Multiple sequence alignment - TraesCS2B01G482200

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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 TraesCS2B01G482200 chr2B 100.000 2237 0 0 1 2237 680062314 680064550 0.000000e+00 4132.0
1 TraesCS2B01G482200 chr2B 90.610 426 33 4 1762 2184 717479939 717480360 1.940000e-155 558.0
2 TraesCS2B01G482200 chr2B 78.034 651 83 35 861 1496 680221223 680221828 2.730000e-94 355.0
3 TraesCS2B01G482200 chr2A 86.007 1072 92 23 602 1649 706918959 706919996 0.000000e+00 1096.0
4 TraesCS2B01G482200 chr2A 82.456 912 63 27 891 1740 706903553 706904429 0.000000e+00 708.0
5 TraesCS2B01G482200 chr2A 87.768 466 27 13 421 875 706902785 706903231 3.290000e-143 518.0
6 TraesCS2B01G482200 chr2A 78.824 595 67 29 925 1504 707040185 707040735 1.640000e-91 346.0
7 TraesCS2B01G482200 chr2A 75.920 598 85 35 824 1388 707168527 707169098 3.690000e-63 252.0
8 TraesCS2B01G482200 chr2A 79.310 319 35 12 819 1128 706922369 706922665 6.300000e-46 195.0
9 TraesCS2B01G482200 chr2A 90.265 113 4 2 1649 1761 706920027 706920132 8.330000e-30 141.0
10 TraesCS2B01G482200 chr2A 88.462 78 6 3 867 943 707040101 707040176 8.510000e-15 91.6
11 TraesCS2B01G482200 chr2D 86.861 959 40 33 481 1396 567051074 567051989 0.000000e+00 994.0
12 TraesCS2B01G482200 chr2D 88.840 457 33 5 1 450 567050632 567051077 1.510000e-151 545.0
13 TraesCS2B01G482200 chr2D 79.755 652 71 33 861 1495 567568876 567569483 1.240000e-112 416.0
14 TraesCS2B01G482200 chr2D 82.535 355 26 11 1372 1705 567051996 567052335 1.690000e-71 279.0
15 TraesCS2B01G482200 chr2D 79.085 306 30 20 832 1128 567057334 567057614 1.770000e-41 180.0
16 TraesCS2B01G482200 chr2D 100.000 31 0 0 1726 1756 567052339 567052369 8.630000e-05 58.4
17 TraesCS2B01G482200 chr4A 91.355 428 30 4 1762 2186 577369225 577368802 1.490000e-161 579.0
18 TraesCS2B01G482200 chr7A 91.885 419 24 7 1764 2178 36365945 36366357 5.360000e-161 577.0
19 TraesCS2B01G482200 chr7A 97.143 35 1 0 12 46 19528195 19528161 2.400000e-05 60.2
20 TraesCS2B01G482200 chr5A 91.274 424 31 2 1762 2183 55262978 55263397 6.930000e-160 573.0
21 TraesCS2B01G482200 chr4B 91.121 428 31 4 1759 2183 90454819 90455242 6.930000e-160 573.0
22 TraesCS2B01G482200 chr4B 88.679 424 40 4 1762 2183 636649268 636649685 5.510000e-141 510.0
23 TraesCS2B01G482200 chr7B 90.909 429 32 4 1758 2183 702326449 702326025 8.960000e-159 569.0
24 TraesCS2B01G482200 chr7B 90.376 426 31 6 1762 2183 517333086 517332667 3.250000e-153 551.0
25 TraesCS2B01G482200 chr1D 91.080 426 29 4 1763 2185 481281774 481281355 3.220000e-158 568.0
26 TraesCS2B01G482200 chr1D 88.946 389 35 5 1795 2181 408542918 408542536 7.230000e-130 473.0
27 TraesCS2B01G482200 chr1B 90.698 430 34 3 1762 2189 681725658 681726083 3.220000e-158 568.0
28 TraesCS2B01G482200 chr1B 90.023 431 35 6 1762 2189 681723552 681723977 3.250000e-153 551.0
29 TraesCS2B01G482200 chr1B 89.116 441 36 6 1747 2184 626697888 626698319 2.530000e-149 538.0
30 TraesCS2B01G482200 chr3A 89.367 442 37 8 1743 2182 713418872 713418439 4.200000e-152 547.0
31 TraesCS2B01G482200 chr3D 89.744 429 34 7 1759 2185 146133791 146133371 7.030000e-150 540.0
32 TraesCS2B01G482200 chr5B 91.667 228 13 4 1762 1988 429636504 429636726 6.000000e-81 311.0
33 TraesCS2B01G482200 chrUn 76.277 274 51 10 973 1237 155033198 155033466 1.390000e-27 134.0
34 TraesCS2B01G482200 chr3B 76.277 274 51 10 973 1237 792434481 792434213 1.390000e-27 134.0
35 TraesCS2B01G482200 chr3B 75.912 274 52 10 973 1237 792344160 792343892 6.480000e-26 128.0


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 TraesCS2B01G482200 chr2B 680062314 680064550 2236 False 4132.000000 4132 100.0000 1 2237 1 chr2B.!!$F1 2236
1 TraesCS2B01G482200 chr2B 680221223 680221828 605 False 355.000000 355 78.0340 861 1496 1 chr2B.!!$F2 635
2 TraesCS2B01G482200 chr2A 706902785 706904429 1644 False 613.000000 708 85.1120 421 1740 2 chr2A.!!$F2 1319
3 TraesCS2B01G482200 chr2A 706918959 706922665 3706 False 477.333333 1096 85.1940 602 1761 3 chr2A.!!$F3 1159
4 TraesCS2B01G482200 chr2A 707168527 707169098 571 False 252.000000 252 75.9200 824 1388 1 chr2A.!!$F1 564
5 TraesCS2B01G482200 chr2A 707040101 707040735 634 False 218.800000 346 83.6430 867 1504 2 chr2A.!!$F4 637
6 TraesCS2B01G482200 chr2D 567050632 567052369 1737 False 469.100000 994 89.5590 1 1756 4 chr2D.!!$F3 1755
7 TraesCS2B01G482200 chr2D 567568876 567569483 607 False 416.000000 416 79.7550 861 1495 1 chr2D.!!$F2 634
8 TraesCS2B01G482200 chr1B 681723552 681726083 2531 False 559.500000 568 90.3605 1762 2189 2 chr1B.!!$F2 427

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
565 578 0.451783 CAGCCAACCTTATCGCCAAC 59.548 55.0 0.0 0.0 0.0 3.77 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1953 2880 0.323451 GGGTTAAACAGCCTCAGGGG 60.323 60.0 0.0 0.0 40.32 4.79 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
92 93 4.092116 AGCATATACTTCCTGGGCTTTC 57.908 45.455 0.00 0.00 0.00 2.62
99 100 2.282462 CCTGGGCTTTCGGCAGTT 60.282 61.111 0.00 0.00 44.01 3.16
136 137 3.693085 CAGGACATGGAGAAGACAAATGG 59.307 47.826 0.00 0.00 0.00 3.16
173 174 6.097270 TCGGCCATAAACTAGTGTAGTGTATT 59.903 38.462 2.24 0.00 37.15 1.89
179 180 9.007252 CATAAACTAGTGTAGTGTATTCGTGTC 57.993 37.037 0.00 0.00 37.15 3.67
188 190 2.930040 GTGTATTCGTGTCATGGAGTGG 59.070 50.000 0.00 0.00 0.00 4.00
202 204 2.512515 GTGGAGCTCCGCATGACC 60.513 66.667 36.03 9.16 45.55 4.02
203 205 4.147449 TGGAGCTCCGCATGACCG 62.147 66.667 27.43 0.00 39.43 4.79
204 206 4.148825 GGAGCTCCGCATGACCGT 62.149 66.667 19.06 0.00 0.00 4.83
216 218 4.724022 GACCGTACGGGCACATAG 57.276 61.111 35.19 8.85 44.50 2.23
332 335 4.494855 GCACGAATTTCATCCTGCTAGTTC 60.495 45.833 0.00 0.00 31.33 3.01
340 343 4.433615 TCATCCTGCTAGTTCGAATTGTC 58.566 43.478 0.00 0.00 0.00 3.18
358 361 6.870971 ATTGTCGTTAAAATATATGCGGGT 57.129 33.333 0.00 0.00 0.00 5.28
360 363 7.783090 TTGTCGTTAAAATATATGCGGGTAA 57.217 32.000 0.00 0.00 0.00 2.85
401 409 3.399181 TCCGCGAATTGGCCTCCT 61.399 61.111 8.23 0.00 0.00 3.69
422 430 2.272447 TGTCTGCGGACGGATGTGA 61.272 57.895 20.49 0.00 44.83 3.58
435 443 6.128391 CGGACGGATGTGAAAGAAAATTTAGA 60.128 38.462 0.00 0.00 0.00 2.10
457 465 4.104831 AGATGCCCTAAGAGGTGTAAACT 58.895 43.478 0.00 0.00 31.93 2.66
525 533 3.063452 GCGACTTGTGTGAAACTCTGAAA 59.937 43.478 0.00 0.00 38.04 2.69
526 534 4.578601 CGACTTGTGTGAAACTCTGAAAC 58.421 43.478 0.00 0.00 38.04 2.78
527 535 4.494199 CGACTTGTGTGAAACTCTGAAACC 60.494 45.833 0.00 0.00 38.04 3.27
529 537 3.254470 TGTGTGAAACTCTGAAACCGA 57.746 42.857 0.00 0.00 38.04 4.69
557 565 1.606313 GCCCAAGCAGCCAACCTTA 60.606 57.895 0.00 0.00 39.53 2.69
562 575 1.032114 AAGCAGCCAACCTTATCGCC 61.032 55.000 0.00 0.00 0.00 5.54
564 577 1.312371 GCAGCCAACCTTATCGCCAA 61.312 55.000 0.00 0.00 0.00 4.52
565 578 0.451783 CAGCCAACCTTATCGCCAAC 59.548 55.000 0.00 0.00 0.00 3.77
566 579 0.679960 AGCCAACCTTATCGCCAACC 60.680 55.000 0.00 0.00 0.00 3.77
567 580 0.679960 GCCAACCTTATCGCCAACCT 60.680 55.000 0.00 0.00 0.00 3.50
717 741 2.441901 GCATCCGCCCCATTCCAA 60.442 61.111 0.00 0.00 0.00 3.53
718 742 2.057408 GCATCCGCCCCATTCCAAA 61.057 57.895 0.00 0.00 0.00 3.28
719 743 1.402107 GCATCCGCCCCATTCCAAAT 61.402 55.000 0.00 0.00 0.00 2.32
720 744 1.122227 CATCCGCCCCATTCCAAATT 58.878 50.000 0.00 0.00 0.00 1.82
721 745 1.485895 CATCCGCCCCATTCCAAATTT 59.514 47.619 0.00 0.00 0.00 1.82
723 747 1.194218 CCGCCCCATTCCAAATTTCT 58.806 50.000 0.00 0.00 0.00 2.52
903 1238 2.466571 CGCCTATAAGAAGCAACGTACG 59.533 50.000 15.01 15.01 0.00 3.67
947 1311 2.051334 AACACAGCCACACAAGCTAA 57.949 45.000 0.00 0.00 38.95 3.09
949 1313 1.949525 ACACAGCCACACAAGCTAAAG 59.050 47.619 0.00 0.00 38.95 1.85
950 1314 0.954452 ACAGCCACACAAGCTAAAGC 59.046 50.000 0.00 0.00 38.95 3.51
951 1315 0.953727 CAGCCACACAAGCTAAAGCA 59.046 50.000 4.54 0.00 45.16 3.91
952 1316 1.337703 CAGCCACACAAGCTAAAGCAA 59.662 47.619 4.54 0.00 45.16 3.91
956 1320 2.880890 CCACACAAGCTAAAGCAAGACT 59.119 45.455 4.54 0.00 45.16 3.24
957 1321 3.304257 CCACACAAGCTAAAGCAAGACTG 60.304 47.826 4.54 0.00 45.16 3.51
1161 1562 4.641645 TTGCCAGACCTGCCGGTG 62.642 66.667 3.79 0.00 45.73 4.94
1226 1627 2.531942 GGTTCCTGGGGTCCCTGT 60.532 66.667 8.15 0.00 36.94 4.00
1227 1628 2.603652 GGTTCCTGGGGTCCCTGTC 61.604 68.421 8.15 0.00 36.94 3.51
1231 1632 2.378634 CCTGGGGTCCCTGTCCATC 61.379 68.421 8.15 0.00 36.94 3.51
1232 1633 2.286121 TGGGGTCCCTGTCCATCC 60.286 66.667 8.15 0.00 36.94 3.51
1233 1634 2.286121 GGGGTCCCTGTCCATCCA 60.286 66.667 8.15 0.00 0.00 3.41
1234 1635 1.697754 GGGGTCCCTGTCCATCCAT 60.698 63.158 8.15 0.00 0.00 3.41
1235 1636 1.533711 GGGTCCCTGTCCATCCATG 59.466 63.158 0.00 0.00 0.00 3.66
1236 1637 0.988145 GGGTCCCTGTCCATCCATGA 60.988 60.000 0.00 0.00 0.00 3.07
1237 1638 0.918983 GGTCCCTGTCCATCCATGAA 59.081 55.000 0.00 0.00 0.00 2.57
1260 1661 6.990908 ACCATGATCATCTCTAGTTCATGA 57.009 37.500 4.86 0.00 43.99 3.07
1340 1755 0.453390 GGCATCGCCCTGAAGAAAAG 59.547 55.000 0.00 0.00 44.06 2.27
1435 1883 0.741915 TTTTCGTTCCTTGGTGTGCC 59.258 50.000 0.00 0.00 0.00 5.01
1504 1960 5.407084 TGCGATCGTCTTCTTGAATAAACAA 59.593 36.000 17.81 0.00 0.00 2.83
1505 1961 6.092122 TGCGATCGTCTTCTTGAATAAACAAT 59.908 34.615 17.81 0.00 0.00 2.71
1507 1963 8.114290 GCGATCGTCTTCTTGAATAAACAATTA 58.886 33.333 17.81 0.00 0.00 1.40
1508 1964 9.967245 CGATCGTCTTCTTGAATAAACAATTAA 57.033 29.630 7.03 0.00 0.00 1.40
1558 2014 9.508642 TCATCAATCGTACTACTCTCTAATCAT 57.491 33.333 0.00 0.00 0.00 2.45
1576 2035 5.779241 ATCATAAAGTCCCAAGTCCAGAA 57.221 39.130 0.00 0.00 0.00 3.02
1580 2039 0.905357 AGTCCCAAGTCCAGAATCGG 59.095 55.000 0.00 0.00 0.00 4.18
1611 2070 2.752903 AGAACCAGCAAGTTTTCGTTGT 59.247 40.909 0.00 0.00 0.00 3.32
1640 2099 7.817418 ACACTAATGCTTTGAAAGAGGTAAA 57.183 32.000 9.48 0.00 0.00 2.01
1641 2100 8.232913 ACACTAATGCTTTGAAAGAGGTAAAA 57.767 30.769 9.48 0.00 0.00 1.52
1642 2101 8.352942 ACACTAATGCTTTGAAAGAGGTAAAAG 58.647 33.333 9.48 0.00 33.67 2.27
1644 2103 6.731292 AATGCTTTGAAAGAGGTAAAAGGT 57.269 33.333 9.48 0.00 31.67 3.50
1645 2104 5.514274 TGCTTTGAAAGAGGTAAAAGGTG 57.486 39.130 9.48 0.00 31.67 4.00
1646 2105 5.197451 TGCTTTGAAAGAGGTAAAAGGTGA 58.803 37.500 9.48 0.00 31.67 4.02
1647 2106 5.833131 TGCTTTGAAAGAGGTAAAAGGTGAT 59.167 36.000 9.48 0.00 31.67 3.06
1677 2165 3.440173 TCATCAACTCTTTCGGATTTGGC 59.560 43.478 0.00 0.00 35.93 4.52
1705 2203 1.078848 GTCTGCGTGGATGGAGCTT 60.079 57.895 0.00 0.00 0.00 3.74
1706 2204 1.086634 GTCTGCGTGGATGGAGCTTC 61.087 60.000 0.00 0.00 0.00 3.86
1707 2205 1.078918 CTGCGTGGATGGAGCTTCA 60.079 57.895 0.00 0.00 0.00 3.02
1708 2206 1.078918 TGCGTGGATGGAGCTTCAG 60.079 57.895 0.00 0.00 0.00 3.02
1709 2207 1.817099 GCGTGGATGGAGCTTCAGG 60.817 63.158 0.00 0.00 0.00 3.86
1710 2208 1.900351 CGTGGATGGAGCTTCAGGA 59.100 57.895 0.00 0.00 0.00 3.86
1711 2209 0.250234 CGTGGATGGAGCTTCAGGAA 59.750 55.000 0.00 0.00 0.00 3.36
1712 2210 1.134280 CGTGGATGGAGCTTCAGGAAT 60.134 52.381 0.00 0.00 0.00 3.01
1713 2211 2.570135 GTGGATGGAGCTTCAGGAATC 58.430 52.381 0.00 0.00 0.00 2.52
1714 2212 2.092753 GTGGATGGAGCTTCAGGAATCA 60.093 50.000 0.00 0.00 0.00 2.57
1715 2213 2.172082 TGGATGGAGCTTCAGGAATCAG 59.828 50.000 0.00 0.00 0.00 2.90
1716 2214 2.486907 GGATGGAGCTTCAGGAATCAGG 60.487 54.545 0.00 0.00 0.00 3.86
1717 2215 1.956869 TGGAGCTTCAGGAATCAGGA 58.043 50.000 0.00 0.00 0.00 3.86
1718 2216 1.556911 TGGAGCTTCAGGAATCAGGAC 59.443 52.381 0.00 0.00 0.00 3.85
1719 2217 1.556911 GGAGCTTCAGGAATCAGGACA 59.443 52.381 0.00 0.00 0.00 4.02
1720 2218 2.172293 GGAGCTTCAGGAATCAGGACAT 59.828 50.000 0.00 0.00 0.00 3.06
1721 2219 3.371380 GGAGCTTCAGGAATCAGGACATT 60.371 47.826 0.00 0.00 0.00 2.71
1724 2222 5.374921 AGCTTCAGGAATCAGGACATTATG 58.625 41.667 0.00 0.00 0.00 1.90
1761 2259 6.313905 GTGTGCATATACATTATGGTAGAGCC 59.686 42.308 0.00 0.00 32.43 4.70
1762 2260 5.520288 GTGCATATACATTATGGTAGAGCCG 59.480 44.000 0.00 0.00 41.21 5.52
1763 2261 5.050490 GCATATACATTATGGTAGAGCCGG 58.950 45.833 0.00 0.00 41.21 6.13
1764 2262 5.163447 GCATATACATTATGGTAGAGCCGGA 60.163 44.000 5.05 0.00 41.21 5.14
1765 2263 6.629515 GCATATACATTATGGTAGAGCCGGAA 60.630 42.308 5.05 0.00 41.21 4.30
1766 2264 5.818678 ATACATTATGGTAGAGCCGGAAA 57.181 39.130 5.05 0.00 41.21 3.13
1784 2282 2.351276 TCCCTTTTGGAGCTCGGC 59.649 61.111 7.83 0.00 44.07 5.54
1887 2386 7.786178 TTACAGATGTACATGAAGGCATAAC 57.214 36.000 14.43 0.00 32.27 1.89
1933 2860 5.054390 TCAAAATACGTTGAAATGAGGGC 57.946 39.130 0.00 0.00 34.59 5.19
1971 3322 0.696501 TCCCCTGAGGCTGTTTAACC 59.303 55.000 0.00 0.00 34.51 2.85
1975 3326 2.369394 CCTGAGGCTGTTTAACCCATC 58.631 52.381 0.00 0.00 0.00 3.51
1995 3346 5.723405 CCATCATACTATTCATCCTCCCAGA 59.277 44.000 0.00 0.00 0.00 3.86
2001 3352 2.268796 TTCATCCTCCCAGACCATGA 57.731 50.000 0.00 0.00 0.00 3.07
2048 3399 6.238566 CGCAACTCAAGGTATTTCATCATGAT 60.239 38.462 1.18 1.18 0.00 2.45
2178 3531 3.431725 CGGCCTCCAAAACGCCTC 61.432 66.667 0.00 0.00 40.70 4.70
2183 3536 0.321671 CCTCCAAAACGCCTCTCTCA 59.678 55.000 0.00 0.00 0.00 3.27
2189 3542 3.366374 CCAAAACGCCTCTCTCAATTTCC 60.366 47.826 0.00 0.00 0.00 3.13
2190 3543 2.859165 AACGCCTCTCTCAATTTCCA 57.141 45.000 0.00 0.00 0.00 3.53
2191 3544 2.393271 ACGCCTCTCTCAATTTCCAG 57.607 50.000 0.00 0.00 0.00 3.86
2192 3545 1.065854 ACGCCTCTCTCAATTTCCAGG 60.066 52.381 0.00 0.00 0.00 4.45
2193 3546 1.065854 CGCCTCTCTCAATTTCCAGGT 60.066 52.381 0.00 0.00 0.00 4.00
2194 3547 2.637947 GCCTCTCTCAATTTCCAGGTC 58.362 52.381 0.00 0.00 0.00 3.85
2195 3548 2.682269 GCCTCTCTCAATTTCCAGGTCC 60.682 54.545 0.00 0.00 0.00 4.46
2200 3553 6.448369 TCTCTCAATTTCCAGGTCCTTTTA 57.552 37.500 0.00 0.00 0.00 1.52
2204 3557 7.010160 TCTCAATTTCCAGGTCCTTTTACAAT 58.990 34.615 0.00 0.00 0.00 2.71
2207 3560 9.320295 TCAATTTCCAGGTCCTTTTACAATTAT 57.680 29.630 0.00 0.00 0.00 1.28
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
22 23 1.413767 CGCTCATCGAAGTGGAACCG 61.414 60.000 0.00 0.00 41.67 4.44
32 33 2.678580 TCCCACACCGCTCATCGA 60.679 61.111 0.00 0.00 41.67 3.59
34 35 2.512515 GCTCCCACACCGCTCATC 60.513 66.667 0.00 0.00 0.00 2.92
92 93 3.114616 CTGCTCACCGAACTGCCG 61.115 66.667 0.00 0.00 0.00 5.69
99 100 4.383861 CTGCAGCCTGCTCACCGA 62.384 66.667 18.96 0.00 45.31 4.69
150 151 6.420008 CGAATACACTACACTAGTTTATGGCC 59.580 42.308 0.00 0.00 36.76 5.36
152 153 7.972277 ACACGAATACACTACACTAGTTTATGG 59.028 37.037 0.00 0.00 36.76 2.74
173 174 0.900182 AGCTCCACTCCATGACACGA 60.900 55.000 0.00 0.00 0.00 4.35
197 199 0.387929 CTATGTGCCCGTACGGTCAT 59.612 55.000 31.24 28.72 34.40 3.06
198 200 1.669049 CCTATGTGCCCGTACGGTCA 61.669 60.000 31.24 24.14 0.00 4.02
199 201 1.066918 CCTATGTGCCCGTACGGTC 59.933 63.158 31.24 21.47 0.00 4.79
200 202 1.259840 AACCTATGTGCCCGTACGGT 61.260 55.000 31.24 16.02 0.00 4.83
201 203 0.108041 AAACCTATGTGCCCGTACGG 60.108 55.000 27.68 27.68 0.00 4.02
202 204 2.195922 GTAAACCTATGTGCCCGTACG 58.804 52.381 8.69 8.69 0.00 3.67
203 205 2.169144 AGGTAAACCTATGTGCCCGTAC 59.831 50.000 0.00 0.00 46.48 3.67
204 206 2.469952 AGGTAAACCTATGTGCCCGTA 58.530 47.619 0.00 0.00 46.48 4.02
246 248 9.471084 CTAAAACCGGAAGAAAACATTTACATT 57.529 29.630 9.46 0.00 0.00 2.71
292 295 1.260297 GTGCAAACACGGCCAAATTTC 59.740 47.619 2.24 0.00 36.98 2.17
340 343 6.790285 ACCTTACCCGCATATATTTTAACG 57.210 37.500 0.00 0.00 0.00 3.18
358 361 1.379309 GGGCCGCCATTCAACCTTA 60.379 57.895 12.58 0.00 0.00 2.69
360 363 2.803593 AATGGGCCGCCATTCAACCT 62.804 55.000 12.58 0.00 35.78 3.50
388 396 1.372087 GACAGCAGGAGGCCAATTCG 61.372 60.000 5.01 0.00 46.50 3.34
392 400 2.752358 CAGACAGCAGGAGGCCAA 59.248 61.111 5.01 0.00 46.50 4.52
401 409 3.381983 ATCCGTCCGCAGACAGCA 61.382 61.111 0.20 0.00 46.13 4.41
420 428 8.877864 TTAGGGCATCTCTAAATTTTCTTTCA 57.122 30.769 0.00 0.00 0.00 2.69
422 430 9.183368 CTCTTAGGGCATCTCTAAATTTTCTTT 57.817 33.333 0.00 0.00 0.00 2.52
435 443 4.104831 AGTTTACACCTCTTAGGGCATCT 58.895 43.478 0.00 0.00 40.58 2.90
480 488 2.749621 CCAAATGACCCAGCTGTTACTC 59.250 50.000 13.81 1.77 0.00 2.59
525 533 4.280019 GGGCCAGTGGGTTTCGGT 62.280 66.667 12.15 0.00 36.17 4.69
526 534 3.801068 TTGGGCCAGTGGGTTTCGG 62.801 63.158 12.15 0.00 36.17 4.30
527 535 2.203422 TTGGGCCAGTGGGTTTCG 60.203 61.111 12.15 0.00 36.17 3.46
529 537 2.524148 GCTTGGGCCAGTGGGTTT 60.524 61.111 12.15 0.00 36.17 3.27
557 565 1.478510 CTGTGAGTAGAGGTTGGCGAT 59.521 52.381 0.00 0.00 0.00 4.58
565 578 1.203523 GCTGTGACCTGTGAGTAGAGG 59.796 57.143 0.00 0.00 42.90 3.69
566 579 1.889170 TGCTGTGACCTGTGAGTAGAG 59.111 52.381 0.00 0.00 0.00 2.43
567 580 1.613925 GTGCTGTGACCTGTGAGTAGA 59.386 52.381 0.00 0.00 0.00 2.59
716 740 4.214545 TCAACGTCGGTGCATTAGAAATTT 59.785 37.500 5.10 0.00 0.00 1.82
717 741 3.749088 TCAACGTCGGTGCATTAGAAATT 59.251 39.130 5.10 0.00 0.00 1.82
718 742 3.124636 GTCAACGTCGGTGCATTAGAAAT 59.875 43.478 5.10 0.00 0.00 2.17
719 743 2.477375 GTCAACGTCGGTGCATTAGAAA 59.523 45.455 5.10 0.00 0.00 2.52
720 744 2.063266 GTCAACGTCGGTGCATTAGAA 58.937 47.619 5.10 0.00 0.00 2.10
721 745 1.000052 TGTCAACGTCGGTGCATTAGA 60.000 47.619 5.10 0.00 0.00 2.10
723 747 1.141645 GTGTCAACGTCGGTGCATTA 58.858 50.000 5.10 0.00 0.00 1.90
769 793 3.415087 CAAGGGCTGGGAGAGGGG 61.415 72.222 0.00 0.00 0.00 4.79
771 795 2.674220 GGTCAAGGGCTGGGAGAGG 61.674 68.421 0.00 0.00 0.00 3.69
855 883 4.974989 GGGTGGCCGTTCGTCGTT 62.975 66.667 0.00 0.00 37.94 3.85
903 1238 4.381411 AGGAGGTAATTTCTTAGCATCGC 58.619 43.478 0.00 0.00 37.72 4.58
947 1311 2.324541 ACTGAGGAGACAGTCTTGCTT 58.675 47.619 4.05 0.00 46.36 3.91
949 1313 2.823154 ACTACTGAGGAGACAGTCTTGC 59.177 50.000 4.05 0.00 46.36 4.01
950 1314 5.883115 TGATACTACTGAGGAGACAGTCTTG 59.117 44.000 4.05 0.00 46.36 3.02
951 1315 6.068461 TGATACTACTGAGGAGACAGTCTT 57.932 41.667 4.05 0.00 46.36 3.01
952 1316 5.427157 TCTGATACTACTGAGGAGACAGTCT 59.573 44.000 1.46 1.46 46.36 3.24
956 1320 6.068461 ACTTCTGATACTACTGAGGAGACA 57.932 41.667 0.00 0.00 0.00 3.41
957 1321 6.600032 TGAACTTCTGATACTACTGAGGAGAC 59.400 42.308 0.00 0.00 0.00 3.36
1026 1409 2.519302 AGCACCACCACCAACAGC 60.519 61.111 0.00 0.00 0.00 4.40
1210 1611 2.603652 GGACAGGGACCCCAGGAAC 61.604 68.421 7.00 0.00 38.92 3.62
1226 1627 4.352893 AGATGATCATGGTTCATGGATGGA 59.647 41.667 14.30 0.00 41.66 3.41
1227 1628 4.663334 AGATGATCATGGTTCATGGATGG 58.337 43.478 14.30 0.00 41.66 3.51
1231 1632 6.111669 ACTAGAGATGATCATGGTTCATGG 57.888 41.667 14.30 5.26 41.66 3.66
1232 1633 7.215085 TGAACTAGAGATGATCATGGTTCATG 58.785 38.462 14.30 7.34 42.60 3.07
1233 1634 7.370905 TGAACTAGAGATGATCATGGTTCAT 57.629 36.000 14.30 10.64 37.66 2.57
1234 1635 6.796785 TGAACTAGAGATGATCATGGTTCA 57.203 37.500 14.30 16.13 38.89 3.18
1235 1636 7.440198 TCATGAACTAGAGATGATCATGGTTC 58.560 38.462 14.30 13.76 44.62 3.62
1236 1637 7.370905 TCATGAACTAGAGATGATCATGGTT 57.629 36.000 14.30 4.07 44.62 3.67
1237 1638 6.518706 GCTCATGAACTAGAGATGATCATGGT 60.519 42.308 14.30 0.00 44.62 3.55
1260 1661 4.580995 AGCTCGTATGTATGTAAGTCAGCT 59.419 41.667 0.00 0.00 0.00 4.24
1331 1746 1.503818 GACGCCGGTGCTTTTCTTCA 61.504 55.000 16.69 0.00 34.43 3.02
1462 1910 7.916977 ACGATCGCACTAACAAAGTATTATGTA 59.083 33.333 16.60 0.00 35.76 2.29
1463 1911 6.755141 ACGATCGCACTAACAAAGTATTATGT 59.245 34.615 16.60 0.00 35.76 2.29
1464 1912 7.161829 ACGATCGCACTAACAAAGTATTATG 57.838 36.000 16.60 0.00 35.76 1.90
1477 1925 3.842732 TTCAAGAAGACGATCGCACTA 57.157 42.857 16.60 0.00 0.00 2.74
1482 1938 9.967245 TTAATTGTTTATTCAAGAAGACGATCG 57.033 29.630 14.88 14.88 0.00 3.69
1525 1981 9.900710 GAGAGTAGTACGATTGATGATACAATT 57.099 33.333 0.00 0.00 40.03 2.32
1526 1982 9.290988 AGAGAGTAGTACGATTGATGATACAAT 57.709 33.333 0.00 0.00 42.19 2.71
1558 2014 3.055385 CCGATTCTGGACTTGGGACTTTA 60.055 47.826 0.00 0.00 0.00 1.85
1576 2035 3.751698 GCTGGTTCTTTTAACAGACCGAT 59.248 43.478 0.00 0.00 32.86 4.18
1580 2039 5.500645 ACTTGCTGGTTCTTTTAACAGAC 57.499 39.130 0.00 0.00 32.86 3.51
1611 2070 6.206634 CCTCTTTCAAAGCATTAGTGTTACCA 59.793 38.462 0.00 0.00 0.00 3.25
1620 2079 7.504238 TCACCTTTTACCTCTTTCAAAGCATTA 59.496 33.333 0.00 0.00 0.00 1.90
1640 2099 8.088463 AGAGTTGATGAGAGATAAATCACCTT 57.912 34.615 0.00 0.00 30.26 3.50
1641 2100 7.673641 AGAGTTGATGAGAGATAAATCACCT 57.326 36.000 0.00 0.00 30.26 4.00
1642 2101 8.729805 AAAGAGTTGATGAGAGATAAATCACC 57.270 34.615 0.00 0.00 30.26 4.02
1644 2103 7.708322 CCGAAAGAGTTGATGAGAGATAAATCA 59.292 37.037 0.00 0.00 0.00 2.57
1645 2104 7.923344 TCCGAAAGAGTTGATGAGAGATAAATC 59.077 37.037 0.00 0.00 0.00 2.17
1646 2105 7.786030 TCCGAAAGAGTTGATGAGAGATAAAT 58.214 34.615 0.00 0.00 0.00 1.40
1647 2106 7.170393 TCCGAAAGAGTTGATGAGAGATAAA 57.830 36.000 0.00 0.00 0.00 1.40
1677 2165 1.329292 TCCACGCAGACAAAGAAAACG 59.671 47.619 0.00 0.00 0.00 3.60
1705 2203 4.721274 TCACCATAATGTCCTGATTCCTGA 59.279 41.667 0.00 0.00 0.00 3.86
1706 2204 5.039920 TCACCATAATGTCCTGATTCCTG 57.960 43.478 0.00 0.00 0.00 3.86
1707 2205 4.445448 GCTCACCATAATGTCCTGATTCCT 60.445 45.833 0.00 0.00 0.00 3.36
1708 2206 3.817647 GCTCACCATAATGTCCTGATTCC 59.182 47.826 0.00 0.00 0.00 3.01
1709 2207 4.454678 TGCTCACCATAATGTCCTGATTC 58.545 43.478 0.00 0.00 0.00 2.52
1710 2208 4.508551 TGCTCACCATAATGTCCTGATT 57.491 40.909 0.00 0.00 0.00 2.57
1711 2209 4.508551 TTGCTCACCATAATGTCCTGAT 57.491 40.909 0.00 0.00 0.00 2.90
1712 2210 3.998913 TTGCTCACCATAATGTCCTGA 57.001 42.857 0.00 0.00 0.00 3.86
1713 2211 4.201657 TGATTGCTCACCATAATGTCCTG 58.798 43.478 0.00 0.00 0.00 3.86
1714 2212 4.080129 ACTGATTGCTCACCATAATGTCCT 60.080 41.667 0.00 0.00 0.00 3.85
1715 2213 4.036027 CACTGATTGCTCACCATAATGTCC 59.964 45.833 0.00 0.00 0.00 4.02
1716 2214 4.637534 ACACTGATTGCTCACCATAATGTC 59.362 41.667 0.00 0.00 0.00 3.06
1717 2215 4.397103 CACACTGATTGCTCACCATAATGT 59.603 41.667 0.00 0.00 0.00 2.71
1718 2216 4.732647 GCACACTGATTGCTCACCATAATG 60.733 45.833 0.00 0.00 37.00 1.90
1719 2217 3.379372 GCACACTGATTGCTCACCATAAT 59.621 43.478 0.00 0.00 37.00 1.28
1720 2218 2.749076 GCACACTGATTGCTCACCATAA 59.251 45.455 0.00 0.00 37.00 1.90
1721 2219 2.290197 TGCACACTGATTGCTCACCATA 60.290 45.455 6.76 0.00 40.86 2.74
1724 2222 1.171308 ATGCACACTGATTGCTCACC 58.829 50.000 0.00 0.00 40.86 4.02
1791 2289 7.537596 TTCAAATTTGAATTTAGAGGCCTCA 57.462 32.000 33.90 17.39 41.88 3.86
1871 2370 5.123820 ACATGTGTGTTATGCCTTCATGTAC 59.876 40.000 0.00 0.00 41.23 2.90
1920 2847 0.961019 TGCACAGCCCTCATTTCAAC 59.039 50.000 0.00 0.00 0.00 3.18
1948 2875 2.470057 AAACAGCCTCAGGGGAAAAA 57.530 45.000 0.00 0.00 37.23 1.94
1949 2876 3.227614 GTTAAACAGCCTCAGGGGAAAA 58.772 45.455 0.00 0.00 37.23 2.29
1950 2877 2.490168 GGTTAAACAGCCTCAGGGGAAA 60.490 50.000 0.00 0.00 37.23 3.13
1952 2879 0.696501 GGTTAAACAGCCTCAGGGGA 59.303 55.000 0.00 0.00 37.23 4.81
1953 2880 0.323451 GGGTTAAACAGCCTCAGGGG 60.323 60.000 0.00 0.00 40.32 4.79
1954 2881 0.404040 TGGGTTAAACAGCCTCAGGG 59.596 55.000 0.00 0.00 44.37 4.45
1955 2882 2.290896 TGATGGGTTAAACAGCCTCAGG 60.291 50.000 0.00 0.00 44.37 3.86
1959 3310 4.862641 AGTATGATGGGTTAAACAGCCT 57.137 40.909 0.00 0.00 44.37 4.58
1971 3322 5.723405 TCTGGGAGGATGAATAGTATGATGG 59.277 44.000 0.00 0.00 0.00 3.51
1975 3326 4.840680 TGGTCTGGGAGGATGAATAGTATG 59.159 45.833 0.00 0.00 0.00 2.39
2020 3371 3.734463 TGAAATACCTTGAGTTGCGACA 58.266 40.909 6.90 0.00 0.00 4.35
2178 3531 6.003950 TGTAAAAGGACCTGGAAATTGAGAG 58.996 40.000 0.00 0.00 0.00 3.20
2189 3542 9.353999 GCAGTTAAATAATTGTAAAAGGACCTG 57.646 33.333 0.00 0.00 0.00 4.00
2190 3543 9.084533 TGCAGTTAAATAATTGTAAAAGGACCT 57.915 29.630 0.00 0.00 0.00 3.85
2191 3544 9.699703 TTGCAGTTAAATAATTGTAAAAGGACC 57.300 29.630 0.00 0.00 28.17 4.46


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

AutoCloner maintained by Alex Coulton.