Multiple sequence alignment - TraesCS5D01G242600

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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 TraesCS5D01G242600 chr5D 100.000 4328 0 0 1 4328 350995222 350999549 0.000000e+00 7993
1 TraesCS5D01G242600 chr5A 93.786 2108 79 15 1890 3969 451466566 451468649 0.000000e+00 3120
2 TraesCS5D01G242600 chr5A 92.291 934 38 15 862 1769 451465522 451466447 0.000000e+00 1295
3 TraesCS5D01G242600 chr5A 91.189 715 31 12 154 863 451464806 451465493 0.000000e+00 942
4 TraesCS5D01G242600 chr5A 95.469 309 13 1 4021 4328 451468666 451468974 3.890000e-135 492
5 TraesCS5D01G242600 chr5A 94.194 155 6 2 1 155 451464460 451464611 2.600000e-57 233
6 TraesCS5D01G242600 chr5A 97.115 104 2 1 1800 1903 451466447 451466549 1.600000e-39 174
7 TraesCS5D01G242600 chr5B 94.551 1725 72 6 2611 4326 411812916 411814627 0.000000e+00 2645
8 TraesCS5D01G242600 chr5B 89.219 1382 56 45 1 1332 411810322 411811660 0.000000e+00 1640
9 TraesCS5D01G242600 chr5B 85.801 993 89 19 1550 2503 411811958 411812937 0.000000e+00 1005


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 TraesCS5D01G242600 chr5D 350995222 350999549 4327 False 7993.000000 7993 100.000000 1 4328 1 chr5D.!!$F1 4327
1 TraesCS5D01G242600 chr5A 451464460 451468974 4514 False 1042.666667 3120 94.007333 1 4328 6 chr5A.!!$F1 4327
2 TraesCS5D01G242600 chr5B 411810322 411814627 4305 False 1763.333333 2645 89.857000 1 4326 3 chr5B.!!$F1 4325

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
972 1208 0.193574 TGGGAGAGGAAGGAGGTTGT 59.806 55.0 0.00 0.0 0.0 3.32 F
2134 2593 0.037734 ACGTTGGCTAAAGGGGGAAG 59.962 55.0 0.33 0.0 0.0 3.46 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2540 3035 0.472044 TTCTACTGCCCTTGCACACA 59.528 50.0 0.00 0.0 44.23 3.72 R
4016 4521 0.323178 AAGCAGACTCAATGGCCTGG 60.323 55.0 3.32 0.0 0.00 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
117 118 9.668497 GAATAGTCAAGGTACCTAATCAGTTTT 57.332 33.333 16.67 2.86 0.00 2.43
128 129 7.595819 ACCTAATCAGTTTTGTTTCATCCAA 57.404 32.000 0.00 0.00 0.00 3.53
131 132 9.492973 CCTAATCAGTTTTGTTTCATCCAAAAT 57.507 29.630 0.00 0.00 42.04 1.82
136 137 8.828644 TCAGTTTTGTTTCATCCAAAATCAATG 58.171 29.630 0.00 0.00 42.04 2.82
140 141 6.185114 TGTTTCATCCAAAATCAATGGGTT 57.815 33.333 0.00 0.00 38.54 4.11
142 143 7.915930 TGTTTCATCCAAAATCAATGGGTTAT 58.084 30.769 0.00 0.00 38.54 1.89
143 144 8.381636 TGTTTCATCCAAAATCAATGGGTTATT 58.618 29.630 0.00 0.00 38.54 1.40
144 145 9.883142 GTTTCATCCAAAATCAATGGGTTATTA 57.117 29.630 0.00 0.00 38.54 0.98
146 147 9.883142 TTCATCCAAAATCAATGGGTTATTAAC 57.117 29.630 0.00 0.00 38.54 2.01
147 148 9.265862 TCATCCAAAATCAATGGGTTATTAACT 57.734 29.630 6.52 0.00 38.54 2.24
187 381 9.155975 ACAAGTTCAGTGTGTGAGATTATAATC 57.844 33.333 16.35 16.35 36.21 1.75
188 382 9.154847 CAAGTTCAGTGTGTGAGATTATAATCA 57.845 33.333 24.00 6.47 37.89 2.57
189 383 9.896645 AAGTTCAGTGTGTGAGATTATAATCAT 57.103 29.630 24.00 11.45 37.89 2.45
231 426 4.029861 CAGTCGTGCAGTTAACGTGTATAC 59.970 45.833 0.00 0.00 41.70 1.47
232 427 3.913763 GTCGTGCAGTTAACGTGTATACA 59.086 43.478 0.08 0.08 41.70 2.29
233 428 4.382457 GTCGTGCAGTTAACGTGTATACAA 59.618 41.667 7.25 0.00 41.70 2.41
234 429 5.061311 GTCGTGCAGTTAACGTGTATACAAT 59.939 40.000 7.25 0.00 41.70 2.71
235 430 6.251163 GTCGTGCAGTTAACGTGTATACAATA 59.749 38.462 7.25 0.00 41.70 1.90
236 431 6.974048 TCGTGCAGTTAACGTGTATACAATAT 59.026 34.615 7.25 0.00 41.70 1.28
237 432 8.127954 TCGTGCAGTTAACGTGTATACAATATA 58.872 33.333 7.25 0.00 41.70 0.86
238 433 8.203346 CGTGCAGTTAACGTGTATACAATATAC 58.797 37.037 7.25 3.08 36.31 1.47
262 457 6.666546 ACATTCAGGGTTCAATTCAATCATCT 59.333 34.615 0.00 0.00 0.00 2.90
264 459 7.870509 TTCAGGGTTCAATTCAATCATCTAG 57.129 36.000 0.00 0.00 0.00 2.43
268 468 9.565090 CAGGGTTCAATTCAATCATCTAGATTA 57.435 33.333 1.33 0.00 45.06 1.75
289 489 9.449719 AGATTACAGTAACCTATTCTTTGGTTG 57.550 33.333 7.56 0.00 45.12 3.77
290 490 7.989416 TTACAGTAACCTATTCTTTGGTTGG 57.011 36.000 7.56 0.99 45.12 3.77
292 492 6.370453 ACAGTAACCTATTCTTTGGTTGGTT 58.630 36.000 7.56 0.00 45.12 3.67
293 493 7.519927 ACAGTAACCTATTCTTTGGTTGGTTA 58.480 34.615 7.56 0.00 45.12 2.85
294 494 8.000127 ACAGTAACCTATTCTTTGGTTGGTTAA 59.000 33.333 7.56 0.00 45.12 2.01
307 507 8.865420 TTTGGTTGGTTAATATGCAGTAACTA 57.135 30.769 14.07 8.10 35.90 2.24
333 533 8.616076 AGAATTCACTGATCAATTCGATAAACC 58.384 33.333 8.44 0.00 41.84 3.27
784 984 3.675225 GCCTTTTCTTTTCTGCCGATTTC 59.325 43.478 0.00 0.00 0.00 2.17
785 985 4.237724 CCTTTTCTTTTCTGCCGATTTCC 58.762 43.478 0.00 0.00 0.00 3.13
786 986 4.021981 CCTTTTCTTTTCTGCCGATTTCCT 60.022 41.667 0.00 0.00 0.00 3.36
787 987 4.766404 TTTCTTTTCTGCCGATTTCCTC 57.234 40.909 0.00 0.00 0.00 3.71
788 988 3.703001 TCTTTTCTGCCGATTTCCTCT 57.297 42.857 0.00 0.00 0.00 3.69
805 1005 3.078305 TCCTCTCCTCTTCCCTTCTCTTT 59.922 47.826 0.00 0.00 0.00 2.52
822 1022 2.032030 TCTTTTCTTTTTGCGCCGAGAG 60.032 45.455 4.18 0.00 0.00 3.20
918 1148 4.850193 CCTGATGGGCCAACAAGT 57.150 55.556 17.73 0.00 0.00 3.16
925 1155 0.539438 TGGGCCAACAAGTGATGGAC 60.539 55.000 2.13 8.30 44.50 4.02
927 1157 0.539438 GGCCAACAAGTGATGGACCA 60.539 55.000 11.48 0.00 39.85 4.02
930 1160 2.094545 GCCAACAAGTGATGGACCAATC 60.095 50.000 11.48 0.00 40.03 2.67
943 1174 1.378762 CCAATCGGTGGTGTTCCCT 59.621 57.895 0.00 0.00 43.20 4.20
972 1208 0.193574 TGGGAGAGGAAGGAGGTTGT 59.806 55.000 0.00 0.00 0.00 3.32
981 1222 3.325135 AGGAAGGAGGTTGTAAGTGTGAG 59.675 47.826 0.00 0.00 0.00 3.51
995 1236 1.123861 TGTGAGCAGCAGGAAGAGGT 61.124 55.000 0.00 0.00 0.00 3.85
1178 1419 2.510238 CTACGAGCACCAGCAGGC 60.510 66.667 0.00 0.00 45.49 4.85
1348 1599 2.590092 GGTGAACCATCTCCCCCG 59.410 66.667 0.00 0.00 33.89 5.73
1349 1600 2.298661 GGTGAACCATCTCCCCCGT 61.299 63.158 0.00 0.00 33.89 5.28
1397 1807 3.129988 GCTGCCACTTTCATTGATAGCTT 59.870 43.478 0.00 0.00 0.00 3.74
1424 1834 1.002134 AGTGGCTGGATTGGGTTCG 60.002 57.895 0.00 0.00 0.00 3.95
1449 1866 7.044641 CGCATTCTAGTATATTCGATCGGAAAG 60.045 40.741 16.41 5.66 38.36 2.62
1502 1919 4.636206 GGTTGATCTGTTAATGGTGAGGAC 59.364 45.833 0.00 0.00 0.00 3.85
1535 1952 1.015109 GCAGAGTGCAGATGTCATGG 58.985 55.000 0.00 0.00 44.26 3.66
1578 1995 3.308331 GGGGGTAGAATCGGTTGGTAAAA 60.308 47.826 0.00 0.00 0.00 1.52
1586 2003 2.690786 TCGGTTGGTAAAATCGTCAGG 58.309 47.619 0.00 0.00 0.00 3.86
1781 2202 8.135529 ACACATAAAAGGAACAAGCTAGAAAAC 58.864 33.333 0.00 0.00 0.00 2.43
1794 2215 3.906601 GCTAGAAAACGTTTTGCTAGTGC 59.093 43.478 32.33 25.35 34.31 4.40
1852 2280 4.164981 TCCATAGTTTACCAGAGGTGTGT 58.835 43.478 0.00 0.00 36.19 3.72
1925 2383 7.053316 TGAAATAAAATACATGATGGGGCAG 57.947 36.000 0.00 0.00 0.00 4.85
1936 2394 1.876156 GATGGGGCAGAACGATGATTC 59.124 52.381 0.00 0.00 0.00 2.52
1937 2395 0.617935 TGGGGCAGAACGATGATTCA 59.382 50.000 0.00 0.00 0.00 2.57
2001 2460 7.807433 TGGAGTTTTTACATCGACATTGAATTG 59.193 33.333 0.00 0.00 0.00 2.32
2014 2473 7.918033 TCGACATTGAATTGTATGTGTTGTTTT 59.082 29.630 6.73 0.00 35.24 2.43
2134 2593 0.037734 ACGTTGGCTAAAGGGGGAAG 59.962 55.000 0.33 0.00 0.00 3.46
2135 2594 0.679960 CGTTGGCTAAAGGGGGAAGG 60.680 60.000 0.00 0.00 0.00 3.46
2136 2595 0.702316 GTTGGCTAAAGGGGGAAGGA 59.298 55.000 0.00 0.00 0.00 3.36
2137 2596 0.702316 TTGGCTAAAGGGGGAAGGAC 59.298 55.000 0.00 0.00 0.00 3.85
2138 2597 0.476808 TGGCTAAAGGGGGAAGGACA 60.477 55.000 0.00 0.00 0.00 4.02
2419 2906 7.499563 GGAAGAACTAATAAGGACTTGGGAATC 59.500 40.741 0.00 0.00 0.00 2.52
2509 3004 7.764331 TGCATCACATGATATTATTGCATACC 58.236 34.615 0.00 0.00 32.63 2.73
2532 3027 8.904099 ACCTTATATTCCTGTACTTATGCAAC 57.096 34.615 0.00 0.00 0.00 4.17
2533 3028 7.656137 ACCTTATATTCCTGTACTTATGCAACG 59.344 37.037 0.00 0.00 0.00 4.10
2534 3029 7.656137 CCTTATATTCCTGTACTTATGCAACGT 59.344 37.037 0.00 0.00 0.00 3.99
2540 3035 3.459145 TGTACTTATGCAACGTGTGTGT 58.541 40.909 0.00 0.00 0.00 3.72
2599 3094 0.608640 CACTAGGCTTCCTTCCACGT 59.391 55.000 0.00 0.00 34.61 4.49
2619 3114 8.622157 TCCACGTTTTATCATTCAGTTTTAACA 58.378 29.630 0.00 0.00 0.00 2.41
2758 3253 7.173390 GGATACCATACACAAGAAAGATAAGGC 59.827 40.741 0.00 0.00 0.00 4.35
2762 3257 7.047891 CCATACACAAGAAAGATAAGGCTACA 58.952 38.462 0.00 0.00 0.00 2.74
2771 3266 3.450904 AGATAAGGCTACAGTGGACCAA 58.549 45.455 0.00 0.00 0.00 3.67
2826 3321 5.123227 ACTTAGCTTGCTTTACAGTTGACA 58.877 37.500 0.00 0.00 0.00 3.58
2998 3493 4.610605 TTTCCTCGTTTGGATGACAGTA 57.389 40.909 0.00 0.00 35.83 2.74
3000 3495 4.819105 TCCTCGTTTGGATGACAGTAAT 57.181 40.909 0.00 0.00 0.00 1.89
3063 3558 7.615582 TGATGAATCTGTCCAAACAATCTAC 57.384 36.000 0.00 0.00 34.24 2.59
3114 3610 0.684535 TCAATGCACTTCTCCGGTCA 59.315 50.000 0.00 0.00 0.00 4.02
3145 3641 8.428063 TCATCAATTTTGTTGATACCAAAAGGT 58.572 29.630 3.23 0.00 42.96 3.50
3146 3642 9.054922 CATCAATTTTGTTGATACCAAAAGGTT 57.945 29.630 3.23 0.00 42.96 3.50
3161 3657 6.183360 ACCAAAAGGTTTAACTACTCCGTTTG 60.183 38.462 12.06 12.06 43.51 2.93
3365 3861 5.640783 TCTGCAGCATACATACATTCTATGC 59.359 40.000 9.47 0.00 42.06 3.14
3459 3958 3.118112 AGCATGTTCTCACCTAATCCCAG 60.118 47.826 0.00 0.00 0.00 4.45
3495 3994 0.689055 ACTGCTGCCACTCTTCATGA 59.311 50.000 0.00 0.00 0.00 3.07
3550 4049 8.836413 GCAAGTACCAATTTTATGATGCTACTA 58.164 33.333 0.00 0.00 0.00 1.82
3639 4138 2.859165 AATCTGCGAGGTTCTTTCCA 57.141 45.000 0.00 0.00 0.00 3.53
3723 4222 4.581868 CCCTCGTAACCAACCTTTTATCA 58.418 43.478 0.00 0.00 0.00 2.15
3741 4240 1.026182 CAGCTTCTGGGCGTTGCATA 61.026 55.000 0.00 0.00 37.29 3.14
3744 4243 1.009829 CTTCTGGGCGTTGCATACTC 58.990 55.000 0.00 0.00 0.00 2.59
3772 4271 4.074970 CAGTAACTGACAAGGCCAAGAAT 58.925 43.478 5.01 0.00 32.44 2.40
3819 4319 7.275779 AGCGATGTAGTAGTACAAATTCAAGTG 59.724 37.037 14.26 0.00 42.54 3.16
3823 4323 7.438564 TGTAGTAGTACAAATTCAAGTGCAGA 58.561 34.615 7.99 0.00 36.15 4.26
3839 4340 2.047679 CAGAACTGCTTGCTTTCTGC 57.952 50.000 17.76 0.00 39.75 4.26
3850 4351 4.396166 GCTTGCTTTCTGCTATTCACCTTA 59.604 41.667 0.00 0.00 43.37 2.69
3913 4414 5.708948 ACTCTCAGAGACTCTTCAAAATCG 58.291 41.667 9.27 0.00 33.32 3.34
3942 4443 1.888215 TTCTTCTTCAGTGCCTGCAG 58.112 50.000 6.78 6.78 0.00 4.41
3970 4475 3.028850 ACATTCATGATTGGCCAAGAGG 58.971 45.455 24.94 14.46 38.23 3.69
3975 4480 1.909700 TGATTGGCCAAGAGGTTCAC 58.090 50.000 24.94 7.82 37.19 3.18
3985 4490 3.545703 CAAGAGGTTCACCAGTGTTCTT 58.454 45.455 0.00 0.00 38.89 2.52
3986 4491 3.477210 AGAGGTTCACCAGTGTTCTTC 57.523 47.619 0.00 0.00 38.89 2.87
3987 4492 3.041946 AGAGGTTCACCAGTGTTCTTCT 58.958 45.455 0.00 1.71 38.89 2.85
3988 4493 3.134458 GAGGTTCACCAGTGTTCTTCTG 58.866 50.000 0.00 0.00 38.89 3.02
3989 4494 2.505819 AGGTTCACCAGTGTTCTTCTGT 59.494 45.455 0.00 0.00 38.89 3.41
3990 4495 3.054361 AGGTTCACCAGTGTTCTTCTGTT 60.054 43.478 0.00 0.00 38.89 3.16
4016 4521 0.106819 AGATCATCAGGCCAACCAGC 60.107 55.000 5.01 0.00 39.06 4.85
4030 4535 1.751927 CCAGCCAGGCCATTGAGTC 60.752 63.158 8.22 0.00 0.00 3.36
4071 4576 5.122869 GTCATGCCCATATATGTGCTTGTAG 59.877 44.000 24.91 11.29 37.50 2.74
4279 4784 1.393603 CTGCTCAGACCACGATAGGA 58.606 55.000 0.00 0.00 43.77 2.94
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
117 118 5.822132 ACCCATTGATTTTGGATGAAACA 57.178 34.783 0.00 0.00 36.26 2.83
143 144 9.575868 TGAACTTGTGATGGGTTATTTTAGTTA 57.424 29.630 0.00 0.00 0.00 2.24
144 145 8.472007 TGAACTTGTGATGGGTTATTTTAGTT 57.528 30.769 0.00 0.00 0.00 2.24
146 147 8.023128 CACTGAACTTGTGATGGGTTATTTTAG 58.977 37.037 0.00 0.00 37.60 1.85
147 148 7.504238 ACACTGAACTTGTGATGGGTTATTTTA 59.496 33.333 0.00 0.00 38.65 1.52
156 350 3.205338 TCACACACTGAACTTGTGATGG 58.795 45.455 9.38 0.00 46.18 3.51
190 384 9.821662 GCACGACTGAAAAGTTAGTTATATTTT 57.178 29.630 0.00 0.00 0.00 1.82
194 388 7.149973 ACTGCACGACTGAAAAGTTAGTTATA 58.850 34.615 0.00 0.00 0.00 0.98
233 428 9.645128 TGATTGAATTGAACCCTGAATGTATAT 57.355 29.630 0.00 0.00 0.00 0.86
234 429 9.645128 ATGATTGAATTGAACCCTGAATGTATA 57.355 29.630 0.00 0.00 0.00 1.47
235 430 7.959658 TGATTGAATTGAACCCTGAATGTAT 57.040 32.000 0.00 0.00 0.00 2.29
236 431 7.835682 AGATGATTGAATTGAACCCTGAATGTA 59.164 33.333 0.00 0.00 0.00 2.29
237 432 6.666546 AGATGATTGAATTGAACCCTGAATGT 59.333 34.615 0.00 0.00 0.00 2.71
238 433 7.108841 AGATGATTGAATTGAACCCTGAATG 57.891 36.000 0.00 0.00 0.00 2.67
264 459 8.674607 CCAACCAAAGAATAGGTTACTGTAATC 58.325 37.037 3.23 2.88 45.93 1.75
268 468 5.948842 ACCAACCAAAGAATAGGTTACTGT 58.051 37.500 0.00 0.00 45.93 3.55
294 494 9.703892 GATCAGTGAATTCTAGTTACTGCATAT 57.296 33.333 14.84 6.62 38.81 1.78
307 507 8.616076 GGTTTATCGAATTGATCAGTGAATTCT 58.384 33.333 13.38 2.24 36.27 2.40
315 515 4.552767 GCACCGGTTTATCGAATTGATCAG 60.553 45.833 2.97 0.00 38.57 2.90
316 516 3.311322 GCACCGGTTTATCGAATTGATCA 59.689 43.478 2.97 0.00 38.57 2.92
333 533 0.739462 TACTGCTCGATTTGGCACCG 60.739 55.000 0.00 0.00 34.57 4.94
464 664 1.915983 GGGTCTCTGTGGGGGATTC 59.084 63.158 0.00 0.00 0.00 2.52
517 717 2.947532 GCTTCCCCAGGCTTTTGGC 61.948 63.158 0.00 0.00 46.43 4.52
520 720 2.283173 CCGCTTCCCCAGGCTTTT 60.283 61.111 0.00 0.00 0.00 2.27
784 984 2.846665 AGAGAAGGGAAGAGGAGAGG 57.153 55.000 0.00 0.00 0.00 3.69
785 985 4.777366 AGAAAAGAGAAGGGAAGAGGAGAG 59.223 45.833 0.00 0.00 0.00 3.20
786 986 4.757692 AGAAAAGAGAAGGGAAGAGGAGA 58.242 43.478 0.00 0.00 0.00 3.71
787 987 5.497464 AAGAAAAGAGAAGGGAAGAGGAG 57.503 43.478 0.00 0.00 0.00 3.69
788 988 5.913946 AAAGAAAAGAGAAGGGAAGAGGA 57.086 39.130 0.00 0.00 0.00 3.71
805 1005 1.234615 CCCTCTCGGCGCAAAAAGAA 61.235 55.000 10.83 0.00 0.00 2.52
822 1022 1.618616 CCAACAACCTATCCAACCCCC 60.619 57.143 0.00 0.00 0.00 5.40
927 1157 3.512219 TTTTAGGGAACACCACCGATT 57.488 42.857 0.00 0.00 43.89 3.34
972 1208 1.970640 TCTTCCTGCTGCTCACACTTA 59.029 47.619 0.00 0.00 0.00 2.24
981 1222 0.250467 TTGTCACCTCTTCCTGCTGC 60.250 55.000 0.00 0.00 0.00 5.25
995 1236 2.741985 CACCTCGCGCCATTGTCA 60.742 61.111 0.00 0.00 0.00 3.58
1397 1807 4.709397 CCCAATCCAGCCACTGTAAATTTA 59.291 41.667 0.00 0.00 0.00 1.40
1424 1834 7.221067 CCTTTCCGATCGAATATACTAGAATGC 59.779 40.741 18.66 0.00 0.00 3.56
1449 1866 4.023291 TGTAAATTCATTGCCTTCTCCCC 58.977 43.478 0.00 0.00 0.00 4.81
1521 1938 5.761726 TCAATATTCTCCATGACATCTGCAC 59.238 40.000 0.00 0.00 0.00 4.57
1530 1947 6.042777 GTGACTCGTTCAATATTCTCCATGA 58.957 40.000 0.00 0.00 35.39 3.07
1531 1948 5.235186 GGTGACTCGTTCAATATTCTCCATG 59.765 44.000 0.00 0.00 35.39 3.66
1532 1949 5.360591 GGTGACTCGTTCAATATTCTCCAT 58.639 41.667 0.00 0.00 35.39 3.41
1533 1950 4.676986 CGGTGACTCGTTCAATATTCTCCA 60.677 45.833 0.00 0.00 35.39 3.86
1534 1951 3.797256 CGGTGACTCGTTCAATATTCTCC 59.203 47.826 0.00 0.00 35.39 3.71
1535 1952 3.797256 CCGGTGACTCGTTCAATATTCTC 59.203 47.826 0.00 0.00 35.39 2.87
1578 1995 4.817517 ACTCGTTACAATTTCCTGACGAT 58.182 39.130 0.00 0.00 38.60 3.73
1586 2003 5.390613 CCACCAATGACTCGTTACAATTTC 58.609 41.667 0.00 0.00 0.00 2.17
1619 2036 6.441284 TCCCAATGAATCAATGACTTTCCAAT 59.559 34.615 0.00 0.00 0.00 3.16
1844 2265 3.616821 GGTTGAAAGCAAAAACACACCTC 59.383 43.478 0.00 0.00 35.42 3.85
1852 2280 1.836802 AGCCCTGGTTGAAAGCAAAAA 59.163 42.857 0.00 0.00 35.42 1.94
1916 2374 1.876156 GAATCATCGTTCTGCCCCATC 59.124 52.381 0.00 0.00 0.00 3.51
1925 2383 5.335127 CCAGGACAAATTGAATCATCGTTC 58.665 41.667 0.00 0.00 0.00 3.95
1936 2394 1.173043 TAAGGCGCCAGGACAAATTG 58.827 50.000 31.54 0.00 0.00 2.32
1937 2395 2.024414 GATAAGGCGCCAGGACAAATT 58.976 47.619 31.54 14.07 0.00 1.82
2135 2594 3.071167 AGTGGACAGTTAAAGGAGGTGTC 59.929 47.826 0.00 0.00 37.41 3.67
2136 2595 3.046374 AGTGGACAGTTAAAGGAGGTGT 58.954 45.455 0.00 0.00 0.00 4.16
2137 2596 3.181454 ACAGTGGACAGTTAAAGGAGGTG 60.181 47.826 0.00 0.00 0.00 4.00
2138 2597 3.046374 ACAGTGGACAGTTAAAGGAGGT 58.954 45.455 0.00 0.00 0.00 3.85
2175 2635 1.999735 CCGCGTTAATTTGCAGAGAGA 59.000 47.619 4.92 0.00 0.00 3.10
2366 2853 6.761099 TCCTAGTTATGACTCAGACTGAAC 57.239 41.667 6.61 4.67 37.33 3.18
2419 2906 2.862541 TCATAATTCCAATGCCTCCCG 58.137 47.619 0.00 0.00 0.00 5.14
2509 3004 8.487970 CACGTTGCATAAGTACAGGAATATAAG 58.512 37.037 0.00 0.00 0.00 1.73
2523 3018 2.031560 ACACACACACACGTTGCATAAG 59.968 45.455 0.00 0.00 0.00 1.73
2524 3019 2.010497 ACACACACACACGTTGCATAA 58.990 42.857 0.00 0.00 0.00 1.90
2531 3026 1.643868 CCTTGCACACACACACACGT 61.644 55.000 0.00 0.00 0.00 4.49
2532 3027 1.062365 CCTTGCACACACACACACG 59.938 57.895 0.00 0.00 0.00 4.49
2533 3028 1.433064 CCCTTGCACACACACACAC 59.567 57.895 0.00 0.00 0.00 3.82
2534 3029 2.413963 GCCCTTGCACACACACACA 61.414 57.895 0.00 0.00 37.47 3.72
2540 3035 0.472044 TTCTACTGCCCTTGCACACA 59.528 50.000 0.00 0.00 44.23 3.72
2571 3066 1.340568 GGAAGCCTAGTGACGGGATAC 59.659 57.143 2.11 0.00 0.00 2.24
2572 3067 1.217183 AGGAAGCCTAGTGACGGGATA 59.783 52.381 2.11 0.00 28.47 2.59
2665 3160 6.797033 CGGATACAAATGAGTCAAGAAAACAC 59.203 38.462 0.00 0.00 0.00 3.32
2758 3253 4.789012 AATGCAAATTGGTCCACTGTAG 57.211 40.909 0.00 0.00 0.00 2.74
2762 3257 3.900601 TGGTAAATGCAAATTGGTCCACT 59.099 39.130 0.00 0.00 0.00 4.00
2771 3266 5.047164 TGCTTCTGATGTGGTAAATGCAAAT 60.047 36.000 0.00 0.00 0.00 2.32
2826 3321 3.117284 ACCACCAAACCCTTGTTATCACT 60.117 43.478 0.00 0.00 33.30 3.41
2998 3493 5.185828 GTGCAACTCCCTATTCAGGAAAATT 59.814 40.000 0.00 0.00 45.91 1.82
3000 3495 4.079253 GTGCAACTCCCTATTCAGGAAAA 58.921 43.478 0.00 0.00 45.91 2.29
3063 3558 1.060266 CTCAGCACGAGCAGATTTTCG 59.940 52.381 7.77 0.00 45.49 3.46
3114 3610 9.775854 TTGGTATCAACAAAATTGATGAAACAT 57.224 25.926 9.68 0.00 42.11 2.71
3428 3924 6.737720 AGGTGAGAACATGCTATCATTCTA 57.262 37.500 0.00 0.00 0.00 2.10
3459 3958 5.053145 CAGCAGTACCATCTTATCTGAACC 58.947 45.833 0.00 0.00 0.00 3.62
3639 4138 4.196971 AGTTGGCGTTCAAGAGTAACTTT 58.803 39.130 0.00 0.00 36.61 2.66
3723 4222 1.026718 GTATGCAACGCCCAGAAGCT 61.027 55.000 0.00 0.00 0.00 3.74
3741 4240 2.598565 TGTCAGTTACTGCAGAGGAGT 58.401 47.619 23.35 5.49 0.00 3.85
3744 4243 2.693069 CCTTGTCAGTTACTGCAGAGG 58.307 52.381 23.35 9.42 0.00 3.69
3772 4271 4.026744 CTGGTCCCTGACTCATTCTTCTA 58.973 47.826 0.00 0.00 32.47 2.10
3819 4319 2.047679 CAGAAAGCAAGCAGTTCTGC 57.952 50.000 18.99 15.88 41.16 4.26
3850 4351 6.952358 TCTACACTCCTTCCAAGTATTACTGT 59.048 38.462 0.00 0.00 0.00 3.55
3913 4414 2.560105 ACTGAAGAAGAATTTGGCTGGC 59.440 45.455 0.00 0.00 0.00 4.85
3942 4443 4.338964 TGGCCAATCATGAATGTGTATGTC 59.661 41.667 0.61 0.00 0.00 3.06
3970 4475 5.585047 ACTTAACAGAAGAACACTGGTGAAC 59.415 40.000 7.78 1.56 39.38 3.18
3975 4480 4.703897 TCCACTTAACAGAAGAACACTGG 58.296 43.478 0.00 0.00 39.38 4.00
3985 4490 4.141846 GCCTGATGATCTCCACTTAACAGA 60.142 45.833 0.00 0.00 0.00 3.41
3986 4491 4.125703 GCCTGATGATCTCCACTTAACAG 58.874 47.826 0.00 0.00 0.00 3.16
3987 4492 3.118261 GGCCTGATGATCTCCACTTAACA 60.118 47.826 0.00 0.00 0.00 2.41
3988 4493 3.118261 TGGCCTGATGATCTCCACTTAAC 60.118 47.826 3.32 0.00 0.00 2.01
3989 4494 3.114606 TGGCCTGATGATCTCCACTTAA 58.885 45.455 3.32 0.00 0.00 1.85
3990 4495 2.763039 TGGCCTGATGATCTCCACTTA 58.237 47.619 3.32 0.00 0.00 2.24
4016 4521 0.323178 AAGCAGACTCAATGGCCTGG 60.323 55.000 3.32 0.00 0.00 4.45
4279 4784 0.537371 CTCACTCCTTGCCGGGTTTT 60.537 55.000 2.18 0.00 0.00 2.43


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

AutoCloner maintained by Alex Coulton.