Multiple sequence alignment - TraesCS7D01G049100

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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 TraesCS7D01G049100 chr7D 100.000 2285 0 0 1 2285 25275896 25278180 0.000000e+00 4220
1 TraesCS7D01G049100 chr7D 84.273 763 86 15 797 1543 25285620 25286364 0.000000e+00 713
2 TraesCS7D01G049100 chr7A 90.601 1415 87 24 762 2144 26049363 26050763 0.000000e+00 1834
3 TraesCS7D01G049100 chr7A 77.229 1133 160 52 1021 2077 26099657 26100767 7.080000e-160 573
4 TraesCS7D01G049100 chr7A 91.333 150 13 0 2136 2285 26051312 26051461 2.980000e-49 206
5 TraesCS7D01G049100 chr4A 90.923 639 36 6 667 1294 709203186 709203813 0.000000e+00 839
6 TraesCS7D01G049100 chr4A 82.702 607 77 14 952 1543 709264430 709265023 4.350000e-142 514
7 TraesCS7D01G049100 chr4A 91.826 367 19 7 294 656 709202848 709203207 3.390000e-138 501
8 TraesCS7D01G049100 chr4A 81.518 606 83 14 952 1543 709262869 709263459 2.660000e-129 472
9 TraesCS7D01G049100 chr4A 90.037 271 16 8 49 311 709202559 709202826 7.820000e-90 340
10 TraesCS7D01G049100 chr4A 86.182 275 27 6 1328 1593 709203818 709204090 1.030000e-73 287
11 TraesCS7D01G049100 chrUn 92.344 209 12 3 1578 1786 470559164 470558960 6.170000e-76 294


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 TraesCS7D01G049100 chr7D 25275896 25278180 2284 False 4220.00 4220 100.000 1 2285 1 chr7D.!!$F1 2284
1 TraesCS7D01G049100 chr7D 25285620 25286364 744 False 713.00 713 84.273 797 1543 1 chr7D.!!$F2 746
2 TraesCS7D01G049100 chr7A 26049363 26051461 2098 False 1020.00 1834 90.967 762 2285 2 chr7A.!!$F2 1523
3 TraesCS7D01G049100 chr7A 26099657 26100767 1110 False 573.00 573 77.229 1021 2077 1 chr7A.!!$F1 1056
4 TraesCS7D01G049100 chr4A 709262869 709265023 2154 False 493.00 514 82.110 952 1543 2 chr4A.!!$F2 591
5 TraesCS7D01G049100 chr4A 709202559 709204090 1531 False 491.75 839 89.742 49 1593 4 chr4A.!!$F1 1544

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
880 930 0.182537 CCCAACTGGACAACCACTCA 59.817 55.0 0.0 0.0 41.77 3.41 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1828 3554 0.100682 GGATCTGACAGTAAGCGCGA 59.899 55.0 12.1 0.0 0.0 5.87 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
36 37 5.505173 GCACAATGCATCAAATAGTAGGT 57.495 39.130 0.00 0.00 44.26 3.08
37 38 5.514279 GCACAATGCATCAAATAGTAGGTC 58.486 41.667 0.00 0.00 44.26 3.85
38 39 5.506317 GCACAATGCATCAAATAGTAGGTCC 60.506 44.000 0.00 0.00 44.26 4.46
39 40 5.824624 CACAATGCATCAAATAGTAGGTCCT 59.175 40.000 0.00 0.00 0.00 3.85
40 41 6.319658 CACAATGCATCAAATAGTAGGTCCTT 59.680 38.462 0.00 0.00 0.00 3.36
41 42 6.891908 ACAATGCATCAAATAGTAGGTCCTTT 59.108 34.615 0.00 0.00 0.00 3.11
42 43 7.397192 ACAATGCATCAAATAGTAGGTCCTTTT 59.603 33.333 0.00 0.00 0.00 2.27
43 44 7.961326 ATGCATCAAATAGTAGGTCCTTTTT 57.039 32.000 0.00 0.00 0.00 1.94
44 45 7.391148 TGCATCAAATAGTAGGTCCTTTTTC 57.609 36.000 0.00 0.00 0.00 2.29
45 46 7.175104 TGCATCAAATAGTAGGTCCTTTTTCT 58.825 34.615 0.00 0.00 0.00 2.52
46 47 7.336931 TGCATCAAATAGTAGGTCCTTTTTCTC 59.663 37.037 0.00 0.00 0.00 2.87
47 48 7.336931 GCATCAAATAGTAGGTCCTTTTTCTCA 59.663 37.037 0.00 0.00 0.00 3.27
48 49 9.231297 CATCAAATAGTAGGTCCTTTTTCTCAA 57.769 33.333 0.00 0.00 0.00 3.02
49 50 9.807921 ATCAAATAGTAGGTCCTTTTTCTCAAA 57.192 29.630 0.00 0.00 0.00 2.69
50 51 9.635404 TCAAATAGTAGGTCCTTTTTCTCAAAA 57.365 29.630 0.00 0.00 0.00 2.44
86 87 2.176247 AGGTCCTGGTCGTGGATATT 57.824 50.000 0.00 0.00 35.87 1.28
99 100 2.228343 GTGGATATTACGACGAGGAGGG 59.772 54.545 0.00 0.00 0.00 4.30
128 130 4.897509 TCTCCCTTGTGCTGGATATATG 57.102 45.455 0.00 0.00 0.00 1.78
141 143 4.541705 TGGATATATGAGGGCTAGAGCTC 58.458 47.826 5.27 5.27 43.28 4.09
162 164 2.225019 CGAGCGTACTGTATTATCCGGT 59.775 50.000 0.00 0.12 0.00 5.28
173 175 5.350633 TGTATTATCCGGTCGTTCGATTTT 58.649 37.500 0.00 0.00 0.00 1.82
230 233 3.751518 TCCTCTCTGTTGTTTTTAGCCC 58.248 45.455 0.00 0.00 0.00 5.19
329 378 3.253188 GCTTTTGAGTATCTTGCACCACA 59.747 43.478 0.00 0.00 34.92 4.17
330 379 4.261572 GCTTTTGAGTATCTTGCACCACAA 60.262 41.667 0.00 0.00 34.92 3.33
331 380 5.565439 GCTTTTGAGTATCTTGCACCACAAT 60.565 40.000 0.00 0.00 37.72 2.71
386 435 5.437289 TTTTTACTGTTCACCAGATGCAG 57.563 39.130 0.00 0.00 44.49 4.41
389 438 1.073964 CTGTTCACCAGATGCAGACG 58.926 55.000 0.00 0.00 44.49 4.18
479 528 4.178540 CAATGGCATTTTGTCACCATCTC 58.821 43.478 10.65 0.00 42.06 2.75
490 539 4.009675 TGTCACCATCTCTTAAATGCCAC 58.990 43.478 0.00 0.00 0.00 5.01
509 558 8.761575 ATGCCACTGTTTCAACTAATAAATTG 57.238 30.769 0.00 0.00 0.00 2.32
553 602 3.205338 AGCATTTTGTTTGTTTGCTCCC 58.795 40.909 0.00 0.00 39.32 4.30
564 613 3.594134 TGTTTGCTCCCTTGTTTTGTTG 58.406 40.909 0.00 0.00 0.00 3.33
598 647 6.131544 TCCTAGTTGAAAAACTTCACAAGC 57.868 37.500 0.00 0.00 34.37 4.01
605 654 5.273170 TGAAAAACTTCACAAGCATCTTCG 58.727 37.500 0.00 0.00 0.00 3.79
610 659 5.078411 ACTTCACAAGCATCTTCGAGTAT 57.922 39.130 0.00 0.00 0.00 2.12
611 660 5.482908 ACTTCACAAGCATCTTCGAGTATT 58.517 37.500 0.00 0.00 0.00 1.89
612 661 5.934625 ACTTCACAAGCATCTTCGAGTATTT 59.065 36.000 0.00 0.00 0.00 1.40
649 698 2.290641 TGTCATTACGGCCAAATCCACT 60.291 45.455 2.24 0.00 0.00 4.00
650 699 2.752903 GTCATTACGGCCAAATCCACTT 59.247 45.455 2.24 0.00 0.00 3.16
651 700 3.192633 GTCATTACGGCCAAATCCACTTT 59.807 43.478 2.24 0.00 0.00 2.66
652 701 3.829601 TCATTACGGCCAAATCCACTTTT 59.170 39.130 2.24 0.00 0.00 2.27
653 702 5.010933 TCATTACGGCCAAATCCACTTTTA 58.989 37.500 2.24 0.00 0.00 1.52
654 703 5.654650 TCATTACGGCCAAATCCACTTTTAT 59.345 36.000 2.24 0.00 0.00 1.40
655 704 5.986501 TTACGGCCAAATCCACTTTTATT 57.013 34.783 2.24 0.00 0.00 1.40
656 705 4.882842 ACGGCCAAATCCACTTTTATTT 57.117 36.364 2.24 0.00 0.00 1.40
657 706 5.222079 ACGGCCAAATCCACTTTTATTTT 57.778 34.783 2.24 0.00 0.00 1.82
658 707 5.616270 ACGGCCAAATCCACTTTTATTTTT 58.384 33.333 2.24 0.00 0.00 1.94
659 708 5.468409 ACGGCCAAATCCACTTTTATTTTTG 59.532 36.000 2.24 0.00 0.00 2.44
660 709 5.616645 CGGCCAAATCCACTTTTATTTTTGC 60.617 40.000 2.24 0.00 0.00 3.68
661 710 5.381477 GCCAAATCCACTTTTATTTTTGCG 58.619 37.500 0.00 0.00 0.00 4.85
662 711 5.616645 GCCAAATCCACTTTTATTTTTGCGG 60.617 40.000 0.00 0.00 0.00 5.69
663 712 5.106752 CCAAATCCACTTTTATTTTTGCGGG 60.107 40.000 0.00 0.00 0.00 6.13
664 713 3.669251 TCCACTTTTATTTTTGCGGGG 57.331 42.857 0.00 0.00 0.00 5.73
665 714 2.300437 TCCACTTTTATTTTTGCGGGGG 59.700 45.455 0.00 0.00 0.00 5.40
666 715 2.037902 CCACTTTTATTTTTGCGGGGGT 59.962 45.455 0.00 0.00 0.00 4.95
667 716 3.258622 CCACTTTTATTTTTGCGGGGGTA 59.741 43.478 0.00 0.00 0.00 3.69
668 717 4.239304 CACTTTTATTTTTGCGGGGGTAC 58.761 43.478 0.00 0.00 0.00 3.34
669 718 3.057386 ACTTTTATTTTTGCGGGGGTACG 60.057 43.478 0.00 0.00 0.00 3.67
670 719 1.461559 TTATTTTTGCGGGGGTACGG 58.538 50.000 0.00 0.00 0.00 4.02
671 720 1.031029 TATTTTTGCGGGGGTACGGC 61.031 55.000 0.00 0.00 44.86 5.68
676 725 4.807631 GCGGGGGTACGGCCAAAT 62.808 66.667 2.24 0.00 39.31 2.32
677 726 2.515290 CGGGGGTACGGCCAAATC 60.515 66.667 2.24 0.00 39.65 2.17
678 727 2.124024 GGGGGTACGGCCAAATCC 60.124 66.667 2.24 0.00 39.65 3.01
679 728 2.678470 GGGGTACGGCCAAATCCA 59.322 61.111 2.24 0.00 39.65 3.41
680 729 1.751544 GGGGTACGGCCAAATCCAC 60.752 63.158 2.24 0.00 39.65 4.02
689 738 3.192633 ACGGCCAAATCCACTTTGATTAC 59.807 43.478 2.24 0.00 45.96 1.89
696 745 6.458210 CAAATCCACTTTGATTACCAGCTTT 58.542 36.000 0.00 0.00 45.96 3.51
721 770 3.318275 ACGTTATCATGTCTCACCGCTAT 59.682 43.478 0.00 0.00 0.00 2.97
722 771 4.517832 ACGTTATCATGTCTCACCGCTATA 59.482 41.667 0.00 0.00 0.00 1.31
724 773 5.334957 CGTTATCATGTCTCACCGCTATAGT 60.335 44.000 0.84 0.00 0.00 2.12
726 775 7.572539 CGTTATCATGTCTCACCGCTATAGTAA 60.573 40.741 0.84 0.00 0.00 2.24
727 776 6.650427 ATCATGTCTCACCGCTATAGTAAA 57.350 37.500 0.84 0.00 0.00 2.01
729 778 5.593095 TCATGTCTCACCGCTATAGTAAAGT 59.407 40.000 0.84 0.00 0.00 2.66
730 779 6.769341 TCATGTCTCACCGCTATAGTAAAGTA 59.231 38.462 0.84 0.00 0.00 2.24
731 780 6.615264 TGTCTCACCGCTATAGTAAAGTAG 57.385 41.667 0.84 0.00 0.00 2.57
732 781 5.008415 TGTCTCACCGCTATAGTAAAGTAGC 59.992 44.000 0.84 0.00 39.86 3.58
733 782 5.239087 GTCTCACCGCTATAGTAAAGTAGCT 59.761 44.000 0.84 0.00 40.82 3.32
734 783 5.826737 TCTCACCGCTATAGTAAAGTAGCTT 59.173 40.000 0.84 0.00 40.82 3.74
735 784 6.017275 TCTCACCGCTATAGTAAAGTAGCTTC 60.017 42.308 0.84 0.00 40.82 3.86
837 887 1.112916 TCAACAGCGACCTCTCACCA 61.113 55.000 0.00 0.00 0.00 4.17
858 908 4.309950 ACCCTTGGCACGACGGTC 62.310 66.667 0.00 0.00 0.00 4.79
865 915 4.612412 GCACGACGGTCCACCCAA 62.612 66.667 1.91 0.00 0.00 4.12
880 930 0.182537 CCCAACTGGACAACCACTCA 59.817 55.000 0.00 0.00 41.77 3.41
913 970 6.487689 AAAAATCAACCTGATCGAGAAGAC 57.512 37.500 0.00 0.00 35.76 3.01
922 979 4.991056 CCTGATCGAGAAGACAACAAAGAA 59.009 41.667 0.00 0.00 0.00 2.52
923 980 5.466728 CCTGATCGAGAAGACAACAAAGAAA 59.533 40.000 0.00 0.00 0.00 2.52
924 981 6.017934 CCTGATCGAGAAGACAACAAAGAAAA 60.018 38.462 0.00 0.00 0.00 2.29
925 982 6.948353 TGATCGAGAAGACAACAAAGAAAAG 58.052 36.000 0.00 0.00 0.00 2.27
926 983 6.538742 TGATCGAGAAGACAACAAAGAAAAGT 59.461 34.615 0.00 0.00 0.00 2.66
927 984 6.106877 TCGAGAAGACAACAAAGAAAAGTG 57.893 37.500 0.00 0.00 0.00 3.16
928 985 5.064707 TCGAGAAGACAACAAAGAAAAGTGG 59.935 40.000 0.00 0.00 0.00 4.00
929 986 5.064707 CGAGAAGACAACAAAGAAAAGTGGA 59.935 40.000 0.00 0.00 0.00 4.02
930 987 6.403200 CGAGAAGACAACAAAGAAAAGTGGAA 60.403 38.462 0.00 0.00 0.00 3.53
968 1035 3.736740 GCTAGCTAGACAACAGGAAGAGC 60.737 52.174 25.15 1.96 0.00 4.09
1312 2970 2.359169 CGTCTAGGGAGCCTGCCAA 61.359 63.158 4.63 0.00 34.61 4.52
1341 3001 8.786898 TGTGATTTCCTCTATTCTTTTCACTTG 58.213 33.333 0.00 0.00 33.79 3.16
1737 3437 1.852942 TCTTGTGCTCAGTCAACGTC 58.147 50.000 0.00 0.00 0.00 4.34
1750 3450 0.948623 CAACGTCGAAGGATGCCACA 60.949 55.000 0.00 0.00 32.12 4.17
1751 3451 0.036388 AACGTCGAAGGATGCCACAT 60.036 50.000 0.00 0.00 32.12 3.21
1752 3452 0.740868 ACGTCGAAGGATGCCACATG 60.741 55.000 0.00 0.00 32.12 3.21
1753 3453 1.723870 GTCGAAGGATGCCACATGC 59.276 57.895 0.00 0.00 41.77 4.06
1788 3489 6.546034 TCCTTCGGTTCAATCTTTCTTTCTTT 59.454 34.615 0.00 0.00 0.00 2.52
1819 3545 4.728350 TGGACACCCCTACTATAGTACTCA 59.272 45.833 8.59 0.00 35.38 3.41
1828 3554 6.602406 CCCTACTATAGTACTCATACCGCATT 59.398 42.308 8.59 0.00 30.88 3.56
1829 3555 7.201714 CCCTACTATAGTACTCATACCGCATTC 60.202 44.444 8.59 0.00 30.88 2.67
1841 3567 4.955238 GCATTCGCGCTTACTGTC 57.045 55.556 5.56 0.00 0.00 3.51
1889 3615 2.313051 TTTGTTCCTCCGGTGCGACA 62.313 55.000 0.00 3.67 0.00 4.35
1896 3622 4.293648 CCGGTGCGACAGGTGTCA 62.294 66.667 10.63 0.00 44.99 3.58
1932 3658 2.158943 GGATTTGAAGAGGAGGTACCCG 60.159 54.545 8.74 0.00 40.05 5.28
1939 3665 0.105607 GAGGAGGTACCCGAGGGAAT 60.106 60.000 16.26 0.00 40.05 3.01
1977 3708 3.610040 TGACGAAATCACTGGCAGTAT 57.390 42.857 21.59 11.36 29.99 2.12
1997 3728 2.603473 CCTGGACACCGGTGAGGA 60.603 66.667 40.21 20.72 45.00 3.71
2119 3861 1.399215 CCGCAACGTCGCTTTGTTTAT 60.399 47.619 0.00 0.00 0.00 1.40
2120 3862 2.159814 CCGCAACGTCGCTTTGTTTATA 60.160 45.455 0.00 0.00 0.00 0.98
2134 3876 7.060633 CGCTTTGTTTATAACACCATTTCTCAC 59.939 37.037 0.00 0.00 41.97 3.51
2165 4464 2.605338 CGACATGGCAAACAAAGTCAGG 60.605 50.000 0.00 0.00 37.78 3.86
2169 4468 1.115326 GGCAAACAAAGTCAGGGGCT 61.115 55.000 0.00 0.00 0.00 5.19
2173 4472 0.853530 AACAAAGTCAGGGGCTCCTT 59.146 50.000 0.00 0.00 42.67 3.36
2187 4486 0.179062 CTCCTTGATTCCTCAGCCCG 60.179 60.000 0.00 0.00 31.68 6.13
2229 4528 4.321974 GCAAGATTCCCCTTCAACGATTTT 60.322 41.667 0.00 0.00 0.00 1.82
2257 4556 2.484889 GTGTTGTGGAGAACTGGAGAC 58.515 52.381 0.00 0.00 0.00 3.36
2264 4563 1.889530 GAGAACTGGAGACCGTGGGG 61.890 65.000 0.00 0.00 40.11 4.96
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
14 15 5.505173 ACCTACTATTTGATGCATTGTGC 57.495 39.130 0.00 0.00 45.29 4.57
15 16 5.824624 AGGACCTACTATTTGATGCATTGTG 59.175 40.000 0.00 0.00 0.00 3.33
16 17 6.006275 AGGACCTACTATTTGATGCATTGT 57.994 37.500 0.00 0.00 0.00 2.71
17 18 6.949352 AAGGACCTACTATTTGATGCATTG 57.051 37.500 0.00 0.00 0.00 2.82
18 19 7.961326 AAAAGGACCTACTATTTGATGCATT 57.039 32.000 0.00 0.00 0.00 3.56
19 20 7.836183 AGAAAAAGGACCTACTATTTGATGCAT 59.164 33.333 0.00 0.00 0.00 3.96
20 21 7.175104 AGAAAAAGGACCTACTATTTGATGCA 58.825 34.615 0.00 0.00 0.00 3.96
21 22 7.336931 TGAGAAAAAGGACCTACTATTTGATGC 59.663 37.037 0.00 0.00 0.00 3.91
22 23 8.792830 TGAGAAAAAGGACCTACTATTTGATG 57.207 34.615 0.00 0.00 0.00 3.07
23 24 9.807921 TTTGAGAAAAAGGACCTACTATTTGAT 57.192 29.630 0.00 0.00 0.00 2.57
24 25 9.635404 TTTTGAGAAAAAGGACCTACTATTTGA 57.365 29.630 0.00 0.00 0.00 2.69
48 49 9.987272 CAGGACCTTCTATTTGAATTTTCTTTT 57.013 29.630 0.00 0.00 33.71 2.27
49 50 8.588472 CCAGGACCTTCTATTTGAATTTTCTTT 58.412 33.333 0.00 0.00 33.71 2.52
50 51 7.730332 ACCAGGACCTTCTATTTGAATTTTCTT 59.270 33.333 0.00 0.00 33.71 2.52
51 52 7.241628 ACCAGGACCTTCTATTTGAATTTTCT 58.758 34.615 0.00 0.00 33.71 2.52
52 53 7.468141 ACCAGGACCTTCTATTTGAATTTTC 57.532 36.000 0.00 0.00 33.71 2.29
53 54 6.151144 CGACCAGGACCTTCTATTTGAATTTT 59.849 38.462 0.00 0.00 33.71 1.82
86 87 0.742281 CGAAGTCCCTCCTCGTCGTA 60.742 60.000 0.00 0.00 32.79 3.43
99 100 1.149148 GCACAAGGGAGAACGAAGTC 58.851 55.000 0.00 0.00 45.00 3.01
128 130 2.903547 CGCTCGAGCTCTAGCCCTC 61.904 68.421 32.88 7.44 43.38 4.30
141 143 2.225019 ACCGGATAATACAGTACGCTCG 59.775 50.000 9.46 0.00 0.00 5.03
154 156 3.847542 TCAAAATCGAACGACCGGATAA 58.152 40.909 9.46 0.00 0.00 1.75
158 160 1.425412 ACTCAAAATCGAACGACCGG 58.575 50.000 0.00 0.00 0.00 5.28
253 256 6.687105 GTGTGAACAGTGTTGCTTAAGTTAAG 59.313 38.462 14.57 16.87 38.80 1.85
255 258 5.065474 GGTGTGAACAGTGTTGCTTAAGTTA 59.935 40.000 14.57 0.00 0.00 2.24
257 260 3.377172 GGTGTGAACAGTGTTGCTTAAGT 59.623 43.478 14.57 0.00 0.00 2.24
258 261 3.243068 GGGTGTGAACAGTGTTGCTTAAG 60.243 47.826 14.57 0.00 0.00 1.85
297 303 0.512952 ACTCAAAAGCGTGATCGTGC 59.487 50.000 0.96 0.96 39.49 5.34
298 304 3.859961 AGATACTCAAAAGCGTGATCGTG 59.140 43.478 0.00 0.00 39.49 4.35
299 305 4.111375 AGATACTCAAAAGCGTGATCGT 57.889 40.909 0.00 0.00 39.49 3.73
301 307 4.093408 TGCAAGATACTCAAAAGCGTGATC 59.907 41.667 0.00 0.00 0.00 2.92
389 438 3.508840 CAATTCGGTGCCGGGCTC 61.509 66.667 21.46 16.86 40.25 4.70
401 450 8.917415 AGGATAGAAAAGCGAAAATTCAATTC 57.083 30.769 0.00 0.00 0.00 2.17
479 528 9.906660 TTATTAGTTGAAACAGTGGCATTTAAG 57.093 29.630 0.00 0.00 0.00 1.85
576 625 5.890334 TGCTTGTGAAGTTTTTCAACTAGG 58.110 37.500 0.00 0.00 42.89 3.02
621 670 3.342377 TGGCCGTAATGACATCAAAGA 57.658 42.857 0.00 0.00 0.00 2.52
622 671 4.433186 TTTGGCCGTAATGACATCAAAG 57.567 40.909 0.00 0.00 0.00 2.77
625 674 2.948979 GGATTTGGCCGTAATGACATCA 59.051 45.455 7.57 0.00 0.00 3.07
649 698 2.230750 CCGTACCCCCGCAAAAATAAAA 59.769 45.455 0.00 0.00 0.00 1.52
650 699 1.817447 CCGTACCCCCGCAAAAATAAA 59.183 47.619 0.00 0.00 0.00 1.40
651 700 1.461559 CCGTACCCCCGCAAAAATAA 58.538 50.000 0.00 0.00 0.00 1.40
652 701 1.031029 GCCGTACCCCCGCAAAAATA 61.031 55.000 0.00 0.00 0.00 1.40
653 702 2.344981 GCCGTACCCCCGCAAAAAT 61.345 57.895 0.00 0.00 0.00 1.82
654 703 2.984718 GCCGTACCCCCGCAAAAA 60.985 61.111 0.00 0.00 0.00 1.94
659 708 4.807631 ATTTGGCCGTACCCCCGC 62.808 66.667 0.00 0.00 37.83 6.13
660 709 2.515290 GATTTGGCCGTACCCCCG 60.515 66.667 0.00 0.00 37.83 5.73
661 710 2.124024 GGATTTGGCCGTACCCCC 60.124 66.667 0.00 0.00 37.83 5.40
662 711 1.751544 GTGGATTTGGCCGTACCCC 60.752 63.158 0.00 0.00 37.83 4.95
663 712 0.323087 AAGTGGATTTGGCCGTACCC 60.323 55.000 0.00 0.00 37.83 3.69
664 713 1.201414 CAAAGTGGATTTGGCCGTACC 59.799 52.381 0.00 0.00 43.88 3.34
665 714 2.156098 TCAAAGTGGATTTGGCCGTAC 58.844 47.619 0.00 0.00 46.93 3.67
666 715 2.570415 TCAAAGTGGATTTGGCCGTA 57.430 45.000 0.00 0.00 46.93 4.02
667 716 1.923356 ATCAAAGTGGATTTGGCCGT 58.077 45.000 0.00 0.00 46.93 5.68
668 717 3.428862 GGTAATCAAAGTGGATTTGGCCG 60.429 47.826 0.00 0.00 46.93 6.13
669 718 3.513515 TGGTAATCAAAGTGGATTTGGCC 59.486 43.478 0.00 0.00 46.93 5.36
670 719 4.747810 CTGGTAATCAAAGTGGATTTGGC 58.252 43.478 0.90 0.00 46.93 4.52
671 720 4.463891 AGCTGGTAATCAAAGTGGATTTGG 59.536 41.667 0.00 0.00 46.93 3.28
673 722 6.295292 GGAAAGCTGGTAATCAAAGTGGATTT 60.295 38.462 0.00 0.00 38.41 2.17
674 723 5.185828 GGAAAGCTGGTAATCAAAGTGGATT 59.814 40.000 0.00 0.00 40.45 3.01
675 724 4.706962 GGAAAGCTGGTAATCAAAGTGGAT 59.293 41.667 0.00 0.00 0.00 3.41
676 725 4.079253 GGAAAGCTGGTAATCAAAGTGGA 58.921 43.478 0.00 0.00 0.00 4.02
677 726 3.826157 TGGAAAGCTGGTAATCAAAGTGG 59.174 43.478 0.00 0.00 0.00 4.00
678 727 4.613622 CGTGGAAAGCTGGTAATCAAAGTG 60.614 45.833 0.00 0.00 0.00 3.16
679 728 3.502211 CGTGGAAAGCTGGTAATCAAAGT 59.498 43.478 0.00 0.00 0.00 2.66
680 729 3.502211 ACGTGGAAAGCTGGTAATCAAAG 59.498 43.478 0.00 0.00 0.00 2.77
689 738 3.009723 ACATGATAACGTGGAAAGCTGG 58.990 45.455 0.00 0.00 37.35 4.85
696 745 2.159296 CGGTGAGACATGATAACGTGGA 60.159 50.000 0.00 0.00 37.35 4.02
721 770 5.408604 GCAAACTGCAGAAGCTACTTTACTA 59.591 40.000 23.35 0.00 44.26 1.82
722 771 4.214332 GCAAACTGCAGAAGCTACTTTACT 59.786 41.667 23.35 0.00 44.26 2.24
724 773 4.749245 GCAAACTGCAGAAGCTACTTTA 57.251 40.909 23.35 0.00 44.26 1.85
776 826 1.079405 TGTCGGTCGAAATGGAGGC 60.079 57.895 0.00 0.00 0.00 4.70
784 834 2.649034 GACCTGCTGTCGGTCGAA 59.351 61.111 0.00 0.00 41.29 3.71
837 887 2.426023 GTCGTGCCAAGGGTGACT 59.574 61.111 0.00 0.00 0.00 3.41
858 908 1.106944 GTGGTTGTCCAGTTGGGTGG 61.107 60.000 0.00 0.00 45.24 4.61
894 951 4.021104 TGTTGTCTTCTCGATCAGGTTGAT 60.021 41.667 0.00 0.00 40.34 2.57
898 955 4.039245 TCTTTGTTGTCTTCTCGATCAGGT 59.961 41.667 0.00 0.00 0.00 4.00
913 970 7.538575 TCTTCTTCTTCCACTTTTCTTTGTTG 58.461 34.615 0.00 0.00 0.00 3.33
922 979 5.041191 TGAGCTTCTTCTTCTTCCACTTT 57.959 39.130 0.00 0.00 0.00 2.66
923 980 4.696479 TGAGCTTCTTCTTCTTCCACTT 57.304 40.909 0.00 0.00 0.00 3.16
924 981 4.640364 CTTGAGCTTCTTCTTCTTCCACT 58.360 43.478 0.00 0.00 0.00 4.00
925 982 3.188254 GCTTGAGCTTCTTCTTCTTCCAC 59.812 47.826 0.00 0.00 38.21 4.02
926 983 3.406764 GCTTGAGCTTCTTCTTCTTCCA 58.593 45.455 0.00 0.00 38.21 3.53
968 1035 2.383855 TCCTTGTGGTTTTCTTGGGTG 58.616 47.619 0.00 0.00 34.23 4.61
1312 2970 6.934645 TGAAAAGAATAGAGGAAATCACACGT 59.065 34.615 0.00 0.00 0.00 4.49
1341 3001 4.319115 CGACACACGTATGTAACAGTACAC 59.681 45.833 0.00 0.00 38.89 2.90
1750 3450 0.463295 CGAAGGAGCCAGTGATGCAT 60.463 55.000 0.00 0.00 0.00 3.96
1751 3451 1.078918 CGAAGGAGCCAGTGATGCA 60.079 57.895 0.00 0.00 0.00 3.96
1752 3452 3.805267 CGAAGGAGCCAGTGATGC 58.195 61.111 0.00 0.00 0.00 3.91
1788 3489 0.104356 TAGGGGTGTCCAAGGTTCCA 60.104 55.000 0.00 0.00 38.24 3.53
1828 3554 0.100682 GGATCTGACAGTAAGCGCGA 59.899 55.000 12.10 0.00 0.00 5.87
1829 3555 0.101399 AGGATCTGACAGTAAGCGCG 59.899 55.000 0.00 0.00 0.00 6.86
1834 3560 1.364678 TGGGGGAGGATCTGACAGTAA 59.635 52.381 1.59 0.00 33.73 2.24
1841 3567 4.756804 TCCATGGGGGAGGATCTG 57.243 61.111 13.02 0.00 42.15 2.90
1889 3615 0.987294 CACCTCCATCCTTGACACCT 59.013 55.000 0.00 0.00 0.00 4.00
1896 3622 1.686236 AATCCACCACCTCCATCCTT 58.314 50.000 0.00 0.00 0.00 3.36
1932 3658 3.308046 GCATATCCCTCTTCCATTCCCTC 60.308 52.174 0.00 0.00 0.00 4.30
1939 3665 2.373169 GTCATGGCATATCCCTCTTCCA 59.627 50.000 0.00 0.00 0.00 3.53
1977 3708 2.123208 TCACCGGTGTCCAGGACA 60.123 61.111 32.74 19.21 40.50 4.02
1997 3728 4.451544 GAGAGTCCTCCCAGTGCT 57.548 61.111 0.00 0.00 33.30 4.40
2102 3844 4.609708 GGTGTTATAAACAAAGCGACGTTG 59.390 41.667 0.00 0.00 44.16 4.10
2105 3847 4.392619 TGGTGTTATAAACAAAGCGACG 57.607 40.909 0.00 0.00 44.16 5.12
2119 3861 5.991606 CAGTCTTGAGTGAGAAATGGTGTTA 59.008 40.000 0.00 0.00 0.00 2.41
2120 3862 4.818546 CAGTCTTGAGTGAGAAATGGTGTT 59.181 41.667 0.00 0.00 0.00 3.32
2134 3876 0.671472 TGCCATGTCGCAGTCTTGAG 60.671 55.000 0.00 0.00 33.92 3.02
2165 4464 0.465278 GCTGAGGAATCAAGGAGCCC 60.465 60.000 0.00 0.00 0.00 5.19
2169 4468 1.907739 CGGGCTGAGGAATCAAGGA 59.092 57.895 0.00 0.00 0.00 3.36
2173 4472 2.244117 GACAGCGGGCTGAGGAATCA 62.244 60.000 26.08 0.00 46.30 2.57
2197 4496 2.025156 GAATCTTGCGCCGCATGG 59.975 61.111 22.45 14.40 38.76 3.66
2202 4501 2.438434 AAGGGGAATCTTGCGCCG 60.438 61.111 4.18 0.00 42.62 6.46
2205 4504 0.447801 CGTTGAAGGGGAATCTTGCG 59.552 55.000 0.00 0.00 0.00 4.85
2211 4510 3.096852 GGGAAAATCGTTGAAGGGGAAT 58.903 45.455 0.00 0.00 0.00 3.01
2229 4528 1.144691 TCTCCACAACACCAATGGGA 58.855 50.000 3.55 0.00 38.05 4.37
2264 4563 3.552132 GAGGGTCTTGGGAGAAAGATC 57.448 52.381 0.00 0.00 38.41 2.75


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

AutoCloner maintained by Alex Coulton.