Multiple sequence alignment - TraesCS7B01G341300

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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 TraesCS7B01G341300 chr7B 100.000 2321 0 0 1 2321 595804997 595802677 0.000000e+00 4287.0
1 TraesCS7B01G341300 chr7B 79.097 421 65 14 917 1327 595798496 595798089 3.800000e-68 268.0
2 TraesCS7B01G341300 chr7B 85.621 153 18 3 262 410 525025011 525025163 8.590000e-35 158.0
3 TraesCS7B01G341300 chr7A 85.325 1833 193 33 10 1777 636907069 636905248 0.000000e+00 1825.0
4 TraesCS7B01G341300 chr7A 77.564 468 76 16 874 1325 636900536 636900082 2.960000e-64 255.0
5 TraesCS7B01G341300 chr7D 86.182 977 55 31 435 1360 550987553 550986606 0.000000e+00 983.0
6 TraesCS7B01G341300 chr7D 78.801 467 72 16 874 1325 550982197 550981743 2.920000e-74 289.0
7 TraesCS7B01G341300 chr7D 84.337 166 23 3 49 213 550987749 550987586 2.390000e-35 159.0
8 TraesCS7B01G341300 chr2D 89.744 507 47 3 1809 2315 471642869 471643370 0.000000e+00 643.0
9 TraesCS7B01G341300 chr2D 87.259 518 59 5 1801 2318 323521183 323520673 3.320000e-163 584.0
10 TraesCS7B01G341300 chr3D 88.340 506 50 6 1811 2315 567669793 567669296 1.190000e-167 599.0
11 TraesCS7B01G341300 chr3D 87.140 521 61 5 1800 2320 602104452 602103938 9.240000e-164 586.0
12 TraesCS7B01G341300 chr1D 88.063 511 54 5 1809 2318 447465050 447464546 1.190000e-167 599.0
13 TraesCS7B01G341300 chr1D 86.727 550 56 10 1781 2320 402303463 402302921 1.540000e-166 595.0
14 TraesCS7B01G341300 chr1D 87.719 513 57 5 1809 2320 481421969 481422476 5.520000e-166 593.0
15 TraesCS7B01G341300 chr6D 87.283 519 58 6 1801 2319 158819812 158820322 9.240000e-164 586.0
16 TraesCS7B01G341300 chr2B 86.081 546 62 9 1782 2320 500647120 500647658 2.000000e-160 575.0
17 TraesCS7B01G341300 chr5B 90.141 142 13 1 270 410 478327849 478327990 1.420000e-42 183.0
18 TraesCS7B01G341300 chr5A 87.662 154 19 0 258 411 533024797 533024950 1.830000e-41 180.0
19 TraesCS7B01G341300 chr3A 87.302 63 7 1 1399 1461 737294855 737294794 1.150000e-08 71.3


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 TraesCS7B01G341300 chr7B 595802677 595804997 2320 True 4287 4287 100.0000 1 2321 1 chr7B.!!$R2 2320
1 TraesCS7B01G341300 chr7A 636905248 636907069 1821 True 1825 1825 85.3250 10 1777 1 chr7A.!!$R2 1767
2 TraesCS7B01G341300 chr7D 550986606 550987749 1143 True 571 983 85.2595 49 1360 2 chr7D.!!$R2 1311
3 TraesCS7B01G341300 chr2D 471642869 471643370 501 False 643 643 89.7440 1809 2315 1 chr2D.!!$F1 506
4 TraesCS7B01G341300 chr2D 323520673 323521183 510 True 584 584 87.2590 1801 2318 1 chr2D.!!$R1 517
5 TraesCS7B01G341300 chr3D 602103938 602104452 514 True 586 586 87.1400 1800 2320 1 chr3D.!!$R2 520
6 TraesCS7B01G341300 chr1D 447464546 447465050 504 True 599 599 88.0630 1809 2318 1 chr1D.!!$R2 509
7 TraesCS7B01G341300 chr1D 402302921 402303463 542 True 595 595 86.7270 1781 2320 1 chr1D.!!$R1 539
8 TraesCS7B01G341300 chr1D 481421969 481422476 507 False 593 593 87.7190 1809 2320 1 chr1D.!!$F1 511
9 TraesCS7B01G341300 chr6D 158819812 158820322 510 False 586 586 87.2830 1801 2319 1 chr6D.!!$F1 518
10 TraesCS7B01G341300 chr2B 500647120 500647658 538 False 575 575 86.0810 1782 2320 1 chr2B.!!$F1 538

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
315 318 0.108756 GGAGTTGTAGCCAGTCCGTC 60.109 60.0 0.0 0.0 0.0 4.79 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1504 1589 0.032678 CGAGCATGGTAGATCCGCTT 59.967 55.0 0.0 0.0 39.52 4.68 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
45 46 4.268359 GTCGGAGTTAAGAAGTAGAGGGA 58.732 47.826 0.00 0.00 0.00 4.20
56 58 1.007359 AGTAGAGGGAGAAGGGTGGTC 59.993 57.143 0.00 0.00 0.00 4.02
58 60 3.003763 AGGGAGAAGGGTGGTCGC 61.004 66.667 0.00 0.00 0.00 5.19
132 135 2.302733 GGTTTTCTGTTGGGCCATGATT 59.697 45.455 7.26 0.00 0.00 2.57
154 157 1.174078 TTGTCTGGGTCTCGCGTGTA 61.174 55.000 5.77 0.00 0.00 2.90
227 230 5.875359 GGTTCGTTCAGTAGATTTCCAATCT 59.125 40.000 4.47 4.47 0.00 2.40
230 233 4.034510 CGTTCAGTAGATTTCCAATCTGCC 59.965 45.833 8.92 0.93 32.25 4.85
265 268 6.493802 AGTTACCAAATATCGCTATCCTGAGA 59.506 38.462 0.00 0.00 0.00 3.27
268 271 5.070446 ACCAAATATCGCTATCCTGAGAACA 59.930 40.000 0.00 0.00 0.00 3.18
279 282 2.126031 GAGAACAGGGCGTCGACC 60.126 66.667 9.89 9.89 0.00 4.79
294 297 2.274104 ACCCGTTGGTTGTGCTGT 59.726 55.556 0.00 0.00 44.75 4.40
303 306 1.102978 GGTTGTGCTGTTGGAGTTGT 58.897 50.000 0.00 0.00 0.00 3.32
309 312 1.160137 GCTGTTGGAGTTGTAGCCAG 58.840 55.000 0.00 0.00 35.23 4.85
310 313 1.543429 GCTGTTGGAGTTGTAGCCAGT 60.543 52.381 0.00 0.00 35.23 4.00
311 314 2.417719 CTGTTGGAGTTGTAGCCAGTC 58.582 52.381 0.00 0.00 35.23 3.51
312 315 1.071699 TGTTGGAGTTGTAGCCAGTCC 59.928 52.381 0.00 0.00 35.23 3.85
315 318 0.108756 GGAGTTGTAGCCAGTCCGTC 60.109 60.000 0.00 0.00 0.00 4.79
317 320 1.445582 GTTGTAGCCAGTCCGTCCG 60.446 63.158 0.00 0.00 0.00 4.79
322 325 4.754667 GCCAGTCCGTCCGGGTTC 62.755 72.222 0.00 0.00 37.00 3.62
329 332 4.493747 CGTCCGGGTTCGAGCCTC 62.494 72.222 18.44 7.43 39.00 4.70
361 364 3.546397 GCGCTCGCGGAGTTTCTC 61.546 66.667 13.56 0.00 40.19 2.87
362 365 3.241059 CGCTCGCGGAGTTTCTCG 61.241 66.667 6.13 0.00 35.56 4.04
367 371 2.906153 CTCGCGGAGTTTCTCGTATAG 58.094 52.381 6.13 0.00 0.00 1.31
379 383 3.777478 TCTCGTATAGAAAAGGCAACGG 58.223 45.455 0.00 0.00 46.39 4.44
380 384 2.864343 CTCGTATAGAAAAGGCAACGGG 59.136 50.000 0.00 0.00 46.39 5.28
381 385 1.937899 CGTATAGAAAAGGCAACGGGG 59.062 52.381 0.00 0.00 46.39 5.73
387 391 1.183030 AAAAGGCAACGGGGGTTAGC 61.183 55.000 0.00 0.00 46.39 3.09
388 392 2.076597 AAAGGCAACGGGGGTTAGCT 62.077 55.000 0.00 0.00 46.39 3.32
391 395 1.449778 GCAACGGGGGTTAGCTCTC 60.450 63.158 0.00 0.00 0.00 3.20
394 398 3.537874 CGGGGGTTAGCTCTCGGG 61.538 72.222 0.00 0.00 0.00 5.14
468 479 1.972075 TCACAACCAGGGAATACGTGA 59.028 47.619 0.00 0.00 37.13 4.35
614 650 1.620822 ACTGCAACTAGGCCAAAAGG 58.379 50.000 5.01 0.00 0.00 3.11
633 669 0.528470 GGGGTGAGACACGAGAGAAG 59.472 60.000 0.00 0.00 34.83 2.85
641 681 4.694037 TGAGACACGAGAGAAGTCGATTTA 59.306 41.667 0.00 0.00 42.85 1.40
729 773 2.437359 GAGCGAGCCCTGCATTGT 60.437 61.111 0.00 0.00 33.85 2.71
842 908 4.402528 CATGGGCCACGGGTTCGA 62.403 66.667 9.28 0.00 40.11 3.71
859 925 2.469826 TCGATGGATGCACGTTATGAC 58.530 47.619 0.00 0.00 0.00 3.06
860 926 2.100749 TCGATGGATGCACGTTATGACT 59.899 45.455 0.00 0.00 0.00 3.41
861 927 2.866156 CGATGGATGCACGTTATGACTT 59.134 45.455 0.00 0.00 0.00 3.01
862 928 4.048504 CGATGGATGCACGTTATGACTTA 58.951 43.478 0.00 0.00 0.00 2.24
863 929 4.686091 CGATGGATGCACGTTATGACTTAT 59.314 41.667 0.00 0.00 0.00 1.73
864 930 5.388786 CGATGGATGCACGTTATGACTTATG 60.389 44.000 0.00 0.00 0.00 1.90
865 931 5.017294 TGGATGCACGTTATGACTTATGA 57.983 39.130 0.00 0.00 0.00 2.15
873 943 6.273825 CACGTTATGACTTATGAGCTACCTT 58.726 40.000 0.00 0.00 0.00 3.50
950 1020 3.594134 CTCACTCTTCACTCCATTGGAC 58.406 50.000 0.00 0.00 0.00 4.02
956 1026 1.348064 TCACTCCATTGGACGACCTT 58.652 50.000 0.00 0.00 37.04 3.50
963 1038 1.535462 CATTGGACGACCTTCACCAAC 59.465 52.381 5.33 0.00 43.60 3.77
979 1054 0.389025 CAACCAAGCAGGAAACCCAC 59.611 55.000 1.83 0.00 41.22 4.61
1204 1286 4.296729 AGGGTGACGACGGGAGGT 62.297 66.667 0.00 0.00 0.00 3.85
1210 1292 2.522436 ACGACGGGAGGTGGTTCA 60.522 61.111 0.00 0.00 33.35 3.18
1224 1306 3.318384 TTCAGGCAGCTGGCGGTA 61.318 61.111 32.96 24.52 46.16 4.02
1245 1327 2.273449 CAGGGGCTGGTGGATGAC 59.727 66.667 0.00 0.00 0.00 3.06
1251 1333 1.327690 GGCTGGTGGATGACCTCGTA 61.328 60.000 0.00 0.00 46.32 3.43
1342 1424 3.245264 ACCTTACCCTGCTAGCACATTTT 60.245 43.478 14.93 0.00 0.00 1.82
1343 1425 4.018779 ACCTTACCCTGCTAGCACATTTTA 60.019 41.667 14.93 0.00 0.00 1.52
1349 1434 6.837312 ACCCTGCTAGCACATTTTATATACA 58.163 36.000 14.93 0.00 0.00 2.29
1371 1456 9.920946 ATACATTGGAGTTTACCATCACTATTT 57.079 29.630 0.00 0.00 39.82 1.40
1409 1494 8.980481 ATGGTATGTTAGAATTTTAGACAGGG 57.020 34.615 0.00 0.00 0.00 4.45
1410 1495 7.924541 TGGTATGTTAGAATTTTAGACAGGGT 58.075 34.615 0.00 0.00 0.00 4.34
1447 1532 8.618702 TTTTTCATGGCAATTTATGTTGATGT 57.381 26.923 0.00 0.00 0.00 3.06
1451 1536 5.327616 TGGCAATTTATGTTGATGTGAGG 57.672 39.130 0.00 0.00 0.00 3.86
1456 1541 7.431249 GCAATTTATGTTGATGTGAGGATGAT 58.569 34.615 0.00 0.00 0.00 2.45
1468 1553 9.465199 TGATGTGAGGATGATAAATTTTCTTGA 57.535 29.630 0.00 0.00 0.00 3.02
1471 1556 7.606073 TGTGAGGATGATAAATTTTCTTGACGA 59.394 33.333 0.00 0.00 0.00 4.20
1472 1557 8.450964 GTGAGGATGATAAATTTTCTTGACGAA 58.549 33.333 0.00 0.00 0.00 3.85
1475 1560 8.237267 AGGATGATAAATTTTCTTGACGAACAC 58.763 33.333 0.00 0.00 0.00 3.32
1476 1561 7.484959 GGATGATAAATTTTCTTGACGAACACC 59.515 37.037 0.00 0.00 0.00 4.16
1498 1583 7.148137 ACACCGTAACTTTCTGACAGAAAAATT 60.148 33.333 26.40 23.76 42.95 1.82
1499 1584 7.165812 CACCGTAACTTTCTGACAGAAAAATTG 59.834 37.037 26.40 18.58 42.95 2.32
1501 1586 8.339714 CCGTAACTTTCTGACAGAAAAATTGTA 58.660 33.333 26.40 13.75 42.95 2.41
1502 1587 9.878599 CGTAACTTTCTGACAGAAAAATTGTAT 57.121 29.630 26.40 15.11 42.95 2.29
1512 1600 8.181573 TGACAGAAAAATTGTATAAAGCGGATC 58.818 33.333 0.00 0.00 0.00 3.36
1520 1608 4.566004 TGTATAAAGCGGATCTACCATGC 58.434 43.478 0.00 0.00 38.90 4.06
1525 1613 1.373497 CGGATCTACCATGCTCGCC 60.373 63.158 0.00 0.00 38.90 5.54
1527 1615 0.106708 GGATCTACCATGCTCGCCAA 59.893 55.000 0.00 0.00 38.79 4.52
1528 1616 1.221414 GATCTACCATGCTCGCCAAC 58.779 55.000 0.00 0.00 0.00 3.77
1529 1617 0.833287 ATCTACCATGCTCGCCAACT 59.167 50.000 0.00 0.00 0.00 3.16
1534 1622 2.017049 ACCATGCTCGCCAACTAAATC 58.983 47.619 0.00 0.00 0.00 2.17
1537 1625 1.086696 TGCTCGCCAACTAAATCTGC 58.913 50.000 0.00 0.00 0.00 4.26
1544 1632 2.619074 GCCAACTAAATCTGCCACCTCT 60.619 50.000 0.00 0.00 0.00 3.69
1551 1639 0.610232 ATCTGCCACCTCTGCAAACC 60.610 55.000 0.00 0.00 38.46 3.27
1555 1643 1.075374 TGCCACCTCTGCAAACCTAAT 59.925 47.619 0.00 0.00 35.40 1.73
1557 1645 2.094545 GCCACCTCTGCAAACCTAATTG 60.095 50.000 0.00 0.00 0.00 2.32
1558 1646 2.493278 CCACCTCTGCAAACCTAATTGG 59.507 50.000 0.00 0.00 42.93 3.16
1559 1647 2.094545 CACCTCTGCAAACCTAATTGGC 60.095 50.000 0.00 0.00 40.22 4.52
1583 1676 7.930865 GGCCATGAAAAATATTTAACATGCCTA 59.069 33.333 25.57 3.78 35.03 3.93
1600 1693 6.209192 ACATGCCTAAAATTCTGATGTTCACA 59.791 34.615 0.00 0.00 0.00 3.58
1604 1697 6.623767 GCCTAAAATTCTGATGTTCACAGGAC 60.624 42.308 0.00 0.00 36.22 3.85
1606 1699 5.954296 AAATTCTGATGTTCACAGGACAG 57.046 39.130 0.00 0.00 36.22 3.51
1609 1702 2.029918 TCTGATGTTCACAGGACAGTCG 60.030 50.000 0.00 0.00 36.22 4.18
1614 1707 1.546476 GTTCACAGGACAGTCGGATCT 59.454 52.381 0.00 0.00 0.00 2.75
1615 1708 2.753452 GTTCACAGGACAGTCGGATCTA 59.247 50.000 0.00 0.00 0.00 1.98
1644 1738 1.369209 CACGAGTGCAAAAGCACCG 60.369 57.895 21.13 21.13 41.19 4.94
1646 1740 0.884704 ACGAGTGCAAAAGCACCGAT 60.885 50.000 26.05 14.38 41.19 4.18
1647 1741 0.238289 CGAGTGCAAAAGCACCGATT 59.762 50.000 16.13 0.00 41.19 3.34
1715 1818 6.044682 AGCTTTGCCTTGATATATTTGTTGC 58.955 36.000 0.00 0.00 0.00 4.17
1731 1834 1.665169 GTTGCTGTTTGTGGGCAAAAG 59.335 47.619 0.00 0.00 45.01 2.27
1732 1835 0.177604 TGCTGTTTGTGGGCAAAAGG 59.822 50.000 0.00 0.00 45.01 3.11
1735 1838 2.031120 CTGTTTGTGGGCAAAAGGAGA 58.969 47.619 0.00 0.00 45.01 3.71
1737 1840 2.167487 TGTTTGTGGGCAAAAGGAGAAC 59.833 45.455 0.00 0.00 45.01 3.01
1741 1844 0.486879 TGGGCAAAAGGAGAACCCAT 59.513 50.000 0.00 0.00 45.65 4.00
1760 1863 8.735692 AACCCATTAAAATTCTGCATATTTGG 57.264 30.769 7.47 6.84 0.00 3.28
1769 1872 9.893634 AAAATTCTGCATATTTGGATTTCATGA 57.106 25.926 7.47 0.00 0.00 3.07
1777 1880 8.553696 GCATATTTGGATTTCATGAAACCATTC 58.446 33.333 27.96 20.18 34.19 2.67
1805 1908 2.203714 CCCCTCGAGATCCCTCCC 60.204 72.222 15.71 0.00 36.04 4.30
1946 2059 1.520342 GATCTTGAGCGAGCGCCTT 60.520 57.895 11.66 0.00 43.17 4.35
1958 2071 3.423154 CGCCTTGGGACGACTTGC 61.423 66.667 0.00 0.00 0.00 4.01
2002 2115 2.969628 CAGGGATGTGACCTCCTCTAT 58.030 52.381 6.85 0.00 35.78 1.98
2052 2165 1.276989 GGATCTTGTCGGTGGGTGTTA 59.723 52.381 0.00 0.00 0.00 2.41
2059 2172 0.611200 TCGGTGGGTGTTACCTCATG 59.389 55.000 0.00 0.00 38.64 3.07
2060 2173 0.392461 CGGTGGGTGTTACCTCATGG 60.392 60.000 0.00 0.00 38.64 3.66
2075 2188 1.852157 ATGGTGGTGGCTTCCCAGA 60.852 57.895 0.00 0.00 43.18 3.86
2104 2217 0.908198 AGTGAAGGAGGAGATGGTGC 59.092 55.000 0.00 0.00 0.00 5.01
2213 2326 0.953471 CCACGCTCCATTGTTTCCGA 60.953 55.000 0.00 0.00 0.00 4.55
2284 2397 1.001764 TCGTAGCCCTCGTTGGAGA 60.002 57.895 0.00 0.00 43.27 3.71
2315 2428 0.767375 CTCCCGGATTGGATGATGGT 59.233 55.000 0.73 0.00 42.00 3.55
2320 2433 0.947244 GGATTGGATGATGGTGACGC 59.053 55.000 0.00 0.00 0.00 5.19
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
1 2 0.036294 AAGTAAACTCTCCGCCCTGC 60.036 55.000 0.00 0.00 0.00 4.85
3 4 0.036294 GCAAGTAAACTCTCCGCCCT 60.036 55.000 0.00 0.00 0.00 5.19
4 5 1.359459 CGCAAGTAAACTCTCCGCCC 61.359 60.000 0.00 0.00 0.00 6.13
5 6 2.079049 CGCAAGTAAACTCTCCGCC 58.921 57.895 0.00 0.00 0.00 6.13
65 67 1.550130 ATACCACCACTCCCCACACG 61.550 60.000 0.00 0.00 0.00 4.49
67 69 0.178888 TCATACCACCACTCCCCACA 60.179 55.000 0.00 0.00 0.00 4.17
132 135 1.300620 CGCGAGACCCAGACAACAA 60.301 57.895 0.00 0.00 0.00 2.83
188 191 2.232298 GAACCTGCTAGCGAGGCTGT 62.232 60.000 24.56 14.74 40.10 4.40
227 230 5.748670 TTTGGTAACTAGAGTATGTGGCA 57.251 39.130 0.00 0.00 37.61 4.92
230 233 8.082852 AGCGATATTTGGTAACTAGAGTATGTG 58.917 37.037 0.00 0.00 37.61 3.21
279 282 1.065600 CCAACAGCACAACCAACGG 59.934 57.895 0.00 0.00 0.00 4.44
291 294 2.417719 GACTGGCTACAACTCCAACAG 58.582 52.381 0.00 0.00 30.98 3.16
294 297 0.320374 CGGACTGGCTACAACTCCAA 59.680 55.000 0.00 0.00 30.98 3.53
303 306 3.892104 AACCCGGACGGACTGGCTA 62.892 63.158 13.13 0.00 43.37 3.93
309 312 4.790861 GCTCGAACCCGGACGGAC 62.791 72.222 13.13 2.68 37.50 4.79
312 315 4.493747 GAGGCTCGAACCCGGACG 62.494 72.222 0.73 6.13 36.24 4.79
361 364 1.937899 CCCCGTTGCCTTTTCTATACG 59.062 52.381 0.00 0.00 0.00 3.06
362 365 2.294979 CCCCCGTTGCCTTTTCTATAC 58.705 52.381 0.00 0.00 0.00 1.47
367 371 0.885879 CTAACCCCCGTTGCCTTTTC 59.114 55.000 0.00 0.00 33.17 2.29
372 376 2.437895 GAGCTAACCCCCGTTGCC 60.438 66.667 0.00 0.00 33.17 4.52
373 377 1.449778 GAGAGCTAACCCCCGTTGC 60.450 63.158 0.00 0.00 33.17 4.17
379 383 1.221021 CAACCCGAGAGCTAACCCC 59.779 63.158 0.00 0.00 0.00 4.95
380 384 1.221021 CCAACCCGAGAGCTAACCC 59.779 63.158 0.00 0.00 0.00 4.11
381 385 0.108281 GACCAACCCGAGAGCTAACC 60.108 60.000 0.00 0.00 0.00 2.85
387 391 2.770164 AAATGAGACCAACCCGAGAG 57.230 50.000 0.00 0.00 0.00 3.20
388 392 3.502123 AAAAATGAGACCAACCCGAGA 57.498 42.857 0.00 0.00 0.00 4.04
444 455 3.263425 ACGTATTCCCTGGTTGTGATTCT 59.737 43.478 0.00 0.00 0.00 2.40
448 459 1.972075 TCACGTATTCCCTGGTTGTGA 59.028 47.619 0.00 0.00 32.93 3.58
458 469 4.571176 GGTCTCCTCAATTTCACGTATTCC 59.429 45.833 0.00 0.00 0.00 3.01
468 479 2.576648 GGTAGGTGGGTCTCCTCAATTT 59.423 50.000 0.00 0.00 36.60 1.82
614 650 0.528470 CTTCTCTCGTGTCTCACCCC 59.472 60.000 0.00 0.00 0.00 4.95
633 669 2.810486 CGGATCGCCCTAAATCGAC 58.190 57.895 0.00 0.00 37.55 4.20
678 718 2.125961 GGGGAGTCGGCGTCAGTAT 61.126 63.158 6.85 0.00 0.00 2.12
729 773 1.581934 GCTGGCAATACGAGTGCATA 58.418 50.000 10.84 0.84 44.07 3.14
783 835 3.295093 TGTGCTCTGATAGAGAAGGAGG 58.705 50.000 9.89 0.00 45.07 4.30
842 908 5.610398 TCATAAGTCATAACGTGCATCCAT 58.390 37.500 0.00 0.00 0.00 3.41
859 925 4.323104 GGGGCAGATAAGGTAGCTCATAAG 60.323 50.000 0.00 0.00 0.00 1.73
860 926 3.583086 GGGGCAGATAAGGTAGCTCATAA 59.417 47.826 0.00 0.00 0.00 1.90
861 927 3.173965 GGGGCAGATAAGGTAGCTCATA 58.826 50.000 0.00 0.00 0.00 2.15
862 928 1.981495 GGGGCAGATAAGGTAGCTCAT 59.019 52.381 0.00 0.00 0.00 2.90
863 929 1.062121 AGGGGCAGATAAGGTAGCTCA 60.062 52.381 0.00 0.00 0.00 4.26
864 930 1.723288 AGGGGCAGATAAGGTAGCTC 58.277 55.000 0.00 0.00 0.00 4.09
865 931 2.050918 GAAGGGGCAGATAAGGTAGCT 58.949 52.381 0.00 0.00 0.00 3.32
873 943 1.112113 GACGTGAGAAGGGGCAGATA 58.888 55.000 0.00 0.00 0.00 1.98
950 1020 0.817634 TGCTTGGTTGGTGAAGGTCG 60.818 55.000 0.00 0.00 0.00 4.79
956 1026 1.398692 GTTTCCTGCTTGGTTGGTGA 58.601 50.000 0.00 0.00 37.07 4.02
963 1038 0.754957 TGTGTGGGTTTCCTGCTTGG 60.755 55.000 0.00 0.00 37.10 3.61
979 1054 4.838152 CGATCGGGGGTGGCTGTG 62.838 72.222 7.38 0.00 0.00 3.66
1053 1135 2.823147 GCAGAGCCGCTCATGCTT 60.823 61.111 25.25 5.64 39.69 3.91
1251 1333 3.137459 CAGACGAGCGCCTCCTCT 61.137 66.667 2.29 3.29 0.00 3.69
1328 1410 9.002600 TCCAATGTATATAAAATGTGCTAGCAG 57.997 33.333 20.03 0.00 0.00 4.24
1407 1492 9.171877 TGCCATGAAAAATTATTTGATTTACCC 57.828 29.630 0.00 0.00 0.00 3.69
1421 1506 9.233649 ACATCAACATAAATTGCCATGAAAAAT 57.766 25.926 0.00 0.00 0.00 1.82
1447 1532 8.450964 GTTCGTCAAGAAAATTTATCATCCTCA 58.549 33.333 0.00 0.00 41.10 3.86
1451 1536 7.216317 CGGTGTTCGTCAAGAAAATTTATCATC 59.784 37.037 0.00 0.00 41.10 2.92
1468 1553 8.770753 TTCTGTCAGAAAGTTACGGTGTTCGT 62.771 42.308 13.00 0.00 42.41 3.85
1471 1556 4.395959 TCTGTCAGAAAGTTACGGTGTT 57.604 40.909 0.00 0.00 0.00 3.32
1472 1557 4.395959 TTCTGTCAGAAAGTTACGGTGT 57.604 40.909 13.00 0.00 29.99 4.16
1475 1560 7.193595 ACAATTTTTCTGTCAGAAAGTTACGG 58.806 34.615 23.53 15.84 44.14 4.02
1476 1561 9.878599 ATACAATTTTTCTGTCAGAAAGTTACG 57.121 29.630 23.53 15.98 44.14 3.18
1482 1567 9.393249 CGCTTTATACAATTTTTCTGTCAGAAA 57.607 29.630 21.59 21.59 42.00 2.52
1484 1569 7.389330 TCCGCTTTATACAATTTTTCTGTCAGA 59.611 33.333 0.00 0.00 0.00 3.27
1488 1573 8.281212 AGATCCGCTTTATACAATTTTTCTGT 57.719 30.769 0.00 0.00 0.00 3.41
1498 1583 4.283467 AGCATGGTAGATCCGCTTTATACA 59.717 41.667 0.00 0.00 39.52 2.29
1499 1584 4.822026 AGCATGGTAGATCCGCTTTATAC 58.178 43.478 0.00 0.00 39.52 1.47
1501 1586 3.615110 CGAGCATGGTAGATCCGCTTTAT 60.615 47.826 0.00 0.00 39.52 1.40
1502 1587 2.288213 CGAGCATGGTAGATCCGCTTTA 60.288 50.000 0.00 0.00 39.52 1.85
1503 1588 1.539065 CGAGCATGGTAGATCCGCTTT 60.539 52.381 0.00 0.00 39.52 3.51
1504 1589 0.032678 CGAGCATGGTAGATCCGCTT 59.967 55.000 0.00 0.00 39.52 4.68
1505 1590 1.662608 CGAGCATGGTAGATCCGCT 59.337 57.895 0.00 0.00 39.52 5.52
1507 1595 1.373497 GGCGAGCATGGTAGATCCG 60.373 63.158 9.34 3.92 39.52 4.18
1512 1600 2.309528 TTAGTTGGCGAGCATGGTAG 57.690 50.000 0.00 0.00 0.00 3.18
1520 1608 1.398390 GTGGCAGATTTAGTTGGCGAG 59.602 52.381 0.00 0.00 42.25 5.03
1525 1613 2.421424 GCAGAGGTGGCAGATTTAGTTG 59.579 50.000 0.00 0.00 0.00 3.16
1527 1615 1.630369 TGCAGAGGTGGCAGATTTAGT 59.370 47.619 0.00 0.00 36.11 2.24
1528 1616 2.408271 TGCAGAGGTGGCAGATTTAG 57.592 50.000 0.00 0.00 36.11 1.85
1529 1617 2.819608 GTTTGCAGAGGTGGCAGATTTA 59.180 45.455 0.00 0.00 43.05 1.40
1534 1622 0.036732 TAGGTTTGCAGAGGTGGCAG 59.963 55.000 0.00 0.00 43.05 4.85
1537 1625 2.493278 CCAATTAGGTTTGCAGAGGTGG 59.507 50.000 0.00 0.00 0.00 4.61
1544 1632 2.533916 TCATGGCCAATTAGGTTTGCA 58.466 42.857 10.96 0.00 40.61 4.08
1555 1643 7.066766 GGCATGTTAAATATTTTTCATGGCCAA 59.933 33.333 32.23 12.30 42.33 4.52
1557 1645 6.767423 AGGCATGTTAAATATTTTTCATGGCC 59.233 34.615 34.73 29.87 45.10 5.36
1558 1646 7.790823 AGGCATGTTAAATATTTTTCATGGC 57.209 32.000 33.45 33.45 44.79 4.40
1575 1668 6.209192 TGTGAACATCAGAATTTTAGGCATGT 59.791 34.615 0.00 0.00 0.00 3.21
1578 1671 5.183713 CCTGTGAACATCAGAATTTTAGGCA 59.816 40.000 0.00 0.00 35.20 4.75
1583 1676 5.829924 ACTGTCCTGTGAACATCAGAATTTT 59.170 36.000 13.44 0.00 35.20 1.82
1587 1680 3.552890 CGACTGTCCTGTGAACATCAGAA 60.553 47.826 1.55 0.00 35.20 3.02
1593 1686 1.272490 GATCCGACTGTCCTGTGAACA 59.728 52.381 1.55 0.00 0.00 3.18
1594 1687 1.546476 AGATCCGACTGTCCTGTGAAC 59.454 52.381 1.55 0.00 0.00 3.18
1596 1689 2.801077 TAGATCCGACTGTCCTGTGA 57.199 50.000 1.55 0.00 0.00 3.58
1600 1693 8.968969 GGTAATAATAATAGATCCGACTGTCCT 58.031 37.037 1.55 0.00 0.00 3.85
1604 1697 8.456471 TCGTGGTAATAATAATAGATCCGACTG 58.544 37.037 0.00 0.00 0.00 3.51
1606 1699 8.457261 ACTCGTGGTAATAATAATAGATCCGAC 58.543 37.037 0.00 0.00 0.00 4.79
1609 1702 8.033038 TGCACTCGTGGTAATAATAATAGATCC 58.967 37.037 0.00 0.00 0.00 3.36
1614 1707 8.339714 GCTTTTGCACTCGTGGTAATAATAATA 58.660 33.333 0.00 0.00 46.58 0.98
1615 1708 7.193595 GCTTTTGCACTCGTGGTAATAATAAT 58.806 34.615 0.00 0.00 46.58 1.28
1644 1738 1.953559 TAAGAGATGGGCGTGCAATC 58.046 50.000 0.00 0.00 0.00 2.67
1646 1740 1.475034 GGATAAGAGATGGGCGTGCAA 60.475 52.381 0.00 0.00 0.00 4.08
1647 1741 0.106708 GGATAAGAGATGGGCGTGCA 59.893 55.000 0.00 0.00 0.00 4.57
1652 1755 3.555168 CGGTAGTTGGATAAGAGATGGGC 60.555 52.174 0.00 0.00 0.00 5.36
1682 1785 9.751542 ATATATCAAGGCAAAGCTATACGTATC 57.248 33.333 12.24 0.00 0.00 2.24
1686 1789 8.721478 ACAAATATATCAAGGCAAAGCTATACG 58.279 33.333 0.00 0.00 0.00 3.06
1696 1799 6.528537 AACAGCAACAAATATATCAAGGCA 57.471 33.333 0.00 0.00 0.00 4.75
1699 1802 7.276218 CCCACAAACAGCAACAAATATATCAAG 59.724 37.037 0.00 0.00 0.00 3.02
1715 1818 2.031120 TCTCCTTTTGCCCACAAACAG 58.969 47.619 0.00 0.00 45.29 3.16
1731 1834 5.659440 TGCAGAATTTTAATGGGTTCTCC 57.341 39.130 0.00 0.00 0.00 3.71
1732 1835 9.822185 AAATATGCAGAATTTTAATGGGTTCTC 57.178 29.630 4.41 0.00 0.00 2.87
1735 1838 8.547173 TCCAAATATGCAGAATTTTAATGGGTT 58.453 29.630 6.99 0.00 0.00 4.11
1737 1840 9.563748 AATCCAAATATGCAGAATTTTAATGGG 57.436 29.630 6.99 5.93 0.00 4.00
1760 1863 5.334724 AGGCTGAATGGTTTCATGAAATC 57.665 39.130 23.05 22.59 40.95 2.17
1765 1868 1.753073 GGGAGGCTGAATGGTTTCATG 59.247 52.381 0.00 0.00 40.95 3.07
1766 1869 1.342374 GGGGAGGCTGAATGGTTTCAT 60.342 52.381 0.00 0.00 40.95 2.57
1767 1870 0.039618 GGGGAGGCTGAATGGTTTCA 59.960 55.000 0.00 0.00 39.54 2.69
1769 1872 0.332972 GAGGGGAGGCTGAATGGTTT 59.667 55.000 0.00 0.00 0.00 3.27
1907 2020 2.972505 CGTCACAGCCACGCCTTT 60.973 61.111 0.00 0.00 0.00 3.11
1985 2098 4.202305 CCAAAGATAGAGGAGGTCACATCC 60.202 50.000 0.00 0.00 37.07 3.51
2002 2115 3.057019 CGACGATGAAGACAACCAAAGA 58.943 45.455 0.00 0.00 0.00 2.52
2038 2151 0.759812 TGAGGTAACACCCACCGACA 60.760 55.000 0.00 0.00 39.75 4.35
2059 2172 2.352805 CTCTGGGAAGCCACCACC 59.647 66.667 0.00 0.00 33.63 4.61
2060 2173 2.352805 CCTCTGGGAAGCCACCAC 59.647 66.667 0.00 0.00 33.63 4.16
2061 2174 2.121963 ACCTCTGGGAAGCCACCA 60.122 61.111 0.00 0.00 36.38 4.17
2075 2188 1.912043 CCTCCTTCACTTGATCCACCT 59.088 52.381 0.00 0.00 0.00 4.00
2104 2217 2.360852 CCACTTCAGCAGCTGGGG 60.361 66.667 22.62 16.55 31.51 4.96
2176 2289 3.717294 GACGCCCCCACCATCACT 61.717 66.667 0.00 0.00 0.00 3.41
2213 2326 2.843113 CCTTCAGATCTGAGGTTTCCCT 59.157 50.000 27.44 0.00 46.66 4.20
2231 2344 0.541863 CCGTCAATGGTAGCCTCCTT 59.458 55.000 0.00 0.00 0.00 3.36
2300 2413 1.220529 CGTCACCATCATCCAATCCG 58.779 55.000 0.00 0.00 0.00 4.18


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

AutoCloner maintained by Alex Coulton.