Multiple sequence alignment - TraesCS2D01G321100

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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 TraesCS2D01G321100 chr2D 100.000 3780 0 0 695 4474 412475422 412471643 0.000000e+00 6981.0
1 TraesCS2D01G321100 chr2D 100.000 342 0 0 1 342 412476116 412475775 2.270000e-177 632.0
2 TraesCS2D01G321100 chr2D 90.654 107 7 2 695 799 126853359 126853254 6.030000e-29 139.0
3 TraesCS2D01G321100 chr2B 92.926 1965 99 22 966 2895 485896279 485894320 0.000000e+00 2822.0
4 TraesCS2D01G321100 chr2B 93.952 1207 54 9 2897 4099 485894157 485892966 0.000000e+00 1807.0
5 TraesCS2D01G321100 chr2B 95.652 115 2 2 854 967 485896441 485896329 9.890000e-42 182.0
6 TraesCS2D01G321100 chr2B 95.745 94 4 0 2267 2360 216462816 216462909 7.750000e-33 152.0
7 TraesCS2D01G321100 chr2A 94.275 1310 60 6 2766 4067 579699079 579697777 0.000000e+00 1989.0
8 TraesCS2D01G321100 chr2A 92.906 1325 52 24 966 2255 579700954 579699637 0.000000e+00 1888.0
9 TraesCS2D01G321100 chr2A 94.236 399 15 4 2376 2772 579699621 579699229 1.780000e-168 603.0
10 TraesCS2D01G321100 chr2A 94.225 329 15 2 4150 4474 579697775 579697447 2.400000e-137 499.0
11 TraesCS2D01G321100 chr2A 91.262 103 9 0 2258 2360 559118409 559118511 1.680000e-29 141.0
12 TraesCS2D01G321100 chr2A 84.348 115 9 4 853 966 579701103 579700997 2.200000e-18 104.0
13 TraesCS2D01G321100 chr3D 96.491 342 12 0 1 342 131595446 131595787 2.340000e-157 566.0
14 TraesCS2D01G321100 chr3D 96.199 342 13 0 1 342 213995136 213995477 1.090000e-155 560.0
15 TraesCS2D01G321100 chr3D 79.470 151 18 11 4172 4315 302293722 302293866 1.320000e-15 95.3
16 TraesCS2D01G321100 chr6D 96.199 342 13 0 1 342 296394338 296394679 1.090000e-155 560.0
17 TraesCS2D01G321100 chr6D 95.858 338 14 0 1 338 347408794 347408457 8.460000e-152 547.0
18 TraesCS2D01G321100 chr6D 95.322 342 16 0 1 342 340967792 340968133 1.090000e-150 544.0
19 TraesCS2D01G321100 chr6D 83.091 550 45 18 1728 2260 122992713 122992195 1.470000e-124 457.0
20 TraesCS2D01G321100 chr6D 91.071 112 8 2 2255 2366 133209835 133209726 2.790000e-32 150.0
21 TraesCS2D01G321100 chr6D 88.136 118 10 3 696 811 340968395 340968510 2.170000e-28 137.0
22 TraesCS2D01G321100 chr6D 94.186 86 5 0 2370 2455 122992110 122992025 1.010000e-26 132.0
23 TraesCS2D01G321100 chr5D 95.906 342 14 0 1 342 380011779 380012120 5.060000e-154 555.0
24 TraesCS2D01G321100 chr7D 95.614 342 15 0 1 342 394989068 394989409 2.350000e-152 549.0
25 TraesCS2D01G321100 chr7D 88.333 240 14 4 1910 2138 518776678 518776442 4.410000e-70 276.0
26 TraesCS2D01G321100 chr7D 86.239 109 9 2 2126 2234 518776423 518776321 3.660000e-21 113.0
27 TraesCS2D01G321100 chr7D 92.208 77 4 1 2379 2455 518776324 518776250 1.700000e-19 108.0
28 TraesCS2D01G321100 chr4D 95.322 342 16 0 1 342 64211655 64211314 1.090000e-150 544.0
29 TraesCS2D01G321100 chr4D 95.322 342 16 0 1 342 173604138 173604479 1.090000e-150 544.0
30 TraesCS2D01G321100 chr6A 83.568 426 32 19 1728 2138 158242429 158242831 9.150000e-97 364.0
31 TraesCS2D01G321100 chr6B 83.294 425 33 15 1728 2138 216634545 216634145 1.530000e-94 357.0
32 TraesCS2D01G321100 chr7B 80.469 384 31 21 1915 2260 589939073 589938696 2.070000e-63 254.0
33 TraesCS2D01G321100 chr7B 93.750 80 5 0 2376 2455 589938689 589938610 2.190000e-23 121.0
34 TraesCS2D01G321100 chr7A 91.589 107 7 2 2267 2373 48103172 48103068 3.610000e-31 147.0
35 TraesCS2D01G321100 chr4B 89.076 119 11 2 2253 2370 71586942 71586825 3.610000e-31 147.0
36 TraesCS2D01G321100 chr1A 93.000 100 6 1 2267 2366 106228083 106228181 1.300000e-30 145.0
37 TraesCS2D01G321100 chr5B 90.654 107 10 0 2254 2360 55370933 55371039 4.670000e-30 143.0
38 TraesCS2D01G321100 chr5B 83.333 108 13 4 695 799 14221039 14220934 1.320000e-15 95.3
39 TraesCS2D01G321100 chr1B 89.286 112 11 1 2255 2366 301273392 301273502 6.030000e-29 139.0
40 TraesCS2D01G321100 chr1B 89.720 107 8 2 695 799 417466211 417466316 2.810000e-27 134.0
41 TraesCS2D01G321100 chr1B 88.785 107 9 2 695 799 341104634 341104529 1.310000e-25 128.0
42 TraesCS2D01G321100 chr3B 83.673 98 14 1 695 790 17186640 17186737 1.710000e-14 91.6


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 TraesCS2D01G321100 chr2D 412471643 412476116 4473 True 3806.500000 6981 100.000000 1 4474 2 chr2D.!!$R2 4473
1 TraesCS2D01G321100 chr2B 485892966 485896441 3475 True 1603.666667 2822 94.176667 854 4099 3 chr2B.!!$R1 3245
2 TraesCS2D01G321100 chr2A 579697447 579701103 3656 True 1016.600000 1989 91.998000 853 4474 5 chr2A.!!$R1 3621
3 TraesCS2D01G321100 chr6D 340967792 340968510 718 False 340.500000 544 91.729000 1 811 2 chr6D.!!$F2 810
4 TraesCS2D01G321100 chr6D 122992025 122992713 688 True 294.500000 457 88.638500 1728 2455 2 chr6D.!!$R3 727

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
79 80 0.465097 ATGCAGGGAAGGAATGCGAG 60.465 55.0 0.00 0.00 42.92 5.03 F
801 804 0.869730 ACACGTGTTTGGCGTTATCC 59.130 50.0 17.22 0.00 40.90 2.59 F
1828 1911 0.330604 AGGACATGCTGCATCCTGTT 59.669 50.0 20.91 1.04 41.47 3.16 F
2362 2517 0.757935 CTAATTCCGGACGGAGGGGA 60.758 60.0 13.64 0.00 46.06 4.81 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1536 1610 0.323957 AGACGGCCTTAGGGTGTTTC 59.676 55.0 0.00 0.00 34.45 2.78 R
2263 2382 0.538118 CAACTAATTCCGGACGGGGA 59.462 55.0 1.83 0.51 36.01 4.81 R
3179 3664 0.843309 TTGACTTTGTGCCTCCTGGA 59.157 50.0 0.00 0.00 34.57 3.86 R
4128 4619 0.539986 GGTTCCCCATGCGAGACTTA 59.460 55.0 0.00 0.00 0.00 2.24 R

All possible primers

Listed here are all possible primers based on the multiple sequence alignment and SNPs generated previously. A lower penalty score indicates a better primer. If the AutoCloner primers did not work during PCR or sequencing, these could be used as alternatives.

Download all possible primers: (Forward) (Reverse)
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
42 43 0.721718 CTCGAGCGAAACATTGACCC 59.278 55.000 0.00 0.00 0.00 4.46
44 45 0.953471 CGAGCGAAACATTGACCCCA 60.953 55.000 0.00 0.00 0.00 4.96
65 66 1.140652 GAGGAGAGGGGAGAAATGCAG 59.859 57.143 0.00 0.00 0.00 4.41
73 74 1.005924 GGGAGAAATGCAGGGAAGGAA 59.994 52.381 0.00 0.00 0.00 3.36
74 75 2.358615 GGGAGAAATGCAGGGAAGGAAT 60.359 50.000 0.00 0.00 0.00 3.01
76 77 2.100418 GAGAAATGCAGGGAAGGAATGC 59.900 50.000 0.00 0.00 40.40 3.56
79 80 0.465097 ATGCAGGGAAGGAATGCGAG 60.465 55.000 0.00 0.00 42.92 5.03
108 109 2.093235 AGGAGCATTACCTTCACTCTGC 60.093 50.000 0.00 0.00 33.55 4.26
155 156 4.773117 GCGAGTCCCACCGACGAC 62.773 72.222 0.00 0.00 46.92 4.34
273 274 3.611766 AGTGGAGAGTAAATGGAACCG 57.388 47.619 0.00 0.00 0.00 4.44
718 719 2.935201 GCACACAAAATCAGCCAAAACA 59.065 40.909 0.00 0.00 0.00 2.83
753 756 2.032799 GCACAAACTGTTGAACGGATGA 59.967 45.455 11.72 0.00 38.20 2.92
754 757 3.849645 GCACAAACTGTTGAACGGATGAG 60.850 47.826 11.72 8.99 38.20 2.90
771 774 1.507141 GAGGGCGTGTGGTTGAGTTG 61.507 60.000 0.00 0.00 0.00 3.16
772 775 2.551912 GGGCGTGTGGTTGAGTTGG 61.552 63.158 0.00 0.00 0.00 3.77
774 777 3.030652 CGTGTGGTTGAGTTGGCC 58.969 61.111 0.00 0.00 0.00 5.36
776 779 1.785041 CGTGTGGTTGAGTTGGCCAG 61.785 60.000 5.11 0.00 32.31 4.85
791 794 3.582120 CAGCGCCCACACGTGTTT 61.582 61.111 20.79 0.00 34.88 2.83
801 804 0.869730 ACACGTGTTTGGCGTTATCC 59.130 50.000 17.22 0.00 40.90 2.59
806 809 3.067040 ACGTGTTTGGCGTTATCCTTTTT 59.933 39.130 0.00 0.00 39.79 1.94
807 810 3.666797 CGTGTTTGGCGTTATCCTTTTTC 59.333 43.478 0.00 0.00 0.00 2.29
808 811 3.666797 GTGTTTGGCGTTATCCTTTTTCG 59.333 43.478 0.00 0.00 0.00 3.46
810 813 4.202030 TGTTTGGCGTTATCCTTTTTCGTT 60.202 37.500 0.00 0.00 0.00 3.85
811 814 4.571372 TTGGCGTTATCCTTTTTCGTTT 57.429 36.364 0.00 0.00 0.00 3.60
812 815 5.686159 TTGGCGTTATCCTTTTTCGTTTA 57.314 34.783 0.00 0.00 0.00 2.01
813 816 5.686159 TGGCGTTATCCTTTTTCGTTTAA 57.314 34.783 0.00 0.00 0.00 1.52
814 817 6.069684 TGGCGTTATCCTTTTTCGTTTAAA 57.930 33.333 0.00 0.00 0.00 1.52
815 818 6.501781 TGGCGTTATCCTTTTTCGTTTAAAA 58.498 32.000 0.00 0.00 35.24 1.52
816 819 6.976925 TGGCGTTATCCTTTTTCGTTTAAAAA 59.023 30.769 0.00 0.00 43.20 1.94
952 958 2.282958 AGGTCACGCCTCCGAGAA 60.283 61.111 0.00 0.00 46.96 2.87
1029 1086 3.036959 GGAGGGGAGGGAGAGGGA 61.037 72.222 0.00 0.00 0.00 4.20
1398 1455 3.068024 TGCTTTCTTTTTGTGCGAGGATT 59.932 39.130 0.00 0.00 0.00 3.01
1463 1535 6.478512 AGGTAGACAAGATTCTGGATTCTC 57.521 41.667 0.00 0.00 0.00 2.87
1474 1546 8.260099 AGATTCTGGATTCTCACAGATTCATA 57.740 34.615 14.90 0.00 42.73 2.15
1520 1593 3.413327 GATCTATCTACGGCTGTCCTCA 58.587 50.000 0.00 0.00 0.00 3.86
1582 1657 5.103940 CCATGAAGGAAGGGAGGATAGAAAA 60.104 44.000 0.00 0.00 41.22 2.29
1617 1692 0.813184 ATGGGAGCGCTTCAAATGTG 59.187 50.000 19.50 0.00 0.00 3.21
1620 1698 1.130561 GGGAGCGCTTCAAATGTGTAC 59.869 52.381 19.50 0.00 0.00 2.90
1642 1724 3.060003 CGTGCAGAAGACTTGAAGAAGTG 60.060 47.826 0.00 0.00 42.80 3.16
1747 1829 3.181495 GCAGCTAGTATAGGATGCCTACG 60.181 52.174 0.00 0.00 39.10 3.51
1828 1911 0.330604 AGGACATGCTGCATCCTGTT 59.669 50.000 20.91 1.04 41.47 3.16
1872 1955 5.163612 GGCAGTGGTCTTTCAAAGAATATCC 60.164 44.000 0.00 0.00 39.67 2.59
1873 1956 5.649831 GCAGTGGTCTTTCAAAGAATATCCT 59.350 40.000 0.00 0.00 39.67 3.24
1874 1957 6.404074 GCAGTGGTCTTTCAAAGAATATCCTG 60.404 42.308 0.00 5.50 39.67 3.86
1912 1999 9.463443 AAAACTGCTAAAGATAAATGAACACAC 57.537 29.630 0.00 0.00 0.00 3.82
2000 2087 2.703007 AGTTCAGAAACTGTCTCTGCCT 59.297 45.455 6.26 2.39 44.13 4.75
2001 2088 2.805099 GTTCAGAAACTGTCTCTGCCTG 59.195 50.000 6.26 0.00 40.18 4.85
2008 2117 1.000283 ACTGTCTCTGCCTGTCTTTCG 60.000 52.381 0.00 0.00 0.00 3.46
2205 2315 7.816640 TGTTGGTCTTTTATAATGCTTCTGTC 58.183 34.615 0.00 0.00 0.00 3.51
2292 2411 3.424433 CCGGAATTAGTTGACGCTCAAAC 60.424 47.826 0.00 0.00 38.22 2.93
2329 2484 7.013369 AGACGTATTTCAGTGCTAGATACATCA 59.987 37.037 0.00 0.00 0.00 3.07
2333 2488 9.319143 GTATTTCAGTGCTAGATACATCAGTTT 57.681 33.333 0.00 0.00 0.00 2.66
2361 2516 1.047034 ACTAATTCCGGACGGAGGGG 61.047 60.000 13.64 8.20 46.06 4.79
2362 2517 0.757935 CTAATTCCGGACGGAGGGGA 60.758 60.000 13.64 0.00 46.06 4.81
2363 2518 0.757935 TAATTCCGGACGGAGGGGAG 60.758 60.000 13.64 0.00 46.06 4.30
2364 2519 2.817420 AATTCCGGACGGAGGGGAGT 62.817 60.000 13.64 0.00 46.06 3.85
2365 2520 1.941403 ATTCCGGACGGAGGGGAGTA 61.941 60.000 13.64 0.00 46.06 2.59
2366 2521 2.043652 CCGGACGGAGGGGAGTAA 60.044 66.667 4.40 0.00 37.50 2.24
2367 2522 2.421399 CCGGACGGAGGGGAGTAAC 61.421 68.421 4.40 0.00 37.50 2.50
2368 2523 1.679977 CGGACGGAGGGGAGTAACA 60.680 63.158 0.00 0.00 0.00 2.41
2369 2524 1.041447 CGGACGGAGGGGAGTAACAT 61.041 60.000 0.00 0.00 0.00 2.71
2370 2525 1.751733 CGGACGGAGGGGAGTAACATA 60.752 57.143 0.00 0.00 0.00 2.29
2374 2529 3.819902 GACGGAGGGGAGTAACATAGTAG 59.180 52.174 0.00 0.00 0.00 2.57
2624 2779 4.918810 AAGGTTTGTGTGTTCAAGGATC 57.081 40.909 0.00 0.00 0.00 3.36
2663 2819 8.948631 TTTTGTGCTGTCCATTAAATGTAAAA 57.051 26.923 0.00 0.00 0.00 1.52
2707 2866 3.710209 AGCATCTGAAGTACAAGCCTT 57.290 42.857 0.00 0.00 0.00 4.35
2824 3140 4.955335 TGAGTCCTAATCTAACTTGGGGA 58.045 43.478 0.00 0.00 0.00 4.81
3041 3518 2.020720 TGTCATGTTCTTGCACGGTTT 58.979 42.857 0.00 0.00 0.00 3.27
3054 3531 3.064820 TGCACGGTTTTCTCTTTCAACTC 59.935 43.478 0.00 0.00 0.00 3.01
3116 3593 7.716998 TCTTCATTATCTTCCATCCTAACTTGC 59.283 37.037 0.00 0.00 0.00 4.01
3129 3606 7.065563 CCATCCTAACTTGCTAGATATTGCATC 59.934 40.741 1.04 0.00 39.07 3.91
3179 3664 5.829391 TGGCATAAATGTCATGATAGTTGCT 59.171 36.000 14.40 0.49 37.51 3.91
3302 3787 0.831307 GGACGGATATATCCCAGGGC 59.169 60.000 23.44 13.21 44.24 5.19
3356 3841 6.382869 AAGAGAGTTGTCAAATTGGTTCTG 57.617 37.500 0.00 0.00 0.00 3.02
3371 3856 3.055819 TGGTTCTGAAGAAGAATCCTCCG 60.056 47.826 0.00 0.00 46.53 4.63
3558 4045 2.944349 GAGTACTACTTGGTCTCTCGGG 59.056 54.545 0.00 0.00 0.00 5.14
3770 4257 3.909776 TTCTTCAATCTTGTGCAGCAG 57.090 42.857 0.00 0.00 0.00 4.24
3822 4309 2.917933 TGTTTCGCTTGCAGCCTATAT 58.082 42.857 0.00 0.00 38.18 0.86
3887 4376 5.294060 GCACAAACAAATGTCAATTTCCTGT 59.706 36.000 0.00 0.00 33.59 4.00
3888 4377 6.183360 GCACAAACAAATGTCAATTTCCTGTT 60.183 34.615 0.00 0.00 33.59 3.16
3889 4378 7.626028 GCACAAACAAATGTCAATTTCCTGTTT 60.626 33.333 0.00 0.00 35.84 2.83
3890 4379 7.904461 CACAAACAAATGTCAATTTCCTGTTTC 59.096 33.333 0.00 0.00 34.37 2.78
3891 4380 7.065683 ACAAACAAATGTCAATTTCCTGTTTCC 59.934 33.333 0.00 0.00 34.37 3.13
3892 4381 6.484364 ACAAATGTCAATTTCCTGTTTCCT 57.516 33.333 0.00 0.00 33.59 3.36
3893 4382 6.282930 ACAAATGTCAATTTCCTGTTTCCTG 58.717 36.000 0.00 0.00 33.59 3.86
3909 4398 3.417069 TCCTGCCATAATGGGTATTCG 57.583 47.619 0.00 0.00 38.19 3.34
4021 4511 3.077359 ACTGTCAGAAATGCTGCTAACC 58.923 45.455 6.91 0.00 44.52 2.85
4025 4516 2.742053 TCAGAAATGCTGCTAACCGAAC 59.258 45.455 0.00 0.00 44.52 3.95
4074 4565 4.569943 ACATCTTGAAAGCTTCGCTCTAA 58.430 39.130 0.00 0.00 38.25 2.10
4101 4592 4.796231 CCGGCAGCGCGACTAAGT 62.796 66.667 12.10 0.00 0.00 2.24
4102 4593 3.248171 CGGCAGCGCGACTAAGTC 61.248 66.667 12.10 0.00 0.00 3.01
4103 4594 2.182030 GGCAGCGCGACTAAGTCT 59.818 61.111 12.10 0.00 0.00 3.24
4104 4595 1.874466 GGCAGCGCGACTAAGTCTC 60.874 63.158 12.10 0.00 0.00 3.36
4105 4596 2.218239 GCAGCGCGACTAAGTCTCG 61.218 63.158 12.10 0.00 42.55 4.04
4143 4634 1.115467 AGACTAAGTCTCGCATGGGG 58.885 55.000 10.21 1.00 38.71 4.96
4144 4635 1.112113 GACTAAGTCTCGCATGGGGA 58.888 55.000 10.21 3.50 0.00 4.81
4145 4636 1.480954 GACTAAGTCTCGCATGGGGAA 59.519 52.381 10.21 0.00 0.00 3.97
4146 4637 1.207329 ACTAAGTCTCGCATGGGGAAC 59.793 52.381 10.21 8.42 0.00 3.62
4172 4663 1.664649 TGCGCGTGGTCTTCTTCTG 60.665 57.895 8.43 0.00 0.00 3.02
4431 4922 9.405587 GAAGATATTTTTGAAATCGTGAACCAA 57.594 29.630 0.00 0.00 0.00 3.67
4442 4933 4.497473 TCGTGAACCAATTCAAATCCAC 57.503 40.909 0.00 0.00 46.40 4.02
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
31 32 2.307098 CTCTCCTCTGGGGTCAATGTTT 59.693 50.000 0.00 0.00 36.25 2.83
42 43 1.767681 CATTTCTCCCCTCTCCTCTGG 59.232 57.143 0.00 0.00 0.00 3.86
44 45 1.274069 TGCATTTCTCCCCTCTCCTCT 60.274 52.381 0.00 0.00 0.00 3.69
65 66 2.125106 ACGCTCGCATTCCTTCCC 60.125 61.111 0.00 0.00 0.00 3.97
73 74 3.376935 CTCCTTCCCACGCTCGCAT 62.377 63.158 0.00 0.00 0.00 4.73
74 75 4.069232 CTCCTTCCCACGCTCGCA 62.069 66.667 0.00 0.00 0.00 5.10
76 77 2.859273 AATGCTCCTTCCCACGCTCG 62.859 60.000 0.00 0.00 0.00 5.03
79 80 1.095807 GGTAATGCTCCTTCCCACGC 61.096 60.000 0.00 0.00 0.00 5.34
108 109 1.883084 GTATTCGCCGGAGTGCCTG 60.883 63.158 5.05 0.00 0.00 4.85
187 188 2.494530 GGCGAGAGGAGAAGGCGAT 61.495 63.158 0.00 0.00 0.00 4.58
694 695 3.199764 GGCTGATTTTGTGTGCCAC 57.800 52.632 0.00 0.00 42.79 5.01
711 712 2.988493 CACGAATCTTGGCATGTTTTGG 59.012 45.455 13.14 7.42 0.00 3.28
718 719 1.246649 TTGTGCACGAATCTTGGCAT 58.753 45.000 13.13 0.00 38.68 4.40
753 756 1.525995 CAACTCAACCACACGCCCT 60.526 57.895 0.00 0.00 0.00 5.19
754 757 2.551912 CCAACTCAACCACACGCCC 61.552 63.158 0.00 0.00 0.00 6.13
774 777 3.582120 AAACACGTGTGGGCGCTG 61.582 61.111 24.16 0.00 34.88 5.18
776 779 4.622456 CCAAACACGTGTGGGCGC 62.622 66.667 24.16 0.00 34.88 6.53
790 793 4.571372 AAACGAAAAAGGATAACGCCAA 57.429 36.364 0.00 0.00 0.00 4.52
791 794 5.686159 TTAAACGAAAAAGGATAACGCCA 57.314 34.783 0.00 0.00 0.00 5.69
845 848 0.948623 TCAACGACGTGGCTTCCATG 60.949 55.000 0.00 3.66 45.34 3.66
846 849 0.036388 ATCAACGACGTGGCTTCCAT 60.036 50.000 0.00 0.00 35.28 3.41
847 850 0.604073 TATCAACGACGTGGCTTCCA 59.396 50.000 0.00 0.00 0.00 3.53
848 851 1.717194 TTATCAACGACGTGGCTTCC 58.283 50.000 0.00 0.00 0.00 3.46
849 852 4.550255 GCTATTTATCAACGACGTGGCTTC 60.550 45.833 0.00 0.00 0.00 3.86
850 853 3.308866 GCTATTTATCAACGACGTGGCTT 59.691 43.478 0.00 0.00 0.00 4.35
851 854 2.864343 GCTATTTATCAACGACGTGGCT 59.136 45.455 0.00 0.00 0.00 4.75
915 921 3.119708 CCTTTTCTGCTGACTATTGGTGC 60.120 47.826 0.00 0.00 0.00 5.01
916 922 4.074970 ACCTTTTCTGCTGACTATTGGTG 58.925 43.478 0.00 0.00 0.00 4.17
948 954 3.181478 CCGGGTACTGTAGTTGGATTCTC 60.181 52.174 0.00 0.00 0.00 2.87
952 958 0.828677 GCCGGGTACTGTAGTTGGAT 59.171 55.000 2.18 0.00 0.00 3.41
1171 1228 2.571757 CAGAAGCAGGTACCGCGA 59.428 61.111 8.23 0.00 0.00 5.87
1378 1435 4.610945 ACAATCCTCGCACAAAAAGAAAG 58.389 39.130 0.00 0.00 0.00 2.62
1398 1455 3.743396 GTGCCAAACAAACAGAACAAACA 59.257 39.130 0.00 0.00 0.00 2.83
1463 1535 6.207417 ACCCTTTGTTTCACTATGAATCTGTG 59.793 38.462 0.00 0.00 36.11 3.66
1474 1546 7.562088 TCCAACTATAAAACCCTTTGTTTCACT 59.438 33.333 0.00 0.00 46.39 3.41
1536 1610 0.323957 AGACGGCCTTAGGGTGTTTC 59.676 55.000 0.00 0.00 34.45 2.78
1617 1692 3.639538 TCTTCAAGTCTTCTGCACGTAC 58.360 45.455 0.00 0.00 0.00 3.67
1620 1698 3.060003 CACTTCTTCAAGTCTTCTGCACG 60.060 47.826 0.00 0.00 41.24 5.34
1747 1829 6.500684 TCACTTCAGATTGTAATTCAAGCC 57.499 37.500 3.36 0.00 42.63 4.35
1828 1911 3.686405 GCCCTGATCATTTCATCAGTGGA 60.686 47.826 16.17 0.00 45.91 4.02
1873 1956 1.953686 GCAGTTTTGCTACTGGGAACA 59.046 47.619 13.49 0.00 46.95 3.18
1874 1957 2.706555 GCAGTTTTGCTACTGGGAAC 57.293 50.000 13.49 0.00 46.95 3.62
1912 1999 5.068460 AGCAAGCACACTATACTTCTCCTAG 59.932 44.000 0.00 0.00 0.00 3.02
2000 2087 7.658167 TGTTTATCACAGGATTAACGAAAGACA 59.342 33.333 0.00 0.00 42.87 3.41
2001 2088 8.025243 TGTTTATCACAGGATTAACGAAAGAC 57.975 34.615 0.00 0.00 42.87 3.01
2171 2281 7.994425 TTATAAAAGACCAACAGCTCAATCA 57.006 32.000 0.00 0.00 0.00 2.57
2172 2282 7.433425 GCATTATAAAAGACCAACAGCTCAATC 59.567 37.037 0.00 0.00 0.00 2.67
2173 2283 7.123247 AGCATTATAAAAGACCAACAGCTCAAT 59.877 33.333 0.00 0.00 0.00 2.57
2174 2284 6.434028 AGCATTATAAAAGACCAACAGCTCAA 59.566 34.615 0.00 0.00 0.00 3.02
2205 2315 1.144503 CCATCCAATCCAAGGAGAGGG 59.855 57.143 9.05 2.36 38.83 4.30
2263 2382 0.538118 CAACTAATTCCGGACGGGGA 59.462 55.000 1.83 0.51 36.01 4.81
2265 2384 1.648504 GTCAACTAATTCCGGACGGG 58.351 55.000 1.83 1.55 35.59 5.28
2292 2411 7.268659 GCACTGAAATACGTCTAGATACATACG 59.731 40.741 0.00 0.00 40.99 3.06
2300 2419 7.713942 TGTATCTAGCACTGAAATACGTCTAGA 59.286 37.037 0.00 0.00 36.50 2.43
2308 2427 9.317936 CAAACTGATGTATCTAGCACTGAAATA 57.682 33.333 0.00 0.00 0.00 1.40
2329 2484 3.432252 CGGAATTAGTTGACGCTCAAACT 59.568 43.478 2.65 1.11 38.22 2.66
2333 2488 1.546923 TCCGGAATTAGTTGACGCTCA 59.453 47.619 0.00 0.00 0.00 4.26
2398 2553 5.048782 GTCATTTAGTCACACAAATGCAGGA 60.049 40.000 9.11 0.00 40.41 3.86
2570 2725 3.376234 TCAATGCATGTAGAGCAGCTTTC 59.624 43.478 0.00 0.00 46.36 2.62
2582 2737 5.049198 CCTTAATGTATCGCTCAATGCATGT 60.049 40.000 0.00 0.00 43.06 3.21
2624 2779 5.978919 ACAGCACAAAATCACTGTAACAATG 59.021 36.000 0.00 0.00 41.41 2.82
2663 2819 9.869757 GCTTTAAGTTGTCCCATAAAATAATGT 57.130 29.630 0.00 0.00 0.00 2.71
2667 2825 9.474313 AGATGCTTTAAGTTGTCCCATAAAATA 57.526 29.630 0.00 0.00 0.00 1.40
2668 2826 8.253113 CAGATGCTTTAAGTTGTCCCATAAAAT 58.747 33.333 0.00 0.00 0.00 1.82
2707 2866 8.642935 TCCATAAGTAATGTTTCACCATTGAA 57.357 30.769 0.00 0.00 35.85 2.69
3017 3494 2.741517 CCGTGCAAGAACATGACATGTA 59.258 45.455 21.10 1.90 44.07 2.29
3041 3518 6.334989 TGTTCAGTAACGAGTTGAAAGAGAA 58.665 36.000 0.00 0.00 38.53 2.87
3054 3531 8.332464 TCAAAGAGTACAAAATGTTCAGTAACG 58.668 33.333 0.00 0.00 38.53 3.18
3129 3606 1.156736 CTTAGTTCCACCCTGCAACG 58.843 55.000 0.00 0.00 0.00 4.10
3179 3664 0.843309 TTGACTTTGTGCCTCCTGGA 59.157 50.000 0.00 0.00 34.57 3.86
3371 3856 1.433471 GCCATAAGCGAACCAAGCC 59.567 57.895 0.00 0.00 34.64 4.35
3714 4201 6.437477 AGATTCTCACCTATGACAGTAACACA 59.563 38.462 0.00 0.00 0.00 3.72
3770 4257 2.221906 CTGCCAGGCACAATTGAGGC 62.222 60.000 19.51 19.51 42.32 4.70
3822 4309 4.358214 TCACAATCCTGTATACCCAGACA 58.642 43.478 0.00 0.00 34.23 3.41
3887 4376 4.141287 CGAATACCCATTATGGCAGGAAA 58.859 43.478 5.57 0.00 35.79 3.13
3888 4377 3.137544 ACGAATACCCATTATGGCAGGAA 59.862 43.478 5.57 0.00 35.79 3.36
3889 4378 2.708861 ACGAATACCCATTATGGCAGGA 59.291 45.455 5.57 0.00 35.79 3.86
3890 4379 3.074412 GACGAATACCCATTATGGCAGG 58.926 50.000 5.57 0.00 35.79 4.85
3891 4380 3.738982 TGACGAATACCCATTATGGCAG 58.261 45.455 5.57 0.00 35.79 4.85
3892 4381 3.847671 TGACGAATACCCATTATGGCA 57.152 42.857 5.57 0.00 35.79 4.92
3893 4382 3.119849 GCATGACGAATACCCATTATGGC 60.120 47.826 5.57 0.00 35.79 4.40
3909 4398 2.874701 AGTCACACTCAAACTGCATGAC 59.125 45.455 0.00 3.64 36.16 3.06
4021 4511 0.947244 GAGCCAGCCATATTGGTTCG 59.053 55.000 0.00 0.00 40.46 3.95
4025 4516 1.177256 GCAGGAGCCAGCCATATTGG 61.177 60.000 0.00 0.00 36.04 3.16
4124 4615 1.115467 CCCCATGCGAGACTTAGTCT 58.885 55.000 15.44 15.44 46.42 3.24
4125 4616 1.112113 TCCCCATGCGAGACTTAGTC 58.888 55.000 3.85 3.85 0.00 2.59
4126 4617 1.207329 GTTCCCCATGCGAGACTTAGT 59.793 52.381 0.00 0.00 0.00 2.24
4127 4618 1.473434 GGTTCCCCATGCGAGACTTAG 60.473 57.143 0.00 0.00 0.00 2.18
4128 4619 0.539986 GGTTCCCCATGCGAGACTTA 59.460 55.000 0.00 0.00 0.00 2.24
4129 4620 1.299976 GGTTCCCCATGCGAGACTT 59.700 57.895 0.00 0.00 0.00 3.01
4130 4621 2.670148 GGGTTCCCCATGCGAGACT 61.670 63.158 0.00 0.00 44.65 3.24
4131 4622 2.124695 GGGTTCCCCATGCGAGAC 60.125 66.667 0.00 0.00 44.65 3.36
4320 4811 6.451064 ACACGAAAAGAGAAAGGAAAACAT 57.549 33.333 0.00 0.00 0.00 2.71
4340 4831 8.421701 ACGAATTTTAAAATATGTTCGCAACAC 58.578 29.630 23.96 0.00 45.50 3.32
4404 4895 7.748683 TGGTTCACGATTTCAAAAATATCTTCG 59.251 33.333 0.00 0.00 0.00 3.79
4422 4913 3.233578 CGTGGATTTGAATTGGTTCACG 58.766 45.455 0.00 0.00 43.72 4.35


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

AutoCloner maintained by Alex Coulton.