Multiple sequence alignment - TraesCS2D01G214700

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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 TraesCS2D01G214700 chr2D 100.000 3000 0 0 1 3000 176165192 176162193 0.000000e+00 5541.0
1 TraesCS2D01G214700 chr2D 88.333 60 5 2 394 451 448447195 448447254 1.490000e-08 71.3
2 TraesCS2D01G214700 chr2A 92.468 1965 71 30 1069 3000 187953425 187951505 0.000000e+00 2737.0
3 TraesCS2D01G214700 chr2A 87.816 632 35 13 18 630 187955357 187954749 0.000000e+00 702.0
4 TraesCS2D01G214700 chr2A 89.796 343 17 7 733 1073 187953819 187953493 9.940000e-115 424.0
5 TraesCS2D01G214700 chr2B 90.399 1979 84 40 660 2596 233269386 233267472 0.000000e+00 2505.0
6 TraesCS2D01G214700 chr2B 98.251 343 1 1 2658 3000 233267474 233267137 1.990000e-166 595.0
7 TraesCS2D01G214700 chr2B 90.789 380 15 7 1 377 233269853 233269491 9.660000e-135 490.0
8 TraesCS2D01G214700 chr2B 91.753 97 6 1 413 509 233269489 233269395 1.880000e-27 134.0
9 TraesCS2D01G214700 chr7D 85.175 1140 110 22 1339 2462 581035091 581036187 0.000000e+00 1114.0
10 TraesCS2D01G214700 chr3D 86.458 480 31 16 2001 2462 604598317 604597854 2.080000e-136 496.0
11 TraesCS2D01G214700 chr3D 87.542 297 28 4 1671 1967 604598600 604598313 4.790000e-88 335.0
12 TraesCS2D01G214700 chr6B 88.889 180 10 3 645 824 594649485 594649654 2.340000e-51 213.0
13 TraesCS2D01G214700 chr6B 88.889 180 10 3 645 824 594650799 594650630 2.340000e-51 213.0
14 TraesCS2D01G214700 chr6B 94.231 104 5 1 530 633 594649125 594649227 1.110000e-34 158.0
15 TraesCS2D01G214700 chr6B 96.471 85 2 1 549 633 594651140 594651057 4.030000e-29 139.0
16 TraesCS2D01G214700 chr6B 92.593 54 2 2 400 451 642350320 642350267 3.210000e-10 76.8
17 TraesCS2D01G214700 chr5A 96.078 51 2 0 399 449 313877741 313877691 1.920000e-12 84.2
18 TraesCS2D01G214700 chr7B 92.593 54 3 1 399 451 500725953 500726006 3.210000e-10 76.8
19 TraesCS2D01G214700 chr4B 94.000 50 3 0 394 443 570739601 570739650 3.210000e-10 76.8
20 TraesCS2D01G214700 chr1D 94.118 51 2 1 399 448 489299983 489300033 3.210000e-10 76.8
21 TraesCS2D01G214700 chr1D 94.118 51 2 1 399 448 489432871 489432921 3.210000e-10 76.8
22 TraesCS2D01G214700 chr5B 95.652 46 2 0 398 443 21154006 21154051 1.150000e-09 75.0


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 TraesCS2D01G214700 chr2D 176162193 176165192 2999 True 5541.000000 5541 100.000000 1 3000 1 chr2D.!!$R1 2999
1 TraesCS2D01G214700 chr2A 187951505 187955357 3852 True 1287.666667 2737 90.026667 18 3000 3 chr2A.!!$R1 2982
2 TraesCS2D01G214700 chr2B 233267137 233269853 2716 True 931.000000 2505 92.798000 1 3000 4 chr2B.!!$R1 2999
3 TraesCS2D01G214700 chr7D 581035091 581036187 1096 False 1114.000000 1114 85.175000 1339 2462 1 chr7D.!!$F1 1123
4 TraesCS2D01G214700 chr3D 604597854 604598600 746 True 415.500000 496 87.000000 1671 2462 2 chr3D.!!$R1 791

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
633 657 0.028902 CATGTCACCATGCATGCGAG 59.971 55.0 21.69 12.41 41.88 5.03 F
872 1744 0.101759 GCTGCGCATCAACCAATCAT 59.898 50.0 12.24 0.00 0.00 2.45 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1482 2430 0.684535 TGGCCGTGTGAATCTGAAGA 59.315 50.000 0.0 0.0 0.00 2.87 R
2630 3649 2.224161 TGCTTTTGGTAACCCACATTGC 60.224 45.455 0.0 0.0 41.67 3.56 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
296 305 2.554032 GGCATCTGGGACGATTATTTGG 59.446 50.000 0.00 0.00 0.00 3.28
331 340 0.689623 CAGTGGGAGCCTTTCTCAGT 59.310 55.000 0.00 0.00 40.74 3.41
332 341 1.902508 CAGTGGGAGCCTTTCTCAGTA 59.097 52.381 0.00 0.00 37.89 2.74
359 370 8.771920 TGTTGAAAGTATCCACTACTGTTATG 57.228 34.615 0.00 0.00 39.87 1.90
382 394 8.644374 ATGAAGTCTTCTATCTATACCACTCC 57.356 38.462 13.67 0.00 0.00 3.85
383 395 7.005296 TGAAGTCTTCTATCTATACCACTCCC 58.995 42.308 13.67 0.00 0.00 4.30
384 396 5.894653 AGTCTTCTATCTATACCACTCCCC 58.105 45.833 0.00 0.00 0.00 4.81
385 397 5.018149 GTCTTCTATCTATACCACTCCCCC 58.982 50.000 0.00 0.00 0.00 5.40
386 398 4.926987 TCTTCTATCTATACCACTCCCCCT 59.073 45.833 0.00 0.00 0.00 4.79
387 399 4.676799 TCTATCTATACCACTCCCCCTG 57.323 50.000 0.00 0.00 0.00 4.45
388 400 3.995077 TCTATCTATACCACTCCCCCTGT 59.005 47.826 0.00 0.00 0.00 4.00
389 401 2.471815 TCTATACCACTCCCCCTGTG 57.528 55.000 0.00 0.00 35.39 3.66
390 402 1.934480 TCTATACCACTCCCCCTGTGA 59.066 52.381 0.00 0.00 37.60 3.58
391 403 2.316677 TCTATACCACTCCCCCTGTGAA 59.683 50.000 0.00 0.00 37.60 3.18
392 404 2.053747 ATACCACTCCCCCTGTGAAA 57.946 50.000 0.00 0.00 37.60 2.69
393 405 1.822425 TACCACTCCCCCTGTGAAAA 58.178 50.000 0.00 0.00 37.60 2.29
394 406 1.158007 ACCACTCCCCCTGTGAAAAT 58.842 50.000 0.00 0.00 37.60 1.82
395 407 2.354328 ACCACTCCCCCTGTGAAAATA 58.646 47.619 0.00 0.00 37.60 1.40
396 408 2.041216 ACCACTCCCCCTGTGAAAATAC 59.959 50.000 0.00 0.00 37.60 1.89
397 409 2.620627 CCACTCCCCCTGTGAAAATACC 60.621 54.545 0.00 0.00 37.60 2.73
404 416 2.620627 CCCTGTGAAAATACCACTCCCC 60.621 54.545 0.00 0.00 35.66 4.81
409 421 2.041081 TGAAAATACCACTCCCCCTGTG 59.959 50.000 0.00 0.00 35.39 3.66
429 441 7.494625 CCCTGTGAAGAAATATAAGAGCGTTTA 59.505 37.037 0.00 0.00 0.00 2.01
430 442 9.046296 CCTGTGAAGAAATATAAGAGCGTTTAT 57.954 33.333 2.15 2.15 0.00 1.40
495 507 0.669932 GCTATGCATCTCAGGGAGCG 60.670 60.000 0.19 0.00 0.00 5.03
509 521 0.243095 GGAGCGTAACTGAACCGACT 59.757 55.000 0.00 0.00 0.00 4.18
510 522 1.615502 GAGCGTAACTGAACCGACTC 58.384 55.000 0.00 0.00 0.00 3.36
511 523 0.956633 AGCGTAACTGAACCGACTCA 59.043 50.000 0.00 0.00 0.00 3.41
512 524 1.058404 GCGTAACTGAACCGACTCAC 58.942 55.000 0.00 0.00 0.00 3.51
566 590 1.202770 CCTGTGAAAAGGAACCGGTCT 60.203 52.381 8.04 0.00 40.02 3.85
601 625 5.794945 CACCAATGCTTATTTGTAGTGAACG 59.205 40.000 0.00 0.00 0.00 3.95
608 632 6.649141 TGCTTATTTGTAGTGAACGTCAGATT 59.351 34.615 0.00 0.00 0.00 2.40
631 655 4.702020 CATGTCACCATGCATGCG 57.298 55.556 21.69 16.19 41.88 4.73
633 657 0.028902 CATGTCACCATGCATGCGAG 59.971 55.000 21.69 12.41 41.88 5.03
634 658 1.099295 ATGTCACCATGCATGCGAGG 61.099 55.000 21.69 22.45 0.00 4.63
637 661 0.461870 TCACCATGCATGCGAGGTAC 60.462 55.000 27.19 0.00 32.01 3.34
639 663 0.462581 ACCATGCATGCGAGGTACTG 60.463 55.000 26.73 6.71 41.55 2.74
641 665 0.933097 CATGCATGCGAGGTACTGTC 59.067 55.000 14.93 0.00 41.55 3.51
643 667 0.389817 TGCATGCGAGGTACTGTCAC 60.390 55.000 14.09 0.00 41.55 3.67
644 668 1.413767 GCATGCGAGGTACTGTCACG 61.414 60.000 0.00 0.00 41.55 4.35
645 669 0.170339 CATGCGAGGTACTGTCACGA 59.830 55.000 0.00 0.00 41.55 4.35
646 670 0.885879 ATGCGAGGTACTGTCACGAA 59.114 50.000 0.00 0.00 41.55 3.85
647 671 0.240145 TGCGAGGTACTGTCACGAAG 59.760 55.000 0.00 0.00 41.55 3.79
648 672 0.456312 GCGAGGTACTGTCACGAAGG 60.456 60.000 0.00 0.00 41.55 3.46
649 673 0.456312 CGAGGTACTGTCACGAAGGC 60.456 60.000 0.00 0.00 41.55 4.35
651 675 1.000506 GAGGTACTGTCACGAAGGCAA 59.999 52.381 0.00 0.00 41.55 4.52
652 676 1.000955 AGGTACTGTCACGAAGGCAAG 59.999 52.381 0.00 0.00 37.18 4.01
653 677 1.429463 GTACTGTCACGAAGGCAAGG 58.571 55.000 0.00 0.00 0.00 3.61
654 678 0.320421 TACTGTCACGAAGGCAAGGC 60.320 55.000 0.00 0.00 0.00 4.35
669 693 1.402968 CAAGGCATATGCACTGTCACC 59.597 52.381 28.07 8.95 44.36 4.02
694 868 3.339547 GGTCCAAACCAGCTTAGCA 57.660 52.632 7.07 0.00 45.68 3.49
695 869 1.616159 GGTCCAAACCAGCTTAGCAA 58.384 50.000 7.07 0.00 45.68 3.91
696 870 1.960689 GGTCCAAACCAGCTTAGCAAA 59.039 47.619 7.07 0.00 45.68 3.68
697 871 2.562738 GGTCCAAACCAGCTTAGCAAAT 59.437 45.455 7.07 0.00 45.68 2.32
698 872 3.761752 GGTCCAAACCAGCTTAGCAAATA 59.238 43.478 7.07 0.00 45.68 1.40
699 873 4.142381 GGTCCAAACCAGCTTAGCAAATAG 60.142 45.833 7.07 0.00 45.68 1.73
700 874 3.443681 TCCAAACCAGCTTAGCAAATAGC 59.556 43.478 7.07 0.00 46.19 2.97
746 1605 5.011329 ACCACTACATCTTCTGGTTTCGTAA 59.989 40.000 0.00 0.00 32.88 3.18
751 1610 6.165659 ACATCTTCTGGTTTCGTAAAATCG 57.834 37.500 0.00 0.00 0.00 3.34
872 1744 0.101759 GCTGCGCATCAACCAATCAT 59.898 50.000 12.24 0.00 0.00 2.45
976 1852 2.634777 CTCGCTCGATCGTCCTCC 59.365 66.667 15.94 0.00 0.00 4.30
1055 1931 0.421904 ACCCAGGTAACCATCCCTCT 59.578 55.000 0.00 0.00 37.17 3.69
1064 1940 1.886422 ACCATCCCTCTCTTCTTCCC 58.114 55.000 0.00 0.00 0.00 3.97
1070 1946 2.680352 TCTCTTCTTCCCGCCGCT 60.680 61.111 0.00 0.00 0.00 5.52
1073 1949 1.945354 CTCTTCTTCCCGCCGCTGTA 61.945 60.000 0.00 0.00 0.00 2.74
1074 1950 1.079405 CTTCTTCCCGCCGCTGTAA 60.079 57.895 0.00 0.00 0.00 2.41
1083 2031 1.632046 CGCCGCTGTAATTTCGGTGT 61.632 55.000 5.41 0.00 45.60 4.16
1126 2074 1.668047 GCTTGCTGAGAACATGTTGGC 60.668 52.381 17.58 14.33 0.00 4.52
1351 2299 3.471806 GGCTCCTTCCTCGTCCCC 61.472 72.222 0.00 0.00 0.00 4.81
1482 2430 1.120530 CAGGGGCTCAAGGTACGTAT 58.879 55.000 0.00 0.00 0.00 3.06
1521 2475 2.109126 GCATGGTCGTTCTGAGGCC 61.109 63.158 0.00 0.00 0.00 5.19
1588 2550 1.677217 GGCCCAGAGTAAGTTGCTGAG 60.677 57.143 0.00 0.00 0.00 3.35
1648 2615 0.471211 TGGAGTCCGACAAGACCCTT 60.471 55.000 4.30 0.00 37.49 3.95
1819 2797 3.502356 CCCTCCTAGTCCTATCTCAACC 58.498 54.545 0.00 0.00 0.00 3.77
2031 3014 2.758089 CGGCAGCAATGCTCACTCC 61.758 63.158 4.03 3.55 36.40 3.85
2073 3056 1.476891 CCAGTCCTAAGAACGCTGCTA 59.523 52.381 0.00 0.00 0.00 3.49
2074 3057 2.531206 CAGTCCTAAGAACGCTGCTAC 58.469 52.381 0.00 0.00 0.00 3.58
2238 3238 7.856415 ACTCTTTCTATAGCTGATCAAACCTT 58.144 34.615 0.00 0.00 0.00 3.50
2270 3279 6.897966 ACATCTCCTGAATCTAGACAACCTAA 59.102 38.462 0.00 0.00 0.00 2.69
2426 3444 4.692625 GCATAGCTTCTCTGTTCAGAAACA 59.307 41.667 0.00 0.00 43.06 2.83
2485 3503 9.508642 AACTTTAATTCTTTCTCCCTAGTTCTG 57.491 33.333 0.00 0.00 0.00 3.02
2528 3546 8.894768 ACATGCCATTCTAATAAGTAGAGAAC 57.105 34.615 0.00 0.00 40.04 3.01
2585 3603 4.142315 CCAGACATGTTAATGCCAGGAAAG 60.142 45.833 0.00 0.00 37.29 2.62
2590 3608 2.224992 TGTTAATGCCAGGAAAGGAGCA 60.225 45.455 0.00 0.00 40.00 4.26
2605 3623 4.851639 AGGAGCAGTTCAGGATAAACAT 57.148 40.909 0.00 0.00 0.00 2.71
2610 3628 4.397417 AGCAGTTCAGGATAAACATCAAGC 59.603 41.667 0.00 0.00 0.00 4.01
2630 3649 8.506140 TCAAGCGTAAAAATGAAGAAATGAAG 57.494 30.769 0.00 0.00 0.00 3.02
2749 3768 2.343544 GCAAACATTCGCATCAAAGCTC 59.656 45.455 0.00 0.00 0.00 4.09
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
18 19 3.009033 TGGAGACCAGGTTGAAATAGTGG 59.991 47.826 0.00 0.00 0.00 4.00
296 305 5.258051 TCCCACTGGGACACAATAAATAAC 58.742 41.667 13.39 0.00 46.17 1.89
313 322 2.327325 TACTGAGAAAGGCTCCCACT 57.673 50.000 0.00 0.00 43.26 4.00
332 341 9.959721 ATAACAGTAGTGGATACTTTCAACAAT 57.040 29.630 1.92 0.00 42.30 2.71
359 370 6.434965 GGGGAGTGGTATAGATAGAAGACTTC 59.565 46.154 7.14 7.14 0.00 3.01
377 389 2.041081 TGGTATTTTCACAGGGGGAGTG 59.959 50.000 0.00 0.00 38.32 3.51
378 390 2.041216 GTGGTATTTTCACAGGGGGAGT 59.959 50.000 0.00 0.00 35.39 3.85
379 391 2.308866 AGTGGTATTTTCACAGGGGGAG 59.691 50.000 0.00 0.00 37.58 4.30
380 392 2.307686 GAGTGGTATTTTCACAGGGGGA 59.692 50.000 0.00 0.00 37.58 4.81
381 393 2.620627 GGAGTGGTATTTTCACAGGGGG 60.621 54.545 0.00 0.00 37.58 5.40
382 394 2.620627 GGGAGTGGTATTTTCACAGGGG 60.621 54.545 0.00 0.00 37.58 4.79
383 395 2.620627 GGGGAGTGGTATTTTCACAGGG 60.621 54.545 0.00 0.00 37.58 4.45
384 396 2.620627 GGGGGAGTGGTATTTTCACAGG 60.621 54.545 0.00 0.00 37.58 4.00
385 397 2.308866 AGGGGGAGTGGTATTTTCACAG 59.691 50.000 0.00 0.00 37.58 3.66
386 398 2.041081 CAGGGGGAGTGGTATTTTCACA 59.959 50.000 0.00 0.00 37.58 3.58
387 399 2.041216 ACAGGGGGAGTGGTATTTTCAC 59.959 50.000 0.00 0.00 35.51 3.18
388 400 2.041081 CACAGGGGGAGTGGTATTTTCA 59.959 50.000 0.00 0.00 33.43 2.69
389 401 2.307686 TCACAGGGGGAGTGGTATTTTC 59.692 50.000 0.00 0.00 37.58 2.29
390 402 2.354328 TCACAGGGGGAGTGGTATTTT 58.646 47.619 0.00 0.00 37.58 1.82
391 403 2.053747 TCACAGGGGGAGTGGTATTT 57.946 50.000 0.00 0.00 37.58 1.40
392 404 1.916181 CTTCACAGGGGGAGTGGTATT 59.084 52.381 0.00 0.00 37.58 1.89
393 405 1.080498 TCTTCACAGGGGGAGTGGTAT 59.920 52.381 0.00 0.00 37.58 2.73
394 406 0.490017 TCTTCACAGGGGGAGTGGTA 59.510 55.000 0.00 0.00 37.58 3.25
395 407 0.401395 TTCTTCACAGGGGGAGTGGT 60.401 55.000 0.00 0.00 37.58 4.16
396 408 0.771127 TTTCTTCACAGGGGGAGTGG 59.229 55.000 0.00 0.00 37.58 4.00
397 409 2.887151 ATTTCTTCACAGGGGGAGTG 57.113 50.000 0.00 0.00 38.32 3.51
404 416 6.910536 AACGCTCTTATATTTCTTCACAGG 57.089 37.500 0.00 0.00 0.00 4.00
495 507 3.382048 AAGGTGAGTCGGTTCAGTTAC 57.618 47.619 0.00 0.00 0.00 2.50
509 521 3.132925 GTGCCGTTTACTACAAAGGTGA 58.867 45.455 0.00 0.00 0.00 4.02
510 522 2.873472 TGTGCCGTTTACTACAAAGGTG 59.127 45.455 0.00 0.00 0.00 4.00
511 523 3.196939 TGTGCCGTTTACTACAAAGGT 57.803 42.857 0.00 0.00 0.00 3.50
512 524 4.691685 TGTATGTGCCGTTTACTACAAAGG 59.308 41.667 0.00 0.00 0.00 3.11
547 571 2.256117 AGACCGGTTCCTTTTCACAG 57.744 50.000 9.42 0.00 0.00 3.66
601 625 4.009675 TGGTGACATGCCTAAAATCTGAC 58.990 43.478 0.00 0.00 33.40 3.51
630 654 0.456312 GCCTTCGTGACAGTACCTCG 60.456 60.000 0.00 0.00 0.00 4.63
631 655 0.601558 TGCCTTCGTGACAGTACCTC 59.398 55.000 0.00 0.00 0.00 3.85
633 657 1.429463 CTTGCCTTCGTGACAGTACC 58.571 55.000 0.00 0.00 0.00 3.34
634 658 1.429463 CCTTGCCTTCGTGACAGTAC 58.571 55.000 0.00 0.00 0.00 2.73
637 661 0.957395 ATGCCTTGCCTTCGTGACAG 60.957 55.000 0.00 0.00 0.00 3.51
638 662 0.323302 TATGCCTTGCCTTCGTGACA 59.677 50.000 0.00 0.00 0.00 3.58
639 663 1.331756 CATATGCCTTGCCTTCGTGAC 59.668 52.381 0.00 0.00 0.00 3.67
641 665 0.029834 GCATATGCCTTGCCTTCGTG 59.970 55.000 17.26 0.00 33.95 4.35
643 667 0.029834 GTGCATATGCCTTGCCTTCG 59.970 55.000 24.54 0.00 39.39 3.79
644 668 1.066605 CAGTGCATATGCCTTGCCTTC 59.933 52.381 24.54 5.43 39.39 3.46
645 669 1.108776 CAGTGCATATGCCTTGCCTT 58.891 50.000 24.54 0.06 39.39 4.35
646 670 0.033796 ACAGTGCATATGCCTTGCCT 60.034 50.000 24.54 9.69 39.39 4.75
647 671 0.383231 GACAGTGCATATGCCTTGCC 59.617 55.000 24.54 11.53 39.39 4.52
648 672 1.097232 TGACAGTGCATATGCCTTGC 58.903 50.000 24.54 16.69 41.18 4.01
649 673 1.402968 GGTGACAGTGCATATGCCTTG 59.597 52.381 24.54 22.30 41.18 3.61
651 675 0.620030 TGGTGACAGTGCATATGCCT 59.380 50.000 24.54 17.40 36.49 4.75
652 676 1.402968 CTTGGTGACAGTGCATATGCC 59.597 52.381 24.54 15.47 44.54 4.40
653 677 1.202222 GCTTGGTGACAGTGCATATGC 60.202 52.381 21.09 21.09 44.54 3.14
654 678 1.402968 GGCTTGGTGACAGTGCATATG 59.597 52.381 0.00 0.00 44.54 1.78
694 868 1.794222 GAGTGCGCCGTTGCTATTT 59.206 52.632 4.18 0.00 35.36 1.40
695 869 2.452813 CGAGTGCGCCGTTGCTATT 61.453 57.895 4.18 0.00 35.36 1.73
696 870 2.885644 CGAGTGCGCCGTTGCTAT 60.886 61.111 4.18 0.00 35.36 2.97
697 871 3.964221 CTCGAGTGCGCCGTTGCTA 62.964 63.158 4.18 0.00 37.46 3.49
700 874 3.470567 GTCTCGAGTGCGCCGTTG 61.471 66.667 13.13 0.00 37.46 4.10
778 1637 2.266055 CCCCCGAGCAGACTTCAC 59.734 66.667 0.00 0.00 0.00 3.18
779 1638 3.706373 GCCCCCGAGCAGACTTCA 61.706 66.667 0.00 0.00 0.00 3.02
780 1639 4.821589 CGCCCCCGAGCAGACTTC 62.822 72.222 0.00 0.00 36.29 3.01
985 1861 3.449227 CATGGTGGCTGGCTGCTG 61.449 66.667 16.14 2.36 42.39 4.41
986 1862 4.753662 CCATGGTGGCTGGCTGCT 62.754 66.667 16.14 0.00 42.39 4.24
1055 1931 1.537814 TTACAGCGGCGGGAAGAAGA 61.538 55.000 9.78 0.00 0.00 2.87
1070 1946 2.029739 TCTCTCGCACACCGAAATTACA 60.030 45.455 0.00 0.00 46.81 2.41
1073 1949 1.714794 CTCTCTCGCACACCGAAATT 58.285 50.000 0.00 0.00 46.81 1.82
1074 1950 0.737715 GCTCTCTCGCACACCGAAAT 60.738 55.000 0.00 0.00 46.81 2.17
1083 2031 3.760035 GAACCCGGCTCTCTCGCA 61.760 66.667 0.00 0.00 0.00 5.10
1095 2043 1.398390 CTCAGCAAGCATAACGAACCC 59.602 52.381 0.00 0.00 0.00 4.11
1147 2095 2.900167 CTTGCACAGCGAGCTTGCA 61.900 57.895 27.59 17.06 44.40 4.08
1199 2147 0.833287 CAGGTGATGTTCCTCGGGAT 59.167 55.000 0.00 0.00 32.37 3.85
1482 2430 0.684535 TGGCCGTGTGAATCTGAAGA 59.315 50.000 0.00 0.00 0.00 2.87
1511 2465 0.877743 GCTTGTGAAGGCCTCAGAAC 59.122 55.000 5.23 2.62 32.60 3.01
1521 2475 4.573607 TCTGCTTGCATATAGCTTGTGAAG 59.426 41.667 10.10 0.00 45.94 3.02
1588 2550 0.813184 CCTGCAACATCCACACCATC 59.187 55.000 0.00 0.00 0.00 3.51
1819 2797 5.182001 ACAATGGATTCTTCAGAAAGGTTCG 59.818 40.000 0.00 0.00 37.61 3.95
2031 3014 3.812053 GCAGGAGGCTTAACATATCACAG 59.188 47.826 0.00 0.00 40.25 3.66
2073 3056 8.091449 GCATTTATAGCAGGAGTAGTCTTATGT 58.909 37.037 0.00 0.00 0.00 2.29
2074 3057 8.090831 TGCATTTATAGCAGGAGTAGTCTTATG 58.909 37.037 0.00 0.00 37.02 1.90
2238 3238 7.178451 TGTCTAGATTCAGGAGATGTGTGTTTA 59.822 37.037 0.00 0.00 0.00 2.01
2290 3299 4.161754 TGCAGATATGCCATCCTATCTCTG 59.838 45.833 10.32 0.00 33.45 3.35
2353 3371 5.564550 AGAGACAGTGGCTTGTATCAATTT 58.435 37.500 0.00 0.00 40.76 1.82
2356 3374 5.016831 TCTAGAGACAGTGGCTTGTATCAA 58.983 41.667 0.00 3.14 40.76 2.57
2426 3444 5.934781 ACTTGATTCAAGAGGAAAGTGTCT 58.065 37.500 28.60 3.14 43.42 3.41
2528 3546 7.538575 GGATGAATTTTAACATATCCGGATGG 58.461 38.462 27.55 20.16 0.00 3.51
2564 3582 4.019174 CCTTTCCTGGCATTAACATGTCT 58.981 43.478 0.00 0.00 35.84 3.41
2585 3603 4.517285 TGATGTTTATCCTGAACTGCTCC 58.483 43.478 0.00 0.00 32.09 4.70
2590 3608 4.579869 ACGCTTGATGTTTATCCTGAACT 58.420 39.130 0.00 0.00 32.09 3.01
2605 3623 7.114811 GCTTCATTTCTTCATTTTTACGCTTGA 59.885 33.333 0.00 0.00 0.00 3.02
2610 3628 8.702438 ACATTGCTTCATTTCTTCATTTTTACG 58.298 29.630 0.00 0.00 0.00 3.18
2630 3649 2.224161 TGCTTTTGGTAACCCACATTGC 60.224 45.455 0.00 0.00 41.67 3.56
2749 3768 9.343539 TCCATGAATGTCCTATATATCTACTCG 57.656 37.037 0.00 0.00 0.00 4.18
2867 3889 5.440610 ACTGTAATGTGGGATTGGATTCTC 58.559 41.667 0.00 0.00 0.00 2.87
2868 3890 5.456921 ACTGTAATGTGGGATTGGATTCT 57.543 39.130 0.00 0.00 0.00 2.40
2869 3891 7.339466 AGTTTACTGTAATGTGGGATTGGATTC 59.661 37.037 0.37 0.00 0.00 2.52
2870 3892 7.182060 AGTTTACTGTAATGTGGGATTGGATT 58.818 34.615 0.37 0.00 0.00 3.01
2871 3893 6.731467 AGTTTACTGTAATGTGGGATTGGAT 58.269 36.000 0.37 0.00 0.00 3.41


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

AutoCloner maintained by Alex Coulton.