Multiple sequence alignment - TraesCS6A01G170300

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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 TraesCS6A01G170300 chr6A 100.000 2471 0 0 1 2471 180626680 180624210 0.000000e+00 4564
1 TraesCS6A01G170300 chr6A 83.624 861 105 23 823 1666 87653937 87653096 0.000000e+00 776
2 TraesCS6A01G170300 chr6A 92.500 480 33 1 992 1471 87906868 87907344 0.000000e+00 684
3 TraesCS6A01G170300 chr6A 86.726 339 44 1 1 338 87546516 87546854 2.320000e-100 375
4 TraesCS6A01G170300 chr6B 88.276 1450 91 35 693 2105 237417208 237415801 0.000000e+00 1663
5 TraesCS6A01G170300 chr6B 83.218 864 110 25 823 1668 144920926 144920080 0.000000e+00 760
6 TraesCS6A01G170300 chr6B 88.455 589 44 12 946 1533 145043594 145044159 0.000000e+00 689
7 TraesCS6A01G170300 chr6B 88.547 358 25 8 2120 2469 237412629 237412280 1.060000e-113 420
8 TraesCS6A01G170300 chr4A 85.836 706 81 9 1 693 497094265 497093566 0.000000e+00 732
9 TraesCS6A01G170300 chr6D 85.185 729 74 21 823 1532 69932987 69932274 0.000000e+00 717
10 TraesCS6A01G170300 chr6D 85.838 692 64 16 800 1472 70634107 70634783 0.000000e+00 704
11 TraesCS6A01G170300 chr2B 88.245 587 55 11 952 1533 756674494 756673917 0.000000e+00 689
12 TraesCS6A01G170300 chr2B 86.420 405 49 5 294 693 506594331 506594734 2.920000e-119 438
13 TraesCS6A01G170300 chr4B 83.000 700 101 10 1 692 575334241 575333552 3.490000e-173 617
14 TraesCS6A01G170300 chr5D 90.000 470 38 5 998 1467 358798383 358798843 1.260000e-167 599
15 TraesCS6A01G170300 chr7B 81.298 647 95 18 63 693 369784992 369785628 3.670000e-138 501
16 TraesCS6A01G170300 chr1D 81.801 544 82 11 157 689 54923158 54922621 8.110000e-120 440


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 TraesCS6A01G170300 chr6A 180624210 180626680 2470 True 4564.0 4564 100.0000 1 2471 1 chr6A.!!$R2 2470
1 TraesCS6A01G170300 chr6A 87653096 87653937 841 True 776.0 776 83.6240 823 1666 1 chr6A.!!$R1 843
2 TraesCS6A01G170300 chr6B 237412280 237417208 4928 True 1041.5 1663 88.4115 693 2469 2 chr6B.!!$R2 1776
3 TraesCS6A01G170300 chr6B 144920080 144920926 846 True 760.0 760 83.2180 823 1668 1 chr6B.!!$R1 845
4 TraesCS6A01G170300 chr6B 145043594 145044159 565 False 689.0 689 88.4550 946 1533 1 chr6B.!!$F1 587
5 TraesCS6A01G170300 chr4A 497093566 497094265 699 True 732.0 732 85.8360 1 693 1 chr4A.!!$R1 692
6 TraesCS6A01G170300 chr6D 69932274 69932987 713 True 717.0 717 85.1850 823 1532 1 chr6D.!!$R1 709
7 TraesCS6A01G170300 chr6D 70634107 70634783 676 False 704.0 704 85.8380 800 1472 1 chr6D.!!$F1 672
8 TraesCS6A01G170300 chr2B 756673917 756674494 577 True 689.0 689 88.2450 952 1533 1 chr2B.!!$R1 581
9 TraesCS6A01G170300 chr4B 575333552 575334241 689 True 617.0 617 83.0000 1 692 1 chr4B.!!$R1 691
10 TraesCS6A01G170300 chr7B 369784992 369785628 636 False 501.0 501 81.2980 63 693 1 chr7B.!!$F1 630
11 TraesCS6A01G170300 chr1D 54922621 54923158 537 True 440.0 440 81.8010 157 689 1 chr1D.!!$R1 532

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
792 810 0.460722 TGAGTTCGACACACCGGAAA 59.539 50.0 9.46 0.0 0.0 3.13 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1950 2037 0.109132 CAATTGCCCGCCAAACTCTC 60.109 55.0 0.0 0.0 36.92 3.2 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
18 19 2.162716 GTTCTTGGCGCGATCTGTT 58.837 52.632 12.10 0.00 0.00 3.16
36 37 0.952010 TTTACGCGGCCAAGTTCTCC 60.952 55.000 12.47 0.00 0.00 3.71
99 100 2.278531 GCGCCACTGCAAAAACGT 60.279 55.556 0.00 0.00 37.32 3.99
106 107 3.483411 GCCACTGCAAAAACGTTTCTTTG 60.483 43.478 15.01 16.39 37.47 2.77
109 111 5.333721 CCACTGCAAAAACGTTTCTTTGTTT 60.334 36.000 20.72 7.28 39.84 2.83
155 157 1.352156 CCTTTGACCGACTAGCACGC 61.352 60.000 4.69 0.00 0.00 5.34
193 195 2.025981 AGAGTTCATGCCCACTATGCAA 60.026 45.455 0.00 0.00 42.92 4.08
224 226 4.582973 TGAAACCATGACCCACATCATA 57.417 40.909 0.00 0.00 37.20 2.15
262 264 2.997315 GGAGGTTTGGGCAAGGGC 60.997 66.667 0.00 0.00 40.13 5.19
338 340 2.143122 GAGTGGTGCATTCGACAAGAA 58.857 47.619 0.00 0.00 43.93 2.52
353 355 5.995282 TCGACAAGAATAAAGTGGACAACAT 59.005 36.000 0.00 0.00 0.00 2.71
387 390 1.551883 GGCCAATTTGCATCCTTGTCT 59.448 47.619 0.00 0.00 0.00 3.41
397 400 2.856222 CATCCTTGTCTTATGGGAGCC 58.144 52.381 0.00 0.00 0.00 4.70
441 444 3.982372 TTCGATGGAGCGACGCCAC 62.982 63.158 17.79 10.43 40.42 5.01
450 453 3.524606 CGACGCCACCTACGGGAT 61.525 66.667 0.00 0.00 36.25 3.85
552 559 2.029964 CGCAACGTGGGGTAGTGT 59.970 61.111 0.00 0.00 0.00 3.55
587 601 1.866015 AGTATGCTGTGGAGTGGCTA 58.134 50.000 0.00 0.00 0.00 3.93
653 670 3.844804 GAGTCTTTCCCTTTCCCTCCTTA 59.155 47.826 0.00 0.00 0.00 2.69
663 680 7.985589 TCCCTTTCCCTCCTTAAATATATGAC 58.014 38.462 0.00 0.00 0.00 3.06
719 736 6.181190 GTTGAATAAAGCTCTAAACTCCCCT 58.819 40.000 0.00 0.00 0.00 4.79
720 737 5.745227 TGAATAAAGCTCTAAACTCCCCTG 58.255 41.667 0.00 0.00 0.00 4.45
721 738 2.498644 AAAGCTCTAAACTCCCCTGC 57.501 50.000 0.00 0.00 0.00 4.85
722 739 1.362224 AAGCTCTAAACTCCCCTGCA 58.638 50.000 0.00 0.00 0.00 4.41
723 740 1.362224 AGCTCTAAACTCCCCTGCAA 58.638 50.000 0.00 0.00 0.00 4.08
726 743 3.092301 GCTCTAAACTCCCCTGCAAAAT 58.908 45.455 0.00 0.00 0.00 1.82
728 745 4.705023 GCTCTAAACTCCCCTGCAAAATAA 59.295 41.667 0.00 0.00 0.00 1.40
731 748 7.604657 TCTAAACTCCCCTGCAAAATAAAAA 57.395 32.000 0.00 0.00 0.00 1.94
732 749 8.201242 TCTAAACTCCCCTGCAAAATAAAAAT 57.799 30.769 0.00 0.00 0.00 1.82
734 751 9.936759 CTAAACTCCCCTGCAAAATAAAAATAA 57.063 29.630 0.00 0.00 0.00 1.40
786 804 1.912110 GCTCGTATGAGTTCGACACAC 59.088 52.381 13.46 0.00 44.48 3.82
790 808 1.200716 GTATGAGTTCGACACACCGGA 59.799 52.381 9.46 0.00 0.00 5.14
792 810 0.460722 TGAGTTCGACACACCGGAAA 59.539 50.000 9.46 0.00 0.00 3.13
794 812 1.725164 GAGTTCGACACACCGGAAATC 59.275 52.381 9.46 0.00 0.00 2.17
796 814 1.459592 GTTCGACACACCGGAAATCTG 59.540 52.381 9.46 0.00 0.00 2.90
798 816 1.341852 TCGACACACCGGAAATCTGAA 59.658 47.619 9.46 0.00 0.00 3.02
815 842 1.295792 GAAATCGCAGCCGTCCATTA 58.704 50.000 0.00 0.00 35.54 1.90
851 879 2.316867 CCATTGCACACTCACGCGA 61.317 57.895 15.93 0.00 0.00 5.87
857 885 1.959899 GCACACTCACGCGAATCCTG 61.960 60.000 15.93 0.00 0.00 3.86
884 920 1.671054 CGCCGCTTCTTCCTTTCCA 60.671 57.895 0.00 0.00 0.00 3.53
945 997 1.502163 CTCCGCAATCTCCAATCGCC 61.502 60.000 0.00 0.00 0.00 5.54
946 998 1.819208 CCGCAATCTCCAATCGCCA 60.819 57.895 0.00 0.00 0.00 5.69
947 999 1.353103 CGCAATCTCCAATCGCCAC 59.647 57.895 0.00 0.00 0.00 5.01
986 1049 1.282157 CCGAATCCTTTCCCTTCCAGT 59.718 52.381 0.00 0.00 0.00 4.00
994 1057 1.708993 TTCCCTTCCAGTGCAGCAGT 61.709 55.000 0.00 0.00 0.00 4.40
996 1059 0.825010 CCCTTCCAGTGCAGCAGTTT 60.825 55.000 0.00 0.00 0.00 2.66
1020 1083 2.512515 GACGCCTCAGCCACCATC 60.513 66.667 0.00 0.00 34.57 3.51
1021 1084 3.315142 GACGCCTCAGCCACCATCA 62.315 63.158 0.00 0.00 34.57 3.07
1026 1089 1.376086 CTCAGCCACCATCACCACA 59.624 57.895 0.00 0.00 0.00 4.17
1033 1096 0.692476 CACCATCACCACAGGGAAGA 59.308 55.000 0.00 0.00 38.05 2.87
1198 1261 2.754658 CCCCTGTCTACCTCGCGT 60.755 66.667 5.77 0.00 0.00 6.01
1356 1419 3.814268 GGCGTCACCATTGCGCAT 61.814 61.111 12.75 0.00 44.76 4.73
1403 1466 0.034670 GTGCTGCTCCCCAAGAAGAT 60.035 55.000 0.00 0.00 31.23 2.40
1406 1469 0.622665 CTGCTCCCCAAGAAGATGGT 59.377 55.000 0.00 0.00 38.91 3.55
1414 1477 2.419297 CCCAAGAAGATGGTCGAGAAGG 60.419 54.545 0.00 0.00 38.91 3.46
1416 1479 1.561643 AGAAGATGGTCGAGAAGGCA 58.438 50.000 0.00 0.00 0.00 4.75
1501 1564 5.399013 GTCGCCTTGCTTAAATTGTTGTAT 58.601 37.500 0.00 0.00 0.00 2.29
1533 1599 1.678728 GGATCGATGGGTGTGCTTCAA 60.679 52.381 0.54 0.00 0.00 2.69
1536 1602 1.202758 TCGATGGGTGTGCTTCAAAGT 60.203 47.619 0.00 0.00 0.00 2.66
1542 1608 1.798813 GGTGTGCTTCAAAGTAGACGG 59.201 52.381 2.87 0.00 36.10 4.79
1556 1622 1.663695 AGACGGTTGTTGTTGGTCTG 58.336 50.000 0.00 0.00 36.66 3.51
1558 1624 0.750182 ACGGTTGTTGTTGGTCTGGG 60.750 55.000 0.00 0.00 0.00 4.45
1589 1655 6.458888 CGCTGTATCTTCTCATCTGTGACTTA 60.459 42.308 0.00 0.00 0.00 2.24
1594 1660 6.840780 TCTTCTCATCTGTGACTTACATGA 57.159 37.500 0.00 0.00 38.92 3.07
1625 1691 8.828863 TGCGTTGCATAAACAATTGTGTTCCT 62.829 38.462 12.82 0.00 39.41 3.36
1635 1701 1.189752 TTGTGTTCCTTTTGCCTGCA 58.810 45.000 0.00 0.00 0.00 4.41
1642 1708 1.977854 TCCTTTTGCCTGCACTCTCTA 59.022 47.619 0.00 0.00 0.00 2.43
1674 1753 7.478322 TGCTTAGATTTGCATCTTTGAGATTC 58.522 34.615 0.00 0.00 40.53 2.52
1779 1859 3.932089 GCATGTTTGAAATATTTGGCGGT 59.068 39.130 5.17 0.00 0.00 5.68
1793 1873 3.504927 CGGTTGTATTTCCCGCCC 58.495 61.111 0.00 0.00 34.62 6.13
1796 1876 0.396556 GGTTGTATTTCCCGCCCCAT 60.397 55.000 0.00 0.00 0.00 4.00
1871 1952 3.680156 GTCCAAATTGGGCGCTCA 58.320 55.556 5.44 5.44 38.32 4.26
1877 1958 0.323725 AAATTGGGCGCTCATGGAGT 60.324 50.000 12.70 0.00 31.39 3.85
1900 1987 0.453390 GCGCCCAAGAGGATTGAAAG 59.547 55.000 0.00 0.00 38.24 2.62
1902 1989 2.012673 CGCCCAAGAGGATTGAAAGAG 58.987 52.381 0.00 0.00 38.24 2.85
1903 1990 2.616510 CGCCCAAGAGGATTGAAAGAGT 60.617 50.000 0.00 0.00 38.24 3.24
1904 1991 3.425659 GCCCAAGAGGATTGAAAGAGTT 58.574 45.455 0.00 0.00 38.24 3.01
1938 2025 2.522372 CAAGATTTGCTGCTCGACTG 57.478 50.000 0.00 0.00 0.00 3.51
1939 2026 2.071540 CAAGATTTGCTGCTCGACTGA 58.928 47.619 0.00 0.00 0.00 3.41
1940 2027 2.462456 AGATTTGCTGCTCGACTGAA 57.538 45.000 0.00 0.00 0.00 3.02
1941 2028 2.983229 AGATTTGCTGCTCGACTGAAT 58.017 42.857 0.00 0.00 0.00 2.57
1942 2029 3.341823 AGATTTGCTGCTCGACTGAATT 58.658 40.909 0.00 0.00 0.00 2.17
1943 2030 3.373439 AGATTTGCTGCTCGACTGAATTC 59.627 43.478 0.00 0.00 0.00 2.17
1944 2031 2.168326 TTGCTGCTCGACTGAATTCA 57.832 45.000 8.12 8.12 0.00 2.57
1967 2054 2.040544 CGAGAGTTTGGCGGGCAAT 61.041 57.895 18.14 3.77 0.00 3.56
1983 2070 4.494484 GGGCAATTGAAAACTGTATCCAC 58.506 43.478 10.34 0.00 0.00 4.02
1992 2079 3.071837 TGTATCCACCGGCGCTCA 61.072 61.111 7.64 0.00 0.00 4.26
2005 2092 2.019984 GGCGCTCAAGGAGAAATTGAT 58.980 47.619 7.64 0.00 36.16 2.57
2017 2104 8.521176 CAAGGAGAAATTGATCAGAAAGTTCAT 58.479 33.333 8.34 0.00 34.83 2.57
2021 2108 7.600065 AGAAATTGATCAGAAAGTTCATGGTG 58.400 34.615 8.34 0.00 34.83 4.17
2025 2112 6.075762 TGATCAGAAAGTTCATGGTGTTTG 57.924 37.500 0.00 0.00 0.00 2.93
2080 2167 2.852449 TGTCAGACGTTCTCTCTCTGT 58.148 47.619 0.00 0.00 34.26 3.41
2087 2174 0.972883 GTTCTCTCTCTGTGCCCACT 59.027 55.000 0.00 0.00 0.00 4.00
2088 2175 2.171840 GTTCTCTCTCTGTGCCCACTA 58.828 52.381 0.00 0.00 0.00 2.74
2091 2178 1.140589 CTCTCTGTGCCCACTAGCG 59.859 63.158 0.00 0.00 34.65 4.26
2113 2200 4.719369 GGTGAGAGCGCCGTCGTT 62.719 66.667 2.29 0.00 38.14 3.85
2114 2201 3.470567 GTGAGAGCGCCGTCGTTG 61.471 66.667 2.29 0.00 38.14 4.10
2134 5378 3.942829 TGCTGGTCCTCAGATTTAACAG 58.057 45.455 0.00 0.00 46.18 3.16
2213 5461 4.711949 ACAAGCCAGCCAGAGCGG 62.712 66.667 0.00 0.00 46.67 5.52
2292 5540 2.941720 GTTCTCAACTGATCTGCCATCC 59.058 50.000 0.00 0.00 0.00 3.51
2295 5543 0.107508 CAACTGATCTGCCATCCGGT 60.108 55.000 0.00 0.00 33.28 5.28
2301 5549 2.503765 TGATCTGCCATCCGGTTTCTTA 59.496 45.455 0.00 0.00 33.28 2.10
2304 5552 2.238646 TCTGCCATCCGGTTTCTTATGT 59.761 45.455 0.00 0.00 33.28 2.29
2328 5576 9.826574 TGTAATCTTAACATCCTATGGTTGTAC 57.173 33.333 1.34 0.00 34.91 2.90
2329 5577 9.826574 GTAATCTTAACATCCTATGGTTGTACA 57.173 33.333 0.00 0.00 34.91 2.90
2330 5578 8.964476 AATCTTAACATCCTATGGTTGTACAG 57.036 34.615 0.00 1.88 34.91 2.74
2331 5579 7.490657 TCTTAACATCCTATGGTTGTACAGT 57.509 36.000 0.00 0.00 34.91 3.55
2333 5581 8.472413 TCTTAACATCCTATGGTTGTACAGTAC 58.528 37.037 3.49 3.49 34.91 2.73
2341 5593 6.980978 CCTATGGTTGTACAGTACATCTTCAG 59.019 42.308 14.34 9.07 38.68 3.02
2345 5597 7.051623 TGGTTGTACAGTACATCTTCAGTTTT 58.948 34.615 14.34 0.00 38.68 2.43
2366 5618 6.817765 TTTTTACCAATCTGTCTAGCAAGG 57.182 37.500 0.00 0.00 0.00 3.61
2417 5669 5.661458 AGTAGTGTACTCCATACATTGTGC 58.339 41.667 0.00 0.00 45.59 4.57
2418 5670 3.521560 AGTGTACTCCATACATTGTGCG 58.478 45.455 0.00 0.00 45.59 5.34
2429 5681 5.333568 CCATACATTGTGCGTGAGTGATATG 60.334 44.000 0.00 0.00 0.00 1.78
2435 5687 1.067669 TGCGTGAGTGATATGCTCCTC 59.932 52.381 0.00 0.00 32.31 3.71
2444 5696 2.158914 TGATATGCTCCTCATGTGCGTT 60.159 45.455 0.00 0.00 36.63 4.84
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
5 6 2.449525 GCGTAAACAGATCGCGCCA 61.450 57.895 0.00 0.00 41.93 5.69
12 13 0.321298 ACTTGGCCGCGTAAACAGAT 60.321 50.000 4.92 0.00 0.00 2.90
18 19 1.375013 GGAGAACTTGGCCGCGTAA 60.375 57.895 4.92 0.00 0.00 3.18
93 94 3.124466 GCCAGCAAACAAAGAAACGTTTT 59.876 39.130 15.89 2.49 33.14 2.43
99 100 2.433604 TGATGGCCAGCAAACAAAGAAA 59.566 40.909 24.04 0.00 0.00 2.52
106 107 3.696051 TCTATTCTTGATGGCCAGCAAAC 59.304 43.478 33.99 12.82 36.18 2.93
109 111 3.117776 ACATCTATTCTTGATGGCCAGCA 60.118 43.478 22.27 22.27 43.88 4.41
155 157 0.545309 TCTGGTGAGGAAGTCCCCTG 60.545 60.000 0.00 0.00 36.49 4.45
193 195 2.552315 GTCATGGTTTCATCGTGTTGGT 59.448 45.455 0.00 0.00 0.00 3.67
262 264 4.488790 GCCCCATAGTCAGGCATG 57.511 61.111 0.00 0.00 46.34 4.06
269 271 0.468226 TGTCCGATTGCCCCATAGTC 59.532 55.000 0.00 0.00 0.00 2.59
282 284 0.971386 GTTGTAGGGGTTCTGTCCGA 59.029 55.000 0.00 0.00 0.00 4.55
338 340 8.947115 GCTAACTTCTTATGTTGTCCACTTTAT 58.053 33.333 0.00 0.00 0.00 1.40
353 355 5.566627 GCAAATTGGCCTTGCTAACTTCTTA 60.567 40.000 18.35 0.00 44.66 2.10
387 390 2.897207 CGTCCACGGCTCCCATAA 59.103 61.111 0.00 0.00 35.37 1.90
397 400 4.444024 CATTGCGGTGCGTCCACG 62.444 66.667 0.00 0.00 43.00 4.94
417 420 0.103208 GTCGCTCCATCGAAGACCAT 59.897 55.000 0.00 0.00 42.51 3.55
467 474 3.473647 CCATGCTCGGGCCTCTCA 61.474 66.667 3.94 0.00 37.74 3.27
496 503 3.133183 CCTCAACTTCCCCTCTTAGTAGC 59.867 52.174 0.00 0.00 0.00 3.58
539 546 0.036732 TACTCGACACTACCCCACGT 59.963 55.000 0.00 0.00 0.00 4.49
552 559 5.984323 CAGCATACTACAGTCTACTACTCGA 59.016 44.000 0.00 0.00 35.76 4.04
587 601 6.426587 ACAAGAATATTTACAGGTGGCTCAT 58.573 36.000 0.00 0.00 0.00 2.90
653 670 4.430007 ACGAGTGTGCGTGTCATATATTT 58.570 39.130 0.00 0.00 43.79 1.40
710 727 9.634021 TTTTATTTTTATTTTGCAGGGGAGTTT 57.366 25.926 0.00 0.00 0.00 2.66
760 778 2.230508 TCGAACTCATACGAGCAGGTTT 59.769 45.455 0.00 0.00 43.66 3.27
786 804 1.268234 GCTGCGATTTCAGATTTCCGG 60.268 52.381 0.00 0.00 36.19 5.14
790 808 1.398390 GACGGCTGCGATTTCAGATTT 59.602 47.619 0.00 0.00 36.19 2.17
792 810 0.811616 GGACGGCTGCGATTTCAGAT 60.812 55.000 0.00 0.00 36.19 2.90
794 812 1.091771 ATGGACGGCTGCGATTTCAG 61.092 55.000 0.00 0.00 37.15 3.02
796 814 1.295792 TAATGGACGGCTGCGATTTC 58.704 50.000 0.00 0.00 0.00 2.17
798 816 1.299541 CTTAATGGACGGCTGCGATT 58.700 50.000 0.00 0.00 0.00 3.34
815 842 0.179018 GGGCGGCTGGATCATAACTT 60.179 55.000 9.56 0.00 0.00 2.66
876 912 5.554350 AGGGGAGTATTTAAACTGGAAAGGA 59.446 40.000 0.00 0.00 0.00 3.36
884 920 4.969999 GAGGAGGAGGGGAGTATTTAAACT 59.030 45.833 0.00 0.00 0.00 2.66
945 997 2.158842 GGAAGTGGGGAGATGAGATGTG 60.159 54.545 0.00 0.00 0.00 3.21
946 998 2.122768 GGAAGTGGGGAGATGAGATGT 58.877 52.381 0.00 0.00 0.00 3.06
947 999 1.419387 GGGAAGTGGGGAGATGAGATG 59.581 57.143 0.00 0.00 0.00 2.90
986 1049 1.531128 TCCATGGCAAACTGCTGCA 60.531 52.632 6.96 0.88 44.28 4.41
994 1057 1.675310 CTGAGGCGTCCATGGCAAA 60.675 57.895 6.96 0.00 36.77 3.68
996 1059 4.783621 GCTGAGGCGTCCATGGCA 62.784 66.667 6.96 0.00 36.77 4.92
1018 1081 1.276421 CTTCGTCTTCCCTGTGGTGAT 59.724 52.381 0.00 0.00 0.00 3.06
1020 1083 0.679505 TCTTCGTCTTCCCTGTGGTG 59.320 55.000 0.00 0.00 0.00 4.17
1021 1084 1.344763 CTTCTTCGTCTTCCCTGTGGT 59.655 52.381 0.00 0.00 0.00 4.16
1026 1089 1.889530 CGCCCTTCTTCGTCTTCCCT 61.890 60.000 0.00 0.00 0.00 4.20
1185 1248 2.359107 ACGGACGCGAGGTAGACA 60.359 61.111 15.93 0.00 0.00 3.41
1403 1466 0.250295 CTTGGTTGCCTTCTCGACCA 60.250 55.000 0.00 0.00 46.12 4.02
1406 1469 0.321671 CTCCTTGGTTGCCTTCTCGA 59.678 55.000 0.00 0.00 0.00 4.04
1414 1477 1.527433 GACTTGGGCTCCTTGGTTGC 61.527 60.000 0.00 0.00 0.00 4.17
1416 1479 1.073199 CGACTTGGGCTCCTTGGTT 59.927 57.895 0.00 0.00 0.00 3.67
1483 1546 7.485913 CCAGCTACATACAACAATTTAAGCAAG 59.514 37.037 0.00 0.00 0.00 4.01
1491 1554 4.889409 CCATCCCAGCTACATACAACAATT 59.111 41.667 0.00 0.00 0.00 2.32
1501 1564 1.620323 CATCGATCCATCCCAGCTACA 59.380 52.381 0.00 0.00 0.00 2.74
1533 1599 3.118519 AGACCAACAACAACCGTCTACTT 60.119 43.478 0.00 0.00 32.15 2.24
1536 1602 2.484065 CCAGACCAACAACAACCGTCTA 60.484 50.000 0.00 0.00 32.64 2.59
1542 1608 1.134175 CACACCCAGACCAACAACAAC 59.866 52.381 0.00 0.00 0.00 3.32
1556 1622 1.204941 AGAAGATACAGCGACACACCC 59.795 52.381 0.00 0.00 0.00 4.61
1558 1624 3.217599 TGAGAAGATACAGCGACACAC 57.782 47.619 0.00 0.00 0.00 3.82
1589 1655 2.505628 TGCAACGCATTGTTTCATGT 57.494 40.000 0.00 0.00 39.29 3.21
1625 1691 3.009473 AGGAATAGAGAGTGCAGGCAAAA 59.991 43.478 0.00 0.00 0.00 2.44
1635 1701 7.281999 GCAAATCTAAGCAAAGGAATAGAGAGT 59.718 37.037 0.00 0.00 0.00 3.24
1642 1708 6.786967 AGATGCAAATCTAAGCAAAGGAAT 57.213 33.333 0.00 0.00 44.88 3.01
1674 1753 6.514947 TCTGGTTGAAATTCAAAAGGACATG 58.485 36.000 10.27 0.00 38.22 3.21
1759 1839 5.546526 ACAACCGCCAAATATTTCAAACAT 58.453 33.333 0.00 0.00 0.00 2.71
1779 1859 2.239681 AAATGGGGCGGGAAATACAA 57.760 45.000 0.00 0.00 0.00 2.41
1855 1936 1.321805 CCATGAGCGCCCAATTTGGA 61.322 55.000 17.24 0.00 40.96 3.53
1871 1952 1.978617 CTTGGGCGCCAAACTCCAT 60.979 57.895 30.85 0.00 43.44 3.41
1877 1958 1.076549 AATCCTCTTGGGCGCCAAA 59.923 52.632 30.85 24.14 43.44 3.28
1904 1991 2.386661 TCTTGCCGCCAAAACAAAAA 57.613 40.000 0.00 0.00 0.00 1.94
1938 2025 3.120165 GCCAAACTCTCGGAACTGAATTC 60.120 47.826 0.00 0.00 36.48 2.17
1939 2026 2.814336 GCCAAACTCTCGGAACTGAATT 59.186 45.455 0.00 0.00 0.00 2.17
1940 2027 2.427506 GCCAAACTCTCGGAACTGAAT 58.572 47.619 0.00 0.00 0.00 2.57
1941 2028 1.872237 CGCCAAACTCTCGGAACTGAA 60.872 52.381 0.00 0.00 0.00 3.02
1942 2029 0.319555 CGCCAAACTCTCGGAACTGA 60.320 55.000 0.00 0.00 0.00 3.41
1943 2030 1.291877 CCGCCAAACTCTCGGAACTG 61.292 60.000 0.00 0.00 45.53 3.16
1944 2031 1.004918 CCGCCAAACTCTCGGAACT 60.005 57.895 0.00 0.00 45.53 3.01
1945 2032 2.033194 CCCGCCAAACTCTCGGAAC 61.033 63.158 1.05 0.00 45.53 3.62
1946 2033 2.345991 CCCGCCAAACTCTCGGAA 59.654 61.111 1.05 0.00 45.53 4.30
1947 2034 4.388499 GCCCGCCAAACTCTCGGA 62.388 66.667 1.05 0.00 45.53 4.55
1948 2035 4.697756 TGCCCGCCAAACTCTCGG 62.698 66.667 0.00 0.00 42.58 4.63
1949 2036 1.586154 AATTGCCCGCCAAACTCTCG 61.586 55.000 0.00 0.00 36.92 4.04
1950 2037 0.109132 CAATTGCCCGCCAAACTCTC 60.109 55.000 0.00 0.00 36.92 3.20
1951 2038 0.539438 TCAATTGCCCGCCAAACTCT 60.539 50.000 0.00 0.00 36.92 3.24
1983 2070 1.026718 AATTTCTCCTTGAGCGCCGG 61.027 55.000 2.29 0.00 0.00 6.13
1992 2079 8.521176 CATGAACTTTCTGATCAATTTCTCCTT 58.479 33.333 0.00 0.00 31.27 3.36
2005 2092 3.698539 TGCAAACACCATGAACTTTCTGA 59.301 39.130 0.00 0.00 0.00 3.27
2017 2104 3.237268 ACTAAATCCCTGCAAACACCA 57.763 42.857 0.00 0.00 0.00 4.17
2021 2108 5.221441 ACCTTCAAACTAAATCCCTGCAAAC 60.221 40.000 0.00 0.00 0.00 2.93
2025 2112 3.367395 GCACCTTCAAACTAAATCCCTGC 60.367 47.826 0.00 0.00 0.00 4.85
2105 2192 4.681978 AGGACCAGCAACGACGGC 62.682 66.667 0.00 0.00 0.00 5.68
2106 2193 2.432628 GAGGACCAGCAACGACGG 60.433 66.667 0.00 0.00 0.00 4.79
2108 2195 0.247736 ATCTGAGGACCAGCAACGAC 59.752 55.000 0.00 0.00 42.62 4.34
2109 2196 0.976641 AATCTGAGGACCAGCAACGA 59.023 50.000 0.00 0.00 42.62 3.85
2111 2198 4.072131 TGTTAAATCTGAGGACCAGCAAC 58.928 43.478 0.00 0.00 42.62 4.17
2112 2199 4.041567 TCTGTTAAATCTGAGGACCAGCAA 59.958 41.667 0.00 0.00 42.62 3.91
2113 2200 3.582647 TCTGTTAAATCTGAGGACCAGCA 59.417 43.478 0.00 0.00 42.62 4.41
2114 2201 4.081420 TCTCTGTTAAATCTGAGGACCAGC 60.081 45.833 0.00 0.00 42.62 4.85
2115 2202 5.667539 TCTCTGTTAAATCTGAGGACCAG 57.332 43.478 0.00 0.00 44.27 4.00
2117 2204 5.639931 GTGTTCTCTGTTAAATCTGAGGACC 59.360 44.000 8.19 0.00 39.54 4.46
2134 5378 3.583806 CTCAGATGTGGACTGTGTTCTC 58.416 50.000 0.00 0.00 36.81 2.87
2243 5491 2.281484 TTGCTCGCCAGTTGACCC 60.281 61.111 0.00 0.00 0.00 4.46
2244 5492 1.891919 TGTTGCTCGCCAGTTGACC 60.892 57.895 0.00 0.00 0.00 4.02
2245 5493 1.160329 AGTGTTGCTCGCCAGTTGAC 61.160 55.000 0.00 0.00 0.00 3.18
2292 5540 9.326413 AGGATGTTAAGATTACATAAGAAACCG 57.674 33.333 0.00 0.00 36.41 4.44
2320 5568 5.801531 ACTGAAGATGTACTGTACAACCA 57.198 39.130 23.03 16.11 42.76 3.67
2345 5597 5.499004 ACCTTGCTAGACAGATTGGTAAA 57.501 39.130 0.00 0.00 0.00 2.01
2400 5652 3.517602 TCACGCACAATGTATGGAGTAC 58.482 45.455 0.00 0.00 0.00 2.73
2401 5653 3.194755 ACTCACGCACAATGTATGGAGTA 59.805 43.478 7.18 0.00 33.01 2.59
2402 5654 2.028112 ACTCACGCACAATGTATGGAGT 60.028 45.455 4.18 4.18 0.00 3.85
2403 5655 2.349580 CACTCACGCACAATGTATGGAG 59.650 50.000 0.00 0.00 0.00 3.86
2404 5656 2.028567 TCACTCACGCACAATGTATGGA 60.029 45.455 0.00 0.00 0.00 3.41
2417 5669 3.243670 ACATGAGGAGCATATCACTCACG 60.244 47.826 0.00 0.00 37.76 4.35
2418 5670 4.056740 CACATGAGGAGCATATCACTCAC 58.943 47.826 0.00 0.41 37.76 3.51
2429 5681 2.010145 TTCTAACGCACATGAGGAGC 57.990 50.000 0.00 0.00 0.00 4.70


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

AutoCloner maintained by Alex Coulton.