Multiple sequence alignment - TraesCS6D01G274600

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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 TraesCS6D01G274600 chr6D 100.000 3759 0 0 1 3759 383229248 383225490 0.000000e+00 6942.0
1 TraesCS6D01G274600 chr6B 93.093 2389 120 28 181 2529 573415968 573413585 0.000000e+00 3456.0
2 TraesCS6D01G274600 chr6B 86.826 1169 66 34 2635 3759 573413584 573412460 0.000000e+00 1225.0
3 TraesCS6D01G274600 chr6A 95.917 2131 52 11 659 2781 525031476 525029373 0.000000e+00 3421.0
4 TraesCS6D01G274600 chr6A 88.086 789 38 13 2878 3648 525029208 525028458 0.000000e+00 885.0
5 TraesCS6D01G274600 chr6A 84.549 576 81 6 45 615 525032127 525031555 7.050000e-157 564.0
6 TraesCS6D01G274600 chr6A 89.873 158 6 4 3604 3759 525028465 525028316 1.070000e-45 195.0
7 TraesCS6D01G274600 chr6A 94.309 123 6 1 1300 1422 74321334 74321213 1.780000e-43 187.0
8 TraesCS6D01G274600 chr6A 100.000 41 0 0 1 41 345616407 345616447 4.030000e-10 76.8
9 TraesCS6D01G274600 chr1B 90.595 1361 104 12 1193 2549 645142627 645141287 0.000000e+00 1783.0
10 TraesCS6D01G274600 chr1B 100.000 41 0 0 1 41 461451342 461451382 4.030000e-10 76.8
11 TraesCS6D01G274600 chr1A 90.318 1322 113 9 1193 2511 559707901 559706592 0.000000e+00 1718.0
12 TraesCS6D01G274600 chr1A 79.304 575 74 25 41 574 27746147 27746717 9.930000e-96 361.0
13 TraesCS6D01G274600 chr1A 100.000 41 0 0 1 41 334077802 334077762 4.030000e-10 76.8
14 TraesCS6D01G274600 chr1D 89.625 1359 117 12 1195 2549 467439116 467437778 0.000000e+00 1707.0
15 TraesCS6D01G274600 chr7D 84.846 1366 176 22 1161 2506 166514266 166512912 0.000000e+00 1347.0
16 TraesCS6D01G274600 chr7D 79.920 503 65 22 45 512 512738208 512737707 1.670000e-88 337.0
17 TraesCS6D01G274600 chr7B 84.053 1367 185 22 1161 2506 130747280 130745926 0.000000e+00 1286.0
18 TraesCS6D01G274600 chr4A 81.656 1401 212 37 1127 2506 24557536 24556160 0.000000e+00 1122.0
19 TraesCS6D01G274600 chr4D 81.912 1360 209 28 1161 2503 443206611 443207950 0.000000e+00 1114.0
20 TraesCS6D01G274600 chr4D 78.534 573 91 15 45 588 351524669 351524100 7.730000e-92 348.0
21 TraesCS6D01G274600 chr4D 81.597 288 47 6 291 575 504113028 504113312 2.260000e-57 233.0
22 TraesCS6D01G274600 chr4D 100.000 41 0 0 1 41 123366762 123366802 4.030000e-10 76.8
23 TraesCS6D01G274600 chr4D 100.000 41 0 0 1 41 123577708 123577748 4.030000e-10 76.8
24 TraesCS6D01G274600 chr3B 78.523 596 104 14 45 617 12130412 12129818 1.650000e-98 370.0
25 TraesCS6D01G274600 chr7A 84.682 346 45 6 45 387 476941738 476942078 4.650000e-89 339.0
26 TraesCS6D01G274600 chr3A 78.299 576 90 22 45 587 696398721 696398148 4.650000e-89 339.0
27 TraesCS6D01G274600 chr3A 83.500 200 29 2 291 489 609378557 609378753 2.310000e-42 183.0
28 TraesCS6D01G274600 chr3D 80.417 480 56 6 45 489 465999137 465999613 7.780000e-87 331.0
29 TraesCS6D01G274600 chr3D 88.664 247 27 1 45 290 431224107 431223861 2.190000e-77 300.0
30 TraesCS6D01G274600 chr3D 82.069 290 44 8 290 574 431223831 431223545 1.350000e-59 241.0
31 TraesCS6D01G274600 chr3D 100.000 41 0 0 1 41 202611066 202611106 4.030000e-10 76.8
32 TraesCS6D01G274600 chr2A 89.300 243 25 1 45 286 324299525 324299767 1.700000e-78 303.0
33 TraesCS6D01G274600 chr5B 79.791 287 50 8 294 574 502031675 502031391 6.370000e-48 202.0
34 TraesCS6D01G274600 chr5D 79.926 269 47 4 291 559 515836608 515836869 1.380000e-44 191.0
35 TraesCS6D01G274600 chrUn 100.000 41 0 0 1 41 231485288 231485248 4.030000e-10 76.8
36 TraesCS6D01G274600 chrUn 100.000 41 0 0 1 41 244847814 244847854 4.030000e-10 76.8
37 TraesCS6D01G274600 chrUn 100.000 41 0 0 1 41 422109038 422109078 4.030000e-10 76.8


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 TraesCS6D01G274600 chr6D 383225490 383229248 3758 True 6942.00 6942 100.00000 1 3759 1 chr6D.!!$R1 3758
1 TraesCS6D01G274600 chr6B 573412460 573415968 3508 True 2340.50 3456 89.95950 181 3759 2 chr6B.!!$R1 3578
2 TraesCS6D01G274600 chr6A 525028316 525032127 3811 True 1266.25 3421 89.60625 45 3759 4 chr6A.!!$R2 3714
3 TraesCS6D01G274600 chr1B 645141287 645142627 1340 True 1783.00 1783 90.59500 1193 2549 1 chr1B.!!$R1 1356
4 TraesCS6D01G274600 chr1A 559706592 559707901 1309 True 1718.00 1718 90.31800 1193 2511 1 chr1A.!!$R2 1318
5 TraesCS6D01G274600 chr1A 27746147 27746717 570 False 361.00 361 79.30400 41 574 1 chr1A.!!$F1 533
6 TraesCS6D01G274600 chr1D 467437778 467439116 1338 True 1707.00 1707 89.62500 1195 2549 1 chr1D.!!$R1 1354
7 TraesCS6D01G274600 chr7D 166512912 166514266 1354 True 1347.00 1347 84.84600 1161 2506 1 chr7D.!!$R1 1345
8 TraesCS6D01G274600 chr7D 512737707 512738208 501 True 337.00 337 79.92000 45 512 1 chr7D.!!$R2 467
9 TraesCS6D01G274600 chr7B 130745926 130747280 1354 True 1286.00 1286 84.05300 1161 2506 1 chr7B.!!$R1 1345
10 TraesCS6D01G274600 chr4A 24556160 24557536 1376 True 1122.00 1122 81.65600 1127 2506 1 chr4A.!!$R1 1379
11 TraesCS6D01G274600 chr4D 443206611 443207950 1339 False 1114.00 1114 81.91200 1161 2503 1 chr4D.!!$F3 1342
12 TraesCS6D01G274600 chr4D 351524100 351524669 569 True 348.00 348 78.53400 45 588 1 chr4D.!!$R1 543
13 TraesCS6D01G274600 chr3B 12129818 12130412 594 True 370.00 370 78.52300 45 617 1 chr3B.!!$R1 572
14 TraesCS6D01G274600 chr3A 696398148 696398721 573 True 339.00 339 78.29900 45 587 1 chr3A.!!$R1 542
15 TraesCS6D01G274600 chr3D 431223545 431224107 562 True 270.50 300 85.36650 45 574 2 chr3D.!!$R1 529

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
634 737 0.109412 GGTTCGATCAAGACGGACGT 60.109 55.0 0.00 0.0 39.77 4.34 F
657 760 0.321387 TGGTTTGCGGCACCGTATTA 60.321 50.0 11.27 0.0 42.09 0.98 F
2529 2676 0.112412 CTAACCAACCCAACCCAGCT 59.888 55.0 0.00 0.0 0.00 4.24 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2511 2657 0.111639 GAGCTGGGTTGGGTTGGTTA 59.888 55.000 0.00 0.0 0.00 2.85 R
2559 2706 0.179105 TGTGTACGAGCCAACGTGTT 60.179 50.000 10.59 0.0 46.02 3.32 R
3454 3732 2.833582 GGAGGACCGGATGAGCGA 60.834 66.667 9.46 0.0 0.00 4.93 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 6.135290 CAAATCAGGTGACTTTGAAGTTGA 57.865 37.500 0.00 0.00 39.88 3.18
24 25 6.563422 CAAATCAGGTGACTTTGAAGTTGAA 58.437 36.000 0.00 0.00 39.88 2.69
25 26 6.382869 AATCAGGTGACTTTGAAGTTGAAG 57.617 37.500 0.00 0.00 39.88 3.02
26 27 3.627577 TCAGGTGACTTTGAAGTTGAAGC 59.372 43.478 0.00 0.00 39.88 3.86
27 28 3.629398 CAGGTGACTTTGAAGTTGAAGCT 59.371 43.478 0.00 0.62 39.88 3.74
28 29 4.096984 CAGGTGACTTTGAAGTTGAAGCTT 59.903 41.667 0.00 0.00 39.88 3.74
29 30 4.096984 AGGTGACTTTGAAGTTGAAGCTTG 59.903 41.667 2.10 0.00 39.88 4.01
30 31 3.793492 GTGACTTTGAAGTTGAAGCTTGC 59.207 43.478 2.10 0.00 39.88 4.01
31 32 3.181487 TGACTTTGAAGTTGAAGCTTGCC 60.181 43.478 2.10 0.00 39.88 4.52
32 33 2.101415 ACTTTGAAGTTGAAGCTTGCCC 59.899 45.455 2.10 0.00 35.21 5.36
33 34 0.667993 TTGAAGTTGAAGCTTGCCCG 59.332 50.000 2.10 0.00 0.00 6.13
34 35 1.081175 GAAGTTGAAGCTTGCCCGC 60.081 57.895 2.10 0.00 0.00 6.13
35 36 1.795170 GAAGTTGAAGCTTGCCCGCA 61.795 55.000 2.10 0.00 0.00 5.69
36 37 1.799258 AAGTTGAAGCTTGCCCGCAG 61.799 55.000 2.10 0.00 0.00 5.18
37 38 2.112928 TTGAAGCTTGCCCGCAGA 59.887 55.556 2.10 0.00 0.00 4.26
38 39 1.528076 TTGAAGCTTGCCCGCAGAA 60.528 52.632 2.10 0.00 0.00 3.02
39 40 1.795170 TTGAAGCTTGCCCGCAGAAC 61.795 55.000 2.10 0.00 0.00 3.01
40 41 3.314388 GAAGCTTGCCCGCAGAACG 62.314 63.158 2.10 0.00 43.15 3.95
43 44 3.793144 CTTGCCCGCAGAACGCTC 61.793 66.667 0.00 0.00 41.76 5.03
87 88 3.365364 CGAGCCCTTGAAATTGAGAACAC 60.365 47.826 0.00 0.00 0.00 3.32
144 145 1.856802 CATCATCGCCGTCTCATTGA 58.143 50.000 0.00 0.00 0.00 2.57
155 156 3.444034 CCGTCTCATTGAAGTACTCCTCA 59.556 47.826 0.00 0.00 0.00 3.86
208 212 7.520451 ACTGCTCGTATATGTACTCCAAATA 57.480 36.000 0.00 0.00 0.00 1.40
239 243 6.127786 CCATTGCTAGAAAGAAGAAGGGAAAG 60.128 42.308 0.00 0.00 0.00 2.62
351 387 4.341783 AGCCTTGCTGGAGCGCTT 62.342 61.111 13.26 0.00 45.83 4.68
382 418 1.002888 AGACGTAGACTTCCGACAGGA 59.997 52.381 0.00 0.00 46.75 3.86
417 457 0.541392 CGGGATGATGGAGTGGTGAA 59.459 55.000 0.00 0.00 0.00 3.18
426 466 1.214175 TGGAGTGGTGAAGAAGGCAAA 59.786 47.619 0.00 0.00 0.00 3.68
439 479 3.571828 AGAAGGCAAAAGAGAAAGAAGGC 59.428 43.478 0.00 0.00 0.00 4.35
452 492 7.684529 AGAGAAAGAAGGCAGAAGAGAAAATA 58.315 34.615 0.00 0.00 0.00 1.40
467 507 3.788142 AGAAAATAGGGAGGATGAAGGCA 59.212 43.478 0.00 0.00 0.00 4.75
471 512 2.367202 GGGAGGATGAAGGCACGGA 61.367 63.158 0.00 0.00 0.00 4.69
489 531 1.272258 GGATTCGGGAAGGGTTTTGGA 60.272 52.381 0.00 0.00 0.00 3.53
501 543 1.853095 TTTTGGATGGACCGGGGGA 60.853 57.895 6.32 0.00 42.61 4.81
538 580 2.997897 GGTGTCCGGACTCCTGCT 60.998 66.667 37.12 0.00 40.71 4.24
550 594 3.567397 GACTCCTGCTAACCTCCTCATA 58.433 50.000 0.00 0.00 0.00 2.15
555 599 4.721776 TCCTGCTAACCTCCTCATATTTGT 59.278 41.667 0.00 0.00 0.00 2.83
556 600 5.059833 CCTGCTAACCTCCTCATATTTGTC 58.940 45.833 0.00 0.00 0.00 3.18
561 605 4.927978 ACCTCCTCATATTTGTCTCGAG 57.072 45.455 5.93 5.93 0.00 4.04
564 608 5.187967 ACCTCCTCATATTTGTCTCGAGTTT 59.812 40.000 13.13 0.00 0.00 2.66
565 609 6.380274 ACCTCCTCATATTTGTCTCGAGTTTA 59.620 38.462 13.13 0.00 0.00 2.01
591 635 4.828829 AGAAAATGTATCCGAACCGTCTT 58.171 39.130 0.00 0.00 0.00 3.01
595 640 1.001068 TGTATCCGAACCGTCTTGCAA 59.999 47.619 0.00 0.00 0.00 4.08
597 642 1.821216 ATCCGAACCGTCTTGCAAAT 58.179 45.000 0.00 0.00 0.00 2.32
620 687 0.386352 TACAGTCTCGCGTTGGTTCG 60.386 55.000 5.77 0.00 0.00 3.95
624 727 0.731514 GTCTCGCGTTGGTTCGATCA 60.732 55.000 5.77 0.00 33.98 2.92
634 737 0.109412 GGTTCGATCAAGACGGACGT 60.109 55.000 0.00 0.00 39.77 4.34
644 747 2.203098 ACGGACGTGGGTGGTTTG 60.203 61.111 0.00 0.00 0.00 2.93
654 757 2.973600 GTGGTTTGCGGCACCGTA 60.974 61.111 11.27 2.77 42.09 4.02
657 760 0.321387 TGGTTTGCGGCACCGTATTA 60.321 50.000 11.27 0.00 42.09 0.98
673 780 4.202326 CCGTATTAAAGATGCCCTACCTGT 60.202 45.833 0.00 0.00 0.00 4.00
858 965 0.901124 CCTCTGCCTGCTTCTGTAGT 59.099 55.000 0.00 0.00 0.00 2.73
1016 1125 2.956987 CCAAAGCTGCTCCCAACG 59.043 61.111 1.00 0.00 0.00 4.10
2511 2657 1.202746 GCTCAAGCATTAGCCTAGCCT 60.203 52.381 0.00 0.00 43.56 4.58
2524 2671 1.340697 CCTAGCCTAACCAACCCAACC 60.341 57.143 0.00 0.00 0.00 3.77
2529 2676 0.112412 CTAACCAACCCAACCCAGCT 59.888 55.000 0.00 0.00 0.00 4.24
2559 2706 2.055838 GTCTCGTGCACATTCGTACAA 58.944 47.619 18.64 0.00 0.00 2.41
2608 2755 0.036952 CACACTCCAGTAGCCACCAG 60.037 60.000 0.00 0.00 0.00 4.00
2638 2785 3.719173 GCACTAGCTAAGGGTGACTAG 57.281 52.381 14.08 0.00 38.44 2.57
2639 2786 2.223852 GCACTAGCTAAGGGTGACTAGC 60.224 54.545 14.08 0.00 36.41 3.42
2640 2787 3.292460 CACTAGCTAAGGGTGACTAGCT 58.708 50.000 9.38 9.38 46.34 3.32
2641 2788 4.462133 CACTAGCTAAGGGTGACTAGCTA 58.538 47.826 10.44 10.44 43.30 3.32
2642 2789 4.888239 CACTAGCTAAGGGTGACTAGCTAA 59.112 45.833 11.58 0.23 44.47 3.09
2645 2792 6.716173 ACTAGCTAAGGGTGACTAGCTAATAC 59.284 42.308 11.58 0.00 44.47 1.89
2654 2801 9.114938 AGGGTGACTAGCTAATACTACTACTAT 57.885 37.037 0.00 0.00 0.00 2.12
2682 2829 0.179179 GACCCGTGCTCTGTACGTAC 60.179 60.000 18.90 18.90 39.80 3.67
2683 2830 1.226211 CCCGTGCTCTGTACGTACG 60.226 63.158 20.18 15.01 39.80 3.67
2684 2831 1.499056 CCGTGCTCTGTACGTACGT 59.501 57.895 25.98 25.98 39.80 3.57
2685 2832 0.721154 CCGTGCTCTGTACGTACGTA 59.279 55.000 23.60 23.60 39.80 3.57
2781 2930 3.874193 GCTTCTCCCTTTTACTTCCCCTG 60.874 52.174 0.00 0.00 0.00 4.45
2782 2931 1.633945 TCTCCCTTTTACTTCCCCTGC 59.366 52.381 0.00 0.00 0.00 4.85
2831 3085 0.675837 AAGACGTGAGATCCCGACGA 60.676 55.000 13.84 0.00 36.90 4.20
2851 3105 1.838077 AGCGATGGTAGCTAGGGTTTT 59.162 47.619 0.00 0.00 44.05 2.43
2866 3120 4.703799 TTTGTGCATGCGCTGGCG 62.704 61.111 29.79 10.80 44.10 5.69
2899 3153 1.187567 AGGGTTTGCATTGGAGCACC 61.188 55.000 0.00 0.00 45.61 5.01
2904 3158 0.035152 TTGCATTGGAGCACCGATCT 60.035 50.000 0.00 0.00 45.61 2.75
2941 3195 1.374631 GTGCTGTGCTCCATCGACA 60.375 57.895 0.00 0.00 0.00 4.35
2959 3213 1.960763 AATGCTCGTGCTTGTGCGA 60.961 52.632 11.19 0.00 43.34 5.10
2999 3253 1.264288 CTTGGTTGCTTCGGTCACTTC 59.736 52.381 0.00 0.00 0.00 3.01
3034 3288 3.741344 ACACTCGTTAGTCGTTACGTACT 59.259 43.478 4.24 9.52 40.80 2.73
3145 3405 0.685458 ATGTTCTTGCCATCCCTGCC 60.685 55.000 0.00 0.00 0.00 4.85
3174 3434 5.634896 GTCCTACGAGTTAATGAAACGAGA 58.365 41.667 0.00 0.00 43.29 4.04
3177 3437 5.966503 CCTACGAGTTAATGAAACGAGAGAG 59.033 44.000 0.00 0.00 43.29 3.20
3195 3466 3.468266 GAGAGAGAGCTGGCTCGCG 62.468 68.421 17.64 0.00 46.90 5.87
3243 3521 0.263765 CCTACCTACCTACCCAGCCA 59.736 60.000 0.00 0.00 0.00 4.75
3253 3531 0.987613 TACCCAGCCATGCTCCATCA 60.988 55.000 0.00 0.00 36.40 3.07
3254 3532 1.076559 CCCAGCCATGCTCCATCAA 60.077 57.895 0.00 0.00 36.40 2.57
3255 3533 0.469331 CCCAGCCATGCTCCATCAAT 60.469 55.000 0.00 0.00 36.40 2.57
3256 3534 1.410004 CCAGCCATGCTCCATCAATT 58.590 50.000 0.00 0.00 36.40 2.32
3316 3594 1.139734 CACCGGACGGATCAGACTG 59.860 63.158 18.80 0.00 38.96 3.51
3317 3595 2.105128 CCGGACGGATCAGACTGC 59.895 66.667 4.40 0.00 37.50 4.40
3318 3596 2.418910 CCGGACGGATCAGACTGCT 61.419 63.158 4.40 0.00 37.50 4.24
3319 3597 1.064946 CGGACGGATCAGACTGCTC 59.935 63.158 0.00 0.00 0.00 4.26
3463 3748 2.588314 CTGCCTGCTCGCTCATCC 60.588 66.667 0.00 0.00 0.00 3.51
3464 3749 4.519437 TGCCTGCTCGCTCATCCG 62.519 66.667 0.00 0.00 0.00 4.18
3471 3756 2.833582 TCGCTCATCCGGTCCTCC 60.834 66.667 0.00 0.00 0.00 4.30
3648 3969 0.734942 GCATGCCATATTGCCATCGC 60.735 55.000 6.36 0.00 32.66 4.58
3707 4035 4.379243 CAGTCCAGCTCGGCCGTT 62.379 66.667 27.15 9.53 33.14 4.44
3708 4036 4.070552 AGTCCAGCTCGGCCGTTC 62.071 66.667 27.15 17.75 33.14 3.95
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 6.135290 TCAACTTCAAAGTCACCTGATTTG 57.865 37.500 0.00 0.00 38.57 2.32
1 2 6.681368 GCTTCAACTTCAAAGTCACCTGATTT 60.681 38.462 0.00 0.00 38.57 2.17
2 3 5.221126 GCTTCAACTTCAAAGTCACCTGATT 60.221 40.000 0.00 0.00 38.57 2.57
3 4 4.276926 GCTTCAACTTCAAAGTCACCTGAT 59.723 41.667 0.00 0.00 38.57 2.90
4 5 3.627577 GCTTCAACTTCAAAGTCACCTGA 59.372 43.478 0.00 0.00 38.57 3.86
5 6 3.629398 AGCTTCAACTTCAAAGTCACCTG 59.371 43.478 0.00 0.00 38.57 4.00
6 7 3.891049 AGCTTCAACTTCAAAGTCACCT 58.109 40.909 0.00 0.00 38.57 4.00
7 8 4.354587 CAAGCTTCAACTTCAAAGTCACC 58.645 43.478 0.00 0.00 38.57 4.02
8 9 3.793492 GCAAGCTTCAACTTCAAAGTCAC 59.207 43.478 0.00 0.00 38.57 3.67
9 10 3.181487 GGCAAGCTTCAACTTCAAAGTCA 60.181 43.478 0.00 0.00 38.57 3.41
10 11 3.375642 GGCAAGCTTCAACTTCAAAGTC 58.624 45.455 0.00 0.00 38.57 3.01
11 12 2.101415 GGGCAAGCTTCAACTTCAAAGT 59.899 45.455 0.00 0.00 42.04 2.66
12 13 2.747436 GGGCAAGCTTCAACTTCAAAG 58.253 47.619 0.00 0.00 0.00 2.77
13 14 1.066908 CGGGCAAGCTTCAACTTCAAA 59.933 47.619 0.00 0.00 0.00 2.69
14 15 0.667993 CGGGCAAGCTTCAACTTCAA 59.332 50.000 0.00 0.00 0.00 2.69
15 16 1.795170 GCGGGCAAGCTTCAACTTCA 61.795 55.000 0.00 0.00 0.00 3.02
16 17 1.081175 GCGGGCAAGCTTCAACTTC 60.081 57.895 0.00 0.00 0.00 3.01
17 18 1.799258 CTGCGGGCAAGCTTCAACTT 61.799 55.000 0.00 0.00 38.13 2.66
18 19 2.203337 TGCGGGCAAGCTTCAACT 60.203 55.556 0.00 0.00 38.13 3.16
19 20 1.795170 TTCTGCGGGCAAGCTTCAAC 61.795 55.000 0.00 0.00 38.13 3.18
20 21 1.528076 TTCTGCGGGCAAGCTTCAA 60.528 52.632 0.00 0.00 38.13 2.69
21 22 2.112928 TTCTGCGGGCAAGCTTCA 59.887 55.556 0.00 0.00 38.13 3.02
22 23 2.563427 GTTCTGCGGGCAAGCTTC 59.437 61.111 0.00 0.00 38.13 3.86
23 24 3.357079 CGTTCTGCGGGCAAGCTT 61.357 61.111 0.00 0.00 38.13 3.74
33 34 2.431601 AGTGCTCGAGCGTTCTGC 60.432 61.111 30.75 16.22 45.83 4.26
34 35 3.760673 GAGTGCTCGAGCGTTCTG 58.239 61.111 30.75 0.00 45.83 3.02
87 88 2.588314 GGAGCATGCAGAGGAGCG 60.588 66.667 21.98 0.00 37.31 5.03
155 156 1.144057 GTCCGACGGCTCATTGGAT 59.856 57.895 9.66 0.00 32.03 3.41
208 212 7.338957 CCTTCTTCTTTCTAGCAATGGATTCTT 59.661 37.037 0.00 0.00 0.00 2.52
239 243 6.667007 ATGTATTGCCAAAGCTAAAAATGC 57.333 33.333 0.00 0.00 40.80 3.56
251 256 4.305769 GCAACTGTTCAATGTATTGCCAA 58.694 39.130 0.00 0.00 37.14 4.52
338 374 2.359107 CCTCAAGCGCTCCAGCAA 60.359 61.111 12.06 0.00 42.21 3.91
351 387 2.046988 TACGTCTCCGTCGCCTCA 60.047 61.111 0.00 0.00 46.28 3.86
356 392 0.373024 GGAAGTCTACGTCTCCGTCG 59.627 60.000 0.00 0.00 46.28 5.12
371 407 1.374758 GCCACACTCCTGTCGGAAG 60.375 63.158 0.00 0.00 39.29 3.46
417 457 3.571828 GCCTTCTTTCTCTTTTGCCTTCT 59.428 43.478 0.00 0.00 0.00 2.85
426 466 5.559148 TTCTCTTCTGCCTTCTTTCTCTT 57.441 39.130 0.00 0.00 0.00 2.85
439 479 6.491714 TCATCCTCCCTATTTTCTCTTCTG 57.508 41.667 0.00 0.00 0.00 3.02
452 492 2.370445 CCGTGCCTTCATCCTCCCT 61.370 63.158 0.00 0.00 0.00 4.20
467 507 0.402887 AAAACCCTTCCCGAATCCGT 59.597 50.000 0.00 0.00 0.00 4.69
471 512 2.456577 CATCCAAAACCCTTCCCGAAT 58.543 47.619 0.00 0.00 0.00 3.34
489 531 2.923634 CTACGACTCCCCCGGTCCAT 62.924 65.000 0.00 0.00 0.00 3.41
538 580 5.892119 ACTCGAGACAAATATGAGGAGGTTA 59.108 40.000 21.68 0.00 0.00 2.85
550 594 4.778534 TCTCCGTAAACTCGAGACAAAT 57.221 40.909 21.68 2.53 0.00 2.32
555 599 5.130292 ACATTTTCTCCGTAAACTCGAGA 57.870 39.130 21.68 0.00 0.00 4.04
556 600 6.198591 GGATACATTTTCTCCGTAAACTCGAG 59.801 42.308 11.84 11.84 0.00 4.04
591 635 2.193447 GCGAGACTGTATCGATTTGCA 58.807 47.619 26.79 0.00 42.76 4.08
595 640 2.451132 CAACGCGAGACTGTATCGATT 58.549 47.619 26.79 16.78 42.76 3.34
597 642 0.098200 CCAACGCGAGACTGTATCGA 59.902 55.000 26.79 0.00 42.76 3.59
620 687 0.736325 CACCCACGTCCGTCTTGATC 60.736 60.000 0.00 0.00 0.00 2.92
624 727 1.974973 AAACCACCCACGTCCGTCTT 61.975 55.000 0.00 0.00 0.00 3.01
644 747 1.333791 GCATCTTTAATACGGTGCCGC 60.334 52.381 10.87 0.00 44.19 6.53
648 751 4.062991 GGTAGGGCATCTTTAATACGGTG 58.937 47.826 0.00 0.00 0.00 4.94
649 752 3.971971 AGGTAGGGCATCTTTAATACGGT 59.028 43.478 0.00 0.00 0.00 4.83
653 756 5.012768 GGCTACAGGTAGGGCATCTTTAATA 59.987 44.000 8.43 0.00 33.87 0.98
654 757 4.202472 GGCTACAGGTAGGGCATCTTTAAT 60.202 45.833 8.43 0.00 33.87 1.40
657 760 1.490910 GGCTACAGGTAGGGCATCTTT 59.509 52.381 8.43 0.00 33.87 2.52
673 780 2.363276 ATGTCGTCCCACCGGCTA 60.363 61.111 0.00 0.00 32.64 3.93
708 815 2.993008 TGCTGGACTGAGCATCCC 59.007 61.111 0.00 0.00 44.16 3.85
858 965 1.667154 CGCCCCGAGAAGAGATCACA 61.667 60.000 0.00 0.00 0.00 3.58
919 1026 3.628032 GGAGGGAGAATTTAAAGAAGCGG 59.372 47.826 0.00 0.00 0.00 5.52
981 1088 2.672996 CTTTGTGGCCTCGTGGGG 60.673 66.667 3.32 0.00 35.12 4.96
1016 1125 0.802222 TCTGTATCGCTTGCGTCTGC 60.802 55.000 14.70 7.92 43.20 4.26
1744 1884 3.335534 ACCACAAGCGCGTTCGAC 61.336 61.111 8.43 0.00 38.10 4.20
2511 2657 0.111639 GAGCTGGGTTGGGTTGGTTA 59.888 55.000 0.00 0.00 0.00 2.85
2559 2706 0.179105 TGTGTACGAGCCAACGTGTT 60.179 50.000 10.59 0.00 46.02 3.32
2629 2776 9.382275 GATAGTAGTAGTATTAGCTAGTCACCC 57.618 40.741 0.00 0.00 0.00 4.61
2630 2777 9.941325 TGATAGTAGTAGTATTAGCTAGTCACC 57.059 37.037 0.00 0.00 0.00 4.02
2637 2784 8.871862 CGATCGTTGATAGTAGTAGTATTAGCT 58.128 37.037 7.03 0.00 0.00 3.32
2638 2785 8.867935 TCGATCGTTGATAGTAGTAGTATTAGC 58.132 37.037 15.94 0.00 0.00 3.09
2640 2787 9.144747 GGTCGATCGTTGATAGTAGTAGTATTA 57.855 37.037 15.94 0.00 0.00 0.98
2641 2788 7.118971 GGGTCGATCGTTGATAGTAGTAGTATT 59.881 40.741 15.94 0.00 0.00 1.89
2642 2789 6.593382 GGGTCGATCGTTGATAGTAGTAGTAT 59.407 42.308 15.94 0.00 0.00 2.12
2645 2792 4.143158 CGGGTCGATCGTTGATAGTAGTAG 60.143 50.000 15.94 0.00 0.00 2.57
2654 2801 2.126228 GCACGGGTCGATCGTTGA 60.126 61.111 15.94 0.00 38.94 3.18
2682 2829 5.052172 GCATGCAGCAATGAATAGTTTTACG 60.052 40.000 14.21 0.00 44.79 3.18
2683 2830 6.264909 GCATGCAGCAATGAATAGTTTTAC 57.735 37.500 14.21 0.00 44.79 2.01
2781 2930 1.788067 AAACGTTTGGTGCGTAGGGC 61.788 55.000 13.81 0.00 42.10 5.19
2782 2931 0.664224 AAAACGTTTGGTGCGTAGGG 59.336 50.000 15.46 0.00 42.10 3.53
2831 3085 1.497161 AAACCCTAGCTACCATCGCT 58.503 50.000 0.00 0.00 41.35 4.93
2941 3195 1.300971 ATCGCACAAGCACGAGCATT 61.301 50.000 7.77 0.00 45.49 3.56
2959 3213 3.755628 ACCTCGTACGTGCCGCAT 61.756 61.111 16.05 0.00 0.00 4.73
2999 3253 1.343465 ACGAGTGTAAACAGACAGGGG 59.657 52.381 0.00 0.00 0.00 4.79
3145 3405 1.086696 TTAACTCGTAGGACGACGGG 58.913 55.000 3.29 3.29 46.73 5.28
3168 3428 2.632377 CAGCTCTCTCTCTCTCTCGTT 58.368 52.381 0.00 0.00 0.00 3.85
3174 3434 0.464373 CGAGCCAGCTCTCTCTCTCT 60.464 60.000 17.06 0.00 40.69 3.10
3177 3437 2.412937 GCGAGCCAGCTCTCTCTC 59.587 66.667 17.06 0.00 40.69 3.20
3243 3521 7.309255 GCAGAGATGAATTAATTGATGGAGCAT 60.309 37.037 5.17 0.82 0.00 3.79
3253 3531 2.031682 GGCGCGCAGAGATGAATTAATT 60.032 45.455 34.42 0.00 0.00 1.40
3254 3532 1.532868 GGCGCGCAGAGATGAATTAAT 59.467 47.619 34.42 0.00 0.00 1.40
3255 3533 0.937304 GGCGCGCAGAGATGAATTAA 59.063 50.000 34.42 0.00 0.00 1.40
3256 3534 1.215014 CGGCGCGCAGAGATGAATTA 61.215 55.000 34.42 0.00 0.00 1.40
3316 3594 2.126307 TTCAGACAGCGAGCGAGC 60.126 61.111 0.00 0.00 37.41 5.03
3317 3595 1.803519 GGTTCAGACAGCGAGCGAG 60.804 63.158 0.00 0.00 0.00 5.03
3318 3596 2.258591 GGTTCAGACAGCGAGCGA 59.741 61.111 0.00 0.00 0.00 4.93
3319 3597 2.811317 GGGTTCAGACAGCGAGCG 60.811 66.667 0.00 0.00 0.00 5.03
3447 3725 4.519437 CGGATGAGCGAGCAGGCA 62.519 66.667 0.00 0.00 34.64 4.75
3451 3729 3.838271 GGACCGGATGAGCGAGCA 61.838 66.667 9.46 0.00 0.00 4.26
3452 3730 3.492311 GAGGACCGGATGAGCGAGC 62.492 68.421 9.46 0.00 0.00 5.03
3454 3732 2.833582 GGAGGACCGGATGAGCGA 60.834 66.667 9.46 0.00 0.00 4.93
3464 3749 3.589881 GCATGCATGCGGAGGACC 61.590 66.667 33.99 8.38 44.67 4.46
3498 3786 4.089239 TCCTGCCGTTGCCGCATA 62.089 61.111 0.00 0.00 36.33 3.14
3539 3827 4.776322 TGATTGGGCTCGCACGGG 62.776 66.667 0.00 0.00 0.00 5.28
3574 3866 3.925238 GGCTTGCCGATACGCACG 61.925 66.667 0.00 0.00 38.83 5.34


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

AutoCloner maintained by Alex Coulton.