Multiple sequence alignment - TraesCS4D01G282800

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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 TraesCS4D01G282800 chr4D 100.000 3530 0 0 1 3530 454440670 454437141 0.000000e+00 6519.0
1 TraesCS4D01G282800 chr4D 93.345 2239 76 28 1257 3464 454413029 454410833 0.000000e+00 3241.0
2 TraesCS4D01G282800 chr4D 90.458 765 47 7 161 900 496335227 496335990 0.000000e+00 985.0
3 TraesCS4D01G282800 chr4D 97.529 526 11 2 1 524 496335154 496335679 0.000000e+00 898.0
4 TraesCS4D01G282800 chr4D 77.086 1366 238 40 1074 2410 455090410 455089091 0.000000e+00 719.0
5 TraesCS4D01G282800 chr4D 81.373 816 123 13 1074 1864 454809752 454808941 3.840000e-179 638.0
6 TraesCS4D01G282800 chr4D 75.427 1054 191 38 1375 2397 451165737 451166753 1.930000e-122 449.0
7 TraesCS4D01G282800 chr4D 82.584 178 13 12 677 847 82022779 82022613 1.320000e-29 141.0
8 TraesCS4D01G282800 chr4A 92.741 2576 94 24 992 3530 13585056 13587575 0.000000e+00 3635.0
9 TraesCS4D01G282800 chr4A 77.622 1354 258 24 1074 2403 13524988 13526320 0.000000e+00 780.0
10 TraesCS4D01G282800 chr4A 77.704 1359 235 39 1074 2403 13150723 13152042 0.000000e+00 769.0
11 TraesCS4D01G282800 chr4A 77.193 1368 248 37 1078 2409 13518020 13519359 0.000000e+00 739.0
12 TraesCS4D01G282800 chr4A 79.315 730 113 14 1074 1766 15784193 15783465 8.870000e-131 477.0
13 TraesCS4D01G282800 chr4A 74.842 1105 229 35 1375 2451 13590349 13589266 4.150000e-124 455.0
14 TraesCS4D01G282800 chr4B 94.780 2069 77 9 896 2944 567193035 567190978 0.000000e+00 3193.0
15 TraesCS4D01G282800 chr4B 92.071 618 37 4 2925 3530 567190965 567190348 0.000000e+00 859.0
16 TraesCS4D01G282800 chr4B 92.939 524 34 3 3 524 139377629 139378151 0.000000e+00 760.0
17 TraesCS4D01G282800 chr4B 77.153 1370 237 49 1074 2403 567590038 567588705 0.000000e+00 726.0
18 TraesCS4D01G282800 chr4B 76.253 1457 273 40 1045 2451 567187217 567188650 0.000000e+00 706.0
19 TraesCS4D01G282800 chr4B 88.258 511 57 3 159 667 139377699 139378208 3.010000e-170 608.0
20 TraesCS4D01G282800 chr4B 81.728 405 60 9 1375 1766 564382507 564382910 3.400000e-85 326.0
21 TraesCS4D01G282800 chr4B 87.432 183 13 2 675 847 139378317 139378499 5.980000e-48 202.0
22 TraesCS4D01G282800 chr4B 93.443 61 4 0 829 889 442585732 442585792 1.350000e-14 91.6
23 TraesCS4D01G282800 chr2B 93.511 524 30 3 3 524 184926196 184926717 0.000000e+00 776.0
24 TraesCS4D01G282800 chr2B 89.453 512 49 4 159 667 184926265 184926774 2.970000e-180 641.0
25 TraesCS4D01G282800 chr2B 86.996 223 7 1 698 898 184926915 184927137 7.620000e-57 231.0
26 TraesCS4D01G282800 chr2B 90.226 133 10 2 1 130 796029571 796029703 1.680000e-38 171.0
27 TraesCS4D01G282800 chr3D 98.015 403 8 0 122 524 100407300 100407702 0.000000e+00 701.0
28 TraesCS4D01G282800 chr3D 90.000 540 41 4 210 747 100407300 100407828 0.000000e+00 686.0
29 TraesCS4D01G282800 chr3D 78.520 838 137 22 1074 1873 435489200 435488368 8.740000e-141 510.0
30 TraesCS4D01G282800 chr1B 90.667 525 47 2 1 524 41698628 41699151 0.000000e+00 697.0
31 TraesCS4D01G282800 chr1B 88.477 512 54 5 159 667 41698699 41699208 6.480000e-172 614.0
32 TraesCS4D01G282800 chr1B 92.053 151 11 1 698 847 41699349 41699499 9.930000e-51 211.0
33 TraesCS4D01G282800 chr1B 96.970 66 2 0 832 897 41699505 41699570 1.040000e-20 111.0
34 TraesCS4D01G282800 chr1A 75.744 1377 264 40 1074 2403 251563953 251562600 2.310000e-176 628.0
35 TraesCS4D01G282800 chr1A 87.179 78 8 2 830 906 30879857 30879933 1.750000e-13 87.9
36 TraesCS4D01G282800 chr1A 78.378 148 22 5 675 822 496647308 496647445 1.750000e-13 87.9
37 TraesCS4D01G282800 chr1D 84.409 186 14 8 677 847 23326234 23326419 6.060000e-38 169.0
38 TraesCS4D01G282800 chr1D 82.723 191 13 11 677 847 54942106 54941916 6.100000e-33 152.0
39 TraesCS4D01G282800 chr1D 81.746 126 12 9 725 842 462285248 462285126 1.040000e-15 95.3
40 TraesCS4D01G282800 chr7A 96.667 60 2 0 830 889 165902618 165902677 2.240000e-17 100.0
41 TraesCS4D01G282800 chr5A 96.667 60 2 0 830 889 698459548 698459489 2.240000e-17 100.0
42 TraesCS4D01G282800 chr3B 89.333 75 7 1 832 906 675570228 675570301 3.750000e-15 93.5
43 TraesCS4D01G282800 chr6B 88.158 76 9 0 833 908 52817713 52817638 1.350000e-14 91.6


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 TraesCS4D01G282800 chr4D 454437141 454440670 3529 True 6519.000000 6519 100.000000 1 3530 1 chr4D.!!$R3 3529
1 TraesCS4D01G282800 chr4D 454410833 454413029 2196 True 3241.000000 3241 93.345000 1257 3464 1 chr4D.!!$R2 2207
2 TraesCS4D01G282800 chr4D 496335154 496335990 836 False 941.500000 985 93.993500 1 900 2 chr4D.!!$F2 899
3 TraesCS4D01G282800 chr4D 455089091 455090410 1319 True 719.000000 719 77.086000 1074 2410 1 chr4D.!!$R5 1336
4 TraesCS4D01G282800 chr4D 454808941 454809752 811 True 638.000000 638 81.373000 1074 1864 1 chr4D.!!$R4 790
5 TraesCS4D01G282800 chr4D 451165737 451166753 1016 False 449.000000 449 75.427000 1375 2397 1 chr4D.!!$F1 1022
6 TraesCS4D01G282800 chr4A 13585056 13587575 2519 False 3635.000000 3635 92.741000 992 3530 1 chr4A.!!$F4 2538
7 TraesCS4D01G282800 chr4A 13524988 13526320 1332 False 780.000000 780 77.622000 1074 2403 1 chr4A.!!$F3 1329
8 TraesCS4D01G282800 chr4A 13150723 13152042 1319 False 769.000000 769 77.704000 1074 2403 1 chr4A.!!$F1 1329
9 TraesCS4D01G282800 chr4A 13518020 13519359 1339 False 739.000000 739 77.193000 1078 2409 1 chr4A.!!$F2 1331
10 TraesCS4D01G282800 chr4A 15783465 15784193 728 True 477.000000 477 79.315000 1074 1766 1 chr4A.!!$R2 692
11 TraesCS4D01G282800 chr4A 13589266 13590349 1083 True 455.000000 455 74.842000 1375 2451 1 chr4A.!!$R1 1076
12 TraesCS4D01G282800 chr4B 567190348 567193035 2687 True 2026.000000 3193 93.425500 896 3530 2 chr4B.!!$R2 2634
13 TraesCS4D01G282800 chr4B 567588705 567590038 1333 True 726.000000 726 77.153000 1074 2403 1 chr4B.!!$R1 1329
14 TraesCS4D01G282800 chr4B 567187217 567188650 1433 False 706.000000 706 76.253000 1045 2451 1 chr4B.!!$F3 1406
15 TraesCS4D01G282800 chr4B 139377629 139378499 870 False 523.333333 760 89.543000 3 847 3 chr4B.!!$F4 844
16 TraesCS4D01G282800 chr2B 184926196 184927137 941 False 549.333333 776 89.986667 3 898 3 chr2B.!!$F2 895
17 TraesCS4D01G282800 chr3D 100407300 100407828 528 False 693.500000 701 94.007500 122 747 2 chr3D.!!$F1 625
18 TraesCS4D01G282800 chr3D 435488368 435489200 832 True 510.000000 510 78.520000 1074 1873 1 chr3D.!!$R1 799
19 TraesCS4D01G282800 chr1B 41698628 41699570 942 False 408.250000 697 92.041750 1 897 4 chr1B.!!$F1 896
20 TraesCS4D01G282800 chr1A 251562600 251563953 1353 True 628.000000 628 75.744000 1074 2403 1 chr1A.!!$R1 1329

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
549 554 0.881118 TGATTTTGCTGGAACGAGCC 59.119 50.0 6.38 0.0 38.28 4.70 F
550 555 0.881118 GATTTTGCTGGAACGAGCCA 59.119 50.0 6.38 0.0 38.28 4.75 F
552 557 1.107114 TTTTGCTGGAACGAGCCAAA 58.893 45.0 6.38 5.4 38.28 3.28 F
2046 2317 0.743345 GGCATACCACCAGGAACGAC 60.743 60.0 0.00 0.0 38.69 4.34 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2038 2309 0.250124 TTGTGCCAATCGTCGTTCCT 60.250 50.000 0.00 0.0 0.00 3.36 R
2047 2318 1.907807 TGTGCCCCTTGTGCCAATC 60.908 57.895 0.00 0.0 0.00 2.67 R
2048 2319 2.200930 TGTGCCCCTTGTGCCAAT 59.799 55.556 0.00 0.0 0.00 3.16 R
3494 3848 1.237954 TGCGCTTGCGGGTATTTCAA 61.238 50.000 16.79 0.0 43.34 2.69 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
60 62 4.478371 CGCTGCTCTCCATGGCCA 62.478 66.667 8.56 8.56 0.00 5.36
63 65 2.934932 TGCTCTCCATGGCCACCA 60.935 61.111 8.16 0.00 38.19 4.17
305 310 1.135689 GCCAGAATGTTTGCTACCACG 60.136 52.381 0.00 0.00 0.00 4.94
373 378 7.102346 TCTTCTTTTGATTTTGCTGAAACCAA 58.898 30.769 0.00 0.00 0.00 3.67
493 498 4.054780 TGCTACCACCGTATCTGATTTC 57.945 45.455 0.00 0.00 0.00 2.17
494 499 3.704566 TGCTACCACCGTATCTGATTTCT 59.295 43.478 0.00 0.00 0.00 2.52
495 500 4.051922 GCTACCACCGTATCTGATTTCTG 58.948 47.826 0.00 0.00 0.00 3.02
496 501 2.906354 ACCACCGTATCTGATTTCTGC 58.094 47.619 0.00 0.00 0.00 4.26
497 502 2.501723 ACCACCGTATCTGATTTCTGCT 59.498 45.455 0.00 0.00 0.00 4.24
498 503 2.868583 CCACCGTATCTGATTTCTGCTG 59.131 50.000 0.00 0.00 0.00 4.41
499 504 2.868583 CACCGTATCTGATTTCTGCTGG 59.131 50.000 0.00 0.00 0.00 4.85
500 505 2.766263 ACCGTATCTGATTTCTGCTGGA 59.234 45.455 0.00 0.00 0.00 3.86
501 506 3.197766 ACCGTATCTGATTTCTGCTGGAA 59.802 43.478 0.00 0.00 0.00 3.53
502 507 3.557595 CCGTATCTGATTTCTGCTGGAAC 59.442 47.826 0.00 0.00 33.13 3.62
503 508 3.557595 CGTATCTGATTTCTGCTGGAACC 59.442 47.826 0.00 0.00 33.13 3.62
504 509 3.726557 ATCTGATTTCTGCTGGAACCA 57.273 42.857 0.00 0.00 33.13 3.67
505 510 3.507162 TCTGATTTCTGCTGGAACCAA 57.493 42.857 0.00 0.00 33.13 3.67
506 511 3.149196 TCTGATTTCTGCTGGAACCAAC 58.851 45.455 0.00 0.00 33.13 3.77
507 512 3.152341 CTGATTTCTGCTGGAACCAACT 58.848 45.455 0.00 0.00 33.13 3.16
508 513 3.565307 TGATTTCTGCTGGAACCAACTT 58.435 40.909 0.00 0.00 33.13 2.66
509 514 4.724399 TGATTTCTGCTGGAACCAACTTA 58.276 39.130 0.00 0.00 33.13 2.24
510 515 5.324409 TGATTTCTGCTGGAACCAACTTAT 58.676 37.500 0.00 0.00 33.13 1.73
511 516 5.774690 TGATTTCTGCTGGAACCAACTTATT 59.225 36.000 0.00 0.00 33.13 1.40
512 517 6.267471 TGATTTCTGCTGGAACCAACTTATTT 59.733 34.615 0.00 0.00 33.13 1.40
513 518 6.478512 TTTCTGCTGGAACCAACTTATTTT 57.521 33.333 0.00 0.00 33.13 1.82
514 519 6.478512 TTCTGCTGGAACCAACTTATTTTT 57.521 33.333 0.00 0.00 0.00 1.94
538 543 6.826893 TGCTACAACTTCTTTTGATTTTGC 57.173 33.333 0.00 0.00 0.00 3.68
539 544 6.572519 TGCTACAACTTCTTTTGATTTTGCT 58.427 32.000 0.00 0.00 0.00 3.91
540 545 6.476380 TGCTACAACTTCTTTTGATTTTGCTG 59.524 34.615 0.00 0.00 0.00 4.41
541 546 6.074142 GCTACAACTTCTTTTGATTTTGCTGG 60.074 38.462 0.00 0.00 0.00 4.85
542 547 5.976458 ACAACTTCTTTTGATTTTGCTGGA 58.024 33.333 0.00 0.00 0.00 3.86
543 548 6.405538 ACAACTTCTTTTGATTTTGCTGGAA 58.594 32.000 0.00 0.00 0.00 3.53
544 549 6.313658 ACAACTTCTTTTGATTTTGCTGGAAC 59.686 34.615 0.00 0.00 0.00 3.62
545 550 5.043248 ACTTCTTTTGATTTTGCTGGAACG 58.957 37.500 0.00 0.00 0.00 3.95
546 551 4.909696 TCTTTTGATTTTGCTGGAACGA 57.090 36.364 0.00 0.00 0.00 3.85
547 552 4.858935 TCTTTTGATTTTGCTGGAACGAG 58.141 39.130 0.00 0.00 0.00 4.18
548 553 2.704725 TTGATTTTGCTGGAACGAGC 57.295 45.000 2.04 2.04 39.62 5.03
549 554 0.881118 TGATTTTGCTGGAACGAGCC 59.119 50.000 6.38 0.00 38.28 4.70
550 555 0.881118 GATTTTGCTGGAACGAGCCA 59.119 50.000 6.38 0.00 38.28 4.75
551 556 1.269448 GATTTTGCTGGAACGAGCCAA 59.731 47.619 6.38 0.00 38.28 4.52
552 557 1.107114 TTTTGCTGGAACGAGCCAAA 58.893 45.000 6.38 5.40 38.28 3.28
553 558 1.107114 TTTGCTGGAACGAGCCAAAA 58.893 45.000 6.38 0.00 38.28 2.44
554 559 1.107114 TTGCTGGAACGAGCCAAAAA 58.893 45.000 6.38 0.00 38.28 1.94
555 560 1.327303 TGCTGGAACGAGCCAAAAAT 58.673 45.000 6.38 0.00 38.28 1.82
556 561 1.686052 TGCTGGAACGAGCCAAAAATT 59.314 42.857 6.38 0.00 38.28 1.82
557 562 2.102252 TGCTGGAACGAGCCAAAAATTT 59.898 40.909 6.38 0.00 38.28 1.82
558 563 3.130633 GCTGGAACGAGCCAAAAATTTT 58.869 40.909 0.00 0.00 37.52 1.82
559 564 3.059665 GCTGGAACGAGCCAAAAATTTTG 60.060 43.478 11.24 11.24 37.52 2.44
560 565 2.869192 TGGAACGAGCCAAAAATTTTGC 59.131 40.909 12.62 4.67 34.31 3.68
561 566 3.130633 GGAACGAGCCAAAAATTTTGCT 58.869 40.909 13.83 13.83 41.24 3.91
562 567 4.202161 TGGAACGAGCCAAAAATTTTGCTA 60.202 37.500 13.90 0.00 39.01 3.49
563 568 4.149922 GGAACGAGCCAAAAATTTTGCTAC 59.850 41.667 13.90 4.89 39.01 3.58
564 569 3.649073 ACGAGCCAAAAATTTTGCTACC 58.351 40.909 13.90 4.49 39.01 3.18
565 570 3.068873 ACGAGCCAAAAATTTTGCTACCA 59.931 39.130 13.90 0.00 39.01 3.25
566 571 3.428534 CGAGCCAAAAATTTTGCTACCAC 59.571 43.478 13.90 3.64 39.01 4.16
567 572 3.738982 AGCCAAAAATTTTGCTACCACC 58.261 40.909 12.62 0.00 37.39 4.61
568 573 2.811431 GCCAAAAATTTTGCTACCACCC 59.189 45.455 12.62 0.00 0.00 4.61
569 574 3.495983 GCCAAAAATTTTGCTACCACCCT 60.496 43.478 12.62 0.00 0.00 4.34
570 575 4.262678 GCCAAAAATTTTGCTACCACCCTA 60.263 41.667 12.62 0.00 0.00 3.53
571 576 5.570641 GCCAAAAATTTTGCTACCACCCTAT 60.571 40.000 12.62 0.00 0.00 2.57
572 577 6.106003 CCAAAAATTTTGCTACCACCCTATC 58.894 40.000 12.62 0.00 0.00 2.08
573 578 6.070824 CCAAAAATTTTGCTACCACCCTATCT 60.071 38.462 12.62 0.00 0.00 1.98
574 579 6.530019 AAAATTTTGCTACCACCCTATCTG 57.470 37.500 1.75 0.00 0.00 2.90
575 580 5.450818 AATTTTGCTACCACCCTATCTGA 57.549 39.130 0.00 0.00 0.00 3.27
576 581 5.653255 ATTTTGCTACCACCCTATCTGAT 57.347 39.130 0.00 0.00 0.00 2.90
577 582 5.450818 TTTTGCTACCACCCTATCTGATT 57.549 39.130 0.00 0.00 0.00 2.57
578 583 5.450818 TTTGCTACCACCCTATCTGATTT 57.549 39.130 0.00 0.00 0.00 2.17
812 928 2.169769 CCCGTGCCAGAGGTTAAAGATA 59.830 50.000 0.00 0.00 0.00 1.98
829 945 3.385115 AGATAAGAGGTTGGGGACGAAT 58.615 45.455 0.00 0.00 0.00 3.34
1173 1326 4.424566 TACTTGGCCGTCCGCGAC 62.425 66.667 8.23 2.72 41.33 5.19
1222 1375 4.680237 CAGGCCGCACCGTCAAGA 62.680 66.667 0.00 0.00 46.52 3.02
1918 2174 5.843421 ACTCTGGAGGATAATGTTGATAGCT 59.157 40.000 0.00 0.00 0.00 3.32
1931 2187 5.664457 TGTTGATAGCTTCGACATCATCTT 58.336 37.500 12.32 0.00 42.69 2.40
2038 2309 2.777114 ACATGTGATAGGCATACCACCA 59.223 45.455 0.00 0.00 39.06 4.17
2046 2317 0.743345 GGCATACCACCAGGAACGAC 60.743 60.000 0.00 0.00 38.69 4.34
2047 2318 1.082117 GCATACCACCAGGAACGACG 61.082 60.000 0.00 0.00 38.69 5.12
2048 2319 0.528924 CATACCACCAGGAACGACGA 59.471 55.000 0.00 0.00 38.69 4.20
2067 2338 4.134785 TGGCACAAGGGGCACACA 62.135 61.111 0.00 0.00 38.55 3.72
2610 2904 1.907807 GACCACCTGCCCATTTGCA 60.908 57.895 0.00 0.00 39.37 4.08
2678 2978 4.263905 ACATCTCTTTTGCCCCTTGATACA 60.264 41.667 0.00 0.00 0.00 2.29
2679 2979 4.380843 TCTCTTTTGCCCCTTGATACAA 57.619 40.909 0.00 0.00 0.00 2.41
3326 3671 3.828921 GTGGGAAGGTTTTGTTCCTACT 58.171 45.455 10.23 0.00 46.71 2.57
3494 3848 8.632679 ACACAATTTGTCACAAGTCATAAATCT 58.367 29.630 0.00 0.00 29.79 2.40
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
9 10 4.221422 GCCATGGGACGAGCGCTA 62.221 66.667 11.50 0.00 0.00 4.26
60 62 4.980573 TGTAGCAAAAATCCTACTGTGGT 58.019 39.130 0.00 0.00 35.95 4.16
63 65 5.381757 TGGTTGTAGCAAAAATCCTACTGT 58.618 37.500 0.00 0.00 35.95 3.55
305 310 5.848406 TGGTTCCAACAAAAATCACATACC 58.152 37.500 0.00 0.00 0.00 2.73
373 378 4.079253 ACGATGGTAGCAAAAATTCTGGT 58.921 39.130 0.00 0.00 0.00 4.00
512 517 8.174422 GCAAAATCAAAAGAAGTTGTAGCAAAA 58.826 29.630 0.00 0.00 0.00 2.44
513 518 7.548780 AGCAAAATCAAAAGAAGTTGTAGCAAA 59.451 29.630 0.00 0.00 0.00 3.68
514 519 7.010367 CAGCAAAATCAAAAGAAGTTGTAGCAA 59.990 33.333 0.00 0.00 0.00 3.91
515 520 6.476380 CAGCAAAATCAAAAGAAGTTGTAGCA 59.524 34.615 0.00 0.00 0.00 3.49
516 521 6.074142 CCAGCAAAATCAAAAGAAGTTGTAGC 60.074 38.462 0.00 0.00 0.00 3.58
517 522 7.202526 TCCAGCAAAATCAAAAGAAGTTGTAG 58.797 34.615 0.00 0.00 0.00 2.74
518 523 7.106439 TCCAGCAAAATCAAAAGAAGTTGTA 57.894 32.000 0.00 0.00 0.00 2.41
519 524 5.976458 TCCAGCAAAATCAAAAGAAGTTGT 58.024 33.333 0.00 0.00 0.00 3.32
520 525 6.508404 CGTTCCAGCAAAATCAAAAGAAGTTG 60.508 38.462 0.00 0.00 0.00 3.16
521 526 5.519927 CGTTCCAGCAAAATCAAAAGAAGTT 59.480 36.000 0.00 0.00 0.00 2.66
522 527 5.043248 CGTTCCAGCAAAATCAAAAGAAGT 58.957 37.500 0.00 0.00 0.00 3.01
523 528 5.280945 TCGTTCCAGCAAAATCAAAAGAAG 58.719 37.500 0.00 0.00 0.00 2.85
524 529 5.255710 TCGTTCCAGCAAAATCAAAAGAA 57.744 34.783 0.00 0.00 0.00 2.52
525 530 4.792704 GCTCGTTCCAGCAAAATCAAAAGA 60.793 41.667 0.00 0.00 39.43 2.52
526 531 3.426525 GCTCGTTCCAGCAAAATCAAAAG 59.573 43.478 0.00 0.00 39.43 2.27
527 532 3.380142 GCTCGTTCCAGCAAAATCAAAA 58.620 40.909 0.00 0.00 39.43 2.44
528 533 2.288152 GGCTCGTTCCAGCAAAATCAAA 60.288 45.455 0.00 0.00 41.65 2.69
529 534 1.269448 GGCTCGTTCCAGCAAAATCAA 59.731 47.619 0.00 0.00 41.65 2.57
530 535 0.881118 GGCTCGTTCCAGCAAAATCA 59.119 50.000 0.00 0.00 41.65 2.57
531 536 0.881118 TGGCTCGTTCCAGCAAAATC 59.119 50.000 0.00 0.00 41.65 2.17
532 537 1.327303 TTGGCTCGTTCCAGCAAAAT 58.673 45.000 0.00 0.00 41.65 1.82
533 538 1.107114 TTTGGCTCGTTCCAGCAAAA 58.893 45.000 0.00 0.00 39.57 2.44
534 539 1.107114 TTTTGGCTCGTTCCAGCAAA 58.893 45.000 0.00 0.00 41.65 3.68
535 540 1.107114 TTTTTGGCTCGTTCCAGCAA 58.893 45.000 0.00 0.00 41.65 3.91
536 541 1.327303 ATTTTTGGCTCGTTCCAGCA 58.673 45.000 0.00 0.00 41.65 4.41
537 542 2.438868 AATTTTTGGCTCGTTCCAGC 57.561 45.000 0.00 0.00 37.44 4.85
538 543 3.059665 GCAAAATTTTTGGCTCGTTCCAG 60.060 43.478 20.36 0.00 37.44 3.86
539 544 2.869192 GCAAAATTTTTGGCTCGTTCCA 59.131 40.909 20.36 0.00 34.26 3.53
540 545 3.130633 AGCAAAATTTTTGGCTCGTTCC 58.869 40.909 20.36 4.43 43.83 3.62
541 546 4.149922 GGTAGCAAAATTTTTGGCTCGTTC 59.850 41.667 20.36 8.25 43.83 3.95
542 547 4.055360 GGTAGCAAAATTTTTGGCTCGTT 58.945 39.130 20.36 0.00 43.83 3.85
543 548 3.068873 TGGTAGCAAAATTTTTGGCTCGT 59.931 39.130 20.36 0.38 43.83 4.18
544 549 3.428534 GTGGTAGCAAAATTTTTGGCTCG 59.571 43.478 20.36 0.04 43.83 5.03
545 550 3.745975 GGTGGTAGCAAAATTTTTGGCTC 59.254 43.478 20.36 10.02 43.83 4.70
547 552 2.811431 GGGTGGTAGCAAAATTTTTGGC 59.189 45.455 20.36 13.58 37.37 4.52
548 553 4.350368 AGGGTGGTAGCAAAATTTTTGG 57.650 40.909 20.36 5.72 0.00 3.28
549 554 6.813152 CAGATAGGGTGGTAGCAAAATTTTTG 59.187 38.462 15.92 15.92 0.00 2.44
550 555 6.723977 TCAGATAGGGTGGTAGCAAAATTTTT 59.276 34.615 0.00 0.00 0.00 1.94
551 556 6.252995 TCAGATAGGGTGGTAGCAAAATTTT 58.747 36.000 0.00 0.00 0.00 1.82
552 557 5.826643 TCAGATAGGGTGGTAGCAAAATTT 58.173 37.500 0.00 0.00 0.00 1.82
553 558 5.450818 TCAGATAGGGTGGTAGCAAAATT 57.549 39.130 0.00 0.00 0.00 1.82
554 559 5.653255 ATCAGATAGGGTGGTAGCAAAAT 57.347 39.130 0.00 0.00 0.00 1.82
555 560 5.450818 AATCAGATAGGGTGGTAGCAAAA 57.549 39.130 0.00 0.00 0.00 2.44
556 561 5.450818 AAATCAGATAGGGTGGTAGCAAA 57.549 39.130 0.00 0.00 0.00 3.68
557 562 5.450818 AAAATCAGATAGGGTGGTAGCAA 57.549 39.130 0.00 0.00 0.00 3.91
558 563 5.192927 CAAAAATCAGATAGGGTGGTAGCA 58.807 41.667 0.00 0.00 0.00 3.49
559 564 4.036852 GCAAAAATCAGATAGGGTGGTAGC 59.963 45.833 0.00 0.00 0.00 3.58
560 565 5.297776 CAGCAAAAATCAGATAGGGTGGTAG 59.702 44.000 0.00 0.00 0.00 3.18
561 566 5.192927 CAGCAAAAATCAGATAGGGTGGTA 58.807 41.667 0.00 0.00 0.00 3.25
562 567 4.019174 CAGCAAAAATCAGATAGGGTGGT 58.981 43.478 0.00 0.00 0.00 4.16
563 568 3.382546 CCAGCAAAAATCAGATAGGGTGG 59.617 47.826 0.00 0.00 36.30 4.61
564 569 4.272489 TCCAGCAAAAATCAGATAGGGTG 58.728 43.478 0.00 0.00 0.00 4.61
565 570 4.591321 TCCAGCAAAAATCAGATAGGGT 57.409 40.909 0.00 0.00 0.00 4.34
566 571 4.098501 GGTTCCAGCAAAAATCAGATAGGG 59.901 45.833 0.00 0.00 0.00 3.53
567 572 4.706476 TGGTTCCAGCAAAAATCAGATAGG 59.294 41.667 0.00 0.00 0.00 2.57
568 573 5.902613 TGGTTCCAGCAAAAATCAGATAG 57.097 39.130 0.00 0.00 0.00 2.08
569 574 5.774690 AGTTGGTTCCAGCAAAAATCAGATA 59.225 36.000 8.28 0.00 37.34 1.98
570 575 4.590222 AGTTGGTTCCAGCAAAAATCAGAT 59.410 37.500 8.28 0.00 37.34 2.90
571 576 3.960102 AGTTGGTTCCAGCAAAAATCAGA 59.040 39.130 8.28 0.00 37.34 3.27
572 577 4.326504 AGTTGGTTCCAGCAAAAATCAG 57.673 40.909 8.28 0.00 37.34 2.90
573 578 4.751767 AAGTTGGTTCCAGCAAAAATCA 57.248 36.364 8.28 0.00 37.34 2.57
574 579 7.728847 AAATAAGTTGGTTCCAGCAAAAATC 57.271 32.000 8.28 0.00 37.34 2.17
575 580 8.518430 AAAAATAAGTTGGTTCCAGCAAAAAT 57.482 26.923 8.28 0.00 37.34 1.82
576 581 7.929941 AAAAATAAGTTGGTTCCAGCAAAAA 57.070 28.000 8.28 0.00 37.34 1.94
617 623 2.071540 TGCAACTTCTCTGATTCTGCG 58.928 47.619 0.00 0.00 0.00 5.18
812 928 0.328258 CCATTCGTCCCCAACCTCTT 59.672 55.000 0.00 0.00 0.00 2.85
829 945 3.083349 CCCCAGCCGTCAGATCCA 61.083 66.667 0.00 0.00 0.00 3.41
1222 1375 2.586792 GGCGAGGCAGAAGGTGAT 59.413 61.111 0.00 0.00 0.00 3.06
1748 1986 4.724279 AGCTTGGGTATCGGGATTAAAT 57.276 40.909 0.00 0.00 0.00 1.40
1918 2174 4.363138 CGAGGATCAAAGATGATGTCGAA 58.637 43.478 11.80 0.00 46.30 3.71
1931 2187 2.759973 AGAGCGGCCGAGGATCAA 60.760 61.111 33.48 0.00 33.17 2.57
2038 2309 0.250124 TTGTGCCAATCGTCGTTCCT 60.250 50.000 0.00 0.00 0.00 3.36
2046 2317 2.676121 TGCCCCTTGTGCCAATCG 60.676 61.111 0.00 0.00 0.00 3.34
2047 2318 1.907807 TGTGCCCCTTGTGCCAATC 60.908 57.895 0.00 0.00 0.00 2.67
2048 2319 2.200930 TGTGCCCCTTGTGCCAAT 59.799 55.556 0.00 0.00 0.00 3.16
2610 2904 0.252284 ACCAGAACAGGATCTCCCGT 60.252 55.000 0.00 0.00 40.87 5.28
2678 2978 3.513515 GAGAAGACCACCACTCTCTGATT 59.486 47.826 0.00 0.00 0.00 2.57
2679 2979 3.096092 GAGAAGACCACCACTCTCTGAT 58.904 50.000 0.00 0.00 0.00 2.90
3326 3671 3.066342 GTCTACTCTACCGCATTAGCACA 59.934 47.826 0.00 0.00 42.27 4.57
3494 3848 1.237954 TGCGCTTGCGGGTATTTCAA 61.238 50.000 16.79 0.00 43.34 2.69


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

AutoCloner maintained by Alex Coulton.