Multiple sequence alignment - TraesCS5B01G177000

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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 TraesCS5B01G177000 chr5B 100.000 2123 0 0 1 2123 322912951 322915073 0.000000e+00 3921
1 TraesCS5B01G177000 chr5D 89.644 2076 128 46 2 2045 285464572 285466592 0.000000e+00 2562
2 TraesCS5B01G177000 chr5D 92.857 126 6 2 2 125 285300698 285300822 1.670000e-41 180
3 TraesCS5B01G177000 chr5A 91.351 1688 91 22 2 1656 377181739 377183404 0.000000e+00 2257
4 TraesCS5B01G177000 chr5A 78.351 194 21 12 1857 2045 377184148 377184325 2.880000e-19 106


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 TraesCS5B01G177000 chr5B 322912951 322915073 2122 False 3921.0 3921 100.000 1 2123 1 chr5B.!!$F1 2122
1 TraesCS5B01G177000 chr5D 285464572 285466592 2020 False 2562.0 2562 89.644 2 2045 1 chr5D.!!$F2 2043
2 TraesCS5B01G177000 chr5A 377181739 377184325 2586 False 1181.5 2257 84.851 2 2045 2 chr5A.!!$F1 2043

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
102 104 0.033601 AGTGCCCTGTGTTTTGACCA 60.034 50.0 0.0 0.0 0.0 4.02 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1986 2589 0.174845 TGCGTAGGATGCAGTACACC 59.825 55.0 0.0 0.0 34.76 4.16 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
68 70 1.070445 ACACAGGAGCAGCAGACAC 59.930 57.895 0.00 0.00 0.00 3.67
80 82 1.152777 CAGACACCCCCTGCACAAA 60.153 57.895 0.00 0.00 0.00 2.83
101 103 1.111277 AAGTGCCCTGTGTTTTGACC 58.889 50.000 0.00 0.00 0.00 4.02
102 104 0.033601 AGTGCCCTGTGTTTTGACCA 60.034 50.000 0.00 0.00 0.00 4.02
166 171 2.147958 TCAAACGGCTACAATGTCCAC 58.852 47.619 0.00 0.00 0.00 4.02
199 204 0.866906 CAACCAAAGCACGCACACAG 60.867 55.000 0.00 0.00 0.00 3.66
267 288 5.948992 AGTGCTTTCCAGTCAAAAGATAC 57.051 39.130 0.03 0.00 36.09 2.24
268 289 4.762251 AGTGCTTTCCAGTCAAAAGATACC 59.238 41.667 0.03 0.00 36.09 2.73
324 348 0.973632 TTCCTAGCAGCTTCCGAACA 59.026 50.000 0.00 0.00 0.00 3.18
339 363 1.144969 GAACAAATCGAGGCGACACA 58.855 50.000 0.00 0.00 39.18 3.72
397 421 8.848474 TCCATAAACTCTTTCCAACTCTTTAG 57.152 34.615 0.00 0.00 0.00 1.85
492 518 3.695060 AGAAGATCTTGGCAATGCAAGAG 59.305 43.478 14.00 9.72 40.27 2.85
573 599 4.530553 TCCAAGTACCAAGATAGACAAGCA 59.469 41.667 0.00 0.00 0.00 3.91
855 881 2.825836 GCGGTTGCATGGGAGGAG 60.826 66.667 0.00 0.00 42.15 3.69
913 939 2.677228 CGGCCTTCCCAGTTCCAT 59.323 61.111 0.00 0.00 0.00 3.41
930 956 1.376543 CATACCACAGCAAGCTCCAG 58.623 55.000 0.00 0.00 0.00 3.86
940 966 1.307691 AAGCTCCAGCCAGGGATCT 60.308 57.895 0.00 0.00 43.38 2.75
970 997 2.748268 GAGCGAACTCTCCTGCTTG 58.252 57.895 0.00 0.00 40.03 4.01
975 1002 1.405256 CGAACTCTCCTGCTTGCATCT 60.405 52.381 0.00 0.00 0.00 2.90
1124 1151 1.612462 CCTTTGCTGGCATGACTGAGA 60.612 52.381 10.05 0.00 0.00 3.27
1147 1178 2.158711 CCAAGCTGCATTCTCCTCCATA 60.159 50.000 1.02 0.00 0.00 2.74
1169 1201 3.159298 CCCATCAAGTCAAGGGTCG 57.841 57.895 0.00 0.00 36.52 4.79
1219 1251 7.604657 AGGGAAGTATCATCAGTTAGTTAGG 57.395 40.000 0.00 0.00 0.00 2.69
1220 1252 7.363031 AGGGAAGTATCATCAGTTAGTTAGGA 58.637 38.462 0.00 0.00 0.00 2.94
1221 1253 7.288158 AGGGAAGTATCATCAGTTAGTTAGGAC 59.712 40.741 0.00 0.00 0.00 3.85
1222 1254 7.288158 GGGAAGTATCATCAGTTAGTTAGGACT 59.712 40.741 0.00 0.00 39.97 3.85
1223 1255 8.697292 GGAAGTATCATCAGTTAGTTAGGACTT 58.303 37.037 0.00 0.00 37.33 3.01
1240 1272 9.671279 GTTAGGACTTAGAGTAGAAGTAGAAGT 57.329 37.037 0.00 0.00 37.27 3.01
1311 1347 8.453238 TTGGTAGACTAGACATTCTATCAGTC 57.547 38.462 0.00 0.00 36.90 3.51
1316 1352 8.734218 AGACTAGACATTCTATCAGTCGTTTA 57.266 34.615 0.00 0.00 37.36 2.01
1317 1353 9.344772 AGACTAGACATTCTATCAGTCGTTTAT 57.655 33.333 0.00 0.00 37.36 1.40
1334 1370 8.665685 AGTCGTTTATTTCACCATGAGTTATTC 58.334 33.333 0.00 0.00 0.00 1.75
1373 1410 3.334583 TTCTCCACCTTTTCTCCGATG 57.665 47.619 0.00 0.00 0.00 3.84
1378 1415 0.673644 ACCTTTTCTCCGATGTGCCG 60.674 55.000 0.00 0.00 0.00 5.69
1400 1439 2.057922 CCCTTAGGCAGTGGGATATGT 58.942 52.381 0.00 0.00 43.47 2.29
1425 1464 5.048083 GGCTGTTGTATCTTTTTGGACATGA 60.048 40.000 0.00 0.00 0.00 3.07
1432 1471 8.806429 TGTATCTTTTTGGACATGATGTGTAT 57.194 30.769 1.23 0.00 42.36 2.29
1443 1482 5.754782 ACATGATGTGTATTGTACCCATGT 58.245 37.500 0.00 0.00 39.91 3.21
1444 1483 5.822519 ACATGATGTGTATTGTACCCATGTC 59.177 40.000 0.00 0.00 39.91 3.06
1490 1529 6.483307 AGTGAAAGAATCAAAGTCGAACATGA 59.517 34.615 0.00 0.00 40.50 3.07
1493 1532 5.613358 AGAATCAAAGTCGAACATGAACC 57.387 39.130 0.00 0.00 0.00 3.62
1502 1541 2.076863 CGAACATGAACCCTTGTCCTC 58.923 52.381 0.00 0.00 31.27 3.71
1506 1545 3.256704 ACATGAACCCTTGTCCTCCTAA 58.743 45.455 0.00 0.00 0.00 2.69
1547 1586 5.593679 TTTATCTTCTTCGGTAGTGGAGG 57.406 43.478 0.00 0.00 0.00 4.30
1548 1587 1.183549 TCTTCTTCGGTAGTGGAGGC 58.816 55.000 0.00 0.00 0.00 4.70
1549 1588 0.895530 CTTCTTCGGTAGTGGAGGCA 59.104 55.000 0.00 0.00 0.00 4.75
1550 1589 1.275291 CTTCTTCGGTAGTGGAGGCAA 59.725 52.381 0.00 0.00 0.00 4.52
1551 1590 1.568504 TCTTCGGTAGTGGAGGCAAT 58.431 50.000 0.00 0.00 0.00 3.56
1552 1591 2.742348 TCTTCGGTAGTGGAGGCAATA 58.258 47.619 0.00 0.00 0.00 1.90
1553 1592 3.305720 TCTTCGGTAGTGGAGGCAATAT 58.694 45.455 0.00 0.00 0.00 1.28
1554 1593 3.069586 TCTTCGGTAGTGGAGGCAATATG 59.930 47.826 0.00 0.00 0.00 1.78
1555 1594 2.673258 TCGGTAGTGGAGGCAATATGA 58.327 47.619 0.00 0.00 0.00 2.15
1558 1597 3.181465 CGGTAGTGGAGGCAATATGAGTT 60.181 47.826 0.00 0.00 0.00 3.01
1563 1602 5.784177 AGTGGAGGCAATATGAGTTATACG 58.216 41.667 0.00 0.00 0.00 3.06
1567 1606 6.094061 GGAGGCAATATGAGTTATACGACTC 58.906 44.000 0.00 0.00 44.97 3.36
1593 1632 8.644318 GAGCTGTCGATAAACTTTTAATCCTA 57.356 34.615 0.00 0.00 0.00 2.94
1627 1666 2.416566 CGCTATATTCTGGAGCTCGCAT 60.417 50.000 7.83 0.00 33.91 4.73
1629 1668 3.616379 GCTATATTCTGGAGCTCGCATTC 59.384 47.826 7.83 0.00 33.28 2.67
1656 1696 6.757897 ATAGAAATAACCATGTGTGTGTGG 57.242 37.500 0.00 0.00 41.35 4.17
1657 1697 3.826157 AGAAATAACCATGTGTGTGTGGG 59.174 43.478 0.00 0.00 39.86 4.61
1658 1698 1.544724 ATAACCATGTGTGTGTGGGC 58.455 50.000 0.00 0.00 39.86 5.36
1659 1699 0.538516 TAACCATGTGTGTGTGGGCC 60.539 55.000 0.00 0.00 39.86 5.80
1660 1700 2.990967 CCATGTGTGTGTGGGCCC 60.991 66.667 17.59 17.59 0.00 5.80
1661 1701 2.203466 CATGTGTGTGTGGGCCCA 60.203 61.111 24.45 24.45 0.00 5.36
1662 1702 2.203480 ATGTGTGTGTGGGCCCAC 60.203 61.111 42.81 42.81 46.33 4.61
1690 1730 2.808206 GGGCGTGAGGTGGGGATAG 61.808 68.421 0.00 0.00 0.00 2.08
1694 1734 1.191535 CGTGAGGTGGGGATAGAACA 58.808 55.000 0.00 0.00 0.00 3.18
1696 1736 2.170607 CGTGAGGTGGGGATAGAACATT 59.829 50.000 0.00 0.00 0.00 2.71
1702 1742 3.714798 GGTGGGGATAGAACATTACCTCA 59.285 47.826 0.00 0.00 0.00 3.86
1708 1748 8.561769 TGGGGATAGAACATTACCTCAATTTTA 58.438 33.333 0.00 0.00 0.00 1.52
1776 2005 4.844349 ATAAATCACTAGGGTGCACAGT 57.156 40.909 20.43 10.97 42.72 3.55
1809 2038 1.270550 CAGGAAGTCCACAAATGCACC 59.729 52.381 0.00 0.00 38.89 5.01
1812 2041 2.545742 GGAAGTCCACAAATGCACCAAC 60.546 50.000 0.00 0.00 35.64 3.77
1825 2054 5.581126 ATGCACCAACTGTAATAACCATG 57.419 39.130 0.00 0.00 0.00 3.66
1867 2470 4.051237 GTTGTCAGAAATTTTGTCCAGGC 58.949 43.478 0.00 0.00 0.00 4.85
1896 2499 7.362662 TGATGAGTTGAAGTGCATAAGAAAAC 58.637 34.615 0.00 0.00 0.00 2.43
1906 2509 7.636150 AGTGCATAAGAAAACAGCTTCATAT 57.364 32.000 0.00 0.00 0.00 1.78
1907 2510 8.737168 AGTGCATAAGAAAACAGCTTCATATA 57.263 30.769 0.00 0.00 0.00 0.86
1908 2511 9.177608 AGTGCATAAGAAAACAGCTTCATATAA 57.822 29.630 0.00 0.00 0.00 0.98
1925 2528 9.443283 CTTCATATAATGTCTTAAGCAGCAAAC 57.557 33.333 0.00 0.00 0.00 2.93
1928 2531 9.013490 CATATAATGTCTTAAGCAGCAAACAAC 57.987 33.333 0.00 0.00 0.00 3.32
1937 2540 0.517316 CAGCAAACAACGGAGCCTAC 59.483 55.000 0.00 0.00 0.00 3.18
1938 2541 0.605589 AGCAAACAACGGAGCCTACC 60.606 55.000 0.00 0.00 0.00 3.18
1939 2542 0.887387 GCAAACAACGGAGCCTACCA 60.887 55.000 0.00 0.00 0.00 3.25
1940 2543 1.156736 CAAACAACGGAGCCTACCAG 58.843 55.000 0.00 0.00 0.00 4.00
1941 2544 0.036306 AAACAACGGAGCCTACCAGG 59.964 55.000 0.00 0.00 38.80 4.45
1942 2545 1.838073 AACAACGGAGCCTACCAGGG 61.838 60.000 0.00 0.00 35.37 4.45
1950 2553 3.477783 GCCTACCAGGGCCTACTAT 57.522 57.895 5.28 0.00 45.92 2.12
1951 2554 1.730851 GCCTACCAGGGCCTACTATT 58.269 55.000 5.28 0.00 45.92 1.73
1952 2555 2.898662 GCCTACCAGGGCCTACTATTA 58.101 52.381 5.28 0.00 45.92 0.98
1953 2556 3.451890 GCCTACCAGGGCCTACTATTAT 58.548 50.000 5.28 0.00 45.92 1.28
1954 2557 4.617593 GCCTACCAGGGCCTACTATTATA 58.382 47.826 5.28 0.00 45.92 0.98
1955 2558 5.217400 GCCTACCAGGGCCTACTATTATAT 58.783 45.833 5.28 0.00 45.92 0.86
1956 2559 6.379579 GCCTACCAGGGCCTACTATTATATA 58.620 44.000 5.28 0.00 45.92 0.86
1967 2570 8.541234 GGCCTACTATTATATAAGCAGTCCTTT 58.459 37.037 13.20 0.00 34.95 3.11
1986 2589 7.228706 AGTCCTTTATTGTCCTTTTGTACTGTG 59.771 37.037 0.00 0.00 0.00 3.66
1999 2607 2.028476 TGTACTGTGGTGTACTGCATCC 60.028 50.000 6.41 0.00 42.22 3.51
2014 2622 2.266554 GCATCCTACGCATCATAGCTC 58.733 52.381 0.00 0.00 0.00 4.09
2015 2623 2.353109 GCATCCTACGCATCATAGCTCA 60.353 50.000 0.00 0.00 0.00 4.26
2016 2624 3.862264 GCATCCTACGCATCATAGCTCAA 60.862 47.826 0.00 0.00 0.00 3.02
2017 2625 4.502016 CATCCTACGCATCATAGCTCAAT 58.498 43.478 0.00 0.00 0.00 2.57
2018 2626 4.607293 TCCTACGCATCATAGCTCAATT 57.393 40.909 0.00 0.00 0.00 2.32
2019 2627 5.722021 TCCTACGCATCATAGCTCAATTA 57.278 39.130 0.00 0.00 0.00 1.40
2020 2628 6.096673 TCCTACGCATCATAGCTCAATTAA 57.903 37.500 0.00 0.00 0.00 1.40
2021 2629 5.926542 TCCTACGCATCATAGCTCAATTAAC 59.073 40.000 0.00 0.00 0.00 2.01
2022 2630 4.715520 ACGCATCATAGCTCAATTAACG 57.284 40.909 0.00 0.00 0.00 3.18
2023 2631 4.119862 ACGCATCATAGCTCAATTAACGT 58.880 39.130 0.00 0.00 0.00 3.99
2024 2632 4.570772 ACGCATCATAGCTCAATTAACGTT 59.429 37.500 5.88 5.88 0.00 3.99
2025 2633 5.064707 ACGCATCATAGCTCAATTAACGTTT 59.935 36.000 5.91 0.00 0.00 3.60
2026 2634 5.393452 CGCATCATAGCTCAATTAACGTTTG 59.607 40.000 5.91 0.00 0.00 2.93
2027 2635 6.258160 GCATCATAGCTCAATTAACGTTTGT 58.742 36.000 5.91 0.00 0.00 2.83
2028 2636 7.406553 GCATCATAGCTCAATTAACGTTTGTA 58.593 34.615 5.91 0.00 0.00 2.41
2029 2637 7.373441 GCATCATAGCTCAATTAACGTTTGTAC 59.627 37.037 5.91 0.00 0.00 2.90
2030 2638 7.892778 TCATAGCTCAATTAACGTTTGTACA 57.107 32.000 5.91 0.00 0.00 2.90
2031 2639 7.735500 TCATAGCTCAATTAACGTTTGTACAC 58.264 34.615 5.91 0.00 0.00 2.90
2032 2640 5.013861 AGCTCAATTAACGTTTGTACACG 57.986 39.130 5.91 0.00 46.04 4.49
2040 2648 2.392611 CGTTTGTACACGTACGCATC 57.607 50.000 16.72 4.34 38.85 3.91
2041 2649 1.714990 CGTTTGTACACGTACGCATCA 59.285 47.619 16.72 7.04 38.85 3.07
2042 2650 2.343246 CGTTTGTACACGTACGCATCAT 59.657 45.455 16.72 0.00 38.85 2.45
2060 2668 6.968904 CGCATCATAGCTGAATTAACTTTTGT 59.031 34.615 0.00 0.00 34.37 2.83
2068 2676 7.570161 AGCTGAATTAACTTTTGTACACGTAC 58.430 34.615 0.00 0.22 36.63 3.67
2069 2677 7.440255 AGCTGAATTAACTTTTGTACACGTACT 59.560 33.333 8.69 0.00 37.00 2.73
2070 2678 8.702438 GCTGAATTAACTTTTGTACACGTACTA 58.298 33.333 8.69 0.00 37.00 1.82
2072 2680 8.702438 TGAATTAACTTTTGTACACGTACTAGC 58.298 33.333 8.69 0.00 37.00 3.42
2073 2681 8.592105 AATTAACTTTTGTACACGTACTAGCA 57.408 30.769 8.69 0.00 37.00 3.49
2074 2682 7.627585 TTAACTTTTGTACACGTACTAGCAG 57.372 36.000 8.69 4.40 37.00 4.24
2075 2683 4.553323 ACTTTTGTACACGTACTAGCAGG 58.447 43.478 8.69 0.00 37.00 4.85
2076 2684 2.642139 TTGTACACGTACTAGCAGGC 57.358 50.000 8.69 0.00 37.00 4.85
2077 2685 1.536940 TGTACACGTACTAGCAGGCA 58.463 50.000 8.69 0.00 37.00 4.75
2078 2686 1.471287 TGTACACGTACTAGCAGGCAG 59.529 52.381 8.69 0.00 37.00 4.85
2079 2687 0.454600 TACACGTACTAGCAGGCAGC 59.545 55.000 0.00 0.00 46.19 5.25
2080 2688 4.339572 GTACACGTACTAGCAGGCAGCA 62.340 54.545 4.24 0.00 38.18 4.41
2081 2689 5.584886 GTACACGTACTAGCAGGCAGCAT 62.585 52.174 4.24 0.00 38.18 3.79
2082 2690 6.274623 GTACACGTACTAGCAGGCAGCATA 62.275 50.000 4.24 0.00 38.18 3.14
2083 2691 7.982013 GTACACGTACTAGCAGGCAGCATAG 62.982 52.000 4.24 5.83 38.18 2.23
2100 2708 5.596845 AGCATAGCTGAACTAGTTTAGAGC 58.403 41.667 26.70 22.89 37.57 4.09
2101 2709 4.747605 GCATAGCTGAACTAGTTTAGAGCC 59.252 45.833 26.70 12.09 33.29 4.70
2102 2710 5.452636 GCATAGCTGAACTAGTTTAGAGCCT 60.453 44.000 26.70 17.50 33.29 4.58
2103 2711 6.239064 GCATAGCTGAACTAGTTTAGAGCCTA 60.239 42.308 26.70 18.77 33.29 3.93
2104 2712 7.684670 GCATAGCTGAACTAGTTTAGAGCCTAA 60.685 40.741 26.70 14.55 33.29 2.69
2105 2713 6.215495 AGCTGAACTAGTTTAGAGCCTAAG 57.785 41.667 26.70 3.60 0.00 2.18
2106 2714 5.717654 AGCTGAACTAGTTTAGAGCCTAAGT 59.282 40.000 26.70 9.02 0.00 2.24
2107 2715 6.890814 AGCTGAACTAGTTTAGAGCCTAAGTA 59.109 38.462 26.70 0.00 0.00 2.24
2108 2716 7.562088 AGCTGAACTAGTTTAGAGCCTAAGTAT 59.438 37.037 26.70 7.88 0.00 2.12
2109 2717 7.863877 GCTGAACTAGTTTAGAGCCTAAGTATC 59.136 40.741 26.70 4.92 0.00 2.24
2110 2718 8.235359 TGAACTAGTTTAGAGCCTAAGTATCC 57.765 38.462 10.02 0.00 0.00 2.59
2111 2719 7.837689 TGAACTAGTTTAGAGCCTAAGTATCCA 59.162 37.037 10.02 0.00 0.00 3.41
2112 2720 8.785184 AACTAGTTTAGAGCCTAAGTATCCAT 57.215 34.615 1.12 0.00 0.00 3.41
2113 2721 8.411991 ACTAGTTTAGAGCCTAAGTATCCATC 57.588 38.462 0.00 0.00 0.00 3.51
2114 2722 6.673839 AGTTTAGAGCCTAAGTATCCATCC 57.326 41.667 0.00 0.00 0.00 3.51
2115 2723 6.143915 AGTTTAGAGCCTAAGTATCCATCCA 58.856 40.000 0.00 0.00 0.00 3.41
2116 2724 6.789959 AGTTTAGAGCCTAAGTATCCATCCAT 59.210 38.462 0.00 0.00 0.00 3.41
2117 2725 6.859112 TTAGAGCCTAAGTATCCATCCATC 57.141 41.667 0.00 0.00 0.00 3.51
2118 2726 4.756564 AGAGCCTAAGTATCCATCCATCA 58.243 43.478 0.00 0.00 0.00 3.07
2119 2727 4.776837 AGAGCCTAAGTATCCATCCATCAG 59.223 45.833 0.00 0.00 0.00 2.90
2120 2728 4.756564 AGCCTAAGTATCCATCCATCAGA 58.243 43.478 0.00 0.00 0.00 3.27
2121 2729 5.158141 AGCCTAAGTATCCATCCATCAGAA 58.842 41.667 0.00 0.00 0.00 3.02
2122 2730 5.248020 AGCCTAAGTATCCATCCATCAGAAG 59.752 44.000 0.00 0.00 0.00 2.85
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 7.334421 TGTTGATTTCTGAGCCTCTGTTAATAC 59.666 37.037 0.00 0.00 0.00 1.89
1 2 7.394016 TGTTGATTTCTGAGCCTCTGTTAATA 58.606 34.615 0.00 0.00 0.00 0.98
2 3 6.240894 TGTTGATTTCTGAGCCTCTGTTAAT 58.759 36.000 0.00 0.00 0.00 1.40
4 5 5.227569 TGTTGATTTCTGAGCCTCTGTTA 57.772 39.130 0.00 0.00 0.00 2.41
6 7 3.777106 TGTTGATTTCTGAGCCTCTGT 57.223 42.857 0.00 0.00 0.00 3.41
7 8 3.377485 CCATGTTGATTTCTGAGCCTCTG 59.623 47.826 0.00 0.00 0.00 3.35
57 59 3.644606 CAGGGGGTGTCTGCTGCT 61.645 66.667 0.00 0.00 0.00 4.24
80 82 2.093711 GGTCAAAACACAGGGCACTTTT 60.094 45.455 0.00 0.00 0.00 2.27
101 103 5.674525 TCCATGTATCTTGCCTAGTTTCTG 58.325 41.667 0.00 0.00 0.00 3.02
102 104 5.957771 TCCATGTATCTTGCCTAGTTTCT 57.042 39.130 0.00 0.00 0.00 2.52
166 171 1.679139 TGGTTGAGGTGCTTGTCTTG 58.321 50.000 0.00 0.00 0.00 3.02
253 274 2.017113 GCCGGGGTATCTTTTGACTGG 61.017 57.143 2.18 0.00 0.00 4.00
324 348 0.320374 TCCTTGTGTCGCCTCGATTT 59.680 50.000 0.00 0.00 38.42 2.17
492 518 1.112113 TGGGAGAACACTAGCGATCC 58.888 55.000 0.00 0.00 0.00 3.36
828 854 0.657840 ATGCAACCGCGCTAATTCTC 59.342 50.000 5.56 0.00 42.97 2.87
870 896 2.439507 CTGGGCTTTTATAGAGGAGGCA 59.560 50.000 0.00 0.00 36.51 4.75
913 939 1.003355 GCTGGAGCTTGCTGTGGTA 60.003 57.895 0.00 0.00 38.21 3.25
930 956 0.543277 TGTGTGATCAGATCCCTGGC 59.457 55.000 8.00 0.00 40.76 4.85
940 966 1.889170 AGTTCGCTCTCTGTGTGATCA 59.111 47.619 0.00 0.00 0.00 2.92
956 983 2.278854 GAGATGCAAGCAGGAGAGTTC 58.721 52.381 0.00 0.00 0.00 3.01
970 997 5.358090 TGATGAACTGAAGAGATGAGATGC 58.642 41.667 0.00 0.00 0.00 3.91
975 1002 5.156608 TGCTTGATGAACTGAAGAGATGA 57.843 39.130 0.00 0.00 0.00 2.92
1056 1083 3.715097 AGCCTGGCTCTGTGCTCC 61.715 66.667 17.22 0.00 42.39 4.70
1124 1151 1.133853 GGAGGAGAATGCAGCTTGGAT 60.134 52.381 0.00 0.00 0.00 3.41
1147 1178 2.887151 CCCTTGACTTGATGGGTTCT 57.113 50.000 0.00 0.00 35.13 3.01
1169 1201 2.983229 AGTGTGACTTCTCCATGCATC 58.017 47.619 0.00 0.00 0.00 3.91
1219 1251 9.889128 TCCTAACTTCTACTTCTACTCTAAGTC 57.111 37.037 0.00 0.00 38.18 3.01
1222 1254 9.683870 CCTTCCTAACTTCTACTTCTACTCTAA 57.316 37.037 0.00 0.00 0.00 2.10
1223 1255 9.055689 TCCTTCCTAACTTCTACTTCTACTCTA 57.944 37.037 0.00 0.00 0.00 2.43
1224 1256 7.931046 TCCTTCCTAACTTCTACTTCTACTCT 58.069 38.462 0.00 0.00 0.00 3.24
1240 1272 2.505819 GAGCATGGGAGTTCCTTCCTAA 59.494 50.000 0.00 0.00 37.40 2.69
1311 1347 7.461107 ACGAATAACTCATGGTGAAATAAACG 58.539 34.615 0.00 0.00 0.00 3.60
1363 1400 1.079405 GGACGGCACATCGGAGAAA 60.079 57.895 0.00 0.00 43.58 2.52
1366 1403 1.672854 TAAGGGACGGCACATCGGAG 61.673 60.000 0.00 0.00 0.00 4.63
1370 1407 1.523938 GCCTAAGGGACGGCACATC 60.524 63.158 0.00 0.00 45.59 3.06
1378 1415 4.147135 TCCCACTGCCTAAGGGAC 57.853 61.111 0.00 0.00 46.42 4.46
1400 1439 4.211125 TGTCCAAAAAGATACAACAGCCA 58.789 39.130 0.00 0.00 0.00 4.75
1443 1482 6.264970 CACTGAATCATCTCTATCAGACCAGA 59.735 42.308 8.48 0.00 41.38 3.86
1444 1483 6.264970 TCACTGAATCATCTCTATCAGACCAG 59.735 42.308 8.48 0.00 41.38 4.00
1490 1529 6.652205 TTTCATATTAGGAGGACAAGGGTT 57.348 37.500 0.00 0.00 0.00 4.11
1493 1532 8.930846 ATTCATTTCATATTAGGAGGACAAGG 57.069 34.615 0.00 0.00 0.00 3.61
1526 1565 3.383825 GCCTCCACTACCGAAGAAGATAA 59.616 47.826 0.00 0.00 0.00 1.75
1536 1575 2.365617 ACTCATATTGCCTCCACTACCG 59.634 50.000 0.00 0.00 0.00 4.02
1540 1579 5.538813 TCGTATAACTCATATTGCCTCCACT 59.461 40.000 0.00 0.00 0.00 4.00
1547 1586 5.284188 GCTCGAGTCGTATAACTCATATTGC 59.716 44.000 15.13 0.00 44.88 3.56
1548 1587 6.521477 CAGCTCGAGTCGTATAACTCATATTG 59.479 42.308 15.13 0.00 44.88 1.90
1549 1588 6.205076 ACAGCTCGAGTCGTATAACTCATATT 59.795 38.462 15.13 0.00 44.88 1.28
1550 1589 5.701750 ACAGCTCGAGTCGTATAACTCATAT 59.298 40.000 15.13 0.00 44.88 1.78
1551 1590 5.055144 ACAGCTCGAGTCGTATAACTCATA 58.945 41.667 15.13 0.00 44.88 2.15
1552 1591 3.878103 ACAGCTCGAGTCGTATAACTCAT 59.122 43.478 15.13 0.00 44.88 2.90
1553 1592 3.268330 ACAGCTCGAGTCGTATAACTCA 58.732 45.455 15.13 0.00 44.88 3.41
1554 1593 3.864163 GACAGCTCGAGTCGTATAACTC 58.136 50.000 15.13 0.00 41.88 3.01
1555 1594 3.948196 GACAGCTCGAGTCGTATAACT 57.052 47.619 15.13 0.00 0.00 2.24
1567 1606 6.255887 AGGATTAAAAGTTTATCGACAGCTCG 59.744 38.462 0.00 0.00 41.65 5.03
1593 1632 5.526479 CAGAATATAGCGAGGCATGCATATT 59.474 40.000 21.36 17.47 33.17 1.28
1603 1642 2.159448 CGAGCTCCAGAATATAGCGAGG 60.159 54.545 8.47 0.00 41.19 4.63
1629 1668 9.773328 CACACACACATGGTTATTTCTATAAAG 57.227 33.333 0.00 0.00 0.00 1.85
1672 1712 2.766651 TATCCCCACCTCACGCCC 60.767 66.667 0.00 0.00 0.00 6.13
1673 1713 1.335132 TTCTATCCCCACCTCACGCC 61.335 60.000 0.00 0.00 0.00 5.68
1674 1714 0.179081 GTTCTATCCCCACCTCACGC 60.179 60.000 0.00 0.00 0.00 5.34
1675 1715 1.191535 TGTTCTATCCCCACCTCACG 58.808 55.000 0.00 0.00 0.00 4.35
1679 1719 3.974642 GAGGTAATGTTCTATCCCCACCT 59.025 47.826 0.00 0.00 37.85 4.00
1733 1958 9.787435 TTTATTCTTGGTGTATAGAAGTTGTGT 57.213 29.630 0.00 0.00 34.17 3.72
1742 1967 9.712305 CCCTAGTGATTTATTCTTGGTGTATAG 57.288 37.037 0.00 0.00 0.00 1.31
1743 1968 9.220906 ACCCTAGTGATTTATTCTTGGTGTATA 57.779 33.333 0.00 0.00 0.00 1.47
1776 2005 3.263425 GGACTTCCTGTTCATTCCCTACA 59.737 47.826 0.00 0.00 0.00 2.74
1836 2065 9.959749 GACAAAATTTCTGACAACCAATAAGTA 57.040 29.630 0.00 0.00 0.00 2.24
1837 2066 7.926018 GGACAAAATTTCTGACAACCAATAAGT 59.074 33.333 0.00 0.00 0.00 2.24
1849 2079 2.956132 TGGCCTGGACAAAATTTCTGA 58.044 42.857 0.00 0.00 0.00 3.27
1850 2080 3.749665 TTGGCCTGGACAAAATTTCTG 57.250 42.857 13.82 0.00 0.00 3.02
1867 2470 4.713824 ATGCACTTCAACTCATCATTGG 57.286 40.909 0.00 0.00 0.00 3.16
1896 2499 7.041576 TGCTGCTTAAGACATTATATGAAGCTG 60.042 37.037 6.67 0.00 37.32 4.24
1906 2509 5.448438 CGTTGTTTGCTGCTTAAGACATTA 58.552 37.500 6.67 0.00 0.00 1.90
1907 2510 4.290155 CGTTGTTTGCTGCTTAAGACATT 58.710 39.130 6.67 0.00 0.00 2.71
1908 2511 3.304659 CCGTTGTTTGCTGCTTAAGACAT 60.305 43.478 6.67 0.00 0.00 3.06
1925 2528 2.584608 CCCTGGTAGGCTCCGTTG 59.415 66.667 0.00 0.00 32.73 4.10
1937 2540 6.384305 ACTGCTTATATAATAGTAGGCCCTGG 59.616 42.308 0.00 0.00 0.00 4.45
1938 2541 7.418025 GGACTGCTTATATAATAGTAGGCCCTG 60.418 44.444 11.57 1.49 44.05 4.45
1939 2542 6.612049 GGACTGCTTATATAATAGTAGGCCCT 59.388 42.308 11.57 0.00 44.05 5.19
1940 2543 6.818233 GGACTGCTTATATAATAGTAGGCCC 58.182 44.000 11.57 5.72 44.05 5.80
1952 2555 9.700831 AAAAGGACAATAAAGGACTGCTTATAT 57.299 29.630 0.00 0.00 0.00 0.86
1953 2556 8.956426 CAAAAGGACAATAAAGGACTGCTTATA 58.044 33.333 0.00 0.00 0.00 0.98
1954 2557 7.451566 ACAAAAGGACAATAAAGGACTGCTTAT 59.548 33.333 0.00 0.00 0.00 1.73
1955 2558 6.775629 ACAAAAGGACAATAAAGGACTGCTTA 59.224 34.615 0.00 0.00 0.00 3.09
1956 2559 5.598417 ACAAAAGGACAATAAAGGACTGCTT 59.402 36.000 0.00 0.00 0.00 3.91
1967 2570 5.686753 ACACCACAGTACAAAAGGACAATA 58.313 37.500 0.00 0.00 0.00 1.90
1986 2589 0.174845 TGCGTAGGATGCAGTACACC 59.825 55.000 0.00 0.00 34.76 4.16
1999 2607 5.402568 ACGTTAATTGAGCTATGATGCGTAG 59.597 40.000 0.00 0.00 38.13 3.51
2022 2630 3.984018 ATGATGCGTACGTGTACAAAC 57.016 42.857 17.90 5.83 35.87 2.93
2023 2631 3.548668 GCTATGATGCGTACGTGTACAAA 59.451 43.478 17.90 0.00 35.87 2.83
2024 2632 3.110358 GCTATGATGCGTACGTGTACAA 58.890 45.455 17.90 0.00 35.87 2.41
2025 2633 2.356695 AGCTATGATGCGTACGTGTACA 59.643 45.455 17.90 12.23 35.87 2.90
2026 2634 2.719556 CAGCTATGATGCGTACGTGTAC 59.280 50.000 17.90 6.99 38.13 2.90
2027 2635 2.614983 TCAGCTATGATGCGTACGTGTA 59.385 45.455 17.90 4.28 38.13 2.90
2028 2636 1.404035 TCAGCTATGATGCGTACGTGT 59.596 47.619 17.90 5.64 38.13 4.49
2029 2637 2.119671 TCAGCTATGATGCGTACGTG 57.880 50.000 17.90 3.74 38.13 4.49
2030 2638 2.863401 TTCAGCTATGATGCGTACGT 57.137 45.000 17.90 0.00 34.73 3.57
2031 2639 5.402568 AGTTAATTCAGCTATGATGCGTACG 59.597 40.000 11.84 11.84 34.73 3.67
2032 2640 6.771188 AGTTAATTCAGCTATGATGCGTAC 57.229 37.500 0.00 0.00 34.73 3.67
2033 2641 7.786178 AAAGTTAATTCAGCTATGATGCGTA 57.214 32.000 0.00 0.00 34.73 4.42
2034 2642 6.683974 AAAGTTAATTCAGCTATGATGCGT 57.316 33.333 0.00 0.00 34.73 5.24
2035 2643 6.968904 ACAAAAGTTAATTCAGCTATGATGCG 59.031 34.615 0.00 0.00 34.73 4.73
2036 2644 9.226345 GTACAAAAGTTAATTCAGCTATGATGC 57.774 33.333 0.00 0.00 34.73 3.91
2039 2647 8.440059 CGTGTACAAAAGTTAATTCAGCTATGA 58.560 33.333 0.00 0.00 0.00 2.15
2040 2648 8.227791 ACGTGTACAAAAGTTAATTCAGCTATG 58.772 33.333 0.00 0.00 0.00 2.23
2041 2649 8.319143 ACGTGTACAAAAGTTAATTCAGCTAT 57.681 30.769 0.00 0.00 0.00 2.97
2042 2650 7.718272 ACGTGTACAAAAGTTAATTCAGCTA 57.282 32.000 0.00 0.00 0.00 3.32
2060 2668 0.454600 GCTGCCTGCTAGTACGTGTA 59.545 55.000 0.00 0.00 38.95 2.90
2077 2685 5.452636 GGCTCTAAACTAGTTCAGCTATGCT 60.453 44.000 23.29 5.38 40.77 3.79
2078 2686 4.747605 GGCTCTAAACTAGTTCAGCTATGC 59.252 45.833 23.29 14.64 0.00 3.14
2079 2687 6.155475 AGGCTCTAAACTAGTTCAGCTATG 57.845 41.667 23.29 8.11 0.00 2.23
2080 2688 7.562088 ACTTAGGCTCTAAACTAGTTCAGCTAT 59.438 37.037 23.29 17.63 0.00 2.97
2081 2689 6.890814 ACTTAGGCTCTAAACTAGTTCAGCTA 59.109 38.462 23.29 15.22 0.00 3.32
2082 2690 5.717654 ACTTAGGCTCTAAACTAGTTCAGCT 59.282 40.000 23.29 15.87 0.00 4.24
2083 2691 5.968254 ACTTAGGCTCTAAACTAGTTCAGC 58.032 41.667 19.10 19.10 0.00 4.26
2084 2692 8.354426 GGATACTTAGGCTCTAAACTAGTTCAG 58.646 40.741 8.95 3.60 0.00 3.02
2085 2693 7.837689 TGGATACTTAGGCTCTAAACTAGTTCA 59.162 37.037 8.95 0.00 37.61 3.18
2086 2694 8.235359 TGGATACTTAGGCTCTAAACTAGTTC 57.765 38.462 8.95 0.00 37.61 3.01
2087 2695 8.785184 ATGGATACTTAGGCTCTAAACTAGTT 57.215 34.615 1.12 1.12 37.61 2.24
2088 2696 7.452189 GGATGGATACTTAGGCTCTAAACTAGT 59.548 40.741 0.00 0.00 37.61 2.57
2089 2697 7.451877 TGGATGGATACTTAGGCTCTAAACTAG 59.548 40.741 0.00 0.00 37.61 2.57
2090 2698 7.302948 TGGATGGATACTTAGGCTCTAAACTA 58.697 38.462 0.00 0.00 37.61 2.24
2091 2699 6.143915 TGGATGGATACTTAGGCTCTAAACT 58.856 40.000 0.00 0.00 37.61 2.66
2092 2700 6.420913 TGGATGGATACTTAGGCTCTAAAC 57.579 41.667 0.00 0.00 37.61 2.01
2093 2701 6.787458 TGATGGATGGATACTTAGGCTCTAAA 59.213 38.462 0.00 0.00 37.61 1.85
2094 2702 6.322931 TGATGGATGGATACTTAGGCTCTAA 58.677 40.000 0.00 0.00 37.61 2.10
2095 2703 5.903923 TGATGGATGGATACTTAGGCTCTA 58.096 41.667 0.00 0.00 37.61 2.43
2096 2704 4.756564 TGATGGATGGATACTTAGGCTCT 58.243 43.478 0.00 0.00 37.61 4.09
2097 2705 4.774726 TCTGATGGATGGATACTTAGGCTC 59.225 45.833 0.00 0.00 37.61 4.70
2098 2706 4.756564 TCTGATGGATGGATACTTAGGCT 58.243 43.478 0.00 0.00 37.61 4.58
2099 2707 5.486526 CTTCTGATGGATGGATACTTAGGC 58.513 45.833 0.00 0.00 37.61 3.93


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

AutoCloner maintained by Alex Coulton.