Multiple sequence alignment - TraesCS2A01G551100

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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 TraesCS2A01G551100 chr2A 100.000 2647 0 0 1 2647 758101601 758104247 0.000000e+00 4889.0
1 TraesCS2A01G551100 chr2B 86.113 2758 186 92 4 2647 769948438 769951112 0.000000e+00 2789.0
2 TraesCS2A01G551100 chr2B 95.122 41 2 0 1223 1263 685736864 685736904 6.120000e-07 65.8
3 TraesCS2A01G551100 chr2D 88.802 1411 74 33 1284 2643 627583188 627584565 0.000000e+00 1653.0
4 TraesCS2A01G551100 chr2D 90.506 1127 63 25 157 1254 627582081 627583192 0.000000e+00 1448.0
5 TraesCS2A01G551100 chr2D 88.344 163 12 4 23 183 627581750 627581907 3.480000e-44 189.0
6 TraesCS2A01G551100 chr6D 83.529 255 33 6 1386 1637 470633209 470632961 2.050000e-56 230.0
7 TraesCS2A01G551100 chr6B 81.754 285 43 6 1356 1637 720502426 720502704 2.050000e-56 230.0
8 TraesCS2A01G551100 chr3D 95.122 41 2 0 1223 1263 324400536 324400496 6.120000e-07 65.8
9 TraesCS2A01G551100 chr3B 95.122 41 2 0 1223 1263 424730866 424730906 6.120000e-07 65.8
10 TraesCS2A01G551100 chr3A 95.000 40 2 0 1224 1263 437879025 437878986 2.200000e-06 63.9
11 TraesCS2A01G551100 chr3A 94.872 39 2 0 1225 1263 437665775 437665737 7.910000e-06 62.1
12 TraesCS2A01G551100 chr4B 92.683 41 3 0 1223 1263 429218897 429218937 2.850000e-05 60.2


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 TraesCS2A01G551100 chr2A 758101601 758104247 2646 False 4889.000000 4889 100.000000 1 2647 1 chr2A.!!$F1 2646
1 TraesCS2A01G551100 chr2B 769948438 769951112 2674 False 2789.000000 2789 86.113000 4 2647 1 chr2B.!!$F2 2643
2 TraesCS2A01G551100 chr2D 627581750 627584565 2815 False 1096.666667 1653 89.217333 23 2643 3 chr2D.!!$F1 2620

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
922 1213 0.103937 CAACACCCAAACGCACCAAT 59.896 50.0 0.0 0.0 0.0 3.16 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2172 2530 0.774685 CGTCGACATCATCATCAGCG 59.225 55.0 17.16 0.0 0.0 5.18 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
19 20 2.246761 TAATCCGTTCCGCCCAGTGG 62.247 60.000 0.63 0.63 33.99 4.00
127 347 1.497991 GATCGCGAATGAAATCCGGA 58.502 50.000 15.24 6.61 0.00 5.14
205 429 2.988839 GCTGGGCTGGGAGTGGAAT 61.989 63.158 0.00 0.00 0.00 3.01
215 439 1.064389 GGGAGTGGAATGAAGGAAGGG 60.064 57.143 0.00 0.00 0.00 3.95
239 468 0.318191 ATCGCGTGTGAGATGGATCG 60.318 55.000 5.77 0.00 33.01 3.69
240 469 1.946156 CGCGTGTGAGATGGATCGG 60.946 63.158 0.00 0.00 0.00 4.18
265 494 1.620739 GCTGTGATGCAGGAGGAGGA 61.621 60.000 0.00 0.00 45.14 3.71
266 495 0.464870 CTGTGATGCAGGAGGAGGAG 59.535 60.000 0.00 0.00 41.42 3.69
269 498 1.074926 GATGCAGGAGGAGGAGGGA 60.075 63.158 0.00 0.00 0.00 4.20
270 499 1.074623 ATGCAGGAGGAGGAGGGAG 60.075 63.158 0.00 0.00 0.00 4.30
271 500 2.445654 GCAGGAGGAGGAGGGAGG 60.446 72.222 0.00 0.00 0.00 4.30
327 556 0.317519 GCACGGAAGGAAACCAAACG 60.318 55.000 0.00 0.00 0.00 3.60
330 559 1.944709 ACGGAAGGAAACCAAACGAAG 59.055 47.619 0.00 0.00 0.00 3.79
362 604 2.586258 CGAATCACGGGTGAATCTCT 57.414 50.000 13.33 0.00 43.58 3.10
379 621 6.693113 TGAATCTCTGAAATCAAGACGTATCG 59.307 38.462 0.00 0.00 0.00 2.92
413 656 6.054295 TCACCCAAAAAGATCCACAATTTTG 58.946 36.000 0.00 0.00 40.62 2.44
481 724 4.142381 CCGGAAAGACCAAATCAAATCCTC 60.142 45.833 0.00 0.00 38.90 3.71
482 725 4.458989 CGGAAAGACCAAATCAAATCCTCA 59.541 41.667 0.00 0.00 38.90 3.86
483 726 5.392380 CGGAAAGACCAAATCAAATCCTCAG 60.392 44.000 0.00 0.00 38.90 3.35
484 727 5.478332 GGAAAGACCAAATCAAATCCTCAGT 59.522 40.000 0.00 0.00 38.79 3.41
485 728 6.015095 GGAAAGACCAAATCAAATCCTCAGTT 60.015 38.462 0.00 0.00 38.79 3.16
488 731 4.154942 ACCAAATCAAATCCTCAGTTGCT 58.845 39.130 0.00 0.00 0.00 3.91
489 732 5.324409 ACCAAATCAAATCCTCAGTTGCTA 58.676 37.500 0.00 0.00 0.00 3.49
493 736 1.667724 CAAATCCTCAGTTGCTAGCCG 59.332 52.381 13.29 0.00 0.00 5.52
494 737 0.179000 AATCCTCAGTTGCTAGCCGG 59.821 55.000 13.29 0.00 0.00 6.13
495 738 0.687757 ATCCTCAGTTGCTAGCCGGA 60.688 55.000 13.29 8.63 0.00 5.14
496 739 0.687757 TCCTCAGTTGCTAGCCGGAT 60.688 55.000 13.29 0.00 0.00 4.18
497 740 1.040646 CCTCAGTTGCTAGCCGGATA 58.959 55.000 13.29 0.50 0.00 2.59
498 741 1.620819 CCTCAGTTGCTAGCCGGATAT 59.379 52.381 13.29 0.00 0.00 1.63
499 742 2.826128 CCTCAGTTGCTAGCCGGATATA 59.174 50.000 13.29 0.00 0.00 0.86
500 743 3.119316 CCTCAGTTGCTAGCCGGATATAG 60.119 52.174 13.29 4.90 0.00 1.31
501 744 3.497332 TCAGTTGCTAGCCGGATATAGT 58.503 45.455 13.29 0.00 0.00 2.12
502 745 4.659115 TCAGTTGCTAGCCGGATATAGTA 58.341 43.478 13.29 0.00 0.00 1.82
503 746 5.262009 TCAGTTGCTAGCCGGATATAGTAT 58.738 41.667 13.29 0.00 0.00 2.12
504 747 6.420638 TCAGTTGCTAGCCGGATATAGTATA 58.579 40.000 13.29 0.00 0.00 1.47
505 748 6.542735 TCAGTTGCTAGCCGGATATAGTATAG 59.457 42.308 13.29 0.00 0.00 1.31
509 752 4.216687 GCTAGCCGGATATAGTATAGCAGG 59.783 50.000 17.30 17.30 35.41 4.85
573 834 2.304092 TGCATGCAAATCTCATCTCCC 58.696 47.619 20.30 0.00 0.00 4.30
618 881 5.833667 GGAAGGAGAGAAAAGAAAAAGGGAA 59.166 40.000 0.00 0.00 0.00 3.97
673 952 4.530857 CGATGGAGGGGGTGACGC 62.531 72.222 0.00 0.00 43.79 5.19
786 1068 4.614036 CACCGGGGGCTGGGTTTT 62.614 66.667 6.32 0.00 33.23 2.43
910 1201 2.802724 GCCAACCCAACCAACACCC 61.803 63.158 0.00 0.00 0.00 4.61
911 1202 1.381872 CCAACCCAACCAACACCCA 60.382 57.895 0.00 0.00 0.00 4.51
913 1204 0.905357 CAACCCAACCAACACCCAAA 59.095 50.000 0.00 0.00 0.00 3.28
915 1206 1.324005 ACCCAACCAACACCCAAACG 61.324 55.000 0.00 0.00 0.00 3.60
916 1207 1.227118 CCAACCAACACCCAAACGC 60.227 57.895 0.00 0.00 0.00 4.84
917 1208 1.513158 CAACCAACACCCAAACGCA 59.487 52.632 0.00 0.00 0.00 5.24
918 1209 0.804156 CAACCAACACCCAAACGCAC 60.804 55.000 0.00 0.00 0.00 5.34
921 1212 1.513158 CAACACCCAAACGCACCAA 59.487 52.632 0.00 0.00 0.00 3.67
922 1213 0.103937 CAACACCCAAACGCACCAAT 59.896 50.000 0.00 0.00 0.00 3.16
924 1215 0.467290 ACACCCAAACGCACCAATCT 60.467 50.000 0.00 0.00 0.00 2.40
925 1216 1.202830 ACACCCAAACGCACCAATCTA 60.203 47.619 0.00 0.00 0.00 1.98
926 1217 2.091541 CACCCAAACGCACCAATCTAT 58.908 47.619 0.00 0.00 0.00 1.98
927 1218 2.491693 CACCCAAACGCACCAATCTATT 59.508 45.455 0.00 0.00 0.00 1.73
928 1219 2.752903 ACCCAAACGCACCAATCTATTC 59.247 45.455 0.00 0.00 0.00 1.75
929 1220 2.752354 CCCAAACGCACCAATCTATTCA 59.248 45.455 0.00 0.00 0.00 2.57
930 1221 3.192422 CCCAAACGCACCAATCTATTCAA 59.808 43.478 0.00 0.00 0.00 2.69
931 1222 4.414852 CCAAACGCACCAATCTATTCAAG 58.585 43.478 0.00 0.00 0.00 3.02
932 1223 3.764885 AACGCACCAATCTATTCAAGC 57.235 42.857 0.00 0.00 0.00 4.01
933 1224 2.017049 ACGCACCAATCTATTCAAGCC 58.983 47.619 0.00 0.00 0.00 4.35
934 1225 2.016318 CGCACCAATCTATTCAAGCCA 58.984 47.619 0.00 0.00 0.00 4.75
935 1226 2.423185 CGCACCAATCTATTCAAGCCAA 59.577 45.455 0.00 0.00 0.00 4.52
936 1227 3.488047 CGCACCAATCTATTCAAGCCAAG 60.488 47.826 0.00 0.00 0.00 3.61
937 1228 3.696051 GCACCAATCTATTCAAGCCAAGA 59.304 43.478 0.00 0.00 0.00 3.02
941 1232 6.151648 CACCAATCTATTCAAGCCAAGAAGAA 59.848 38.462 0.00 0.00 0.00 2.52
945 1236 5.181748 TCTATTCAAGCCAAGAAGAAGAGC 58.818 41.667 0.00 0.00 31.38 4.09
962 1253 0.753262 AGCTCTTCGCCGTTCCATAT 59.247 50.000 0.00 0.00 40.39 1.78
970 1261 4.233123 TCGCCGTTCCATATTACTACTG 57.767 45.455 0.00 0.00 0.00 2.74
973 1264 4.377897 GCCGTTCCATATTACTACTGCTT 58.622 43.478 0.00 0.00 0.00 3.91
976 1267 6.281405 CCGTTCCATATTACTACTGCTTCTT 58.719 40.000 0.00 0.00 0.00 2.52
978 1269 6.142480 CGTTCCATATTACTACTGCTTCTTCG 59.858 42.308 0.00 0.00 0.00 3.79
979 1270 6.085555 TCCATATTACTACTGCTTCTTCGG 57.914 41.667 0.00 0.00 0.00 4.30
982 1273 1.456296 TACTACTGCTTCTTCGGCGA 58.544 50.000 4.99 4.99 0.00 5.54
983 1274 0.171455 ACTACTGCTTCTTCGGCGAG 59.829 55.000 10.46 4.79 0.00 5.03
984 1275 0.452184 CTACTGCTTCTTCGGCGAGA 59.548 55.000 10.46 7.33 0.00 4.04
1161 1464 4.087892 CAGGTCCAGGTCCAGGCG 62.088 72.222 5.43 0.00 0.00 5.52
1260 1563 5.152623 ACAGAGGTGAGAAATCGAATCAA 57.847 39.130 0.00 0.00 0.00 2.57
1324 1633 1.198178 GCTACTCGATCCATCCTCGTC 59.802 57.143 0.00 0.00 37.40 4.20
1338 1649 5.507482 CCATCCTCGTCGTACATGTTCTAAT 60.507 44.000 2.30 0.00 0.00 1.73
1351 1663 6.711277 ACATGTTCTAATCTGCCTTGTTCTA 58.289 36.000 0.00 0.00 0.00 2.10
1367 1679 5.468540 TGTTCTATGTTGCAGTGACTACT 57.531 39.130 0.00 0.00 37.75 2.57
1382 1694 1.169577 CTACTGTGGACTCTGCGACT 58.830 55.000 0.00 0.00 0.00 4.18
1663 1975 1.586564 GATGAACCGTCTCTCGCCG 60.587 63.158 0.00 0.00 38.35 6.46
1665 1977 4.415332 GAACCGTCTCTCGCCGCA 62.415 66.667 0.00 0.00 38.35 5.69
1666 1978 4.719369 AACCGTCTCTCGCCGCAC 62.719 66.667 0.00 0.00 38.35 5.34
1677 1989 4.856801 GCCGCACCCGTGGATCAT 62.857 66.667 0.00 0.00 46.55 2.45
1678 1990 2.588877 CCGCACCCGTGGATCATC 60.589 66.667 0.00 0.00 46.55 2.92
1679 1991 2.501128 CGCACCCGTGGATCATCT 59.499 61.111 0.00 0.00 0.00 2.90
1706 2018 7.015389 ACGGAGGAGGATTAATTCTTAAGTAGG 59.985 40.741 1.63 0.00 0.00 3.18
1707 2019 7.232941 CGGAGGAGGATTAATTCTTAAGTAGGA 59.767 40.741 1.63 0.00 0.00 2.94
1760 2088 1.367840 GGACATAGATCCGCCGCTT 59.632 57.895 0.00 0.00 0.00 4.68
1815 2147 4.464597 GGGGTCCTAGTAGATGATGATGAC 59.535 50.000 0.00 0.00 0.00 3.06
1861 2197 2.330440 TGTGTGCTCTGCTTCTTCAA 57.670 45.000 0.00 0.00 0.00 2.69
1874 2210 4.874970 GCTTCTTCAAAGATGCCAAGAAA 58.125 39.130 15.95 0.00 45.35 2.52
1953 2289 4.229304 TGTTGTTCAGAGAAGTTTCCCA 57.771 40.909 0.00 0.00 0.00 4.37
1963 2299 4.289672 AGAGAAGTTTCCCATCTTGGCTAA 59.710 41.667 0.00 0.00 35.79 3.09
2005 2353 3.561310 TCAGAGCAACATGTTGACAGTTC 59.439 43.478 36.65 23.71 42.93 3.01
2051 2407 5.391950 GCAACAATTAACCATCATCGTCTGT 60.392 40.000 0.00 0.00 0.00 3.41
2052 2408 6.183360 GCAACAATTAACCATCATCGTCTGTA 60.183 38.462 0.00 0.00 0.00 2.74
2055 2411 6.420903 ACAATTAACCATCATCGTCTGTATCG 59.579 38.462 0.00 0.00 0.00 2.92
2057 2413 1.957177 ACCATCATCGTCTGTATCGCT 59.043 47.619 0.00 0.00 0.00 4.93
2066 2422 3.311871 TCGTCTGTATCGCTTCTCCTTAC 59.688 47.826 0.00 0.00 0.00 2.34
2068 2424 4.201930 CGTCTGTATCGCTTCTCCTTACTT 60.202 45.833 0.00 0.00 0.00 2.24
2074 2430 7.426410 TGTATCGCTTCTCCTTACTTAATCTG 58.574 38.462 0.00 0.00 0.00 2.90
2081 2437 5.674525 TCTCCTTACTTAATCTGCACATGG 58.325 41.667 0.00 0.00 0.00 3.66
2084 2440 4.271049 CCTTACTTAATCTGCACATGGTCG 59.729 45.833 0.00 0.00 0.00 4.79
2086 2442 1.331756 CTTAATCTGCACATGGTCGCC 59.668 52.381 0.00 0.00 0.00 5.54
2091 2447 4.541482 GCACATGGTCGCCGCATG 62.541 66.667 0.00 3.60 0.00 4.06
2092 2448 4.541482 CACATGGTCGCCGCATGC 62.541 66.667 7.91 7.91 0.00 4.06
2094 2450 4.246206 CATGGTCGCCGCATGCAG 62.246 66.667 19.57 7.69 41.33 4.41
2099 2455 3.422303 TCGCCGCATGCAGTTCAC 61.422 61.111 19.57 0.00 41.33 3.18
2102 2458 3.725459 CCGCATGCAGTTCACGCA 61.725 61.111 19.57 0.00 44.94 5.24
2148 2505 1.396648 TCTGCCACGCGATACAATTTG 59.603 47.619 15.93 0.00 0.00 2.32
2149 2506 0.449786 TGCCACGCGATACAATTTGG 59.550 50.000 15.93 8.68 0.00 3.28
2172 2530 8.169977 TGGATGATTGATTGTTAAATAGCTCC 57.830 34.615 0.00 0.00 0.00 4.70
2173 2531 7.041167 TGGATGATTGATTGTTAAATAGCTCCG 60.041 37.037 0.00 0.00 0.00 4.63
2174 2532 6.060028 TGATTGATTGTTAAATAGCTCCGC 57.940 37.500 0.00 0.00 0.00 5.54
2175 2533 5.822519 TGATTGATTGTTAAATAGCTCCGCT 59.177 36.000 0.00 0.00 43.41 5.52
2176 2534 5.484173 TTGATTGTTAAATAGCTCCGCTG 57.516 39.130 0.00 0.00 40.10 5.18
2177 2535 4.765273 TGATTGTTAAATAGCTCCGCTGA 58.235 39.130 0.00 0.00 40.10 4.26
2244 2611 2.347150 TCGTACGTGCGTATCTCGTAAA 59.653 45.455 24.94 0.00 45.10 2.01
2261 2628 9.929180 ATCTCGTAAATGTACATATACAATGCT 57.071 29.630 9.21 0.00 44.47 3.79
2340 2710 1.656587 AAGGCCGGAGCATATATGGA 58.343 50.000 5.05 0.00 42.56 3.41
2341 2711 1.198713 AGGCCGGAGCATATATGGAG 58.801 55.000 5.05 0.00 42.56 3.86
2342 2712 0.179000 GGCCGGAGCATATATGGAGG 59.821 60.000 5.05 0.00 42.56 4.30
2343 2713 0.905357 GCCGGAGCATATATGGAGGT 59.095 55.000 5.05 0.00 39.53 3.85
2344 2714 2.108168 GCCGGAGCATATATGGAGGTA 58.892 52.381 5.05 0.00 39.53 3.08
2345 2715 2.101582 GCCGGAGCATATATGGAGGTAG 59.898 54.545 5.05 0.00 39.53 3.18
2346 2716 2.695666 CCGGAGCATATATGGAGGTAGG 59.304 54.545 14.51 0.00 0.00 3.18
2347 2717 2.695666 CGGAGCATATATGGAGGTAGGG 59.304 54.545 14.51 0.00 0.00 3.53
2348 2718 3.627492 CGGAGCATATATGGAGGTAGGGA 60.627 52.174 14.51 0.00 0.00 4.20
2349 2719 3.964031 GGAGCATATATGGAGGTAGGGAG 59.036 52.174 14.51 0.00 0.00 4.30
2350 2720 4.326212 GGAGCATATATGGAGGTAGGGAGA 60.326 50.000 14.51 0.00 0.00 3.71
2351 2721 5.463154 GAGCATATATGGAGGTAGGGAGAT 58.537 45.833 14.51 0.00 0.00 2.75
2352 2722 6.412142 GGAGCATATATGGAGGTAGGGAGATA 60.412 46.154 14.51 0.00 0.00 1.98
2353 2723 7.185863 AGCATATATGGAGGTAGGGAGATAT 57.814 40.000 14.51 0.00 0.00 1.63
2354 2724 7.015680 AGCATATATGGAGGTAGGGAGATATG 58.984 42.308 14.51 0.00 31.93 1.78
2501 2891 6.330278 GCTGGATTAAACTGGGAATAAACAC 58.670 40.000 0.00 0.00 0.00 3.32
2550 2940 3.329231 GCGTGCAGCTGTGTGTTA 58.671 55.556 16.64 0.00 44.04 2.41
2576 2968 9.239551 AGTTATTAGGTTGGGTTCTGATTTTAC 57.760 33.333 0.00 0.00 0.00 2.01
2616 3008 1.459592 CGTGGAATGTCAAAGTCGGAC 59.540 52.381 0.00 0.00 35.83 4.79
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
6 7 3.485346 TTCCACCACTGGGCGGAAC 62.485 63.158 14.46 0.00 46.04 3.62
8 9 3.636231 CTTCCACCACTGGGCGGA 61.636 66.667 0.00 2.16 43.74 5.54
9 10 4.722700 CCTTCCACCACTGGGCGG 62.723 72.222 0.00 0.00 38.25 6.13
10 11 4.722700 CCCTTCCACCACTGGGCG 62.723 72.222 0.00 0.00 38.25 6.13
11 12 3.256960 TCCCTTCCACCACTGGGC 61.257 66.667 0.00 0.00 39.49 5.36
12 13 0.916358 ATCTCCCTTCCACCACTGGG 60.916 60.000 0.00 0.00 38.25 4.45
15 16 1.280457 GTGATCTCCCTTCCACCACT 58.720 55.000 0.00 0.00 0.00 4.00
19 20 1.519455 CGCGTGATCTCCCTTCCAC 60.519 63.158 0.00 0.00 0.00 4.02
127 347 2.515523 GCGTGCATGGCAGGATCT 60.516 61.111 14.32 0.00 45.68 2.75
152 372 3.995669 CACCAACGTCGTGCCGTG 61.996 66.667 0.00 1.92 41.65 4.94
155 375 3.645975 CACCACCAACGTCGTGCC 61.646 66.667 0.00 0.00 0.00 5.01
205 429 1.115467 GCGATCTCTCCCTTCCTTCA 58.885 55.000 0.00 0.00 0.00 3.02
215 439 1.599171 CCATCTCACACGCGATCTCTC 60.599 57.143 15.93 0.00 0.00 3.20
239 468 1.211969 CTGCATCACAGCTGTTGCC 59.788 57.895 30.90 18.35 40.91 4.52
240 469 1.211969 CCTGCATCACAGCTGTTGC 59.788 57.895 28.71 28.71 45.78 4.17
270 499 1.660917 CTTCGATACGAGGAGCCCC 59.339 63.158 0.00 0.00 37.14 5.80
271 500 1.660917 CCTTCGATACGAGGAGCCC 59.339 63.158 4.96 0.00 37.14 5.19
279 508 0.174845 TCACTTGCCCCTTCGATACG 59.825 55.000 0.00 0.00 0.00 3.06
327 556 2.209838 TTCGTGAGATCATCGGCTTC 57.790 50.000 0.00 0.00 41.60 3.86
330 559 1.789464 GTGATTCGTGAGATCATCGGC 59.211 52.381 0.00 0.00 41.60 5.54
362 604 2.927477 GGCACGATACGTCTTGATTTCA 59.073 45.455 0.00 0.00 38.32 2.69
413 656 2.121538 GGGCTCGGGGATTTGCTTC 61.122 63.158 0.00 0.00 0.00 3.86
481 724 3.944055 ACTATATCCGGCTAGCAACTG 57.056 47.619 18.24 2.73 0.00 3.16
482 725 5.299782 GCTATACTATATCCGGCTAGCAACT 59.700 44.000 18.24 0.15 32.41 3.16
483 726 5.067413 TGCTATACTATATCCGGCTAGCAAC 59.933 44.000 18.24 0.00 37.68 4.17
484 727 5.198207 TGCTATACTATATCCGGCTAGCAA 58.802 41.667 18.24 1.14 37.68 3.91
485 728 4.788679 TGCTATACTATATCCGGCTAGCA 58.211 43.478 18.24 0.00 38.14 3.49
488 731 5.641789 TCCTGCTATACTATATCCGGCTA 57.358 43.478 0.00 0.00 0.00 3.93
489 732 4.521536 TCCTGCTATACTATATCCGGCT 57.478 45.455 0.00 0.00 0.00 5.52
557 818 1.064463 GTGGGGGAGATGAGATTTGCA 60.064 52.381 0.00 0.00 0.00 4.08
573 834 4.994756 GGGGTGTGGGCAAGTGGG 62.995 72.222 0.00 0.00 0.00 4.61
618 881 2.357637 GCTGTCTGCGTATCTTCTCTCT 59.642 50.000 0.00 0.00 0.00 3.10
665 931 4.090057 GCTTTCGCTGCGTCACCC 62.090 66.667 22.48 4.48 0.00 4.61
770 1049 2.859971 TAAAACCCAGCCCCCGGT 60.860 61.111 0.00 0.00 0.00 5.28
771 1050 2.361992 GTAAAACCCAGCCCCCGG 60.362 66.667 0.00 0.00 0.00 5.73
861 1143 1.068127 GGCGGTATATATACAGGGGCG 59.932 57.143 21.56 16.25 34.98 6.13
910 1201 3.853671 GCTTGAATAGATTGGTGCGTTTG 59.146 43.478 0.00 0.00 0.00 2.93
911 1202 3.119495 GGCTTGAATAGATTGGTGCGTTT 60.119 43.478 0.00 0.00 0.00 3.60
913 1204 2.017049 GGCTTGAATAGATTGGTGCGT 58.983 47.619 0.00 0.00 0.00 5.24
915 1206 3.696051 TCTTGGCTTGAATAGATTGGTGC 59.304 43.478 0.00 0.00 0.00 5.01
916 1207 5.649395 TCTTCTTGGCTTGAATAGATTGGTG 59.351 40.000 0.00 0.00 0.00 4.17
917 1208 5.819991 TCTTCTTGGCTTGAATAGATTGGT 58.180 37.500 0.00 0.00 0.00 3.67
918 1209 6.600822 TCTTCTTCTTGGCTTGAATAGATTGG 59.399 38.462 0.00 0.00 0.00 3.16
921 1212 5.821995 GCTCTTCTTCTTGGCTTGAATAGAT 59.178 40.000 0.00 0.00 0.00 1.98
922 1213 5.046014 AGCTCTTCTTCTTGGCTTGAATAGA 60.046 40.000 0.00 0.00 0.00 1.98
924 1215 5.046014 AGAGCTCTTCTTCTTGGCTTGAATA 60.046 40.000 11.45 0.00 33.13 1.75
925 1216 4.009002 GAGCTCTTCTTCTTGGCTTGAAT 58.991 43.478 6.43 0.00 33.13 2.57
926 1217 3.072184 AGAGCTCTTCTTCTTGGCTTGAA 59.928 43.478 11.45 0.00 33.13 2.69
927 1218 2.636893 AGAGCTCTTCTTCTTGGCTTGA 59.363 45.455 11.45 0.00 33.13 3.02
928 1219 3.056588 AGAGCTCTTCTTCTTGGCTTG 57.943 47.619 11.45 0.00 33.13 4.01
929 1220 3.786368 AAGAGCTCTTCTTCTTGGCTT 57.214 42.857 23.49 0.00 42.54 4.35
945 1236 3.978687 AGTAATATGGAACGGCGAAGAG 58.021 45.455 16.62 0.00 0.00 2.85
962 1253 1.814394 TCGCCGAAGAAGCAGTAGTAA 59.186 47.619 0.00 0.00 0.00 2.24
970 1261 0.109039 AACTCTCTCGCCGAAGAAGC 60.109 55.000 0.00 0.00 0.00 3.86
973 1264 1.244816 TCAAACTCTCTCGCCGAAGA 58.755 50.000 0.00 0.00 0.00 2.87
976 1267 0.098905 CGATCAAACTCTCTCGCCGA 59.901 55.000 0.00 0.00 0.00 5.54
978 1269 1.133407 AGTCGATCAAACTCTCTCGCC 59.867 52.381 0.00 0.00 0.00 5.54
979 1270 2.159503 TCAGTCGATCAAACTCTCTCGC 60.160 50.000 0.00 0.00 0.00 5.03
982 1273 3.430098 GCCATCAGTCGATCAAACTCTCT 60.430 47.826 0.00 0.00 0.00 3.10
983 1274 2.863137 GCCATCAGTCGATCAAACTCTC 59.137 50.000 0.00 0.00 0.00 3.20
984 1275 2.419297 GGCCATCAGTCGATCAAACTCT 60.419 50.000 0.00 0.00 0.00 3.24
1206 1509 0.465705 GGAGGATCTTGGCGATGACA 59.534 55.000 0.00 0.00 33.73 3.58
1260 1563 2.124570 AGCGCGGCTTGATTGGAT 60.125 55.556 8.83 0.00 33.89 3.41
1324 1633 4.870426 ACAAGGCAGATTAGAACATGTACG 59.130 41.667 0.00 0.00 0.00 3.67
1338 1649 3.138884 TGCAACATAGAACAAGGCAGA 57.861 42.857 0.00 0.00 0.00 4.26
1484 1796 1.507174 CTCCGACGACTCCTTGACC 59.493 63.158 0.00 0.00 0.00 4.02
1663 1975 0.597637 CGTAGATGATCCACGGGTGC 60.598 60.000 5.50 0.00 32.19 5.01
1668 1980 1.537638 CTCCTCCGTAGATGATCCACG 59.462 57.143 6.43 6.43 35.50 4.94
1670 1982 1.780919 TCCTCCTCCGTAGATGATCCA 59.219 52.381 0.00 0.00 0.00 3.41
1671 1983 2.588464 TCCTCCTCCGTAGATGATCC 57.412 55.000 0.00 0.00 0.00 3.36
1672 1984 6.783708 ATTAATCCTCCTCCGTAGATGATC 57.216 41.667 0.00 0.00 0.00 2.92
1673 1985 6.957020 AGAATTAATCCTCCTCCGTAGATGAT 59.043 38.462 0.00 0.00 0.00 2.45
1674 1986 6.315714 AGAATTAATCCTCCTCCGTAGATGA 58.684 40.000 0.00 0.00 0.00 2.92
1675 1987 6.597832 AGAATTAATCCTCCTCCGTAGATG 57.402 41.667 0.00 0.00 0.00 2.90
1676 1988 8.722622 TTAAGAATTAATCCTCCTCCGTAGAT 57.277 34.615 0.00 0.00 35.24 1.98
1677 1989 7.783596 ACTTAAGAATTAATCCTCCTCCGTAGA 59.216 37.037 10.09 0.00 40.24 2.59
1678 1990 7.953752 ACTTAAGAATTAATCCTCCTCCGTAG 58.046 38.462 10.09 0.00 40.24 3.51
1679 1991 7.909485 ACTTAAGAATTAATCCTCCTCCGTA 57.091 36.000 10.09 0.00 40.24 4.02
1815 2147 6.294620 GGGGACGAACTAACATCCTAATCTAG 60.295 46.154 0.00 0.00 0.00 2.43
1877 2213 8.028938 CCGGATGAATACTCTGTTTTGATTTTT 58.971 33.333 0.00 0.00 0.00 1.94
1882 2218 3.938963 GCCGGATGAATACTCTGTTTTGA 59.061 43.478 5.05 0.00 0.00 2.69
1883 2219 3.065371 GGCCGGATGAATACTCTGTTTTG 59.935 47.826 5.05 0.00 0.00 2.44
1884 2220 3.279434 GGCCGGATGAATACTCTGTTTT 58.721 45.455 5.05 0.00 0.00 2.43
1900 2236 2.562738 AGATTTCCTTTCTTTTGGCCGG 59.437 45.455 0.00 0.00 0.00 6.13
1953 2289 4.202050 GCCATTTCGACATTTAGCCAAGAT 60.202 41.667 0.00 0.00 0.00 2.40
1963 2299 2.036958 TCCGATGCCATTTCGACATT 57.963 45.000 0.00 0.00 38.88 2.71
2005 2353 7.268199 TGCAAAAGATTAGCTCTGATTATGG 57.732 36.000 0.00 0.00 33.29 2.74
2051 2407 6.040504 TGCAGATTAAGTAAGGAGAAGCGATA 59.959 38.462 0.00 0.00 0.00 2.92
2052 2408 5.163405 TGCAGATTAAGTAAGGAGAAGCGAT 60.163 40.000 0.00 0.00 0.00 4.58
2055 2411 5.178797 TGTGCAGATTAAGTAAGGAGAAGC 58.821 41.667 0.00 0.00 0.00 3.86
2057 2413 6.115446 CCATGTGCAGATTAAGTAAGGAGAA 58.885 40.000 0.00 0.00 0.00 2.87
2066 2422 1.331756 GGCGACCATGTGCAGATTAAG 59.668 52.381 0.00 0.00 0.00 1.85
2068 2424 0.809636 CGGCGACCATGTGCAGATTA 60.810 55.000 0.00 0.00 0.00 1.75
2074 2430 4.541482 CATGCGGCGACCATGTGC 62.541 66.667 12.98 0.00 35.54 4.57
2092 2448 4.291047 AGGCAGATGCGTGAACTG 57.709 55.556 0.00 0.00 43.26 3.16
2101 2457 1.228184 GATCAGGGGCAGGCAGATG 60.228 63.158 0.00 0.00 0.00 2.90
2102 2458 1.066585 ATGATCAGGGGCAGGCAGAT 61.067 55.000 0.09 0.00 0.00 2.90
2116 2472 1.202110 CGTGGCAGACAAAGCATGATC 60.202 52.381 0.00 0.00 0.00 2.92
2148 2505 7.301054 CGGAGCTATTTAACAATCAATCATCC 58.699 38.462 0.00 0.00 0.00 3.51
2169 2527 1.000938 TCGACATCATCATCAGCGGAG 60.001 52.381 0.00 0.00 0.00 4.63
2170 2528 1.032014 TCGACATCATCATCAGCGGA 58.968 50.000 0.00 0.00 0.00 5.54
2172 2530 0.774685 CGTCGACATCATCATCAGCG 59.225 55.000 17.16 0.00 0.00 5.18
2173 2531 2.049959 CTCGTCGACATCATCATCAGC 58.950 52.381 17.16 0.00 0.00 4.26
2174 2532 2.049959 GCTCGTCGACATCATCATCAG 58.950 52.381 17.16 0.00 0.00 2.90
2175 2533 1.678101 AGCTCGTCGACATCATCATCA 59.322 47.619 17.16 0.00 0.00 3.07
2176 2534 2.414058 AGCTCGTCGACATCATCATC 57.586 50.000 17.16 0.00 0.00 2.92
2177 2535 3.990318 TTAGCTCGTCGACATCATCAT 57.010 42.857 17.16 0.00 0.00 2.45
2258 2625 1.493022 ACCTAAGACAACCCACAAGCA 59.507 47.619 0.00 0.00 0.00 3.91
2259 2626 1.880027 CACCTAAGACAACCCACAAGC 59.120 52.381 0.00 0.00 0.00 4.01
2260 2627 3.403038 CTCACCTAAGACAACCCACAAG 58.597 50.000 0.00 0.00 0.00 3.16
2261 2628 2.486548 GCTCACCTAAGACAACCCACAA 60.487 50.000 0.00 0.00 0.00 3.33
2309 2677 1.203001 TCCGGCCTTTGGACTTTTCAT 60.203 47.619 0.00 0.00 0.00 2.57
2340 2710 6.445139 CCATTCATTACCATATCTCCCTACCT 59.555 42.308 0.00 0.00 0.00 3.08
2341 2711 6.353082 CCCATTCATTACCATATCTCCCTACC 60.353 46.154 0.00 0.00 0.00 3.18
2342 2712 6.353082 CCCCATTCATTACCATATCTCCCTAC 60.353 46.154 0.00 0.00 0.00 3.18
2343 2713 5.731187 CCCCATTCATTACCATATCTCCCTA 59.269 44.000 0.00 0.00 0.00 3.53
2344 2714 4.541714 CCCCATTCATTACCATATCTCCCT 59.458 45.833 0.00 0.00 0.00 4.20
2345 2715 4.325344 CCCCCATTCATTACCATATCTCCC 60.325 50.000 0.00 0.00 0.00 4.30
2346 2716 4.860022 CCCCCATTCATTACCATATCTCC 58.140 47.826 0.00 0.00 0.00 3.71
2347 2717 4.263905 TGCCCCCATTCATTACCATATCTC 60.264 45.833 0.00 0.00 0.00 2.75
2348 2718 3.662148 TGCCCCCATTCATTACCATATCT 59.338 43.478 0.00 0.00 0.00 1.98
2349 2719 3.763897 GTGCCCCCATTCATTACCATATC 59.236 47.826 0.00 0.00 0.00 1.63
2350 2720 3.402366 AGTGCCCCCATTCATTACCATAT 59.598 43.478 0.00 0.00 0.00 1.78
2351 2721 2.788807 AGTGCCCCCATTCATTACCATA 59.211 45.455 0.00 0.00 0.00 2.74
2352 2722 1.575304 AGTGCCCCCATTCATTACCAT 59.425 47.619 0.00 0.00 0.00 3.55
2353 2723 1.006813 AGTGCCCCCATTCATTACCA 58.993 50.000 0.00 0.00 0.00 3.25
2354 2724 1.341976 ACAGTGCCCCCATTCATTACC 60.342 52.381 0.00 0.00 0.00 2.85
2501 2891 1.248486 TATCTTCTCCCTGATCCGCG 58.752 55.000 0.00 0.00 0.00 6.46
2550 2940 9.239551 GTAAAATCAGAACCCAACCTAATAACT 57.760 33.333 0.00 0.00 0.00 2.24
2576 2968 3.249091 CGAGACAAGACACAGAATCAGG 58.751 50.000 0.00 0.00 0.00 3.86


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

AutoCloner maintained by Alex Coulton.