Multiple sequence alignment - TraesCS5B01G283800

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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 TraesCS5B01G283800 chr5B 100.000 4651 0 0 1 4651 469409081 469404431 0.000000e+00 8589.0
1 TraesCS5B01G283800 chr5B 92.522 575 34 7 4080 4651 661288972 661289540 0.000000e+00 815.0
2 TraesCS5B01G283800 chr5D 95.560 3378 106 18 733 4078 389527119 389523754 0.000000e+00 5367.0
3 TraesCS5B01G283800 chr5D 91.679 685 48 4 19 698 389528256 389527576 0.000000e+00 941.0
4 TraesCS5B01G283800 chr5D 87.209 430 42 9 1 421 221737112 221737537 1.170000e-130 477.0
5 TraesCS5B01G283800 chr5A 93.345 3366 145 24 766 4078 492829256 492825917 0.000000e+00 4902.0
6 TraesCS5B01G283800 chr2D 88.596 2464 189 46 1478 3918 226599215 226601609 0.000000e+00 2909.0
7 TraesCS5B01G283800 chr2D 87.822 427 45 5 1 421 318502565 318502990 1.160000e-135 494.0
8 TraesCS5B01G283800 chr2D 85.549 173 19 5 546 717 536380944 536381111 4.780000e-40 176.0
9 TraesCS5B01G283800 chr2A 86.609 1038 92 24 1478 2497 271887793 271886785 0.000000e+00 1103.0
10 TraesCS5B01G283800 chr2A 90.296 845 66 9 3069 3908 271869167 271868334 0.000000e+00 1092.0
11 TraesCS5B01G283800 chr2A 90.871 482 44 0 2589 3070 271886785 271886304 0.000000e+00 647.0
12 TraesCS5B01G283800 chr4A 93.654 583 27 8 4071 4651 713946039 713946613 0.000000e+00 863.0
13 TraesCS5B01G283800 chr7B 93.902 574 29 4 4078 4651 43698826 43698259 0.000000e+00 861.0
14 TraesCS5B01G283800 chr7B 89.044 429 38 7 1 421 181628704 181629131 1.480000e-144 523.0
15 TraesCS5B01G283800 chr1B 93.739 575 26 8 4079 4651 1696478 1695912 0.000000e+00 854.0
16 TraesCS5B01G283800 chr1B 92.650 585 32 9 4071 4651 432807648 432808225 0.000000e+00 832.0
17 TraesCS5B01G283800 chr1B 86.916 428 40 12 4 421 4264545 4264124 2.530000e-127 466.0
18 TraesCS5B01G283800 chr4B 93.576 576 27 6 4079 4651 367849375 367848807 0.000000e+00 850.0
19 TraesCS5B01G283800 chr4B 93.043 575 31 8 4080 4651 576181845 576181277 0.000000e+00 832.0
20 TraesCS5B01G283800 chr4B 92.535 576 35 5 4078 4651 517364206 517363637 0.000000e+00 819.0
21 TraesCS5B01G283800 chr3B 93.565 575 29 5 4079 4651 15126465 15127033 0.000000e+00 850.0
22 TraesCS5B01G283800 chr3B 84.685 111 16 1 549 659 805637294 805637185 4.920000e-20 110.0
23 TraesCS5B01G283800 chr7D 88.372 430 40 8 1 421 218181634 218181206 4.150000e-140 508.0
24 TraesCS5B01G283800 chr7D 88.140 430 38 9 4 422 544477275 544476848 2.500000e-137 499.0
25 TraesCS5B01G283800 chr1D 87.671 438 46 6 1 431 196100232 196099796 1.930000e-138 503.0
26 TraesCS5B01G283800 chr3D 86.605 433 45 9 1 421 492598886 492598455 2.530000e-127 466.0
27 TraesCS5B01G283800 chr6D 86.111 180 23 2 550 729 7453852 7453675 4.750000e-45 193.0
28 TraesCS5B01G283800 chr2B 88.820 161 8 6 996 1149 296064745 296064902 6.140000e-44 189.0
29 TraesCS5B01G283800 chr2B 83.735 166 24 2 552 717 637776209 637776371 2.240000e-33 154.0
30 TraesCS5B01G283800 chrUn 85.981 107 15 0 549 655 398557346 398557240 1.060000e-21 115.0
31 TraesCS5B01G283800 chrUn 84.071 113 18 0 543 655 61914612 61914724 4.920000e-20 110.0
32 TraesCS5B01G283800 chrUn 85.047 107 16 0 549 655 197806121 197806015 4.920000e-20 110.0
33 TraesCS5B01G283800 chrUn 84.071 113 18 0 543 655 206534259 206534371 4.920000e-20 110.0
34 TraesCS5B01G283800 chrUn 84.071 113 18 0 543 655 208960149 208960261 4.920000e-20 110.0
35 TraesCS5B01G283800 chrUn 84.071 113 18 0 543 655 367296941 367297053 4.920000e-20 110.0
36 TraesCS5B01G283800 chrUn 90.385 52 3 2 483 532 197806209 197806158 3.000000e-07 67.6
37 TraesCS5B01G283800 chrUn 97.436 39 1 0 483 521 206534177 206534215 3.000000e-07 67.6
38 TraesCS5B01G283800 chrUn 97.436 39 1 0 483 521 208960067 208960105 3.000000e-07 67.6
39 TraesCS5B01G283800 chrUn 97.436 39 1 0 483 521 367296859 367296897 3.000000e-07 67.6
40 TraesCS5B01G283800 chrUn 97.436 39 1 0 483 521 381076117 381076155 3.000000e-07 67.6
41 TraesCS5B01G283800 chrUn 90.385 52 3 2 483 532 398557434 398557383 3.000000e-07 67.6


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 TraesCS5B01G283800 chr5B 469404431 469409081 4650 True 8589 8589 100.0000 1 4651 1 chr5B.!!$R1 4650
1 TraesCS5B01G283800 chr5B 661288972 661289540 568 False 815 815 92.5220 4080 4651 1 chr5B.!!$F1 571
2 TraesCS5B01G283800 chr5D 389523754 389528256 4502 True 3154 5367 93.6195 19 4078 2 chr5D.!!$R1 4059
3 TraesCS5B01G283800 chr5A 492825917 492829256 3339 True 4902 4902 93.3450 766 4078 1 chr5A.!!$R1 3312
4 TraesCS5B01G283800 chr2D 226599215 226601609 2394 False 2909 2909 88.5960 1478 3918 1 chr2D.!!$F1 2440
5 TraesCS5B01G283800 chr2A 271868334 271869167 833 True 1092 1092 90.2960 3069 3908 1 chr2A.!!$R1 839
6 TraesCS5B01G283800 chr2A 271886304 271887793 1489 True 875 1103 88.7400 1478 3070 2 chr2A.!!$R2 1592
7 TraesCS5B01G283800 chr4A 713946039 713946613 574 False 863 863 93.6540 4071 4651 1 chr4A.!!$F1 580
8 TraesCS5B01G283800 chr7B 43698259 43698826 567 True 861 861 93.9020 4078 4651 1 chr7B.!!$R1 573
9 TraesCS5B01G283800 chr1B 1695912 1696478 566 True 854 854 93.7390 4079 4651 1 chr1B.!!$R1 572
10 TraesCS5B01G283800 chr1B 432807648 432808225 577 False 832 832 92.6500 4071 4651 1 chr1B.!!$F1 580
11 TraesCS5B01G283800 chr4B 367848807 367849375 568 True 850 850 93.5760 4079 4651 1 chr4B.!!$R1 572
12 TraesCS5B01G283800 chr4B 576181277 576181845 568 True 832 832 93.0430 4080 4651 1 chr4B.!!$R3 571
13 TraesCS5B01G283800 chr4B 517363637 517364206 569 True 819 819 92.5350 4078 4651 1 chr4B.!!$R2 573
14 TraesCS5B01G283800 chr3B 15126465 15127033 568 False 850 850 93.5650 4079 4651 1 chr3B.!!$F1 572

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
490 496 0.325296 TAGCAGTCCCCGTCCTTGAT 60.325 55.000 0.0 0.0 0.00 2.57 F
722 1162 0.533951 ACTAAGGGTTTACTCCGCCG 59.466 55.000 0.0 0.0 0.00 6.46 F
1257 1714 0.667487 ACTGCGTGGTTCAGTCGATG 60.667 55.000 0.0 0.0 40.47 3.84 F
2289 2771 1.065199 TCGCTTTCTCTGCCCATCATT 60.065 47.619 0.0 0.0 0.00 2.57 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2221 2703 1.208614 GCTGGCAGAAGTTGAAGCG 59.791 57.895 20.86 0.0 31.21 4.68 R
2289 2771 4.503714 AGGTGGTCTTCAGTTTCTCAAA 57.496 40.909 0.00 0.0 0.00 2.69 R
2968 3483 3.245016 ACTCTTGGGATGTGATTCTGCAA 60.245 43.478 0.00 0.0 0.00 4.08 R
3995 4524 0.037419 TTACGTCACCGGCCTTTACC 60.037 55.000 0.00 0.0 38.78 2.85 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
46 47 8.133024 TCTATCAATTGCCCAACAGTAATTTT 57.867 30.769 0.00 0.00 30.78 1.82
47 48 8.592809 TCTATCAATTGCCCAACAGTAATTTTT 58.407 29.630 0.00 0.00 30.78 1.94
51 52 8.592809 TCAATTGCCCAACAGTAATTTTTCTAT 58.407 29.630 0.00 0.00 30.78 1.98
52 53 9.218440 CAATTGCCCAACAGTAATTTTTCTATT 57.782 29.630 0.00 0.00 30.78 1.73
57 58 7.027161 CCCAACAGTAATTTTTCTATTCACCG 58.973 38.462 0.00 0.00 0.00 4.94
64 65 9.174166 AGTAATTTTTCTATTCACCGTATGCTT 57.826 29.630 0.00 0.00 0.00 3.91
92 93 5.049398 TCGAGAGAAGCTTCTAGTGAAAC 57.951 43.478 28.53 14.23 37.73 2.78
93 94 4.762765 TCGAGAGAAGCTTCTAGTGAAACT 59.237 41.667 28.53 18.65 45.55 2.66
94 95 5.938710 TCGAGAGAAGCTTCTAGTGAAACTA 59.061 40.000 28.53 3.51 41.65 2.24
95 96 6.600032 TCGAGAGAAGCTTCTAGTGAAACTAT 59.400 38.462 28.53 2.33 43.40 2.12
96 97 7.414651 TCGAGAGAAGCTTCTAGTGAAACTATG 60.415 40.741 28.53 14.38 43.40 2.23
222 228 7.754924 ACCATACAATTCAATTTTGCTCGTAAG 59.245 33.333 0.00 0.00 0.00 2.34
243 249 1.153539 TCAAGGGATTGACAACCCCA 58.846 50.000 20.53 0.00 46.64 4.96
269 275 1.748493 GCGATGGGTTGCAAGGATTTA 59.252 47.619 0.00 0.00 34.69 1.40
271 277 3.181476 GCGATGGGTTGCAAGGATTTATT 60.181 43.478 0.00 0.00 34.69 1.40
283 289 5.409214 GCAAGGATTTATTGTTTGTGTGCAT 59.591 36.000 0.00 0.00 0.00 3.96
285 291 4.931002 AGGATTTATTGTTTGTGTGCATGC 59.069 37.500 11.82 11.82 0.00 4.06
348 354 9.658799 TTGATAACCTTGATTCTTAACTGAGAG 57.341 33.333 0.00 0.00 0.00 3.20
378 384 8.879342 ACTTATTTCTACTGTACTGCATCATC 57.121 34.615 0.00 0.00 0.00 2.92
380 386 5.939764 TTTCTACTGTACTGCATCATCCT 57.060 39.130 0.00 0.00 0.00 3.24
381 387 5.521906 TTCTACTGTACTGCATCATCCTC 57.478 43.478 0.00 0.00 0.00 3.71
390 396 1.685517 TGCATCATCCTCTCCTCTTCG 59.314 52.381 0.00 0.00 0.00 3.79
402 408 1.982226 TCCTCTTCGGTGAAATCCCAA 59.018 47.619 0.00 0.00 0.00 4.12
405 411 1.071071 TCTTCGGTGAAATCCCAACGT 59.929 47.619 0.00 0.00 46.41 3.99
423 429 3.639538 ACGTAGTTCACAAGTAGCACAG 58.360 45.455 0.00 0.00 37.78 3.66
481 487 3.372554 GACGTGGCTAGCAGTCCCC 62.373 68.421 18.24 0.00 0.00 4.81
490 496 0.325296 TAGCAGTCCCCGTCCTTGAT 60.325 55.000 0.00 0.00 0.00 2.57
517 523 4.754667 GCCCTCCCGTCGAACACC 62.755 72.222 0.00 0.00 0.00 4.16
518 524 4.078516 CCCTCCCGTCGAACACCC 62.079 72.222 0.00 0.00 0.00 4.61
547 553 3.381983 AGCCGAGCACGATGACCA 61.382 61.111 4.70 0.00 42.66 4.02
584 590 1.603455 CCGGCTTGGTCACCATTGT 60.603 57.895 0.00 0.00 31.53 2.71
603 609 2.968206 GCGGGGGCGTATAGTAGG 59.032 66.667 0.00 0.00 0.00 3.18
605 611 1.962144 CGGGGGCGTATAGTAGGTG 59.038 63.158 0.00 0.00 0.00 4.00
606 612 0.825010 CGGGGGCGTATAGTAGGTGT 60.825 60.000 0.00 0.00 0.00 4.16
607 613 1.417288 GGGGGCGTATAGTAGGTGTT 58.583 55.000 0.00 0.00 0.00 3.32
610 616 1.949525 GGGCGTATAGTAGGTGTTCGA 59.050 52.381 0.00 0.00 0.00 3.71
611 617 2.555757 GGGCGTATAGTAGGTGTTCGAT 59.444 50.000 0.00 0.00 0.00 3.59
612 618 3.562505 GGCGTATAGTAGGTGTTCGATG 58.437 50.000 0.00 0.00 0.00 3.84
613 619 3.251729 GGCGTATAGTAGGTGTTCGATGA 59.748 47.826 0.00 0.00 0.00 2.92
634 640 7.967854 CGATGAAATGTATGAGCCAAAACTAAA 59.032 33.333 0.00 0.00 0.00 1.85
693 699 8.071368 GTCCGACAAGATCTTATAGTGAAGTAG 58.929 40.741 7.86 0.00 0.00 2.57
720 1160 3.698539 ACTCTACTAAGGGTTTACTCCGC 59.301 47.826 0.00 0.00 29.55 5.54
721 1161 3.026694 TCTACTAAGGGTTTACTCCGCC 58.973 50.000 0.00 0.00 0.00 6.13
722 1162 0.533951 ACTAAGGGTTTACTCCGCCG 59.466 55.000 0.00 0.00 0.00 6.46
723 1163 0.808847 CTAAGGGTTTACTCCGCCGC 60.809 60.000 0.00 0.00 0.00 6.53
724 1164 1.543065 TAAGGGTTTACTCCGCCGCA 61.543 55.000 0.00 0.00 0.00 5.69
725 1165 2.124860 GGGTTTACTCCGCCGCAT 60.125 61.111 0.00 0.00 0.00 4.73
726 1166 2.469516 GGGTTTACTCCGCCGCATG 61.470 63.158 0.00 0.00 0.00 4.06
727 1167 2.403586 GTTTACTCCGCCGCATGC 59.596 61.111 7.91 7.91 0.00 4.06
728 1168 2.106683 GTTTACTCCGCCGCATGCT 61.107 57.895 17.13 0.00 38.05 3.79
729 1169 2.106074 TTTACTCCGCCGCATGCTG 61.106 57.895 17.13 10.87 38.05 4.41
730 1170 2.514510 TTTACTCCGCCGCATGCTGA 62.515 55.000 17.13 6.05 38.05 4.26
731 1171 2.514510 TTACTCCGCCGCATGCTGAA 62.515 55.000 17.13 0.00 38.05 3.02
753 1193 9.983804 CTGAAAATCGGTTAGAAATAACCTTAC 57.016 33.333 13.68 3.85 45.51 2.34
771 1211 4.834496 CCTTACTACCCGGGATAATGTGTA 59.166 45.833 32.02 14.91 0.00 2.90
779 1219 5.126384 ACCCGGGATAATGTGTATTTGTTTG 59.874 40.000 32.02 0.00 0.00 2.93
859 1307 0.945813 CGTCACCGGCCTTTGTTTTA 59.054 50.000 0.00 0.00 0.00 1.52
956 1409 2.430694 TCGAGAGAGAGAGAGAGTCCTG 59.569 54.545 0.00 0.00 34.84 3.86
961 1414 1.379309 GAGAGAGAGTCCTGCCCGT 60.379 63.158 0.00 0.00 0.00 5.28
1077 1530 2.362503 ATCGGAGGCCACGAGTCA 60.363 61.111 23.70 5.28 44.24 3.41
1101 1554 1.216710 CAGGCTCCTCGAGTCCAAC 59.783 63.158 12.31 0.00 34.41 3.77
1105 1558 0.968393 GCTCCTCGAGTCCAACCTCT 60.968 60.000 12.31 0.00 31.39 3.69
1125 1578 1.078848 CCCCGAGCTCTTCAAGGTG 60.079 63.158 12.85 0.00 35.33 4.00
1130 1583 1.351153 GAGCTCTTCAAGGTGCGTAC 58.649 55.000 6.43 0.00 35.33 3.67
1161 1614 0.817634 GCTCGCTAGCTCCTCAGAGA 60.818 60.000 13.93 0.00 45.85 3.10
1197 1650 2.046292 CCTGGTTGGTTGGGTGAAATT 58.954 47.619 0.00 0.00 0.00 1.82
1200 1653 3.876320 CTGGTTGGTTGGGTGAAATTTTG 59.124 43.478 0.00 0.00 0.00 2.44
1257 1714 0.667487 ACTGCGTGGTTCAGTCGATG 60.667 55.000 0.00 0.00 40.47 3.84
1263 1720 2.598637 CGTGGTTCAGTCGATGTGTATG 59.401 50.000 0.00 0.00 0.00 2.39
1383 1841 1.328680 CGATTGATTCAGTGCGGGAAG 59.671 52.381 0.00 0.00 0.00 3.46
1423 1885 4.562757 CCTGTGTTCGGGATCTGTTTTCTA 60.563 45.833 0.00 0.00 42.46 2.10
1510 1976 7.868415 GTGATCTATTGTTCAGGTACCTGTATC 59.132 40.741 35.34 26.07 43.96 2.24
1684 2161 2.592102 ATTGTGCACACCCTCTTGAT 57.408 45.000 21.56 4.62 0.00 2.57
1887 2366 8.037758 TGTTTGCCTTCTCTTGTTTGAAAATTA 58.962 29.630 0.00 0.00 0.00 1.40
1995 2474 5.590259 GGCCTAATTCAGAACTCAATTGCTA 59.410 40.000 0.00 0.00 0.00 3.49
2107 2586 7.445707 TGTCAATATTTTGTGCTTACAGGTACA 59.554 33.333 0.00 0.00 34.32 2.90
2156 2636 4.101942 GTTCTCTTGTGACTCTATCTGCG 58.898 47.826 0.00 0.00 0.00 5.18
2188 2670 5.416271 TCAAACCTGGTGTCCTATTAGTC 57.584 43.478 0.00 0.00 0.00 2.59
2189 2671 5.091552 TCAAACCTGGTGTCCTATTAGTCT 58.908 41.667 0.00 0.00 0.00 3.24
2289 2771 1.065199 TCGCTTTCTCTGCCCATCATT 60.065 47.619 0.00 0.00 0.00 2.57
3241 3756 6.762661 ACATGGCATTTGTTATTATTTCTGCC 59.237 34.615 0.00 3.36 46.29 4.85
3243 3758 4.209080 GGCATTTGTTATTATTTCTGCCGC 59.791 41.667 0.00 0.00 38.61 6.53
3706 4224 2.876581 TGCCCTTTCCCTTCTTTTCTC 58.123 47.619 0.00 0.00 0.00 2.87
3874 4393 3.415212 CCACACAATGGCCCATAGATAG 58.585 50.000 0.00 0.00 43.24 2.08
3918 4437 4.570772 ACATTATGGATGTCGCACAACTAC 59.429 41.667 0.00 0.00 45.88 2.73
3922 4441 1.079405 ATGTCGCACAACTACGGGG 60.079 57.895 0.00 0.00 0.00 5.73
3995 4524 4.450122 GCGCACATGTCAGCCACG 62.450 66.667 0.30 2.97 0.00 4.94
4038 4567 1.276421 AGAGAATCCACAACCCGACTG 59.724 52.381 0.00 0.00 33.66 3.51
4041 4570 0.324943 AATCCACAACCCGACTGAGG 59.675 55.000 0.00 0.00 0.00 3.86
4069 4598 2.746362 GTCCAAAGAGATGAACAGCTGG 59.254 50.000 19.93 0.00 0.00 4.85
4107 4636 3.566742 TCGAAAAAGGGTTTTACTCCAGC 59.433 43.478 0.00 0.00 37.07 4.85
4108 4637 3.305131 CGAAAAAGGGTTTTACTCCAGCC 60.305 47.826 0.00 0.00 37.07 4.85
4109 4638 3.612795 AAAAGGGTTTTACTCCAGCCT 57.387 42.857 0.00 0.00 42.96 4.58
4110 4639 4.734843 AAAAGGGTTTTACTCCAGCCTA 57.265 40.909 0.00 0.00 40.12 3.93
4111 4640 4.302559 AAAGGGTTTTACTCCAGCCTAG 57.697 45.455 0.00 0.00 40.12 3.02
4177 4707 4.640771 ATCCAGCTAACAAGTCTCCAAA 57.359 40.909 0.00 0.00 0.00 3.28
4229 4763 2.359900 AGAGCCAAATAGAAAGCCACG 58.640 47.619 0.00 0.00 0.00 4.94
4283 4818 4.157246 TGCCTATCCTATTACATGACCGT 58.843 43.478 0.00 0.00 0.00 4.83
4303 4838 3.489398 CGTCATCCAAACCGGTTGAAAAA 60.489 43.478 23.08 5.59 43.62 1.94
4360 4896 2.201210 CAAACACCCCCTGGCCTT 59.799 61.111 3.32 0.00 33.59 4.35
4364 4900 3.966543 CACCCCCTGGCCTTCGTT 61.967 66.667 3.32 0.00 33.59 3.85
4405 4941 2.040544 GGATCAACACTGTGGCCCG 61.041 63.158 13.09 0.00 0.00 6.13
4522 5058 3.833442 CACGAATGTGCCTCGCTATATA 58.167 45.455 0.00 0.00 39.67 0.86
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
11 12 9.002600 GTTGGGCAATTGATAGAAAAGAAAAAT 57.997 29.630 10.34 0.00 0.00 1.82
12 13 7.989741 TGTTGGGCAATTGATAGAAAAGAAAAA 59.010 29.630 10.34 0.00 0.00 1.94
13 14 7.504403 TGTTGGGCAATTGATAGAAAAGAAAA 58.496 30.769 10.34 0.00 0.00 2.29
14 15 7.060383 TGTTGGGCAATTGATAGAAAAGAAA 57.940 32.000 10.34 0.00 0.00 2.52
15 16 6.267471 ACTGTTGGGCAATTGATAGAAAAGAA 59.733 34.615 10.34 0.00 0.00 2.52
16 17 5.774690 ACTGTTGGGCAATTGATAGAAAAGA 59.225 36.000 10.34 0.00 0.00 2.52
17 18 6.029346 ACTGTTGGGCAATTGATAGAAAAG 57.971 37.500 10.34 2.98 0.00 2.27
22 23 8.776376 AAAAATTACTGTTGGGCAATTGATAG 57.224 30.769 10.34 0.00 0.00 2.08
64 65 6.016192 TCACTAGAAGCTTCTCTCGAGAAAAA 60.016 38.462 31.67 12.48 45.75 1.94
92 93 4.696479 AAAGATAGACCTGGTGCCATAG 57.304 45.455 2.82 0.00 0.00 2.23
93 94 6.763715 ATAAAAGATAGACCTGGTGCCATA 57.236 37.500 2.82 0.00 0.00 2.74
94 95 5.653255 ATAAAAGATAGACCTGGTGCCAT 57.347 39.130 2.82 0.00 0.00 4.40
95 96 5.450818 AATAAAAGATAGACCTGGTGCCA 57.549 39.130 2.82 0.00 0.00 4.92
207 213 4.475944 CCTTGACCTTACGAGCAAAATTG 58.524 43.478 0.00 0.00 0.00 2.32
210 216 2.105134 TCCCTTGACCTTACGAGCAAAA 59.895 45.455 0.00 0.00 0.00 2.44
243 249 1.240641 TTGCAACCCATCGCGAACAT 61.241 50.000 15.24 0.00 0.00 2.71
269 275 0.032403 AGCGCATGCACACAAACAAT 59.968 45.000 19.57 0.00 46.23 2.71
271 277 1.299240 CAGCGCATGCACACAAACA 60.299 52.632 19.57 0.00 46.23 2.83
283 289 3.594775 CACCTTGTTGGCAGCGCA 61.595 61.111 11.47 0.00 40.22 6.09
285 291 3.119193 AACACCTTGTTGGCAGCG 58.881 55.556 0.00 0.00 39.45 5.18
293 299 2.024414 GAGAACCAAGCAACACCTTGT 58.976 47.619 0.00 0.00 40.40 3.16
295 301 1.215423 AGGAGAACCAAGCAACACCTT 59.785 47.619 0.00 0.00 38.94 3.50
359 365 5.204292 AGAGGATGATGCAGTACAGTAGAA 58.796 41.667 0.00 0.00 0.00 2.10
366 372 3.230134 AGAGGAGAGGATGATGCAGTAC 58.770 50.000 0.00 0.00 0.00 2.73
378 384 2.159028 GGATTTCACCGAAGAGGAGAGG 60.159 54.545 0.00 0.00 45.00 3.69
380 386 1.831736 GGGATTTCACCGAAGAGGAGA 59.168 52.381 0.00 0.00 45.00 3.71
381 387 1.555075 TGGGATTTCACCGAAGAGGAG 59.445 52.381 0.00 0.00 45.00 3.69
390 396 3.187842 GTGAACTACGTTGGGATTTCACC 59.812 47.826 15.38 0.00 37.80 4.02
402 408 3.552273 CCTGTGCTACTTGTGAACTACGT 60.552 47.826 0.00 0.00 0.00 3.57
405 411 3.305131 CGTCCTGTGCTACTTGTGAACTA 60.305 47.826 0.00 0.00 0.00 2.24
475 481 1.613630 AGCATCAAGGACGGGGACT 60.614 57.895 0.00 0.00 0.00 3.85
481 487 1.376424 ACCAGCAGCATCAAGGACG 60.376 57.895 0.00 0.00 0.00 4.79
530 536 3.362399 CTGGTCATCGTGCTCGGCT 62.362 63.158 8.49 0.00 37.69 5.52
595 601 9.908152 CATACATTTCATCGAACACCTACTATA 57.092 33.333 0.00 0.00 0.00 1.31
603 609 4.332543 TGGCTCATACATTTCATCGAACAC 59.667 41.667 0.00 0.00 0.00 3.32
605 611 5.484173 TTGGCTCATACATTTCATCGAAC 57.516 39.130 0.00 0.00 0.00 3.95
606 612 6.150976 AGTTTTGGCTCATACATTTCATCGAA 59.849 34.615 0.00 0.00 0.00 3.71
607 613 5.647658 AGTTTTGGCTCATACATTTCATCGA 59.352 36.000 0.00 0.00 0.00 3.59
611 617 9.995003 AAATTTAGTTTTGGCTCATACATTTCA 57.005 25.926 0.00 0.00 0.00 2.69
661 667 1.404843 AGATCTTGTCGGACCTAGCC 58.595 55.000 5.55 0.00 0.00 3.93
693 699 8.134261 CGGAGTAAACCCTTAGTAGAGTATTTC 58.866 40.741 0.00 0.00 0.00 2.17
699 1139 3.067883 GGCGGAGTAAACCCTTAGTAGAG 59.932 52.174 0.00 0.00 0.00 2.43
720 1160 0.171007 AACCGATTTTCAGCATGCGG 59.829 50.000 13.01 12.49 43.95 5.69
721 1161 2.351418 TCTAACCGATTTTCAGCATGCG 59.649 45.455 13.01 7.64 34.76 4.73
722 1162 4.355543 TTCTAACCGATTTTCAGCATGC 57.644 40.909 10.51 10.51 34.76 4.06
723 1163 7.432252 GGTTATTTCTAACCGATTTTCAGCATG 59.568 37.037 0.00 0.00 45.59 4.06
724 1164 7.480810 GGTTATTTCTAACCGATTTTCAGCAT 58.519 34.615 0.00 0.00 45.59 3.79
725 1165 6.848451 GGTTATTTCTAACCGATTTTCAGCA 58.152 36.000 0.00 0.00 45.59 4.41
753 1193 5.617252 ACAAATACACATTATCCCGGGTAG 58.383 41.667 22.86 9.53 0.00 3.18
771 1211 2.495669 CGGTGGGGATTAGCAAACAAAT 59.504 45.455 0.00 0.00 0.00 2.32
779 1219 1.600916 GGATGCGGTGGGGATTAGC 60.601 63.158 0.00 0.00 0.00 3.09
851 1299 2.688958 CCGGCGGGGATTATAAAACAAA 59.311 45.455 20.56 0.00 38.47 2.83
877 1325 4.574013 CGAGCAGATTTCTCCTTGCTTAAT 59.426 41.667 0.00 0.00 32.34 1.40
956 1409 2.428085 GGAGGAGAGAGGAACGGGC 61.428 68.421 0.00 0.00 0.00 6.13
961 1414 0.395036 CTCGCAGGAGGAGAGAGGAA 60.395 60.000 0.00 0.00 45.27 3.36
1077 1530 2.601666 TCGAGGAGCCTGTGCAGT 60.602 61.111 0.00 0.00 41.13 4.40
1101 1554 2.042435 AAGAGCTCGGGGGAGAGG 60.042 66.667 8.37 0.00 38.63 3.69
1105 1558 1.990060 CCTTGAAGAGCTCGGGGGA 60.990 63.158 8.37 0.00 0.00 4.81
1257 1714 4.080863 AGTTCATCAGGTTCCTCCATACAC 60.081 45.833 0.00 0.00 39.02 2.90
1263 1720 4.762289 ACATAGTTCATCAGGTTCCTCC 57.238 45.455 0.00 0.00 0.00 4.30
1510 1976 7.857569 TCGGAAATAAAGTACAGTGTGAAAAG 58.142 34.615 5.88 0.00 0.00 2.27
1684 2161 4.659172 CCGGGCAGGGAAACAGCA 62.659 66.667 0.00 0.00 34.92 4.41
1779 2256 7.667575 AGATCAGTTCATAATCTACCACAGT 57.332 36.000 0.00 0.00 0.00 3.55
1995 2474 4.037923 AGCAAAATGACAAGTCGTTGGAAT 59.962 37.500 8.31 0.00 38.69 3.01
2107 2586 7.669722 ACCACAACTAAATCACCAATGTTAGAT 59.330 33.333 0.00 0.00 0.00 1.98
2156 2636 4.816392 ACACCAGGTTTGAAAACAAAGAC 58.184 39.130 8.11 0.00 40.63 3.01
2188 2670 5.347342 CCAAGCAGAGTCTCATACACTTAG 58.653 45.833 1.94 0.00 0.00 2.18
2189 2671 4.382040 GCCAAGCAGAGTCTCATACACTTA 60.382 45.833 1.94 0.00 0.00 2.24
2221 2703 1.208614 GCTGGCAGAAGTTGAAGCG 59.791 57.895 20.86 0.00 31.21 4.68
2289 2771 4.503714 AGGTGGTCTTCAGTTTCTCAAA 57.496 40.909 0.00 0.00 0.00 2.69
2968 3483 3.245016 ACTCTTGGGATGTGATTCTGCAA 60.245 43.478 0.00 0.00 0.00 4.08
3874 4393 6.249035 TGTAAATCCAACCACGATTCTTTC 57.751 37.500 0.00 0.00 0.00 2.62
3939 4458 1.442769 AGCCAGACGCATGTAACTTG 58.557 50.000 0.00 0.00 41.38 3.16
3947 4466 3.437795 GCAGCAAGCCAGACGCAT 61.438 61.111 0.00 0.00 41.38 4.73
3951 4470 0.170561 CAAGATGCAGCAAGCCAGAC 59.829 55.000 4.07 0.00 44.83 3.51
3953 4472 0.601558 AACAAGATGCAGCAAGCCAG 59.398 50.000 4.07 0.00 44.83 4.85
3995 4524 0.037419 TTACGTCACCGGCCTTTACC 60.037 55.000 0.00 0.00 38.78 2.85
4004 4533 2.983402 TTCTCTGACTTACGTCACCG 57.017 50.000 0.00 0.00 44.85 4.94
4010 4539 3.927142 GGTTGTGGATTCTCTGACTTACG 59.073 47.826 0.00 0.00 0.00 3.18
4030 4559 1.482593 GACAATGATCCTCAGTCGGGT 59.517 52.381 0.00 0.00 0.00 5.28
4038 4567 5.678583 TCATCTCTTTGGACAATGATCCTC 58.321 41.667 1.76 0.00 39.75 3.71
4041 4570 6.677431 GCTGTTCATCTCTTTGGACAATGATC 60.677 42.308 1.76 0.00 34.72 2.92
4047 4576 3.405831 CAGCTGTTCATCTCTTTGGACA 58.594 45.455 5.25 0.00 33.99 4.02
4092 4621 1.560146 GCTAGGCTGGAGTAAAACCCT 59.440 52.381 0.43 0.00 0.00 4.34
4107 4636 2.433604 TCTTTCTGATGCAGAGGCTAGG 59.566 50.000 0.00 0.00 41.75 3.02
4108 4637 3.815856 TCTTTCTGATGCAGAGGCTAG 57.184 47.619 0.00 0.00 41.75 3.42
4109 4638 4.069300 CATCTTTCTGATGCAGAGGCTA 57.931 45.455 0.00 0.00 44.96 3.93
4110 4639 2.920524 CATCTTTCTGATGCAGAGGCT 58.079 47.619 0.00 0.00 44.96 4.58
4163 4693 6.097915 ACTTCGAGATTTGGAGACTTGTTA 57.902 37.500 0.00 0.00 0.00 2.41
4177 4707 7.955864 GCGTTTGTTTATTTCTTACTTCGAGAT 59.044 33.333 0.00 0.00 0.00 2.75
4229 4763 2.959507 ATTTTATTTGCCAGCCGGTC 57.040 45.000 1.90 0.00 33.28 4.79
4303 4838 2.022035 TGGGAGATGGTAGGTCAGGATT 60.022 50.000 0.00 0.00 0.00 3.01
4311 4846 3.147772 CTACCCGATGGGAGATGGTAGG 61.148 59.091 9.30 0.00 46.90 3.18
4348 4883 3.966543 CAACGAAGGCCAGGGGGT 61.967 66.667 5.01 0.00 36.17 4.95
4360 4896 0.520404 GTCGCTACTCACTCCAACGA 59.480 55.000 0.00 0.00 0.00 3.85
4364 4900 0.538746 TGTGGTCGCTACTCACTCCA 60.539 55.000 10.01 0.00 31.73 3.86
4405 4941 5.705609 TCACTTTTTGCAGGTTATCTTCC 57.294 39.130 0.00 0.00 0.00 3.46
4481 5017 4.438148 GTGTTGGTGTTTGTGCCTTATTT 58.562 39.130 0.00 0.00 0.00 1.40
4496 5032 1.227999 CGAGGCACATTCGTGTTGGT 61.228 55.000 0.00 0.00 45.50 3.67
4522 5058 1.341383 GGCTTGATGGGGTTGACTCAT 60.341 52.381 0.00 0.00 0.00 2.90
4607 5143 2.236146 TCCGCTGGCTAAGATTCTTTGA 59.764 45.455 11.35 0.00 0.00 2.69


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

AutoCloner maintained by Alex Coulton.