Multiple sequence alignment - TraesCS3D01G274500

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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 TraesCS3D01G274500 chr3D 100.000 3761 0 0 1 3761 380597760 380594000 0.000000e+00 6946.0
1 TraesCS3D01G274500 chr3A 93.123 2443 116 23 797 3214 503839049 503836634 0.000000e+00 3533.0
2 TraesCS3D01G274500 chr3A 89.851 404 25 6 1 390 503841932 503841531 4.340000e-139 505.0
3 TraesCS3D01G274500 chr3A 93.023 43 2 1 89 131 508387629 508387670 1.130000e-05 62.1
4 TraesCS3D01G274500 chr3B 97.219 1007 16 5 2251 3250 495817696 495816695 0.000000e+00 1694.0
5 TraesCS3D01G274500 chr3B 95.418 1004 31 6 852 1845 495819234 495818236 0.000000e+00 1585.0
6 TraesCS3D01G274500 chr3B 95.376 519 14 2 3251 3761 495816662 495816146 0.000000e+00 817.0
7 TraesCS3D01G274500 chr3B 96.763 278 9 0 1990 2267 495817989 495817712 7.360000e-127 464.0
8 TraesCS3D01G274500 chr3B 99.174 121 1 0 1874 1994 495818237 495818117 6.320000e-53 219.0
9 TraesCS3D01G274500 chr1D 80.921 304 29 22 108 392 52325786 52325493 2.940000e-51 213.0
10 TraesCS3D01G274500 chr7D 76.435 331 44 25 54 368 232079146 232079458 8.420000e-32 148.0
11 TraesCS3D01G274500 chr4D 78.788 198 27 10 66 249 215249683 215249879 6.600000e-23 119.0
12 TraesCS3D01G274500 chr4D 83.333 72 9 3 61 131 462502340 462502271 3.140000e-06 63.9
13 TraesCS3D01G274500 chr4A 86.111 72 9 1 61 132 6451829 6451759 4.030000e-10 76.8
14 TraesCS3D01G274500 chr5D 85.915 71 9 1 61 131 437445306 437445237 1.450000e-09 75.0
15 TraesCS3D01G274500 chr6A 97.222 36 0 1 3213 3247 214565320 214565355 4.060000e-05 60.2
16 TraesCS3D01G274500 chr1A 88.000 50 6 0 74 123 6024820 6024869 4.060000e-05 60.2
17 TraesCS3D01G274500 chr2D 96.970 33 1 0 482 514 598302794 598302826 5.250000e-04 56.5
18 TraesCS3D01G274500 chr2D 96.970 33 1 0 482 514 642058390 642058422 5.250000e-04 56.5
19 TraesCS3D01G274500 chr7B 88.636 44 4 1 112 154 731187490 731187447 7.000000e-03 52.8


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 TraesCS3D01G274500 chr3D 380594000 380597760 3760 True 6946.0 6946 100.000 1 3761 1 chr3D.!!$R1 3760
1 TraesCS3D01G274500 chr3A 503836634 503841932 5298 True 2019.0 3533 91.487 1 3214 2 chr3A.!!$R1 3213
2 TraesCS3D01G274500 chr3B 495816146 495819234 3088 True 955.8 1694 96.790 852 3761 5 chr3B.!!$R1 2909

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
791 1846 0.042581 CCCAAAATAAGGGGGCTGGT 59.957 55.0 0.0 0.0 42.90 4.00 F
843 3036 0.111253 CTTGTTGGAGTTCCCTGCCT 59.889 55.0 0.0 0.0 35.38 4.75 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2025 4367 1.053424 AACAGCCTGACTCCCGTAAA 58.947 50.000 0.00 0.0 0.00 2.01 R
2835 5211 1.592081 GAACTCGCAGATCAGCACATC 59.408 52.381 10.95 0.0 33.89 3.06 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
31 32 3.617263 CCTTCTATTCCGAAGTGTTTCCG 59.383 47.826 0.00 0.00 38.95 4.30
48 50 6.746364 GTGTTTCCGTACAAAACATTACAACA 59.254 34.615 20.28 1.06 45.42 3.33
52 54 7.086230 TCCGTACAAAACATTACAACACTTT 57.914 32.000 0.00 0.00 0.00 2.66
55 57 8.735837 CCGTACAAAACATTACAACACTTTTAC 58.264 33.333 0.00 0.00 0.00 2.01
149 154 9.606631 ATCATCAACTCCACTACTTTATTTCTC 57.393 33.333 0.00 0.00 0.00 2.87
207 213 3.275617 TGCACACATCCCACTATAACC 57.724 47.619 0.00 0.00 0.00 2.85
209 215 3.201930 TGCACACATCCCACTATAACCAT 59.798 43.478 0.00 0.00 0.00 3.55
215 221 8.375506 CACACATCCCACTATAACCATAATACT 58.624 37.037 0.00 0.00 0.00 2.12
350 365 9.850628 TCAAATTGAAGACAATCAAATCTCATC 57.149 29.630 0.00 0.00 44.67 2.92
356 371 9.239551 TGAAGACAATCAAATCTCATCAGAAAT 57.760 29.630 0.00 0.00 30.24 2.17
390 405 3.130633 GCTTTTTCCCACATGTTTCCAC 58.869 45.455 0.00 0.00 0.00 4.02
391 406 3.380142 CTTTTTCCCACATGTTTCCACG 58.620 45.455 0.00 0.00 0.00 4.94
392 407 2.060050 TTTCCCACATGTTTCCACGT 57.940 45.000 0.00 0.00 0.00 4.49
393 408 1.313772 TTCCCACATGTTTCCACGTG 58.686 50.000 9.08 9.08 44.52 4.49
395 410 1.073125 TCCCACATGTTTCCACGTGAT 59.927 47.619 19.30 0.00 41.91 3.06
396 411 2.303311 TCCCACATGTTTCCACGTGATA 59.697 45.455 19.30 1.05 41.91 2.15
397 412 2.418628 CCCACATGTTTCCACGTGATAC 59.581 50.000 19.30 12.02 41.91 2.24
437 452 9.950680 TTAGACTCATTTCAAATTGAAGACAAC 57.049 29.630 8.51 1.74 37.70 3.32
438 453 7.428826 AGACTCATTTCAAATTGAAGACAACC 58.571 34.615 8.51 0.02 37.70 3.77
439 454 7.068593 AGACTCATTTCAAATTGAAGACAACCA 59.931 33.333 8.51 0.00 37.70 3.67
440 455 7.555087 ACTCATTTCAAATTGAAGACAACCAA 58.445 30.769 8.51 0.00 37.70 3.67
441 456 8.040132 ACTCATTTCAAATTGAAGACAACCAAA 58.960 29.630 8.51 0.00 37.70 3.28
442 457 8.961294 TCATTTCAAATTGAAGACAACCAAAT 57.039 26.923 8.51 0.00 37.70 2.32
443 458 9.044150 TCATTTCAAATTGAAGACAACCAAATC 57.956 29.630 8.51 0.00 37.70 2.17
444 459 9.048446 CATTTCAAATTGAAGACAACCAAATCT 57.952 29.630 8.51 0.00 37.70 2.40
445 460 8.647143 TTTCAAATTGAAGACAACCAAATCTC 57.353 30.769 8.51 0.00 37.70 2.75
446 461 7.345422 TCAAATTGAAGACAACCAAATCTCA 57.655 32.000 0.00 0.00 38.90 3.27
447 462 7.954835 TCAAATTGAAGACAACCAAATCTCAT 58.045 30.769 0.00 0.00 38.90 2.90
448 463 8.084073 TCAAATTGAAGACAACCAAATCTCATC 58.916 33.333 0.00 0.00 38.90 2.92
449 464 7.528996 AATTGAAGACAACCAAATCTCATCA 57.471 32.000 0.00 0.00 38.90 3.07
450 465 6.564709 TTGAAGACAACCAAATCTCATCAG 57.435 37.500 0.00 0.00 0.00 2.90
451 466 5.868454 TGAAGACAACCAAATCTCATCAGA 58.132 37.500 0.00 0.00 0.00 3.27
452 467 6.298361 TGAAGACAACCAAATCTCATCAGAA 58.702 36.000 0.00 0.00 30.24 3.02
453 468 6.772233 TGAAGACAACCAAATCTCATCAGAAA 59.228 34.615 0.00 0.00 30.24 2.52
454 469 7.449395 TGAAGACAACCAAATCTCATCAGAAAT 59.551 33.333 0.00 0.00 30.24 2.17
455 470 8.868522 AAGACAACCAAATCTCATCAGAAATA 57.131 30.769 0.00 0.00 30.24 1.40
456 471 8.868522 AGACAACCAAATCTCATCAGAAATAA 57.131 30.769 0.00 0.00 30.24 1.40
457 472 9.471702 AGACAACCAAATCTCATCAGAAATAAT 57.528 29.630 0.00 0.00 30.24 1.28
468 483 8.347771 TCTCATCAGAAATAATATTGTTGCAGC 58.652 33.333 5.78 0.00 0.00 5.25
469 484 8.229253 TCATCAGAAATAATATTGTTGCAGCT 57.771 30.769 5.78 0.00 0.00 4.24
470 485 8.689061 TCATCAGAAATAATATTGTTGCAGCTT 58.311 29.630 5.78 0.00 0.00 3.74
471 486 9.309516 CATCAGAAATAATATTGTTGCAGCTTT 57.690 29.630 5.78 0.00 0.00 3.51
472 487 9.880157 ATCAGAAATAATATTGTTGCAGCTTTT 57.120 25.926 5.78 0.00 0.00 2.27
473 488 9.709495 TCAGAAATAATATTGTTGCAGCTTTTT 57.291 25.926 5.78 0.00 0.00 1.94
474 489 9.962759 CAGAAATAATATTGTTGCAGCTTTTTC 57.037 29.630 5.78 0.00 0.00 2.29
475 490 9.933723 AGAAATAATATTGTTGCAGCTTTTTCT 57.066 25.926 5.78 1.42 0.00 2.52
477 492 9.709495 AAATAATATTGTTGCAGCTTTTTCTCA 57.291 25.926 1.17 0.00 0.00 3.27
478 493 8.693542 ATAATATTGTTGCAGCTTTTTCTCAC 57.306 30.769 1.17 0.00 0.00 3.51
479 494 3.865011 TTGTTGCAGCTTTTTCTCACA 57.135 38.095 1.17 0.00 0.00 3.58
480 495 4.389890 TTGTTGCAGCTTTTTCTCACAT 57.610 36.364 1.17 0.00 0.00 3.21
481 496 3.708890 TGTTGCAGCTTTTTCTCACATG 58.291 40.909 1.17 0.00 0.00 3.21
482 497 3.130869 TGTTGCAGCTTTTTCTCACATGT 59.869 39.130 1.17 0.00 0.00 3.21
483 498 4.114794 GTTGCAGCTTTTTCTCACATGTT 58.885 39.130 0.00 0.00 0.00 2.71
484 499 4.389890 TGCAGCTTTTTCTCACATGTTT 57.610 36.364 0.00 0.00 0.00 2.83
485 500 4.362279 TGCAGCTTTTTCTCACATGTTTC 58.638 39.130 0.00 0.00 0.00 2.78
486 501 3.737774 GCAGCTTTTTCTCACATGTTTCC 59.262 43.478 0.00 0.00 0.00 3.13
487 502 4.737352 GCAGCTTTTTCTCACATGTTTCCA 60.737 41.667 0.00 0.00 0.00 3.53
488 503 4.741676 CAGCTTTTTCTCACATGTTTCCAC 59.258 41.667 0.00 0.00 0.00 4.02
489 504 4.402155 AGCTTTTTCTCACATGTTTCCACA 59.598 37.500 0.00 0.00 37.31 4.17
490 505 5.105392 AGCTTTTTCTCACATGTTTCCACAA 60.105 36.000 0.00 0.00 36.16 3.33
491 506 5.005682 GCTTTTTCTCACATGTTTCCACAAC 59.994 40.000 0.00 0.00 36.16 3.32
492 507 5.651387 TTTTCTCACATGTTTCCACAACA 57.349 34.783 0.00 0.00 36.16 3.33
493 508 5.651387 TTTCTCACATGTTTCCACAACAA 57.349 34.783 0.00 0.00 36.16 2.83
494 509 5.850557 TTCTCACATGTTTCCACAACAAT 57.149 34.783 0.00 0.00 36.16 2.71
495 510 5.185668 TCTCACATGTTTCCACAACAATG 57.814 39.130 0.00 0.00 36.16 2.82
520 535 4.799917 GCGGGGTATCATCTACTTTCTTCC 60.800 50.000 0.00 0.00 0.00 3.46
521 536 4.344102 CGGGGTATCATCTACTTTCTTCCA 59.656 45.833 0.00 0.00 0.00 3.53
523 538 6.210784 CGGGGTATCATCTACTTTCTTCCATA 59.789 42.308 0.00 0.00 0.00 2.74
531 551 0.107848 CTTTCTTCCATACGCCCCGT 60.108 55.000 0.00 0.00 44.35 5.28
540 560 1.600485 CATACGCCCCGTCCATTAAAC 59.400 52.381 0.00 0.00 41.54 2.01
541 561 0.612229 TACGCCCCGTCCATTAAACA 59.388 50.000 0.00 0.00 41.54 2.83
542 562 0.956902 ACGCCCCGTCCATTAAACAC 60.957 55.000 0.00 0.00 33.69 3.32
546 566 2.510613 CCCCGTCCATTAAACACAACT 58.489 47.619 0.00 0.00 0.00 3.16
550 570 4.379394 CCCGTCCATTAAACACAACTGATG 60.379 45.833 0.00 0.00 0.00 3.07
556 576 5.406175 CCATTAAACACAACTGATGCAAAGG 59.594 40.000 0.00 0.00 0.00 3.11
559 579 2.653726 ACACAACTGATGCAAAGGTGA 58.346 42.857 21.11 0.00 35.82 4.02
643 663 4.274147 TGGCCGACATGTTTATAATTGGT 58.726 39.130 0.00 0.00 0.00 3.67
644 664 4.336993 TGGCCGACATGTTTATAATTGGTC 59.663 41.667 0.00 0.00 0.00 4.02
706 1755 2.597510 GCTGGACACGGCCCTTTT 60.598 61.111 0.00 0.00 43.36 2.27
707 1756 2.200337 GCTGGACACGGCCCTTTTT 61.200 57.895 0.00 0.00 43.36 1.94
755 1809 5.626142 TGTATTAGCTCTTCCAAACAACCA 58.374 37.500 0.00 0.00 0.00 3.67
769 1824 5.220951 CCAAACAACCAAAATAGGCCAAAAC 60.221 40.000 5.01 0.00 0.00 2.43
779 1834 4.991789 ATAGGCCAAAACAACCCAAAAT 57.008 36.364 5.01 0.00 0.00 1.82
780 1835 6.441088 AATAGGCCAAAACAACCCAAAATA 57.559 33.333 5.01 0.00 0.00 1.40
791 1846 0.042581 CCCAAAATAAGGGGGCTGGT 59.957 55.000 0.00 0.00 42.90 4.00
795 1850 2.529930 AAATAAGGGGGCTGGTGGGC 62.530 60.000 0.00 0.00 40.05 5.36
831 3024 1.743394 GCCGTCCTATTTCCTTGTTGG 59.257 52.381 0.00 0.00 37.10 3.77
832 3025 2.617021 GCCGTCCTATTTCCTTGTTGGA 60.617 50.000 0.00 0.00 44.51 3.53
842 3035 0.895559 CCTTGTTGGAGTTCCCTGCC 60.896 60.000 0.00 0.00 38.35 4.85
843 3036 0.111253 CTTGTTGGAGTTCCCTGCCT 59.889 55.000 0.00 0.00 35.38 4.75
844 3037 0.178992 TTGTTGGAGTTCCCTGCCTG 60.179 55.000 0.00 0.00 35.38 4.85
845 3038 1.973812 GTTGGAGTTCCCTGCCTGC 60.974 63.158 0.00 0.00 35.38 4.85
847 3040 4.432741 GGAGTTCCCTGCCTGCCC 62.433 72.222 0.00 0.00 0.00 5.36
848 3041 4.432741 GAGTTCCCTGCCTGCCCC 62.433 72.222 0.00 0.00 0.00 5.80
875 3068 3.253838 TGCCTGGCCCGTTTAGGT 61.254 61.111 17.53 0.00 38.74 3.08
988 3191 4.813526 CGCTCTGACCGACCGTCG 62.814 72.222 14.15 14.15 45.23 5.12
1330 3539 1.903404 TGCTCGCTGAGTGACTGGA 60.903 57.895 0.00 0.00 31.39 3.86
1646 3855 1.878102 CGAGAGTTTGGGAAGTGTGGG 60.878 57.143 0.00 0.00 0.00 4.61
1674 3883 2.046507 GACACTGCTCTGGCCCAG 60.047 66.667 3.69 3.69 37.74 4.45
1771 3981 7.012515 TGCCTGTTTTTCTTCGTAACTCATAAA 59.987 33.333 0.00 0.00 0.00 1.40
1835 4045 8.390354 GGTTATTTGATTCAAAAGGCTAATTGC 58.610 33.333 15.34 0.25 36.90 3.56
1902 4112 1.067821 GTTTGATGCCAAAACACCGGA 59.932 47.619 9.46 0.00 43.18 5.14
2236 4578 7.759433 ACCATTGGCGTTATTTAGAAAATTGAG 59.241 33.333 1.54 0.00 0.00 3.02
2730 5106 2.094078 GCCAGCAAAATCAGTATTGGCA 60.094 45.455 7.65 0.00 46.64 4.92
2737 5113 6.767423 AGCAAAATCAGTATTGGCAAAAACTT 59.233 30.769 13.97 1.40 31.78 2.66
2791 5167 8.719648 CAGTGCTGGAGATTCTATGATATTTTC 58.280 37.037 0.00 0.00 0.00 2.29
2793 5169 7.663081 GTGCTGGAGATTCTATGATATTTTCCA 59.337 37.037 0.00 0.00 0.00 3.53
2835 5211 4.580167 TGTGGATTCTCTTTTTGTCACTGG 59.420 41.667 0.00 0.00 0.00 4.00
3221 5614 2.706190 AGAATTCCAATCTACTCCCCCG 59.294 50.000 0.65 0.00 0.00 5.73
3222 5615 2.191981 ATTCCAATCTACTCCCCCGT 57.808 50.000 0.00 0.00 0.00 5.28
3223 5616 1.492764 TTCCAATCTACTCCCCCGTC 58.507 55.000 0.00 0.00 0.00 4.79
3224 5617 0.398098 TCCAATCTACTCCCCCGTCC 60.398 60.000 0.00 0.00 0.00 4.79
3225 5618 1.408453 CCAATCTACTCCCCCGTCCC 61.408 65.000 0.00 0.00 0.00 4.46
3226 5619 0.689745 CAATCTACTCCCCCGTCCCA 60.690 60.000 0.00 0.00 0.00 4.37
3227 5620 0.267960 AATCTACTCCCCCGTCCCAT 59.732 55.000 0.00 0.00 0.00 4.00
3228 5621 1.164313 ATCTACTCCCCCGTCCCATA 58.836 55.000 0.00 0.00 0.00 2.74
3279 5704 4.841246 GGGAGTATGTCTATGTCCTTGGAT 59.159 45.833 0.00 0.00 0.00 3.41
3291 5716 5.176407 TGTCCTTGGATTTGTTTACGTTG 57.824 39.130 0.00 0.00 0.00 4.10
3302 5727 7.436970 GGATTTGTTTACGTTGTCCAAATTTCT 59.563 33.333 13.02 0.00 36.24 2.52
3339 5764 6.015010 AGGATTATACGCTTGCTTACTCTCAT 60.015 38.462 0.00 0.00 0.00 2.90
3345 5770 4.697352 ACGCTTGCTTACTCTCATTCATTT 59.303 37.500 0.00 0.00 0.00 2.32
3371 5796 1.929230 TGAAGTTCACGCGTTTCTCA 58.071 45.000 10.22 5.55 0.00 3.27
3413 5838 4.238514 CCTTCAGACTCAGTTTTCCGTAG 58.761 47.826 0.00 0.00 0.00 3.51
3477 5910 7.459795 TTCACAATTATGTAGAACCATTGCA 57.540 32.000 0.00 0.00 37.82 4.08
3483 5916 4.785346 ATGTAGAACCATTGCATCCTCT 57.215 40.909 0.00 0.00 0.00 3.69
3578 6011 8.579850 AGATGGCATGAAAAACAGTAATCTAA 57.420 30.769 3.81 0.00 0.00 2.10
3703 6136 8.519526 GGGTATTTTAGTCATGTCAAAATCACA 58.480 33.333 13.86 0.00 34.57 3.58
3726 6159 7.863375 CACAGAAAACGTGGATACCAAAATTTA 59.137 33.333 0.00 0.00 34.18 1.40
3733 6166 8.217131 ACGTGGATACCAAAATTTAGATTACC 57.783 34.615 0.00 0.00 34.18 2.85
3734 6167 8.050930 ACGTGGATACCAAAATTTAGATTACCT 58.949 33.333 0.00 0.00 34.18 3.08
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
356 371 8.072321 TGTGGGAAAAAGCAGCAATAATATTA 57.928 30.769 0.00 0.00 0.00 0.98
359 374 5.991933 TGTGGGAAAAAGCAGCAATAATA 57.008 34.783 0.00 0.00 0.00 0.98
366 381 2.531522 AACATGTGGGAAAAAGCAGC 57.468 45.000 0.00 0.00 0.00 5.25
368 383 2.768527 TGGAAACATGTGGGAAAAAGCA 59.231 40.909 0.00 0.00 33.40 3.91
370 385 3.380142 CGTGGAAACATGTGGGAAAAAG 58.620 45.455 0.00 0.00 46.14 2.27
411 426 9.950680 GTTGTCTTCAATTTGAAATGAGTCTAA 57.049 29.630 12.62 0.56 35.73 2.10
412 427 8.567948 GGTTGTCTTCAATTTGAAATGAGTCTA 58.432 33.333 12.62 0.00 35.73 2.59
413 428 7.068593 TGGTTGTCTTCAATTTGAAATGAGTCT 59.931 33.333 12.62 0.00 35.73 3.24
414 429 7.202526 TGGTTGTCTTCAATTTGAAATGAGTC 58.797 34.615 12.62 0.84 35.73 3.36
415 430 7.111247 TGGTTGTCTTCAATTTGAAATGAGT 57.889 32.000 12.62 0.00 35.73 3.41
416 431 8.422973 TTTGGTTGTCTTCAATTTGAAATGAG 57.577 30.769 12.62 1.91 35.73 2.90
417 432 8.961294 ATTTGGTTGTCTTCAATTTGAAATGA 57.039 26.923 12.62 5.34 35.73 2.57
418 433 9.048446 AGATTTGGTTGTCTTCAATTTGAAATG 57.952 29.630 12.62 3.15 35.73 2.32
419 434 9.264719 GAGATTTGGTTGTCTTCAATTTGAAAT 57.735 29.630 12.62 0.92 35.73 2.17
420 435 8.256605 TGAGATTTGGTTGTCTTCAATTTGAAA 58.743 29.630 12.62 2.45 35.73 2.69
421 436 7.780064 TGAGATTTGGTTGTCTTCAATTTGAA 58.220 30.769 11.19 11.19 35.92 2.69
422 437 7.345422 TGAGATTTGGTTGTCTTCAATTTGA 57.655 32.000 0.00 0.00 35.92 2.69
423 438 7.868922 TGATGAGATTTGGTTGTCTTCAATTTG 59.131 33.333 0.00 0.00 35.92 2.32
424 439 7.954835 TGATGAGATTTGGTTGTCTTCAATTT 58.045 30.769 0.00 0.00 35.92 1.82
425 440 7.449395 TCTGATGAGATTTGGTTGTCTTCAATT 59.551 33.333 0.00 0.00 35.92 2.32
426 441 6.944290 TCTGATGAGATTTGGTTGTCTTCAAT 59.056 34.615 0.00 0.00 35.92 2.57
427 442 6.298361 TCTGATGAGATTTGGTTGTCTTCAA 58.702 36.000 0.00 0.00 0.00 2.69
428 443 5.868454 TCTGATGAGATTTGGTTGTCTTCA 58.132 37.500 0.00 0.00 0.00 3.02
429 444 6.808008 TTCTGATGAGATTTGGTTGTCTTC 57.192 37.500 0.00 0.00 0.00 2.87
430 445 7.771927 ATTTCTGATGAGATTTGGTTGTCTT 57.228 32.000 0.00 0.00 0.00 3.01
431 446 8.868522 TTATTTCTGATGAGATTTGGTTGTCT 57.131 30.769 0.00 0.00 0.00 3.41
442 457 8.347771 GCTGCAACAATATTATTTCTGATGAGA 58.652 33.333 0.00 0.00 0.00 3.27
443 458 8.350722 AGCTGCAACAATATTATTTCTGATGAG 58.649 33.333 1.02 0.00 0.00 2.90
444 459 8.229253 AGCTGCAACAATATTATTTCTGATGA 57.771 30.769 1.02 0.00 0.00 2.92
445 460 8.867112 AAGCTGCAACAATATTATTTCTGATG 57.133 30.769 1.02 0.00 0.00 3.07
446 461 9.880157 AAAAGCTGCAACAATATTATTTCTGAT 57.120 25.926 1.02 0.00 0.00 2.90
447 462 9.709495 AAAAAGCTGCAACAATATTATTTCTGA 57.291 25.926 1.02 0.00 0.00 3.27
448 463 9.962759 GAAAAAGCTGCAACAATATTATTTCTG 57.037 29.630 1.02 0.00 0.00 3.02
449 464 9.933723 AGAAAAAGCTGCAACAATATTATTTCT 57.066 25.926 1.02 0.00 0.00 2.52
451 466 9.709495 TGAGAAAAAGCTGCAACAATATTATTT 57.291 25.926 1.02 0.00 0.00 1.40
452 467 9.143631 GTGAGAAAAAGCTGCAACAATATTATT 57.856 29.630 1.02 0.00 0.00 1.40
453 468 8.306038 TGTGAGAAAAAGCTGCAACAATATTAT 58.694 29.630 1.02 0.00 0.00 1.28
454 469 7.656412 TGTGAGAAAAAGCTGCAACAATATTA 58.344 30.769 1.02 0.00 0.00 0.98
455 470 6.514947 TGTGAGAAAAAGCTGCAACAATATT 58.485 32.000 1.02 0.00 0.00 1.28
456 471 6.088016 TGTGAGAAAAAGCTGCAACAATAT 57.912 33.333 1.02 0.00 0.00 1.28
457 472 5.512753 TGTGAGAAAAAGCTGCAACAATA 57.487 34.783 1.02 0.00 0.00 1.90
458 473 4.389890 TGTGAGAAAAAGCTGCAACAAT 57.610 36.364 1.02 0.00 0.00 2.71
459 474 3.865011 TGTGAGAAAAAGCTGCAACAA 57.135 38.095 1.02 0.00 0.00 2.83
460 475 3.130869 ACATGTGAGAAAAAGCTGCAACA 59.869 39.130 0.00 0.00 0.00 3.33
461 476 3.709987 ACATGTGAGAAAAAGCTGCAAC 58.290 40.909 0.00 0.00 0.00 4.17
462 477 4.389890 AACATGTGAGAAAAAGCTGCAA 57.610 36.364 0.00 0.00 0.00 4.08
463 478 4.362279 GAAACATGTGAGAAAAAGCTGCA 58.638 39.130 0.00 0.00 0.00 4.41
464 479 3.737774 GGAAACATGTGAGAAAAAGCTGC 59.262 43.478 0.00 0.00 0.00 5.25
465 480 4.741676 GTGGAAACATGTGAGAAAAAGCTG 59.258 41.667 0.00 0.00 46.14 4.24
466 481 4.402155 TGTGGAAACATGTGAGAAAAAGCT 59.598 37.500 0.00 0.00 46.14 3.74
467 482 4.681744 TGTGGAAACATGTGAGAAAAAGC 58.318 39.130 0.00 0.00 46.14 3.51
468 483 6.098679 TGTTGTGGAAACATGTGAGAAAAAG 58.901 36.000 0.00 0.00 46.14 2.27
469 484 6.030548 TGTTGTGGAAACATGTGAGAAAAA 57.969 33.333 0.00 0.00 46.14 1.94
470 485 5.651387 TGTTGTGGAAACATGTGAGAAAA 57.349 34.783 0.00 0.00 46.14 2.29
471 486 5.651387 TTGTTGTGGAAACATGTGAGAAA 57.349 34.783 0.00 0.00 46.14 2.52
472 487 5.590145 CATTGTTGTGGAAACATGTGAGAA 58.410 37.500 0.00 0.00 46.14 2.87
473 488 4.499526 GCATTGTTGTGGAAACATGTGAGA 60.500 41.667 0.00 0.00 46.14 3.27
474 489 3.737266 GCATTGTTGTGGAAACATGTGAG 59.263 43.478 0.00 0.00 46.14 3.51
475 490 3.715495 GCATTGTTGTGGAAACATGTGA 58.285 40.909 0.00 0.00 46.14 3.58
476 491 2.472115 CGCATTGTTGTGGAAACATGTG 59.528 45.455 0.00 0.00 46.14 3.21
477 492 2.741612 CGCATTGTTGTGGAAACATGT 58.258 42.857 0.00 0.00 46.14 3.21
478 493 1.456544 GCGCATTGTTGTGGAAACATG 59.543 47.619 0.30 0.00 46.14 3.21
479 494 1.782044 GCGCATTGTTGTGGAAACAT 58.218 45.000 0.30 0.00 46.14 2.71
480 495 0.593518 CGCGCATTGTTGTGGAAACA 60.594 50.000 8.75 0.00 33.82 2.83
481 496 1.274798 CCGCGCATTGTTGTGGAAAC 61.275 55.000 8.75 0.00 38.00 2.78
482 497 1.007964 CCGCGCATTGTTGTGGAAA 60.008 52.632 8.75 0.00 38.00 3.13
483 498 2.642129 CCGCGCATTGTTGTGGAA 59.358 55.556 8.75 0.00 38.00 3.53
484 499 3.361158 CCCGCGCATTGTTGTGGA 61.361 61.111 8.75 0.00 38.00 4.02
485 500 4.418401 CCCCGCGCATTGTTGTGG 62.418 66.667 8.75 0.00 33.82 4.17
486 501 1.653094 ATACCCCGCGCATTGTTGTG 61.653 55.000 8.75 0.00 36.41 3.33
487 502 1.373590 GATACCCCGCGCATTGTTGT 61.374 55.000 8.75 0.00 0.00 3.32
488 503 1.355210 GATACCCCGCGCATTGTTG 59.645 57.895 8.75 0.00 0.00 3.33
489 504 0.465460 ATGATACCCCGCGCATTGTT 60.465 50.000 8.75 0.00 0.00 2.83
490 505 0.884704 GATGATACCCCGCGCATTGT 60.885 55.000 8.75 2.69 0.00 2.71
491 506 0.603707 AGATGATACCCCGCGCATTG 60.604 55.000 8.75 0.00 0.00 2.82
492 507 0.973632 TAGATGATACCCCGCGCATT 59.026 50.000 8.75 0.00 0.00 3.56
493 508 0.246635 GTAGATGATACCCCGCGCAT 59.753 55.000 8.75 0.00 0.00 4.73
494 509 0.826256 AGTAGATGATACCCCGCGCA 60.826 55.000 8.75 0.00 0.00 6.09
495 510 0.317479 AAGTAGATGATACCCCGCGC 59.683 55.000 0.00 0.00 0.00 6.86
520 535 1.600485 GTTTAATGGACGGGGCGTATG 59.400 52.381 0.00 0.00 41.37 2.39
521 536 1.209990 TGTTTAATGGACGGGGCGTAT 59.790 47.619 0.00 0.00 41.37 3.06
523 538 0.956902 GTGTTTAATGGACGGGGCGT 60.957 55.000 0.00 0.00 45.10 5.68
531 551 5.781210 TTGCATCAGTTGTGTTTAATGGA 57.219 34.783 0.00 0.00 0.00 3.41
540 560 2.287788 GGTCACCTTTGCATCAGTTGTG 60.288 50.000 0.00 0.00 0.00 3.33
541 561 1.956477 GGTCACCTTTGCATCAGTTGT 59.044 47.619 0.00 0.00 0.00 3.32
542 562 1.955778 TGGTCACCTTTGCATCAGTTG 59.044 47.619 0.00 0.00 0.00 3.16
546 566 2.299582 CCATTTGGTCACCTTTGCATCA 59.700 45.455 0.00 0.00 0.00 3.07
550 570 0.320683 GCCCATTTGGTCACCTTTGC 60.321 55.000 0.00 0.00 36.04 3.68
556 576 2.282887 ACCGGCCCATTTGGTCAC 60.283 61.111 0.00 0.00 39.41 3.67
584 604 1.996786 GCATGTGGGCCATCAAGACG 61.997 60.000 10.70 2.25 0.00 4.18
585 605 1.811860 GCATGTGGGCCATCAAGAC 59.188 57.895 10.70 0.00 0.00 3.01
620 640 4.892934 ACCAATTATAAACATGTCGGCCAT 59.107 37.500 2.24 0.00 0.00 4.40
624 644 5.498159 CACGACCAATTATAAACATGTCGG 58.502 41.667 22.59 13.86 36.32 4.79
679 700 3.075005 TGTCCAGCCTCGTAGCCC 61.075 66.667 0.00 0.00 0.00 5.19
733 1782 6.569179 TTGGTTGTTTGGAAGAGCTAATAC 57.431 37.500 0.00 0.00 0.00 1.89
740 1794 5.230182 GCCTATTTTGGTTGTTTGGAAGAG 58.770 41.667 0.00 0.00 0.00 2.85
746 1800 5.355350 TGTTTTGGCCTATTTTGGTTGTTTG 59.645 36.000 3.32 0.00 0.00 2.93
752 1806 3.181449 GGGTTGTTTTGGCCTATTTTGGT 60.181 43.478 3.32 0.00 0.00 3.67
755 1809 4.779993 TTGGGTTGTTTTGGCCTATTTT 57.220 36.364 3.32 0.00 0.00 1.82
769 1824 1.554617 CAGCCCCCTTATTTTGGGTTG 59.445 52.381 0.00 0.00 42.92 3.77
779 1834 2.791731 TTAGCCCACCAGCCCCCTTA 62.792 60.000 0.00 0.00 0.00 2.69
780 1835 4.693915 TAGCCCACCAGCCCCCTT 62.694 66.667 0.00 0.00 0.00 3.95
787 1842 2.192605 GGCATGTTTAGCCCACCAG 58.807 57.895 0.00 0.00 46.50 4.00
788 1843 4.432601 GGCATGTTTAGCCCACCA 57.567 55.556 0.00 0.00 46.50 4.17
831 3024 4.432741 GGGGCAGGCAGGGAACTC 62.433 72.222 0.00 0.00 40.21 3.01
836 3029 3.995506 CTAAACGGGGCAGGCAGGG 62.996 68.421 0.00 0.00 0.00 4.45
837 3030 2.438434 CTAAACGGGGCAGGCAGG 60.438 66.667 0.00 0.00 0.00 4.85
838 3031 2.438434 CCTAAACGGGGCAGGCAG 60.438 66.667 0.00 0.00 0.00 4.85
845 3038 3.728373 AGGCAGGCCTAAACGGGG 61.728 66.667 11.95 0.00 46.14 5.73
847 3040 2.438434 CCAGGCAGGCCTAAACGG 60.438 66.667 13.37 6.26 46.28 4.44
857 3050 1.906105 TACCTAAACGGGCCAGGCAG 61.906 60.000 15.19 9.33 36.97 4.85
1082 3285 2.770130 GGTGGGAAGGGATGGCAA 59.230 61.111 0.00 0.00 0.00 4.52
1145 3354 3.419759 CGAGGGTGAAAACGGGCG 61.420 66.667 0.00 0.00 0.00 6.13
1146 3355 2.031465 TCGAGGGTGAAAACGGGC 59.969 61.111 0.00 0.00 0.00 6.13
1147 3356 2.025418 CGTCGAGGGTGAAAACGGG 61.025 63.158 0.00 0.00 0.00 5.28
1148 3357 1.007038 TCGTCGAGGGTGAAAACGG 60.007 57.895 5.12 0.00 34.30 4.44
1149 3358 1.280206 GGTCGTCGAGGGTGAAAACG 61.280 60.000 5.12 0.00 34.80 3.60
1150 3359 1.280206 CGGTCGTCGAGGGTGAAAAC 61.280 60.000 5.12 0.00 42.43 2.43
1646 3855 2.757868 AGAGCAGTGTCTCAGTATCACC 59.242 50.000 14.37 0.00 35.59 4.02
1674 3883 3.620488 TGTGAAGCCAATTACCATCTCC 58.380 45.455 0.00 0.00 0.00 3.71
1771 3981 3.370978 CGATGCAGTTACGAAAGGTTGAT 59.629 43.478 0.00 0.00 0.00 2.57
1835 4045 5.880887 AGACGAAAAATAAAGGCTAGAAGGG 59.119 40.000 0.00 0.00 0.00 3.95
2025 4367 1.053424 AACAGCCTGACTCCCGTAAA 58.947 50.000 0.00 0.00 0.00 2.01
2084 4426 8.982091 AAAGGAAAGGAAAGGCTATAAGATAC 57.018 34.615 0.00 0.00 0.00 2.24
2186 4528 4.895297 ACAAAATTCTCAGCAAGGGAAGAA 59.105 37.500 0.00 0.00 0.00 2.52
2236 4578 6.472686 ACAGAAGTCTAGGGATGTATTCAC 57.527 41.667 0.00 0.00 0.00 3.18
2730 5106 6.432472 TGCCAAAAATCAAGTCCAAAGTTTTT 59.568 30.769 0.00 0.00 31.23 1.94
2737 5113 5.678583 TCAAATGCCAAAAATCAAGTCCAA 58.321 33.333 0.00 0.00 0.00 3.53
2835 5211 1.592081 GAACTCGCAGATCAGCACATC 59.408 52.381 10.95 0.00 33.89 3.06
3187 5580 2.758979 TGGAATTCTGGACCGAGAGTAC 59.241 50.000 5.23 0.00 0.00 2.73
3221 5614 5.352643 AAAACGCGCTTATATTATGGGAC 57.647 39.130 5.73 0.00 0.00 4.46
3222 5615 5.527951 TCAAAAACGCGCTTATATTATGGGA 59.472 36.000 5.73 0.00 0.00 4.37
3223 5616 5.623673 GTCAAAAACGCGCTTATATTATGGG 59.376 40.000 5.73 0.00 0.00 4.00
3224 5617 5.623673 GGTCAAAAACGCGCTTATATTATGG 59.376 40.000 5.73 0.00 0.00 2.74
3225 5618 5.623673 GGGTCAAAAACGCGCTTATATTATG 59.376 40.000 5.73 0.00 0.00 1.90
3226 5619 5.754778 GGGTCAAAAACGCGCTTATATTAT 58.245 37.500 5.73 0.00 0.00 1.28
3227 5620 5.159399 GGGTCAAAAACGCGCTTATATTA 57.841 39.130 5.73 0.00 0.00 0.98
3228 5621 4.023739 GGGTCAAAAACGCGCTTATATT 57.976 40.909 5.73 0.00 0.00 1.28
3279 5704 6.035112 GCAGAAATTTGGACAACGTAAACAAA 59.965 34.615 0.00 9.14 35.76 2.83
3291 5716 4.657075 CAGCAAATGCAGAAATTTGGAC 57.343 40.909 8.28 0.00 44.30 4.02
3339 5764 6.370593 GCGTGAACTTCATACTTGAAATGAA 58.629 36.000 0.00 0.00 41.22 2.57
3345 5770 3.021269 ACGCGTGAACTTCATACTTGA 57.979 42.857 12.93 0.00 0.00 3.02
3371 5796 2.897326 GGGGCTTGTAACTTGGTGAAAT 59.103 45.455 0.00 0.00 0.00 2.17
3477 5910 7.741554 AGACCTTTCATAACTGTTAGAGGAT 57.258 36.000 19.84 10.77 0.00 3.24
3703 6136 8.398878 TCTAAATTTTGGTATCCACGTTTTCT 57.601 30.769 0.00 0.00 30.78 2.52
3726 6159 5.907662 TCATGAAATCCAGGAGAGGTAATCT 59.092 40.000 0.00 0.00 42.61 2.40
3733 6166 6.770746 ACAAATTCATGAAATCCAGGAGAG 57.229 37.500 13.09 0.00 36.87 3.20
3734 6167 8.827832 ATTACAAATTCATGAAATCCAGGAGA 57.172 30.769 13.09 0.00 36.87 3.71


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

AutoCloner maintained by Alex Coulton.