Multiple sequence alignment - TraesCS3A01G047600

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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 TraesCS3A01G047600 chr3A 100.000 5204 0 0 1 5204 25182353 25187556 0.000000e+00 9611
1 TraesCS3A01G047600 chr3A 95.894 414 16 1 466 879 742921600 742922012 0.000000e+00 669
2 TraesCS3A01G047600 chr3A 95.652 414 18 0 466 879 16235687 16235274 0.000000e+00 665
3 TraesCS3A01G047600 chr3A 84.462 251 24 2 3674 3924 21275214 21274979 3.130000e-57 233
4 TraesCS3A01G047600 chr3B 97.501 3121 71 2 880 3995 17086545 17083427 0.000000e+00 5325
5 TraesCS3A01G047600 chr3B 95.339 708 28 4 4011 4718 17083441 17082739 0.000000e+00 1120
6 TraesCS3A01G047600 chr3B 95.943 419 11 2 4792 5204 16956967 16956549 0.000000e+00 675
7 TraesCS3A01G047600 chr3B 86.051 509 41 15 4725 5204 17082372 17081865 2.150000e-143 520
8 TraesCS3A01G047600 chr3B 82.705 584 90 4 1146 1727 17118240 17118814 4.650000e-140 508
9 TraesCS3A01G047600 chr3B 78.458 506 65 30 4726 5204 17057043 17056555 1.830000e-74 291
10 TraesCS3A01G047600 chr3B 78.717 343 43 17 4884 5204 16950234 16949900 8.840000e-48 202
11 TraesCS3A01G047600 chr3D 87.273 3143 361 22 880 3995 15026912 15030042 0.000000e+00 3552
12 TraesCS3A01G047600 chr3D 90.258 2135 190 9 1878 3995 11818016 11815883 0.000000e+00 2774
13 TraesCS3A01G047600 chr3D 87.368 570 67 4 880 1449 11818579 11818015 0.000000e+00 649
14 TraesCS3A01G047600 chr3D 83.248 585 85 6 1146 1727 11853699 11854273 4.620000e-145 525
15 TraesCS3A01G047600 chr3D 81.931 321 37 11 4011 4314 11815897 11815581 8.650000e-63 252
16 TraesCS3A01G047600 chr3D 79.056 339 37 16 4011 4319 15030028 15030362 8.840000e-48 202
17 TraesCS3A01G047600 chr5A 98.586 495 6 1 1 494 564736135 564736629 0.000000e+00 874
18 TraesCS3A01G047600 chr6B 97.782 496 9 2 1 494 101663075 101662580 0.000000e+00 854
19 TraesCS3A01G047600 chr6B 94.444 414 23 0 466 879 101662645 101662232 5.680000e-179 638
20 TraesCS3A01G047600 chr4D 97.576 495 11 1 1 494 356250147 356249653 0.000000e+00 846
21 TraesCS3A01G047600 chr6D 97.741 487 9 2 9 494 428954431 428954916 0.000000e+00 837
22 TraesCS3A01G047600 chr6D 96.860 414 13 0 466 879 428954851 428955264 0.000000e+00 693
23 TraesCS3A01G047600 chr5B 97.177 496 12 2 1 494 522481032 522481527 0.000000e+00 837
24 TraesCS3A01G047600 chr5B 96.177 497 15 3 1 494 507931141 507931636 0.000000e+00 809
25 TraesCS3A01G047600 chr5B 94.774 421 21 1 466 886 522481462 522481881 0.000000e+00 654
26 TraesCS3A01G047600 chr6A 96.976 496 13 2 1 494 573038452 573037957 0.000000e+00 832
27 TraesCS3A01G047600 chr6A 95.894 414 16 1 466 879 573038022 573037610 0.000000e+00 669
28 TraesCS3A01G047600 chr1B 96.982 497 12 2 1 494 51537863 51538359 0.000000e+00 832
29 TraesCS3A01G047600 chr2D 96.364 495 11 2 1 494 10035297 10034809 0.000000e+00 808
30 TraesCS3A01G047600 chr4A 95.894 414 16 1 466 879 605029186 605028774 0.000000e+00 669
31 TraesCS3A01G047600 chr1A 94.471 416 22 1 466 881 533300423 533300837 1.580000e-179 640
32 TraesCS3A01G047600 chr7A 94.217 415 22 2 466 879 552986787 552987200 2.640000e-177 632


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 TraesCS3A01G047600 chr3A 25182353 25187556 5203 False 9611.000000 9611 100.000000 1 5204 1 chr3A.!!$F1 5203
1 TraesCS3A01G047600 chr3B 17081865 17086545 4680 True 2321.666667 5325 92.963667 880 5204 3 chr3B.!!$R4 4324
2 TraesCS3A01G047600 chr3B 17118240 17118814 574 False 508.000000 508 82.705000 1146 1727 1 chr3B.!!$F1 581
3 TraesCS3A01G047600 chr3D 15026912 15030362 3450 False 1877.000000 3552 83.164500 880 4319 2 chr3D.!!$F2 3439
4 TraesCS3A01G047600 chr3D 11815581 11818579 2998 True 1225.000000 2774 86.519000 880 4314 3 chr3D.!!$R1 3434
5 TraesCS3A01G047600 chr3D 11853699 11854273 574 False 525.000000 525 83.248000 1146 1727 1 chr3D.!!$F1 581
6 TraesCS3A01G047600 chr6B 101662232 101663075 843 True 746.000000 854 96.113000 1 879 2 chr6B.!!$R1 878
7 TraesCS3A01G047600 chr6D 428954431 428955264 833 False 765.000000 837 97.300500 9 879 2 chr6D.!!$F1 870
8 TraesCS3A01G047600 chr5B 522481032 522481881 849 False 745.500000 837 95.975500 1 886 2 chr5B.!!$F2 885
9 TraesCS3A01G047600 chr6A 573037610 573038452 842 True 750.500000 832 96.435000 1 879 2 chr6A.!!$R1 878

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
770 773 0.032130 GATGAAGCTATGCCGACGGA 59.968 55.000 20.50 2.93 0.00 4.69 F
1311 1318 2.158711 TGATCTGATTCATGACCTGGCC 60.159 50.000 0.00 0.00 0.00 5.36 F
1440 1447 2.203280 TGGAACACAAGTGCCCGG 60.203 61.111 0.00 0.00 43.60 5.73 F
3177 3198 0.704076 ACATAACAGGGTGCCCACAT 59.296 50.000 10.26 0.00 38.92 3.21 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1776 1785 1.473258 TCATGCCATGTGGTAAAGCC 58.527 50.000 4.31 0.0 37.57 4.35 R
2336 2345 1.964223 ACTCAGTCCAATCGTCACAGT 59.036 47.619 0.00 0.0 0.00 3.55 R
3314 3341 2.213499 GACTCCGTGATATTGCCAAGG 58.787 52.381 0.00 0.0 35.03 3.61 R
4660 4733 0.388649 CGCAGCCGGTCAGATATACC 60.389 60.000 1.90 0.0 0.00 2.73 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
468 471 6.716934 CCGTAGGCATAGATGGATAACTAT 57.283 41.667 0.00 0.00 46.14 2.12
469 472 6.507900 CCGTAGGCATAGATGGATAACTATG 58.492 44.000 0.00 0.00 46.14 2.23
476 479 7.334844 CATAGATGGATAACTATGCCTACGA 57.665 40.000 0.00 0.00 39.24 3.43
477 480 5.646577 AGATGGATAACTATGCCTACGAC 57.353 43.478 0.00 0.00 0.00 4.34
478 481 5.326069 AGATGGATAACTATGCCTACGACT 58.674 41.667 0.00 0.00 0.00 4.18
479 482 5.775701 AGATGGATAACTATGCCTACGACTT 59.224 40.000 0.00 0.00 0.00 3.01
480 483 5.864418 TGGATAACTATGCCTACGACTTT 57.136 39.130 0.00 0.00 0.00 2.66
481 484 5.597806 TGGATAACTATGCCTACGACTTTG 58.402 41.667 0.00 0.00 0.00 2.77
482 485 4.448060 GGATAACTATGCCTACGACTTTGC 59.552 45.833 0.00 0.00 0.00 3.68
483 486 2.311124 ACTATGCCTACGACTTTGCC 57.689 50.000 0.00 0.00 0.00 4.52
484 487 1.209128 CTATGCCTACGACTTTGCCG 58.791 55.000 0.00 0.00 0.00 5.69
485 488 0.533491 TATGCCTACGACTTTGCCGT 59.467 50.000 0.00 0.00 43.26 5.68
486 489 0.739813 ATGCCTACGACTTTGCCGTC 60.740 55.000 0.00 0.00 40.95 4.79
770 773 0.032130 GATGAAGCTATGCCGACGGA 59.968 55.000 20.50 2.93 0.00 4.69
909 912 5.014755 ACATCCAGGTTTACAGGTTATTGGA 59.985 40.000 0.00 0.00 37.82 3.53
1029 1032 7.014134 TCAGTTTTGCTAAGTGATGAATGGAAA 59.986 33.333 5.81 0.00 0.00 3.13
1195 1198 5.710099 TGGATATCACAAGGTTTTGTTCCTC 59.290 40.000 4.83 0.00 45.01 3.71
1311 1318 2.158711 TGATCTGATTCATGACCTGGCC 60.159 50.000 0.00 0.00 0.00 5.36
1440 1447 2.203280 TGGAACACAAGTGCCCGG 60.203 61.111 0.00 0.00 43.60 5.73
1565 1574 7.548780 TGATGAAGGGTTTTCTGAAACTTTTTG 59.451 33.333 1.58 0.00 43.68 2.44
1622 1631 7.201384 CGTTTTGAGGTTATCCGTACTAACTTC 60.201 40.741 8.03 8.03 36.35 3.01
1764 1773 5.525378 CCAGGTTCTTGATGTAGAGTATTGC 59.475 44.000 0.00 0.00 0.00 3.56
1776 1785 3.448686 AGAGTATTGCGTGGATCTTTCG 58.551 45.455 0.00 0.00 0.00 3.46
1987 1996 8.125978 TCTTGCAATTTACAATCTGGAGAATT 57.874 30.769 0.00 0.00 0.00 2.17
2009 2018 5.370875 TTGGGTAGTAGAGAGGAGTCTAC 57.629 47.826 3.30 3.30 46.47 2.59
2047 2056 8.685257 AAGGGACAAGATATACATCCATGATA 57.315 34.615 0.00 0.00 0.00 2.15
2129 2138 4.401925 CTTGAGGGTCTTCATCCAAGTTT 58.598 43.478 0.00 0.00 33.27 2.66
2336 2345 6.872020 GCTTCAACAGAAGTACCAGTTATGTA 59.128 38.462 7.04 0.00 40.66 2.29
2721 2730 7.598493 GTGAAATTAACAATTGCAAGCTTCCTA 59.402 33.333 4.94 0.00 38.14 2.94
2765 2774 4.378874 GGAAAATTTCAGCCGACTTCTCTG 60.379 45.833 8.09 0.00 0.00 3.35
2975 2996 0.895100 GCATCCTTGGCAGTTGGTGA 60.895 55.000 0.00 0.00 0.00 4.02
3045 3066 3.592059 GACAATTGATGGCTTGTTGCAT 58.408 40.909 13.59 0.00 45.15 3.96
3053 3074 1.005805 TGGCTTGTTGCATATCCCACT 59.994 47.619 0.00 0.00 45.15 4.00
3088 3109 3.621268 TCGGCTTGAGTATTTGTGCATAC 59.379 43.478 0.00 0.00 0.00 2.39
3177 3198 0.704076 ACATAACAGGGTGCCCACAT 59.296 50.000 10.26 0.00 38.92 3.21
3213 3240 5.634118 TGGACAGAAAAAGAATCCAGTGAT 58.366 37.500 0.00 0.00 34.50 3.06
3314 3341 5.344743 TCTAATCTCACCTCATTGTCCAC 57.655 43.478 0.00 0.00 0.00 4.02
3352 3379 3.898123 GAGTCCAGGGCTGACATCTATTA 59.102 47.826 0.00 0.00 0.00 0.98
3748 3788 5.163854 CGTTCACAGAAGAACAAGACAAAGT 60.164 40.000 7.49 0.00 46.32 2.66
3750 3790 7.412563 CGTTCACAGAAGAACAAGACAAAGTAA 60.413 37.037 7.49 0.00 46.32 2.24
3935 3975 2.613977 GGAGCTGTATGTGAGCAACTGT 60.614 50.000 0.00 0.00 39.05 3.55
3998 4039 6.476243 ACGTTAGATGCGTTTATGTTCTTT 57.524 33.333 0.00 0.00 39.79 2.52
3999 4040 7.585286 ACGTTAGATGCGTTTATGTTCTTTA 57.415 32.000 0.00 0.00 39.79 1.85
4000 4041 8.193250 ACGTTAGATGCGTTTATGTTCTTTAT 57.807 30.769 0.00 0.00 39.79 1.40
4001 4042 8.325997 ACGTTAGATGCGTTTATGTTCTTTATC 58.674 33.333 0.00 0.00 39.79 1.75
4002 4043 7.522884 CGTTAGATGCGTTTATGTTCTTTATCG 59.477 37.037 0.00 0.00 0.00 2.92
4003 4044 8.537223 GTTAGATGCGTTTATGTTCTTTATCGA 58.463 33.333 0.00 0.00 0.00 3.59
4004 4045 7.534085 AGATGCGTTTATGTTCTTTATCGAA 57.466 32.000 0.00 0.00 0.00 3.71
4005 4046 7.970384 AGATGCGTTTATGTTCTTTATCGAAA 58.030 30.769 0.00 0.00 0.00 3.46
4006 4047 8.447833 AGATGCGTTTATGTTCTTTATCGAAAA 58.552 29.630 0.00 0.00 0.00 2.29
4007 4048 8.958175 ATGCGTTTATGTTCTTTATCGAAAAA 57.042 26.923 0.00 0.00 0.00 1.94
4186 4247 1.545582 TGCTGGCTTGCTTAATTCACC 59.454 47.619 4.89 0.00 0.00 4.02
4237 4309 9.947433 TTCTGATGGAAATTGCAAAATAAATCT 57.053 25.926 1.71 0.00 0.00 2.40
4238 4310 9.373603 TCTGATGGAAATTGCAAAATAAATCTG 57.626 29.630 1.71 8.88 0.00 2.90
4266 4338 7.716998 GTGGTGATTGATAGTCTATTTCATGGT 59.283 37.037 0.00 0.00 0.00 3.55
4308 4381 5.279156 GCTCTTTGATGAAATCCCAAAGTGT 60.279 40.000 17.30 0.00 44.73 3.55
4324 4397 6.040391 CCCAAAGTGTAGATGGTTTCAAGAAA 59.960 38.462 0.00 0.00 32.13 2.52
4470 4543 1.068121 ACTTCCCCCTTCTCTTGTGG 58.932 55.000 0.00 0.00 0.00 4.17
4496 4569 6.811170 CGGTTTGCCAGTTATTTGTTGATAAT 59.189 34.615 0.00 0.00 34.09 1.28
4571 4644 9.616156 TTTCTGAACTGTAATGTAGTTTTGGTA 57.384 29.630 0.00 0.00 38.42 3.25
4660 4733 3.438087 TGCACAAACCACAAAAACCATTG 59.562 39.130 0.00 0.00 36.37 2.82
4671 4744 7.093945 ACCACAAAAACCATTGGTATATCTGAC 60.094 37.037 9.20 0.00 40.69 3.51
4672 4745 7.257722 CACAAAAACCATTGGTATATCTGACC 58.742 38.462 9.20 0.00 33.12 4.02
4737 5171 9.630098 TTTTATTTCTGATCAGCAAACAGAATC 57.370 29.630 18.36 0.00 45.62 2.52
4740 5174 7.984422 TTTCTGATCAGCAAACAGAATCTTA 57.016 32.000 18.36 0.00 45.62 2.10
4751 5185 6.127786 GCAAACAGAATCTTAAATCAGCTCCT 60.128 38.462 0.00 0.00 0.00 3.69
4793 5227 3.431905 CCAGAGGAGATGTGTTGGAGATG 60.432 52.174 0.00 0.00 0.00 2.90
4881 5315 1.903860 ACTGGTAAGTCGGGCACATTA 59.096 47.619 0.00 0.00 26.77 1.90
4883 5317 2.676342 CTGGTAAGTCGGGCACATTAAC 59.324 50.000 0.00 0.00 0.00 2.01
4885 5319 2.676342 GGTAAGTCGGGCACATTAACAG 59.324 50.000 0.00 0.00 0.00 3.16
4888 5322 1.623811 AGTCGGGCACATTAACAGAGT 59.376 47.619 0.00 0.00 0.00 3.24
4889 5323 2.829720 AGTCGGGCACATTAACAGAGTA 59.170 45.455 0.00 0.00 0.00 2.59
4890 5324 3.259876 AGTCGGGCACATTAACAGAGTAA 59.740 43.478 0.00 0.00 0.00 2.24
4891 5325 3.617263 GTCGGGCACATTAACAGAGTAAG 59.383 47.826 0.00 0.00 0.00 2.34
4892 5326 3.512329 TCGGGCACATTAACAGAGTAAGA 59.488 43.478 0.00 0.00 0.00 2.10
4910 5349 2.498167 AGAATCCTTGTGTCTGTGCAC 58.502 47.619 10.75 10.75 39.65 4.57
4915 5354 1.473965 CCTTGTGTCTGTGCACTCTGT 60.474 52.381 19.41 0.00 39.89 3.41
4920 5359 3.809279 TGTGTCTGTGCACTCTGTTATTG 59.191 43.478 19.41 0.00 39.89 1.90
4923 5362 2.068519 CTGTGCACTCTGTTATTGCGA 58.931 47.619 19.41 0.00 36.59 5.10
4931 5370 2.543012 CTCTGTTATTGCGAGATGGCAG 59.457 50.000 0.00 0.00 44.94 4.85
4960 5399 2.291365 TGCTACAGCTCGTCCGTAATA 58.709 47.619 2.44 0.00 42.66 0.98
4962 5401 3.317149 TGCTACAGCTCGTCCGTAATATT 59.683 43.478 2.44 0.00 42.66 1.28
4984 5423 1.521580 TCGCATGTTGTTCTGATGCA 58.478 45.000 0.00 0.00 42.20 3.96
4999 5438 2.079158 GATGCACTTCAAGCTGCTACA 58.921 47.619 0.90 0.00 34.29 2.74
5009 5448 4.087182 TCAAGCTGCTACAACCTACTAGT 58.913 43.478 0.90 0.00 0.00 2.57
5010 5449 5.258841 TCAAGCTGCTACAACCTACTAGTA 58.741 41.667 0.90 1.89 0.00 1.82
5011 5450 5.713389 TCAAGCTGCTACAACCTACTAGTAA 59.287 40.000 0.90 0.00 0.00 2.24
5012 5451 5.579564 AGCTGCTACAACCTACTAGTAAC 57.420 43.478 0.00 0.00 0.00 2.50
5014 5453 5.657302 AGCTGCTACAACCTACTAGTAACAT 59.343 40.000 0.00 0.00 0.00 2.71
5017 5477 6.860080 TGCTACAACCTACTAGTAACATGAC 58.140 40.000 3.76 0.00 0.00 3.06
5023 5483 7.616150 ACAACCTACTAGTAACATGACTCAGAT 59.384 37.037 3.76 0.00 0.00 2.90
5049 5509 3.257375 AGTGTTTGTATGTAGCTGTCCGA 59.743 43.478 0.00 0.00 0.00 4.55
5090 5550 3.200605 AGACACCAATGCATGTAGGATCA 59.799 43.478 17.20 0.00 0.00 2.92
5103 5563 3.384789 TGTAGGATCATGTGAGTAGCCAC 59.615 47.826 0.00 0.00 37.55 5.01
5104 5564 1.765314 AGGATCATGTGAGTAGCCACC 59.235 52.381 0.00 0.00 36.26 4.61
5109 5569 1.003580 CATGTGAGTAGCCACCCAACT 59.996 52.381 0.00 0.00 36.26 3.16
5127 5587 5.443185 CAACTGATTTGGTTGAGTCATGT 57.557 39.130 0.00 0.00 44.58 3.21
5139 5599 6.017192 TGGTTGAGTCATGTGTTATTGAAGTG 60.017 38.462 0.00 0.00 0.00 3.16
5149 5609 5.705441 TGTGTTATTGAAGTGATTCCAGGAC 59.295 40.000 0.00 0.00 0.00 3.85
5166 5627 1.067142 GGACTGGTGTATGAAGCGTGA 60.067 52.381 0.00 0.00 0.00 4.35
5174 5635 3.927142 GTGTATGAAGCGTGAGTTTAGCT 59.073 43.478 0.00 0.00 43.90 3.32
5186 5648 5.230942 GTGAGTTTAGCTGAGTCTAAAGCA 58.769 41.667 0.00 7.85 42.06 3.91
5190 5652 7.708322 TGAGTTTAGCTGAGTCTAAAGCATATG 59.292 37.037 0.00 0.00 42.06 1.78
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
228 230 9.793259 TGGGTAGAATTTTCCATAGATTATGAC 57.207 33.333 0.00 0.00 38.45 3.06
454 457 6.482524 AGTCGTAGGCATAGTTATCCATCTA 58.517 40.000 0.00 0.00 0.00 1.98
455 458 5.326069 AGTCGTAGGCATAGTTATCCATCT 58.674 41.667 0.00 0.00 0.00 2.90
456 459 5.646577 AGTCGTAGGCATAGTTATCCATC 57.353 43.478 0.00 0.00 0.00 3.51
457 460 6.223852 CAAAGTCGTAGGCATAGTTATCCAT 58.776 40.000 0.00 0.00 0.00 3.41
458 461 5.597806 CAAAGTCGTAGGCATAGTTATCCA 58.402 41.667 0.00 0.00 0.00 3.41
459 462 4.448060 GCAAAGTCGTAGGCATAGTTATCC 59.552 45.833 0.00 0.00 0.00 2.59
460 463 4.448060 GGCAAAGTCGTAGGCATAGTTATC 59.552 45.833 0.00 0.00 0.00 1.75
461 464 4.377897 GGCAAAGTCGTAGGCATAGTTAT 58.622 43.478 0.00 0.00 0.00 1.89
462 465 3.735820 CGGCAAAGTCGTAGGCATAGTTA 60.736 47.826 0.00 0.00 0.00 2.24
463 466 2.629051 GGCAAAGTCGTAGGCATAGTT 58.371 47.619 0.00 0.00 0.00 2.24
464 467 1.470979 CGGCAAAGTCGTAGGCATAGT 60.471 52.381 0.00 0.00 0.00 2.12
465 468 1.209128 CGGCAAAGTCGTAGGCATAG 58.791 55.000 0.00 0.00 0.00 2.23
466 469 0.533491 ACGGCAAAGTCGTAGGCATA 59.467 50.000 0.00 0.00 43.84 3.14
467 470 0.739813 GACGGCAAAGTCGTAGGCAT 60.740 55.000 0.00 0.00 46.30 4.40
468 471 1.373748 GACGGCAAAGTCGTAGGCA 60.374 57.895 0.00 0.00 46.30 4.75
469 472 3.471399 GACGGCAAAGTCGTAGGC 58.529 61.111 0.00 0.00 46.30 3.93
482 485 2.231478 AGTTATCCATCTATGCCGACGG 59.769 50.000 10.29 10.29 0.00 4.79
483 486 3.577649 AGTTATCCATCTATGCCGACG 57.422 47.619 0.00 0.00 0.00 5.12
489 492 6.507900 CCGTAGGCATAGTTATCCATCTATG 58.492 44.000 7.54 7.54 46.14 2.23
490 493 6.716934 CCGTAGGCATAGTTATCCATCTAT 57.283 41.667 0.00 0.00 46.14 1.98
770 773 4.510340 GTGAATACCGTCGGCATAGAAAAT 59.490 41.667 12.28 0.00 0.00 1.82
909 912 0.324943 ACTTGTTGGCTATCCGCTGT 59.675 50.000 0.00 0.00 39.13 4.40
1013 1016 4.156556 GCTGCAGTTTCCATTCATCACTTA 59.843 41.667 16.64 0.00 0.00 2.24
1195 1198 4.033709 TCCTCCATTCTCTTACTTCCAGG 58.966 47.826 0.00 0.00 0.00 4.45
1311 1318 9.529325 TGACATTCGTCTAAAGAAACTATATGG 57.471 33.333 0.00 0.00 43.06 2.74
1361 1368 2.693074 GTTGGGTGACATGTTCCACTTT 59.307 45.455 15.09 0.00 33.99 2.66
1440 1447 8.632679 TGAAAGTTATCATTGGGAGAATAATGC 58.367 33.333 0.00 0.00 34.96 3.56
1565 1574 2.819608 TGCACCTCTTTGAATACCTTGC 59.180 45.455 0.00 0.00 0.00 4.01
1622 1631 5.126222 TCACTAAGAAGAGTGTCTATGCTGG 59.874 44.000 3.66 0.00 45.88 4.85
1764 1773 1.664151 GGTAAAGCCGAAAGATCCACG 59.336 52.381 0.00 0.00 0.00 4.94
1776 1785 1.473258 TCATGCCATGTGGTAAAGCC 58.527 50.000 4.31 0.00 37.57 4.35
1987 1996 4.141756 CGTAGACTCCTCTCTACTACCCAA 60.142 50.000 0.00 0.00 40.36 4.12
2009 2018 2.917933 TGTCCCTTAATCCAGCATTCG 58.082 47.619 0.00 0.00 0.00 3.34
2047 2056 6.594788 ATTCTTACACCATGAAAGCAACAT 57.405 33.333 0.00 0.00 0.00 2.71
2336 2345 1.964223 ACTCAGTCCAATCGTCACAGT 59.036 47.619 0.00 0.00 0.00 3.55
2765 2774 6.467677 TCCATAATTACCAGCATCTCTAAGC 58.532 40.000 0.00 0.00 0.00 3.09
2975 2996 6.011122 AGCTGAAATTCCCAGTAATCAGAT 57.989 37.500 4.87 0.00 37.14 2.90
3045 3066 5.163343 CCGATTTAAGAGGTCAAGTGGGATA 60.163 44.000 0.00 0.00 0.00 2.59
3053 3074 4.253685 CTCAAGCCGATTTAAGAGGTCAA 58.746 43.478 0.00 0.00 0.00 3.18
3190 3214 5.047566 TCACTGGATTCTTTTTCTGTCCA 57.952 39.130 0.00 0.00 37.41 4.02
3191 3215 6.183360 GCTATCACTGGATTCTTTTTCTGTCC 60.183 42.308 0.00 0.00 34.89 4.02
3213 3240 2.416787 TGGTAGGAGGGACCAGCTA 58.583 57.895 0.00 0.00 42.15 3.32
3314 3341 2.213499 GACTCCGTGATATTGCCAAGG 58.787 52.381 0.00 0.00 35.03 3.61
3352 3379 7.114754 TCTAAAGATGTGCAAGAATGGAGAAT 58.885 34.615 0.00 0.00 0.00 2.40
3647 3674 5.415701 CCTACAAGTTCACCAATGCAACTAT 59.584 40.000 0.00 0.00 30.68 2.12
3750 3790 9.911788 AATATGAAGAGATGTAAGGTGACAAAT 57.088 29.630 0.00 0.00 31.83 2.32
3791 3831 3.503891 CAGCGATATGAGATCAGAGCAG 58.496 50.000 0.00 0.00 0.00 4.24
3935 3975 7.592885 ACACTGTTCCTTTAGTTCTGTACTA 57.407 36.000 0.00 0.00 38.33 1.82
3976 4017 7.522884 CGATAAAGAACATAAACGCATCTAACG 59.477 37.037 0.00 0.00 0.00 3.18
3977 4018 8.537223 TCGATAAAGAACATAAACGCATCTAAC 58.463 33.333 0.00 0.00 0.00 2.34
3979 4020 8.637281 TTCGATAAAGAACATAAACGCATCTA 57.363 30.769 0.00 0.00 0.00 1.98
3980 4021 7.534085 TTCGATAAAGAACATAAACGCATCT 57.466 32.000 0.00 0.00 0.00 2.90
3981 4022 8.595781 TTTTCGATAAAGAACATAAACGCATC 57.404 30.769 0.00 0.00 0.00 3.91
3982 4023 8.958175 TTTTTCGATAAAGAACATAAACGCAT 57.042 26.923 0.00 0.00 0.00 4.73
4008 4049 9.850628 CATGTCAATCAACATAAACTCATCTTT 57.149 29.630 0.00 0.00 37.78 2.52
4009 4050 7.972277 GCATGTCAATCAACATAAACTCATCTT 59.028 33.333 0.00 0.00 37.78 2.40
4015 4056 5.865552 GCTTGCATGTCAATCAACATAAACT 59.134 36.000 1.14 0.00 37.78 2.66
4028 4069 4.520111 AGTTATGAACTTGCTTGCATGTCA 59.480 37.500 13.21 12.63 39.04 3.58
4237 4309 7.619965 TGAAATAGACTATCAATCACCACACA 58.380 34.615 0.00 0.00 0.00 3.72
4238 4310 8.554528 CATGAAATAGACTATCAATCACCACAC 58.445 37.037 0.00 0.00 0.00 3.82
4266 4338 3.071602 AGAGCTGTTTCTGCCACTTCTTA 59.928 43.478 0.00 0.00 0.00 2.10
4308 4381 8.463930 AGACAATGTTTTCTTGAAACCATCTA 57.536 30.769 6.60 0.00 45.66 1.98
4351 4424 9.823647 CAACAGTCACAGGAGACTATTATTATT 57.176 33.333 0.00 0.00 46.65 1.40
4353 4426 8.362464 ACAACAGTCACAGGAGACTATTATTA 57.638 34.615 0.00 0.00 46.65 0.98
4355 4428 6.859112 ACAACAGTCACAGGAGACTATTAT 57.141 37.500 0.00 0.00 46.65 1.28
4356 4429 6.946583 AGTACAACAGTCACAGGAGACTATTA 59.053 38.462 0.00 0.00 46.65 0.98
4357 4430 5.775701 AGTACAACAGTCACAGGAGACTATT 59.224 40.000 0.00 0.00 46.65 1.73
4358 4431 5.326069 AGTACAACAGTCACAGGAGACTAT 58.674 41.667 0.00 0.00 46.65 2.12
4359 4432 4.726583 AGTACAACAGTCACAGGAGACTA 58.273 43.478 0.00 0.00 46.65 2.59
4420 4493 3.636679 AGATAGTGGTCTGCTGCTCTTA 58.363 45.455 0.00 0.00 0.00 2.10
4470 4543 2.432206 ACAAATAACTGGCAAACCGC 57.568 45.000 0.00 0.00 39.70 5.68
4496 4569 6.897966 ACCTCATGAGTTTCCAGAGTCTATAA 59.102 38.462 21.11 0.00 0.00 0.98
4499 4572 4.678256 ACCTCATGAGTTTCCAGAGTCTA 58.322 43.478 21.11 0.00 0.00 2.59
4571 4644 7.890127 TGAAGAAAGAAATCCTGTAATGATGGT 59.110 33.333 0.00 0.00 0.00 3.55
4660 4733 0.388649 CGCAGCCGGTCAGATATACC 60.389 60.000 1.90 0.00 0.00 2.73
4706 4779 8.081633 TGTTTGCTGATCAGAAATAAAAACGAT 58.918 29.630 27.04 0.00 0.00 3.73
4708 4781 7.591057 TCTGTTTGCTGATCAGAAATAAAAACG 59.409 33.333 27.04 17.25 35.65 3.60
4714 4787 8.571461 AAGATTCTGTTTGCTGATCAGAAATA 57.429 30.769 27.04 18.08 46.41 1.40
4718 4791 7.984422 TTTAAGATTCTGTTTGCTGATCAGA 57.016 32.000 27.04 8.75 36.59 3.27
4719 4792 8.456471 TGATTTAAGATTCTGTTTGCTGATCAG 58.544 33.333 18.84 18.84 0.00 2.90
4720 4793 8.339344 TGATTTAAGATTCTGTTTGCTGATCA 57.661 30.769 0.00 0.00 0.00 2.92
4721 4794 7.431668 GCTGATTTAAGATTCTGTTTGCTGATC 59.568 37.037 0.00 0.00 0.00 2.92
4722 4795 7.122353 AGCTGATTTAAGATTCTGTTTGCTGAT 59.878 33.333 0.00 0.00 0.00 2.90
4723 4796 6.432162 AGCTGATTTAAGATTCTGTTTGCTGA 59.568 34.615 0.00 0.00 0.00 4.26
4724 4797 6.618811 AGCTGATTTAAGATTCTGTTTGCTG 58.381 36.000 0.00 0.00 0.00 4.41
4726 4799 6.032717 GGAGCTGATTTAAGATTCTGTTTGC 58.967 40.000 0.00 0.00 0.00 3.68
4727 4800 7.388460 AGGAGCTGATTTAAGATTCTGTTTG 57.612 36.000 0.00 0.00 0.00 2.93
4737 5171 7.495279 GCCATCATAGATAGGAGCTGATTTAAG 59.505 40.741 0.00 0.00 0.00 1.85
4740 5174 5.339035 GGCCATCATAGATAGGAGCTGATTT 60.339 44.000 0.00 0.00 0.00 2.17
4751 5185 3.973305 TGGTGAGTTGGCCATCATAGATA 59.027 43.478 16.12 0.00 0.00 1.98
4793 5227 3.383185 ACTCTGCATACTTAGCTCTGGAC 59.617 47.826 0.00 0.00 0.00 4.02
4806 5240 3.319137 GTGGAACTGACACTCTGCATA 57.681 47.619 0.00 0.00 35.98 3.14
4842 5276 7.483580 ACCAGTAACTCTAAGATTACTTGCT 57.516 36.000 0.00 0.00 39.15 3.91
4881 5315 6.183361 ACAGACACAAGGATTCTTACTCTGTT 60.183 38.462 11.76 1.73 37.14 3.16
4883 5317 5.636965 CACAGACACAAGGATTCTTACTCTG 59.363 44.000 10.82 10.82 35.38 3.35
4885 5319 4.390297 GCACAGACACAAGGATTCTTACTC 59.610 45.833 0.00 0.00 0.00 2.59
4888 5322 4.065088 GTGCACAGACACAAGGATTCTTA 58.935 43.478 13.17 0.00 40.40 2.10
4889 5323 2.880890 GTGCACAGACACAAGGATTCTT 59.119 45.455 13.17 0.00 40.40 2.52
4890 5324 2.105477 AGTGCACAGACACAAGGATTCT 59.895 45.455 21.04 0.00 43.23 2.40
4891 5325 2.481952 GAGTGCACAGACACAAGGATTC 59.518 50.000 21.04 0.00 43.23 2.52
4892 5326 2.105477 AGAGTGCACAGACACAAGGATT 59.895 45.455 21.04 0.00 43.23 3.01
4910 5349 2.543012 CTGCCATCTCGCAATAACAGAG 59.457 50.000 0.00 0.00 38.56 3.35
4915 5354 3.819564 AGTACTGCCATCTCGCAATAA 57.180 42.857 0.00 0.00 38.56 1.40
4920 5359 2.010145 TGAAAGTACTGCCATCTCGC 57.990 50.000 0.00 0.00 0.00 5.03
4923 5362 3.641434 AGCATGAAAGTACTGCCATCT 57.359 42.857 0.00 1.03 36.56 2.90
4931 5370 3.512680 ACGAGCTGTAGCATGAAAGTAC 58.487 45.455 6.65 0.00 45.16 2.73
4960 5399 4.386652 GCATCAGAACAACATGCGAAAAAT 59.613 37.500 0.00 0.00 34.01 1.82
4962 5401 3.243334 TGCATCAGAACAACATGCGAAAA 60.243 39.130 0.00 0.00 44.99 2.29
4984 5423 2.938956 AGGTTGTAGCAGCTTGAAGT 57.061 45.000 0.00 0.00 0.00 3.01
4999 5438 9.344772 CTATCTGAGTCATGTTACTAGTAGGTT 57.655 37.037 2.23 0.00 0.00 3.50
5009 5448 8.367911 ACAAACACTTCTATCTGAGTCATGTTA 58.632 33.333 5.23 0.00 0.00 2.41
5010 5449 7.220030 ACAAACACTTCTATCTGAGTCATGTT 58.780 34.615 0.00 0.00 0.00 2.71
5011 5450 6.763355 ACAAACACTTCTATCTGAGTCATGT 58.237 36.000 0.00 0.00 0.00 3.21
5012 5451 8.815189 CATACAAACACTTCTATCTGAGTCATG 58.185 37.037 0.00 0.00 0.00 3.07
5014 5453 7.896811 ACATACAAACACTTCTATCTGAGTCA 58.103 34.615 0.00 0.00 0.00 3.41
5017 5477 8.194104 AGCTACATACAAACACTTCTATCTGAG 58.806 37.037 0.00 0.00 0.00 3.35
5023 5483 6.395629 GGACAGCTACATACAAACACTTCTA 58.604 40.000 0.00 0.00 0.00 2.10
5049 5509 2.835764 TCTACCTACGGCTCAACCAAAT 59.164 45.455 0.00 0.00 39.03 2.32
5090 5550 1.003580 CAGTTGGGTGGCTACTCACAT 59.996 52.381 0.47 0.00 36.92 3.21
5109 5569 7.230309 TCAATAACACATGACTCAACCAAATCA 59.770 33.333 0.00 0.00 0.00 2.57
5118 5578 7.119699 GGAATCACTTCAATAACACATGACTCA 59.880 37.037 0.00 0.00 32.70 3.41
5127 5587 5.939883 CAGTCCTGGAATCACTTCAATAACA 59.060 40.000 0.00 0.00 32.70 2.41
5149 5609 2.370281 ACTCACGCTTCATACACCAG 57.630 50.000 0.00 0.00 0.00 4.00
5155 5615 4.082190 ACTCAGCTAAACTCACGCTTCATA 60.082 41.667 0.00 0.00 0.00 2.15
5156 5616 3.257393 CTCAGCTAAACTCACGCTTCAT 58.743 45.455 0.00 0.00 0.00 2.57
5157 5617 2.035961 ACTCAGCTAAACTCACGCTTCA 59.964 45.455 0.00 0.00 0.00 3.02
5160 5621 1.889829 AGACTCAGCTAAACTCACGCT 59.110 47.619 0.00 0.00 0.00 5.07
5166 5627 6.481644 GCATATGCTTTAGACTCAGCTAAACT 59.518 38.462 20.64 0.00 35.91 2.66


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

AutoCloner maintained by Alex Coulton.