Multiple sequence alignment - TraesCS3A01G256300

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 TraesCS3A01G256300 chr3A 100.000 3446 0 0 1 3446 478244264 478240819 0.000000e+00 6364.0
1 TraesCS3A01G256300 chr3D 89.529 2378 125 46 1 2295 358566009 358563673 0.000000e+00 2898.0
2 TraesCS3A01G256300 chr3D 83.293 820 51 34 2501 3268 358563571 358562786 0.000000e+00 676.0
3 TraesCS3A01G256300 chr3D 93.333 120 4 2 2329 2445 358563681 358563563 1.270000e-39 174.0
4 TraesCS3A01G256300 chr3D 80.102 196 12 8 3263 3446 358561127 358560947 1.680000e-23 121.0
5 TraesCS3A01G256300 chr3B 90.497 2052 96 38 462 2443 464617665 464615643 0.000000e+00 2617.0
6 TraesCS3A01G256300 chr3B 89.362 470 28 7 17 476 464619066 464618609 3.860000e-159 571.0
7 TraesCS3A01G256300 chr3B 87.527 465 31 10 3001 3446 464614726 464614270 2.370000e-141 512.0
8 TraesCS3A01G256300 chr3B 81.520 487 33 25 2501 2954 464615649 464615187 7.080000e-92 348.0
9 TraesCS3A01G256300 chr1D 80.715 783 129 17 1005 1773 451063124 451062350 1.070000e-164 590.0
10 TraesCS3A01G256300 chr1D 77.789 995 170 31 1005 1960 450579207 450580189 1.800000e-157 566.0
11 TraesCS3A01G256300 chr1D 77.350 883 169 19 1013 1869 450739241 450740118 8.590000e-136 494.0
12 TraesCS3A01G256300 chr1D 75.897 975 181 38 1027 1956 450462948 450461983 1.890000e-122 449.0
13 TraesCS3A01G256300 chr1B 77.800 1000 167 39 1005 1960 618316840 618317828 1.800000e-157 566.0
14 TraesCS3A01G256300 chr1B 79.461 779 143 13 1005 1773 618542995 618543766 1.410000e-148 536.0
15 TraesCS3A01G256300 chr1B 77.309 996 170 34 1002 1960 618908054 618907078 1.410000e-148 536.0
16 TraesCS3A01G256300 chr1B 77.071 990 183 27 1005 1960 618698924 618697945 6.550000e-147 531.0
17 TraesCS3A01G256300 chr1B 78.146 874 148 26 1014 1855 618196982 618197844 1.830000e-142 516.0
18 TraesCS3A01G256300 chr1B 75.951 973 178 38 1027 1956 617968623 617967664 1.890000e-122 449.0
19 TraesCS3A01G256300 chr1A 76.118 984 183 30 1021 1960 545752041 545753016 5.210000e-128 468.0
20 TraesCS3A01G256300 chr1A 75.905 967 175 40 1040 1959 545649134 545648179 3.160000e-120 442.0
21 TraesCS3A01G256300 chr4D 90.385 52 4 1 2450 2500 28110854 28110905 2.220000e-07 67.6


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 TraesCS3A01G256300 chr3A 478240819 478244264 3445 True 6364.00 6364 100.00000 1 3446 1 chr3A.!!$R1 3445
1 TraesCS3A01G256300 chr3D 358560947 358566009 5062 True 967.25 2898 86.56425 1 3446 4 chr3D.!!$R1 3445
2 TraesCS3A01G256300 chr3B 464614270 464619066 4796 True 1012.00 2617 87.22650 17 3446 4 chr3B.!!$R1 3429
3 TraesCS3A01G256300 chr1D 451062350 451063124 774 True 590.00 590 80.71500 1005 1773 1 chr1D.!!$R2 768
4 TraesCS3A01G256300 chr1D 450579207 450580189 982 False 566.00 566 77.78900 1005 1960 1 chr1D.!!$F1 955
5 TraesCS3A01G256300 chr1D 450739241 450740118 877 False 494.00 494 77.35000 1013 1869 1 chr1D.!!$F2 856
6 TraesCS3A01G256300 chr1D 450461983 450462948 965 True 449.00 449 75.89700 1027 1956 1 chr1D.!!$R1 929
7 TraesCS3A01G256300 chr1B 618316840 618317828 988 False 566.00 566 77.80000 1005 1960 1 chr1B.!!$F2 955
8 TraesCS3A01G256300 chr1B 618542995 618543766 771 False 536.00 536 79.46100 1005 1773 1 chr1B.!!$F3 768
9 TraesCS3A01G256300 chr1B 618907078 618908054 976 True 536.00 536 77.30900 1002 1960 1 chr1B.!!$R3 958
10 TraesCS3A01G256300 chr1B 618697945 618698924 979 True 531.00 531 77.07100 1005 1960 1 chr1B.!!$R2 955
11 TraesCS3A01G256300 chr1B 618196982 618197844 862 False 516.00 516 78.14600 1014 1855 1 chr1B.!!$F1 841
12 TraesCS3A01G256300 chr1B 617967664 617968623 959 True 449.00 449 75.95100 1027 1956 1 chr1B.!!$R1 929
13 TraesCS3A01G256300 chr1A 545752041 545753016 975 False 468.00 468 76.11800 1021 1960 1 chr1A.!!$F1 939
14 TraesCS3A01G256300 chr1A 545648179 545649134 955 True 442.00 442 75.90500 1040 1959 1 chr1A.!!$R1 919

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
525 1505 0.108424 AGGACACTGATTCGCTGAGC 60.108 55.0 0.00 0.0 0.0 4.26 F
526 1506 0.390340 GGACACTGATTCGCTGAGCA 60.390 55.0 4.88 0.0 0.0 4.26 F
2189 3294 0.518636 CGCCAGATCCAAGTGTGTTG 59.481 55.0 0.00 0.0 0.0 3.33 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2103 3202 0.933097 CATCCTCTGCGTCCAATTCG 59.067 55.000 0.00 0.0 0.0 3.34 R
2265 3373 1.070909 CGCGGCAAAATTTGTGGAAAC 60.071 47.619 7.60 0.0 0.0 2.78 R
3130 4700 0.527600 TCGTACTCATCGCATGTGGC 60.528 55.000 6.39 0.0 39.9 5.01 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
194 196 2.433838 CGCAGCTGACCTGACAGG 60.434 66.667 20.43 20.45 44.64 4.00
203 205 3.390521 CCTGACAGGCACGCCCTA 61.391 66.667 8.99 0.00 44.09 3.53
204 206 2.735772 CCTGACAGGCACGCCCTAT 61.736 63.158 8.99 0.00 44.09 2.57
249 264 4.095334 TGCTTCACATGTGTGCATCTATTC 59.905 41.667 30.22 11.89 45.25 1.75
257 272 2.871022 GTGTGCATCTATTCTGGCTCAG 59.129 50.000 0.00 0.00 31.39 3.35
298 313 0.796927 TCTGTACTGACGCTCGTGAG 59.203 55.000 7.31 7.31 35.49 3.51
303 318 3.669036 CTGACGCTCGTGAGTCCCG 62.669 68.421 16.85 6.23 41.36 5.14
333 348 1.544691 ACGGAAATCACGAGCAGTACT 59.455 47.619 0.00 0.00 34.93 2.73
334 349 2.751259 ACGGAAATCACGAGCAGTACTA 59.249 45.455 0.00 0.00 34.93 1.82
336 351 3.106672 GGAAATCACGAGCAGTACTACG 58.893 50.000 12.46 12.46 0.00 3.51
337 352 3.427233 GGAAATCACGAGCAGTACTACGT 60.427 47.826 13.48 13.48 39.53 3.57
450 467 6.029607 ACGCAGAGTGCATATTGTATTTTTG 58.970 36.000 0.00 0.00 45.36 2.44
459 476 3.866883 ATTGTATTTTTGGGCCTCACG 57.133 42.857 4.53 0.00 0.00 4.35
502 1477 0.737715 TGCACCGCCACAAAAACAAC 60.738 50.000 0.00 0.00 0.00 3.32
510 1488 2.792749 CCACAAAAACAACACGAGGAC 58.207 47.619 0.00 0.00 0.00 3.85
512 1490 3.168193 CACAAAAACAACACGAGGACAC 58.832 45.455 0.00 0.00 0.00 3.67
525 1505 0.108424 AGGACACTGATTCGCTGAGC 60.108 55.000 0.00 0.00 0.00 4.26
526 1506 0.390340 GGACACTGATTCGCTGAGCA 60.390 55.000 4.88 0.00 0.00 4.26
539 1519 1.063174 GCTGAGCAGGCAGAAATAACG 59.937 52.381 0.00 0.00 38.14 3.18
541 1521 2.346803 TGAGCAGGCAGAAATAACGAC 58.653 47.619 0.00 0.00 0.00 4.34
543 1523 1.067142 AGCAGGCAGAAATAACGACGA 60.067 47.619 0.00 0.00 0.00 4.20
544 1524 1.060698 GCAGGCAGAAATAACGACGAC 59.939 52.381 0.00 0.00 0.00 4.34
567 1547 3.543641 GGGATGCATGGGCCAAGC 61.544 66.667 25.97 25.97 40.13 4.01
579 1559 4.789075 CCAAGCGCCTGCATGTGC 62.789 66.667 18.42 18.42 46.23 4.57
688 1704 3.959975 CCCACACAAACGCACGGG 61.960 66.667 0.00 0.00 0.00 5.28
703 1725 2.857104 GCACGGGAAAAAGAAGGAAACG 60.857 50.000 0.00 0.00 0.00 3.60
818 1840 0.613853 CCGATCGGCCCCCTAATCTA 60.614 60.000 23.37 0.00 0.00 1.98
819 1841 1.263356 CGATCGGCCCCCTAATCTAA 58.737 55.000 7.38 0.00 0.00 2.10
820 1842 1.067071 CGATCGGCCCCCTAATCTAAC 60.067 57.143 7.38 0.00 0.00 2.34
821 1843 1.975680 GATCGGCCCCCTAATCTAACA 59.024 52.381 0.00 0.00 0.00 2.41
866 1888 1.602771 GTCTTCCCCTTCCCCTTCG 59.397 63.158 0.00 0.00 0.00 3.79
872 1911 2.751837 CCTTCCCCTTCGCTTGCC 60.752 66.667 0.00 0.00 0.00 4.52
911 1950 3.297620 GCAACCACAGCCCACCAG 61.298 66.667 0.00 0.00 0.00 4.00
941 1980 3.422862 CGCACACCAAACAAAAACAACAG 60.423 43.478 0.00 0.00 0.00 3.16
942 1981 3.120373 GCACACCAAACAAAAACAACAGG 60.120 43.478 0.00 0.00 0.00 4.00
946 1985 3.991121 ACCAAACAAAAACAACAGGAACG 59.009 39.130 0.00 0.00 0.00 3.95
987 2026 2.179547 CAGAGCAACCACACACGCA 61.180 57.895 0.00 0.00 0.00 5.24
1720 2774 3.197790 CCATGTGCTTCGCGAGGG 61.198 66.667 20.46 13.07 0.00 4.30
1974 3073 2.049156 CTCGGCGAGCAGTGTGAA 60.049 61.111 25.31 0.00 0.00 3.18
2103 3202 0.534203 TCGGCACCCTTTCAAGTGAC 60.534 55.000 0.00 0.00 38.73 3.67
2189 3294 0.518636 CGCCAGATCCAAGTGTGTTG 59.481 55.000 0.00 0.00 0.00 3.33
2203 3308 6.169094 CAAGTGTGTTGGAGTTCAGATAGAT 58.831 40.000 0.00 0.00 0.00 1.98
2208 3316 7.223582 GTGTGTTGGAGTTCAGATAGATATGTG 59.776 40.741 0.00 0.00 0.00 3.21
2222 3330 8.595421 AGATAGATATGTGCTTTCATCATCACT 58.405 33.333 0.00 0.00 0.00 3.41
2246 3354 6.638096 TGTACCCTGTAATAATCGAATCGA 57.362 37.500 8.12 8.12 41.13 3.59
2262 3370 6.705782 TCGAATCGATGCAATAGAAAAGTTC 58.294 36.000 0.00 0.00 29.85 3.01
2265 3373 3.621268 TCGATGCAATAGAAAAGTTCCGG 59.379 43.478 0.00 0.00 0.00 5.14
2277 3385 4.746535 AAAGTTCCGGTTTCCACAAATT 57.253 36.364 0.00 0.00 0.00 1.82
2282 3390 1.870402 CCGGTTTCCACAAATTTTGCC 59.130 47.619 9.04 0.78 0.00 4.52
2284 3392 1.262950 GGTTTCCACAAATTTTGCCGC 59.737 47.619 9.04 0.00 0.00 6.53
2301 3409 1.141019 GCGCCGTTCTGACCATCTA 59.859 57.895 0.00 0.00 0.00 1.98
2356 3464 9.570488 GTTCTGATAGACTACGTACTGAATTTT 57.430 33.333 0.00 0.00 0.00 1.82
2386 3497 2.031163 GGAGAACACAGTGCGCCT 59.969 61.111 4.18 0.00 27.95 5.52
2390 3501 0.882042 AGAACACAGTGCGCCTTCTG 60.882 55.000 18.16 18.16 37.65 3.02
2418 3529 6.254157 CACTCCAACTCACAACAAAAATCTTG 59.746 38.462 0.00 0.00 0.00 3.02
2446 3557 8.862550 ACAACTTACACAACTACAGTACTAAC 57.137 34.615 0.00 0.00 0.00 2.34
2447 3558 8.689972 ACAACTTACACAACTACAGTACTAACT 58.310 33.333 0.00 0.00 35.91 2.24
2448 3559 9.178427 CAACTTACACAACTACAGTACTAACTC 57.822 37.037 0.00 0.00 31.97 3.01
2449 3560 8.688747 ACTTACACAACTACAGTACTAACTCT 57.311 34.615 0.00 0.00 31.97 3.24
2450 3561 9.129532 ACTTACACAACTACAGTACTAACTCTT 57.870 33.333 0.00 0.00 31.97 2.85
2451 3562 9.962783 CTTACACAACTACAGTACTAACTCTTT 57.037 33.333 0.00 0.00 31.97 2.52
2485 3596 4.864334 CACCCCGGGCTCTGCATC 62.864 72.222 17.73 0.00 0.00 3.91
2487 3598 4.113815 CCCCGGGCTCTGCATCAA 62.114 66.667 17.73 0.00 0.00 2.57
2488 3599 2.045045 CCCGGGCTCTGCATCAAA 60.045 61.111 8.08 0.00 0.00 2.69
2489 3600 1.678635 CCCGGGCTCTGCATCAAAA 60.679 57.895 8.08 0.00 0.00 2.44
2490 3601 1.508088 CCGGGCTCTGCATCAAAAC 59.492 57.895 0.00 0.00 0.00 2.43
2491 3602 1.135315 CGGGCTCTGCATCAAAACG 59.865 57.895 0.00 0.00 0.00 3.60
2492 3603 1.298157 CGGGCTCTGCATCAAAACGA 61.298 55.000 0.00 0.00 0.00 3.85
2493 3604 1.098050 GGGCTCTGCATCAAAACGAT 58.902 50.000 0.00 0.00 33.27 3.73
2504 3615 4.973396 CATCAAAACGATGCATACACAGT 58.027 39.130 0.00 0.00 44.95 3.55
2505 3616 6.105657 CATCAAAACGATGCATACACAGTA 57.894 37.500 0.00 0.00 44.95 2.74
2506 3617 5.524511 TCAAAACGATGCATACACAGTAC 57.475 39.130 0.00 0.00 0.00 2.73
2507 3618 5.234752 TCAAAACGATGCATACACAGTACT 58.765 37.500 0.00 0.00 0.00 2.73
2508 3619 6.391537 TCAAAACGATGCATACACAGTACTA 58.608 36.000 0.00 0.00 0.00 1.82
2509 3620 6.869388 TCAAAACGATGCATACACAGTACTAA 59.131 34.615 0.00 0.00 0.00 2.24
2510 3621 6.642683 AAACGATGCATACACAGTACTAAC 57.357 37.500 0.00 0.00 0.00 2.34
2511 3622 5.578005 ACGATGCATACACAGTACTAACT 57.422 39.130 0.00 0.00 35.91 2.24
2518 3629 6.134730 GCATACACAGTACTAACTAGTAGCG 58.865 44.000 0.00 0.00 39.29 4.26
2560 3679 0.037605 AAGAGCATTGCTTTGCCTGC 60.038 50.000 13.35 0.00 43.83 4.85
2587 3706 2.100749 CACGGCAAGAAAAGAAAACCCT 59.899 45.455 0.00 0.00 0.00 4.34
2589 3708 2.288213 CGGCAAGAAAAGAAAACCCTCC 60.288 50.000 0.00 0.00 0.00 4.30
2590 3709 2.288213 GGCAAGAAAAGAAAACCCTCCG 60.288 50.000 0.00 0.00 0.00 4.63
2591 3710 2.862530 GCAAGAAAAGAAAACCCTCCGC 60.863 50.000 0.00 0.00 0.00 5.54
2592 3711 2.358322 AGAAAAGAAAACCCTCCGCA 57.642 45.000 0.00 0.00 0.00 5.69
2596 3715 2.882927 AAGAAAACCCTCCGCAAAAC 57.117 45.000 0.00 0.00 0.00 2.43
2662 3781 1.821759 TGCGGTTTATCCCATGCCG 60.822 57.895 1.79 1.79 44.60 5.69
2675 3794 2.300433 CCATGCCGAAGAATTCCATCA 58.700 47.619 0.65 0.00 43.81 3.07
2676 3795 2.033801 CCATGCCGAAGAATTCCATCAC 59.966 50.000 0.65 0.00 43.81 3.06
2677 3796 2.488204 TGCCGAAGAATTCCATCACA 57.512 45.000 0.65 0.33 43.81 3.58
2678 3797 2.358957 TGCCGAAGAATTCCATCACAG 58.641 47.619 0.65 0.00 43.81 3.66
2679 3798 1.672881 GCCGAAGAATTCCATCACAGG 59.327 52.381 0.65 0.17 43.81 4.00
2682 3801 2.604914 CGAAGAATTCCATCACAGGTCG 59.395 50.000 0.65 0.00 43.81 4.79
2683 3802 3.676049 CGAAGAATTCCATCACAGGTCGA 60.676 47.826 0.65 0.00 43.81 4.20
2684 3803 4.446371 GAAGAATTCCATCACAGGTCGAT 58.554 43.478 0.65 0.00 39.83 3.59
2685 3804 5.601662 GAAGAATTCCATCACAGGTCGATA 58.398 41.667 0.65 0.00 39.83 2.92
2686 3805 5.614324 AGAATTCCATCACAGGTCGATAA 57.386 39.130 0.65 0.00 0.00 1.75
2687 3806 5.360591 AGAATTCCATCACAGGTCGATAAC 58.639 41.667 0.65 0.00 0.00 1.89
2688 3807 4.753516 ATTCCATCACAGGTCGATAACA 57.246 40.909 0.00 0.00 0.00 2.41
2689 3808 3.520290 TCCATCACAGGTCGATAACAC 57.480 47.619 0.00 0.00 0.00 3.32
2690 3809 2.159296 TCCATCACAGGTCGATAACACG 60.159 50.000 0.00 0.00 0.00 4.49
2692 3811 0.455464 TCACAGGTCGATAACACGCG 60.455 55.000 3.53 3.53 0.00 6.01
2693 3812 1.153901 ACAGGTCGATAACACGCGG 60.154 57.895 12.47 1.27 0.00 6.46
2694 3813 2.202703 AGGTCGATAACACGCGGC 60.203 61.111 12.47 0.00 0.00 6.53
2695 3814 3.259751 GGTCGATAACACGCGGCC 61.260 66.667 12.47 0.00 45.61 6.13
2696 3815 3.613702 GTCGATAACACGCGGCCG 61.614 66.667 24.05 24.05 41.14 6.13
2697 3816 4.858433 TCGATAACACGCGGCCGG 62.858 66.667 29.38 19.49 39.22 6.13
2698 3817 4.858433 CGATAACACGCGGCCGGA 62.858 66.667 29.38 1.03 39.22 5.14
2699 3818 2.279918 GATAACACGCGGCCGGAT 60.280 61.111 29.38 7.65 39.22 4.18
2874 4018 2.672996 TCCGCTCAAGCAAAGGGC 60.673 61.111 2.50 0.00 42.21 5.19
2890 4045 1.700186 AGGGCGGAGAAGAAAAGAAGT 59.300 47.619 0.00 0.00 0.00 3.01
2891 4046 2.077627 GGGCGGAGAAGAAAAGAAGTC 58.922 52.381 0.00 0.00 0.00 3.01
2892 4047 2.077627 GGCGGAGAAGAAAAGAAGTCC 58.922 52.381 0.00 0.00 0.00 3.85
2894 4049 2.866855 GCGGAGAAGAAAAGAAGTCCGT 60.867 50.000 10.05 0.00 46.87 4.69
2895 4050 3.613432 GCGGAGAAGAAAAGAAGTCCGTA 60.613 47.826 10.05 0.00 46.87 4.02
2911 4066 1.153568 GTACGTACCCGCCCCTTTC 60.154 63.158 15.00 0.00 37.70 2.62
2992 4170 1.101331 CGGGGAGACACCTGTACTAC 58.899 60.000 0.00 0.00 38.98 2.73
2993 4171 1.482954 GGGGAGACACCTGTACTACC 58.517 60.000 0.00 0.00 38.98 3.18
2999 4568 4.142138 GGAGACACCTGTACTACCATCTTG 60.142 50.000 0.00 0.00 35.41 3.02
3044 4614 4.479993 GCATCTCTGGGTGGCGCT 62.480 66.667 7.64 0.00 0.00 5.92
3130 4700 4.156622 CATCACGCCGCACTGCTG 62.157 66.667 0.00 0.00 0.00 4.41
3157 4727 1.939785 GATGAGTACGAGCACGGCG 60.940 63.158 4.80 4.80 44.46 6.46
3242 4817 1.794785 CGTGTGCGTACGTGTCGAT 60.795 57.895 17.90 0.00 39.13 3.59
3245 4820 2.574999 TGCGTACGTGTCGATCGC 60.575 61.111 17.90 19.68 45.13 4.58
3300 6539 2.743928 GCCGCCAAGTCTGTCTGG 60.744 66.667 0.00 0.00 0.00 3.86
3313 6552 1.005630 GTCTGGTTCTGCAGCTCGT 60.006 57.895 9.47 0.00 0.00 4.18
3329 6578 0.028902 TCGTGCACCTATCATCGTCG 59.971 55.000 12.15 0.00 0.00 5.12
3355 6604 0.030101 TTTTGCAACTTTCGGGAGCG 59.970 50.000 0.00 0.00 0.00 5.03
3358 6607 4.445545 CAACTTTCGGGAGCGCGC 62.446 66.667 26.66 26.66 0.00 6.86
3363 6612 3.982372 TTTCGGGAGCGCGCTGTAG 62.982 63.158 41.82 27.20 0.00 2.74
3412 6663 1.614413 GGGCGGATAAGGACTACTCTG 59.386 57.143 0.00 0.00 0.00 3.35
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
18 19 0.948623 TCAAGATTGGACGTGCACCG 60.949 55.000 10.12 9.19 44.03 4.94
19 20 0.517316 GTCAAGATTGGACGTGCACC 59.483 55.000 10.12 4.77 0.00 5.01
63 65 2.959372 GTGCCCGCCCACTTAAAC 59.041 61.111 0.00 0.00 33.02 2.01
103 105 2.414138 GTCGTTAATTCCGGGTGAGTTG 59.586 50.000 0.00 0.00 0.00 3.16
104 106 2.613725 GGTCGTTAATTCCGGGTGAGTT 60.614 50.000 0.00 0.00 0.00 3.01
105 107 1.066645 GGTCGTTAATTCCGGGTGAGT 60.067 52.381 0.00 0.00 0.00 3.41
106 108 1.206371 AGGTCGTTAATTCCGGGTGAG 59.794 52.381 0.00 0.00 0.00 3.51
107 109 1.205417 GAGGTCGTTAATTCCGGGTGA 59.795 52.381 0.00 0.00 0.00 4.02
108 110 1.066716 TGAGGTCGTTAATTCCGGGTG 60.067 52.381 0.00 0.00 0.00 4.61
194 196 0.868406 GTGCAATAGATAGGGCGTGC 59.132 55.000 0.00 0.00 0.00 5.34
201 203 4.621991 AGCGTGGTTAGTGCAATAGATAG 58.378 43.478 0.00 0.00 0.00 2.08
202 204 4.617959 GAGCGTGGTTAGTGCAATAGATA 58.382 43.478 0.00 0.00 0.00 1.98
203 205 3.458189 GAGCGTGGTTAGTGCAATAGAT 58.542 45.455 0.00 0.00 0.00 1.98
204 206 2.734175 CGAGCGTGGTTAGTGCAATAGA 60.734 50.000 0.00 0.00 0.00 1.98
268 283 4.201724 GCGTCAGTACAGAGCAAAAATAGG 60.202 45.833 0.00 0.00 0.00 2.57
303 318 5.272167 TCGTGATTTCCGTGTGATTAAAC 57.728 39.130 0.00 0.00 0.00 2.01
316 331 3.756069 ACGTAGTACTGCTCGTGATTTC 58.244 45.455 17.14 0.00 41.94 2.17
450 467 2.747855 CTCCTTTGCGTGAGGCCC 60.748 66.667 0.00 0.00 42.61 5.80
459 476 5.218139 GCAATACAATATGCTCTCCTTTGC 58.782 41.667 0.00 0.00 39.46 3.68
502 1477 0.109086 AGCGAATCAGTGTCCTCGTG 60.109 55.000 11.09 0.00 33.87 4.35
510 1488 1.703438 GCCTGCTCAGCGAATCAGTG 61.703 60.000 0.00 0.00 0.00 3.66
512 1490 1.429927 CTGCCTGCTCAGCGAATCAG 61.430 60.000 0.00 0.00 0.00 2.90
525 1505 2.092211 GTGTCGTCGTTATTTCTGCCTG 59.908 50.000 0.00 0.00 0.00 4.85
526 1506 2.288579 TGTGTCGTCGTTATTTCTGCCT 60.289 45.455 0.00 0.00 0.00 4.75
539 1519 0.391661 ATGCATCCCACTGTGTCGTC 60.392 55.000 7.08 0.00 0.00 4.20
541 1521 1.371337 CCATGCATCCCACTGTGTCG 61.371 60.000 7.08 0.00 0.00 4.35
543 1523 1.000521 CCCATGCATCCCACTGTGT 60.001 57.895 7.08 0.00 0.00 3.72
544 1524 2.420568 GCCCATGCATCCCACTGTG 61.421 63.158 0.00 0.00 37.47 3.66
574 1554 0.337773 TCCTCTCCTCTCCTGCACAT 59.662 55.000 0.00 0.00 0.00 3.21
575 1555 0.324183 CTCCTCTCCTCTCCTGCACA 60.324 60.000 0.00 0.00 0.00 4.57
576 1556 0.033601 TCTCCTCTCCTCTCCTGCAC 60.034 60.000 0.00 0.00 0.00 4.57
579 1559 1.498576 TCCATCTCCTCTCCTCTCCTG 59.501 57.143 0.00 0.00 0.00 3.86
638 1646 2.750888 GGCTCAATCAACCGACGGC 61.751 63.158 15.39 0.00 0.00 5.68
688 1704 2.603892 GGACGCCGTTTCCTTCTTTTTC 60.604 50.000 0.00 0.00 0.00 2.29
818 1840 2.837591 GCTAATTGGGTGGGGATTTGTT 59.162 45.455 0.00 0.00 0.00 2.83
819 1841 2.044353 AGCTAATTGGGTGGGGATTTGT 59.956 45.455 0.00 0.00 0.00 2.83
820 1842 2.695147 GAGCTAATTGGGTGGGGATTTG 59.305 50.000 0.00 0.00 0.00 2.32
821 1843 2.359249 GGAGCTAATTGGGTGGGGATTT 60.359 50.000 0.00 0.00 0.00 2.17
866 1888 5.065218 CGTTTATATATCCATGGAGGCAAGC 59.935 44.000 21.33 10.10 37.29 4.01
872 1911 3.242944 CGCGCGTTTATATATCCATGGAG 59.757 47.826 24.19 3.98 0.00 3.86
904 1943 2.983592 GCGTTGGGTTCTGGTGGG 60.984 66.667 0.00 0.00 0.00 4.61
910 1949 0.681564 TTTGGTGTGCGTTGGGTTCT 60.682 50.000 0.00 0.00 0.00 3.01
911 1950 0.526739 GTTTGGTGTGCGTTGGGTTC 60.527 55.000 0.00 0.00 0.00 3.62
941 1980 2.582498 CGCCGGTGATCTCGTTCC 60.582 66.667 10.20 0.00 0.00 3.62
942 1981 3.255379 GCGCCGGTGATCTCGTTC 61.255 66.667 21.76 0.00 0.00 3.95
946 1985 2.663188 GGATGCGCCGGTGATCTC 60.663 66.667 21.76 11.12 0.00 2.75
987 2026 1.896220 TCGCCATTCTTGCTTGTCTT 58.104 45.000 0.00 0.00 0.00 3.01
1230 2278 2.599408 ACTCGAGGAAGAGGTGGTAA 57.401 50.000 18.41 0.00 42.31 2.85
1972 3071 1.806542 TGGTGAATCGCAAGCTTCTTC 59.193 47.619 0.00 0.00 42.66 2.87
1973 3072 1.808945 CTGGTGAATCGCAAGCTTCTT 59.191 47.619 0.00 0.00 42.66 2.52
1974 3073 1.446907 CTGGTGAATCGCAAGCTTCT 58.553 50.000 0.00 0.00 42.66 2.85
2060 3159 3.485431 CTGCGTCTTCAGCTGGCG 61.485 66.667 15.13 14.14 35.28 5.69
2103 3202 0.933097 CATCCTCTGCGTCCAATTCG 59.067 55.000 0.00 0.00 0.00 3.34
2189 3294 7.212976 TGAAAGCACATATCTATCTGAACTCC 58.787 38.462 0.00 0.00 0.00 3.85
2193 3298 9.433153 GATGATGAAAGCACATATCTATCTGAA 57.567 33.333 0.00 0.00 30.93 3.02
2203 3308 6.316140 GGTACAAGTGATGATGAAAGCACATA 59.684 38.462 0.00 0.00 30.93 2.29
2208 3316 4.095483 CAGGGTACAAGTGATGATGAAAGC 59.905 45.833 0.00 0.00 0.00 3.51
2222 3330 7.041635 TCGATTCGATTATTACAGGGTACAA 57.958 36.000 4.29 0.00 0.00 2.41
2246 3354 5.336451 GGAAACCGGAACTTTTCTATTGCAT 60.336 40.000 9.46 0.00 33.10 3.96
2262 3370 1.870402 GGCAAAATTTGTGGAAACCGG 59.130 47.619 7.60 0.00 0.00 5.28
2265 3373 1.070909 CGCGGCAAAATTTGTGGAAAC 60.071 47.619 7.60 0.00 0.00 2.78
2282 3390 2.607668 TAGATGGTCAGAACGGCGCG 62.608 60.000 6.90 0.00 0.00 6.86
2284 3392 1.338337 AGATAGATGGTCAGAACGGCG 59.662 52.381 4.80 4.80 0.00 6.46
2296 3404 5.218885 CAGAGTAGGAACGCAAGATAGATG 58.781 45.833 0.00 0.00 43.62 2.90
2301 3409 3.511934 AGAACAGAGTAGGAACGCAAGAT 59.488 43.478 0.00 0.00 43.62 2.40
2356 3464 1.604308 TTCTCCACGCACGGGTAGA 60.604 57.895 0.00 0.00 0.00 2.59
2386 3497 4.081365 TGTTGTGAGTTGGAGTGTACAGAA 60.081 41.667 0.00 0.00 0.00 3.02
2390 3501 5.554822 TTTTGTTGTGAGTTGGAGTGTAC 57.445 39.130 0.00 0.00 0.00 2.90
2418 3529 7.144000 AGTACTGTAGTTGTGTAAGTTGTAGC 58.856 38.462 0.00 0.00 0.00 3.58
2468 3579 4.864334 GATGCAGAGCCCGGGGTG 62.864 72.222 34.05 18.64 0.00 4.61
2470 3581 3.643595 TTTGATGCAGAGCCCGGGG 62.644 63.158 25.28 9.31 0.00 5.73
2471 3582 1.678635 TTTTGATGCAGAGCCCGGG 60.679 57.895 19.09 19.09 0.00 5.73
2472 3583 1.508088 GTTTTGATGCAGAGCCCGG 59.492 57.895 0.00 0.00 0.00 5.73
2473 3584 1.135315 CGTTTTGATGCAGAGCCCG 59.865 57.895 0.00 0.00 0.00 6.13
2474 3585 1.098050 ATCGTTTTGATGCAGAGCCC 58.902 50.000 0.00 0.00 35.45 5.19
2483 3594 5.874810 AGTACTGTGTATGCATCGTTTTGAT 59.125 36.000 0.19 0.00 38.01 2.57
2484 3595 5.234752 AGTACTGTGTATGCATCGTTTTGA 58.765 37.500 0.19 0.00 0.00 2.69
2485 3596 5.530519 AGTACTGTGTATGCATCGTTTTG 57.469 39.130 0.19 0.00 0.00 2.44
2486 3597 6.872020 AGTTAGTACTGTGTATGCATCGTTTT 59.128 34.615 0.19 0.00 31.99 2.43
2487 3598 6.395629 AGTTAGTACTGTGTATGCATCGTTT 58.604 36.000 0.19 0.00 31.99 3.60
2488 3599 5.962433 AGTTAGTACTGTGTATGCATCGTT 58.038 37.500 0.19 0.00 31.99 3.85
2489 3600 5.578005 AGTTAGTACTGTGTATGCATCGT 57.422 39.130 0.19 0.00 31.99 3.73
2490 3601 6.726230 ACTAGTTAGTACTGTGTATGCATCG 58.274 40.000 0.19 0.00 35.78 3.84
2491 3602 7.804129 GCTACTAGTTAGTACTGTGTATGCATC 59.196 40.741 0.19 0.00 37.73 3.91
2492 3603 7.520131 CGCTACTAGTTAGTACTGTGTATGCAT 60.520 40.741 5.39 3.79 37.73 3.96
2493 3604 6.238293 CGCTACTAGTTAGTACTGTGTATGCA 60.238 42.308 5.39 0.00 37.73 3.96
2494 3605 6.134730 CGCTACTAGTTAGTACTGTGTATGC 58.865 44.000 5.39 0.08 37.73 3.14
2495 3606 6.481313 TCCGCTACTAGTTAGTACTGTGTATG 59.519 42.308 5.39 0.00 37.73 2.39
2496 3607 6.586344 TCCGCTACTAGTTAGTACTGTGTAT 58.414 40.000 5.39 0.00 37.73 2.29
2497 3608 5.977635 TCCGCTACTAGTTAGTACTGTGTA 58.022 41.667 5.39 1.09 37.73 2.90
2498 3609 4.836825 TCCGCTACTAGTTAGTACTGTGT 58.163 43.478 5.39 0.00 37.73 3.72
2499 3610 7.226325 ACTTATCCGCTACTAGTTAGTACTGTG 59.774 40.741 5.39 0.00 37.73 3.66
2500 3611 7.226325 CACTTATCCGCTACTAGTTAGTACTGT 59.774 40.741 5.39 0.00 37.73 3.55
2501 3612 7.440556 TCACTTATCCGCTACTAGTTAGTACTG 59.559 40.741 5.39 0.00 37.73 2.74
2502 3613 7.440856 GTCACTTATCCGCTACTAGTTAGTACT 59.559 40.741 0.00 0.00 37.73 2.73
2503 3614 7.307692 GGTCACTTATCCGCTACTAGTTAGTAC 60.308 44.444 0.00 0.00 37.73 2.73
2504 3615 6.708054 GGTCACTTATCCGCTACTAGTTAGTA 59.292 42.308 0.00 0.00 37.73 1.82
2505 3616 5.530543 GGTCACTTATCCGCTACTAGTTAGT 59.469 44.000 0.00 0.00 40.24 2.24
2506 3617 5.530171 TGGTCACTTATCCGCTACTAGTTAG 59.470 44.000 0.00 0.00 0.00 2.34
2507 3618 5.297776 GTGGTCACTTATCCGCTACTAGTTA 59.702 44.000 0.00 0.00 0.00 2.24
2508 3619 4.097589 GTGGTCACTTATCCGCTACTAGTT 59.902 45.833 0.00 0.00 0.00 2.24
2509 3620 3.631227 GTGGTCACTTATCCGCTACTAGT 59.369 47.826 0.00 0.00 0.00 2.57
2510 3621 3.303857 CGTGGTCACTTATCCGCTACTAG 60.304 52.174 0.00 0.00 32.71 2.57
2511 3622 2.615447 CGTGGTCACTTATCCGCTACTA 59.385 50.000 0.00 0.00 32.71 1.82
2518 3629 2.426024 TCTACTGCGTGGTCACTTATCC 59.574 50.000 0.00 0.00 0.00 2.59
2560 3679 1.999735 TCTTTTCTTGCCGTGCTATCG 59.000 47.619 0.00 0.00 0.00 2.92
2575 3694 3.527533 GTTTTGCGGAGGGTTTTCTTTT 58.472 40.909 0.00 0.00 0.00 2.27
2587 3706 0.658897 GGAAACAGTCGTTTTGCGGA 59.341 50.000 0.00 0.00 45.40 5.54
2589 3708 2.108700 CAAGGAAACAGTCGTTTTGCG 58.891 47.619 0.00 0.00 45.40 4.85
2590 3709 2.851824 CACAAGGAAACAGTCGTTTTGC 59.148 45.455 0.00 0.00 45.40 3.68
2591 3710 2.851824 GCACAAGGAAACAGTCGTTTTG 59.148 45.455 0.00 0.00 45.40 2.44
2592 3711 2.490115 TGCACAAGGAAACAGTCGTTTT 59.510 40.909 0.00 0.00 45.40 2.43
2596 3715 1.528586 CTCTGCACAAGGAAACAGTCG 59.471 52.381 0.00 0.00 0.00 4.18
2662 3781 3.861840 TCGACCTGTGATGGAATTCTTC 58.138 45.455 5.23 3.91 0.00 2.87
2675 3794 1.153901 CCGCGTGTTATCGACCTGT 60.154 57.895 4.92 0.00 0.00 4.00
2676 3795 2.514013 GCCGCGTGTTATCGACCTG 61.514 63.158 4.92 0.00 0.00 4.00
2677 3796 2.202703 GCCGCGTGTTATCGACCT 60.203 61.111 4.92 0.00 0.00 3.85
2678 3797 3.259751 GGCCGCGTGTTATCGACC 61.260 66.667 4.92 0.00 0.00 4.79
2679 3798 3.613702 CGGCCGCGTGTTATCGAC 61.614 66.667 14.67 0.00 0.00 4.20
2682 3801 2.279918 ATCCGGCCGCGTGTTATC 60.280 61.111 22.85 0.00 0.00 1.75
2683 3802 2.587753 CATCCGGCCGCGTGTTAT 60.588 61.111 22.85 2.42 0.00 1.89
2684 3803 4.823419 CCATCCGGCCGCGTGTTA 62.823 66.667 22.85 0.00 0.00 2.41
2692 3811 2.340443 GAGACGATCCATCCGGCC 59.660 66.667 0.00 0.00 35.21 6.13
2693 3812 2.049985 CGAGACGATCCATCCGGC 60.050 66.667 0.00 0.00 34.76 6.13
2694 3813 2.645567 CCGAGACGATCCATCCGG 59.354 66.667 0.00 0.00 0.00 5.14
2695 3814 2.049985 GCCGAGACGATCCATCCG 60.050 66.667 0.00 0.00 0.00 4.18
2696 3815 2.148558 GAGGCCGAGACGATCCATCC 62.149 65.000 0.00 0.00 0.00 3.51
2697 3816 1.175983 AGAGGCCGAGACGATCCATC 61.176 60.000 0.00 0.00 0.00 3.51
2698 3817 1.152652 AGAGGCCGAGACGATCCAT 60.153 57.895 0.00 0.00 0.00 3.41
2699 3818 1.824329 GAGAGGCCGAGACGATCCA 60.824 63.158 0.00 0.00 0.00 3.41
2771 3896 6.435430 TTCATTCATTAATCAAGTGGACGG 57.565 37.500 0.00 0.00 0.00 4.79
2874 4018 3.027974 ACGGACTTCTTTTCTTCTCCG 57.972 47.619 2.43 2.43 45.01 4.63
2878 4033 4.618912 GGTACGTACGGACTTCTTTTCTTC 59.381 45.833 28.62 5.56 0.00 2.87
2892 4047 2.889154 GAAAGGGGCGGGTACGTACG 62.889 65.000 18.98 15.01 43.45 3.67
2894 4049 1.190833 TTGAAAGGGGCGGGTACGTA 61.191 55.000 0.00 0.00 43.45 3.57
2895 4050 1.844544 ATTGAAAGGGGCGGGTACGT 61.845 55.000 0.00 0.00 43.45 3.57
2911 4066 1.502231 CTGACCCCTATCGCGAATTG 58.498 55.000 15.24 6.11 0.00 2.32
2974 4152 1.272872 TGGTAGTACAGGTGTCTCCCC 60.273 57.143 2.06 0.00 36.75 4.81
2981 4159 4.683832 GCTACAAGATGGTAGTACAGGTG 58.316 47.826 2.06 0.00 42.18 4.00
2992 4170 2.240500 GCCGCTCGCTACAAGATGG 61.241 63.158 0.00 0.00 0.00 3.51
2993 4171 2.580470 CGCCGCTCGCTACAAGATG 61.580 63.158 0.00 0.00 34.21 2.90
3023 4592 1.527844 GCCACCCAGAGATGCATCC 60.528 63.158 23.06 14.22 0.00 3.51
3025 4594 2.191375 CGCCACCCAGAGATGCAT 59.809 61.111 0.00 0.00 0.00 3.96
3027 4596 4.479993 AGCGCCACCCAGAGATGC 62.480 66.667 2.29 0.00 0.00 3.91
3028 4597 2.202987 GAGCGCCACCCAGAGATG 60.203 66.667 2.29 0.00 0.00 2.90
3029 4598 3.842923 CGAGCGCCACCCAGAGAT 61.843 66.667 2.29 0.00 0.00 2.75
3130 4700 0.527600 TCGTACTCATCGCATGTGGC 60.528 55.000 6.39 0.00 39.90 5.01
3179 4749 3.599285 GACGGCCGGACAATCACCA 62.599 63.158 31.76 0.00 0.00 4.17
3313 6552 1.067416 GGCGACGATGATAGGTGCA 59.933 57.895 0.00 0.00 0.00 4.57
3329 6578 2.476241 CCGAAAGTTGCAAAATCTTGGC 59.524 45.455 0.00 0.00 32.76 4.52
3358 6607 4.554363 CGGCGCCCGTCTCTACAG 62.554 72.222 23.46 0.00 42.73 2.74
3390 6639 1.006454 GTAGTCCTTATCCGCCCGC 60.006 63.158 0.00 0.00 0.00 6.13
3395 6644 2.287909 GCAGCAGAGTAGTCCTTATCCG 60.288 54.545 0.00 0.00 0.00 4.18
3396 6645 2.962421 AGCAGCAGAGTAGTCCTTATCC 59.038 50.000 0.00 0.00 0.00 2.59
3412 6663 1.211818 CTCGCATCTTCCGTAGCAGC 61.212 60.000 0.00 0.00 0.00 5.25


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

AutoCloner maintained by Alex Coulton.