Multiple sequence alignment - TraesCS5D01G409200

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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 TraesCS5D01G409200 chr5D 100.000 3455 0 0 1 3455 473095614 473099068 0.000000e+00 6381.0
1 TraesCS5D01G409200 chr5D 87.838 74 7 2 3173 3244 528755021 528755094 6.140000e-13 86.1
2 TraesCS5D01G409200 chr5A 93.506 2972 82 28 567 3455 593077828 593080771 0.000000e+00 4316.0
3 TraesCS5D01G409200 chr5A 86.471 170 17 3 125 288 593076919 593077088 7.620000e-42 182.0
4 TraesCS5D01G409200 chr5B 96.624 2251 45 6 575 2798 580490308 580492554 0.000000e+00 3707.0
5 TraesCS5D01G409200 chr5B 88.842 475 48 4 1 471 580488335 580488808 2.310000e-161 579.0
6 TraesCS5D01G409200 chr7A 95.946 370 13 1 2784 3151 130440619 130440250 1.770000e-167 599.0
7 TraesCS5D01G409200 chr7A 95.673 208 8 1 3249 3455 130440221 130440014 1.990000e-87 333.0
8 TraesCS5D01G409200 chr7A 89.394 66 7 0 3173 3238 14373478 14373543 2.210000e-12 84.2
9 TraesCS5D01G409200 chr6A 95.946 370 13 1 2784 3151 26755720 26756089 1.770000e-167 599.0
10 TraesCS5D01G409200 chr6A 96.635 208 6 1 3249 3455 26756118 26756325 9.180000e-91 344.0
11 TraesCS5D01G409200 chrUn 79.265 381 76 3 2488 2865 413095334 413094954 2.640000e-66 263.0
12 TraesCS5D01G409200 chr6B 79.265 381 76 3 2488 2865 560700949 560700569 2.640000e-66 263.0
13 TraesCS5D01G409200 chr6B 79.265 381 76 3 2488 2865 560740396 560740016 2.640000e-66 263.0
14 TraesCS5D01G409200 chr6B 78.740 381 78 3 2488 2865 560793302 560792922 5.720000e-63 252.0
15 TraesCS5D01G409200 chr7D 87.179 78 8 1 3173 3248 625355910 625355833 1.710000e-13 87.9
16 TraesCS5D01G409200 chr1A 88.732 71 6 2 3177 3245 558188247 558188317 6.140000e-13 86.1
17 TraesCS5D01G409200 chr3D 83.871 93 7 4 3160 3244 131489161 131489253 7.950000e-12 82.4
18 TraesCS5D01G409200 chr3D 88.235 68 8 0 3173 3240 267028089 267028022 7.950000e-12 82.4
19 TraesCS5D01G409200 chr3D 86.486 74 8 1 3173 3244 389633203 389633130 2.860000e-11 80.5
20 TraesCS5D01G409200 chr3A 86.486 74 8 2 3173 3244 224976042 224976115 2.860000e-11 80.5


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 TraesCS5D01G409200 chr5D 473095614 473099068 3454 False 6381.0 6381 100.0000 1 3455 1 chr5D.!!$F1 3454
1 TraesCS5D01G409200 chr5A 593076919 593080771 3852 False 2249.0 4316 89.9885 125 3455 2 chr5A.!!$F1 3330
2 TraesCS5D01G409200 chr5B 580488335 580492554 4219 False 2143.0 3707 92.7330 1 2798 2 chr5B.!!$F1 2797
3 TraesCS5D01G409200 chr7A 130440014 130440619 605 True 466.0 599 95.8095 2784 3455 2 chr7A.!!$R1 671
4 TraesCS5D01G409200 chr6A 26755720 26756325 605 False 471.5 599 96.2905 2784 3455 2 chr6A.!!$F1 671

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
465 476 0.109723 TTAGGGCCGAAGTGCTTTGT 59.890 50.0 0.00 0.00 0.00 2.83 F
710 2187 0.396278 GGCCATTTTCTCCCCCTCAG 60.396 60.0 0.00 0.00 0.00 3.35 F
723 2200 0.518636 CCCTCAGTCGACGACGTTTA 59.481 55.0 21.44 8.14 37.67 2.01 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2084 3614 0.811616 GCGGAAGACCCTGTATGCTG 60.812 60.000 0.00 0.00 0.0 4.41 R
2232 3762 0.870393 CAGAGAACGTGTGCATGCTT 59.130 50.000 20.33 3.73 0.0 3.91 R
2587 4117 7.234577 ACACCATGGCCTTAATAAAAAGAGAAA 59.765 33.333 13.04 0.00 0.0 2.52 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 1.746615 CACTGGCAATGACGAGGGG 60.747 63.158 0.00 0.00 0.00 4.79
59 62 9.654663 ACTGGTATTCTTATCTGTAACTTTCAC 57.345 33.333 0.00 0.00 0.00 3.18
62 65 9.530633 GGTATTCTTATCTGTAACTTTCACGAT 57.469 33.333 0.00 0.00 0.00 3.73
107 110 7.054491 TGGTTCTACTCCGTACTTTTTAACT 57.946 36.000 0.00 0.00 0.00 2.24
118 121 7.119553 TCCGTACTTTTTAACTGTTGTTCACTT 59.880 33.333 2.69 0.00 37.59 3.16
150 153 5.244755 GTCCATTAATTTGTTGGCATGGTT 58.755 37.500 0.00 0.00 0.00 3.67
206 210 1.006043 TCGAGATCTCCACCCTCAGTT 59.994 52.381 17.13 0.00 0.00 3.16
207 211 1.135915 CGAGATCTCCACCCTCAGTTG 59.864 57.143 17.13 0.00 0.00 3.16
244 251 3.492656 GGATTTGACGCTGGTGCTATCTA 60.493 47.826 0.00 0.00 36.97 1.98
296 305 3.532641 AGTGCAATCTTTTCCCTTCCT 57.467 42.857 0.00 0.00 0.00 3.36
305 314 5.179452 TCTTTTCCCTTCCTGATAAGTGG 57.821 43.478 0.00 0.00 0.00 4.00
308 317 2.492025 TCCCTTCCTGATAAGTGGCAT 58.508 47.619 0.00 0.00 0.00 4.40
310 319 3.391296 TCCCTTCCTGATAAGTGGCATAC 59.609 47.826 0.00 0.00 0.00 2.39
316 325 4.021456 TCCTGATAAGTGGCATACGTATGG 60.021 45.833 31.14 16.47 34.69 2.74
334 343 1.627879 GGCACAAACATATGGCAACG 58.372 50.000 7.80 0.00 40.91 4.10
337 346 2.504868 CACAAACATATGGCAACGTCG 58.495 47.619 7.80 0.00 42.51 5.12
351 360 1.935199 AACGTCGAACGGTTTTGATGT 59.065 42.857 13.08 13.08 39.21 3.06
382 391 3.184581 GTGACGTGAGGATGACAACTTTC 59.815 47.826 0.00 0.00 0.00 2.62
386 396 4.881850 ACGTGAGGATGACAACTTTCTTTT 59.118 37.500 0.00 0.00 0.00 2.27
392 402 5.244626 AGGATGACAACTTTCTTTTGGATGG 59.755 40.000 0.00 0.00 0.00 3.51
400 410 6.866010 ACTTTCTTTTGGATGGCAAATTTC 57.134 33.333 0.00 0.00 0.00 2.17
408 418 8.688747 TTTTGGATGGCAAATTTCAGTTTATT 57.311 26.923 0.00 0.00 0.00 1.40
412 422 8.566260 TGGATGGCAAATTTCAGTTTATTTTTG 58.434 29.630 0.00 0.00 0.00 2.44
415 425 6.264067 TGGCAAATTTCAGTTTATTTTTGGGG 59.736 34.615 0.00 0.00 0.00 4.96
458 469 1.971481 AAAAACGTTAGGGCCGAAGT 58.029 45.000 0.00 0.00 0.00 3.01
459 470 1.232119 AAAACGTTAGGGCCGAAGTG 58.768 50.000 0.00 0.00 0.00 3.16
460 471 1.232621 AAACGTTAGGGCCGAAGTGC 61.233 55.000 0.00 0.00 0.00 4.40
461 472 2.108278 AACGTTAGGGCCGAAGTGCT 62.108 55.000 0.00 0.00 0.00 4.40
462 473 1.375523 CGTTAGGGCCGAAGTGCTT 60.376 57.895 0.00 0.00 0.00 3.91
463 474 0.953960 CGTTAGGGCCGAAGTGCTTT 60.954 55.000 0.00 0.00 0.00 3.51
464 475 0.521735 GTTAGGGCCGAAGTGCTTTG 59.478 55.000 0.00 0.00 0.00 2.77
465 476 0.109723 TTAGGGCCGAAGTGCTTTGT 59.890 50.000 0.00 0.00 0.00 2.83
466 477 0.605319 TAGGGCCGAAGTGCTTTGTG 60.605 55.000 0.00 0.00 0.00 3.33
467 478 2.050077 GGCCGAAGTGCTTTGTGC 60.050 61.111 0.00 2.48 43.25 4.57
468 479 2.555547 GGCCGAAGTGCTTTGTGCT 61.556 57.895 0.00 0.00 43.37 4.40
469 480 1.234615 GGCCGAAGTGCTTTGTGCTA 61.235 55.000 0.00 0.00 43.37 3.49
470 481 0.804989 GCCGAAGTGCTTTGTGCTAT 59.195 50.000 0.00 0.00 43.37 2.97
471 482 1.200020 GCCGAAGTGCTTTGTGCTATT 59.800 47.619 0.00 0.00 43.37 1.73
472 483 2.351738 GCCGAAGTGCTTTGTGCTATTT 60.352 45.455 0.00 0.00 43.37 1.40
473 484 3.857010 GCCGAAGTGCTTTGTGCTATTTT 60.857 43.478 0.00 0.00 43.37 1.82
474 485 4.614993 GCCGAAGTGCTTTGTGCTATTTTA 60.615 41.667 0.00 0.00 43.37 1.52
475 486 5.640732 CCGAAGTGCTTTGTGCTATTTTAT 58.359 37.500 0.00 0.00 43.37 1.40
476 487 6.092748 CCGAAGTGCTTTGTGCTATTTTATT 58.907 36.000 0.00 0.00 43.37 1.40
477 488 6.586082 CCGAAGTGCTTTGTGCTATTTTATTT 59.414 34.615 0.00 0.00 43.37 1.40
478 489 7.201350 CCGAAGTGCTTTGTGCTATTTTATTTC 60.201 37.037 0.00 0.00 43.37 2.17
479 490 7.538678 CGAAGTGCTTTGTGCTATTTTATTTCT 59.461 33.333 0.00 0.00 43.37 2.52
480 491 8.748380 AAGTGCTTTGTGCTATTTTATTTCTC 57.252 30.769 0.00 0.00 43.37 2.87
481 492 7.315890 AGTGCTTTGTGCTATTTTATTTCTCC 58.684 34.615 0.00 0.00 43.37 3.71
482 493 6.531594 GTGCTTTGTGCTATTTTATTTCTCCC 59.468 38.462 0.00 0.00 43.37 4.30
483 494 6.437162 TGCTTTGTGCTATTTTATTTCTCCCT 59.563 34.615 0.00 0.00 43.37 4.20
484 495 6.975197 GCTTTGTGCTATTTTATTTCTCCCTC 59.025 38.462 0.00 0.00 38.95 4.30
485 496 6.677781 TTGTGCTATTTTATTTCTCCCTCG 57.322 37.500 0.00 0.00 0.00 4.63
486 497 4.574828 TGTGCTATTTTATTTCTCCCTCGC 59.425 41.667 0.00 0.00 0.00 5.03
487 498 4.574828 GTGCTATTTTATTTCTCCCTCGCA 59.425 41.667 0.00 0.00 0.00 5.10
488 499 5.065988 GTGCTATTTTATTTCTCCCTCGCAA 59.934 40.000 0.00 0.00 0.00 4.85
489 500 5.650266 TGCTATTTTATTTCTCCCTCGCAAA 59.350 36.000 0.00 0.00 0.00 3.68
490 501 6.151985 TGCTATTTTATTTCTCCCTCGCAAAA 59.848 34.615 0.00 0.00 0.00 2.44
491 502 7.033185 GCTATTTTATTTCTCCCTCGCAAAAA 58.967 34.615 0.00 0.00 0.00 1.94
513 524 3.990318 AAAGGAAGTGCTTTGTGCTAC 57.010 42.857 0.00 0.00 43.37 3.58
580 2032 2.858768 AGAGGAGGGGCATTATTTTCCA 59.141 45.455 0.00 0.00 0.00 3.53
703 2180 1.821136 CTTCCACAGGCCATTTTCTCC 59.179 52.381 5.01 0.00 0.00 3.71
710 2187 0.396278 GGCCATTTTCTCCCCCTCAG 60.396 60.000 0.00 0.00 0.00 3.35
723 2200 0.518636 CCCTCAGTCGACGACGTTTA 59.481 55.000 21.44 8.14 37.67 2.01
951 2481 1.447314 GAAGTACGGGGGTTCTGCG 60.447 63.158 0.00 0.00 0.00 5.18
986 2516 0.530650 CAGTGTCAGCGTGTGGAAGT 60.531 55.000 0.00 0.00 0.00 3.01
1104 2634 2.397413 CTGTGGACGCCTTTGACCCT 62.397 60.000 0.00 0.00 0.00 4.34
1416 2946 2.400399 GTCAATGTCGAGACGTTTGGA 58.600 47.619 7.87 1.87 38.39 3.53
1644 3174 1.065410 TCTTGCTTGAGGGTTGGGGA 61.065 55.000 0.00 0.00 0.00 4.81
1695 3225 3.834813 AGGTCTACAGTGAGATGCTTGAA 59.165 43.478 0.00 0.00 0.00 2.69
1752 3282 2.673775 TGGTTGATTCCCTCTGCAAA 57.326 45.000 0.00 0.00 0.00 3.68
2076 3606 6.916360 AACAAGATGATTAGCCTTGGAAAA 57.084 33.333 0.00 0.00 40.99 2.29
2084 3614 5.126061 TGATTAGCCTTGGAAAAGATGAAGC 59.874 40.000 0.00 0.00 0.00 3.86
2587 4117 6.676950 TGTTATTGTTTGTCGAGCATGATTT 58.323 32.000 0.00 0.00 0.00 2.17
2752 4282 8.529476 CCAACTACAGTTACTTCATAAGTACCT 58.471 37.037 0.00 0.00 43.30 3.08
2898 4428 6.899393 ATTTATTTCACAGCAGGAGACAAA 57.101 33.333 0.00 0.00 0.00 2.83
2918 4448 8.325046 AGACAAAGGCTAATAGTGATTCTTCTT 58.675 33.333 0.00 0.00 0.00 2.52
2924 4454 8.592809 AGGCTAATAGTGATTCTTCTTCATAGG 58.407 37.037 0.00 0.00 0.00 2.57
3034 4572 9.934190 AAAATTGTACATTTTTGTTTGATCAGC 57.066 25.926 21.59 0.00 0.00 4.26
3071 4609 1.767759 AACAAAGCAGAGCCACAAGT 58.232 45.000 0.00 0.00 0.00 3.16
3072 4610 2.638480 ACAAAGCAGAGCCACAAGTA 57.362 45.000 0.00 0.00 0.00 2.24
3073 4611 2.222027 ACAAAGCAGAGCCACAAGTAC 58.778 47.619 0.00 0.00 0.00 2.73
3074 4612 2.221169 CAAAGCAGAGCCACAAGTACA 58.779 47.619 0.00 0.00 0.00 2.90
3075 4613 2.175878 AAGCAGAGCCACAAGTACAG 57.824 50.000 0.00 0.00 0.00 2.74
3076 4614 1.051812 AGCAGAGCCACAAGTACAGT 58.948 50.000 0.00 0.00 0.00 3.55
3085 4629 4.755123 AGCCACAAGTACAGTTGTATTGAC 59.245 41.667 15.14 0.31 38.65 3.18
3154 4700 8.806429 TTGATTACTCCATTTTCTAGATTGCA 57.194 30.769 0.00 0.00 0.00 4.08
3155 4701 8.213518 TGATTACTCCATTTTCTAGATTGCAC 57.786 34.615 0.00 0.00 0.00 4.57
3157 4703 4.579869 ACTCCATTTTCTAGATTGCACGT 58.420 39.130 0.00 0.00 0.00 4.49
3158 4704 5.003804 ACTCCATTTTCTAGATTGCACGTT 58.996 37.500 0.00 0.00 0.00 3.99
3159 4705 6.170506 ACTCCATTTTCTAGATTGCACGTTA 58.829 36.000 0.00 0.00 0.00 3.18
3160 4706 6.653320 ACTCCATTTTCTAGATTGCACGTTAA 59.347 34.615 0.00 0.00 0.00 2.01
3161 4707 6.837992 TCCATTTTCTAGATTGCACGTTAAC 58.162 36.000 0.00 0.00 0.00 2.01
3162 4708 6.653320 TCCATTTTCTAGATTGCACGTTAACT 59.347 34.615 3.71 0.00 0.00 2.24
3164 4710 8.612619 CCATTTTCTAGATTGCACGTTAACTAT 58.387 33.333 3.71 0.00 0.00 2.12
3165 4711 9.988350 CATTTTCTAGATTGCACGTTAACTATT 57.012 29.630 3.71 0.00 0.00 1.73
3168 4714 9.865321 TTTCTAGATTGCACGTTAACTATTACT 57.135 29.630 3.71 0.00 0.00 2.24
3169 4715 9.512435 TTCTAGATTGCACGTTAACTATTACTC 57.488 33.333 3.71 0.00 0.00 2.59
3170 4716 8.133627 TCTAGATTGCACGTTAACTATTACTCC 58.866 37.037 3.71 0.00 0.00 3.85
3171 4717 6.047231 AGATTGCACGTTAACTATTACTCCC 58.953 40.000 3.71 0.00 0.00 4.30
3172 4718 5.410355 TTGCACGTTAACTATTACTCCCT 57.590 39.130 3.71 0.00 0.00 4.20
3173 4719 5.002464 TGCACGTTAACTATTACTCCCTC 57.998 43.478 3.71 0.00 0.00 4.30
3174 4720 4.142093 TGCACGTTAACTATTACTCCCTCC 60.142 45.833 3.71 0.00 0.00 4.30
3175 4721 4.604976 CACGTTAACTATTACTCCCTCCG 58.395 47.826 3.71 0.00 0.00 4.63
3176 4722 4.096984 CACGTTAACTATTACTCCCTCCGT 59.903 45.833 3.71 0.00 0.00 4.69
3177 4723 5.296780 CACGTTAACTATTACTCCCTCCGTA 59.703 44.000 3.71 0.00 0.00 4.02
3178 4724 6.016777 CACGTTAACTATTACTCCCTCCGTAT 60.017 42.308 3.71 0.00 0.00 3.06
3179 4725 6.547510 ACGTTAACTATTACTCCCTCCGTATT 59.452 38.462 3.71 0.00 0.00 1.89
3180 4726 7.719633 ACGTTAACTATTACTCCCTCCGTATTA 59.280 37.037 3.71 0.00 0.00 0.98
3181 4727 8.233190 CGTTAACTATTACTCCCTCCGTATTAG 58.767 40.741 3.71 0.00 31.80 1.73
3182 4728 9.072375 GTTAACTATTACTCCCTCCGTATTAGT 57.928 37.037 0.00 0.00 36.42 2.24
3183 4729 9.646522 TTAACTATTACTCCCTCCGTATTAGTT 57.353 33.333 15.65 15.65 41.69 2.24
3184 4730 7.521871 ACTATTACTCCCTCCGTATTAGTTG 57.478 40.000 0.00 0.00 33.59 3.16
3185 4731 7.065504 ACTATTACTCCCTCCGTATTAGTTGT 58.934 38.462 0.00 0.00 33.59 3.32
3186 4732 5.841957 TTACTCCCTCCGTATTAGTTGTC 57.158 43.478 0.00 0.00 0.00 3.18
3206 4752 8.280497 AGTTGTCGCTAATTTAGTACAAAGTTG 58.720 33.333 19.29 0.00 36.38 3.16
3221 4767 6.930667 ACAAAGTTGTACTAAATCAACGGT 57.069 33.333 0.00 0.00 45.56 4.83
3284 4832 5.170748 GGCATGTACAGATTTCCTTTTTGG 58.829 41.667 0.33 0.00 37.10 3.28
3341 4889 3.240069 GCTAAAATGCACAGTGCTCTTG 58.760 45.455 25.83 12.06 45.31 3.02
3359 4907 7.903431 GTGCTCTTGTTATAATTGGTTTCGTAG 59.097 37.037 0.00 0.00 0.00 3.51
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
5 6 3.645660 TGCCCCTCGTCATTGCCA 61.646 61.111 0.00 0.00 0.00 4.92
6 7 3.134127 GTGCCCCTCGTCATTGCC 61.134 66.667 0.00 0.00 0.00 4.52
71 74 5.619533 CGGAGTAGAACCAACTACAGACTTC 60.620 48.000 0.00 0.00 43.38 3.01
107 110 4.142773 GGACGAAAAGACAAGTGAACAACA 60.143 41.667 0.00 0.00 0.00 3.33
118 121 6.920758 CCAACAAATTAATGGACGAAAAGACA 59.079 34.615 0.00 0.00 36.27 3.41
150 153 8.030692 CAGATTTTCCATTTTGATGCTGAGTTA 58.969 33.333 0.00 0.00 0.00 2.24
206 210 3.769739 AATCCAGTGTGAGTTACTGCA 57.230 42.857 0.00 0.00 43.19 4.41
207 211 4.065088 TCAAATCCAGTGTGAGTTACTGC 58.935 43.478 0.00 0.00 43.19 4.40
266 273 8.088365 AGGGAAAAGATTGCACTTGTATTAAAC 58.912 33.333 0.00 0.00 0.00 2.01
274 283 3.575687 AGGAAGGGAAAAGATTGCACTTG 59.424 43.478 0.00 0.00 0.00 3.16
289 298 3.744660 GTATGCCACTTATCAGGAAGGG 58.255 50.000 0.00 0.00 0.00 3.95
296 305 3.070302 TGCCATACGTATGCCACTTATCA 59.930 43.478 26.79 11.95 32.40 2.15
305 314 3.691049 ATGTTTGTGCCATACGTATGC 57.309 42.857 26.79 21.64 32.40 3.14
308 317 3.562141 GCCATATGTTTGTGCCATACGTA 59.438 43.478 0.00 0.00 0.00 3.57
310 319 2.357323 TGCCATATGTTTGTGCCATACG 59.643 45.455 1.24 0.00 0.00 3.06
316 325 2.250188 GACGTTGCCATATGTTTGTGC 58.750 47.619 1.24 0.00 0.00 4.57
325 334 0.319727 AACCGTTCGACGTTGCCATA 60.320 50.000 0.00 0.00 40.58 2.74
329 338 0.026544 TCAAAACCGTTCGACGTTGC 59.973 50.000 0.00 0.00 40.58 4.17
333 342 1.523515 TGACATCAAAACCGTTCGACG 59.476 47.619 0.00 0.00 42.11 5.12
334 343 3.001939 ACTTGACATCAAAACCGTTCGAC 59.998 43.478 0.00 0.00 35.15 4.20
337 346 6.413818 CACTAAACTTGACATCAAAACCGTTC 59.586 38.462 0.00 0.00 35.15 3.95
341 350 5.907391 CGTCACTAAACTTGACATCAAAACC 59.093 40.000 3.58 0.00 43.09 3.27
351 360 4.279922 TCATCCTCACGTCACTAAACTTGA 59.720 41.667 0.00 0.00 0.00 3.02
382 391 6.622833 AAACTGAAATTTGCCATCCAAAAG 57.377 33.333 0.00 0.00 45.80 2.27
386 396 8.566260 CAAAAATAAACTGAAATTTGCCATCCA 58.434 29.630 0.00 0.00 0.00 3.41
392 402 7.270757 ACCCCAAAAATAAACTGAAATTTGC 57.729 32.000 0.00 0.00 0.00 3.68
447 458 0.605319 CACAAAGCACTTCGGCCCTA 60.605 55.000 0.00 0.00 0.00 3.53
459 470 6.867550 AGGGAGAAATAAAATAGCACAAAGC 58.132 36.000 0.00 0.00 46.19 3.51
460 471 7.189512 CGAGGGAGAAATAAAATAGCACAAAG 58.810 38.462 0.00 0.00 0.00 2.77
461 472 6.404293 GCGAGGGAGAAATAAAATAGCACAAA 60.404 38.462 0.00 0.00 0.00 2.83
462 473 5.065988 GCGAGGGAGAAATAAAATAGCACAA 59.934 40.000 0.00 0.00 0.00 3.33
463 474 4.574828 GCGAGGGAGAAATAAAATAGCACA 59.425 41.667 0.00 0.00 0.00 4.57
464 475 4.574828 TGCGAGGGAGAAATAAAATAGCAC 59.425 41.667 0.00 0.00 0.00 4.40
465 476 4.776349 TGCGAGGGAGAAATAAAATAGCA 58.224 39.130 0.00 0.00 0.00 3.49
466 477 5.751243 TTGCGAGGGAGAAATAAAATAGC 57.249 39.130 0.00 0.00 0.00 2.97
543 554 4.224818 CCTCCTCTCCTCTGTTTCTTTCAT 59.775 45.833 0.00 0.00 0.00 2.57
544 555 3.580458 CCTCCTCTCCTCTGTTTCTTTCA 59.420 47.826 0.00 0.00 0.00 2.69
545 556 3.055458 CCCTCCTCTCCTCTGTTTCTTTC 60.055 52.174 0.00 0.00 0.00 2.62
547 558 2.545810 CCCTCCTCTCCTCTGTTTCTT 58.454 52.381 0.00 0.00 0.00 2.52
548 559 1.273552 CCCCTCCTCTCCTCTGTTTCT 60.274 57.143 0.00 0.00 0.00 2.52
556 567 2.522013 AATAATGCCCCTCCTCTCCT 57.478 50.000 0.00 0.00 0.00 3.69
703 2180 2.138656 AAACGTCGTCGACTGAGGGG 62.139 60.000 22.18 8.74 40.62 4.79
710 2187 1.836555 CGGAATCTAAACGTCGTCGAC 59.163 52.381 15.51 15.51 40.62 4.20
723 2200 3.528370 CGGAGGCCGTCGGAATCT 61.528 66.667 17.49 8.73 42.73 2.40
743 2220 0.533032 CCCTCTCAACCTTCTCGTCC 59.467 60.000 0.00 0.00 0.00 4.79
907 2437 1.153862 CACTGAGGTCTCGCTCTGC 60.154 63.158 0.00 0.00 0.00 4.26
951 2481 4.687215 TGCTGTGGTGGAGCTCGC 62.687 66.667 7.83 4.02 37.35 5.03
986 2516 1.300931 GCCATTCTGCTATCGCCGA 60.301 57.895 0.00 0.00 34.43 5.54
1005 2535 0.391597 GACCAGTGAGACGGAAACCA 59.608 55.000 0.00 0.00 0.00 3.67
1006 2536 0.680061 AGACCAGTGAGACGGAAACC 59.320 55.000 0.00 0.00 0.00 3.27
1092 2622 2.597217 TTGGCAGGGTCAAAGGCG 60.597 61.111 0.00 0.00 0.00 5.52
1095 2625 2.956987 CGCTTGGCAGGGTCAAAG 59.043 61.111 0.00 0.00 0.00 2.77
1104 2634 4.953010 TTGCAGAGGCGCTTGGCA 62.953 61.111 7.64 9.57 46.16 4.92
1503 3033 1.082104 GTTGAAAGCGGCGAGGTTG 60.082 57.895 12.98 0.00 40.91 3.77
1644 3174 1.204146 TTGGGAGATTAGGCGCTCTT 58.796 50.000 7.64 0.00 0.00 2.85
1752 3282 1.810412 GCTTCCTCAACACGACCTGTT 60.810 52.381 0.00 0.00 44.51 3.16
1758 3288 1.040646 AGACAGCTTCCTCAACACGA 58.959 50.000 0.00 0.00 0.00 4.35
2076 3606 1.842562 ACCCTGTATGCTGCTTCATCT 59.157 47.619 0.00 0.00 0.00 2.90
2084 3614 0.811616 GCGGAAGACCCTGTATGCTG 60.812 60.000 0.00 0.00 0.00 4.41
2232 3762 0.870393 CAGAGAACGTGTGCATGCTT 59.130 50.000 20.33 3.73 0.00 3.91
2587 4117 7.234577 ACACCATGGCCTTAATAAAAAGAGAAA 59.765 33.333 13.04 0.00 0.00 2.52
2869 4399 8.730680 GTCTCCTGCTGTGAAATAAATAAAAGA 58.269 33.333 0.00 0.00 0.00 2.52
2898 4428 8.592809 CCTATGAAGAAGAATCACTATTAGCCT 58.407 37.037 0.00 0.00 0.00 4.58
3029 4559 0.908198 GACTGAACCTGAGGGCTGAT 59.092 55.000 2.38 0.00 35.63 2.90
3034 4572 3.165875 TGTTAGAGACTGAACCTGAGGG 58.834 50.000 2.38 0.00 38.88 4.30
3071 4609 4.968259 ACTGCAAGGTCAATACAACTGTA 58.032 39.130 0.00 0.00 39.30 2.74
3072 4610 3.820557 ACTGCAAGGTCAATACAACTGT 58.179 40.909 0.00 0.00 39.30 3.55
3073 4611 4.997395 ACTACTGCAAGGTCAATACAACTG 59.003 41.667 0.00 0.00 39.30 3.16
3074 4612 5.221641 TGACTACTGCAAGGTCAATACAACT 60.222 40.000 11.84 0.00 39.30 3.16
3075 4613 4.994852 TGACTACTGCAAGGTCAATACAAC 59.005 41.667 11.84 0.00 39.30 3.32
3076 4614 5.011635 TCTGACTACTGCAAGGTCAATACAA 59.988 40.000 14.16 0.74 35.27 2.41
3085 4629 4.734398 ATCTTCTCTGACTACTGCAAGG 57.266 45.455 0.00 0.00 39.30 3.61
3151 4697 4.142093 GGAGGGAGTAATAGTTAACGTGCA 60.142 45.833 0.00 0.00 0.00 4.57
3152 4698 4.366586 GGAGGGAGTAATAGTTAACGTGC 58.633 47.826 0.00 0.00 0.00 5.34
3153 4699 4.096984 ACGGAGGGAGTAATAGTTAACGTG 59.903 45.833 0.00 0.00 0.00 4.49
3154 4700 4.273318 ACGGAGGGAGTAATAGTTAACGT 58.727 43.478 0.00 0.00 0.00 3.99
3155 4701 4.907879 ACGGAGGGAGTAATAGTTAACG 57.092 45.455 0.00 0.00 0.00 3.18
3157 4703 9.646522 AACTAATACGGAGGGAGTAATAGTTAA 57.353 33.333 12.43 0.00 43.39 2.01
3158 4704 9.071276 CAACTAATACGGAGGGAGTAATAGTTA 57.929 37.037 13.25 0.00 43.37 2.24
3159 4705 7.562821 ACAACTAATACGGAGGGAGTAATAGTT 59.437 37.037 9.67 9.67 44.78 2.24
3160 4706 7.065504 ACAACTAATACGGAGGGAGTAATAGT 58.934 38.462 0.00 0.00 40.50 2.12
3161 4707 7.521871 ACAACTAATACGGAGGGAGTAATAG 57.478 40.000 0.00 0.00 35.06 1.73
3162 4708 6.205464 CGACAACTAATACGGAGGGAGTAATA 59.795 42.308 0.00 0.00 0.00 0.98
3164 4710 4.336433 CGACAACTAATACGGAGGGAGTAA 59.664 45.833 0.00 0.00 0.00 2.24
3165 4711 3.879295 CGACAACTAATACGGAGGGAGTA 59.121 47.826 0.00 0.00 0.00 2.59
3167 4713 2.543238 GCGACAACTAATACGGAGGGAG 60.543 54.545 0.00 0.00 0.00 4.30
3168 4714 1.406539 GCGACAACTAATACGGAGGGA 59.593 52.381 0.00 0.00 0.00 4.20
3169 4715 1.407979 AGCGACAACTAATACGGAGGG 59.592 52.381 0.00 0.00 0.00 4.30
3170 4716 2.865343 AGCGACAACTAATACGGAGG 57.135 50.000 0.00 0.00 0.00 4.30
3171 4717 6.823678 AAATTAGCGACAACTAATACGGAG 57.176 37.500 0.00 0.00 41.03 4.63
3172 4718 7.483307 ACTAAATTAGCGACAACTAATACGGA 58.517 34.615 0.00 0.00 41.03 4.69
3173 4719 7.689953 ACTAAATTAGCGACAACTAATACGG 57.310 36.000 0.00 0.00 41.03 4.02
3174 4720 9.225201 TGTACTAAATTAGCGACAACTAATACG 57.775 33.333 0.00 0.00 41.03 3.06
3178 4724 9.480053 ACTTTGTACTAAATTAGCGACAACTAA 57.520 29.630 16.10 6.10 35.75 2.24
3179 4725 9.480053 AACTTTGTACTAAATTAGCGACAACTA 57.520 29.630 16.10 6.60 35.75 2.24
3180 4726 7.958053 ACTTTGTACTAAATTAGCGACAACT 57.042 32.000 16.10 6.38 35.75 3.16
3181 4727 8.066000 ACAACTTTGTACTAAATTAGCGACAAC 58.934 33.333 16.10 3.19 40.16 3.32
3182 4728 8.145316 ACAACTTTGTACTAAATTAGCGACAA 57.855 30.769 13.72 13.72 40.16 3.18
3183 4729 7.718272 ACAACTTTGTACTAAATTAGCGACA 57.282 32.000 0.00 2.39 40.16 4.35
3202 4748 9.933723 ATTAGTTACCGTTGATTTAGTACAACT 57.066 29.630 0.00 0.00 42.53 3.16
3218 4764 3.321682 TCCCCGTTCCATATTAGTTACCG 59.678 47.826 0.00 0.00 0.00 4.02
3220 4766 5.541953 ACTCCCCGTTCCATATTAGTTAC 57.458 43.478 0.00 0.00 0.00 2.50
3221 4767 6.613699 TCTACTCCCCGTTCCATATTAGTTA 58.386 40.000 0.00 0.00 0.00 2.24
3284 4832 0.818296 ACAGATGGACAGAGTACGGC 59.182 55.000 0.00 0.00 0.00 5.68
3341 4889 6.579491 AGACGCTACGAAACCAATTATAAC 57.421 37.500 0.00 0.00 0.00 1.89
3359 4907 7.007995 GCAAGTAAATAAACCAACATAAGACGC 59.992 37.037 0.00 0.00 0.00 5.19


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

AutoCloner maintained by Alex Coulton.