Multiple sequence alignment - TraesCS2A01G192500

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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 TraesCS2A01G192500 chr2A 100.000 2943 0 0 1 2943 159938967 159936025 0 5435
1 TraesCS2A01G192500 chr2B 88.196 2982 164 100 57 2943 199124380 199121492 0 3384
2 TraesCS2A01G192500 chr2D 92.096 1999 69 45 975 2943 141191502 141193441 0 2734
3 TraesCS2A01G192500 chr2D 84.067 954 72 42 27 931 141190565 141191487 0 846


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 TraesCS2A01G192500 chr2A 159936025 159938967 2942 True 5435 5435 100.0000 1 2943 1 chr2A.!!$R1 2942
1 TraesCS2A01G192500 chr2B 199121492 199124380 2888 True 3384 3384 88.1960 57 2943 1 chr2B.!!$R1 2886
2 TraesCS2A01G192500 chr2D 141190565 141193441 2876 False 1790 2734 88.0815 27 2943 2 chr2D.!!$F1 2916

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
766 849 0.035739 TTCTTTCCTGCCCGTACACC 59.964 55.0 0.0 0.0 0.0 4.16 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1960 2124 0.109412 GGCAGATCAGTTGCAGTTGC 60.109 55.0 7.62 0.0 43.28 4.17 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
17 18 2.501128 ATCCATGCCGTCCAGTCG 59.499 61.111 0.00 0.00 0.00 4.18
18 19 2.058001 ATCCATGCCGTCCAGTCGA 61.058 57.895 0.00 0.00 0.00 4.20
19 20 2.021068 ATCCATGCCGTCCAGTCGAG 62.021 60.000 0.00 0.00 0.00 4.04
20 21 2.573869 CATGCCGTCCAGTCGAGT 59.426 61.111 0.00 0.00 0.00 4.18
21 22 1.663379 CCATGCCGTCCAGTCGAGTA 61.663 60.000 0.00 0.00 0.00 2.59
22 23 0.172578 CATGCCGTCCAGTCGAGTAA 59.827 55.000 0.00 0.00 0.00 2.24
23 24 0.172803 ATGCCGTCCAGTCGAGTAAC 59.827 55.000 0.00 0.00 0.00 2.50
24 25 1.174078 TGCCGTCCAGTCGAGTAACA 61.174 55.000 0.00 0.00 0.00 2.41
25 26 0.456312 GCCGTCCAGTCGAGTAACAG 60.456 60.000 0.00 0.00 0.00 3.16
164 171 4.811206 TGACCAAATCACCGGTGG 57.189 55.556 33.40 20.12 34.99 4.61
182 189 1.742510 GCTAACCACGGCGCCTAAA 60.743 57.895 26.68 2.64 0.00 1.85
183 190 1.093496 GCTAACCACGGCGCCTAAAT 61.093 55.000 26.68 9.35 0.00 1.40
186 193 2.047002 AACCACGGCGCCTAAATAAT 57.953 45.000 26.68 1.13 0.00 1.28
282 305 2.054799 ACCCAACCTGTCATACACACT 58.945 47.619 0.00 0.00 0.00 3.55
285 308 3.007506 CCCAACCTGTCATACACACTACA 59.992 47.826 0.00 0.00 0.00 2.74
291 314 3.634283 TGTCATACACACTACACACACG 58.366 45.455 0.00 0.00 0.00 4.49
293 316 3.667261 GTCATACACACTACACACACGAC 59.333 47.826 0.00 0.00 0.00 4.34
294 317 2.780065 TACACACTACACACACGACC 57.220 50.000 0.00 0.00 0.00 4.79
300 323 2.659757 CACTACACACACGACCAATACG 59.340 50.000 0.00 0.00 0.00 3.06
301 324 2.553602 ACTACACACACGACCAATACGA 59.446 45.455 0.00 0.00 34.70 3.43
316 339 0.311477 TACGACGCACAAGTACAGCA 59.689 50.000 0.00 0.00 0.00 4.41
323 346 0.859232 CACAAGTACAGCACACGGAC 59.141 55.000 0.00 0.00 0.00 4.79
324 347 0.596600 ACAAGTACAGCACACGGACG 60.597 55.000 0.00 0.00 0.00 4.79
325 348 0.318360 CAAGTACAGCACACGGACGA 60.318 55.000 0.00 0.00 0.00 4.20
326 349 0.039437 AAGTACAGCACACGGACGAG 60.039 55.000 0.00 0.00 0.00 4.18
328 351 2.632544 TACAGCACACGGACGAGGG 61.633 63.158 0.00 0.00 0.00 4.30
332 355 4.129737 CACACGGACGAGGGCGAT 62.130 66.667 0.00 0.00 41.64 4.58
333 356 4.129737 ACACGGACGAGGGCGATG 62.130 66.667 0.00 0.00 41.64 3.84
372 395 1.506493 GATGCTTAGCGAGGGACATG 58.494 55.000 0.00 0.00 0.00 3.21
373 396 0.107456 ATGCTTAGCGAGGGACATGG 59.893 55.000 0.00 0.00 0.00 3.66
374 397 0.975556 TGCTTAGCGAGGGACATGGA 60.976 55.000 0.00 0.00 0.00 3.41
526 579 2.879907 CAACCATTCGCAGGCAGG 59.120 61.111 0.00 0.00 0.00 4.85
527 580 3.064324 AACCATTCGCAGGCAGGC 61.064 61.111 0.00 0.00 0.00 4.85
528 581 3.866379 AACCATTCGCAGGCAGGCA 62.866 57.895 0.00 0.00 0.00 4.75
529 582 3.515286 CCATTCGCAGGCAGGCAG 61.515 66.667 0.00 0.00 0.00 4.85
565 632 0.036577 GGCCATCCATCTGAGATCGG 60.037 60.000 0.00 0.00 0.00 4.18
568 635 1.274728 CCATCCATCTGAGATCGGTCC 59.725 57.143 9.64 0.00 0.00 4.46
604 671 2.839486 TCCGATTCAGTCAAGTTGCT 57.161 45.000 0.00 0.00 0.00 3.91
605 672 2.416747 TCCGATTCAGTCAAGTTGCTG 58.583 47.619 16.52 16.52 0.00 4.41
606 673 1.135859 CCGATTCAGTCAAGTTGCTGC 60.136 52.381 17.37 0.00 33.09 5.25
643 710 1.751924 CGAGCTGGCTATCCCCTATAC 59.248 57.143 0.00 0.00 0.00 1.47
644 711 2.621929 CGAGCTGGCTATCCCCTATACT 60.622 54.545 0.00 0.00 0.00 2.12
645 712 3.371702 CGAGCTGGCTATCCCCTATACTA 60.372 52.174 0.00 0.00 0.00 1.82
646 713 4.211920 GAGCTGGCTATCCCCTATACTAG 58.788 52.174 0.00 0.00 0.00 2.57
647 714 2.696187 GCTGGCTATCCCCTATACTAGC 59.304 54.545 0.00 0.00 36.66 3.42
648 715 2.952978 CTGGCTATCCCCTATACTAGCG 59.047 54.545 0.00 0.00 37.94 4.26
649 716 2.579400 TGGCTATCCCCTATACTAGCGA 59.421 50.000 0.00 0.00 37.94 4.93
650 717 2.950975 GGCTATCCCCTATACTAGCGAC 59.049 54.545 0.00 0.00 37.94 5.19
651 718 2.950975 GCTATCCCCTATACTAGCGACC 59.049 54.545 0.00 0.00 0.00 4.79
652 719 3.371810 GCTATCCCCTATACTAGCGACCT 60.372 52.174 0.00 0.00 0.00 3.85
653 720 3.829728 ATCCCCTATACTAGCGACCTT 57.170 47.619 0.00 0.00 0.00 3.50
654 721 3.607490 TCCCCTATACTAGCGACCTTT 57.393 47.619 0.00 0.00 0.00 3.11
655 722 3.494332 TCCCCTATACTAGCGACCTTTC 58.506 50.000 0.00 0.00 0.00 2.62
674 744 6.887002 ACCTTTCTTTGTTCTCTTTGTTCTCT 59.113 34.615 0.00 0.00 0.00 3.10
675 745 7.394641 ACCTTTCTTTGTTCTCTTTGTTCTCTT 59.605 33.333 0.00 0.00 0.00 2.85
676 746 8.246871 CCTTTCTTTGTTCTCTTTGTTCTCTTT 58.753 33.333 0.00 0.00 0.00 2.52
677 747 8.970691 TTTCTTTGTTCTCTTTGTTCTCTTTG 57.029 30.769 0.00 0.00 0.00 2.77
684 754 4.757149 TCTCTTTGTTCTCTTTGCTAAGCC 59.243 41.667 2.75 0.00 0.00 4.35
697 767 1.480683 GCTAAGCCCCCTTTATTCCCC 60.481 57.143 0.00 0.00 32.47 4.81
717 787 3.551846 CCCCATTAAACTATGCCTTCGT 58.448 45.455 0.00 0.00 0.00 3.85
750 823 2.102578 CAAATTCGGCCCAATCCTTCT 58.897 47.619 0.00 0.00 0.00 2.85
756 839 1.478631 GGCCCAATCCTTCTTTCCTG 58.521 55.000 0.00 0.00 0.00 3.86
759 842 1.478631 CCAATCCTTCTTTCCTGCCC 58.521 55.000 0.00 0.00 0.00 5.36
761 844 0.698818 AATCCTTCTTTCCTGCCCGT 59.301 50.000 0.00 0.00 0.00 5.28
762 845 1.580059 ATCCTTCTTTCCTGCCCGTA 58.420 50.000 0.00 0.00 0.00 4.02
764 847 0.323629 CCTTCTTTCCTGCCCGTACA 59.676 55.000 0.00 0.00 0.00 2.90
765 848 1.439679 CTTCTTTCCTGCCCGTACAC 58.560 55.000 0.00 0.00 0.00 2.90
766 849 0.035739 TTCTTTCCTGCCCGTACACC 59.964 55.000 0.00 0.00 0.00 4.16
767 850 1.740296 CTTTCCTGCCCGTACACCG 60.740 63.158 0.00 0.00 0.00 4.94
768 851 3.887335 TTTCCTGCCCGTACACCGC 62.887 63.158 0.00 0.00 34.38 5.68
797 880 4.393778 GTCCGTCCCTCCCCTCCA 62.394 72.222 0.00 0.00 0.00 3.86
798 881 4.075793 TCCGTCCCTCCCCTCCAG 62.076 72.222 0.00 0.00 0.00 3.86
799 882 4.075793 CCGTCCCTCCCCTCCAGA 62.076 72.222 0.00 0.00 0.00 3.86
800 883 2.283809 CGTCCCTCCCCTCCAGAT 59.716 66.667 0.00 0.00 0.00 2.90
874 977 2.768344 CCGCCTCCCCCTACACAT 60.768 66.667 0.00 0.00 0.00 3.21
877 980 0.463833 CGCCTCCCCCTACACATTTC 60.464 60.000 0.00 0.00 0.00 2.17
897 1000 1.681793 CCCTTACGACATCCTCGACAT 59.318 52.381 0.00 0.00 46.14 3.06
903 1006 1.841450 GACATCCTCGACATTCGACC 58.159 55.000 0.00 0.00 44.82 4.79
904 1007 1.134367 GACATCCTCGACATTCGACCA 59.866 52.381 0.00 0.00 44.82 4.02
906 1009 2.196749 CATCCTCGACATTCGACCAAG 58.803 52.381 0.00 0.00 44.82 3.61
908 1011 0.389817 CCTCGACATTCGACCAAGCA 60.390 55.000 0.00 0.00 44.82 3.91
946 1051 2.204151 AGGGAGGGGGACTGGTTG 60.204 66.667 0.00 0.00 0.00 3.77
964 1069 1.746991 GCTTACTGCCTGAGTGCCC 60.747 63.158 0.00 0.00 35.96 5.36
1097 1236 1.305219 TGTGCTCGGTTGCTTATGCC 61.305 55.000 0.00 0.00 38.71 4.40
1118 1257 2.114616 ACTGATTGGTTTGGGTTTGCA 58.885 42.857 0.00 0.00 0.00 4.08
1122 1261 0.107459 TTGGTTTGGGTTTGCAAGGC 60.107 50.000 0.00 0.00 0.00 4.35
1123 1262 0.980231 TGGTTTGGGTTTGCAAGGCT 60.980 50.000 0.00 0.00 0.00 4.58
1124 1263 0.532640 GGTTTGGGTTTGCAAGGCTG 60.533 55.000 0.00 0.00 0.00 4.85
1125 1264 0.177836 GTTTGGGTTTGCAAGGCTGT 59.822 50.000 0.00 0.00 0.00 4.40
1126 1265 0.908198 TTTGGGTTTGCAAGGCTGTT 59.092 45.000 0.00 0.00 0.00 3.16
1127 1266 0.177604 TTGGGTTTGCAAGGCTGTTG 59.822 50.000 0.00 0.00 0.00 3.33
1128 1267 0.685785 TGGGTTTGCAAGGCTGTTGA 60.686 50.000 0.00 0.00 0.00 3.18
1129 1268 0.681175 GGGTTTGCAAGGCTGTTGAT 59.319 50.000 0.00 0.00 0.00 2.57
1130 1269 1.070601 GGGTTTGCAAGGCTGTTGATT 59.929 47.619 0.00 0.00 0.00 2.57
1131 1270 2.407090 GGTTTGCAAGGCTGTTGATTC 58.593 47.619 0.00 0.00 0.00 2.52
1132 1271 2.036346 GGTTTGCAAGGCTGTTGATTCT 59.964 45.455 0.00 0.00 0.00 2.40
1133 1272 3.493176 GGTTTGCAAGGCTGTTGATTCTT 60.493 43.478 0.00 0.00 0.00 2.52
1134 1273 3.374220 TTGCAAGGCTGTTGATTCTTG 57.626 42.857 0.00 0.00 39.46 3.02
1136 1275 1.973138 CAAGGCTGTTGATTCTTGCG 58.027 50.000 0.00 0.00 31.73 4.85
1137 1276 1.267806 CAAGGCTGTTGATTCTTGCGT 59.732 47.619 0.00 0.00 31.73 5.24
1138 1277 1.160137 AGGCTGTTGATTCTTGCGTC 58.840 50.000 0.00 0.00 0.00 5.19
1139 1278 0.179215 GGCTGTTGATTCTTGCGTCG 60.179 55.000 0.00 0.00 0.00 5.12
1140 1279 0.790207 GCTGTTGATTCTTGCGTCGA 59.210 50.000 0.00 0.00 0.00 4.20
1141 1280 1.201855 GCTGTTGATTCTTGCGTCGAG 60.202 52.381 0.00 0.00 0.00 4.04
1142 1281 1.391485 CTGTTGATTCTTGCGTCGAGG 59.609 52.381 0.00 0.00 0.00 4.63
1143 1282 1.270094 TGTTGATTCTTGCGTCGAGGT 60.270 47.619 7.01 0.00 0.00 3.85
1144 1283 1.390463 GTTGATTCTTGCGTCGAGGTC 59.610 52.381 7.01 0.04 0.00 3.85
1820 1984 1.290324 GACTGCCTGCTCAAGACGA 59.710 57.895 0.00 0.00 0.00 4.20
1876 2040 1.493311 CAAGGCGCTCAAGAACGTC 59.507 57.895 7.64 0.00 0.00 4.34
1943 2107 1.338200 GCAGGAGGTTGTTCGAGTGAT 60.338 52.381 0.00 0.00 0.00 3.06
1944 2108 2.341257 CAGGAGGTTGTTCGAGTGATG 58.659 52.381 0.00 0.00 0.00 3.07
1945 2109 2.029020 CAGGAGGTTGTTCGAGTGATGA 60.029 50.000 0.00 0.00 0.00 2.92
1953 2117 4.427096 TGTTCGAGTGATGAGAAGAGAC 57.573 45.455 0.00 0.00 0.00 3.36
1959 2123 2.170187 AGTGATGAGAAGAGACCATGCC 59.830 50.000 0.00 0.00 0.00 4.40
1960 2124 1.137675 TGATGAGAAGAGACCATGCCG 59.862 52.381 0.00 0.00 0.00 5.69
1983 2150 1.271762 ACTGCAACTGATCTGCCACAT 60.272 47.619 3.24 0.00 39.13 3.21
2112 2279 1.635844 CATGATCCCGAACGAACGAA 58.364 50.000 0.14 0.00 35.09 3.85
2114 2281 0.730155 TGATCCCGAACGAACGAACG 60.730 55.000 0.14 6.10 39.31 3.95
2281 2449 9.906660 TTTTCCACTGTCAATTGTGAATTATAC 57.093 29.630 5.13 0.00 34.87 1.47
2309 2477 5.788450 ACTTATGAGCTACTCCATGTATGC 58.212 41.667 0.00 0.00 0.00 3.14
2331 2499 0.965439 TTTCCATGGACTTTTGCCCG 59.035 50.000 15.91 0.00 0.00 6.13
2335 2503 1.135024 CCATGGACTTTTGCCCGATTG 60.135 52.381 5.56 0.00 0.00 2.67
2353 2525 2.408333 GCCCTGTGCATACATCCAC 58.592 57.895 0.00 0.00 40.77 4.02
2405 2577 4.083431 CCGGTCGTATCGTATCTCATTCTT 60.083 45.833 0.00 0.00 0.00 2.52
2406 2578 5.080731 CGGTCGTATCGTATCTCATTCTTC 58.919 45.833 0.00 0.00 0.00 2.87
2450 2622 1.453745 CCCCCACATTCCACCATCG 60.454 63.158 0.00 0.00 0.00 3.84
2456 2628 0.253044 ACATTCCACCATCGTCAGGG 59.747 55.000 0.00 0.00 0.00 4.45
2492 2664 6.478588 GCTAAGATTTGTGTCGGTTCATTAG 58.521 40.000 0.00 0.00 0.00 1.73
2575 2752 2.864343 AGAGAGGAAACAAACAACGACG 59.136 45.455 0.00 0.00 0.00 5.12
2608 2785 0.036306 AGGCTACCTTTTCACACCCG 59.964 55.000 0.00 0.00 0.00 5.28
2635 2812 1.627550 GAGAAACGTGCGGAGAAGCC 61.628 60.000 0.00 0.00 36.02 4.35
2641 2818 4.802051 TGCGGAGAAGCCATGGCC 62.802 66.667 33.14 18.87 43.17 5.36
2657 2834 2.193536 GCCAAGCAACCGGTGAACT 61.194 57.895 8.52 2.50 0.00 3.01
2658 2835 1.654220 CCAAGCAACCGGTGAACTG 59.346 57.895 8.52 3.06 0.00 3.16
2659 2836 0.817634 CCAAGCAACCGGTGAACTGA 60.818 55.000 8.52 0.00 0.00 3.41
2660 2837 1.021202 CAAGCAACCGGTGAACTGAA 58.979 50.000 8.52 0.00 0.00 3.02
2661 2838 1.021968 AAGCAACCGGTGAACTGAAC 58.978 50.000 8.52 0.00 0.00 3.18
2781 2958 1.518572 CATGTCGCCGGACCTGTAC 60.519 63.158 5.05 0.00 42.73 2.90
2805 2982 1.379977 TAGCGTGGGGAGAGACAGG 60.380 63.158 0.00 0.00 0.00 4.00
2882 3063 2.662857 TGAGCTGCAGTGCGTGAC 60.663 61.111 16.64 3.05 38.13 3.67
2902 3083 3.695606 GGAGTGGCCGACAGCTCA 61.696 66.667 0.00 0.00 43.05 4.26
2926 3109 3.760684 GGAACTGATGCAACCTCTGAAAT 59.239 43.478 0.00 0.00 0.00 2.17
2927 3110 4.943705 GGAACTGATGCAACCTCTGAAATA 59.056 41.667 0.00 0.00 0.00 1.40
2928 3111 5.065731 GGAACTGATGCAACCTCTGAAATAG 59.934 44.000 0.00 0.00 0.00 1.73
2929 3112 5.171339 ACTGATGCAACCTCTGAAATAGT 57.829 39.130 0.00 0.00 0.00 2.12
2932 3115 6.048732 TGATGCAACCTCTGAAATAGTACA 57.951 37.500 0.00 0.00 0.00 2.90
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 2.021068 CTCGACTGGACGGCATGGAT 62.021 60.000 0.00 0.00 0.00 3.41
1 2 2.678580 TCGACTGGACGGCATGGA 60.679 61.111 0.00 0.00 0.00 3.41
2 3 1.663379 TACTCGACTGGACGGCATGG 61.663 60.000 0.00 0.00 0.00 3.66
3 4 0.172578 TTACTCGACTGGACGGCATG 59.827 55.000 0.00 0.00 0.00 4.06
4 5 0.172803 GTTACTCGACTGGACGGCAT 59.827 55.000 0.00 0.00 0.00 4.40
5 6 1.174078 TGTTACTCGACTGGACGGCA 61.174 55.000 0.00 0.00 0.00 5.69
6 7 0.456312 CTGTTACTCGACTGGACGGC 60.456 60.000 0.00 0.00 0.00 5.68
7 8 0.879765 ACTGTTACTCGACTGGACGG 59.120 55.000 0.00 0.00 0.00 4.79
8 9 1.534163 TGACTGTTACTCGACTGGACG 59.466 52.381 0.00 0.00 0.00 4.79
9 10 2.095161 CCTGACTGTTACTCGACTGGAC 60.095 54.545 0.00 0.00 0.00 4.02
10 11 2.160205 CCTGACTGTTACTCGACTGGA 58.840 52.381 0.00 0.00 0.00 3.86
11 12 2.160205 TCCTGACTGTTACTCGACTGG 58.840 52.381 0.00 0.00 0.00 4.00
12 13 3.917329 TTCCTGACTGTTACTCGACTG 57.083 47.619 0.00 0.00 0.00 3.51
13 14 4.618965 GTTTTCCTGACTGTTACTCGACT 58.381 43.478 0.00 0.00 0.00 4.18
14 15 3.424529 CGTTTTCCTGACTGTTACTCGAC 59.575 47.826 0.00 0.00 0.00 4.20
15 16 3.316029 TCGTTTTCCTGACTGTTACTCGA 59.684 43.478 0.00 0.00 0.00 4.04
16 17 3.635331 TCGTTTTCCTGACTGTTACTCG 58.365 45.455 0.00 0.00 0.00 4.18
17 18 4.085210 CGTTCGTTTTCCTGACTGTTACTC 60.085 45.833 0.00 0.00 0.00 2.59
18 19 3.800506 CGTTCGTTTTCCTGACTGTTACT 59.199 43.478 0.00 0.00 0.00 2.24
19 20 3.603173 GCGTTCGTTTTCCTGACTGTTAC 60.603 47.826 0.00 0.00 0.00 2.50
20 21 2.540931 GCGTTCGTTTTCCTGACTGTTA 59.459 45.455 0.00 0.00 0.00 2.41
21 22 1.329599 GCGTTCGTTTTCCTGACTGTT 59.670 47.619 0.00 0.00 0.00 3.16
22 23 0.935196 GCGTTCGTTTTCCTGACTGT 59.065 50.000 0.00 0.00 0.00 3.55
23 24 0.111266 CGCGTTCGTTTTCCTGACTG 60.111 55.000 0.00 0.00 0.00 3.51
24 25 1.219522 CCGCGTTCGTTTTCCTGACT 61.220 55.000 4.92 0.00 0.00 3.41
25 26 1.203313 CCGCGTTCGTTTTCCTGAC 59.797 57.895 4.92 0.00 0.00 3.51
164 171 1.093496 ATTTAGGCGCCGTGGTTAGC 61.093 55.000 23.20 0.00 0.00 3.09
172 179 1.944024 TGGTTGATTATTTAGGCGCCG 59.056 47.619 23.20 0.00 0.00 6.46
182 189 1.217942 GGGGGAAGGCTGGTTGATTAT 59.782 52.381 0.00 0.00 0.00 1.28
183 190 0.629058 GGGGGAAGGCTGGTTGATTA 59.371 55.000 0.00 0.00 0.00 1.75
186 193 2.121506 AGGGGGAAGGCTGGTTGA 60.122 61.111 0.00 0.00 0.00 3.18
282 305 2.665245 CGTCGTATTGGTCGTGTGTGTA 60.665 50.000 0.00 0.00 0.00 2.90
285 308 1.005294 GCGTCGTATTGGTCGTGTGT 61.005 55.000 0.00 0.00 0.00 3.72
291 314 1.425412 ACTTGTGCGTCGTATTGGTC 58.575 50.000 0.00 0.00 0.00 4.02
293 316 2.330286 TGTACTTGTGCGTCGTATTGG 58.670 47.619 0.00 0.00 0.00 3.16
294 317 2.222508 GCTGTACTTGTGCGTCGTATTG 60.223 50.000 0.00 0.00 0.00 1.90
300 323 0.232303 GTGTGCTGTACTTGTGCGTC 59.768 55.000 0.00 0.00 0.00 5.19
301 324 1.487452 CGTGTGCTGTACTTGTGCGT 61.487 55.000 0.00 0.00 0.00 5.24
316 339 4.129737 CATCGCCCTCGTCCGTGT 62.130 66.667 0.00 0.00 36.96 4.49
328 351 3.558411 GTCTCGTGGCTGCATCGC 61.558 66.667 0.50 0.00 0.00 4.58
330 353 1.875813 CTCGTCTCGTGGCTGCATC 60.876 63.158 0.50 0.00 0.00 3.91
331 354 1.670949 ATCTCGTCTCGTGGCTGCAT 61.671 55.000 0.50 0.00 0.00 3.96
332 355 1.877576 AATCTCGTCTCGTGGCTGCA 61.878 55.000 0.50 0.00 0.00 4.41
333 356 1.142778 GAATCTCGTCTCGTGGCTGC 61.143 60.000 0.00 0.00 0.00 5.25
334 357 0.863538 CGAATCTCGTCTCGTGGCTG 60.864 60.000 0.00 0.00 34.72 4.85
335 358 1.025113 TCGAATCTCGTCTCGTGGCT 61.025 55.000 0.00 0.00 41.35 4.75
336 359 0.029567 ATCGAATCTCGTCTCGTGGC 59.970 55.000 0.00 0.00 41.35 5.01
337 360 1.747956 CATCGAATCTCGTCTCGTGG 58.252 55.000 0.00 0.00 41.35 4.94
338 361 1.116436 GCATCGAATCTCGTCTCGTG 58.884 55.000 0.00 0.00 41.35 4.35
339 362 1.018148 AGCATCGAATCTCGTCTCGT 58.982 50.000 0.00 0.00 41.35 4.18
340 363 2.112475 AAGCATCGAATCTCGTCTCG 57.888 50.000 0.00 0.00 41.35 4.04
341 364 2.977169 GCTAAGCATCGAATCTCGTCTC 59.023 50.000 0.00 0.00 41.35 3.36
342 365 2.603412 CGCTAAGCATCGAATCTCGTCT 60.603 50.000 0.00 0.00 41.35 4.18
343 366 1.711298 CGCTAAGCATCGAATCTCGTC 59.289 52.381 0.00 0.00 41.35 4.20
372 395 2.969238 CATGCATCGCCCTCGTCC 60.969 66.667 0.00 0.00 36.96 4.79
373 396 3.643978 GCATGCATCGCCCTCGTC 61.644 66.667 14.21 0.00 36.96 4.20
374 397 3.762429 ATGCATGCATCGCCCTCGT 62.762 57.895 27.46 2.73 36.96 4.18
424 477 2.188817 GGGAGCATATATTCCGTCCCT 58.811 52.381 9.73 0.00 40.58 4.20
425 478 1.209747 GGGGAGCATATATTCCGTCCC 59.790 57.143 8.90 8.90 42.69 4.46
426 479 2.188817 AGGGGAGCATATATTCCGTCC 58.811 52.381 0.00 0.00 34.17 4.79
427 480 5.416271 TTTAGGGGAGCATATATTCCGTC 57.584 43.478 0.00 0.00 34.17 4.79
482 535 2.747855 CTGTGAAAGGGCGAGGGC 60.748 66.667 0.00 0.00 38.90 5.19
485 538 2.037136 CAGGCTGTGAAAGGGCGAG 61.037 63.158 6.28 0.00 0.00 5.03
526 579 1.663702 CCAGTTGCTTGCTTGCTGC 60.664 57.895 0.00 0.00 43.25 5.25
527 580 1.663702 GCCAGTTGCTTGCTTGCTG 60.664 57.895 3.47 0.37 36.87 4.41
528 581 2.732658 GCCAGTTGCTTGCTTGCT 59.267 55.556 3.47 0.00 36.87 3.91
529 582 2.732094 CGCCAGTTGCTTGCTTGC 60.732 61.111 0.00 0.00 38.05 4.01
542 609 3.089217 TCAGATGGATGGCCGCCA 61.089 61.111 16.17 16.17 40.24 5.69
554 621 2.278332 TCGATGGACCGATCTCAGAT 57.722 50.000 0.00 0.00 33.14 2.90
565 632 2.397413 ATTGGGGGCGATCGATGGAC 62.397 60.000 21.57 8.36 0.00 4.02
568 635 1.237285 GGAATTGGGGGCGATCGATG 61.237 60.000 21.57 0.00 0.00 3.84
643 710 4.561105 AGAGAACAAAGAAAGGTCGCTAG 58.439 43.478 0.00 0.00 0.00 3.42
644 711 4.602340 AGAGAACAAAGAAAGGTCGCTA 57.398 40.909 0.00 0.00 0.00 4.26
645 712 3.477210 AGAGAACAAAGAAAGGTCGCT 57.523 42.857 0.00 0.00 0.00 4.93
646 713 4.201920 ACAAAGAGAACAAAGAAAGGTCGC 60.202 41.667 0.00 0.00 0.00 5.19
647 714 5.485662 ACAAAGAGAACAAAGAAAGGTCG 57.514 39.130 0.00 0.00 0.00 4.79
648 715 7.066404 AGAGAACAAAGAGAACAAAGAAAGGTC 59.934 37.037 0.00 0.00 0.00 3.85
649 716 6.887002 AGAGAACAAAGAGAACAAAGAAAGGT 59.113 34.615 0.00 0.00 0.00 3.50
650 717 7.326968 AGAGAACAAAGAGAACAAAGAAAGG 57.673 36.000 0.00 0.00 0.00 3.11
651 718 9.070149 CAAAGAGAACAAAGAGAACAAAGAAAG 57.930 33.333 0.00 0.00 0.00 2.62
652 719 7.542130 GCAAAGAGAACAAAGAGAACAAAGAAA 59.458 33.333 0.00 0.00 0.00 2.52
653 720 7.029563 GCAAAGAGAACAAAGAGAACAAAGAA 58.970 34.615 0.00 0.00 0.00 2.52
654 721 6.375455 AGCAAAGAGAACAAAGAGAACAAAGA 59.625 34.615 0.00 0.00 0.00 2.52
655 722 6.558909 AGCAAAGAGAACAAAGAGAACAAAG 58.441 36.000 0.00 0.00 0.00 2.77
674 744 3.371034 GGAATAAAGGGGGCTTAGCAAA 58.629 45.455 6.53 0.00 0.00 3.68
675 745 2.358826 GGGAATAAAGGGGGCTTAGCAA 60.359 50.000 6.53 0.00 0.00 3.91
676 746 1.216930 GGGAATAAAGGGGGCTTAGCA 59.783 52.381 6.53 0.00 0.00 3.49
677 747 1.480683 GGGGAATAAAGGGGGCTTAGC 60.481 57.143 0.00 0.00 0.00 3.09
697 767 4.036380 GGAACGAAGGCATAGTTTAATGGG 59.964 45.833 0.00 0.00 0.00 4.00
717 787 2.083774 CGAATTTGCTGGCTAGTGGAA 58.916 47.619 0.00 0.00 0.00 3.53
750 823 2.344500 CGGTGTACGGGCAGGAAA 59.656 61.111 0.00 0.00 39.42 3.13
761 844 2.745037 GAAGGTGGTGGCGGTGTA 59.255 61.111 0.00 0.00 0.00 2.90
762 845 4.265056 GGAAGGTGGTGGCGGTGT 62.265 66.667 0.00 0.00 0.00 4.16
768 851 3.584868 GACGGACGGAAGGTGGTGG 62.585 68.421 0.00 0.00 0.00 4.61
784 867 2.050918 CTTTATCTGGAGGGGAGGGAC 58.949 57.143 0.00 0.00 0.00 4.46
793 876 3.244491 CCTGGCAGGATCTTTATCTGGAG 60.244 52.174 29.96 0.00 37.67 3.86
794 877 2.707791 CCTGGCAGGATCTTTATCTGGA 59.292 50.000 29.96 0.00 37.67 3.86
797 880 2.106166 CAGCCTGGCAGGATCTTTATCT 59.894 50.000 37.07 18.22 37.67 1.98
798 881 2.502295 CAGCCTGGCAGGATCTTTATC 58.498 52.381 37.07 16.15 37.67 1.75
799 882 1.478288 GCAGCCTGGCAGGATCTTTAT 60.478 52.381 37.07 9.70 37.67 1.40
800 883 0.107017 GCAGCCTGGCAGGATCTTTA 60.107 55.000 37.07 0.00 37.67 1.85
874 977 2.953466 CGAGGATGTCGTAAGGGAAA 57.047 50.000 0.00 0.00 44.20 3.13
893 996 1.400242 GCTTGTGCTTGGTCGAATGTC 60.400 52.381 0.00 0.00 36.03 3.06
897 1000 1.785041 GCTGCTTGTGCTTGGTCGAA 61.785 55.000 0.00 0.00 40.48 3.71
903 1006 1.335810 TCTCTTTGCTGCTTGTGCTTG 59.664 47.619 0.00 0.00 40.48 4.01
904 1007 1.336125 GTCTCTTTGCTGCTTGTGCTT 59.664 47.619 0.00 0.00 40.48 3.91
906 1009 0.385223 CGTCTCTTTGCTGCTTGTGC 60.385 55.000 0.00 0.00 40.20 4.57
908 1011 0.815213 TGCGTCTCTTTGCTGCTTGT 60.815 50.000 0.00 0.00 0.00 3.16
946 1051 1.746991 GGGCACTCAGGCAGTAAGC 60.747 63.158 0.00 0.00 46.44 3.09
1083 1188 0.323302 TCAGTGGCATAAGCAACCGA 59.677 50.000 0.00 0.00 46.34 4.69
1086 1191 3.155093 CCAATCAGTGGCATAAGCAAC 57.845 47.619 0.00 0.00 45.47 4.17
1097 1236 2.158986 TGCAAACCCAAACCAATCAGTG 60.159 45.455 0.00 0.00 0.00 3.66
1118 1257 1.537202 GACGCAAGAATCAACAGCCTT 59.463 47.619 0.00 0.00 43.62 4.35
1122 1261 1.391485 CCTCGACGCAAGAATCAACAG 59.609 52.381 0.00 0.00 43.62 3.16
1123 1262 1.270094 ACCTCGACGCAAGAATCAACA 60.270 47.619 0.00 0.00 43.62 3.33
1124 1263 1.390463 GACCTCGACGCAAGAATCAAC 59.610 52.381 0.00 0.00 43.62 3.18
1125 1264 1.710013 GACCTCGACGCAAGAATCAA 58.290 50.000 0.00 0.00 43.62 2.57
1126 1265 0.456142 CGACCTCGACGCAAGAATCA 60.456 55.000 0.00 0.00 43.02 2.57
1127 1266 0.179171 TCGACCTCGACGCAAGAATC 60.179 55.000 0.00 0.00 44.22 2.52
1128 1267 0.179161 CTCGACCTCGACGCAAGAAT 60.179 55.000 0.00 0.00 44.22 2.40
1129 1268 1.209383 CTCGACCTCGACGCAAGAA 59.791 57.895 0.00 0.00 44.22 2.52
1130 1269 2.687805 CCTCGACCTCGACGCAAGA 61.688 63.158 0.00 0.00 44.22 3.02
1131 1270 2.202492 CCTCGACCTCGACGCAAG 60.202 66.667 0.00 0.00 44.22 4.01
1132 1271 2.974489 GACCTCGACCTCGACGCAA 61.974 63.158 0.00 0.00 44.22 4.85
1133 1272 3.429141 GACCTCGACCTCGACGCA 61.429 66.667 0.00 0.00 44.22 5.24
1134 1273 4.517703 CGACCTCGACCTCGACGC 62.518 72.222 1.47 0.00 44.22 5.19
1135 1274 2.800581 CTCGACCTCGACCTCGACG 61.801 68.421 5.73 0.00 44.22 5.12
1136 1275 2.462782 CCTCGACCTCGACCTCGAC 61.463 68.421 5.73 0.00 44.22 4.20
1137 1276 2.125229 CCTCGACCTCGACCTCGA 60.125 66.667 8.88 8.88 44.22 4.04
1138 1277 1.096386 ATTCCTCGACCTCGACCTCG 61.096 60.000 0.00 1.30 44.22 4.63
1139 1278 0.382515 CATTCCTCGACCTCGACCTC 59.617 60.000 0.00 0.00 44.22 3.85
1140 1279 1.668101 GCATTCCTCGACCTCGACCT 61.668 60.000 0.00 0.00 44.22 3.85
1141 1280 1.227002 GCATTCCTCGACCTCGACC 60.227 63.158 0.00 0.00 44.22 4.79
1142 1281 1.586564 CGCATTCCTCGACCTCGAC 60.587 63.158 0.00 0.00 44.22 4.20
1144 1283 1.874019 CACGCATTCCTCGACCTCG 60.874 63.158 0.00 0.00 41.45 4.63
1943 2107 1.219124 GCGGCATGGTCTCTTCTCA 59.781 57.895 0.00 0.00 0.00 3.27
1944 2108 0.391661 TTGCGGCATGGTCTCTTCTC 60.392 55.000 2.28 0.00 0.00 2.87
1945 2109 0.674895 GTTGCGGCATGGTCTCTTCT 60.675 55.000 2.28 0.00 0.00 2.85
1953 2117 2.431260 GTTGCAGTTGCGGCATGG 60.431 61.111 2.28 0.00 45.83 3.66
1959 2123 0.453950 GCAGATCAGTTGCAGTTGCG 60.454 55.000 0.00 0.00 45.83 4.85
1960 2124 0.109412 GGCAGATCAGTTGCAGTTGC 60.109 55.000 7.62 0.00 43.28 4.17
2112 2279 5.378332 AGTACAAGCTGGTAGATAGATCGT 58.622 41.667 0.00 0.00 0.00 3.73
2114 2281 7.989416 AGTAGTACAAGCTGGTAGATAGATC 57.011 40.000 0.00 0.00 0.00 2.75
2286 2454 5.305386 TGCATACATGGAGTAGCTCATAAGT 59.695 40.000 0.00 0.00 35.85 2.24
2287 2455 5.787380 TGCATACATGGAGTAGCTCATAAG 58.213 41.667 0.00 0.00 35.85 1.73
2292 2460 5.049129 GGAAAATGCATACATGGAGTAGCTC 60.049 44.000 0.00 0.00 36.36 4.09
2296 2464 6.638096 CATGGAAAATGCATACATGGAGTA 57.362 37.500 18.40 0.00 36.36 2.59
2297 2465 5.524971 CATGGAAAATGCATACATGGAGT 57.475 39.130 18.40 0.00 36.36 3.85
2301 2469 5.524971 AGTCCATGGAAAATGCATACATG 57.475 39.130 18.20 18.87 36.36 3.21
2307 2475 3.401182 GCAAAAGTCCATGGAAAATGCA 58.599 40.909 26.03 0.00 0.00 3.96
2309 2477 3.337358 GGGCAAAAGTCCATGGAAAATG 58.663 45.455 18.20 14.10 0.00 2.32
2335 2503 2.408333 GTGGATGTATGCACAGGGC 58.592 57.895 11.02 0.00 46.68 5.19
2405 2577 1.271163 ACGATTCGCCAAAAAGGAGGA 60.271 47.619 5.86 0.00 41.22 3.71
2406 2578 1.135689 CACGATTCGCCAAAAAGGAGG 60.136 52.381 5.86 0.00 41.22 4.30
2450 2622 1.433879 CGGTCGATGAGTCCCTGAC 59.566 63.158 0.00 0.00 0.00 3.51
2456 2628 3.357166 AATCTTAGCGGTCGATGAGTC 57.643 47.619 0.00 0.00 0.00 3.36
2492 2664 3.066203 TCTTCTTCTTGGTGCCGTTTTTC 59.934 43.478 0.00 0.00 0.00 2.29
2575 2752 5.984695 AGGTAGCCTTCCTTTCATTTTTC 57.015 39.130 0.00 0.00 30.18 2.29
2608 2785 1.730593 CGCACGTTTCTCCGATCGTC 61.731 60.000 15.09 0.00 34.30 4.20
2635 2812 2.990967 ACCGGTTGCTTGGCCATG 60.991 61.111 6.09 11.02 0.00 3.66
2641 2818 1.021202 TTCAGTTCACCGGTTGCTTG 58.979 50.000 2.97 1.44 0.00 4.01
2658 2835 4.683334 GTGCTTGCCACGCGGTTC 62.683 66.667 12.47 0.00 34.22 3.62
2764 2941 2.718073 GGTACAGGTCCGGCGACAT 61.718 63.158 9.30 0.00 41.13 3.06
2781 2958 2.125673 CTCCCCACGCTACAACGG 60.126 66.667 0.00 0.00 37.37 4.44
2805 2982 0.591659 GTGAAAGAAACGGGAGCACC 59.408 55.000 0.00 0.00 0.00 5.01
2861 3042 1.004080 ACGCACTGCAGCTCAGATT 60.004 52.632 15.27 0.00 45.72 2.40
2882 3063 2.743928 GCTGTCGGCCACTCCAAG 60.744 66.667 2.24 0.00 34.27 3.61
2902 3083 2.373169 TCAGAGGTTGCATCAGTTCCTT 59.627 45.455 0.00 0.00 0.00 3.36


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

AutoCloner maintained by Alex Coulton.