Multiple sequence alignment - TraesCS1B01G309400

Loading Multiple Alignment...

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 TraesCS1B01G309400 chr1B 100.000 3419 0 0 1 3419 532174978 532171560 0.000000e+00 6314.0
1 TraesCS1B01G309400 chr1B 87.692 65 6 2 579 643 659319423 659319485 1.320000e-09 75.0
2 TraesCS1B01G309400 chr1D 94.838 2809 101 14 644 3419 397081812 397079015 0.000000e+00 4344.0
3 TraesCS1B01G309400 chr1D 91.379 580 40 5 1 576 397082389 397081816 0.000000e+00 785.0
4 TraesCS1B01G309400 chr1A 94.042 2786 107 15 667 3419 494451939 494449180 0.000000e+00 4170.0
5 TraesCS1B01G309400 chr1A 90.893 582 41 7 1 576 494452532 494451957 0.000000e+00 771.0
6 TraesCS1B01G309400 chr3A 80.072 828 154 8 992 1810 595434916 595435741 3.770000e-169 604.0
7 TraesCS1B01G309400 chr2D 87.037 432 44 8 1622 2049 520042415 520042838 8.580000e-131 477.0
8 TraesCS1B01G309400 chr2D 88.889 261 18 7 1327 1579 520042158 520042415 9.210000e-81 311.0
9 TraesCS1B01G309400 chr2D 81.285 358 46 9 3077 3415 307019485 307019840 1.560000e-68 270.0
10 TraesCS1B01G309400 chr2B 86.605 433 45 7 1622 2049 612067830 612068254 1.860000e-127 466.0
11 TraesCS1B01G309400 chr2B 86.461 421 45 6 1634 2049 612074157 612074570 5.200000e-123 451.0
12 TraesCS1B01G309400 chr2B 89.764 254 16 4 1327 1579 612067586 612067830 1.980000e-82 316.0
13 TraesCS1B01G309400 chr6B 78.417 417 61 17 3013 3408 511741167 511740759 9.480000e-61 244.0
14 TraesCS1B01G309400 chr6B 79.297 256 30 17 2970 3217 713312708 713312468 1.270000e-34 158.0
15 TraesCS1B01G309400 chr6A 75.385 325 46 15 3111 3416 452621401 452621710 3.580000e-25 126.0
16 TraesCS1B01G309400 chr6A 88.732 71 4 3 576 643 104118409 104118340 2.190000e-12 84.2
17 TraesCS1B01G309400 chr3D 80.925 173 15 6 3260 3415 566130070 566130241 1.670000e-23 121.0
18 TraesCS1B01G309400 chr3D 89.855 69 7 0 576 644 567408805 567408737 4.700000e-14 89.8
19 TraesCS1B01G309400 chr3B 80.814 172 17 5 3260 3415 754721940 754721769 1.670000e-23 121.0
20 TraesCS1B01G309400 chr3B 87.671 73 9 0 571 643 628472955 628473027 6.080000e-13 86.1
21 TraesCS1B01G309400 chr5A 86.842 76 10 0 570 645 680077928 680078003 6.080000e-13 86.1
22 TraesCS1B01G309400 chr5A 85.714 77 8 1 579 652 594959630 594959706 1.020000e-10 78.7
23 TraesCS1B01G309400 chr5B 86.667 75 6 3 570 643 453878004 453877933 2.830000e-11 80.5
24 TraesCS1B01G309400 chr5D 87.143 70 5 3 579 645 45654424 45654356 3.660000e-10 76.8
25 TraesCS1B01G309400 chr6D 86.567 67 9 0 578 644 104767511 104767445 1.320000e-09 75.0


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 TraesCS1B01G309400 chr1B 532171560 532174978 3418 True 6314.0 6314 100.0000 1 3419 1 chr1B.!!$R1 3418
1 TraesCS1B01G309400 chr1D 397079015 397082389 3374 True 2564.5 4344 93.1085 1 3419 2 chr1D.!!$R1 3418
2 TraesCS1B01G309400 chr1A 494449180 494452532 3352 True 2470.5 4170 92.4675 1 3419 2 chr1A.!!$R1 3418
3 TraesCS1B01G309400 chr3A 595434916 595435741 825 False 604.0 604 80.0720 992 1810 1 chr3A.!!$F1 818
4 TraesCS1B01G309400 chr2D 520042158 520042838 680 False 394.0 477 87.9630 1327 2049 2 chr2D.!!$F2 722
5 TraesCS1B01G309400 chr2B 612067586 612068254 668 False 391.0 466 88.1845 1327 2049 2 chr2B.!!$F2 722

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
409 414 0.108585 TGCAGAGGACACCCAGTTTC 59.891 55.0 0.0 0.0 33.88 2.78 F
1695 1720 0.249238 CTGAGTACAGATGCCCTCGC 60.249 60.0 0.0 0.0 46.03 5.03 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1785 1810 0.324943 CCGGCTTCCTATACCATGGG 59.675 60.0 18.09 0.0 0.00 4.00 R
3319 3364 0.250467 CCATCACCATCCACCGGATC 60.250 60.0 9.46 0.0 40.98 3.36 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
40 41 1.890894 CTCCACCACACGTAGGAGG 59.109 63.158 14.11 14.11 43.07 4.30
41 42 0.611062 CTCCACCACACGTAGGAGGA 60.611 60.000 19.43 19.43 43.07 3.71
42 43 0.178955 TCCACCACACGTAGGAGGAA 60.179 55.000 18.69 6.76 41.98 3.36
43 44 0.246635 CCACCACACGTAGGAGGAAG 59.753 60.000 14.87 0.01 38.99 3.46
204 205 1.084289 GGACTTGGGAATTCCGTTCG 58.916 55.000 18.30 8.94 37.73 3.95
296 298 3.940209 TTGGAATCTGCGAGCATTTTT 57.060 38.095 0.00 0.00 0.00 1.94
303 305 4.410492 TCTGCGAGCATTTTTCTTTCTC 57.590 40.909 0.00 0.00 0.00 2.87
324 326 5.582269 TCTCTATTTTGTCGCCTCAATTCTG 59.418 40.000 0.00 0.00 0.00 3.02
329 331 1.092345 GTCGCCTCAATTCTGGGAGC 61.092 60.000 0.00 0.00 0.00 4.70
368 370 1.269448 GACCCGATTGCACAATGTTGT 59.731 47.619 0.00 0.00 43.36 3.32
381 386 5.907391 GCACAATGTTGTAGTTACACTTGTC 59.093 40.000 0.00 4.69 39.91 3.18
409 414 0.108585 TGCAGAGGACACCCAGTTTC 59.891 55.000 0.00 0.00 33.88 2.78
479 484 2.334977 TCTCAGAGTTTGCCCTGGTAA 58.665 47.619 0.00 0.00 0.00 2.85
480 485 2.303022 TCTCAGAGTTTGCCCTGGTAAG 59.697 50.000 0.00 0.00 0.00 2.34
484 489 1.474077 GAGTTTGCCCTGGTAAGCATG 59.526 52.381 3.94 0.00 39.11 4.06
494 499 0.535102 GGTAAGCATGTGGGATCCCG 60.535 60.000 26.03 12.57 39.42 5.14
528 533 5.547465 TCTCTGCGTTCTTCTTATGGAAAA 58.453 37.500 0.00 0.00 33.07 2.29
550 555 2.161609 GTGGGTTGGATGTTCGATTCAC 59.838 50.000 0.00 0.00 0.00 3.18
551 556 2.224646 TGGGTTGGATGTTCGATTCACA 60.225 45.455 0.00 0.00 0.00 3.58
553 558 3.254657 GGGTTGGATGTTCGATTCACAAA 59.745 43.478 0.00 0.00 0.00 2.83
554 559 4.082245 GGGTTGGATGTTCGATTCACAAAT 60.082 41.667 0.00 0.00 0.00 2.32
555 560 5.469479 GGTTGGATGTTCGATTCACAAATT 58.531 37.500 0.00 0.00 0.00 1.82
561 567 9.949174 TGGATGTTCGATTCACAAATTATAATG 57.051 29.630 0.00 0.00 0.00 1.90
563 569 8.801715 ATGTTCGATTCACAAATTATAATGGC 57.198 30.769 0.00 0.00 0.00 4.40
576 582 9.751542 CAAATTATAATGGCGGGTGTAAAAATA 57.248 29.630 0.00 0.00 0.00 1.40
578 584 8.700439 ATTATAATGGCGGGTGTAAAAATACT 57.300 30.769 0.00 0.00 0.00 2.12
581 587 4.556592 TGGCGGGTGTAAAAATACTACT 57.443 40.909 0.00 0.00 0.00 2.57
582 588 4.506758 TGGCGGGTGTAAAAATACTACTC 58.493 43.478 0.00 0.00 0.00 2.59
583 589 3.873361 GGCGGGTGTAAAAATACTACTCC 59.127 47.826 0.00 0.00 33.86 3.85
584 590 3.873361 GCGGGTGTAAAAATACTACTCCC 59.127 47.826 9.20 9.20 44.44 4.30
585 591 4.383444 GCGGGTGTAAAAATACTACTCCCT 60.383 45.833 14.81 0.00 45.17 4.20
586 592 5.354767 CGGGTGTAAAAATACTACTCCCTC 58.645 45.833 14.81 0.00 45.17 4.30
587 593 5.678583 GGGTGTAAAAATACTACTCCCTCC 58.321 45.833 11.23 0.00 44.47 4.30
588 594 5.427806 GGGTGTAAAAATACTACTCCCTCCT 59.572 44.000 11.23 0.00 44.47 3.69
589 595 6.346896 GGTGTAAAAATACTACTCCCTCCTG 58.653 44.000 0.00 0.00 30.14 3.86
590 596 6.070366 GGTGTAAAAATACTACTCCCTCCTGT 60.070 42.308 0.00 0.00 30.14 4.00
591 597 7.040494 GTGTAAAAATACTACTCCCTCCTGTC 58.960 42.308 0.00 0.00 0.00 3.51
592 598 5.695424 AAAAATACTACTCCCTCCTGTCC 57.305 43.478 0.00 0.00 0.00 4.02
593 599 4.348020 AAATACTACTCCCTCCTGTCCA 57.652 45.455 0.00 0.00 0.00 4.02
594 600 4.561254 AATACTACTCCCTCCTGTCCAT 57.439 45.455 0.00 0.00 0.00 3.41
595 601 5.681494 AATACTACTCCCTCCTGTCCATA 57.319 43.478 0.00 0.00 0.00 2.74
596 602 5.887480 ATACTACTCCCTCCTGTCCATAT 57.113 43.478 0.00 0.00 0.00 1.78
597 603 4.561254 ACTACTCCCTCCTGTCCATATT 57.439 45.455 0.00 0.00 0.00 1.28
598 604 5.681494 ACTACTCCCTCCTGTCCATATTA 57.319 43.478 0.00 0.00 0.00 0.98
599 605 6.039415 ACTACTCCCTCCTGTCCATATTAA 57.961 41.667 0.00 0.00 0.00 1.40
600 606 6.635021 ACTACTCCCTCCTGTCCATATTAAT 58.365 40.000 0.00 0.00 0.00 1.40
601 607 7.082972 ACTACTCCCTCCTGTCCATATTAATT 58.917 38.462 0.00 0.00 0.00 1.40
602 608 6.192970 ACTCCCTCCTGTCCATATTAATTG 57.807 41.667 0.00 0.00 0.00 2.32
603 609 5.672194 ACTCCCTCCTGTCCATATTAATTGT 59.328 40.000 0.00 0.00 0.00 2.71
604 610 6.183361 ACTCCCTCCTGTCCATATTAATTGTC 60.183 42.308 0.00 0.00 0.00 3.18
605 611 4.997395 CCCTCCTGTCCATATTAATTGTCG 59.003 45.833 0.00 0.00 0.00 4.35
606 612 4.452455 CCTCCTGTCCATATTAATTGTCGC 59.548 45.833 0.00 0.00 0.00 5.19
607 613 5.290493 TCCTGTCCATATTAATTGTCGCT 57.710 39.130 0.00 0.00 0.00 4.93
608 614 5.056480 TCCTGTCCATATTAATTGTCGCTG 58.944 41.667 0.00 0.00 0.00 5.18
609 615 5.056480 CCTGTCCATATTAATTGTCGCTGA 58.944 41.667 0.00 0.00 0.00 4.26
610 616 5.702670 CCTGTCCATATTAATTGTCGCTGAT 59.297 40.000 0.00 0.00 0.00 2.90
611 617 6.205464 CCTGTCCATATTAATTGTCGCTGATT 59.795 38.462 0.00 0.00 0.00 2.57
612 618 7.255242 CCTGTCCATATTAATTGTCGCTGATTT 60.255 37.037 0.00 0.00 0.00 2.17
613 619 8.669946 TGTCCATATTAATTGTCGCTGATTTA 57.330 30.769 0.00 0.00 0.00 1.40
614 620 8.773645 TGTCCATATTAATTGTCGCTGATTTAG 58.226 33.333 0.00 0.00 0.00 1.85
615 621 8.774586 GTCCATATTAATTGTCGCTGATTTAGT 58.225 33.333 0.00 0.00 0.00 2.24
616 622 9.990360 TCCATATTAATTGTCGCTGATTTAGTA 57.010 29.630 0.00 0.00 0.00 1.82
626 632 9.982291 TTGTCGCTGATTTAGTACAAATTAATC 57.018 29.630 0.00 0.00 34.01 1.75
627 633 9.378551 TGTCGCTGATTTAGTACAAATTAATCT 57.621 29.630 0.00 0.00 0.00 2.40
628 634 9.638300 GTCGCTGATTTAGTACAAATTAATCTG 57.362 33.333 0.00 0.00 0.00 2.90
629 635 8.826710 TCGCTGATTTAGTACAAATTAATCTGG 58.173 33.333 0.00 0.00 0.00 3.86
630 636 8.826710 CGCTGATTTAGTACAAATTAATCTGGA 58.173 33.333 0.00 0.00 0.00 3.86
636 642 9.627123 TTTAGTACAAATTAATCTGGATGGGAG 57.373 33.333 0.00 0.00 0.00 4.30
637 643 6.605119 AGTACAAATTAATCTGGATGGGAGG 58.395 40.000 0.00 0.00 0.00 4.30
638 644 4.808042 ACAAATTAATCTGGATGGGAGGG 58.192 43.478 0.00 0.00 0.00 4.30
639 645 4.482025 ACAAATTAATCTGGATGGGAGGGA 59.518 41.667 0.00 0.00 0.00 4.20
640 646 5.075493 CAAATTAATCTGGATGGGAGGGAG 58.925 45.833 0.00 0.00 0.00 4.30
641 647 3.438131 TTAATCTGGATGGGAGGGAGT 57.562 47.619 0.00 0.00 0.00 3.85
642 648 4.569676 TTAATCTGGATGGGAGGGAGTA 57.430 45.455 0.00 0.00 0.00 2.59
643 649 2.407340 ATCTGGATGGGAGGGAGTAC 57.593 55.000 0.00 0.00 0.00 2.73
644 650 0.264955 TCTGGATGGGAGGGAGTACC 59.735 60.000 0.00 0.00 40.67 3.34
676 682 4.261155 CCGAAGATTTGTCATGTGTGTGTT 60.261 41.667 0.00 0.00 0.00 3.32
698 704 4.754372 ATACACTTGCACATGTGTTCTG 57.246 40.909 26.01 17.46 44.14 3.02
711 717 8.119226 GCACATGTGTTCTGATCTAGTTTATTC 58.881 37.037 26.01 0.00 0.00 1.75
727 733 9.167311 CTAGTTTATTCTGTTTTGCAGGTAGAT 57.833 33.333 0.00 0.00 45.08 1.98
765 771 2.508526 GGCTGAAGGTGATTCACTTGT 58.491 47.619 16.02 2.39 43.09 3.16
773 779 0.867746 TGATTCACTTGTGCTCGTGC 59.132 50.000 1.71 1.71 40.20 5.34
794 800 2.941720 CTGGAAGAGGCAATTGTCTAGC 59.058 50.000 13.63 1.10 34.07 3.42
852 860 0.608130 CGGTTCTGATGAGTGGTGGA 59.392 55.000 0.00 0.00 0.00 4.02
936 944 5.186021 GGGACTCTGTCTTCTCTAACATTCA 59.814 44.000 0.00 0.00 32.47 2.57
941 949 7.106439 TCTGTCTTCTCTAACATTCATCTCC 57.894 40.000 0.00 0.00 0.00 3.71
954 963 2.525368 TCATCTCCGAGTCTGAACCAA 58.475 47.619 0.00 0.00 0.00 3.67
960 969 2.029020 TCCGAGTCTGAACCAATCTGTG 60.029 50.000 0.00 0.00 0.00 3.66
1013 1022 7.671302 TGTGCTTATATAATGGAAGAGAGGAC 58.329 38.462 0.00 0.00 0.00 3.85
1105 1117 2.540361 CGCAATCTAGCAAATGGTCAGC 60.540 50.000 0.00 0.00 0.00 4.26
1191 1203 4.599041 AGAGGGAGATCTCGATAATGAGG 58.401 47.826 16.46 0.00 38.71 3.86
1194 1206 5.200483 AGGGAGATCTCGATAATGAGGATC 58.800 45.833 16.46 1.43 36.61 3.36
1258 1270 5.590259 GCTACCAGGAGCAAGATTTATTTCA 59.410 40.000 0.00 0.00 42.36 2.69
1367 1382 7.070447 TCACCAGTTGATCTCTGCTATAGATTT 59.930 37.037 3.21 0.00 33.82 2.17
1571 1594 0.951558 AAAGGCTACAACGGTGCAAG 59.048 50.000 0.00 0.00 0.00 4.01
1695 1720 0.249238 CTGAGTACAGATGCCCTCGC 60.249 60.000 0.00 0.00 46.03 5.03
1716 1741 4.083324 CGCTATTTTTCCACTGAGCTGAAA 60.083 41.667 0.00 0.00 0.00 2.69
1785 1810 3.249559 CCATCGCAAGGATAAAGAGAAGC 59.750 47.826 0.00 0.00 32.85 3.86
1788 1813 2.680805 CGCAAGGATAAAGAGAAGCCCA 60.681 50.000 0.00 0.00 0.00 5.36
1836 1861 3.561725 CACCACTGAGAAAAGACAAGACC 59.438 47.826 0.00 0.00 0.00 3.85
2063 2091 5.393027 CCCAACGCATCAAGCTTAAAGTTAT 60.393 40.000 0.00 0.00 42.61 1.89
2133 2161 6.441088 AAGAAGGGTACTCTTGAGTTTGAT 57.559 37.500 14.12 0.00 0.00 2.57
2268 2296 2.610232 GGACATTGTTTGGTCATGGCAC 60.610 50.000 0.00 0.00 35.74 5.01
2279 2307 2.824041 ATGGCACGGCGATGTTCC 60.824 61.111 16.62 7.29 0.00 3.62
2438 2466 9.764363 ACAATAATCTAACTGAAATCGCTATCA 57.236 29.630 0.00 0.00 0.00 2.15
2513 2543 2.267174 ATGTGCTTGCAGTTCTCACT 57.733 45.000 0.00 0.00 0.00 3.41
2754 2784 3.002246 TGACTGTTGCGATTTGTGAACTC 59.998 43.478 0.00 0.00 0.00 3.01
2781 2811 6.888430 ACTTAAGAAACTATCAGCGTTTGTG 58.112 36.000 10.09 0.00 34.94 3.33
2902 2935 5.360714 TGGCTAGAGGAAATAAAATGGCAAG 59.639 40.000 0.00 0.00 0.00 4.01
2903 2936 5.594317 GGCTAGAGGAAATAAAATGGCAAGA 59.406 40.000 0.00 0.00 0.00 3.02
2904 2937 6.096846 GGCTAGAGGAAATAAAATGGCAAGAA 59.903 38.462 0.00 0.00 0.00 2.52
2927 2960 2.693074 GCTTGTTGAAAGGGAAGAACCA 59.307 45.455 0.00 0.00 41.20 3.67
2938 2971 6.560003 AAGGGAAGAACCAGAAACAAAAAT 57.440 33.333 0.00 0.00 41.20 1.82
2998 3043 0.253207 CCCCAGGAGGAAACCCTAGT 60.253 60.000 0.00 0.00 38.24 2.57
3009 3054 2.042843 CCCTAGTGTCGCCTCCCT 60.043 66.667 0.00 0.00 0.00 4.20
3132 3177 3.710722 CGCCTCTCCCTGCTTGGT 61.711 66.667 0.00 0.00 0.00 3.67
3133 3178 2.045536 GCCTCTCCCTGCTTGGTG 60.046 66.667 0.00 0.00 0.00 4.17
3134 3179 2.673523 CCTCTCCCTGCTTGGTGG 59.326 66.667 0.00 0.00 0.00 4.61
3135 3180 2.045536 CTCTCCCTGCTTGGTGGC 60.046 66.667 0.00 0.00 0.00 5.01
3136 3181 3.965539 CTCTCCCTGCTTGGTGGCG 62.966 68.421 0.00 0.00 34.52 5.69
3137 3182 4.335647 CTCCCTGCTTGGTGGCGT 62.336 66.667 0.00 0.00 34.52 5.68
3138 3183 4.329545 TCCCTGCTTGGTGGCGTC 62.330 66.667 0.00 0.00 34.52 5.19
3224 3269 4.421554 CCTCCCCTCCCTCCAGCA 62.422 72.222 0.00 0.00 0.00 4.41
3244 3289 2.132352 GTCTCGGGGGCTTCGGTAT 61.132 63.158 0.00 0.00 0.00 2.73
3258 3303 0.179009 CGGTATCCAGGGGTCGACTA 60.179 60.000 16.46 0.00 0.00 2.59
3285 3330 0.913451 ATCTGGCCTCCTGCTCTGTT 60.913 55.000 3.32 0.00 40.92 3.16
3342 3403 0.532862 CGGTGGATGGTGATGGTAGC 60.533 60.000 0.00 0.00 0.00 3.58
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
40 41 1.265454 TTCTCCGGCTCCCTTCCTTC 61.265 60.000 0.00 0.00 0.00 3.46
41 42 1.229529 TTCTCCGGCTCCCTTCCTT 60.230 57.895 0.00 0.00 0.00 3.36
42 43 1.687493 CTTCTCCGGCTCCCTTCCT 60.687 63.158 0.00 0.00 0.00 3.36
43 44 2.904131 CTTCTCCGGCTCCCTTCC 59.096 66.667 0.00 0.00 0.00 3.46
149 150 3.211803 TCGATTGGATTATACCGCGAG 57.788 47.619 8.23 0.00 0.00 5.03
204 205 3.971245 AACCTCACCTGATCTGAAGAC 57.029 47.619 0.38 0.00 0.00 3.01
296 298 5.147330 TGAGGCGACAAAATAGAGAAAGA 57.853 39.130 0.00 0.00 0.00 2.52
303 305 4.201950 CCCAGAATTGAGGCGACAAAATAG 60.202 45.833 0.00 0.00 33.44 1.73
329 331 2.079049 GCGGAACAGGAGCGTTAAG 58.921 57.895 0.00 0.00 0.00 1.85
345 347 2.749865 ATTGTGCAATCGGGTCGCG 61.750 57.895 0.00 0.00 0.00 5.87
348 350 1.269448 ACAACATTGTGCAATCGGGTC 59.731 47.619 0.00 0.00 40.49 4.46
350 352 2.487762 ACTACAACATTGTGCAATCGGG 59.512 45.455 7.53 0.00 42.31 5.14
368 370 7.115805 CTGCAAGATTTACGACAAGTGTAACTA 59.884 37.037 0.00 0.00 43.06 2.24
381 386 2.673368 GGTGTCCTCTGCAAGATTTACG 59.327 50.000 0.00 0.00 45.62 3.18
409 414 3.434319 ATGGCCAAAGCTCGCACG 61.434 61.111 10.96 0.00 39.73 5.34
479 484 0.765903 ATCTCGGGATCCCACATGCT 60.766 55.000 30.42 6.67 35.37 3.79
480 485 0.976641 TATCTCGGGATCCCACATGC 59.023 55.000 30.42 2.23 35.37 4.06
484 489 7.007723 AGAGATATATTATCTCGGGATCCCAC 58.992 42.308 30.42 4.64 46.74 4.61
528 533 2.039746 TGAATCGAACATCCAACCCACT 59.960 45.455 0.00 0.00 0.00 4.00
550 555 8.655651 ATTTTTACACCCGCCATTATAATTTG 57.344 30.769 0.00 0.00 0.00 2.32
551 556 9.752961 GTATTTTTACACCCGCCATTATAATTT 57.247 29.630 0.00 0.00 0.00 1.82
553 558 8.700439 AGTATTTTTACACCCGCCATTATAAT 57.300 30.769 0.00 0.00 0.00 1.28
554 559 9.054922 GTAGTATTTTTACACCCGCCATTATAA 57.945 33.333 0.00 0.00 0.00 0.98
555 560 8.431222 AGTAGTATTTTTACACCCGCCATTATA 58.569 33.333 0.00 0.00 0.00 0.98
561 567 3.873361 GGAGTAGTATTTTTACACCCGCC 59.127 47.826 0.00 0.00 0.00 6.13
576 582 4.561254 AATATGGACAGGAGGGAGTAGT 57.439 45.455 0.00 0.00 0.00 2.73
578 584 6.849697 ACAATTAATATGGACAGGAGGGAGTA 59.150 38.462 0.00 0.00 0.00 2.59
581 587 5.221641 CGACAATTAATATGGACAGGAGGGA 60.222 44.000 0.00 0.00 0.00 4.20
582 588 4.997395 CGACAATTAATATGGACAGGAGGG 59.003 45.833 0.00 0.00 0.00 4.30
583 589 4.452455 GCGACAATTAATATGGACAGGAGG 59.548 45.833 0.00 0.00 0.00 4.30
584 590 5.178252 CAGCGACAATTAATATGGACAGGAG 59.822 44.000 0.00 0.00 0.00 3.69
585 591 5.056480 CAGCGACAATTAATATGGACAGGA 58.944 41.667 0.00 0.00 0.00 3.86
586 592 5.056480 TCAGCGACAATTAATATGGACAGG 58.944 41.667 0.00 0.00 0.00 4.00
587 593 6.791887 ATCAGCGACAATTAATATGGACAG 57.208 37.500 0.00 0.00 0.00 3.51
588 594 7.566760 AAATCAGCGACAATTAATATGGACA 57.433 32.000 0.00 0.00 0.00 4.02
589 595 8.774586 ACTAAATCAGCGACAATTAATATGGAC 58.225 33.333 0.00 0.00 0.00 4.02
590 596 8.902540 ACTAAATCAGCGACAATTAATATGGA 57.097 30.769 0.00 0.00 0.00 3.41
600 606 9.982291 GATTAATTTGTACTAAATCAGCGACAA 57.018 29.630 0.00 0.00 33.66 3.18
601 607 9.378551 AGATTAATTTGTACTAAATCAGCGACA 57.621 29.630 0.00 0.00 0.00 4.35
602 608 9.638300 CAGATTAATTTGTACTAAATCAGCGAC 57.362 33.333 0.00 0.00 0.00 5.19
603 609 8.826710 CCAGATTAATTTGTACTAAATCAGCGA 58.173 33.333 5.36 0.00 0.00 4.93
604 610 8.826710 TCCAGATTAATTTGTACTAAATCAGCG 58.173 33.333 5.36 0.00 0.00 5.18
610 616 9.627123 CTCCCATCCAGATTAATTTGTACTAAA 57.373 33.333 5.36 0.00 0.00 1.85
611 617 8.217799 CCTCCCATCCAGATTAATTTGTACTAA 58.782 37.037 5.36 0.00 0.00 2.24
612 618 7.202186 CCCTCCCATCCAGATTAATTTGTACTA 60.202 40.741 5.36 0.00 0.00 1.82
613 619 6.410853 CCCTCCCATCCAGATTAATTTGTACT 60.411 42.308 5.36 0.00 0.00 2.73
614 620 5.770162 CCCTCCCATCCAGATTAATTTGTAC 59.230 44.000 5.36 0.00 0.00 2.90
615 621 5.674496 TCCCTCCCATCCAGATTAATTTGTA 59.326 40.000 5.36 0.00 0.00 2.41
616 622 4.482025 TCCCTCCCATCCAGATTAATTTGT 59.518 41.667 5.36 0.00 0.00 2.83
617 623 5.065613 TCCCTCCCATCCAGATTAATTTG 57.934 43.478 0.00 0.00 0.00 2.32
618 624 4.733988 ACTCCCTCCCATCCAGATTAATTT 59.266 41.667 0.00 0.00 0.00 1.82
619 625 4.319515 ACTCCCTCCCATCCAGATTAATT 58.680 43.478 0.00 0.00 0.00 1.40
620 626 3.959920 ACTCCCTCCCATCCAGATTAAT 58.040 45.455 0.00 0.00 0.00 1.40
621 627 3.438131 ACTCCCTCCCATCCAGATTAA 57.562 47.619 0.00 0.00 0.00 1.40
622 628 3.439558 GGTACTCCCTCCCATCCAGATTA 60.440 52.174 0.00 0.00 0.00 1.75
623 629 2.695585 GTACTCCCTCCCATCCAGATT 58.304 52.381 0.00 0.00 0.00 2.40
624 630 1.132689 GGTACTCCCTCCCATCCAGAT 60.133 57.143 0.00 0.00 0.00 2.90
625 631 0.264955 GGTACTCCCTCCCATCCAGA 59.735 60.000 0.00 0.00 0.00 3.86
626 632 2.841595 GGTACTCCCTCCCATCCAG 58.158 63.158 0.00 0.00 0.00 3.86
637 643 0.398098 TCGGGGAATGAGGGTACTCC 60.398 60.000 0.00 0.00 43.29 3.85
638 644 1.413077 CTTCGGGGAATGAGGGTACTC 59.587 57.143 0.00 0.00 44.23 2.59
639 645 1.007963 TCTTCGGGGAATGAGGGTACT 59.992 52.381 0.00 0.00 0.00 2.73
640 646 1.492764 TCTTCGGGGAATGAGGGTAC 58.507 55.000 0.00 0.00 0.00 3.34
641 647 2.489528 ATCTTCGGGGAATGAGGGTA 57.510 50.000 0.00 0.00 0.00 3.69
642 648 1.596496 AATCTTCGGGGAATGAGGGT 58.404 50.000 0.00 0.00 0.00 4.34
643 649 2.301346 CAAATCTTCGGGGAATGAGGG 58.699 52.381 0.00 0.00 0.00 4.30
644 650 2.945668 GACAAATCTTCGGGGAATGAGG 59.054 50.000 0.00 0.00 0.00 3.86
645 651 3.609853 TGACAAATCTTCGGGGAATGAG 58.390 45.455 0.00 0.00 0.00 2.90
693 699 9.548208 GCAAAACAGAATAAACTAGATCAGAAC 57.452 33.333 0.00 0.00 0.00 3.01
711 717 5.830912 TGACAAAATCTACCTGCAAAACAG 58.169 37.500 0.00 0.00 46.77 3.16
717 723 2.040278 AGCCTGACAAAATCTACCTGCA 59.960 45.455 0.00 0.00 0.00 4.41
727 733 0.817634 CCGTCACCAGCCTGACAAAA 60.818 55.000 0.00 0.00 40.67 2.44
746 752 2.351157 GCACAAGTGAATCACCTTCAGC 60.351 50.000 10.12 4.86 44.44 4.26
765 771 2.659016 CCTCTTCCAGCACGAGCA 59.341 61.111 7.77 0.00 45.49 4.26
773 779 2.941720 GCTAGACAATTGCCTCTTCCAG 59.058 50.000 5.05 0.00 0.00 3.86
794 800 1.151777 ACGCAGTGGTGACTTTGTCG 61.152 55.000 0.00 0.00 42.51 4.35
852 860 3.256631 GTGGAATGAAACCAGTCTGCAAT 59.743 43.478 0.00 0.00 38.14 3.56
936 944 3.131933 CAGATTGGTTCAGACTCGGAGAT 59.868 47.826 12.86 0.00 33.89 2.75
941 949 2.029020 TCCACAGATTGGTTCAGACTCG 60.029 50.000 0.00 0.00 46.97 4.18
960 969 7.449704 AGCCTGAATTTTTATGATGGTCTATCC 59.550 37.037 0.00 0.00 34.77 2.59
1013 1022 2.811431 TCATAACGCTGGGTCAAAACAG 59.189 45.455 0.00 0.00 37.76 3.16
1191 1203 1.143305 CATTCGGATGCCTCACGATC 58.857 55.000 0.00 0.00 36.43 3.69
1194 1206 0.652592 GAACATTCGGATGCCTCACG 59.347 55.000 2.75 0.00 36.72 4.35
1258 1270 3.495100 CCGCCTTTAGCATACTCCAGAAT 60.495 47.826 0.00 0.00 44.04 2.40
1367 1382 3.290948 AAACACCTCTACTGTGGCAAA 57.709 42.857 0.00 0.00 38.05 3.68
1571 1594 2.292267 CACAAGACCATACATCTGCCC 58.708 52.381 0.00 0.00 0.00 5.36
1695 1720 6.622462 GCTCTTTCAGCTCAGTGGAAAAATAG 60.622 42.308 0.00 0.00 45.83 1.73
1716 1741 3.359110 AGGATCCCATTAAGGAGCTCT 57.641 47.619 14.64 0.00 42.19 4.09
1785 1810 0.324943 CCGGCTTCCTATACCATGGG 59.675 60.000 18.09 0.00 0.00 4.00
1788 1813 2.368875 CTCAACCGGCTTCCTATACCAT 59.631 50.000 0.00 0.00 0.00 3.55
1836 1861 1.591059 AGCAGCTTCGCTCGCATAG 60.591 57.895 0.00 0.00 37.91 2.23
1887 1912 4.812476 TTCATGCTCGCCGGTCCG 62.812 66.667 3.60 3.60 0.00 4.79
2063 2091 5.487433 TCATCGCTCCATTGTCTTTCTTTA 58.513 37.500 0.00 0.00 0.00 1.85
2133 2161 2.477825 GCGAGCTCATAGATTTCTGCA 58.522 47.619 15.40 0.00 0.00 4.41
2199 2227 4.641396 TCAACAGTTTCTGGTACTCCATG 58.359 43.478 0.00 0.00 43.43 3.66
2294 2322 0.539051 CCACTGTGGATCCTGAGGTC 59.461 60.000 22.33 0.00 40.96 3.85
2438 2466 6.071952 GGTCTCACCATGAAATATGTGTGTTT 60.072 38.462 0.00 0.00 38.42 2.83
2754 2784 8.656849 ACAAACGCTGATAGTTTCTTAAGTATG 58.343 33.333 1.63 0.00 39.50 2.39
2781 2811 1.505353 GTTGCCACAGAGCATGCTC 59.495 57.895 35.57 35.57 43.64 4.26
2902 2935 3.222603 TCTTCCCTTTCAACAAGCCTTC 58.777 45.455 0.00 0.00 0.00 3.46
2903 2936 3.312736 TCTTCCCTTTCAACAAGCCTT 57.687 42.857 0.00 0.00 0.00 4.35
2904 2937 2.959030 GTTCTTCCCTTTCAACAAGCCT 59.041 45.455 0.00 0.00 0.00 4.58
2927 2960 6.693315 TTCTTCCTCGTCATTTTTGTTTCT 57.307 33.333 0.00 0.00 0.00 2.52
2938 2971 2.132762 GAAGCGTTTTCTTCCTCGTCA 58.867 47.619 0.00 0.00 37.17 4.35
3121 3166 4.329545 GACGCCACCAAGCAGGGA 62.330 66.667 0.10 0.00 43.89 4.20
3160 3205 2.698788 TAGGAGGGAGAGGGCCGA 60.699 66.667 0.00 0.00 0.00 5.54
3235 3280 1.446366 GACCCCTGGATACCGAAGC 59.554 63.158 0.00 0.00 0.00 3.86
3236 3281 0.754217 TCGACCCCTGGATACCGAAG 60.754 60.000 0.00 0.00 0.00 3.79
3237 3282 1.039233 GTCGACCCCTGGATACCGAA 61.039 60.000 3.51 0.00 0.00 4.30
3238 3283 1.454479 GTCGACCCCTGGATACCGA 60.454 63.158 3.51 0.00 0.00 4.69
3244 3289 2.439701 CGCTAGTCGACCCCTGGA 60.440 66.667 13.01 0.00 41.67 3.86
3285 3330 1.767036 CCAACCACCACCATCCAGA 59.233 57.895 0.00 0.00 0.00 3.86
3318 3363 0.469494 CATCACCATCCACCGGATCA 59.531 55.000 9.46 0.00 40.98 2.92
3319 3364 0.250467 CCATCACCATCCACCGGATC 60.250 60.000 9.46 0.00 40.98 3.36
3342 3403 4.489771 GACCACCCCTGCCATCGG 62.490 72.222 0.00 0.00 0.00 4.18
3367 3428 1.167851 CATCACCACCACCACATCAC 58.832 55.000 0.00 0.00 0.00 3.06
3394 3455 2.091112 CACCAGAGCAGCGAGAACG 61.091 63.158 0.00 0.00 42.93 3.95


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

AutoCloner maintained by Alex Coulton.