Multiple sequence alignment - TraesCS5D01G432000

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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 TraesCS5D01G432000 chr5D 100.000 2582 0 0 1 2582 488354687 488357268 0.000000e+00 4769.0
1 TraesCS5D01G432000 chr5D 100.000 44 0 0 183 226 38197381 38197338 5.920000e-12 82.4
2 TraesCS5D01G432000 chr5B 86.127 865 68 21 652 1493 601344235 601345070 0.000000e+00 885.0
3 TraesCS5D01G432000 chr5B 91.158 622 46 9 1891 2506 601346278 601346896 0.000000e+00 835.0
4 TraesCS5D01G432000 chr5B 80.153 1043 118 41 594 1584 601337338 601338343 0.000000e+00 697.0
5 TraesCS5D01G432000 chr5B 88.930 271 16 2 238 508 601337071 601337327 3.210000e-84 322.0
6 TraesCS5D01G432000 chr5B 89.593 221 20 3 1638 1857 601345384 601345602 7.040000e-71 278.0
7 TraesCS5D01G432000 chr5B 92.073 164 9 3 1 163 601336812 601336972 7.190000e-56 228.0
8 TraesCS5D01G432000 chr5B 89.888 178 12 4 1446 1620 601345239 601345413 9.300000e-55 224.0
9 TraesCS5D01G432000 chr5B 90.541 148 12 2 1645 1792 601338357 601338502 7.290000e-46 195.0
10 TraesCS5D01G432000 chr5B 86.184 152 16 4 1 152 601339682 601339828 2.660000e-35 159.0
11 TraesCS5D01G432000 chr5B 100.000 33 0 0 1855 1887 701525332 701525364 7.710000e-06 62.1
12 TraesCS5D01G432000 chr5A 88.595 719 53 11 793 1493 609211457 609212164 0.000000e+00 846.0
13 TraesCS5D01G432000 chr5A 90.256 626 45 8 1891 2508 609213409 609214026 0.000000e+00 804.0
14 TraesCS5D01G432000 chr5A 79.514 864 102 36 610 1410 609240527 609241378 1.750000e-151 545.0
15 TraesCS5D01G432000 chr5A 94.628 242 12 1 1646 1887 609212346 609212586 8.720000e-100 374.0
16 TraesCS5D01G432000 chr5A 95.858 169 6 1 183 351 609210929 609211096 3.270000e-69 272.0
17 TraesCS5D01G432000 chr5A 89.071 183 14 6 1448 1628 609212191 609212369 3.340000e-54 222.0
18 TraesCS5D01G432000 chr5A 86.486 185 13 5 480 660 609211158 609211334 2.620000e-45 193.0
19 TraesCS5D01G432000 chr5A 92.481 133 10 0 1 133 609240009 609240141 9.430000e-45 191.0
20 TraesCS5D01G432000 chr5A 84.663 163 5 2 1 163 609210708 609210850 7.450000e-31 145.0
21 TraesCS5D01G432000 chr5A 88.525 122 3 4 643 764 609211345 609211455 1.250000e-28 137.0
22 TraesCS5D01G432000 chr5A 91.026 78 5 2 367 442 609211085 609211162 1.260000e-18 104.0
23 TraesCS5D01G432000 chr5A 100.000 44 0 0 2503 2546 351723068 351723111 5.920000e-12 82.4
24 TraesCS5D01G432000 chr2B 97.917 48 1 0 179 226 112826512 112826559 1.650000e-12 84.2
25 TraesCS5D01G432000 chr2B 87.500 64 6 2 2484 2546 706020643 706020705 3.560000e-09 73.1
26 TraesCS5D01G432000 chrUn 100.000 44 0 0 183 226 86516615 86516658 5.920000e-12 82.4
27 TraesCS5D01G432000 chrUn 100.000 44 0 0 183 226 206784133 206784176 5.920000e-12 82.4
28 TraesCS5D01G432000 chrUn 100.000 44 0 0 183 226 345389165 345389122 5.920000e-12 82.4
29 TraesCS5D01G432000 chr7D 97.917 48 0 1 2500 2546 361175194 361175241 5.920000e-12 82.4
30 TraesCS5D01G432000 chr7B 100.000 44 0 0 2505 2548 229411438 229411481 5.920000e-12 82.4
31 TraesCS5D01G432000 chr7B 96.774 31 1 0 1857 1887 748011359 748011329 5.000000e-03 52.8
32 TraesCS5D01G432000 chr4D 100.000 44 0 0 183 226 123320960 123321003 5.920000e-12 82.4
33 TraesCS5D01G432000 chr4D 100.000 44 0 0 183 226 407656296 407656253 5.920000e-12 82.4
34 TraesCS5D01G432000 chr4D 94.118 51 0 3 2499 2546 367421022 367420972 9.910000e-10 75.0
35 TraesCS5D01G432000 chr4B 100.000 44 0 0 2505 2548 288595676 288595719 5.920000e-12 82.4
36 TraesCS5D01G432000 chr3D 100.000 44 0 0 183 226 213395619 213395662 5.920000e-12 82.4
37 TraesCS5D01G432000 chr3D 100.000 44 0 0 2503 2546 581694798 581694755 5.920000e-12 82.4
38 TraesCS5D01G432000 chr7A 100.000 43 0 0 2504 2546 605673455 605673497 2.130000e-11 80.5
39 TraesCS5D01G432000 chr3A 97.826 46 1 0 2505 2550 426771871 426771826 2.130000e-11 80.5
40 TraesCS5D01G432000 chr3A 100.000 29 0 0 1858 1886 608148633 608148605 1.000000e-03 54.7
41 TraesCS5D01G432000 chr1A 92.500 40 3 0 2468 2507 115970324 115970363 9.980000e-05 58.4


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 TraesCS5D01G432000 chr5D 488354687 488357268 2581 False 4769.000000 4769 100.000000 1 2582 1 chr5D.!!$F1 2581
1 TraesCS5D01G432000 chr5B 601344235 601346896 2661 False 555.500000 885 89.191500 652 2506 4 chr5B.!!$F3 1854
2 TraesCS5D01G432000 chr5B 601336812 601339828 3016 False 320.200000 697 87.576200 1 1792 5 chr5B.!!$F2 1791
3 TraesCS5D01G432000 chr5A 609240009 609241378 1369 False 368.000000 545 85.997500 1 1410 2 chr5A.!!$F3 1409
4 TraesCS5D01G432000 chr5A 609210708 609214026 3318 False 344.111111 846 89.900889 1 2508 9 chr5A.!!$F2 2507

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
418 589 0.107831 AACACGAGCCTGGCACTTTA 59.892 50.0 22.65 0.0 0.00 1.85 F
1290 1613 0.736325 CTCTGGGTAAACGCTGTCCG 60.736 60.0 0.00 0.0 44.21 4.79 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1526 2065 0.037734 AACTCCCGGGCGAAATCTTT 59.962 50.0 19.65 0.00 0.0 2.52 R
2530 4044 0.390209 GGCGCTCCACATTTGCAAAT 60.390 50.0 18.99 18.99 0.0 2.32 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
132 134 3.279434 GGAATTCCACCGACTTTATGCT 58.721 45.455 20.04 0.00 35.64 3.79
133 135 3.312697 GGAATTCCACCGACTTTATGCTC 59.687 47.826 20.04 0.00 35.64 4.26
134 136 3.627395 ATTCCACCGACTTTATGCTCA 57.373 42.857 0.00 0.00 0.00 4.26
179 313 6.464749 ATGAAAAGGATTTGTTCCATTGCACT 60.465 34.615 0.00 0.00 42.27 4.40
230 381 2.007399 CTTCGCTCGCTCGCTTTCAG 62.007 60.000 0.00 0.00 0.00 3.02
256 407 1.527034 CCTGTCACCAGACCAACATG 58.473 55.000 0.00 0.00 44.33 3.21
290 441 2.096248 AGTCAGTAGCTTCCTTCTCCG 58.904 52.381 0.00 0.00 0.00 4.63
297 448 1.623811 AGCTTCCTTCTCCGCAAGTTA 59.376 47.619 0.00 0.00 0.00 2.24
410 581 3.502211 ACTTTATTCCAAACACGAGCCTG 59.498 43.478 0.00 0.00 0.00 4.85
418 589 0.107831 AACACGAGCCTGGCACTTTA 59.892 50.000 22.65 0.00 0.00 1.85
502 673 0.968405 TTCCACAGCCCAATTTCTGC 59.032 50.000 0.00 0.00 33.80 4.26
532 703 0.810031 GCGTGGCATACCTACCTGTG 60.810 60.000 0.00 0.00 36.63 3.66
534 705 1.066430 CGTGGCATACCTACCTGTGTT 60.066 52.381 0.00 0.00 36.63 3.32
535 706 2.629051 GTGGCATACCTACCTGTGTTC 58.371 52.381 0.00 0.00 36.63 3.18
540 711 3.447586 GCATACCTACCTGTGTTCTCTCA 59.552 47.826 0.00 0.00 0.00 3.27
740 978 6.833041 TCTCTTCGATTCCTCTGTAGATACT 58.167 40.000 0.00 0.00 0.00 2.12
741 979 6.708502 TCTCTTCGATTCCTCTGTAGATACTG 59.291 42.308 0.00 0.00 0.00 2.74
742 980 6.358178 TCTTCGATTCCTCTGTAGATACTGT 58.642 40.000 0.00 0.00 0.00 3.55
743 981 7.506971 TCTTCGATTCCTCTGTAGATACTGTA 58.493 38.462 0.00 0.00 0.00 2.74
744 982 7.441760 TCTTCGATTCCTCTGTAGATACTGTAC 59.558 40.741 0.00 0.00 0.00 2.90
787 1025 4.626081 CCCGGCCGGCTAATCCTG 62.626 72.222 39.46 18.81 0.00 3.86
899 1150 3.681835 GACTCGGAGCGTGGGTGT 61.682 66.667 4.58 0.00 0.00 4.16
908 1166 1.525077 GCGTGGGTGTTGTCTTCCA 60.525 57.895 0.00 0.00 0.00 3.53
937 1201 7.283127 GGAGCATATACACACATAAATATGGGG 59.717 40.741 7.53 1.23 41.37 4.96
954 1226 2.579201 GCGCCTGAGCTTCTACCA 59.421 61.111 0.00 0.00 36.60 3.25
964 1236 3.006430 TGAGCTTCTACCAAATCACGTCA 59.994 43.478 0.00 0.00 0.00 4.35
968 1240 5.473504 AGCTTCTACCAAATCACGTCAATTT 59.526 36.000 0.00 0.00 0.00 1.82
988 1263 2.879907 CTGGACGCCATTTGCCAG 59.120 61.111 0.00 0.00 41.62 4.85
1166 1474 1.000486 CACGAAGAGGAGAGGGGGA 60.000 63.158 0.00 0.00 0.00 4.81
1170 1478 1.869452 AAGAGGAGAGGGGGAGGGT 60.869 63.158 0.00 0.00 0.00 4.34
1172 1480 1.233659 GAGGAGAGGGGGAGGGTAC 59.766 68.421 0.00 0.00 0.00 3.34
1248 1565 4.579869 AGCTGGATGACATACTTTCGTTT 58.420 39.130 0.00 0.00 0.00 3.60
1290 1613 0.736325 CTCTGGGTAAACGCTGTCCG 60.736 60.000 0.00 0.00 44.21 4.79
1299 1622 2.050351 CGCTGTCCGTCACTCGTT 60.050 61.111 0.00 0.00 37.94 3.85
1357 1680 1.361993 CGGGAGAAGATGAGGCGAG 59.638 63.158 0.00 0.00 0.00 5.03
1413 1736 3.006644 CAGAGGTCACCGATGATGATGAT 59.993 47.826 0.00 0.00 37.14 2.45
1416 1739 3.581770 AGGTCACCGATGATGATGATGAT 59.418 43.478 0.00 0.00 37.14 2.45
1526 2065 2.926242 ACGGGGAAGAGGCCGAAA 60.926 61.111 0.00 0.00 0.00 3.46
1545 2084 0.037734 AAAGATTTCGCCCGGGAGTT 59.962 50.000 29.31 8.14 0.00 3.01
1560 2099 1.678101 GGAGTTGTCAAGCAAGCAAGT 59.322 47.619 0.00 0.00 37.83 3.16
1586 2125 6.255950 GCGTTAAGAAAATAACTTAGGCCTG 58.744 40.000 17.99 0.87 34.35 4.85
1587 2126 6.128090 GCGTTAAGAAAATAACTTAGGCCTGT 60.128 38.462 17.99 1.70 34.35 4.00
1589 2128 7.749126 CGTTAAGAAAATAACTTAGGCCTGTTG 59.251 37.037 17.99 7.77 34.35 3.33
1591 2130 5.887754 AGAAAATAACTTAGGCCTGTTGGA 58.112 37.500 17.99 0.00 34.57 3.53
1593 2132 6.954102 AGAAAATAACTTAGGCCTGTTGGATT 59.046 34.615 17.99 6.82 34.57 3.01
1594 2133 8.113462 AGAAAATAACTTAGGCCTGTTGGATTA 58.887 33.333 17.99 5.89 34.57 1.75
1595 2134 7.881775 AAATAACTTAGGCCTGTTGGATTAG 57.118 36.000 17.99 2.22 34.57 1.73
1596 2135 4.929146 AACTTAGGCCTGTTGGATTAGT 57.071 40.909 17.99 2.85 34.57 2.24
1597 2136 4.929146 ACTTAGGCCTGTTGGATTAGTT 57.071 40.909 17.99 0.00 34.57 2.24
1598 2137 5.256806 ACTTAGGCCTGTTGGATTAGTTT 57.743 39.130 17.99 0.00 34.57 2.66
1599 2138 5.641155 ACTTAGGCCTGTTGGATTAGTTTT 58.359 37.500 17.99 0.00 34.57 2.43
1600 2139 6.786122 ACTTAGGCCTGTTGGATTAGTTTTA 58.214 36.000 17.99 0.00 34.57 1.52
1601 2140 6.884836 ACTTAGGCCTGTTGGATTAGTTTTAG 59.115 38.462 17.99 0.00 34.57 1.85
1602 2141 5.256806 AGGCCTGTTGGATTAGTTTTAGT 57.743 39.130 3.11 0.00 34.57 2.24
1603 2142 5.641155 AGGCCTGTTGGATTAGTTTTAGTT 58.359 37.500 3.11 0.00 34.57 2.24
1604 2143 5.476945 AGGCCTGTTGGATTAGTTTTAGTTG 59.523 40.000 3.11 0.00 34.57 3.16
1605 2144 5.243060 GGCCTGTTGGATTAGTTTTAGTTGT 59.757 40.000 0.00 0.00 34.57 3.32
1606 2145 6.239204 GGCCTGTTGGATTAGTTTTAGTTGTT 60.239 38.462 0.00 0.00 34.57 2.83
1607 2146 6.640907 GCCTGTTGGATTAGTTTTAGTTGTTG 59.359 38.462 0.00 0.00 34.57 3.33
1608 2147 7.145323 CCTGTTGGATTAGTTTTAGTTGTTGG 58.855 38.462 0.00 0.00 34.57 3.77
1609 2148 7.013846 CCTGTTGGATTAGTTTTAGTTGTTGGA 59.986 37.037 0.00 0.00 34.57 3.53
1610 2149 8.472007 TGTTGGATTAGTTTTAGTTGTTGGAT 57.528 30.769 0.00 0.00 0.00 3.41
1611 2150 8.919145 TGTTGGATTAGTTTTAGTTGTTGGATT 58.081 29.630 0.00 0.00 0.00 3.01
1614 2153 9.802039 TGGATTAGTTTTAGTTGTTGGATTAGT 57.198 29.630 0.00 0.00 0.00 2.24
1706 2249 5.114081 ACCGCAGTTTATGGTACTGTATTC 58.886 41.667 0.00 0.00 43.81 1.75
1767 2310 7.062371 GTGATGTGTACACTGATCTTAACTGAC 59.938 40.741 25.60 10.18 35.66 3.51
1858 2401 1.752683 TCGGCTCTTCCACTCTACTC 58.247 55.000 0.00 0.00 34.01 2.59
1860 2403 1.853963 GGCTCTTCCACTCTACTCCA 58.146 55.000 0.00 0.00 34.01 3.86
1912 3419 4.777366 AGCTATAATGCAACCAGGGTTTTT 59.223 37.500 0.00 0.00 36.00 1.94
1966 3473 3.292460 AGAGTCCGCATTAGCTTAGACT 58.708 45.455 0.00 0.00 42.31 3.24
2010 3517 4.691685 GCAATCAGACCAAAATTGATGCAA 59.308 37.500 0.00 0.00 33.22 4.08
2011 3518 5.179742 GCAATCAGACCAAAATTGATGCAAA 59.820 36.000 0.00 0.00 33.22 3.68
2046 3556 7.837689 ACACCCTTGAAGACTATAGTACATACA 59.162 37.037 5.09 0.05 0.00 2.29
2047 3557 8.353684 CACCCTTGAAGACTATAGTACATACAG 58.646 40.741 5.09 2.36 0.00 2.74
2096 3606 8.073355 ACGACACAGAAGACTTACATAAAAAG 57.927 34.615 0.00 0.00 0.00 2.27
2103 3613 8.930760 CAGAAGACTTACATAAAAAGGTCTCAG 58.069 37.037 0.00 0.00 0.00 3.35
2122 3632 0.889186 GTGAGCGGTGGTGGTCAATT 60.889 55.000 0.00 0.00 46.76 2.32
2135 3645 8.931775 GGTGGTGGTCAATTTTAAAATATGAAC 58.068 33.333 21.61 21.61 0.00 3.18
2154 3665 2.197465 ACTCAGTTTGGGGAGGTATCC 58.803 52.381 0.00 0.00 45.85 2.59
2191 3702 1.466855 GCGCAGTTTTGACAGTTGTC 58.533 50.000 0.30 5.33 44.97 3.18
2221 3732 9.847224 TCTTTATTAAGTTCAATCCATAGGGTC 57.153 33.333 0.00 0.00 32.43 4.46
2263 3774 0.366871 CACGAATTCAAGGCTCGACG 59.633 55.000 6.22 0.00 36.45 5.12
2316 3827 8.656849 CAAGGCATAATTACATACGGATAAGAC 58.343 37.037 0.00 0.00 0.00 3.01
2514 4028 7.479352 TGCAATTAATCTTGGAAAAGGATGA 57.521 32.000 0.00 0.00 0.00 2.92
2516 4030 8.542080 TGCAATTAATCTTGGAAAAGGATGAAT 58.458 29.630 0.00 0.00 0.00 2.57
2527 4041 0.849417 AGGATGAATGAGGGAAGGCC 59.151 55.000 0.00 0.00 0.00 5.19
2528 4042 0.849417 GGATGAATGAGGGAAGGCCT 59.151 55.000 0.00 0.00 0.00 5.19
2530 4044 2.443255 GGATGAATGAGGGAAGGCCTTA 59.557 50.000 20.54 1.80 0.00 2.69
2531 4045 3.075134 GGATGAATGAGGGAAGGCCTTAT 59.925 47.826 20.54 7.60 0.00 1.73
2532 4046 4.448347 GGATGAATGAGGGAAGGCCTTATT 60.448 45.833 20.54 14.22 0.00 1.40
2533 4047 4.608170 TGAATGAGGGAAGGCCTTATTT 57.392 40.909 20.54 6.38 0.00 1.40
2534 4048 4.280819 TGAATGAGGGAAGGCCTTATTTG 58.719 43.478 20.54 0.00 0.00 2.32
2535 4049 2.143876 TGAGGGAAGGCCTTATTTGC 57.856 50.000 20.54 5.12 0.00 3.68
2536 4050 1.357420 TGAGGGAAGGCCTTATTTGCA 59.643 47.619 20.54 10.57 0.00 4.08
2537 4051 2.225242 TGAGGGAAGGCCTTATTTGCAA 60.225 45.455 20.54 0.00 0.00 4.08
2538 4052 2.831526 GAGGGAAGGCCTTATTTGCAAA 59.168 45.455 20.54 15.44 0.00 3.68
2542 4056 3.934579 GGAAGGCCTTATTTGCAAATGTG 59.065 43.478 30.43 21.90 0.00 3.21
2544 4058 3.172339 AGGCCTTATTTGCAAATGTGGA 58.828 40.909 31.67 15.77 0.00 4.02
2545 4059 3.196254 AGGCCTTATTTGCAAATGTGGAG 59.804 43.478 31.67 23.26 0.00 3.86
2546 4060 2.931969 GCCTTATTTGCAAATGTGGAGC 59.068 45.455 31.67 23.46 0.00 4.70
2547 4061 3.181397 CCTTATTTGCAAATGTGGAGCG 58.819 45.455 30.43 14.06 0.00 5.03
2550 4064 2.433231 TTTGCAAATGTGGAGCGCCC 62.433 55.000 8.05 5.76 0.00 6.13
2551 4065 4.133796 GCAAATGTGGAGCGCCCC 62.134 66.667 2.29 0.34 0.00 5.80
2552 4066 3.451894 CAAATGTGGAGCGCCCCC 61.452 66.667 5.13 7.58 0.00 5.40
2571 4085 1.141053 CCCCCTTCCTAGTCCAATTCG 59.859 57.143 0.00 0.00 0.00 3.34
2572 4086 1.141053 CCCCTTCCTAGTCCAATTCGG 59.859 57.143 0.00 0.00 0.00 4.30
2573 4087 2.116238 CCCTTCCTAGTCCAATTCGGA 58.884 52.381 0.00 0.00 43.61 4.55
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
132 134 6.824704 TCATTCAATAGCAAGTGTGATGATGA 59.175 34.615 0.00 0.00 0.00 2.92
133 135 7.023197 TCATTCAATAGCAAGTGTGATGATG 57.977 36.000 0.00 0.00 0.00 3.07
134 136 7.634671 TTCATTCAATAGCAAGTGTGATGAT 57.365 32.000 0.00 0.00 30.60 2.45
176 310 1.296715 CCCTTCCCTCACCGAAGTG 59.703 63.158 0.00 0.00 46.00 3.16
177 311 1.918800 CCCCTTCCCTCACCGAAGT 60.919 63.158 0.00 0.00 35.90 3.01
179 313 2.609610 CCCCCTTCCCTCACCGAA 60.610 66.667 0.00 0.00 0.00 4.30
256 407 6.578023 AGCTACTGACTGATAAGTTCCATTC 58.422 40.000 0.00 0.00 0.00 2.67
290 441 7.491048 TCAAATTCTTGTGAAAAGGTAACTTGC 59.509 33.333 0.00 0.00 44.41 4.01
435 606 4.047059 CAAAGCCACGCAGCCCAG 62.047 66.667 0.00 0.00 0.00 4.45
436 607 4.577677 TCAAAGCCACGCAGCCCA 62.578 61.111 0.00 0.00 0.00 5.36
600 805 3.127589 GGTGGCGTTTGTTATGCTTTTT 58.872 40.909 0.00 0.00 38.86 1.94
601 806 2.547007 GGGTGGCGTTTGTTATGCTTTT 60.547 45.455 0.00 0.00 38.86 2.27
602 807 1.000394 GGGTGGCGTTTGTTATGCTTT 60.000 47.619 0.00 0.00 38.86 3.51
603 808 0.601057 GGGTGGCGTTTGTTATGCTT 59.399 50.000 0.00 0.00 38.86 3.91
604 809 0.538516 TGGGTGGCGTTTGTTATGCT 60.539 50.000 0.00 0.00 38.86 3.79
605 810 0.530288 ATGGGTGGCGTTTGTTATGC 59.470 50.000 0.00 0.00 38.08 3.14
606 811 1.202132 CGATGGGTGGCGTTTGTTATG 60.202 52.381 0.00 0.00 0.00 1.90
607 812 1.091537 CGATGGGTGGCGTTTGTTAT 58.908 50.000 0.00 0.00 0.00 1.89
608 813 0.956410 CCGATGGGTGGCGTTTGTTA 60.956 55.000 0.00 0.00 0.00 2.41
609 814 2.265182 CCGATGGGTGGCGTTTGTT 61.265 57.895 0.00 0.00 0.00 2.83
610 815 2.671619 CCGATGGGTGGCGTTTGT 60.672 61.111 0.00 0.00 0.00 2.83
611 816 3.439540 CCCGATGGGTGGCGTTTG 61.440 66.667 0.00 0.00 38.25 2.93
643 852 2.740506 TTCTCCCCCTTCGTTTGTTT 57.259 45.000 0.00 0.00 0.00 2.83
645 854 1.818131 GCTTTCTCCCCCTTCGTTTGT 60.818 52.381 0.00 0.00 0.00 2.83
693 931 0.245539 AAGGCACGCACAGTACGTAT 59.754 50.000 0.00 0.00 42.96 3.06
740 978 0.599558 CCCGTCCTCTCAAACGTACA 59.400 55.000 0.00 0.00 37.19 2.90
741 979 0.108945 CCCCGTCCTCTCAAACGTAC 60.109 60.000 0.00 0.00 37.19 3.67
742 980 0.540365 ACCCCGTCCTCTCAAACGTA 60.540 55.000 0.00 0.00 37.19 3.57
743 981 1.405272 AACCCCGTCCTCTCAAACGT 61.405 55.000 0.00 0.00 37.19 3.99
744 982 0.669625 GAACCCCGTCCTCTCAAACG 60.670 60.000 0.00 0.00 38.58 3.60
787 1025 1.066143 TCCAGAATGAACTCGGGCTTC 60.066 52.381 0.00 0.00 39.69 3.86
899 1150 1.271856 TATGCTCCGGTGGAAGACAA 58.728 50.000 0.00 0.00 0.00 3.18
908 1166 4.948341 TTATGTGTGTATATGCTCCGGT 57.052 40.909 0.00 0.00 0.00 5.28
937 1201 0.673644 TTTGGTAGAAGCTCAGGCGC 60.674 55.000 0.00 0.00 44.37 6.53
954 1226 2.811431 TCCAGCGAAATTGACGTGATTT 59.189 40.909 0.00 0.00 0.00 2.17
988 1263 1.596260 CATCGACATGAGGATGTGCAC 59.404 52.381 10.75 10.75 43.22 4.57
995 1270 3.068732 GGTGATCTTCATCGACATGAGGA 59.931 47.826 0.00 3.64 46.18 3.71
1038 1319 0.652071 TGATGTGATTTGCTAGCGCG 59.348 50.000 10.77 0.00 39.65 6.86
1074 1382 1.474330 TCATCGAGCTGTTCAGGCTA 58.526 50.000 0.00 0.00 40.40 3.93
1077 1385 1.649664 CCTTCATCGAGCTGTTCAGG 58.350 55.000 0.00 0.00 0.00 3.86
1078 1386 1.005340 GCCTTCATCGAGCTGTTCAG 58.995 55.000 0.00 0.00 0.00 3.02
1079 1387 0.391661 GGCCTTCATCGAGCTGTTCA 60.392 55.000 0.00 0.00 0.00 3.18
1080 1388 0.391661 TGGCCTTCATCGAGCTGTTC 60.392 55.000 3.32 0.00 0.00 3.18
1081 1389 0.674895 GTGGCCTTCATCGAGCTGTT 60.675 55.000 3.32 0.00 0.00 3.16
1166 1474 1.081462 TTCCCCACATCCGTACCCT 59.919 57.895 0.00 0.00 0.00 4.34
1170 1478 1.646912 TCTTGTTCCCCACATCCGTA 58.353 50.000 0.00 0.00 34.43 4.02
1172 1480 1.003118 TCTTCTTGTTCCCCACATCCG 59.997 52.381 0.00 0.00 34.43 4.18
1277 1600 1.058404 GAGTGACGGACAGCGTTTAC 58.942 55.000 0.00 0.00 0.00 2.01
1299 1622 1.266178 TCATCTTCTCCAACTCGCCA 58.734 50.000 0.00 0.00 0.00 5.69
1357 1680 2.029828 CGTAGCCCATGATCTGGTACTC 60.030 54.545 0.00 0.00 44.30 2.59
1413 1736 3.559811 CCACCAATGTGTCTTCCTCATCA 60.560 47.826 0.00 0.00 41.09 3.07
1416 1739 1.545428 GCCACCAATGTGTCTTCCTCA 60.545 52.381 0.00 0.00 41.09 3.86
1526 2065 0.037734 AACTCCCGGGCGAAATCTTT 59.962 50.000 19.65 0.00 0.00 2.52
1545 2084 1.735360 GCCACTTGCTTGCTTGACA 59.265 52.632 0.00 0.00 36.87 3.58
1560 2099 5.124297 GGCCTAAGTTATTTTCTTAACGCCA 59.876 40.000 0.00 0.00 39.74 5.69
1682 2225 5.857471 ATACAGTACCATAAACTGCGGTA 57.143 39.130 0.00 0.00 46.73 4.02
1684 2227 5.234329 CAGAATACAGTACCATAAACTGCGG 59.766 44.000 3.24 0.00 46.73 5.69
1706 2249 7.291411 AGGCCTAAGTTATACTACATGACAG 57.709 40.000 1.29 0.00 0.00 3.51
1767 2310 3.250762 CACCCTAATACATGGATTGCACG 59.749 47.826 13.77 0.87 0.00 5.34
1839 2382 1.682394 GGAGTAGAGTGGAAGAGCCGA 60.682 57.143 0.00 0.00 40.66 5.54
1858 2401 8.904099 AAAGACTTATAATTAGGAACGGATGG 57.096 34.615 0.00 0.00 0.00 3.51
1887 2430 5.324832 AACCCTGGTTGCATTATAGCTAT 57.675 39.130 11.77 11.77 36.91 2.97
1888 2431 4.788925 AACCCTGGTTGCATTATAGCTA 57.211 40.909 0.00 0.00 36.91 3.32
1889 2432 3.669939 AACCCTGGTTGCATTATAGCT 57.330 42.857 0.00 0.00 36.91 3.32
1912 3419 5.141182 TCTACATTTTGTTAGGTTGCCCAA 58.859 37.500 0.00 0.00 0.00 4.12
1951 3458 2.131183 GAGCCAGTCTAAGCTAATGCG 58.869 52.381 0.00 0.00 45.42 4.73
2010 3517 3.835395 TCTTCAAGGGTGTGTTTGGTTTT 59.165 39.130 0.00 0.00 0.00 2.43
2011 3518 3.194755 GTCTTCAAGGGTGTGTTTGGTTT 59.805 43.478 0.00 0.00 0.00 3.27
2046 3556 3.549070 GTGTTCGTCGTTGTGTTTCTACT 59.451 43.478 0.00 0.00 0.00 2.57
2047 3557 3.549070 AGTGTTCGTCGTTGTGTTTCTAC 59.451 43.478 0.00 0.00 0.00 2.59
2055 3565 0.099259 TCGTCAGTGTTCGTCGTTGT 59.901 50.000 9.38 0.00 0.00 3.32
2096 3606 2.262915 CCACCGCTCACTGAGACC 59.737 66.667 10.45 0.00 0.00 3.85
2103 3613 0.889186 AATTGACCACCACCGCTCAC 60.889 55.000 0.00 0.00 0.00 3.51
2122 3632 8.713708 TCCCCAAACTGAGTTCATATTTTAAA 57.286 30.769 0.00 0.00 0.00 1.52
2210 3721 3.779183 CTGCTCATATGGACCCTATGGAT 59.221 47.826 14.65 0.00 34.81 3.41
2221 3732 5.240844 TGAGATTTGATTGCTGCTCATATGG 59.759 40.000 2.13 0.00 0.00 2.74
2430 3943 2.418368 TGGATACACCATTGGAGTGC 57.582 50.000 15.13 7.52 46.17 4.40
2489 4003 8.081517 TCATCCTTTTCCAAGATTAATTGCAT 57.918 30.769 0.00 0.00 30.57 3.96
2499 4013 4.292041 TCCCTCATTCATCCTTTTCCAAGA 59.708 41.667 0.00 0.00 30.57 3.02
2511 4025 4.821532 AATAAGGCCTTCCCTCATTCAT 57.178 40.909 24.49 3.14 45.62 2.57
2514 4028 3.033909 GCAAATAAGGCCTTCCCTCATT 58.966 45.455 24.49 13.11 45.62 2.57
2516 4030 1.357420 TGCAAATAAGGCCTTCCCTCA 59.643 47.619 24.49 11.98 45.62 3.86
2527 4041 2.599973 GCGCTCCACATTTGCAAATAAG 59.400 45.455 23.69 17.76 0.00 1.73
2528 4042 2.605030 GCGCTCCACATTTGCAAATAA 58.395 42.857 23.69 9.41 0.00 1.40
2530 4044 0.390209 GGCGCTCCACATTTGCAAAT 60.390 50.000 18.99 18.99 0.00 2.32
2531 4045 1.006337 GGCGCTCCACATTTGCAAA 60.006 52.632 15.44 15.44 0.00 3.68
2532 4046 2.650196 GGCGCTCCACATTTGCAA 59.350 55.556 7.64 0.00 0.00 4.08
2533 4047 3.372730 GGGCGCTCCACATTTGCA 61.373 61.111 7.64 0.00 35.00 4.08
2534 4048 4.133796 GGGGCGCTCCACATTTGC 62.134 66.667 24.98 0.00 35.23 3.68
2535 4049 3.451894 GGGGGCGCTCCACATTTG 61.452 66.667 31.11 0.00 39.29 2.32
2551 4065 1.141053 CGAATTGGACTAGGAAGGGGG 59.859 57.143 0.00 0.00 0.00 5.40
2552 4066 1.141053 CCGAATTGGACTAGGAAGGGG 59.859 57.143 0.00 0.00 42.00 4.79
2553 4067 2.116238 TCCGAATTGGACTAGGAAGGG 58.884 52.381 0.00 0.00 43.74 3.95


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

AutoCloner maintained by Alex Coulton.