Multiple sequence alignment - TraesCS1B01G283300

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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 TraesCS1B01G283300 chr1B 100.000 3323 0 0 1 3323 492305316 492308638 0.000000e+00 6137.0
1 TraesCS1B01G283300 chr1B 82.222 90 14 2 2087 2175 28764932 28764844 3.550000e-10 76.8
2 TraesCS1B01G283300 chr1B 93.750 48 3 0 2084 2131 13592270 13592317 4.600000e-09 73.1
3 TraesCS1B01G283300 chr1B 93.182 44 3 0 2086 2129 585166585 585166628 7.700000e-07 65.8
4 TraesCS1B01G283300 chr1D 92.833 2093 90 30 384 2450 367847140 367849198 0.000000e+00 2979.0
5 TraesCS1B01G283300 chr1D 93.594 843 44 5 2448 3288 367849279 367850113 0.000000e+00 1249.0
6 TraesCS1B01G283300 chr1D 88.372 344 21 7 21 353 367846708 367847043 2.400000e-106 396.0
7 TraesCS1B01G283300 chr1D 100.000 62 0 0 1 62 367846648 367846709 7.530000e-22 115.0
8 TraesCS1B01G283300 chr1D 76.923 130 30 0 1865 1994 433253063 433253192 1.280000e-09 75.0
9 TraesCS1B01G283300 chr1A 90.117 1973 134 29 1360 3285 467184977 467186935 0.000000e+00 2507.0
10 TraesCS1B01G283300 chr1A 83.413 1254 68 48 140 1354 467183777 467184929 0.000000e+00 1035.0
11 TraesCS1B01G283300 chr1A 96.491 114 4 0 21 134 467183563 467183676 4.380000e-44 189.0
12 TraesCS1B01G283300 chr1A 100.000 62 0 0 1 62 467183503 467183564 7.530000e-22 115.0
13 TraesCS1B01G283300 chr1A 82.418 91 14 2 2086 2175 21024736 21024647 9.880000e-11 78.7
14 TraesCS1B01G283300 chr1A 82.955 88 13 2 2086 2172 531643644 531643730 9.880000e-11 78.7
15 TraesCS1B01G283300 chr1A 100.000 37 0 0 3287 3323 382594729 382594693 5.950000e-08 69.4
16 TraesCS1B01G283300 chr1A 85.075 67 5 5 3262 3323 14611198 14611132 2.770000e-06 63.9
17 TraesCS1B01G283300 chr3A 87.368 95 12 0 1043 1137 746351509 746351603 3.500000e-20 110.0
18 TraesCS1B01G283300 chr3A 87.368 95 12 0 1043 1137 746363950 746363856 3.500000e-20 110.0
19 TraesCS1B01G283300 chr3A 86.316 95 13 0 1043 1137 746313267 746313361 1.630000e-18 104.0
20 TraesCS1B01G283300 chr3A 83.838 99 14 2 1256 1353 746351602 746351699 3.530000e-15 93.5
21 TraesCS1B01G283300 chr3A 88.462 78 7 2 1277 1353 746363836 746363760 3.530000e-15 93.5
22 TraesCS1B01G283300 chr3A 79.231 130 27 0 1864 1993 746351866 746351995 1.270000e-14 91.6
23 TraesCS1B01G283300 chr3A 81.250 112 21 0 1882 1993 746363575 746363464 1.270000e-14 91.6
24 TraesCS1B01G283300 chr3A 87.931 58 7 0 1864 1921 746313624 746313681 5.950000e-08 69.4
25 TraesCS1B01G283300 chr3D 90.667 75 7 0 1063 1137 611568453 611568379 2.110000e-17 100.0
26 TraesCS1B01G283300 chr3D 79.389 131 25 2 1864 1993 611558997 611559126 1.270000e-14 91.6
27 TraesCS1B01G283300 chr3D 89.855 69 7 0 1285 1353 611558762 611558830 4.570000e-14 89.8
28 TraesCS1B01G283300 chr3D 89.855 69 7 0 1285 1353 611568264 611568196 4.570000e-14 89.8
29 TraesCS1B01G283300 chr3B 88.462 78 7 2 1277 1353 829288982 829288906 3.530000e-15 93.5
30 TraesCS1B01G283300 chr3B 76.744 129 30 0 1864 1992 829273919 829274047 4.600000e-09 73.1
31 TraesCS1B01G283300 chr3B 78.378 111 24 0 1882 1992 829288721 829288611 4.600000e-09 73.1
32 TraesCS1B01G283300 chr6B 97.727 44 0 1 3281 3323 704788936 704788893 1.280000e-09 75.0
33 TraesCS1B01G283300 chr6B 93.333 45 1 2 3281 3323 699982994 699983038 7.700000e-07 65.8
34 TraesCS1B01G283300 chrUn 76.744 129 30 0 1864 1992 480633118 480633246 4.600000e-09 73.1
35 TraesCS1B01G283300 chr6D 86.885 61 8 0 2086 2146 356598478 356598418 5.950000e-08 69.4
36 TraesCS1B01G283300 chr5B 100.000 37 0 0 3287 3323 531360741 531360777 5.950000e-08 69.4
37 TraesCS1B01G283300 chr5B 91.837 49 0 4 3277 3323 469810474 469810520 7.700000e-07 65.8
38 TraesCS1B01G283300 chr4B 91.667 48 2 2 3277 3323 68661669 68661623 7.700000e-07 65.8
39 TraesCS1B01G283300 chr4B 91.489 47 3 1 3278 3323 126329447 126329493 2.770000e-06 63.9
40 TraesCS1B01G283300 chr2B 100.000 34 0 0 3290 3323 52411535 52411502 2.770000e-06 63.9


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 TraesCS1B01G283300 chr1B 492305316 492308638 3322 False 6137.00 6137 100.00000 1 3323 1 chr1B.!!$F2 3322
1 TraesCS1B01G283300 chr1D 367846648 367850113 3465 False 1184.75 2979 93.69975 1 3288 4 chr1D.!!$F2 3287
2 TraesCS1B01G283300 chr1A 467183503 467186935 3432 False 961.50 2507 92.50525 1 3285 4 chr1A.!!$F2 3284

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
382 560 0.110238 CAACATTCACTGGGCGTTCG 60.110 55.0 0.00 0.00 0.00 3.95 F
1354 1611 0.106894 GACCGGGATGATCAAGGTCC 59.893 60.0 20.73 15.39 40.17 4.46 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1410 1709 0.321021 AGGCAGATGATGATCTCGGC 59.679 55.000 9.02 9.02 36.75 5.54 R
3110 3537 1.271379 GGGCTCACCACTTTGCTAAGA 60.271 52.381 14.98 0.00 39.85 2.10 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
112 153 2.249535 ATTGGCAGCAGCGCTATCG 61.250 57.895 10.99 1.46 43.41 2.92
138 179 4.640364 TGACATGCATCGGCTTATTCATA 58.360 39.130 0.00 0.00 41.91 2.15
142 183 6.985117 ACATGCATCGGCTTATTCATAATTT 58.015 32.000 0.00 0.00 41.91 1.82
143 184 7.086376 ACATGCATCGGCTTATTCATAATTTC 58.914 34.615 0.00 0.00 41.91 2.17
144 185 6.012658 TGCATCGGCTTATTCATAATTTCC 57.987 37.500 0.00 0.00 41.91 3.13
146 187 6.088824 GCATCGGCTTATTCATAATTTCCTG 58.911 40.000 0.00 0.00 36.96 3.86
147 188 6.615088 CATCGGCTTATTCATAATTTCCTGG 58.385 40.000 0.00 0.00 0.00 4.45
258 396 0.242286 AGATCGATCTGAATCCGGCG 59.758 55.000 26.78 0.00 35.42 6.46
273 411 2.480555 GCGCCTGTTCGTCCATTG 59.519 61.111 0.00 0.00 0.00 2.82
274 412 2.325082 GCGCCTGTTCGTCCATTGT 61.325 57.895 0.00 0.00 0.00 2.71
275 413 1.852067 GCGCCTGTTCGTCCATTGTT 61.852 55.000 0.00 0.00 0.00 2.83
276 414 1.434555 CGCCTGTTCGTCCATTGTTA 58.565 50.000 0.00 0.00 0.00 2.41
277 415 1.393539 CGCCTGTTCGTCCATTGTTAG 59.606 52.381 0.00 0.00 0.00 2.34
279 417 2.415512 GCCTGTTCGTCCATTGTTAGAC 59.584 50.000 0.00 0.00 0.00 2.59
280 418 3.000727 CCTGTTCGTCCATTGTTAGACC 58.999 50.000 0.00 0.00 0.00 3.85
281 419 3.556213 CCTGTTCGTCCATTGTTAGACCA 60.556 47.826 0.00 0.00 0.00 4.02
283 421 3.181464 TGTTCGTCCATTGTTAGACCACA 60.181 43.478 0.00 0.00 0.00 4.17
284 422 3.755112 TCGTCCATTGTTAGACCACAA 57.245 42.857 0.00 0.00 40.92 3.33
285 423 4.280436 TCGTCCATTGTTAGACCACAAT 57.720 40.909 0.00 0.00 46.34 2.71
286 424 4.250464 TCGTCCATTGTTAGACCACAATC 58.750 43.478 0.00 0.00 44.08 2.67
340 484 1.051812 CTCCCAACACCTCTGACTGT 58.948 55.000 0.00 0.00 0.00 3.55
341 485 1.417890 CTCCCAACACCTCTGACTGTT 59.582 52.381 0.00 0.00 0.00 3.16
375 553 3.545703 GGGGAGTATCAACATTCACTGG 58.454 50.000 0.00 0.00 36.25 4.00
382 560 0.110238 CAACATTCACTGGGCGTTCG 60.110 55.000 0.00 0.00 0.00 3.95
404 614 4.619227 CCACAGGCGGTTCACGGT 62.619 66.667 0.00 0.00 44.51 4.83
426 638 1.131883 AGCTGATTTGTGCTTCGATGC 59.868 47.619 15.88 15.88 35.86 3.91
436 648 3.233578 GTGCTTCGATGCGAAATGAAAA 58.766 40.909 17.33 0.00 45.23 2.29
437 649 3.853671 GTGCTTCGATGCGAAATGAAAAT 59.146 39.130 17.33 0.00 45.23 1.82
440 652 6.033407 GTGCTTCGATGCGAAATGAAAATAAA 59.967 34.615 17.33 0.00 45.23 1.40
441 653 6.751425 TGCTTCGATGCGAAATGAAAATAAAT 59.249 30.769 17.33 0.00 45.23 1.40
442 654 7.044117 TGCTTCGATGCGAAATGAAAATAAATC 60.044 33.333 17.33 0.00 45.23 2.17
451 665 7.050811 CGAAATGAAAATAAATCAATTCGCGG 58.949 34.615 6.13 0.00 46.63 6.46
452 666 6.826893 AATGAAAATAAATCAATTCGCGGG 57.173 33.333 6.13 0.00 0.00 6.13
741 985 5.009610 AGTTGCCCAGTTTGTTTATACTGTG 59.990 40.000 0.00 0.00 40.06 3.66
742 986 4.465886 TGCCCAGTTTGTTTATACTGTGT 58.534 39.130 0.00 0.00 40.06 3.72
748 992 8.788806 CCCAGTTTGTTTATACTGTGTTTATGA 58.211 33.333 0.00 0.00 40.06 2.15
838 1088 3.803082 GCACGACACCGCATGCAT 61.803 61.111 19.57 1.32 37.61 3.96
839 1089 2.869646 CACGACACCGCATGCATT 59.130 55.556 19.57 0.00 39.95 3.56
911 1164 0.821517 CCCCTATATATGCACGCCGA 59.178 55.000 0.00 0.00 0.00 5.54
994 1248 2.493907 AAGCAGCGACCTCCTTCGAC 62.494 60.000 0.00 0.00 41.78 4.20
1168 1423 1.212616 CCATTTCGTCTCAGATCCGC 58.787 55.000 0.00 0.00 0.00 5.54
1172 1427 4.933064 CGTCTCAGATCCGCCCGC 62.933 72.222 0.00 0.00 0.00 6.13
1248 1505 3.443045 CCCTTGCGCGAATTGGCT 61.443 61.111 12.10 0.00 0.00 4.75
1354 1611 0.106894 GACCGGGATGATCAAGGTCC 59.893 60.000 20.73 15.39 40.17 4.46
1364 1662 5.392057 GGATGATCAAGGTCCGAAACTTTTC 60.392 44.000 0.00 0.00 0.00 2.29
1381 1679 6.186420 ACTTTTCCCCTGTTAATTTGCATT 57.814 33.333 0.00 0.00 0.00 3.56
1403 1702 1.472026 GCATGGGCATGAATGTGTTCC 60.472 52.381 0.00 0.00 41.20 3.62
1404 1703 2.104967 CATGGGCATGAATGTGTTCCT 58.895 47.619 0.00 0.00 41.20 3.36
1405 1704 1.548081 TGGGCATGAATGTGTTCCTG 58.452 50.000 0.00 0.00 34.34 3.86
1406 1705 1.075212 TGGGCATGAATGTGTTCCTGA 59.925 47.619 0.00 0.00 33.39 3.86
1407 1706 1.474077 GGGCATGAATGTGTTCCTGAC 59.526 52.381 0.00 0.00 37.29 3.51
1410 1709 2.094894 GCATGAATGTGTTCCTGACTCG 59.905 50.000 0.00 0.00 33.39 4.18
1411 1710 1.795768 TGAATGTGTTCCTGACTCGC 58.204 50.000 0.00 0.00 33.26 5.03
1545 1844 0.033503 TCCTCGTCCTCATGCAGGTA 60.034 55.000 0.00 0.00 43.95 3.08
1547 1846 1.207089 CCTCGTCCTCATGCAGGTAAA 59.793 52.381 0.00 0.00 43.95 2.01
1556 1855 4.758674 CCTCATGCAGGTAAATGAATCGAT 59.241 41.667 0.00 0.00 37.53 3.59
1557 1856 5.240183 CCTCATGCAGGTAAATGAATCGATT 59.760 40.000 11.20 11.20 37.53 3.34
1582 1881 1.303309 CTCCAATCATGCTCCGGTTC 58.697 55.000 0.00 0.00 0.00 3.62
1584 1883 1.134401 TCCAATCATGCTCCGGTTCTC 60.134 52.381 0.00 0.00 0.00 2.87
1612 1911 6.996509 AGTGCAAATTAACAATCCTGTCAAT 58.003 32.000 0.00 0.00 33.45 2.57
1613 1912 8.121305 AGTGCAAATTAACAATCCTGTCAATA 57.879 30.769 0.00 0.00 33.45 1.90
1641 1940 0.035820 TCTGCATTACCCACCGTTCC 60.036 55.000 0.00 0.00 0.00 3.62
1651 1950 0.865769 CCACCGTTCCTTTTCTGACG 59.134 55.000 0.00 0.00 35.44 4.35
1654 1953 1.411612 ACCGTTCCTTTTCTGACGACT 59.588 47.619 0.00 0.00 37.69 4.18
1657 1956 1.531578 GTTCCTTTTCTGACGACTGCC 59.468 52.381 0.00 0.00 0.00 4.85
1693 2001 4.314740 TTTCATTTCAAACCAGGAACCG 57.685 40.909 0.00 0.00 0.00 4.44
1750 2058 1.719600 GCCTCATGCCTATGATCGAC 58.280 55.000 0.00 0.00 42.19 4.20
1807 2115 5.448632 CCAAGTGTACAAGTCAACTTTCCAC 60.449 44.000 0.00 1.37 33.11 4.02
1928 2239 1.295423 CCCCGAGTACCACAACCTG 59.705 63.158 0.00 0.00 0.00 4.00
2012 2323 1.789078 CGCATACCATTGCCTGCCTC 61.789 60.000 0.00 0.00 39.52 4.70
2040 2355 4.379652 GCATTTCCACAACCTTTTCATGT 58.620 39.130 0.00 0.00 0.00 3.21
2049 2364 6.430925 CCACAACCTTTTCATGTATCTTCAGA 59.569 38.462 0.00 0.00 0.00 3.27
2113 2428 5.159273 AGAAGAATGAGAACAAGGAGGTC 57.841 43.478 0.00 0.00 0.00 3.85
2161 2476 2.747460 GCTCGTGCTGCCATCCAA 60.747 61.111 1.41 0.00 36.03 3.53
2291 2606 4.202245 TCTTTTTCAGGGATCTGTACGG 57.798 45.455 0.00 0.00 41.59 4.02
2338 2653 4.261363 GGCGGTAGAGTGTGTACTATTACC 60.261 50.000 0.00 0.00 40.45 2.85
2389 2704 2.025887 GGAAGCAAAGAAGATCCCCTCA 60.026 50.000 0.00 0.00 0.00 3.86
2469 2867 7.447374 TTGTATTAGCCATATTTTCCCATCG 57.553 36.000 0.00 0.00 0.00 3.84
2747 3157 8.231692 TCAAATTTGTATTGAAGACCTTGTGA 57.768 30.769 17.47 0.00 34.04 3.58
2748 3158 8.690884 TCAAATTTGTATTGAAGACCTTGTGAA 58.309 29.630 17.47 0.00 34.04 3.18
2755 3165 2.158475 TGAAGACCTTGTGAATTGGCCT 60.158 45.455 3.32 0.00 0.00 5.19
2865 3280 9.350357 CTTGTCAGATTGATTATTTTTGGTCTG 57.650 33.333 0.00 0.00 34.63 3.51
2887 3302 9.034544 GTCTGCAAACTTCAAAATTGAATAAGT 57.965 29.630 8.88 1.70 45.26 2.24
2917 3332 5.519927 CCATCTTTTTAATTCCGGACATTGC 59.480 40.000 1.83 0.00 0.00 3.56
2955 3378 4.481368 TTGGAGTCGTACCAATGCTAAT 57.519 40.909 0.00 0.00 41.64 1.73
3002 3429 0.842635 GGCCATCCAGGTCATCTTCT 59.157 55.000 0.00 0.00 43.39 2.85
3024 3451 5.869344 TCTGCAACATCATGTACTTGTAGAC 59.131 40.000 5.01 0.00 27.67 2.59
3040 3467 6.770785 ACTTGTAGACTGGATGCTAAACAAAA 59.229 34.615 0.00 0.00 0.00 2.44
3042 3469 7.144722 TGTAGACTGGATGCTAAACAAAATG 57.855 36.000 0.00 0.00 0.00 2.32
3080 3507 8.621286 CCTATTTGTTTACTGAGTGTGAGTTTT 58.379 33.333 0.00 0.00 0.00 2.43
3132 3559 1.651737 TAGCAAAGTGGTGAGCCCTA 58.348 50.000 0.00 0.00 0.00 3.53
3159 3587 4.876107 TCTCACAAACTCAGACTGGTTTTC 59.124 41.667 15.30 0.00 34.01 2.29
3270 3698 6.724263 CCCTTTTGTTTAAGGTTGATTTTGC 58.276 36.000 0.00 0.00 42.63 3.68
3277 3705 8.140677 TGTTTAAGGTTGATTTTGCAAAGATG 57.859 30.769 12.41 0.00 0.00 2.90
3285 3713 8.814235 GGTTGATTTTGCAAAGATGATGATAAG 58.186 33.333 12.41 0.00 0.00 1.73
3286 3714 9.577110 GTTGATTTTGCAAAGATGATGATAAGA 57.423 29.630 12.41 0.00 0.00 2.10
3290 3718 9.760077 ATTTTGCAAAGATGATGATAAGATTCC 57.240 29.630 12.41 0.00 0.00 3.01
3291 3719 6.549912 TGCAAAGATGATGATAAGATTCCG 57.450 37.500 0.00 0.00 0.00 4.30
3292 3720 6.290605 TGCAAAGATGATGATAAGATTCCGA 58.709 36.000 0.00 0.00 0.00 4.55
3293 3721 6.767423 TGCAAAGATGATGATAAGATTCCGAA 59.233 34.615 0.00 0.00 0.00 4.30
3294 3722 7.282901 TGCAAAGATGATGATAAGATTCCGAAA 59.717 33.333 0.00 0.00 0.00 3.46
3295 3723 8.131100 GCAAAGATGATGATAAGATTCCGAAAA 58.869 33.333 0.00 0.00 0.00 2.29
3298 3726 8.388484 AGATGATGATAAGATTCCGAAAAAGG 57.612 34.615 0.00 0.00 0.00 3.11
3299 3727 6.942532 TGATGATAAGATTCCGAAAAAGGG 57.057 37.500 0.00 0.00 0.00 3.95
3300 3728 6.423182 TGATGATAAGATTCCGAAAAAGGGT 58.577 36.000 0.00 0.00 0.00 4.34
3301 3729 6.889722 TGATGATAAGATTCCGAAAAAGGGTT 59.110 34.615 0.00 0.00 0.00 4.11
3302 3730 7.396055 TGATGATAAGATTCCGAAAAAGGGTTT 59.604 33.333 0.00 0.00 0.00 3.27
3303 3731 7.153217 TGATAAGATTCCGAAAAAGGGTTTC 57.847 36.000 0.00 0.00 0.00 2.78
3304 3732 4.866508 AAGATTCCGAAAAAGGGTTTCC 57.133 40.909 0.00 0.00 0.00 3.13
3305 3733 3.162666 AGATTCCGAAAAAGGGTTTCCC 58.837 45.455 0.00 0.00 45.90 3.97
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
112 153 0.820891 AAGCCGATGCATGTCATCCC 60.821 55.000 2.46 12.45 46.93 3.85
127 168 6.073003 CGAGTCCAGGAAATTATGAATAAGCC 60.073 42.308 0.00 0.00 0.00 4.35
134 175 2.429250 TCGCGAGTCCAGGAAATTATGA 59.571 45.455 3.71 0.00 0.00 2.15
138 179 0.895530 TCTCGCGAGTCCAGGAAATT 59.104 50.000 33.33 0.00 0.00 1.82
142 183 2.033602 TGTCTCGCGAGTCCAGGA 59.966 61.111 33.33 12.73 0.00 3.86
143 184 2.179517 GTGTCTCGCGAGTCCAGG 59.820 66.667 33.33 10.33 0.00 4.45
144 185 2.179517 GGTGTCTCGCGAGTCCAG 59.820 66.667 33.33 11.12 0.00 3.86
210 348 4.454504 ACACAAGTCGAGTTCAGTGTTTTT 59.545 37.500 18.46 2.29 36.91 1.94
211 349 4.000988 ACACAAGTCGAGTTCAGTGTTTT 58.999 39.130 18.46 2.57 36.91 2.43
218 356 6.321848 TCTACATAACACAAGTCGAGTTCA 57.678 37.500 1.51 0.00 30.49 3.18
258 396 2.415512 GTCTAACAATGGACGAACAGGC 59.584 50.000 0.00 0.00 0.00 4.85
273 411 4.876107 CCACTATGGTGATTGTGGTCTAAC 59.124 45.833 11.31 0.00 45.39 2.34
274 412 5.097742 CCACTATGGTGATTGTGGTCTAA 57.902 43.478 11.31 0.00 45.39 2.10
275 413 4.753516 CCACTATGGTGATTGTGGTCTA 57.246 45.455 11.31 0.00 45.39 2.59
276 414 3.634397 CCACTATGGTGATTGTGGTCT 57.366 47.619 11.31 0.00 45.39 3.85
280 418 2.505407 TCCCTCCACTATGGTGATTGTG 59.495 50.000 11.31 0.00 45.61 3.33
281 419 2.845659 TCCCTCCACTATGGTGATTGT 58.154 47.619 11.31 0.00 45.61 2.71
283 421 2.173569 GCTTCCCTCCACTATGGTGATT 59.826 50.000 11.31 0.00 45.61 2.57
284 422 1.771255 GCTTCCCTCCACTATGGTGAT 59.229 52.381 11.31 0.00 45.61 3.06
285 423 1.204146 GCTTCCCTCCACTATGGTGA 58.796 55.000 11.31 0.00 45.61 4.02
286 424 1.207791 AGCTTCCCTCCACTATGGTG 58.792 55.000 1.49 1.49 39.03 4.17
340 484 3.589951 ACTCCCCGCTGTACTAGATAA 57.410 47.619 0.00 0.00 0.00 1.75
341 485 4.287845 TGATACTCCCCGCTGTACTAGATA 59.712 45.833 0.00 0.00 0.00 1.98
375 553 3.414700 CTGTGGACTGCGAACGCC 61.415 66.667 16.27 1.79 41.09 5.68
382 560 3.050275 GAACCGCCTGTGGACTGC 61.050 66.667 3.27 0.00 0.00 4.40
404 614 2.168326 TCGAAGCACAAATCAGCTCA 57.832 45.000 0.00 0.00 40.90 4.26
436 648 4.439563 GGTTTGTCCCGCGAATTGATTTAT 60.440 41.667 8.23 0.00 0.00 1.40
437 649 3.119779 GGTTTGTCCCGCGAATTGATTTA 60.120 43.478 8.23 0.00 0.00 1.40
440 652 0.808755 GGTTTGTCCCGCGAATTGAT 59.191 50.000 8.23 0.00 0.00 2.57
441 653 1.570347 CGGTTTGTCCCGCGAATTGA 61.570 55.000 8.23 0.00 41.78 2.57
442 654 1.154301 CGGTTTGTCCCGCGAATTG 60.154 57.895 8.23 0.00 41.78 2.32
451 665 1.452470 ACCACACACCGGTTTGTCC 60.452 57.895 23.26 0.00 30.53 4.02
452 666 1.720694 CCACCACACACCGGTTTGTC 61.721 60.000 23.26 0.00 33.25 3.18
464 680 2.367648 AGTGACCCACCCACCACA 60.368 61.111 0.00 0.00 34.49 4.17
502 718 1.234821 TCATCGTGTCAACTTTGGGC 58.765 50.000 0.00 0.00 0.00 5.36
534 751 0.109643 CACACGCCACCATGTTCATG 60.110 55.000 5.88 5.88 0.00 3.07
590 807 2.359107 CCACTGGCACGATGCTGT 60.359 61.111 9.31 6.63 44.28 4.40
633 863 2.104331 ACTAGGCGCCATCGTTCG 59.896 61.111 31.54 5.84 38.14 3.95
715 959 4.522789 AGTATAAACAAACTGGGCAACTGG 59.477 41.667 0.00 0.00 0.00 4.00
741 985 5.997385 ACACCGTCAACAGAAATCATAAAC 58.003 37.500 0.00 0.00 0.00 2.01
742 986 6.434596 CAACACCGTCAACAGAAATCATAAA 58.565 36.000 0.00 0.00 0.00 1.40
748 992 2.357637 CACCAACACCGTCAACAGAAAT 59.642 45.455 0.00 0.00 0.00 2.17
752 996 0.376852 CACACCAACACCGTCAACAG 59.623 55.000 0.00 0.00 0.00 3.16
821 1071 3.326889 AATGCATGCGGTGTCGTGC 62.327 57.895 14.09 1.36 38.39 5.34
822 1072 1.226101 GAATGCATGCGGTGTCGTG 60.226 57.895 14.09 0.00 38.89 4.35
823 1073 2.739704 CGAATGCATGCGGTGTCGT 61.740 57.895 19.95 0.00 38.89 4.34
825 1075 1.060937 GTCGAATGCATGCGGTGTC 59.939 57.895 26.54 11.21 0.00 3.67
826 1076 2.739704 CGTCGAATGCATGCGGTGT 61.740 57.895 26.54 0.00 0.00 4.16
827 1077 2.021793 CGTCGAATGCATGCGGTG 59.978 61.111 26.54 15.30 0.00 4.94
828 1078 2.125713 TCGTCGAATGCATGCGGT 60.126 55.556 26.54 2.35 0.00 5.68
829 1079 2.321060 GTCGTCGAATGCATGCGG 59.679 61.111 26.54 11.95 0.00 5.69
830 1080 2.054840 CGTCGTCGAATGCATGCG 60.055 61.111 21.64 21.64 39.71 4.73
831 1081 3.383861 TCGTCGTCGAATGCATGC 58.616 55.556 11.82 11.82 43.34 4.06
839 1089 3.999333 TGAACGCGTCGTCGTCGA 61.999 61.111 14.44 0.00 42.46 4.20
885 1137 3.634448 CGTGCATATATAGGGGAGAGAGG 59.366 52.174 0.00 0.00 0.00 3.69
961 1215 1.081892 CTGCTTAATCTGCTGCGTGT 58.918 50.000 0.00 0.00 0.00 4.49
994 1248 0.250234 TTGTCCTGGCTCATCTTCGG 59.750 55.000 0.00 0.00 0.00 4.30
1354 1611 5.176774 GCAAATTAACAGGGGAAAAGTTTCG 59.823 40.000 0.00 0.00 38.06 3.46
1364 1662 2.027377 TGCCAATGCAAATTAACAGGGG 60.027 45.455 0.00 0.00 46.66 4.79
1381 1679 0.615261 ACACATTCATGCCCATGCCA 60.615 50.000 3.41 0.00 38.65 4.92
1403 1702 0.665298 TGATGATCTCGGCGAGTCAG 59.335 55.000 33.31 12.16 0.00 3.51
1404 1703 1.268079 GATGATGATCTCGGCGAGTCA 59.732 52.381 33.31 31.32 0.00 3.41
1405 1704 1.539388 AGATGATGATCTCGGCGAGTC 59.461 52.381 33.31 27.60 33.20 3.36
1406 1705 1.269174 CAGATGATGATCTCGGCGAGT 59.731 52.381 33.31 21.83 36.75 4.18
1407 1706 1.979897 CAGATGATGATCTCGGCGAG 58.020 55.000 30.10 30.10 36.75 5.03
1410 1709 0.321021 AGGCAGATGATGATCTCGGC 59.679 55.000 9.02 9.02 36.75 5.54
1411 1710 1.940294 GCAGGCAGATGATGATCTCGG 60.940 57.143 0.00 0.00 36.75 4.63
1545 1844 6.573664 TTGGAGTGTTGAATCGATTCATTT 57.426 33.333 34.66 22.13 45.30 2.32
1547 1846 5.882000 TGATTGGAGTGTTGAATCGATTCAT 59.118 36.000 34.66 23.10 45.30 2.57
1556 1855 3.084039 GGAGCATGATTGGAGTGTTGAA 58.916 45.455 0.00 0.00 0.00 2.69
1557 1856 2.715046 GGAGCATGATTGGAGTGTTGA 58.285 47.619 0.00 0.00 0.00 3.18
1582 1881 6.364165 CAGGATTGTTAATTTGCACTTGTGAG 59.636 38.462 4.79 0.00 0.00 3.51
1584 1883 5.984926 ACAGGATTGTTAATTTGCACTTGTG 59.015 36.000 0.00 0.00 32.28 3.33
1612 1911 2.159014 GGGTAATGCAGACGGTGATGTA 60.159 50.000 0.00 0.00 0.00 2.29
1613 1912 1.406887 GGGTAATGCAGACGGTGATGT 60.407 52.381 0.00 0.00 0.00 3.06
1641 1940 1.871080 ACAGGCAGTCGTCAGAAAAG 58.129 50.000 0.00 0.00 0.00 2.27
1651 1950 9.807649 ATGAAATGAAATAATTAACAGGCAGTC 57.192 29.630 0.00 0.00 0.00 3.51
1750 2058 0.451783 GATTGGTTTAGCGTGCCTGG 59.548 55.000 0.00 0.00 0.00 4.45
1807 2115 1.676615 GCTTGATGCCAAAATGGTGGG 60.677 52.381 0.00 0.00 40.46 4.61
1854 2162 5.240403 CCTTCTCTCCCTGTTCAAGAAAAAG 59.760 44.000 0.00 0.00 0.00 2.27
1863 2174 2.834549 TGTCATCCTTCTCTCCCTGTTC 59.165 50.000 0.00 0.00 0.00 3.18
1928 2239 0.459489 AGAGCTCGCTGAGATGGTTC 59.541 55.000 8.37 0.43 0.00 3.62
2012 2323 2.086869 AGGTTGTGGAAATGCGAGATG 58.913 47.619 0.00 0.00 0.00 2.90
2040 2355 4.528206 TCAGGCACTTGAAGTCTGAAGATA 59.472 41.667 12.61 0.00 34.60 1.98
2049 2364 3.152341 CCAAGAATCAGGCACTTGAAGT 58.848 45.455 0.00 0.00 42.12 3.01
2113 2428 1.009389 GGAGGAAGTCGTTGACAGCG 61.009 60.000 5.21 5.21 34.60 5.18
2161 2476 3.771479 TGATGAGAGCTTACATGGAGTGT 59.229 43.478 10.51 0.00 44.95 3.55
2203 2518 5.875910 TCGAGGACTCTCTGTCTTTAACTAG 59.124 44.000 0.00 0.00 44.74 2.57
2206 2521 4.142556 CCTCGAGGACTCTCTGTCTTTAAC 60.143 50.000 28.21 0.00 44.74 2.01
2291 2606 3.490348 AGGCTGTGCATAATGTATTCCC 58.510 45.455 0.00 0.00 0.00 3.97
2318 2633 9.662947 AAAAATGGTAATAGTACACACTCTACC 57.337 33.333 2.37 8.20 40.57 3.18
2338 2653 3.306989 GGAGGAAGGGCAAAGGAAAAATG 60.307 47.826 0.00 0.00 0.00 2.32
2389 2704 5.573219 TGTTCATCAGATCCCAAATGTTCT 58.427 37.500 0.00 0.00 0.00 3.01
2469 2867 8.338259 CAAATTTGAGATACATAGTACCACAGC 58.662 37.037 13.08 0.00 0.00 4.40
2517 2915 8.407064 AGTAAGAACTGAAGATAATACACGAGG 58.593 37.037 0.00 0.00 33.57 4.63
2747 3157 4.858850 TGAAGATGATACACAGGCCAATT 58.141 39.130 5.01 0.00 0.00 2.32
2748 3158 4.080129 ACTGAAGATGATACACAGGCCAAT 60.080 41.667 5.01 0.00 33.57 3.16
2887 3302 4.464597 CCGGAATTAAAAAGATGGGGTCAA 59.535 41.667 0.00 0.00 0.00 3.18
2917 3332 1.745087 CCAAATGGAATGAGGGACACG 59.255 52.381 0.00 0.00 37.39 4.49
2955 3378 2.501723 CCTCTTAGGAAACTAGGCAGCA 59.498 50.000 0.00 0.00 45.45 4.41
3002 3429 5.639082 CAGTCTACAAGTACATGATGTTGCA 59.361 40.000 2.29 0.00 0.00 4.08
3024 3451 6.917533 ACTTCTCATTTTGTTTAGCATCCAG 58.082 36.000 0.00 0.00 0.00 3.86
3052 3479 6.929606 ACTCACACTCAGTAAACAAATAGGTC 59.070 38.462 0.00 0.00 0.00 3.85
3110 3537 1.271379 GGGCTCACCACTTTGCTAAGA 60.271 52.381 14.98 0.00 39.85 2.10
3132 3559 4.285517 ACCAGTCTGAGTTTGTGAGATGAT 59.714 41.667 0.00 0.00 0.00 2.45
3159 3587 8.381636 ACCTTCCATGATATATCTTCCTTTCAG 58.618 37.037 13.79 0.95 0.00 3.02
3277 3705 6.944234 ACCCTTTTTCGGAATCTTATCATC 57.056 37.500 0.00 0.00 0.00 2.92


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

AutoCloner maintained by Alex Coulton.