Multiple sequence alignment - TraesCS7A01G411300

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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 TraesCS7A01G411300 chr7A 100.000 3113 0 0 1 3113 602097802 602100914 0.000000e+00 5749
1 TraesCS7A01G411300 chr7A 77.453 479 53 25 1001 1470 602659033 602658601 5.190000e-58 235
2 TraesCS7A01G411300 chr7B 93.078 1358 59 7 213 1539 555654701 555656054 0.000000e+00 1954
3 TraesCS7A01G411300 chr7B 92.083 720 42 8 1534 2251 555656081 555656787 0.000000e+00 1000
4 TraesCS7A01G411300 chr7B 83.558 815 65 22 2293 3087 555656798 555657563 0.000000e+00 699
5 TraesCS7A01G411300 chr7B 79.630 594 76 28 1537 2126 556333129 556332577 4.870000e-103 385
6 TraesCS7A01G411300 chr7B 77.149 477 71 17 1001 1470 556333680 556333235 3.100000e-60 243
7 TraesCS7A01G411300 chr7B 93.130 131 6 2 102 230 555654555 555654684 4.100000e-44 189
8 TraesCS7A01G411300 chr7D 93.820 1165 40 9 403 1539 521762844 521764004 0.000000e+00 1724
9 TraesCS7A01G411300 chr7D 90.190 948 58 17 1534 2465 521764037 521764965 0.000000e+00 1203
10 TraesCS7A01G411300 chr7D 86.342 637 54 19 2458 3086 521764995 521765606 0.000000e+00 664
11 TraesCS7A01G411300 chr7D 77.393 606 74 24 1533 2129 522154460 522153909 5.050000e-78 302
12 TraesCS7A01G411300 chr1D 77.778 333 37 18 488 814 37528511 37528210 1.480000e-38 171


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 TraesCS7A01G411300 chr7A 602097802 602100914 3112 False 5749.0 5749 100.000000 1 3113 1 chr7A.!!$F1 3112
1 TraesCS7A01G411300 chr7B 555654555 555657563 3008 False 960.5 1954 90.462250 102 3087 4 chr7B.!!$F1 2985
2 TraesCS7A01G411300 chr7B 556332577 556333680 1103 True 314.0 385 78.389500 1001 2126 2 chr7B.!!$R1 1125
3 TraesCS7A01G411300 chr7D 521762844 521765606 2762 False 1197.0 1724 90.117333 403 3086 3 chr7D.!!$F1 2683
4 TraesCS7A01G411300 chr7D 522153909 522154460 551 True 302.0 302 77.393000 1533 2129 1 chr7D.!!$R1 596


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
20 21 0.878086 GTAGCTCCGAGCAGGCAATC 60.878 60.0 22.29 1.31 45.56 2.67 F
23 24 1.028868 GCTCCGAGCAGGCAATCTTT 61.029 55.0 15.78 0.00 41.89 2.52 F
955 1037 1.159285 CCAACGACATGCACACAGAT 58.841 50.0 0.00 0.00 0.00 2.90 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1145 1232 0.390472 CGTGCCTTTCTCACCCTCTC 60.390 60.0 0.00 0.00 0.00 3.20 R
1587 1743 0.752054 GACATCTCCAGGAGCCTCTG 59.248 60.0 12.26 8.78 34.70 3.35 R
2183 2371 0.662619 TTTTTGTCCTCTGCGTGCAG 59.337 50.0 15.59 15.59 44.86 4.41 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
17 18 3.826754 CGTAGCTCCGAGCAGGCA 61.827 66.667 22.29 1.79 45.56 4.75
18 19 2.579201 GTAGCTCCGAGCAGGCAA 59.421 61.111 22.29 0.00 45.56 4.52
19 20 1.144936 GTAGCTCCGAGCAGGCAAT 59.855 57.895 22.29 3.05 45.56 3.56
20 21 0.878086 GTAGCTCCGAGCAGGCAATC 60.878 60.000 22.29 1.31 45.56 2.67
21 22 1.045350 TAGCTCCGAGCAGGCAATCT 61.045 55.000 22.29 1.58 45.56 2.40
22 23 1.451028 GCTCCGAGCAGGCAATCTT 60.451 57.895 15.78 0.00 41.89 2.40
23 24 1.028868 GCTCCGAGCAGGCAATCTTT 61.029 55.000 15.78 0.00 41.89 2.52
24 25 1.457346 CTCCGAGCAGGCAATCTTTT 58.543 50.000 0.00 0.00 40.77 2.27
25 26 2.632377 CTCCGAGCAGGCAATCTTTTA 58.368 47.619 0.00 0.00 40.77 1.52
26 27 2.352960 CTCCGAGCAGGCAATCTTTTAC 59.647 50.000 0.00 0.00 40.77 2.01
27 28 2.083774 CCGAGCAGGCAATCTTTTACA 58.916 47.619 0.00 0.00 0.00 2.41
28 29 2.487762 CCGAGCAGGCAATCTTTTACAA 59.512 45.455 0.00 0.00 0.00 2.41
29 30 3.129287 CCGAGCAGGCAATCTTTTACAAT 59.871 43.478 0.00 0.00 0.00 2.71
30 31 4.380867 CCGAGCAGGCAATCTTTTACAATT 60.381 41.667 0.00 0.00 0.00 2.32
31 32 4.795278 CGAGCAGGCAATCTTTTACAATTC 59.205 41.667 0.00 0.00 0.00 2.17
32 33 5.077134 AGCAGGCAATCTTTTACAATTCC 57.923 39.130 0.00 0.00 0.00 3.01
33 34 3.859386 GCAGGCAATCTTTTACAATTCCG 59.141 43.478 0.00 0.00 0.00 4.30
34 35 4.618227 GCAGGCAATCTTTTACAATTCCGT 60.618 41.667 0.00 0.00 0.00 4.69
35 36 4.858692 CAGGCAATCTTTTACAATTCCGTG 59.141 41.667 0.00 0.00 0.00 4.94
36 37 4.082245 AGGCAATCTTTTACAATTCCGTGG 60.082 41.667 0.00 0.00 0.00 4.94
37 38 4.321675 GGCAATCTTTTACAATTCCGTGGT 60.322 41.667 0.00 0.00 0.00 4.16
38 39 4.621034 GCAATCTTTTACAATTCCGTGGTG 59.379 41.667 0.00 0.00 0.00 4.17
39 40 5.563867 GCAATCTTTTACAATTCCGTGGTGA 60.564 40.000 0.00 0.00 0.00 4.02
40 41 6.442952 CAATCTTTTACAATTCCGTGGTGAA 58.557 36.000 0.00 0.00 0.00 3.18
41 42 6.834168 ATCTTTTACAATTCCGTGGTGAAT 57.166 33.333 0.00 0.00 36.53 2.57
42 43 6.642707 TCTTTTACAATTCCGTGGTGAATT 57.357 33.333 0.00 0.00 43.84 2.17
43 44 7.747155 TCTTTTACAATTCCGTGGTGAATTA 57.253 32.000 0.00 0.00 41.74 1.40
44 45 8.343168 TCTTTTACAATTCCGTGGTGAATTAT 57.657 30.769 0.00 0.00 41.74 1.28
45 46 9.451002 TCTTTTACAATTCCGTGGTGAATTATA 57.549 29.630 0.00 0.00 41.74 0.98
46 47 9.498307 CTTTTACAATTCCGTGGTGAATTATAC 57.502 33.333 0.00 0.00 41.74 1.47
47 48 8.795842 TTTACAATTCCGTGGTGAATTATACT 57.204 30.769 0.00 0.00 41.74 2.12
48 49 9.887629 TTTACAATTCCGTGGTGAATTATACTA 57.112 29.630 0.00 0.00 41.74 1.82
49 50 9.887629 TTACAATTCCGTGGTGAATTATACTAA 57.112 29.630 0.00 0.00 41.74 2.24
50 51 8.974060 ACAATTCCGTGGTGAATTATACTAAT 57.026 30.769 0.00 0.00 41.74 1.73
54 55 8.542497 TTCCGTGGTGAATTATACTAATATGC 57.458 34.615 0.00 0.00 0.00 3.14
55 56 7.672240 TCCGTGGTGAATTATACTAATATGCA 58.328 34.615 0.00 0.00 0.00 3.96
56 57 8.151596 TCCGTGGTGAATTATACTAATATGCAA 58.848 33.333 0.00 0.00 0.00 4.08
57 58 8.227791 CCGTGGTGAATTATACTAATATGCAAC 58.772 37.037 0.00 0.00 0.00 4.17
58 59 8.769891 CGTGGTGAATTATACTAATATGCAACA 58.230 33.333 0.00 0.00 0.00 3.33
59 60 9.878599 GTGGTGAATTATACTAATATGCAACAC 57.121 33.333 0.00 0.00 34.81 3.32
60 61 9.845740 TGGTGAATTATACTAATATGCAACACT 57.154 29.630 0.00 0.00 0.00 3.55
74 75 9.950680 AATATGCAACACTAATTAAGTACATGC 57.049 29.630 0.00 9.32 39.14 4.06
75 76 6.809630 TGCAACACTAATTAAGTACATGCA 57.190 33.333 9.66 9.66 42.83 3.96
76 77 7.389803 TGCAACACTAATTAAGTACATGCAT 57.610 32.000 0.00 0.00 41.47 3.96
77 78 8.499403 TGCAACACTAATTAAGTACATGCATA 57.501 30.769 0.00 0.00 41.47 3.14
78 79 8.951243 TGCAACACTAATTAAGTACATGCATAA 58.049 29.630 0.00 0.00 41.47 1.90
79 80 9.781834 GCAACACTAATTAAGTACATGCATAAA 57.218 29.630 0.00 0.00 38.81 1.40
112 113 2.073816 ACATGTACCCTTTCGCTTTCG 58.926 47.619 0.00 0.00 0.00 3.46
142 143 1.893137 GGAAATTCAAGGGTGGACCAC 59.107 52.381 16.86 16.86 43.89 4.16
158 159 3.006967 GGACCACTTTCAAGTCTAGCTCA 59.993 47.826 0.00 0.00 37.08 4.26
162 163 3.426859 CACTTTCAAGTCTAGCTCACACG 59.573 47.826 0.00 0.00 37.08 4.49
163 164 3.318275 ACTTTCAAGTCTAGCTCACACGA 59.682 43.478 0.00 0.00 32.86 4.35
164 165 3.560902 TTCAAGTCTAGCTCACACGAG 57.439 47.619 0.00 0.00 42.66 4.18
239 275 6.822073 TGAAAATGTCTATCGTTATGACCG 57.178 37.500 0.00 0.00 0.00 4.79
249 285 3.281158 TCGTTATGACCGACCACAGATA 58.719 45.455 0.00 0.00 0.00 1.98
252 288 4.274214 CGTTATGACCGACCACAGATACTA 59.726 45.833 0.00 0.00 0.00 1.82
256 292 4.784177 TGACCGACCACAGATACTACATA 58.216 43.478 0.00 0.00 0.00 2.29
358 396 4.846779 ACAAATTGACAACGCCAATACT 57.153 36.364 0.00 0.00 33.51 2.12
397 435 4.723248 CGTGCCTTTCCTTCTTGTAAATC 58.277 43.478 0.00 0.00 0.00 2.17
407 459 5.013079 TCCTTCTTGTAAATCTTCTCCAGCA 59.987 40.000 0.00 0.00 0.00 4.41
452 504 3.885484 ATGAGTGCGTTTTGTCTGAAG 57.115 42.857 0.00 0.00 0.00 3.02
484 536 3.387225 GAGGGCGCACTACCTTCCC 62.387 68.421 14.87 0.00 37.18 3.97
595 652 5.239306 TCATAAATCCGGTTTCATGATCTGC 59.761 40.000 6.95 0.00 0.00 4.26
609 666 5.123344 TCATGATCTGCACAAACTTCTCATG 59.877 40.000 0.00 0.00 39.86 3.07
703 760 8.361889 TGCTACTTTGTACTGATGTAACTGTTA 58.638 33.333 0.00 0.00 0.00 2.41
793 851 4.067896 TCTCAGAAAGGCAAAGATCACAC 58.932 43.478 0.00 0.00 0.00 3.82
846 919 6.824305 TGAGAAAACCAATCTCAGGATTTC 57.176 37.500 2.27 6.80 46.23 2.17
955 1037 1.159285 CCAACGACATGCACACAGAT 58.841 50.000 0.00 0.00 0.00 2.90
1067 1151 2.357952 AGCACCGAAACAAAAGTTCCTC 59.642 45.455 0.00 0.00 0.00 3.71
1145 1232 3.074412 ACCCTGATTTTGTGAGCTAACG 58.926 45.455 0.00 0.00 0.00 3.18
1221 1309 1.268079 GCCACAGAAAGAACCAAGCTC 59.732 52.381 0.00 0.00 0.00 4.09
1409 1497 4.507916 TCCTCCTCCTCCTCGCCG 62.508 72.222 0.00 0.00 0.00 6.46
1514 1632 4.401022 TGTGTGCATCAATCTCCTCTTTT 58.599 39.130 0.00 0.00 0.00 2.27
1518 1636 4.335037 GTGCATCAATCTCCTCTTTTCTCC 59.665 45.833 0.00 0.00 0.00 3.71
1587 1743 2.899900 ACTTTTCCAGAAATCCAAGGCC 59.100 45.455 0.00 0.00 0.00 5.19
1605 1761 2.913463 CAGAGGCTCCTGGAGATGT 58.087 57.895 27.53 10.31 0.00 3.06
1611 1767 0.667993 GCTCCTGGAGATGTCGAGAG 59.332 60.000 27.53 1.31 30.18 3.20
1823 1979 2.607187 GCGCTCAGCTTCTAAAGTACA 58.393 47.619 0.00 0.00 44.04 2.90
1824 1980 2.600867 GCGCTCAGCTTCTAAAGTACAG 59.399 50.000 0.00 0.00 44.04 2.74
1947 2111 9.392259 GTTGTTTACTGGCTAGTATTTATCCTT 57.608 33.333 11.07 0.00 39.08 3.36
1959 2123 9.817809 CTAGTATTTATCCTTTCTGTGTGCTTA 57.182 33.333 0.00 0.00 0.00 3.09
1997 2181 9.686683 AATTACCAAGCTATGTTTAGTCAGATT 57.313 29.630 0.00 0.00 0.00 2.40
2052 2236 5.416271 AAGTATGTACACCAAGGAATCGT 57.584 39.130 0.00 0.00 0.00 3.73
2183 2371 5.718649 ACAGTATGCACGTATTTGACATC 57.281 39.130 0.00 0.00 42.53 3.06
2215 2403 9.691362 GCAGAGGACAAAAATATTTTGAGTTAA 57.309 29.630 19.24 0.00 33.83 2.01
2230 2418 8.723942 TTTTGAGTTAAAGAGATAGAGATGCC 57.276 34.615 0.00 0.00 0.00 4.40
2251 2439 4.414852 CCATATGGAAGCAAAACTGAACG 58.585 43.478 17.49 0.00 37.39 3.95
2252 2440 2.422276 ATGGAAGCAAAACTGAACGC 57.578 45.000 0.00 0.00 0.00 4.84
2254 2442 2.566913 TGGAAGCAAAACTGAACGCTA 58.433 42.857 0.00 0.00 33.45 4.26
2255 2443 2.289547 TGGAAGCAAAACTGAACGCTAC 59.710 45.455 0.00 0.00 33.45 3.58
2256 2444 2.350484 GGAAGCAAAACTGAACGCTACC 60.350 50.000 0.00 0.00 33.45 3.18
2257 2445 2.256117 AGCAAAACTGAACGCTACCT 57.744 45.000 0.00 0.00 31.60 3.08
2259 2447 2.290641 AGCAAAACTGAACGCTACCTTG 59.709 45.455 0.00 0.00 31.60 3.61
2260 2448 2.032924 GCAAAACTGAACGCTACCTTGT 59.967 45.455 0.00 0.00 0.00 3.16
2261 2449 3.848554 GCAAAACTGAACGCTACCTTGTC 60.849 47.826 0.00 0.00 0.00 3.18
2262 2450 2.902705 AACTGAACGCTACCTTGTCA 57.097 45.000 0.00 0.00 0.00 3.58
2263 2451 2.902705 ACTGAACGCTACCTTGTCAA 57.097 45.000 0.00 0.00 0.00 3.18
2264 2452 3.402628 ACTGAACGCTACCTTGTCAAT 57.597 42.857 0.00 0.00 0.00 2.57
2276 2464 6.712547 GCTACCTTGTCAATAATATCAAGCCT 59.287 38.462 0.00 0.00 36.82 4.58
2277 2465 6.949352 ACCTTGTCAATAATATCAAGCCTG 57.051 37.500 0.00 0.00 36.82 4.85
2299 2487 5.912892 TGCGAGTTATGAAATCTGGATGTA 58.087 37.500 0.00 0.00 0.00 2.29
2316 2504 6.346096 TGGATGTAAGCAGTATTACCAACTC 58.654 40.000 0.00 0.00 35.23 3.01
2319 2507 8.148351 GGATGTAAGCAGTATTACCAACTCATA 58.852 37.037 0.00 0.00 35.23 2.15
2418 2614 8.575565 TTGTTAGCTAACTTAGAATATGCTCG 57.424 34.615 31.14 0.00 37.12 5.03
2423 2619 3.113260 ACTTAGAATATGCTCGGTGGC 57.887 47.619 0.00 0.00 0.00 5.01
2428 2624 2.036475 AGAATATGCTCGGTGGCTACAG 59.964 50.000 1.52 0.00 0.00 2.74
2456 2652 2.517166 GGGCAAATCGGAGAGGCC 60.517 66.667 0.00 0.00 46.79 5.19
2459 2693 0.965363 GGCAAATCGGAGAGGCCAAA 60.965 55.000 5.01 0.00 46.75 3.28
2494 2729 6.149308 CACACTCCACATGATTAGTTTGCTAA 59.851 38.462 0.00 0.00 40.98 3.09
2533 2768 5.348451 GCCTTTAAACACACCAAATAGCATG 59.652 40.000 0.00 0.00 0.00 4.06
2613 2848 4.654262 TGATACAAGGGAAGTGGGTATCTC 59.346 45.833 0.00 0.00 40.42 2.75
2630 2865 6.375455 GGGTATCTCAGACAAATTGTGTTCAT 59.625 38.462 2.20 0.00 41.96 2.57
2645 2880 5.564768 TGTGTTCATTGTTAGTTTGACACG 58.435 37.500 0.00 0.00 30.72 4.49
2648 2883 5.351740 TGTTCATTGTTAGTTTGACACGACA 59.648 36.000 0.00 0.00 0.00 4.35
2669 2904 6.127758 CGACAAAGATACCCAAATGAAATCCA 60.128 38.462 0.00 0.00 0.00 3.41
2673 2908 7.510549 AAGATACCCAAATGAAATCCATACG 57.489 36.000 0.00 0.00 34.45 3.06
2703 2938 2.158449 GCGGTTCAGACTCTGTTGAATG 59.842 50.000 5.94 0.00 35.91 2.67
2733 2968 8.928270 ATTTGCAGAATTTTCAAATGCAAAAA 57.072 23.077 23.32 11.19 42.62 1.94
2734 2969 7.737525 TTGCAGAATTTTCAAATGCAAAAAC 57.262 28.000 13.04 0.00 34.18 2.43
2735 2970 7.086230 TGCAGAATTTTCAAATGCAAAAACT 57.914 28.000 0.00 0.00 0.00 2.66
2736 2971 8.206325 TGCAGAATTTTCAAATGCAAAAACTA 57.794 26.923 0.00 0.00 0.00 2.24
2737 2972 8.336806 TGCAGAATTTTCAAATGCAAAAACTAG 58.663 29.630 0.00 0.00 0.00 2.57
2795 3033 7.117379 GCGGGCTTTAATCGTAATAAATCTAGT 59.883 37.037 0.00 0.00 0.00 2.57
2820 3058 6.229936 AGCAATGCAGATAAACAATTCCAT 57.770 33.333 8.35 0.00 0.00 3.41
2841 3079 3.855858 TCGCCCATTAAAAAGCCATTTC 58.144 40.909 0.00 0.00 0.00 2.17
2869 3110 9.764363 AGAAAGAAAAGGTCAATTTTATTGGTC 57.236 29.630 0.00 0.00 34.70 4.02
3001 3244 8.539674 GTCTGATTTTAAAATTTGACCACACAC 58.460 33.333 22.82 9.41 31.18 3.82
3017 3261 6.696411 ACCACACACTTCAAAAAGAAATCAA 58.304 32.000 0.00 0.00 35.40 2.57
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 2.635229 ATTGCCTGCTCGGAGCTACG 62.635 60.000 28.42 13.63 42.97 3.51
1 2 0.878086 GATTGCCTGCTCGGAGCTAC 60.878 60.000 28.42 18.22 42.97 3.58
2 3 1.045350 AGATTGCCTGCTCGGAGCTA 61.045 55.000 28.42 15.06 42.97 3.32
3 4 1.908340 AAGATTGCCTGCTCGGAGCT 61.908 55.000 28.42 9.16 42.97 4.09
4 5 1.028868 AAAGATTGCCTGCTCGGAGC 61.029 55.000 22.78 22.78 42.82 4.70
5 6 1.457346 AAAAGATTGCCTGCTCGGAG 58.543 50.000 0.00 0.00 33.16 4.63
6 7 2.290008 TGTAAAAGATTGCCTGCTCGGA 60.290 45.455 0.00 0.00 33.16 4.55
7 8 2.083774 TGTAAAAGATTGCCTGCTCGG 58.916 47.619 0.00 0.00 0.00 4.63
8 9 3.829886 TTGTAAAAGATTGCCTGCTCG 57.170 42.857 0.00 0.00 0.00 5.03
9 10 5.105063 GGAATTGTAAAAGATTGCCTGCTC 58.895 41.667 0.00 0.00 0.00 4.26
10 11 4.380867 CGGAATTGTAAAAGATTGCCTGCT 60.381 41.667 0.00 0.00 0.00 4.24
11 12 3.859386 CGGAATTGTAAAAGATTGCCTGC 59.141 43.478 0.00 0.00 0.00 4.85
12 13 4.858692 CACGGAATTGTAAAAGATTGCCTG 59.141 41.667 0.00 0.00 0.00 4.85
13 14 4.082245 CCACGGAATTGTAAAAGATTGCCT 60.082 41.667 0.00 0.00 0.00 4.75
14 15 4.173256 CCACGGAATTGTAAAAGATTGCC 58.827 43.478 0.00 0.00 0.00 4.52
15 16 4.621034 CACCACGGAATTGTAAAAGATTGC 59.379 41.667 0.00 0.00 0.00 3.56
16 17 6.007936 TCACCACGGAATTGTAAAAGATTG 57.992 37.500 0.00 0.00 0.00 2.67
17 18 6.642707 TTCACCACGGAATTGTAAAAGATT 57.357 33.333 0.00 0.00 0.00 2.40
18 19 6.834168 ATTCACCACGGAATTGTAAAAGAT 57.166 33.333 0.00 0.00 33.85 2.40
19 20 6.642707 AATTCACCACGGAATTGTAAAAGA 57.357 33.333 0.00 0.00 43.79 2.52
20 21 9.498307 GTATAATTCACCACGGAATTGTAAAAG 57.502 33.333 10.49 0.00 44.77 2.27
21 22 9.233649 AGTATAATTCACCACGGAATTGTAAAA 57.766 29.630 10.49 0.00 44.77 1.52
22 23 8.795842 AGTATAATTCACCACGGAATTGTAAA 57.204 30.769 10.49 0.00 44.77 2.01
23 24 9.887629 TTAGTATAATTCACCACGGAATTGTAA 57.112 29.630 10.49 2.69 44.77 2.41
25 26 8.974060 ATTAGTATAATTCACCACGGAATTGT 57.026 30.769 10.49 7.12 44.77 2.71
28 29 9.162764 GCATATTAGTATAATTCACCACGGAAT 57.837 33.333 0.00 0.00 39.11 3.01
29 30 8.151596 TGCATATTAGTATAATTCACCACGGAA 58.848 33.333 0.00 0.00 0.00 4.30
30 31 7.672240 TGCATATTAGTATAATTCACCACGGA 58.328 34.615 0.00 0.00 0.00 4.69
31 32 7.899178 TGCATATTAGTATAATTCACCACGG 57.101 36.000 0.00 0.00 0.00 4.94
32 33 8.769891 TGTTGCATATTAGTATAATTCACCACG 58.230 33.333 0.00 0.00 0.00 4.94
33 34 9.878599 GTGTTGCATATTAGTATAATTCACCAC 57.121 33.333 0.00 0.00 0.00 4.16
34 35 9.845740 AGTGTTGCATATTAGTATAATTCACCA 57.154 29.630 0.00 0.00 0.00 4.17
48 49 9.950680 GCATGTACTTAATTAGTGTTGCATATT 57.049 29.630 0.00 0.00 37.73 1.28
49 50 9.119418 TGCATGTACTTAATTAGTGTTGCATAT 57.881 29.630 11.26 0.00 39.87 1.78
50 51 8.499403 TGCATGTACTTAATTAGTGTTGCATA 57.501 30.769 11.26 0.00 39.87 3.14
51 52 7.389803 TGCATGTACTTAATTAGTGTTGCAT 57.610 32.000 11.26 8.29 39.87 3.96
52 53 6.809630 TGCATGTACTTAATTAGTGTTGCA 57.190 33.333 11.26 11.26 41.17 4.08
53 54 9.781834 TTTATGCATGTACTTAATTAGTGTTGC 57.218 29.630 10.16 7.99 37.73 4.17
77 78 9.984590 AAGGGTACATGTACTTAATGGTATTTT 57.015 29.630 29.89 9.60 36.36 1.82
78 79 9.984590 AAAGGGTACATGTACTTAATGGTATTT 57.015 29.630 29.89 16.08 36.36 1.40
79 80 9.623000 GAAAGGGTACATGTACTTAATGGTATT 57.377 33.333 29.89 14.71 36.36 1.89
80 81 7.929785 CGAAAGGGTACATGTACTTAATGGTAT 59.070 37.037 29.89 11.07 36.36 2.73
81 82 7.267128 CGAAAGGGTACATGTACTTAATGGTA 58.733 38.462 29.89 0.00 36.36 3.25
82 83 6.110707 CGAAAGGGTACATGTACTTAATGGT 58.889 40.000 29.89 12.91 36.36 3.55
83 84 5.007332 GCGAAAGGGTACATGTACTTAATGG 59.993 44.000 29.89 18.36 36.36 3.16
84 85 5.815740 AGCGAAAGGGTACATGTACTTAATG 59.184 40.000 29.89 18.39 36.36 1.90
85 86 5.985911 AGCGAAAGGGTACATGTACTTAAT 58.014 37.500 29.89 17.06 36.36 1.40
86 87 5.410355 AGCGAAAGGGTACATGTACTTAA 57.590 39.130 29.89 0.00 36.36 1.85
87 88 5.410355 AAGCGAAAGGGTACATGTACTTA 57.590 39.130 29.89 0.00 36.36 2.24
88 89 3.975168 AGCGAAAGGGTACATGTACTT 57.025 42.857 29.89 19.27 36.36 2.24
89 90 3.975168 AAGCGAAAGGGTACATGTACT 57.025 42.857 29.89 14.43 36.36 2.73
90 91 3.061697 CGAAAGCGAAAGGGTACATGTAC 59.938 47.826 25.00 25.00 40.82 2.90
91 92 3.056678 TCGAAAGCGAAAGGGTACATGTA 60.057 43.478 0.08 0.08 44.78 2.29
92 93 2.073816 CGAAAGCGAAAGGGTACATGT 58.926 47.619 2.69 2.69 40.82 3.21
93 94 2.343101 TCGAAAGCGAAAGGGTACATG 58.657 47.619 0.00 0.00 44.78 3.21
94 95 2.754946 TCGAAAGCGAAAGGGTACAT 57.245 45.000 0.00 0.00 44.78 2.29
112 113 4.584743 ACCCTTGAATTTCCACTTCACTTC 59.415 41.667 0.00 0.00 32.57 3.01
142 143 3.902150 TCGTGTGAGCTAGACTTGAAAG 58.098 45.455 0.00 0.00 0.00 2.62
239 275 7.841956 AGGCATATTATGTAGTATCTGTGGTC 58.158 38.462 5.60 0.00 0.00 4.02
249 285 8.807948 AAGTGTCAAAAGGCATATTATGTAGT 57.192 30.769 5.60 0.00 0.00 2.73
252 288 8.584157 TCAAAAGTGTCAAAAGGCATATTATGT 58.416 29.630 5.60 0.00 0.00 2.29
358 396 4.457496 GCCTAGCTGCGCCACTGA 62.457 66.667 4.18 0.00 0.00 3.41
376 414 5.966742 AGATTTACAAGAAGGAAAGGCAC 57.033 39.130 0.00 0.00 0.00 5.01
377 415 6.306987 AGAAGATTTACAAGAAGGAAAGGCA 58.693 36.000 0.00 0.00 0.00 4.75
380 418 7.361628 GCTGGAGAAGATTTACAAGAAGGAAAG 60.362 40.741 0.00 0.00 0.00 2.62
397 435 3.997021 ACGTTATTTCTGTGCTGGAGAAG 59.003 43.478 0.00 0.00 31.17 2.85
407 459 4.866508 TGAGAGTGGACGTTATTTCTGT 57.133 40.909 0.00 0.00 0.00 3.41
452 504 1.311651 GCCCTCTTTTCAGAGCAGGC 61.312 60.000 4.40 4.40 44.96 4.85
484 536 6.808008 AAAGAATGATGTTACCACTGAGTG 57.192 37.500 5.42 5.42 0.00 3.51
595 652 2.480419 GTCGGGTCATGAGAAGTTTGTG 59.520 50.000 0.00 0.00 0.00 3.33
609 666 6.980051 AAGAAAATAGTACATTGTCGGGTC 57.020 37.500 0.00 0.00 0.00 4.46
793 851 1.290324 CGATCAGCAGGGGATACGG 59.710 63.158 0.00 0.00 37.60 4.02
1031 1115 1.590932 GTGCTCTATGGCATCACTGG 58.409 55.000 1.65 0.00 44.34 4.00
1067 1151 2.192624 CCCAAAACGAGCAACAGTTTG 58.807 47.619 0.00 0.00 40.07 2.93
1079 1163 0.824182 TTAGCACCACCCCCAAAACG 60.824 55.000 0.00 0.00 0.00 3.60
1111 1198 2.431954 TCAGGGTTAGTACTCTCCCG 57.568 55.000 21.89 17.96 44.13 5.14
1145 1232 0.390472 CGTGCCTTTCTCACCCTCTC 60.390 60.000 0.00 0.00 0.00 3.20
1254 1342 4.950050 GCAGCTAGCTAAGATAAGACCAA 58.050 43.478 18.86 0.00 41.15 3.67
1409 1497 1.750399 ATGTGCCATGGGAAGCGAC 60.750 57.895 15.13 0.00 0.00 5.19
1514 1632 9.357161 GTAAGAGATATGAAGAAAGTAGGGAGA 57.643 37.037 0.00 0.00 0.00 3.71
1587 1743 0.752054 GACATCTCCAGGAGCCTCTG 59.248 60.000 12.26 8.78 34.70 3.35
1605 1761 1.593787 CAAGCTTCCTGGCTCTCGA 59.406 57.895 0.00 0.00 42.24 4.04
1611 1767 3.376918 GTGCCCAAGCTTCCTGGC 61.377 66.667 19.53 19.53 44.27 4.85
1820 1976 3.368013 CCCGCAACAAGATCAGTACTGTA 60.368 47.826 21.99 9.79 0.00 2.74
1821 1977 2.612972 CCCGCAACAAGATCAGTACTGT 60.613 50.000 21.99 9.95 0.00 3.55
1822 1978 2.002586 CCCGCAACAAGATCAGTACTG 58.997 52.381 17.17 17.17 0.00 2.74
1823 1979 1.623811 ACCCGCAACAAGATCAGTACT 59.376 47.619 0.00 0.00 0.00 2.73
1824 1980 1.732259 CACCCGCAACAAGATCAGTAC 59.268 52.381 0.00 0.00 0.00 2.73
1947 2111 6.578944 TCAAGAACTTACTAAGCACACAGAA 58.421 36.000 0.00 0.00 0.00 3.02
1959 2123 9.167311 CATAGCTTGGTAATTCAAGAACTTACT 57.833 33.333 10.29 1.20 44.98 2.24
1997 2181 6.003326 TGTTATAGGACGATAATCCGGTACA 58.997 40.000 0.00 0.00 44.22 2.90
2162 2350 5.731278 CAGATGTCAAATACGTGCATACTG 58.269 41.667 0.00 0.00 0.00 2.74
2171 2359 1.393196 TGCGTGCAGATGTCAAATACG 59.607 47.619 0.00 0.00 0.00 3.06
2183 2371 0.662619 TTTTTGTCCTCTGCGTGCAG 59.337 50.000 15.59 15.59 44.86 4.41
2215 2403 6.352051 GCTTCCATATGGCATCTCTATCTCTT 60.352 42.308 17.58 0.00 34.44 2.85
2216 2404 5.129155 GCTTCCATATGGCATCTCTATCTCT 59.871 44.000 17.58 0.00 34.44 3.10
2217 2405 5.105023 TGCTTCCATATGGCATCTCTATCTC 60.105 44.000 17.58 0.00 34.44 2.75
2218 2406 4.781621 TGCTTCCATATGGCATCTCTATCT 59.218 41.667 17.58 0.00 34.44 1.98
2219 2407 5.095145 TGCTTCCATATGGCATCTCTATC 57.905 43.478 17.58 0.00 34.44 2.08
2230 2418 3.853671 GCGTTCAGTTTTGCTTCCATATG 59.146 43.478 0.00 0.00 0.00 1.78
2251 2439 6.712547 AGGCTTGATATTATTGACAAGGTAGC 59.287 38.462 0.00 0.00 39.70 3.58
2252 2440 7.308229 GCAGGCTTGATATTATTGACAAGGTAG 60.308 40.741 0.00 0.00 39.70 3.18
2254 2442 5.300286 GCAGGCTTGATATTATTGACAAGGT 59.700 40.000 0.00 0.00 39.70 3.50
2255 2443 5.561532 CGCAGGCTTGATATTATTGACAAGG 60.562 44.000 0.00 0.00 39.70 3.61
2256 2444 5.237127 TCGCAGGCTTGATATTATTGACAAG 59.763 40.000 0.00 0.00 41.46 3.16
2257 2445 5.122519 TCGCAGGCTTGATATTATTGACAA 58.877 37.500 0.00 0.00 0.00 3.18
2259 2447 4.752101 ACTCGCAGGCTTGATATTATTGAC 59.248 41.667 0.00 0.00 0.00 3.18
2260 2448 4.960938 ACTCGCAGGCTTGATATTATTGA 58.039 39.130 0.00 0.00 0.00 2.57
2261 2449 5.679734 AACTCGCAGGCTTGATATTATTG 57.320 39.130 0.00 0.00 0.00 1.90
2262 2450 7.161404 TCATAACTCGCAGGCTTGATATTATT 58.839 34.615 0.00 0.00 0.00 1.40
2263 2451 6.701340 TCATAACTCGCAGGCTTGATATTAT 58.299 36.000 0.00 0.00 0.00 1.28
2264 2452 6.096673 TCATAACTCGCAGGCTTGATATTA 57.903 37.500 0.00 0.00 0.00 0.98
2276 2464 4.769688 ACATCCAGATTTCATAACTCGCA 58.230 39.130 0.00 0.00 0.00 5.10
2277 2465 6.564873 GCTTACATCCAGATTTCATAACTCGC 60.565 42.308 0.00 0.00 0.00 5.03
2299 2487 8.023021 TCTGATATGAGTTGGTAATACTGCTT 57.977 34.615 0.00 0.00 0.00 3.91
2316 2504 9.674824 GCAAATTGACCTAGAAAATCTGATATG 57.325 33.333 0.00 0.00 0.00 1.78
2319 2507 7.613022 TCTGCAAATTGACCTAGAAAATCTGAT 59.387 33.333 0.00 0.00 0.00 2.90
2332 2520 3.244976 CGGTTTCATCTGCAAATTGACC 58.755 45.455 0.00 0.00 0.00 4.02
2418 2614 2.691409 TTAGCATGTCTGTAGCCACC 57.309 50.000 0.00 0.00 0.00 4.61
2423 2619 3.198409 TGCCCATTAGCATGTCTGTAG 57.802 47.619 0.00 0.00 38.00 2.74
2428 2624 2.287788 CCGATTTGCCCATTAGCATGTC 60.288 50.000 0.00 0.00 43.64 3.06
2459 2693 7.765695 ATCATGTGGAGTGTGTTAGAATTTT 57.234 32.000 0.00 0.00 0.00 1.82
2465 2699 7.521529 CAAACTAATCATGTGGAGTGTGTTAG 58.478 38.462 0.00 0.00 0.00 2.34
2494 2729 7.540745 GTGTTTAAAGGCATGTAAATTCATCGT 59.459 33.333 0.00 0.00 0.00 3.73
2551 2786 8.057623 AGTTCCAATATCAATCCAAGAAGATGT 58.942 33.333 0.00 0.00 0.00 3.06
2552 2787 8.350722 CAGTTCCAATATCAATCCAAGAAGATG 58.649 37.037 0.00 0.00 0.00 2.90
2613 2848 8.633075 AACTAACAATGAACACAATTTGTCTG 57.367 30.769 0.00 0.00 37.51 3.51
2630 2865 6.671614 ATCTTTGTCGTGTCAAACTAACAA 57.328 33.333 0.00 0.00 34.30 2.83
2645 2880 7.169158 TGGATTTCATTTGGGTATCTTTGTC 57.831 36.000 0.00 0.00 0.00 3.18
2648 2883 7.777910 TCGTATGGATTTCATTTGGGTATCTTT 59.222 33.333 0.00 0.00 37.30 2.52
2669 2904 2.355132 CTGAACCGCTGTAGAGTCGTAT 59.645 50.000 3.77 0.00 0.00 3.06
2673 2908 1.813786 AGTCTGAACCGCTGTAGAGTC 59.186 52.381 0.00 0.00 0.00 3.36
2731 2966 5.805728 ACCTTATGTGTTGCTAGCTAGTTT 58.194 37.500 21.62 0.00 0.00 2.66
2732 2967 5.422214 ACCTTATGTGTTGCTAGCTAGTT 57.578 39.130 21.62 0.00 0.00 2.24
2733 2968 5.422214 AACCTTATGTGTTGCTAGCTAGT 57.578 39.130 21.62 2.93 0.00 2.57
2734 2969 5.643777 ACAAACCTTATGTGTTGCTAGCTAG 59.356 40.000 16.84 16.84 0.00 3.42
2735 2970 5.556915 ACAAACCTTATGTGTTGCTAGCTA 58.443 37.500 17.23 5.31 0.00 3.32
2736 2971 4.398319 ACAAACCTTATGTGTTGCTAGCT 58.602 39.130 17.23 0.00 0.00 3.32
2737 2972 4.215399 TGACAAACCTTATGTGTTGCTAGC 59.785 41.667 8.10 8.10 0.00 3.42
2795 3033 7.167924 TGGAATTGTTTATCTGCATTGCTAA 57.832 32.000 10.49 0.00 0.00 3.09
2820 3058 3.513515 AGAAATGGCTTTTTAATGGGCGA 59.486 39.130 0.00 0.00 0.00 5.54
2977 3220 8.647143 AGTGTGTGGTCAAATTTTAAAATCAG 57.353 30.769 13.68 9.48 0.00 2.90
2989 3232 5.713792 TCTTTTTGAAGTGTGTGGTCAAA 57.286 34.783 0.00 0.00 39.00 2.69



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

AutoCloner maintained by Alex Coulton.