Multiple sequence alignment - TraesCS7D01G268100

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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 TraesCS7D01G268100 chr7D 100.000 2321 0 0 1 2321 252030851 252033171 0.000000e+00 4287
1 TraesCS7D01G268100 chr7D 89.812 373 33 1 1 368 251509753 251510125 7.510000e-130 473
2 TraesCS7D01G268100 chr7D 83.398 518 51 12 361 852 251516227 251516735 4.550000e-122 448
3 TraesCS7D01G268100 chr7D 92.254 142 10 1 787 928 251516735 251516875 1.410000e-47 200
4 TraesCS7D01G268100 chr7A 92.509 1375 60 11 1 1349 269279287 269277930 0.000000e+00 1929
5 TraesCS7D01G268100 chr7A 84.068 885 83 18 4 852 269958921 269958059 0.000000e+00 800
6 TraesCS7D01G268100 chr7A 84.456 386 23 16 1472 1849 598328307 598328663 1.710000e-91 346
7 TraesCS7D01G268100 chr7A 96.939 196 5 1 1528 1722 269275359 269275164 6.180000e-86 327
8 TraesCS7D01G268100 chr7A 94.656 131 5 2 1726 1855 269273108 269272979 3.910000e-48 202
9 TraesCS7D01G268100 chr7A 88.276 145 10 3 787 931 269958059 269957922 1.430000e-37 167
10 TraesCS7D01G268100 chr7A 93.827 81 4 1 2242 2321 483941949 483942029 1.130000e-23 121
11 TraesCS7D01G268100 chr7A 98.387 62 1 0 1475 1536 269277809 269277748 2.440000e-20 110
12 TraesCS7D01G268100 chr7B 94.411 984 44 7 1 974 228786197 228787179 0.000000e+00 1502
13 TraesCS7D01G268100 chr7B 84.667 900 82 14 1 852 228393134 228394025 0.000000e+00 846
14 TraesCS7D01G268100 chr7B 90.372 457 36 6 1862 2316 481834703 481835153 5.520000e-166 593
15 TraesCS7D01G268100 chr7B 95.238 357 14 1 980 1336 228787351 228787704 1.560000e-156 562
16 TraesCS7D01G268100 chr7B 92.254 142 10 1 787 928 228394025 228394165 1.410000e-47 200
17 TraesCS7D01G268100 chr5B 92.641 462 28 4 1862 2321 79801097 79800640 0.000000e+00 660
18 TraesCS7D01G268100 chr5D 86.031 451 36 10 1867 2316 45132675 45133099 2.100000e-125 459
19 TraesCS7D01G268100 chr5D 89.811 265 23 2 1868 2131 13293951 13293690 1.030000e-88 337
20 TraesCS7D01G268100 chr5D 97.895 95 1 1 2228 2321 13293431 13293337 1.850000e-36 163
21 TraesCS7D01G268100 chrUn 85.422 391 42 11 1472 1854 12175172 12175555 2.160000e-105 392
22 TraesCS7D01G268100 chr3D 86.510 341 33 9 1523 1854 167381122 167381458 1.700000e-96 363
23 TraesCS7D01G268100 chr3B 87.859 313 28 5 1862 2170 781215155 781215461 2.190000e-95 359
24 TraesCS7D01G268100 chr3B 89.011 273 21 7 1586 1854 242668822 242669089 1.720000e-86 329
25 TraesCS7D01G268100 chr3B 97.753 89 2 0 2228 2316 781215628 781215716 1.110000e-33 154
26 TraesCS7D01G268100 chr3A 86.310 336 32 10 1529 1854 202598647 202598316 1.020000e-93 353
27 TraesCS7D01G268100 chr3A 83.812 383 27 14 1475 1851 9050310 9049957 4.780000e-87 331
28 TraesCS7D01G268100 chr2B 84.475 219 25 7 1472 1684 98580464 98580679 8.410000e-50 207
29 TraesCS7D01G268100 chr2B 96.629 89 3 0 2228 2316 21781730 21781642 5.170000e-32 148
30 TraesCS7D01G268100 chr1A 95.062 81 3 1 2242 2321 17828541 17828621 2.420000e-25 126


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 TraesCS7D01G268100 chr7D 252030851 252033171 2320 False 4287.0 4287 100.00000 1 2321 1 chr7D.!!$F2 2320
1 TraesCS7D01G268100 chr7D 251516227 251516875 648 False 324.0 448 87.82600 361 928 2 chr7D.!!$F3 567
2 TraesCS7D01G268100 chr7A 269272979 269279287 6308 True 642.0 1929 95.62275 1 1855 4 chr7A.!!$R1 1854
3 TraesCS7D01G268100 chr7A 269957922 269958921 999 True 483.5 800 86.17200 4 931 2 chr7A.!!$R2 927
4 TraesCS7D01G268100 chr7B 228786197 228787704 1507 False 1032.0 1502 94.82450 1 1336 2 chr7B.!!$F3 1335
5 TraesCS7D01G268100 chr7B 228393134 228394165 1031 False 523.0 846 88.46050 1 928 2 chr7B.!!$F2 927
6 TraesCS7D01G268100 chr5D 13293337 13293951 614 True 250.0 337 93.85300 1868 2321 2 chr5D.!!$R1 453
7 TraesCS7D01G268100 chr3B 781215155 781215716 561 False 256.5 359 92.80600 1862 2316 2 chr3B.!!$F2 454

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
725 779 0.250467 TCAGTCCCTTGCAGCTCAAC 60.25 55.0 0.0 0.0 0.0 3.18 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2108 6895 0.17899 AGGGGAGCTTGTGTTGGTTC 60.179 55.0 0.0 0.0 0.0 3.62 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
195 212 3.616956 TTAGGTCAGCAGAGGTGATTG 57.383 47.619 2.01 0.00 42.05 2.67
196 213 0.617413 AGGTCAGCAGAGGTGATTGG 59.383 55.000 2.01 0.00 42.05 3.16
265 282 8.739039 TGAAGTTTACTACAAATGATGGAATGG 58.261 33.333 0.00 0.00 0.00 3.16
304 326 1.672356 GGCTCATGTGGTGCTTCGT 60.672 57.895 0.00 0.00 36.29 3.85
318 340 2.616376 TGCTTCGTGTGCATAAGTTTGT 59.384 40.909 0.00 0.00 35.31 2.83
513 558 7.203910 CCAGAGTCTAAGCGTTTGTATAGATT 58.796 38.462 0.00 0.00 0.00 2.40
546 591 3.142174 CCAGAGAAAACCTTCCAGTGAC 58.858 50.000 0.00 0.00 31.28 3.67
609 654 3.637432 TCTTACAATTGCAACCGCTTTG 58.363 40.909 0.00 4.57 39.64 2.77
656 701 6.659242 TCTTGGTTGGATTAGATCAACTTTCC 59.341 38.462 0.00 0.00 41.91 3.13
725 779 0.250467 TCAGTCCCTTGCAGCTCAAC 60.250 55.000 0.00 0.00 0.00 3.18
804 859 3.627577 GTCCGAATATGCAACCACATTCT 59.372 43.478 0.00 0.00 33.68 2.40
830 885 3.829026 AGCTCCAAGGATCTTCCAAAAAC 59.171 43.478 0.00 0.00 39.61 2.43
890 1010 1.487976 GCAACCATCTCCATCCTCTCA 59.512 52.381 0.00 0.00 0.00 3.27
897 1017 0.690411 CTCCATCCTCTCACCCTGCT 60.690 60.000 0.00 0.00 0.00 4.24
920 1040 0.324091 AGCCAAGCAAGGAATCCCTG 60.324 55.000 0.00 0.00 43.48 4.45
962 1088 4.819761 GCCAGCTCGATCGCACCA 62.820 66.667 11.09 0.00 0.00 4.17
974 1100 2.406401 GCACCAAGCTGCTATGCG 59.594 61.111 14.98 7.71 41.15 4.73
1065 1357 1.142097 GCTGGACTACTTCCTCGCC 59.858 63.158 0.00 0.00 46.10 5.54
1113 1405 1.818785 GGTGAGGCTGCTCATCTGC 60.819 63.158 0.00 0.00 35.65 4.26
1123 1415 4.100084 TCATCTGCGCCCTGGTGG 62.100 66.667 4.18 0.00 37.09 4.61
1211 1509 1.307343 AGGACATGGAGGTCTGGGG 60.307 63.158 0.00 0.00 37.91 4.96
1340 1638 1.227002 GTCCTAGCACGCTGGCTAC 60.227 63.158 0.72 0.00 43.70 3.58
1349 1647 2.933906 GCACGCTGGCTACTTATTGTAA 59.066 45.455 0.00 0.00 0.00 2.41
1350 1648 3.560068 GCACGCTGGCTACTTATTGTAAT 59.440 43.478 0.00 0.00 0.00 1.89
1351 1649 4.035208 GCACGCTGGCTACTTATTGTAATT 59.965 41.667 0.00 0.00 0.00 1.40
1352 1650 5.448632 GCACGCTGGCTACTTATTGTAATTT 60.449 40.000 0.00 0.00 0.00 1.82
1353 1651 5.965334 CACGCTGGCTACTTATTGTAATTTG 59.035 40.000 0.00 0.00 0.00 2.32
1354 1652 5.646360 ACGCTGGCTACTTATTGTAATTTGT 59.354 36.000 0.00 0.00 0.00 2.83
1355 1653 6.819649 ACGCTGGCTACTTATTGTAATTTGTA 59.180 34.615 0.00 0.00 0.00 2.41
1356 1654 7.334921 ACGCTGGCTACTTATTGTAATTTGTAA 59.665 33.333 0.00 0.00 0.00 2.41
1372 1670 9.417284 GTAATTTGTAATGTTCGTATTTCCTCG 57.583 33.333 0.00 0.00 0.00 4.63
1375 1673 4.930405 TGTAATGTTCGTATTTCCTCGCAA 59.070 37.500 0.00 0.00 0.00 4.85
1377 1675 5.365403 AATGTTCGTATTTCCTCGCAAAA 57.635 34.783 0.00 0.00 0.00 2.44
1408 1729 2.619074 GCTTGCTCCATCCAGGTTAGTT 60.619 50.000 0.00 0.00 39.02 2.24
1414 1735 4.876679 GCTCCATCCAGGTTAGTTAGTTTC 59.123 45.833 0.00 0.00 39.02 2.78
1416 1737 6.636454 TCCATCCAGGTTAGTTAGTTTCAT 57.364 37.500 0.00 0.00 39.02 2.57
1417 1738 7.027874 TCCATCCAGGTTAGTTAGTTTCATT 57.972 36.000 0.00 0.00 39.02 2.57
1418 1739 7.466804 TCCATCCAGGTTAGTTAGTTTCATTT 58.533 34.615 0.00 0.00 39.02 2.32
1419 1740 7.947890 TCCATCCAGGTTAGTTAGTTTCATTTT 59.052 33.333 0.00 0.00 39.02 1.82
1420 1741 8.585018 CCATCCAGGTTAGTTAGTTTCATTTTT 58.415 33.333 0.00 0.00 0.00 1.94
1441 1762 3.349879 TTTTTGCGGGGGAGGTTAG 57.650 52.632 0.00 0.00 0.00 2.34
1442 1763 0.479378 TTTTTGCGGGGGAGGTTAGT 59.521 50.000 0.00 0.00 0.00 2.24
1443 1764 0.479378 TTTTGCGGGGGAGGTTAGTT 59.521 50.000 0.00 0.00 0.00 2.24
1444 1765 1.360185 TTTGCGGGGGAGGTTAGTTA 58.640 50.000 0.00 0.00 0.00 2.24
1445 1766 0.906775 TTGCGGGGGAGGTTAGTTAG 59.093 55.000 0.00 0.00 0.00 2.34
1446 1767 0.252375 TGCGGGGGAGGTTAGTTAGT 60.252 55.000 0.00 0.00 0.00 2.24
1447 1768 0.907486 GCGGGGGAGGTTAGTTAGTT 59.093 55.000 0.00 0.00 0.00 2.24
1448 1769 1.280133 GCGGGGGAGGTTAGTTAGTTT 59.720 52.381 0.00 0.00 0.00 2.66
1449 1770 2.679059 GCGGGGGAGGTTAGTTAGTTTC 60.679 54.545 0.00 0.00 0.00 2.78
1450 1771 2.568509 CGGGGGAGGTTAGTTAGTTTCA 59.431 50.000 0.00 0.00 0.00 2.69
1451 1772 3.199289 CGGGGGAGGTTAGTTAGTTTCAT 59.801 47.826 0.00 0.00 0.00 2.57
1452 1773 4.324022 CGGGGGAGGTTAGTTAGTTTCATT 60.324 45.833 0.00 0.00 0.00 2.57
1467 1788 3.520290 TTCATTACACGAGAGCGGATT 57.480 42.857 0.00 0.00 43.17 3.01
1472 1793 5.704053 TCATTACACGAGAGCGGATTATCTA 59.296 40.000 0.00 0.00 43.17 1.98
1473 1794 5.608676 TTACACGAGAGCGGATTATCTAG 57.391 43.478 0.00 0.00 43.17 2.43
1504 1839 3.583276 CTGCGCCGTGGTCAGGTTA 62.583 63.158 4.18 0.00 0.00 2.85
1536 1871 3.330701 ACCATTTGTAGTGTCAGGTCCAT 59.669 43.478 0.00 0.00 0.00 3.41
1538 1873 2.472695 TTGTAGTGTCAGGTCCATGC 57.527 50.000 0.00 0.00 0.00 4.06
1539 1874 0.246360 TGTAGTGTCAGGTCCATGCG 59.754 55.000 0.00 0.00 0.00 4.73
1580 4312 4.713792 ACTCCATCCCAGAAATATGTCC 57.286 45.455 0.00 0.00 0.00 4.02
1592 4324 8.844244 CCCAGAAATATGTCCTCTTATTTCTTG 58.156 37.037 17.99 15.84 46.64 3.02
1625 4357 8.757982 AACAAATTAGATGCCTGATATCTTGT 57.242 30.769 3.98 0.00 36.38 3.16
1784 6570 6.921857 TCGAAGTCCTAACTTAAGAACACAAG 59.078 38.462 10.09 0.00 45.80 3.16
1793 6579 9.382244 CTAACTTAAGAACACAAGTATGCAAAC 57.618 33.333 10.09 0.00 33.92 2.93
1800 6586 4.545610 ACACAAGTATGCAAACGAATTGG 58.454 39.130 0.00 0.00 39.54 3.16
1860 6646 9.451002 TTCTAACATTAAAATCAATGGTACGGA 57.549 29.630 1.36 0.00 39.71 4.69
1866 6652 7.762588 TTAAAATCAATGGTACGGAAAAGGA 57.237 32.000 0.00 0.00 0.00 3.36
1882 6668 2.600475 GGAAAACGTTGCGAGCCGA 61.600 57.895 0.00 0.00 0.00 5.54
1934 6720 2.362120 ATGCTGGCAGCTCCAACC 60.362 61.111 36.50 9.94 46.01 3.77
1952 6739 2.204461 CCCCACGAAACAAACCCCC 61.204 63.158 0.00 0.00 0.00 5.40
1955 6742 2.124236 ACGAAACAAACCCCCGCA 60.124 55.556 0.00 0.00 0.00 5.69
1971 6758 1.257936 CCGCATAAGACATGTGTACGC 59.742 52.381 1.15 1.87 0.00 4.42
1996 6783 3.953775 CTCACACAACCGCCCCCT 61.954 66.667 0.00 0.00 0.00 4.79
2022 6809 4.174051 TCCTATCCTTATCCTTTCCCTGGA 59.826 45.833 0.00 0.00 38.06 3.86
2046 6833 6.653020 ACTTTCCTTTTGGCTTTTCTTCAAT 58.347 32.000 0.00 0.00 40.12 2.57
2096 6883 3.835395 AGAACCACGATTTTCTCTCCTCT 59.165 43.478 0.00 0.00 0.00 3.69
2107 6894 1.133945 TCTCTCCTCTACGCTGCTCAT 60.134 52.381 0.00 0.00 0.00 2.90
2108 6895 1.001487 CTCTCCTCTACGCTGCTCATG 60.001 57.143 0.00 0.00 0.00 3.07
2114 6901 1.275010 TCTACGCTGCTCATGAACCAA 59.725 47.619 0.00 0.00 0.00 3.67
2131 6918 0.890996 CAACACAAGCTCCCCTCACC 60.891 60.000 0.00 0.00 0.00 4.02
2144 6931 4.652131 TCACCGGCGGCCATTGTT 62.652 61.111 28.71 0.15 0.00 2.83
2146 6933 3.679738 ACCGGCGGCCATTGTTTG 61.680 61.111 28.71 0.00 0.00 2.93
2147 6934 3.679738 CCGGCGGCCATTGTTTGT 61.680 61.111 20.71 0.00 0.00 2.83
2148 6935 2.126502 CGGCGGCCATTGTTTGTC 60.127 61.111 20.71 0.00 0.00 3.18
2149 6936 2.126502 GGCGGCCATTGTTTGTCG 60.127 61.111 15.62 0.00 0.00 4.35
2150 6937 2.804931 GCGGCCATTGTTTGTCGC 60.805 61.111 2.24 0.00 38.34 5.19
2157 6947 1.066908 CCATTGTTTGTCGCAACCAGT 59.933 47.619 0.00 0.00 0.00 4.00
2159 6949 3.554524 CATTGTTTGTCGCAACCAGTAG 58.445 45.455 0.00 0.00 0.00 2.57
2165 6955 0.108804 GTCGCAACCAGTAGCTGCTA 60.109 55.000 3.21 5.02 33.82 3.49
2176 6966 4.228567 GCTGCTAGCGGGGGAGAC 62.229 72.222 24.73 3.25 0.00 3.36
2189 6979 4.862823 GAGACCGGGGGAGGGGAG 62.863 77.778 6.32 0.00 35.02 4.30
2212 7169 0.767375 GGGCTCTGGATATGCTGGAA 59.233 55.000 1.37 0.00 0.00 3.53
2225 7182 1.293498 CTGGAACCAGAGTCCACGG 59.707 63.158 14.94 0.00 46.30 4.94
2226 7183 2.047179 GGAACCAGAGTCCACGGC 60.047 66.667 0.00 0.00 0.00 5.68
2227 7184 2.584391 GGAACCAGAGTCCACGGCT 61.584 63.158 0.00 0.00 0.00 5.52
2228 7185 1.079750 GAACCAGAGTCCACGGCTC 60.080 63.158 0.00 0.79 0.00 4.70
2229 7186 2.508586 GAACCAGAGTCCACGGCTCC 62.509 65.000 4.53 0.00 33.69 4.70
2230 7187 2.997315 CCAGAGTCCACGGCTCCA 60.997 66.667 4.53 0.00 33.69 3.86
2231 7188 2.262915 CAGAGTCCACGGCTCCAC 59.737 66.667 4.53 0.00 33.69 4.02
2232 7189 3.374402 AGAGTCCACGGCTCCACG 61.374 66.667 4.53 0.00 40.31 4.94
2318 7275 2.281484 GCTGGAACCAGACGGCAA 60.281 61.111 22.96 0.00 46.30 4.52
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
195 212 1.017387 GATCCGACCAATCTGTTGCC 58.983 55.000 0.00 0.00 33.90 4.52
196 213 1.667724 CAGATCCGACCAATCTGTTGC 59.332 52.381 5.20 0.00 43.32 4.17
304 326 2.741612 GCAGCAACAAACTTATGCACA 58.258 42.857 0.00 0.00 42.45 4.57
333 355 1.455383 AAAGCACCGGTGAAGCTTGG 61.455 55.000 38.30 9.57 46.95 3.61
409 431 3.243035 CGCTTGTTGAAAATGACACCTCA 60.243 43.478 0.00 0.00 0.00 3.86
412 434 1.786579 GCGCTTGTTGAAAATGACACC 59.213 47.619 0.00 0.00 0.00 4.16
513 558 8.650143 AAGGTTTTCTCTGGCATCTAAAATTA 57.350 30.769 0.00 0.00 0.00 1.40
546 591 7.482654 TGTTCATAGGAAGCGAAATCTTATG 57.517 36.000 0.00 7.76 37.89 1.90
609 654 7.823149 AGATTTGCCGGTTTATATATACGAC 57.177 36.000 1.90 1.27 0.00 4.34
656 701 7.576750 TGAGCAAAGTAAAAGTATAGTGTCG 57.423 36.000 0.00 0.00 0.00 4.35
725 779 3.618780 GAGTGGGCTCAGGTGCAGG 62.619 68.421 0.00 0.00 41.29 4.85
804 859 4.927267 TGGAAGATCCTTGGAGCTTTTA 57.073 40.909 19.37 10.19 37.46 1.52
890 1010 2.437897 CTTGGCTTGGAGCAGGGT 59.562 61.111 2.04 0.00 44.75 4.34
897 1017 1.549203 GATTCCTTGCTTGGCTTGGA 58.451 50.000 0.00 0.00 0.00 3.53
962 1088 1.364626 GCAGTCACGCATAGCAGCTT 61.365 55.000 0.00 0.00 0.00 3.74
996 1288 1.216178 GCCCATGCACACCATTGTC 59.784 57.895 0.00 0.00 37.47 3.18
1065 1357 3.598562 GCGACGACGATGAGCACG 61.599 66.667 12.29 0.00 42.66 5.34
1174 1472 2.482374 GTCGGTGTCGGTAGTCGG 59.518 66.667 0.00 0.00 39.77 4.79
1179 1477 2.034879 GTCCTCGTCGGTGTCGGTA 61.035 63.158 0.00 0.00 36.95 4.02
1211 1509 3.521529 ATATCCAGCTCCGTGCCGC 62.522 63.158 0.00 0.00 44.23 6.53
1349 1647 6.092944 TGCGAGGAAATACGAACATTACAAAT 59.907 34.615 0.00 0.00 0.00 2.32
1350 1648 5.408909 TGCGAGGAAATACGAACATTACAAA 59.591 36.000 0.00 0.00 0.00 2.83
1351 1649 4.930405 TGCGAGGAAATACGAACATTACAA 59.070 37.500 0.00 0.00 0.00 2.41
1352 1650 4.496360 TGCGAGGAAATACGAACATTACA 58.504 39.130 0.00 0.00 0.00 2.41
1353 1651 5.459110 TTGCGAGGAAATACGAACATTAC 57.541 39.130 0.00 0.00 0.00 1.89
1354 1652 6.483385 TTTTGCGAGGAAATACGAACATTA 57.517 33.333 0.00 0.00 0.00 1.90
1355 1653 5.365403 TTTTGCGAGGAAATACGAACATT 57.635 34.783 0.00 0.00 0.00 2.71
1356 1654 5.365403 TTTTTGCGAGGAAATACGAACAT 57.635 34.783 0.00 0.00 0.00 2.71
1377 1675 3.445096 GGATGGAGCAAGCAGTACATTTT 59.555 43.478 0.00 0.00 0.00 1.82
1379 1677 2.025981 TGGATGGAGCAAGCAGTACATT 60.026 45.455 0.00 0.00 0.00 2.71
1380 1678 1.561076 TGGATGGAGCAAGCAGTACAT 59.439 47.619 0.00 0.00 0.00 2.29
1382 1680 1.661341 CTGGATGGAGCAAGCAGTAC 58.339 55.000 0.00 0.00 0.00 2.73
1384 1682 1.302285 CCTGGATGGAGCAAGCAGT 59.698 57.895 0.00 0.00 38.35 4.40
1385 1683 0.323178 AACCTGGATGGAGCAAGCAG 60.323 55.000 0.00 0.00 39.71 4.24
1423 1744 0.479378 ACTAACCTCCCCCGCAAAAA 59.521 50.000 0.00 0.00 0.00 1.94
1424 1745 0.479378 AACTAACCTCCCCCGCAAAA 59.521 50.000 0.00 0.00 0.00 2.44
1425 1746 1.279846 CTAACTAACCTCCCCCGCAAA 59.720 52.381 0.00 0.00 0.00 3.68
1426 1747 0.906775 CTAACTAACCTCCCCCGCAA 59.093 55.000 0.00 0.00 0.00 4.85
1427 1748 0.252375 ACTAACTAACCTCCCCCGCA 60.252 55.000 0.00 0.00 0.00 5.69
1428 1749 0.907486 AACTAACTAACCTCCCCCGC 59.093 55.000 0.00 0.00 0.00 6.13
1429 1750 2.568509 TGAAACTAACTAACCTCCCCCG 59.431 50.000 0.00 0.00 0.00 5.73
1430 1751 4.857130 ATGAAACTAACTAACCTCCCCC 57.143 45.455 0.00 0.00 0.00 5.40
1431 1752 6.596888 GTGTAATGAAACTAACTAACCTCCCC 59.403 42.308 0.00 0.00 0.00 4.81
1432 1753 6.312180 CGTGTAATGAAACTAACTAACCTCCC 59.688 42.308 0.00 0.00 0.00 4.30
1433 1754 7.092716 TCGTGTAATGAAACTAACTAACCTCC 58.907 38.462 0.00 0.00 0.00 4.30
1434 1755 8.025445 TCTCGTGTAATGAAACTAACTAACCTC 58.975 37.037 0.00 0.00 0.00 3.85
1435 1756 7.889469 TCTCGTGTAATGAAACTAACTAACCT 58.111 34.615 0.00 0.00 0.00 3.50
1436 1757 7.201418 GCTCTCGTGTAATGAAACTAACTAACC 60.201 40.741 0.00 0.00 0.00 2.85
1437 1758 7.461156 CGCTCTCGTGTAATGAAACTAACTAAC 60.461 40.741 0.00 0.00 0.00 2.34
1438 1759 6.525628 CGCTCTCGTGTAATGAAACTAACTAA 59.474 38.462 0.00 0.00 0.00 2.24
1439 1760 6.025896 CGCTCTCGTGTAATGAAACTAACTA 58.974 40.000 0.00 0.00 0.00 2.24
1440 1761 4.857588 CGCTCTCGTGTAATGAAACTAACT 59.142 41.667 0.00 0.00 0.00 2.24
1441 1762 4.031426 CCGCTCTCGTGTAATGAAACTAAC 59.969 45.833 0.00 0.00 0.00 2.34
1442 1763 4.082625 TCCGCTCTCGTGTAATGAAACTAA 60.083 41.667 0.00 0.00 0.00 2.24
1443 1764 3.441222 TCCGCTCTCGTGTAATGAAACTA 59.559 43.478 0.00 0.00 0.00 2.24
1444 1765 2.230508 TCCGCTCTCGTGTAATGAAACT 59.769 45.455 0.00 0.00 0.00 2.66
1445 1766 2.602878 TCCGCTCTCGTGTAATGAAAC 58.397 47.619 0.00 0.00 0.00 2.78
1446 1767 3.520290 ATCCGCTCTCGTGTAATGAAA 57.480 42.857 0.00 0.00 0.00 2.69
1447 1768 3.520290 AATCCGCTCTCGTGTAATGAA 57.480 42.857 0.00 0.00 0.00 2.57
1448 1769 4.519350 AGATAATCCGCTCTCGTGTAATGA 59.481 41.667 0.00 0.00 0.00 2.57
1449 1770 4.799678 AGATAATCCGCTCTCGTGTAATG 58.200 43.478 0.00 0.00 0.00 1.90
1450 1771 5.392165 GCTAGATAATCCGCTCTCGTGTAAT 60.392 44.000 0.00 0.00 0.00 1.89
1451 1772 4.083431 GCTAGATAATCCGCTCTCGTGTAA 60.083 45.833 0.00 0.00 0.00 2.41
1452 1773 3.436015 GCTAGATAATCCGCTCTCGTGTA 59.564 47.826 0.00 0.00 0.00 2.90
1467 1788 2.039418 AGAACATGCACGGGCTAGATA 58.961 47.619 12.74 0.00 41.91 1.98
1504 1839 5.376625 ACACTACAAATGGTTCTGACACAT 58.623 37.500 0.00 0.00 0.00 3.21
1538 1873 0.757188 ATAGAGAGAGGTGGGGCACG 60.757 60.000 0.00 0.00 34.83 5.34
1539 1874 2.365941 GTTATAGAGAGAGGTGGGGCAC 59.634 54.545 0.00 0.00 0.00 5.01
1592 4324 7.930217 TCAGGCATCTAATTTGTTTACATAGC 58.070 34.615 0.00 0.00 0.00 2.97
1756 6541 7.765360 TGTGTTCTTAAGTTAGGACTTCGAAAA 59.235 33.333 0.00 0.00 44.75 2.29
1760 6545 6.700520 ACTTGTGTTCTTAAGTTAGGACTTCG 59.299 38.462 1.63 0.00 44.75 3.79
1784 6570 6.942886 TTGATTTCCAATTCGTTTGCATAC 57.057 33.333 0.00 0.00 33.73 2.39
1793 6579 8.763356 TGAACTGAAAATTTGATTTCCAATTCG 58.237 29.630 0.00 0.00 38.30 3.34
1847 6633 5.335348 CGTTTTCCTTTTCCGTACCATTGAT 60.335 40.000 0.00 0.00 0.00 2.57
1848 6634 4.023878 CGTTTTCCTTTTCCGTACCATTGA 60.024 41.667 0.00 0.00 0.00 2.57
1849 6635 4.223659 CGTTTTCCTTTTCCGTACCATTG 58.776 43.478 0.00 0.00 0.00 2.82
1851 6637 3.479489 ACGTTTTCCTTTTCCGTACCAT 58.521 40.909 0.00 0.00 0.00 3.55
1852 6638 2.916640 ACGTTTTCCTTTTCCGTACCA 58.083 42.857 0.00 0.00 0.00 3.25
1854 6640 3.038017 GCAACGTTTTCCTTTTCCGTAC 58.962 45.455 0.00 0.00 0.00 3.67
1855 6641 2.286301 CGCAACGTTTTCCTTTTCCGTA 60.286 45.455 0.00 0.00 0.00 4.02
1856 6642 1.532298 CGCAACGTTTTCCTTTTCCGT 60.532 47.619 0.00 0.00 0.00 4.69
1857 6643 1.117234 CGCAACGTTTTCCTTTTCCG 58.883 50.000 0.00 0.00 0.00 4.30
1858 6644 2.381589 CTCGCAACGTTTTCCTTTTCC 58.618 47.619 0.00 0.00 0.00 3.13
1859 6645 1.779157 GCTCGCAACGTTTTCCTTTTC 59.221 47.619 0.00 0.00 0.00 2.29
1860 6646 1.535226 GGCTCGCAACGTTTTCCTTTT 60.535 47.619 0.00 0.00 0.00 2.27
1866 6652 2.101209 CTGTCGGCTCGCAACGTTTT 62.101 55.000 0.00 0.00 0.00 2.43
1882 6668 1.600916 GAAAGCTTGGCCGGTCTGT 60.601 57.895 7.97 0.00 0.00 3.41
1925 6711 2.457323 TTTCGTGGGGGTTGGAGCT 61.457 57.895 0.00 0.00 0.00 4.09
1926 6712 2.114411 TTTCGTGGGGGTTGGAGC 59.886 61.111 0.00 0.00 0.00 4.70
1927 6713 0.466555 TTGTTTCGTGGGGGTTGGAG 60.467 55.000 0.00 0.00 0.00 3.86
1934 6720 2.204461 GGGGGTTTGTTTCGTGGGG 61.204 63.158 0.00 0.00 0.00 4.96
1952 6739 1.072154 CGCGTACACATGTCTTATGCG 60.072 52.381 25.15 25.15 36.96 4.73
1955 6742 2.536365 CACCGCGTACACATGTCTTAT 58.464 47.619 4.92 0.00 0.00 1.73
1971 6758 1.597027 GGTTGTGTGAGGTCCACCG 60.597 63.158 0.00 0.00 45.09 4.94
1996 6783 6.323737 CAGGGAAAGGATAAGGATAGGAGTA 58.676 44.000 0.00 0.00 0.00 2.59
2022 6809 5.675684 TGAAGAAAAGCCAAAAGGAAAGT 57.324 34.783 0.00 0.00 0.00 2.66
2096 6883 1.270571 TGTTGGTTCATGAGCAGCGTA 60.271 47.619 11.93 0.00 39.50 4.42
2107 6894 0.467290 GGGGAGCTTGTGTTGGTTCA 60.467 55.000 0.00 0.00 0.00 3.18
2108 6895 0.178990 AGGGGAGCTTGTGTTGGTTC 60.179 55.000 0.00 0.00 0.00 3.62
2114 6901 2.883828 CGGTGAGGGGAGCTTGTGT 61.884 63.158 0.00 0.00 0.00 3.72
2131 6918 2.126502 GACAAACAATGGCCGCCG 60.127 61.111 4.58 0.00 0.00 6.46
2140 6927 1.332375 GCTACTGGTTGCGACAAACAA 59.668 47.619 6.39 0.00 0.00 2.83
2142 6929 1.069906 CAGCTACTGGTTGCGACAAAC 60.070 52.381 6.39 1.33 36.47 2.93
2144 6931 1.227999 GCAGCTACTGGTTGCGACAA 61.228 55.000 6.39 0.00 41.87 3.18
2146 6933 3.169198 GCAGCTACTGGTTGCGAC 58.831 61.111 0.00 0.00 41.87 5.19
2150 6937 0.807667 CCGCTAGCAGCTACTGGTTG 60.808 60.000 16.45 4.35 42.44 3.77
2157 6947 2.521950 CTCCCCCGCTAGCAGCTA 60.522 66.667 16.45 1.13 39.60 3.32
2159 6949 4.228567 GTCTCCCCCGCTAGCAGC 62.229 72.222 16.45 0.00 38.02 5.25
2172 6962 4.862823 CTCCCCTCCCCCGGTCTC 62.863 77.778 0.00 0.00 0.00 3.36
2191 6981 1.377994 CAGCATATCCAGAGCCCCC 59.622 63.158 0.00 0.00 0.00 5.40
2192 6982 1.130054 TCCAGCATATCCAGAGCCCC 61.130 60.000 0.00 0.00 0.00 5.80
2193 6983 0.767375 TTCCAGCATATCCAGAGCCC 59.233 55.000 0.00 0.00 0.00 5.19
2194 6984 1.544314 GGTTCCAGCATATCCAGAGCC 60.544 57.143 0.00 0.00 0.00 4.70
2203 7160 1.555075 GTGGACTCTGGTTCCAGCATA 59.445 52.381 13.44 0.00 33.74 3.14
2212 7169 2.997897 GGAGCCGTGGACTCTGGT 60.998 66.667 9.25 0.00 34.46 4.00
2226 7183 4.374702 GTTGCAGCACGCGTGGAG 62.375 66.667 37.47 16.07 46.97 3.86
2229 7186 4.671549 CTGGTTGCAGCACGCGTG 62.672 66.667 34.01 34.01 46.97 5.34


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

AutoCloner maintained by Alex Coulton.