Multiple sequence alignment - TraesCS7D01G423200

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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 TraesCS7D01G423200 chr7D 100.000 4391 0 0 1 4391 543628138 543623748 0.000000e+00 8109
1 TraesCS7D01G423200 chr7D 86.922 2554 309 16 888 3428 543563745 543561204 0.000000e+00 2843
2 TraesCS7D01G423200 chr7D 87.332 2305 286 4 1182 3483 543610521 543608220 0.000000e+00 2634
3 TraesCS7D01G423200 chr7A 97.178 2764 73 2 910 3669 625604031 625601269 0.000000e+00 4667
4 TraesCS7D01G423200 chr7A 88.992 3225 294 24 92 3272 617739464 617736257 0.000000e+00 3932
5 TraesCS7D01G423200 chr7A 88.739 2957 295 20 559 3483 625540231 625537281 0.000000e+00 3581
6 TraesCS7D01G423200 chr7A 87.993 2457 286 6 979 3428 625535259 625532805 0.000000e+00 2894
7 TraesCS7D01G423200 chr7A 88.163 2264 260 5 1162 3418 617705325 617703063 0.000000e+00 2689
8 TraesCS7D01G423200 chr7A 85.386 2607 338 30 981 3567 625617233 625614650 0.000000e+00 2663
9 TraesCS7D01G423200 chr7A 83.889 1049 119 32 138 1166 617732007 617730989 0.000000e+00 955
10 TraesCS7D01G423200 chr7A 89.612 645 29 9 3766 4374 625601150 625600508 0.000000e+00 785
11 TraesCS7D01G423200 chr7A 80.779 796 98 26 138 915 625610027 625609269 4.930000e-159 571
12 TraesCS7D01G423200 chr7A 85.579 423 21 14 92 492 625540663 625540259 1.470000e-109 407
13 TraesCS7D01G423200 chr7A 86.861 137 17 1 3856 3991 625613877 625613741 7.610000e-33 152
14 TraesCS7D01G423200 chr7A 97.143 70 1 1 3698 3766 14447514 14447583 2.770000e-22 117
15 TraesCS7D01G423200 chr7B 89.537 2743 271 10 738 3472 586969095 586966361 0.000000e+00 3461
16 TraesCS7D01G423200 chr7B 87.602 613 38 19 92 693 586969685 586969100 0.000000e+00 676
17 TraesCS7D01G423200 chr7B 98.507 67 1 0 3705 3771 57323363 57323297 7.710000e-23 119
18 TraesCS7D01G423200 chr7B 94.667 75 1 3 3693 3766 34680510 34680582 3.590000e-21 113
19 TraesCS7D01G423200 chr6B 82.317 2426 400 22 985 3397 694667799 694665390 0.000000e+00 2076
20 TraesCS7D01G423200 chr1A 97.826 92 2 0 4 95 498452757 498452666 4.550000e-35 159
21 TraesCS7D01G423200 chr2D 96.774 93 3 0 1 93 247820425 247820517 5.880000e-34 156
22 TraesCS7D01G423200 chr2D 94.118 102 5 1 1 102 599946138 599946238 2.110000e-33 154
23 TraesCS7D01G423200 chr2D 95.946 74 3 0 3705 3778 532706684 532706611 2.140000e-23 121
24 TraesCS7D01G423200 chr4D 96.667 90 3 0 4 93 494876001 494875912 2.740000e-32 150
25 TraesCS7D01G423200 chr4B 94.845 97 3 2 4 98 564869557 564869461 2.740000e-32 150
26 TraesCS7D01G423200 chr4B 98.507 67 1 0 3705 3771 472131267 472131201 7.710000e-23 119
27 TraesCS7D01G423200 chr3A 95.699 93 4 0 1 93 24029981 24030073 2.740000e-32 150
28 TraesCS7D01G423200 chr1D 95.699 93 4 0 4 96 184046494 184046402 2.740000e-32 150
29 TraesCS7D01G423200 chr1D 100.000 68 0 0 3705 3772 367688960 367688893 4.610000e-25 126
30 TraesCS7D01G423200 chr1B 94.792 96 5 0 1 96 151091097 151091192 2.740000e-32 150
31 TraesCS7D01G423200 chr4A 91.509 106 7 1 1 104 589013517 589013622 1.270000e-30 145
32 TraesCS7D01G423200 chr6A 100.000 65 0 0 3705 3769 550063133 550063069 2.140000e-23 121
33 TraesCS7D01G423200 chr2A 97.222 72 1 1 3705 3776 498091717 498091647 2.140000e-23 121
34 TraesCS7D01G423200 chr6D 100.000 64 0 0 3705 3768 37049094 37049157 7.710000e-23 119


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 TraesCS7D01G423200 chr7D 543623748 543628138 4390 True 8109.000000 8109 100.0000 1 4391 1 chr7D.!!$R3 4390
1 TraesCS7D01G423200 chr7D 543561204 543563745 2541 True 2843.000000 2843 86.9220 888 3428 1 chr7D.!!$R1 2540
2 TraesCS7D01G423200 chr7D 543608220 543610521 2301 True 2634.000000 2634 87.3320 1182 3483 1 chr7D.!!$R2 2301
3 TraesCS7D01G423200 chr7A 617736257 617739464 3207 True 3932.000000 3932 88.9920 92 3272 1 chr7A.!!$R3 3180
4 TraesCS7D01G423200 chr7A 625600508 625604031 3523 True 2726.000000 4667 93.3950 910 4374 2 chr7A.!!$R5 3464
5 TraesCS7D01G423200 chr7A 617703063 617705325 2262 True 2689.000000 2689 88.1630 1162 3418 1 chr7A.!!$R1 2256
6 TraesCS7D01G423200 chr7A 625532805 625540663 7858 True 2294.000000 3581 87.4370 92 3483 3 chr7A.!!$R4 3391
7 TraesCS7D01G423200 chr7A 625609269 625617233 7964 True 1128.666667 2663 84.3420 138 3991 3 chr7A.!!$R6 3853
8 TraesCS7D01G423200 chr7A 617730989 617732007 1018 True 955.000000 955 83.8890 138 1166 1 chr7A.!!$R2 1028
9 TraesCS7D01G423200 chr7B 586966361 586969685 3324 True 2068.500000 3461 88.5695 92 3472 2 chr7B.!!$R2 3380
10 TraesCS7D01G423200 chr6B 694665390 694667799 2409 True 2076.000000 2076 82.3170 985 3397 1 chr6B.!!$R1 2412

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
83 84 0.237498 GGGACAAGCTTTTTCGGACG 59.763 55.000 0.00 0.0 0.00 4.79 F
84 85 0.237498 GGACAAGCTTTTTCGGACGG 59.763 55.000 0.00 0.0 0.00 4.79 F
87 88 0.517316 CAAGCTTTTTCGGACGGAGG 59.483 55.000 0.00 0.0 0.00 4.30 F
1151 1229 0.030638 GCGCTTGGCTTCTTCAACAA 59.969 50.000 0.00 0.0 39.11 2.83 F
2166 2251 2.016318 TGTGCACAAGTTTGTCTGAGG 58.984 47.619 19.28 0.0 39.91 3.86 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1131 1209 1.100463 TGTTGAAGAAGCCAAGCGCA 61.100 50.000 11.47 0.0 41.38 6.09 R
1151 1229 1.466851 GGAGGGTTTGCTGCTGCTTT 61.467 55.000 17.00 0.0 40.48 3.51 R
1215 1293 2.556622 CCACGCAGAAGTAAATTTGGGT 59.443 45.455 0.00 0.0 37.21 4.51 R
2958 3047 2.243736 TCGGCTAAATTCCCTTCCCAAT 59.756 45.455 0.00 0.0 0.00 3.16 R
3822 9115 0.170561 GCAGTCTTGCTTGCCATCAG 59.829 55.000 0.00 0.0 46.95 2.90 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
23 24 6.983906 TCTCTCAAATGGATGTATCTAGCA 57.016 37.500 0.00 0.00 0.00 3.49
24 25 6.753180 TCTCTCAAATGGATGTATCTAGCAC 58.247 40.000 0.00 0.00 0.00 4.40
25 26 5.858381 TCTCAAATGGATGTATCTAGCACC 58.142 41.667 0.00 0.00 0.00 5.01
26 27 5.366477 TCTCAAATGGATGTATCTAGCACCA 59.634 40.000 0.00 0.00 0.00 4.17
27 28 6.000246 TCAAATGGATGTATCTAGCACCAA 58.000 37.500 0.00 0.00 0.00 3.67
28 29 6.422333 TCAAATGGATGTATCTAGCACCAAA 58.578 36.000 0.00 0.00 0.00 3.28
29 30 7.062322 TCAAATGGATGTATCTAGCACCAAAT 58.938 34.615 0.00 0.00 0.00 2.32
30 31 7.560991 TCAAATGGATGTATCTAGCACCAAATT 59.439 33.333 0.00 0.00 0.00 1.82
31 32 8.849168 CAAATGGATGTATCTAGCACCAAATTA 58.151 33.333 0.00 0.00 0.00 1.40
32 33 8.627208 AATGGATGTATCTAGCACCAAATTAG 57.373 34.615 0.00 0.00 0.00 1.73
33 34 7.136822 TGGATGTATCTAGCACCAAATTAGT 57.863 36.000 0.00 0.00 0.00 2.24
34 35 6.992123 TGGATGTATCTAGCACCAAATTAGTG 59.008 38.462 4.54 4.54 38.30 2.74
56 57 5.762825 GCTAGATGCATCCATTTGAGAAA 57.237 39.130 23.06 0.00 42.31 2.52
57 58 5.517904 GCTAGATGCATCCATTTGAGAAAC 58.482 41.667 23.06 0.00 42.31 2.78
58 59 5.066893 GCTAGATGCATCCATTTGAGAAACA 59.933 40.000 23.06 0.00 42.31 2.83
59 60 5.988310 AGATGCATCCATTTGAGAAACAA 57.012 34.783 23.06 0.00 36.65 2.83
60 61 5.962433 AGATGCATCCATTTGAGAAACAAG 58.038 37.500 23.06 0.00 39.77 3.16
61 62 3.916761 TGCATCCATTTGAGAAACAAGC 58.083 40.909 0.00 0.00 39.77 4.01
62 63 3.575256 TGCATCCATTTGAGAAACAAGCT 59.425 39.130 0.00 0.00 39.77 3.74
63 64 4.039488 TGCATCCATTTGAGAAACAAGCTT 59.961 37.500 0.00 0.00 39.77 3.74
64 65 4.387862 GCATCCATTTGAGAAACAAGCTTG 59.612 41.667 24.84 24.84 39.77 4.01
65 66 4.589216 TCCATTTGAGAAACAAGCTTGG 57.411 40.909 29.18 12.28 39.77 3.61
66 67 3.321682 TCCATTTGAGAAACAAGCTTGGG 59.678 43.478 29.18 16.37 39.77 4.12
67 68 3.321682 CCATTTGAGAAACAAGCTTGGGA 59.678 43.478 29.18 7.03 39.77 4.37
68 69 4.301628 CATTTGAGAAACAAGCTTGGGAC 58.698 43.478 29.18 18.46 39.77 4.46
69 70 2.727123 TGAGAAACAAGCTTGGGACA 57.273 45.000 29.18 17.71 0.00 4.02
70 71 3.360867 TTGAGAAACAAGCTTGGGACAA 58.639 40.909 29.18 21.59 37.48 3.18
71 72 3.381272 TTGAGAAACAAGCTTGGGACAAG 59.619 43.478 29.18 3.71 37.48 3.16
72 73 6.232513 TTGAGAAACAAGCTTGGGACAAGC 62.233 45.833 29.18 22.54 43.31 4.01
81 82 3.811031 TGGGACAAGCTTTTTCGGA 57.189 47.368 0.00 0.00 31.92 4.55
82 83 1.314730 TGGGACAAGCTTTTTCGGAC 58.685 50.000 0.00 0.00 31.92 4.79
83 84 0.237498 GGGACAAGCTTTTTCGGACG 59.763 55.000 0.00 0.00 0.00 4.79
84 85 0.237498 GGACAAGCTTTTTCGGACGG 59.763 55.000 0.00 0.00 0.00 4.79
85 86 1.223187 GACAAGCTTTTTCGGACGGA 58.777 50.000 0.00 0.00 0.00 4.69
86 87 1.194772 GACAAGCTTTTTCGGACGGAG 59.805 52.381 0.00 0.00 0.00 4.63
87 88 0.517316 CAAGCTTTTTCGGACGGAGG 59.483 55.000 0.00 0.00 0.00 4.30
88 89 0.605589 AAGCTTTTTCGGACGGAGGG 60.606 55.000 0.00 0.00 0.00 4.30
89 90 1.004200 GCTTTTTCGGACGGAGGGA 60.004 57.895 0.00 0.00 0.00 4.20
90 91 1.019805 GCTTTTTCGGACGGAGGGAG 61.020 60.000 0.00 0.00 0.00 4.30
336 347 6.371595 AGATTTCTTTGGACAGAGAGACAT 57.628 37.500 0.00 0.00 0.00 3.06
487 515 4.671234 ACAGAGTTGTAGCCTCGTGAGAG 61.671 52.174 0.00 0.00 46.49 3.20
543 573 1.963515 GTCATGGTTGTTGCCCTCTTT 59.036 47.619 0.00 0.00 0.00 2.52
607 647 9.109393 CACTTTACAGCAGTGTATAATACCAAT 57.891 33.333 0.00 0.00 38.98 3.16
673 713 8.288689 TCCTTAAAAATATGGCACCTTAAGAC 57.711 34.615 3.36 0.00 31.13 3.01
719 759 6.818142 CCACATACTTGTCATGTTGTGATAGA 59.182 38.462 21.86 0.00 39.48 1.98
720 760 7.201556 CCACATACTTGTCATGTTGTGATAGAC 60.202 40.741 21.86 0.00 39.48 2.59
761 823 2.158986 CGCATGTCTCTTTCCTCTCCAT 60.159 50.000 0.00 0.00 0.00 3.41
766 828 6.514947 CATGTCTCTTTCCTCTCCATTCTAG 58.485 44.000 0.00 0.00 0.00 2.43
839 906 3.198853 AGCAAGGAGTCCAGAATAAGACC 59.801 47.826 12.86 0.00 33.29 3.85
840 907 3.055094 GCAAGGAGTCCAGAATAAGACCA 60.055 47.826 12.86 0.00 33.29 4.02
849 916 5.591877 GTCCAGAATAAGACCATTGATGCTT 59.408 40.000 0.00 0.00 0.00 3.91
937 1006 4.910195 ACTGCTATGACCAGACAATTGAA 58.090 39.130 13.59 0.00 34.47 2.69
966 1035 8.341892 TGAGCACTTATATCTGTAGTATCTGG 57.658 38.462 0.00 0.00 0.00 3.86
1104 1182 2.715005 GCACTTGCTGTCAACGCA 59.285 55.556 0.00 0.00 38.21 5.24
1131 1209 3.016736 CGTCTCCAAAAATGGCAGGTAT 58.983 45.455 0.00 0.00 0.00 2.73
1151 1229 0.030638 GCGCTTGGCTTCTTCAACAA 59.969 50.000 0.00 0.00 39.11 2.83
1215 1293 6.061441 CCTTGGCATATGGTTCAATACAGTA 58.939 40.000 4.56 0.00 0.00 2.74
1233 1311 4.454504 ACAGTACCCAAATTTACTTCTGCG 59.545 41.667 0.00 0.00 0.00 5.18
1397 1475 3.515502 ACCACTGCTATGCTCTTGAGTAA 59.484 43.478 0.00 0.00 0.00 2.24
2166 2251 2.016318 TGTGCACAAGTTTGTCTGAGG 58.984 47.619 19.28 0.00 39.91 3.86
2269 2354 6.752815 GCTAGAATGTAGTGGTACTTCAAGTC 59.247 42.308 0.00 0.00 29.44 3.01
2958 3047 2.041620 AGACTTTGGGATGGCAAAGCTA 59.958 45.455 0.00 0.00 40.85 3.32
3444 8087 7.924541 TGTATAAGGAAAACTAGATGGGTTGT 58.075 34.615 0.00 0.00 0.00 3.32
3571 8226 7.994425 TGCGGTTGTATTCCATATATTGAAT 57.006 32.000 14.53 14.53 35.48 2.57
3698 8963 9.936759 TGTTACAAGACAGATGTGTATATTCAA 57.063 29.630 0.00 0.00 36.88 2.69
3730 8995 8.958060 AACATAGTCTAGGGATATGTGTATGT 57.042 34.615 12.94 0.00 39.46 2.29
3736 9001 9.742144 AGTCTAGGGATATGTGTATGTTACTAG 57.258 37.037 0.00 0.00 0.00 2.57
3737 9002 9.517868 GTCTAGGGATATGTGTATGTTACTAGT 57.482 37.037 0.00 0.00 0.00 2.57
3738 9003 9.516546 TCTAGGGATATGTGTATGTTACTAGTG 57.483 37.037 5.39 0.00 0.00 2.74
3739 9004 9.298250 CTAGGGATATGTGTATGTTACTAGTGT 57.702 37.037 5.39 0.00 0.00 3.55
3741 9006 9.824216 AGGGATATGTGTATGTTACTAGTGTAT 57.176 33.333 5.39 0.00 0.00 2.29
3752 9017 8.818622 ATGTTACTAGTGTATGTTACTCTCCA 57.181 34.615 5.39 0.00 34.65 3.86
3753 9018 8.818622 TGTTACTAGTGTATGTTACTCTCCAT 57.181 34.615 5.39 0.00 34.65 3.41
3754 9019 9.251440 TGTTACTAGTGTATGTTACTCTCCATT 57.749 33.333 5.39 0.00 34.65 3.16
3755 9020 9.517609 GTTACTAGTGTATGTTACTCTCCATTG 57.482 37.037 5.39 0.00 34.65 2.82
3756 9021 7.719871 ACTAGTGTATGTTACTCTCCATTGT 57.280 36.000 0.00 0.00 34.65 2.71
3757 9022 7.548097 ACTAGTGTATGTTACTCTCCATTGTG 58.452 38.462 0.00 0.00 34.65 3.33
3758 9023 5.734720 AGTGTATGTTACTCTCCATTGTGG 58.265 41.667 0.00 0.00 39.43 4.17
3759 9024 4.332819 GTGTATGTTACTCTCCATTGTGGC 59.667 45.833 0.00 0.00 37.47 5.01
3760 9025 4.225042 TGTATGTTACTCTCCATTGTGGCT 59.775 41.667 0.00 0.00 37.47 4.75
3761 9026 5.423931 TGTATGTTACTCTCCATTGTGGCTA 59.576 40.000 0.00 0.00 37.47 3.93
3762 9027 4.471904 TGTTACTCTCCATTGTGGCTAG 57.528 45.455 0.00 0.00 37.47 3.42
3763 9028 3.838317 TGTTACTCTCCATTGTGGCTAGT 59.162 43.478 7.76 7.76 37.47 2.57
3764 9029 4.081642 TGTTACTCTCCATTGTGGCTAGTC 60.082 45.833 6.40 0.00 37.47 2.59
3787 9080 4.130857 TCACATTTTCTCCGCTTACAACA 58.869 39.130 0.00 0.00 0.00 3.33
3802 9095 6.142817 GCTTACAACAGTAACACCAAATCTG 58.857 40.000 0.00 0.00 0.00 2.90
3822 9115 0.796927 GTAGTTTCACCCTTGCTCGC 59.203 55.000 0.00 0.00 0.00 5.03
3827 9120 0.674581 TTCACCCTTGCTCGCTGATG 60.675 55.000 0.00 0.00 0.00 3.07
3892 9186 2.202623 GTGAGACGCGGTAGCAGG 60.203 66.667 12.47 0.00 45.49 4.85
3988 9283 7.142995 AGGGGAAAATTAGATAAGAGTCCAG 57.857 40.000 0.00 0.00 0.00 3.86
4015 9310 2.496070 CACTATGAGACCGGTCTGGAAA 59.504 50.000 40.88 22.76 40.61 3.13
4122 9443 2.054799 TGCTTTTGTAGAGGGAGGTGT 58.945 47.619 0.00 0.00 0.00 4.16
4125 9446 3.326747 CTTTTGTAGAGGGAGGTGTTCG 58.673 50.000 0.00 0.00 0.00 3.95
4355 12054 3.003173 TCAGGGGAAGGCCTGACG 61.003 66.667 5.69 0.00 38.03 4.35
4359 12058 3.706373 GGGAAGGCCTGACGAGCA 61.706 66.667 5.69 0.00 0.00 4.26
4382 12081 4.235762 CGGTGGGCGTAGGGATGG 62.236 72.222 0.00 0.00 0.00 3.51
4383 12082 4.564110 GGTGGGCGTAGGGATGGC 62.564 72.222 0.00 0.00 36.41 4.40
4384 12083 3.792736 GTGGGCGTAGGGATGGCA 61.793 66.667 0.00 0.00 38.91 4.92
4385 12084 3.012119 TGGGCGTAGGGATGGCAA 61.012 61.111 0.00 0.00 38.91 4.52
4386 12085 2.382770 TGGGCGTAGGGATGGCAAT 61.383 57.895 0.00 0.00 38.91 3.56
4387 12086 1.898574 GGGCGTAGGGATGGCAATG 60.899 63.158 0.00 0.00 38.91 2.82
4388 12087 1.898574 GGCGTAGGGATGGCAATGG 60.899 63.158 0.00 0.00 37.11 3.16
4389 12088 1.148273 GCGTAGGGATGGCAATGGA 59.852 57.895 0.00 0.00 0.00 3.41
4390 12089 0.250901 GCGTAGGGATGGCAATGGAT 60.251 55.000 0.00 0.00 0.00 3.41
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 6.239430 GGTGCTAGATACATCCATTTGAGAGA 60.239 42.308 0.00 0.00 0.00 3.10
2 3 5.366477 TGGTGCTAGATACATCCATTTGAGA 59.634 40.000 0.00 0.00 0.00 3.27
5 6 6.698008 TTTGGTGCTAGATACATCCATTTG 57.302 37.500 0.00 0.00 0.00 2.32
6 7 7.902920 AATTTGGTGCTAGATACATCCATTT 57.097 32.000 0.00 0.00 0.00 2.32
7 8 8.220559 ACTAATTTGGTGCTAGATACATCCATT 58.779 33.333 0.00 0.00 0.00 3.16
8 9 7.663081 CACTAATTTGGTGCTAGATACATCCAT 59.337 37.037 0.00 0.00 0.00 3.41
9 10 6.992123 CACTAATTTGGTGCTAGATACATCCA 59.008 38.462 0.00 0.00 0.00 3.41
10 11 7.426929 CACTAATTTGGTGCTAGATACATCC 57.573 40.000 0.00 0.00 0.00 3.51
33 34 8.712463 TTGTTTCTCAAATGGATGCATCTAGCA 61.712 37.037 25.28 15.62 44.90 3.49
34 35 5.066893 TGTTTCTCAAATGGATGCATCTAGC 59.933 40.000 25.28 10.32 45.96 3.42
35 36 6.688637 TGTTTCTCAAATGGATGCATCTAG 57.311 37.500 25.28 8.89 0.00 2.43
36 37 6.405065 GCTTGTTTCTCAAATGGATGCATCTA 60.405 38.462 25.28 20.79 35.48 1.98
37 38 5.623824 GCTTGTTTCTCAAATGGATGCATCT 60.624 40.000 25.28 4.53 35.48 2.90
38 39 4.565564 GCTTGTTTCTCAAATGGATGCATC 59.434 41.667 18.81 18.81 35.48 3.91
39 40 4.222145 AGCTTGTTTCTCAAATGGATGCAT 59.778 37.500 0.00 0.00 35.48 3.96
40 41 3.575256 AGCTTGTTTCTCAAATGGATGCA 59.425 39.130 0.00 0.00 35.48 3.96
41 42 4.184079 AGCTTGTTTCTCAAATGGATGC 57.816 40.909 0.00 0.00 35.48 3.91
42 43 4.927425 CCAAGCTTGTTTCTCAAATGGATG 59.073 41.667 24.35 0.00 36.92 3.51
43 44 4.020839 CCCAAGCTTGTTTCTCAAATGGAT 60.021 41.667 24.35 0.00 36.92 3.41
44 45 3.321682 CCCAAGCTTGTTTCTCAAATGGA 59.678 43.478 24.35 0.00 36.92 3.41
45 46 3.321682 TCCCAAGCTTGTTTCTCAAATGG 59.678 43.478 24.35 14.01 35.48 3.16
46 47 4.202141 TGTCCCAAGCTTGTTTCTCAAATG 60.202 41.667 24.35 5.47 35.48 2.32
47 48 3.960102 TGTCCCAAGCTTGTTTCTCAAAT 59.040 39.130 24.35 0.00 35.48 2.32
48 49 3.360867 TGTCCCAAGCTTGTTTCTCAAA 58.639 40.909 24.35 0.00 35.48 2.69
49 50 3.011566 TGTCCCAAGCTTGTTTCTCAA 57.988 42.857 24.35 1.41 34.61 3.02
50 51 2.727123 TGTCCCAAGCTTGTTTCTCA 57.273 45.000 24.35 12.85 0.00 3.27
51 52 2.287849 GCTTGTCCCAAGCTTGTTTCTC 60.288 50.000 24.35 10.65 40.01 2.87
52 53 1.683385 GCTTGTCCCAAGCTTGTTTCT 59.317 47.619 24.35 0.00 40.01 2.52
53 54 2.140065 GCTTGTCCCAAGCTTGTTTC 57.860 50.000 24.35 13.85 40.01 2.78
60 61 1.602920 CCGAAAAAGCTTGTCCCAAGC 60.603 52.381 18.69 18.69 43.31 4.01
61 62 1.953686 TCCGAAAAAGCTTGTCCCAAG 59.046 47.619 0.00 0.00 0.00 3.61
62 63 1.679153 GTCCGAAAAAGCTTGTCCCAA 59.321 47.619 0.00 0.00 0.00 4.12
63 64 1.314730 GTCCGAAAAAGCTTGTCCCA 58.685 50.000 0.00 0.00 0.00 4.37
64 65 0.237498 CGTCCGAAAAAGCTTGTCCC 59.763 55.000 0.00 0.00 0.00 4.46
65 66 0.237498 CCGTCCGAAAAAGCTTGTCC 59.763 55.000 0.00 0.00 0.00 4.02
66 67 1.194772 CTCCGTCCGAAAAAGCTTGTC 59.805 52.381 0.00 0.00 0.00 3.18
67 68 1.226746 CTCCGTCCGAAAAAGCTTGT 58.773 50.000 0.00 0.00 0.00 3.16
68 69 0.517316 CCTCCGTCCGAAAAAGCTTG 59.483 55.000 0.00 0.00 0.00 4.01
69 70 0.605589 CCCTCCGTCCGAAAAAGCTT 60.606 55.000 0.00 0.00 0.00 3.74
70 71 1.003718 CCCTCCGTCCGAAAAAGCT 60.004 57.895 0.00 0.00 0.00 3.74
71 72 1.004200 TCCCTCCGTCCGAAAAAGC 60.004 57.895 0.00 0.00 0.00 3.51
72 73 0.320697 ACTCCCTCCGTCCGAAAAAG 59.679 55.000 0.00 0.00 0.00 2.27
73 74 1.631405 TACTCCCTCCGTCCGAAAAA 58.369 50.000 0.00 0.00 0.00 1.94
74 75 1.856629 ATACTCCCTCCGTCCGAAAA 58.143 50.000 0.00 0.00 0.00 2.29
75 76 1.856629 AATACTCCCTCCGTCCGAAA 58.143 50.000 0.00 0.00 0.00 3.46
76 77 1.753073 GAAATACTCCCTCCGTCCGAA 59.247 52.381 0.00 0.00 0.00 4.30
77 78 1.064166 AGAAATACTCCCTCCGTCCGA 60.064 52.381 0.00 0.00 0.00 4.55
78 79 1.400737 AGAAATACTCCCTCCGTCCG 58.599 55.000 0.00 0.00 0.00 4.79
79 80 3.564264 ACTAGAAATACTCCCTCCGTCC 58.436 50.000 0.00 0.00 0.00 4.79
80 81 6.897706 AATACTAGAAATACTCCCTCCGTC 57.102 41.667 0.00 0.00 0.00 4.79
81 82 7.949006 ACATAATACTAGAAATACTCCCTCCGT 59.051 37.037 0.00 0.00 0.00 4.69
82 83 8.350852 ACATAATACTAGAAATACTCCCTCCG 57.649 38.462 0.00 0.00 0.00 4.63
83 84 9.310449 TGACATAATACTAGAAATACTCCCTCC 57.690 37.037 0.00 0.00 0.00 4.30
85 86 9.884814 AGTGACATAATACTAGAAATACTCCCT 57.115 33.333 0.00 0.00 0.00 4.20
223 224 5.343058 CGAATCCATTTGCACAGTTAGTTTG 59.657 40.000 0.00 0.00 0.00 2.93
336 347 6.808321 AAGCCTTATACCTATTGTCAGTCA 57.192 37.500 0.00 0.00 0.00 3.41
509 537 9.859427 CAACAACCATGACATATTTCAGTTTAT 57.141 29.630 0.00 0.00 0.00 1.40
543 573 9.344772 ACACTGTTGGTATTCTTTTGTGTATTA 57.655 29.630 0.00 0.00 34.88 0.98
612 652 8.175716 GCCAGTTAATACAAGTCATGTTAAGTC 58.824 37.037 0.00 0.00 43.63 3.01
624 664 8.856247 GGAAAAATAAACGCCAGTTAATACAAG 58.144 33.333 0.00 0.00 40.18 3.16
719 759 3.378112 CGTGGGCATGATCAAAGTATTGT 59.622 43.478 0.00 0.00 37.79 2.71
720 760 3.793129 GCGTGGGCATGATCAAAGTATTG 60.793 47.826 0.00 0.00 39.62 1.90
761 823 1.174783 GCGTGGTGGAGACTCTAGAA 58.825 55.000 1.74 0.00 0.00 2.10
766 828 1.228657 GGTTTGCGTGGTGGAGACTC 61.229 60.000 0.00 0.00 0.00 3.36
839 906 4.682860 GTGGAAAACTGTGAAGCATCAATG 59.317 41.667 0.00 0.00 37.30 2.82
840 907 4.262164 GGTGGAAAACTGTGAAGCATCAAT 60.262 41.667 0.00 0.00 37.30 2.57
849 916 1.746220 CAAACCGGTGGAAAACTGTGA 59.254 47.619 8.52 0.00 32.74 3.58
937 1006 6.723298 ACTACAGATATAAGTGCTCAAGCT 57.277 37.500 3.32 0.00 42.66 3.74
966 1035 0.743097 GATGGCAAACCTGAGGATGC 59.257 55.000 20.40 20.40 37.95 3.91
1103 1181 3.568538 CCATTTTTGGAGACGAGCTTTG 58.431 45.455 0.00 0.00 0.00 2.77
1104 1182 2.029918 GCCATTTTTGGAGACGAGCTTT 60.030 45.455 0.00 0.00 0.00 3.51
1131 1209 1.100463 TGTTGAAGAAGCCAAGCGCA 61.100 50.000 11.47 0.00 41.38 6.09
1151 1229 1.466851 GGAGGGTTTGCTGCTGCTTT 61.467 55.000 17.00 0.00 40.48 3.51
1215 1293 2.556622 CCACGCAGAAGTAAATTTGGGT 59.443 45.455 0.00 0.00 37.21 4.51
1233 1311 3.380320 GTGTATCCCTATTTGCAACCCAC 59.620 47.826 0.00 0.00 0.00 4.61
1355 1433 6.040842 AGTGGTGCTATTTCTTGTGATGTTTT 59.959 34.615 0.00 0.00 0.00 2.43
1397 1475 7.637511 AGAGTCTGTTAGGATGAAATTTCCAT 58.362 34.615 15.48 8.91 35.59 3.41
2269 2354 4.974399 AGGTAAAGAGTTTCTCCAGTTGG 58.026 43.478 0.00 0.00 0.00 3.77
2508 2597 4.942761 ATCTGTGAATTTTGTTGTGGCT 57.057 36.364 0.00 0.00 0.00 4.75
2674 2763 6.237313 ACCGACAAGCTTAACTAAATTGAC 57.763 37.500 0.00 0.00 0.00 3.18
2958 3047 2.243736 TCGGCTAAATTCCCTTCCCAAT 59.756 45.455 0.00 0.00 0.00 3.16
3444 8087 9.601810 ACATCTGTATTATAACATCTCCAGGTA 57.398 33.333 0.00 0.00 0.00 3.08
3580 8235 7.956420 ACGACAATACTGAGTACATTCAAAA 57.044 32.000 0.00 0.00 0.00 2.44
3635 8900 1.789523 TCTAGTTTCCCTATGGCGCT 58.210 50.000 7.64 0.00 0.00 5.92
3706 8971 8.958060 AACATACACATATCCCTAGACTATGT 57.042 34.615 0.00 0.00 36.72 2.29
3710 8975 9.742144 CTAGTAACATACACATATCCCTAGACT 57.258 37.037 0.00 0.00 0.00 3.24
3711 8976 9.517868 ACTAGTAACATACACATATCCCTAGAC 57.482 37.037 0.00 0.00 0.00 2.59
3713 8978 9.298250 ACACTAGTAACATACACATATCCCTAG 57.702 37.037 0.00 0.00 0.00 3.02
3716 8981 9.856488 CATACACTAGTAACATACACATATCCC 57.144 37.037 0.00 0.00 33.13 3.85
3726 8991 9.910267 TGGAGAGTAACATACACTAGTAACATA 57.090 33.333 0.00 0.00 33.13 2.29
3728 8993 8.818622 ATGGAGAGTAACATACACTAGTAACA 57.181 34.615 0.00 0.00 33.13 2.41
3729 8994 9.517609 CAATGGAGAGTAACATACACTAGTAAC 57.482 37.037 0.00 0.00 33.13 2.50
3730 8995 9.251440 ACAATGGAGAGTAACATACACTAGTAA 57.749 33.333 0.00 0.00 33.13 2.24
3735 9000 5.734720 CCACAATGGAGAGTAACATACACT 58.265 41.667 0.00 0.00 40.96 3.55
3736 9001 4.332819 GCCACAATGGAGAGTAACATACAC 59.667 45.833 0.00 0.00 40.96 2.90
3737 9002 4.225042 AGCCACAATGGAGAGTAACATACA 59.775 41.667 0.00 0.00 40.96 2.29
3738 9003 4.770795 AGCCACAATGGAGAGTAACATAC 58.229 43.478 0.00 0.00 40.96 2.39
3739 9004 5.661312 ACTAGCCACAATGGAGAGTAACATA 59.339 40.000 0.00 0.00 40.96 2.29
3740 9005 4.471386 ACTAGCCACAATGGAGAGTAACAT 59.529 41.667 0.00 0.00 40.96 2.71
3741 9006 3.838317 ACTAGCCACAATGGAGAGTAACA 59.162 43.478 0.00 0.00 40.96 2.41
3744 9009 3.954904 GAGACTAGCCACAATGGAGAGTA 59.045 47.826 0.00 0.00 40.96 2.59
3745 9010 2.763448 GAGACTAGCCACAATGGAGAGT 59.237 50.000 0.00 0.46 40.96 3.24
3746 9011 2.762887 TGAGACTAGCCACAATGGAGAG 59.237 50.000 0.00 0.00 40.96 3.20
3748 9013 2.234661 TGTGAGACTAGCCACAATGGAG 59.765 50.000 9.80 0.00 40.96 3.86
3751 9016 5.413833 AGAAAATGTGAGACTAGCCACAATG 59.586 40.000 14.48 0.00 45.08 2.82
3752 9017 5.564550 AGAAAATGTGAGACTAGCCACAAT 58.435 37.500 14.48 6.35 45.08 2.71
3753 9018 4.973168 AGAAAATGTGAGACTAGCCACAA 58.027 39.130 14.48 2.77 45.08 3.33
3754 9019 4.563580 GGAGAAAATGTGAGACTAGCCACA 60.564 45.833 13.32 13.32 45.85 4.17
3755 9020 3.935828 GGAGAAAATGTGAGACTAGCCAC 59.064 47.826 0.00 0.00 0.00 5.01
3756 9021 3.368427 CGGAGAAAATGTGAGACTAGCCA 60.368 47.826 0.00 0.00 0.00 4.75
3757 9022 3.190874 CGGAGAAAATGTGAGACTAGCC 58.809 50.000 0.00 0.00 0.00 3.93
3758 9023 2.605366 GCGGAGAAAATGTGAGACTAGC 59.395 50.000 0.00 0.00 0.00 3.42
3759 9024 4.116747 AGCGGAGAAAATGTGAGACTAG 57.883 45.455 0.00 0.00 0.00 2.57
3760 9025 4.537135 AAGCGGAGAAAATGTGAGACTA 57.463 40.909 0.00 0.00 0.00 2.59
3761 9026 3.409026 AAGCGGAGAAAATGTGAGACT 57.591 42.857 0.00 0.00 0.00 3.24
3762 9027 3.994392 TGTAAGCGGAGAAAATGTGAGAC 59.006 43.478 0.00 0.00 0.00 3.36
3763 9028 4.265904 TGTAAGCGGAGAAAATGTGAGA 57.734 40.909 0.00 0.00 0.00 3.27
3764 9029 4.213270 TGTTGTAAGCGGAGAAAATGTGAG 59.787 41.667 0.00 0.00 0.00 3.51
3802 9095 1.439679 CGAGCAAGGGTGAAACTACC 58.560 55.000 0.00 0.00 40.10 3.18
3822 9115 0.170561 GCAGTCTTGCTTGCCATCAG 59.829 55.000 0.00 0.00 46.95 2.90
3845 9138 2.545946 GTGAGTTTCTGTGCAACCTCTC 59.454 50.000 0.00 0.00 34.36 3.20
3988 9283 1.878522 CGGTCTCATAGTGCGCCAC 60.879 63.158 4.18 3.02 34.10 5.01
4032 9353 1.522569 GAGGTGAGGTTGGGATCGG 59.477 63.158 0.00 0.00 0.00 4.18
4068 9389 2.703798 CCAGCGAGTTTGCCCATGG 61.704 63.158 4.14 4.14 34.65 3.66
4122 9443 1.964373 GACTTTCCTTGCCCGCGAA 60.964 57.895 8.23 0.00 0.00 4.70
4125 9446 3.431725 CCGACTTTCCTTGCCCGC 61.432 66.667 0.00 0.00 0.00 6.13


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

AutoCloner maintained by Alex Coulton.