Multiple sequence alignment - TraesCS1B01G409800

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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 TraesCS1B01G409800 chr1B 100.000 2523 0 0 1 2523 636837299 636839821 0.000000e+00 4660.0
1 TraesCS1B01G409800 chr1B 84.360 211 27 4 2216 2422 636838977 636839185 4.260000e-48 202.0
2 TraesCS1B01G409800 chr1B 84.360 211 27 4 1679 1887 636839514 636839720 4.260000e-48 202.0
3 TraesCS1B01G409800 chr1B 81.765 170 24 4 2262 2425 637329284 637329452 4.380000e-28 135.0
4 TraesCS1B01G409800 chr1D 93.234 1818 102 12 724 2523 462200252 462202066 0.000000e+00 2656.0
5 TraesCS1B01G409800 chr1D 85.337 416 47 8 94 499 462199450 462199861 3.880000e-113 418.0
6 TraesCS1B01G409800 chr1D 85.470 234 27 6 503 733 462199935 462200164 1.170000e-58 237.0
7 TraesCS1B01G409800 chr1D 84.834 211 30 2 1679 1887 462201755 462201965 7.070000e-51 211.0
8 TraesCS1B01G409800 chr1D 86.294 197 20 4 2231 2422 462201229 462201423 9.150000e-50 207.0
9 TraesCS1B01G409800 chr1D 88.430 121 13 1 1767 1886 462287257 462287377 7.270000e-31 145.0
10 TraesCS1B01G409800 chr1D 81.250 160 25 4 391 547 464730546 464730389 9.480000e-25 124.0
11 TraesCS1B01G409800 chr1A 92.765 1700 85 13 839 2523 554061212 554062888 0.000000e+00 2423.0
12 TraesCS1B01G409800 chr1A 86.265 648 51 28 104 733 554060433 554061060 0.000000e+00 669.0
13 TraesCS1B01G409800 chr1A 85.782 211 28 2 1679 1887 554062577 554062787 3.270000e-54 222.0
14 TraesCS1B01G409800 chr1A 85.784 204 20 5 2224 2422 554062046 554062245 9.150000e-50 207.0
15 TraesCS1B01G409800 chrUn 81.414 382 53 18 1001 1377 74596104 74596472 1.900000e-76 296.0
16 TraesCS1B01G409800 chr7A 80.513 390 65 10 1001 1388 108809303 108808923 3.180000e-74 289.0
17 TraesCS1B01G409800 chr6D 79.592 392 59 20 1001 1377 431846326 431846711 6.920000e-66 261.0
18 TraesCS1B01G409800 chr6B 79.634 383 62 13 1001 1377 651987354 651987726 6.920000e-66 261.0
19 TraesCS1B01G409800 chr3B 86.441 236 30 2 1154 1388 632817480 632817714 8.950000e-65 257.0
20 TraesCS1B01G409800 chr3B 78.341 217 28 13 339 547 705145762 705145967 3.410000e-24 122.0
21 TraesCS1B01G409800 chr2D 86.861 137 17 1 1156 1291 382446518 382446382 4.350000e-33 152.0
22 TraesCS1B01G409800 chr7B 78.899 218 41 4 318 535 497923540 497923328 2.620000e-30 143.0
23 TraesCS1B01G409800 chr5A 78.125 224 33 14 339 555 586315622 586315836 7.330000e-26 128.0
24 TraesCS1B01G409800 chr3A 78.646 192 25 14 365 546 635238049 635237864 2.050000e-21 113.0
25 TraesCS1B01G409800 chr3A 77.143 210 34 11 339 541 35666995 35666793 2.650000e-20 110.0
26 TraesCS1B01G409800 chr4D 77.670 206 31 14 357 553 305829431 305829630 7.380000e-21 111.0
27 TraesCS1B01G409800 chr5B 78.472 144 18 13 503 641 450088835 450088700 5.780000e-12 82.4
28 TraesCS1B01G409800 chr2A 80.769 104 10 9 502 601 738283076 738282979 3.480000e-09 73.1


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 TraesCS1B01G409800 chr1B 636837299 636839821 2522 False 1688.00 4660 89.573333 1 2523 3 chr1B.!!$F2 2522
1 TraesCS1B01G409800 chr1D 462199450 462202066 2616 False 745.80 2656 87.033800 94 2523 5 chr1D.!!$F2 2429
2 TraesCS1B01G409800 chr1A 554060433 554062888 2455 False 880.25 2423 87.649000 104 2523 4 chr1A.!!$F1 2419

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
136 137 0.596082 GGGAGCAGTTTTTAAGCGCA 59.404 50.0 11.47 0.00 0.00 6.09 F
1113 1338 0.109735 TGTCGATCAGTGCTGTCGTC 60.110 55.0 16.97 13.99 36.37 4.20 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1394 1619 0.037326 AAAGGCGCAATCGAGTGAGA 60.037 50.000 20.66 0.0 38.1 3.27 R
2375 2623 3.228188 AGGCTGTGAAGAATTGGTCAA 57.772 42.857 0.00 0.0 0.0 3.18 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
50 51 9.877222 AGGGAGAAGTAAATTTCTTTAAAAGGA 57.123 29.630 0.00 0.00 37.53 3.36
57 58 9.374711 AGTAAATTTCTTTAAAAGGATGGGTCA 57.625 29.630 0.00 0.00 0.00 4.02
58 59 9.990360 GTAAATTTCTTTAAAAGGATGGGTCAA 57.010 29.630 0.00 0.00 0.00 3.18
60 61 8.491045 AATTTCTTTAAAAGGATGGGTCAAGA 57.509 30.769 0.00 0.00 0.00 3.02
61 62 6.894339 TTCTTTAAAAGGATGGGTCAAGAC 57.106 37.500 0.00 0.00 0.00 3.01
73 74 2.479566 GTCAAGACCATGCTTGGAGA 57.520 50.000 24.48 13.05 46.92 3.71
74 75 2.354259 GTCAAGACCATGCTTGGAGAG 58.646 52.381 24.48 11.16 46.92 3.20
75 76 2.027745 GTCAAGACCATGCTTGGAGAGA 60.028 50.000 24.48 13.05 46.92 3.10
76 77 2.639347 TCAAGACCATGCTTGGAGAGAA 59.361 45.455 24.48 4.90 46.92 2.87
77 78 3.072915 TCAAGACCATGCTTGGAGAGAAA 59.927 43.478 24.48 3.42 46.92 2.52
78 79 3.795688 AGACCATGCTTGGAGAGAAAA 57.204 42.857 24.48 0.00 46.92 2.29
79 80 4.104383 AGACCATGCTTGGAGAGAAAAA 57.896 40.909 24.48 0.00 46.92 1.94
80 81 3.823304 AGACCATGCTTGGAGAGAAAAAC 59.177 43.478 24.48 5.03 46.92 2.43
81 82 3.565307 ACCATGCTTGGAGAGAAAAACA 58.435 40.909 24.48 0.00 46.92 2.83
82 83 4.154942 ACCATGCTTGGAGAGAAAAACAT 58.845 39.130 24.48 0.00 46.92 2.71
83 84 5.324409 ACCATGCTTGGAGAGAAAAACATA 58.676 37.500 24.48 0.00 46.92 2.29
84 85 5.416952 ACCATGCTTGGAGAGAAAAACATAG 59.583 40.000 24.48 0.00 46.92 2.23
85 86 5.416952 CCATGCTTGGAGAGAAAAACATAGT 59.583 40.000 13.33 0.00 46.92 2.12
86 87 5.947228 TGCTTGGAGAGAAAAACATAGTG 57.053 39.130 0.00 0.00 0.00 2.74
87 88 5.376625 TGCTTGGAGAGAAAAACATAGTGT 58.623 37.500 0.00 0.00 0.00 3.55
88 89 5.827797 TGCTTGGAGAGAAAAACATAGTGTT 59.172 36.000 0.00 0.00 43.41 3.32
89 90 6.995686 TGCTTGGAGAGAAAAACATAGTGTTA 59.004 34.615 0.00 0.00 40.14 2.41
90 91 7.041372 TGCTTGGAGAGAAAAACATAGTGTTAC 60.041 37.037 0.00 0.00 40.14 2.50
91 92 7.173390 GCTTGGAGAGAAAAACATAGTGTTACT 59.827 37.037 0.00 0.00 40.14 2.24
92 93 9.706691 CTTGGAGAGAAAAACATAGTGTTACTA 57.293 33.333 0.00 0.00 40.14 1.82
93 94 9.706691 TTGGAGAGAAAAACATAGTGTTACTAG 57.293 33.333 0.00 0.00 40.14 2.57
94 95 8.311836 TGGAGAGAAAAACATAGTGTTACTAGG 58.688 37.037 0.00 0.00 40.14 3.02
95 96 8.529476 GGAGAGAAAAACATAGTGTTACTAGGA 58.471 37.037 7.54 0.00 40.14 2.94
136 137 0.596082 GGGAGCAGTTTTTAAGCGCA 59.404 50.000 11.47 0.00 0.00 6.09
137 138 1.202348 GGGAGCAGTTTTTAAGCGCAT 59.798 47.619 11.47 0.00 0.00 4.73
145 146 5.726413 GCAGTTTTTAAGCGCATGTTGTTTT 60.726 36.000 11.47 0.00 0.00 2.43
146 147 5.895889 CAGTTTTTAAGCGCATGTTGTTTTC 59.104 36.000 11.47 0.00 0.00 2.29
150 151 3.715628 AAGCGCATGTTGTTTTCTCTT 57.284 38.095 11.47 0.00 0.00 2.85
244 255 8.159344 TCTTTGGTCTTCTCATTCTTTCTTTC 57.841 34.615 0.00 0.00 0.00 2.62
247 258 8.525290 TTGGTCTTCTCATTCTTTCTTTCTTT 57.475 30.769 0.00 0.00 0.00 2.52
290 301 4.212213 TCGGTTTTATGTGTCGGTTTTG 57.788 40.909 0.00 0.00 0.00 2.44
314 325 6.598850 TGTTTTGGTTTTCTACGTTCCTTACT 59.401 34.615 0.00 0.00 0.00 2.24
321 332 8.347771 GGTTTTCTACGTTCCTTACTCATTTTT 58.652 33.333 0.00 0.00 0.00 1.94
322 333 9.378597 GTTTTCTACGTTCCTTACTCATTTTTC 57.621 33.333 0.00 0.00 0.00 2.29
377 390 6.764308 AACACATTGTCCATTTCTCCTATG 57.236 37.500 0.00 0.00 0.00 2.23
423 436 8.635877 ACACGTTTAGCAATTTTAAAACATGA 57.364 26.923 15.99 0.00 31.53 3.07
424 437 9.255304 ACACGTTTAGCAATTTTAAAACATGAT 57.745 25.926 15.99 13.08 31.53 2.45
563 652 9.985318 TTAACATTTTGAAAACATTGCTTTGAG 57.015 25.926 0.00 0.00 0.00 3.02
728 916 7.477144 TGGACTGAAAAACATATGCTATACG 57.523 36.000 1.58 0.00 0.00 3.06
794 1000 2.092375 GCCTTTTATCTACAGGCCCAGT 60.092 50.000 0.00 0.15 46.55 4.00
871 1095 2.101783 CAAATCACTAGCCCAATGCCA 58.898 47.619 0.00 0.00 42.71 4.92
983 1208 4.760047 CCACCACCTTCCTCGGCG 62.760 72.222 0.00 0.00 0.00 6.46
1073 1298 0.976641 CTGGGCTACAAGAGGTGACA 59.023 55.000 0.00 0.00 0.00 3.58
1095 1320 2.014068 GCCATCTCCCTTCTCCGTTTG 61.014 57.143 0.00 0.00 0.00 2.93
1102 1327 1.067142 CCCTTCTCCGTTTGTCGATCA 60.067 52.381 0.00 0.00 42.86 2.92
1113 1338 0.109735 TGTCGATCAGTGCTGTCGTC 60.110 55.000 16.97 13.99 36.37 4.20
1115 1340 2.500442 CGATCAGTGCTGTCGTCGC 61.500 63.158 12.52 0.00 33.10 5.19
1179 1404 1.402456 CCAAGTCGAACCAGTACGAGG 60.402 57.143 5.93 5.93 39.16 4.63
1403 1628 3.444034 CCATGGTAAAGTCTCTCACTCGA 59.556 47.826 2.57 0.00 32.30 4.04
1413 1638 0.037326 TCTCACTCGATTGCGCCTTT 60.037 50.000 4.18 0.00 37.46 3.11
1427 1652 0.179156 GCCTTTGCACATCATCGTGG 60.179 55.000 0.00 0.00 37.37 4.94
1451 1676 0.537143 TCGTGCCCTTTGCTGATGTT 60.537 50.000 0.00 0.00 42.00 2.71
1452 1677 0.387622 CGTGCCCTTTGCTGATGTTG 60.388 55.000 0.00 0.00 42.00 3.33
1453 1678 0.037975 GTGCCCTTTGCTGATGTTGG 60.038 55.000 0.00 0.00 42.00 3.77
1460 1685 3.430651 CCTTTGCTGATGTTGGTGTTGTT 60.431 43.478 0.00 0.00 0.00 2.83
1461 1686 2.867287 TGCTGATGTTGGTGTTGTTG 57.133 45.000 0.00 0.00 0.00 3.33
1473 1698 2.545742 GGTGTTGTTGGGTGATTCTTGC 60.546 50.000 0.00 0.00 0.00 4.01
1556 1781 8.589701 TGTGTCCTGATACTAATTCTTCAGTA 57.410 34.615 0.00 0.00 35.01 2.74
1562 1787 9.685828 CCTGATACTAATTCTTCAGTAGCTTAC 57.314 37.037 0.00 0.00 35.27 2.34
1578 1803 4.923893 AGCTTACGCACGTATAATGTGTA 58.076 39.130 3.43 7.31 41.02 2.90
1581 1818 6.477688 AGCTTACGCACGTATAATGTGTATTT 59.522 34.615 3.43 1.24 41.39 1.40
1582 1819 6.568601 GCTTACGCACGTATAATGTGTATTTG 59.431 38.462 3.43 7.24 41.39 2.32
1583 1820 7.522901 TTACGCACGTATAATGTGTATTTGT 57.477 32.000 3.43 4.97 41.39 2.83
1584 1821 6.411630 ACGCACGTATAATGTGTATTTGTT 57.588 33.333 0.00 0.00 38.98 2.83
1585 1822 6.833839 ACGCACGTATAATGTGTATTTGTTT 58.166 32.000 0.00 0.00 38.98 2.83
1586 1823 6.957077 ACGCACGTATAATGTGTATTTGTTTC 59.043 34.615 0.00 0.00 38.98 2.78
1587 1824 6.956520 CGCACGTATAATGTGTATTTGTTTCA 59.043 34.615 7.87 0.00 37.43 2.69
1588 1825 7.161900 CGCACGTATAATGTGTATTTGTTTCAG 59.838 37.037 7.87 0.00 37.43 3.02
1589 1826 7.960738 GCACGTATAATGTGTATTTGTTTCAGT 59.039 33.333 7.87 0.00 37.43 3.41
1590 1827 9.261318 CACGTATAATGTGTATTTGTTTCAGTG 57.739 33.333 0.00 0.00 30.72 3.66
1591 1828 9.210329 ACGTATAATGTGTATTTGTTTCAGTGA 57.790 29.630 0.00 0.00 0.00 3.41
1633 1870 2.091541 ACGACCATGGCCTAATTTGTG 58.908 47.619 13.04 0.00 0.00 3.33
1689 1927 6.203915 ACTGTTATACGTTTTGATTGCTGTGA 59.796 34.615 0.00 0.00 0.00 3.58
1730 1973 2.765689 TTTGGGGGAAGCTCTTTCAA 57.234 45.000 0.00 0.00 37.54 2.69
1818 2061 2.885266 TGGTCTCATAGTACGAGGATGC 59.115 50.000 0.00 0.00 0.00 3.91
1849 2093 3.733224 CGATGATTTCTCACCGATCAGTC 59.267 47.826 0.00 0.00 41.19 3.51
1851 2095 4.808414 TGATTTCTCACCGATCAGTCTT 57.192 40.909 0.00 0.00 0.00 3.01
1887 2131 2.436417 CAGTGACCCCCATACTTGTTG 58.564 52.381 0.00 0.00 0.00 3.33
1893 2137 3.694566 GACCCCCATACTTGTTGAATCAC 59.305 47.826 0.00 0.00 0.00 3.06
1917 2161 5.499004 ACCCTTATAATCGTGGCATGTAT 57.501 39.130 6.60 1.05 0.00 2.29
1924 2168 9.302345 CTTATAATCGTGGCATGTATAGTTAGG 57.698 37.037 6.60 0.00 0.00 2.69
1931 2175 5.869888 GTGGCATGTATAGTTAGGATGTAGC 59.130 44.000 0.00 0.00 0.00 3.58
1934 2178 6.387465 GCATGTATAGTTAGGATGTAGCGAA 58.613 40.000 0.00 0.00 0.00 4.70
1960 2204 6.371548 TGGTGAGATTTGTTTGCTGTACTATC 59.628 38.462 0.00 0.00 0.00 2.08
1973 2217 7.924103 TGCTGTACTATCGTGTATACATTTG 57.076 36.000 9.18 2.77 0.00 2.32
1986 2230 9.358872 CGTGTATACATTTGTAGCATCATCTAT 57.641 33.333 9.18 0.00 33.52 1.98
2082 2326 4.277476 TGTTTCCCTTGTGAACTTGATGT 58.723 39.130 0.00 0.00 0.00 3.06
2098 2346 9.167311 GAACTTGATGTATTGAACCAGATAACT 57.833 33.333 0.00 0.00 0.00 2.24
2099 2347 8.498054 ACTTGATGTATTGAACCAGATAACTG 57.502 34.615 0.00 0.00 43.12 3.16
2174 2422 5.120674 TGAAATCAGTTCACGCATAGTCAAG 59.879 40.000 0.00 0.00 41.47 3.02
2209 2457 8.730680 TCTAGGCATGAACTATTTCTGTTTTTC 58.269 33.333 0.00 0.00 32.36 2.29
2369 2617 3.270027 CGAGGATGTGCTTTGGTTGATA 58.730 45.455 0.00 0.00 0.00 2.15
2370 2618 3.063997 CGAGGATGTGCTTTGGTTGATAC 59.936 47.826 0.00 0.00 0.00 2.24
2371 2619 4.265073 GAGGATGTGCTTTGGTTGATACT 58.735 43.478 0.00 0.00 0.00 2.12
2372 2620 4.265073 AGGATGTGCTTTGGTTGATACTC 58.735 43.478 0.00 0.00 0.00 2.59
2373 2621 4.009675 GGATGTGCTTTGGTTGATACTCA 58.990 43.478 0.00 0.00 0.00 3.41
2374 2622 4.641989 GGATGTGCTTTGGTTGATACTCAT 59.358 41.667 0.00 0.00 0.00 2.90
2375 2623 5.126061 GGATGTGCTTTGGTTGATACTCATT 59.874 40.000 0.00 0.00 0.00 2.57
2410 2662 2.054453 GCCTTGCCTCCAATGACCC 61.054 63.158 0.00 0.00 0.00 4.46
2457 2709 8.011844 AGTGTATCACTCATGCAGTAAGATTA 57.988 34.615 0.00 0.00 41.21 1.75
2485 2737 7.139896 TGCTTGTTGTACCATTGTATACTTG 57.860 36.000 4.17 2.24 0.00 3.16
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
24 25 9.877222 TCCTTTTAAAGAAATTTACTTCTCCCT 57.123 29.630 6.24 0.00 34.49 4.20
31 32 9.374711 TGACCCATCCTTTTAAAGAAATTTACT 57.625 29.630 6.24 0.00 0.00 2.24
32 33 9.990360 TTGACCCATCCTTTTAAAGAAATTTAC 57.010 29.630 6.24 0.00 0.00 2.01
34 35 8.933653 TCTTGACCCATCCTTTTAAAGAAATTT 58.066 29.630 6.24 0.00 0.00 1.82
35 36 8.367911 GTCTTGACCCATCCTTTTAAAGAAATT 58.632 33.333 6.24 0.00 0.00 1.82
36 37 7.039011 GGTCTTGACCCATCCTTTTAAAGAAAT 60.039 37.037 6.24 0.00 0.00 2.17
37 38 6.266786 GGTCTTGACCCATCCTTTTAAAGAAA 59.733 38.462 6.24 0.00 0.00 2.52
38 39 5.773176 GGTCTTGACCCATCCTTTTAAAGAA 59.227 40.000 6.24 0.00 0.00 2.52
39 40 5.163034 TGGTCTTGACCCATCCTTTTAAAGA 60.163 40.000 16.23 0.00 0.00 2.52
40 41 5.076873 TGGTCTTGACCCATCCTTTTAAAG 58.923 41.667 16.23 0.00 0.00 1.85
41 42 5.068215 TGGTCTTGACCCATCCTTTTAAA 57.932 39.130 16.23 0.00 0.00 1.52
42 43 4.733077 TGGTCTTGACCCATCCTTTTAA 57.267 40.909 16.23 0.00 0.00 1.52
43 44 4.599041 CATGGTCTTGACCCATCCTTTTA 58.401 43.478 16.23 0.00 40.76 1.52
44 45 3.434309 CATGGTCTTGACCCATCCTTTT 58.566 45.455 16.23 0.00 40.76 2.27
45 46 2.885554 GCATGGTCTTGACCCATCCTTT 60.886 50.000 16.23 0.00 40.76 3.11
46 47 1.341383 GCATGGTCTTGACCCATCCTT 60.341 52.381 16.23 0.00 40.76 3.36
47 48 0.257039 GCATGGTCTTGACCCATCCT 59.743 55.000 16.23 0.00 40.76 3.24
48 49 0.257039 AGCATGGTCTTGACCCATCC 59.743 55.000 16.23 2.12 40.76 3.51
49 50 1.747355 CAAGCATGGTCTTGACCCATC 59.253 52.381 16.23 5.91 44.61 3.51
50 51 1.617804 CCAAGCATGGTCTTGACCCAT 60.618 52.381 16.23 7.83 44.61 4.00
51 52 0.251297 CCAAGCATGGTCTTGACCCA 60.251 55.000 16.23 5.98 44.61 4.51
52 53 2.571548 CCAAGCATGGTCTTGACCC 58.428 57.895 16.23 2.37 44.61 4.46
62 63 6.072286 ACACTATGTTTTTCTCTCCAAGCATG 60.072 38.462 0.00 0.00 0.00 4.06
63 64 6.006449 ACACTATGTTTTTCTCTCCAAGCAT 58.994 36.000 0.00 0.00 0.00 3.79
64 65 5.376625 ACACTATGTTTTTCTCTCCAAGCA 58.623 37.500 0.00 0.00 0.00 3.91
65 66 5.948992 ACACTATGTTTTTCTCTCCAAGC 57.051 39.130 0.00 0.00 0.00 4.01
66 67 8.608844 AGTAACACTATGTTTTTCTCTCCAAG 57.391 34.615 0.00 0.00 41.45 3.61
67 68 9.706691 CTAGTAACACTATGTTTTTCTCTCCAA 57.293 33.333 0.00 0.00 41.45 3.53
68 69 8.311836 CCTAGTAACACTATGTTTTTCTCTCCA 58.688 37.037 0.00 0.00 41.45 3.86
69 70 8.529476 TCCTAGTAACACTATGTTTTTCTCTCC 58.471 37.037 0.00 0.00 41.45 3.71
71 72 9.877178 CATCCTAGTAACACTATGTTTTTCTCT 57.123 33.333 0.00 0.00 41.45 3.10
72 73 9.871238 TCATCCTAGTAACACTATGTTTTTCTC 57.129 33.333 0.00 0.00 41.45 2.87
73 74 9.654663 GTCATCCTAGTAACACTATGTTTTTCT 57.345 33.333 0.00 0.50 41.45 2.52
74 75 8.880750 GGTCATCCTAGTAACACTATGTTTTTC 58.119 37.037 0.00 0.00 41.45 2.29
75 76 7.827729 GGGTCATCCTAGTAACACTATGTTTTT 59.172 37.037 0.00 0.00 41.45 1.94
76 77 7.037873 TGGGTCATCCTAGTAACACTATGTTTT 60.038 37.037 0.00 0.00 37.85 2.43
77 78 6.442564 TGGGTCATCCTAGTAACACTATGTTT 59.557 38.462 0.00 0.00 37.85 2.83
78 79 5.962031 TGGGTCATCCTAGTAACACTATGTT 59.038 40.000 0.00 0.00 39.22 2.71
79 80 5.525484 TGGGTCATCCTAGTAACACTATGT 58.475 41.667 0.00 0.00 36.20 2.29
80 81 6.479972 TTGGGTCATCCTAGTAACACTATG 57.520 41.667 0.00 0.00 36.20 2.23
81 82 8.816894 CATATTGGGTCATCCTAGTAACACTAT 58.183 37.037 0.00 0.00 36.20 2.12
82 83 7.234782 CCATATTGGGTCATCCTAGTAACACTA 59.765 40.741 0.00 0.00 32.67 2.74
83 84 6.043243 CCATATTGGGTCATCCTAGTAACACT 59.957 42.308 0.00 0.00 32.67 3.55
84 85 6.231211 CCATATTGGGTCATCCTAGTAACAC 58.769 44.000 0.00 0.00 32.67 3.32
85 86 6.433847 CCATATTGGGTCATCCTAGTAACA 57.566 41.667 0.00 0.00 32.67 2.41
131 132 3.316308 AGAAAGAGAAAACAACATGCGCT 59.684 39.130 9.73 0.00 0.00 5.92
188 190 5.346181 AAAGAAAAATCGAAAACCCCACA 57.654 34.783 0.00 0.00 0.00 4.17
189 191 6.741109 TCTAAAGAAAAATCGAAAACCCCAC 58.259 36.000 0.00 0.00 0.00 4.61
199 201 9.774742 CCAAAGATAACCTCTAAAGAAAAATCG 57.225 33.333 0.00 0.00 32.41 3.34
247 258 7.916450 ACCGAATGAAAAGAAATAAACAACGAA 59.084 29.630 0.00 0.00 0.00 3.85
267 278 5.216648 CAAAACCGACACATAAAACCGAAT 58.783 37.500 0.00 0.00 0.00 3.34
277 288 3.878160 ACCAAAACAAAACCGACACAT 57.122 38.095 0.00 0.00 0.00 3.21
290 301 7.019774 AGTAAGGAACGTAGAAAACCAAAAC 57.980 36.000 0.00 0.00 0.00 2.43
354 367 5.126061 GCATAGGAGAAATGGACAATGTGTT 59.874 40.000 0.00 0.00 0.00 3.32
683 774 1.673767 ACATGGTCTTGACCCATCCT 58.326 50.000 16.23 0.00 40.76 3.24
708 799 8.764287 TCATCACGTATAGCATATGTTTTTCAG 58.236 33.333 4.29 0.00 0.00 3.02
709 800 8.547894 GTCATCACGTATAGCATATGTTTTTCA 58.452 33.333 4.29 0.00 0.00 2.69
728 916 2.545952 CCGTGTGGGCTATAGTCATCAC 60.546 54.545 16.14 16.14 0.00 3.06
871 1095 2.264794 GGACGGTCCAGATTGCGT 59.735 61.111 22.10 0.00 36.28 5.24
954 1178 3.182263 TGGTGGTGGGAAGTGGGG 61.182 66.667 0.00 0.00 0.00 4.96
958 1182 1.716028 GGAAGGTGGTGGTGGGAAGT 61.716 60.000 0.00 0.00 0.00 3.01
1073 1298 1.764054 CGGAGAAGGGAGATGGCCT 60.764 63.158 3.32 0.00 0.00 5.19
1095 1320 1.128724 CGACGACAGCACTGATCGAC 61.129 60.000 21.15 16.25 37.46 4.20
1102 1327 4.406173 CCTCGCGACGACAGCACT 62.406 66.667 3.71 0.00 34.19 4.40
1253 1478 2.028748 GGTCTTGGCCTTGTAGACGTAA 60.029 50.000 3.32 0.00 39.30 3.18
1388 1613 2.600731 CGCAATCGAGTGAGAGACTTT 58.399 47.619 18.43 0.00 38.10 2.66
1389 1614 1.734047 GCGCAATCGAGTGAGAGACTT 60.734 52.381 20.66 0.00 38.10 3.01
1394 1619 0.037326 AAAGGCGCAATCGAGTGAGA 60.037 50.000 20.66 0.00 38.10 3.27
1396 1621 1.911293 GCAAAGGCGCAATCGAGTGA 61.911 55.000 18.43 0.00 38.10 3.41
1398 1623 1.965930 TGCAAAGGCGCAATCGAGT 60.966 52.632 10.83 0.00 45.35 4.18
1413 1638 0.321346 ACAGACCACGATGATGTGCA 59.679 50.000 0.00 0.00 38.55 4.57
1427 1652 2.946762 GCAAAGGGCACGACAGAC 59.053 61.111 0.00 0.00 43.97 3.51
1451 1676 2.692557 CAAGAATCACCCAACAACACCA 59.307 45.455 0.00 0.00 0.00 4.17
1452 1677 2.545742 GCAAGAATCACCCAACAACACC 60.546 50.000 0.00 0.00 0.00 4.16
1453 1678 2.362077 AGCAAGAATCACCCAACAACAC 59.638 45.455 0.00 0.00 0.00 3.32
1460 1685 0.401356 TGCAGAGCAAGAATCACCCA 59.599 50.000 0.00 0.00 34.76 4.51
1461 1686 1.093159 CTGCAGAGCAAGAATCACCC 58.907 55.000 8.42 0.00 38.41 4.61
1473 1698 0.676151 GACCTTCTTGCCCTGCAGAG 60.676 60.000 17.39 1.83 40.61 3.35
1562 1787 6.956520 TGAAACAAATACACATTATACGTGCG 59.043 34.615 0.00 0.00 37.93 5.34
1578 1803 6.219417 TGGACAACAATCACTGAAACAAAT 57.781 33.333 0.00 0.00 0.00 2.32
1581 1818 5.850557 AATGGACAACAATCACTGAAACA 57.149 34.783 0.00 0.00 0.00 2.83
1582 1819 7.648142 TCTAAATGGACAACAATCACTGAAAC 58.352 34.615 0.00 0.00 0.00 2.78
1583 1820 7.815840 TCTAAATGGACAACAATCACTGAAA 57.184 32.000 0.00 0.00 0.00 2.69
1584 1821 8.946085 GTATCTAAATGGACAACAATCACTGAA 58.054 33.333 0.00 0.00 0.00 3.02
1585 1822 7.552687 GGTATCTAAATGGACAACAATCACTGA 59.447 37.037 0.00 0.00 0.00 3.41
1586 1823 7.554118 AGGTATCTAAATGGACAACAATCACTG 59.446 37.037 0.00 0.00 0.00 3.66
1587 1824 7.633789 AGGTATCTAAATGGACAACAATCACT 58.366 34.615 0.00 0.00 0.00 3.41
1588 1825 7.865706 AGGTATCTAAATGGACAACAATCAC 57.134 36.000 0.00 0.00 0.00 3.06
1589 1826 7.709182 CGTAGGTATCTAAATGGACAACAATCA 59.291 37.037 0.00 0.00 0.00 2.57
1590 1827 7.924412 TCGTAGGTATCTAAATGGACAACAATC 59.076 37.037 0.00 0.00 0.00 2.67
1591 1828 7.709613 GTCGTAGGTATCTAAATGGACAACAAT 59.290 37.037 0.00 0.00 0.00 2.71
1592 1829 7.037438 GTCGTAGGTATCTAAATGGACAACAA 58.963 38.462 0.00 0.00 0.00 2.83
1660 1898 8.604035 CAGCAATCAAAACGTATAACAGTCTAT 58.396 33.333 0.00 0.00 0.00 1.98
1689 1927 1.382146 CATGGGGCCCTTGAATGCT 60.382 57.895 29.73 0.00 31.33 3.79
1730 1973 3.733337 CCTGCAGGTATTTCGAAGCTAT 58.267 45.455 25.53 0.00 0.00 2.97
1818 2061 2.672874 TGAGAAATCATCGACCAAAGCG 59.327 45.455 0.00 0.00 0.00 4.68
1869 2113 2.871096 TCAACAAGTATGGGGGTCAC 57.129 50.000 0.00 0.00 0.00 3.67
1887 2131 5.277828 GCCACGATTATAAGGGTTGTGATTC 60.278 44.000 6.53 0.00 30.45 2.52
1893 2137 3.882888 ACATGCCACGATTATAAGGGTTG 59.117 43.478 0.00 0.00 0.00 3.77
1917 2161 4.891168 TCACCATTCGCTACATCCTAACTA 59.109 41.667 0.00 0.00 0.00 2.24
1924 2168 4.572389 ACAAATCTCACCATTCGCTACATC 59.428 41.667 0.00 0.00 0.00 3.06
1931 2175 3.916172 CAGCAAACAAATCTCACCATTCG 59.084 43.478 0.00 0.00 0.00 3.34
1934 2178 5.072741 AGTACAGCAAACAAATCTCACCAT 58.927 37.500 0.00 0.00 0.00 3.55
1960 2204 7.643528 AGATGATGCTACAAATGTATACACG 57.356 36.000 7.96 2.50 0.00 4.49
1973 2217 5.063186 CGCAGATTGGAATAGATGATGCTAC 59.937 44.000 0.00 0.00 0.00 3.58
1986 2230 4.748892 TCAAACAAAAACGCAGATTGGAA 58.251 34.783 0.00 0.00 0.00 3.53
2082 2326 6.539173 ACCAACACAGTTATCTGGTTCAATA 58.461 36.000 5.80 0.00 45.14 1.90
2369 2617 5.278660 GCTGTGAAGAATTGGTCAAATGAGT 60.279 40.000 0.00 0.00 0.00 3.41
2370 2618 5.159209 GCTGTGAAGAATTGGTCAAATGAG 58.841 41.667 0.00 0.00 0.00 2.90
2371 2619 4.022068 GGCTGTGAAGAATTGGTCAAATGA 60.022 41.667 0.00 0.00 0.00 2.57
2372 2620 4.021719 AGGCTGTGAAGAATTGGTCAAATG 60.022 41.667 0.00 0.00 0.00 2.32
2373 2621 4.154942 AGGCTGTGAAGAATTGGTCAAAT 58.845 39.130 0.00 0.00 0.00 2.32
2374 2622 3.565307 AGGCTGTGAAGAATTGGTCAAA 58.435 40.909 0.00 0.00 0.00 2.69
2375 2623 3.228188 AGGCTGTGAAGAATTGGTCAA 57.772 42.857 0.00 0.00 0.00 3.18
2410 2662 8.889717 ACACTAACGAGAAATAACAAATATGGG 58.110 33.333 0.00 0.00 0.00 4.00
2485 2737 9.744468 AAAACATCTCAAATACCTAAACAACAC 57.256 29.630 0.00 0.00 0.00 3.32


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

AutoCloner maintained by Alex Coulton.