Multiple sequence alignment - TraesCS3D01G238300

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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 TraesCS3D01G238300 chr3D 100.000 3045 0 0 1 3045 329604881 329601837 0.000000e+00 5624.0
1 TraesCS3D01G238300 chr3A 92.726 2021 72 17 496 2492 444650625 444648656 0.000000e+00 2848.0
2 TraesCS3D01G238300 chr3A 91.922 359 27 2 2644 3001 444549508 444549151 4.530000e-138 501.0
3 TraesCS3D01G238300 chr3B 92.679 1762 72 26 503 2225 427164059 427162316 0.000000e+00 2486.0
4 TraesCS3D01G238300 chr3B 90.354 508 30 7 2557 3045 427156645 427156138 0.000000e+00 649.0
5 TraesCS3D01G238300 chr3B 87.234 423 44 10 7 424 427164546 427164129 9.880000e-130 473.0
6 TraesCS3D01G238300 chr3B 93.286 283 7 6 2268 2540 427161530 427161250 1.020000e-109 407.0
7 TraesCS3D01G238300 chr3B 97.143 35 1 0 2223 2257 427162234 427162200 3.280000e-05 60.2
8 TraesCS3D01G238300 chrUn 81.752 411 53 18 28 421 294376819 294376414 1.050000e-84 324.0
9 TraesCS3D01G238300 chrUn 100.000 28 0 0 379 406 478521103 478521130 5.000000e-03 52.8
10 TraesCS3D01G238300 chr7B 77.865 384 62 16 29 390 641691032 641690650 1.840000e-52 217.0
11 TraesCS3D01G238300 chr7A 78.187 353 63 12 77 419 19927896 19927548 2.380000e-51 213.0
12 TraesCS3D01G238300 chr7A 89.655 58 4 2 2497 2552 143353143 143353200 4.210000e-09 73.1
13 TraesCS3D01G238300 chr6A 78.933 356 28 30 77 421 461650151 461649832 6.660000e-47 198.0
14 TraesCS3D01G238300 chr7D 89.041 146 6 4 2503 2639 124879225 124879081 4.040000e-39 172.0
15 TraesCS3D01G238300 chr7D 75.938 320 50 19 26 337 590120455 590120755 4.090000e-29 139.0
16 TraesCS3D01G238300 chr7D 100.000 28 0 0 379 406 29039751 29039778 5.000000e-03 52.8
17 TraesCS3D01G238300 chr4A 87.333 150 10 1 2504 2644 446620638 446620489 2.430000e-36 163.0
18 TraesCS3D01G238300 chr4A 100.000 28 0 0 379 406 701117789 701117762 5.000000e-03 52.8
19 TraesCS3D01G238300 chr4A 100.000 28 0 0 379 406 702857424 702857451 5.000000e-03 52.8
20 TraesCS3D01G238300 chr1B 89.623 106 9 2 1595 1699 662016747 662016851 1.900000e-27 134.0
21 TraesCS3D01G238300 chr1A 89.423 104 11 0 1595 1698 571737848 571737951 6.850000e-27 132.0
22 TraesCS3D01G238300 chr1A 84.800 125 16 3 1593 1716 571725102 571725224 4.120000e-24 122.0
23 TraesCS3D01G238300 chr1A 89.610 77 6 2 1623 1698 571744136 571744211 2.500000e-16 97.1
24 TraesCS3D01G238300 chr1D 90.000 100 8 2 1600 1698 475919062 475919160 8.860000e-26 128.0
25 TraesCS3D01G238300 chr1D 87.850 107 12 1 1593 1699 475864161 475864266 1.150000e-24 124.0
26 TraesCS3D01G238300 chr5D 82.143 140 25 0 1378 1517 434544566 434544705 1.480000e-23 121.0
27 TraesCS3D01G238300 chr2A 84.426 122 10 2 2504 2616 607947675 607947554 8.920000e-21 111.0
28 TraesCS3D01G238300 chr2B 83.486 109 13 4 1593 1699 99520980 99521085 2.500000e-16 97.1
29 TraesCS3D01G238300 chr2D 86.765 68 5 4 2572 2638 557667017 557666953 4.210000e-09 73.1


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 TraesCS3D01G238300 chr3D 329601837 329604881 3044 True 5624.00 5624 100.0000 1 3045 1 chr3D.!!$R1 3044
1 TraesCS3D01G238300 chr3A 444648656 444650625 1969 True 2848.00 2848 92.7260 496 2492 1 chr3A.!!$R2 1996
2 TraesCS3D01G238300 chr3B 427161250 427164546 3296 True 856.55 2486 92.5855 7 2540 4 chr3B.!!$R2 2533
3 TraesCS3D01G238300 chr3B 427156138 427156645 507 True 649.00 649 90.3540 2557 3045 1 chr3B.!!$R1 488

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
474 501 0.106149 AAAGTCCTGGAGCGAACGTT 59.894 50.0 0.00 0.00 0.0 3.99 F
475 502 0.319641 AAGTCCTGGAGCGAACGTTC 60.320 55.0 18.47 18.47 0.0 3.95 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1805 1848 0.244178 GTCTTCTGTCCCACGGAGAC 59.756 60.0 0.0 0.0 34.53 3.36 R
2445 3264 1.014352 CAATTCACGATTCCGACCCC 58.986 55.0 0.0 0.0 39.50 4.95 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
20 21 3.460857 CCTTTGGAATAGGGAGAGACG 57.539 52.381 0.00 0.00 0.00 4.18
50 51 2.649531 TACACTTTGGTCCTGGTTGG 57.350 50.000 0.00 0.00 37.10 3.77
62 63 2.316677 TCCTGGTTGGAGATACACCCTA 59.683 50.000 0.00 0.00 40.56 3.53
63 64 2.434702 CCTGGTTGGAGATACACCCTAC 59.565 54.545 0.00 0.00 38.35 3.18
64 65 3.104512 CTGGTTGGAGATACACCCTACA 58.895 50.000 0.00 0.00 31.33 2.74
65 66 2.835764 TGGTTGGAGATACACCCTACAC 59.164 50.000 0.00 0.00 31.33 2.90
67 68 2.756760 GTTGGAGATACACCCTACACGA 59.243 50.000 0.00 0.00 0.00 4.35
68 69 2.651455 TGGAGATACACCCTACACGAG 58.349 52.381 0.00 0.00 0.00 4.18
69 70 1.955080 GGAGATACACCCTACACGAGG 59.045 57.143 0.00 0.00 46.25 4.63
144 145 8.211629 AGAATAAACCTGACTTTCTTGTACACT 58.788 33.333 0.00 0.00 0.00 3.55
150 151 5.921408 CCTGACTTTCTTGTACACTAGTGTC 59.079 44.000 31.11 21.50 43.74 3.67
163 164 9.990360 TGTACACTAGTGTCTAAATTTTCATGA 57.010 29.630 31.11 6.52 43.74 3.07
199 200 3.370104 TGACTTCAGGGCAAAAAGGAAA 58.630 40.909 0.00 0.00 0.00 3.13
200 201 3.772025 TGACTTCAGGGCAAAAAGGAAAA 59.228 39.130 0.00 0.00 0.00 2.29
240 241 7.680730 AGAGGTCACTATTCACACTATTTTGT 58.319 34.615 0.00 0.00 0.00 2.83
241 242 8.157476 AGAGGTCACTATTCACACTATTTTGTT 58.843 33.333 0.00 0.00 0.00 2.83
243 244 7.936847 AGGTCACTATTCACACTATTTTGTTCA 59.063 33.333 0.00 0.00 0.00 3.18
280 281 7.832187 TCTTTTTGTAAAGAAGACAAGAGGGAA 59.168 33.333 0.00 0.00 45.08 3.97
284 285 8.533569 TTGTAAAGAAGACAAGAGGGAATTTT 57.466 30.769 0.00 0.00 33.03 1.82
286 287 8.630037 TGTAAAGAAGACAAGAGGGAATTTTTC 58.370 33.333 0.00 0.00 0.00 2.29
288 289 8.996651 AAAGAAGACAAGAGGGAATTTTTCTA 57.003 30.769 0.00 0.00 0.00 2.10
323 326 5.630121 TCACAAGTACAATGGAAGGTCAAT 58.370 37.500 0.00 0.00 0.00 2.57
410 416 5.585047 GTGTAGATACATCCAGGAACCAAAC 59.415 44.000 0.00 0.00 38.63 2.93
411 417 4.927267 AGATACATCCAGGAACCAAACA 57.073 40.909 0.00 0.00 0.00 2.83
448 474 1.026182 TGTGCGCAGGGATCAACATC 61.026 55.000 12.22 0.00 0.00 3.06
453 479 1.522355 CAGGGATCAACATCGCGCT 60.522 57.895 5.56 0.00 44.84 5.92
467 494 2.394563 GCGCTGAAAGTCCTGGAGC 61.395 63.158 0.00 0.00 35.30 4.70
468 495 2.097038 CGCTGAAAGTCCTGGAGCG 61.097 63.158 10.66 10.66 45.60 5.03
469 496 1.293498 GCTGAAAGTCCTGGAGCGA 59.707 57.895 0.00 0.00 35.30 4.93
470 497 0.320771 GCTGAAAGTCCTGGAGCGAA 60.321 55.000 0.00 0.00 35.30 4.70
471 498 1.433534 CTGAAAGTCCTGGAGCGAAC 58.566 55.000 0.00 0.00 0.00 3.95
472 499 0.319555 TGAAAGTCCTGGAGCGAACG 60.320 55.000 0.00 0.00 0.00 3.95
473 500 0.319641 GAAAGTCCTGGAGCGAACGT 60.320 55.000 0.00 0.00 0.00 3.99
474 501 0.106149 AAAGTCCTGGAGCGAACGTT 59.894 50.000 0.00 0.00 0.00 3.99
475 502 0.319641 AAGTCCTGGAGCGAACGTTC 60.320 55.000 18.47 18.47 0.00 3.95
485 512 2.447408 CGAACGTTCGCCCAATACA 58.553 52.632 34.54 0.00 44.26 2.29
486 513 0.791422 CGAACGTTCGCCCAATACAA 59.209 50.000 34.54 0.00 44.26 2.41
487 514 1.395608 CGAACGTTCGCCCAATACAAT 59.604 47.619 34.54 0.00 44.26 2.71
488 515 2.159626 CGAACGTTCGCCCAATACAATT 60.160 45.455 34.54 0.00 44.26 2.32
489 516 3.668491 CGAACGTTCGCCCAATACAATTT 60.668 43.478 34.54 0.00 44.26 1.82
490 517 4.435784 CGAACGTTCGCCCAATACAATTTA 60.436 41.667 34.54 0.00 44.26 1.40
491 518 4.345271 ACGTTCGCCCAATACAATTTAC 57.655 40.909 0.00 0.00 0.00 2.01
492 519 3.181518 ACGTTCGCCCAATACAATTTACG 60.182 43.478 0.00 0.00 0.00 3.18
493 520 3.181518 CGTTCGCCCAATACAATTTACGT 60.182 43.478 0.00 0.00 0.00 3.57
494 521 4.669708 CGTTCGCCCAATACAATTTACGTT 60.670 41.667 0.00 0.00 0.00 3.99
499 526 7.536855 TCGCCCAATACAATTTACGTTAAAAT 58.463 30.769 0.00 0.00 0.00 1.82
523 550 6.959639 AACCTTTCTCTTCATTGTAAGCAA 57.040 33.333 0.00 0.00 39.16 3.91
562 589 1.644786 GACCAACCAGCACGGCATAC 61.645 60.000 0.00 0.00 39.03 2.39
573 600 0.389426 ACGGCATACAACTGACCGAC 60.389 55.000 6.76 0.00 46.71 4.79
596 623 7.506328 ACCACTAACACCAAAAGAGAAATAC 57.494 36.000 0.00 0.00 0.00 1.89
689 716 1.886313 CAGCATCGCTAGTGCCCAG 60.886 63.158 0.00 0.00 43.50 4.45
695 722 4.496336 GCTAGTGCCCAGCCCCAG 62.496 72.222 0.00 0.00 32.68 4.45
740 769 8.023128 GCATTTGAATATTACACACACAAGTCT 58.977 33.333 0.00 0.00 0.00 3.24
752 781 1.069906 CACAAGTCTTTTCCTTCCGCG 60.070 52.381 0.00 0.00 0.00 6.46
827 856 2.435586 ATCCAGTGACGCTGCAGC 60.436 61.111 29.12 29.12 43.71 5.25
921 953 3.118454 CATCACGACCGCCCACAC 61.118 66.667 0.00 0.00 0.00 3.82
952 984 2.508439 CGTATGAACGCCGGCACT 60.508 61.111 28.98 12.90 43.12 4.40
976 1008 4.427661 GCTGACGGCTGAGCGAGT 62.428 66.667 0.00 3.92 38.06 4.18
983 1015 4.154347 GCTGAGCGAGTGGGAGGG 62.154 72.222 0.00 0.00 0.00 4.30
984 1016 2.363018 CTGAGCGAGTGGGAGGGA 60.363 66.667 0.00 0.00 0.00 4.20
985 1017 2.680352 TGAGCGAGTGGGAGGGAC 60.680 66.667 0.00 0.00 0.00 4.46
986 1018 3.827898 GAGCGAGTGGGAGGGACG 61.828 72.222 0.00 0.00 0.00 4.79
987 1019 4.361971 AGCGAGTGGGAGGGACGA 62.362 66.667 0.00 0.00 0.00 4.20
988 1020 3.827898 GCGAGTGGGAGGGACGAG 61.828 72.222 0.00 0.00 0.00 4.18
989 1021 3.141488 CGAGTGGGAGGGACGAGG 61.141 72.222 0.00 0.00 0.00 4.63
990 1022 2.037527 GAGTGGGAGGGACGAGGT 59.962 66.667 0.00 0.00 0.00 3.85
991 1023 2.283966 AGTGGGAGGGACGAGGTG 60.284 66.667 0.00 0.00 0.00 4.00
992 1024 2.603776 GTGGGAGGGACGAGGTGT 60.604 66.667 0.00 0.00 0.00 4.16
993 1025 2.603473 TGGGAGGGACGAGGTGTG 60.603 66.667 0.00 0.00 0.00 3.82
994 1026 4.083862 GGGAGGGACGAGGTGTGC 62.084 72.222 0.00 0.00 38.37 4.57
995 1027 3.311110 GGAGGGACGAGGTGTGCA 61.311 66.667 0.00 0.00 41.41 4.57
996 1028 2.262915 GAGGGACGAGGTGTGCAG 59.737 66.667 0.00 0.00 41.41 4.41
997 1029 3.941657 GAGGGACGAGGTGTGCAGC 62.942 68.421 0.00 0.00 41.41 5.25
998 1030 4.008933 GGGACGAGGTGTGCAGCT 62.009 66.667 3.35 3.35 41.41 4.24
1182 1214 2.355837 ATGTCGTCGTGCTGCGTT 60.356 55.556 0.00 0.00 42.13 4.84
1347 1379 6.698766 GCCTAAATCCAAGCTTGTTGATTATG 59.301 38.462 24.35 18.67 0.00 1.90
1409 1441 2.113774 CAGCCCAAGTGGAGCACA 59.886 61.111 11.73 0.00 36.74 4.57
1475 1507 1.488393 GGCTTCAGCTGGAGGAAGTAT 59.512 52.381 23.72 0.00 41.93 2.12
1520 1552 0.830444 AGTACCCAAGGTCAGCGACA 60.830 55.000 10.14 0.00 37.09 4.35
1522 1554 0.320374 TACCCAAGGTCAGCGACAAG 59.680 55.000 10.14 1.03 37.09 3.16
1549 1592 1.165907 CGAGCACCTCAAACCAAGCA 61.166 55.000 0.00 0.00 0.00 3.91
1560 1603 1.826385 AACCAAGCAAGCGAGCTATT 58.174 45.000 6.37 0.15 45.89 1.73
1699 1742 1.129998 CTCTTCGACGTCGTGTACCAT 59.870 52.381 34.40 0.00 40.80 3.55
1743 1786 1.450531 AAGCACTGCAACAGCCAGAC 61.451 55.000 3.30 0.00 34.37 3.51
1828 1871 1.080705 CGTGGGACAGAAGACCGAC 60.081 63.158 0.00 0.00 41.80 4.79
2171 2226 1.171549 TGCATGCCGCTTGTTCTGAA 61.172 50.000 16.68 0.00 43.06 3.02
2187 2254 5.869344 TGTTCTGAATCCATTAAGTGACGAG 59.131 40.000 0.00 0.00 0.00 4.18
2445 3264 0.450983 GTCACTAGTCGGGGTCTTCG 59.549 60.000 0.00 0.00 0.00 3.79
2487 3306 0.608130 TTCCCATCGTCTGTCTGGTG 59.392 55.000 0.00 0.00 0.00 4.17
2489 3308 1.448540 CCATCGTCTGTCTGGTGCC 60.449 63.158 0.00 0.00 0.00 5.01
2490 3309 1.593787 CATCGTCTGTCTGGTGCCT 59.406 57.895 0.00 0.00 0.00 4.75
2492 3311 1.204704 CATCGTCTGTCTGGTGCCTTA 59.795 52.381 0.00 0.00 0.00 2.69
2535 3363 4.994852 GCTTGGATGCGGTGTATTCTAATA 59.005 41.667 0.00 0.00 0.00 0.98
2536 3364 5.107065 GCTTGGATGCGGTGTATTCTAATAC 60.107 44.000 6.00 6.00 41.24 1.89
2537 3365 5.538849 TGGATGCGGTGTATTCTAATACA 57.461 39.130 10.73 10.73 46.51 2.29
2567 3395 9.256477 GTATTTATTCTACACATCGGTCATGAA 57.744 33.333 0.00 0.00 36.21 2.57
2570 3398 4.529109 TCTACACATCGGTCATGAACAA 57.471 40.909 12.13 0.00 36.21 2.83
2572 3400 5.487433 TCTACACATCGGTCATGAACAAAT 58.513 37.500 12.13 0.32 36.21 2.32
2578 3406 4.764679 TCGGTCATGAACAAATTTCCAG 57.235 40.909 12.13 0.00 0.00 3.86
2613 3441 3.673594 CGACGAGCAGAGACCTGTATTTT 60.674 47.826 0.00 0.00 42.35 1.82
2644 3472 5.121298 GGGTATTTGAGACAGAAACGGTAAC 59.879 44.000 0.00 0.00 0.00 2.50
2645 3473 5.697633 GGTATTTGAGACAGAAACGGTAACA 59.302 40.000 0.00 0.00 0.00 2.41
2647 3475 4.395959 TTGAGACAGAAACGGTAACACT 57.604 40.909 0.00 0.00 0.00 3.55
2648 3476 4.395959 TGAGACAGAAACGGTAACACTT 57.604 40.909 0.00 0.00 0.00 3.16
2649 3477 4.116961 TGAGACAGAAACGGTAACACTTG 58.883 43.478 0.00 0.00 0.00 3.16
2707 3552 2.288025 GCCAAGGTCCTCGGTGGTA 61.288 63.158 9.43 0.00 37.07 3.25
2716 3561 2.100197 TCCTCGGTGGTACATCAAGAG 58.900 52.381 0.00 0.00 41.34 2.85
2721 3566 2.680805 CGGTGGTACATCAAGAGCCATT 60.681 50.000 0.00 0.00 41.34 3.16
2725 3570 4.449068 GTGGTACATCAAGAGCCATTATCG 59.551 45.833 0.00 0.00 44.52 2.92
2727 3572 3.198409 ACATCAAGAGCCATTATCGCA 57.802 42.857 0.00 0.00 0.00 5.10
2745 3590 0.659427 CATGAAGTGGAATCGCGCAT 59.341 50.000 8.75 0.00 0.00 4.73
2751 3597 1.134818 AGTGGAATCGCGCATAGAACA 60.135 47.619 8.75 0.00 0.00 3.18
2757 3603 1.075542 TCGCGCATAGAACAGTTTGG 58.924 50.000 8.75 0.00 0.00 3.28
2783 3629 5.527951 CCACGAGCAATCTACTACTCTTAGA 59.472 44.000 0.00 0.00 0.00 2.10
2829 3675 4.679654 GGAAGTTTGTTGGCTAATTGTTCG 59.320 41.667 0.00 0.00 0.00 3.95
2873 3719 2.048312 GAATGCTTCCGCGGGCTTAC 62.048 60.000 27.83 11.36 39.65 2.34
2889 3735 2.285977 CTTACGTGGAGGCCCAAATAC 58.714 52.381 0.00 0.00 45.59 1.89
2897 3743 2.378038 GAGGCCCAAATACTTGCATGA 58.622 47.619 6.60 0.00 0.00 3.07
2910 3756 5.184892 ACTTGCATGAAAAGGATCCTAGT 57.815 39.130 16.55 8.50 0.00 2.57
2939 3785 5.120830 ACTCAAGTATGTCGCTGATTTGTTC 59.879 40.000 0.00 0.00 0.00 3.18
2944 3790 1.376683 TCGCTGATTTGTTCCCCCG 60.377 57.895 0.00 0.00 0.00 5.73
2948 3795 0.322456 CTGATTTGTTCCCCCGCTCA 60.322 55.000 0.00 0.00 0.00 4.26
2965 3812 2.355132 GCTCATCAAAGCACCTGATCAG 59.645 50.000 16.24 16.24 42.05 2.90
3007 3854 3.880610 AGTTTACGTGAAATCCAAACGC 58.119 40.909 0.00 0.00 40.90 4.84
3025 3872 0.811616 GCCATCGCGAAAGTCTCCAT 60.812 55.000 15.24 0.00 0.00 3.41
3034 3881 2.936498 CGAAAGTCTCCATAATTGCCGT 59.064 45.455 0.00 0.00 0.00 5.68
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 2.103263 CCGTCTCTCCCTATTCCAAAGG 59.897 54.545 0.00 0.00 0.00 3.11
1 2 2.103263 CCCGTCTCTCCCTATTCCAAAG 59.897 54.545 0.00 0.00 0.00 2.77
2 3 2.116238 CCCGTCTCTCCCTATTCCAAA 58.884 52.381 0.00 0.00 0.00 3.28
3 4 1.789523 CCCGTCTCTCCCTATTCCAA 58.210 55.000 0.00 0.00 0.00 3.53
4 5 0.759436 GCCCGTCTCTCCCTATTCCA 60.759 60.000 0.00 0.00 0.00 3.53
5 6 0.470268 AGCCCGTCTCTCCCTATTCC 60.470 60.000 0.00 0.00 0.00 3.01
20 21 1.824852 CCAAAGTGTATTTCCCAGCCC 59.175 52.381 0.00 0.00 0.00 5.19
117 118 8.837389 GTGTACAAGAAAGTCAGGTTTATTCTT 58.163 33.333 0.00 0.00 40.06 2.52
127 128 6.740110 AGACACTAGTGTACAAGAAAGTCAG 58.260 40.000 27.98 0.00 45.05 3.51
161 162 7.925483 CCTGAAGTCAACATTGGTTTATTTTCA 59.075 33.333 0.00 0.00 34.21 2.69
163 164 7.216494 CCCTGAAGTCAACATTGGTTTATTTT 58.784 34.615 0.00 0.00 34.21 1.82
167 168 3.572255 GCCCTGAAGTCAACATTGGTTTA 59.428 43.478 0.00 0.00 34.21 2.01
209 210 9.869667 ATAGTGTGAATAGTGACCTCTAATAGT 57.130 33.333 0.00 0.00 0.00 2.12
255 256 7.568199 TCCCTCTTGTCTTCTTTACAAAAAG 57.432 36.000 0.00 0.00 42.99 2.27
269 270 7.888250 ATCCATAGAAAAATTCCCTCTTGTC 57.112 36.000 0.00 0.00 0.00 3.18
396 402 1.955208 GCGGATGTTTGGTTCCTGGAT 60.955 52.381 0.00 0.00 0.00 3.41
397 403 0.608035 GCGGATGTTTGGTTCCTGGA 60.608 55.000 0.00 0.00 0.00 3.86
431 457 1.815003 CGATGTTGATCCCTGCGCA 60.815 57.895 10.98 10.98 0.00 6.09
448 474 2.048222 TCCAGGACTTTCAGCGCG 60.048 61.111 0.00 0.00 0.00 6.86
453 479 0.319555 CGTTCGCTCCAGGACTTTCA 60.320 55.000 0.00 0.00 0.00 2.69
468 495 3.481112 AATTGTATTGGGCGAACGTTC 57.519 42.857 18.47 18.47 0.00 3.95
469 496 3.926821 AAATTGTATTGGGCGAACGTT 57.073 38.095 0.00 0.00 0.00 3.99
470 497 3.181518 CGTAAATTGTATTGGGCGAACGT 60.182 43.478 0.00 0.00 0.00 3.99
471 498 3.181518 ACGTAAATTGTATTGGGCGAACG 60.182 43.478 0.00 0.00 0.00 3.95
472 499 4.345271 ACGTAAATTGTATTGGGCGAAC 57.655 40.909 0.00 0.00 0.00 3.95
473 500 6.492007 TTAACGTAAATTGTATTGGGCGAA 57.508 33.333 0.00 0.00 0.00 4.70
474 501 6.492007 TTTAACGTAAATTGTATTGGGCGA 57.508 33.333 0.00 0.00 0.00 5.54
475 502 7.743520 ATTTTAACGTAAATTGTATTGGGCG 57.256 32.000 0.00 0.00 0.00 6.13
490 517 9.893305 CAATGAAGAGAAAGGTTATTTTAACGT 57.107 29.630 0.00 0.00 0.00 3.99
491 518 9.893305 ACAATGAAGAGAAAGGTTATTTTAACG 57.107 29.630 0.00 0.00 0.00 3.18
499 526 8.635765 ATTGCTTACAATGAAGAGAAAGGTTA 57.364 30.769 0.00 0.00 44.90 2.85
523 550 3.441572 GTCCATGCAGCTTACACTTTGAT 59.558 43.478 0.00 0.00 0.00 2.57
562 589 2.132762 GTGTTAGTGGTCGGTCAGTTG 58.867 52.381 0.00 0.00 0.00 3.16
573 600 7.745620 AGTATTTCTCTTTTGGTGTTAGTGG 57.254 36.000 0.00 0.00 0.00 4.00
596 623 0.106335 ATCTGCAGATCGGCTGGAAG 59.894 55.000 23.75 10.05 44.82 3.46
689 716 2.035783 GGTCTTTGGTCCTGGGGC 59.964 66.667 0.00 0.00 0.00 5.80
740 769 0.326927 ATTCTCCCGCGGAAGGAAAA 59.673 50.000 30.73 9.16 31.49 2.29
752 781 3.769844 TGACTGGACTAACAGATTCTCCC 59.230 47.826 0.00 0.00 40.97 4.30
827 856 2.897350 GGGGAGGCAAAGATCGCG 60.897 66.667 0.00 0.00 0.00 5.87
921 953 1.446099 ATACGACACAGCAGGCGTG 60.446 57.895 13.91 1.01 40.32 5.34
976 1008 2.603473 CACACCTCGTCCCTCCCA 60.603 66.667 0.00 0.00 0.00 4.37
983 1015 1.079543 ATCAGCTGCACACCTCGTC 60.080 57.895 9.47 0.00 0.00 4.20
984 1016 1.375140 CATCAGCTGCACACCTCGT 60.375 57.895 9.47 0.00 0.00 4.18
985 1017 2.104859 CCATCAGCTGCACACCTCG 61.105 63.158 9.47 0.00 0.00 4.63
986 1018 0.743701 CTCCATCAGCTGCACACCTC 60.744 60.000 9.47 0.00 0.00 3.85
987 1019 1.298993 CTCCATCAGCTGCACACCT 59.701 57.895 9.47 0.00 0.00 4.00
988 1020 1.748122 CCTCCATCAGCTGCACACC 60.748 63.158 9.47 0.00 0.00 4.16
989 1021 0.743701 CTCCTCCATCAGCTGCACAC 60.744 60.000 9.47 0.00 0.00 3.82
990 1022 0.906282 TCTCCTCCATCAGCTGCACA 60.906 55.000 9.47 0.00 0.00 4.57
991 1023 0.179078 CTCTCCTCCATCAGCTGCAC 60.179 60.000 9.47 0.00 0.00 4.57
992 1024 1.335882 CCTCTCCTCCATCAGCTGCA 61.336 60.000 9.47 0.00 0.00 4.41
993 1025 1.336632 ACCTCTCCTCCATCAGCTGC 61.337 60.000 9.47 0.00 0.00 5.25
994 1026 0.464870 CACCTCTCCTCCATCAGCTG 59.535 60.000 7.63 7.63 0.00 4.24
995 1027 1.336632 GCACCTCTCCTCCATCAGCT 61.337 60.000 0.00 0.00 0.00 4.24
996 1028 1.145819 GCACCTCTCCTCCATCAGC 59.854 63.158 0.00 0.00 0.00 4.26
997 1029 1.440893 CGCACCTCTCCTCCATCAG 59.559 63.158 0.00 0.00 0.00 2.90
998 1030 2.725312 GCGCACCTCTCCTCCATCA 61.725 63.158 0.30 0.00 0.00 3.07
1347 1379 4.638865 ACCATCTTAATACCAAGAAACGGC 59.361 41.667 0.00 0.00 38.03 5.68
1409 1441 0.324943 CGGAATTCACCCTCACCTGT 59.675 55.000 7.93 0.00 0.00 4.00
1496 1528 0.400213 CTGACCTTGGGTACTTGGCA 59.600 55.000 0.00 0.00 35.25 4.92
1520 1552 2.049063 GGTGCTCGAGCGTCACTT 60.049 61.111 30.75 0.00 45.83 3.16
1522 1554 2.505118 GAGGTGCTCGAGCGTCAC 60.505 66.667 30.75 22.96 45.83 3.67
1549 1592 5.755861 GTCCTCTTGAAATAATAGCTCGCTT 59.244 40.000 0.00 0.00 0.00 4.68
1560 1603 9.658799 CTCAATTTAGTCAGTCCTCTTGAAATA 57.341 33.333 0.00 0.00 0.00 1.40
1699 1742 4.164087 ACGCACGTGTGGTTCCCA 62.164 61.111 30.74 0.00 0.00 4.37
1805 1848 0.244178 GTCTTCTGTCCCACGGAGAC 59.756 60.000 0.00 0.00 34.53 3.36
2171 2226 4.100035 TCATCTGCTCGTCACTTAATGGAT 59.900 41.667 0.00 0.00 0.00 3.41
2445 3264 1.014352 CAATTCACGATTCCGACCCC 58.986 55.000 0.00 0.00 39.50 4.95
2487 3306 2.587522 CCTAAGGGATTTGCCTAAGGC 58.412 52.381 0.00 0.00 41.65 4.35
2489 3308 2.587522 GGCCTAAGGGATTTGCCTAAG 58.412 52.381 0.00 0.00 39.05 2.18
2490 3309 1.133915 CGGCCTAAGGGATTTGCCTAA 60.134 52.381 0.00 0.00 39.97 2.69
2492 3311 1.227383 CGGCCTAAGGGATTTGCCT 59.773 57.895 0.00 0.00 39.97 4.75
2501 3329 3.757248 ATCCAAGCGCGGCCTAAGG 62.757 63.158 8.83 3.58 0.00 2.69
2517 3345 6.868864 ACATCTGTATTAGAATACACCGCATC 59.131 38.462 10.39 0.00 44.52 3.91
2535 3363 8.421784 ACCGATGTGTAGAATAAATACATCTGT 58.578 33.333 12.17 9.50 43.21 3.41
2536 3364 8.818141 ACCGATGTGTAGAATAAATACATCTG 57.182 34.615 12.17 8.98 43.21 2.90
2537 3365 8.638873 TGACCGATGTGTAGAATAAATACATCT 58.361 33.333 12.17 0.00 43.21 2.90
2538 3366 8.812147 TGACCGATGTGTAGAATAAATACATC 57.188 34.615 0.00 0.00 42.42 3.06
2539 3367 9.208022 CATGACCGATGTGTAGAATAAATACAT 57.792 33.333 0.00 0.00 35.69 2.29
2540 3368 8.417884 TCATGACCGATGTGTAGAATAAATACA 58.582 33.333 0.00 0.00 33.29 2.29
2541 3369 8.812147 TCATGACCGATGTGTAGAATAAATAC 57.188 34.615 0.00 0.00 33.29 1.89
2542 3370 9.256477 GTTCATGACCGATGTGTAGAATAAATA 57.744 33.333 0.00 0.00 33.29 1.40
2543 3371 7.768582 TGTTCATGACCGATGTGTAGAATAAAT 59.231 33.333 0.00 0.00 33.29 1.40
2544 3372 7.100409 TGTTCATGACCGATGTGTAGAATAAA 58.900 34.615 0.00 0.00 33.29 1.40
2545 3373 6.635755 TGTTCATGACCGATGTGTAGAATAA 58.364 36.000 0.00 0.00 33.29 1.40
2546 3374 6.215495 TGTTCATGACCGATGTGTAGAATA 57.785 37.500 0.00 0.00 33.29 1.75
2547 3375 5.084818 TGTTCATGACCGATGTGTAGAAT 57.915 39.130 0.00 0.00 33.29 2.40
2548 3376 4.529109 TGTTCATGACCGATGTGTAGAA 57.471 40.909 0.00 0.00 33.29 2.10
2549 3377 4.529109 TTGTTCATGACCGATGTGTAGA 57.471 40.909 0.00 0.00 33.29 2.59
2550 3378 5.801350 ATTTGTTCATGACCGATGTGTAG 57.199 39.130 0.00 0.00 33.29 2.74
2551 3379 6.348950 GGAAATTTGTTCATGACCGATGTGTA 60.349 38.462 0.00 0.00 33.29 2.90
2552 3380 5.452078 AAATTTGTTCATGACCGATGTGT 57.548 34.783 0.00 0.00 33.29 3.72
2553 3381 4.858692 GGAAATTTGTTCATGACCGATGTG 59.141 41.667 0.00 0.00 33.29 3.21
2554 3382 4.522405 TGGAAATTTGTTCATGACCGATGT 59.478 37.500 0.00 0.00 33.29 3.06
2555 3383 5.058149 TGGAAATTTGTTCATGACCGATG 57.942 39.130 0.00 0.00 0.00 3.84
2578 3406 0.383860 CTCGTCGTTTTGTTTCCGGC 60.384 55.000 0.00 0.00 0.00 6.13
2613 3441 7.041644 CGTTTCTGTCTCAAATACCCTTGTAAA 60.042 37.037 0.00 0.00 0.00 2.01
2648 3476 2.055042 AACTTTTGTGGTGCGCCCA 61.055 52.632 15.15 12.86 42.51 5.36
2649 3477 1.591327 CAACTTTTGTGGTGCGCCC 60.591 57.895 15.15 6.44 0.00 6.13
2707 3552 3.198409 TGCGATAATGGCTCTTGATGT 57.802 42.857 0.00 0.00 0.00 3.06
2716 3561 2.221169 TCCACTTCATGCGATAATGGC 58.779 47.619 0.00 0.00 0.00 4.40
2721 3566 2.135139 GCGATTCCACTTCATGCGATA 58.865 47.619 0.00 0.00 0.00 2.92
2725 3570 1.297893 GCGCGATTCCACTTCATGC 60.298 57.895 12.10 0.00 0.00 4.06
2727 3572 2.138320 CTATGCGCGATTCCACTTCAT 58.862 47.619 12.10 2.37 0.00 2.57
2745 3590 2.547218 GCTCGTGGTCCAAACTGTTCTA 60.547 50.000 0.00 0.00 0.00 2.10
2751 3597 1.072331 AGATTGCTCGTGGTCCAAACT 59.928 47.619 0.00 0.00 0.00 2.66
2757 3603 3.628487 AGAGTAGTAGATTGCTCGTGGTC 59.372 47.826 0.00 0.00 33.57 4.02
2799 3645 1.538849 GCCAACAAACTTCCAGCTTGG 60.539 52.381 0.00 0.00 39.43 3.61
2873 3719 1.094785 CAAGTATTTGGGCCTCCACG 58.905 55.000 4.53 0.00 43.94 4.94
2889 3735 4.201990 GCACTAGGATCCTTTTCATGCAAG 60.202 45.833 22.03 10.24 0.00 4.01
2897 3743 3.327757 TGAGTGTGCACTAGGATCCTTTT 59.672 43.478 22.03 4.01 42.66 2.27
2910 3756 1.000843 AGCGACATACTTGAGTGTGCA 59.999 47.619 7.67 0.00 40.25 4.57
2939 3785 2.045045 TGCTTTGATGAGCGGGGG 60.045 61.111 0.00 0.00 45.64 5.40
2944 3790 2.355132 CTGATCAGGTGCTTTGATGAGC 59.645 50.000 15.38 0.00 43.00 4.26
2948 3795 2.502142 TGCTGATCAGGTGCTTTGAT 57.498 45.000 23.89 0.00 37.96 2.57
2965 3812 2.206750 TCTTAAATACGTCGGCCATGC 58.793 47.619 2.24 0.00 0.00 4.06
3007 3854 2.509052 TATGGAGACTTTCGCGATGG 57.491 50.000 10.88 8.58 0.00 3.51
3016 3863 4.481368 TGTACGGCAATTATGGAGACTT 57.519 40.909 0.00 0.00 0.00 3.01


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

AutoCloner maintained by Alex Coulton.