Multiple sequence alignment - TraesCS6A01G055400

Loading Multiple Alignment...

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 TraesCS6A01G055400 chr6A 100.000 2312 0 0 1 2312 29080969 29083280 0.000000e+00 4270.0
1 TraesCS6A01G055400 chr6A 88.779 606 43 19 730 1319 31264731 31264135 0.000000e+00 719.0
2 TraesCS6A01G055400 chr6A 88.213 526 40 18 736 1244 28773810 28773290 1.960000e-170 608.0
3 TraesCS6A01G055400 chr6A 84.615 169 17 3 1368 1536 28772894 28772735 2.380000e-35 159.0
4 TraesCS6A01G055400 chr6A 82.857 175 23 7 1568 1736 28772808 28772635 1.430000e-32 150.0
5 TraesCS6A01G055400 chrUn 90.055 1086 51 20 476 1539 103527969 103526919 0.000000e+00 1354.0
6 TraesCS6A01G055400 chrUn 90.280 607 39 15 730 1319 103772388 103771785 0.000000e+00 776.0
7 TraesCS6A01G055400 chrUn 89.127 607 41 14 736 1319 103670333 103670937 0.000000e+00 732.0
8 TraesCS6A01G055400 chrUn 93.595 484 22 7 3 478 103528509 103528027 0.000000e+00 713.0
9 TraesCS6A01G055400 chrUn 93.750 176 10 1 1615 1790 103526916 103526742 1.760000e-66 263.0
10 TraesCS6A01G055400 chrUn 98.113 53 1 0 1568 1620 103526996 103526944 2.450000e-15 93.5
11 TraesCS6A01G055400 chr6B 90.100 798 41 9 739 1514 54877223 54876442 0.000000e+00 1002.0
12 TraesCS6A01G055400 chr6B 89.417 737 24 11 1615 2310 54876414 54875691 0.000000e+00 880.0
13 TraesCS6A01G055400 chr6B 86.336 827 83 17 730 1539 54663210 54662397 0.000000e+00 874.0
14 TraesCS6A01G055400 chr6B 89.322 590 47 15 736 1319 55436287 55436866 0.000000e+00 726.0
15 TraesCS6A01G055400 chr6B 85.352 710 60 29 740 1406 55651502 55650794 0.000000e+00 695.0
16 TraesCS6A01G055400 chr6B 86.755 604 42 26 734 1319 60928161 60928744 2.510000e-179 638.0
17 TraesCS6A01G055400 chr6B 92.996 257 13 4 476 730 54881890 54881637 1.010000e-98 370.0
18 TraesCS6A01G055400 chr6B 90.650 246 20 3 20 263 54887791 54887547 7.970000e-85 324.0
19 TraesCS6A01G055400 chr6B 77.049 244 33 14 1941 2181 613613828 613614051 4.040000e-23 119.0
20 TraesCS6A01G055400 chr6B 98.000 50 1 0 1571 1620 54876491 54876442 1.140000e-13 87.9
21 TraesCS6A01G055400 chr6B 94.340 53 3 0 1568 1620 55694782 55694730 5.290000e-12 82.4
22 TraesCS6A01G055400 chr1B 87.170 569 54 14 767 1319 398836449 398837014 1.510000e-176 628.0
23 TraesCS6A01G055400 chr7A 86.195 594 57 22 742 1313 628483508 628484098 9.070000e-174 619.0
24 TraesCS6A01G055400 chr5D 84.921 630 63 21 742 1344 331842423 331841799 1.960000e-170 608.0
25 TraesCS6A01G055400 chr7B 86.596 567 48 20 779 1319 589740771 589740207 3.290000e-168 601.0
26 TraesCS6A01G055400 chr6D 86.759 506 34 18 1001 1477 29757005 29757506 1.220000e-147 532.0
27 TraesCS6A01G055400 chr4A 76.423 246 29 14 1948 2189 676923365 676923145 3.140000e-19 106.0


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 TraesCS6A01G055400 chr6A 29080969 29083280 2311 False 4270.000000 4270 100.000000 1 2312 1 chr6A.!!$F1 2311
1 TraesCS6A01G055400 chr6A 31264135 31264731 596 True 719.000000 719 88.779000 730 1319 1 chr6A.!!$R1 589
2 TraesCS6A01G055400 chr6A 28772635 28773810 1175 True 305.666667 608 85.228333 736 1736 3 chr6A.!!$R2 1000
3 TraesCS6A01G055400 chrUn 103771785 103772388 603 True 776.000000 776 90.280000 730 1319 1 chrUn.!!$R1 589
4 TraesCS6A01G055400 chrUn 103670333 103670937 604 False 732.000000 732 89.127000 736 1319 1 chrUn.!!$F1 583
5 TraesCS6A01G055400 chrUn 103526742 103528509 1767 True 605.875000 1354 93.878250 3 1790 4 chrUn.!!$R2 1787
6 TraesCS6A01G055400 chr6B 54662397 54663210 813 True 874.000000 874 86.336000 730 1539 1 chr6B.!!$R1 809
7 TraesCS6A01G055400 chr6B 55436287 55436866 579 False 726.000000 726 89.322000 736 1319 1 chr6B.!!$F1 583
8 TraesCS6A01G055400 chr6B 55650794 55651502 708 True 695.000000 695 85.352000 740 1406 1 chr6B.!!$R4 666
9 TraesCS6A01G055400 chr6B 54875691 54877223 1532 True 656.633333 1002 92.505667 739 2310 3 chr6B.!!$R6 1571
10 TraesCS6A01G055400 chr6B 60928161 60928744 583 False 638.000000 638 86.755000 734 1319 1 chr6B.!!$F2 585
11 TraesCS6A01G055400 chr1B 398836449 398837014 565 False 628.000000 628 87.170000 767 1319 1 chr1B.!!$F1 552
12 TraesCS6A01G055400 chr7A 628483508 628484098 590 False 619.000000 619 86.195000 742 1313 1 chr7A.!!$F1 571
13 TraesCS6A01G055400 chr5D 331841799 331842423 624 True 608.000000 608 84.921000 742 1344 1 chr5D.!!$R1 602
14 TraesCS6A01G055400 chr7B 589740207 589740771 564 True 601.000000 601 86.596000 779 1319 1 chr7B.!!$R1 540
15 TraesCS6A01G055400 chr6D 29757005 29757506 501 False 532.000000 532 86.759000 1001 1477 1 chr6D.!!$F1 476

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
362 365 0.174845 TGTATTCTTGGAGACCGGCG 59.825 55.0 0.0 0.0 0.0 6.46 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1661 2126 0.034337 TCAACCGTACACTGAAGCCC 59.966 55.0 0.0 0.0 0.0 5.19 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
28 29 1.072266 TACACCAGAAATGCCACCCT 58.928 50.000 0.00 0.00 0.00 4.34
65 66 1.482182 CCATCGACATGTTCTCCTCCA 59.518 52.381 0.00 0.00 0.00 3.86
79 80 3.194968 TCTCCTCCACACGTTATTTCTCC 59.805 47.826 0.00 0.00 0.00 3.71
80 81 3.170717 TCCTCCACACGTTATTTCTCCT 58.829 45.455 0.00 0.00 0.00 3.69
90 93 4.079327 ACGTTATTTCTCCTCCCCTCTCTA 60.079 45.833 0.00 0.00 0.00 2.43
94 97 3.390175 TTCTCCTCCCCTCTCTACTTG 57.610 52.381 0.00 0.00 0.00 3.16
116 119 3.020274 TGTGTGTGAGAGAGATAGAGGC 58.980 50.000 0.00 0.00 0.00 4.70
127 130 1.274728 AGATAGAGGCGATGCATGACC 59.725 52.381 2.46 5.00 0.00 4.02
129 132 0.760567 TAGAGGCGATGCATGACCCT 60.761 55.000 2.46 6.50 0.00 4.34
145 148 4.969484 TGACCCTTTTCTAGGTTTCTGAC 58.031 43.478 0.00 0.00 43.07 3.51
165 168 2.725641 CACTCACCACGTCCGTCA 59.274 61.111 0.00 0.00 0.00 4.35
219 222 0.242825 CACGCCTCCTTGTACTTCGA 59.757 55.000 0.00 0.00 0.00 3.71
234 237 1.530283 TCGACCATCGAGCTCCCTA 59.470 57.895 8.47 0.00 44.82 3.53
236 239 1.797211 CGACCATCGAGCTCCCTACC 61.797 65.000 8.47 0.00 43.74 3.18
244 247 4.103928 GCTCCCTACCCCTCCCCA 62.104 72.222 0.00 0.00 0.00 4.96
246 249 1.321943 CTCCCTACCCCTCCCCAAT 59.678 63.158 0.00 0.00 0.00 3.16
322 325 2.678324 GCATATCAGGACGAGGTAAGC 58.322 52.381 0.00 0.00 0.00 3.09
331 334 1.126296 GACGAGGTAAGCGTTTTCTGC 59.874 52.381 0.00 0.00 42.77 4.26
362 365 0.174845 TGTATTCTTGGAGACCGGCG 59.825 55.000 0.00 0.00 0.00 6.46
391 394 7.026562 TCAACTTTTGATACTTGTGTTGTGTG 58.973 34.615 0.00 0.00 35.98 3.82
519 588 8.365060 TGATTCTGGTATTCAACATGGATTTT 57.635 30.769 0.00 0.00 0.00 1.82
571 640 6.459257 TTGTTTGCACACACAAGTTTTTAG 57.541 33.333 4.89 0.00 30.32 1.85
712 782 0.391597 ACACGTCCAGGTCAATTCGT 59.608 50.000 0.00 0.00 0.00 3.85
728 798 1.010580 TCGTGCGAAAACACACATGT 58.989 45.000 0.00 0.00 40.73 3.21
958 1059 2.411290 CGCAACAACCACCACCAC 59.589 61.111 0.00 0.00 0.00 4.16
964 1081 1.756172 CAACCACCACCACCAGCAA 60.756 57.895 0.00 0.00 0.00 3.91
966 1083 2.123939 CCACCACCACCAGCAACA 60.124 61.111 0.00 0.00 0.00 3.33
1349 1518 1.580942 CCACCACCAGATTTGTGCG 59.419 57.895 0.00 0.00 32.30 5.34
1439 1888 5.680619 ACTGTTGTTTGGATGTAGTTCTGA 58.319 37.500 0.00 0.00 0.00 3.27
1459 1923 6.860080 TCTGAGATGGAATTGAAATTGAAGC 58.140 36.000 0.00 0.00 0.00 3.86
1460 1924 6.434965 TCTGAGATGGAATTGAAATTGAAGCA 59.565 34.615 0.00 0.00 0.00 3.91
1462 1926 5.416947 AGATGGAATTGAAATTGAAGCAGC 58.583 37.500 0.00 0.00 0.00 5.25
1481 1945 4.095632 GCAGCTTACCCTTGAATTCTTCTC 59.904 45.833 7.05 0.00 0.00 2.87
1503 1967 3.622163 CCAATCTCTCACTCTGTTGATGC 59.378 47.826 0.00 0.00 0.00 3.91
1514 1978 4.023450 ACTCTGTTGATGCTGATTTGTGTG 60.023 41.667 0.00 0.00 0.00 3.82
1515 1979 4.136051 TCTGTTGATGCTGATTTGTGTGA 58.864 39.130 0.00 0.00 0.00 3.58
1517 1981 3.240069 GTTGATGCTGATTTGTGTGAGC 58.760 45.455 0.00 0.00 0.00 4.26
1518 1982 2.506444 TGATGCTGATTTGTGTGAGCA 58.494 42.857 0.00 0.00 45.12 4.26
1521 1985 2.300433 TGCTGATTTGTGTGAGCAGTT 58.700 42.857 0.00 0.00 36.54 3.16
1525 1989 4.214119 GCTGATTTGTGTGAGCAGTTAGAA 59.786 41.667 0.00 0.00 0.00 2.10
1554 2018 8.803397 ACTAATTTCCCACTCTGTAATTTACC 57.197 34.615 4.17 0.00 0.00 2.85
1555 2019 7.832685 ACTAATTTCCCACTCTGTAATTTACCC 59.167 37.037 4.17 0.00 0.00 3.69
1556 2020 4.579647 TTCCCACTCTGTAATTTACCCC 57.420 45.455 4.17 0.00 0.00 4.95
1557 2021 3.810623 TCCCACTCTGTAATTTACCCCT 58.189 45.455 4.17 0.00 0.00 4.79
1558 2022 3.521937 TCCCACTCTGTAATTTACCCCTG 59.478 47.826 4.17 0.00 0.00 4.45
1559 2023 3.521937 CCCACTCTGTAATTTACCCCTGA 59.478 47.826 4.17 0.00 0.00 3.86
1560 2024 4.018779 CCCACTCTGTAATTTACCCCTGAA 60.019 45.833 4.17 0.00 0.00 3.02
1561 2025 5.340027 CCCACTCTGTAATTTACCCCTGAAT 60.340 44.000 4.17 0.00 0.00 2.57
1562 2026 6.187682 CCACTCTGTAATTTACCCCTGAATT 58.812 40.000 4.17 0.00 0.00 2.17
1563 2027 7.343357 CCACTCTGTAATTTACCCCTGAATTA 58.657 38.462 4.17 0.00 0.00 1.40
1564 2028 7.282450 CCACTCTGTAATTTACCCCTGAATTAC 59.718 40.741 4.17 10.47 43.76 1.89
1565 2029 8.047310 CACTCTGTAATTTACCCCTGAATTACT 58.953 37.037 15.70 0.00 43.80 2.24
1566 2030 9.275572 ACTCTGTAATTTACCCCTGAATTACTA 57.724 33.333 15.70 7.16 43.80 1.82
1567 2031 9.765795 CTCTGTAATTTACCCCTGAATTACTAG 57.234 37.037 15.70 12.31 43.80 2.57
1568 2032 9.275572 TCTGTAATTTACCCCTGAATTACTAGT 57.724 33.333 15.70 0.00 43.80 2.57
1569 2033 9.901172 CTGTAATTTACCCCTGAATTACTAGTT 57.099 33.333 0.00 0.00 43.80 2.24
1573 2037 9.690913 AATTTACCCCTGAATTACTAGTTTACC 57.309 33.333 0.00 0.00 0.00 2.85
1574 2038 5.705397 ACCCCTGAATTACTAGTTTACCC 57.295 43.478 0.00 0.00 0.00 3.69
1575 2039 5.356575 ACCCCTGAATTACTAGTTTACCCT 58.643 41.667 0.00 0.00 0.00 4.34
1576 2040 5.794289 ACCCCTGAATTACTAGTTTACCCTT 59.206 40.000 0.00 0.00 0.00 3.95
1577 2041 6.120220 CCCCTGAATTACTAGTTTACCCTTG 58.880 44.000 0.00 0.00 0.00 3.61
1578 2042 6.069847 CCCCTGAATTACTAGTTTACCCTTGA 60.070 42.308 0.00 0.00 0.00 3.02
1579 2043 7.399634 CCCTGAATTACTAGTTTACCCTTGAA 58.600 38.462 0.00 0.00 0.00 2.69
1580 2044 8.053355 CCCTGAATTACTAGTTTACCCTTGAAT 58.947 37.037 0.00 0.00 0.00 2.57
1581 2045 9.462606 CCTGAATTACTAGTTTACCCTTGAATT 57.537 33.333 0.00 0.00 0.00 2.17
1587 2051 9.720769 TTACTAGTTTACCCTTGAATTCTTCTG 57.279 33.333 0.00 0.00 0.00 3.02
1588 2052 5.966742 AGTTTACCCTTGAATTCTTCTGC 57.033 39.130 7.05 0.00 0.00 4.26
1589 2053 5.385198 AGTTTACCCTTGAATTCTTCTGCA 58.615 37.500 7.05 0.00 0.00 4.41
1590 2054 5.833131 AGTTTACCCTTGAATTCTTCTGCAA 59.167 36.000 7.05 0.00 0.00 4.08
1591 2055 6.494835 AGTTTACCCTTGAATTCTTCTGCAAT 59.505 34.615 7.05 0.00 0.00 3.56
1592 2056 6.515272 TTACCCTTGAATTCTTCTGCAATC 57.485 37.500 7.05 0.00 0.00 2.67
1593 2057 4.670765 ACCCTTGAATTCTTCTGCAATCT 58.329 39.130 7.05 0.00 0.00 2.40
1594 2058 4.704057 ACCCTTGAATTCTTCTGCAATCTC 59.296 41.667 7.05 0.00 0.00 2.75
1595 2059 4.948621 CCCTTGAATTCTTCTGCAATCTCT 59.051 41.667 7.05 0.00 0.00 3.10
1596 2060 5.066246 CCCTTGAATTCTTCTGCAATCTCTC 59.934 44.000 7.05 0.00 0.00 3.20
1597 2061 5.646793 CCTTGAATTCTTCTGCAATCTCTCA 59.353 40.000 7.05 0.00 0.00 3.27
1598 2062 6.403418 CCTTGAATTCTTCTGCAATCTCTCAC 60.403 42.308 7.05 0.00 0.00 3.51
1599 2063 5.802465 TGAATTCTTCTGCAATCTCTCACT 58.198 37.500 7.05 0.00 0.00 3.41
1600 2064 5.873712 TGAATTCTTCTGCAATCTCTCACTC 59.126 40.000 7.05 0.00 0.00 3.51
1601 2065 5.680594 ATTCTTCTGCAATCTCTCACTCT 57.319 39.130 0.00 0.00 0.00 3.24
1602 2066 4.453177 TCTTCTGCAATCTCTCACTCTG 57.547 45.455 0.00 0.00 0.00 3.35
1603 2067 3.831333 TCTTCTGCAATCTCTCACTCTGT 59.169 43.478 0.00 0.00 0.00 3.41
1604 2068 4.282957 TCTTCTGCAATCTCTCACTCTGTT 59.717 41.667 0.00 0.00 0.00 3.16
1605 2069 3.922910 TCTGCAATCTCTCACTCTGTTG 58.077 45.455 0.00 0.00 0.00 3.33
1606 2070 3.575687 TCTGCAATCTCTCACTCTGTTGA 59.424 43.478 0.00 0.00 0.00 3.18
1607 2071 4.222366 TCTGCAATCTCTCACTCTGTTGAT 59.778 41.667 0.00 0.00 0.00 2.57
1608 2072 4.251268 TGCAATCTCTCACTCTGTTGATG 58.749 43.478 0.00 0.00 0.00 3.07
1609 2073 4.252073 GCAATCTCTCACTCTGTTGATGT 58.748 43.478 0.00 0.00 0.00 3.06
1610 2074 4.694509 GCAATCTCTCACTCTGTTGATGTT 59.305 41.667 0.00 0.00 0.00 2.71
1611 2075 5.390673 GCAATCTCTCACTCTGTTGATGTTG 60.391 44.000 0.00 0.00 0.00 3.33
1612 2076 5.735285 ATCTCTCACTCTGTTGATGTTGA 57.265 39.130 0.00 0.00 0.00 3.18
1613 2077 5.735285 TCTCTCACTCTGTTGATGTTGAT 57.265 39.130 0.00 0.00 0.00 2.57
1614 2078 6.106648 TCTCTCACTCTGTTGATGTTGATT 57.893 37.500 0.00 0.00 0.00 2.57
1615 2079 6.528321 TCTCTCACTCTGTTGATGTTGATTT 58.472 36.000 0.00 0.00 0.00 2.17
1616 2080 6.426025 TCTCTCACTCTGTTGATGTTGATTTG 59.574 38.462 0.00 0.00 0.00 2.32
1617 2081 6.057533 TCTCACTCTGTTGATGTTGATTTGT 58.942 36.000 0.00 0.00 0.00 2.83
1647 2111 1.354031 TCTGTAATTTGCTGCCTCCCA 59.646 47.619 0.00 0.00 0.00 4.37
1661 2126 1.269448 CCTCCCAAAATCAACCGTGTG 59.731 52.381 0.00 0.00 0.00 3.82
1754 2219 5.562890 GCTTGTCCTGAACATTTTCTGTACC 60.563 44.000 0.00 0.00 36.98 3.34
1758 2223 3.408634 CTGAACATTTTCTGTACCCCGT 58.591 45.455 0.00 0.00 36.98 5.28
1800 2265 1.180029 AGACATGTGCTGCCCATTTC 58.820 50.000 1.15 3.49 0.00 2.17
1808 2273 1.450531 GCTGCCCATTTCGGATCTGG 61.451 60.000 0.62 0.00 36.56 3.86
1809 2274 0.107017 CTGCCCATTTCGGATCTGGT 60.107 55.000 0.62 0.00 36.56 4.00
1841 2306 1.654954 CTGTCATGGGAAGCAGCTGC 61.655 60.000 31.53 31.53 42.49 5.25
1890 2369 4.822685 TGCCTACCTAAATCAACCGTAA 57.177 40.909 0.00 0.00 0.00 3.18
1904 2383 2.762745 ACCGTAACAAGTGTAAGCTGG 58.237 47.619 0.00 0.00 0.00 4.85
1922 2401 2.557924 CTGGTTTGCTTGGCTGAACATA 59.442 45.455 9.86 1.57 31.02 2.29
1923 2402 2.557924 TGGTTTGCTTGGCTGAACATAG 59.442 45.455 9.86 0.00 31.02 2.23
1959 2438 5.185056 CCTACCCCAACTTTTTGAATCGATT 59.815 40.000 11.20 11.20 34.24 3.34
1995 2474 8.658609 TGATTTCTTTTGCTTAAAATGCATAGC 58.341 29.630 11.51 11.51 40.34 2.97
1996 2475 7.959689 TTTCTTTTGCTTAAAATGCATAGCA 57.040 28.000 16.14 16.14 44.86 3.49
2145 2624 1.283613 TCTGCCCCCAAATACAATCGT 59.716 47.619 0.00 0.00 0.00 3.73
2169 2649 1.985159 TGCTTCAGTGTACCCTGGATT 59.015 47.619 5.47 0.00 33.14 3.01
2183 2663 1.737236 CTGGATTCGAACCAAATCGCA 59.263 47.619 16.68 4.62 42.44 5.10
2209 2713 4.933330 TCTCGACACTTAATATGCTGACC 58.067 43.478 0.00 0.00 0.00 4.02
2247 2751 1.475280 TGATGGCAAGCTGCTGATTTC 59.525 47.619 1.35 0.00 44.28 2.17
2260 2766 4.379652 TGCTGATTTCTTTTGGCCTTTTC 58.620 39.130 3.32 0.00 0.00 2.29
2310 2816 4.064388 TGATGTGTCTTTCTGAATTGCGA 58.936 39.130 0.00 0.00 0.00 5.10
2311 2817 4.696877 TGATGTGTCTTTCTGAATTGCGAT 59.303 37.500 0.00 0.00 0.00 4.58
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
28 29 1.125093 TGGAGAAAACCGAGGGAGCA 61.125 55.000 0.00 0.00 0.00 4.26
65 66 2.500504 GAGGGGAGGAGAAATAACGTGT 59.499 50.000 0.00 0.00 0.00 4.49
79 80 2.232452 CACACACAAGTAGAGAGGGGAG 59.768 54.545 0.00 0.00 0.00 4.30
80 81 2.248248 CACACACAAGTAGAGAGGGGA 58.752 52.381 0.00 0.00 0.00 4.81
90 93 5.073428 TCTATCTCTCTCACACACACAAGT 58.927 41.667 0.00 0.00 0.00 3.16
94 97 3.181491 GCCTCTATCTCTCTCACACACAC 60.181 52.174 0.00 0.00 0.00 3.82
116 119 2.874701 CCTAGAAAAGGGTCATGCATCG 59.125 50.000 0.00 0.00 42.32 3.84
129 132 3.135994 GTGGCGTCAGAAACCTAGAAAA 58.864 45.455 0.00 0.00 0.00 2.29
219 222 1.457831 GGGTAGGGAGCTCGATGGT 60.458 63.158 7.83 0.00 0.00 3.55
234 237 1.619669 GGAGACATTGGGGAGGGGT 60.620 63.158 0.00 0.00 0.00 4.95
236 239 0.030092 TAGGGAGACATTGGGGAGGG 60.030 60.000 0.00 0.00 0.00 4.30
244 247 2.695666 CGGTGAGATGTAGGGAGACATT 59.304 50.000 0.00 0.00 40.18 2.71
246 249 1.685180 CCGGTGAGATGTAGGGAGACA 60.685 57.143 0.00 0.00 0.00 3.41
322 325 4.396166 ACATATTTGGAGAGGCAGAAAACG 59.604 41.667 0.00 0.00 0.00 3.60
331 334 7.739825 TCTCCAAGAATACATATTTGGAGAGG 58.260 38.462 23.67 6.99 45.57 3.69
362 365 7.222611 ACAACACAAGTATCAAAAGTTGAATGC 59.777 33.333 9.09 0.00 43.95 3.56
441 450 8.370493 TGCATCGGATTTTTAAATGAACAAAA 57.630 26.923 0.00 0.00 0.00 2.44
543 612 5.938438 ACTTGTGTGTGCAAACAATTTTT 57.062 30.435 12.34 0.00 35.82 1.94
544 613 5.938438 AACTTGTGTGTGCAAACAATTTT 57.062 30.435 12.34 0.00 35.82 1.82
545 614 5.938438 AAACTTGTGTGTGCAAACAATTT 57.062 30.435 12.34 9.24 35.82 1.82
546 615 5.938438 AAAACTTGTGTGTGCAAACAATT 57.062 30.435 12.34 3.39 35.82 2.32
547 616 5.938438 AAAAACTTGTGTGTGCAAACAAT 57.062 30.435 12.34 0.00 35.82 2.71
550 619 6.364976 ACTTCTAAAAACTTGTGTGTGCAAAC 59.635 34.615 0.00 0.00 0.00 2.93
557 626 8.801715 AATATGCACTTCTAAAAACTTGTGTG 57.198 30.769 0.00 0.00 0.00 3.82
712 782 4.120589 TGTACTACATGTGTGTTTTCGCA 58.879 39.130 9.11 1.01 39.77 5.10
728 798 5.542635 AGGTGTGTTTTCTCAGGATGTACTA 59.457 40.000 0.00 0.00 37.40 1.82
958 1059 0.319297 GAGCTTGGCTTTGTTGCTGG 60.319 55.000 0.00 0.00 39.88 4.85
964 1081 3.357079 CGGCGAGCTTGGCTTTGT 61.357 61.111 23.91 0.00 39.88 2.83
966 1083 4.329545 TCCGGCGAGCTTGGCTTT 62.330 61.111 23.91 0.00 39.88 3.51
1290 1445 3.136123 CCGCCGAACCCGTAGAGA 61.136 66.667 0.00 0.00 0.00 3.10
1349 1518 0.443869 CATGAACACTACACAGCCGC 59.556 55.000 0.00 0.00 0.00 6.53
1439 1888 5.187186 AGCTGCTTCAATTTCAATTCCATCT 59.813 36.000 0.00 0.00 0.00 2.90
1481 1945 3.622163 GCATCAACAGAGTGAGAGATTGG 59.378 47.826 0.00 0.00 0.00 3.16
1503 1967 5.929697 TTCTAACTGCTCACACAAATCAG 57.070 39.130 0.00 0.00 0.00 2.90
1539 2003 8.047310 AGTAATTCAGGGGTAAATTACAGAGTG 58.953 37.037 16.12 0.00 44.87 3.51
1541 2005 9.765795 CTAGTAATTCAGGGGTAAATTACAGAG 57.234 37.037 16.12 10.73 44.87 3.35
1543 2007 9.901172 AACTAGTAATTCAGGGGTAAATTACAG 57.099 33.333 16.12 13.53 44.87 2.74
1547 2011 9.690913 GGTAAACTAGTAATTCAGGGGTAAATT 57.309 33.333 0.00 0.00 0.00 1.82
1548 2012 8.277197 GGGTAAACTAGTAATTCAGGGGTAAAT 58.723 37.037 0.00 0.00 0.00 1.40
1549 2013 7.462006 AGGGTAAACTAGTAATTCAGGGGTAAA 59.538 37.037 0.00 0.00 0.00 2.01
1550 2014 6.967652 AGGGTAAACTAGTAATTCAGGGGTAA 59.032 38.462 0.00 0.00 0.00 2.85
1551 2015 6.514863 AGGGTAAACTAGTAATTCAGGGGTA 58.485 40.000 0.00 0.00 0.00 3.69
1552 2016 5.356575 AGGGTAAACTAGTAATTCAGGGGT 58.643 41.667 0.00 0.00 0.00 4.95
1553 2017 5.970501 AGGGTAAACTAGTAATTCAGGGG 57.029 43.478 0.00 0.00 0.00 4.79
1554 2018 6.954232 TCAAGGGTAAACTAGTAATTCAGGG 58.046 40.000 0.00 0.00 0.00 4.45
1555 2019 9.462606 AATTCAAGGGTAAACTAGTAATTCAGG 57.537 33.333 0.00 0.00 0.00 3.86
1578 2042 5.875910 CAGAGTGAGAGATTGCAGAAGAATT 59.124 40.000 0.00 0.00 0.00 2.17
1579 2043 5.046448 ACAGAGTGAGAGATTGCAGAAGAAT 60.046 40.000 0.00 0.00 0.00 2.40
1580 2044 4.282957 ACAGAGTGAGAGATTGCAGAAGAA 59.717 41.667 0.00 0.00 0.00 2.52
1581 2045 3.831333 ACAGAGTGAGAGATTGCAGAAGA 59.169 43.478 0.00 0.00 0.00 2.87
1582 2046 4.191033 ACAGAGTGAGAGATTGCAGAAG 57.809 45.455 0.00 0.00 0.00 2.85
1583 2047 4.039609 TCAACAGAGTGAGAGATTGCAGAA 59.960 41.667 0.00 0.00 0.00 3.02
1584 2048 3.575687 TCAACAGAGTGAGAGATTGCAGA 59.424 43.478 0.00 0.00 0.00 4.26
1585 2049 3.922910 TCAACAGAGTGAGAGATTGCAG 58.077 45.455 0.00 0.00 0.00 4.41
1586 2050 4.251268 CATCAACAGAGTGAGAGATTGCA 58.749 43.478 0.00 0.00 0.00 4.08
1587 2051 4.252073 ACATCAACAGAGTGAGAGATTGC 58.748 43.478 0.00 0.00 0.00 3.56
1588 2052 5.930569 TCAACATCAACAGAGTGAGAGATTG 59.069 40.000 0.00 0.00 0.00 2.67
1589 2053 6.106648 TCAACATCAACAGAGTGAGAGATT 57.893 37.500 0.00 0.00 0.00 2.40
1590 2054 5.735285 TCAACATCAACAGAGTGAGAGAT 57.265 39.130 0.00 0.00 0.00 2.75
1591 2055 5.735285 ATCAACATCAACAGAGTGAGAGA 57.265 39.130 0.00 0.00 0.00 3.10
1592 2056 6.204301 ACAAATCAACATCAACAGAGTGAGAG 59.796 38.462 0.00 0.00 0.00 3.20
1593 2057 6.017687 CACAAATCAACATCAACAGAGTGAGA 60.018 38.462 0.00 0.00 0.00 3.27
1594 2058 6.140786 CACAAATCAACATCAACAGAGTGAG 58.859 40.000 0.00 0.00 0.00 3.51
1595 2059 5.589855 ACACAAATCAACATCAACAGAGTGA 59.410 36.000 0.00 0.00 0.00 3.41
1596 2060 5.824429 ACACAAATCAACATCAACAGAGTG 58.176 37.500 0.00 0.00 0.00 3.51
1597 2061 5.824624 AGACACAAATCAACATCAACAGAGT 59.175 36.000 0.00 0.00 0.00 3.24
1598 2062 6.204301 AGAGACACAAATCAACATCAACAGAG 59.796 38.462 0.00 0.00 0.00 3.35
1599 2063 6.057533 AGAGACACAAATCAACATCAACAGA 58.942 36.000 0.00 0.00 0.00 3.41
1600 2064 6.309712 AGAGACACAAATCAACATCAACAG 57.690 37.500 0.00 0.00 0.00 3.16
1601 2065 5.050159 CGAGAGACACAAATCAACATCAACA 60.050 40.000 0.00 0.00 0.00 3.33
1602 2066 5.377358 CGAGAGACACAAATCAACATCAAC 58.623 41.667 0.00 0.00 0.00 3.18
1603 2067 4.083855 GCGAGAGACACAAATCAACATCAA 60.084 41.667 0.00 0.00 0.00 2.57
1604 2068 3.433274 GCGAGAGACACAAATCAACATCA 59.567 43.478 0.00 0.00 0.00 3.07
1605 2069 3.681897 AGCGAGAGACACAAATCAACATC 59.318 43.478 0.00 0.00 0.00 3.06
1606 2070 3.668447 AGCGAGAGACACAAATCAACAT 58.332 40.909 0.00 0.00 0.00 2.71
1607 2071 3.059884 GAGCGAGAGACACAAATCAACA 58.940 45.455 0.00 0.00 0.00 3.33
1608 2072 3.122613 CAGAGCGAGAGACACAAATCAAC 59.877 47.826 0.00 0.00 0.00 3.18
1609 2073 3.243873 ACAGAGCGAGAGACACAAATCAA 60.244 43.478 0.00 0.00 0.00 2.57
1610 2074 2.297315 ACAGAGCGAGAGACACAAATCA 59.703 45.455 0.00 0.00 0.00 2.57
1611 2075 2.953020 ACAGAGCGAGAGACACAAATC 58.047 47.619 0.00 0.00 0.00 2.17
1612 2076 4.521130 TTACAGAGCGAGAGACACAAAT 57.479 40.909 0.00 0.00 0.00 2.32
1613 2077 4.521130 ATTACAGAGCGAGAGACACAAA 57.479 40.909 0.00 0.00 0.00 2.83
1614 2078 4.521130 AATTACAGAGCGAGAGACACAA 57.479 40.909 0.00 0.00 0.00 3.33
1615 2079 4.237724 CAAATTACAGAGCGAGAGACACA 58.762 43.478 0.00 0.00 0.00 3.72
1616 2080 3.061429 GCAAATTACAGAGCGAGAGACAC 59.939 47.826 0.00 0.00 0.00 3.67
1617 2081 3.056536 AGCAAATTACAGAGCGAGAGACA 60.057 43.478 0.00 0.00 0.00 3.41
1647 2111 1.339929 GAAGCCCACACGGTTGATTTT 59.660 47.619 0.00 0.00 0.00 1.82
1661 2126 0.034337 TCAACCGTACACTGAAGCCC 59.966 55.000 0.00 0.00 0.00 5.19
1692 2157 1.387756 CGCAAGCTACAAAAATGCAGC 59.612 47.619 5.25 0.00 36.84 5.25
1734 2199 3.756963 GGGGTACAGAAAATGTTCAGGAC 59.243 47.826 0.00 0.00 39.96 3.85
1754 2219 1.675552 AACTTGGTTCAACTGACGGG 58.324 50.000 0.00 0.00 0.00 5.28
1758 2223 7.226720 GTCTTATCTGAAACTTGGTTCAACTGA 59.773 37.037 2.62 0.00 37.08 3.41
1800 2265 2.086869 ACAAATTGCTCACCAGATCCG 58.913 47.619 0.00 0.00 0.00 4.18
1808 2273 4.379813 CCCATGACAGTACAAATTGCTCAC 60.380 45.833 0.00 0.00 0.00 3.51
1809 2274 3.758023 CCCATGACAGTACAAATTGCTCA 59.242 43.478 0.00 0.00 0.00 4.26
1841 2306 1.332375 TCGAAACGAGCACAAAAAGGG 59.668 47.619 0.00 0.00 0.00 3.95
1890 2369 2.654863 AGCAAACCAGCTTACACTTGT 58.345 42.857 0.00 0.00 43.70 3.16
1904 2383 4.708726 ATCTATGTTCAGCCAAGCAAAC 57.291 40.909 0.00 0.00 0.00 2.93
1959 2438 5.072741 AGCAAAAGAAATCAACTGCTCCTA 58.927 37.500 0.00 0.00 35.25 2.94
1994 2473 2.876550 TCAGTATGCATTCAGCTCATGC 59.123 45.455 17.29 17.29 46.25 4.06
1995 2474 5.690997 AATCAGTATGCATTCAGCTCATG 57.309 39.130 3.54 0.00 45.94 3.07
1996 2475 5.241064 GGAAATCAGTATGCATTCAGCTCAT 59.759 40.000 3.54 0.00 45.94 2.90
2012 2491 6.822676 AGAGCAACTTATTGAGAGGAAATCAG 59.177 38.462 0.00 0.00 38.15 2.90
2121 2600 3.534357 TTGTATTTGGGGGCAGAGAAA 57.466 42.857 0.00 0.00 0.00 2.52
2145 2624 2.571212 CAGGGTACACTGAAGCAAACA 58.429 47.619 21.03 0.00 40.97 2.83
2169 2649 3.444916 GAGAGTATGCGATTTGGTTCGA 58.555 45.455 0.00 0.00 41.62 3.71
2183 2663 7.364200 GTCAGCATATTAAGTGTCGAGAGTAT 58.636 38.462 0.00 0.00 0.00 2.12
2209 2713 4.521010 CATCATCACAATTCGAATGTCCG 58.479 43.478 12.25 3.64 0.00 4.79


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

AutoCloner maintained by Alex Coulton.