Multiple sequence alignment - TraesCS2D01G488300

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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 TraesCS2D01G488300 chr2D 100.000 4463 0 0 1 4463 587705118 587700656 0.000000e+00 8242
1 TraesCS2D01G488300 chr2A 92.344 2508 138 34 1277 3755 722525693 722523211 0.000000e+00 3518
2 TraesCS2D01G488300 chr2A 91.081 583 24 8 3898 4463 722523085 722522514 0.000000e+00 763
3 TraesCS2D01G488300 chr2A 89.752 605 29 12 721 1305 722526286 722525695 0.000000e+00 743
4 TraesCS2D01G488300 chr2A 89.486 428 25 6 1 415 722527056 722526636 1.420000e-144 523
5 TraesCS2D01G488300 chr2B 91.222 2119 89 39 2406 4463 710286780 710284698 0.000000e+00 2793
6 TraesCS2D01G488300 chr2B 91.572 1768 101 27 679 2409 710288617 710286861 0.000000e+00 2396
7 TraesCS2D01G488300 chr2B 90.640 203 12 6 421 620 710288888 710288690 3.420000e-66 263
8 TraesCS2D01G488300 chr2B 88.710 124 5 3 584 702 710288675 710288556 4.650000e-30 143
9 TraesCS2D01G488300 chr6B 90.351 114 6 5 4326 4435 424292566 424292678 1.290000e-30 145
10 TraesCS2D01G488300 chr6B 88.793 116 8 5 4324 4435 424069033 424069147 2.170000e-28 137
11 TraesCS2D01G488300 chrUn 86.957 115 7 5 4324 4434 401085934 401086044 6.060000e-24 122
12 TraesCS2D01G488300 chrUn 86.957 115 7 5 4324 4434 408002379 408002269 6.060000e-24 122
13 TraesCS2D01G488300 chrUn 86.957 115 7 5 4324 4434 446902183 446902293 6.060000e-24 122
14 TraesCS2D01G488300 chrUn 86.957 115 7 5 4324 4434 465860458 465860348 6.060000e-24 122
15 TraesCS2D01G488300 chr1B 86.957 115 7 5 4324 4434 628945837 628945727 6.060000e-24 122


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 TraesCS2D01G488300 chr2D 587700656 587705118 4462 True 8242.00 8242 100.00000 1 4463 1 chr2D.!!$R1 4462
1 TraesCS2D01G488300 chr2A 722522514 722527056 4542 True 1386.75 3518 90.66575 1 4463 4 chr2A.!!$R1 4462
2 TraesCS2D01G488300 chr2B 710284698 710288888 4190 True 1398.75 2793 90.53600 421 4463 4 chr2B.!!$R1 4042

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
417 431 0.247185 CTTTTCATTGGGCGCCATGT 59.753 50.0 30.85 10.13 31.53 3.21 F
1080 1310 0.248702 GGAAGCGCTCGAGAGGTAAG 60.249 60.0 21.10 3.05 0.00 2.34 F
2904 3293 0.899717 ACAAGTGCCATTTCGCCCAT 60.900 50.0 0.00 0.00 0.00 4.00 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1558 1839 0.036164 TCACCATCACCTTTCCCACG 59.964 55.000 0.0 0.0 0.0 4.94 R
2926 3315 1.202698 GGACATGTAGGAGGATGGTGC 60.203 57.143 0.0 0.0 0.0 5.01 R
4132 4599 0.106918 GGAGGAGAGAAGAGCGGAGA 60.107 60.000 0.0 0.0 0.0 3.71 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
34 35 5.011635 TGGATGCGATACTTTGGCTATTCTA 59.988 40.000 0.00 0.00 0.00 2.10
56 57 7.366513 TCTAGCTCTTCGATATGTTCAATCAG 58.633 38.462 0.00 0.00 0.00 2.90
132 133 4.498009 CCTTTGAGCACGTCAAGATTTGTT 60.498 41.667 0.00 0.00 46.09 2.83
133 134 3.607422 TGAGCACGTCAAGATTTGTTG 57.393 42.857 0.00 0.00 29.64 3.33
152 165 2.777094 TGACGATCTTCAATTGGCACA 58.223 42.857 5.42 0.00 0.00 4.57
159 172 2.093921 TCTTCAATTGGCACATGCATGG 60.094 45.455 29.41 19.00 44.36 3.66
166 179 2.181125 TGGCACATGCATGGAAATCTT 58.819 42.857 29.41 4.72 44.36 2.40
171 184 5.818857 GGCACATGCATGGAAATCTTAAAAT 59.181 36.000 29.41 1.63 44.36 1.82
179 192 6.201615 GCATGGAAATCTTAAAATAGGCTTGC 59.798 38.462 0.00 0.00 0.00 4.01
182 195 6.600032 TGGAAATCTTAAAATAGGCTTGCGTA 59.400 34.615 0.00 0.00 0.00 4.42
247 260 8.412456 CCATATAGAGATGTTGCGAAGATCTAT 58.588 37.037 0.00 7.89 41.13 1.98
249 262 4.305769 AGAGATGTTGCGAAGATCTATGC 58.694 43.478 11.21 11.21 41.13 3.14
262 275 1.121407 TCTATGCCGATGGGGGACTG 61.121 60.000 0.00 0.00 39.90 3.51
268 281 1.685765 CGATGGGGGACTGTCCAGA 60.686 63.158 26.94 11.15 38.64 3.86
269 282 1.680522 CGATGGGGGACTGTCCAGAG 61.681 65.000 26.94 8.95 38.64 3.35
274 288 1.492993 GGGGACTGTCCAGAGGCTTT 61.493 60.000 26.94 0.00 38.64 3.51
294 308 4.439305 TTGCTATGCAACCATTCTTCAC 57.561 40.909 0.45 0.00 43.99 3.18
307 321 4.513442 CATTCTTCACGGGGTAGATCAAA 58.487 43.478 0.00 0.00 0.00 2.69
311 325 1.475280 TCACGGGGTAGATCAAAGTCG 59.525 52.381 0.00 0.00 0.00 4.18
347 361 7.078249 AGAAGGTTTCTTTTGGCCATAAAAT 57.922 32.000 6.09 0.00 36.36 1.82
389 403 1.863454 CACATGCTCTAGCTAAAGCCG 59.137 52.381 16.36 9.93 43.38 5.52
410 424 3.671702 CGCTTCTTCTCTTTTCATTGGGC 60.672 47.826 0.00 0.00 0.00 5.36
415 429 0.819582 CTCTTTTCATTGGGCGCCAT 59.180 50.000 30.85 11.77 31.53 4.40
416 430 0.531657 TCTTTTCATTGGGCGCCATG 59.468 50.000 30.85 23.81 31.53 3.66
417 431 0.247185 CTTTTCATTGGGCGCCATGT 59.753 50.000 30.85 10.13 31.53 3.21
418 432 0.683973 TTTTCATTGGGCGCCATGTT 59.316 45.000 30.85 6.69 31.53 2.71
419 433 0.683973 TTTCATTGGGCGCCATGTTT 59.316 45.000 30.85 4.60 31.53 2.83
437 451 6.813152 CCATGTTTGGCTTTCTAATTTACCTG 59.187 38.462 0.00 0.00 35.85 4.00
484 501 8.234546 ACTTTTTGTTTAGAATGTATGCCTACG 58.765 33.333 0.00 0.00 0.00 3.51
498 515 5.551760 ATGCCTACGAACTTTGAGATTTG 57.448 39.130 0.00 0.00 0.00 2.32
519 536 3.196901 TGAATAAAGCCCGCTCTCTAACA 59.803 43.478 0.00 0.00 0.00 2.41
602 786 1.854743 CAGATTGATGCCGTGTAGTCG 59.145 52.381 0.00 0.00 0.00 4.18
669 899 3.994392 TGAGAAAGTGTAGTCGATTTGGC 59.006 43.478 0.00 0.00 0.00 4.52
695 925 4.545823 TTTTGTTGAGAAAGTGTAGCCG 57.454 40.909 0.00 0.00 0.00 5.52
696 926 3.462483 TTGTTGAGAAAGTGTAGCCGA 57.538 42.857 0.00 0.00 0.00 5.54
697 927 3.678056 TGTTGAGAAAGTGTAGCCGAT 57.322 42.857 0.00 0.00 0.00 4.18
698 928 4.002906 TGTTGAGAAAGTGTAGCCGATT 57.997 40.909 0.00 0.00 0.00 3.34
699 929 4.385825 TGTTGAGAAAGTGTAGCCGATTT 58.614 39.130 0.00 0.00 0.00 2.17
700 930 4.213270 TGTTGAGAAAGTGTAGCCGATTTG 59.787 41.667 0.00 0.00 0.00 2.32
701 931 3.334691 TGAGAAAGTGTAGCCGATTTGG 58.665 45.455 0.00 0.00 42.50 3.28
764 994 1.647545 CGTCTACGTAACTGGGCCGA 61.648 60.000 0.00 0.00 34.11 5.54
768 998 3.023119 TCTACGTAACTGGGCCGAAATA 58.977 45.455 0.00 0.00 0.00 1.40
778 1008 0.949397 GGCCGAAATACGAATTCCCC 59.051 55.000 0.00 0.00 45.77 4.81
779 1009 0.949397 GCCGAAATACGAATTCCCCC 59.051 55.000 0.00 0.00 45.77 5.40
789 1019 0.461516 GAATTCCCCCGTCGGAGTTC 60.462 60.000 14.39 1.78 40.24 3.01
795 1025 4.493747 CCGTCGGAGTTCGGGAGC 62.494 72.222 4.91 0.00 40.61 4.70
855 1085 3.536956 CTTATAAAGCCCAGTCACCGA 57.463 47.619 0.00 0.00 0.00 4.69
861 1091 2.035442 GCCCAGTCACCGAAAGAGC 61.035 63.158 0.00 0.00 0.00 4.09
1080 1310 0.248702 GGAAGCGCTCGAGAGGTAAG 60.249 60.000 21.10 3.05 0.00 2.34
1084 1314 2.816012 GCTCGAGAGGTAAGGCCC 59.184 66.667 18.75 0.00 38.26 5.80
1136 1371 2.033049 TGCTTTCTATAGGTCTCGTCGC 59.967 50.000 0.00 0.00 0.00 5.19
1196 1431 4.889807 GCCTCGGCTCTCTCTAGA 57.110 61.111 0.00 0.00 38.26 2.43
1240 1490 1.153901 CGTGTCGTGCCGTTATCCT 60.154 57.895 0.00 0.00 0.00 3.24
1354 1634 7.673180 AGGTTGATAATTATGCCAAATCCATG 58.327 34.615 1.78 0.00 0.00 3.66
1425 1705 2.393768 CCACCTGCATCGTGTCTGC 61.394 63.158 11.81 0.00 40.10 4.26
1447 1727 6.694447 TGCTACCGTAATGAAATACCTATCC 58.306 40.000 0.00 0.00 0.00 2.59
1520 1800 5.608449 AGAGCAGGACGTACTAAAAAGTTT 58.392 37.500 0.00 0.00 0.00 2.66
1527 1808 9.199982 CAGGACGTACTAAAAAGTTTATCAAGA 57.800 33.333 0.00 0.00 0.00 3.02
1542 1823 6.780706 TTATCAAGACGAGGTTTCTTTGAC 57.219 37.500 0.00 0.00 30.56 3.18
1558 1839 6.436843 TCTTTGACAAGAAGGAAAGAACAC 57.563 37.500 0.00 0.00 35.99 3.32
1603 1884 6.033341 GGGAAACAAATTTGGAAAAGCAAAC 58.967 36.000 21.74 1.76 0.00 2.93
1663 1944 2.555325 TGCAAGAAGAGAAACATGGCAG 59.445 45.455 0.00 0.00 0.00 4.85
1668 1949 1.985473 AGAGAAACATGGCAGCACAA 58.015 45.000 0.00 0.00 0.00 3.33
1682 1963 4.386652 GGCAGCACAAGTTAAACATCATTG 59.613 41.667 0.00 0.00 0.00 2.82
1689 1970 9.571810 GCACAAGTTAAACATCATTGATGAATA 57.428 29.630 28.81 18.44 42.09 1.75
1731 2014 7.703621 AGTTATCATGTTTCAACAATATGCAGC 59.296 33.333 0.00 0.00 43.03 5.25
1734 2020 3.820689 TGTTTCAACAATATGCAGCGTC 58.179 40.909 0.00 0.00 35.67 5.19
1735 2021 2.804421 TTCAACAATATGCAGCGTCG 57.196 45.000 0.00 0.00 0.00 5.12
1828 2114 7.249858 TGTTCATTCATCACATTTATTGGACG 58.750 34.615 0.00 0.00 0.00 4.79
2061 2348 7.175990 TGCAGTTACGAATTAAATTCTTCCCTT 59.824 33.333 0.00 0.00 37.13 3.95
2094 2383 1.871039 TGGTGCAGAAGCTTTACGAAC 59.129 47.619 0.00 0.00 42.74 3.95
2119 2408 5.178996 TGTTGCAAATTGTAATTCATGCACC 59.821 36.000 13.38 9.24 40.10 5.01
2123 2412 2.917701 TTGTAATTCATGCACCGCAG 57.082 45.000 0.00 0.00 43.65 5.18
2150 2439 6.603237 TGCCAAATGATCAAAGTAGATACG 57.397 37.500 0.00 0.00 0.00 3.06
2218 2507 8.650143 AATAGTACCTCAATTCACATTTGGTT 57.350 30.769 0.00 0.00 32.05 3.67
2223 2512 5.305128 ACCTCAATTCACATTTGGTTCATGT 59.695 36.000 0.00 0.00 35.10 3.21
2295 2587 6.014925 TGAGTCTGCACTAACATGGTTTAGTA 60.015 38.462 8.06 0.00 39.77 1.82
2298 2590 7.883311 AGTCTGCACTAACATGGTTTAGTAATT 59.117 33.333 8.06 0.00 39.77 1.40
2329 2621 4.870363 TGAAAGCATCCTTTTAAGCACAC 58.130 39.130 0.00 0.00 41.22 3.82
2340 2632 7.984391 TCCTTTTAAGCACACACATATACATG 58.016 34.615 0.00 0.00 38.21 3.21
2342 2634 7.910162 CCTTTTAAGCACACACATATACATGTC 59.090 37.037 0.00 0.00 43.73 3.06
2377 2671 2.303022 TGGTCTCTGTGGATCTTGGTTC 59.697 50.000 0.00 0.00 0.00 3.62
2383 2677 4.836825 TCTGTGGATCTTGGTTCAATCTC 58.163 43.478 0.00 0.00 0.00 2.75
2495 2874 4.107622 GCCATTTGCACTGATAACATGTC 58.892 43.478 0.00 0.00 40.77 3.06
2501 2880 6.421377 TTGCACTGATAACATGTCATACAC 57.579 37.500 0.00 0.00 0.00 2.90
2514 2893 3.056891 TGTCATACACGTGATCTTCTGCA 60.057 43.478 25.01 7.53 0.00 4.41
2519 2898 3.402110 ACACGTGATCTTCTGCATTTGA 58.598 40.909 25.01 0.00 0.00 2.69
2520 2899 3.814842 ACACGTGATCTTCTGCATTTGAA 59.185 39.130 25.01 0.00 0.00 2.69
2543 2925 9.554395 TGAACACTGTTATCTTGTTATGAGAAA 57.446 29.630 0.00 0.00 33.59 2.52
2565 2947 5.939764 ATCTTCTGTCTTGGTATACAGCA 57.060 39.130 5.01 0.00 42.31 4.41
2573 2955 4.868734 GTCTTGGTATACAGCACTACAACC 59.131 45.833 5.01 0.00 0.00 3.77
2610 2999 2.001812 TCGCTCAGTTCTCATTGCTC 57.998 50.000 0.00 0.00 0.00 4.26
2611 3000 1.273327 TCGCTCAGTTCTCATTGCTCA 59.727 47.619 0.00 0.00 0.00 4.26
2614 3003 3.242349 CGCTCAGTTCTCATTGCTCATTC 60.242 47.826 0.00 0.00 0.00 2.67
2632 3021 8.016497 GCTCATTCAGCTATCATTACTTACTG 57.984 38.462 0.00 0.00 45.83 2.74
2721 3110 3.490348 CTTTGGTGAGGGATGTCACTTT 58.510 45.455 4.14 0.00 45.34 2.66
2904 3293 0.899717 ACAAGTGCCATTTCGCCCAT 60.900 50.000 0.00 0.00 0.00 4.00
2926 3315 3.013932 AGAGGGAGCTTGGCAGGG 61.014 66.667 0.00 0.00 0.00 4.45
2994 3383 0.314302 GTGGTCGATATGGAGGTCGG 59.686 60.000 0.00 0.00 38.34 4.79
3054 3443 2.183858 GAAACTTTGGCGCCTCGTCC 62.184 60.000 29.70 12.64 0.00 4.79
3078 3467 1.242076 GCAAGGTCAGTGTTGATGCT 58.758 50.000 0.00 0.00 35.15 3.79
3108 3497 1.694169 AGGCATCATCGGGAAGGGT 60.694 57.895 0.00 0.00 0.00 4.34
3213 3602 2.071778 TTGAGCTGGAAGGCAGTTTT 57.928 45.000 0.00 0.00 34.17 2.43
3294 3683 2.342279 CCGTCGAAGAACCCTGCA 59.658 61.111 0.00 0.00 39.69 4.41
3489 3893 3.002583 TGCTGCGGTGGATCCTCA 61.003 61.111 14.23 4.98 0.00 3.86
3495 3899 2.022240 GCGGTGGATCCTCACTCCTC 62.022 65.000 14.23 0.00 37.75 3.71
3659 4064 4.282703 TCCCAGTGTAGTTAGTCACCTTTC 59.717 45.833 0.00 0.00 35.45 2.62
3680 4091 5.514274 TCGAGTTTTCTCCTTGCATTTTT 57.486 34.783 0.00 0.00 43.49 1.94
3681 4092 6.627395 TCGAGTTTTCTCCTTGCATTTTTA 57.373 33.333 0.00 0.00 43.49 1.52
3683 4094 7.657336 TCGAGTTTTCTCCTTGCATTTTTATT 58.343 30.769 0.00 0.00 43.49 1.40
3684 4095 8.141268 TCGAGTTTTCTCCTTGCATTTTTATTT 58.859 29.630 0.00 0.00 43.49 1.40
3690 4101 2.095692 CCTTGCATTTTTATTTGGCGGC 59.904 45.455 0.00 0.00 0.00 6.53
3748 4166 2.286872 CAGCAGATGGGTCACTGATTC 58.713 52.381 0.00 0.00 34.49 2.52
3756 4174 2.038952 TGGGTCACTGATTCCTCTGTTG 59.961 50.000 3.88 0.00 31.84 3.33
3762 4180 5.350914 GTCACTGATTCCTCTGTTGATTCTG 59.649 44.000 0.00 0.00 31.84 3.02
3768 4186 6.213397 TGATTCCTCTGTTGATTCTGAGGTTA 59.787 38.462 15.46 8.55 46.53 2.85
3795 4213 8.870116 TGTTCTATGATGCTACATAATACACCT 58.130 33.333 5.32 0.00 33.26 4.00
3798 4216 8.674607 TCTATGATGCTACATAATACACCTACG 58.325 37.037 5.32 0.00 33.26 3.51
3806 4224 7.278424 GCTACATAATACACCTACGTTCCAAAA 59.722 37.037 0.00 0.00 0.00 2.44
3807 4225 9.321562 CTACATAATACACCTACGTTCCAAAAT 57.678 33.333 0.00 0.00 0.00 1.82
3808 4226 8.570068 ACATAATACACCTACGTTCCAAAATT 57.430 30.769 0.00 0.00 0.00 1.82
3809 4227 8.671028 ACATAATACACCTACGTTCCAAAATTC 58.329 33.333 0.00 0.00 0.00 2.17
3810 4228 6.505044 AATACACCTACGTTCCAAAATTCC 57.495 37.500 0.00 0.00 0.00 3.01
3811 4229 3.822940 ACACCTACGTTCCAAAATTCCA 58.177 40.909 0.00 0.00 0.00 3.53
3812 4230 4.208746 ACACCTACGTTCCAAAATTCCAA 58.791 39.130 0.00 0.00 0.00 3.53
3813 4231 4.645588 ACACCTACGTTCCAAAATTCCAAA 59.354 37.500 0.00 0.00 0.00 3.28
3814 4232 5.127356 ACACCTACGTTCCAAAATTCCAAAA 59.873 36.000 0.00 0.00 0.00 2.44
3952 4410 6.985188 TTGGTTGCTATTGTAGATCTTGAC 57.015 37.500 0.00 0.00 0.00 3.18
3954 4412 6.653020 TGGTTGCTATTGTAGATCTTGACAT 58.347 36.000 0.00 0.00 0.00 3.06
3956 4414 7.611467 TGGTTGCTATTGTAGATCTTGACATTT 59.389 33.333 0.00 0.00 0.00 2.32
4045 4512 1.002502 GTGGGGCCAGTTACACCTC 60.003 63.158 4.39 0.00 0.00 3.85
4132 4599 0.453793 CCACGACATCTCGAGCTCTT 59.546 55.000 12.85 0.00 43.06 2.85
4133 4600 1.532921 CCACGACATCTCGAGCTCTTC 60.533 57.143 12.85 0.39 43.06 2.87
4134 4601 1.400142 CACGACATCTCGAGCTCTTCT 59.600 52.381 12.85 0.00 43.06 2.85
4135 4602 1.668751 ACGACATCTCGAGCTCTTCTC 59.331 52.381 12.85 0.00 43.06 2.87
4136 4603 1.002900 CGACATCTCGAGCTCTTCTCC 60.003 57.143 12.85 0.00 43.06 3.71
4137 4604 1.002900 GACATCTCGAGCTCTTCTCCG 60.003 57.143 12.85 0.00 38.62 4.63
4138 4605 0.317770 CATCTCGAGCTCTTCTCCGC 60.318 60.000 12.85 0.00 38.62 5.54
4139 4606 0.465460 ATCTCGAGCTCTTCTCCGCT 60.465 55.000 12.85 0.00 38.62 5.52
4140 4607 1.092921 TCTCGAGCTCTTCTCCGCTC 61.093 60.000 12.85 0.00 46.91 5.03
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
34 35 5.069648 TCCTGATTGAACATATCGAAGAGCT 59.930 40.000 0.00 0.00 43.63 4.09
56 57 1.648467 GCACCCGAGCAAGTTCATCC 61.648 60.000 0.00 0.00 0.00 3.51
132 133 2.777094 TGTGCCAATTGAAGATCGTCA 58.223 42.857 7.12 7.29 0.00 4.35
133 134 3.688272 CATGTGCCAATTGAAGATCGTC 58.312 45.455 7.12 1.20 0.00 4.20
136 137 3.513680 TGCATGTGCCAATTGAAGATC 57.486 42.857 7.12 0.00 41.18 2.75
152 165 7.607615 AGCCTATTTTAAGATTTCCATGCAT 57.392 32.000 0.00 0.00 0.00 3.96
159 172 9.813080 CTATACGCAAGCCTATTTTAAGATTTC 57.187 33.333 0.00 0.00 45.62 2.17
166 179 5.849510 TCAGCTATACGCAAGCCTATTTTA 58.150 37.500 0.00 0.00 41.02 1.52
171 184 2.554462 CTCTCAGCTATACGCAAGCCTA 59.446 50.000 0.00 0.00 41.02 3.93
188 201 1.809547 GCCTTTTGGAAGTGAGCTCTC 59.190 52.381 16.19 11.84 44.07 3.20
189 202 1.143684 TGCCTTTTGGAAGTGAGCTCT 59.856 47.619 16.19 0.00 44.07 4.09
190 203 1.538950 CTGCCTTTTGGAAGTGAGCTC 59.461 52.381 6.82 6.82 40.57 4.09
191 204 1.613836 CTGCCTTTTGGAAGTGAGCT 58.386 50.000 0.00 0.00 40.57 4.09
228 241 3.431572 GGCATAGATCTTCGCAACATCTC 59.568 47.826 15.55 0.00 0.00 2.75
247 260 3.399181 GACAGTCCCCCATCGGCA 61.399 66.667 0.00 0.00 0.00 5.69
249 262 2.687200 TGGACAGTCCCCCATCGG 60.687 66.667 17.59 0.00 35.03 4.18
262 275 1.020437 GCATAGCAAAGCCTCTGGAC 58.980 55.000 0.00 0.00 0.00 4.02
274 288 2.419673 CGTGAAGAATGGTTGCATAGCA 59.580 45.455 0.00 0.00 38.87 3.49
294 308 2.165845 AGTTCGACTTTGATCTACCCCG 59.834 50.000 0.00 0.00 0.00 5.73
347 361 3.804036 CCTAAGTCATTGTTATCCCGCA 58.196 45.455 0.00 0.00 0.00 5.69
389 403 3.671702 CGCCCAATGAAAAGAGAAGAAGC 60.672 47.826 0.00 0.00 0.00 3.86
415 429 7.775053 ATCAGGTAAATTAGAAAGCCAAACA 57.225 32.000 0.00 0.00 0.00 2.83
416 430 9.952188 GATATCAGGTAAATTAGAAAGCCAAAC 57.048 33.333 0.00 0.00 0.00 2.93
417 431 9.693739 TGATATCAGGTAAATTAGAAAGCCAAA 57.306 29.630 0.00 0.00 0.00 3.28
418 432 9.866655 ATGATATCAGGTAAATTAGAAAGCCAA 57.133 29.630 11.78 0.00 0.00 4.52
419 433 9.866655 AATGATATCAGGTAAATTAGAAAGCCA 57.133 29.630 11.78 0.00 0.00 4.75
464 479 6.636705 AGTTCGTAGGCATACATTCTAAACA 58.363 36.000 9.48 0.00 31.76 2.83
465 480 7.535489 AAGTTCGTAGGCATACATTCTAAAC 57.465 36.000 9.48 3.26 31.76 2.01
484 501 6.528072 CGGGCTTTATTCAAATCTCAAAGTTC 59.472 38.462 0.00 0.00 0.00 3.01
498 515 3.793559 TGTTAGAGAGCGGGCTTTATTC 58.206 45.455 0.00 0.00 0.00 1.75
564 581 3.589988 TCTGAGCTCGATTTTCTCAACC 58.410 45.455 9.64 0.00 36.54 3.77
636 866 3.976015 ACACTTTCTCAACCCCTCAAAA 58.024 40.909 0.00 0.00 0.00 2.44
677 907 3.678056 ATCGGCTACACTTTCTCAACA 57.322 42.857 0.00 0.00 0.00 3.33
678 908 4.378459 CCAAATCGGCTACACTTTCTCAAC 60.378 45.833 0.00 0.00 0.00 3.18
680 910 3.334691 CCAAATCGGCTACACTTTCTCA 58.665 45.455 0.00 0.00 0.00 3.27
706 936 4.636648 TCGGCTACACTTTCTCAACAAAAA 59.363 37.500 0.00 0.00 0.00 1.94
707 937 4.193090 TCGGCTACACTTTCTCAACAAAA 58.807 39.130 0.00 0.00 0.00 2.44
708 938 3.799366 TCGGCTACACTTTCTCAACAAA 58.201 40.909 0.00 0.00 0.00 2.83
727 957 0.443869 CGCTTCTGTCACCCAAATCG 59.556 55.000 0.00 0.00 0.00 3.34
764 994 1.473788 CCGACGGGGGAATTCGTATTT 60.474 52.381 5.81 0.00 39.88 1.40
768 998 2.681064 TCCGACGGGGGAATTCGT 60.681 61.111 15.25 0.00 42.67 3.85
779 1009 4.493747 GGCTCCCGAACTCCGACG 62.494 72.222 0.00 0.00 41.76 5.12
849 1079 1.371183 CAGGTGGCTCTTTCGGTGA 59.629 57.895 0.00 0.00 0.00 4.02
855 1085 1.529244 GGTGTGCAGGTGGCTCTTT 60.529 57.895 0.00 0.00 45.15 2.52
861 1091 4.248842 TCGTGGGTGTGCAGGTGG 62.249 66.667 0.00 0.00 0.00 4.61
1084 1314 2.184579 GGAGAGACGGGAAAGCGG 59.815 66.667 0.00 0.00 0.00 5.52
1136 1371 1.972223 ACGACAGGACGAGACCCAG 60.972 63.158 0.00 0.00 37.03 4.45
1240 1490 7.508687 TGCAGGCAAATCTTATCTTATACAGA 58.491 34.615 0.00 0.00 35.33 3.41
1425 1705 7.893658 ACTGGATAGGTATTTCATTACGGTAG 58.106 38.462 0.00 0.00 0.00 3.18
1461 1741 3.327757 TCAGACTTGGGTTGTCAAGCTAT 59.672 43.478 14.11 0.00 45.77 2.97
1475 1755 6.459066 TCTTAGATGAGTTGGTTCAGACTTG 58.541 40.000 0.00 0.00 0.00 3.16
1520 1800 5.849510 TGTCAAAGAAACCTCGTCTTGATA 58.150 37.500 0.00 0.00 35.50 2.15
1542 1823 2.290641 CCCACGTGTTCTTTCCTTCTTG 59.709 50.000 15.65 0.00 0.00 3.02
1558 1839 0.036164 TCACCATCACCTTTCCCACG 59.964 55.000 0.00 0.00 0.00 4.94
1603 1884 3.998341 CCATTTTGATCAAAAGCAGGTGG 59.002 43.478 31.05 27.87 42.72 4.61
1643 1924 2.670509 GCTGCCATGTTTCTCTTCTTGC 60.671 50.000 0.00 0.00 0.00 4.01
1647 1928 1.881973 TGTGCTGCCATGTTTCTCTTC 59.118 47.619 0.00 0.00 0.00 2.87
1650 1931 1.610522 ACTTGTGCTGCCATGTTTCTC 59.389 47.619 0.00 0.00 0.00 2.87
1663 1944 7.872163 TTCATCAATGATGTTTAACTTGTGC 57.128 32.000 21.13 0.00 40.55 4.57
1714 1997 2.840176 CGACGCTGCATATTGTTGAAAC 59.160 45.455 0.00 0.00 0.00 2.78
1735 2021 4.614306 GCAGAAAACGGTTATGGTTACACC 60.614 45.833 0.00 0.00 39.22 4.16
1746 2032 2.488153 GCTTATCCTGCAGAAAACGGTT 59.512 45.455 17.39 0.00 0.00 4.44
1750 2036 2.819608 TGGTGCTTATCCTGCAGAAAAC 59.180 45.455 17.39 2.72 41.41 2.43
2036 2323 7.085052 AGGGAAGAATTTAATTCGTAACTGC 57.915 36.000 11.43 2.21 43.92 4.40
2056 2343 6.071984 TGCACCAAAATAAAAGTAGAAGGGA 58.928 36.000 0.00 0.00 0.00 4.20
2061 2348 6.490040 AGCTTCTGCACCAAAATAAAAGTAGA 59.510 34.615 0.00 0.00 42.74 2.59
2094 2383 6.301108 GTGCATGAATTACAATTTGCAACAG 58.699 36.000 13.04 0.00 41.25 3.16
2195 2484 7.227873 TGAACCAAATGTGAATTGAGGTACTA 58.772 34.615 0.00 0.00 41.55 1.82
2295 2587 9.783081 AAAAGGATGCTTTCATTACTCAAAATT 57.217 25.926 13.01 0.00 31.96 1.82
2298 2590 9.912634 CTTAAAAGGATGCTTTCATTACTCAAA 57.087 29.630 13.01 0.00 31.96 2.69
2340 2632 5.464722 CAGAGACCACAATACTGCATATGAC 59.535 44.000 6.97 0.00 0.00 3.06
2342 2634 5.235831 CACAGAGACCACAATACTGCATATG 59.764 44.000 0.00 0.00 32.67 1.78
2377 2671 2.110967 CCAGGCAGGTGCGAGATTG 61.111 63.158 0.00 0.00 43.26 2.67
2383 2677 1.971505 TAGGAATCCAGGCAGGTGCG 61.972 60.000 0.61 0.00 43.26 5.34
2495 2874 5.063817 TCAAATGCAGAAGATCACGTGTATG 59.936 40.000 16.51 4.75 0.00 2.39
2501 2880 4.083643 AGTGTTCAAATGCAGAAGATCACG 60.084 41.667 14.96 0.00 36.39 4.35
2520 2899 9.950496 AGATTTCTCATAACAAGATAACAGTGT 57.050 29.630 0.00 0.00 0.00 3.55
2543 2925 5.423610 AGTGCTGTATACCAAGACAGAAGAT 59.576 40.000 6.22 0.00 45.87 2.40
2565 2947 4.677673 AGTTACAAAGGACGGTTGTAGT 57.322 40.909 0.00 0.00 41.26 2.73
2573 2955 3.985925 AGCGAACTTAGTTACAAAGGACG 59.014 43.478 0.00 0.00 33.30 4.79
2712 3101 1.405105 ACAAAGTGCGCAAAGTGACAT 59.595 42.857 14.00 0.00 0.00 3.06
2721 3110 2.594303 CCAGGGACAAAGTGCGCA 60.594 61.111 5.66 5.66 0.00 6.09
2904 3293 3.393970 CCAAGCTCCCTCTCGCCA 61.394 66.667 0.00 0.00 0.00 5.69
2926 3315 1.202698 GGACATGTAGGAGGATGGTGC 60.203 57.143 0.00 0.00 0.00 5.01
3096 3485 3.015145 ACCCCACCCTTCCCGATG 61.015 66.667 0.00 0.00 0.00 3.84
3108 3497 1.227823 CTGCTTCGTGTTGACCCCA 60.228 57.895 0.00 0.00 0.00 4.96
3213 3602 2.819608 GTTGGCTTGCTTTATCTGGTCA 59.180 45.455 0.00 0.00 0.00 4.02
3489 3893 0.610687 GTAGCAGCACAAGGAGGAGT 59.389 55.000 0.00 0.00 0.00 3.85
3495 3899 1.151668 GTCACAGTAGCAGCACAAGG 58.848 55.000 0.00 0.00 0.00 3.61
3612 4016 2.289002 ACAGCAAGAAAGTTCTGAAGCG 59.711 45.455 0.00 0.83 37.65 4.68
3659 4064 7.873739 AATAAAAATGCAAGGAGAAAACTCG 57.126 32.000 0.00 0.00 0.00 4.18
3680 4091 0.607762 TGTGAAGCAGCCGCCAAATA 60.608 50.000 0.00 0.00 39.83 1.40
3681 4092 1.870055 CTGTGAAGCAGCCGCCAAAT 61.870 55.000 0.00 0.00 38.52 2.32
3683 4094 2.979676 CTGTGAAGCAGCCGCCAA 60.980 61.111 0.00 0.00 38.52 4.52
3704 4122 5.240623 GTCAACACAACTGGATAATCACCAA 59.759 40.000 0.00 0.00 36.95 3.67
3756 4174 7.877097 AGCATCATAGAACATAACCTCAGAATC 59.123 37.037 0.00 0.00 0.00 2.52
3762 4180 9.929180 TTATGTAGCATCATAGAACATAACCTC 57.071 33.333 0.00 0.00 37.83 3.85
3768 4186 9.658799 GGTGTATTATGTAGCATCATAGAACAT 57.341 33.333 14.29 0.00 33.61 2.71
4045 4512 1.202313 GGAGAGAGAAATGACCGTCGG 60.202 57.143 10.48 10.48 0.00 4.79
4132 4599 0.106918 GGAGGAGAGAAGAGCGGAGA 60.107 60.000 0.00 0.00 0.00 3.71
4133 4600 1.106944 GGGAGGAGAGAAGAGCGGAG 61.107 65.000 0.00 0.00 0.00 4.63
4134 4601 1.076632 GGGAGGAGAGAAGAGCGGA 60.077 63.158 0.00 0.00 0.00 5.54
4135 4602 2.131067 GGGGAGGAGAGAAGAGCGG 61.131 68.421 0.00 0.00 0.00 5.52
4136 4603 1.076339 AGGGGAGGAGAGAAGAGCG 60.076 63.158 0.00 0.00 0.00 5.03
4137 4604 1.106944 CGAGGGGAGGAGAGAAGAGC 61.107 65.000 0.00 0.00 0.00 4.09
4138 4605 0.467290 CCGAGGGGAGGAGAGAAGAG 60.467 65.000 0.00 0.00 34.06 2.85
4139 4606 1.615814 CCGAGGGGAGGAGAGAAGA 59.384 63.158 0.00 0.00 34.06 2.87
4140 4607 2.131067 GCCGAGGGGAGGAGAGAAG 61.131 68.421 0.00 0.00 34.06 2.85
4141 4608 2.042843 GCCGAGGGGAGGAGAGAA 60.043 66.667 0.00 0.00 34.06 2.87
4393 4872 2.285743 AACAGGAGAGGGGGAGGC 60.286 66.667 0.00 0.00 0.00 4.70


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

AutoCloner maintained by Alex Coulton.