.18 18.72 36.23 4.30
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
33 38 2.147315 GATAGCAGCGCCGAGGATCA 62.147 60.000 2.29 0.00 33.17 2.92
34 39 1.445238 GATAGCAGCGCCGAGGATC 60.445 63.158 2.29 0.00 0.00 3.36
35 40 0.609406 TAGATAGCAGCGCCGAGGAT 60.609 55.000 2.29 0.00 0.00 3.24
46 51 6.012745 TCACCTTGCAGATAGATAGATAGCA 58.987 40.000 0.00 0.00 0.00 3.49
113 122 2.069273 CCAAAACAGACGACTAGCTGG 58.931 52.381 0.00 0.00 36.47 4.85
133 142 4.671590 CCAAACCCGTCCACCCCC 62.672 72.222 0.00 0.00 0.00 5.40
134 143 3.440162 AACCAAACCCGTCCACCCC 62.440 63.158 0.00 0.00 0.00 4.95
135 144 1.900016 GAACCAAACCCGTCCACCC 60.900 63.158 0.00 0.00 0.00 4.61
136 145 2.255881 CGAACCAAACCCGTCCACC 61.256 63.158 0.00 0.00 0.00 4.61
137 146 2.255881 CCGAACCAAACCCGTCCAC 61.256 63.158 0.00 0.00 0.00 4.02
138 147 2.111460 CCGAACCAAACCCGTCCA 59.889 61.111 0.00 0.00 0.00 4.02
139 148 2.111669 ACCGAACCAAACCCGTCC 59.888 61.111 0.00 0.00 0.00 4.79
140 149 2.255881 CCACCGAACCAAACCCGTC 61.256 63.158 0.00 0.00 0.00 4.79
141 150 2.059345 ATCCACCGAACCAAACCCGT 62.059 55.000 0.00 0.00 0.00 5.28
142 151 0.891904 AATCCACCGAACCAAACCCG 60.892 55.000 0.00 0.00 0.00 5.28
184 193 3.597255 CCATGGGATGAATCTCGATCTG 58.403 50.000 2.85 0.00 0.00 2.90
191 200 0.109342 GACGGCCATGGGATGAATCT 59.891 55.000 15.13 0.00 0.00 2.40
200 209 0.962356 AGAAGCAAAGACGGCCATGG 60.962 55.000 7.63 7.63 0.00 3.66
235 244 2.522193 GTCCCCGCTCTCCCCTAG 60.522 72.222 0.00 0.00 0.00 3.02
245 254 0.243636 CCATGAAAACTTGTCCCCGC 59.756 55.000 0.00 0.00 0.00 6.13
275 284 8.210954 CTGACGTGAAAAACAGAGAGAGAATCT 61.211 40.741 0.00 0.00 42.61 2.40
276 285 5.692204 TGACGTGAAAAACAGAGAGAGAATC 59.308 40.000 0.00 0.00 0.00 2.52
277 286 5.601662 TGACGTGAAAAACAGAGAGAGAAT 58.398 37.500 0.00 0.00 0.00 2.40
278 287 5.006153 TGACGTGAAAAACAGAGAGAGAA 57.994 39.130 0.00 0.00 0.00 2.87
285 294 5.175859 AGAGAAACTGACGTGAAAAACAGA 58.824 37.500 6.68 0.00 34.88 3.41
288 297 5.433005 GCTAGAGAAACTGACGTGAAAAAC 58.567 41.667 0.00 0.00 0.00 2.43
293 302 2.235891 TGGCTAGAGAAACTGACGTGA 58.764 47.619 0.00 0.00 0.00 4.35
294 303 2.724977 TGGCTAGAGAAACTGACGTG 57.275 50.000 0.00 0.00 0.00 4.49
295 304 3.746045 TTTGGCTAGAGAAACTGACGT 57.254 42.857 0.00 0.00 0.00 4.34
296 305 4.690748 TGAATTTGGCTAGAGAAACTGACG 59.309 41.667 0.00 0.00 0.00 4.35
317 334 2.048601 TCCTTACGAACCAAACCCTGA 58.951 47.619 0.00 0.00 0.00 3.86
322 339 3.059393 CGGAAAGTCCTTACGAACCAAAC 60.059 47.826 0.00 0.00 33.30 2.93
327 344 3.181523 GCAATCGGAAAGTCCTTACGAAC 60.182 47.826 9.70 2.22 36.31 3.95
330 347 1.323534 CGCAATCGGAAAGTCCTTACG 59.676 52.381 0.00 0.00 33.30 3.18
370 387 4.097892 GGAGAATTGCACCCGAAATATTGT 59.902 41.667 0.00 0.00 0.00 2.71
373 390 3.897239 TGGAGAATTGCACCCGAAATAT 58.103 40.909 0.00 0.00 0.00 1.28
391 408 4.771577 AGGCAATTGATTGTTGTACATGGA 59.228 37.500 10.34 0.00 39.88 3.41
396 413 4.990426 AGCAAAGGCAATTGATTGTTGTAC 59.010 37.500 10.34 0.00 44.61 2.90
399 416 4.151689 CAGAGCAAAGGCAATTGATTGTTG 59.848 41.667 10.34 8.22 44.61 3.33
411 428 0.823356 TTGGGACACAGAGCAAAGGC 60.823 55.000 0.00 0.00 39.29 4.35
428 445 4.675510 CATTCGGAAATGGAGTTGGATTG 58.324 43.478 0.00 0.00 38.91 2.67
464 481 9.506018 TCACAAAGTTGAAGATCAGAAATATCA 57.494 29.630 0.00 0.00 0.00 2.15
500 519 2.031012 CACAACCGCTGGAGCTGA 59.969 61.111 0.00 0.00 39.32 4.26
501 520 0.602638 TAACACAACCGCTGGAGCTG 60.603 55.000 0.00 0.00 39.32 4.24
502 521 0.320771 CTAACACAACCGCTGGAGCT 60.321 55.000 1.50 0.00 39.32 4.09
503 522 1.298859 CCTAACACAACCGCTGGAGC 61.299 60.000 1.50 0.00 37.78 4.70
504 523 0.034896 ACCTAACACAACCGCTGGAG 59.965 55.000 1.50 0.00 0.00 3.86
505 524 0.250124 CACCTAACACAACCGCTGGA 60.250 55.000 1.50 0.00 0.00 3.86
528 547 4.780021 AGCCCTATCTCTCTGAAAGAAACA 59.220 41.667 0.00 0.00 46.34 2.83
551 570 2.357075 TGGTTGTCACAAGTAAACGCA 58.643 42.857 0.00 0.00 0.00 5.24
575 594 5.640357 GCTGATCATTTTGCAGAAATGGAAA 59.360 36.000 22.68 12.02 38.00 3.13
586 610 3.864243 TCCCATTTGCTGATCATTTTGC 58.136 40.909 0.00 0.00 0.00 3.68
587 611 4.439057 CCTCCCATTTGCTGATCATTTTG 58.561 43.478 0.00 0.00 0.00 2.44
634 658 9.807649 AAGATAATATGGAAAATGTGAAGCAAC 57.192 29.630 0.00 0.00 0.00 4.17
643 673 6.151691 CACGGGCAAGATAATATGGAAAATG 58.848 40.000 0.00 0.00 0.00 2.32
674 704 1.760029 TCACTAGGCCATGATTACGCA 59.240 47.619 5.01 0.00 0.00 5.24
676 706 3.735237 ACTCACTAGGCCATGATTACG 57.265 47.619 5.01 0.00 0.00 3.18
677 707 5.304614 TCCTAACTCACTAGGCCATGATTAC 59.695 44.000 5.01 0.00 38.73 1.89
685 715 6.630638 GCCATATTATCCTAACTCACTAGGCC 60.631 46.154 0.00 0.00 38.73 5.19
686 716 6.155393 AGCCATATTATCCTAACTCACTAGGC 59.845 42.308 0.00 0.00 38.73 3.93
722 752 2.289547 TGAAGCTGAACTACCGTTTTGC 59.710 45.455 0.00 0.00 32.39 3.68
849 884 2.674796 AACTTAGTGATCGCTGACCC 57.325 50.000 19.11 0.00 0.00 4.46
928 963 8.709308 AGGCTGTCAGATAAGAATTGTATACTT 58.291 33.333 3.32 0.00 0.00 2.24
930 965 7.095439 GCAGGCTGTCAGATAAGAATTGTATAC 60.095 40.741 17.16 0.00 0.00 1.47
931 966 6.931281 GCAGGCTGTCAGATAAGAATTGTATA 59.069 38.462 17.16 0.00 0.00 1.47
934 969 3.944015 GCAGGCTGTCAGATAAGAATTGT 59.056 43.478 17.16 0.00 0.00 2.71
1075 1110 1.005450 TGGAAGGGACCAGGCAAATAC 59.995 52.381 0.00 0.00 34.77 1.89
1103 1138 2.404361 GCGTATAAGAACGGAGAATCGC 59.596 50.000 0.00 0.00 43.06 4.58
1105 1140 5.978322 AGAAAGCGTATAAGAACGGAGAATC 59.022 40.000 0.00 0.00 43.06 2.52
1136 1171 8.641498 ATGTTCACCTGAGATTAAGAAACAAT 57.359 30.769 0.00 0.00 0.00 2.71
1146 1181 5.745312 TCACACTATGTTCACCTGAGATT 57.255 39.130 0.00 0.00 0.00 2.40
1147 1182 5.337894 CCTTCACACTATGTTCACCTGAGAT 60.338 44.000 0.00 0.00 0.00 2.75
1312 1347 9.777297 AATGTTAGCAAAAGGTGTTTGATAATT 57.223 25.926 11.35 2.68 40.73 1.40
1475 1510 2.740714 GCATCCGACAAGCGTGACC 61.741 63.158 6.65 0.00 38.67 4.02
1490 1525 1.001641 GGACCCTTCAGCACAGCAT 60.002 57.895 0.00 0.00 0.00 3.79
1611 1646 3.611766 AGTACGAGAACCAATGAAGGG 57.388 47.619 0.00 0.00 0.00 3.95
1624 1659 4.733850 TGCAGAACATCTGTAAGTACGAG 58.266 43.478 8.97 0.00 45.94 4.18
2034 2069 8.788806 AGAAGAACTCCATAACTATAGATGTCG 58.211 37.037 6.78 0.00 0.00 4.35
2052 2087 5.215252 TGACGATTTCCAAGAGAAGAACT 57.785 39.130 0.00 0.00 35.40 3.01
2166 2204 7.001674 ACTGACACCATTTTGTATTCAGGTTA 58.998 34.615 0.00 0.00 34.28 2.85
2199 2237 6.821665 GGTGAACTTATGGTATAGTTGCTTCA 59.178 38.462 0.00 0.00 34.88 3.02
2229 2267 5.450376 TCAGCATTATTCTTCGAACGTTC 57.550 39.130 18.47 18.47 0.00 3.95
2272 2310 3.788227 TGCCCATGTCTGTAGAAAAGT 57.212 42.857 0.00 0.00 0.00 2.66
2451 2489 1.188219 TGGAGACGCTCTTGCTTCCT 61.188 55.000 6.78 0.00 38.09 3.36
2571 2609 3.787394 TCCGTGGTGGAGAAGGAC 58.213 61.111 0.00 0.00 43.74 3.85
2589 2627 2.294791 CGACGAGAAGGGCTCAGATATT 59.705 50.000 0.00 0.00 44.15 1.28
2595 2633 2.687805 CGACGACGAGAAGGGCTCA 61.688 63.158 0.00 0.00 44.15 4.26
2649 2687 0.377203 GAACGCCGCTAATTTCCTGG 59.623 55.000 0.00 0.00 0.00 4.45
2663 2701 3.081445 CGACAATGTACAAATCGAACGC 58.919 45.455 17.23 0.00 34.77 4.84
2772 2821 2.593436 AAACGACAGGTTGCCCCG 60.593 61.111 0.00 0.00 39.30 5.73
2820 2872 5.923204 AGAACCTATGTTGATCATCTCCAC 58.077 41.667 0.00 0.00 37.91 4.02
2834 2886 8.288208 GTGAATCATATCTTGCAAGAACCTATG 58.712 37.037 31.55 29.25 38.77 2.23
2840 2892 8.151141 GAGATGTGAATCATATCTTGCAAGAA 57.849 34.615 31.55 20.53 41.22 2.52
2855 2933 5.247110 ACAGTAGTGGTTCAGAGATGTGAAT 59.753 40.000 1.92 0.00 38.68 2.57
2913 3005 2.365293 CCGACCCATGTCAGTCATCATA 59.635 50.000 8.09 0.00 41.85 2.15
2923 3015 4.101448 AGCAGGCCGACCCATGTC 62.101 66.667 0.00 0.00 38.18 3.06
2963 3055 4.421365 GGTCATGCTTGGCCTCAA 57.579 55.556 15.66 0.00 44.72 3.02
3001 3093 4.744631 GTGTGTCCATTCCAAATTGTTCAC 59.255 41.667 0.00 0.00 0.00 3.18
3025 3118 4.885907 AGATTGCAGATGAATTTGGTCGAT 59.114 37.500 0.00 0.00 0.00 3.59
3042 3135 2.350772 CCGTTTCAAGGTGTGAGATTGC 60.351 50.000 0.00 0.00 37.61 3.56
3050 3143 2.193536 GCAGCCCGTTTCAAGGTGT 61.194 57.895 0.00 0.00 0.00 4.16
3120 3231 1.216710 CACGGAGCCAGTTCTCTCC 59.783 63.158 0.00 0.00 44.14 3.71
3212 3358 5.018539 TCCGTTCTTCACTTCTTTCTCAA 57.981 39.130 0.00 0.00 0.00 3.02
3213 3359 4.665833 TCCGTTCTTCACTTCTTTCTCA 57.334 40.909 0.00 0.00 0.00 3.27
3226 3376 8.499403 TTTTTGGAAATTTTTGATCCGTTCTT 57.501 26.923 0.00 0.00 35.96 2.52
3248 3398 3.119388 CGGCAGGTTGACATGATGATTTT 60.119 43.478 0.00 0.00 0.00 1.82
3255 3405 1.346395 ACTTACGGCAGGTTGACATGA 59.654 47.619 0.00 0.00 0.00 3.07
3340 3508 3.006110 TCCCACTTTAACGAGTTGACGAT 59.994 43.478 0.00 0.00 37.03 3.73
3360 3528 2.324332 TTCGATCGCTCGCTGTCTCC 62.324 60.000 11.09 0.00 44.65 3.71
3401 3579 4.103103 CGACCGCTCGCTGTCTCA 62.103 66.667 10.86 0.00 31.91 3.27
3415 3593 1.601903 TGACTTGTGCATTGGTTCGAC 59.398 47.619 0.00 0.00 0.00 4.20
3442 3620 1.883638 GCTGGTGTGGATGTGTGTGAT 60.884 52.381 0.00 0.00 0.00 3.06
3484 3662 4.778415 CAGGACGTGTCTCCGGCG 62.778 72.222 0.00 0.00 36.47 6.46
3486 3664 2.709125 TTTGCAGGACGTGTCTCCGG 62.709 60.000 0.00 0.00 35.20 5.14
3490 3668 0.107410 TGGTTTTGCAGGACGTGTCT 60.107 50.000 0.00 0.00 0.00 3.41
3493 3671 1.010125 CGTGGTTTTGCAGGACGTG 60.010 57.895 0.00 0.00 0.00 4.49
3543 3722 3.127548 GCCTCGCTTTTGATGATTCTTCA 59.872 43.478 0.00 0.00 36.00 3.02
3606 3788 3.966543 CAGTTTGACCCGGGGCCT 61.967 66.667 27.91 11.70 0.00 5.19
3608 3790 1.802337 GAAACAGTTTGACCCGGGGC 61.802 60.000 27.92 25.98 0.00 5.80


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

AutoCloner maintained by Alex Coulton.