Multiple sequence alignment - TraesCS4D01G128900

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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 TraesCS4D01G128900 chr4D 100.000 4028 0 0 1 4028 113234211 113238238 0.000000e+00 7439.0
1 TraesCS4D01G128900 chr4B 94.029 2060 82 17 1702 3731 173967821 173969869 0.000000e+00 3085.0
2 TraesCS4D01G128900 chr4B 92.189 1946 96 21 1 1917 173966173 173968091 0.000000e+00 2700.0
3 TraesCS4D01G128900 chr4B 95.604 91 4 0 3769 3859 173969869 173969959 3.240000e-31 147.0
4 TraesCS4D01G128900 chr4A 95.246 1851 65 14 1702 3531 463924715 463922867 0.000000e+00 2909.0
5 TraesCS4D01G128900 chr4A 91.619 1933 68 35 4 1917 463926302 463924445 0.000000e+00 2586.0
6 TraesCS4D01G128900 chr4A 85.930 398 33 8 3596 3984 463922608 463922225 1.740000e-108 403.0
7 TraesCS4D01G128900 chr4A 100.000 47 0 0 3982 4028 463922150 463922104 1.990000e-13 87.9
8 TraesCS4D01G128900 chr5D 75.422 1245 134 83 1921 3050 226941161 226939974 2.860000e-121 446.0
9 TraesCS4D01G128900 chr5D 75.202 371 54 17 1359 1701 226941471 226941111 1.510000e-29 141.0
10 TraesCS4D01G128900 chr5A 75.040 1246 137 86 1920 3052 300964879 300963695 6.230000e-113 418.0
11 TraesCS4D01G128900 chr5A 75.610 369 53 18 1359 1701 300965185 300964828 9.020000e-32 148.0
12 TraesCS4D01G128900 chr5B 74.800 1250 131 82 1921 3052 244976936 244978119 1.050000e-105 394.0
13 TraesCS4D01G128900 chr5B 76.164 365 52 17 1359 1701 244976635 244976986 4.170000e-35 159.0


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

query scaffold start end length rev.comp avg.bitscore max.bitscore avg.percent.identical query.start query.end num_hsp groupid homo_length
0 TraesCS4D01G128900 chr4D 113234211 113238238 4027 False 7439.000000 7439 100.000000 1 4028 1 chr4D.!!$F1 4027
1 TraesCS4D01G128900 chr4B 173966173 173969959 3786 False 1977.333333 3085 93.940667 1 3859 3 chr4B.!!$F1 3858
2 TraesCS4D01G128900 chr4A 463922104 463926302 4198 True 1496.475000 2909 93.198750 4 4028 4 chr4A.!!$R1 4024
3 TraesCS4D01G128900 chr5D 226939974 226941471 1497 True 293.500000 446 75.312000 1359 3050 2 chr5D.!!$R1 1691
4 TraesCS4D01G128900 chr5A 300963695 300965185 1490 True 283.000000 418 75.325000 1359 3052 2 chr5A.!!$R1 1693
5 TraesCS4D01G128900 chr5B 244976635 244978119 1484 False 276.500000 394 75.482000 1359 3052 2 chr5B.!!$F1 1693

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
436 455 0.390998 GTTCAGCCTCTGTCTCTGCC 60.391 60.0 0.0 0.0 32.61 4.85 F
1384 1431 0.381089 GTACCAGACCTCCATCGACG 59.619 60.0 0.0 0.0 0.00 5.12 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1793 1873 0.463295 CGCACCCTTCATCTGCATCT 60.463 55.000 0.00 0.0 0.0 2.9 R
3086 3314 1.001888 TTGCCCCATGTCATGCCAT 59.998 52.632 7.35 0.0 0.0 4.4 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
34 35 1.742831 TGGCACCGACAATAGAAATGC 59.257 47.619 0.00 0.00 0.00 3.56
123 125 6.678540 ATTAACCACGTCAAAATTTTACGC 57.321 33.333 21.85 9.33 40.18 4.42
138 140 3.307339 TTACGCTCAAAACACACGTTC 57.693 42.857 0.00 0.00 38.12 3.95
160 162 2.125512 CCCGTGCTACACTGCTCC 60.126 66.667 0.00 0.00 31.34 4.70
185 187 3.181504 GCAAACCATGTACCGTATGAACC 60.182 47.826 0.00 0.00 0.00 3.62
197 199 6.610075 ACCGTATGAACCTTTTAACCTCTA 57.390 37.500 0.00 0.00 0.00 2.43
199 201 6.875726 ACCGTATGAACCTTTTAACCTCTAAC 59.124 38.462 0.00 0.00 0.00 2.34
200 202 7.101700 CCGTATGAACCTTTTAACCTCTAACT 58.898 38.462 0.00 0.00 0.00 2.24
225 232 2.591571 AGGACCTAACGGCGTATTTC 57.408 50.000 15.20 7.65 0.00 2.17
316 324 6.152379 CAGGAGAACAAGACAAATAAAAGGC 58.848 40.000 0.00 0.00 0.00 4.35
403 419 1.407618 CCGCAGTTTTATAAAGCCCCC 59.592 52.381 8.28 0.00 0.00 5.40
436 455 0.390998 GTTCAGCCTCTGTCTCTGCC 60.391 60.000 0.00 0.00 32.61 4.85
478 497 7.969536 TTAGCAACTCTGATCCATATTTAGC 57.030 36.000 0.00 0.00 0.00 3.09
536 559 0.887933 GCGAAAGGCTTCCAATCCAA 59.112 50.000 0.00 0.00 39.11 3.53
537 560 1.478105 GCGAAAGGCTTCCAATCCAAT 59.522 47.619 0.00 0.00 39.11 3.16
538 561 2.480244 GCGAAAGGCTTCCAATCCAATC 60.480 50.000 0.00 0.00 39.11 2.67
539 562 2.099756 CGAAAGGCTTCCAATCCAATCC 59.900 50.000 0.00 0.00 0.00 3.01
540 563 2.925966 AAGGCTTCCAATCCAATCCA 57.074 45.000 0.00 0.00 0.00 3.41
561 584 2.000048 TCCCCAAAGCCCAAAGACTAT 59.000 47.619 0.00 0.00 0.00 2.12
636 661 6.936900 GCACAAGATAGAGATAGAGAGAGAGT 59.063 42.308 0.00 0.00 0.00 3.24
638 663 6.936900 ACAAGATAGAGATAGAGAGAGAGTGC 59.063 42.308 0.00 0.00 0.00 4.40
639 664 6.054860 AGATAGAGATAGAGAGAGAGTGCC 57.945 45.833 0.00 0.00 0.00 5.01
640 665 3.508845 AGAGATAGAGAGAGAGTGCCC 57.491 52.381 0.00 0.00 0.00 5.36
735 770 1.541672 CCCCCTCTCCTCTCTCTCC 59.458 68.421 0.00 0.00 0.00 3.71
736 771 1.292941 CCCCCTCTCCTCTCTCTCCA 61.293 65.000 0.00 0.00 0.00 3.86
737 772 0.859760 CCCCTCTCCTCTCTCTCCAT 59.140 60.000 0.00 0.00 0.00 3.41
743 778 2.158682 TCTCCTCTCTCTCCATTCTCCG 60.159 54.545 0.00 0.00 0.00 4.63
962 999 2.653448 CAGATCTGCGCTCGTCCG 60.653 66.667 10.38 0.00 0.00 4.79
963 1000 3.134792 AGATCTGCGCTCGTCCGT 61.135 61.111 9.73 0.00 0.00 4.69
964 1001 2.951745 GATCTGCGCTCGTCCGTG 60.952 66.667 9.73 0.00 0.00 4.94
965 1002 4.498520 ATCTGCGCTCGTCCGTGG 62.499 66.667 9.73 0.00 0.00 4.94
988 1025 4.090057 GCTGCTGCGTTTCGGTCC 62.090 66.667 0.00 0.00 0.00 4.46
1059 1096 1.421268 TCCTTGCTTTGCTTCCTCTCA 59.579 47.619 0.00 0.00 0.00 3.27
1099 1136 3.005155 GCATGTTCCTTCTTGTTTCTGCT 59.995 43.478 0.00 0.00 0.00 4.24
1169 1210 0.384230 CATGCCGTTCGTGTGTGTTC 60.384 55.000 0.00 0.00 0.00 3.18
1280 1321 9.376075 CTCAGCAAGATCGATGGTAAATAATAT 57.624 33.333 0.54 0.00 0.00 1.28
1329 1375 1.066454 GTTTTGTTGTTCCGTGGGGAG 59.934 52.381 0.00 0.00 44.98 4.30
1375 1422 2.943978 GCAGGCGTGTACCAGACCT 61.944 63.158 8.40 0.00 0.00 3.85
1384 1431 0.381089 GTACCAGACCTCCATCGACG 59.619 60.000 0.00 0.00 0.00 5.12
1755 1835 0.465824 AGCAGATGCAGATGAAGGGC 60.466 55.000 7.68 0.00 45.16 5.19
1790 1870 3.362797 GCTTCAGCAGCTGCAGCA 61.363 61.111 38.24 21.89 46.72 4.41
1791 1871 2.871099 CTTCAGCAGCTGCAGCAG 59.129 61.111 38.24 31.89 45.16 4.24
1808 1888 1.309950 CAGCAGATGCAGATGAAGGG 58.690 55.000 7.68 0.00 45.16 3.95
1809 1889 0.917533 AGCAGATGCAGATGAAGGGT 59.082 50.000 7.68 0.00 45.16 4.34
1810 1890 1.022735 GCAGATGCAGATGAAGGGTG 58.977 55.000 5.17 0.00 41.59 4.61
1811 1891 1.022735 CAGATGCAGATGAAGGGTGC 58.977 55.000 0.00 0.00 37.73 5.01
1812 1892 0.463295 AGATGCAGATGAAGGGTGCG 60.463 55.000 0.00 0.00 40.23 5.34
1813 1893 2.056481 GATGCAGATGAAGGGTGCGC 62.056 60.000 0.00 0.00 40.23 6.09
1814 1894 3.512516 GCAGATGAAGGGTGCGCC 61.513 66.667 8.12 8.12 0.00 6.53
1815 1895 3.197790 CAGATGAAGGGTGCGCCG 61.198 66.667 10.86 0.00 34.97 6.46
1816 1896 3.390521 AGATGAAGGGTGCGCCGA 61.391 61.111 10.86 0.00 34.97 5.54
1817 1897 3.195698 GATGAAGGGTGCGCCGAC 61.196 66.667 10.86 4.66 34.97 4.79
1945 2025 4.754667 CGCAGCAGCTCCAGCAGA 62.755 66.667 0.00 0.00 45.16 4.26
2076 2156 0.395312 TCAAGTTCAACCTCCCCGAC 59.605 55.000 0.00 0.00 0.00 4.79
2295 2384 2.291996 TGGAGGAAACGAGATCCCTGTA 60.292 50.000 0.00 0.00 37.71 2.74
2406 2519 2.510918 GGTAAGAACGGAGGCGGC 60.511 66.667 0.00 0.00 0.00 6.53
3059 3287 3.055719 CACCGCCGCTCATGGTTT 61.056 61.111 0.00 0.00 32.48 3.27
3086 3314 3.657398 AGACCATGATGAATCTGGCAA 57.343 42.857 0.00 0.00 32.10 4.52
3123 3352 3.437049 GCAACAACAAGTCCCATCTAGAC 59.563 47.826 0.00 0.00 34.31 2.59
3162 3391 4.957759 TTTAGCTTCTACATTTTCGCCC 57.042 40.909 0.00 0.00 0.00 6.13
3373 3608 4.024725 TGTGTTTACATTCTGCGTTGGTAC 60.025 41.667 0.00 0.00 0.00 3.34
3406 3641 4.564769 GTGAGATGTCCAGAAGAAACGATC 59.435 45.833 0.00 0.00 0.00 3.69
3428 3663 9.066939 CGATCGTAGAAATGTAGAAAGGATATG 57.933 37.037 7.03 0.00 43.58 1.78
3431 3666 9.914131 TCGTAGAAATGTAGAAAGGATATGATG 57.086 33.333 0.00 0.00 0.00 3.07
3434 3669 7.520798 AGAAATGTAGAAAGGATATGATGGCA 58.479 34.615 0.00 0.00 0.00 4.92
3435 3670 7.664731 AGAAATGTAGAAAGGATATGATGGCAG 59.335 37.037 0.00 0.00 0.00 4.85
3436 3671 5.894298 TGTAGAAAGGATATGATGGCAGT 57.106 39.130 0.00 0.00 0.00 4.40
3437 3672 6.252599 TGTAGAAAGGATATGATGGCAGTT 57.747 37.500 0.00 0.00 0.00 3.16
3438 3673 6.291377 TGTAGAAAGGATATGATGGCAGTTC 58.709 40.000 0.00 0.00 0.00 3.01
3441 3676 1.696336 AGGATATGATGGCAGTTCGCT 59.304 47.619 0.00 0.00 41.91 4.93
3443 3678 2.996621 GGATATGATGGCAGTTCGCTAC 59.003 50.000 0.00 0.00 41.91 3.58
3444 3679 3.554960 GGATATGATGGCAGTTCGCTACA 60.555 47.826 0.00 0.00 41.91 2.74
3445 3680 2.627515 ATGATGGCAGTTCGCTACAT 57.372 45.000 0.00 0.00 41.91 2.29
3446 3681 2.401583 TGATGGCAGTTCGCTACATT 57.598 45.000 0.00 0.00 41.91 2.71
3447 3682 2.710377 TGATGGCAGTTCGCTACATTT 58.290 42.857 0.00 0.00 41.91 2.32
3448 3683 3.081061 TGATGGCAGTTCGCTACATTTT 58.919 40.909 0.00 0.00 41.91 1.82
3449 3684 3.505680 TGATGGCAGTTCGCTACATTTTT 59.494 39.130 0.00 0.00 41.91 1.94
3466 3707 4.268720 TTTTTGAGGGGCGCAGTT 57.731 50.000 10.83 0.00 0.00 3.16
3467 3708 2.037871 TTTTTGAGGGGCGCAGTTC 58.962 52.632 10.83 3.26 0.00 3.01
3531 3772 1.059913 AAGACTCCCCACTGGACTTG 58.940 55.000 0.00 0.00 38.61 3.16
3533 3774 2.352805 CTCCCCACTGGACTTGGC 59.647 66.667 0.00 0.00 38.61 4.52
3541 4041 1.068333 CACTGGACTTGGCCAATTTCG 60.068 52.381 20.85 9.98 37.52 3.46
3618 4122 1.747367 CATTTCCGCCCGGTAAGCA 60.747 57.895 6.61 0.00 36.47 3.91
3684 4188 0.508641 CGATTTCTGCCCGATAAGCG 59.491 55.000 0.00 0.00 40.47 4.68
3710 4214 1.000938 CACAACTTGCCCAAGCTTCTC 60.001 52.381 7.88 0.00 41.99 2.87
3719 4223 0.239347 CCAAGCTTCTCGCAAAGGTG 59.761 55.000 0.00 0.00 42.61 4.00
3739 4243 2.025719 GCCTTAGCTGAATTCCGCC 58.974 57.895 17.09 0.00 35.50 6.13
3740 4244 1.448119 GCCTTAGCTGAATTCCGCCC 61.448 60.000 17.09 0.00 35.50 6.13
3741 4245 1.160329 CCTTAGCTGAATTCCGCCCG 61.160 60.000 17.09 6.89 0.00 6.13
3742 4246 0.179084 CTTAGCTGAATTCCGCCCGA 60.179 55.000 17.09 1.95 0.00 5.14
3743 4247 0.461339 TTAGCTGAATTCCGCCCGAC 60.461 55.000 17.09 0.00 0.00 4.79
3744 4248 1.609635 TAGCTGAATTCCGCCCGACA 61.610 55.000 17.09 0.00 0.00 4.35
3745 4249 2.038269 GCTGAATTCCGCCCGACAA 61.038 57.895 10.49 0.00 0.00 3.18
3746 4250 1.982073 GCTGAATTCCGCCCGACAAG 61.982 60.000 10.49 0.00 0.00 3.16
3747 4251 1.982073 CTGAATTCCGCCCGACAAGC 61.982 60.000 2.27 0.00 0.00 4.01
3748 4252 1.745489 GAATTCCGCCCGACAAGCT 60.745 57.895 0.00 0.00 0.00 3.74
3749 4253 0.461339 GAATTCCGCCCGACAAGCTA 60.461 55.000 0.00 0.00 0.00 3.32
3750 4254 0.180406 AATTCCGCCCGACAAGCTAT 59.820 50.000 0.00 0.00 0.00 2.97
3751 4255 0.532862 ATTCCGCCCGACAAGCTATG 60.533 55.000 0.00 0.00 0.00 2.23
3753 4257 2.173669 CCGCCCGACAAGCTATGTG 61.174 63.158 6.31 0.00 44.12 3.21
3754 4258 2.173669 CGCCCGACAAGCTATGTGG 61.174 63.158 6.31 5.47 44.12 4.17
3755 4259 1.220749 GCCCGACAAGCTATGTGGA 59.779 57.895 10.88 0.00 44.12 4.02
3756 4260 1.090052 GCCCGACAAGCTATGTGGAC 61.090 60.000 10.88 2.39 44.12 4.02
3757 4261 0.249120 CCCGACAAGCTATGTGGACA 59.751 55.000 10.88 0.00 44.12 4.02
3758 4262 1.338674 CCCGACAAGCTATGTGGACAA 60.339 52.381 10.88 0.00 44.12 3.18
3759 4263 1.732259 CCGACAAGCTATGTGGACAAC 59.268 52.381 10.88 0.00 44.12 3.32
3760 4264 2.612972 CCGACAAGCTATGTGGACAACT 60.613 50.000 10.88 0.00 44.12 3.16
3761 4265 3.067106 CGACAAGCTATGTGGACAACTT 58.933 45.455 6.31 0.00 44.12 2.66
3762 4266 3.123621 CGACAAGCTATGTGGACAACTTC 59.876 47.826 6.31 0.00 44.12 3.01
3763 4267 3.412386 ACAAGCTATGTGGACAACTTCC 58.588 45.455 0.00 0.00 46.13 3.46
3764 4268 3.073062 ACAAGCTATGTGGACAACTTCCT 59.927 43.478 0.00 0.00 46.10 3.36
3765 4269 3.618690 AGCTATGTGGACAACTTCCTC 57.381 47.619 0.00 0.00 46.10 3.71
3766 4270 3.177228 AGCTATGTGGACAACTTCCTCT 58.823 45.455 0.00 0.00 46.10 3.69
3767 4271 4.353777 AGCTATGTGGACAACTTCCTCTA 58.646 43.478 0.00 0.00 46.10 2.43
3824 4328 4.202101 CCAACGTCTCTATGAGCTCATCTT 60.202 45.833 31.92 13.13 37.76 2.40
3869 4373 1.556911 GTGCCATCTCTCCTCCTCAAA 59.443 52.381 0.00 0.00 0.00 2.69
3879 4383 5.960811 TCTCTCCTCCTCAAACTTGACATAT 59.039 40.000 0.00 0.00 32.90 1.78
3890 4394 7.592938 TCAAACTTGACATATCGAAAGCATTT 58.407 30.769 0.00 0.00 34.41 2.32
3929 4433 2.609046 CCTCTTGGAGGTACTGGGG 58.391 63.158 5.49 0.00 44.25 4.96
3930 4434 0.983378 CCTCTTGGAGGTACTGGGGG 60.983 65.000 5.49 0.00 44.25 5.40
3931 4435 0.252742 CTCTTGGAGGTACTGGGGGT 60.253 60.000 0.00 0.00 41.55 4.95
3932 4436 0.195096 TCTTGGAGGTACTGGGGGTT 59.805 55.000 0.00 0.00 41.55 4.11
3945 4458 0.898326 GGGGGTTTGGCTACAAGTGG 60.898 60.000 0.00 0.00 37.97 4.00
3979 4492 1.469335 TTGCTCCTCCGTTCGTCCTT 61.469 55.000 0.00 0.00 0.00 3.36
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
2 3 1.689813 TCGGTGCCAAGAGTGAAAGTA 59.310 47.619 0.00 0.00 0.00 2.24
14 15 1.742831 GCATTTCTATTGTCGGTGCCA 59.257 47.619 0.00 0.00 0.00 4.92
34 35 2.681660 ATGTGACGCATGACCGATG 58.318 52.632 0.00 0.00 36.26 3.84
185 187 8.781196 GGTCCTTTGTTAGTTAGAGGTTAAAAG 58.219 37.037 0.00 0.00 0.00 2.27
197 199 3.405831 GCCGTTAGGTCCTTTGTTAGTT 58.594 45.455 0.00 0.00 40.50 2.24
199 201 1.997606 CGCCGTTAGGTCCTTTGTTAG 59.002 52.381 0.00 0.00 40.50 2.34
200 202 1.344114 ACGCCGTTAGGTCCTTTGTTA 59.656 47.619 0.00 0.00 40.50 2.41
204 211 3.264947 GAAATACGCCGTTAGGTCCTTT 58.735 45.455 0.00 0.00 40.50 3.11
316 324 1.202222 CCGCTGCCAATTCTTTAGCTG 60.202 52.381 0.00 0.00 32.43 4.24
403 419 2.007049 GCTGAACATGTGAGGTACCCG 61.007 57.143 8.74 0.00 0.00 5.28
436 455 0.250727 AAACATGGACCGGTCAGTGG 60.251 55.000 34.40 22.02 0.00 4.00
499 518 2.036475 TCGCTTTTGCTCTCTCTCAACT 59.964 45.455 0.00 0.00 44.80 3.16
500 519 2.408050 TCGCTTTTGCTCTCTCTCAAC 58.592 47.619 0.00 0.00 44.80 3.18
536 559 0.417035 TTTGGGCTTTGGGGATGGAT 59.583 50.000 0.00 0.00 0.00 3.41
537 560 0.252193 CTTTGGGCTTTGGGGATGGA 60.252 55.000 0.00 0.00 0.00 3.41
538 561 0.252193 TCTTTGGGCTTTGGGGATGG 60.252 55.000 0.00 0.00 0.00 3.51
539 562 0.897621 GTCTTTGGGCTTTGGGGATG 59.102 55.000 0.00 0.00 0.00 3.51
540 563 0.786435 AGTCTTTGGGCTTTGGGGAT 59.214 50.000 0.00 0.00 0.00 3.85
561 584 6.481643 ACCCTTTTCAAGATTTATTCCTCGA 58.518 36.000 0.00 0.00 0.00 4.04
636 661 2.041265 GGAGGAAGGAGAGGGGCA 59.959 66.667 0.00 0.00 0.00 5.36
638 663 3.157949 GCGGAGGAAGGAGAGGGG 61.158 72.222 0.00 0.00 0.00 4.79
639 664 3.157949 GGCGGAGGAAGGAGAGGG 61.158 72.222 0.00 0.00 0.00 4.30
640 665 3.157949 GGGCGGAGGAAGGAGAGG 61.158 72.222 0.00 0.00 0.00 3.69
724 759 1.847088 TCGGAGAATGGAGAGAGAGGA 59.153 52.381 0.00 0.00 0.00 3.71
725 760 2.229792 CTCGGAGAATGGAGAGAGAGG 58.770 57.143 0.00 0.00 34.09 3.69
727 762 1.064389 TGCTCGGAGAATGGAGAGAGA 60.064 52.381 9.69 0.00 34.09 3.10
731 766 1.107114 GAGTGCTCGGAGAATGGAGA 58.893 55.000 9.69 0.00 34.09 3.71
732 767 3.657956 GAGTGCTCGGAGAATGGAG 57.342 57.895 9.69 0.00 34.09 3.86
765 800 0.248289 AATAAGTGTCCCGTCCCACG 59.752 55.000 0.00 0.00 42.11 4.94
966 1003 4.043200 GAAACGCAGCAGCCCACC 62.043 66.667 0.00 0.00 37.52 4.61
971 1008 4.090057 GGACCGAAACGCAGCAGC 62.090 66.667 0.00 0.00 37.42 5.25
988 1025 0.674581 TTGCTCATGGCTGACTTCCG 60.675 55.000 7.54 0.00 42.39 4.30
1059 1096 0.322546 GCGGGGGAATGTCTTGAGTT 60.323 55.000 0.00 0.00 0.00 3.01
1099 1136 4.686191 ACCTCACAAAAATTTCATGGCA 57.314 36.364 8.33 0.00 0.00 4.92
1169 1210 1.068816 GGATTTGGGGACGAACAAACG 60.069 52.381 0.00 0.00 39.15 3.60
1280 1321 6.832384 ACGGATAAACAGAACTCCATCTACTA 59.168 38.462 0.00 0.00 0.00 1.82
1291 1332 6.031471 ACAAAACAACACGGATAAACAGAAC 58.969 36.000 0.00 0.00 0.00 3.01
1375 1422 3.209812 CTCCTCCGCGTCGATGGA 61.210 66.667 4.92 5.34 0.00 3.41
1384 1431 4.785453 CACCTTGCCCTCCTCCGC 62.785 72.222 0.00 0.00 0.00 5.54
1789 1869 1.309950 CCCTTCATCTGCATCTGCTG 58.690 55.000 3.53 3.22 42.66 4.41
1790 1870 0.917533 ACCCTTCATCTGCATCTGCT 59.082 50.000 3.53 0.00 42.66 4.24
1791 1871 1.022735 CACCCTTCATCTGCATCTGC 58.977 55.000 0.00 0.00 42.50 4.26
1792 1872 1.022735 GCACCCTTCATCTGCATCTG 58.977 55.000 0.00 0.00 0.00 2.90
1793 1873 0.463295 CGCACCCTTCATCTGCATCT 60.463 55.000 0.00 0.00 0.00 2.90
1794 1874 2.020131 CGCACCCTTCATCTGCATC 58.980 57.895 0.00 0.00 0.00 3.91
1795 1875 2.117156 GCGCACCCTTCATCTGCAT 61.117 57.895 0.30 0.00 0.00 3.96
1796 1876 2.747460 GCGCACCCTTCATCTGCA 60.747 61.111 0.30 0.00 0.00 4.41
1797 1877 3.512516 GGCGCACCCTTCATCTGC 61.513 66.667 10.83 0.00 0.00 4.26
1798 1878 3.197790 CGGCGCACCCTTCATCTG 61.198 66.667 10.83 0.00 0.00 2.90
1799 1879 3.390521 TCGGCGCACCCTTCATCT 61.391 61.111 10.83 0.00 0.00 2.90
1800 1880 3.195698 GTCGGCGCACCCTTCATC 61.196 66.667 10.83 0.00 0.00 2.92
2295 2384 1.299976 GCCGTTCCCCTTGATCTGT 59.700 57.895 0.00 0.00 0.00 3.41
2973 3191 2.924290 GCTGAAGTAGTTGTAAGGCTCG 59.076 50.000 0.00 0.00 0.00 5.03
3059 3287 5.434408 CAGATTCATCATGGTCTTCCTTCA 58.566 41.667 0.00 0.00 34.23 3.02
3086 3314 1.001888 TTGCCCCATGTCATGCCAT 59.998 52.632 7.35 0.00 0.00 4.40
3123 3352 9.278734 GAAGCTAAATTAATCAAGAAGAAACGG 57.721 33.333 0.00 0.00 0.00 4.44
3373 3608 3.653344 TGGACATCTCACTTTTCAGTCG 58.347 45.455 0.00 0.00 0.00 4.18
3406 3641 9.144747 CCATCATATCCTTTCTACATTTCTACG 57.855 37.037 0.00 0.00 0.00 3.51
3449 3684 1.791103 CGAACTGCGCCCCTCAAAAA 61.791 55.000 4.18 0.00 0.00 1.94
3450 3685 2.258013 CGAACTGCGCCCCTCAAAA 61.258 57.895 4.18 0.00 0.00 2.44
3466 3707 3.849911 CTTGGTTGAGAAGATGTAGCGA 58.150 45.455 0.00 0.00 0.00 4.93
3467 3708 2.349886 GCTTGGTTGAGAAGATGTAGCG 59.650 50.000 0.00 0.00 0.00 4.26
3533 3774 0.310854 GCTTATCGGGCCGAAATTGG 59.689 55.000 34.58 20.62 39.99 3.16
3589 4093 1.455383 GCGGAAATGGGCTATGGTGG 61.455 60.000 0.00 0.00 0.00 4.61
3591 4095 1.152756 GGCGGAAATGGGCTATGGT 60.153 57.895 0.00 0.00 0.00 3.55
3594 4098 2.113139 CGGGCGGAAATGGGCTAT 59.887 61.111 0.00 0.00 0.00 2.97
3600 4104 1.101049 ATGCTTACCGGGCGGAAATG 61.101 55.000 6.32 0.00 38.96 2.32
3618 4122 0.469705 TTGGGGAAGCTGTGCACAAT 60.470 50.000 21.98 9.80 35.79 2.71
3721 4225 1.448119 GGGCGGAATTCAGCTAAGGC 61.448 60.000 26.17 11.80 37.23 4.35
3723 4227 0.179084 TCGGGCGGAATTCAGCTAAG 60.179 55.000 26.17 18.12 37.23 2.18
3724 4228 0.461339 GTCGGGCGGAATTCAGCTAA 60.461 55.000 26.17 11.91 37.23 3.09
3725 4229 1.143183 GTCGGGCGGAATTCAGCTA 59.857 57.895 26.17 12.22 37.23 3.32
3726 4230 2.125106 GTCGGGCGGAATTCAGCT 60.125 61.111 26.17 0.00 37.23 4.24
3727 4231 1.982073 CTTGTCGGGCGGAATTCAGC 61.982 60.000 20.68 20.68 36.32 4.26
3728 4232 1.982073 GCTTGTCGGGCGGAATTCAG 61.982 60.000 7.93 4.27 0.00 3.02
3729 4233 2.038269 GCTTGTCGGGCGGAATTCA 61.038 57.895 7.93 0.00 0.00 2.57
3730 4234 0.461339 TAGCTTGTCGGGCGGAATTC 60.461 55.000 0.00 0.00 34.52 2.17
3731 4235 0.180406 ATAGCTTGTCGGGCGGAATT 59.820 50.000 0.00 0.00 34.52 2.17
3732 4236 0.532862 CATAGCTTGTCGGGCGGAAT 60.533 55.000 0.00 0.00 34.52 3.01
3733 4237 1.153449 CATAGCTTGTCGGGCGGAA 60.153 57.895 0.00 0.00 34.52 4.30
3734 4238 2.355986 ACATAGCTTGTCGGGCGGA 61.356 57.895 0.00 0.00 30.89 5.54
3735 4239 2.173669 CACATAGCTTGTCGGGCGG 61.174 63.158 0.00 0.00 36.00 6.13
3736 4240 2.173669 CCACATAGCTTGTCGGGCG 61.174 63.158 0.00 0.00 36.00 6.13
3737 4241 1.090052 GTCCACATAGCTTGTCGGGC 61.090 60.000 0.00 0.00 36.00 6.13
3738 4242 0.249120 TGTCCACATAGCTTGTCGGG 59.751 55.000 0.00 0.00 36.00 5.14
3739 4243 1.732259 GTTGTCCACATAGCTTGTCGG 59.268 52.381 0.00 1.89 36.00 4.79
3740 4244 2.688507 AGTTGTCCACATAGCTTGTCG 58.311 47.619 0.00 0.00 36.00 4.35
3741 4245 3.437049 GGAAGTTGTCCACATAGCTTGTC 59.563 47.826 0.00 0.00 46.97 3.18
3742 4246 3.412386 GGAAGTTGTCCACATAGCTTGT 58.588 45.455 0.00 0.00 46.97 3.16
3752 4256 7.762128 GCAAGAAGCTAGAGGAAGTTGTCCA 62.762 48.000 0.00 0.00 44.58 4.02
3753 4257 5.390821 GCAAGAAGCTAGAGGAAGTTGTCC 61.391 50.000 0.00 0.00 43.30 4.02
3754 4258 3.682377 GCAAGAAGCTAGAGGAAGTTGTC 59.318 47.826 0.00 0.00 41.15 3.18
3755 4259 3.071602 TGCAAGAAGCTAGAGGAAGTTGT 59.928 43.478 0.00 0.00 45.94 3.32
3756 4260 3.668447 TGCAAGAAGCTAGAGGAAGTTG 58.332 45.455 0.00 0.00 45.94 3.16
3757 4261 4.357918 TTGCAAGAAGCTAGAGGAAGTT 57.642 40.909 0.00 0.00 45.94 2.66
3758 4262 4.322567 CTTTGCAAGAAGCTAGAGGAAGT 58.677 43.478 0.00 0.00 45.94 3.01
3759 4263 3.688673 CCTTTGCAAGAAGCTAGAGGAAG 59.311 47.826 0.00 0.00 45.94 3.46
3760 4264 3.073062 ACCTTTGCAAGAAGCTAGAGGAA 59.927 43.478 14.85 0.00 45.94 3.36
3761 4265 2.639839 ACCTTTGCAAGAAGCTAGAGGA 59.360 45.455 14.85 0.00 45.94 3.71
3762 4266 2.746362 CACCTTTGCAAGAAGCTAGAGG 59.254 50.000 7.79 7.79 45.94 3.69
3786 4290 1.143183 TTGGGCTAGTCGATTCGCC 59.857 57.895 14.25 14.25 41.75 5.54
3787 4291 1.480219 CGTTGGGCTAGTCGATTCGC 61.480 60.000 0.00 0.00 0.00 4.70
3824 4328 0.400213 ACGAATGCTCTTTGGGGACA 59.600 50.000 0.00 0.00 39.83 4.02
3869 4373 6.741992 TCAAATGCTTTCGATATGTCAAGT 57.258 33.333 0.00 0.00 0.00 3.16
3890 4394 2.715749 ATGACCATGCCTCGAAATCA 57.284 45.000 0.00 0.00 0.00 2.57
3923 4427 0.112412 CTTGTAGCCAAACCCCCAGT 59.888 55.000 0.00 0.00 0.00 4.00
3926 4430 0.898326 CCACTTGTAGCCAAACCCCC 60.898 60.000 0.00 0.00 0.00 5.40
3927 4431 0.111639 TCCACTTGTAGCCAAACCCC 59.888 55.000 0.00 0.00 0.00 4.95
3928 4432 2.092323 GATCCACTTGTAGCCAAACCC 58.908 52.381 0.00 0.00 0.00 4.11
3929 4433 2.790433 TGATCCACTTGTAGCCAAACC 58.210 47.619 0.00 0.00 0.00 3.27
3930 4434 4.702131 AGATTGATCCACTTGTAGCCAAAC 59.298 41.667 0.00 0.00 0.00 2.93
3931 4435 4.922206 AGATTGATCCACTTGTAGCCAAA 58.078 39.130 0.00 0.00 0.00 3.28
3932 4436 4.019411 TGAGATTGATCCACTTGTAGCCAA 60.019 41.667 0.00 0.00 0.00 4.52
3945 4458 4.706035 AGGAGCAAGTGATGAGATTGATC 58.294 43.478 0.00 0.00 38.33 2.92


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

AutoCloner maintained by Alex Coulton.