Multiple sequence alignment - TraesCS6A01G299700

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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 TraesCS6A01G299700 chr6A 100.000 2360 0 0 1 2360 532870123 532872482 0.000000e+00 4359
1 TraesCS6A01G299700 chr6A 97.713 1312 27 1 73 1384 502339364 502340672 0.000000e+00 2254
2 TraesCS6A01G299700 chr6A 95.604 91 1 3 1 89 207563509 207563420 2.440000e-30 143
3 TraesCS6A01G299700 chr3D 98.171 1312 24 0 73 1384 69660501 69661812 0.000000e+00 2290
4 TraesCS6A01G299700 chr2B 97.184 1314 35 1 73 1384 717931228 717929915 0.000000e+00 2220
5 TraesCS6A01G299700 chr7B 97.178 1311 36 1 73 1383 84527337 84528646 0.000000e+00 2215
6 TraesCS6A01G299700 chr3A 96.951 1312 39 1 73 1384 681100795 681099485 0.000000e+00 2200
7 TraesCS6A01G299700 chr3A 72.968 603 118 34 1626 2217 359367287 359366719 4.030000e-38 169
8 TraesCS6A01G299700 chr3A 97.647 85 1 1 1 85 399871865 399871948 6.800000e-31 145
9 TraesCS6A01G299700 chr3A 95.506 89 3 1 1 89 233261747 233261660 8.790000e-30 141
10 TraesCS6A01G299700 chr4A 96.570 1312 45 0 73 1384 107232212 107230901 0.000000e+00 2174
11 TraesCS6A01G299700 chr4A 73.254 587 118 32 1638 2217 237098092 237098646 6.700000e-41 178
12 TraesCS6A01G299700 chr2D 96.692 1300 42 1 85 1384 609915227 609916525 0.000000e+00 2161
13 TraesCS6A01G299700 chr2D 74.210 601 113 33 1627 2219 601980832 601981398 1.840000e-51 213
14 TraesCS6A01G299700 chr2A 95.887 1313 45 5 73 1384 148651719 148653023 0.000000e+00 2117
15 TraesCS6A01G299700 chr6B 95.579 1312 58 0 73 1384 695056725 695058036 0.000000e+00 2102
16 TraesCS6A01G299700 chr6D 87.315 473 49 3 1391 1863 387727300 387727761 4.470000e-147 531
17 TraesCS6A01G299700 chr6D 92.466 146 10 1 2213 2358 387728701 387728845 8.550000e-50 207
18 TraesCS6A01G299700 chr7D 79.638 663 109 16 1524 2184 154914041 154914679 9.940000e-124 453
19 TraesCS6A01G299700 chr7D 84.097 371 51 7 1424 1787 58354362 58354731 3.730000e-93 351
20 TraesCS6A01G299700 chr7D 74.037 597 107 38 1641 2219 590901319 590901885 1.430000e-47 200
21 TraesCS6A01G299700 chr7D 76.157 432 68 24 1572 1993 461815175 461814769 6.660000e-46 195
22 TraesCS6A01G299700 chr7D 75.291 429 70 25 1809 2228 625636628 625636227 3.120000e-39 172
23 TraesCS6A01G299700 chr7A 80.602 299 56 2 1455 1751 156561331 156561033 1.820000e-56 230
24 TraesCS6A01G299700 chr7A 73.884 605 113 35 1627 2217 32179443 32180016 1.430000e-47 200
25 TraesCS6A01G299700 chr7A 92.632 95 5 2 1 95 173014198 173014106 4.090000e-28 135
26 TraesCS6A01G299700 chr4D 74.333 600 120 27 1627 2217 459924841 459925415 8.490000e-55 224
27 TraesCS6A01G299700 chr5D 76.897 290 52 5 1624 1910 420981035 420980758 1.460000e-32 150
28 TraesCS6A01G299700 chr5B 96.552 87 2 1 1 86 125804454 125804368 2.440000e-30 143
29 TraesCS6A01G299700 chr5B 93.000 100 2 3 3 101 110991224 110991129 8.790000e-30 141
30 TraesCS6A01G299700 chr1A 92.233 103 5 2 1 102 364548415 364548315 2.440000e-30 143
31 TraesCS6A01G299700 chr1A 92.857 98 4 3 1 98 239853117 239853211 3.160000e-29 139
32 TraesCS6A01G299700 chr1D 72.194 597 117 34 1638 2219 233919491 233918929 1.140000e-28 137
33 TraesCS6A01G299700 chrUn 91.837 98 5 3 1 98 13040435 13040341 1.470000e-27 134
34 TraesCS6A01G299700 chrUn 75.427 293 58 13 1642 1928 51210671 51210387 1.900000e-26 130
35 TraesCS6A01G299700 chr1B 75.083 301 68 7 1624 1920 368568023 368567726 1.470000e-27 134
36 TraesCS6A01G299700 chr1B 74.733 281 44 18 1649 1922 534231506 534231246 1.490000e-17 100


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 TraesCS6A01G299700 chr6A 532870123 532872482 2359 False 4359 4359 100.0000 1 2360 1 chr6A.!!$F2 2359
1 TraesCS6A01G299700 chr6A 502339364 502340672 1308 False 2254 2254 97.7130 73 1384 1 chr6A.!!$F1 1311
2 TraesCS6A01G299700 chr3D 69660501 69661812 1311 False 2290 2290 98.1710 73 1384 1 chr3D.!!$F1 1311
3 TraesCS6A01G299700 chr2B 717929915 717931228 1313 True 2220 2220 97.1840 73 1384 1 chr2B.!!$R1 1311
4 TraesCS6A01G299700 chr7B 84527337 84528646 1309 False 2215 2215 97.1780 73 1383 1 chr7B.!!$F1 1310
5 TraesCS6A01G299700 chr3A 681099485 681100795 1310 True 2200 2200 96.9510 73 1384 1 chr3A.!!$R3 1311
6 TraesCS6A01G299700 chr4A 107230901 107232212 1311 True 2174 2174 96.5700 73 1384 1 chr4A.!!$R1 1311
7 TraesCS6A01G299700 chr2D 609915227 609916525 1298 False 2161 2161 96.6920 85 1384 1 chr2D.!!$F2 1299
8 TraesCS6A01G299700 chr2D 601980832 601981398 566 False 213 213 74.2100 1627 2219 1 chr2D.!!$F1 592
9 TraesCS6A01G299700 chr2A 148651719 148653023 1304 False 2117 2117 95.8870 73 1384 1 chr2A.!!$F1 1311
10 TraesCS6A01G299700 chr6B 695056725 695058036 1311 False 2102 2102 95.5790 73 1384 1 chr6B.!!$F1 1311
11 TraesCS6A01G299700 chr6D 387727300 387728845 1545 False 369 531 89.8905 1391 2358 2 chr6D.!!$F1 967
12 TraesCS6A01G299700 chr7D 154914041 154914679 638 False 453 453 79.6380 1524 2184 1 chr7D.!!$F2 660
13 TraesCS6A01G299700 chr4D 459924841 459925415 574 False 224 224 74.3330 1627 2217 1 chr4D.!!$F1 590

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
36 37 0.109272 TGCCTCTAAGTCGTGCTTCG 60.109 55.0 0.0 0.0 38.57 3.79 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1436 1437 0.321671 CATGTCGGGACACCAGAAGT 59.678 55.0 3.22 0.0 45.05 3.01 R

All possible primers

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

Download all possible primers: (Forward) (Reverse)
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
19 20 2.276472 TGCTTTCAATGCGGTTATGC 57.724 45.000 0.00 0.00 0.00 3.14
20 21 1.135141 TGCTTTCAATGCGGTTATGCC 60.135 47.619 0.00 0.00 0.00 4.40
21 22 1.134946 GCTTTCAATGCGGTTATGCCT 59.865 47.619 0.00 0.00 34.25 4.75
22 23 2.796032 GCTTTCAATGCGGTTATGCCTC 60.796 50.000 0.00 0.00 34.25 4.70
23 24 2.418368 TTCAATGCGGTTATGCCTCT 57.582 45.000 0.00 0.00 34.25 3.69
24 25 3.552132 TTCAATGCGGTTATGCCTCTA 57.448 42.857 0.00 0.00 34.25 2.43
25 26 3.552132 TCAATGCGGTTATGCCTCTAA 57.448 42.857 0.00 0.00 34.25 2.10
26 27 3.466836 TCAATGCGGTTATGCCTCTAAG 58.533 45.455 0.00 0.00 34.25 2.18
27 28 3.118408 TCAATGCGGTTATGCCTCTAAGT 60.118 43.478 0.00 0.00 34.25 2.24
28 29 2.596904 TGCGGTTATGCCTCTAAGTC 57.403 50.000 0.00 0.00 34.25 3.01
29 30 1.202371 TGCGGTTATGCCTCTAAGTCG 60.202 52.381 0.00 0.00 34.25 4.18
30 31 1.202382 GCGGTTATGCCTCTAAGTCGT 60.202 52.381 0.00 0.00 34.25 4.34
31 32 2.460918 CGGTTATGCCTCTAAGTCGTG 58.539 52.381 0.00 0.00 34.25 4.35
32 33 2.202566 GGTTATGCCTCTAAGTCGTGC 58.797 52.381 0.00 0.00 0.00 5.34
33 34 2.159085 GGTTATGCCTCTAAGTCGTGCT 60.159 50.000 0.00 0.00 0.00 4.40
34 35 3.522553 GTTATGCCTCTAAGTCGTGCTT 58.477 45.455 0.00 1.30 41.05 3.91
35 36 2.301577 ATGCCTCTAAGTCGTGCTTC 57.698 50.000 0.00 0.00 38.57 3.86
36 37 0.109272 TGCCTCTAAGTCGTGCTTCG 60.109 55.000 0.00 0.00 38.57 3.79
37 38 0.170561 GCCTCTAAGTCGTGCTTCGA 59.829 55.000 0.92 0.92 46.83 3.71
46 47 2.028484 GTGCTTCGACACGTGGGA 59.972 61.111 21.57 13.88 0.00 4.37
47 48 2.022129 GTGCTTCGACACGTGGGAG 61.022 63.158 21.57 8.15 0.00 4.30
48 49 2.197605 TGCTTCGACACGTGGGAGA 61.198 57.895 21.57 12.82 0.00 3.71
49 50 1.215647 GCTTCGACACGTGGGAGAT 59.784 57.895 21.57 0.00 0.00 2.75
50 51 0.454600 GCTTCGACACGTGGGAGATA 59.545 55.000 21.57 1.34 0.00 1.98
51 52 1.067212 GCTTCGACACGTGGGAGATAT 59.933 52.381 21.57 0.00 0.00 1.63
52 53 2.292569 GCTTCGACACGTGGGAGATATA 59.707 50.000 21.57 0.63 0.00 0.86
53 54 3.609644 GCTTCGACACGTGGGAGATATAG 60.610 52.174 21.57 11.01 0.00 1.31
54 55 1.878088 TCGACACGTGGGAGATATAGC 59.122 52.381 21.57 0.00 0.00 2.97
55 56 1.068472 CGACACGTGGGAGATATAGCC 60.068 57.143 21.57 0.00 0.00 3.93
56 57 0.959553 ACACGTGGGAGATATAGCCG 59.040 55.000 21.57 0.00 0.00 5.52
57 58 0.388649 CACGTGGGAGATATAGCCGC 60.389 60.000 7.95 0.00 0.00 6.53
58 59 0.826256 ACGTGGGAGATATAGCCGCA 60.826 55.000 0.00 0.00 0.00 5.69
59 60 0.532573 CGTGGGAGATATAGCCGCAT 59.467 55.000 0.00 0.00 0.00 4.73
60 61 1.469940 CGTGGGAGATATAGCCGCATC 60.470 57.143 0.00 0.00 0.00 3.91
61 62 0.817654 TGGGAGATATAGCCGCATCG 59.182 55.000 0.00 0.00 0.00 3.84
62 63 1.103803 GGGAGATATAGCCGCATCGA 58.896 55.000 0.00 0.00 0.00 3.59
63 64 1.066303 GGGAGATATAGCCGCATCGAG 59.934 57.143 0.00 0.00 0.00 4.04
64 65 1.066303 GGAGATATAGCCGCATCGAGG 59.934 57.143 0.00 0.00 0.00 4.63
65 66 1.066303 GAGATATAGCCGCATCGAGGG 59.934 57.143 0.00 0.00 0.00 4.30
232 233 4.270317 AGGATTTTGGCCATTCCACTAT 57.730 40.909 24.23 7.71 46.55 2.12
683 684 4.262164 CCTTCCAGAACAACAAATCCAAGG 60.262 45.833 0.00 0.00 0.00 3.61
735 736 1.733360 GCAACGACGGCTTGGTATTTA 59.267 47.619 0.00 0.00 0.00 1.40
935 936 4.495422 GGATTTGATAGTGACACACTCGT 58.505 43.478 8.59 0.00 41.21 4.18
1013 1014 6.095440 GCTAATGAAAAGATGGACCTTTGCTA 59.905 38.462 0.00 0.00 36.57 3.49
1060 1061 3.450457 TGCAGTGAGGTTTGGTTTGAATT 59.550 39.130 0.00 0.00 0.00 2.17
1094 1095 5.348986 TGTCGGATGTAGTAAGATTGAAGC 58.651 41.667 0.00 0.00 0.00 3.86
1303 1304 2.026262 AGTGTTTGGATGGATAACGCCT 60.026 45.455 0.00 0.00 33.86 5.52
1416 1417 3.052109 TGAGTATGTACATCCACTCCCCT 60.052 47.826 25.62 8.01 37.25 4.79
1424 1425 2.126882 CATCCACTCCCCTAACATGGA 58.873 52.381 0.00 0.00 43.42 3.41
1436 1437 3.716195 CATGGAGGCGGTGTGGGA 61.716 66.667 0.00 0.00 0.00 4.37
1439 1440 3.637273 GGAGGCGGTGTGGGACTT 61.637 66.667 0.00 0.00 0.00 3.01
1465 1466 4.335214 CCGACATGGGATTTGGCA 57.665 55.556 0.00 0.00 0.00 4.92
1497 1498 5.131142 TGACCTTCCTCCTTAAATCTCCATC 59.869 44.000 0.00 0.00 0.00 3.51
1507 1508 1.753930 AATCTCCATCGCAATGTGCA 58.246 45.000 0.61 0.00 45.36 4.57
1540 1541 2.159448 CGTTGTTTGAAGCTGTTGGTGA 60.159 45.455 0.00 0.00 0.00 4.02
1555 1557 1.341852 TGGTGACGATCGGTTCTTTCA 59.658 47.619 20.98 9.89 0.00 2.69
1565 1567 1.723220 GGTTCTTTCACGGCTCTACC 58.277 55.000 0.00 0.00 0.00 3.18
1636 1640 8.882736 CAAAGACTGTGATATGCATGTAACTAA 58.117 33.333 10.16 0.00 0.00 2.24
1714 1721 5.417754 TCTCAAGCATCAGTCTTGATCTT 57.582 39.130 5.98 0.00 45.96 2.40
1767 1775 4.019771 TGGTTATATCTGGCAATGGCGATA 60.020 41.667 17.73 17.73 42.47 2.92
1777 1785 3.300009 GCAATGGCGATACTTATTGTGC 58.700 45.455 0.00 0.00 34.04 4.57
1787 1795 5.978919 CGATACTTATTGTGCCGTTACCTTA 59.021 40.000 0.00 0.00 0.00 2.69
1794 1802 4.274602 TGTGCCGTTACCTTATTGAAGA 57.725 40.909 0.00 0.00 34.25 2.87
1802 1810 6.128007 CCGTTACCTTATTGAAGACATTGCTT 60.128 38.462 0.00 0.00 34.25 3.91
1804 1812 7.360861 CGTTACCTTATTGAAGACATTGCTTGA 60.361 37.037 0.00 0.00 34.25 3.02
1812 1820 5.603596 TGAAGACATTGCTTGAATTTGCTT 58.396 33.333 0.00 0.00 0.00 3.91
1818 1826 4.405116 TTGCTTGAATTTGCTTGGACTT 57.595 36.364 0.00 0.00 0.00 3.01
1822 1830 4.571984 GCTTGAATTTGCTTGGACTTGTTT 59.428 37.500 0.00 0.00 0.00 2.83
1863 1871 3.874383 TCTGGTCTTTGATGGTTGGAA 57.126 42.857 0.00 0.00 0.00 3.53
1865 1873 3.138283 TCTGGTCTTTGATGGTTGGAACT 59.862 43.478 0.00 0.00 0.00 3.01
1939 2628 2.425143 ATCCTTGTCGAGGTACCGTA 57.575 50.000 6.18 0.00 46.39 4.02
1940 2629 1.453155 TCCTTGTCGAGGTACCGTAC 58.547 55.000 6.18 6.81 46.39 3.67
1961 2650 3.686241 ACCGATGATGTCAAGTGATTGTG 59.314 43.478 0.00 0.00 0.00 3.33
1971 2660 1.671979 AGTGATTGTGGATGCGGATG 58.328 50.000 0.00 0.00 0.00 3.51
1975 2664 1.386525 ATTGTGGATGCGGATGTGGC 61.387 55.000 0.00 0.00 0.00 5.01
1983 2672 0.250510 TGCGGATGTGGCTGTTGTTA 60.251 50.000 0.00 0.00 0.00 2.41
2048 2739 6.903883 TTATTCCGTCAAGACATAGCTTTC 57.096 37.500 0.00 0.00 0.00 2.62
2074 2765 5.820423 TCTTGTTTGACTTTGCTAGTTGCTA 59.180 36.000 0.00 0.00 43.37 3.49
2075 2766 6.486657 TCTTGTTTGACTTTGCTAGTTGCTAT 59.513 34.615 0.00 0.00 43.37 2.97
2079 2770 6.633500 TTGACTTTGCTAGTTGCTATTGTT 57.367 33.333 0.00 0.00 43.37 2.83
2081 2772 7.921786 TGACTTTGCTAGTTGCTATTGTTAT 57.078 32.000 0.00 0.00 43.37 1.89
2111 2803 3.055747 TGTGTGTGTGAGAGTTGGTTGTA 60.056 43.478 0.00 0.00 0.00 2.41
2116 2808 3.058914 GTGTGAGAGTTGGTTGTATGCAC 60.059 47.826 0.00 0.00 0.00 4.57
2123 2815 3.841845 AGTTGGTTGTATGCACCCTAGTA 59.158 43.478 0.00 0.00 0.00 1.82
2124 2816 4.473559 AGTTGGTTGTATGCACCCTAGTAT 59.526 41.667 0.00 0.00 0.00 2.12
2126 2818 5.444744 TGGTTGTATGCACCCTAGTATTT 57.555 39.130 0.00 0.00 0.00 1.40
2127 2819 6.563037 TGGTTGTATGCACCCTAGTATTTA 57.437 37.500 0.00 0.00 0.00 1.40
2128 2820 7.144234 TGGTTGTATGCACCCTAGTATTTAT 57.856 36.000 0.00 0.00 0.00 1.40
2129 2821 6.995686 TGGTTGTATGCACCCTAGTATTTATG 59.004 38.462 0.00 0.00 0.00 1.90
2130 2822 6.996282 GGTTGTATGCACCCTAGTATTTATGT 59.004 38.462 0.00 0.00 0.00 2.29
2131 2823 8.152246 GGTTGTATGCACCCTAGTATTTATGTA 58.848 37.037 0.00 0.00 0.00 2.29
2132 2824 9.204570 GTTGTATGCACCCTAGTATTTATGTAG 57.795 37.037 0.00 0.00 0.00 2.74
2133 2825 8.486942 TGTATGCACCCTAGTATTTATGTAGT 57.513 34.615 0.00 0.00 0.00 2.73
2160 2854 0.318955 GGGTGTGTTGCTCATTGTGC 60.319 55.000 3.79 3.79 0.00 4.57
2167 2861 4.037803 TGTGTTGCTCATTGTGCTTGTATT 59.962 37.500 11.58 0.00 0.00 1.89
2169 2863 3.745332 TGCTCATTGTGCTTGTATTCG 57.255 42.857 11.58 0.00 0.00 3.34
2187 2881 3.921119 TCGCTTGATGCTTCATTTTGT 57.079 38.095 2.75 0.00 40.11 2.83
2189 2883 3.252944 TCGCTTGATGCTTCATTTTGTGA 59.747 39.130 2.75 4.39 40.11 3.58
2190 2884 4.082625 TCGCTTGATGCTTCATTTTGTGAT 60.083 37.500 2.75 0.00 40.11 3.06
2319 3020 0.832135 ACGGAGGAACAAGCAGAGGA 60.832 55.000 0.00 0.00 0.00 3.71
2326 3027 2.125350 CAAGCAGAGGAGCCGTCC 60.125 66.667 0.00 0.00 44.33 4.79
2358 3059 5.616383 CGTATTCGTAATGAACTCGAGTCTC 59.384 44.000 20.33 17.72 40.00 3.36
2359 3060 5.821516 ATTCGTAATGAACTCGAGTCTCT 57.178 39.130 20.33 2.57 40.00 3.10
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 1.135141 GGCATAACCGCATTGAAAGCA 60.135 47.619 0.00 0.00 0.00 3.91
1 2 1.134946 AGGCATAACCGCATTGAAAGC 59.865 47.619 0.00 0.00 46.52 3.51
2 3 2.684881 AGAGGCATAACCGCATTGAAAG 59.315 45.455 0.00 0.00 46.52 2.62
3 4 2.722094 AGAGGCATAACCGCATTGAAA 58.278 42.857 0.00 0.00 46.52 2.69
4 5 2.418368 AGAGGCATAACCGCATTGAA 57.582 45.000 0.00 0.00 46.52 2.69
5 6 3.118408 ACTTAGAGGCATAACCGCATTGA 60.118 43.478 0.00 0.00 46.52 2.57
6 7 3.206150 ACTTAGAGGCATAACCGCATTG 58.794 45.455 0.00 0.00 46.52 2.82
7 8 3.467803 GACTTAGAGGCATAACCGCATT 58.532 45.455 0.00 0.00 46.52 3.56
8 9 2.545952 CGACTTAGAGGCATAACCGCAT 60.546 50.000 0.00 0.00 46.52 4.73
9 10 1.202371 CGACTTAGAGGCATAACCGCA 60.202 52.381 0.00 0.00 46.52 5.69
10 11 1.202382 ACGACTTAGAGGCATAACCGC 60.202 52.381 0.00 0.00 46.52 5.68
11 12 2.460918 CACGACTTAGAGGCATAACCG 58.539 52.381 0.00 0.00 46.52 4.44
12 13 2.159085 AGCACGACTTAGAGGCATAACC 60.159 50.000 0.00 0.00 39.61 2.85
13 14 3.166489 AGCACGACTTAGAGGCATAAC 57.834 47.619 0.00 0.00 0.00 1.89
14 15 3.733988 CGAAGCACGACTTAGAGGCATAA 60.734 47.826 0.00 0.00 45.77 1.90
15 16 2.223502 CGAAGCACGACTTAGAGGCATA 60.224 50.000 0.00 0.00 45.77 3.14
16 17 1.469940 CGAAGCACGACTTAGAGGCAT 60.470 52.381 0.00 0.00 45.77 4.40
17 18 0.109272 CGAAGCACGACTTAGAGGCA 60.109 55.000 0.00 0.00 45.77 4.75
18 19 0.170561 TCGAAGCACGACTTAGAGGC 59.829 55.000 2.09 0.00 46.45 4.70
29 30 2.022129 CTCCCACGTGTCGAAGCAC 61.022 63.158 15.65 0.00 36.12 4.40
30 31 1.532604 ATCTCCCACGTGTCGAAGCA 61.533 55.000 15.65 0.00 0.00 3.91
31 32 0.454600 TATCTCCCACGTGTCGAAGC 59.545 55.000 15.65 0.00 0.00 3.86
32 33 3.609644 GCTATATCTCCCACGTGTCGAAG 60.610 52.174 15.65 6.13 0.00 3.79
33 34 2.292569 GCTATATCTCCCACGTGTCGAA 59.707 50.000 15.65 0.00 0.00 3.71
34 35 1.878088 GCTATATCTCCCACGTGTCGA 59.122 52.381 15.65 8.55 0.00 4.20
35 36 1.068472 GGCTATATCTCCCACGTGTCG 60.068 57.143 15.65 4.04 0.00 4.35
36 37 1.068472 CGGCTATATCTCCCACGTGTC 60.068 57.143 15.65 0.00 0.00 3.67
37 38 0.959553 CGGCTATATCTCCCACGTGT 59.040 55.000 15.65 0.00 0.00 4.49
38 39 0.388649 GCGGCTATATCTCCCACGTG 60.389 60.000 9.08 9.08 0.00 4.49
39 40 0.826256 TGCGGCTATATCTCCCACGT 60.826 55.000 0.00 0.00 0.00 4.49
40 41 0.532573 ATGCGGCTATATCTCCCACG 59.467 55.000 0.00 0.00 0.00 4.94
41 42 1.469940 CGATGCGGCTATATCTCCCAC 60.470 57.143 0.00 0.00 0.00 4.61
42 43 0.817654 CGATGCGGCTATATCTCCCA 59.182 55.000 0.00 0.00 0.00 4.37
43 44 1.066303 CTCGATGCGGCTATATCTCCC 59.934 57.143 0.00 0.00 0.00 4.30
44 45 1.066303 CCTCGATGCGGCTATATCTCC 59.934 57.143 0.00 0.00 0.00 3.71
45 46 1.066303 CCCTCGATGCGGCTATATCTC 59.934 57.143 0.00 0.00 0.00 2.75
46 47 1.107114 CCCTCGATGCGGCTATATCT 58.893 55.000 0.00 0.00 0.00 1.98
47 48 0.528684 GCCCTCGATGCGGCTATATC 60.529 60.000 10.26 0.00 42.21 1.63
48 49 1.517832 GCCCTCGATGCGGCTATAT 59.482 57.895 10.26 0.00 42.21 0.86
49 50 2.970639 GCCCTCGATGCGGCTATA 59.029 61.111 10.26 0.00 42.21 1.31
56 57 2.171725 GGTGTAACGCCCTCGATGC 61.172 63.158 0.00 0.00 38.12 3.91
57 58 0.527817 GAGGTGTAACGCCCTCGATG 60.528 60.000 0.00 0.00 38.06 3.84
58 59 1.814527 GAGGTGTAACGCCCTCGAT 59.185 57.895 0.00 0.00 38.06 3.59
59 60 3.281240 GAGGTGTAACGCCCTCGA 58.719 61.111 0.00 0.00 38.06 4.04
61 62 1.538419 GCTATGAGGTGTAACGCCCTC 60.538 57.143 1.66 1.66 46.20 4.30
62 63 0.464452 GCTATGAGGTGTAACGCCCT 59.536 55.000 0.00 0.00 38.12 5.19
63 64 0.532196 GGCTATGAGGTGTAACGCCC 60.532 60.000 0.00 0.00 38.12 6.13
64 65 0.532196 GGGCTATGAGGTGTAACGCC 60.532 60.000 0.00 0.00 38.12 5.68
65 66 0.177141 TGGGCTATGAGGTGTAACGC 59.823 55.000 0.00 0.00 38.12 4.84
66 67 2.277084 GTTGGGCTATGAGGTGTAACG 58.723 52.381 0.00 0.00 38.12 3.18
67 68 3.343941 TGTTGGGCTATGAGGTGTAAC 57.656 47.619 0.00 0.00 0.00 2.50
68 69 3.585289 TCTTGTTGGGCTATGAGGTGTAA 59.415 43.478 0.00 0.00 0.00 2.41
69 70 3.178046 TCTTGTTGGGCTATGAGGTGTA 58.822 45.455 0.00 0.00 0.00 2.90
70 71 1.985159 TCTTGTTGGGCTATGAGGTGT 59.015 47.619 0.00 0.00 0.00 4.16
71 72 2.787473 TCTTGTTGGGCTATGAGGTG 57.213 50.000 0.00 0.00 0.00 4.00
106 107 2.529632 AGAAAGAAGATTGTTGCCCCC 58.470 47.619 0.00 0.00 0.00 5.40
232 233 7.713942 CAGGAAATCTGTCATCTCATGTAATGA 59.286 37.037 8.17 8.17 44.02 2.57
279 280 0.321653 ATCGCACTGTGAAAGTCCCC 60.322 55.000 12.86 0.00 36.83 4.81
683 684 2.142357 GAACTTCGGCAAGCCCAACC 62.142 60.000 5.34 0.00 32.09 3.77
735 736 5.184864 TGTCAATTTTCGCCTTTCATACCAT 59.815 36.000 0.00 0.00 0.00 3.55
891 892 4.222886 CCGCGTCAACATTTAATTTCACA 58.777 39.130 4.92 0.00 0.00 3.58
935 936 4.640201 GGATAACTGCTCCAAATGTTGCTA 59.360 41.667 0.00 0.00 32.72 3.49
1013 1014 0.384309 TTCTGCTGTGAACGAGTCGT 59.616 50.000 13.56 13.56 43.97 4.34
1060 1061 6.216801 ACTACATCCGACAGTATTAGCAAA 57.783 37.500 0.00 0.00 0.00 3.68
1094 1095 1.409412 CTCCACGCTATCCGAATTCG 58.591 55.000 20.92 20.92 41.02 3.34
1384 1385 4.182693 TGTACATACTCAACACGAAGGG 57.817 45.455 0.00 0.00 0.00 3.95
1385 1386 4.804139 GGATGTACATACTCAACACGAAGG 59.196 45.833 11.08 0.00 0.00 3.46
1386 1387 5.288712 GTGGATGTACATACTCAACACGAAG 59.711 44.000 18.90 0.00 0.00 3.79
1387 1388 5.047590 AGTGGATGTACATACTCAACACGAA 60.048 40.000 18.90 0.00 33.78 3.85
1388 1389 4.461431 AGTGGATGTACATACTCAACACGA 59.539 41.667 18.90 0.00 33.78 4.35
1389 1390 4.744570 AGTGGATGTACATACTCAACACG 58.255 43.478 18.90 0.00 33.78 4.49
1396 1397 3.708236 AGGGGAGTGGATGTACATACT 57.292 47.619 18.90 14.50 0.00 2.12
1399 1400 3.731431 TGTTAGGGGAGTGGATGTACAT 58.269 45.455 8.43 8.43 0.00 2.29
1416 1417 1.298340 CCACACCGCCTCCATGTTA 59.702 57.895 0.00 0.00 0.00 2.41
1424 1425 2.526873 AGAAGTCCCACACCGCCT 60.527 61.111 0.00 0.00 0.00 5.52
1426 1427 2.358737 CCAGAAGTCCCACACCGC 60.359 66.667 0.00 0.00 0.00 5.68
1436 1437 0.321671 CATGTCGGGACACCAGAAGT 59.678 55.000 3.22 0.00 45.05 3.01
1439 1440 3.387716 CCATGTCGGGACACCAGA 58.612 61.111 3.22 0.00 45.05 3.86
1450 1451 2.019984 GAGACTGCCAAATCCCATGTC 58.980 52.381 0.00 0.00 0.00 3.06
1465 1466 0.612453 GGAGGAAGGTCACCGAGACT 60.612 60.000 7.70 0.00 46.72 3.24
1507 1508 3.283751 TCAAACAACGAAGGTCACCATT 58.716 40.909 0.00 0.00 0.00 3.16
1540 1541 1.012486 GCCGTGAAAGAACCGATCGT 61.012 55.000 15.09 0.00 0.00 3.73
1636 1640 1.153168 CCACTTTCCGCGATCCCAT 60.153 57.895 8.23 0.00 0.00 4.00
1767 1775 6.174760 TCAATAAGGTAACGGCACAATAAGT 58.825 36.000 0.00 0.00 46.39 2.24
1777 1785 5.354234 AGCAATGTCTTCAATAAGGTAACGG 59.646 40.000 0.00 0.00 46.39 4.44
1787 1795 6.228258 AGCAAATTCAAGCAATGTCTTCAAT 58.772 32.000 0.00 0.00 0.00 2.57
1794 1802 4.060205 GTCCAAGCAAATTCAAGCAATGT 58.940 39.130 0.00 0.00 0.00 2.71
1802 1810 6.169094 TGAAAAACAAGTCCAAGCAAATTCA 58.831 32.000 0.00 0.00 0.00 2.57
1822 1830 7.380536 CCAGATCATTGGTTTTCATCTTGAAA 58.619 34.615 0.00 0.00 43.84 2.69
1939 2628 3.686241 CACAATCACTTGACATCATCGGT 59.314 43.478 0.00 0.00 36.20 4.69
1940 2629 3.064408 CCACAATCACTTGACATCATCGG 59.936 47.826 0.00 0.00 36.20 4.18
1941 2630 3.934579 TCCACAATCACTTGACATCATCG 59.065 43.478 0.00 0.00 36.20 3.84
1942 2631 5.732528 GCATCCACAATCACTTGACATCATC 60.733 44.000 0.00 0.00 36.20 2.92
1961 2650 1.750399 AACAGCCACATCCGCATCC 60.750 57.895 0.00 0.00 0.00 3.51
1971 2660 6.494893 TCAACAATCTATAACAACAGCCAC 57.505 37.500 0.00 0.00 0.00 5.01
2038 2729 5.057149 AGTCAAACAAGACGAAAGCTATGT 58.943 37.500 0.00 0.00 43.24 2.29
2048 2739 4.795970 ACTAGCAAAGTCAAACAAGACG 57.204 40.909 0.00 0.00 43.24 4.18
2079 2770 9.729023 CAACTCTCACACACACAAATAAAAATA 57.271 29.630 0.00 0.00 0.00 1.40
2081 2772 7.032580 CCAACTCTCACACACACAAATAAAAA 58.967 34.615 0.00 0.00 0.00 1.94
2088 2779 2.746904 CAACCAACTCTCACACACACAA 59.253 45.455 0.00 0.00 0.00 3.33
2111 2803 8.951614 TCTACTACATAAATACTAGGGTGCAT 57.048 34.615 0.00 0.00 0.00 3.96
2116 2808 6.095160 CGGCCTCTACTACATAAATACTAGGG 59.905 46.154 0.00 0.00 0.00 3.53
2123 2815 3.323979 CACCCGGCCTCTACTACATAAAT 59.676 47.826 0.00 0.00 0.00 1.40
2124 2816 2.696707 CACCCGGCCTCTACTACATAAA 59.303 50.000 0.00 0.00 0.00 1.40
2126 2818 1.216175 ACACCCGGCCTCTACTACATA 59.784 52.381 0.00 0.00 0.00 2.29
2127 2819 0.032416 ACACCCGGCCTCTACTACAT 60.032 55.000 0.00 0.00 0.00 2.29
2128 2820 0.968901 CACACCCGGCCTCTACTACA 60.969 60.000 0.00 0.00 0.00 2.74
2129 2821 0.969409 ACACACCCGGCCTCTACTAC 60.969 60.000 0.00 0.00 0.00 2.73
2130 2822 0.251922 AACACACCCGGCCTCTACTA 60.252 55.000 0.00 0.00 0.00 1.82
2131 2823 1.535687 AACACACCCGGCCTCTACT 60.536 57.895 0.00 0.00 0.00 2.57
2132 2824 1.375523 CAACACACCCGGCCTCTAC 60.376 63.158 0.00 0.00 0.00 2.59
2133 2825 3.065306 CAACACACCCGGCCTCTA 58.935 61.111 0.00 0.00 0.00 2.43
2167 2861 3.252944 TCACAAAATGAAGCATCAAGCGA 59.747 39.130 0.00 0.00 39.72 4.93
2169 2863 7.766219 ATTATCACAAAATGAAGCATCAAGC 57.234 32.000 0.00 0.00 41.93 4.01
2242 2943 9.878599 GGAAATTATACAAACCATCGACTATTG 57.121 33.333 0.00 0.00 0.00 1.90
2246 2947 9.675464 TTTAGGAAATTATACAAACCATCGACT 57.325 29.630 0.00 0.00 0.00 4.18
2276 2977 2.355444 TGGTCCGTTCCGTTTCTTTTTC 59.645 45.455 0.00 0.00 0.00 2.29
2277 2978 2.356695 CTGGTCCGTTCCGTTTCTTTTT 59.643 45.455 0.00 0.00 0.00 1.94
2278 2979 1.944709 CTGGTCCGTTCCGTTTCTTTT 59.055 47.619 0.00 0.00 0.00 2.27
2326 3027 5.311858 GTTCATTACGAATACGGACTCCGG 61.312 50.000 21.52 0.00 43.22 5.14
2331 3032 4.591202 TCGAGTTCATTACGAATACGGAC 58.409 43.478 0.00 0.00 44.46 4.79
2337 3038 5.821516 AGAGACTCGAGTTCATTACGAAT 57.178 39.130 21.08 0.00 35.63 3.34


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

AutoCloner maintained by Alex Coulton.