Multiple sequence alignment - TraesCS2A01G312000

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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 TraesCS2A01G312000 chr2A 100.000 2441 0 0 1 2441 535737913 535740353 0.000000e+00 4508
1 TraesCS2A01G312000 chr2D 92.751 1145 44 16 788 1932 398507746 398508851 0.000000e+00 1618
2 TraesCS2A01G312000 chr2D 93.225 679 30 7 40 708 398507074 398507746 0.000000e+00 985
3 TraesCS2A01G312000 chr2D 94.508 437 10 1 1931 2353 398509957 398510393 0.000000e+00 662
4 TraesCS2A01G312000 chr2B 90.587 903 53 14 788 1673 471436348 471435461 0.000000e+00 1168
5 TraesCS2A01G312000 chr2B 86.226 726 46 23 3 699 471437050 471436350 0.000000e+00 737
6 TraesCS2A01G312000 chr2B 90.000 410 37 3 1839 2244 471435363 471434954 5.980000e-146 527
7 TraesCS2A01G312000 chr4A 97.727 88 2 0 703 790 743279139 743279052 4.200000e-33 152
8 TraesCS2A01G312000 chr7A 97.701 87 2 0 703 789 321626504 321626418 1.510000e-32 150
9 TraesCS2A01G312000 chr7A 93.878 98 3 3 697 793 173487556 173487651 7.030000e-31 145
10 TraesCS2A01G312000 chr7A 93.000 100 6 1 695 794 556151907 556152005 7.030000e-31 145
11 TraesCS2A01G312000 chr5A 94.845 97 4 1 697 793 78157218 78157123 1.510000e-32 150
12 TraesCS2A01G312000 chr5A 91.346 104 6 3 703 806 477706782 477706682 3.270000e-29 139
13 TraesCS2A01G312000 chr4D 97.701 87 2 0 703 789 446912623 446912537 1.510000e-32 150
14 TraesCS2A01G312000 chr3A 95.699 93 4 0 697 789 697737663 697737755 1.510000e-32 150
15 TraesCS2A01G312000 chr5B 94.792 96 3 2 701 795 371270674 371270580 5.440000e-32 148


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 TraesCS2A01G312000 chr2A 535737913 535740353 2440 False 4508.000000 4508 100.000000 1 2441 1 chr2A.!!$F1 2440
1 TraesCS2A01G312000 chr2D 398507074 398510393 3319 False 1088.333333 1618 93.494667 40 2353 3 chr2D.!!$F1 2313
2 TraesCS2A01G312000 chr2B 471434954 471437050 2096 True 810.666667 1168 88.937667 3 2244 3 chr2B.!!$R1 2241

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
970 1021 0.039437 TCGTCACGGAAAGAGCAGAC 60.039 55.0 0.0 0.0 0.0 3.51 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2353 3545 0.459237 ATCTGCTTCAGAAGACGCGG 60.459 55.0 14.86 4.9 44.04 6.46 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
33 34 3.415087 ACTGCATCCAGCCCTCCC 61.415 66.667 0.00 0.00 43.02 4.30
34 35 3.095163 CTGCATCCAGCCCTCCCT 61.095 66.667 0.00 0.00 44.83 4.20
35 36 2.614969 TGCATCCAGCCCTCCCTT 60.615 61.111 0.00 0.00 44.83 3.95
36 37 2.220786 CTGCATCCAGCCCTCCCTTT 62.221 60.000 0.00 0.00 44.83 3.11
37 38 1.454663 GCATCCAGCCCTCCCTTTC 60.455 63.158 0.00 0.00 37.23 2.62
38 39 1.228510 CATCCAGCCCTCCCTTTCC 59.771 63.158 0.00 0.00 0.00 3.13
47 48 3.682292 CTCCCTTTCCCCGCCTTCG 62.682 68.421 0.00 0.00 0.00 3.79
213 215 3.194116 TCGGTTTCACCAGGTAGACATAC 59.806 47.826 0.00 0.00 38.47 2.39
214 216 3.056393 CGGTTTCACCAGGTAGACATACA 60.056 47.826 0.00 0.00 38.47 2.29
215 217 4.251268 GGTTTCACCAGGTAGACATACAC 58.749 47.826 0.00 0.00 38.42 2.90
216 218 4.262721 GGTTTCACCAGGTAGACATACACA 60.263 45.833 0.00 0.00 38.42 3.72
243 245 4.953269 TCGATTTTTACGTTGACATCTGC 58.047 39.130 0.00 0.00 0.00 4.26
312 319 5.733226 TGCTTACATACATACACATGTGC 57.267 39.130 25.68 7.36 45.17 4.57
531 569 7.065443 CCTGTTTACTCGTAGGAAAATTTAGGG 59.935 40.741 0.00 0.00 31.91 3.53
620 658 6.180472 TCCCTTTTTCTATGGCTTTACAGAG 58.820 40.000 0.00 0.00 0.00 3.35
707 748 5.839606 AGGAAAAGACTGGTTACTGAGTACT 59.160 40.000 0.00 0.00 0.00 2.73
708 749 6.015265 AGGAAAAGACTGGTTACTGAGTACTC 60.015 42.308 16.32 16.32 0.00 2.59
709 750 5.725325 AAAGACTGGTTACTGAGTACTCC 57.275 43.478 20.11 4.76 0.00 3.85
710 751 3.699413 AGACTGGTTACTGAGTACTCCC 58.301 50.000 20.11 13.43 0.00 4.30
711 752 3.334280 AGACTGGTTACTGAGTACTCCCT 59.666 47.826 20.11 7.46 0.00 4.20
712 753 3.695556 GACTGGTTACTGAGTACTCCCTC 59.304 52.174 20.11 4.83 0.00 4.30
713 754 3.334280 ACTGGTTACTGAGTACTCCCTCT 59.666 47.826 20.11 2.56 32.50 3.69
714 755 3.697045 CTGGTTACTGAGTACTCCCTCTG 59.303 52.174 20.11 7.70 36.71 3.35
715 756 3.075582 TGGTTACTGAGTACTCCCTCTGT 59.924 47.826 20.11 12.51 43.42 3.41
716 757 4.290459 TGGTTACTGAGTACTCCCTCTGTA 59.710 45.833 20.11 11.65 41.85 2.74
717 758 5.222192 TGGTTACTGAGTACTCCCTCTGTAA 60.222 44.000 20.11 15.92 45.57 2.41
719 760 6.830873 TTACTGAGTACTCCCTCTGTAAAC 57.169 41.667 20.11 0.00 45.18 2.01
720 761 5.000570 ACTGAGTACTCCCTCTGTAAACT 57.999 43.478 20.11 0.00 40.52 2.66
721 762 6.137104 ACTGAGTACTCCCTCTGTAAACTA 57.863 41.667 20.11 0.00 40.52 2.24
722 763 6.550163 ACTGAGTACTCCCTCTGTAAACTAA 58.450 40.000 20.11 0.00 40.52 2.24
723 764 7.183460 ACTGAGTACTCCCTCTGTAAACTAAT 58.817 38.462 20.11 0.00 40.52 1.73
724 765 8.334734 ACTGAGTACTCCCTCTGTAAACTAATA 58.665 37.037 20.11 0.00 40.52 0.98
725 766 9.357161 CTGAGTACTCCCTCTGTAAACTAATAT 57.643 37.037 20.11 0.00 32.50 1.28
785 826 8.777578 TGCTCTTATATTAGTTTACAGAGGGA 57.222 34.615 0.00 0.00 0.00 4.20
786 827 8.861086 TGCTCTTATATTAGTTTACAGAGGGAG 58.139 37.037 0.00 0.00 0.00 4.30
792 833 8.785184 ATATTAGTTTACAGAGGGAGTAGCTT 57.215 34.615 0.00 0.00 0.00 3.74
908 955 0.106708 ACCAAAGCTGCTTCGACTCA 59.893 50.000 16.28 0.00 0.00 3.41
970 1021 0.039437 TCGTCACGGAAAGAGCAGAC 60.039 55.000 0.00 0.00 0.00 3.51
990 1043 5.008415 CAGACAGAGGTATCAAATTCCATGC 59.992 44.000 0.00 0.00 0.00 4.06
1029 1082 2.079925 AGCGCAAGAAATGAGTCTTCC 58.920 47.619 11.47 0.00 35.63 3.46
1157 1210 3.823330 GTCGTCGTCATCGCCCCT 61.823 66.667 0.00 0.00 36.96 4.79
1179 1232 1.811266 CATGGTTCTGCCGTCCGAG 60.811 63.158 0.00 0.00 41.21 4.63
1467 1520 7.854557 AACTAGTACGTCCTTTTCTTGTTTT 57.145 32.000 0.00 0.00 0.00 2.43
1520 1574 4.646040 TGGAATCAAGTTTATGCCCATCAG 59.354 41.667 0.00 0.00 0.00 2.90
1530 1584 0.991146 TGCCCATCAGTTGAAGCCTA 59.009 50.000 0.00 0.00 0.00 3.93
1553 1607 0.965866 GGTACCTGCTGCTTTTCCCC 60.966 60.000 4.06 0.00 0.00 4.81
1554 1608 0.965866 GTACCTGCTGCTTTTCCCCC 60.966 60.000 0.00 0.00 0.00 5.40
1568 1622 6.159751 TGCTTTTCCCCCTATACTAAATGAGT 59.840 38.462 0.00 0.00 42.69 3.41
1659 1713 6.697455 GCCTTCTTTATTAACTATGCTTTGCC 59.303 38.462 0.00 0.00 0.00 4.52
1681 1735 6.136071 GCCATATTAGCACGAAACATTGTAG 58.864 40.000 0.00 0.00 0.00 2.74
1684 1738 8.273557 CCATATTAGCACGAAACATTGTAGTAC 58.726 37.037 0.00 0.00 0.00 2.73
1685 1739 8.813282 CATATTAGCACGAAACATTGTAGTACA 58.187 33.333 0.00 0.00 0.00 2.90
1687 1741 5.591643 AGCACGAAACATTGTAGTACAAG 57.408 39.130 19.87 14.08 41.94 3.16
1688 1742 4.451096 AGCACGAAACATTGTAGTACAAGG 59.549 41.667 22.57 22.57 44.54 3.61
1689 1743 4.449743 GCACGAAACATTGTAGTACAAGGA 59.550 41.667 28.96 5.21 41.91 3.36
1690 1744 5.389516 GCACGAAACATTGTAGTACAAGGAG 60.390 44.000 28.96 18.79 41.91 3.69
1693 1747 6.590292 ACGAAACATTGTAGTACAAGGAGATG 59.410 38.462 28.96 19.43 41.91 2.90
1694 1748 6.811665 CGAAACATTGTAGTACAAGGAGATGA 59.188 38.462 28.96 2.31 41.91 2.92
1695 1749 7.330946 CGAAACATTGTAGTACAAGGAGATGAA 59.669 37.037 28.96 1.60 41.91 2.57
1696 1750 9.167311 GAAACATTGTAGTACAAGGAGATGAAT 57.833 33.333 28.96 12.73 41.91 2.57
1697 1751 9.520515 AAACATTGTAGTACAAGGAGATGAATT 57.479 29.630 28.96 15.06 41.91 2.17
1698 1752 9.520515 AACATTGTAGTACAAGGAGATGAATTT 57.479 29.630 28.96 11.19 41.91 1.82
1702 1756 7.833786 TGTAGTACAAGGAGATGAATTTACGT 58.166 34.615 0.00 0.00 0.00 3.57
1703 1757 8.959548 TGTAGTACAAGGAGATGAATTTACGTA 58.040 33.333 0.00 0.00 0.00 3.57
1704 1758 9.962783 GTAGTACAAGGAGATGAATTTACGTAT 57.037 33.333 0.00 0.00 0.00 3.06
1706 1760 9.886132 AGTACAAGGAGATGAATTTACGTATTT 57.114 29.630 0.00 0.00 0.00 1.40
1787 1854 1.480954 TCACTATGGTTCGAGGCTTCC 59.519 52.381 0.00 0.00 0.00 3.46
1800 1867 0.610232 GGCTTCCAGCACCTGATTGT 60.610 55.000 0.00 0.00 44.75 2.71
1801 1868 0.524862 GCTTCCAGCACCTGATTGTG 59.475 55.000 0.00 0.00 41.89 3.33
1802 1869 1.883638 GCTTCCAGCACCTGATTGTGA 60.884 52.381 0.00 0.00 41.89 3.58
1805 1872 3.159213 TCCAGCACCTGATTGTGAAAT 57.841 42.857 0.00 0.00 38.55 2.17
1806 1873 3.499338 TCCAGCACCTGATTGTGAAATT 58.501 40.909 0.00 0.00 38.55 1.82
1810 1877 6.041409 TCCAGCACCTGATTGTGAAATTTTTA 59.959 34.615 0.00 0.00 38.55 1.52
1812 1879 7.388500 CCAGCACCTGATTGTGAAATTTTTATT 59.612 33.333 0.00 0.00 38.55 1.40
1813 1880 9.421806 CAGCACCTGATTGTGAAATTTTTATTA 57.578 29.630 0.00 0.00 38.55 0.98
1874 1941 3.808728 TCTTGTGATACCAGGCAATAGC 58.191 45.455 0.00 0.00 41.10 2.97
1877 1944 4.235079 TGTGATACCAGGCAATAGCTTT 57.765 40.909 0.00 0.00 41.70 3.51
2020 3194 4.022068 TCAGCAACTTGTTTTCCCATGATC 60.022 41.667 0.00 0.00 0.00 2.92
2047 3223 0.165295 CTGCGACAGTGTCAAGCATG 59.835 55.000 22.66 13.61 37.20 4.06
2175 3352 2.187163 GCTAGTGGCTTCCGGTCC 59.813 66.667 0.00 1.92 38.06 4.46
2357 3549 2.259618 GTATGTAGATGCATACCCGCG 58.740 52.381 0.00 0.00 43.09 6.46
2358 3550 0.679505 ATGTAGATGCATACCCGCGT 59.320 50.000 4.92 0.00 33.35 6.01
2359 3551 0.031585 TGTAGATGCATACCCGCGTC 59.968 55.000 4.92 0.00 46.32 5.19
2361 3553 4.438346 GATGCATACCCGCGTCTT 57.562 55.556 4.92 0.00 43.30 3.01
2362 3554 2.226269 GATGCATACCCGCGTCTTC 58.774 57.895 4.92 0.00 43.30 2.87
2363 3555 0.249489 GATGCATACCCGCGTCTTCT 60.249 55.000 4.92 0.00 43.30 2.85
2364 3556 0.530650 ATGCATACCCGCGTCTTCTG 60.531 55.000 4.92 0.00 33.35 3.02
2365 3557 1.141019 GCATACCCGCGTCTTCTGA 59.859 57.895 4.92 0.00 0.00 3.27
2366 3558 0.459585 GCATACCCGCGTCTTCTGAA 60.460 55.000 4.92 0.00 0.00 3.02
2367 3559 1.560923 CATACCCGCGTCTTCTGAAG 58.439 55.000 11.18 11.18 0.00 3.02
2368 3560 0.179108 ATACCCGCGTCTTCTGAAGC 60.179 55.000 12.54 7.08 42.76 3.86
2369 3561 1.529152 TACCCGCGTCTTCTGAAGCA 61.529 55.000 12.54 0.00 45.66 3.91
2370 3562 2.097038 CCCGCGTCTTCTGAAGCAG 61.097 63.158 12.54 9.54 45.66 4.24
2371 3563 1.080501 CCGCGTCTTCTGAAGCAGA 60.081 57.895 12.54 0.00 45.66 4.26
2372 3564 0.459237 CCGCGTCTTCTGAAGCAGAT 60.459 55.000 12.54 0.00 45.66 2.90
2373 3565 0.919981 CGCGTCTTCTGAAGCAGATC 59.080 55.000 12.54 0.00 45.66 2.75
2374 3566 1.285578 GCGTCTTCTGAAGCAGATCC 58.714 55.000 12.54 0.00 44.93 3.36
2375 3567 1.134848 GCGTCTTCTGAAGCAGATCCT 60.135 52.381 12.54 0.00 44.93 3.24
2376 3568 2.808244 CGTCTTCTGAAGCAGATCCTC 58.192 52.381 12.54 0.00 40.39 3.71
2377 3569 2.481104 CGTCTTCTGAAGCAGATCCTCC 60.481 54.545 12.54 0.00 40.39 4.30
2378 3570 2.499289 GTCTTCTGAAGCAGATCCTCCA 59.501 50.000 12.54 0.00 40.39 3.86
2379 3571 3.055530 GTCTTCTGAAGCAGATCCTCCAA 60.056 47.826 12.54 0.00 40.39 3.53
2380 3572 3.584406 TCTTCTGAAGCAGATCCTCCAAA 59.416 43.478 12.54 0.00 40.39 3.28
2381 3573 3.340814 TCTGAAGCAGATCCTCCAAAC 57.659 47.619 0.00 0.00 35.39 2.93
2382 3574 2.909006 TCTGAAGCAGATCCTCCAAACT 59.091 45.455 0.00 0.00 35.39 2.66
2383 3575 3.008330 CTGAAGCAGATCCTCCAAACTG 58.992 50.000 0.00 0.00 32.44 3.16
2384 3576 2.290514 TGAAGCAGATCCTCCAAACTGG 60.291 50.000 0.00 0.00 39.43 4.00
2385 3577 1.366319 AGCAGATCCTCCAAACTGGT 58.634 50.000 0.00 0.00 39.03 4.00
2386 3578 1.707427 AGCAGATCCTCCAAACTGGTT 59.293 47.619 0.00 0.00 39.03 3.67
2387 3579 2.108952 AGCAGATCCTCCAAACTGGTTT 59.891 45.455 0.00 0.00 39.03 3.27
2388 3580 3.330701 AGCAGATCCTCCAAACTGGTTTA 59.669 43.478 0.00 0.00 39.03 2.01
2389 3581 3.691609 GCAGATCCTCCAAACTGGTTTAG 59.308 47.826 0.00 0.00 39.03 1.85
2390 3582 3.691609 CAGATCCTCCAAACTGGTTTAGC 59.308 47.826 0.00 0.00 39.03 3.09
2391 3583 3.589288 AGATCCTCCAAACTGGTTTAGCT 59.411 43.478 0.00 0.00 39.03 3.32
2392 3584 3.140325 TCCTCCAAACTGGTTTAGCTG 57.860 47.619 0.00 0.00 39.03 4.24
2393 3585 2.708861 TCCTCCAAACTGGTTTAGCTGA 59.291 45.455 0.00 0.00 39.03 4.26
2394 3586 3.137544 TCCTCCAAACTGGTTTAGCTGAA 59.862 43.478 0.00 0.00 39.03 3.02
2395 3587 3.253432 CCTCCAAACTGGTTTAGCTGAAC 59.747 47.826 12.74 12.74 39.03 3.18
2397 3589 2.296190 CCAAACTGGTTTAGCTGAACCC 59.704 50.000 31.18 17.25 46.85 4.11
2398 3590 3.222603 CAAACTGGTTTAGCTGAACCCT 58.777 45.455 31.18 17.31 46.85 4.34
2399 3591 4.394729 CAAACTGGTTTAGCTGAACCCTA 58.605 43.478 31.18 16.82 46.85 3.53
2400 3592 3.983044 ACTGGTTTAGCTGAACCCTAG 57.017 47.619 31.18 25.30 46.85 3.02
2401 3593 3.248888 ACTGGTTTAGCTGAACCCTAGT 58.751 45.455 31.18 25.85 46.85 2.57
2402 3594 4.422984 ACTGGTTTAGCTGAACCCTAGTA 58.577 43.478 31.18 15.53 46.85 1.82
2403 3595 4.842380 ACTGGTTTAGCTGAACCCTAGTAA 59.158 41.667 31.18 14.89 46.85 2.24
2404 3596 5.046520 ACTGGTTTAGCTGAACCCTAGTAAG 60.047 44.000 31.18 23.52 46.85 2.34
2405 3597 4.842380 TGGTTTAGCTGAACCCTAGTAAGT 59.158 41.667 31.18 0.00 46.85 2.24
2406 3598 6.018469 TGGTTTAGCTGAACCCTAGTAAGTA 58.982 40.000 31.18 11.64 46.85 2.24
2407 3599 6.154021 TGGTTTAGCTGAACCCTAGTAAGTAG 59.846 42.308 31.18 0.00 46.85 2.57
2408 3600 8.723682 TGGTTTAGCTGAACCCTAGTAAGTAGG 61.724 44.444 31.18 0.00 46.85 3.18
2409 3601 4.334208 AGCTGAACCCTAGTAAGTAGGT 57.666 45.455 3.53 0.00 46.66 3.08
2410 3602 4.685807 AGCTGAACCCTAGTAAGTAGGTT 58.314 43.478 3.53 0.00 46.66 3.50
2411 3603 4.710865 AGCTGAACCCTAGTAAGTAGGTTC 59.289 45.833 15.55 15.55 46.66 3.62
2412 3604 4.439837 GCTGAACCCTAGTAAGTAGGTTCG 60.440 50.000 16.65 13.42 46.66 3.95
2413 3605 4.019174 TGAACCCTAGTAAGTAGGTTCGG 58.981 47.826 16.65 0.00 46.66 4.30
2414 3606 3.746792 ACCCTAGTAAGTAGGTTCGGT 57.253 47.619 3.53 0.00 46.66 4.69
2415 3607 4.053009 ACCCTAGTAAGTAGGTTCGGTT 57.947 45.455 3.53 0.00 46.66 4.44
2416 3608 4.420206 ACCCTAGTAAGTAGGTTCGGTTT 58.580 43.478 3.53 0.00 46.66 3.27
2417 3609 4.840680 ACCCTAGTAAGTAGGTTCGGTTTT 59.159 41.667 3.53 0.00 46.66 2.43
2418 3610 6.016555 ACCCTAGTAAGTAGGTTCGGTTTTA 58.983 40.000 3.53 0.00 46.66 1.52
2419 3611 6.669591 ACCCTAGTAAGTAGGTTCGGTTTTAT 59.330 38.462 3.53 0.00 46.66 1.40
2420 3612 7.180946 ACCCTAGTAAGTAGGTTCGGTTTTATT 59.819 37.037 3.53 0.00 46.66 1.40
2421 3613 8.043113 CCCTAGTAAGTAGGTTCGGTTTTATTT 58.957 37.037 3.53 0.00 46.66 1.40
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
33 34 0.605589 AAGAACGAAGGCGGGGAAAG 60.606 55.000 0.00 0.00 43.17 2.62
34 35 0.179012 AAAGAACGAAGGCGGGGAAA 60.179 50.000 0.00 0.00 43.17 3.13
35 36 0.179012 AAAAGAACGAAGGCGGGGAA 60.179 50.000 0.00 0.00 43.17 3.97
36 37 0.179012 AAAAAGAACGAAGGCGGGGA 60.179 50.000 0.00 0.00 43.17 4.81
37 38 0.240145 GAAAAAGAACGAAGGCGGGG 59.760 55.000 0.00 0.00 43.17 5.73
38 39 1.235724 AGAAAAAGAACGAAGGCGGG 58.764 50.000 0.00 0.00 43.17 6.13
47 48 5.704978 AGATGAGAGCAGGAAGAAAAAGAAC 59.295 40.000 0.00 0.00 0.00 3.01
146 148 1.679680 CTGGGCATCAAGCTTGGTATG 59.320 52.381 25.73 21.92 44.79 2.39
213 215 5.058008 GTCAACGTAAAAATCGAAGCATGTG 59.942 40.000 0.00 0.00 0.00 3.21
214 216 5.144359 GTCAACGTAAAAATCGAAGCATGT 58.856 37.500 0.00 0.00 0.00 3.21
215 217 5.143660 TGTCAACGTAAAAATCGAAGCATG 58.856 37.500 0.00 0.00 0.00 4.06
216 218 5.351233 TGTCAACGTAAAAATCGAAGCAT 57.649 34.783 0.00 0.00 0.00 3.79
243 245 9.842775 AAATAGATATACCATCACATGCATAGG 57.157 33.333 0.00 0.00 0.00 2.57
257 264 7.781548 ACACACCGACAAAAATAGATATACC 57.218 36.000 0.00 0.00 0.00 2.73
312 319 1.269166 ACTGATTACGAGCTTTCGCG 58.731 50.000 0.00 0.00 42.32 5.87
390 421 9.474313 AGGTAGGACAAAAATAGCAATCAAATA 57.526 29.630 0.00 0.00 0.00 1.40
391 422 8.366359 AGGTAGGACAAAAATAGCAATCAAAT 57.634 30.769 0.00 0.00 0.00 2.32
759 800 9.381038 TCCCTCTGTAAACTAATATAAGAGCAT 57.619 33.333 0.00 0.00 0.00 3.79
760 801 8.777578 TCCCTCTGTAAACTAATATAAGAGCA 57.222 34.615 0.00 0.00 0.00 4.26
761 802 8.862085 ACTCCCTCTGTAAACTAATATAAGAGC 58.138 37.037 0.00 0.00 0.00 4.09
765 806 9.878737 AGCTACTCCCTCTGTAAACTAATATAA 57.121 33.333 0.00 0.00 0.00 0.98
766 807 9.878737 AAGCTACTCCCTCTGTAAACTAATATA 57.121 33.333 0.00 0.00 0.00 0.86
767 808 8.643324 CAAGCTACTCCCTCTGTAAACTAATAT 58.357 37.037 0.00 0.00 0.00 1.28
768 809 7.837689 TCAAGCTACTCCCTCTGTAAACTAATA 59.162 37.037 0.00 0.00 0.00 0.98
769 810 6.668283 TCAAGCTACTCCCTCTGTAAACTAAT 59.332 38.462 0.00 0.00 0.00 1.73
770 811 6.014647 TCAAGCTACTCCCTCTGTAAACTAA 58.985 40.000 0.00 0.00 0.00 2.24
771 812 5.577100 TCAAGCTACTCCCTCTGTAAACTA 58.423 41.667 0.00 0.00 0.00 2.24
772 813 4.417437 TCAAGCTACTCCCTCTGTAAACT 58.583 43.478 0.00 0.00 0.00 2.66
773 814 4.803098 TCAAGCTACTCCCTCTGTAAAC 57.197 45.455 0.00 0.00 0.00 2.01
774 815 5.734720 CAATCAAGCTACTCCCTCTGTAAA 58.265 41.667 0.00 0.00 0.00 2.01
775 816 4.383118 GCAATCAAGCTACTCCCTCTGTAA 60.383 45.833 0.00 0.00 0.00 2.41
776 817 3.133003 GCAATCAAGCTACTCCCTCTGTA 59.867 47.826 0.00 0.00 0.00 2.74
777 818 2.093235 GCAATCAAGCTACTCCCTCTGT 60.093 50.000 0.00 0.00 0.00 3.41
778 819 2.170187 AGCAATCAAGCTACTCCCTCTG 59.830 50.000 0.00 0.00 44.50 3.35
779 820 2.476199 AGCAATCAAGCTACTCCCTCT 58.524 47.619 0.00 0.00 44.50 3.69
780 821 2.998316 AGCAATCAAGCTACTCCCTC 57.002 50.000 0.00 0.00 44.50 4.30
781 822 2.573462 TGAAGCAATCAAGCTACTCCCT 59.427 45.455 0.00 0.00 45.89 4.20
782 823 2.680339 GTGAAGCAATCAAGCTACTCCC 59.320 50.000 0.00 0.00 45.89 4.30
783 824 3.338249 TGTGAAGCAATCAAGCTACTCC 58.662 45.455 0.00 0.00 45.89 3.85
784 825 4.730035 GCATGTGAAGCAATCAAGCTACTC 60.730 45.833 0.00 0.00 45.89 2.59
785 826 3.128242 GCATGTGAAGCAATCAAGCTACT 59.872 43.478 0.00 0.00 45.89 2.57
786 827 3.128242 AGCATGTGAAGCAATCAAGCTAC 59.872 43.478 11.18 0.00 45.89 3.58
792 833 5.187687 TCTTATCAGCATGTGAAGCAATCA 58.812 37.500 0.00 0.00 39.19 2.57
872 913 2.103373 TGGTAGCTCAGAATTCTCGCT 58.897 47.619 24.33 24.33 35.06 4.93
908 955 1.952621 TAGGGCAGTGGTAGAGCTTT 58.047 50.000 0.00 0.00 0.00 3.51
917 964 0.254178 AGTGCAAGATAGGGCAGTGG 59.746 55.000 0.00 0.00 41.84 4.00
970 1021 5.180868 GCTAGCATGGAATTTGATACCTCTG 59.819 44.000 10.63 0.00 0.00 3.35
990 1043 3.456280 GCTCAAGAACATGAGGAGCTAG 58.544 50.000 0.00 0.00 45.60 3.42
1157 1210 3.918253 GACGGCAGAACCATGGGCA 62.918 63.158 18.09 0.00 39.03 5.36
1179 1232 1.227999 TGCTGTACCGTGCTTTCTGC 61.228 55.000 0.00 0.00 43.25 4.26
1467 1520 6.081356 ACCCTATCACCAAATCCAAAAGAAA 58.919 36.000 0.00 0.00 0.00 2.52
1481 1534 4.593206 TGATTCCATGACTACCCTATCACC 59.407 45.833 0.00 0.00 0.00 4.02
1520 1574 3.863041 CAGGTACCTTCTAGGCTTCAAC 58.137 50.000 13.15 0.00 39.63 3.18
1530 1584 2.553247 GGAAAAGCAGCAGGTACCTTCT 60.553 50.000 13.15 10.61 0.00 2.85
1568 1622 6.613699 AGCTGGACAAATCCCATGATAAATA 58.386 36.000 0.00 0.00 45.59 1.40
1659 1713 8.813282 TGTACTACAATGTTTCGTGCTAATATG 58.187 33.333 0.00 0.00 0.00 1.78
1666 1720 4.449743 TCCTTGTACTACAATGTTTCGTGC 59.550 41.667 2.02 0.00 37.48 5.34
1684 1738 9.931210 GGTAAAATACGTAAATTCATCTCCTTG 57.069 33.333 0.00 0.00 0.00 3.61
1685 1739 9.675464 TGGTAAAATACGTAAATTCATCTCCTT 57.325 29.630 0.00 0.00 0.00 3.36
1687 1741 9.878599 CATGGTAAAATACGTAAATTCATCTCC 57.121 33.333 0.00 0.00 0.00 3.71
1754 1821 3.134804 ACCATAGTGAGCCCTGTGTATTC 59.865 47.826 0.00 0.00 0.00 1.75
1787 1854 7.894376 ATAAAAATTTCACAATCAGGTGCTG 57.106 32.000 0.00 0.00 38.66 4.41
1830 1897 4.273148 ACAAGTGAGAATAACGAAGGCT 57.727 40.909 0.00 0.00 0.00 4.58
1831 1898 5.179555 AGAAACAAGTGAGAATAACGAAGGC 59.820 40.000 0.00 0.00 0.00 4.35
1834 1901 7.279090 TCACAAGAAACAAGTGAGAATAACGAA 59.721 33.333 0.00 0.00 37.36 3.85
1835 1902 6.759356 TCACAAGAAACAAGTGAGAATAACGA 59.241 34.615 0.00 0.00 37.36 3.85
1836 1903 6.943981 TCACAAGAAACAAGTGAGAATAACG 58.056 36.000 0.00 0.00 37.36 3.18
1837 1904 9.813080 GTATCACAAGAAACAAGTGAGAATAAC 57.187 33.333 0.00 0.00 44.51 1.89
1874 1941 6.187125 AGCAGCTGTAAACATACATGAAAG 57.813 37.500 16.64 0.00 0.00 2.62
1877 1944 5.729510 TGTAGCAGCTGTAAACATACATGA 58.270 37.500 16.64 0.00 0.00 3.07
2020 3194 1.734477 CACTGTCGCAGGAGGAACG 60.734 63.158 10.80 0.00 35.51 3.95
2139 3316 1.937899 GCGCTTATGTGGGAACGTATT 59.062 47.619 0.00 0.00 0.00 1.89
2175 3352 8.072567 GCTAATATTACATGTTTCAAGCAGGAG 58.927 37.037 2.30 0.00 0.00 3.69
2314 3506 5.525378 ACTTTTACTGAGCTTTCTGACACAG 59.475 40.000 0.00 0.00 0.00 3.66
2353 3545 0.459237 ATCTGCTTCAGAAGACGCGG 60.459 55.000 14.86 4.90 44.04 6.46
2354 3546 0.919981 GATCTGCTTCAGAAGACGCG 59.080 55.000 14.86 3.53 44.04 6.01
2355 3547 1.134848 AGGATCTGCTTCAGAAGACGC 60.135 52.381 14.86 0.00 44.04 5.19
2356 3548 2.481104 GGAGGATCTGCTTCAGAAGACG 60.481 54.545 14.86 3.73 44.04 4.18
2357 3549 2.499289 TGGAGGATCTGCTTCAGAAGAC 59.501 50.000 14.86 6.04 44.04 3.01
2358 3550 2.825223 TGGAGGATCTGCTTCAGAAGA 58.175 47.619 14.86 0.00 44.04 2.87
2359 3551 3.623906 TTGGAGGATCTGCTTCAGAAG 57.376 47.619 5.72 5.72 44.04 2.85
2360 3552 3.328931 AGTTTGGAGGATCTGCTTCAGAA 59.671 43.478 0.27 0.00 44.04 3.02
2361 3553 2.909006 AGTTTGGAGGATCTGCTTCAGA 59.091 45.455 0.00 0.00 44.99 3.27
2362 3554 3.008330 CAGTTTGGAGGATCTGCTTCAG 58.992 50.000 0.00 0.00 33.73 3.02
2363 3555 2.290514 CCAGTTTGGAGGATCTGCTTCA 60.291 50.000 0.00 0.00 40.96 3.02
2364 3556 2.290577 ACCAGTTTGGAGGATCTGCTTC 60.291 50.000 1.40 0.00 40.96 3.86
2365 3557 1.707427 ACCAGTTTGGAGGATCTGCTT 59.293 47.619 1.40 0.00 40.96 3.91
2366 3558 1.366319 ACCAGTTTGGAGGATCTGCT 58.634 50.000 1.40 0.00 40.96 4.24
2367 3559 2.206576 AACCAGTTTGGAGGATCTGC 57.793 50.000 1.40 0.00 40.96 4.26
2368 3560 3.691609 GCTAAACCAGTTTGGAGGATCTG 59.308 47.826 10.42 0.00 40.96 2.90
2369 3561 3.589288 AGCTAAACCAGTTTGGAGGATCT 59.411 43.478 10.42 0.00 40.96 2.75
2370 3562 3.691609 CAGCTAAACCAGTTTGGAGGATC 59.308 47.826 10.42 0.00 40.96 3.36
2371 3563 3.330701 TCAGCTAAACCAGTTTGGAGGAT 59.669 43.478 10.42 0.00 40.96 3.24
2372 3564 2.708861 TCAGCTAAACCAGTTTGGAGGA 59.291 45.455 10.42 4.24 40.96 3.71
2373 3565 3.140325 TCAGCTAAACCAGTTTGGAGG 57.860 47.619 10.42 2.16 40.96 4.30
2374 3566 3.253432 GGTTCAGCTAAACCAGTTTGGAG 59.747 47.826 14.39 0.47 46.62 3.86
2375 3567 3.219281 GGTTCAGCTAAACCAGTTTGGA 58.781 45.455 14.39 0.00 46.62 3.53
2376 3568 3.643159 GGTTCAGCTAAACCAGTTTGG 57.357 47.619 14.39 4.23 46.62 3.28
2383 3575 5.417754 ACTTACTAGGGTTCAGCTAAACC 57.582 43.478 10.68 10.68 46.41 3.27
2384 3576 6.154192 ACCTACTTACTAGGGTTCAGCTAAAC 59.846 42.308 0.00 0.00 46.21 2.01
2385 3577 6.259123 ACCTACTTACTAGGGTTCAGCTAAA 58.741 40.000 0.00 0.00 46.21 1.85
2386 3578 5.835582 ACCTACTTACTAGGGTTCAGCTAA 58.164 41.667 0.00 0.00 46.21 3.09
2387 3579 5.463051 ACCTACTTACTAGGGTTCAGCTA 57.537 43.478 0.00 0.00 46.21 3.32
2388 3580 4.334208 ACCTACTTACTAGGGTTCAGCT 57.666 45.455 0.00 0.00 46.21 4.24
2389 3581 5.008619 GAACCTACTTACTAGGGTTCAGC 57.991 47.826 16.84 0.00 43.46 4.26
2392 3584 4.019858 ACCGAACCTACTTACTAGGGTTC 58.980 47.826 13.44 13.44 43.46 3.62
2393 3585 4.053009 ACCGAACCTACTTACTAGGGTT 57.947 45.455 0.00 0.00 43.46 4.11
2394 3586 3.746792 ACCGAACCTACTTACTAGGGT 57.253 47.619 0.00 0.00 46.51 4.34
2395 3587 5.411831 AAAACCGAACCTACTTACTAGGG 57.588 43.478 0.00 0.00 46.21 3.53


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

AutoCloner maintained by Alex Coulton.