Multiple sequence alignment - TraesCS3B01G258900

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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 TraesCS3B01G258900 chr3B 100.000 2585 0 0 1 2585 416564831 416567415 0.000000e+00 4774
1 TraesCS3B01G258900 chr3D 88.105 1715 131 34 30 1723 305318833 305317171 0.000000e+00 1969
2 TraesCS3B01G258900 chr3D 87.950 639 52 9 1745 2359 340722406 340723043 0.000000e+00 730
3 TraesCS3B01G258900 chr3A 94.221 1021 47 8 716 1724 429490675 429491695 0.000000e+00 1548
4 TraesCS3B01G258900 chr3A 86.905 504 51 10 89 587 429485669 429486162 3.760000e-153 551
5 TraesCS3B01G258900 chr2A 89.385 895 57 10 1727 2585 773578252 773579144 0.000000e+00 1092
6 TraesCS3B01G258900 chr2A 89.441 161 15 2 1727 1886 716823460 716823619 4.360000e-48 202
7 TraesCS3B01G258900 chr6A 91.407 675 42 7 1727 2385 97317397 97318071 0.000000e+00 911
8 TraesCS3B01G258900 chr6A 87.805 164 18 2 1727 1889 534691058 534690896 9.440000e-45 191
9 TraesCS3B01G258900 chr4D 89.193 657 46 9 1727 2359 364549536 364550191 0.000000e+00 797
10 TraesCS3B01G258900 chr4D 89.058 658 47 9 1727 2359 47662874 47663531 0.000000e+00 793
11 TraesCS3B01G258900 chr1D 89.058 658 47 3 1727 2359 355103965 355104622 0.000000e+00 793
12 TraesCS3B01G258900 chr6D 87.994 658 51 8 1727 2359 331531347 331530693 0.000000e+00 752
13 TraesCS3B01G258900 chr6B 94.393 321 6 4 2039 2350 172020398 172020715 1.390000e-132 483
14 TraesCS3B01G258900 chr6B 98.444 257 4 0 2329 2585 172022365 172022621 1.090000e-123 453
15 TraesCS3B01G258900 chr1A 89.441 161 15 2 1727 1886 21411015 21411174 4.360000e-48 202
16 TraesCS3B01G258900 chr7A 88.415 164 17 2 1727 1889 26572117 26571955 2.030000e-46 196


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 TraesCS3B01G258900 chr3B 416564831 416567415 2584 False 4774 4774 100.0000 1 2585 1 chr3B.!!$F1 2584
1 TraesCS3B01G258900 chr3D 305317171 305318833 1662 True 1969 1969 88.1050 30 1723 1 chr3D.!!$R1 1693
2 TraesCS3B01G258900 chr3D 340722406 340723043 637 False 730 730 87.9500 1745 2359 1 chr3D.!!$F1 614
3 TraesCS3B01G258900 chr3A 429490675 429491695 1020 False 1548 1548 94.2210 716 1724 1 chr3A.!!$F2 1008
4 TraesCS3B01G258900 chr2A 773578252 773579144 892 False 1092 1092 89.3850 1727 2585 1 chr2A.!!$F2 858
5 TraesCS3B01G258900 chr6A 97317397 97318071 674 False 911 911 91.4070 1727 2385 1 chr6A.!!$F1 658
6 TraesCS3B01G258900 chr4D 364549536 364550191 655 False 797 797 89.1930 1727 2359 1 chr4D.!!$F2 632
7 TraesCS3B01G258900 chr4D 47662874 47663531 657 False 793 793 89.0580 1727 2359 1 chr4D.!!$F1 632
8 TraesCS3B01G258900 chr1D 355103965 355104622 657 False 793 793 89.0580 1727 2359 1 chr1D.!!$F1 632
9 TraesCS3B01G258900 chr6D 331530693 331531347 654 True 752 752 87.9940 1727 2359 1 chr6D.!!$R1 632
10 TraesCS3B01G258900 chr6B 172020398 172022621 2223 False 468 483 96.4185 2039 2585 2 chr6B.!!$F1 546

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
237 252 0.029035 TCCGAATTCTCGCTACGCTC 59.971 55.0 3.52 0.0 44.04 5.03 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2037 2098 0.321021 ACTCTCCTGTGCTCAAGCTG 59.679 55.0 3.32 0.0 42.66 4.24 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
19 20 1.177401 CTCCAGCCTGCTTAAAACCC 58.823 55.000 0.00 0.00 0.00 4.11
20 21 0.777446 TCCAGCCTGCTTAAAACCCT 59.223 50.000 0.00 0.00 0.00 4.34
21 22 1.146982 TCCAGCCTGCTTAAAACCCTT 59.853 47.619 0.00 0.00 0.00 3.95
22 23 1.546029 CCAGCCTGCTTAAAACCCTTC 59.454 52.381 0.00 0.00 0.00 3.46
23 24 2.519013 CAGCCTGCTTAAAACCCTTCT 58.481 47.619 0.00 0.00 0.00 2.85
24 25 2.489722 CAGCCTGCTTAAAACCCTTCTC 59.510 50.000 0.00 0.00 0.00 2.87
25 26 1.819288 GCCTGCTTAAAACCCTTCTCC 59.181 52.381 0.00 0.00 0.00 3.71
26 27 2.084546 CCTGCTTAAAACCCTTCTCCG 58.915 52.381 0.00 0.00 0.00 4.63
27 28 2.552373 CCTGCTTAAAACCCTTCTCCGT 60.552 50.000 0.00 0.00 0.00 4.69
28 29 3.146847 CTGCTTAAAACCCTTCTCCGTT 58.853 45.455 0.00 0.00 0.00 4.44
29 30 3.558033 TGCTTAAAACCCTTCTCCGTTT 58.442 40.909 0.00 0.00 33.69 3.60
30 31 3.316868 TGCTTAAAACCCTTCTCCGTTTG 59.683 43.478 0.00 0.00 32.65 2.93
31 32 3.855895 GCTTAAAACCCTTCTCCGTTTGC 60.856 47.826 0.00 0.00 32.65 3.68
32 33 1.770294 AAAACCCTTCTCCGTTTGCA 58.230 45.000 0.00 0.00 32.65 4.08
45 46 3.509575 TCCGTTTGCAAGCTTATTCCATT 59.490 39.130 11.70 0.00 0.00 3.16
71 72 1.407989 CCCTTGCAAGACATCTCTCCC 60.408 57.143 28.05 0.00 0.00 4.30
74 75 0.820226 TGCAAGACATCTCTCCCTCG 59.180 55.000 0.00 0.00 0.00 4.63
76 77 0.248825 CAAGACATCTCTCCCTCGCG 60.249 60.000 0.00 0.00 0.00 5.87
77 78 0.681564 AAGACATCTCTCCCTCGCGT 60.682 55.000 5.77 0.00 0.00 6.01
92 107 1.611977 TCGCGTCTTCTTTCCTCTCAA 59.388 47.619 5.77 0.00 0.00 3.02
128 143 4.530857 CGGCCGGCAGGTTCCTAG 62.531 72.222 30.85 3.27 40.50 3.02
129 144 3.400054 GGCCGGCAGGTTCCTAGT 61.400 66.667 30.85 0.00 40.50 2.57
134 149 2.125106 GCAGGTTCCTAGTGCCGG 60.125 66.667 0.00 0.00 0.00 6.13
139 154 1.143401 GTTCCTAGTGCCGGTAGCC 59.857 63.158 1.90 0.00 42.71 3.93
142 157 1.825191 CCTAGTGCCGGTAGCCGTA 60.825 63.158 1.90 0.00 46.80 4.02
149 164 2.541120 CCGGTAGCCGTAGTCCTCG 61.541 68.421 6.82 0.00 46.80 4.63
150 165 2.720605 GGTAGCCGTAGTCCTCGC 59.279 66.667 0.00 0.00 0.00 5.03
152 167 2.517875 TAGCCGTAGTCCTCGCCC 60.518 66.667 0.00 0.00 0.00 6.13
172 187 3.667282 GCGTAGATAGCCGCGGGA 61.667 66.667 29.38 0.00 40.56 5.14
173 188 2.561885 CGTAGATAGCCGCGGGAG 59.438 66.667 29.38 0.83 0.00 4.30
174 189 1.964891 CGTAGATAGCCGCGGGAGA 60.965 63.158 29.38 0.00 0.00 3.71
178 193 3.256716 GATAGCCGCGGGAGAGTCG 62.257 68.421 29.38 0.00 0.00 4.18
193 208 3.020984 AGAGTCGAGATCCTCAGGTTTC 58.979 50.000 3.88 0.00 0.00 2.78
201 216 1.584724 TCCTCAGGTTTCCATCTCCC 58.415 55.000 0.00 0.00 0.00 4.30
205 220 1.203428 TCAGGTTTCCATCTCCCTCCA 60.203 52.381 0.00 0.00 0.00 3.86
209 224 2.423517 GGTTTCCATCTCCCTCCATTCC 60.424 54.545 0.00 0.00 0.00 3.01
226 241 0.902531 TCCCAGGTGAGTCCGAATTC 59.097 55.000 0.00 0.00 41.99 2.17
228 243 1.134670 CCCAGGTGAGTCCGAATTCTC 60.135 57.143 3.52 0.00 41.99 2.87
229 244 1.469940 CCAGGTGAGTCCGAATTCTCG 60.470 57.143 3.52 0.00 45.02 4.04
232 247 1.404391 GGTGAGTCCGAATTCTCGCTA 59.596 52.381 3.52 0.00 44.04 4.26
233 248 2.452105 GTGAGTCCGAATTCTCGCTAC 58.548 52.381 3.52 0.00 44.04 3.58
235 250 0.248539 AGTCCGAATTCTCGCTACGC 60.249 55.000 3.52 0.00 44.04 4.42
236 251 0.248539 GTCCGAATTCTCGCTACGCT 60.249 55.000 3.52 0.00 44.04 5.07
237 252 0.029035 TCCGAATTCTCGCTACGCTC 59.971 55.000 3.52 0.00 44.04 5.03
245 260 0.041224 CTCGCTACGCTCGCTGAATA 60.041 55.000 0.00 0.00 0.00 1.75
248 263 1.663161 CGCTACGCTCGCTGAATATGA 60.663 52.381 0.00 0.00 0.00 2.15
284 299 6.477033 CGTGGTTAGTGATTTCTCTTATCAGG 59.523 42.308 0.00 0.00 32.96 3.86
325 340 1.531739 TTCTTGCGACCCAATTGCCC 61.532 55.000 0.00 0.00 36.80 5.36
337 352 2.020720 CAATTGCCCGGTAATGCTGTA 58.979 47.619 0.00 0.00 0.00 2.74
342 357 1.940613 GCCCGGTAATGCTGTAAGAAG 59.059 52.381 0.00 0.00 34.07 2.85
373 388 3.328237 TTCGTTTTCCTGCGTTTCTTC 57.672 42.857 0.00 0.00 0.00 2.87
395 410 8.293157 TCTTCGCATTTGTTGAACATGTTATTA 58.707 29.630 11.95 0.00 0.00 0.98
396 411 8.446489 TTCGCATTTGTTGAACATGTTATTAG 57.554 30.769 11.95 0.00 0.00 1.73
397 412 7.589395 TCGCATTTGTTGAACATGTTATTAGT 58.411 30.769 11.95 0.00 0.00 2.24
398 413 8.079203 TCGCATTTGTTGAACATGTTATTAGTT 58.921 29.630 11.95 0.00 0.00 2.24
399 414 8.698854 CGCATTTGTTGAACATGTTATTAGTTT 58.301 29.630 11.95 0.00 0.00 2.66
400 415 9.796062 GCATTTGTTGAACATGTTATTAGTTTG 57.204 29.630 11.95 6.59 0.00 2.93
433 448 4.546570 TGTATCGCTGATTCGATTCGATT 58.453 39.130 9.96 6.37 45.81 3.34
434 449 4.617223 TGTATCGCTGATTCGATTCGATTC 59.383 41.667 19.09 19.09 45.81 2.52
435 450 2.044135 TCGCTGATTCGATTCGATTCG 58.956 47.619 20.58 20.58 38.54 3.34
436 451 2.044135 CGCTGATTCGATTCGATTCGA 58.956 47.619 24.07 24.07 45.75 3.71
437 452 2.658802 CGCTGATTCGATTCGATTCGAT 59.341 45.455 27.13 18.71 46.55 3.59
438 453 3.241177 CGCTGATTCGATTCGATTCGATC 60.241 47.826 27.13 23.88 46.55 3.69
454 469 1.089920 GATCGACTTGTGCATGCCTT 58.910 50.000 16.68 0.00 0.00 4.35
455 470 0.806868 ATCGACTTGTGCATGCCTTG 59.193 50.000 16.68 5.40 0.00 3.61
456 471 0.250252 TCGACTTGTGCATGCCTTGA 60.250 50.000 16.68 0.45 0.00 3.02
479 497 4.454504 ACCTAAGTCAGTGTTTATTTGCGG 59.545 41.667 0.00 0.00 0.00 5.69
491 509 5.354234 TGTTTATTTGCGGAAGGAAGAGATC 59.646 40.000 0.00 0.00 44.06 2.75
549 567 3.457234 GTGTTTGCAGAAGGAAAAAGGG 58.543 45.455 0.00 0.00 36.80 3.95
556 574 3.157881 CAGAAGGAAAAAGGGGAGTTCC 58.842 50.000 0.00 0.00 41.03 3.62
568 586 0.733223 GGAGTTCCGAGACGTGCTTC 60.733 60.000 0.00 0.00 0.00 3.86
572 590 1.541310 TTCCGAGACGTGCTTCCCAT 61.541 55.000 0.00 0.00 0.00 4.00
579 597 2.968574 AGACGTGCTTCCCATATCATCT 59.031 45.455 0.00 0.00 0.00 2.90
580 598 3.389329 AGACGTGCTTCCCATATCATCTT 59.611 43.478 0.00 0.00 0.00 2.40
587 605 5.537295 TGCTTCCCATATCATCTTCCAAATG 59.463 40.000 0.00 0.00 0.00 2.32
588 606 5.537674 GCTTCCCATATCATCTTCCAAATGT 59.462 40.000 0.00 0.00 0.00 2.71
589 607 6.041296 GCTTCCCATATCATCTTCCAAATGTT 59.959 38.462 0.00 0.00 0.00 2.71
590 608 7.587037 TTCCCATATCATCTTCCAAATGTTC 57.413 36.000 0.00 0.00 0.00 3.18
591 609 6.914665 TCCCATATCATCTTCCAAATGTTCT 58.085 36.000 0.00 0.00 0.00 3.01
592 610 8.044574 TCCCATATCATCTTCCAAATGTTCTA 57.955 34.615 0.00 0.00 0.00 2.10
593 611 8.672329 TCCCATATCATCTTCCAAATGTTCTAT 58.328 33.333 0.00 0.00 0.00 1.98
594 612 8.954350 CCCATATCATCTTCCAAATGTTCTATC 58.046 37.037 0.00 0.00 0.00 2.08
595 613 8.954350 CCATATCATCTTCCAAATGTTCTATCC 58.046 37.037 0.00 0.00 0.00 2.59
596 614 9.736414 CATATCATCTTCCAAATGTTCTATCCT 57.264 33.333 0.00 0.00 0.00 3.24
599 617 8.324191 TCATCTTCCAAATGTTCTATCCTAGT 57.676 34.615 0.00 0.00 0.00 2.57
600 618 9.434275 TCATCTTCCAAATGTTCTATCCTAGTA 57.566 33.333 0.00 0.00 0.00 1.82
605 623 9.627123 TTCCAAATGTTCTATCCTAGTATTTGG 57.373 33.333 15.90 15.90 43.67 3.28
606 624 8.217799 TCCAAATGTTCTATCCTAGTATTTGGG 58.782 37.037 19.69 7.18 43.24 4.12
607 625 7.998964 CCAAATGTTCTATCCTAGTATTTGGGT 59.001 37.037 14.76 0.00 41.78 4.51
615 633 8.591072 TCTATCCTAGTATTTGGGTATTTTCCG 58.409 37.037 0.00 0.00 0.00 4.30
616 634 5.370679 TCCTAGTATTTGGGTATTTTCCGC 58.629 41.667 0.00 0.00 0.00 5.54
625 643 2.484947 GGGTATTTTCCGCCAGACCTAG 60.485 54.545 0.00 0.00 0.00 3.02
626 644 2.484947 GGTATTTTCCGCCAGACCTAGG 60.485 54.545 7.41 7.41 0.00 3.02
627 645 1.580059 ATTTTCCGCCAGACCTAGGA 58.420 50.000 17.98 0.00 0.00 2.94
628 646 1.580059 TTTTCCGCCAGACCTAGGAT 58.420 50.000 17.98 0.00 32.19 3.24
631 649 1.227674 CCGCCAGACCTAGGATTGC 60.228 63.158 17.98 11.19 0.00 3.56
647 665 4.531732 AGGATTGCTCTTCTCTTCTTCTGT 59.468 41.667 0.00 0.00 0.00 3.41
648 666 4.869861 GGATTGCTCTTCTCTTCTTCTGTC 59.130 45.833 0.00 0.00 0.00 3.51
659 677 7.356641 TCTCTTCTTCTGTCGAAATGATTTG 57.643 36.000 0.00 0.00 0.00 2.32
660 678 6.931281 TCTCTTCTTCTGTCGAAATGATTTGT 59.069 34.615 0.00 0.00 0.00 2.83
710 728 8.140677 AGTTAGCTACAACTACGTCTATACTG 57.859 38.462 0.00 0.00 36.99 2.74
711 729 7.768120 AGTTAGCTACAACTACGTCTATACTGT 59.232 37.037 0.00 0.00 36.99 3.55
712 730 9.035607 GTTAGCTACAACTACGTCTATACTGTA 57.964 37.037 0.00 0.00 0.00 2.74
713 731 7.712264 AGCTACAACTACGTCTATACTGTAG 57.288 40.000 0.00 3.71 38.40 2.74
789 811 4.653341 TCAAACCAAAACCATCAGTCCATT 59.347 37.500 0.00 0.00 0.00 3.16
858 890 5.220228 GCGTGACATTGTACTACTGAATCAC 60.220 44.000 0.00 0.00 0.00 3.06
917 949 2.426024 TCGCTGACCATGTACTACTTCC 59.574 50.000 0.00 0.00 0.00 3.46
1014 1046 3.047280 GCAATGGCGTCGTCACCA 61.047 61.111 0.00 0.00 41.06 4.17
1050 1082 3.535962 CTCTGCGAGGAGGAGCCC 61.536 72.222 0.00 0.00 38.29 5.19
1509 1541 3.423162 CTTCTCGCGGGCCAGAGAG 62.423 68.421 26.51 26.51 43.42 3.20
1592 1630 2.047179 GGGGCGGTGACAGAGTTC 60.047 66.667 0.00 0.00 0.00 3.01
1630 1669 5.170748 GCCTTGCTAATTGTTTTGTGCTAT 58.829 37.500 0.00 0.00 0.00 2.97
1633 1672 7.009540 GCCTTGCTAATTGTTTTGTGCTATAAG 59.990 37.037 0.00 0.00 0.00 1.73
1716 1757 1.135199 GGTGATCGACAAGAACCGCTA 60.135 52.381 0.00 0.00 0.00 4.26
1720 1761 3.616821 TGATCGACAAGAACCGCTATTTG 59.383 43.478 0.00 0.00 0.00 2.32
1723 1764 3.678072 TCGACAAGAACCGCTATTTGAAG 59.322 43.478 0.00 0.00 0.00 3.02
1724 1765 3.678072 CGACAAGAACCGCTATTTGAAGA 59.322 43.478 0.00 0.00 0.00 2.87
1725 1766 4.201628 CGACAAGAACCGCTATTTGAAGAG 60.202 45.833 0.00 0.00 0.00 2.85
1821 1862 3.658705 ACCTCTCTAATCCCGGTCTATCT 59.341 47.826 0.00 0.00 0.00 1.98
1886 1927 1.962807 CCAGGATCTCGCTTCTCTCAT 59.037 52.381 0.00 0.00 0.00 2.90
1930 1971 3.685214 GACGCACGTGAGGATCGCT 62.685 63.158 22.23 0.00 45.19 4.93
1996 2057 3.515286 CTCTGCTGCATTGGCCCG 61.515 66.667 1.31 0.00 40.13 6.13
2031 2092 1.927527 AGAGGCCATTCCCAGCAGT 60.928 57.895 5.01 0.00 34.51 4.40
2114 2176 2.898705 CCAGAGTCTGGCAGTCAATAC 58.101 52.381 26.03 4.70 45.13 1.89
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 1.177401 GGGTTTTAAGCAGGCTGGAG 58.823 55.000 17.64 0.00 0.00 3.86
1 2 0.777446 AGGGTTTTAAGCAGGCTGGA 59.223 50.000 17.64 0.00 0.00 3.86
4 5 2.555448 GGAGAAGGGTTTTAAGCAGGCT 60.555 50.000 0.00 0.00 0.00 4.58
5 6 1.819288 GGAGAAGGGTTTTAAGCAGGC 59.181 52.381 0.00 0.00 0.00 4.85
6 7 2.084546 CGGAGAAGGGTTTTAAGCAGG 58.915 52.381 0.00 0.00 0.00 4.85
7 8 2.779506 ACGGAGAAGGGTTTTAAGCAG 58.220 47.619 0.00 0.00 0.00 4.24
8 9 2.943036 ACGGAGAAGGGTTTTAAGCA 57.057 45.000 0.00 0.00 0.00 3.91
9 10 3.855895 GCAAACGGAGAAGGGTTTTAAGC 60.856 47.826 0.00 0.00 34.33 3.09
10 11 3.316868 TGCAAACGGAGAAGGGTTTTAAG 59.683 43.478 0.00 0.00 34.33 1.85
11 12 3.288964 TGCAAACGGAGAAGGGTTTTAA 58.711 40.909 0.00 0.00 34.33 1.52
12 13 2.933573 TGCAAACGGAGAAGGGTTTTA 58.066 42.857 0.00 0.00 34.33 1.52
13 14 1.770294 TGCAAACGGAGAAGGGTTTT 58.230 45.000 0.00 0.00 34.33 2.43
14 15 1.681264 CTTGCAAACGGAGAAGGGTTT 59.319 47.619 0.00 0.00 36.85 3.27
15 16 1.318576 CTTGCAAACGGAGAAGGGTT 58.681 50.000 0.00 0.00 0.00 4.11
16 17 1.172812 GCTTGCAAACGGAGAAGGGT 61.173 55.000 0.00 0.00 0.00 4.34
17 18 0.890996 AGCTTGCAAACGGAGAAGGG 60.891 55.000 0.00 0.00 0.00 3.95
18 19 0.954452 AAGCTTGCAAACGGAGAAGG 59.046 50.000 0.00 0.00 0.00 3.46
19 20 4.406943 GAATAAGCTTGCAAACGGAGAAG 58.593 43.478 9.86 0.00 0.00 2.85
20 21 3.190535 GGAATAAGCTTGCAAACGGAGAA 59.809 43.478 9.86 0.00 0.00 2.87
21 22 2.747446 GGAATAAGCTTGCAAACGGAGA 59.253 45.455 9.86 0.00 0.00 3.71
22 23 2.487762 TGGAATAAGCTTGCAAACGGAG 59.512 45.455 9.86 0.00 0.00 4.63
23 24 2.509569 TGGAATAAGCTTGCAAACGGA 58.490 42.857 9.86 0.00 0.00 4.69
24 25 3.508744 ATGGAATAAGCTTGCAAACGG 57.491 42.857 9.86 0.00 0.00 4.44
25 26 3.859386 GGAATGGAATAAGCTTGCAAACG 59.141 43.478 9.86 0.00 0.00 3.60
26 27 3.859386 CGGAATGGAATAAGCTTGCAAAC 59.141 43.478 9.86 0.00 0.00 2.93
27 28 3.675775 GCGGAATGGAATAAGCTTGCAAA 60.676 43.478 9.86 0.00 0.00 3.68
28 29 2.159254 GCGGAATGGAATAAGCTTGCAA 60.159 45.455 9.86 0.00 0.00 4.08
29 30 1.405105 GCGGAATGGAATAAGCTTGCA 59.595 47.619 9.86 0.00 0.00 4.08
30 31 1.269257 GGCGGAATGGAATAAGCTTGC 60.269 52.381 9.86 0.00 0.00 4.01
31 32 1.338020 GGGCGGAATGGAATAAGCTTG 59.662 52.381 9.86 0.00 0.00 4.01
32 33 1.692411 GGGCGGAATGGAATAAGCTT 58.308 50.000 3.48 3.48 0.00 3.74
45 46 4.344865 GTCTTGCAAGGGGGCGGA 62.345 66.667 25.73 2.20 36.28 5.54
71 72 1.200252 TGAGAGGAAAGAAGACGCGAG 59.800 52.381 15.93 0.00 0.00 5.03
74 75 2.070028 GGTTGAGAGGAAAGAAGACGC 58.930 52.381 0.00 0.00 0.00 5.19
76 77 3.318886 GACGGTTGAGAGGAAAGAAGAC 58.681 50.000 0.00 0.00 0.00 3.01
77 78 2.030185 CGACGGTTGAGAGGAAAGAAGA 60.030 50.000 0.00 0.00 0.00 2.87
112 127 3.400054 ACTAGGAACCTGCCGGCC 61.400 66.667 26.77 7.68 0.00 6.13
113 128 2.125106 CACTAGGAACCTGCCGGC 60.125 66.667 22.73 22.73 0.00 6.13
114 129 2.125106 GCACTAGGAACCTGCCGG 60.125 66.667 0.00 0.00 0.00 6.13
115 130 2.125106 GGCACTAGGAACCTGCCG 60.125 66.667 5.63 0.00 35.86 5.69
116 131 2.125106 CGGCACTAGGAACCTGCC 60.125 66.667 10.54 10.54 41.84 4.85
117 132 1.610554 TACCGGCACTAGGAACCTGC 61.611 60.000 0.00 0.00 0.00 4.85
118 133 0.460311 CTACCGGCACTAGGAACCTG 59.540 60.000 0.00 0.00 0.00 4.00
119 134 1.328430 GCTACCGGCACTAGGAACCT 61.328 60.000 0.00 0.00 41.35 3.50
120 135 1.143401 GCTACCGGCACTAGGAACC 59.857 63.158 0.00 0.00 41.35 3.62
121 136 1.143401 GGCTACCGGCACTAGGAAC 59.857 63.158 0.00 0.00 44.01 3.62
122 137 2.420568 CGGCTACCGGCACTAGGAA 61.421 63.158 0.00 0.00 44.15 3.36
123 138 2.831742 CGGCTACCGGCACTAGGA 60.832 66.667 0.00 0.00 44.15 2.94
157 172 0.890090 ACTCTCCCGCGGCTATCTAC 60.890 60.000 22.85 0.00 0.00 2.59
169 184 1.604604 CTGAGGATCTCGACTCTCCC 58.395 60.000 2.87 0.00 34.84 4.30
170 185 1.133915 ACCTGAGGATCTCGACTCTCC 60.134 57.143 4.99 0.00 34.84 3.71
171 186 2.341846 ACCTGAGGATCTCGACTCTC 57.658 55.000 4.99 0.00 34.84 3.20
172 187 2.818751 AACCTGAGGATCTCGACTCT 57.181 50.000 4.99 0.00 34.84 3.24
173 188 2.100087 GGAAACCTGAGGATCTCGACTC 59.900 54.545 4.99 0.00 34.92 3.36
174 189 2.104170 GGAAACCTGAGGATCTCGACT 58.896 52.381 4.99 0.00 34.92 4.18
178 193 3.070878 GGAGATGGAAACCTGAGGATCTC 59.929 52.174 15.25 15.25 36.59 2.75
193 208 0.769873 CTGGGAATGGAGGGAGATGG 59.230 60.000 0.00 0.00 0.00 3.51
201 216 0.543749 GGACTCACCTGGGAATGGAG 59.456 60.000 0.00 0.00 35.41 3.86
205 220 1.584724 ATTCGGACTCACCTGGGAAT 58.415 50.000 0.00 0.00 36.31 3.01
209 224 1.469940 CGAGAATTCGGACTCACCTGG 60.470 57.143 0.00 0.00 43.05 4.45
232 247 2.130395 CATGTCATATTCAGCGAGCGT 58.870 47.619 0.00 0.00 0.00 5.07
233 248 1.136419 GCATGTCATATTCAGCGAGCG 60.136 52.381 0.00 0.00 0.00 5.03
235 250 1.802960 GGGCATGTCATATTCAGCGAG 59.197 52.381 0.00 0.00 0.00 5.03
236 251 1.140652 TGGGCATGTCATATTCAGCGA 59.859 47.619 0.00 0.00 0.00 4.93
237 252 1.596603 TGGGCATGTCATATTCAGCG 58.403 50.000 0.00 0.00 0.00 5.18
245 260 2.122797 CCACGCATGGGCATGTCAT 61.123 57.895 10.10 0.00 43.04 3.06
284 299 1.591619 GCTAAACGCGGGACTTATGTC 59.408 52.381 12.47 0.10 42.22 3.06
289 304 1.154197 GAAAGCTAAACGCGGGACTT 58.846 50.000 12.47 3.54 45.59 3.01
373 388 7.795431 ACTAATAACATGTTCAACAAATGCG 57.205 32.000 15.85 0.00 0.00 4.73
395 410 2.871096 TACATTCGGCTTCCCAAACT 57.129 45.000 0.00 0.00 0.00 2.66
396 411 2.031683 CGATACATTCGGCTTCCCAAAC 59.968 50.000 0.00 0.00 44.28 2.93
397 412 2.285083 CGATACATTCGGCTTCCCAAA 58.715 47.619 0.00 0.00 44.28 3.28
398 413 1.948104 CGATACATTCGGCTTCCCAA 58.052 50.000 0.00 0.00 44.28 4.12
399 414 3.678921 CGATACATTCGGCTTCCCA 57.321 52.632 0.00 0.00 44.28 4.37
433 448 1.083806 GGCATGCACAAGTCGATCGA 61.084 55.000 21.36 15.15 0.00 3.59
434 449 1.086067 AGGCATGCACAAGTCGATCG 61.086 55.000 21.36 9.36 0.00 3.69
435 450 1.089920 AAGGCATGCACAAGTCGATC 58.910 50.000 21.36 0.00 0.00 3.69
436 451 0.806868 CAAGGCATGCACAAGTCGAT 59.193 50.000 21.36 0.00 0.00 3.59
437 452 0.250252 TCAAGGCATGCACAAGTCGA 60.250 50.000 21.36 2.60 0.00 4.20
438 453 0.110056 GTCAAGGCATGCACAAGTCG 60.110 55.000 21.36 0.03 0.00 4.18
440 455 0.178981 AGGTCAAGGCATGCACAAGT 60.179 50.000 21.36 0.00 0.00 3.16
442 457 2.161855 CTTAGGTCAAGGCATGCACAA 58.838 47.619 21.36 0.00 0.00 3.33
443 458 1.073763 ACTTAGGTCAAGGCATGCACA 59.926 47.619 21.36 0.00 38.70 4.57
444 459 1.740025 GACTTAGGTCAAGGCATGCAC 59.260 52.381 21.36 8.78 42.49 4.57
445 460 2.113860 GACTTAGGTCAAGGCATGCA 57.886 50.000 21.36 0.00 42.49 3.96
455 470 5.390567 CCGCAAATAAACACTGACTTAGGTC 60.391 44.000 0.00 0.00 42.42 3.85
456 471 4.454504 CCGCAAATAAACACTGACTTAGGT 59.545 41.667 0.00 0.00 0.00 3.08
470 488 5.097742 TGATCTCTTCCTTCCGCAAATAA 57.902 39.130 0.00 0.00 0.00 1.40
477 495 2.102252 CCCTCTTGATCTCTTCCTTCCG 59.898 54.545 0.00 0.00 0.00 4.30
479 497 4.679372 CGTTCCCTCTTGATCTCTTCCTTC 60.679 50.000 0.00 0.00 0.00 3.46
524 542 3.414549 TTTCCTTCTGCAAACACGTTC 57.585 42.857 0.00 0.00 0.00 3.95
534 552 2.294449 ACTCCCCTTTTTCCTTCTGC 57.706 50.000 0.00 0.00 0.00 4.26
549 567 0.733223 GAAGCACGTCTCGGAACTCC 60.733 60.000 0.00 0.00 0.00 3.85
556 574 1.067060 TGATATGGGAAGCACGTCTCG 59.933 52.381 0.00 0.00 0.00 4.04
568 586 8.874744 ATAGAACATTTGGAAGATGATATGGG 57.125 34.615 0.00 0.00 0.00 4.00
589 607 8.591072 CGGAAAATACCCAAATACTAGGATAGA 58.409 37.037 0.00 0.00 42.77 1.98
590 608 7.333672 GCGGAAAATACCCAAATACTAGGATAG 59.666 40.741 0.00 0.00 46.50 2.08
591 609 7.163441 GCGGAAAATACCCAAATACTAGGATA 58.837 38.462 0.00 0.00 0.00 2.59
592 610 6.002082 GCGGAAAATACCCAAATACTAGGAT 58.998 40.000 0.00 0.00 0.00 3.24
593 611 5.370679 GCGGAAAATACCCAAATACTAGGA 58.629 41.667 0.00 0.00 0.00 2.94
594 612 4.517832 GGCGGAAAATACCCAAATACTAGG 59.482 45.833 0.00 0.00 0.00 3.02
595 613 5.127491 TGGCGGAAAATACCCAAATACTAG 58.873 41.667 0.00 0.00 0.00 2.57
596 614 5.104444 TCTGGCGGAAAATACCCAAATACTA 60.104 40.000 0.00 0.00 0.00 1.82
597 615 3.951680 CTGGCGGAAAATACCCAAATACT 59.048 43.478 0.00 0.00 0.00 2.12
598 616 3.949113 TCTGGCGGAAAATACCCAAATAC 59.051 43.478 0.00 0.00 0.00 1.89
599 617 3.949113 GTCTGGCGGAAAATACCCAAATA 59.051 43.478 0.00 0.00 0.00 1.40
600 618 2.758423 GTCTGGCGGAAAATACCCAAAT 59.242 45.455 0.00 0.00 0.00 2.32
601 619 2.164338 GTCTGGCGGAAAATACCCAAA 58.836 47.619 0.00 0.00 0.00 3.28
602 620 1.614850 GGTCTGGCGGAAAATACCCAA 60.615 52.381 0.00 0.00 0.00 4.12
603 621 0.034863 GGTCTGGCGGAAAATACCCA 60.035 55.000 0.00 0.00 0.00 4.51
604 622 0.255033 AGGTCTGGCGGAAAATACCC 59.745 55.000 0.00 0.00 0.00 3.69
605 623 2.484947 CCTAGGTCTGGCGGAAAATACC 60.485 54.545 0.00 0.00 0.00 2.73
606 624 2.433239 TCCTAGGTCTGGCGGAAAATAC 59.567 50.000 9.08 0.00 0.00 1.89
607 625 2.754465 TCCTAGGTCTGGCGGAAAATA 58.246 47.619 9.08 0.00 0.00 1.40
608 626 1.580059 TCCTAGGTCTGGCGGAAAAT 58.420 50.000 9.08 0.00 0.00 1.82
609 627 1.580059 ATCCTAGGTCTGGCGGAAAA 58.420 50.000 9.08 0.00 0.00 2.29
615 633 1.127343 AGAGCAATCCTAGGTCTGGC 58.873 55.000 9.08 7.01 41.82 4.85
616 634 3.037549 AGAAGAGCAATCCTAGGTCTGG 58.962 50.000 9.08 0.00 42.50 3.86
625 643 4.831107 ACAGAAGAAGAGAAGAGCAATCC 58.169 43.478 0.00 0.00 0.00 3.01
626 644 4.562394 CGACAGAAGAAGAGAAGAGCAATC 59.438 45.833 0.00 0.00 0.00 2.67
627 645 4.219507 TCGACAGAAGAAGAGAAGAGCAAT 59.780 41.667 0.00 0.00 0.00 3.56
628 646 3.570125 TCGACAGAAGAAGAGAAGAGCAA 59.430 43.478 0.00 0.00 0.00 3.91
631 649 6.385843 TCATTTCGACAGAAGAAGAGAAGAG 58.614 40.000 0.00 0.00 37.70 2.85
697 715 9.726232 TTAAAATGTGCTACAGTATAGACGTAG 57.274 33.333 12.25 12.25 36.55 3.51
700 718 9.901724 CTTTTAAAATGTGCTACAGTATAGACG 57.098 33.333 0.09 0.00 0.00 4.18
703 721 8.673711 TGCCTTTTAAAATGTGCTACAGTATAG 58.326 33.333 0.09 0.00 0.00 1.31
706 724 6.488683 ACTGCCTTTTAAAATGTGCTACAGTA 59.511 34.615 0.09 0.00 32.13 2.74
707 725 5.301805 ACTGCCTTTTAAAATGTGCTACAGT 59.698 36.000 0.09 4.74 0.00 3.55
708 726 5.772521 ACTGCCTTTTAAAATGTGCTACAG 58.227 37.500 0.09 4.18 0.00 2.74
710 728 6.581166 GTGTACTGCCTTTTAAAATGTGCTAC 59.419 38.462 0.09 5.71 0.00 3.58
711 729 6.566942 CGTGTACTGCCTTTTAAAATGTGCTA 60.567 38.462 0.09 0.00 0.00 3.49
712 730 5.528870 GTGTACTGCCTTTTAAAATGTGCT 58.471 37.500 0.09 0.00 0.00 4.40
713 731 4.381566 CGTGTACTGCCTTTTAAAATGTGC 59.618 41.667 0.09 5.80 0.00 4.57
714 732 4.381566 GCGTGTACTGCCTTTTAAAATGTG 59.618 41.667 0.09 0.01 0.00 3.21
858 890 4.636206 GGGTTGGAGACAGTAATTAAGCTG 59.364 45.833 0.00 2.39 44.54 4.24
917 949 4.038402 ACTTCTTGCCTGGAATCAACAAAG 59.962 41.667 0.00 0.53 0.00 2.77
995 1027 3.047280 GTGACGACGCCATTGCCA 61.047 61.111 0.00 0.00 0.00 4.92
1389 1421 3.358111 TCCCCGAGCAAATTTACATCA 57.642 42.857 0.00 0.00 0.00 3.07
1523 1561 3.625897 CGTCCCTGACCACCTGCA 61.626 66.667 0.00 0.00 0.00 4.41
1544 1582 1.835693 CCATCCTCTTGGGGCTCTC 59.164 63.158 0.00 0.00 35.33 3.20
1630 1669 1.281353 CCGCGTGCAACAAAGCTTA 59.719 52.632 4.92 0.00 35.74 3.09
1633 1672 3.024043 CACCGCGTGCAACAAAGC 61.024 61.111 4.92 0.00 35.74 3.51
1709 1750 7.362660 GGTTTATTTCCTCTTCAAATAGCGGTT 60.363 37.037 0.00 0.00 29.50 4.44
1716 1757 7.470192 TCTCAGGGTTTATTTCCTCTTCAAAT 58.530 34.615 0.00 0.00 0.00 2.32
1720 1761 6.887002 ACAATCTCAGGGTTTATTTCCTCTTC 59.113 38.462 0.00 0.00 0.00 2.87
1723 1764 7.565680 TCTACAATCTCAGGGTTTATTTCCTC 58.434 38.462 0.00 0.00 0.00 3.71
1724 1765 7.366011 CCTCTACAATCTCAGGGTTTATTTCCT 60.366 40.741 0.00 0.00 0.00 3.36
1725 1766 6.768381 CCTCTACAATCTCAGGGTTTATTTCC 59.232 42.308 0.00 0.00 0.00 3.13
1821 1862 2.568062 TGCCAAACGTATCTAGGGTTCA 59.432 45.455 0.00 0.00 0.00 3.18
1919 1960 2.541178 CGTGTAGGTAAGCGATCCTCAC 60.541 54.545 0.00 7.73 35.51 3.51
1930 1971 1.735198 GCAGTGCGCGTGTAGGTAA 60.735 57.895 8.43 0.00 0.00 2.85
2037 2098 0.321021 ACTCTCCTGTGCTCAAGCTG 59.679 55.000 3.32 0.00 42.66 4.24
2114 2176 1.148310 ACAAGAAGAACGTCGCCATG 58.852 50.000 0.00 0.00 0.00 3.66
2519 4290 2.666098 GGCGGCTTGGTCTTCCCTA 61.666 63.158 0.00 0.00 0.00 3.53


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

AutoCloner maintained by Alex Coulton.