Multiple sequence alignment - TraesCS1D01G199600

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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 TraesCS1D01G199600 chr1D 100.000 5593 0 0 1 5593 282290139 282284547 0.000000e+00 10329.0
1 TraesCS1D01G199600 chr1A 97.734 4810 88 10 798 5593 354302847 354298045 0.000000e+00 8259.0
2 TraesCS1D01G199600 chr1A 95.532 470 18 3 1 467 354303928 354303459 0.000000e+00 749.0
3 TraesCS1D01G199600 chr1A 92.248 129 8 2 668 794 354303279 354303151 1.240000e-41 182.0
4 TraesCS1D01G199600 chr1B 95.885 2916 97 10 693 3595 383800122 383797217 0.000000e+00 4698.0
5 TraesCS1D01G199600 chr1B 97.799 1999 35 4 3600 5593 383797166 383795172 0.000000e+00 3439.0
6 TraesCS1D01G199600 chr1B 93.725 510 28 3 1 506 383800717 383800208 0.000000e+00 761.0
7 TraesCS1D01G199600 chr1B 100.000 29 0 0 474 502 304179240 304179268 3.000000e-03 54.7
8 TraesCS1D01G199600 chr7A 97.059 34 0 1 469 502 172205565 172205533 7.830000e-04 56.5
9 TraesCS1D01G199600 chr3D 96.970 33 1 0 470 502 591662323 591662291 7.830000e-04 56.5
10 TraesCS1D01G199600 chr2A 100.000 29 0 0 474 502 777041151 777041123 3.000000e-03 54.7
11 TraesCS1D01G199600 chr5D 100.000 28 0 0 475 502 480842375 480842348 1.000000e-02 52.8


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 TraesCS1D01G199600 chr1D 282284547 282290139 5592 True 10329.000000 10329 100.000000 1 5593 1 chr1D.!!$R1 5592
1 TraesCS1D01G199600 chr1A 354298045 354303928 5883 True 3063.333333 8259 95.171333 1 5593 3 chr1A.!!$R1 5592
2 TraesCS1D01G199600 chr1B 383795172 383800717 5545 True 2966.000000 4698 95.803000 1 5593 3 chr1B.!!$R1 5592

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
540 555 0.036010 AAGATCTTCACGCACCCCTG 60.036 55.0 0.88 0.00 0.00 4.45 F
547 562 0.105964 TCACGCACCCCTGTATATGC 59.894 55.0 0.00 0.00 34.66 3.14 F
660 675 0.305313 TGCACACTTTAACCGTTCGC 59.695 50.0 0.00 0.00 0.00 4.70 F
1782 2144 0.321298 TAAGCGAGGCCTGTCAAACC 60.321 55.0 12.00 0.00 0.00 3.27 F
1818 2180 0.390472 GTTCTGGCTCTTCTCCCACG 60.390 60.0 0.00 0.00 0.00 4.94 F
2643 3005 0.611618 TGGAAGGCGCCAATGTTCAT 60.612 50.0 31.54 0.76 34.31 2.57 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1812 2174 0.759812 TGTAAGTCACCACCGTGGGA 60.760 55.000 21.77 12.73 43.37 4.37 R
1815 2177 1.214367 GTGTGTAAGTCACCACCGTG 58.786 55.000 0.00 0.00 45.61 4.94 R
2298 2660 1.937223 CTTGTGACAACACTGCGGTAA 59.063 47.619 0.00 0.00 46.07 2.85 R
3186 3548 0.247736 ACTGCCTCATTCTCGGTGTC 59.752 55.000 0.00 0.00 0.00 3.67 R
3744 4156 3.126514 CACAATCTCTCGCATTTGAGCTT 59.873 43.478 0.00 0.00 35.90 3.74 R
4773 5190 5.726793 TGCCCCTCTAGACTTTCTATTTCTT 59.273 40.000 0.00 0.00 0.00 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
101 102 2.202810 GCAGAGGGCGTCACTAGC 60.203 66.667 10.15 4.31 0.00 3.42
143 145 2.107950 TCTGTAATCCAGCGGTTTGG 57.892 50.000 0.00 0.00 41.25 3.28
260 264 0.364515 GCTGCGTACGGTTTCTAACG 59.635 55.000 18.39 0.00 38.34 3.18
263 267 2.252747 TGCGTACGGTTTCTAACGATG 58.747 47.619 18.39 0.00 37.53 3.84
389 393 2.855570 GCATGCATCAATTTCGATCGCA 60.856 45.455 14.21 0.00 35.44 5.10
442 447 9.666626 CATACTCTATCTACTTGTAAAACCTCG 57.333 37.037 0.00 0.00 0.00 4.63
446 451 7.983307 TCTATCTACTTGTAAAACCTCGAGAC 58.017 38.462 15.71 3.91 0.00 3.36
447 452 5.039480 TCTACTTGTAAAACCTCGAGACG 57.961 43.478 15.71 0.00 0.00 4.18
455 460 2.080286 AACCTCGAGACGAAACCATG 57.920 50.000 15.71 0.00 34.74 3.66
462 467 2.411547 CGAGACGAAACCATGCAACTTC 60.412 50.000 0.00 0.00 0.00 3.01
467 472 2.095768 CGAAACCATGCAACTTCGACAT 60.096 45.455 14.13 0.00 42.44 3.06
490 497 8.079809 ACATATAGTAACAACAACAACAAAGCC 58.920 33.333 0.00 0.00 0.00 4.35
506 513 5.660460 ACAAAGCCTTTAGTTTCAACTTGG 58.340 37.500 0.00 0.47 40.37 3.61
507 514 5.186992 ACAAAGCCTTTAGTTTCAACTTGGT 59.813 36.000 0.00 0.00 40.37 3.67
508 515 5.932619 AAGCCTTTAGTTTCAACTTGGTT 57.067 34.783 0.00 0.00 40.37 3.67
509 516 7.093684 ACAAAGCCTTTAGTTTCAACTTGGTTA 60.094 33.333 0.00 0.00 40.37 2.85
510 517 6.635030 AGCCTTTAGTTTCAACTTGGTTAG 57.365 37.500 0.00 0.00 40.37 2.34
511 518 6.362248 AGCCTTTAGTTTCAACTTGGTTAGA 58.638 36.000 0.00 0.00 40.37 2.10
513 520 6.294010 GCCTTTAGTTTCAACTTGGTTAGAGG 60.294 42.308 0.00 0.00 40.37 3.69
515 522 7.255139 CCTTTAGTTTCAACTTGGTTAGAGGTG 60.255 40.741 0.00 0.00 40.37 4.00
516 523 3.883489 AGTTTCAACTTGGTTAGAGGTGC 59.117 43.478 0.00 0.00 35.21 5.01
529 544 5.301555 GTTAGAGGTGCCCATAAGATCTTC 58.698 45.833 12.24 0.00 0.00 2.87
530 545 3.387962 AGAGGTGCCCATAAGATCTTCA 58.612 45.455 12.24 0.00 0.00 3.02
531 546 3.135530 AGAGGTGCCCATAAGATCTTCAC 59.864 47.826 12.24 12.89 0.00 3.18
532 547 2.158900 AGGTGCCCATAAGATCTTCACG 60.159 50.000 12.24 1.46 0.00 4.35
533 548 1.599542 GTGCCCATAAGATCTTCACGC 59.400 52.381 12.24 10.12 0.00 5.34
534 549 1.209261 TGCCCATAAGATCTTCACGCA 59.791 47.619 12.24 12.55 0.00 5.24
537 552 2.213499 CCATAAGATCTTCACGCACCC 58.787 52.381 12.24 0.00 0.00 4.61
538 553 2.213499 CATAAGATCTTCACGCACCCC 58.787 52.381 12.24 0.00 0.00 4.95
540 555 0.036010 AAGATCTTCACGCACCCCTG 60.036 55.000 0.88 0.00 0.00 4.45
542 557 0.535335 GATCTTCACGCACCCCTGTA 59.465 55.000 0.00 0.00 0.00 2.74
543 558 1.139058 GATCTTCACGCACCCCTGTAT 59.861 52.381 0.00 0.00 0.00 2.29
546 561 2.102420 TCTTCACGCACCCCTGTATATG 59.898 50.000 0.00 0.00 0.00 1.78
547 562 0.105964 TCACGCACCCCTGTATATGC 59.894 55.000 0.00 0.00 34.66 3.14
556 571 4.348168 CACCCCTGTATATGCCTAGTCTTT 59.652 45.833 0.00 0.00 0.00 2.52
557 572 4.975794 ACCCCTGTATATGCCTAGTCTTTT 59.024 41.667 0.00 0.00 0.00 2.27
560 575 5.765182 CCCTGTATATGCCTAGTCTTTTTGG 59.235 44.000 0.00 0.00 0.00 3.28
561 576 6.357367 CCTGTATATGCCTAGTCTTTTTGGT 58.643 40.000 0.00 0.00 0.00 3.67
562 577 6.260936 CCTGTATATGCCTAGTCTTTTTGGTG 59.739 42.308 0.00 0.00 0.00 4.17
563 578 6.953101 TGTATATGCCTAGTCTTTTTGGTGA 58.047 36.000 0.00 0.00 0.00 4.02
564 579 7.573710 TGTATATGCCTAGTCTTTTTGGTGAT 58.426 34.615 0.00 0.00 0.00 3.06
565 580 8.710239 TGTATATGCCTAGTCTTTTTGGTGATA 58.290 33.333 0.00 0.00 0.00 2.15
566 581 9.726438 GTATATGCCTAGTCTTTTTGGTGATAT 57.274 33.333 0.00 0.00 0.00 1.63
568 583 7.961326 ATGCCTAGTCTTTTTGGTGATATTT 57.039 32.000 0.00 0.00 0.00 1.40
569 584 7.391148 TGCCTAGTCTTTTTGGTGATATTTC 57.609 36.000 0.00 0.00 0.00 2.17
570 585 6.945435 TGCCTAGTCTTTTTGGTGATATTTCA 59.055 34.615 0.00 0.00 0.00 2.69
571 586 7.121168 TGCCTAGTCTTTTTGGTGATATTTCAG 59.879 37.037 0.00 0.00 30.85 3.02
572 587 7.121315 GCCTAGTCTTTTTGGTGATATTTCAGT 59.879 37.037 0.00 0.00 30.85 3.41
573 588 8.669243 CCTAGTCTTTTTGGTGATATTTCAGTC 58.331 37.037 0.00 0.00 30.85 3.51
574 589 7.454260 AGTCTTTTTGGTGATATTTCAGTCC 57.546 36.000 0.00 0.00 30.85 3.85
575 590 7.234355 AGTCTTTTTGGTGATATTTCAGTCCT 58.766 34.615 0.00 0.00 30.85 3.85
576 591 7.725844 AGTCTTTTTGGTGATATTTCAGTCCTT 59.274 33.333 0.00 0.00 30.85 3.36
577 592 8.360390 GTCTTTTTGGTGATATTTCAGTCCTTT 58.640 33.333 0.00 0.00 30.85 3.11
578 593 9.581289 TCTTTTTGGTGATATTTCAGTCCTTTA 57.419 29.630 0.00 0.00 30.85 1.85
615 630 6.801862 CGGACTCTTTCATGTTAAATTTGGTC 59.198 38.462 0.00 0.00 0.00 4.02
616 631 7.308589 CGGACTCTTTCATGTTAAATTTGGTCT 60.309 37.037 0.00 0.00 0.00 3.85
629 644 6.911250 AAATTTGGTCTATCCCGAACTTTT 57.089 33.333 0.00 0.00 30.59 2.27
657 672 7.551262 TGATATTATCTGCACACTTTAACCGTT 59.449 33.333 5.33 0.00 0.00 4.44
660 675 0.305313 TGCACACTTTAACCGTTCGC 59.695 50.000 0.00 0.00 0.00 4.70
665 680 2.414138 ACACTTTAACCGTTCGCTATGC 59.586 45.455 0.00 0.00 0.00 3.14
680 715 3.495193 GCTATGCACATTGAATATGCCG 58.505 45.455 5.92 0.00 38.63 5.69
684 719 4.031418 TGCACATTGAATATGCCGAAAG 57.969 40.909 5.92 0.00 38.63 2.62
725 761 8.730680 TGGATAAGCTTCTTTGACAGATTTAAC 58.269 33.333 0.00 0.00 0.00 2.01
796 1133 7.645340 CCAGACAGTCAAAAGAAAATGTTACTG 59.355 37.037 2.66 0.00 39.14 2.74
903 1247 4.157958 CGGCGCTTGCTTGCTCTC 62.158 66.667 7.64 0.00 39.13 3.20
1173 1523 1.294780 CTTCTTCCTCTGGTGCGCT 59.705 57.895 9.73 0.00 0.00 5.92
1653 2015 2.033448 TGTTGCAGTAAGGCCGGG 59.967 61.111 2.18 0.00 0.00 5.73
1669 2031 2.742116 GGGACCATGGCCGAGCTAA 61.742 63.158 13.04 0.00 0.00 3.09
1714 2076 4.711949 CGGGCCAGCAGCTCACTT 62.712 66.667 4.39 0.00 45.13 3.16
1716 2078 2.033141 GGCCAGCAGCTCACTTCA 59.967 61.111 0.00 0.00 43.05 3.02
1765 2127 0.324943 GTGCAGTGAGGGAAGGCTAA 59.675 55.000 0.00 0.00 0.00 3.09
1766 2128 0.615331 TGCAGTGAGGGAAGGCTAAG 59.385 55.000 0.00 0.00 0.00 2.18
1777 2139 2.202946 GGCTAAGCGAGGCCTGTC 60.203 66.667 12.00 0.03 45.09 3.51
1782 2144 0.321298 TAAGCGAGGCCTGTCAAACC 60.321 55.000 12.00 0.00 0.00 3.27
1812 2174 1.004440 GGTGCGTTCTGGCTCTTCT 60.004 57.895 0.00 0.00 0.00 2.85
1815 2177 1.448717 GCGTTCTGGCTCTTCTCCC 60.449 63.158 0.00 0.00 0.00 4.30
1818 2180 0.390472 GTTCTGGCTCTTCTCCCACG 60.390 60.000 0.00 0.00 0.00 4.94
1916 2278 0.971959 ATGGCATCCAACGGTTGCAT 60.972 50.000 15.31 9.73 46.69 3.96
1920 2282 0.680921 CATCCAACGGTTGCATCCCT 60.681 55.000 15.31 0.00 0.00 4.20
2178 2540 1.425066 TGCAAGTCAGGGTTTCCATCT 59.575 47.619 0.00 0.00 34.83 2.90
2199 2561 4.640771 TGAAGCCCTTCAGTTCTACATT 57.359 40.909 6.62 0.00 43.90 2.71
2298 2660 4.411540 AGGATAGATCATGCAGTCAACCTT 59.588 41.667 0.00 0.00 0.00 3.50
2324 2686 2.033801 GCAGTGTTGTCACAAGCAATCT 59.966 45.455 0.00 0.00 46.01 2.40
2441 2803 6.616017 TGCGTCAAAATTATGCACTTGATAA 58.384 32.000 0.00 0.00 34.03 1.75
2502 2864 2.226437 TCATTTTGTTCAAGAGGCTCGC 59.774 45.455 9.22 0.00 0.00 5.03
2643 3005 0.611618 TGGAAGGCGCCAATGTTCAT 60.612 50.000 31.54 0.76 34.31 2.57
2721 3083 2.483877 CAGTTCGGCAACAGCTTTGATA 59.516 45.455 11.34 0.00 34.60 2.15
2918 3280 5.124457 ACAAGCTTGCTGTTTATGGTATCTG 59.876 40.000 26.27 0.00 0.00 2.90
3017 3379 8.680903 CACAGAGATCCTTGCTATAACATTTTT 58.319 33.333 0.00 0.00 0.00 1.94
3186 3548 4.678287 GTGAGACATGTGCAGTTTGATTTG 59.322 41.667 1.15 0.00 0.00 2.32
3260 3622 8.829612 TGACACAATGCTGATGTACTATATTTG 58.170 33.333 0.00 0.00 0.00 2.32
3344 3706 8.685838 TTGCAGGTATACTTTAGTTGTTTCTT 57.314 30.769 2.25 0.00 0.00 2.52
3445 3811 8.494347 GTTTGAACTATGCAATGCACAATTTTA 58.506 29.630 11.23 0.00 43.04 1.52
3446 3812 8.774890 TTGAACTATGCAATGCACAATTTTAT 57.225 26.923 11.23 0.00 43.04 1.40
3447 3813 8.774890 TGAACTATGCAATGCACAATTTTATT 57.225 26.923 11.23 0.00 43.04 1.40
3448 3814 9.217278 TGAACTATGCAATGCACAATTTTATTT 57.783 25.926 11.23 0.00 43.04 1.40
3605 4017 7.408910 TGTGCACAAACATTTCTATGATATCG 58.591 34.615 19.28 0.00 35.65 2.92
3744 4156 6.998074 AGAGTTGTGACCAAAGAATGACATTA 59.002 34.615 0.00 0.00 30.94 1.90
4727 5144 6.464222 CAATCCTTTGTAGTACCTGTGAAGA 58.536 40.000 0.00 0.00 0.00 2.87
4773 5190 6.317312 TGGTGAGTCTACTTTAGTAAGGGAA 58.683 40.000 0.00 0.00 35.61 3.97
5334 5751 2.042831 GGAAGCAGATGCCTTGCGT 61.043 57.895 0.14 0.00 43.38 5.24
5523 5940 2.429610 GTTAGCATACCGGTCAGAAGGA 59.570 50.000 12.40 0.00 0.00 3.36
5547 5964 1.434188 TGCCTTCAAACCTCTGAGGA 58.566 50.000 29.71 4.61 37.67 3.71
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
442 447 2.411547 CGAAGTTGCATGGTTTCGTCTC 60.412 50.000 11.74 0.00 38.03 3.36
446 451 1.262950 TGTCGAAGTTGCATGGTTTCG 59.737 47.619 13.05 13.05 42.61 3.46
447 452 3.559238 ATGTCGAAGTTGCATGGTTTC 57.441 42.857 0.00 0.00 0.00 2.78
455 460 7.285783 TGTTGTTACTATATGTCGAAGTTGC 57.714 36.000 0.00 0.00 0.00 4.17
462 467 9.313323 CTTTGTTGTTGTTGTTACTATATGTCG 57.687 33.333 0.00 0.00 0.00 4.35
467 472 7.811117 AGGCTTTGTTGTTGTTGTTACTATA 57.189 32.000 0.00 0.00 0.00 1.31
490 497 7.639945 CACCTCTAACCAAGTTGAAACTAAAG 58.360 38.462 3.87 0.00 38.57 1.85
513 520 1.599542 GCGTGAAGATCTTATGGGCAC 59.400 52.381 8.25 10.67 0.00 5.01
515 522 1.599542 GTGCGTGAAGATCTTATGGGC 59.400 52.381 8.25 10.19 0.00 5.36
516 523 2.213499 GGTGCGTGAAGATCTTATGGG 58.787 52.381 8.25 0.00 0.00 4.00
529 544 0.884704 GGCATATACAGGGGTGCGTG 60.885 60.000 0.00 0.00 38.43 5.34
530 545 1.054406 AGGCATATACAGGGGTGCGT 61.054 55.000 0.00 0.00 38.43 5.24
531 546 0.973632 TAGGCATATACAGGGGTGCG 59.026 55.000 0.00 0.00 38.43 5.34
532 547 1.978580 ACTAGGCATATACAGGGGTGC 59.021 52.381 0.00 0.00 36.88 5.01
533 548 3.511477 AGACTAGGCATATACAGGGGTG 58.489 50.000 0.00 0.00 0.00 4.61
534 549 3.925261 AGACTAGGCATATACAGGGGT 57.075 47.619 0.00 0.00 0.00 4.95
537 552 6.260936 CACCAAAAAGACTAGGCATATACAGG 59.739 42.308 0.00 0.00 0.00 4.00
538 553 7.047891 TCACCAAAAAGACTAGGCATATACAG 58.952 38.462 0.00 0.00 0.00 2.74
540 555 9.726438 ATATCACCAAAAAGACTAGGCATATAC 57.274 33.333 0.00 0.00 0.00 1.47
542 557 9.646522 AAATATCACCAAAAAGACTAGGCATAT 57.353 29.630 0.00 0.00 0.00 1.78
543 558 9.120538 GAAATATCACCAAAAAGACTAGGCATA 57.879 33.333 0.00 0.00 0.00 3.14
546 561 7.121315 ACTGAAATATCACCAAAAAGACTAGGC 59.879 37.037 0.00 0.00 0.00 3.93
547 562 8.567285 ACTGAAATATCACCAAAAAGACTAGG 57.433 34.615 0.00 0.00 0.00 3.02
586 601 9.672086 CAAATTTAACATGAAAGAGTCCGTAAA 57.328 29.630 0.00 0.00 0.00 2.01
587 602 8.293867 CCAAATTTAACATGAAAGAGTCCGTAA 58.706 33.333 0.00 0.00 0.00 3.18
588 603 7.446013 ACCAAATTTAACATGAAAGAGTCCGTA 59.554 33.333 0.00 0.00 0.00 4.02
589 604 6.264518 ACCAAATTTAACATGAAAGAGTCCGT 59.735 34.615 0.00 0.00 0.00 4.69
590 605 6.677913 ACCAAATTTAACATGAAAGAGTCCG 58.322 36.000 0.00 0.00 0.00 4.79
591 606 7.886338 AGACCAAATTTAACATGAAAGAGTCC 58.114 34.615 0.00 0.00 0.00 3.85
595 610 8.966868 GGGATAGACCAAATTTAACATGAAAGA 58.033 33.333 0.00 0.00 41.20 2.52
596 611 7.915397 CGGGATAGACCAAATTTAACATGAAAG 59.085 37.037 0.00 0.00 41.20 2.62
597 612 7.612244 TCGGGATAGACCAAATTTAACATGAAA 59.388 33.333 0.00 0.00 41.20 2.69
605 620 8.411991 AAAAAGTTCGGGATAGACCAAATTTA 57.588 30.769 0.00 0.00 41.20 1.40
629 644 8.394877 CGGTTAAAGTGTGCAGATAATATCAAA 58.605 33.333 2.84 0.00 0.00 2.69
640 655 1.659211 GCGAACGGTTAAAGTGTGCAG 60.659 52.381 0.00 0.00 0.00 4.41
641 656 0.305313 GCGAACGGTTAAAGTGTGCA 59.695 50.000 0.00 0.00 0.00 4.57
646 661 2.414138 GTGCATAGCGAACGGTTAAAGT 59.586 45.455 3.96 0.00 0.00 2.66
647 662 2.413796 TGTGCATAGCGAACGGTTAAAG 59.586 45.455 3.96 0.00 0.00 1.85
652 667 0.726827 CAATGTGCATAGCGAACGGT 59.273 50.000 4.11 4.11 0.00 4.83
654 669 2.804421 TTCAATGTGCATAGCGAACG 57.196 45.000 0.00 0.00 0.00 3.95
657 672 4.408993 GCATATTCAATGTGCATAGCGA 57.591 40.909 13.85 0.00 45.37 4.93
688 723 4.872691 AGAAGCTTATCCAACATCGTTGAG 59.127 41.667 0.00 0.00 0.00 3.02
738 774 6.156748 ACATTGATGGATCATTTCACATGG 57.843 37.500 0.00 0.00 36.56 3.66
796 1133 3.194116 TCCCAAATACGAGTACTGGACAC 59.806 47.826 12.28 0.00 0.00 3.67
891 1235 0.612229 TGGAGAGGAGAGCAAGCAAG 59.388 55.000 0.00 0.00 0.00 4.01
903 1247 2.353357 TGCCTAATTGCATGGAGAGG 57.647 50.000 7.33 7.33 36.04 3.69
923 1267 2.555448 CGGGGAGGAGCTCAGTGATATA 60.555 54.545 17.19 0.00 31.08 0.86
1488 1850 1.591183 GTAGTTGGGCGACGGGTTA 59.409 57.895 0.00 0.00 0.00 2.85
1653 2015 1.510480 GCATTAGCTCGGCCATGGTC 61.510 60.000 14.67 10.70 37.91 4.02
1669 2031 1.434622 GCATACGACAGCAGCTGCAT 61.435 55.000 38.24 26.73 45.16 3.96
1714 2076 1.005037 GACACGTCCACATGGCTGA 60.005 57.895 0.00 0.00 34.44 4.26
1716 2078 1.293498 GAGACACGTCCACATGGCT 59.707 57.895 0.00 0.00 36.68 4.75
1765 2127 2.032681 GGTTTGACAGGCCTCGCT 59.967 61.111 0.00 0.00 0.00 4.93
1766 2128 3.056328 GGGTTTGACAGGCCTCGC 61.056 66.667 0.00 0.00 0.00 5.03
1777 2139 2.168313 GCACCATATTTCCCAGGGTTTG 59.832 50.000 5.01 0.00 0.00 2.93
1782 2144 1.676006 GAACGCACCATATTTCCCAGG 59.324 52.381 0.00 0.00 0.00 4.45
1812 2174 0.759812 TGTAAGTCACCACCGTGGGA 60.760 55.000 21.77 12.73 43.37 4.37
1815 2177 1.214367 GTGTGTAAGTCACCACCGTG 58.786 55.000 0.00 0.00 45.61 4.94
1916 2278 7.446106 ACATTATACATAACAAGGTCAGGGA 57.554 36.000 0.00 0.00 0.00 4.20
2178 2540 4.041567 TCAATGTAGAACTGAAGGGCTTCA 59.958 41.667 0.00 0.00 46.27 3.02
2199 2561 4.544683 TGATGCCCAAACCAATCATATCA 58.455 39.130 0.00 0.00 0.00 2.15
2298 2660 1.937223 CTTGTGACAACACTGCGGTAA 59.063 47.619 0.00 0.00 46.07 2.85
2502 2864 6.000891 TCCTTCATCTTGTCAAACAAATCG 57.999 37.500 0.00 0.00 37.69 3.34
2643 3005 6.239204 CCACGTTGAATGAGGTACTATCCATA 60.239 42.308 0.00 0.00 41.55 2.74
2721 3083 5.108187 TGCCTAGATTGAGCATTTCTCTT 57.892 39.130 0.00 0.00 42.38 2.85
2900 3262 4.588899 AGTGCAGATACCATAAACAGCAA 58.411 39.130 0.00 0.00 32.03 3.91
2918 3280 8.741101 TTGTATCAATTACATCACAAAAGTGC 57.259 30.769 0.00 0.00 40.46 4.40
3017 3379 2.282180 GTTGGGCGCTTCAAGGGA 60.282 61.111 7.64 0.00 0.00 4.20
3186 3548 0.247736 ACTGCCTCATTCTCGGTGTC 59.752 55.000 0.00 0.00 0.00 3.67
3260 3622 7.631717 AAATCATTTAGGTGTAAGCCTCTTC 57.368 36.000 0.00 0.00 39.94 2.87
3302 3664 6.393171 ACCTGCAATTTCTTTCAAATCTAGC 58.607 36.000 0.00 0.00 0.00 3.42
3398 3760 9.647797 TCAAACTTATGTAACGATGATACACTT 57.352 29.630 0.00 0.00 36.19 3.16
3454 3820 7.093945 TGGGAAATTCCTAAACTGCAAATAGTC 60.094 37.037 12.28 0.00 36.57 2.59
3532 3898 9.472361 GATAGTGCTAAAACGGATACAGAAATA 57.528 33.333 0.00 0.00 0.00 1.40
3581 3947 6.358030 GCGATATCATAGAAATGTTTGTGCAC 59.642 38.462 10.75 10.75 34.50 4.57
3605 4017 4.101741 ACCACTCCTATTCAGACCAATAGC 59.898 45.833 0.00 0.00 35.70 2.97
3744 4156 3.126514 CACAATCTCTCGCATTTGAGCTT 59.873 43.478 0.00 0.00 35.90 3.74
4773 5190 5.726793 TGCCCCTCTAGACTTTCTATTTCTT 59.273 40.000 0.00 0.00 0.00 2.52
5523 5940 4.015084 CTCAGAGGTTTGAAGGCATTGAT 58.985 43.478 0.00 0.00 0.00 2.57


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

AutoCloner maintained by Alex Coulton.