Multiple sequence alignment - TraesCS5D01G104200

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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 TraesCS5D01G104200 chr5D 100.000 3311 0 0 1 3311 118006867 118010177 0.000000e+00 6115.0
1 TraesCS5D01G104200 chr5D 81.871 171 27 4 2992 3160 118007904 118008072 1.240000e-29 141.0
2 TraesCS5D01G104200 chr5D 81.765 170 29 2 1038 1206 118009858 118010026 1.240000e-29 141.0
3 TraesCS5D01G104200 chr5D 86.076 79 11 0 433 511 55019723 55019801 5.890000e-13 86.1
4 TraesCS5D01G104200 chr5D 100.000 28 0 0 499 526 108084938 108084965 6.000000e-03 52.8
5 TraesCS5D01G104200 chr5B 90.377 2837 154 42 530 3311 128856309 128853537 0.000000e+00 3616.0
6 TraesCS5D01G104200 chr5B 84.118 170 25 2 1038 1206 128853856 128853688 2.640000e-36 163.0
7 TraesCS5D01G104200 chr5B 83.444 151 25 0 3010 3160 128855767 128855617 1.240000e-29 141.0
8 TraesCS5D01G104200 chr5B 82.828 99 17 0 413 511 361014268 361014170 4.550000e-14 89.8
9 TraesCS5D01G104200 chr5A 91.235 1449 69 24 632 2060 127519373 127520783 0.000000e+00 1919.0
10 TraesCS5D01G104200 chr5A 89.562 1188 65 22 2150 3311 127532199 127533353 0.000000e+00 1452.0
11 TraesCS5D01G104200 chr5A 84.118 170 25 2 1038 1206 127533033 127533201 2.640000e-36 163.0
12 TraesCS5D01G104200 chr5A 83.444 151 25 0 3010 3160 127519803 127519953 1.240000e-29 141.0
13 TraesCS5D01G104200 chr4D 88.086 512 56 5 1 510 122691179 122690671 1.310000e-168 603.0
14 TraesCS5D01G104200 chr6A 84.241 514 74 7 1 510 324289810 324290320 8.250000e-136 494.0
15 TraesCS5D01G104200 chr2B 84.405 513 62 11 1 511 257530705 257530209 3.840000e-134 488.0
16 TraesCS5D01G104200 chr6D 82.592 517 80 7 1 511 80507986 80507474 6.520000e-122 448.0
17 TraesCS5D01G104200 chr6D 83.516 455 68 7 15 465 262183212 262182761 5.110000e-113 418.0
18 TraesCS5D01G104200 chrUn 84.950 299 40 5 29 324 316647383 316647087 6.950000e-77 298.0
19 TraesCS5D01G104200 chr3B 84.950 299 40 5 29 324 35039967 35039671 6.950000e-77 298.0
20 TraesCS5D01G104200 chr3B 84.950 299 40 5 29 324 35121153 35120857 6.950000e-77 298.0
21 TraesCS5D01G104200 chr3D 83.886 211 31 3 303 511 116330733 116330524 7.250000e-47 198.0
22 TraesCS5D01G104200 chr4B 82.819 227 32 7 287 510 491831686 491831908 2.610000e-46 196.0
23 TraesCS5D01G104200 chr1A 81.043 211 34 5 303 510 576382182 576382389 2.640000e-36 163.0
24 TraesCS5D01G104200 chr4A 75.532 282 55 10 233 511 663420978 663420708 3.470000e-25 126.0


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 TraesCS5D01G104200 chr5D 118006867 118010177 3310 False 2132.333333 6115 87.878667 1 3311 3 chr5D.!!$F3 3310
1 TraesCS5D01G104200 chr5B 128853537 128856309 2772 True 1306.666667 3616 85.979667 530 3311 3 chr5B.!!$R2 2781
2 TraesCS5D01G104200 chr5A 127519373 127520783 1410 False 1030.000000 1919 87.339500 632 3160 2 chr5A.!!$F1 2528
3 TraesCS5D01G104200 chr5A 127532199 127533353 1154 False 807.500000 1452 86.840000 1038 3311 2 chr5A.!!$F2 2273
4 TraesCS5D01G104200 chr4D 122690671 122691179 508 True 603.000000 603 88.086000 1 510 1 chr4D.!!$R1 509
5 TraesCS5D01G104200 chr6A 324289810 324290320 510 False 494.000000 494 84.241000 1 510 1 chr6A.!!$F1 509
6 TraesCS5D01G104200 chr6D 80507474 80507986 512 True 448.000000 448 82.592000 1 511 1 chr6D.!!$R1 510

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
661 672 0.104304 AACGAGCGACCAAGTCAAGT 59.896 50.0 0.00 0.0 32.09 3.16 F
928 958 0.248784 GCTGCGCTTCCATTCCATTC 60.249 55.0 9.73 0.0 0.00 2.67 F
930 960 0.323269 TGCGCTTCCATTCCATTCCA 60.323 50.0 9.73 0.0 0.00 3.53 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1914 1983 0.391661 TCTCTGCGTGATGCCTTTCC 60.392 55.000 0.0 0.0 45.6 3.13 R
2200 2270 0.875059 CAGCAAGGTTCGGGAAAGTC 59.125 55.000 0.0 0.0 0.0 3.01 R
2509 2603 1.417517 ACACTGTTCTGATGAGGCACA 59.582 47.619 0.0 0.0 0.0 4.57 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
81 82 3.314331 CCTCCAGTGGCCTGTCGT 61.314 66.667 3.51 0.00 36.95 4.34
109 110 1.300233 CGGCTAGATCCGCTCCAAC 60.300 63.158 0.00 0.00 43.18 3.77
160 163 1.816863 GAGGGTTGGACAGCTCGTGA 61.817 60.000 0.00 0.00 0.00 4.35
284 288 2.240414 GGGGGAATAGAAAAAGGGACGA 59.760 50.000 0.00 0.00 0.00 4.20
285 289 3.276857 GGGGAATAGAAAAAGGGACGAC 58.723 50.000 0.00 0.00 0.00 4.34
300 304 1.099295 ACGACTGTGTCACCGACAGA 61.099 55.000 8.08 0.00 43.57 3.41
301 305 0.241213 CGACTGTGTCACCGACAGAT 59.759 55.000 8.08 0.00 43.57 2.90
378 382 0.457851 CAAACACGGCCCAAACTTGA 59.542 50.000 0.00 0.00 0.00 3.02
390 394 2.517959 CAAACTTGAGCCAGGAATGGA 58.482 47.619 0.00 0.00 0.00 3.41
398 402 2.100418 GAGCCAGGAATGGATCAAAAGC 59.900 50.000 7.63 0.00 43.36 3.51
399 403 1.202336 GCCAGGAATGGATCAAAAGCG 60.202 52.381 0.00 0.00 0.00 4.68
415 419 0.601841 AGCGGACCGAAAACGAACAT 60.602 50.000 20.50 0.00 0.00 2.71
421 425 3.002965 GGACCGAAAACGAACATTTGTCT 59.997 43.478 0.00 0.00 0.00 3.41
422 426 3.947626 ACCGAAAACGAACATTTGTCTG 58.052 40.909 0.00 0.00 0.00 3.51
465 469 4.461198 CAAGGTTTCTGTCTGTTTACCCT 58.539 43.478 0.00 0.00 0.00 4.34
469 473 4.515567 GGTTTCTGTCTGTTTACCCTCAAG 59.484 45.833 0.00 0.00 0.00 3.02
495 499 1.378119 GGGTGGACGATTTGGGGTC 60.378 63.158 0.00 0.00 0.00 4.46
496 500 1.743995 GGTGGACGATTTGGGGTCG 60.744 63.158 0.00 0.00 44.26 4.79
510 514 2.604174 GGTCGTGCGTTGGAGTTGG 61.604 63.158 0.00 0.00 0.00 3.77
511 515 1.593209 GTCGTGCGTTGGAGTTGGA 60.593 57.895 0.00 0.00 0.00 3.53
512 516 1.300620 TCGTGCGTTGGAGTTGGAG 60.301 57.895 0.00 0.00 0.00 3.86
513 517 1.594293 CGTGCGTTGGAGTTGGAGT 60.594 57.895 0.00 0.00 0.00 3.85
514 518 1.157870 CGTGCGTTGGAGTTGGAGTT 61.158 55.000 0.00 0.00 0.00 3.01
515 519 0.307760 GTGCGTTGGAGTTGGAGTTG 59.692 55.000 0.00 0.00 0.00 3.16
516 520 0.817634 TGCGTTGGAGTTGGAGTTGG 60.818 55.000 0.00 0.00 0.00 3.77
517 521 0.534203 GCGTTGGAGTTGGAGTTGGA 60.534 55.000 0.00 0.00 0.00 3.53
518 522 1.512926 CGTTGGAGTTGGAGTTGGAG 58.487 55.000 0.00 0.00 0.00 3.86
519 523 1.202651 CGTTGGAGTTGGAGTTGGAGT 60.203 52.381 0.00 0.00 0.00 3.85
520 524 2.745152 CGTTGGAGTTGGAGTTGGAGTT 60.745 50.000 0.00 0.00 0.00 3.01
521 525 2.618709 GTTGGAGTTGGAGTTGGAGTTG 59.381 50.000 0.00 0.00 0.00 3.16
522 526 1.142870 TGGAGTTGGAGTTGGAGTTGG 59.857 52.381 0.00 0.00 0.00 3.77
523 527 1.239347 GAGTTGGAGTTGGAGTTGGC 58.761 55.000 0.00 0.00 0.00 4.52
524 528 0.178990 AGTTGGAGTTGGAGTTGGCC 60.179 55.000 0.00 0.00 0.00 5.36
525 529 0.178990 GTTGGAGTTGGAGTTGGCCT 60.179 55.000 3.32 0.00 0.00 5.19
526 530 0.178992 TTGGAGTTGGAGTTGGCCTG 60.179 55.000 3.32 0.00 0.00 4.85
527 531 1.059584 TGGAGTTGGAGTTGGCCTGA 61.060 55.000 3.32 0.00 0.00 3.86
528 532 0.329596 GGAGTTGGAGTTGGCCTGAT 59.670 55.000 3.32 0.00 0.00 2.90
540 544 1.691219 GCCTGATGAGGGTTTGGGA 59.309 57.895 0.00 0.00 40.19 4.37
545 549 0.259938 GATGAGGGTTTGGGATGGCT 59.740 55.000 0.00 0.00 0.00 4.75
548 552 3.076916 GGGTTTGGGATGGCTGGC 61.077 66.667 0.00 0.00 0.00 4.85
559 563 0.549950 ATGGCTGGCTGTAGATGCTT 59.450 50.000 2.00 0.00 0.00 3.91
572 576 6.474102 GCTGTAGATGCTTTGAGTCTACTTAC 59.526 42.308 11.61 0.68 42.89 2.34
652 663 1.134694 GATTTGCCAACGAGCGACC 59.865 57.895 0.00 0.00 34.65 4.79
658 669 1.300620 CCAACGAGCGACCAAGTCA 60.301 57.895 0.00 0.00 32.09 3.41
660 671 0.508641 CAACGAGCGACCAAGTCAAG 59.491 55.000 0.00 0.00 32.09 3.02
661 672 0.104304 AACGAGCGACCAAGTCAAGT 59.896 50.000 0.00 0.00 32.09 3.16
663 674 0.508641 CGAGCGACCAAGTCAAGTTG 59.491 55.000 0.00 0.00 32.09 3.16
693 707 2.169832 TGAGTAGCAACCACAGCTTC 57.830 50.000 0.00 0.00 43.25 3.86
698 712 0.882042 AGCAACCACAGCTTCGACAG 60.882 55.000 0.00 0.00 39.87 3.51
726 740 0.523335 GCAAAGCCGGCGAAATACAG 60.523 55.000 23.20 7.51 0.00 2.74
752 766 1.521457 GGCAATGCAGGACGATCGA 60.521 57.895 24.34 0.00 0.00 3.59
926 956 2.475466 CGCTGCGCTTCCATTCCAT 61.475 57.895 9.88 0.00 0.00 3.41
927 957 1.811860 GCTGCGCTTCCATTCCATT 59.188 52.632 9.73 0.00 0.00 3.16
928 958 0.248784 GCTGCGCTTCCATTCCATTC 60.249 55.000 9.73 0.00 0.00 2.67
929 959 0.383231 CTGCGCTTCCATTCCATTCC 59.617 55.000 9.73 0.00 0.00 3.01
930 960 0.323269 TGCGCTTCCATTCCATTCCA 60.323 50.000 9.73 0.00 0.00 3.53
941 971 1.153628 CCATTCCAGACCCGTCGAC 60.154 63.158 5.18 5.18 34.09 4.20
1224 1263 4.856801 CCAGGTGCGCGCCCTATT 62.857 66.667 35.27 15.43 0.00 1.73
1225 1264 3.272334 CAGGTGCGCGCCCTATTC 61.272 66.667 35.27 10.57 0.00 1.75
1244 1283 2.184579 CTTCCCTCCCTCGCGTTC 59.815 66.667 5.77 0.00 0.00 3.95
1255 1294 1.982073 CTCGCGTTCCCAGAATTGGC 61.982 60.000 5.77 0.00 43.58 4.52
1285 1324 1.398198 CGATCGGATTCGTACGGAGAC 60.398 57.143 16.52 5.20 37.69 3.36
1289 1328 2.609459 TCGGATTCGTACGGAGACTTAC 59.391 50.000 16.52 0.00 37.69 2.34
1301 1340 2.928116 GGAGACTTACCGGTCGATTTTG 59.072 50.000 12.40 0.00 40.76 2.44
1399 1441 4.463879 AAGGAGCTCTGCGCGCAT 62.464 61.111 36.48 20.97 45.59 4.73
1416 1458 4.917998 CGCGCATGTAGATTTCTGTACTAT 59.082 41.667 8.75 0.00 0.00 2.12
1421 1463 9.678941 CGCATGTAGATTTCTGTACTATTCTTA 57.321 33.333 0.00 0.00 0.00 2.10
1442 1484 8.076714 TCTTATGGTCGTAGTAGTACAATACG 57.923 38.462 13.25 13.25 42.70 3.06
1443 1485 5.679734 ATGGTCGTAGTAGTACAATACGG 57.320 43.478 17.23 4.67 41.88 4.02
1444 1486 4.513442 TGGTCGTAGTAGTACAATACGGT 58.487 43.478 17.23 0.00 41.88 4.83
1445 1487 5.666462 TGGTCGTAGTAGTACAATACGGTA 58.334 41.667 17.23 0.00 41.88 4.02
1524 1566 0.818852 TGGACGCGTATGATCCCGTA 60.819 55.000 13.97 0.00 33.63 4.02
1675 1740 6.049149 CGAATCACACTTACCCTACATCAAT 58.951 40.000 0.00 0.00 0.00 2.57
1676 1741 6.201044 CGAATCACACTTACCCTACATCAATC 59.799 42.308 0.00 0.00 0.00 2.67
1677 1742 6.560003 ATCACACTTACCCTACATCAATCA 57.440 37.500 0.00 0.00 0.00 2.57
1812 1881 1.073897 GAGCAAGGGCAGTGAACCT 59.926 57.895 0.00 0.00 44.61 3.50
1941 2010 2.015736 ATCACGCAGAGATGTTGGTC 57.984 50.000 0.00 0.00 36.27 4.02
2083 2153 4.467198 TCTCTCTTAAGCCTAAAACCCG 57.533 45.455 0.00 0.00 0.00 5.28
2084 2154 3.836562 TCTCTCTTAAGCCTAAAACCCGT 59.163 43.478 0.00 0.00 0.00 5.28
2114 2184 3.802948 ATCCATGAACTAGTGTCGTCC 57.197 47.619 0.00 0.00 0.00 4.79
2133 2203 6.150140 GTCGTCCTCTTAGTTAAACACCTCTA 59.850 42.308 0.00 0.00 0.00 2.43
2135 2205 6.150809 CGTCCTCTTAGTTAAACACCTCTAGT 59.849 42.308 0.00 0.00 0.00 2.57
2170 2240 9.423061 CAAAATATCTTCCCTGTTTTACTTTGG 57.577 33.333 0.00 0.00 0.00 3.28
2188 2258 2.291365 TGGATTGTCCATCATTGCTCG 58.709 47.619 0.00 0.00 42.67 5.03
2194 2264 0.829990 TCCATCATTGCTCGCCTGTA 59.170 50.000 0.00 0.00 0.00 2.74
2200 2270 3.317150 TCATTGCTCGCCTGTATTATCG 58.683 45.455 0.00 0.00 0.00 2.92
2208 2278 3.057734 CGCCTGTATTATCGACTTTCCC 58.942 50.000 0.00 0.00 0.00 3.97
2232 2302 1.584380 CTTGCTGCAGGGCTGTTCTC 61.584 60.000 17.12 0.00 0.00 2.87
2346 2416 0.759346 ACTCTTCGCTGAACCCAGTT 59.241 50.000 0.00 0.00 42.35 3.16
2347 2417 1.141053 ACTCTTCGCTGAACCCAGTTT 59.859 47.619 0.00 0.00 42.35 2.66
2348 2418 1.532868 CTCTTCGCTGAACCCAGTTTG 59.467 52.381 0.00 0.00 42.35 2.93
2351 2421 1.008538 CGCTGAACCCAGTTTGTGC 60.009 57.895 0.00 0.00 42.35 4.57
2352 2422 1.723608 CGCTGAACCCAGTTTGTGCA 61.724 55.000 0.00 0.00 42.35 4.57
2353 2423 0.675633 GCTGAACCCAGTTTGTGCAT 59.324 50.000 0.00 0.00 42.35 3.96
2354 2424 1.336240 GCTGAACCCAGTTTGTGCATC 60.336 52.381 0.00 0.00 42.35 3.91
2357 2427 3.030291 TGAACCCAGTTTGTGCATCTTT 58.970 40.909 0.00 0.00 0.00 2.52
2358 2428 3.181477 TGAACCCAGTTTGTGCATCTTTG 60.181 43.478 0.00 0.00 0.00 2.77
2359 2429 2.387757 ACCCAGTTTGTGCATCTTTGT 58.612 42.857 0.00 0.00 0.00 2.83
2360 2430 2.101249 ACCCAGTTTGTGCATCTTTGTG 59.899 45.455 0.00 0.00 0.00 3.33
2393 2479 6.497437 CATCTTTGTGAATAAATGGATCGCA 58.503 36.000 0.00 0.00 0.00 5.10
2401 2487 5.467735 TGAATAAATGGATCGCAGATGTCAG 59.532 40.000 0.00 0.00 45.12 3.51
2403 2489 2.816204 ATGGATCGCAGATGTCAGAG 57.184 50.000 0.00 0.00 45.12 3.35
2404 2490 1.478631 TGGATCGCAGATGTCAGAGT 58.521 50.000 0.00 0.00 45.12 3.24
2405 2491 1.827344 TGGATCGCAGATGTCAGAGTT 59.173 47.619 0.00 0.00 45.12 3.01
2406 2492 2.159184 TGGATCGCAGATGTCAGAGTTC 60.159 50.000 0.00 0.00 45.12 3.01
2407 2493 2.115595 GATCGCAGATGTCAGAGTTCG 58.884 52.381 0.00 0.00 45.12 3.95
2408 2494 0.456824 TCGCAGATGTCAGAGTTCGC 60.457 55.000 0.00 0.00 0.00 4.70
2409 2495 0.733909 CGCAGATGTCAGAGTTCGCA 60.734 55.000 0.00 0.00 0.00 5.10
2410 2496 1.432514 GCAGATGTCAGAGTTCGCAA 58.567 50.000 0.00 0.00 0.00 4.85
2411 2497 1.127582 GCAGATGTCAGAGTTCGCAAC 59.872 52.381 0.00 0.00 0.00 4.17
2416 2502 2.473816 TGTCAGAGTTCGCAACTTCAG 58.526 47.619 3.56 0.00 43.03 3.02
2419 2505 3.183373 GTCAGAGTTCGCAACTTCAGAAG 59.817 47.826 8.77 8.77 43.03 2.85
2462 2556 5.848406 GCAAGTAGCAGACAATATCCTAGT 58.152 41.667 0.00 0.00 44.79 2.57
2463 2557 6.982852 GCAAGTAGCAGACAATATCCTAGTA 58.017 40.000 0.00 0.00 44.79 1.82
2464 2558 6.864165 GCAAGTAGCAGACAATATCCTAGTAC 59.136 42.308 0.00 0.00 44.79 2.73
2465 2559 7.470147 GCAAGTAGCAGACAATATCCTAGTACA 60.470 40.741 0.00 0.00 44.79 2.90
2466 2560 8.580720 CAAGTAGCAGACAATATCCTAGTACAT 58.419 37.037 0.00 0.00 0.00 2.29
2467 2561 8.116651 AGTAGCAGACAATATCCTAGTACATG 57.883 38.462 0.00 0.00 0.00 3.21
2468 2562 5.788450 AGCAGACAATATCCTAGTACATGC 58.212 41.667 0.00 0.00 0.00 4.06
2490 2584 6.124340 TGCTACATGTGGATTCTTGATTGAT 58.876 36.000 14.15 0.00 0.00 2.57
2537 2631 6.294176 GCCTCATCAGAACAGTGTTATTTGTT 60.294 38.462 8.88 1.05 40.04 2.83
2572 2666 4.094739 TCAATTGCACGAATCCTGTATGTG 59.905 41.667 0.00 0.00 0.00 3.21
2813 2914 3.866356 GGTACAAACCGTCCGCTC 58.134 61.111 0.00 0.00 35.62 5.03
2814 2915 1.005867 GGTACAAACCGTCCGCTCA 60.006 57.895 0.00 0.00 35.62 4.26
2850 2951 6.432162 TCCCTTCTTTTCTTGTTCATCATCAG 59.568 38.462 0.00 0.00 0.00 2.90
3058 3167 3.599584 AGCTACTACGCGCTGGAA 58.400 55.556 5.73 0.00 34.69 3.53
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
78 79 0.739462 CTAGCCGGATTTGTGCACGA 60.739 55.000 13.13 7.71 0.00 4.35
81 82 1.475034 GGATCTAGCCGGATTTGTGCA 60.475 52.381 5.05 0.00 0.00 4.57
115 117 2.979676 CCTTCAGCGCAACAGGCA 60.980 61.111 11.47 0.00 45.17 4.75
142 144 1.194781 ATCACGAGCTGTCCAACCCT 61.195 55.000 0.00 0.00 0.00 4.34
160 163 3.649277 GACCGCGTGCTCTCCACAT 62.649 63.158 4.92 0.00 44.91 3.21
246 249 2.234296 CCTCCCCCAAACTCCAGCT 61.234 63.158 0.00 0.00 0.00 4.24
249 252 2.534272 CCCCTCCCCCAAACTCCA 60.534 66.667 0.00 0.00 0.00 3.86
284 288 0.318441 CCATCTGTCGGTGACACAGT 59.682 55.000 8.08 0.00 37.67 3.55
285 289 0.390340 CCCATCTGTCGGTGACACAG 60.390 60.000 8.08 3.28 37.67 3.66
314 318 4.415501 GCGACGCGTGCTCTTGTG 62.416 66.667 20.70 0.00 0.00 3.33
335 339 4.578898 AACGGACACGCGCAGACA 62.579 61.111 5.73 0.00 46.04 3.41
378 382 2.105766 GCTTTTGATCCATTCCTGGCT 58.894 47.619 0.00 0.00 42.80 4.75
390 394 1.069500 CGTTTTCGGTCCGCTTTTGAT 60.069 47.619 6.34 0.00 39.94 2.57
393 397 1.015868 TTCGTTTTCGGTCCGCTTTT 58.984 45.000 6.34 0.00 44.25 2.27
398 402 2.286536 ACAAATGTTCGTTTTCGGTCCG 60.287 45.455 4.39 4.39 44.25 4.79
399 403 3.002965 AGACAAATGTTCGTTTTCGGTCC 59.997 43.478 0.00 0.00 44.25 4.46
441 445 4.204799 GGTAAACAGACAGAAACCTTGGT 58.795 43.478 0.00 0.00 0.00 3.67
444 448 4.165372 TGAGGGTAAACAGACAGAAACCTT 59.835 41.667 0.00 0.00 0.00 3.50
445 449 3.714798 TGAGGGTAAACAGACAGAAACCT 59.285 43.478 0.00 0.00 0.00 3.50
446 450 4.081322 TGAGGGTAAACAGACAGAAACC 57.919 45.455 0.00 0.00 0.00 3.27
495 499 1.157870 AACTCCAACTCCAACGCACG 61.158 55.000 0.00 0.00 0.00 5.34
496 500 0.307760 CAACTCCAACTCCAACGCAC 59.692 55.000 0.00 0.00 0.00 5.34
499 503 1.202651 ACTCCAACTCCAACTCCAACG 60.203 52.381 0.00 0.00 0.00 4.10
510 514 1.003580 TCATCAGGCCAACTCCAACTC 59.996 52.381 5.01 0.00 0.00 3.01
511 515 1.004044 CTCATCAGGCCAACTCCAACT 59.996 52.381 5.01 0.00 0.00 3.16
512 516 1.457346 CTCATCAGGCCAACTCCAAC 58.543 55.000 5.01 0.00 0.00 3.77
513 517 0.329261 CCTCATCAGGCCAACTCCAA 59.671 55.000 5.01 0.00 30.98 3.53
514 518 1.565390 CCCTCATCAGGCCAACTCCA 61.565 60.000 5.01 0.00 38.72 3.86
515 519 1.225704 CCCTCATCAGGCCAACTCC 59.774 63.158 5.01 0.00 38.72 3.85
516 520 0.329596 AACCCTCATCAGGCCAACTC 59.670 55.000 5.01 0.00 38.72 3.01
517 521 0.779997 AAACCCTCATCAGGCCAACT 59.220 50.000 5.01 0.00 38.72 3.16
518 522 0.890683 CAAACCCTCATCAGGCCAAC 59.109 55.000 5.01 0.00 38.72 3.77
519 523 0.251742 CCAAACCCTCATCAGGCCAA 60.252 55.000 5.01 0.00 38.72 4.52
520 524 1.383799 CCAAACCCTCATCAGGCCA 59.616 57.895 5.01 0.00 38.72 5.36
521 525 1.380380 CCCAAACCCTCATCAGGCC 60.380 63.158 0.00 0.00 38.72 5.19
522 526 0.259938 ATCCCAAACCCTCATCAGGC 59.740 55.000 0.00 0.00 38.72 4.85
523 527 1.410648 CCATCCCAAACCCTCATCAGG 60.411 57.143 0.00 0.00 39.98 3.86
524 528 2.025863 GCCATCCCAAACCCTCATCAG 61.026 57.143 0.00 0.00 0.00 2.90
525 529 0.033208 GCCATCCCAAACCCTCATCA 60.033 55.000 0.00 0.00 0.00 3.07
526 530 0.259938 AGCCATCCCAAACCCTCATC 59.740 55.000 0.00 0.00 0.00 2.92
527 531 0.032813 CAGCCATCCCAAACCCTCAT 60.033 55.000 0.00 0.00 0.00 2.90
528 532 1.383799 CAGCCATCCCAAACCCTCA 59.616 57.895 0.00 0.00 0.00 3.86
540 544 0.549950 AAGCATCTACAGCCAGCCAT 59.450 50.000 0.00 0.00 0.00 4.40
545 549 2.568956 AGACTCAAAGCATCTACAGCCA 59.431 45.455 0.00 0.00 0.00 4.75
548 552 6.975772 GGTAAGTAGACTCAAAGCATCTACAG 59.024 42.308 11.94 0.00 44.83 2.74
559 563 6.000219 ACTTGTCGTAGGTAAGTAGACTCAA 59.000 40.000 6.20 0.00 33.22 3.02
572 576 3.526931 ATGGATCACACTTGTCGTAGG 57.473 47.619 0.00 0.00 0.00 3.18
613 624 3.732212 CATTGCCTCAATGGATCTACGA 58.268 45.455 10.74 0.00 45.03 3.43
646 657 1.498865 CGCAACTTGACTTGGTCGCT 61.499 55.000 0.00 0.00 34.95 4.93
652 663 2.802247 TCACTCATCGCAACTTGACTTG 59.198 45.455 0.00 0.00 0.00 3.16
658 669 3.325293 ACTCATCACTCATCGCAACTT 57.675 42.857 0.00 0.00 0.00 2.66
660 671 2.537625 GCTACTCATCACTCATCGCAAC 59.462 50.000 0.00 0.00 0.00 4.17
661 672 2.166254 TGCTACTCATCACTCATCGCAA 59.834 45.455 0.00 0.00 0.00 4.85
663 674 2.498807 TGCTACTCATCACTCATCGC 57.501 50.000 0.00 0.00 0.00 4.58
693 707 1.135859 GCTTTGCCTGTCATTCTGTCG 60.136 52.381 0.00 0.00 0.00 4.35
752 766 0.329596 GTTGAGGCTCCTGTGGGATT 59.670 55.000 12.86 0.00 41.36 3.01
926 956 1.228337 TCTGTCGACGGGTCTGGAA 60.228 57.895 23.78 0.00 0.00 3.53
927 957 1.970114 GTCTGTCGACGGGTCTGGA 60.970 63.158 23.78 0.47 0.00 3.86
928 958 2.567049 GTCTGTCGACGGGTCTGG 59.433 66.667 23.78 1.99 0.00 3.86
929 959 2.567049 GGTCTGTCGACGGGTCTG 59.433 66.667 23.78 3.66 41.16 3.51
930 960 3.054503 CGGTCTGTCGACGGGTCT 61.055 66.667 23.78 0.00 41.16 3.85
1222 1261 1.395826 CGCGAGGGAGGGAAGAGAAT 61.396 60.000 0.00 0.00 0.00 2.40
1223 1262 2.052690 CGCGAGGGAGGGAAGAGAA 61.053 63.158 0.00 0.00 0.00 2.87
1224 1263 2.440430 CGCGAGGGAGGGAAGAGA 60.440 66.667 0.00 0.00 0.00 3.10
1225 1264 2.286127 GAACGCGAGGGAGGGAAGAG 62.286 65.000 15.93 0.00 0.00 2.85
1244 1283 2.885676 CGCGATCGCCAATTCTGGG 61.886 63.158 32.63 12.68 43.74 4.45
1285 1324 7.042925 CCTTATAAGTCAAAATCGACCGGTAAG 60.043 40.741 7.34 4.86 36.52 2.34
1289 1328 5.006358 CACCTTATAAGTCAAAATCGACCGG 59.994 44.000 11.50 0.00 36.52 5.28
1301 1340 0.103572 TCCGCGGCACCTTATAAGTC 59.896 55.000 23.51 0.71 0.00 3.01
1416 1458 8.551205 CGTATTGTACTACTACGACCATAAGAA 58.449 37.037 13.58 0.00 40.38 2.52
1421 1463 5.126067 ACCGTATTGTACTACTACGACCAT 58.874 41.667 17.90 4.56 40.38 3.55
1457 1499 8.500753 ACACCGATTTTAGCAATATTCAAGTA 57.499 30.769 0.00 0.00 0.00 2.24
1532 1574 2.809446 TCAAGATCATACGCGTCCTTG 58.191 47.619 18.63 20.59 34.11 3.61
1621 1663 8.863872 ACAAAGCAAACTCCTTTATACTGTAT 57.136 30.769 5.53 5.53 31.70 2.29
1622 1664 9.781633 TTACAAAGCAAACTCCTTTATACTGTA 57.218 29.630 0.00 0.00 31.70 2.74
1626 1668 9.698617 CGTATTACAAAGCAAACTCCTTTATAC 57.301 33.333 0.00 0.00 31.70 1.47
1637 1702 7.197071 AGTGTGATTCGTATTACAAAGCAAA 57.803 32.000 1.21 0.00 32.74 3.68
1638 1703 6.795098 AGTGTGATTCGTATTACAAAGCAA 57.205 33.333 1.21 0.00 32.74 3.91
1914 1983 0.391661 TCTCTGCGTGATGCCTTTCC 60.392 55.000 0.00 0.00 45.60 3.13
1941 2010 2.045438 TAGCCATGGTTGCCCACG 60.045 61.111 14.67 0.00 45.65 4.94
2060 2130 5.051153 CGGGTTTTAGGCTTAAGAGAGATC 58.949 45.833 6.67 0.00 0.00 2.75
2061 2131 4.470304 ACGGGTTTTAGGCTTAAGAGAGAT 59.530 41.667 6.67 0.00 0.00 2.75
2068 2138 3.505480 TTCCACGGGTTTTAGGCTTAA 57.495 42.857 0.00 0.00 0.00 1.85
2083 2153 8.739972 ACACTAGTTCATGGATTTATTTTCCAC 58.260 33.333 0.00 0.00 45.71 4.02
2084 2154 8.877864 ACACTAGTTCATGGATTTATTTTCCA 57.122 30.769 0.00 0.00 46.86 3.53
2101 2171 7.013655 TGTTTAACTAAGAGGACGACACTAGTT 59.986 37.037 0.00 0.00 0.00 2.24
2133 2203 8.960591 CAGGGAAGATATTTTGTGTTGAATACT 58.039 33.333 0.00 0.00 0.00 2.12
2135 2205 8.877864 ACAGGGAAGATATTTTGTGTTGAATA 57.122 30.769 0.00 0.00 0.00 1.75
2170 2240 1.002033 GGCGAGCAATGATGGACAATC 60.002 52.381 0.00 0.00 35.67 2.67
2188 2258 3.057734 CGGGAAAGTCGATAATACAGGC 58.942 50.000 0.00 0.00 0.00 4.85
2194 2264 4.189231 CAAGGTTCGGGAAAGTCGATAAT 58.811 43.478 0.00 0.00 36.49 1.28
2200 2270 0.875059 CAGCAAGGTTCGGGAAAGTC 59.125 55.000 0.00 0.00 0.00 3.01
2208 2278 3.741476 GCCCTGCAGCAAGGTTCG 61.741 66.667 11.90 0.00 35.34 3.95
2232 2302 1.920574 CAGTAATCGCTCACACTTCCG 59.079 52.381 0.00 0.00 0.00 4.30
2346 2416 4.270566 GCACAAATTCACAAAGATGCACAA 59.729 37.500 0.00 0.00 0.00 3.33
2347 2417 3.803231 GCACAAATTCACAAAGATGCACA 59.197 39.130 0.00 0.00 0.00 4.57
2348 2418 3.803231 TGCACAAATTCACAAAGATGCAC 59.197 39.130 0.00 0.00 36.94 4.57
2351 2421 7.042321 ACAAAGATGCACAAATTCACAAAGATG 60.042 33.333 0.00 0.00 0.00 2.90
2352 2422 6.987992 ACAAAGATGCACAAATTCACAAAGAT 59.012 30.769 0.00 0.00 0.00 2.40
2353 2423 6.256104 CACAAAGATGCACAAATTCACAAAGA 59.744 34.615 0.00 0.00 0.00 2.52
2354 2424 6.256104 TCACAAAGATGCACAAATTCACAAAG 59.744 34.615 0.00 0.00 0.00 2.77
2357 2427 5.259832 TCACAAAGATGCACAAATTCACA 57.740 34.783 0.00 0.00 0.00 3.58
2358 2428 6.774354 ATTCACAAAGATGCACAAATTCAC 57.226 33.333 0.00 0.00 0.00 3.18
2359 2429 8.883954 TTTATTCACAAAGATGCACAAATTCA 57.116 26.923 0.00 0.00 0.00 2.57
2360 2430 9.749490 CATTTATTCACAAAGATGCACAAATTC 57.251 29.630 0.00 0.00 0.00 2.17
2393 2479 3.243873 TGAAGTTGCGAACTCTGACATCT 60.244 43.478 2.65 0.00 41.91 2.90
2410 2496 3.706594 TCACCACTCTGAACTTCTGAAGT 59.293 43.478 17.00 17.00 45.46 3.01
2411 2497 4.327982 TCACCACTCTGAACTTCTGAAG 57.672 45.455 15.59 15.59 0.00 3.02
2428 2514 1.443802 GCTACTTGCAGGAGTTCACC 58.556 55.000 1.40 0.00 42.31 4.02
2448 2534 8.526978 CATGTAGCATGTACTAGGATATTGTCT 58.473 37.037 0.00 0.00 0.00 3.41
2449 2535 8.307483 ACATGTAGCATGTACTAGGATATTGTC 58.693 37.037 12.42 0.00 0.00 3.18
2459 2553 6.731292 AGAATCCACATGTAGCATGTACTA 57.269 37.500 13.49 4.24 0.00 1.82
2460 2554 5.620738 AGAATCCACATGTAGCATGTACT 57.379 39.130 13.49 6.78 0.00 2.73
2461 2555 5.817296 TCAAGAATCCACATGTAGCATGTAC 59.183 40.000 13.49 0.00 0.00 2.90
2462 2556 5.988287 TCAAGAATCCACATGTAGCATGTA 58.012 37.500 13.49 1.47 0.00 2.29
2463 2557 4.847198 TCAAGAATCCACATGTAGCATGT 58.153 39.130 8.75 8.75 0.00 3.21
2464 2558 6.038936 TCAATCAAGAATCCACATGTAGCATG 59.961 38.462 0.00 7.48 0.00 4.06
2465 2559 6.124340 TCAATCAAGAATCCACATGTAGCAT 58.876 36.000 0.00 0.00 0.00 3.79
2466 2560 5.499313 TCAATCAAGAATCCACATGTAGCA 58.501 37.500 0.00 0.00 0.00 3.49
2467 2561 6.630444 ATCAATCAAGAATCCACATGTAGC 57.370 37.500 0.00 0.00 0.00 3.58
2468 2562 8.727910 CCATATCAATCAAGAATCCACATGTAG 58.272 37.037 0.00 0.00 0.00 2.74
2490 2584 5.764686 GGCACATCATCAGTTATTCACCATA 59.235 40.000 0.00 0.00 0.00 2.74
2509 2603 1.417517 ACACTGTTCTGATGAGGCACA 59.582 47.619 0.00 0.00 0.00 4.57
2563 2657 7.042456 GCAGTCTTGATTACATACACATACAGG 60.042 40.741 0.00 0.00 0.00 4.00
2572 2666 6.595716 AGGAACTTGCAGTCTTGATTACATAC 59.404 38.462 0.00 0.00 27.25 2.39
2704 2804 5.863935 GTCCTGTGGCTATCAAATTTTGTTC 59.136 40.000 8.89 0.00 0.00 3.18
2813 2914 2.125773 AGAAGGGAAGCAGCTGATTG 57.874 50.000 24.07 0.00 0.00 2.67
2814 2915 2.895242 AAGAAGGGAAGCAGCTGATT 57.105 45.000 18.77 18.77 0.00 2.57
2850 2951 2.338785 GCCTGAACTTGGCTGGCTC 61.339 63.158 2.00 0.00 46.38 4.70
3007 3116 3.092511 ATCCCCAGCACCATCGCT 61.093 61.111 0.00 0.00 45.21 4.93


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

AutoCloner maintained by Alex Coulton.