Multiple sequence alignment - TraesCS7D01G118800

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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 TraesCS7D01G118800 chr7D 100.000 4245 0 0 1 4245 73613746 73609502 0.000000e+00 7840.0
1 TraesCS7D01G118800 chr7D 88.752 809 51 14 2606 3413 73563689 73562920 0.000000e+00 953.0
2 TraesCS7D01G118800 chr7D 88.079 755 55 11 3421 4163 73562885 73562154 0.000000e+00 863.0
3 TraesCS7D01G118800 chr7D 77.732 1446 213 60 2006 3398 82447993 82446604 0.000000e+00 785.0
4 TraesCS7D01G118800 chr7D 85.813 726 77 13 2698 3410 73369698 73370410 0.000000e+00 747.0
5 TraesCS7D01G118800 chr7D 83.355 769 78 22 792 1527 73367758 73368509 0.000000e+00 665.0
6 TraesCS7D01G118800 chr7D 80.252 714 73 35 783 1467 73178003 73178677 3.840000e-130 475.0
7 TraesCS7D01G118800 chr7D 78.682 713 89 29 784 1467 73212873 73213551 2.360000e-112 416.0
8 TraesCS7D01G118800 chr7D 79.935 618 73 27 784 1378 73217955 73218544 1.420000e-109 407.0
9 TraesCS7D01G118800 chr7D 79.528 508 86 12 974 1475 82349161 82348666 3.140000e-91 346.0
10 TraesCS7D01G118800 chr7D 89.231 260 27 1 1 259 73554193 73554452 1.470000e-84 324.0
11 TraesCS7D01G118800 chr7D 88.462 260 29 1 1 259 73554901 73555160 3.190000e-81 313.0
12 TraesCS7D01G118800 chr7D 81.370 365 44 9 1593 1951 73368697 73369043 4.180000e-70 276.0
13 TraesCS7D01G118800 chr7D 98.039 51 1 0 3908 3958 73370990 73371040 5.850000e-14 89.8
14 TraesCS7D01G118800 chr7A 97.234 1229 26 3 1744 2971 78134630 78133409 0.000000e+00 2074.0
15 TraesCS7D01G118800 chr7A 98.935 657 7 0 2968 3624 78133328 78132672 0.000000e+00 1175.0
16 TraesCS7D01G118800 chr7A 94.422 735 29 6 1 732 78135346 78134621 0.000000e+00 1120.0
17 TraesCS7D01G118800 chr7A 83.095 1260 152 35 2682 3899 77916701 77917941 0.000000e+00 1090.0
18 TraesCS7D01G118800 chr7A 87.828 838 61 13 3421 4240 78078252 78077438 0.000000e+00 944.0
19 TraesCS7D01G118800 chr7A 95.221 565 6 10 3690 4245 78132673 78132121 0.000000e+00 874.0
20 TraesCS7D01G118800 chr7A 82.665 773 76 17 792 1527 77915005 77915756 2.150000e-177 632.0
21 TraesCS7D01G118800 chr7A 89.091 495 32 5 2932 3413 78078772 78078287 2.830000e-166 595.0
22 TraesCS7D01G118800 chr7A 82.172 617 47 28 793 1373 78080880 78080291 4.970000e-129 472.0
23 TraesCS7D01G118800 chr7A 80.235 597 75 13 902 1467 77731744 77732328 3.950000e-110 409.0
24 TraesCS7D01G118800 chr7A 88.150 346 25 2 2534 2879 78079102 78078773 8.550000e-107 398.0
25 TraesCS7D01G118800 chr7A 89.615 260 25 2 1 259 78073229 78073487 3.160000e-86 329.0
26 TraesCS7D01G118800 chr7A 81.644 365 43 9 1593 1951 77915960 77916306 8.990000e-72 281.0
27 TraesCS7D01G118800 chr7A 84.906 159 20 4 1812 1968 78390768 78390924 1.580000e-34 158.0
28 TraesCS7D01G118800 chr7A 77.778 207 30 12 2294 2494 78394608 78394804 3.470000e-21 113.0
29 TraesCS7D01G118800 chr7A 98.039 51 1 0 3908 3958 77917991 77918041 5.850000e-14 89.8
30 TraesCS7D01G118800 chr7A 95.556 45 0 2 2191 2234 78218915 78218958 2.120000e-08 71.3
31 TraesCS7D01G118800 chr7A 97.297 37 1 0 2087 2123 19982976 19983012 3.540000e-06 63.9
32 TraesCS7D01G118800 chr7A 97.222 36 1 0 2088 2123 681749104 681749139 1.270000e-05 62.1
33 TraesCS7D01G118800 chr7A 100.000 32 0 0 2959 2990 78395478 78395509 4.580000e-05 60.2
34 TraesCS7D01G118800 chr7B 88.071 1400 93 32 2888 4245 16734044 16735411 0.000000e+00 1592.0
35 TraesCS7D01G118800 chr7B 91.691 1035 61 12 1570 2598 16733035 16734050 0.000000e+00 1411.0
36 TraesCS7D01G118800 chr7B 90.338 1066 30 18 504 1524 16731845 16732882 0.000000e+00 1330.0
37 TraesCS7D01G118800 chr7B 88.318 1070 90 18 2534 3580 16827925 16828982 0.000000e+00 1251.0
38 TraesCS7D01G118800 chr7B 77.801 1446 213 63 2006 3398 29828704 29827314 0.000000e+00 793.0
39 TraesCS7D01G118800 chr7B 77.457 1455 211 70 2006 3398 30764903 30763504 0.000000e+00 761.0
40 TraesCS7D01G118800 chr7B 76.475 1458 212 72 2006 3398 31442822 31441431 0.000000e+00 671.0
41 TraesCS7D01G118800 chr7B 84.412 680 74 17 2749 3410 16525893 16526558 1.290000e-179 640.0
42 TraesCS7D01G118800 chr7B 85.285 632 59 13 757 1373 16826147 16826759 4.660000e-174 621.0
43 TraesCS7D01G118800 chr7B 82.993 588 66 13 902 1467 15935313 15935888 6.340000e-138 501.0
44 TraesCS7D01G118800 chr7B 83.594 512 39 10 789 1276 16524188 16524678 5.040000e-119 438.0
45 TraesCS7D01G118800 chr7B 86.284 401 30 8 3814 4198 16829066 16829457 3.050000e-111 412.0
46 TraesCS7D01G118800 chr7B 83.733 375 32 12 1593 1959 16525103 16525456 1.140000e-85 327.0
47 TraesCS7D01G118800 chr7B 74.942 858 135 51 2019 2846 31444828 31444021 1.900000e-83 320.0
48 TraesCS7D01G118800 chr7B 77.228 505 51 36 2006 2467 31446850 31446367 1.970000e-58 237.0
49 TraesCS7D01G118800 chr7B 90.728 151 12 2 339 488 16716903 16717052 2.590000e-47 200.0
50 TraesCS7D01G118800 chr7B 75.688 436 69 26 1697 2130 16951850 16952250 2.610000e-42 183.0
51 TraesCS7D01G118800 chr7B 85.057 174 19 2 111 284 16716556 16716722 2.030000e-38 171.0
52 TraesCS7D01G118800 chr7B 90.517 116 10 1 1 115 16716078 16716193 7.350000e-33 152.0
53 TraesCS7D01G118800 chr7B 98.039 51 1 0 3908 3958 16527127 16527177 5.850000e-14 89.8
54 TraesCS7D01G118800 chr7B 97.778 45 0 1 3595 3638 16828979 16829023 4.550000e-10 76.8
55 TraesCS7D01G118800 chr1B 90.230 522 40 6 2652 3172 15262915 15262404 0.000000e+00 671.0
56 TraesCS7D01G118800 chr2D 86.000 150 19 2 2681 2829 33047333 33047185 4.390000e-35 159.0
57 TraesCS7D01G118800 chr2D 81.006 179 27 6 1814 1989 33580232 33580058 7.400000e-28 135.0
58 TraesCS7D01G118800 chr2D 100.000 28 0 0 2092 2119 34986236 34986209 8.000000e-03 52.8
59 TraesCS7D01G118800 chr2B 86.232 138 19 0 1814 1951 54786419 54786282 2.640000e-32 150.0
60 TraesCS7D01G118800 chr2A 81.111 180 27 6 1813 1989 36410902 36410727 2.060000e-28 137.0
61 TraesCS7D01G118800 chr4A 78.873 213 33 7 2285 2494 644637768 644637971 2.660000e-27 134.0
62 TraesCS7D01G118800 chr4A 100.000 32 0 0 1438 1469 606808588 606808619 4.580000e-05 60.2
63 TraesCS7D01G118800 chr4B 87.129 101 11 2 2685 2784 14523069 14522970 3.470000e-21 113.0
64 TraesCS7D01G118800 chr6A 87.778 90 8 3 2050 2137 31880688 31880776 7.510000e-18 102.0
65 TraesCS7D01G118800 chr6D 86.667 90 9 3 2050 2137 30746438 30746526 3.490000e-16 97.1
66 TraesCS7D01G118800 chr6B 93.878 49 0 3 2188 2234 471051892 471051845 2.120000e-08 71.3


These results show the homologous regions that are presented in the multiple sequence alignment. HSPs from the BLAST search that are within 2000 bases of each other have been grouped together. Homologous regions that are purely upstream or downstream may be removed if they don't overlap both primers.

query scaffold start end length rev.comp avg.bitscore max.bitscore avg.percent.identical query.start query.end num_hsp groupid homo_length
0 TraesCS7D01G118800 chr7D 73609502 73613746 4244 True 7840.000000 7840 100.000000 1 4245 1 chr7D.!!$R1 4244
1 TraesCS7D01G118800 chr7D 73562154 73563689 1535 True 908.000000 953 88.415500 2606 4163 2 chr7D.!!$R4 1557
2 TraesCS7D01G118800 chr7D 82446604 82447993 1389 True 785.000000 785 77.732000 2006 3398 1 chr7D.!!$R3 1392
3 TraesCS7D01G118800 chr7D 73178003 73178677 674 False 475.000000 475 80.252000 783 1467 1 chr7D.!!$F1 684
4 TraesCS7D01G118800 chr7D 73367758 73371040 3282 False 444.450000 747 87.144250 792 3958 4 chr7D.!!$F4 3166
5 TraesCS7D01G118800 chr7D 73212873 73213551 678 False 416.000000 416 78.682000 784 1467 1 chr7D.!!$F2 683
6 TraesCS7D01G118800 chr7D 73217955 73218544 589 False 407.000000 407 79.935000 784 1378 1 chr7D.!!$F3 594
7 TraesCS7D01G118800 chr7D 73554193 73555160 967 False 318.500000 324 88.846500 1 259 2 chr7D.!!$F5 258
8 TraesCS7D01G118800 chr7A 78132121 78135346 3225 True 1310.750000 2074 96.453000 1 4245 4 chr7A.!!$R2 4244
9 TraesCS7D01G118800 chr7A 78077438 78080880 3442 True 602.250000 944 86.810250 793 4240 4 chr7A.!!$R1 3447
10 TraesCS7D01G118800 chr7A 77915005 77918041 3036 False 523.200000 1090 86.360750 792 3958 4 chr7A.!!$F6 3166
11 TraesCS7D01G118800 chr7A 77731744 77732328 584 False 409.000000 409 80.235000 902 1467 1 chr7A.!!$F2 565
12 TraesCS7D01G118800 chr7B 16731845 16735411 3566 False 1444.333333 1592 90.033333 504 4245 3 chr7B.!!$F5 3741
13 TraesCS7D01G118800 chr7B 29827314 29828704 1390 True 793.000000 793 77.801000 2006 3398 1 chr7B.!!$R1 1392
14 TraesCS7D01G118800 chr7B 30763504 30764903 1399 True 761.000000 761 77.457000 2006 3398 1 chr7B.!!$R2 1392
15 TraesCS7D01G118800 chr7B 16826147 16829457 3310 False 590.200000 1251 89.416250 757 4198 4 chr7B.!!$F6 3441
16 TraesCS7D01G118800 chr7B 15935313 15935888 575 False 501.000000 501 82.993000 902 1467 1 chr7B.!!$F1 565
17 TraesCS7D01G118800 chr7B 31441431 31446850 5419 True 409.333333 671 76.215000 2006 3398 3 chr7B.!!$R3 1392
18 TraesCS7D01G118800 chr7B 16524188 16527177 2989 False 373.700000 640 87.444500 789 3958 4 chr7B.!!$F3 3169
19 TraesCS7D01G118800 chr1B 15262404 15262915 511 True 671.000000 671 90.230000 2652 3172 1 chr1B.!!$R1 520

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
437 442 0.519077 GCTAGAGCAAACACCAGCAC 59.481 55.0 0.00 0.00 41.59 4.40 F
1399 1535 0.108992 CGGCAAGTACCTACGCTTGA 60.109 55.0 8.27 0.00 43.29 3.02 F
2159 2683 0.961019 TGGAATTGTCTGCAGCAACC 59.039 50.0 20.74 18.44 0.00 3.77 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1571 1832 0.935196 GAGTCGCAGAAAACCAACGT 59.065 50.000 0.0 0.0 39.69 3.99 R
2388 3040 7.397892 TTTCTCACAGGTTATTCAACACAAA 57.602 32.000 0.0 0.0 36.29 2.83 R
3677 8984 2.699954 CTCACAACAAGAACCCGCTAT 58.300 47.619 0.0 0.0 0.00 2.97 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
36 37 3.651803 AGTGTCCAAGACGAGAAGAAG 57.348 47.619 0.00 0.00 34.95 2.85
107 109 2.119495 GGGAGATGGGAAGCAAGAGTA 58.881 52.381 0.00 0.00 0.00 2.59
110 112 4.385754 GGGAGATGGGAAGCAAGAGTAATT 60.386 45.833 0.00 0.00 0.00 1.40
176 178 3.681897 CACAAGAGAACTAGACACCATGC 59.318 47.826 0.00 0.00 0.00 4.06
180 182 3.003480 GAGAACTAGACACCATGCCAAC 58.997 50.000 0.00 0.00 0.00 3.77
188 190 1.255882 CACCATGCCAACCTTAGCAA 58.744 50.000 0.00 0.00 43.36 3.91
195 197 2.557924 TGCCAACCTTAGCAACAGAATG 59.442 45.455 0.00 0.00 36.54 2.67
291 294 2.290260 TGTCGAAACATGAATGGCTCCT 60.290 45.455 0.00 0.00 0.00 3.69
296 299 2.885135 ACATGAATGGCTCCTCAACA 57.115 45.000 0.00 0.00 0.00 3.33
361 365 3.496160 GGTAACTCCACATCACCACAACT 60.496 47.826 0.00 0.00 35.97 3.16
424 428 8.091449 AGTAATTGAGATAAAATCGGGCTAGAG 58.909 37.037 0.00 0.00 0.00 2.43
434 438 1.021390 CGGGCTAGAGCAAACACCAG 61.021 60.000 3.54 0.00 44.36 4.00
437 442 0.519077 GCTAGAGCAAACACCAGCAC 59.481 55.000 0.00 0.00 41.59 4.40
450 455 3.292936 AGCACACAAGCAGGCAGC 61.293 61.111 0.00 0.00 46.19 5.25
601 607 0.981183 ATCTGACGGTGGTTTGCCTA 59.019 50.000 0.00 0.00 35.27 3.93
679 685 1.682257 GCAGGGCAAGGAGAGAAGT 59.318 57.895 0.00 0.00 0.00 3.01
681 687 1.134551 GCAGGGCAAGGAGAGAAGTAG 60.135 57.143 0.00 0.00 0.00 2.57
685 691 1.406205 GGCAAGGAGAGAAGTAGTGCC 60.406 57.143 0.00 0.00 42.88 5.01
689 695 1.605058 GGAGAGAAGTAGTGCCGCCA 61.605 60.000 0.00 0.00 0.00 5.69
787 816 1.455959 CGGGAATCGGAGGAGAGGT 60.456 63.158 0.00 0.00 34.75 3.85
843 880 2.915137 GCAGGCCCGAAACCCAAA 60.915 61.111 0.00 0.00 0.00 3.28
844 881 2.931068 GCAGGCCCGAAACCCAAAG 61.931 63.158 0.00 0.00 0.00 2.77
846 883 3.691342 GGCCCGAAACCCAAAGCC 61.691 66.667 0.00 0.00 0.00 4.35
847 884 3.691342 GCCCGAAACCCAAAGCCC 61.691 66.667 0.00 0.00 0.00 5.19
848 885 2.117423 CCCGAAACCCAAAGCCCT 59.883 61.111 0.00 0.00 0.00 5.19
850 887 2.275380 CCGAAACCCAAAGCCCTGG 61.275 63.158 0.00 0.00 36.10 4.45
851 888 2.931068 CGAAACCCAAAGCCCTGGC 61.931 63.158 0.00 0.00 42.33 4.85
867 904 3.972227 GCTGAACAGCGATGGTGT 58.028 55.556 5.32 0.00 46.58 4.16
868 905 1.790387 GCTGAACAGCGATGGTGTC 59.210 57.895 5.32 0.00 43.73 3.67
869 906 0.950555 GCTGAACAGCGATGGTGTCA 60.951 55.000 5.32 4.70 43.73 3.58
898 955 2.821625 GCACCTTCAAATACCCCACCTT 60.822 50.000 0.00 0.00 0.00 3.50
1152 1252 2.740714 GCACATCGACCAAGGCGAC 61.741 63.158 0.00 0.00 40.94 5.19
1153 1253 2.126071 ACATCGACCAAGGCGACG 60.126 61.111 0.00 0.00 40.94 5.12
1154 1254 3.554692 CATCGACCAAGGCGACGC 61.555 66.667 12.43 12.43 40.94 5.19
1387 1523 1.599797 GGCAAGTACACCGGCAAGT 60.600 57.895 0.00 0.00 0.00 3.16
1390 1526 1.435577 CAAGTACACCGGCAAGTACC 58.564 55.000 21.77 9.76 41.07 3.34
1391 1527 1.001633 CAAGTACACCGGCAAGTACCT 59.998 52.381 21.77 11.56 41.07 3.08
1392 1528 2.220653 AGTACACCGGCAAGTACCTA 57.779 50.000 21.77 0.00 41.07 3.08
1395 1531 1.808390 CACCGGCAAGTACCTACGC 60.808 63.158 0.00 0.00 0.00 4.42
1396 1532 1.980772 ACCGGCAAGTACCTACGCT 60.981 57.895 0.00 0.00 0.00 5.07
1397 1533 1.217244 CCGGCAAGTACCTACGCTT 59.783 57.895 0.00 0.00 0.00 4.68
1398 1534 1.082117 CCGGCAAGTACCTACGCTTG 61.082 60.000 0.00 0.00 43.42 4.01
1399 1535 0.108992 CGGCAAGTACCTACGCTTGA 60.109 55.000 8.27 0.00 43.29 3.02
1400 1536 1.670674 CGGCAAGTACCTACGCTTGAA 60.671 52.381 8.27 0.00 43.29 2.69
1401 1537 2.000447 GGCAAGTACCTACGCTTGAAG 59.000 52.381 8.27 0.00 43.29 3.02
1402 1538 2.353406 GGCAAGTACCTACGCTTGAAGA 60.353 50.000 8.27 0.00 43.29 2.87
1403 1539 3.323243 GCAAGTACCTACGCTTGAAGAA 58.677 45.455 8.27 0.00 43.29 2.52
1491 1630 1.303888 AGACCCGAACAGTCCGCTA 60.304 57.895 0.00 0.00 34.67 4.26
1537 1787 2.167487 AGTTCGCCTGAGAGAAATCTCC 59.833 50.000 6.81 0.28 43.88 3.71
1540 1790 3.677002 CCTGAGAGAAATCTCCGGC 57.323 57.895 6.81 0.00 43.88 6.13
1571 1832 2.287547 GCCGAATTTGTGCAGTTCTTGA 60.288 45.455 0.00 0.00 0.00 3.02
1808 2200 3.849951 CACCCCGACATCCTCCCG 61.850 72.222 0.00 0.00 0.00 5.14
2156 2680 2.030371 TGTTTGGAATTGTCTGCAGCA 58.970 42.857 9.47 7.85 0.00 4.41
2157 2681 2.429971 TGTTTGGAATTGTCTGCAGCAA 59.570 40.909 20.64 20.64 0.00 3.91
2158 2682 2.796593 GTTTGGAATTGTCTGCAGCAAC 59.203 45.455 20.74 11.32 0.00 4.17
2159 2683 0.961019 TGGAATTGTCTGCAGCAACC 59.039 50.000 20.74 18.44 0.00 3.77
2160 2684 1.251251 GGAATTGTCTGCAGCAACCT 58.749 50.000 20.74 13.45 0.00 3.50
2161 2685 1.615392 GGAATTGTCTGCAGCAACCTT 59.385 47.619 20.74 14.31 0.00 3.50
2162 2686 2.608752 GGAATTGTCTGCAGCAACCTTG 60.609 50.000 20.74 0.00 0.00 3.61
2163 2687 1.985473 ATTGTCTGCAGCAACCTTGA 58.015 45.000 20.74 3.80 0.00 3.02
2164 2688 1.761449 TTGTCTGCAGCAACCTTGAA 58.239 45.000 9.47 0.00 0.00 2.69
2388 3040 6.265577 GTTTTACGCATTGAGCCTATTTCAT 58.734 36.000 0.00 0.00 41.38 2.57
2410 3062 6.770303 TCATTTGTGTTGAATAACCTGTGAGA 59.230 34.615 0.00 0.00 35.92 3.27
2619 3281 6.372659 GGTCTTGAATCTCTTTTGTGCAGATA 59.627 38.462 0.00 0.00 0.00 1.98
2629 3291 9.453572 TCTCTTTTGTGCAGATATTAGATTTGT 57.546 29.630 0.00 0.00 0.00 2.83
2929 7923 7.922811 AGTTCCACATTTCTTTTCTTGATTCAC 59.077 33.333 0.00 0.00 0.00 3.18
2930 7924 6.748132 TCCACATTTCTTTTCTTGATTCACC 58.252 36.000 0.00 0.00 0.00 4.02
3517 8758 1.355381 TGTGGTGCTTCCTGGATGAAT 59.645 47.619 13.34 0.00 37.07 2.57
3672 8979 5.523916 AGGCTATGAACTTACTACAAATGCG 59.476 40.000 0.00 0.00 0.00 4.73
3784 9091 9.658475 TTTGTAACGTATGAACAAAATTCAGAG 57.342 29.630 14.02 0.00 39.46 3.35
3874 9181 6.266330 ACATAAGCTGCCTTCTTTTTCTTTCT 59.734 34.615 0.00 0.00 32.47 2.52
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
9 10 0.597637 CGTCTTGGACACTTGACGCT 60.598 55.000 0.00 0.00 44.00 5.07
107 109 0.400594 GGCATCCCCGCTAGGTAATT 59.599 55.000 0.00 0.00 35.12 1.40
110 112 2.525877 GGGCATCCCCGCTAGGTA 60.526 66.667 0.00 0.00 42.67 3.08
176 178 5.183713 TCATTCATTCTGTTGCTAAGGTTGG 59.816 40.000 0.00 0.00 0.00 3.77
180 182 5.885230 TGTCATTCATTCTGTTGCTAAGG 57.115 39.130 0.00 0.00 0.00 2.69
188 190 6.458751 GGCAACGATAATGTCATTCATTCTGT 60.459 38.462 0.07 0.00 44.50 3.41
195 197 5.484173 TCTTGGCAACGATAATGTCATTC 57.516 39.130 0.07 0.00 42.51 2.67
291 294 5.705441 GGAAGTACATGGATCTTGTTGTTGA 59.295 40.000 0.00 0.00 0.00 3.18
296 299 5.882557 GTGATGGAAGTACATGGATCTTGTT 59.117 40.000 0.00 0.00 0.00 2.83
407 411 4.574828 TGTTTGCTCTAGCCCGATTTTATC 59.425 41.667 0.00 0.00 41.18 1.75
410 414 2.488153 GTGTTTGCTCTAGCCCGATTTT 59.512 45.455 0.00 0.00 41.18 1.82
424 428 1.147557 GCTTGTGTGCTGGTGTTTGC 61.148 55.000 0.00 0.00 0.00 3.68
434 438 3.553437 CTGCTGCCTGCTTGTGTGC 62.553 63.158 0.00 0.00 43.37 4.57
437 442 2.596631 ACCTGCTGCCTGCTTGTG 60.597 61.111 0.00 0.00 43.37 3.33
450 455 4.624364 TGGCCTGCGTGACACCTG 62.624 66.667 3.32 0.00 0.00 4.00
489 494 2.103647 GTGTGCGTGTGTGACACCA 61.104 57.895 13.85 0.83 45.93 4.17
844 881 3.984193 ATCGCTGTTCAGCCAGGGC 62.984 63.158 17.42 0.97 43.10 5.19
846 883 2.110967 CCATCGCTGTTCAGCCAGG 61.111 63.158 17.42 12.93 32.92 4.45
847 884 1.376424 ACCATCGCTGTTCAGCCAG 60.376 57.895 17.42 6.34 35.49 4.85
848 885 1.672030 CACCATCGCTGTTCAGCCA 60.672 57.895 17.42 6.88 0.00 4.75
850 887 0.950555 TGACACCATCGCTGTTCAGC 60.951 55.000 13.97 13.97 0.00 4.26
851 888 1.073964 CTGACACCATCGCTGTTCAG 58.926 55.000 0.00 0.00 0.00 3.02
852 889 0.392706 ACTGACACCATCGCTGTTCA 59.607 50.000 0.00 0.00 0.00 3.18
854 891 0.106708 ACACTGACACCATCGCTGTT 59.893 50.000 0.00 0.00 0.00 3.16
855 892 0.319900 GACACTGACACCATCGCTGT 60.320 55.000 0.00 0.00 0.00 4.40
856 893 0.319813 TGACACTGACACCATCGCTG 60.320 55.000 0.00 0.00 0.00 5.18
857 894 0.037882 CTGACACTGACACCATCGCT 60.038 55.000 0.00 0.00 0.00 4.93
858 895 1.016130 CCTGACACTGACACCATCGC 61.016 60.000 0.00 0.00 0.00 4.58
859 896 1.016130 GCCTGACACTGACACCATCG 61.016 60.000 0.00 0.00 0.00 3.84
860 897 0.035317 TGCCTGACACTGACACCATC 59.965 55.000 0.00 0.00 0.00 3.51
861 898 0.250467 GTGCCTGACACTGACACCAT 60.250 55.000 0.00 0.00 46.41 3.55
862 899 1.146041 GTGCCTGACACTGACACCA 59.854 57.895 0.00 0.00 46.41 4.17
863 900 4.049393 GTGCCTGACACTGACACC 57.951 61.111 0.00 0.00 46.41 4.16
1378 1514 1.538687 AAGCGTAGGTACTTGCCGGT 61.539 55.000 1.90 0.00 41.75 5.28
1379 1515 1.082117 CAAGCGTAGGTACTTGCCGG 61.082 60.000 0.00 0.00 41.75 6.13
1384 1520 3.005155 ACGTTCTTCAAGCGTAGGTACTT 59.995 43.478 0.00 0.00 41.75 2.24
1387 1523 2.553602 TGACGTTCTTCAAGCGTAGGTA 59.446 45.455 0.00 0.00 39.06 3.08
1390 1526 1.719780 GGTGACGTTCTTCAAGCGTAG 59.280 52.381 0.00 0.00 39.06 3.51
1391 1527 1.774639 GGTGACGTTCTTCAAGCGTA 58.225 50.000 0.00 0.00 39.06 4.42
1392 1528 2.601562 GGTGACGTTCTTCAAGCGT 58.398 52.632 0.00 0.00 41.81 5.07
1540 1790 3.558505 CACAAATTCGGCAAGAACAGAG 58.441 45.455 0.00 0.00 42.39 3.35
1571 1832 0.935196 GAGTCGCAGAAAACCAACGT 59.065 50.000 0.00 0.00 39.69 3.99
1808 2200 1.060937 GCACATGGCGATGTCGAAC 59.939 57.895 11.83 0.00 41.12 3.95
2133 2657 1.686052 TGCAGACAATTCCAAACACCC 59.314 47.619 0.00 0.00 0.00 4.61
2156 2680 4.160252 ACTGCAAGACAACAATTCAAGGTT 59.840 37.500 0.00 0.00 37.43 3.50
2157 2681 3.701040 ACTGCAAGACAACAATTCAAGGT 59.299 39.130 0.00 0.00 37.43 3.50
2158 2682 4.311816 ACTGCAAGACAACAATTCAAGG 57.688 40.909 0.00 0.00 37.43 3.61
2159 2683 7.935338 ATAAACTGCAAGACAACAATTCAAG 57.065 32.000 0.00 0.00 37.43 3.02
2160 2684 7.763528 ACAATAAACTGCAAGACAACAATTCAA 59.236 29.630 0.00 0.00 37.43 2.69
2161 2685 7.264221 ACAATAAACTGCAAGACAACAATTCA 58.736 30.769 0.00 0.00 37.43 2.57
2162 2686 7.698836 ACAATAAACTGCAAGACAACAATTC 57.301 32.000 0.00 0.00 37.43 2.17
2163 2687 7.763528 TGAACAATAAACTGCAAGACAACAATT 59.236 29.630 0.00 0.00 37.43 2.32
2164 2688 7.264221 TGAACAATAAACTGCAAGACAACAAT 58.736 30.769 0.00 0.00 37.43 2.71
2388 3040 7.397892 TTTCTCACAGGTTATTCAACACAAA 57.602 32.000 0.00 0.00 36.29 2.83
2683 3513 8.868635 AACACTCACTAAAGTAACACTCTAAC 57.131 34.615 0.00 0.00 0.00 2.34
3517 8758 4.566907 GCAAGAACCCCTACAGGTAAATGA 60.567 45.833 0.00 0.00 40.05 2.57
3672 8979 5.353123 TCACAACAAGAACCCGCTATATTTC 59.647 40.000 0.00 0.00 0.00 2.17
3677 8984 2.699954 CTCACAACAAGAACCCGCTAT 58.300 47.619 0.00 0.00 0.00 2.97
3784 9091 3.682858 TCTTGTAGCGCTGTTGGATAAAC 59.317 43.478 22.90 7.25 39.41 2.01
3874 9181 3.118629 AGTGTCTGCTCAAACAAGACAGA 60.119 43.478 5.04 0.00 39.72 3.41


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

AutoCloner maintained by Alex Coulton.