Multiple sequence alignment - TraesCS5B01G197400

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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 TraesCS5B01G197400 chr5B 100.000 4489 0 0 1 4489 355901425 355905913 0.000000e+00 8290
1 TraesCS5B01G197400 chr5D 94.959 2817 108 20 712 3520 310033734 310036524 0.000000e+00 4385
2 TraesCS5B01G197400 chr5D 89.888 623 32 11 1 621 310033105 310033698 0.000000e+00 773
3 TraesCS5B01G197400 chr5A 94.196 2843 128 17 712 3520 403701025 403703864 0.000000e+00 4301
4 TraesCS5B01G197400 chr5A 98.866 970 11 0 3520 4489 32752988 32753957 0.000000e+00 1731
5 TraesCS5B01G197400 chr5A 84.986 706 52 27 1 672 403700344 403701029 0.000000e+00 667
6 TraesCS5B01G197400 chr4B 98.774 979 10 1 3513 4489 439735987 439736965 0.000000e+00 1740
7 TraesCS5B01G197400 chr2B 98.971 972 8 1 3520 4489 161707309 161706338 0.000000e+00 1738
8 TraesCS5B01G197400 chr2B 98.866 970 11 0 3517 4486 575371444 575372413 0.000000e+00 1731
9 TraesCS5B01G197400 chr6A 98.970 971 8 1 3519 4489 569701807 569700839 0.000000e+00 1736
10 TraesCS5B01G197400 chr6A 98.969 970 9 1 3520 4489 569117589 569116621 0.000000e+00 1735
11 TraesCS5B01G197400 chr1A 98.970 971 9 1 3519 4489 580985939 580984970 0.000000e+00 1736
12 TraesCS5B01G197400 chr4A 98.969 970 8 1 3520 4489 441957506 441956539 0.000000e+00 1735
13 TraesCS5B01G197400 chr3A 98.866 970 9 1 3520 4489 730996633 730997600 0.000000e+00 1729
14 TraesCS5B01G197400 chrUn 86.709 158 21 0 1298 1455 11818654 11818811 4.620000e-40 176
15 TraesCS5B01G197400 chrUn 86.709 158 21 0 1298 1455 11821200 11821357 4.620000e-40 176
16 TraesCS5B01G197400 chrUn 86.709 158 21 0 1298 1455 385071643 385071800 4.620000e-40 176
17 TraesCS5B01G197400 chrUn 86.076 158 22 0 1298 1455 377579916 377579759 2.150000e-38 171


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 TraesCS5B01G197400 chr5B 355901425 355905913 4488 False 8290 8290 100.0000 1 4489 1 chr5B.!!$F1 4488
1 TraesCS5B01G197400 chr5D 310033105 310036524 3419 False 2579 4385 92.4235 1 3520 2 chr5D.!!$F1 3519
2 TraesCS5B01G197400 chr5A 403700344 403703864 3520 False 2484 4301 89.5910 1 3520 2 chr5A.!!$F2 3519
3 TraesCS5B01G197400 chr5A 32752988 32753957 969 False 1731 1731 98.8660 3520 4489 1 chr5A.!!$F1 969
4 TraesCS5B01G197400 chr4B 439735987 439736965 978 False 1740 1740 98.7740 3513 4489 1 chr4B.!!$F1 976
5 TraesCS5B01G197400 chr2B 161706338 161707309 971 True 1738 1738 98.9710 3520 4489 1 chr2B.!!$R1 969
6 TraesCS5B01G197400 chr2B 575371444 575372413 969 False 1731 1731 98.8660 3517 4486 1 chr2B.!!$F1 969
7 TraesCS5B01G197400 chr6A 569700839 569701807 968 True 1736 1736 98.9700 3519 4489 1 chr6A.!!$R2 970
8 TraesCS5B01G197400 chr6A 569116621 569117589 968 True 1735 1735 98.9690 3520 4489 1 chr6A.!!$R1 969
9 TraesCS5B01G197400 chr1A 580984970 580985939 969 True 1736 1736 98.9700 3519 4489 1 chr1A.!!$R1 970
10 TraesCS5B01G197400 chr4A 441956539 441957506 967 True 1735 1735 98.9690 3520 4489 1 chr4A.!!$R1 969
11 TraesCS5B01G197400 chr3A 730996633 730997600 967 False 1729 1729 98.8660 3520 4489 1 chr3A.!!$F1 969

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
211 224 0.532573 ACTCTATGCCACGTGTCCAG 59.467 55.0 15.65 6.11 0.00 3.86 F
1423 1492 0.597118 CATAGCGTCTGAGCTCAGGC 60.597 60.0 36.92 35.39 45.67 4.85 F
2644 2713 0.537188 CATGGTCAGCCTCTACGGTT 59.463 55.0 0.00 0.00 35.27 4.44 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1476 1545 0.531532 CCGACTCCACAGATGCATCC 60.532 60.000 23.06 5.58 0.00 3.51 R
2658 2727 2.417097 GCTTTGGCGTGGTTGCTT 59.583 55.556 0.00 0.00 34.52 3.91 R
4208 4292 1.270305 CCGTGACACTCATTGGTCTGT 60.270 52.381 3.68 0.00 35.11 3.41 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
22 23 2.395690 GCACACGCGAATTCTCCG 59.604 61.111 15.93 12.10 0.00 4.63
131 143 2.361610 CCAGCCATCGCCCAAAGT 60.362 61.111 0.00 0.00 34.57 2.66
132 144 2.409870 CCAGCCATCGCCCAAAGTC 61.410 63.158 0.00 0.00 34.57 3.01
133 145 1.675310 CAGCCATCGCCCAAAGTCA 60.675 57.895 0.00 0.00 34.57 3.41
134 146 1.033746 CAGCCATCGCCCAAAGTCAT 61.034 55.000 0.00 0.00 34.57 3.06
135 147 0.546122 AGCCATCGCCCAAAGTCATA 59.454 50.000 0.00 0.00 34.57 2.15
136 148 1.143684 AGCCATCGCCCAAAGTCATAT 59.856 47.619 0.00 0.00 34.57 1.78
137 149 1.267806 GCCATCGCCCAAAGTCATATG 59.732 52.381 0.00 0.00 0.00 1.78
185 197 2.437359 GCTGCAATGCCTCGGACT 60.437 61.111 1.53 0.00 0.00 3.85
203 216 3.304794 GGACTCGACATACTCTATGCCAC 60.305 52.174 0.00 0.00 39.79 5.01
208 221 3.372954 GACATACTCTATGCCACGTGTC 58.627 50.000 15.65 0.98 39.79 3.67
211 224 0.532573 ACTCTATGCCACGTGTCCAG 59.467 55.000 15.65 6.11 0.00 3.86
319 333 2.465920 CGAAACGAGCACGACTGC 59.534 61.111 11.40 0.00 44.63 4.40
335 349 2.746362 GACTGCACCATCTTCCTTCTTG 59.254 50.000 0.00 0.00 0.00 3.02
368 382 1.801771 CGGTTGCGTAGACCAAATGAA 59.198 47.619 5.91 0.00 36.99 2.57
369 383 2.224549 CGGTTGCGTAGACCAAATGAAA 59.775 45.455 5.91 0.00 36.99 2.69
370 384 3.119990 CGGTTGCGTAGACCAAATGAAAT 60.120 43.478 5.91 0.00 36.99 2.17
371 385 4.165779 GGTTGCGTAGACCAAATGAAATG 58.834 43.478 1.23 0.00 37.14 2.32
372 386 4.083003 GGTTGCGTAGACCAAATGAAATGA 60.083 41.667 1.23 0.00 37.14 2.57
384 398 3.051392 GAAATGAGGTTGCCCGGCG 62.051 63.158 4.58 0.00 35.12 6.46
413 427 2.911143 CCCACCCCGATGAAGAGG 59.089 66.667 0.00 0.00 0.00 3.69
455 469 3.321111 ACTCTTCCTCGTTCACAAAGCTA 59.679 43.478 0.00 0.00 0.00 3.32
456 470 3.650139 TCTTCCTCGTTCACAAAGCTAC 58.350 45.455 0.00 0.00 0.00 3.58
457 471 3.321111 TCTTCCTCGTTCACAAAGCTACT 59.679 43.478 0.00 0.00 0.00 2.57
487 505 4.884668 TGTAACCAAGTCGAAGGAATCT 57.115 40.909 6.80 0.00 0.00 2.40
492 510 7.558807 TGTAACCAAGTCGAAGGAATCTATCTA 59.441 37.037 6.80 0.00 0.00 1.98
621 668 1.197055 GACATGCATGCATCAAAGCG 58.803 50.000 30.07 19.46 37.31 4.68
622 669 0.812549 ACATGCATGCATCAAAGCGA 59.187 45.000 30.07 0.00 37.31 4.93
623 670 1.202256 ACATGCATGCATCAAAGCGAG 60.202 47.619 30.07 18.04 37.31 5.03
624 671 1.064952 CATGCATGCATCAAAGCGAGA 59.935 47.619 30.07 0.00 37.31 4.04
629 676 3.618698 CATGCATCAAAGCGAGATCAAG 58.381 45.455 0.00 0.00 37.31 3.02
650 697 1.815003 GCCATAGCCCATATCTGCAAC 59.185 52.381 0.00 0.00 0.00 4.17
660 707 4.946157 CCCATATCTGCAACAAGAAAGTCT 59.054 41.667 0.00 0.00 0.00 3.24
692 739 2.697431 GCACCACTATGCAAACGAAA 57.303 45.000 0.00 0.00 45.39 3.46
693 740 3.006659 GCACCACTATGCAAACGAAAA 57.993 42.857 0.00 0.00 45.39 2.29
694 741 2.724174 GCACCACTATGCAAACGAAAAC 59.276 45.455 0.00 0.00 45.39 2.43
695 742 3.793801 GCACCACTATGCAAACGAAAACA 60.794 43.478 0.00 0.00 45.39 2.83
696 743 4.355437 CACCACTATGCAAACGAAAACAA 58.645 39.130 0.00 0.00 0.00 2.83
697 744 4.800993 CACCACTATGCAAACGAAAACAAA 59.199 37.500 0.00 0.00 0.00 2.83
698 745 5.289675 CACCACTATGCAAACGAAAACAAAA 59.710 36.000 0.00 0.00 0.00 2.44
699 746 5.289917 ACCACTATGCAAACGAAAACAAAAC 59.710 36.000 0.00 0.00 0.00 2.43
700 747 5.411222 CACTATGCAAACGAAAACAAAACG 58.589 37.500 0.00 0.00 0.00 3.60
701 748 2.771210 TGCAAACGAAAACAAAACGC 57.229 40.000 0.00 0.00 0.00 4.84
702 749 1.057847 TGCAAACGAAAACAAAACGCG 59.942 42.857 3.53 3.53 0.00 6.01
703 750 1.587847 GCAAACGAAAACAAAACGCGG 60.588 47.619 12.47 0.00 0.00 6.46
704 751 1.912110 CAAACGAAAACAAAACGCGGA 59.088 42.857 12.47 0.00 0.00 5.54
705 752 2.478547 AACGAAAACAAAACGCGGAT 57.521 40.000 12.47 0.00 0.00 4.18
706 753 2.478547 ACGAAAACAAAACGCGGATT 57.521 40.000 12.47 1.50 0.00 3.01
707 754 3.605743 ACGAAAACAAAACGCGGATTA 57.394 38.095 12.47 0.00 0.00 1.75
708 755 3.290748 ACGAAAACAAAACGCGGATTAC 58.709 40.909 12.47 0.00 0.00 1.89
709 756 3.002553 ACGAAAACAAAACGCGGATTACT 59.997 39.130 12.47 0.00 0.00 2.24
710 757 3.969981 CGAAAACAAAACGCGGATTACTT 59.030 39.130 12.47 0.00 0.00 2.24
711 758 5.138788 CGAAAACAAAACGCGGATTACTTA 58.861 37.500 12.47 0.00 0.00 2.24
712 759 5.791480 CGAAAACAAAACGCGGATTACTTAT 59.209 36.000 12.47 0.00 0.00 1.73
713 760 6.954852 CGAAAACAAAACGCGGATTACTTATA 59.045 34.615 12.47 0.00 0.00 0.98
714 761 7.161418 CGAAAACAAAACGCGGATTACTTATAG 59.839 37.037 12.47 0.00 0.00 1.31
715 762 6.973229 AACAAAACGCGGATTACTTATAGT 57.027 33.333 12.47 0.00 0.00 2.12
716 763 6.340537 ACAAAACGCGGATTACTTATAGTG 57.659 37.500 12.47 0.47 0.00 2.74
717 764 6.101332 ACAAAACGCGGATTACTTATAGTGA 58.899 36.000 12.47 0.00 0.00 3.41
718 765 6.759827 ACAAAACGCGGATTACTTATAGTGAT 59.240 34.615 12.47 0.00 0.00 3.06
719 766 6.764877 AAACGCGGATTACTTATAGTGATG 57.235 37.500 12.47 0.00 0.00 3.07
720 767 5.449107 ACGCGGATTACTTATAGTGATGT 57.551 39.130 12.47 0.00 0.00 3.06
721 768 6.564709 ACGCGGATTACTTATAGTGATGTA 57.435 37.500 12.47 0.00 0.00 2.29
722 769 6.609533 ACGCGGATTACTTATAGTGATGTAG 58.390 40.000 12.47 0.00 0.00 2.74
723 770 6.028368 CGCGGATTACTTATAGTGATGTAGG 58.972 44.000 0.00 0.00 0.00 3.18
724 771 6.349115 CGCGGATTACTTATAGTGATGTAGGT 60.349 42.308 0.00 0.00 0.00 3.08
725 772 6.807230 GCGGATTACTTATAGTGATGTAGGTG 59.193 42.308 0.00 0.00 0.00 4.00
726 773 6.807230 CGGATTACTTATAGTGATGTAGGTGC 59.193 42.308 0.00 0.00 0.00 5.01
727 774 7.523216 CGGATTACTTATAGTGATGTAGGTGCA 60.523 40.741 0.00 0.00 0.00 4.57
728 775 7.599245 GGATTACTTATAGTGATGTAGGTGCAC 59.401 40.741 8.80 8.80 0.00 4.57
882 944 2.132762 CTGTCTGGTAACACGTGTTCC 58.867 52.381 35.40 31.09 46.17 3.62
898 960 3.132467 GTGTTCCGCCTCCTCTATAAGTT 59.868 47.826 0.00 0.00 0.00 2.66
902 964 1.336056 CGCCTCCTCTATAAGTTCGCC 60.336 57.143 0.00 0.00 0.00 5.54
905 967 1.619332 CTCCTCTATAAGTTCGCCCCC 59.381 57.143 0.00 0.00 0.00 5.40
920 982 3.905678 CCCCGCGCTCCTCACTAG 61.906 72.222 5.56 0.00 0.00 2.57
922 984 3.826754 CCGCGCTCCTCACTAGCA 61.827 66.667 5.56 0.00 40.08 3.49
924 986 1.227089 CGCGCTCCTCACTAGCAAT 60.227 57.895 5.56 0.00 40.08 3.56
967 1036 7.482169 TCTCTCTTGAGCTTACTCCATTTTA 57.518 36.000 0.00 0.00 42.74 1.52
977 1046 1.340991 ACTCCATTTTATGCGCCCACT 60.341 47.619 4.18 0.00 0.00 4.00
978 1047 2.092646 ACTCCATTTTATGCGCCCACTA 60.093 45.455 4.18 0.00 0.00 2.74
998 1067 5.998363 CACTATACTTCCCTTAATCCAAGCC 59.002 44.000 0.00 0.00 32.41 4.35
1356 1425 0.904865 TGAGGTTCCTGCTCACGGAT 60.905 55.000 0.00 0.00 0.00 4.18
1423 1492 0.597118 CATAGCGTCTGAGCTCAGGC 60.597 60.000 36.92 35.39 45.67 4.85
1466 1535 3.190849 CATGGACGTGCTGCCGAG 61.191 66.667 8.99 1.59 0.00 4.63
1476 1545 3.190849 CTGCCGAGGTGCATCGTG 61.191 66.667 8.75 2.22 41.16 4.35
1478 1547 4.451150 GCCGAGGTGCATCGTGGA 62.451 66.667 13.93 0.00 41.12 4.02
1531 1600 1.461091 GGTATCGGATCAGGCGTGGA 61.461 60.000 6.56 0.00 0.00 4.02
1785 1854 3.057596 TCAACAATTTGATGGCGTTCCTC 60.058 43.478 2.79 0.00 36.79 3.71
1920 1989 2.438868 TCACACTGGAACTCATGACG 57.561 50.000 0.00 0.00 0.00 4.35
1926 1995 0.834261 TGGAACTCATGACGGACCCA 60.834 55.000 0.00 0.00 0.00 4.51
2112 2181 2.359602 TCGCTTCCCGAGACGAGT 60.360 61.111 0.00 0.00 41.89 4.18
2207 2276 0.874607 GCCGTTAGCTACATCGTGGG 60.875 60.000 0.00 0.00 38.99 4.61
2208 2277 0.874607 CCGTTAGCTACATCGTGGGC 60.875 60.000 0.00 0.00 0.00 5.36
2250 2319 2.707849 GGAGCGTAGGAAGGCGACA 61.708 63.158 0.00 0.00 41.40 4.35
2346 2415 2.289532 GCTGTGCCTCCTCTCCTGT 61.290 63.158 0.00 0.00 0.00 4.00
2354 2423 1.410365 CCTCCTCTCCTGTATGGACGT 60.410 57.143 0.00 0.00 40.56 4.34
2644 2713 0.537188 CATGGTCAGCCTCTACGGTT 59.463 55.000 0.00 0.00 35.27 4.44
2652 2721 0.741221 GCCTCTACGGTTTGCTCCAG 60.741 60.000 0.00 0.00 34.25 3.86
2658 2727 2.843545 GGTTTGCTCCAGTCCCCA 59.156 61.111 0.00 0.00 0.00 4.96
2709 2778 3.297620 GTGGTGGTGCTTGCTGGG 61.298 66.667 0.00 0.00 0.00 4.45
2835 2904 1.935327 GCCTAGTCGCTCACCTCGTT 61.935 60.000 0.00 0.00 0.00 3.85
2904 2973 1.450531 GGCTGCTTGTCTTGCTGTGT 61.451 55.000 0.00 0.00 0.00 3.72
2907 2976 0.461870 TGCTTGTCTTGCTGTGTCGT 60.462 50.000 0.00 0.00 0.00 4.34
2925 2994 4.124351 CACGGCGGCGAGAAGGTA 62.124 66.667 38.93 0.00 0.00 3.08
2929 2998 2.707849 GGCGGCGAGAAGGTAGTCA 61.708 63.158 12.98 0.00 0.00 3.41
2979 3048 1.661821 GTCACTGCACTCGCTCGTT 60.662 57.895 0.00 0.00 39.64 3.85
3048 3117 0.537653 TGATCCACCGGCATTACGAA 59.462 50.000 0.00 0.00 35.47 3.85
3120 3189 2.547798 GGTGACCGTTTCGTTCGC 59.452 61.111 0.00 0.00 0.00 4.70
3328 3400 1.455786 CCGCTATTGCTATACACGTGC 59.544 52.381 17.22 0.77 36.97 5.34
3334 3406 5.388475 GCTATTGCTATACACGTGCATACAC 60.388 44.000 17.22 6.31 38.67 2.90
3375 3451 9.738832 GTTTGTAACACCTTTGTTGTACATATT 57.261 29.630 0.00 0.00 45.91 1.28
3383 3459 6.995686 ACCTTTGTTGTACATATTCTGTGTCA 59.004 34.615 0.00 0.00 38.92 3.58
3391 3467 8.039603 TGTACATATTCTGTGTCAAATTGGAC 57.960 34.615 5.98 5.98 38.92 4.02
3448 3525 5.768164 TGGAAGAAGATAGTTGTGGGAAAAC 59.232 40.000 0.00 0.00 0.00 2.43
3491 3569 6.002062 ACTTTCTCGCTCGAAAATGAAAAT 57.998 33.333 6.11 0.00 32.95 1.82
3540 3618 4.919774 TGTAAGACAATAGGCTTTGGGA 57.080 40.909 0.00 0.00 0.00 4.37
3880 3964 4.500887 GCAGAAAGGTATGTAGCACCGATA 60.501 45.833 0.00 0.00 41.21 2.92
4064 4148 4.287067 TCAGGTTAGAGCCAAAGAAGACAT 59.713 41.667 0.00 0.00 0.00 3.06
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
9 10 0.389948 AAAGCTCGGAGAATTCGCGT 60.390 50.000 9.69 0.00 36.69 6.01
17 18 1.544825 CCTCCACCAAAGCTCGGAGA 61.545 60.000 9.69 4.74 46.71 3.71
22 23 1.676967 CTGGCCTCCACCAAAGCTC 60.677 63.158 3.32 0.00 39.86 4.09
131 143 3.454447 CCGCCAAGGGGATATACATATGA 59.546 47.826 10.38 0.00 37.91 2.15
132 144 3.808728 CCGCCAAGGGGATATACATATG 58.191 50.000 4.54 0.00 37.91 1.78
133 145 2.172717 GCCGCCAAGGGGATATACATAT 59.827 50.000 4.54 0.00 41.48 1.78
134 146 1.557832 GCCGCCAAGGGGATATACATA 59.442 52.381 4.54 0.00 41.48 2.29
135 147 0.328258 GCCGCCAAGGGGATATACAT 59.672 55.000 4.54 0.00 41.48 2.29
136 148 0.766674 AGCCGCCAAGGGGATATACA 60.767 55.000 4.54 0.00 41.48 2.29
137 149 0.321653 CAGCCGCCAAGGGGATATAC 60.322 60.000 4.54 0.00 41.48 1.47
178 190 3.120477 GCATAGAGTATGTCGAGTCCGAG 60.120 52.174 0.00 0.00 46.52 4.63
182 194 3.607310 CGTGGCATAGAGTATGTCGAGTC 60.607 52.174 0.00 0.00 43.54 3.36
185 197 2.032924 CACGTGGCATAGAGTATGTCGA 59.967 50.000 7.95 0.00 43.54 4.20
203 216 4.436998 GACCGCTCCCTGGACACG 62.437 72.222 0.00 0.00 0.00 4.49
261 275 3.895041 TGGTCATGGATATCGTAAGCTCA 59.105 43.478 0.00 0.00 37.18 4.26
291 305 1.934589 CTCGTTTCGCCATGGTCATA 58.065 50.000 14.67 0.00 0.00 2.15
319 333 2.486982 CAGCACAAGAAGGAAGATGGTG 59.513 50.000 0.00 0.00 0.00 4.17
335 349 3.726517 AACCGACGCATGCAGCAC 61.727 61.111 19.57 4.50 46.13 4.40
413 427 5.299531 AGAGTTGAAACTTAGAAGCAAACCC 59.700 40.000 0.00 0.00 39.88 4.11
477 495 8.321716 CGAACAAAAGTTAGATAGATTCCTTCG 58.678 37.037 0.00 0.00 0.00 3.79
478 496 9.152595 ACGAACAAAAGTTAGATAGATTCCTTC 57.847 33.333 0.00 0.00 0.00 3.46
547 594 2.032528 CGAGGGCATGTGTGGTGT 59.967 61.111 0.00 0.00 0.00 4.16
672 719 1.890876 TTCGTTTGCATAGTGGTGCT 58.109 45.000 0.00 0.00 45.27 4.40
673 720 2.697431 TTTCGTTTGCATAGTGGTGC 57.303 45.000 0.00 0.00 45.25 5.01
674 721 3.958704 TGTTTTCGTTTGCATAGTGGTG 58.041 40.909 0.00 0.00 0.00 4.17
676 723 5.553581 CGTTTTGTTTTCGTTTGCATAGTGG 60.554 40.000 0.00 0.00 0.00 4.00
677 724 5.411222 CGTTTTGTTTTCGTTTGCATAGTG 58.589 37.500 0.00 0.00 0.00 2.74
678 725 4.027214 GCGTTTTGTTTTCGTTTGCATAGT 60.027 37.500 0.00 0.00 0.00 2.12
679 726 4.433079 GCGTTTTGTTTTCGTTTGCATAG 58.567 39.130 0.00 0.00 0.00 2.23
681 728 2.284741 CGCGTTTTGTTTTCGTTTGCAT 60.285 40.909 0.00 0.00 0.00 3.96
682 729 1.057847 CGCGTTTTGTTTTCGTTTGCA 59.942 42.857 0.00 0.00 0.00 4.08
683 730 1.587847 CCGCGTTTTGTTTTCGTTTGC 60.588 47.619 4.92 0.00 0.00 3.68
684 731 1.912110 TCCGCGTTTTGTTTTCGTTTG 59.088 42.857 4.92 0.00 0.00 2.93
685 732 2.259505 TCCGCGTTTTGTTTTCGTTT 57.740 40.000 4.92 0.00 0.00 3.60
687 734 2.478547 AATCCGCGTTTTGTTTTCGT 57.521 40.000 4.92 0.00 0.00 3.85
688 735 3.547601 AGTAATCCGCGTTTTGTTTTCG 58.452 40.909 4.92 0.00 0.00 3.46
689 736 7.959109 ACTATAAGTAATCCGCGTTTTGTTTTC 59.041 33.333 4.92 0.00 0.00 2.29
690 737 7.747357 CACTATAAGTAATCCGCGTTTTGTTTT 59.253 33.333 4.92 0.00 0.00 2.43
691 738 7.118101 TCACTATAAGTAATCCGCGTTTTGTTT 59.882 33.333 4.92 0.58 0.00 2.83
692 739 6.591062 TCACTATAAGTAATCCGCGTTTTGTT 59.409 34.615 4.92 0.00 0.00 2.83
693 740 6.101332 TCACTATAAGTAATCCGCGTTTTGT 58.899 36.000 4.92 0.00 0.00 2.83
694 741 6.578020 TCACTATAAGTAATCCGCGTTTTG 57.422 37.500 4.92 0.00 0.00 2.44
695 742 6.759827 ACATCACTATAAGTAATCCGCGTTTT 59.240 34.615 4.92 0.00 0.00 2.43
696 743 6.278363 ACATCACTATAAGTAATCCGCGTTT 58.722 36.000 4.92 0.40 0.00 3.60
697 744 5.839621 ACATCACTATAAGTAATCCGCGTT 58.160 37.500 4.92 0.00 0.00 4.84
698 745 5.449107 ACATCACTATAAGTAATCCGCGT 57.551 39.130 4.92 0.00 0.00 6.01
699 746 6.028368 CCTACATCACTATAAGTAATCCGCG 58.972 44.000 0.00 0.00 0.00 6.46
700 747 6.807230 CACCTACATCACTATAAGTAATCCGC 59.193 42.308 0.00 0.00 0.00 5.54
701 748 6.807230 GCACCTACATCACTATAAGTAATCCG 59.193 42.308 0.00 0.00 0.00 4.18
702 749 7.599245 GTGCACCTACATCACTATAAGTAATCC 59.401 40.741 5.22 0.00 0.00 3.01
703 750 7.599245 GGTGCACCTACATCACTATAAGTAATC 59.401 40.741 29.12 0.00 0.00 1.75
704 751 7.070696 TGGTGCACCTACATCACTATAAGTAAT 59.929 37.037 34.75 0.00 36.82 1.89
705 752 6.381707 TGGTGCACCTACATCACTATAAGTAA 59.618 38.462 34.75 6.60 36.82 2.24
706 753 5.894964 TGGTGCACCTACATCACTATAAGTA 59.105 40.000 34.75 6.97 36.82 2.24
707 754 4.714802 TGGTGCACCTACATCACTATAAGT 59.285 41.667 34.75 0.00 36.82 2.24
708 755 5.276461 TGGTGCACCTACATCACTATAAG 57.724 43.478 34.75 0.00 36.82 1.73
709 756 5.365314 TGATGGTGCACCTACATCACTATAA 59.635 40.000 34.75 11.74 44.19 0.98
710 757 4.898861 TGATGGTGCACCTACATCACTATA 59.101 41.667 34.75 11.96 44.19 1.31
711 758 3.711190 TGATGGTGCACCTACATCACTAT 59.289 43.478 34.75 17.59 44.19 2.12
712 759 3.103742 TGATGGTGCACCTACATCACTA 58.896 45.455 34.75 13.29 44.19 2.74
713 760 1.908619 TGATGGTGCACCTACATCACT 59.091 47.619 34.75 10.40 44.19 3.41
714 761 2.401583 TGATGGTGCACCTACATCAC 57.598 50.000 34.75 17.76 44.19 3.06
716 763 3.198409 TGATGATGGTGCACCTACATC 57.802 47.619 38.14 38.14 42.89 3.06
717 764 3.483421 CATGATGATGGTGCACCTACAT 58.517 45.455 34.75 33.23 36.10 2.29
718 765 2.421811 CCATGATGATGGTGCACCTACA 60.422 50.000 34.75 30.66 43.98 2.74
719 766 2.224606 CCATGATGATGGTGCACCTAC 58.775 52.381 34.75 26.66 43.98 3.18
720 767 2.643995 CCATGATGATGGTGCACCTA 57.356 50.000 34.75 21.96 43.98 3.08
721 768 3.507675 CCATGATGATGGTGCACCT 57.492 52.632 34.75 21.08 43.98 4.00
745 792 1.740380 GCATGGCAGCTTCTTCGTCTA 60.740 52.381 0.00 0.00 0.00 2.59
882 944 1.336056 GGCGAACTTATAGAGGAGGCG 60.336 57.143 0.00 0.00 0.00 5.52
905 967 2.635229 ATTGCTAGTGAGGAGCGCGG 62.635 60.000 8.83 0.00 43.19 6.46
907 969 1.373570 AAATTGCTAGTGAGGAGCGC 58.626 50.000 0.00 0.00 43.19 5.92
910 972 3.873952 GGCTGTAAATTGCTAGTGAGGAG 59.126 47.826 0.00 0.00 0.00 3.69
912 974 2.945668 GGGCTGTAAATTGCTAGTGAGG 59.054 50.000 0.00 0.00 0.00 3.86
913 975 3.375299 GTGGGCTGTAAATTGCTAGTGAG 59.625 47.826 0.00 0.00 0.00 3.51
914 976 3.343617 GTGGGCTGTAAATTGCTAGTGA 58.656 45.455 0.00 0.00 0.00 3.41
916 978 2.308866 AGGTGGGCTGTAAATTGCTAGT 59.691 45.455 0.00 0.00 0.00 2.57
919 981 1.355720 AGAGGTGGGCTGTAAATTGCT 59.644 47.619 0.00 0.00 0.00 3.91
920 982 1.745653 GAGAGGTGGGCTGTAAATTGC 59.254 52.381 0.00 0.00 0.00 3.56
922 984 3.806949 TTGAGAGGTGGGCTGTAAATT 57.193 42.857 0.00 0.00 0.00 1.82
924 986 2.912956 AGATTGAGAGGTGGGCTGTAAA 59.087 45.455 0.00 0.00 0.00 2.01
967 1036 0.396811 GGGAAGTATAGTGGGCGCAT 59.603 55.000 10.83 0.00 0.00 4.73
977 1046 4.979039 TGGGCTTGGATTAAGGGAAGTATA 59.021 41.667 0.00 0.00 36.87 1.47
978 1047 3.791545 TGGGCTTGGATTAAGGGAAGTAT 59.208 43.478 0.00 0.00 36.87 2.12
998 1067 4.752879 CGGCCGGTGTAGTGGTGG 62.753 72.222 20.10 0.00 0.00 4.61
1013 1082 2.537560 GGCATCGCAGATGAACCGG 61.538 63.158 18.54 0.00 45.12 5.28
1122 1191 4.719106 ACGACGGAGGCGAGGAGT 62.719 66.667 1.02 0.00 0.00 3.85
1214 1283 3.188786 CGAGGCGTACTGCTTGGC 61.189 66.667 9.06 0.00 45.43 4.52
1423 1492 1.078759 GCGACGGATCCAAGACACAG 61.079 60.000 13.41 0.00 0.00 3.66
1476 1545 0.531532 CCGACTCCACAGATGCATCC 60.532 60.000 23.06 5.58 0.00 3.51
1478 1547 1.524002 CCCGACTCCACAGATGCAT 59.476 57.895 0.00 0.00 0.00 3.96
1485 1554 4.316823 AGCTCCCCCGACTCCACA 62.317 66.667 0.00 0.00 0.00 4.17
1506 1575 1.290324 CTGATCCGATACCAGCCGG 59.710 63.158 0.00 0.00 46.57 6.13
1697 1766 1.544724 GGAGAGCTCGCCATCTAGAT 58.455 55.000 29.33 0.00 35.76 1.98
1698 1767 0.886938 CGGAGAGCTCGCCATCTAGA 60.887 60.000 32.15 0.00 35.39 2.43
1920 1989 2.342648 GACACGGTCACTGGGTCC 59.657 66.667 7.94 0.00 32.09 4.46
1926 1995 3.612681 CCGGTGGACACGGTCACT 61.613 66.667 8.82 0.00 46.03 3.41
2112 2181 4.263572 CCGTGGTGGTGCCTGGAA 62.264 66.667 0.00 0.00 36.12 3.53
2207 2276 3.644399 GACCCCGTCGAGAACTGGC 62.644 68.421 0.00 0.00 31.17 4.85
2208 2277 2.572284 GACCCCGTCGAGAACTGG 59.428 66.667 0.00 0.00 32.28 4.00
2644 2713 2.436109 GCTTGGGGACTGGAGCAA 59.564 61.111 0.00 0.00 35.29 3.91
2652 2721 3.670377 GCGTGGTTGCTTGGGGAC 61.670 66.667 0.00 0.00 0.00 4.46
2658 2727 2.417097 GCTTTGGCGTGGTTGCTT 59.583 55.556 0.00 0.00 34.52 3.91
2709 2778 2.815647 CGGTCGCTGGAAAGGAGC 60.816 66.667 0.00 0.00 0.00 4.70
2739 2808 4.357947 GAGACGGTGTCGCAGGCA 62.358 66.667 0.00 0.00 43.93 4.75
2862 2931 2.982130 CAGTGGTCCTTCCCGGAG 59.018 66.667 0.73 0.00 44.20 4.63
2964 3033 3.038417 GCAACGAGCGAGTGCAGT 61.038 61.111 14.83 0.00 46.23 4.40
3120 3189 2.429236 CGGCGCTATAGCACGAGG 60.429 66.667 25.91 11.53 41.51 4.63
3328 3400 4.433615 ACTGCAACTCTAATCCGTGTATG 58.566 43.478 0.00 0.00 0.00 2.39
3334 3406 5.178623 TGTTACAAACTGCAACTCTAATCCG 59.821 40.000 0.00 0.00 0.00 4.18
3335 3407 6.371389 GTGTTACAAACTGCAACTCTAATCC 58.629 40.000 0.00 0.00 0.00 3.01
3375 3451 3.627123 CACACAGTCCAATTTGACACAGA 59.373 43.478 11.85 0.00 37.73 3.41
3383 3459 4.336433 CAGAGTGAACACACAGTCCAATTT 59.664 41.667 7.68 0.00 40.03 1.82
3391 3467 5.467735 TCAAATCATCAGAGTGAACACACAG 59.532 40.000 7.68 0.00 37.04 3.66
3448 3525 1.522668 TTCAGTCGCCACCAAATCTG 58.477 50.000 0.00 0.00 0.00 2.90
3491 3569 6.463360 TGCAATCATGTAAGTACAGTCAAGA 58.537 36.000 0.00 0.00 39.92 3.02
3540 3618 3.175710 AGGGTTGTGCCGGTTCCT 61.176 61.111 1.90 0.00 38.44 3.36
3880 3964 5.256474 CCTCCTGTTCTTTGGTGTGATAAT 58.744 41.667 0.00 0.00 0.00 1.28
4208 4292 1.270305 CCGTGACACTCATTGGTCTGT 60.270 52.381 3.68 0.00 35.11 3.41


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

AutoCloner maintained by Alex Coulton.