Multiple sequence alignment - TraesCS7D01G127300

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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 TraesCS7D01G127300 chr7D 100.000 2246 0 0 1 2246 79624456 79626701 0.000000e+00 4148.0
1 TraesCS7D01G127300 chr7B 89.758 1074 53 14 717 1741 26874222 26875287 0.000000e+00 1321.0
2 TraesCS7D01G127300 chr7B 92.273 220 13 3 2025 2242 26877298 26877515 2.170000e-80 309.0
3 TraesCS7D01G127300 chr7B 85.612 278 20 7 1735 1993 26875340 26875616 7.900000e-70 274.0
4 TraesCS7D01G127300 chr2D 85.847 537 66 8 45 579 18192769 18192241 1.510000e-156 562.0
5 TraesCS7D01G127300 chr6B 86.011 529 67 6 49 575 101544313 101544836 5.420000e-156 560.0
6 TraesCS7D01G127300 chr6B 83.962 530 74 6 45 574 461997903 461997385 4.310000e-137 497.0
7 TraesCS7D01G127300 chr7A 85.122 531 74 3 45 573 700813415 700813942 2.540000e-149 538.0
8 TraesCS7D01G127300 chr7A 88.914 442 24 10 956 1381 82504891 82505323 2.560000e-144 521.0
9 TraesCS7D01G127300 chr7A 93.631 314 9 6 659 967 82504571 82504878 2.030000e-125 459.0
10 TraesCS7D01G127300 chr7A 84.052 464 52 17 1383 1826 82505361 82505822 5.730000e-116 427.0
11 TraesCS7D01G127300 chr1D 83.531 589 84 11 1 584 341270704 341270124 2.540000e-149 538.0
12 TraesCS7D01G127300 chrUn 85.094 530 73 5 45 572 69883237 69883762 9.130000e-149 536.0
13 TraesCS7D01G127300 chr6D 85.094 530 74 5 45 573 348045584 348045059 9.130000e-149 536.0
14 TraesCS7D01G127300 chr3D 85.122 531 71 4 44 571 261750104 261750629 9.130000e-149 536.0
15 TraesCS7D01G127300 chr3A 84.387 538 74 10 45 578 514566507 514565976 9.190000e-144 520.0
16 TraesCS7D01G127300 chr3A 100.000 34 0 0 1 34 514566572 514566539 1.860000e-06 63.9
17 TraesCS7D01G127300 chr2A 93.103 58 4 0 1 58 579994564 579994621 3.970000e-13 86.1


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 TraesCS7D01G127300 chr7D 79624456 79626701 2245 False 4148.000000 4148 100.000000 1 2246 1 chr7D.!!$F1 2245
1 TraesCS7D01G127300 chr7B 26874222 26877515 3293 False 634.666667 1321 89.214333 717 2242 3 chr7B.!!$F1 1525
2 TraesCS7D01G127300 chr2D 18192241 18192769 528 True 562.000000 562 85.847000 45 579 1 chr2D.!!$R1 534
3 TraesCS7D01G127300 chr6B 101544313 101544836 523 False 560.000000 560 86.011000 49 575 1 chr6B.!!$F1 526
4 TraesCS7D01G127300 chr6B 461997385 461997903 518 True 497.000000 497 83.962000 45 574 1 chr6B.!!$R1 529
5 TraesCS7D01G127300 chr7A 700813415 700813942 527 False 538.000000 538 85.122000 45 573 1 chr7A.!!$F1 528
6 TraesCS7D01G127300 chr7A 82504571 82505822 1251 False 469.000000 521 88.865667 659 1826 3 chr7A.!!$F2 1167
7 TraesCS7D01G127300 chr1D 341270124 341270704 580 True 538.000000 538 83.531000 1 584 1 chr1D.!!$R1 583
8 TraesCS7D01G127300 chrUn 69883237 69883762 525 False 536.000000 536 85.094000 45 572 1 chrUn.!!$F1 527
9 TraesCS7D01G127300 chr6D 348045059 348045584 525 True 536.000000 536 85.094000 45 573 1 chr6D.!!$R1 528
10 TraesCS7D01G127300 chr3D 261750104 261750629 525 False 536.000000 536 85.122000 44 571 1 chr3D.!!$F1 527
11 TraesCS7D01G127300 chr3A 514565976 514566572 596 True 291.950000 520 92.193500 1 578 2 chr3A.!!$R1 577

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
614 649 0.038343 ACAATGTTTCCATGCGTGCC 60.038 50.0 0.0 0.0 0.0 5.01 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2159 4047 0.109781 CGTTTGCAATTCCCAGACCG 60.11 55.0 0.0 0.0 0.0 4.79 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
71 94 8.859236 AGTTATGGTAGAAAACTTAAAGGGTC 57.141 34.615 0.00 0.00 29.25 4.46
98 121 6.013639 AGCTAGTTAACTTGGTAGTCATGGTT 60.014 38.462 18.09 0.00 31.99 3.67
103 126 4.008074 ACTTGGTAGTCATGGTTGTCAG 57.992 45.455 0.00 0.00 0.00 3.51
104 127 2.472695 TGGTAGTCATGGTTGTCAGC 57.527 50.000 0.00 0.00 0.00 4.26
108 131 4.041075 TGGTAGTCATGGTTGTCAGCTTTA 59.959 41.667 0.00 0.00 0.00 1.85
110 133 5.106673 GGTAGTCATGGTTGTCAGCTTTAAC 60.107 44.000 0.00 0.00 0.00 2.01
153 179 8.080417 GGCGATCATACTACACAGACTAATAAA 58.920 37.037 0.00 0.00 0.00 1.40
239 269 5.029807 TCGTTGAAATGTAGCCATATGGA 57.970 39.130 26.47 4.45 37.39 3.41
246 276 7.397221 TGAAATGTAGCCATATGGAATCTAGG 58.603 38.462 26.47 0.00 37.39 3.02
279 309 0.584396 TCGCGACAAACACAATGGTC 59.416 50.000 3.71 0.00 0.00 4.02
343 373 5.886474 GGATTTTAGAAAATTCCGAGACCCT 59.114 40.000 1.93 0.00 38.64 4.34
367 397 0.896923 AAATGCATGCACGTGGGATT 59.103 45.000 25.37 8.74 0.00 3.01
375 405 0.109597 GCACGTGGGATTTTGCTGAG 60.110 55.000 18.88 0.00 32.00 3.35
376 406 1.522668 CACGTGGGATTTTGCTGAGA 58.477 50.000 7.95 0.00 0.00 3.27
377 407 1.879380 CACGTGGGATTTTGCTGAGAA 59.121 47.619 7.95 0.00 0.00 2.87
453 484 5.560724 CTTTCCTCTTTTGTCAGGTATCCA 58.439 41.667 0.00 0.00 0.00 3.41
472 503 1.332375 CACTTTTGAAACGCGGGAGAA 59.668 47.619 12.47 0.00 0.00 2.87
474 505 2.031157 ACTTTTGAAACGCGGGAGAATG 60.031 45.455 12.47 3.70 0.00 2.67
482 513 1.154205 CGCGGGAGAATGGTAGCAAG 61.154 60.000 0.00 0.00 0.00 4.01
485 516 1.802880 CGGGAGAATGGTAGCAAGACG 60.803 57.143 0.00 0.00 0.00 4.18
491 522 0.459899 ATGGTAGCAAGACGATCGCA 59.540 50.000 16.60 1.53 0.00 5.10
494 525 2.100087 TGGTAGCAAGACGATCGCAATA 59.900 45.455 16.60 0.00 0.00 1.90
497 529 4.211374 GGTAGCAAGACGATCGCAATAAAT 59.789 41.667 16.60 0.00 0.00 1.40
575 610 9.542462 CAGCTGCACTAATAAGTATTTAGGTAA 57.458 33.333 0.00 0.00 33.48 2.85
612 647 4.792528 AAAAACAATGTTTCCATGCGTG 57.207 36.364 12.11 0.00 0.00 5.34
613 648 1.782044 AACAATGTTTCCATGCGTGC 58.218 45.000 0.00 0.00 0.00 5.34
614 649 0.038343 ACAATGTTTCCATGCGTGCC 60.038 50.000 0.00 0.00 0.00 5.01
615 650 0.244450 CAATGTTTCCATGCGTGCCT 59.756 50.000 0.00 0.00 0.00 4.75
616 651 0.244450 AATGTTTCCATGCGTGCCTG 59.756 50.000 0.00 0.00 0.00 4.85
617 652 2.126346 GTTTCCATGCGTGCCTGC 60.126 61.111 0.00 0.00 0.00 4.85
618 653 3.372730 TTTCCATGCGTGCCTGCC 61.373 61.111 0.00 0.00 0.00 4.85
619 654 3.866379 TTTCCATGCGTGCCTGCCT 62.866 57.895 0.00 0.00 0.00 4.75
634 669 2.597217 CCTGCCTGGGTTGCGAAA 60.597 61.111 0.00 0.00 0.00 3.46
635 670 2.629656 CCTGCCTGGGTTGCGAAAG 61.630 63.158 0.00 0.00 0.00 2.62
636 671 2.597217 TGCCTGGGTTGCGAAAGG 60.597 61.111 0.00 0.00 0.00 3.11
637 672 2.282180 GCCTGGGTTGCGAAAGGA 60.282 61.111 0.00 0.00 30.92 3.36
638 673 1.678970 GCCTGGGTTGCGAAAGGAT 60.679 57.895 0.00 0.00 30.92 3.24
639 674 1.250840 GCCTGGGTTGCGAAAGGATT 61.251 55.000 0.00 0.00 30.92 3.01
640 675 0.527565 CCTGGGTTGCGAAAGGATTG 59.472 55.000 0.00 0.00 30.92 2.67
641 676 0.527565 CTGGGTTGCGAAAGGATTGG 59.472 55.000 0.00 0.00 0.00 3.16
642 677 0.897863 TGGGTTGCGAAAGGATTGGG 60.898 55.000 0.00 0.00 0.00 4.12
643 678 0.610785 GGGTTGCGAAAGGATTGGGA 60.611 55.000 0.00 0.00 0.00 4.37
644 679 0.811281 GGTTGCGAAAGGATTGGGAG 59.189 55.000 0.00 0.00 0.00 4.30
645 680 1.613255 GGTTGCGAAAGGATTGGGAGA 60.613 52.381 0.00 0.00 0.00 3.71
646 681 2.369394 GTTGCGAAAGGATTGGGAGAT 58.631 47.619 0.00 0.00 0.00 2.75
647 682 2.042686 TGCGAAAGGATTGGGAGATG 57.957 50.000 0.00 0.00 0.00 2.90
648 683 0.665298 GCGAAAGGATTGGGAGATGC 59.335 55.000 0.00 0.00 0.00 3.91
649 684 2.018644 GCGAAAGGATTGGGAGATGCA 61.019 52.381 0.00 0.00 0.00 3.96
650 685 1.945394 CGAAAGGATTGGGAGATGCAG 59.055 52.381 0.00 0.00 0.00 4.41
651 686 1.680207 GAAAGGATTGGGAGATGCAGC 59.320 52.381 0.00 0.00 0.00 5.25
652 687 0.106318 AAGGATTGGGAGATGCAGCC 60.106 55.000 0.00 0.00 0.00 4.85
653 688 1.228228 GGATTGGGAGATGCAGCCA 59.772 57.895 0.00 0.00 0.00 4.75
654 689 0.396139 GGATTGGGAGATGCAGCCAA 60.396 55.000 0.00 0.00 0.00 4.52
655 690 1.030457 GATTGGGAGATGCAGCCAAG 58.970 55.000 0.00 0.00 0.00 3.61
656 691 0.396695 ATTGGGAGATGCAGCCAAGG 60.397 55.000 0.00 0.00 0.00 3.61
657 692 2.832201 GGGAGATGCAGCCAAGGC 60.832 66.667 2.02 2.02 42.33 4.35
678 713 2.119671 TGCAGTGTACGCTATGATCG 57.880 50.000 8.97 0.00 0.00 3.69
687 722 2.408050 ACGCTATGATCGAAATCAGGC 58.592 47.619 0.00 0.00 44.90 4.85
847 882 2.485479 CCGAAGCCAGCAACCACTATAT 60.485 50.000 0.00 0.00 0.00 0.86
848 883 3.206150 CGAAGCCAGCAACCACTATATT 58.794 45.455 0.00 0.00 0.00 1.28
875 910 6.824305 ATATATAGTGCTGCCATTGTTTCC 57.176 37.500 0.00 0.00 0.00 3.13
939 979 1.007271 CAACGAGCTCCACGACACT 60.007 57.895 8.47 0.00 34.70 3.55
952 992 1.549170 ACGACACTTTACTAGGGGCTG 59.451 52.381 0.00 0.00 30.63 4.85
1008 1072 2.656069 CGTTGGTCCGATGGAGGGT 61.656 63.158 0.00 0.00 29.39 4.34
1107 1171 2.032681 AGAGGCTTCACCAACGCC 59.967 61.111 0.00 0.00 43.14 5.68
1331 1407 4.634199 TGGGTTAGTAGTTTCTCGTTTGG 58.366 43.478 0.00 0.00 0.00 3.28
1400 1520 2.488204 TGTGTGGGTGTGGACATATG 57.512 50.000 0.00 0.00 0.00 1.78
1441 1568 9.999009 ACATATATAGTGCACGTACATACATAC 57.001 33.333 12.01 0.00 0.00 2.39
1446 1573 5.340803 AGTGCACGTACATACATACAGAAG 58.659 41.667 12.01 0.00 0.00 2.85
1461 1588 7.953752 ACATACAGAAGTTAGGAAGGTATAGC 58.046 38.462 0.00 0.00 0.00 2.97
1495 1622 1.207791 TTCCTCTCCTCTCCAATGGC 58.792 55.000 0.00 0.00 0.00 4.40
1497 1624 1.138568 CCTCTCCTCTCCAATGGCAT 58.861 55.000 0.00 0.00 0.00 4.40
1578 1706 4.433186 TGCTTGGACAAATTAATCCACG 57.567 40.909 9.58 9.30 44.80 4.94
1601 1743 5.237127 CGAGGAATTACTTCATGCTGCATTA 59.763 40.000 13.38 1.64 32.70 1.90
1602 1744 6.238456 CGAGGAATTACTTCATGCTGCATTAA 60.238 38.462 13.38 10.74 32.70 1.40
1603 1745 7.521099 CGAGGAATTACTTCATGCTGCATTAAT 60.521 37.037 13.38 11.38 32.70 1.40
1604 1746 8.015185 AGGAATTACTTCATGCTGCATTAATT 57.985 30.769 21.19 21.19 32.70 1.40
1709 1866 9.746711 GATATAATTGCTCGTGTATTAAAGCTG 57.253 33.333 0.00 0.00 35.76 4.24
1733 1890 5.462068 GTCCCAAACTGAGCAAATGTTTTAC 59.538 40.000 0.00 0.00 32.42 2.01
1766 1984 5.815222 GCATATAAACTTCCCCGCAAAAATT 59.185 36.000 0.00 0.00 0.00 1.82
1838 2072 9.751542 AATCTAGGAATACTACAAACTTCGATG 57.248 33.333 0.00 0.00 0.00 3.84
1844 2078 7.760340 GGAATACTACAAACTTCGATGAAGAGT 59.240 37.037 13.13 7.99 41.71 3.24
1853 2087 9.107367 CAAACTTCGATGAAGAGTTTTTCATAC 57.893 33.333 13.13 0.00 45.30 2.39
1871 2105 9.515226 TTTTCATACTTTGCTACTCCAGTTAAT 57.485 29.630 0.00 0.00 0.00 1.40
1875 2109 6.115448 ACTTTGCTACTCCAGTTAATCTGT 57.885 37.500 4.93 0.00 42.19 3.41
1877 2111 6.428159 ACTTTGCTACTCCAGTTAATCTGTTG 59.572 38.462 4.93 0.00 42.19 3.33
1879 2113 4.253685 GCTACTCCAGTTAATCTGTTGCA 58.746 43.478 0.00 0.00 42.19 4.08
1897 2132 2.092753 TGCAGGAAAATCTAGAGCCCTG 60.093 50.000 19.80 19.80 42.88 4.45
1928 2163 3.953766 TCTCTGAACTCGACGATAATGC 58.046 45.455 0.00 0.00 0.00 3.56
1934 2170 5.168569 TGAACTCGACGATAATGCTCTTTT 58.831 37.500 0.00 0.00 0.00 2.27
1936 2172 3.307242 ACTCGACGATAATGCTCTTTTGC 59.693 43.478 0.00 0.00 0.00 3.68
1948 2184 2.289547 GCTCTTTTGCAACGGTCTACAA 59.710 45.455 0.00 0.00 0.00 2.41
1952 2188 0.250553 TTGCAACGGTCTACAAGGGG 60.251 55.000 0.00 0.00 0.00 4.79
1958 2194 0.107848 CGGTCTACAAGGGGCGAAAT 60.108 55.000 0.00 0.00 0.00 2.17
1960 2196 1.209747 GGTCTACAAGGGGCGAAATCT 59.790 52.381 0.00 0.00 0.00 2.40
1980 2216 4.645535 TCTCACCTGAACTTTTCCATCAG 58.354 43.478 0.00 0.00 40.17 2.90
1993 2229 3.184382 TCCATCAGACCTCACCAACTA 57.816 47.619 0.00 0.00 0.00 2.24
1994 2230 3.724478 TCCATCAGACCTCACCAACTAT 58.276 45.455 0.00 0.00 0.00 2.12
1995 2231 3.706594 TCCATCAGACCTCACCAACTATC 59.293 47.826 0.00 0.00 0.00 2.08
1996 2232 3.708631 CCATCAGACCTCACCAACTATCT 59.291 47.826 0.00 0.00 0.00 1.98
1997 2233 4.202202 CCATCAGACCTCACCAACTATCTC 60.202 50.000 0.00 0.00 0.00 2.75
2000 2236 3.131933 CAGACCTCACCAACTATCTCCAG 59.868 52.174 0.00 0.00 0.00 3.86
2001 2237 2.432510 GACCTCACCAACTATCTCCAGG 59.567 54.545 0.00 0.00 0.00 4.45
2002 2238 1.139853 CCTCACCAACTATCTCCAGGC 59.860 57.143 0.00 0.00 0.00 4.85
2003 2239 2.114616 CTCACCAACTATCTCCAGGCT 58.885 52.381 0.00 0.00 0.00 4.58
2004 2240 1.833630 TCACCAACTATCTCCAGGCTG 59.166 52.381 7.75 7.75 0.00 4.85
2006 2242 1.834263 ACCAACTATCTCCAGGCTGAC 59.166 52.381 17.94 0.00 0.00 3.51
2009 2245 2.080654 ACTATCTCCAGGCTGACCTC 57.919 55.000 17.94 0.00 46.34 3.85
2010 2246 1.289231 ACTATCTCCAGGCTGACCTCA 59.711 52.381 17.94 0.00 46.34 3.86
2011 2247 2.292521 ACTATCTCCAGGCTGACCTCAA 60.293 50.000 17.94 0.00 46.34 3.02
2012 2248 0.908198 ATCTCCAGGCTGACCTCAAC 59.092 55.000 17.94 0.00 46.34 3.18
2013 2249 1.194781 TCTCCAGGCTGACCTCAACC 61.195 60.000 17.94 0.00 46.34 3.77
2014 2250 2.046892 CCAGGCTGACCTCAACCG 60.047 66.667 17.94 0.00 46.34 4.44
2015 2251 2.743718 CAGGCTGACCTCAACCGT 59.256 61.111 9.42 0.00 46.34 4.83
2018 2254 2.741092 GCTGACCTCAACCGTCCA 59.259 61.111 0.00 0.00 0.00 4.02
2019 2255 1.296715 GCTGACCTCAACCGTCCAT 59.703 57.895 0.00 0.00 0.00 3.41
2020 2256 0.741221 GCTGACCTCAACCGTCCATC 60.741 60.000 0.00 0.00 0.00 3.51
2021 2257 0.608130 CTGACCTCAACCGTCCATCA 59.392 55.000 0.00 0.00 0.00 3.07
2022 2258 1.001974 CTGACCTCAACCGTCCATCAA 59.998 52.381 0.00 0.00 0.00 2.57
2023 2259 1.418264 TGACCTCAACCGTCCATCAAA 59.582 47.619 0.00 0.00 0.00 2.69
2036 3922 7.907389 ACCGTCCATCAAATGTACTCATATAT 58.093 34.615 0.00 0.00 33.49 0.86
2085 3971 0.599204 CTTGCTTGCCAAACCAGCAG 60.599 55.000 0.00 0.00 42.17 4.24
2086 3972 2.030490 TTGCTTGCCAAACCAGCAGG 62.030 55.000 0.00 0.00 42.17 4.85
2114 4002 2.665185 AGGGCGTTGCTCGAACAC 60.665 61.111 6.11 0.00 42.86 3.32
2120 4008 1.599419 GCGTTGCTCGAACACCAAATT 60.599 47.619 6.11 0.00 42.86 1.82
2134 4022 1.059657 CAAATTGCTCGCAACGACCG 61.060 55.000 6.46 0.00 38.88 4.79
2159 4047 2.827642 GCCTGGATCAGCCTGTGC 60.828 66.667 0.00 0.00 37.63 4.57
2170 4058 2.671070 CCTGTGCGGTCTGGGAAT 59.329 61.111 0.00 0.00 0.00 3.01
2171 4059 1.002134 CCTGTGCGGTCTGGGAATT 60.002 57.895 0.00 0.00 0.00 2.17
2237 4125 4.074259 ACAGAGCACAGCATACATTGAAA 58.926 39.130 0.00 0.00 0.00 2.69
2242 4130 6.039047 AGAGCACAGCATACATTGAAAATAGG 59.961 38.462 0.00 0.00 0.00 2.57
2243 4131 5.653769 AGCACAGCATACATTGAAAATAGGT 59.346 36.000 0.00 0.00 0.00 3.08
2244 4132 6.828273 AGCACAGCATACATTGAAAATAGGTA 59.172 34.615 0.00 0.00 0.00 3.08
2245 4133 7.503566 AGCACAGCATACATTGAAAATAGGTAT 59.496 33.333 0.00 0.00 0.00 2.73
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
34 35 5.657474 TCTACCATAACTAGTTTCGCCTTG 58.343 41.667 14.49 2.98 0.00 3.61
71 94 6.313905 CCATGACTACCAAGTTAACTAGCTTG 59.686 42.308 8.92 3.23 42.07 4.01
98 121 3.187637 CGAAAATCCCGTTAAAGCTGACA 59.812 43.478 0.00 0.00 0.00 3.58
103 126 4.149910 TCAACGAAAATCCCGTTAAAGC 57.850 40.909 0.00 0.00 46.85 3.51
104 127 6.483687 CCTATCAACGAAAATCCCGTTAAAG 58.516 40.000 0.00 0.00 46.85 1.85
110 133 1.260561 CGCCTATCAACGAAAATCCCG 59.739 52.381 0.00 0.00 0.00 5.14
215 245 5.295787 TCCATATGGCTACATTTCAACGAAC 59.704 40.000 17.58 0.00 38.53 3.95
218 248 5.749596 TTCCATATGGCTACATTTCAACG 57.250 39.130 17.58 0.00 38.53 4.10
226 256 6.328934 TCAAACCTAGATTCCATATGGCTACA 59.671 38.462 17.58 0.00 34.44 2.74
230 260 6.299141 TCTTCAAACCTAGATTCCATATGGC 58.701 40.000 17.58 3.19 34.44 4.40
239 269 5.582665 GCGATGAGTTCTTCAAACCTAGATT 59.417 40.000 0.00 0.00 39.77 2.40
246 276 2.475111 TGTCGCGATGAGTTCTTCAAAC 59.525 45.455 14.06 0.00 39.77 2.93
279 309 3.178814 CGTCGGTTTTCAAATCCGTTTTG 59.821 43.478 17.28 4.73 45.08 2.44
295 325 0.663568 CTTTTGACTCGAGCGTCGGT 60.664 55.000 13.61 0.00 40.88 4.69
296 326 0.663568 ACTTTTGACTCGAGCGTCGG 60.664 55.000 13.61 1.36 40.88 4.79
334 364 4.320494 GCATGCATTTATTTAGGGTCTCGG 60.320 45.833 14.21 0.00 0.00 4.63
335 365 4.275689 TGCATGCATTTATTTAGGGTCTCG 59.724 41.667 18.46 0.00 0.00 4.04
338 368 4.202010 ACGTGCATGCATTTATTTAGGGTC 60.202 41.667 25.64 4.79 0.00 4.46
343 373 3.696548 TCCCACGTGCATGCATTTATTTA 59.303 39.130 25.64 4.53 0.00 1.40
367 397 1.750193 CCCCGCTATTTCTCAGCAAA 58.250 50.000 0.00 0.00 39.04 3.68
375 405 0.250081 CCTCTCTGCCCCGCTATTTC 60.250 60.000 0.00 0.00 0.00 2.17
376 406 0.691078 TCCTCTCTGCCCCGCTATTT 60.691 55.000 0.00 0.00 0.00 1.40
377 407 0.691078 TTCCTCTCTGCCCCGCTATT 60.691 55.000 0.00 0.00 0.00 1.73
453 484 1.670791 TTCTCCCGCGTTTCAAAAGT 58.329 45.000 4.92 0.00 0.00 2.66
472 503 0.459899 TGCGATCGTCTTGCTACCAT 59.540 50.000 17.81 0.00 35.06 3.55
474 505 1.571919 ATTGCGATCGTCTTGCTACC 58.428 50.000 17.81 0.00 35.06 3.18
482 513 8.621921 ATCTCAGTATATTTATTGCGATCGTC 57.378 34.615 17.81 9.69 0.00 4.20
485 516 7.915923 TCCGATCTCAGTATATTTATTGCGATC 59.084 37.037 7.92 7.92 35.00 3.69
491 522 6.153000 AGCCGTCCGATCTCAGTATATTTATT 59.847 38.462 0.00 0.00 0.00 1.40
494 525 3.827302 AGCCGTCCGATCTCAGTATATTT 59.173 43.478 0.00 0.00 0.00 1.40
497 529 2.552743 CAAGCCGTCCGATCTCAGTATA 59.447 50.000 0.00 0.00 0.00 1.47
600 635 2.126346 GCAGGCACGCATGGAAAC 60.126 61.111 5.77 0.00 0.00 2.78
601 636 3.372730 GGCAGGCACGCATGGAAA 61.373 61.111 5.77 0.00 0.00 3.13
602 637 4.349503 AGGCAGGCACGCATGGAA 62.350 61.111 5.77 0.00 0.00 3.53
617 652 2.597217 TTTCGCAACCCAGGCAGG 60.597 61.111 0.00 0.00 37.03 4.85
618 653 2.629656 CCTTTCGCAACCCAGGCAG 61.630 63.158 0.00 0.00 0.00 4.85
619 654 2.424842 ATCCTTTCGCAACCCAGGCA 62.425 55.000 0.00 0.00 0.00 4.75
620 655 1.250840 AATCCTTTCGCAACCCAGGC 61.251 55.000 0.00 0.00 0.00 4.85
621 656 0.527565 CAATCCTTTCGCAACCCAGG 59.472 55.000 0.00 0.00 0.00 4.45
622 657 0.527565 CCAATCCTTTCGCAACCCAG 59.472 55.000 0.00 0.00 0.00 4.45
623 658 0.897863 CCCAATCCTTTCGCAACCCA 60.898 55.000 0.00 0.00 0.00 4.51
624 659 0.610785 TCCCAATCCTTTCGCAACCC 60.611 55.000 0.00 0.00 0.00 4.11
625 660 0.811281 CTCCCAATCCTTTCGCAACC 59.189 55.000 0.00 0.00 0.00 3.77
626 661 1.821216 TCTCCCAATCCTTTCGCAAC 58.179 50.000 0.00 0.00 0.00 4.17
627 662 2.368439 CATCTCCCAATCCTTTCGCAA 58.632 47.619 0.00 0.00 0.00 4.85
628 663 2.018644 GCATCTCCCAATCCTTTCGCA 61.019 52.381 0.00 0.00 0.00 5.10
629 664 0.665298 GCATCTCCCAATCCTTTCGC 59.335 55.000 0.00 0.00 0.00 4.70
630 665 1.945394 CTGCATCTCCCAATCCTTTCG 59.055 52.381 0.00 0.00 0.00 3.46
631 666 1.680207 GCTGCATCTCCCAATCCTTTC 59.320 52.381 0.00 0.00 0.00 2.62
632 667 1.687368 GGCTGCATCTCCCAATCCTTT 60.687 52.381 0.50 0.00 0.00 3.11
633 668 0.106318 GGCTGCATCTCCCAATCCTT 60.106 55.000 0.50 0.00 0.00 3.36
634 669 1.284111 TGGCTGCATCTCCCAATCCT 61.284 55.000 0.50 0.00 0.00 3.24
635 670 0.396139 TTGGCTGCATCTCCCAATCC 60.396 55.000 0.50 0.00 33.92 3.01
636 671 1.030457 CTTGGCTGCATCTCCCAATC 58.970 55.000 0.50 0.00 37.92 2.67
637 672 0.396695 CCTTGGCTGCATCTCCCAAT 60.397 55.000 0.50 0.00 37.92 3.16
638 673 1.000521 CCTTGGCTGCATCTCCCAA 60.001 57.895 0.50 7.69 37.13 4.12
639 674 2.679092 CCTTGGCTGCATCTCCCA 59.321 61.111 0.50 0.00 0.00 4.37
640 675 2.832201 GCCTTGGCTGCATCTCCC 60.832 66.667 4.11 0.00 0.00 4.30
641 676 1.455217 ATGCCTTGGCTGCATCTCC 60.455 57.895 13.18 0.00 46.04 3.71
642 677 1.734137 CATGCCTTGGCTGCATCTC 59.266 57.895 13.18 0.00 46.04 2.75
643 678 2.423898 GCATGCCTTGGCTGCATCT 61.424 57.895 21.96 0.00 46.04 2.90
644 679 2.106332 GCATGCCTTGGCTGCATC 59.894 61.111 21.96 0.00 46.04 3.91
646 681 3.378602 CTGCATGCCTTGGCTGCA 61.379 61.111 25.29 25.29 43.20 4.41
647 682 3.379445 ACTGCATGCCTTGGCTGC 61.379 61.111 16.68 20.87 36.45 5.25
648 683 0.961857 TACACTGCATGCCTTGGCTG 60.962 55.000 16.68 9.44 35.41 4.85
649 684 0.962356 GTACACTGCATGCCTTGGCT 60.962 55.000 16.68 0.00 0.00 4.75
650 685 1.508088 GTACACTGCATGCCTTGGC 59.492 57.895 16.68 4.43 0.00 4.52
651 686 1.796151 CGTACACTGCATGCCTTGG 59.204 57.895 16.68 4.68 0.00 3.61
652 687 1.135315 GCGTACACTGCATGCCTTG 59.865 57.895 16.68 14.42 0.00 3.61
653 688 0.249120 TAGCGTACACTGCATGCCTT 59.751 50.000 16.68 0.00 33.85 4.35
654 689 0.465705 ATAGCGTACACTGCATGCCT 59.534 50.000 16.68 4.59 33.85 4.75
655 690 0.583438 CATAGCGTACACTGCATGCC 59.417 55.000 16.68 0.00 33.85 4.40
656 691 1.570813 TCATAGCGTACACTGCATGC 58.429 50.000 11.82 11.82 33.85 4.06
657 692 2.406357 CGATCATAGCGTACACTGCATG 59.594 50.000 0.00 0.00 33.85 4.06
678 713 1.887707 CTACCGCCCGCCTGATTTC 60.888 63.158 0.00 0.00 0.00 2.17
687 722 1.007271 CATGTAGCTCTACCGCCCG 60.007 63.158 0.00 0.00 35.26 6.13
857 892 2.584835 AGGAAACAATGGCAGCACTA 57.415 45.000 0.00 0.00 0.00 2.74
858 893 1.615392 GAAGGAAACAATGGCAGCACT 59.385 47.619 0.00 0.00 0.00 4.40
873 908 1.004745 GTGCTTGGATCTTGGGAAGGA 59.995 52.381 0.00 0.00 0.00 3.36
875 910 2.205022 TGTGCTTGGATCTTGGGAAG 57.795 50.000 0.00 0.00 0.00 3.46
939 979 1.278127 GTGTGAGCAGCCCCTAGTAAA 59.722 52.381 0.00 0.00 0.00 2.01
952 992 0.933097 CTGACTGTGTGTGTGTGAGC 59.067 55.000 0.00 0.00 0.00 4.26
1400 1520 8.659491 CACTATATATGTTGATGCACCACATAC 58.341 37.037 13.85 0.00 39.84 2.39
1441 1568 6.821388 ACATGCTATACCTTCCTAACTTCTG 58.179 40.000 0.00 0.00 0.00 3.02
1446 1573 9.587772 CATATGTACATGCTATACCTTCCTAAC 57.412 37.037 18.81 0.00 0.00 2.34
1461 1588 6.294473 AGGAGAGGAAAAGCATATGTACATG 58.706 40.000 18.81 5.31 0.00 3.21
1495 1622 6.178324 AGCATACACAGATCCATATCCAATG 58.822 40.000 0.00 0.00 31.98 2.82
1497 1624 5.830799 AGCATACACAGATCCATATCCAA 57.169 39.130 0.00 0.00 31.98 3.53
1539 1667 7.386299 GTCCAAGCATCGATAACATTTCTCTAT 59.614 37.037 0.00 0.00 0.00 1.98
1578 1706 5.511234 AATGCAGCATGAAGTAATTCCTC 57.489 39.130 9.18 0.00 39.69 3.71
1709 1866 3.733443 AACATTTGCTCAGTTTGGGAC 57.267 42.857 0.00 0.00 0.00 4.46
1733 1890 6.347402 CGGGGAAGTTTATATGCTGTAATTCG 60.347 42.308 0.00 0.00 0.00 3.34
1827 2045 9.107367 GTATGAAAAACTCTTCATCGAAGTTTG 57.893 33.333 11.78 0.00 43.42 2.93
1829 2047 8.608844 AGTATGAAAAACTCTTCATCGAAGTT 57.391 30.769 2.25 0.00 43.42 2.66
1838 2072 8.231161 GGAGTAGCAAAGTATGAAAAACTCTTC 58.769 37.037 0.00 0.00 0.00 2.87
1844 2078 7.817418 AACTGGAGTAGCAAAGTATGAAAAA 57.183 32.000 0.00 0.00 0.00 1.94
1871 2105 4.256920 GCTCTAGATTTTCCTGCAACAGA 58.743 43.478 0.00 0.00 32.44 3.41
1875 2109 2.578021 AGGGCTCTAGATTTTCCTGCAA 59.422 45.455 0.00 0.00 0.00 4.08
1877 2111 2.171448 TCAGGGCTCTAGATTTTCCTGC 59.829 50.000 18.33 7.38 40.93 4.85
1879 2113 3.454082 CACTCAGGGCTCTAGATTTTCCT 59.546 47.826 0.00 0.00 0.00 3.36
1928 2163 3.058914 CCTTGTAGACCGTTGCAAAAGAG 60.059 47.826 0.00 0.00 0.00 2.85
1934 2170 1.373435 CCCCTTGTAGACCGTTGCA 59.627 57.895 0.00 0.00 0.00 4.08
1936 2172 1.740296 CGCCCCTTGTAGACCGTTG 60.740 63.158 0.00 0.00 0.00 4.10
1952 2188 4.467735 GAAAAGTTCAGGTGAGATTTCGC 58.532 43.478 0.00 0.00 0.00 4.70
1958 2194 4.347876 TCTGATGGAAAAGTTCAGGTGAGA 59.652 41.667 0.00 0.00 0.00 3.27
1960 2196 4.389374 GTCTGATGGAAAAGTTCAGGTGA 58.611 43.478 0.00 0.00 0.00 4.02
1980 2216 2.432510 CCTGGAGATAGTTGGTGAGGTC 59.567 54.545 0.00 0.00 0.00 3.85
2000 2236 2.047179 GGACGGTTGAGGTCAGCC 60.047 66.667 2.85 2.85 42.88 4.85
2001 2237 0.741221 GATGGACGGTTGAGGTCAGC 60.741 60.000 0.00 0.00 36.12 4.26
2002 2238 0.608130 TGATGGACGGTTGAGGTCAG 59.392 55.000 0.00 0.00 36.12 3.51
2003 2239 1.052617 TTGATGGACGGTTGAGGTCA 58.947 50.000 0.00 0.00 36.12 4.02
2004 2240 2.178912 TTTGATGGACGGTTGAGGTC 57.821 50.000 0.00 0.00 0.00 3.85
2006 2242 2.436417 ACATTTGATGGACGGTTGAGG 58.564 47.619 0.00 0.00 33.60 3.86
2036 3922 2.614481 GCCCTCCGTCAAATGTACTCAA 60.614 50.000 0.00 0.00 0.00 3.02
2085 3971 2.895372 CGCCCTGTCGTTATGGCC 60.895 66.667 0.00 0.00 40.87 5.36
2086 3972 2.125269 ACGCCCTGTCGTTATGGC 60.125 61.111 0.00 0.00 40.07 4.40
2104 3990 1.266718 GAGCAATTTGGTGTTCGAGCA 59.733 47.619 5.71 0.00 0.00 4.26
2114 4002 2.712077 GTCGTTGCGAGCAATTTGG 58.288 52.632 13.89 4.63 36.23 3.28
2134 4022 1.517257 CTGATCCAGGCACGACGAC 60.517 63.158 0.00 0.00 0.00 4.34
2159 4047 0.109781 CGTTTGCAATTCCCAGACCG 60.110 55.000 0.00 0.00 0.00 4.79


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

AutoCloner maintained by Alex Coulton.