Multiple sequence alignment - TraesCS1A01G035300

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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 TraesCS1A01G035300 chr1A 100.000 2528 0 0 1 2528 18488023 18485496 0.000000e+00 4669
1 TraesCS1A01G035300 chr1D 92.441 1561 65 16 1 1537 17194967 17193436 0.000000e+00 2180
2 TraesCS1A01G035300 chr1D 85.241 996 90 26 1552 2527 17193476 17192518 0.000000e+00 972
3 TraesCS1A01G035300 chr1B 90.155 1290 77 14 285 1534 24989791 24988512 0.000000e+00 1633
4 TraesCS1A01G035300 chr1B 85.681 859 60 28 1558 2384 24988543 24987716 0.000000e+00 846
5 TraesCS1A01G035300 chr5B 88.462 520 57 1 1001 1520 612015077 612014561 2.140000e-175 625
6 TraesCS1A01G035300 chr3D 86.034 537 65 7 1001 1537 438604264 438603738 3.650000e-158 568
7 TraesCS1A01G035300 chr5D 87.324 497 57 2 1024 1520 495373539 495373049 4.720000e-157 564
8 TraesCS1A01G035300 chr5A 87.277 448 52 3 943 1390 619476694 619476252 8.070000e-140 507


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 TraesCS1A01G035300 chr1A 18485496 18488023 2527 True 4669.0 4669 100.000 1 2528 1 chr1A.!!$R1 2527
1 TraesCS1A01G035300 chr1D 17192518 17194967 2449 True 1576.0 2180 88.841 1 2527 2 chr1D.!!$R1 2526
2 TraesCS1A01G035300 chr1B 24987716 24989791 2075 True 1239.5 1633 87.918 285 2384 2 chr1B.!!$R1 2099
3 TraesCS1A01G035300 chr5B 612014561 612015077 516 True 625.0 625 88.462 1001 1520 1 chr5B.!!$R1 519
4 TraesCS1A01G035300 chr3D 438603738 438604264 526 True 568.0 568 86.034 1001 1537 1 chr3D.!!$R1 536

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
278 279 0.035056 AGGCTGTGATTAGTGGCCAC 60.035 55.0 29.22 29.22 44.60 5.01 F
1257 1311 0.036875 AGCCTAACAGCACCAAGGAC 59.963 55.0 0.00 0.00 34.23 3.85 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1407 1461 0.106819 CATCCTTCAGCCCTTCCTGG 60.107 60.0 0.0 0.0 33.64 4.45 R
2463 2556 0.105224 AATGACACAACACCCGTCGA 59.895 50.0 0.0 0.0 32.17 4.20 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
177 178 1.821136 GCTTCAGTTTCCCCATCTTGG 59.179 52.381 0.00 0.00 37.25 3.61
185 186 3.652057 TTCCCCATCTTGGAGTTGATC 57.348 47.619 0.00 0.00 40.96 2.92
206 207 1.216710 GTGGCTCTGTCTAAGCGCT 59.783 57.895 2.64 2.64 40.77 5.92
219 220 1.446907 AAGCGCTGGAGATGAACAAG 58.553 50.000 12.58 0.00 0.00 3.16
223 224 2.146342 CGCTGGAGATGAACAAGTGTT 58.854 47.619 0.00 0.00 41.64 3.32
248 249 4.082787 GCTGCTAGTTTTGTAATCCTGCAA 60.083 41.667 0.00 0.00 0.00 4.08
265 266 4.262164 CCTGCAATTTTTAGTTCAGGCTGT 60.262 41.667 15.27 0.00 35.29 4.40
278 279 0.035056 AGGCTGTGATTAGTGGCCAC 60.035 55.000 29.22 29.22 44.60 5.01
347 348 1.339055 CCCGAAAAGGCTCAGATGACA 60.339 52.381 0.00 0.00 39.21 3.58
353 354 3.996921 AAGGCTCAGATGACATTCACT 57.003 42.857 0.00 0.00 0.00 3.41
376 377 3.999705 CTGCCCCTCTCCTCCTGCT 63.000 68.421 0.00 0.00 0.00 4.24
431 432 4.394712 CTGGGGGTGTCACCGAGC 62.395 72.222 15.93 2.07 39.83 5.03
456 466 1.134965 CGTTGCCTCTAGGACTCAAGG 60.135 57.143 0.00 0.00 37.39 3.61
457 467 2.180276 GTTGCCTCTAGGACTCAAGGA 58.820 52.381 0.00 0.00 37.39 3.36
458 468 2.151502 TGCCTCTAGGACTCAAGGAG 57.848 55.000 0.00 0.00 37.39 3.69
459 469 1.342474 TGCCTCTAGGACTCAAGGAGG 60.342 57.143 0.00 0.00 44.41 4.30
460 470 1.408969 CCTCTAGGACTCAAGGAGGC 58.591 60.000 0.00 0.00 37.37 4.70
557 576 4.641541 TCTGATTGTTTCATGCAGTATGGG 59.358 41.667 0.00 0.00 37.39 4.00
559 578 4.398988 TGATTGTTTCATGCAGTATGGGTC 59.601 41.667 0.00 0.00 37.39 4.46
588 607 2.304761 ACGTGGTATGGGTTTGTGATCT 59.695 45.455 0.00 0.00 0.00 2.75
589 608 3.244770 ACGTGGTATGGGTTTGTGATCTT 60.245 43.478 0.00 0.00 0.00 2.40
590 609 3.374058 CGTGGTATGGGTTTGTGATCTTC 59.626 47.826 0.00 0.00 0.00 2.87
591 610 4.589908 GTGGTATGGGTTTGTGATCTTCT 58.410 43.478 0.00 0.00 0.00 2.85
592 611 4.396166 GTGGTATGGGTTTGTGATCTTCTG 59.604 45.833 0.00 0.00 0.00 3.02
593 612 4.042809 TGGTATGGGTTTGTGATCTTCTGT 59.957 41.667 0.00 0.00 0.00 3.41
594 613 5.010282 GGTATGGGTTTGTGATCTTCTGTT 58.990 41.667 0.00 0.00 0.00 3.16
595 614 6.177610 GGTATGGGTTTGTGATCTTCTGTTA 58.822 40.000 0.00 0.00 0.00 2.41
596 615 6.093633 GGTATGGGTTTGTGATCTTCTGTTAC 59.906 42.308 0.00 0.00 0.00 2.50
597 616 4.062293 TGGGTTTGTGATCTTCTGTTACG 58.938 43.478 0.00 0.00 0.00 3.18
681 700 1.479323 ACGCTTAGCTAAATCCGTGGA 59.521 47.619 19.38 0.00 0.00 4.02
732 751 5.546499 AGGTGTTTGATAAAGTCCCTCTGTA 59.454 40.000 0.00 0.00 0.00 2.74
736 755 7.606456 GTGTTTGATAAAGTCCCTCTGTAATGA 59.394 37.037 0.00 0.00 0.00 2.57
759 778 1.956477 ACACTGAATGGGTGCTTTGTC 59.044 47.619 0.00 0.00 38.14 3.18
808 827 1.909700 AACTCGCACATGGTTTCCAT 58.090 45.000 0.00 0.00 46.37 3.41
838 857 1.434622 GCCACATCGCATCCTGAGTG 61.435 60.000 0.00 0.00 0.00 3.51
860 879 2.093869 CAGGCTTACCATTTGCAGCAAT 60.094 45.455 9.12 0.00 39.06 3.56
873 892 2.223782 TGCAGCAATTTCACTGTGTTCC 60.224 45.455 7.79 0.00 36.26 3.62
935 983 6.940739 ACTTGATACACTATGCTCTTCTTGT 58.059 36.000 0.00 0.00 0.00 3.16
967 1015 3.999001 GGTTAATTAATCGTCGATCCCCC 59.001 47.826 8.45 0.00 0.00 5.40
986 1034 2.188817 CCTAAGGAGGTTGCTGTAGGT 58.811 52.381 0.00 0.00 38.16 3.08
1257 1311 0.036875 AGCCTAACAGCACCAAGGAC 59.963 55.000 0.00 0.00 34.23 3.85
1296 1350 3.265479 AGCCTAGTTTGCTTGAGGATCTT 59.735 43.478 0.00 0.00 34.87 2.40
1407 1461 5.419471 AGTGAAGAACTATGTGGAGACCTAC 59.581 44.000 0.00 0.00 37.36 3.18
1496 1550 2.267961 GGGACCATCGACACCACC 59.732 66.667 0.00 0.00 0.00 4.61
1497 1551 2.291043 GGGACCATCGACACCACCT 61.291 63.158 0.00 0.00 0.00 4.00
1498 1552 1.218316 GGACCATCGACACCACCTC 59.782 63.158 0.00 0.00 0.00 3.85
1499 1553 1.218316 GACCATCGACACCACCTCC 59.782 63.158 0.00 0.00 0.00 4.30
1500 1554 1.535444 ACCATCGACACCACCTCCA 60.535 57.895 0.00 0.00 0.00 3.86
1501 1555 1.079127 CCATCGACACCACCTCCAC 60.079 63.158 0.00 0.00 0.00 4.02
1502 1556 1.079127 CATCGACACCACCTCCACC 60.079 63.158 0.00 0.00 0.00 4.61
1503 1557 1.535444 ATCGACACCACCTCCACCA 60.535 57.895 0.00 0.00 0.00 4.17
1504 1558 1.827399 ATCGACACCACCTCCACCAC 61.827 60.000 0.00 0.00 0.00 4.16
1505 1559 2.430367 GACACCACCTCCACCACC 59.570 66.667 0.00 0.00 0.00 4.61
1506 1560 3.530910 GACACCACCTCCACCACCG 62.531 68.421 0.00 0.00 0.00 4.94
1520 1574 4.856801 ACCGCCACCGCCATCATC 62.857 66.667 0.00 0.00 0.00 2.92
1523 1577 3.272334 GCCACCGCCATCATCGTC 61.272 66.667 0.00 0.00 0.00 4.20
1524 1578 2.186644 CCACCGCCATCATCGTCA 59.813 61.111 0.00 0.00 0.00 4.35
1525 1579 1.227645 CCACCGCCATCATCGTCAT 60.228 57.895 0.00 0.00 0.00 3.06
1526 1580 1.501337 CCACCGCCATCATCGTCATG 61.501 60.000 0.00 0.00 0.00 3.07
1527 1581 0.530431 CACCGCCATCATCGTCATGA 60.530 55.000 0.00 0.00 43.45 3.07
1528 1582 0.530650 ACCGCCATCATCGTCATGAC 60.531 55.000 16.21 16.21 42.05 3.06
1529 1583 1.224069 CCGCCATCATCGTCATGACC 61.224 60.000 20.03 2.51 42.05 4.02
1530 1584 0.249615 CGCCATCATCGTCATGACCT 60.250 55.000 20.03 5.02 42.05 3.85
1531 1585 1.807755 CGCCATCATCGTCATGACCTT 60.808 52.381 20.03 4.83 42.05 3.50
1532 1586 1.600957 GCCATCATCGTCATGACCTTG 59.399 52.381 20.03 16.50 42.05 3.61
1533 1587 2.910199 CCATCATCGTCATGACCTTGT 58.090 47.619 20.03 6.21 42.05 3.16
1534 1588 3.741075 GCCATCATCGTCATGACCTTGTA 60.741 47.826 20.03 8.29 42.05 2.41
1535 1589 4.635223 CCATCATCGTCATGACCTTGTAT 58.365 43.478 20.03 9.89 42.05 2.29
1536 1590 4.687948 CCATCATCGTCATGACCTTGTATC 59.312 45.833 20.03 0.00 42.05 2.24
1537 1591 3.964909 TCATCGTCATGACCTTGTATCG 58.035 45.455 20.03 6.03 33.80 2.92
1538 1592 3.630312 TCATCGTCATGACCTTGTATCGA 59.370 43.478 20.03 11.36 33.80 3.59
1539 1593 3.416119 TCGTCATGACCTTGTATCGAC 57.584 47.619 20.03 0.00 0.00 4.20
1540 1594 2.109463 CGTCATGACCTTGTATCGACG 58.891 52.381 20.03 0.46 38.79 5.12
1541 1595 1.852895 GTCATGACCTTGTATCGACGC 59.147 52.381 15.31 0.00 0.00 5.19
1542 1596 1.202371 TCATGACCTTGTATCGACGCC 60.202 52.381 0.00 0.00 0.00 5.68
1543 1597 0.821517 ATGACCTTGTATCGACGCCA 59.178 50.000 0.00 0.00 0.00 5.69
1544 1598 0.108992 TGACCTTGTATCGACGCCAC 60.109 55.000 0.00 0.00 0.00 5.01
1545 1599 0.804933 GACCTTGTATCGACGCCACC 60.805 60.000 0.00 0.00 0.00 4.61
1546 1600 1.255667 ACCTTGTATCGACGCCACCT 61.256 55.000 0.00 0.00 0.00 4.00
1547 1601 0.527817 CCTTGTATCGACGCCACCTC 60.528 60.000 0.00 0.00 0.00 3.85
1548 1602 0.527817 CTTGTATCGACGCCACCTCC 60.528 60.000 0.00 0.00 0.00 4.30
1549 1603 1.252215 TTGTATCGACGCCACCTCCA 61.252 55.000 0.00 0.00 0.00 3.86
1550 1604 1.226888 GTATCGACGCCACCTCCAC 60.227 63.158 0.00 0.00 0.00 4.02
1551 1605 2.420568 TATCGACGCCACCTCCACC 61.421 63.158 0.00 0.00 0.00 4.61
1631 1692 7.928307 TTATCATTAGAACTTGCAGCTTCTT 57.072 32.000 11.91 0.00 0.00 2.52
1669 1730 3.402628 TCAGAAGTTGGGTAGAACAGC 57.597 47.619 0.00 0.00 0.00 4.40
1670 1731 2.972713 TCAGAAGTTGGGTAGAACAGCT 59.027 45.455 0.00 0.00 0.00 4.24
1678 1739 2.829720 TGGGTAGAACAGCTAACGATGT 59.170 45.455 0.00 0.00 42.50 3.06
1720 1784 8.558973 AAAAAGATCTTCATGAGTAGGTCTTG 57.441 34.615 19.17 0.00 40.44 3.02
1773 1837 5.285651 GTGACCTACACTGCTATGAAGATC 58.714 45.833 0.00 0.00 45.13 2.75
1798 1862 0.179059 TCAGCTTGTCTCGGTTGCAA 60.179 50.000 0.00 0.00 0.00 4.08
1820 1884 2.837591 TCATTCCCTTCTCCATCGACAA 59.162 45.455 0.00 0.00 0.00 3.18
1850 1915 3.450028 CCTTCTAGGCTGTGTGCTC 57.550 57.895 0.00 0.00 42.39 4.26
1851 1916 0.901124 CCTTCTAGGCTGTGTGCTCT 59.099 55.000 0.00 0.00 42.39 4.09
1852 1917 1.277557 CCTTCTAGGCTGTGTGCTCTT 59.722 52.381 0.00 0.00 42.39 2.85
1853 1918 2.344950 CTTCTAGGCTGTGTGCTCTTG 58.655 52.381 0.00 0.00 42.39 3.02
1854 1919 0.036952 TCTAGGCTGTGTGCTCTTGC 60.037 55.000 0.00 0.00 42.39 4.01
1855 1920 1.003355 TAGGCTGTGTGCTCTTGCC 60.003 57.895 0.00 0.00 43.52 4.52
1862 1929 1.238439 GTGTGCTCTTGCCTTGCTAA 58.762 50.000 0.00 0.00 38.71 3.09
1893 1963 2.629017 AGGCCCATCCTGTCATTTTT 57.371 45.000 0.00 0.00 45.54 1.94
1937 2015 3.367025 CCTTGATCGTCGTTGGTACTTTC 59.633 47.826 0.00 0.00 0.00 2.62
1942 2020 3.411446 TCGTCGTTGGTACTTTCTAGGA 58.589 45.455 0.00 0.00 0.00 2.94
1979 2057 3.885724 TGAACGAGATGCCATTCACTA 57.114 42.857 0.00 0.00 0.00 2.74
1984 2062 2.096565 CGAGATGCCATTCACTATTGCG 60.097 50.000 0.00 0.00 0.00 4.85
1986 2064 2.158769 AGATGCCATTCACTATTGCGGA 60.159 45.455 0.00 0.00 0.00 5.54
2048 2127 0.956633 CTTGTTCATGTGCTGCTGGT 59.043 50.000 0.00 0.00 0.00 4.00
2051 2130 0.801251 GTTCATGTGCTGCTGGTCTC 59.199 55.000 0.00 0.00 0.00 3.36
2112 2191 0.891373 GCTGCAGAGTACAGAGGTCA 59.109 55.000 20.43 0.00 37.32 4.02
2119 2198 3.894427 CAGAGTACAGAGGTCAGCCATAT 59.106 47.826 0.00 0.00 37.19 1.78
2120 2199 5.073428 CAGAGTACAGAGGTCAGCCATATA 58.927 45.833 0.00 0.00 37.19 0.86
2123 2202 6.210385 AGAGTACAGAGGTCAGCCATATAATG 59.790 42.308 0.00 0.00 37.19 1.90
2128 2207 5.481824 CAGAGGTCAGCCATATAATGTCCTA 59.518 44.000 0.00 0.00 33.48 2.94
2230 2311 1.070758 CTGCCTGGTCGCCATATAGTT 59.929 52.381 0.00 0.00 30.82 2.24
2302 2395 2.624364 TCGTGGTTGCTGTAGTCTAACA 59.376 45.455 0.00 0.00 0.00 2.41
2328 2421 0.034476 TCTCTGCAGTGCCTGACAAG 59.966 55.000 14.67 1.71 32.44 3.16
2329 2422 0.250209 CTCTGCAGTGCCTGACAAGT 60.250 55.000 14.67 0.00 32.44 3.16
2391 2484 2.831366 GCAGCGTAGTCCGATCCGA 61.831 63.158 0.00 0.00 39.56 4.55
2392 2485 1.009900 CAGCGTAGTCCGATCCGAC 60.010 63.158 6.12 6.12 39.56 4.79
2417 2510 1.708993 TTGTCCTTGCAGCAGGAGGT 61.709 55.000 7.42 0.00 44.11 3.85
2427 2520 2.467880 CAGCAGGAGGTCTAGGGTTTA 58.532 52.381 0.00 0.00 0.00 2.01
2430 2523 2.093606 GCAGGAGGTCTAGGGTTTACAC 60.094 54.545 0.00 0.00 0.00 2.90
2433 2526 4.081586 CAGGAGGTCTAGGGTTTACACTTC 60.082 50.000 0.00 0.00 0.00 3.01
2440 2533 6.035217 GTCTAGGGTTTACACTTCGAATCTC 58.965 44.000 0.00 0.00 0.00 2.75
2441 2534 5.950549 TCTAGGGTTTACACTTCGAATCTCT 59.049 40.000 0.00 0.00 0.00 3.10
2442 2535 5.074584 AGGGTTTACACTTCGAATCTCTC 57.925 43.478 0.00 0.00 0.00 3.20
2506 2599 2.261361 CGTGGCGGTCACATCTCA 59.739 61.111 13.79 0.00 46.36 3.27
2509 2602 1.453155 GTGGCGGTCACATCTCAAAT 58.547 50.000 8.05 0.00 45.39 2.32
2511 2604 1.017387 GGCGGTCACATCTCAAATCC 58.983 55.000 0.00 0.00 0.00 3.01
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
177 178 2.021355 CAGAGCCACTGGATCAACTC 57.979 55.000 15.72 4.06 41.08 3.01
188 189 3.787458 GCGCTTAGACAGAGCCAC 58.213 61.111 0.00 0.00 42.30 5.01
206 207 3.316029 CAGCAAACACTTGTTCATCTCCA 59.684 43.478 0.00 0.00 37.25 3.86
219 220 5.629435 GGATTACAAAACTAGCAGCAAACAC 59.371 40.000 0.00 0.00 0.00 3.32
223 224 4.082787 GCAGGATTACAAAACTAGCAGCAA 60.083 41.667 0.00 0.00 0.00 3.91
248 249 7.094205 CCACTAATCACAGCCTGAACTAAAAAT 60.094 37.037 0.00 0.00 30.60 1.82
265 266 2.125310 CCGCGTGGCCACTAATCA 60.125 61.111 32.28 0.00 0.00 2.57
347 348 0.326264 GAGGGGCAGTGACAGTGAAT 59.674 55.000 14.64 0.00 0.00 2.57
353 354 1.610673 GAGGAGAGGGGCAGTGACA 60.611 63.158 0.00 0.00 0.00 3.58
362 363 1.342819 CGATTTAGCAGGAGGAGAGGG 59.657 57.143 0.00 0.00 0.00 4.30
376 377 1.143183 GCGAGTGGGAGGCGATTTA 59.857 57.895 0.00 0.00 0.00 1.40
398 399 3.444805 AGAGCCCAGAGTCGACGC 61.445 66.667 11.72 11.72 0.00 5.19
431 432 2.050350 TCCTAGAGGCAACGTCGGG 61.050 63.158 0.00 0.00 46.39 5.14
438 439 2.461695 CTCCTTGAGTCCTAGAGGCAA 58.538 52.381 0.00 0.00 34.44 4.52
456 466 1.471851 GCCTAGAAAGAAGGTCGCCTC 60.472 57.143 0.00 0.00 36.43 4.70
457 467 0.537653 GCCTAGAAAGAAGGTCGCCT 59.462 55.000 0.00 0.00 36.43 5.52
458 468 0.537653 AGCCTAGAAAGAAGGTCGCC 59.462 55.000 0.00 0.00 36.43 5.54
459 469 2.388310 AAGCCTAGAAAGAAGGTCGC 57.612 50.000 0.00 0.00 36.43 5.19
460 470 4.722361 AGTAAGCCTAGAAAGAAGGTCG 57.278 45.455 0.00 0.00 36.43 4.79
495 514 7.572168 GCTCAGTTTCTGGACAGAGAAATTAAC 60.572 40.741 1.92 3.63 42.49 2.01
496 515 6.428159 GCTCAGTTTCTGGACAGAGAAATTAA 59.572 38.462 1.92 0.00 42.49 1.40
497 516 5.934625 GCTCAGTTTCTGGACAGAGAAATTA 59.065 40.000 1.92 0.00 42.49 1.40
498 517 4.759183 GCTCAGTTTCTGGACAGAGAAATT 59.241 41.667 1.92 0.00 42.49 1.82
499 518 4.322567 GCTCAGTTTCTGGACAGAGAAAT 58.677 43.478 1.92 0.00 42.49 2.17
500 519 3.495100 GGCTCAGTTTCTGGACAGAGAAA 60.495 47.826 1.92 0.00 39.20 2.52
501 520 2.037772 GGCTCAGTTTCTGGACAGAGAA 59.962 50.000 1.92 0.00 38.88 2.87
502 521 1.620819 GGCTCAGTTTCTGGACAGAGA 59.379 52.381 1.92 0.00 38.88 3.10
503 522 1.622811 AGGCTCAGTTTCTGGACAGAG 59.377 52.381 1.92 0.00 38.88 3.35
557 576 3.118884 ACCCATACCACGTGAATACAGAC 60.119 47.826 19.30 0.00 0.00 3.51
559 578 3.536956 ACCCATACCACGTGAATACAG 57.463 47.619 19.30 0.71 0.00 2.74
588 607 7.249147 GCTCTCTTATACAGAACGTAACAGAA 58.751 38.462 0.00 0.00 32.59 3.02
589 608 6.456584 CGCTCTCTTATACAGAACGTAACAGA 60.457 42.308 0.00 0.00 32.59 3.41
590 609 5.677612 CGCTCTCTTATACAGAACGTAACAG 59.322 44.000 0.00 0.00 32.59 3.16
591 610 5.122869 ACGCTCTCTTATACAGAACGTAACA 59.877 40.000 7.31 0.00 35.14 2.41
592 611 5.567552 ACGCTCTCTTATACAGAACGTAAC 58.432 41.667 7.31 0.00 35.14 2.50
593 612 5.220739 GGACGCTCTCTTATACAGAACGTAA 60.221 44.000 8.58 0.00 36.35 3.18
594 613 4.272018 GGACGCTCTCTTATACAGAACGTA 59.728 45.833 8.58 0.00 36.35 3.57
595 614 3.065095 GGACGCTCTCTTATACAGAACGT 59.935 47.826 8.41 8.41 37.98 3.99
596 615 3.064958 TGGACGCTCTCTTATACAGAACG 59.935 47.826 3.26 3.26 0.00 3.95
597 616 4.634184 TGGACGCTCTCTTATACAGAAC 57.366 45.455 0.00 0.00 0.00 3.01
681 700 6.819146 GCCTACATAAGCAAAGTAAAGAGAGT 59.181 38.462 0.00 0.00 0.00 3.24
732 751 2.297033 GCACCCATTCAGTGTGTTCATT 59.703 45.455 0.00 0.00 37.56 2.57
736 755 2.071778 AAGCACCCATTCAGTGTGTT 57.928 45.000 0.00 0.00 37.56 3.32
759 778 1.238439 AACTGGATGTCCTGCAAACG 58.762 50.000 5.91 0.00 38.38 3.60
808 827 2.822561 TGCGATGTGGCAGGAAATTTTA 59.177 40.909 0.00 0.00 38.17 1.52
838 857 0.459063 GCTGCAAATGGTAAGCCTGC 60.459 55.000 0.00 0.00 34.97 4.85
860 879 5.120399 ACAATAAGACGGAACACAGTGAAA 58.880 37.500 7.81 0.00 0.00 2.69
903 922 6.109359 AGCATAGTGTATCAAGTCTTTGGAC 58.891 40.000 0.00 0.00 42.41 4.02
910 929 7.038659 ACAAGAAGAGCATAGTGTATCAAGTC 58.961 38.462 0.00 0.00 0.00 3.01
911 930 6.940739 ACAAGAAGAGCATAGTGTATCAAGT 58.059 36.000 0.00 0.00 0.00 3.16
915 959 6.640499 CAGCTACAAGAAGAGCATAGTGTATC 59.360 42.308 0.00 0.00 41.36 2.24
917 961 5.419155 ACAGCTACAAGAAGAGCATAGTGTA 59.581 40.000 0.00 0.00 41.36 2.90
920 964 4.753233 CACAGCTACAAGAAGAGCATAGT 58.247 43.478 0.00 0.00 41.36 2.12
935 983 5.424757 ACGATTAATTAACCTGCACAGCTA 58.575 37.500 0.00 0.00 0.00 3.32
967 1015 2.678190 GCACCTACAGCAACCTCCTTAG 60.678 54.545 0.00 0.00 0.00 2.18
986 1034 4.761227 TGAACTTCATGCTACTTGATTGCA 59.239 37.500 0.00 0.00 43.40 4.08
1257 1311 3.146847 AGGCTCACTTTTAGTTTTCCCG 58.853 45.455 0.00 0.00 0.00 5.14
1407 1461 0.106819 CATCCTTCAGCCCTTCCTGG 60.107 60.000 0.00 0.00 33.64 4.45
1503 1557 4.856801 GATGATGGCGGTGGCGGT 62.857 66.667 0.00 0.00 41.24 5.68
1506 1560 3.272334 GACGATGATGGCGGTGGC 61.272 66.667 0.00 0.00 38.90 5.01
1507 1561 1.227645 ATGACGATGATGGCGGTGG 60.228 57.895 0.00 0.00 0.00 4.61
1508 1562 0.530431 TCATGACGATGATGGCGGTG 60.530 55.000 0.00 0.00 33.40 4.94
1509 1563 0.530650 GTCATGACGATGATGGCGGT 60.531 55.000 10.69 0.00 40.78 5.68
1510 1564 1.224069 GGTCATGACGATGATGGCGG 61.224 60.000 19.33 0.00 40.78 6.13
1511 1565 0.249615 AGGTCATGACGATGATGGCG 60.250 55.000 19.33 0.00 40.78 5.69
1512 1566 1.600957 CAAGGTCATGACGATGATGGC 59.399 52.381 19.33 3.21 40.78 4.40
1513 1567 2.910199 ACAAGGTCATGACGATGATGG 58.090 47.619 26.81 13.01 40.78 3.51
1514 1568 4.383948 CGATACAAGGTCATGACGATGATG 59.616 45.833 26.81 18.93 40.78 3.07
1515 1569 4.278419 TCGATACAAGGTCATGACGATGAT 59.722 41.667 26.81 18.24 40.78 2.45
1516 1570 3.630312 TCGATACAAGGTCATGACGATGA 59.370 43.478 26.81 15.47 36.16 2.92
1517 1571 3.731216 GTCGATACAAGGTCATGACGATG 59.269 47.826 19.33 20.51 0.00 3.84
1518 1572 3.966154 GTCGATACAAGGTCATGACGAT 58.034 45.455 19.33 8.03 0.00 3.73
1519 1573 3.416119 GTCGATACAAGGTCATGACGA 57.584 47.619 19.33 8.14 0.00 4.20
1520 1574 2.109463 CGTCGATACAAGGTCATGACG 58.891 52.381 19.33 8.60 41.15 4.35
1521 1575 1.852895 GCGTCGATACAAGGTCATGAC 59.147 52.381 17.91 17.91 0.00 3.06
1522 1576 1.202371 GGCGTCGATACAAGGTCATGA 60.202 52.381 0.00 0.00 0.00 3.07
1523 1577 1.209128 GGCGTCGATACAAGGTCATG 58.791 55.000 0.00 0.00 0.00 3.07
1524 1578 0.821517 TGGCGTCGATACAAGGTCAT 59.178 50.000 0.00 0.00 0.00 3.06
1525 1579 0.108992 GTGGCGTCGATACAAGGTCA 60.109 55.000 0.00 0.00 0.00 4.02
1526 1580 0.804933 GGTGGCGTCGATACAAGGTC 60.805 60.000 0.00 0.00 0.00 3.85
1527 1581 1.217244 GGTGGCGTCGATACAAGGT 59.783 57.895 0.00 0.00 0.00 3.50
1528 1582 0.527817 GAGGTGGCGTCGATACAAGG 60.528 60.000 0.00 0.00 0.00 3.61
1529 1583 0.527817 GGAGGTGGCGTCGATACAAG 60.528 60.000 0.00 0.00 0.00 3.16
1530 1584 1.252215 TGGAGGTGGCGTCGATACAA 61.252 55.000 0.00 0.00 0.00 2.41
1531 1585 1.679641 TGGAGGTGGCGTCGATACA 60.680 57.895 0.00 0.00 0.00 2.29
1532 1586 1.226888 GTGGAGGTGGCGTCGATAC 60.227 63.158 0.00 0.00 0.00 2.24
1533 1587 2.420568 GGTGGAGGTGGCGTCGATA 61.421 63.158 0.00 0.00 0.00 2.92
1534 1588 3.771160 GGTGGAGGTGGCGTCGAT 61.771 66.667 0.00 0.00 0.00 3.59
1537 1591 4.699522 GGTGGTGGAGGTGGCGTC 62.700 72.222 0.00 0.00 0.00 5.19
1564 1624 0.249615 CTCATGACGATGATGGCGGT 60.250 55.000 0.00 0.00 37.97 5.68
1621 1682 9.618890 AAGAGAATATATAAACAAGAAGCTGCA 57.381 29.630 1.02 0.00 0.00 4.41
1642 1703 6.724441 TGTTCTACCCAACTTCTGATAAGAGA 59.276 38.462 0.00 0.00 0.00 3.10
1657 1718 2.829720 ACATCGTTAGCTGTTCTACCCA 59.170 45.455 0.00 0.00 0.00 4.51
1669 1730 3.242543 GGAAATGAGCAGCACATCGTTAG 60.243 47.826 5.73 0.00 0.00 2.34
1670 1731 2.677836 GGAAATGAGCAGCACATCGTTA 59.322 45.455 5.73 0.00 0.00 3.18
1700 1764 5.596845 GTCCAAGACCTACTCATGAAGATC 58.403 45.833 0.00 0.00 0.00 2.75
1724 1788 2.562635 CCAGATCAGCAGATGGACAAG 58.437 52.381 0.00 0.00 33.72 3.16
1773 1837 1.063806 CCGAGACAAGCTGAAGAACG 58.936 55.000 0.00 0.00 0.00 3.95
1798 1862 3.041211 TGTCGATGGAGAAGGGAATGAT 58.959 45.455 0.00 0.00 0.00 2.45
1820 1884 1.202268 CCTAGAAGGCGTCGATTTCGT 60.202 52.381 0.00 0.00 40.80 3.85
1850 1915 4.681744 TGTTTCTGTTTTAGCAAGGCAAG 58.318 39.130 0.00 0.00 0.00 4.01
1851 1916 4.727507 TGTTTCTGTTTTAGCAAGGCAA 57.272 36.364 0.00 0.00 0.00 4.52
1852 1917 4.727507 TTGTTTCTGTTTTAGCAAGGCA 57.272 36.364 0.00 0.00 0.00 4.75
1853 1918 4.507756 CCTTTGTTTCTGTTTTAGCAAGGC 59.492 41.667 0.00 0.00 0.00 4.35
1854 1919 4.507756 GCCTTTGTTTCTGTTTTAGCAAGG 59.492 41.667 0.00 0.00 0.00 3.61
1855 1920 4.507756 GGCCTTTGTTTCTGTTTTAGCAAG 59.492 41.667 0.00 0.00 0.00 4.01
1862 1929 2.368548 GGATGGGCCTTTGTTTCTGTTT 59.631 45.455 4.53 0.00 0.00 2.83
1893 1963 3.243035 GGCGCACATTGCAGATACATAAA 60.243 43.478 10.83 0.00 45.36 1.40
1896 1966 0.664761 GGCGCACATTGCAGATACAT 59.335 50.000 10.83 0.00 45.36 2.29
1897 1967 1.375853 GGGCGCACATTGCAGATACA 61.376 55.000 10.83 0.00 45.36 2.29
1898 1968 1.097547 AGGGCGCACATTGCAGATAC 61.098 55.000 14.57 0.00 45.36 2.24
1900 1970 1.679977 AAGGGCGCACATTGCAGAT 60.680 52.632 14.57 0.00 45.36 2.90
1937 2015 6.108687 TCAAATACTGTGCTTGTCATCCTAG 58.891 40.000 0.00 0.00 0.00 3.02
1942 2020 4.754618 TCGTTCAAATACTGTGCTTGTCAT 59.245 37.500 0.00 0.00 0.00 3.06
1979 2057 5.220854 GCAGACATACAAATAAGTCCGCAAT 60.221 40.000 0.00 0.00 34.18 3.56
1984 2062 8.391106 CAACTAAGCAGACATACAAATAAGTCC 58.609 37.037 0.00 0.00 30.73 3.85
1986 2064 8.721478 CACAACTAAGCAGACATACAAATAAGT 58.279 33.333 0.00 0.00 0.00 2.24
2048 2127 2.201921 ACAGCTCACCTAACTCGAGA 57.798 50.000 21.68 0.00 0.00 4.04
2051 2130 2.732597 GCAGTACAGCTCACCTAACTCG 60.733 54.545 2.52 0.00 0.00 4.18
2152 2231 5.163499 TGCTTGGTACCCTACAAACAAAAAG 60.163 40.000 10.07 2.69 0.00 2.27
2191 2272 6.769341 CAGGCAGATATATAATAAGCCATGCA 59.231 38.462 16.35 0.00 42.90 3.96
2192 2273 6.206243 CCAGGCAGATATATAATAAGCCATGC 59.794 42.308 16.35 0.00 42.90 4.06
2230 2311 9.990868 TGTACTGCTAGATATATAGATTTGGGA 57.009 33.333 8.58 0.00 0.00 4.37
2257 2342 7.425224 ACTAAGCCTACATCAATCAGTAACT 57.575 36.000 0.00 0.00 0.00 2.24
2302 2395 1.373999 GCACTGCAGAGACGAGCTT 60.374 57.895 23.35 0.00 0.00 3.74
2345 2438 1.856597 GTACAGTTTCGACACGTTGCT 59.143 47.619 4.93 0.00 0.00 3.91
2391 2484 1.959085 CTGCAAGGACAAATGGCGT 59.041 52.632 0.00 0.00 0.00 5.68
2392 2485 1.444895 GCTGCAAGGACAAATGGCG 60.445 57.895 0.00 0.00 0.00 5.69
2417 2510 5.950549 AGAGATTCGAAGTGTAAACCCTAGA 59.049 40.000 3.35 0.00 0.00 2.43
2440 2533 9.459640 TCGACTATATTATTTCCAAACTTCGAG 57.540 33.333 0.00 0.00 0.00 4.04
2441 2534 9.241317 GTCGACTATATTATTTCCAAACTTCGA 57.759 33.333 8.70 0.00 0.00 3.71
2442 2535 8.205948 CGTCGACTATATTATTTCCAAACTTCG 58.794 37.037 14.70 0.00 0.00 3.79
2443 2536 8.485591 CCGTCGACTATATTATTTCCAAACTTC 58.514 37.037 14.70 0.00 0.00 3.01
2444 2537 7.440255 CCCGTCGACTATATTATTTCCAAACTT 59.560 37.037 14.70 0.00 0.00 2.66
2446 2539 6.703165 ACCCGTCGACTATATTATTTCCAAAC 59.297 38.462 14.70 0.00 0.00 2.93
2447 2540 6.702723 CACCCGTCGACTATATTATTTCCAAA 59.297 38.462 14.70 0.00 0.00 3.28
2463 2556 0.105224 AATGACACAACACCCGTCGA 59.895 50.000 0.00 0.00 32.17 4.20
2464 2557 0.941542 AAATGACACAACACCCGTCG 59.058 50.000 0.00 0.00 32.17 5.12
2506 2599 1.642513 GGCCCTAGGGGTTCGGATTT 61.643 60.000 29.57 0.00 46.51 2.17
2509 2602 3.262778 AAGGCCCTAGGGGTTCGGA 62.263 63.158 29.57 0.00 46.51 4.55


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

AutoCloner maintained by Alex Coulton.