Multiple sequence alignment - TraesCS1D01G393100

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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 TraesCS1D01G393100 chr1D 100.000 2786 0 0 1 2786 462752989 462755774 0.000000e+00 5145.0
1 TraesCS1D01G393100 chr1D 81.126 959 151 20 998 1953 462862573 462863504 0.000000e+00 741.0
2 TraesCS1D01G393100 chr1D 78.919 740 108 23 1484 2210 462854911 462855615 2.530000e-125 459.0
3 TraesCS1D01G393100 chr1D 85.545 422 57 2 2359 2780 462855686 462856103 3.290000e-119 438.0
4 TraesCS1D01G393100 chr1D 80.381 525 77 16 463 975 462854384 462854894 2.620000e-100 375.0
5 TraesCS1D01G393100 chr1D 77.860 271 34 12 2143 2403 480443541 480443795 8.040000e-31 145.0
6 TraesCS1D01G393100 chr1D 84.375 128 15 2 199 326 462854164 462854286 1.360000e-23 121.0
7 TraesCS1D01G393100 chr1D 100.000 46 0 0 2741 2786 470209756 470209711 4.940000e-13 86.1
8 TraesCS1D01G393100 chr1B 88.681 2032 129 38 71 2077 637881826 637883781 0.000000e+00 2385.0
9 TraesCS1D01G393100 chr1B 79.832 1552 222 44 237 1776 637895405 637896877 0.000000e+00 1048.0
10 TraesCS1D01G393100 chr1B 93.171 659 38 2 2128 2786 637884080 637884731 0.000000e+00 961.0
11 TraesCS1D01G393100 chr1B 80.607 428 75 6 1329 1752 637903732 637904155 9.620000e-85 324.0
12 TraesCS1D01G393100 chr1B 78.092 283 36 12 2144 2416 668781514 668781780 3.720000e-34 156.0
13 TraesCS1D01G393100 chr1B 83.582 67 7 3 1676 1740 637918272 637918336 3.000000e-05 60.2
14 TraesCS1D01G393100 chr1A 90.524 1678 113 16 191 1837 554541678 554543340 0.000000e+00 2176.0
15 TraesCS1D01G393100 chr1A 92.857 812 34 2 1829 2619 554557869 554558677 0.000000e+00 1157.0
16 TraesCS1D01G393100 chr1A 82.442 860 124 18 385 1236 554572798 554573638 0.000000e+00 726.0
17 TraesCS1D01G393100 chr1A 77.366 1321 175 53 416 1665 554642899 554644166 0.000000e+00 669.0
18 TraesCS1D01G393100 chr1A 97.037 135 4 0 2652 2786 554558679 554558813 7.760000e-56 228.0
19 TraesCS1D01G393100 chr1A 76.944 360 63 13 534 889 554799023 554799366 1.320000e-43 187.0


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 TraesCS1D01G393100 chr1D 462752989 462755774 2785 False 5145.00 5145 100.000 1 2786 1 chr1D.!!$F1 2785
1 TraesCS1D01G393100 chr1D 462862573 462863504 931 False 741.00 741 81.126 998 1953 1 chr1D.!!$F2 955
2 TraesCS1D01G393100 chr1D 462854164 462856103 1939 False 348.25 459 82.305 199 2780 4 chr1D.!!$F4 2581
3 TraesCS1D01G393100 chr1B 637881826 637884731 2905 False 1673.00 2385 90.926 71 2786 2 chr1B.!!$F5 2715
4 TraesCS1D01G393100 chr1B 637895405 637896877 1472 False 1048.00 1048 79.832 237 1776 1 chr1B.!!$F1 1539
5 TraesCS1D01G393100 chr1A 554541678 554543340 1662 False 2176.00 2176 90.524 191 1837 1 chr1A.!!$F1 1646
6 TraesCS1D01G393100 chr1A 554572798 554573638 840 False 726.00 726 82.442 385 1236 1 chr1A.!!$F2 851
7 TraesCS1D01G393100 chr1A 554557869 554558813 944 False 692.50 1157 94.947 1829 2786 2 chr1A.!!$F5 957
8 TraesCS1D01G393100 chr1A 554642899 554644166 1267 False 669.00 669 77.366 416 1665 1 chr1A.!!$F3 1249

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
38 39 0.099613 CGCTGCGTAGTGAGATGAGT 59.900 55.0 14.93 0.0 36.52 3.41 F
46 47 0.108424 AGTGAGATGAGTTCGCCAGC 60.108 55.0 0.00 0.0 0.00 4.85 F
354 402 0.177141 TCGGCCGGAAAAATCGATCT 59.823 50.0 27.83 0.0 0.00 2.75 F
1271 1402 0.386985 GACGTCTTCGGTGAGGACAC 60.387 60.0 8.70 0.0 45.27 3.67 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1001 1128 0.543410 TCCTTCGTAGCAACCCTCCA 60.543 55.000 0.00 0.0 0.0 3.86 R
1482 1625 0.588252 CAAACAACCTCTCCGTGCAG 59.412 55.000 0.00 0.0 0.0 4.41 R
1674 1821 1.662026 CCGTTTTTGCCGTACTTGAGC 60.662 52.381 0.00 0.0 0.0 4.26 R
2430 2854 0.106521 GTTTGTGGGGCATGTGCTTT 59.893 50.000 4.84 0.0 41.7 3.51 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
20 21 1.844357 CGAGGTTATTACGTGACAGCG 59.156 52.381 0.00 0.00 37.94 5.18
21 22 1.587034 GAGGTTATTACGTGACAGCGC 59.413 52.381 0.00 0.00 34.88 5.92
22 23 1.203994 AGGTTATTACGTGACAGCGCT 59.796 47.619 2.64 2.64 34.88 5.92
23 24 1.323534 GGTTATTACGTGACAGCGCTG 59.676 52.381 34.89 34.89 34.88 5.18
24 25 0.996462 TTATTACGTGACAGCGCTGC 59.004 50.000 36.28 27.34 34.88 5.25
25 26 1.137459 TATTACGTGACAGCGCTGCG 61.137 55.000 36.28 31.01 34.88 5.18
26 27 3.719471 TATTACGTGACAGCGCTGCGT 62.719 52.381 36.28 34.33 39.23 5.24
27 28 2.460837 TTACGTGACAGCGCTGCGTA 62.461 55.000 36.28 33.33 37.05 4.42
28 29 2.844224 TACGTGACAGCGCTGCGTAG 62.844 60.000 36.28 25.83 37.05 3.51
29 30 2.430921 GTGACAGCGCTGCGTAGT 60.431 61.111 36.28 17.71 0.00 2.73
30 31 2.430751 TGACAGCGCTGCGTAGTG 60.431 61.111 36.28 19.40 37.49 2.74
31 32 2.126463 GACAGCGCTGCGTAGTGA 60.126 61.111 36.28 0.00 36.52 3.41
32 33 2.126307 ACAGCGCTGCGTAGTGAG 60.126 61.111 36.28 10.83 36.52 3.51
33 34 2.179267 CAGCGCTGCGTAGTGAGA 59.821 61.111 26.68 0.00 36.52 3.27
34 35 1.226802 CAGCGCTGCGTAGTGAGAT 60.227 57.895 26.68 0.00 36.52 2.75
35 36 1.226802 AGCGCTGCGTAGTGAGATG 60.227 57.895 24.04 0.00 36.52 2.90
36 37 1.226688 GCGCTGCGTAGTGAGATGA 60.227 57.895 24.04 0.00 36.52 2.92
37 38 1.205485 GCGCTGCGTAGTGAGATGAG 61.205 60.000 24.04 0.00 36.52 2.90
38 39 0.099613 CGCTGCGTAGTGAGATGAGT 59.900 55.000 14.93 0.00 36.52 3.41
39 40 1.468224 CGCTGCGTAGTGAGATGAGTT 60.468 52.381 14.93 0.00 36.52 3.01
40 41 2.189342 GCTGCGTAGTGAGATGAGTTC 58.811 52.381 1.53 0.00 0.00 3.01
41 42 2.445316 CTGCGTAGTGAGATGAGTTCG 58.555 52.381 0.00 0.00 0.00 3.95
42 43 1.192793 GCGTAGTGAGATGAGTTCGC 58.807 55.000 0.00 0.00 36.06 4.70
43 44 1.828832 CGTAGTGAGATGAGTTCGCC 58.171 55.000 0.00 0.00 0.00 5.54
44 45 1.132453 CGTAGTGAGATGAGTTCGCCA 59.868 52.381 0.00 0.00 0.00 5.69
45 46 2.792890 CGTAGTGAGATGAGTTCGCCAG 60.793 54.545 0.00 0.00 0.00 4.85
46 47 0.108424 AGTGAGATGAGTTCGCCAGC 60.108 55.000 0.00 0.00 0.00 4.85
47 48 0.390340 GTGAGATGAGTTCGCCAGCA 60.390 55.000 0.00 0.00 0.00 4.41
48 49 0.538584 TGAGATGAGTTCGCCAGCAT 59.461 50.000 0.00 0.00 0.00 3.79
49 50 1.065926 TGAGATGAGTTCGCCAGCATT 60.066 47.619 0.00 0.00 0.00 3.56
50 51 2.168313 TGAGATGAGTTCGCCAGCATTA 59.832 45.455 0.00 0.00 0.00 1.90
51 52 3.181462 TGAGATGAGTTCGCCAGCATTAT 60.181 43.478 0.00 0.00 0.00 1.28
52 53 3.812053 GAGATGAGTTCGCCAGCATTATT 59.188 43.478 0.00 0.00 0.00 1.40
53 54 4.202441 AGATGAGTTCGCCAGCATTATTT 58.798 39.130 0.00 0.00 0.00 1.40
54 55 5.368145 AGATGAGTTCGCCAGCATTATTTA 58.632 37.500 0.00 0.00 0.00 1.40
55 56 4.875544 TGAGTTCGCCAGCATTATTTAC 57.124 40.909 0.00 0.00 0.00 2.01
56 57 3.625764 TGAGTTCGCCAGCATTATTTACC 59.374 43.478 0.00 0.00 0.00 2.85
57 58 3.616219 AGTTCGCCAGCATTATTTACCA 58.384 40.909 0.00 0.00 0.00 3.25
58 59 4.207165 AGTTCGCCAGCATTATTTACCAT 58.793 39.130 0.00 0.00 0.00 3.55
59 60 4.275936 AGTTCGCCAGCATTATTTACCATC 59.724 41.667 0.00 0.00 0.00 3.51
60 61 3.146066 TCGCCAGCATTATTTACCATCC 58.854 45.455 0.00 0.00 0.00 3.51
61 62 2.095768 CGCCAGCATTATTTACCATCCG 60.096 50.000 0.00 0.00 0.00 4.18
62 63 2.351738 GCCAGCATTATTTACCATCCGC 60.352 50.000 0.00 0.00 0.00 5.54
63 64 2.095768 CCAGCATTATTTACCATCCGCG 60.096 50.000 0.00 0.00 0.00 6.46
64 65 2.805671 CAGCATTATTTACCATCCGCGA 59.194 45.455 8.23 0.00 0.00 5.87
65 66 3.067106 AGCATTATTTACCATCCGCGAG 58.933 45.455 8.23 0.00 0.00 5.03
66 67 3.064207 GCATTATTTACCATCCGCGAGA 58.936 45.455 8.23 3.13 0.00 4.04
67 68 3.120649 GCATTATTTACCATCCGCGAGAC 60.121 47.826 8.23 0.00 0.00 3.36
68 69 2.806608 TATTTACCATCCGCGAGACC 57.193 50.000 8.23 0.00 0.00 3.85
69 70 0.249322 ATTTACCATCCGCGAGACCG 60.249 55.000 8.23 0.00 39.16 4.79
70 71 1.597797 TTTACCATCCGCGAGACCGT 61.598 55.000 8.23 5.71 38.24 4.83
71 72 2.274232 TTACCATCCGCGAGACCGTG 62.274 60.000 8.23 0.00 45.12 4.94
108 109 0.874607 GTCAAAGCGTCCGTCACTGT 60.875 55.000 0.00 0.00 0.00 3.55
109 110 0.669619 TCAAAGCGTCCGTCACTGTA 59.330 50.000 0.00 0.00 0.00 2.74
110 111 1.060713 CAAAGCGTCCGTCACTGTAG 58.939 55.000 0.00 0.00 0.00 2.74
136 138 4.481930 TTTTAGGCAATCGTCACTGTTG 57.518 40.909 0.00 0.00 0.00 3.33
141 143 1.334960 GCAATCGTCACTGTTGGTTGG 60.335 52.381 1.24 0.00 0.00 3.77
152 154 2.428171 CTGTTGGTTGGATTGGGCTATG 59.572 50.000 0.00 0.00 0.00 2.23
153 155 1.756538 GTTGGTTGGATTGGGCTATGG 59.243 52.381 0.00 0.00 0.00 2.74
154 156 0.396974 TGGTTGGATTGGGCTATGGC 60.397 55.000 0.00 0.00 37.82 4.40
197 199 3.760684 GTCTCAGTTTTGGGCTCATCAAT 59.239 43.478 0.00 0.00 0.00 2.57
198 200 4.012374 TCTCAGTTTTGGGCTCATCAATC 58.988 43.478 0.00 0.00 0.00 2.67
199 201 3.760151 CTCAGTTTTGGGCTCATCAATCA 59.240 43.478 0.00 0.00 0.00 2.57
200 202 3.507233 TCAGTTTTGGGCTCATCAATCAC 59.493 43.478 0.00 0.00 0.00 3.06
201 203 3.508793 CAGTTTTGGGCTCATCAATCACT 59.491 43.478 0.00 0.00 0.00 3.41
202 204 3.760684 AGTTTTGGGCTCATCAATCACTC 59.239 43.478 0.00 0.00 0.00 3.51
203 205 2.425143 TTGGGCTCATCAATCACTCC 57.575 50.000 0.00 0.00 0.00 3.85
204 206 1.288188 TGGGCTCATCAATCACTCCA 58.712 50.000 0.00 0.00 0.00 3.86
208 210 2.621998 GGCTCATCAATCACTCCAATGG 59.378 50.000 0.00 0.00 0.00 3.16
241 247 2.886523 CCCATGATAATCCATGCACGTT 59.113 45.455 0.00 0.00 41.83 3.99
278 284 1.228552 GGCCCAAAACCAGCAGAGA 60.229 57.895 0.00 0.00 0.00 3.10
279 285 1.527433 GGCCCAAAACCAGCAGAGAC 61.527 60.000 0.00 0.00 0.00 3.36
297 303 1.679680 GACATCCCTGATCCGTAACGA 59.320 52.381 0.00 0.00 0.00 3.85
329 377 0.599204 TTCGCACCGGAGAACAAGAC 60.599 55.000 9.46 0.00 0.00 3.01
330 378 2.372690 CGCACCGGAGAACAAGACG 61.373 63.158 9.46 0.00 0.00 4.18
333 381 0.666577 CACCGGAGAACAAGACGTCC 60.667 60.000 9.46 0.00 0.00 4.79
334 382 1.111116 ACCGGAGAACAAGACGTCCA 61.111 55.000 9.46 0.00 0.00 4.02
335 383 0.246635 CCGGAGAACAAGACGTCCAT 59.753 55.000 13.01 0.00 0.00 3.41
336 384 1.630148 CGGAGAACAAGACGTCCATC 58.370 55.000 13.01 5.69 0.00 3.51
337 385 1.630148 GGAGAACAAGACGTCCATCG 58.370 55.000 13.01 0.46 46.00 3.84
338 386 1.630148 GAGAACAAGACGTCCATCGG 58.370 55.000 13.01 0.00 44.69 4.18
344 392 4.137872 GACGTCCATCGGCCGGAA 62.138 66.667 27.83 7.28 42.54 4.30
345 393 3.652539 GACGTCCATCGGCCGGAAA 62.653 63.158 27.83 6.34 42.54 3.13
346 394 2.435234 CGTCCATCGGCCGGAAAA 60.435 61.111 27.83 5.87 33.29 2.29
347 395 2.036006 CGTCCATCGGCCGGAAAAA 61.036 57.895 27.83 5.39 33.29 1.94
348 396 1.373590 CGTCCATCGGCCGGAAAAAT 61.374 55.000 27.83 8.08 33.29 1.82
349 397 0.380733 GTCCATCGGCCGGAAAAATC 59.619 55.000 27.83 6.61 33.29 2.17
350 398 1.092921 TCCATCGGCCGGAAAAATCG 61.093 55.000 27.83 3.37 0.00 3.34
351 399 1.092921 CCATCGGCCGGAAAAATCGA 61.093 55.000 27.83 1.69 0.00 3.59
352 400 0.944386 CATCGGCCGGAAAAATCGAT 59.056 50.000 27.83 4.59 40.57 3.59
353 401 1.069906 CATCGGCCGGAAAAATCGATC 60.070 52.381 27.83 0.00 38.32 3.69
354 402 0.177141 TCGGCCGGAAAAATCGATCT 59.823 50.000 27.83 0.00 0.00 2.75
355 403 0.582005 CGGCCGGAAAAATCGATCTC 59.418 55.000 20.10 0.00 0.00 2.75
356 404 1.663695 GGCCGGAAAAATCGATCTCA 58.336 50.000 5.05 0.00 0.00 3.27
357 405 1.330829 GGCCGGAAAAATCGATCTCAC 59.669 52.381 5.05 0.00 0.00 3.51
476 527 1.758514 GCCATCTCCTCTCCCGTCA 60.759 63.158 0.00 0.00 0.00 4.35
719 808 2.113774 CCACAAGCTGGACCTGCA 59.886 61.111 23.61 0.00 43.95 4.41
720 809 2.263741 CCACAAGCTGGACCTGCAC 61.264 63.158 23.61 0.00 43.95 4.57
846 938 0.899720 TCGCCACGGGAAATCTAAGT 59.100 50.000 0.00 0.00 0.00 2.24
857 952 1.210538 AATCTAAGTTCCCCGGGGAC 58.789 55.000 42.89 32.99 45.11 4.46
889 994 3.020026 CTCGCGTACGACACCGAGT 62.020 63.158 25.20 0.00 45.12 4.18
891 996 2.866028 GCGTACGACACCGAGTCT 59.134 61.111 21.65 0.00 45.32 3.24
1001 1128 3.038280 TCGTGGGTGACTTGGATGATAT 58.962 45.455 0.00 0.00 0.00 1.63
1131 1258 2.356125 CCCATCGACACTCCCTTTCAAT 60.356 50.000 0.00 0.00 0.00 2.57
1271 1402 0.386985 GACGTCTTCGGTGAGGACAC 60.387 60.000 8.70 0.00 45.27 3.67
1411 1546 0.464373 CCACAAGGCGCATGGATACT 60.464 55.000 10.83 0.00 35.33 2.12
1412 1547 1.382522 CACAAGGCGCATGGATACTT 58.617 50.000 10.83 0.00 37.61 2.24
1419 1554 2.289694 GGCGCATGGATACTTAGATGGT 60.290 50.000 10.83 0.00 37.61 3.55
1438 1577 2.159099 GGTTACATCTCCTCATGCGACA 60.159 50.000 0.00 0.00 0.00 4.35
1482 1625 2.747855 CAGCCGGCCTGGAAGTTC 60.748 66.667 26.15 0.00 42.00 3.01
1500 1643 0.468226 TCTGCACGGAGAGGTTGTTT 59.532 50.000 0.00 0.00 0.00 2.83
1559 1702 0.737715 CACGTCCCAGCTAGTCTTGC 60.738 60.000 0.00 0.00 0.00 4.01
1628 1775 0.530870 AGATTTAAGCGGAGGCGCTC 60.531 55.000 7.64 2.45 45.26 5.03
1674 1821 3.431912 TGATCCGTTTGTCGATGTTTCAG 59.568 43.478 0.00 0.00 42.86 3.02
1731 1878 2.982130 CACAGGCCTAACCGCTCT 59.018 61.111 3.98 0.00 46.52 4.09
1812 1959 0.106894 TGTATGGCACCACGTGTTGA 59.893 50.000 18.10 0.00 35.75 3.18
1822 1972 0.039346 CACGTGTTGAATGCATGGCA 60.039 50.000 7.58 0.00 44.86 4.92
1867 2017 7.976135 ATCTCCTGTGAATTGCTACAATATC 57.024 36.000 0.00 0.00 0.00 1.63
1971 2142 4.009675 TGGACTACATGAATTTCTGGTGC 58.990 43.478 0.00 0.00 0.00 5.01
2101 2276 5.897377 AACTGTTTTGTCTAGTGTGCTTT 57.103 34.783 0.00 0.00 0.00 3.51
2147 2570 1.078709 GTGCATGAGTAAAGCGCTGA 58.921 50.000 12.58 0.00 35.97 4.26
2322 2746 0.036732 AGTTGGTCGTGGCATCACAT 59.963 50.000 0.00 0.00 43.79 3.21
2340 2764 9.173939 GCATCACATCATTAAACTATAAAGCAC 57.826 33.333 0.00 0.00 0.00 4.40
2430 2854 5.888724 TGAAAACCCAGTGTTGATTCAACTA 59.111 36.000 25.49 12.56 43.85 2.24
2431 2855 6.378564 TGAAAACCCAGTGTTGATTCAACTAA 59.621 34.615 25.49 8.05 43.85 2.24
2441 2865 4.439305 TGATTCAACTAAAGCACATGCC 57.561 40.909 0.00 0.00 43.38 4.40
2480 2904 6.041865 TGGTTCTTCCATGTGACAATTGATTT 59.958 34.615 13.59 0.00 41.93 2.17
2494 2918 6.870769 ACAATTGATTTCTCCATGATTCCAC 58.129 36.000 13.59 0.00 0.00 4.02
2593 3021 1.602377 GGAGAATTTTATCCCACCGCG 59.398 52.381 0.00 0.00 32.46 6.46
2594 3022 1.002792 GAGAATTTTATCCCACCGCGC 60.003 52.381 0.00 0.00 0.00 6.86
2595 3023 0.736053 GAATTTTATCCCACCGCGCA 59.264 50.000 8.75 0.00 0.00 6.09
2596 3024 0.454196 AATTTTATCCCACCGCGCAC 59.546 50.000 8.75 0.00 0.00 5.34
2645 3073 9.645128 ATTTATGGGTCAAGATTGATCACATAA 57.355 29.630 18.48 18.48 40.07 1.90
2650 3078 7.781219 TGGGTCAAGATTGATCACATAATTGAT 59.219 33.333 8.04 0.00 40.07 2.57
2727 3155 6.071728 ACCTAATCTGGCAAGAAACAAATGAG 60.072 38.462 0.00 0.00 35.59 2.90
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
3 4 1.323534 CAGCGCTGTCACGTAATAACC 59.676 52.381 29.24 0.00 34.88 2.85
4 5 1.266891 GCAGCGCTGTCACGTAATAAC 60.267 52.381 35.80 12.95 34.88 1.89
5 6 0.996462 GCAGCGCTGTCACGTAATAA 59.004 50.000 35.80 0.00 34.88 1.40
8 9 2.460837 TACGCAGCGCTGTCACGTAA 62.461 55.000 32.25 21.38 36.39 3.18
10 11 4.337060 TACGCAGCGCTGTCACGT 62.337 61.111 33.00 33.00 40.53 4.49
12 13 2.430921 ACTACGCAGCGCTGTCAC 60.431 61.111 35.80 20.02 0.00 3.67
13 14 2.430751 CACTACGCAGCGCTGTCA 60.431 61.111 35.80 20.79 0.00 3.58
14 15 2.126463 TCACTACGCAGCGCTGTC 60.126 61.111 35.80 26.28 0.00 3.51
15 16 1.938657 ATCTCACTACGCAGCGCTGT 61.939 55.000 35.80 21.44 0.00 4.40
16 17 1.226802 ATCTCACTACGCAGCGCTG 60.227 57.895 32.83 32.83 0.00 5.18
17 18 1.226802 CATCTCACTACGCAGCGCT 60.227 57.895 16.61 2.64 0.00 5.92
18 19 1.205485 CTCATCTCACTACGCAGCGC 61.205 60.000 16.61 0.00 0.00 5.92
19 20 0.099613 ACTCATCTCACTACGCAGCG 59.900 55.000 14.82 14.82 0.00 5.18
20 21 2.189342 GAACTCATCTCACTACGCAGC 58.811 52.381 0.00 0.00 0.00 5.25
21 22 2.445316 CGAACTCATCTCACTACGCAG 58.555 52.381 0.00 0.00 0.00 5.18
22 23 1.467543 GCGAACTCATCTCACTACGCA 60.468 52.381 0.00 0.00 43.35 5.24
23 24 1.192793 GCGAACTCATCTCACTACGC 58.807 55.000 0.00 0.00 38.23 4.42
24 25 1.132453 TGGCGAACTCATCTCACTACG 59.868 52.381 0.00 0.00 0.00 3.51
25 26 2.803451 CTGGCGAACTCATCTCACTAC 58.197 52.381 0.00 0.00 0.00 2.73
26 27 1.135139 GCTGGCGAACTCATCTCACTA 59.865 52.381 0.00 0.00 0.00 2.74
27 28 0.108424 GCTGGCGAACTCATCTCACT 60.108 55.000 0.00 0.00 0.00 3.41
28 29 0.390340 TGCTGGCGAACTCATCTCAC 60.390 55.000 0.00 0.00 0.00 3.51
29 30 0.538584 ATGCTGGCGAACTCATCTCA 59.461 50.000 0.00 0.00 0.00 3.27
30 31 1.661341 AATGCTGGCGAACTCATCTC 58.339 50.000 0.00 0.00 0.00 2.75
31 32 2.988010 TAATGCTGGCGAACTCATCT 57.012 45.000 0.00 0.00 0.00 2.90
32 33 4.558538 AAATAATGCTGGCGAACTCATC 57.441 40.909 0.00 0.00 0.00 2.92
33 34 4.275936 GGTAAATAATGCTGGCGAACTCAT 59.724 41.667 0.00 0.00 0.00 2.90
34 35 3.625764 GGTAAATAATGCTGGCGAACTCA 59.374 43.478 0.00 0.00 0.00 3.41
35 36 3.625764 TGGTAAATAATGCTGGCGAACTC 59.374 43.478 0.00 0.00 0.00 3.01
36 37 3.616219 TGGTAAATAATGCTGGCGAACT 58.384 40.909 0.00 0.00 0.00 3.01
37 38 4.537015 GATGGTAAATAATGCTGGCGAAC 58.463 43.478 0.00 0.00 0.00 3.95
38 39 3.568007 GGATGGTAAATAATGCTGGCGAA 59.432 43.478 0.00 0.00 0.00 4.70
39 40 3.146066 GGATGGTAAATAATGCTGGCGA 58.854 45.455 0.00 0.00 0.00 5.54
40 41 2.095768 CGGATGGTAAATAATGCTGGCG 60.096 50.000 0.00 0.00 0.00 5.69
41 42 2.351738 GCGGATGGTAAATAATGCTGGC 60.352 50.000 0.00 0.00 0.00 4.85
42 43 2.095768 CGCGGATGGTAAATAATGCTGG 60.096 50.000 0.00 0.00 0.00 4.85
43 44 2.805671 TCGCGGATGGTAAATAATGCTG 59.194 45.455 6.13 0.00 0.00 4.41
44 45 3.067106 CTCGCGGATGGTAAATAATGCT 58.933 45.455 6.13 0.00 0.00 3.79
45 46 3.064207 TCTCGCGGATGGTAAATAATGC 58.936 45.455 6.13 0.00 0.00 3.56
46 47 3.432252 GGTCTCGCGGATGGTAAATAATG 59.568 47.826 6.13 0.00 0.00 1.90
47 48 3.660865 GGTCTCGCGGATGGTAAATAAT 58.339 45.455 6.13 0.00 0.00 1.28
48 49 2.544277 CGGTCTCGCGGATGGTAAATAA 60.544 50.000 6.13 0.00 0.00 1.40
49 50 1.001048 CGGTCTCGCGGATGGTAAATA 60.001 52.381 6.13 0.00 0.00 1.40
50 51 0.249322 CGGTCTCGCGGATGGTAAAT 60.249 55.000 6.13 0.00 0.00 1.40
51 52 1.140161 CGGTCTCGCGGATGGTAAA 59.860 57.895 6.13 0.00 0.00 2.01
52 53 2.048023 ACGGTCTCGCGGATGGTAA 61.048 57.895 6.13 0.00 40.63 2.85
53 54 2.438975 ACGGTCTCGCGGATGGTA 60.439 61.111 6.13 0.00 40.63 3.25
54 55 4.129737 CACGGTCTCGCGGATGGT 62.130 66.667 6.13 2.20 40.63 3.55
55 56 4.873129 CCACGGTCTCGCGGATGG 62.873 72.222 6.13 3.86 40.76 3.51
59 60 4.554363 CTAGCCACGGTCTCGCGG 62.554 72.222 6.13 0.00 41.19 6.46
61 62 4.874977 GGCTAGCCACGGTCTCGC 62.875 72.222 29.33 0.00 40.63 5.03
62 63 1.822613 TAGGCTAGCCACGGTCTCG 60.823 63.158 34.70 0.00 43.02 4.04
63 64 1.035932 TGTAGGCTAGCCACGGTCTC 61.036 60.000 34.70 15.98 38.92 3.36
64 65 1.000019 TGTAGGCTAGCCACGGTCT 60.000 57.895 34.70 16.07 38.92 3.85
65 66 1.141234 GTGTAGGCTAGCCACGGTC 59.859 63.158 34.70 18.87 38.92 4.79
66 67 1.608336 TGTGTAGGCTAGCCACGGT 60.608 57.895 34.70 17.23 38.92 4.83
67 68 1.153628 GTGTGTAGGCTAGCCACGG 60.154 63.158 34.70 0.00 38.92 4.94
68 69 0.458543 CAGTGTGTAGGCTAGCCACG 60.459 60.000 34.70 15.44 38.92 4.94
69 70 0.741221 GCAGTGTGTAGGCTAGCCAC 60.741 60.000 34.70 27.48 38.92 5.01
70 71 1.596934 GCAGTGTGTAGGCTAGCCA 59.403 57.895 34.70 18.26 38.92 4.75
71 72 1.519455 CGCAGTGTGTAGGCTAGCC 60.519 63.158 27.19 27.19 0.00 3.93
72 73 1.215647 ACGCAGTGTGTAGGCTAGC 59.784 57.895 7.76 6.04 42.51 3.42
118 120 1.346395 ACCAACAGTGACGATTGCCTA 59.654 47.619 0.00 0.00 0.00 3.93
125 127 2.217750 CAATCCAACCAACAGTGACGA 58.782 47.619 0.00 0.00 0.00 4.20
136 138 1.455383 CGCCATAGCCCAATCCAACC 61.455 60.000 0.00 0.00 34.57 3.77
197 199 0.907704 AGTACGGGCCATTGGAGTGA 60.908 55.000 6.95 0.00 0.00 3.41
198 200 0.744414 CAGTACGGGCCATTGGAGTG 60.744 60.000 6.95 0.00 0.00 3.51
199 201 0.907704 TCAGTACGGGCCATTGGAGT 60.908 55.000 6.95 5.55 0.00 3.85
200 202 0.179073 CTCAGTACGGGCCATTGGAG 60.179 60.000 6.95 0.00 0.00 3.86
201 203 1.904771 CTCAGTACGGGCCATTGGA 59.095 57.895 6.95 0.00 0.00 3.53
202 204 1.819632 GCTCAGTACGGGCCATTGG 60.820 63.158 4.39 0.00 0.00 3.16
203 205 1.819632 GGCTCAGTACGGGCCATTG 60.820 63.158 19.55 0.00 44.69 2.82
204 206 2.590092 GGCTCAGTACGGGCCATT 59.410 61.111 19.55 0.00 44.69 3.16
208 210 2.044806 ATCATGGGCTCAGTACGGGC 62.045 60.000 0.00 1.54 0.00 6.13
241 247 2.825532 GCCTTAATTTGAGTGGAAGCCA 59.174 45.455 0.00 0.00 0.00 4.75
278 284 1.771565 TCGTTACGGATCAGGGATGT 58.228 50.000 4.53 0.00 0.00 3.06
279 285 2.743938 CTTCGTTACGGATCAGGGATG 58.256 52.381 4.53 0.00 0.00 3.51
297 303 0.385974 GTGCGAAACTGCGAATGCTT 60.386 50.000 0.00 0.00 43.34 3.91
330 378 0.380733 GATTTTTCCGGCCGATGGAC 59.619 55.000 30.73 7.84 34.56 4.02
333 381 0.944386 ATCGATTTTTCCGGCCGATG 59.056 50.000 30.73 11.63 38.37 3.84
334 382 1.202651 AGATCGATTTTTCCGGCCGAT 60.203 47.619 30.73 12.19 41.85 4.18
335 383 0.177141 AGATCGATTTTTCCGGCCGA 59.823 50.000 30.73 10.38 0.00 5.54
336 384 0.582005 GAGATCGATTTTTCCGGCCG 59.418 55.000 21.04 21.04 0.00 6.13
337 385 1.330829 GTGAGATCGATTTTTCCGGCC 59.669 52.381 0.00 0.00 0.00 6.13
338 386 1.330829 GGTGAGATCGATTTTTCCGGC 59.669 52.381 0.00 0.00 0.00 6.13
339 387 2.627945 TGGTGAGATCGATTTTTCCGG 58.372 47.619 0.00 0.00 0.00 5.14
340 388 3.181510 GGTTGGTGAGATCGATTTTTCCG 60.182 47.826 0.00 0.00 0.00 4.30
341 389 3.128764 GGGTTGGTGAGATCGATTTTTCC 59.871 47.826 0.00 1.54 0.00 3.13
342 390 4.010349 AGGGTTGGTGAGATCGATTTTTC 58.990 43.478 0.00 0.00 0.00 2.29
343 391 4.034285 AGGGTTGGTGAGATCGATTTTT 57.966 40.909 0.00 0.00 0.00 1.94
344 392 3.721087 AGGGTTGGTGAGATCGATTTT 57.279 42.857 0.00 0.00 0.00 1.82
345 393 3.432326 GCTAGGGTTGGTGAGATCGATTT 60.432 47.826 0.00 0.00 0.00 2.17
346 394 2.103263 GCTAGGGTTGGTGAGATCGATT 59.897 50.000 0.00 0.00 0.00 3.34
347 395 1.689273 GCTAGGGTTGGTGAGATCGAT 59.311 52.381 0.00 0.00 0.00 3.59
348 396 1.112113 GCTAGGGTTGGTGAGATCGA 58.888 55.000 0.00 0.00 0.00 3.59
349 397 0.824109 TGCTAGGGTTGGTGAGATCG 59.176 55.000 0.00 0.00 0.00 3.69
350 398 1.474143 GCTGCTAGGGTTGGTGAGATC 60.474 57.143 0.00 0.00 0.00 2.75
351 399 0.543749 GCTGCTAGGGTTGGTGAGAT 59.456 55.000 0.00 0.00 0.00 2.75
352 400 0.545309 AGCTGCTAGGGTTGGTGAGA 60.545 55.000 0.00 0.00 0.00 3.27
353 401 0.107945 GAGCTGCTAGGGTTGGTGAG 60.108 60.000 0.15 0.00 0.00 3.51
354 402 1.553690 GGAGCTGCTAGGGTTGGTGA 61.554 60.000 0.15 0.00 0.00 4.02
355 403 1.078143 GGAGCTGCTAGGGTTGGTG 60.078 63.158 0.15 0.00 0.00 4.17
356 404 0.042731 TAGGAGCTGCTAGGGTTGGT 59.957 55.000 11.40 0.00 0.00 3.67
357 405 0.755686 CTAGGAGCTGCTAGGGTTGG 59.244 60.000 29.29 8.28 0.00 3.77
532 604 0.393944 TCGGACGACATGTAGCTCCT 60.394 55.000 18.21 0.00 0.00 3.69
646 728 2.168728 GGTACAGATGTCCCTTCCTGTC 59.831 54.545 0.00 0.00 40.07 3.51
657 739 0.532573 CGAGCACCAGGTACAGATGT 59.467 55.000 0.00 0.00 0.00 3.06
889 994 0.760567 ATGATAGACAGCCCCGCAGA 60.761 55.000 0.00 0.00 0.00 4.26
891 996 1.748403 GATGATAGACAGCCCCGCA 59.252 57.895 0.00 0.00 0.00 5.69
988 1115 4.392940 CAACCCTCCATATCATCCAAGTC 58.607 47.826 0.00 0.00 0.00 3.01
1001 1128 0.543410 TCCTTCGTAGCAACCCTCCA 60.543 55.000 0.00 0.00 0.00 3.86
1131 1258 3.430556 CGATCGACAACATTTGGTACACA 59.569 43.478 10.26 0.00 39.29 3.72
1226 1357 3.204827 CATCGCCTTTGCCCTCGG 61.205 66.667 0.00 0.00 0.00 4.63
1271 1402 4.798682 AGTAGGTGCGGGAGGGGG 62.799 72.222 0.00 0.00 0.00 5.40
1321 1456 1.117150 GGTAGACCCCACTCGCAATA 58.883 55.000 0.00 0.00 0.00 1.90
1419 1554 3.384467 TGATGTCGCATGAGGAGATGTAA 59.616 43.478 0.00 0.00 0.00 2.41
1431 1570 2.292267 GTGGGAGAAATGATGTCGCAT 58.708 47.619 0.00 0.00 44.38 4.73
1482 1625 0.588252 CAAACAACCTCTCCGTGCAG 59.412 55.000 0.00 0.00 0.00 4.41
1538 1681 2.202623 GACTAGCTGGGACGTGCG 60.203 66.667 0.85 0.00 35.70 5.34
1559 1702 1.822990 AGGTACTGTCACCCATGTACG 59.177 52.381 0.00 0.00 39.62 3.67
1630 1777 2.436646 CTTGCTACCGGTGCTGGG 60.437 66.667 19.93 9.17 0.00 4.45
1674 1821 1.662026 CCGTTTTTGCCGTACTTGAGC 60.662 52.381 0.00 0.00 0.00 4.26
1731 1878 8.224720 CCCTCATTATATTTGGGAAAGAGGTAA 58.775 37.037 0.00 0.00 40.23 2.85
1812 1959 3.977134 TTTAACCATGTGCCATGCATT 57.023 38.095 0.00 8.17 41.91 3.56
1867 2017 1.909302 ACCCACCAGACAACCTCATAG 59.091 52.381 0.00 0.00 0.00 2.23
1971 2142 3.555966 ACAAGTTTCACTTCTTCCCAGG 58.444 45.455 0.00 0.00 36.03 4.45
2147 2570 5.648092 CACCCAAAATAGAGAGGACGAAATT 59.352 40.000 0.00 0.00 0.00 1.82
2369 2793 4.629634 CGCCTCTTCACAACATGTATTGTA 59.370 41.667 0.00 0.00 40.89 2.41
2378 2802 2.370281 GAGATCGCCTCTTCACAACA 57.630 50.000 0.00 0.00 38.86 3.33
2430 2854 0.106521 GTTTGTGGGGCATGTGCTTT 59.893 50.000 4.84 0.00 41.70 3.51
2431 2855 1.047596 TGTTTGTGGGGCATGTGCTT 61.048 50.000 4.84 0.00 41.70 3.91
2441 2865 5.011533 TGGAAGAACCATAATTGTTTGTGGG 59.988 40.000 6.47 0.00 45.67 4.61
2480 2904 3.099905 AGAAGTCGTGGAATCATGGAGA 58.900 45.455 0.00 0.00 0.00 3.71
2494 2918 3.664107 TCATTCTGGTTCCAAGAAGTCG 58.336 45.455 0.00 0.00 0.00 4.18
2523 2947 5.961395 TCACTTCTTCGTGTACAAAAGTC 57.039 39.130 15.30 0.00 36.33 3.01
2587 3011 0.454285 CAAAGTATTGGTGCGCGGTG 60.454 55.000 8.83 0.00 32.69 4.94
2619 3047 9.645128 TTATGTGATCAATCTTGACCCATAAAT 57.355 29.630 0.00 6.68 40.49 1.40


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

AutoCloner maintained by Alex Coulton.