Multiple sequence alignment - TraesCS6A01G168600

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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 TraesCS6A01G168600 chr6A 100.000 2597 0 0 1 2597 175628374 175630970 0.000000e+00 4796
1 TraesCS6A01G168600 chr6A 99.087 876 8 0 1722 2597 97398564 97397689 0.000000e+00 1574
2 TraesCS6A01G168600 chr6A 83.559 517 64 14 982 1492 175621926 175622427 5.060000e-127 464
3 TraesCS6A01G168600 chr4A 99.543 876 4 0 1722 2597 644772685 644771810 0.000000e+00 1596
4 TraesCS6A01G168600 chr4A 99.087 876 8 0 1722 2597 612039984 612040859 0.000000e+00 1574
5 TraesCS6A01G168600 chr5A 99.429 876 5 0 1722 2597 637101780 637100905 0.000000e+00 1591
6 TraesCS6A01G168600 chr5A 99.088 877 8 0 1721 2597 69232549 69231673 0.000000e+00 1576
7 TraesCS6A01G168600 chr1A 99.429 876 5 0 1722 2597 582543179 582542304 0.000000e+00 1591
8 TraesCS6A01G168600 chr1A 99.316 877 5 1 1721 2597 521287690 521286815 0.000000e+00 1585
9 TraesCS6A01G168600 chr2A 99.315 876 6 0 1722 2597 72953333 72954208 0.000000e+00 1585
10 TraesCS6A01G168600 chr7B 98.973 876 9 0 1722 2597 122624256 122625131 0.000000e+00 1568
11 TraesCS6A01G168600 chr6B 93.902 820 36 6 902 1721 233023611 233024416 0.000000e+00 1225
12 TraesCS6A01G168600 chr6B 83.065 620 61 14 1 601 233022711 233023305 8.230000e-145 523
13 TraesCS6A01G168600 chr6B 81.506 611 81 23 991 1597 233013887 233014469 8.410000e-130 473
14 TraesCS6A01G168600 chr6B 78.595 598 84 27 908 1492 233010404 233010970 3.180000e-94 355
15 TraesCS6A01G168600 chr6B 86.294 197 19 4 673 866 233023422 233023613 9.420000e-50 207
16 TraesCS6A01G168600 chr6D 90.122 820 58 11 902 1721 134688830 134689626 0.000000e+00 1044
17 TraesCS6A01G168600 chr6D 90.000 820 57 12 902 1721 134283639 134284433 0.000000e+00 1037
18 TraesCS6A01G168600 chr6D 81.290 620 84 23 982 1597 134279456 134280047 8.410000e-130 473
19 TraesCS6A01G168600 chr6D 83.399 506 63 15 991 1493 134682681 134683168 1.420000e-122 449
20 TraesCS6A01G168600 chr6D 87.861 173 14 5 697 866 134688664 134688832 2.040000e-46 196
21 TraesCS6A01G168600 chr6D 86.705 173 16 5 697 866 134283473 134283641 4.410000e-43 185


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 TraesCS6A01G168600 chr6A 175628374 175630970 2596 False 4796.000000 4796 100.000000 1 2597 1 chr6A.!!$F2 2596
1 TraesCS6A01G168600 chr6A 97397689 97398564 875 True 1574.000000 1574 99.087000 1722 2597 1 chr6A.!!$R1 875
2 TraesCS6A01G168600 chr6A 175621926 175622427 501 False 464.000000 464 83.559000 982 1492 1 chr6A.!!$F1 510
3 TraesCS6A01G168600 chr4A 644771810 644772685 875 True 1596.000000 1596 99.543000 1722 2597 1 chr4A.!!$R1 875
4 TraesCS6A01G168600 chr4A 612039984 612040859 875 False 1574.000000 1574 99.087000 1722 2597 1 chr4A.!!$F1 875
5 TraesCS6A01G168600 chr5A 637100905 637101780 875 True 1591.000000 1591 99.429000 1722 2597 1 chr5A.!!$R2 875
6 TraesCS6A01G168600 chr5A 69231673 69232549 876 True 1576.000000 1576 99.088000 1721 2597 1 chr5A.!!$R1 876
7 TraesCS6A01G168600 chr1A 582542304 582543179 875 True 1591.000000 1591 99.429000 1722 2597 1 chr1A.!!$R2 875
8 TraesCS6A01G168600 chr1A 521286815 521287690 875 True 1585.000000 1585 99.316000 1721 2597 1 chr1A.!!$R1 876
9 TraesCS6A01G168600 chr2A 72953333 72954208 875 False 1585.000000 1585 99.315000 1722 2597 1 chr2A.!!$F1 875
10 TraesCS6A01G168600 chr7B 122624256 122625131 875 False 1568.000000 1568 98.973000 1722 2597 1 chr7B.!!$F1 875
11 TraesCS6A01G168600 chr6B 233022711 233024416 1705 False 651.666667 1225 87.753667 1 1721 3 chr6B.!!$F2 1720
12 TraesCS6A01G168600 chr6B 233010404 233014469 4065 False 414.000000 473 80.050500 908 1597 2 chr6B.!!$F1 689
13 TraesCS6A01G168600 chr6D 134688664 134689626 962 False 620.000000 1044 88.991500 697 1721 2 chr6D.!!$F3 1024
14 TraesCS6A01G168600 chr6D 134279456 134284433 4977 False 565.000000 1037 85.998333 697 1721 3 chr6D.!!$F2 1024

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
961 7678 0.234884 CCAAGTCGCAACGAACTTCC 59.765 55.0 0.0 0.0 37.72 3.46 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2171 8905 2.770232 CCTAACCCTAACCCTGTACTGG 59.23 54.545 11.71 11.71 0.0 4.0 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
28 29 0.777446 ACCCACCAGCACCAGTTAAT 59.223 50.000 0.00 0.00 0.00 1.40
78 79 1.271934 CCATCTCCGTCATGCTCCTAG 59.728 57.143 0.00 0.00 0.00 3.02
82 83 1.035385 TCCGTCATGCTCCTAGCGAA 61.035 55.000 0.00 0.00 46.26 4.70
97 98 1.870016 CGAAGCCTCTTCGAGACGC 60.870 63.158 20.43 0.00 43.97 5.19
98 99 1.517475 GAAGCCTCTTCGAGACGCC 60.517 63.158 0.00 0.00 28.34 5.68
99 100 1.939769 GAAGCCTCTTCGAGACGCCT 61.940 60.000 0.00 0.00 28.34 5.52
107 108 1.512996 TTCGAGACGCCTTGAGTCGT 61.513 55.000 0.00 0.00 42.97 4.34
115 116 1.228657 GCCTTGAGTCGTGACCAACC 61.229 60.000 0.00 0.00 0.00 3.77
138 139 1.037579 TCGCCATGTCTCCATCTCGT 61.038 55.000 0.00 0.00 0.00 4.18
148 149 2.485677 CCATCTCGTGGCTTTGCAT 58.514 52.632 0.00 0.00 42.12 3.96
172 190 1.651987 ATTAGTTGTCATGCGGGTCG 58.348 50.000 0.00 0.00 0.00 4.79
185 203 0.941542 CGGGTCGAGAAAAGCAAACA 59.058 50.000 0.00 0.00 0.00 2.83
244 262 7.340122 TCTTCATTTGTGTTGGTAAATGACA 57.660 32.000 10.80 0.94 46.85 3.58
258 276 7.681679 TGGTAAATGACATGAACTAAGTACCA 58.318 34.615 0.00 5.63 35.96 3.25
282 300 6.268847 CACCTATACCTATTTCTCAAGGCTCT 59.731 42.308 0.00 0.00 36.24 4.09
292 310 2.705658 TCTCAAGGCTCTGAAAGTTGGA 59.294 45.455 0.00 0.00 33.76 3.53
324 342 3.542712 ACATGTTTGTCGACATCTTGC 57.457 42.857 20.80 8.52 38.15 4.01
325 343 2.226437 ACATGTTTGTCGACATCTTGCC 59.774 45.455 20.80 4.56 38.15 4.52
326 344 1.960417 TGTTTGTCGACATCTTGCCA 58.040 45.000 20.80 7.11 0.00 4.92
327 345 2.293170 TGTTTGTCGACATCTTGCCAA 58.707 42.857 20.80 5.73 0.00 4.52
328 346 2.685388 TGTTTGTCGACATCTTGCCAAA 59.315 40.909 20.80 4.92 0.00 3.28
329 347 3.317711 TGTTTGTCGACATCTTGCCAAAT 59.682 39.130 20.80 0.00 0.00 2.32
331 349 2.503331 TGTCGACATCTTGCCAAATGT 58.497 42.857 15.76 5.36 38.78 2.71
332 350 3.669536 TGTCGACATCTTGCCAAATGTA 58.330 40.909 15.76 0.00 36.28 2.29
333 351 4.260985 TGTCGACATCTTGCCAAATGTAT 58.739 39.130 15.76 0.00 36.28 2.29
334 352 5.423886 TGTCGACATCTTGCCAAATGTATA 58.576 37.500 15.76 0.00 36.28 1.47
335 353 6.054941 TGTCGACATCTTGCCAAATGTATAT 58.945 36.000 15.76 0.00 36.28 0.86
339 357 7.281999 TCGACATCTTGCCAAATGTATATCAAA 59.718 33.333 5.59 0.00 36.28 2.69
391 409 6.239908 CACTATGATGTGTGTAAGCAAACA 57.760 37.500 0.00 0.00 45.89 2.83
399 417 7.821846 TGATGTGTGTAAGCAAACACTATATCA 59.178 33.333 18.73 19.08 44.78 2.15
409 427 8.079211 AGCAAACACTATATCAGAGTTAAGGA 57.921 34.615 0.00 0.00 37.11 3.36
415 433 9.702253 ACACTATATCAGAGTTAAGGAAGAAGA 57.298 33.333 0.00 0.00 0.00 2.87
427 445 9.061435 AGTTAAGGAAGAAGAAGAAGAAATGTG 57.939 33.333 0.00 0.00 0.00 3.21
431 449 7.056635 AGGAAGAAGAAGAAGAAATGTGTTCA 58.943 34.615 0.00 0.00 29.35 3.18
434 452 9.392021 GAAGAAGAAGAAGAAATGTGTTCATTC 57.608 33.333 0.00 0.00 42.60 2.67
435 453 8.688747 AGAAGAAGAAGAAATGTGTTCATTCT 57.311 30.769 0.00 0.00 42.60 2.40
445 463 9.046296 AGAAATGTGTTCATTCTCGTATTATCC 57.954 33.333 0.00 0.00 42.60 2.59
450 468 4.414999 TCATTCTCGTATTATCCGACGG 57.585 45.455 7.84 7.84 39.53 4.79
525 543 9.389755 AGGTGCTTTTGTTATTGTTAATGTTTT 57.610 25.926 0.00 0.00 0.00 2.43
580 598 6.266131 AGGCCCATAGTTTATTCTGATGAA 57.734 37.500 0.00 0.00 36.54 2.57
583 601 7.068716 AGGCCCATAGTTTATTCTGATGAAAAC 59.931 37.037 0.00 0.00 35.63 2.43
593 611 6.659361 ATTCTGATGAAAACTGATCGACAG 57.341 37.500 11.80 11.80 42.58 3.51
610 628 3.822735 CGACAGTATAATAGGGTTCCCGA 59.177 47.826 1.91 0.00 0.00 5.14
614 632 4.587684 CAGTATAATAGGGTTCCCGACTGT 59.412 45.833 1.91 0.00 0.00 3.55
618 636 4.914177 AATAGGGTTCCCGACTGTTTAA 57.086 40.909 1.91 0.00 0.00 1.52
619 637 2.556144 AGGGTTCCCGACTGTTTAAC 57.444 50.000 1.91 0.00 0.00 2.01
621 639 3.242011 AGGGTTCCCGACTGTTTAACTA 58.758 45.455 1.91 0.00 0.00 2.24
625 643 5.279456 GGGTTCCCGACTGTTTAACTAAGTA 60.279 44.000 0.00 0.00 0.00 2.24
629 647 5.481473 TCCCGACTGTTTAACTAAGTATGGT 59.519 40.000 0.00 0.00 0.00 3.55
631 649 6.976925 CCCGACTGTTTAACTAAGTATGGTAG 59.023 42.308 0.00 0.00 0.00 3.18
633 651 8.246180 CCGACTGTTTAACTAAGTATGGTAGAA 58.754 37.037 0.00 0.00 0.00 2.10
647 665 8.240267 AGTATGGTAGAAAGAGATAGAACCAC 57.760 38.462 0.00 0.00 38.28 4.16
650 668 7.496346 TGGTAGAAAGAGATAGAACCACATT 57.504 36.000 0.00 0.00 30.84 2.71
653 671 8.669243 GGTAGAAAGAGATAGAACCACATTTTG 58.331 37.037 0.00 0.00 0.00 2.44
656 674 9.525826 AGAAAGAGATAGAACCACATTTTGATT 57.474 29.630 0.00 0.00 0.00 2.57
659 677 6.660521 AGAGATAGAACCACATTTTGATTGCA 59.339 34.615 0.00 0.00 0.00 4.08
660 678 7.341256 AGAGATAGAACCACATTTTGATTGCAT 59.659 33.333 0.00 0.00 0.00 3.96
661 679 7.486647 AGATAGAACCACATTTTGATTGCATC 58.513 34.615 0.00 0.00 0.00 3.91
663 681 6.045072 AGAACCACATTTTGATTGCATCAT 57.955 33.333 0.00 0.00 39.39 2.45
665 683 5.155278 ACCACATTTTGATTGCATCATGT 57.845 34.783 0.00 0.00 39.39 3.21
666 684 5.553123 ACCACATTTTGATTGCATCATGTT 58.447 33.333 0.00 0.00 39.39 2.71
667 685 5.640357 ACCACATTTTGATTGCATCATGTTC 59.360 36.000 0.00 0.00 39.39 3.18
669 687 6.147985 CCACATTTTGATTGCATCATGTTCAA 59.852 34.615 0.00 0.00 39.39 2.69
671 734 7.532546 CACATTTTGATTGCATCATGTTCAAAC 59.467 33.333 10.32 0.00 39.39 2.93
674 737 4.239304 TGATTGCATCATGTTCAAACTGC 58.761 39.130 0.00 0.00 33.59 4.40
680 743 4.201551 GCATCATGTTCAAACTGCATTTCG 60.202 41.667 0.00 0.00 0.00 3.46
681 744 3.307674 TCATGTTCAAACTGCATTTCGC 58.692 40.909 0.00 0.00 42.89 4.70
703 4025 9.865321 TTCGCAGTTTATAACTTAGTGTAATCT 57.135 29.630 0.00 0.00 40.46 2.40
736 4060 4.700213 GGAATGAATTCTCAGTTTTCCCGA 59.300 41.667 7.05 0.00 34.28 5.14
739 4063 5.689383 TGAATTCTCAGTTTTCCCGAAAG 57.311 39.130 7.05 0.00 0.00 2.62
743 4067 6.709018 ATTCTCAGTTTTCCCGAAAGAAAA 57.291 33.333 4.51 4.51 42.07 2.29
828 4153 6.950842 AGGATTGAAGTGATAAGTCATGTCA 58.049 36.000 0.00 0.00 36.60 3.58
866 4191 5.186603 ACTTCTCTGATCTCAGCACATAACA 59.813 40.000 2.21 0.00 43.46 2.41
867 4192 5.665916 TCTCTGATCTCAGCACATAACAA 57.334 39.130 2.21 0.00 43.46 2.83
868 4193 6.041423 TCTCTGATCTCAGCACATAACAAA 57.959 37.500 2.21 0.00 43.46 2.83
869 4194 5.871524 TCTCTGATCTCAGCACATAACAAAC 59.128 40.000 2.21 0.00 43.46 2.93
870 4195 4.937620 TCTGATCTCAGCACATAACAAACC 59.062 41.667 2.21 0.00 43.46 3.27
871 4196 4.910195 TGATCTCAGCACATAACAAACCT 58.090 39.130 0.00 0.00 0.00 3.50
872 4197 5.316167 TGATCTCAGCACATAACAAACCTT 58.684 37.500 0.00 0.00 0.00 3.50
873 4198 5.769662 TGATCTCAGCACATAACAAACCTTT 59.230 36.000 0.00 0.00 0.00 3.11
874 4199 6.939730 TGATCTCAGCACATAACAAACCTTTA 59.060 34.615 0.00 0.00 0.00 1.85
875 4200 7.611467 TGATCTCAGCACATAACAAACCTTTAT 59.389 33.333 0.00 0.00 0.00 1.40
876 4201 9.109393 GATCTCAGCACATAACAAACCTTTATA 57.891 33.333 0.00 0.00 0.00 0.98
877 4202 9.632638 ATCTCAGCACATAACAAACCTTTATAT 57.367 29.630 0.00 0.00 0.00 0.86
883 4208 9.537848 GCACATAACAAACCTTTATATATACGC 57.462 33.333 0.00 0.00 0.00 4.42
888 4213 7.572502 ACAAACCTTTATATATACGCTACGC 57.427 36.000 0.00 0.00 0.00 4.42
889 4214 7.373493 ACAAACCTTTATATATACGCTACGCT 58.627 34.615 0.00 0.00 0.00 5.07
890 4215 7.540055 ACAAACCTTTATATATACGCTACGCTC 59.460 37.037 0.00 0.00 0.00 5.03
891 4216 6.748333 ACCTTTATATATACGCTACGCTCA 57.252 37.500 0.00 0.00 0.00 4.26
892 4217 7.149569 ACCTTTATATATACGCTACGCTCAA 57.850 36.000 0.00 0.00 0.00 3.02
893 4218 7.596494 ACCTTTATATATACGCTACGCTCAAA 58.404 34.615 0.00 0.00 0.00 2.69
894 4219 8.084073 ACCTTTATATATACGCTACGCTCAAAA 58.916 33.333 0.00 0.00 0.00 2.44
895 4220 8.918658 CCTTTATATATACGCTACGCTCAAAAA 58.081 33.333 0.00 0.00 0.00 1.94
939 4264 4.860022 CAACCATCCTTTAACCTCTCCAT 58.140 43.478 0.00 0.00 0.00 3.41
946 4271 6.500589 TCCTTTAACCTCTCCATATCCAAG 57.499 41.667 0.00 0.00 0.00 3.61
947 4272 5.970640 TCCTTTAACCTCTCCATATCCAAGT 59.029 40.000 0.00 0.00 0.00 3.16
948 4273 6.099845 TCCTTTAACCTCTCCATATCCAAGTC 59.900 42.308 0.00 0.00 0.00 3.01
949 4274 5.531122 TTAACCTCTCCATATCCAAGTCG 57.469 43.478 0.00 0.00 0.00 4.18
961 7678 0.234884 CCAAGTCGCAACGAACTTCC 59.765 55.000 0.00 0.00 37.72 3.46
982 7699 7.653311 ACTTCCAAAAATATTCTCAACACTTGC 59.347 33.333 0.00 0.00 0.00 4.01
983 7700 7.048629 TCCAAAAATATTCTCAACACTTGCA 57.951 32.000 0.00 0.00 0.00 4.08
1112 7837 1.680522 GGATCGCTGAAGGAGCTCCA 61.681 60.000 33.90 13.39 46.64 3.86
1113 7838 0.392336 GATCGCTGAAGGAGCTCCAT 59.608 55.000 33.90 23.93 46.64 3.41
1173 7898 3.179939 GCCGCGTCCTTCTTCGTC 61.180 66.667 4.92 0.00 0.00 4.20
1201 7926 1.714414 GACGCGCTCTACTTCGAGA 59.286 57.895 5.73 0.00 32.74 4.04
1209 7934 1.679153 CTCTACTTCGAGAAGAGCCCC 59.321 57.143 18.54 0.00 40.79 5.80
1236 7961 1.152398 GGCATCCGGGGAGGTACTA 60.152 63.158 0.00 0.00 41.55 1.82
1248 7973 4.519437 GTACTACGGCCGGGGCAC 62.519 72.222 31.76 17.81 44.11 5.01
1551 8285 2.684843 GCGGCTGAAGGTGAAGCTG 61.685 63.158 0.00 0.00 46.56 4.24
1552 8286 1.004560 CGGCTGAAGGTGAAGCTGA 60.005 57.895 0.00 0.00 46.74 4.26
1553 8287 0.392193 CGGCTGAAGGTGAAGCTGAT 60.392 55.000 0.00 0.00 46.74 2.90
1554 8288 1.093159 GGCTGAAGGTGAAGCTGATG 58.907 55.000 0.00 0.00 39.46 3.07
1555 8289 0.450983 GCTGAAGGTGAAGCTGATGC 59.549 55.000 0.00 0.00 36.47 3.91
1600 8334 0.320247 AGAGGTTGCTGAGTGAAGCG 60.320 55.000 0.00 0.00 46.65 4.68
1607 8341 1.818674 TGCTGAGTGAAGCGTATCTCA 59.181 47.619 6.22 6.22 46.65 3.27
1609 8343 2.857152 GCTGAGTGAAGCGTATCTCAAG 59.143 50.000 7.40 4.40 36.67 3.02
1810 8544 2.139917 GCGTGTCAGTACCAACATTGA 58.860 47.619 1.67 0.00 0.00 2.57
2171 8905 1.444553 CAGACGGTCTCAACGAGGC 60.445 63.158 7.89 0.00 32.92 4.70
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
9 10 0.777446 ATTAACTGGTGCTGGTGGGT 59.223 50.000 0.00 0.00 0.00 4.51
16 17 4.634012 TGGTAACAGATTAACTGGTGCT 57.366 40.909 0.00 0.00 46.95 4.40
67 68 1.045350 AGGCTTCGCTAGGAGCATGA 61.045 55.000 0.00 0.00 42.58 3.07
89 90 1.964891 ACGACTCAAGGCGTCTCGA 60.965 57.895 4.78 0.00 35.59 4.04
97 98 0.105964 TGGTTGGTCACGACTCAAGG 59.894 55.000 0.00 0.00 0.00 3.61
98 99 1.217882 GTGGTTGGTCACGACTCAAG 58.782 55.000 0.00 0.00 31.52 3.02
99 100 0.537653 TGTGGTTGGTCACGACTCAA 59.462 50.000 0.00 0.00 40.31 3.02
107 108 0.959867 CATGGCGATGTGGTTGGTCA 60.960 55.000 0.00 0.00 0.00 4.02
115 116 4.939399 TGGAGACATGGCGATGTG 57.061 55.556 19.79 0.00 43.22 3.21
138 139 2.818921 ACTAATTCCCATGCAAAGCCA 58.181 42.857 0.00 0.00 0.00 4.75
148 149 2.364632 CCGCATGACAACTAATTCCCA 58.635 47.619 0.00 0.00 0.00 4.37
231 249 8.448615 GGTACTTAGTTCATGTCATTTACCAAC 58.551 37.037 0.00 0.00 0.00 3.77
244 262 9.893975 AATAGGTATAGGTGGTACTTAGTTCAT 57.106 33.333 0.00 0.00 0.00 2.57
258 276 6.268847 CAGAGCCTTGAGAAATAGGTATAGGT 59.731 42.308 0.00 0.00 33.91 3.08
334 352 9.211485 CAAAAGCTTCATTTTCCTACATTTGAT 57.789 29.630 0.00 0.00 30.01 2.57
335 353 8.203485 ACAAAAGCTTCATTTTCCTACATTTGA 58.797 29.630 0.00 0.00 30.01 2.69
339 357 7.725251 TGAACAAAAGCTTCATTTTCCTACAT 58.275 30.769 0.00 0.00 30.01 2.29
399 417 9.500785 CATTTCTTCTTCTTCTTCCTTAACTCT 57.499 33.333 0.00 0.00 0.00 3.24
409 427 9.129532 AGAATGAACACATTTCTTCTTCTTCTT 57.870 29.630 0.00 0.00 34.86 2.52
415 433 6.867662 ACGAGAATGAACACATTTCTTCTT 57.132 33.333 0.00 0.00 34.86 2.52
416 434 8.553459 AATACGAGAATGAACACATTTCTTCT 57.447 30.769 0.00 0.00 34.86 2.85
419 437 9.046296 GGATAATACGAGAATGAACACATTTCT 57.954 33.333 0.00 0.00 34.86 2.52
420 438 8.004344 CGGATAATACGAGAATGAACACATTTC 58.996 37.037 0.00 0.00 34.86 2.17
427 445 4.615961 CCGTCGGATAATACGAGAATGAAC 59.384 45.833 4.91 0.00 41.50 3.18
431 449 3.415212 TCCCGTCGGATAATACGAGAAT 58.585 45.455 14.39 0.00 41.50 2.40
434 452 3.303406 GTTTCCCGTCGGATAATACGAG 58.697 50.000 14.39 0.00 41.50 4.18
435 453 2.034558 GGTTTCCCGTCGGATAATACGA 59.965 50.000 14.39 0.00 41.55 3.43
450 468 4.368565 ACTTAGAAGGAACTGGGTTTCC 57.631 45.455 0.00 0.00 44.96 3.13
491 509 8.816640 ACAATAACAAAAGCACCTAATCTTTG 57.183 30.769 0.00 0.00 33.29 2.77
535 553 7.313951 CCTTTGAGAAGGTGCTTAATCTTAG 57.686 40.000 0.00 0.00 46.16 2.18
554 572 6.547141 TCATCAGAATAAACTATGGGCCTTTG 59.453 38.462 4.53 1.57 0.00 2.77
555 573 6.672593 TCATCAGAATAAACTATGGGCCTTT 58.327 36.000 4.53 0.00 0.00 3.11
564 582 9.869757 TCGATCAGTTTTCATCAGAATAAACTA 57.130 29.630 0.00 0.00 34.29 2.24
603 621 6.312180 CCATACTTAGTTAAACAGTCGGGAAC 59.688 42.308 0.00 0.00 0.00 3.62
604 622 6.014327 ACCATACTTAGTTAAACAGTCGGGAA 60.014 38.462 0.00 0.00 0.00 3.97
605 623 5.481473 ACCATACTTAGTTAAACAGTCGGGA 59.519 40.000 0.00 0.00 0.00 5.14
606 624 5.727434 ACCATACTTAGTTAAACAGTCGGG 58.273 41.667 0.00 0.00 0.00 5.14
621 639 8.697292 GTGGTTCTATCTCTTTCTACCATACTT 58.303 37.037 0.00 0.00 36.66 2.24
625 643 7.682787 ATGTGGTTCTATCTCTTTCTACCAT 57.317 36.000 0.00 0.00 36.66 3.55
631 649 9.565213 CAATCAAAATGTGGTTCTATCTCTTTC 57.435 33.333 0.00 0.00 0.00 2.62
633 651 7.177216 TGCAATCAAAATGTGGTTCTATCTCTT 59.823 33.333 0.00 0.00 0.00 2.85
635 653 6.855836 TGCAATCAAAATGTGGTTCTATCTC 58.144 36.000 0.00 0.00 0.00 2.75
637 655 7.689953 GATGCAATCAAAATGTGGTTCTATC 57.310 36.000 0.00 0.00 44.70 2.08
653 671 4.239304 TGCAGTTTGAACATGATGCAATC 58.761 39.130 0.00 0.31 45.83 2.67
655 673 3.729862 TGCAGTTTGAACATGATGCAA 57.270 38.095 0.00 0.00 40.43 4.08
656 674 3.945981 ATGCAGTTTGAACATGATGCA 57.054 38.095 0.00 9.84 46.50 3.96
659 677 3.922240 GCGAAATGCAGTTTGAACATGAT 59.078 39.130 18.07 0.00 45.45 2.45
660 678 3.307674 GCGAAATGCAGTTTGAACATGA 58.692 40.909 18.07 0.00 45.45 3.07
661 679 3.693300 GCGAAATGCAGTTTGAACATG 57.307 42.857 18.07 0.00 45.45 3.21
712 4036 4.437390 CGGGAAAACTGAGAATTCATTCCG 60.437 45.833 8.44 4.12 39.39 4.30
718 4042 5.941948 TCTTTCGGGAAAACTGAGAATTC 57.058 39.130 0.00 0.00 35.48 2.17
792 4116 5.360714 TCACTTCAATCCTTTGCTTCTTGTT 59.639 36.000 0.00 0.00 32.61 2.83
828 4153 4.164221 TCAGAGAAGTGACAAGAAAAGGGT 59.836 41.667 0.00 0.00 0.00 4.34
899 4224 8.789762 GGATGGTTGCGTATATATAAAGGTTTT 58.210 33.333 0.00 0.00 0.00 2.43
900 4225 8.161425 AGGATGGTTGCGTATATATAAAGGTTT 58.839 33.333 0.00 0.00 0.00 3.27
901 4226 7.686434 AGGATGGTTGCGTATATATAAAGGTT 58.314 34.615 0.00 0.00 0.00 3.50
902 4227 7.253905 AGGATGGTTGCGTATATATAAAGGT 57.746 36.000 0.00 0.00 0.00 3.50
903 4228 8.561738 AAAGGATGGTTGCGTATATATAAAGG 57.438 34.615 0.00 0.00 0.00 3.11
906 4231 9.439500 GGTTAAAGGATGGTTGCGTATATATAA 57.561 33.333 0.00 0.00 0.00 0.98
918 4243 6.183361 GGATATGGAGAGGTTAAAGGATGGTT 60.183 42.308 0.00 0.00 0.00 3.67
931 4256 1.688735 TGCGACTTGGATATGGAGAGG 59.311 52.381 0.00 0.00 0.00 3.69
939 4264 2.736144 AGTTCGTTGCGACTTGGATA 57.264 45.000 1.84 0.00 34.89 2.59
946 4271 2.461897 TTTTGGAAGTTCGTTGCGAC 57.538 45.000 0.00 0.00 34.89 5.19
947 4272 3.701532 ATTTTTGGAAGTTCGTTGCGA 57.298 38.095 0.00 0.00 0.00 5.10
948 4273 5.856455 AGAATATTTTTGGAAGTTCGTTGCG 59.144 36.000 0.00 0.00 0.00 4.85
949 4274 6.861055 TGAGAATATTTTTGGAAGTTCGTTGC 59.139 34.615 0.00 0.00 0.00 4.17
961 7678 7.222417 TGTGTGCAAGTGTTGAGAATATTTTTG 59.778 33.333 0.00 0.00 0.00 2.44
982 7699 2.587956 CATGGAATCTTTGCGTGTGTG 58.412 47.619 0.00 0.00 33.85 3.82
983 7700 1.541147 CCATGGAATCTTTGCGTGTGT 59.459 47.619 5.56 0.00 36.41 3.72
1013 7738 1.970640 GGTGGTTGGAAAAGCAGGAAT 59.029 47.619 0.00 0.00 0.00 3.01
1236 7961 2.845317 TATATGTGCCCCGGCCGT 60.845 61.111 26.12 5.81 41.09 5.68
1248 7973 1.935300 GCCGGGAGCACGAAGTATATG 60.935 57.143 2.18 0.00 41.61 1.78
1411 8139 2.636412 CGTCTTCCACCTCCTCGCA 61.636 63.158 0.00 0.00 0.00 5.10
1551 8285 2.889503 AGAGCGCGCTTCAGCATC 60.890 61.111 36.87 20.61 42.21 3.91
1552 8286 3.193614 CAGAGCGCGCTTCAGCAT 61.194 61.111 36.87 11.56 42.21 3.79
1553 8287 4.362476 TCAGAGCGCGCTTCAGCA 62.362 61.111 36.87 14.88 42.21 4.41
1554 8288 2.874010 TACTCAGAGCGCGCTTCAGC 62.874 60.000 36.87 22.43 37.78 4.26
1555 8289 0.248825 ATACTCAGAGCGCGCTTCAG 60.249 55.000 36.87 29.59 0.00 3.02
1556 8290 0.248661 GATACTCAGAGCGCGCTTCA 60.249 55.000 36.87 20.38 0.00 3.02
1810 8544 8.688747 TTAGTCCAATTTGCAAAAATTTGGAT 57.311 26.923 32.73 25.65 38.31 3.41
2171 8905 2.770232 CCTAACCCTAACCCTGTACTGG 59.230 54.545 11.71 11.71 0.00 4.00


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

AutoCloner maintained by Alex Coulton.