Multiple sequence alignment - TraesCS5D01G262300

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 TraesCS5D01G262300 chr5D 100.000 4307 0 0 1 4307 368298483 368302789 0.000000e+00 7954
1 TraesCS5D01G262300 chr5D 84.544 2685 305 61 716 3320 368290305 368292959 0.000000e+00 2558
2 TraesCS5D01G262300 chr5D 84.019 413 35 16 207 597 368289898 368290301 6.800000e-98 368
3 TraesCS5D01G262300 chr5D 84.138 145 22 1 3747 3890 435935500 435935644 5.810000e-29 139
4 TraesCS5D01G262300 chr5A 92.477 2765 140 22 739 3461 470184012 470186750 0.000000e+00 3892
5 TraesCS5D01G262300 chr5A 84.086 2702 291 53 716 3320 470174781 470177440 0.000000e+00 2479
6 TraesCS5D01G262300 chr5A 87.983 724 43 20 3594 4307 470186747 470187436 0.000000e+00 815
7 TraesCS5D01G262300 chr5A 88.095 504 26 9 171 656 470183528 470184015 6.250000e-158 568
8 TraesCS5D01G262300 chr5A 80.317 315 32 17 269 570 470174458 470174755 1.210000e-50 211
9 TraesCS5D01G262300 chr5B 92.812 2560 134 15 630 3151 436244142 436246689 0.000000e+00 3663
10 TraesCS5D01G262300 chr5B 84.473 2692 288 55 719 3320 436213591 436216242 0.000000e+00 2536
11 TraesCS5D01G262300 chr5B 93.158 570 26 5 1 565 436243575 436244136 0.000000e+00 824
12 TraesCS5D01G262300 chr5B 86.765 408 34 11 3907 4307 436247241 436247635 1.840000e-118 436
13 TraesCS5D01G262300 chr5B 90.526 285 14 4 237 510 436213229 436213511 8.800000e-97 364
14 TraesCS5D01G262300 chr5B 94.241 191 9 2 3135 3324 436246704 436246893 1.520000e-74 291
15 TraesCS5D01G262300 chr3D 93.701 127 8 0 591 717 14846661 14846787 1.580000e-44 191
16 TraesCS5D01G262300 chr3D 86.614 127 13 3 3768 3890 572442744 572442870 2.090000e-28 137
17 TraesCS5D01G262300 chr1A 92.683 123 9 0 598 720 168567636 168567514 1.230000e-40 178
18 TraesCS5D01G262300 chr1A 90.000 130 11 1 601 728 498452785 498452656 2.660000e-37 167
19 TraesCS5D01G262300 chr4D 91.473 129 9 2 601 728 367720770 367720897 4.430000e-40 176
20 TraesCS5D01G262300 chr7A 92.562 121 9 0 601 721 721098350 721098230 1.590000e-39 174
21 TraesCS5D01G262300 chr6B 93.220 118 8 0 600 717 617675164 617675281 1.590000e-39 174
22 TraesCS5D01G262300 chr6B 93.162 117 8 0 601 717 292242 292358 5.730000e-39 172
23 TraesCS5D01G262300 chr6D 87.248 149 17 2 3747 3893 2625191 2625339 7.410000e-38 169
24 TraesCS5D01G262300 chr7D 88.406 138 13 2 601 737 31949675 31949810 3.450000e-36 163
25 TraesCS5D01G262300 chr2B 83.832 167 24 3 3727 3890 731257596 731257430 5.770000e-34 156
26 TraesCS5D01G262300 chr3A 87.402 127 12 2 3768 3890 706426395 706426269 4.490000e-30 143
27 TraesCS5D01G262300 chr3A 86.614 127 13 3 3768 3890 706193446 706193320 2.090000e-28 137
28 TraesCS5D01G262300 chr2A 84.496 129 17 3 3764 3890 37967023 37966896 1.630000e-24 124


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 TraesCS5D01G262300 chr5D 368298483 368302789 4306 False 7954.000000 7954 100.000000 1 4307 1 chr5D.!!$F1 4306
1 TraesCS5D01G262300 chr5D 368289898 368292959 3061 False 1463.000000 2558 84.281500 207 3320 2 chr5D.!!$F3 3113
2 TraesCS5D01G262300 chr5A 470183528 470187436 3908 False 1758.333333 3892 89.518333 171 4307 3 chr5A.!!$F2 4136
3 TraesCS5D01G262300 chr5A 470174458 470177440 2982 False 1345.000000 2479 82.201500 269 3320 2 chr5A.!!$F1 3051
4 TraesCS5D01G262300 chr5B 436213229 436216242 3013 False 1450.000000 2536 87.499500 237 3320 2 chr5B.!!$F1 3083
5 TraesCS5D01G262300 chr5B 436243575 436247635 4060 False 1303.500000 3663 91.744000 1 4307 4 chr5B.!!$F2 4306

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
840 924 0.376502 GCGATTTCTTCAGCTCCTGC 59.623 55.0 0.0 0.0 40.05 4.85 F
1417 1503 0.881159 CGCCAAACCCGTCAAGTACA 60.881 55.0 0.0 0.0 0.00 2.90 F
1418 1504 1.310904 GCCAAACCCGTCAAGTACAA 58.689 50.0 0.0 0.0 0.00 2.41 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1644 1730 2.355716 GGTTAGCCAGTACATTGCTCCA 60.356 50.000 7.02 0.00 36.57 3.86 R
3270 3521 2.389998 GACGAATCGAATCTGGAGCTC 58.610 52.381 10.55 4.71 0.00 4.09 R
3427 3688 1.446966 GAGACCACGGCTTGCTCTC 60.447 63.158 1.13 1.13 0.00 3.20 R

All possible primers

Listed here are all possible primers based on the multiple sequence alignment and SNPs generated previously. A lower penalty score indicates a better primer. If the AutoCloner primers did not work during PCR or sequencing, these could be used as alternatives.

Download all possible primers: (Forward) (Reverse)
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
86 91 0.396556 AAAACCCACAGGAAACCGCT 60.397 50.000 0.00 0.00 36.73 5.52
89 94 1.373435 CCCACAGGAAACCGCTACA 59.627 57.895 0.00 0.00 33.47 2.74
151 156 4.315803 ACAATATGACCAACGCTATAGGC 58.684 43.478 1.04 0.00 37.64 3.93
163 168 0.468226 CTATAGGCGCCACAAAGGGA 59.532 55.000 31.54 2.84 38.09 4.20
358 381 1.799548 GCGGAGGAGTTCGTCTGAATC 60.800 57.143 13.30 0.00 38.92 2.52
393 431 1.074395 CTCCCCTCCCCTAACTCCC 60.074 68.421 0.00 0.00 0.00 4.30
426 465 2.028020 CCCTTCCTCTACGTTTTCTGCT 60.028 50.000 0.00 0.00 0.00 4.24
429 468 3.482722 TCCTCTACGTTTTCTGCTACG 57.517 47.619 0.00 0.00 43.08 3.51
656 715 6.747414 ATGGATGTATCTAGCACCAAGTTA 57.253 37.500 0.00 0.00 0.00 2.24
679 738 3.567164 GTGCCAGATACATCCATTTGAGG 59.433 47.826 0.00 0.00 0.00 3.86
685 744 6.066690 CAGATACATCCATTTGAGGGACAAT 58.933 40.000 0.00 0.00 37.23 2.71
717 776 2.084546 GTTTTTCGGATGGAGGGAGTG 58.915 52.381 0.00 0.00 0.00 3.51
726 785 4.335594 CGGATGGAGGGAGTGTTTTATTTC 59.664 45.833 0.00 0.00 0.00 2.17
784 846 4.706476 TCATGGATTGTTTGATGAACCTCC 59.294 41.667 0.00 0.00 38.55 4.30
791 869 5.152623 TGTTTGATGAACCTCCTAGTCAG 57.847 43.478 0.00 0.00 37.45 3.51
819 900 6.949117 AGAGGGATAATGTTGAGAGCATAT 57.051 37.500 0.00 0.00 0.00 1.78
820 901 6.709281 AGAGGGATAATGTTGAGAGCATATG 58.291 40.000 0.00 0.00 0.00 1.78
840 924 0.376502 GCGATTTCTTCAGCTCCTGC 59.623 55.000 0.00 0.00 40.05 4.85
853 937 1.129917 CTCCTGCTCTGATCCCATGT 58.870 55.000 0.00 0.00 0.00 3.21
859 943 3.499338 TGCTCTGATCCCATGTTGTTTT 58.501 40.909 0.00 0.00 0.00 2.43
890 974 6.952743 ACGATGAATGATCTTACTTTCATGC 58.047 36.000 12.19 0.00 41.39 4.06
923 1008 6.092807 GCAGAGTTTATTCAGTCTCCGAATTT 59.907 38.462 0.00 0.00 34.89 1.82
928 1013 8.290325 AGTTTATTCAGTCTCCGAATTTGTTTC 58.710 33.333 0.00 0.00 34.89 2.78
1005 1091 1.031571 GCTTCGATGGAACCATGGCA 61.032 55.000 13.04 1.62 36.70 4.92
1063 1149 2.733552 CCGCAAGATATCATCGAACTGG 59.266 50.000 5.32 0.00 43.02 4.00
1208 1294 4.320641 CCTTTTATTTTTCCAACGAGGCGA 60.321 41.667 0.00 0.00 37.29 5.54
1215 1301 1.471119 TCCAACGAGGCGAGACTTAT 58.529 50.000 0.00 0.00 37.29 1.73
1262 1348 1.005215 CCTCTTTGATGAGGCCTGGTT 59.995 52.381 12.00 0.00 45.84 3.67
1306 1392 3.949754 GGTGATTGAGCCTGATGATTTCA 59.050 43.478 0.00 0.00 0.00 2.69
1311 1397 3.959293 TGAGCCTGATGATTTCATGTGT 58.041 40.909 0.00 0.00 36.57 3.72
1417 1503 0.881159 CGCCAAACCCGTCAAGTACA 60.881 55.000 0.00 0.00 0.00 2.90
1418 1504 1.310904 GCCAAACCCGTCAAGTACAA 58.689 50.000 0.00 0.00 0.00 2.41
1425 1511 1.429463 CCGTCAAGTACAAGCACTCC 58.571 55.000 0.00 0.00 0.00 3.85
1427 1513 2.612972 CCGTCAAGTACAAGCACTCCAT 60.613 50.000 0.00 0.00 0.00 3.41
1430 1516 2.637382 TCAAGTACAAGCACTCCATGGA 59.363 45.455 15.27 15.27 0.00 3.41
1557 1643 6.038161 CCTTCAGTGTCATTCAAGTTTACACA 59.962 38.462 0.00 0.00 42.21 3.72
1644 1730 2.264794 GGGGTCGTCAACGCTGAT 59.735 61.111 0.00 0.00 40.55 2.90
1848 1937 4.577875 CTGTTCAAGCCAGAAGAGATTCT 58.422 43.478 6.98 0.00 40.30 2.40
1910 2002 1.615384 GGTGAAGCAAAGCTGGATCCT 60.615 52.381 14.23 0.00 39.62 3.24
1939 2031 7.989741 AGCATAGTATTGAGTTATCAGCACTTT 59.010 33.333 0.00 0.00 36.61 2.66
2161 2256 3.254024 AAGAAGGCCGGCATCGTGT 62.254 57.895 30.85 5.51 33.95 4.49
2508 2619 8.746052 ATATTGGATCAACATTTCCTTACGAA 57.254 30.769 0.00 0.00 32.95 3.85
2528 2643 7.519032 ACGAATTTGGAGTGAGGATTTTTAA 57.481 32.000 0.00 0.00 0.00 1.52
2678 2801 6.822667 TCTTTCAGCAGAATCATTTTGCTA 57.177 33.333 14.75 0.00 45.75 3.49
2820 2958 6.655930 AGGTTTGTGAAGACCTAACTTACAA 58.344 36.000 0.00 0.00 44.26 2.41
2838 2976 7.124052 ACTTACAATTACTCTAGTAGCCTCCA 58.876 38.462 0.00 0.00 0.00 3.86
2941 3084 6.886459 AGTATGATGGTATTCACTTTTGCAGT 59.114 34.615 0.00 0.00 35.35 4.40
3064 3239 4.370364 AAAGACGCACACAAAAGTTGAT 57.630 36.364 0.00 0.00 0.00 2.57
3270 3521 1.639298 CCAAGCGAAAGAGGAAGCCG 61.639 60.000 0.00 0.00 0.00 5.52
3427 3688 1.066858 ACTGTATGGTGCCAAGACTCG 60.067 52.381 0.00 0.00 0.00 4.18
3452 3713 1.464997 CAAGCCGTGGTCTCTTTTAGC 59.535 52.381 0.00 0.00 0.00 3.09
3453 3714 0.977395 AGCCGTGGTCTCTTTTAGCT 59.023 50.000 0.00 0.00 0.00 3.32
3454 3715 1.066787 AGCCGTGGTCTCTTTTAGCTC 60.067 52.381 0.00 0.00 0.00 4.09
3455 3716 1.337823 GCCGTGGTCTCTTTTAGCTCA 60.338 52.381 0.00 0.00 0.00 4.26
3456 3717 2.678190 GCCGTGGTCTCTTTTAGCTCAT 60.678 50.000 0.00 0.00 0.00 2.90
3458 3719 4.755411 CCGTGGTCTCTTTTAGCTCATAA 58.245 43.478 0.00 0.00 0.00 1.90
3459 3720 4.806247 CCGTGGTCTCTTTTAGCTCATAAG 59.194 45.833 0.00 0.00 0.00 1.73
3477 3738 8.273780 CTCATAAGCAGATTTAAACCAAGACT 57.726 34.615 0.00 0.00 0.00 3.24
3478 3739 8.268850 TCATAAGCAGATTTAAACCAAGACTC 57.731 34.615 0.00 0.00 0.00 3.36
3479 3740 5.613358 AAGCAGATTTAAACCAAGACTCG 57.387 39.130 0.00 0.00 0.00 4.18
3480 3741 4.642429 AGCAGATTTAAACCAAGACTCGT 58.358 39.130 0.00 0.00 0.00 4.18
3481 3742 4.452455 AGCAGATTTAAACCAAGACTCGTG 59.548 41.667 0.00 0.00 0.00 4.35
3482 3743 4.712763 CAGATTTAAACCAAGACTCGTGC 58.287 43.478 0.00 0.00 0.00 5.34
3483 3744 4.452455 CAGATTTAAACCAAGACTCGTGCT 59.548 41.667 0.00 0.00 0.00 4.40
3484 3745 5.049405 CAGATTTAAACCAAGACTCGTGCTT 60.049 40.000 0.00 0.00 0.00 3.91
3485 3746 6.147164 CAGATTTAAACCAAGACTCGTGCTTA 59.853 38.462 0.00 0.00 0.00 3.09
3486 3747 6.708949 AGATTTAAACCAAGACTCGTGCTTAA 59.291 34.615 0.00 0.00 0.00 1.85
3487 3748 5.917541 TTAAACCAAGACTCGTGCTTAAG 57.082 39.130 0.00 0.00 0.00 1.85
3488 3749 3.470645 AACCAAGACTCGTGCTTAAGT 57.529 42.857 4.02 0.00 0.00 2.24
3501 3762 3.057946 GTGCTTAAGTCTTGCCAAAGGAG 60.058 47.826 4.02 0.00 33.90 3.69
3511 3773 2.726821 TGCCAAAGGAGAAATAGCAGG 58.273 47.619 0.00 0.00 0.00 4.85
3518 3780 4.388378 AGGAGAAATAGCAGGTCGTAAC 57.612 45.455 0.00 0.00 0.00 2.50
3519 3781 4.024670 AGGAGAAATAGCAGGTCGTAACT 58.975 43.478 0.00 0.00 0.00 2.24
3520 3782 4.466726 AGGAGAAATAGCAGGTCGTAACTT 59.533 41.667 0.00 0.00 0.00 2.66
3521 3783 4.567159 GGAGAAATAGCAGGTCGTAACTTG 59.433 45.833 0.00 0.00 35.67 3.16
3544 3806 5.759763 TGCTGTGGCACAATAGTATCATAAG 59.240 40.000 22.31 6.06 44.16 1.73
3561 3823 6.964807 TCATAAGTAGGAGCATTACGGTTA 57.035 37.500 0.00 0.00 0.00 2.85
3569 3831 4.750098 AGGAGCATTACGGTTATGATTTCG 59.250 41.667 11.03 0.00 0.00 3.46
3623 3889 2.148916 TCTTCAGTAGGCGTTGTGTG 57.851 50.000 0.00 0.00 0.00 3.82
3624 3890 0.512952 CTTCAGTAGGCGTTGTGTGC 59.487 55.000 0.00 0.00 0.00 4.57
3626 3892 0.179070 TCAGTAGGCGTTGTGTGCAA 60.179 50.000 0.00 0.00 0.00 4.08
3628 3894 1.064803 CAGTAGGCGTTGTGTGCAAAA 59.935 47.619 0.00 0.00 36.22 2.44
3630 3896 1.849829 GTAGGCGTTGTGTGCAAAAAC 59.150 47.619 0.00 0.00 36.22 2.43
3637 3903 3.481628 CGTTGTGTGCAAAAACATGTGTG 60.482 43.478 0.00 0.00 36.22 3.82
3671 3937 6.822442 ACCGGTGTTTATCAAAAAGGAAAAT 58.178 32.000 6.12 0.00 0.00 1.82
3674 3940 9.430623 CCGGTGTTTATCAAAAAGGAAAATATT 57.569 29.630 0.00 0.00 0.00 1.28
3687 3959 7.544804 AAGGAAAATATTTGTGCTCCTCTTT 57.455 32.000 16.14 3.41 32.04 2.52
3734 4006 1.884075 AAGATGCCGCGTCACCACTA 61.884 55.000 14.97 0.00 0.00 2.74
3749 4021 6.627287 CGTCACCACTAGAATTTCCTCATACA 60.627 42.308 0.00 0.00 0.00 2.29
3760 4032 1.064240 TCCTCATACACCGAGTGCCTA 60.064 52.381 4.23 0.00 36.98 3.93
3767 4039 0.179124 CACCGAGTGCCTAGCTCTTC 60.179 60.000 0.00 0.00 32.35 2.87
3771 4043 2.583593 GTGCCTAGCTCTTCGCCG 60.584 66.667 0.00 0.00 40.39 6.46
3784 4056 1.161563 TTCGCCGAGAACCAAACCAC 61.162 55.000 0.00 0.00 33.14 4.16
3787 4059 1.070105 CCGAGAACCAAACCACGGA 59.930 57.895 0.00 0.00 42.40 4.69
3801 4073 2.664851 CGGACACTCGGCAAAGCA 60.665 61.111 0.00 0.00 0.00 3.91
3834 4106 4.802876 GAGGAAAACTCGGCAATAGATG 57.197 45.455 0.00 0.00 36.29 2.90
3835 4107 3.002759 GAGGAAAACTCGGCAATAGATGC 59.997 47.826 0.00 0.00 44.84 3.91
3836 4108 5.218587 GAGGAAAACTCGGCAATAGATGCT 61.219 45.833 0.01 0.00 44.90 3.79
3837 4109 5.968988 GAGGAAAACTCGGCAATAGATGCTA 60.969 44.000 0.01 0.00 44.90 3.49
3838 4110 7.933715 GAGGAAAACTCGGCAATAGATGCTAC 61.934 46.154 0.01 0.00 44.90 3.58
3839 4111 9.978740 GAGGAAAACTCGGCAATAGATGCTACT 62.979 44.444 0.01 0.00 44.90 2.57
3850 4122 0.370273 GATGCTACTCGGCAAACACG 59.630 55.000 0.00 0.00 45.68 4.49
3851 4123 1.019278 ATGCTACTCGGCAAACACGG 61.019 55.000 0.00 0.00 45.68 4.94
3852 4124 2.388232 GCTACTCGGCAAACACGGG 61.388 63.158 0.00 0.00 37.94 5.28
3937 4217 1.205655 CTCCATCTGCTCAGAAACCGA 59.794 52.381 3.47 0.00 41.36 4.69
3959 4239 1.139989 GATGCGTACCATGATGTCCG 58.860 55.000 0.00 0.00 33.29 4.79
3969 4249 2.202932 GATGTCCGCCACGCTGAT 60.203 61.111 0.00 0.00 0.00 2.90
3975 4255 4.569023 CGCCACGCTGATCCGCTA 62.569 66.667 7.56 0.00 0.00 4.26
4043 4328 4.677673 TGACATGACCAGTCTATCCATG 57.322 45.455 0.00 0.00 40.12 3.66
4106 4395 2.355716 CGATGGGCCTTCTGTTTTCCTA 60.356 50.000 16.47 0.00 0.00 2.94
4107 4396 3.697166 GATGGGCCTTCTGTTTTCCTAA 58.303 45.455 11.96 0.00 0.00 2.69
4117 4406 3.003275 TCTGTTTTCCTAACTTTGCAGCG 59.997 43.478 0.00 0.00 0.00 5.18
4120 4409 2.543777 TTCCTAACTTTGCAGCGAGT 57.456 45.000 0.00 0.00 0.00 4.18
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
69 74 0.250597 GTAGCGGTTTCCTGTGGGTT 60.251 55.000 0.00 0.00 0.00 4.11
99 104 5.589050 GTCTCTAAAATAAACCGCTTCCCAT 59.411 40.000 0.00 0.00 0.00 4.00
151 156 2.350458 CCCCAATCCCTTTGTGGCG 61.350 63.158 0.00 0.00 33.15 5.69
163 168 2.489073 GGATACGGCTTCAATCCCCAAT 60.489 50.000 0.00 0.00 34.30 3.16
246 258 1.800681 GGTATTTGACCGCCTGTGC 59.199 57.895 0.00 0.00 38.87 4.57
257 269 0.876342 GAGAGGGAGCGCGGTATTTG 60.876 60.000 12.41 0.00 0.00 2.32
350 373 1.519455 CTCACGGGCGGATTCAGAC 60.519 63.158 0.00 0.00 0.00 3.51
393 431 2.166664 AGAGGAAGGGAAAACGAGATCG 59.833 50.000 0.00 0.00 46.33 3.69
429 468 2.819595 TGATGCGGAAGAAGCGCC 60.820 61.111 2.29 0.00 37.44 6.53
617 676 1.066143 TCCATTCGAGGGACAAGCTTC 60.066 52.381 0.00 0.00 0.00 3.86
621 680 2.698855 ACATCCATTCGAGGGACAAG 57.301 50.000 9.77 6.38 37.23 3.16
656 715 4.458397 CTCAAATGGATGTATCTGGCACT 58.542 43.478 0.00 0.00 0.00 4.40
661 720 5.039920 TGTCCCTCAAATGGATGTATCTG 57.960 43.478 0.00 0.00 33.65 2.90
679 738 2.586648 ACCTTGTCCCAAGATTGTCC 57.413 50.000 5.57 0.00 0.00 4.02
685 744 2.092321 TCCGAAAAACCTTGTCCCAAGA 60.092 45.455 5.57 0.00 0.00 3.02
704 763 5.358160 CAGAAATAAAACACTCCCTCCATCC 59.642 44.000 0.00 0.00 0.00 3.51
784 846 9.703892 CAACATTATCCCTCTTTATCTGACTAG 57.296 37.037 0.00 0.00 0.00 2.57
791 869 7.220030 TGCTCTCAACATTATCCCTCTTTATC 58.780 38.462 0.00 0.00 0.00 1.75
819 900 0.615331 AGGAGCTGAAGAAATCGCCA 59.385 50.000 0.00 0.00 0.00 5.69
820 901 1.012841 CAGGAGCTGAAGAAATCGCC 58.987 55.000 0.00 0.00 32.44 5.54
842 926 8.859156 CGTAATTTTAAAACAACATGGGATCAG 58.141 33.333 1.97 0.00 0.00 2.90
890 974 7.814642 AGACTGAATAAACTCTGCAGAAAATG 58.185 34.615 18.85 8.55 0.00 2.32
923 1008 0.107410 ACGGACTGGCAAGTGAAACA 60.107 50.000 0.00 0.00 41.43 2.83
928 1013 0.307760 GTTTGACGGACTGGCAAGTG 59.692 55.000 0.00 0.00 36.52 3.16
954 1039 1.761784 AGCTACCAGATCCTTCTGCTG 59.238 52.381 0.00 0.00 46.76 4.41
955 1040 2.038659 GAGCTACCAGATCCTTCTGCT 58.961 52.381 0.00 0.00 46.76 4.24
1005 1091 4.122046 GTTTCTTCTTTGTTGGCTGCATT 58.878 39.130 0.50 0.00 0.00 3.56
1063 1149 0.320697 ACCGGAAGCCTCACAAGTAC 59.679 55.000 9.46 0.00 0.00 2.73
1208 1294 3.636153 GGAAGGACTTGCCATAAGTCT 57.364 47.619 16.55 1.54 44.49 3.24
1277 1363 2.690778 GGCTCAATCACCGGCACAC 61.691 63.158 0.00 0.00 0.00 3.82
1284 1370 3.949754 TGAAATCATCAGGCTCAATCACC 59.050 43.478 0.00 0.00 33.04 4.02
1417 1503 2.508716 AGTGATCATCCATGGAGTGCTT 59.491 45.455 21.33 0.00 0.00 3.91
1418 1504 2.104451 GAGTGATCATCCATGGAGTGCT 59.896 50.000 21.33 11.50 0.00 4.40
1425 1511 4.691175 AGAACGAAGAGTGATCATCCATG 58.309 43.478 0.00 0.00 0.00 3.66
1427 1513 4.705023 TGTAGAACGAAGAGTGATCATCCA 59.295 41.667 0.00 0.00 0.00 3.41
1430 1516 4.400884 AGCTGTAGAACGAAGAGTGATCAT 59.599 41.667 0.00 0.00 0.00 2.45
1557 1643 0.904865 TCCACTTCTCATCGCCCAGT 60.905 55.000 0.00 0.00 0.00 4.00
1644 1730 2.355716 GGTTAGCCAGTACATTGCTCCA 60.356 50.000 7.02 0.00 36.57 3.86
1753 1839 3.264104 CAAATGCAGGATCCGCAAAAAT 58.736 40.909 27.06 13.51 43.84 1.82
1910 2002 7.439356 GTGCTGATAACTCAATACTATGCTTCA 59.561 37.037 0.00 0.00 0.00 3.02
1939 2031 6.582636 AGATGAAATGCGGTCTTAGAATGTA 58.417 36.000 0.00 0.00 0.00 2.29
2161 2256 3.192954 CTTTTCGCCTTGGCGTGCA 62.193 57.895 29.41 14.77 34.52 4.57
2508 2619 8.704668 ACACTTTTAAAAATCCTCACTCCAAAT 58.295 29.630 1.66 0.00 0.00 2.32
2528 2643 3.057736 GCTGCATTCACATCAGACACTTT 60.058 43.478 0.00 0.00 0.00 2.66
2678 2801 7.013559 TGTCAAATTCACAACATCAGAGACAAT 59.986 33.333 0.00 0.00 0.00 2.71
2808 2942 8.911965 GGCTACTAGAGTAATTGTAAGTTAGGT 58.088 37.037 0.00 0.00 0.00 3.08
2820 2958 6.136857 TGAACATGGAGGCTACTAGAGTAAT 58.863 40.000 0.00 0.00 0.00 1.89
2941 3084 2.480037 CTGAACTGCACATGTAGCGAAA 59.520 45.455 0.00 0.00 33.85 3.46
3270 3521 2.389998 GACGAATCGAATCTGGAGCTC 58.610 52.381 10.55 4.71 0.00 4.09
3427 3688 1.446966 GAGACCACGGCTTGCTCTC 60.447 63.158 1.13 1.13 0.00 3.20
3452 3713 8.273780 AGTCTTGGTTTAAATCTGCTTATGAG 57.726 34.615 0.00 0.00 0.00 2.90
3453 3714 7.064609 CGAGTCTTGGTTTAAATCTGCTTATGA 59.935 37.037 0.00 0.00 0.00 2.15
3454 3715 7.148407 ACGAGTCTTGGTTTAAATCTGCTTATG 60.148 37.037 0.00 0.00 0.00 1.90
3455 3716 6.879458 ACGAGTCTTGGTTTAAATCTGCTTAT 59.121 34.615 0.00 0.00 0.00 1.73
3456 3717 6.147164 CACGAGTCTTGGTTTAAATCTGCTTA 59.853 38.462 0.00 0.00 0.00 3.09
3458 3719 4.452455 CACGAGTCTTGGTTTAAATCTGCT 59.548 41.667 0.00 0.00 0.00 4.24
3459 3720 4.712763 CACGAGTCTTGGTTTAAATCTGC 58.287 43.478 0.00 0.00 0.00 4.26
3460 3721 4.452455 AGCACGAGTCTTGGTTTAAATCTG 59.548 41.667 0.00 0.00 0.00 2.90
3461 3722 4.642429 AGCACGAGTCTTGGTTTAAATCT 58.358 39.130 0.00 0.00 0.00 2.40
3462 3723 5.358298 AAGCACGAGTCTTGGTTTAAATC 57.642 39.130 8.14 0.00 30.54 2.17
3463 3724 6.485648 ACTTAAGCACGAGTCTTGGTTTAAAT 59.514 34.615 17.76 0.00 36.19 1.40
3464 3725 5.818857 ACTTAAGCACGAGTCTTGGTTTAAA 59.181 36.000 17.76 7.72 36.19 1.52
3465 3726 5.362263 ACTTAAGCACGAGTCTTGGTTTAA 58.638 37.500 17.76 9.97 36.19 1.52
3466 3727 4.952460 ACTTAAGCACGAGTCTTGGTTTA 58.048 39.130 17.76 9.27 36.19 2.01
3467 3728 3.805207 ACTTAAGCACGAGTCTTGGTTT 58.195 40.909 17.76 0.00 36.19 3.27
3468 3729 3.391049 GACTTAAGCACGAGTCTTGGTT 58.609 45.455 16.90 16.90 39.30 3.67
3469 3730 3.027974 GACTTAAGCACGAGTCTTGGT 57.972 47.619 1.29 0.00 39.30 3.67
3474 3735 1.727335 GGCAAGACTTAAGCACGAGTC 59.273 52.381 1.29 5.53 41.99 3.36
3475 3736 1.070134 TGGCAAGACTTAAGCACGAGT 59.930 47.619 1.29 0.00 0.00 4.18
3476 3737 1.795768 TGGCAAGACTTAAGCACGAG 58.204 50.000 1.29 0.00 0.00 4.18
3477 3738 2.248280 TTGGCAAGACTTAAGCACGA 57.752 45.000 1.29 0.00 0.00 4.35
3478 3739 2.350772 CCTTTGGCAAGACTTAAGCACG 60.351 50.000 1.29 0.00 30.57 5.34
3479 3740 2.884639 TCCTTTGGCAAGACTTAAGCAC 59.115 45.455 1.29 0.00 30.57 4.40
3480 3741 3.149196 CTCCTTTGGCAAGACTTAAGCA 58.851 45.455 1.29 0.00 30.57 3.91
3481 3742 3.412386 TCTCCTTTGGCAAGACTTAAGC 58.588 45.455 1.29 0.00 30.57 3.09
3482 3743 6.581171 ATTTCTCCTTTGGCAAGACTTAAG 57.419 37.500 0.00 0.00 30.57 1.85
3483 3744 6.151144 GCTATTTCTCCTTTGGCAAGACTTAA 59.849 38.462 0.00 0.00 30.57 1.85
3484 3745 5.648092 GCTATTTCTCCTTTGGCAAGACTTA 59.352 40.000 0.00 0.00 30.57 2.24
3485 3746 4.460731 GCTATTTCTCCTTTGGCAAGACTT 59.539 41.667 0.00 0.00 30.57 3.01
3486 3747 4.013050 GCTATTTCTCCTTTGGCAAGACT 58.987 43.478 0.00 0.00 30.57 3.24
3487 3748 3.758554 TGCTATTTCTCCTTTGGCAAGAC 59.241 43.478 0.00 0.00 30.57 3.01
3488 3749 4.012374 CTGCTATTTCTCCTTTGGCAAGA 58.988 43.478 0.00 0.00 30.57 3.02
3501 3762 4.260334 GCAAGTTACGACCTGCTATTTC 57.740 45.455 0.00 0.00 39.58 2.17
3521 3783 5.760253 ACTTATGATACTATTGTGCCACAGC 59.240 40.000 0.00 0.00 40.48 4.40
3522 3784 7.600375 CCTACTTATGATACTATTGTGCCACAG 59.400 40.741 0.00 0.00 0.00 3.66
3523 3785 7.289084 TCCTACTTATGATACTATTGTGCCACA 59.711 37.037 0.00 0.00 0.00 4.17
3524 3786 7.667557 TCCTACTTATGATACTATTGTGCCAC 58.332 38.462 0.00 0.00 0.00 5.01
3534 3796 6.720288 ACCGTAATGCTCCTACTTATGATACT 59.280 38.462 0.00 0.00 0.00 2.12
3536 3798 7.534723 AACCGTAATGCTCCTACTTATGATA 57.465 36.000 0.00 0.00 0.00 2.15
3544 3806 6.128902 CGAAATCATAACCGTAATGCTCCTAC 60.129 42.308 0.00 0.00 0.00 3.18
3561 3823 4.696877 TGACAGAATGAGTTGCGAAATCAT 59.303 37.500 6.16 6.16 46.99 2.45
3623 3889 5.964887 ACAACATACACACATGTTTTTGC 57.035 34.783 0.00 0.00 44.75 3.68
3624 3890 7.305705 CGGTTACAACATACACACATGTTTTTG 60.306 37.037 0.00 0.00 44.75 2.44
3626 3892 6.202937 CGGTTACAACATACACACATGTTTT 58.797 36.000 0.00 0.00 44.75 2.43
3630 3896 3.749088 ACCGGTTACAACATACACACATG 59.251 43.478 0.00 0.00 0.00 3.21
3637 3903 6.724694 TGATAAACACCGGTTACAACATAC 57.275 37.500 2.97 0.00 35.82 2.39
3648 3914 8.996024 ATATTTTCCTTTTTGATAAACACCGG 57.004 30.769 0.00 0.00 0.00 5.28
3695 3967 6.620877 TCTTCTCAAAGCTCAAATAGGGTA 57.379 37.500 0.00 0.00 32.18 3.69
3699 3971 5.503683 CGGCATCTTCTCAAAGCTCAAATAG 60.504 44.000 0.00 0.00 32.18 1.73
3700 3972 4.333649 CGGCATCTTCTCAAAGCTCAAATA 59.666 41.667 0.00 0.00 32.18 1.40
3701 3973 3.128242 CGGCATCTTCTCAAAGCTCAAAT 59.872 43.478 0.00 0.00 32.18 2.32
3704 3976 1.730501 CGGCATCTTCTCAAAGCTCA 58.269 50.000 0.00 0.00 32.18 4.26
3705 3977 0.376502 GCGGCATCTTCTCAAAGCTC 59.623 55.000 0.00 0.00 32.18 4.09
3706 3978 1.364626 CGCGGCATCTTCTCAAAGCT 61.365 55.000 0.00 0.00 32.18 3.74
3707 3979 1.061570 CGCGGCATCTTCTCAAAGC 59.938 57.895 0.00 0.00 32.18 3.51
3708 3980 0.371645 GACGCGGCATCTTCTCAAAG 59.628 55.000 7.34 0.00 0.00 2.77
3711 3983 1.446099 GTGACGCGGCATCTTCTCA 60.446 57.895 22.20 1.95 0.00 3.27
3734 4006 4.759782 CACTCGGTGTATGAGGAAATTCT 58.240 43.478 0.00 0.00 37.79 2.40
3749 4021 1.658686 CGAAGAGCTAGGCACTCGGT 61.659 60.000 0.00 0.00 41.75 4.69
3767 4039 2.943653 GTGGTTTGGTTCTCGGCG 59.056 61.111 0.00 0.00 0.00 6.46
3771 4043 0.942252 GTGTCCGTGGTTTGGTTCTC 59.058 55.000 0.00 0.00 0.00 2.87
3784 4056 1.781025 TTTGCTTTGCCGAGTGTCCG 61.781 55.000 0.00 0.00 0.00 4.79
3787 4059 1.961793 TACTTTGCTTTGCCGAGTGT 58.038 45.000 0.00 0.00 0.00 3.55
3801 4073 4.316645 GAGTTTTCCTCTCGGCTTACTTT 58.683 43.478 0.00 0.00 37.22 2.66
3826 4098 3.871006 TGTTTGCCGAGTAGCATCTATTG 59.129 43.478 0.00 0.00 43.64 1.90
3827 4099 3.871594 GTGTTTGCCGAGTAGCATCTATT 59.128 43.478 0.00 0.00 43.64 1.73
3828 4100 3.458189 GTGTTTGCCGAGTAGCATCTAT 58.542 45.455 0.00 0.00 43.64 1.98
3829 4101 2.734175 CGTGTTTGCCGAGTAGCATCTA 60.734 50.000 0.00 0.00 43.64 1.98
3830 4102 1.726853 GTGTTTGCCGAGTAGCATCT 58.273 50.000 0.00 0.00 43.64 2.90
3831 4103 0.370273 CGTGTTTGCCGAGTAGCATC 59.630 55.000 0.00 0.00 43.64 3.91
3832 4104 1.019278 CCGTGTTTGCCGAGTAGCAT 61.019 55.000 0.00 0.00 43.64 3.79
3833 4105 1.666553 CCGTGTTTGCCGAGTAGCA 60.667 57.895 0.00 0.00 42.17 3.49
3834 4106 2.388232 CCCGTGTTTGCCGAGTAGC 61.388 63.158 0.00 0.00 0.00 3.58
3835 4107 2.388232 GCCCGTGTTTGCCGAGTAG 61.388 63.158 0.00 0.00 0.00 2.57
3836 4108 2.357760 GCCCGTGTTTGCCGAGTA 60.358 61.111 0.00 0.00 0.00 2.59
3837 4109 3.842925 ATGCCCGTGTTTGCCGAGT 62.843 57.895 0.00 0.00 0.00 4.18
3838 4110 2.141122 AAATGCCCGTGTTTGCCGAG 62.141 55.000 0.00 0.00 0.00 4.63
3839 4111 0.889638 TAAATGCCCGTGTTTGCCGA 60.890 50.000 0.00 0.00 0.00 5.54
3840 4112 0.731174 GTAAATGCCCGTGTTTGCCG 60.731 55.000 0.00 0.00 0.00 5.69
3841 4113 0.389296 GGTAAATGCCCGTGTTTGCC 60.389 55.000 0.00 0.00 33.93 4.52
3850 4122 2.552315 CACATGGTATCGGTAAATGCCC 59.448 50.000 0.00 0.00 30.94 5.36
3851 4123 2.031157 GCACATGGTATCGGTAAATGCC 60.031 50.000 0.00 0.00 32.49 4.40
3852 4124 2.616376 TGCACATGGTATCGGTAAATGC 59.384 45.455 0.00 0.00 0.00 3.56
3884 4156 0.936600 AACAACGGCAAGCATTTTGC 59.063 45.000 3.39 3.39 45.46 3.68
3885 4157 1.526464 GGAACAACGGCAAGCATTTTG 59.474 47.619 0.00 0.00 0.00 2.44
3937 4217 2.483714 GGACATCATGGTACGCATCTGT 60.484 50.000 0.00 7.93 0.00 3.41
3959 4239 2.962253 GTAGCGGATCAGCGTGGC 60.962 66.667 12.29 0.80 43.00 5.01
3986 4266 9.664332 GCCATTCATCATATAGACAATAGACTT 57.336 33.333 0.00 0.00 0.00 3.01
3988 4268 8.263640 AGGCCATTCATCATATAGACAATAGAC 58.736 37.037 5.01 0.00 0.00 2.59
3989 4269 8.262933 CAGGCCATTCATCATATAGACAATAGA 58.737 37.037 5.01 0.00 0.00 1.98
3991 4271 7.037370 ACCAGGCCATTCATCATATAGACAATA 60.037 37.037 5.01 0.00 0.00 1.90
3992 4272 6.185511 CCAGGCCATTCATCATATAGACAAT 58.814 40.000 5.01 0.00 0.00 2.71
3993 4273 5.073554 ACCAGGCCATTCATCATATAGACAA 59.926 40.000 5.01 0.00 0.00 3.18
4083 4368 1.586154 AAAACAGAAGGCCCATCGCG 61.586 55.000 0.00 0.00 38.94 5.87
4106 4395 1.291877 CCGCTACTCGCTGCAAAGTT 61.292 55.000 9.58 0.00 36.73 2.66
4107 4396 1.738099 CCGCTACTCGCTGCAAAGT 60.738 57.895 9.30 9.30 36.73 2.66
4229 4522 0.460811 TCGATGACACCTGCATCTGC 60.461 55.000 0.00 0.00 39.91 4.26
4230 4523 1.134877 ACTCGATGACACCTGCATCTG 60.135 52.381 0.00 0.00 39.91 2.90
4231 4524 1.134877 CACTCGATGACACCTGCATCT 60.135 52.381 0.00 0.00 39.91 2.90
4232 4525 1.284657 CACTCGATGACACCTGCATC 58.715 55.000 0.00 0.00 38.95 3.91
4233 4526 0.742281 GCACTCGATGACACCTGCAT 60.742 55.000 0.00 0.00 0.00 3.96
4234 4527 1.374631 GCACTCGATGACACCTGCA 60.375 57.895 0.00 0.00 0.00 4.41


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

AutoCloner maintained by Alex Coulton.