Multiple sequence alignment - TraesCS4D01G040300

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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 TraesCS4D01G040300 chr4D 100.000 4563 0 0 1 4563 18722953 18727515 0.000000e+00 8427.0
1 TraesCS4D01G040300 chr4D 91.411 163 13 1 1471 1633 75266748 75266909 5.940000e-54 222.0
2 TraesCS4D01G040300 chr4D 91.411 163 12 2 1471 1633 416761696 416761856 5.940000e-54 222.0
3 TraesCS4D01G040300 chr4A 93.084 3369 167 28 486 3827 582510683 582507354 0.000000e+00 4870.0
4 TraesCS4D01G040300 chr4A 88.668 503 42 6 1 491 582511245 582510746 2.350000e-167 599.0
5 TraesCS4D01G040300 chr4A 90.244 164 14 2 1471 1633 5222460 5222622 3.580000e-51 213.0
6 TraesCS4D01G040300 chr4A 76.471 255 27 16 3887 4112 582507322 582507072 1.740000e-19 108.0
7 TraesCS4D01G040300 chr4B 93.773 2200 110 16 1634 3827 30837897 30840075 0.000000e+00 3278.0
8 TraesCS4D01G040300 chr4B 91.994 662 35 5 734 1392 30837167 30837813 0.000000e+00 913.0
9 TraesCS4D01G040300 chr4B 86.541 743 45 26 3850 4548 30840053 30840784 0.000000e+00 767.0
10 TraesCS4D01G040300 chr4B 89.959 488 30 8 1 470 30836490 30836976 3.020000e-171 612.0
11 TraesCS4D01G040300 chr4B 90.148 203 15 4 498 696 30836970 30837171 4.530000e-65 259.0
12 TraesCS4D01G040300 chr3B 91.124 169 11 3 1470 1638 257782111 257781947 4.590000e-55 226.0
13 TraesCS4D01G040300 chr2D 91.018 167 13 2 1470 1636 318563895 318563731 1.650000e-54 224.0
14 TraesCS4D01G040300 chr2D 89.412 170 15 3 1464 1633 22450788 22450954 1.290000e-50 211.0
15 TraesCS4D01G040300 chr3D 89.881 168 15 2 1471 1637 128214007 128214173 9.940000e-52 215.0
16 TraesCS4D01G040300 chr7D 90.244 164 15 1 1471 1634 566026575 566026737 3.580000e-51 213.0
17 TraesCS4D01G040300 chr7A 82.407 108 16 3 361 467 155963517 155963622 1.750000e-14 91.6


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 TraesCS4D01G040300 chr4D 18722953 18727515 4562 False 8427.0 8427 100.000000 1 4563 1 chr4D.!!$F1 4562
1 TraesCS4D01G040300 chr4A 582507072 582511245 4173 True 1859.0 4870 86.074333 1 4112 3 chr4A.!!$R1 4111
2 TraesCS4D01G040300 chr4B 30836490 30840784 4294 False 1165.8 3278 90.483000 1 4548 5 chr4B.!!$F1 4547

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
552 642 0.179086 TGTTTGACGAGAGCTGCACA 60.179 50.0 1.02 0.00 0.00 4.57 F
1773 1883 0.319986 TCAACATGGTGCGCTTCGTA 60.320 50.0 9.73 0.00 0.00 3.43 F
2075 2194 0.380378 GCATTTTTGGCGCCTCGATA 59.620 50.0 29.70 9.68 0.00 2.92 F
3034 3154 0.263765 AGAACCGGTATGGGGAGCTA 59.736 55.0 8.00 0.00 44.64 3.32 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2109 2228 0.551396 AGCAGGCCAACCCCTATAAC 59.449 55.000 5.01 0.0 36.11 1.89 R
2739 2859 0.036388 GCTGGAATCGTGGACCTCAA 60.036 55.000 0.00 0.0 0.00 3.02 R
3359 3479 0.389391 TAGCAGATAGGGACAAGCGC 59.611 55.000 0.00 0.0 0.00 5.92 R
4540 4749 1.003718 AAGCCTTGGACGGTACAGC 60.004 57.895 0.00 0.0 0.00 4.40 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 2.072487 ATGGACGGTGGGGAGATGG 61.072 63.158 0.00 0.00 0.00 3.51
73 74 5.265191 AGCAGATCGATGTATATGGTAGGT 58.735 41.667 0.54 0.00 27.72 3.08
82 83 7.232737 TCGATGTATATGGTAGGTGTTCTTCAT 59.767 37.037 0.00 0.00 0.00 2.57
86 87 7.785028 TGTATATGGTAGGTGTTCTTCATCTCT 59.215 37.037 0.00 0.00 38.58 3.10
184 187 7.067494 ACCATGCCATAAAAGACTACTCAAATC 59.933 37.037 0.00 0.00 0.00 2.17
200 203 5.936956 ACTCAAATCAGACATGGAGTTTCTC 59.063 40.000 0.00 0.00 32.04 2.87
229 232 8.668353 TCTGAGATCAAATACAACATTGTAAGC 58.332 33.333 8.47 0.00 45.74 3.09
341 360 9.243105 TCTTAATCTTCTGGGAAAAATCGATTT 57.757 29.630 17.60 17.60 0.00 2.17
426 445 4.987285 CAGACCTCCACAAATATGATCTCG 59.013 45.833 0.00 0.00 0.00 4.04
465 484 5.238650 ACGCTAACAGAAAAGTAAGCAATGT 59.761 36.000 0.00 0.00 0.00 2.71
471 490 8.856490 AACAGAAAAGTAAGCAATGTTAGTTG 57.144 30.769 0.00 0.00 0.00 3.16
472 491 8.220755 ACAGAAAAGTAAGCAATGTTAGTTGA 57.779 30.769 0.00 0.00 0.00 3.18
475 494 9.736023 AGAAAAGTAAGCAATGTTAGTTGAAAG 57.264 29.630 0.00 0.00 0.00 2.62
552 642 0.179086 TGTTTGACGAGAGCTGCACA 60.179 50.000 1.02 0.00 0.00 4.57
553 643 0.510359 GTTTGACGAGAGCTGCACAG 59.490 55.000 1.02 0.00 0.00 3.66
662 753 3.243771 CGAGTACACCTTTCACCTCAACT 60.244 47.826 0.00 0.00 0.00 3.16
710 801 0.927537 GTTTTGCCTGGAAAACACGC 59.072 50.000 18.34 3.37 42.80 5.34
842 934 2.699938 ATTCCCCGCCCCCTCATT 60.700 61.111 0.00 0.00 0.00 2.57
874 966 2.032071 CCCACGAGTTCCACACCC 59.968 66.667 0.00 0.00 0.00 4.61
880 972 1.185618 CGAGTTCCACACCCTCCTCA 61.186 60.000 0.00 0.00 0.00 3.86
923 1019 2.756283 CCCTCTCGCCGACTTCCT 60.756 66.667 0.00 0.00 0.00 3.36
925 1021 2.405594 CTCTCGCCGACTTCCTCG 59.594 66.667 0.00 0.00 42.54 4.63
967 1063 0.390472 GAACTACTGCCTGCTCGCTT 60.390 55.000 0.00 0.00 0.00 4.68
1012 1108 2.409870 CGTGGCATGGCTTCTTCCC 61.410 63.158 21.08 0.00 0.00 3.97
1368 1472 4.380973 CCTTGATCTCTCTGCAGTTCGTAA 60.381 45.833 14.67 1.55 0.00 3.18
1388 1492 8.867112 TCGTAAGATATGCTAAAGGTGTTAAG 57.133 34.615 0.00 0.00 45.01 1.85
1403 1507 1.559149 TTAAGAAACGGCGGCGTCAC 61.559 55.000 37.44 29.99 0.00 3.67
1449 1556 3.482786 CATTGTTCAGTAGCGCAACTTC 58.517 45.455 11.47 0.00 0.00 3.01
1464 1571 4.653004 GCAACTTCGCTAGGAAAATTCTC 58.347 43.478 0.00 0.00 33.34 2.87
1471 1578 6.961360 TCGCTAGGAAAATTCTCTGATCTA 57.039 37.500 0.00 0.00 0.00 1.98
1497 1604 7.059202 TCCCTCCGTTTCTAAATATAAGACC 57.941 40.000 0.00 0.00 0.00 3.85
1534 1641 3.028094 AGGGACTACATACGGATGTGT 57.972 47.619 23.85 17.96 46.11 3.72
1535 1642 2.693591 AGGGACTACATACGGATGTGTG 59.306 50.000 23.85 17.20 46.11 3.82
1536 1643 2.470821 GGACTACATACGGATGTGTGC 58.529 52.381 23.85 18.69 46.11 4.57
1541 1650 0.923403 CATACGGATGTGTGCAGACG 59.077 55.000 9.70 0.00 35.01 4.18
1565 1674 7.172532 ACGCATTTTAAAGTGTAGATTCACTCA 59.827 33.333 11.77 0.00 46.25 3.41
1577 1686 3.438087 AGATTCACTCATTTTGCTCCGTG 59.562 43.478 0.00 0.00 0.00 4.94
1595 1704 6.037172 GCTCCGTGTGTAGTTCATATTGAAAT 59.963 38.462 0.00 0.00 38.22 2.17
1596 1705 7.534085 TCCGTGTGTAGTTCATATTGAAATC 57.466 36.000 0.00 0.00 38.22 2.17
1676 1786 3.941483 ACTCAGTGTTTGACAACTTCCTG 59.059 43.478 0.00 0.00 33.58 3.86
1679 1789 4.764823 TCAGTGTTTGACAACTTCCTGTTT 59.235 37.500 0.00 0.00 36.63 2.83
1752 1862 2.738521 CTCACAGAACCCGCGGTG 60.739 66.667 26.12 18.26 35.34 4.94
1773 1883 0.319986 TCAACATGGTGCGCTTCGTA 60.320 50.000 9.73 0.00 0.00 3.43
1965 2075 4.314740 ACGCCTTCTTGCACAATTTTTA 57.685 36.364 0.00 0.00 0.00 1.52
1993 2104 3.643320 TGTTGTAATGGTGGAATTGGCAA 59.357 39.130 0.68 0.68 0.00 4.52
1994 2105 4.244862 GTTGTAATGGTGGAATTGGCAAG 58.755 43.478 5.96 0.00 0.00 4.01
2008 2119 2.778299 TGGCAAGTGTTGTGGAGATAC 58.222 47.619 0.00 0.00 0.00 2.24
2013 2124 4.631813 GCAAGTGTTGTGGAGATACCTAAG 59.368 45.833 0.00 0.00 39.86 2.18
2014 2125 5.178797 CAAGTGTTGTGGAGATACCTAAGG 58.821 45.833 0.00 0.00 39.86 2.69
2021 2132 6.485830 TGTGGAGATACCTAAGGAAATCTG 57.514 41.667 0.00 0.00 39.86 2.90
2048 2167 2.027745 ACAGGTGATAGTTGTGCCTCTG 60.028 50.000 0.00 0.00 0.00 3.35
2075 2194 0.380378 GCATTTTTGGCGCCTCGATA 59.620 50.000 29.70 9.68 0.00 2.92
2109 2228 1.002087 GGTTCGGGGCCATAGTATCAG 59.998 57.143 4.39 0.00 0.00 2.90
2184 2303 4.749245 AAGCATTTAGTCGTGTTCCTTG 57.251 40.909 0.00 0.00 0.00 3.61
2321 2440 7.945033 AAATATTTTACCAATAGCAATGCCG 57.055 32.000 0.00 0.00 0.00 5.69
2390 2509 6.780706 TCGTCTTTTCAGAGATTTGGTTAC 57.219 37.500 0.00 0.00 0.00 2.50
2631 2750 2.493675 TCCGATATCCACTATGCTGCTC 59.506 50.000 0.00 0.00 0.00 4.26
2701 2821 2.173782 TCAGGTCCTTGTTGTGGCTTTA 59.826 45.455 0.00 0.00 0.00 1.85
2711 2831 4.643463 TGTTGTGGCTTTAACCTCGATAA 58.357 39.130 0.00 0.00 0.00 1.75
2733 2853 3.981211 TCTGGTTTTTGCTCAAAGATGC 58.019 40.909 0.00 0.00 0.00 3.91
2737 2857 3.742882 GGTTTTTGCTCAAAGATGCCTTC 59.257 43.478 0.00 0.00 0.00 3.46
2739 2859 1.896220 TTGCTCAAAGATGCCTTCGT 58.104 45.000 0.00 0.00 0.00 3.85
2773 2893 2.358957 TCCAGCTTTGAATCATGGACG 58.641 47.619 0.00 0.00 35.16 4.79
3012 3132 4.759693 ACTGAAACTGCAATCGTTTATGGA 59.240 37.500 2.83 0.00 34.94 3.41
3034 3154 0.263765 AGAACCGGTATGGGGAGCTA 59.736 55.000 8.00 0.00 44.64 3.32
3109 3229 3.775316 AGCTGCCCTTGTACTATGTAAGT 59.225 43.478 0.00 0.00 42.62 2.24
3121 3241 9.502091 TTGTACTATGTAAGTTTGATGCTTCTT 57.498 29.630 0.88 0.00 39.80 2.52
3149 3269 5.230097 GCTTTGTTCTGTGCTTTTGTAGTTC 59.770 40.000 0.00 0.00 0.00 3.01
3156 3276 6.503524 TCTGTGCTTTTGTAGTTCCATTTTC 58.496 36.000 0.00 0.00 0.00 2.29
3169 3289 7.636150 AGTTCCATTTTCATATTCAGACAGG 57.364 36.000 0.00 0.00 0.00 4.00
3189 3309 2.095372 GGCAATACCTTGACGTAAGTGC 59.905 50.000 0.00 0.00 44.56 4.40
3359 3479 1.672356 CCCACTGAAACGGCAGGAG 60.672 63.158 7.05 0.43 40.20 3.69
3488 3608 0.318445 CCTGTGCTCTTTTGTGCTGC 60.318 55.000 0.00 0.00 39.44 5.25
3643 3763 6.292114 GCAACTGTATGTAAACCAAAACAAGC 60.292 38.462 0.00 0.00 0.00 4.01
3657 3777 3.838244 AACAAGCGGCCTTATATCTGA 57.162 42.857 0.00 0.00 0.00 3.27
3661 3781 2.320781 AGCGGCCTTATATCTGACACT 58.679 47.619 0.00 0.00 0.00 3.55
3675 3795 3.953612 TCTGACACTTGCTTTGGTTCATT 59.046 39.130 0.00 0.00 0.00 2.57
3718 3838 2.413453 GCGTTTGCTCTACAGAGAAAGG 59.587 50.000 10.46 12.46 44.74 3.11
3760 3880 3.308904 GGAGGTTAGTTGCCATTTAGGGT 60.309 47.826 0.00 0.00 38.09 4.34
3764 3884 4.514066 GGTTAGTTGCCATTTAGGGTATCG 59.486 45.833 0.00 0.00 38.09 2.92
3821 3941 9.507329 AGTGCCCAGTATATATTAGAAAATGTG 57.493 33.333 0.00 0.00 0.00 3.21
3822 3942 8.730680 GTGCCCAGTATATATTAGAAAATGTGG 58.269 37.037 0.00 0.00 0.00 4.17
3823 3943 7.393234 TGCCCAGTATATATTAGAAAATGTGGC 59.607 37.037 0.00 0.00 0.00 5.01
3824 3944 7.393234 GCCCAGTATATATTAGAAAATGTGGCA 59.607 37.037 0.00 0.00 0.00 4.92
3825 3945 9.466497 CCCAGTATATATTAGAAAATGTGGCAT 57.534 33.333 0.00 0.00 0.00 4.40
3833 3953 9.807649 ATATTAGAAAATGTGGCATTGTCTTTC 57.192 29.630 16.73 7.55 0.00 2.62
3834 3954 4.886579 AGAAAATGTGGCATTGTCTTTCC 58.113 39.130 8.33 0.00 0.00 3.13
3835 3955 3.683365 AAATGTGGCATTGTCTTTCCC 57.317 42.857 0.00 0.00 0.00 3.97
3836 3956 1.560505 ATGTGGCATTGTCTTTCCCC 58.439 50.000 0.00 0.00 0.00 4.81
3837 3957 0.482446 TGTGGCATTGTCTTTCCCCT 59.518 50.000 0.00 0.00 0.00 4.79
3838 3958 1.133199 TGTGGCATTGTCTTTCCCCTT 60.133 47.619 0.00 0.00 0.00 3.95
3839 3959 1.970640 GTGGCATTGTCTTTCCCCTTT 59.029 47.619 0.00 0.00 0.00 3.11
3840 3960 2.368548 GTGGCATTGTCTTTCCCCTTTT 59.631 45.455 0.00 0.00 0.00 2.27
3841 3961 3.044894 TGGCATTGTCTTTCCCCTTTTT 58.955 40.909 0.00 0.00 0.00 1.94
3842 3962 3.181456 TGGCATTGTCTTTCCCCTTTTTG 60.181 43.478 0.00 0.00 0.00 2.44
3843 3963 3.070878 GGCATTGTCTTTCCCCTTTTTGA 59.929 43.478 0.00 0.00 0.00 2.69
3844 3964 4.444164 GGCATTGTCTTTCCCCTTTTTGAA 60.444 41.667 0.00 0.00 0.00 2.69
3845 3965 5.122519 GCATTGTCTTTCCCCTTTTTGAAA 58.877 37.500 0.00 0.00 0.00 2.69
3846 3966 5.588246 GCATTGTCTTTCCCCTTTTTGAAAA 59.412 36.000 0.00 0.00 30.65 2.29
3847 3967 6.094742 GCATTGTCTTTCCCCTTTTTGAAAAA 59.905 34.615 2.83 2.83 30.65 1.94
3927 4065 1.001378 GGTGTAAAGTGGCAACTGCAG 60.001 52.381 13.48 13.48 44.36 4.41
3997 4135 8.803235 ACGTAGCAAGGATGATAGTAAATGATA 58.197 33.333 0.00 0.00 0.00 2.15
4000 4138 8.539770 AGCAAGGATGATAGTAAATGATAACG 57.460 34.615 0.00 0.00 0.00 3.18
4003 4163 7.004555 AGGATGATAGTAAATGATAACGCCA 57.995 36.000 0.00 0.00 0.00 5.69
4036 4196 6.886178 ATATTGTAAGTCTGTTGGTAGGGT 57.114 37.500 0.00 0.00 0.00 4.34
4041 4201 6.314120 TGTAAGTCTGTTGGTAGGGTTACTA 58.686 40.000 0.00 0.00 0.00 1.82
4137 4302 8.432013 TGTAGTGCTGAAATCATCATACCTTAT 58.568 33.333 0.00 0.00 37.44 1.73
4287 4452 5.616488 GCAAAATGCAATTGTTCCAATCT 57.384 34.783 14.73 0.00 44.26 2.40
4288 4453 5.387279 GCAAAATGCAATTGTTCCAATCTG 58.613 37.500 14.73 0.00 44.26 2.90
4289 4454 5.618195 GCAAAATGCAATTGTTCCAATCTGG 60.618 40.000 14.73 0.00 44.26 3.86
4290 4455 4.895668 AATGCAATTGTTCCAATCTGGT 57.104 36.364 7.40 0.00 35.04 4.00
4291 4456 3.940209 TGCAATTGTTCCAATCTGGTC 57.060 42.857 7.40 0.00 39.03 4.02
4292 4457 2.562298 TGCAATTGTTCCAATCTGGTCC 59.438 45.455 7.40 0.00 39.03 4.46
4293 4458 2.562298 GCAATTGTTCCAATCTGGTCCA 59.438 45.455 7.40 0.00 39.03 4.02
4323 4488 6.884295 TCAGGGATTCCAACTGTTACATTTAG 59.116 38.462 4.80 0.00 34.02 1.85
4354 4519 8.005192 AGATTTTCTTGATCTTCATTAAGGGC 57.995 34.615 0.00 0.00 33.22 5.19
4516 4725 0.625849 AGCTTGTATTGGGTGGAGGG 59.374 55.000 0.00 0.00 0.00 4.30
4517 4726 0.623723 GCTTGTATTGGGTGGAGGGA 59.376 55.000 0.00 0.00 0.00 4.20
4518 4727 1.408822 GCTTGTATTGGGTGGAGGGAG 60.409 57.143 0.00 0.00 0.00 4.30
4519 4728 1.212935 CTTGTATTGGGTGGAGGGAGG 59.787 57.143 0.00 0.00 0.00 4.30
4534 4743 4.079730 GGAGGGAGGAATGGTTTAGATTGT 60.080 45.833 0.00 0.00 0.00 2.71
4540 4749 0.732571 ATGGTTTAGATTGTGCCGCG 59.267 50.000 0.00 0.00 0.00 6.46
4553 4762 4.728102 CCGCGCTGTACCGTCCAA 62.728 66.667 5.56 0.00 0.00 3.53
4554 4763 3.179265 CGCGCTGTACCGTCCAAG 61.179 66.667 5.56 0.00 0.00 3.61
4555 4764 2.813908 GCGCTGTACCGTCCAAGG 60.814 66.667 0.00 0.00 37.30 3.61
4556 4765 2.813908 CGCTGTACCGTCCAAGGC 60.814 66.667 0.00 0.00 33.69 4.35
4557 4766 2.663196 GCTGTACCGTCCAAGGCT 59.337 61.111 0.00 0.00 33.69 4.58
4558 4767 1.003718 GCTGTACCGTCCAAGGCTT 60.004 57.895 0.00 0.00 33.69 4.35
4559 4768 1.298859 GCTGTACCGTCCAAGGCTTG 61.299 60.000 20.31 20.31 33.69 4.01
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
34 35 1.689273 CTGCTATGACTCCTACCCCAC 59.311 57.143 0.00 0.00 0.00 4.61
73 74 4.399303 TCATCGTAGCAGAGATGAAGAACA 59.601 41.667 13.24 0.00 46.93 3.18
82 83 4.500375 CCAATGACATCATCGTAGCAGAGA 60.500 45.833 0.00 0.00 35.10 3.10
86 87 3.457234 GTCCAATGACATCATCGTAGCA 58.543 45.455 0.00 0.00 41.37 3.49
200 203 8.048534 ACAATGTTGTATTTGATCTCAGAAGG 57.951 34.615 0.00 0.00 40.16 3.46
266 285 4.981674 AGGTGTGCATAAAATTGAACAACG 59.018 37.500 0.00 0.00 45.94 4.10
267 286 6.214205 CAGGTGTGCATAAAATTGAACAAC 57.786 37.500 0.00 0.00 42.35 3.32
310 329 9.794685 GATTTTTCCCAGAAGATTAAGAATGTC 57.205 33.333 0.00 0.00 0.00 3.06
341 360 1.133363 TTGTGGAGGTCTTTCGGGAA 58.867 50.000 0.00 0.00 0.00 3.97
346 365 8.710835 TTTAACAAAATTTGTGGAGGTCTTTC 57.289 30.769 12.50 0.00 44.59 2.62
426 445 6.580791 TCTGTTAGCGTGCAAATTTTTATGAC 59.419 34.615 0.00 0.00 0.00 3.06
488 509 9.856488 GAAGGTTTCCTACTAATTCCAAAATTC 57.144 33.333 0.00 0.00 33.27 2.17
491 512 8.002459 ACTGAAGGTTTCCTACTAATTCCAAAA 58.998 33.333 0.00 0.00 31.13 2.44
492 513 7.523415 ACTGAAGGTTTCCTACTAATTCCAAA 58.477 34.615 0.00 0.00 31.13 3.28
495 516 7.166167 TGAACTGAAGGTTTCCTACTAATTCC 58.834 38.462 0.00 0.00 38.41 3.01
552 642 1.816835 TCTCGTCTGATGTTTACGGCT 59.183 47.619 0.00 0.00 37.24 5.52
553 643 2.273370 TCTCGTCTGATGTTTACGGC 57.727 50.000 0.00 0.00 37.24 5.68
633 723 2.064014 GAAAGGTGTACTCGTTTCCGG 58.936 52.381 23.03 0.00 36.69 5.14
646 736 2.498167 CAGGAGTTGAGGTGAAAGGTG 58.502 52.381 0.00 0.00 0.00 4.00
662 753 4.408821 GCGGGTGACATGGCAGGA 62.409 66.667 0.00 0.00 0.00 3.86
710 801 0.317519 GTGTTTTGCGAGTTTCCGGG 60.318 55.000 0.00 0.00 0.00 5.73
842 934 2.117206 GGGGGTGTGAATGTGGCA 59.883 61.111 0.00 0.00 0.00 4.92
895 991 0.673437 GCGAGAGGGAGGATTCTCTG 59.327 60.000 0.00 0.00 40.12 3.35
896 992 0.469144 GGCGAGAGGGAGGATTCTCT 60.469 60.000 0.00 0.00 42.44 3.10
897 993 1.801309 CGGCGAGAGGGAGGATTCTC 61.801 65.000 0.00 0.00 39.25 2.87
904 1000 2.776913 GGAAGTCGGCGAGAGGGAG 61.777 68.421 11.20 0.00 0.00 4.30
906 1002 2.756283 AGGAAGTCGGCGAGAGGG 60.756 66.667 11.20 0.00 0.00 4.30
923 1019 4.097437 ACTTCACTGTCTGTAAGTGTTCGA 59.903 41.667 10.65 0.00 44.42 3.71
925 1021 6.736123 TCTACTTCACTGTCTGTAAGTGTTC 58.264 40.000 10.65 0.00 44.42 3.18
1272 1368 0.673956 GGGTCTTCTTGGAGGCGAAC 60.674 60.000 0.00 0.00 0.00 3.95
1368 1472 7.280205 CCGTTTCTTAACACCTTTAGCATATCT 59.720 37.037 0.00 0.00 33.75 1.98
1392 1496 4.499023 CAATTCGTGACGCCGCCG 62.499 66.667 0.00 0.00 41.14 6.46
1403 1507 1.850377 TTGTTGCTTGTGCCAATTCG 58.150 45.000 0.00 0.00 38.71 3.34
1405 1509 4.060205 GAGAATTGTTGCTTGTGCCAATT 58.940 39.130 0.00 0.00 40.84 2.32
1449 1556 6.744112 AGTAGATCAGAGAATTTTCCTAGCG 58.256 40.000 0.00 0.00 0.00 4.26
1460 1567 2.510382 ACGGAGGGAGTAGATCAGAGAA 59.490 50.000 0.00 0.00 0.00 2.87
1464 1571 3.292460 AGAAACGGAGGGAGTAGATCAG 58.708 50.000 0.00 0.00 0.00 2.90
1471 1578 7.201983 GGTCTTATATTTAGAAACGGAGGGAGT 60.202 40.741 0.00 0.00 0.00 3.85
1525 1632 2.738521 GCGTCTGCACACATCCGT 60.739 61.111 0.00 0.00 42.15 4.69
1535 1642 5.277601 TCTACACTTTAAAATGCGTCTGC 57.722 39.130 0.00 0.00 43.20 4.26
1536 1643 7.478667 GTGAATCTACACTTTAAAATGCGTCTG 59.521 37.037 0.00 0.00 37.73 3.51
1552 1661 4.631377 CGGAGCAAAATGAGTGAATCTACA 59.369 41.667 0.00 0.00 0.00 2.74
1565 1674 3.472652 TGAACTACACACGGAGCAAAAT 58.527 40.909 0.00 0.00 0.00 1.82
1611 1720 6.705863 TCTACTCCCTCCGTTTCTAAATAC 57.294 41.667 0.00 0.00 0.00 1.89
1623 1732 6.732896 TTGATACTGAATTCTACTCCCTCC 57.267 41.667 7.05 0.00 0.00 4.30
1679 1789 3.056250 TGCTGCAGAAAACAGGAACAAAA 60.056 39.130 20.43 0.00 35.62 2.44
1752 1862 0.725784 CGAAGCGCACCATGTTGAAC 60.726 55.000 11.47 0.00 0.00 3.18
1773 1883 1.152881 GAAGGGGATGGCTGCGATT 60.153 57.895 0.00 0.00 0.00 3.34
1965 2075 6.295236 CCAATTCCACCATTACAACAGAACAT 60.295 38.462 0.00 0.00 0.00 2.71
1981 2092 2.472816 CACAACACTTGCCAATTCCAC 58.527 47.619 0.00 0.00 0.00 4.02
1993 2104 4.684724 TCCTTAGGTATCTCCACAACACT 58.315 43.478 0.00 0.00 39.02 3.55
1994 2105 5.416271 TTCCTTAGGTATCTCCACAACAC 57.584 43.478 0.00 0.00 39.02 3.32
2021 2132 3.058914 GCACAACTATCACCTGTTCACAC 60.059 47.826 0.00 0.00 0.00 3.82
2048 2167 1.328374 GCGCCAAAAATGCCATCAATC 59.672 47.619 0.00 0.00 0.00 2.67
2075 2194 0.606401 CGAACCAAGTCAGCATGGGT 60.606 55.000 0.00 0.00 40.03 4.51
2109 2228 0.551396 AGCAGGCCAACCCCTATAAC 59.449 55.000 5.01 0.00 36.11 1.89
2210 2329 5.817296 TCTGAATTCCATTATGAGGACAACG 59.183 40.000 2.27 0.00 34.19 4.10
2319 2438 2.351738 GGAGTGCTTTGAATTGGTTCGG 60.352 50.000 0.00 0.00 37.15 4.30
2321 2440 4.488879 GATGGAGTGCTTTGAATTGGTTC 58.511 43.478 0.00 0.00 34.85 3.62
2631 2750 5.887598 TCCCATTTGTGACCAAGATGATTAG 59.112 40.000 0.00 0.00 0.00 1.73
2660 2780 5.303845 CCTGAATGATAGATGGTCAGTGAGA 59.696 44.000 0.00 0.00 35.07 3.27
2701 2821 5.010282 AGCAAAAACCAGATTATCGAGGTT 58.990 37.500 15.72 15.72 39.91 3.50
2711 2831 4.562143 GGCATCTTTGAGCAAAAACCAGAT 60.562 41.667 0.00 0.00 0.00 2.90
2733 2853 0.246635 ATCGTGGACCTCAACGAAGG 59.753 55.000 8.94 0.00 42.55 3.46
2737 2857 0.037697 TGGAATCGTGGACCTCAACG 60.038 55.000 0.00 0.00 0.00 4.10
2739 2859 0.036388 GCTGGAATCGTGGACCTCAA 60.036 55.000 0.00 0.00 0.00 3.02
2773 2893 2.413634 CGAATCCCAAAGCGTACCAAAC 60.414 50.000 0.00 0.00 0.00 2.93
2952 3072 1.884464 CGCTACCATCTGCGCACAT 60.884 57.895 5.66 0.00 45.50 3.21
3012 3132 2.033208 GCTCCCCATACCGGTTCTAGT 61.033 57.143 15.04 0.00 0.00 2.57
3034 3154 2.568623 AAGAGGAACCAAGCGAATGT 57.431 45.000 0.00 0.00 0.00 2.71
3109 3229 3.068024 ACAAAGCGGAAAGAAGCATCAAA 59.932 39.130 0.00 0.00 35.48 2.69
3121 3241 1.388547 AAGCACAGAACAAAGCGGAA 58.611 45.000 0.00 0.00 0.00 4.30
3149 3269 5.840243 TGCCTGTCTGAATATGAAAATGG 57.160 39.130 0.00 0.00 0.00 3.16
3169 3289 3.000727 AGCACTTACGTCAAGGTATTGC 58.999 45.455 0.00 1.12 38.70 3.56
3179 3299 6.801367 TTGATTAATACGAGCACTTACGTC 57.199 37.500 0.00 0.00 42.61 4.34
3183 3303 8.600625 GTTGTGATTGATTAATACGAGCACTTA 58.399 33.333 17.07 8.49 38.41 2.24
3199 3319 6.808829 AGCTTGAAGATTTTGTTGTGATTGA 58.191 32.000 0.00 0.00 0.00 2.57
3359 3479 0.389391 TAGCAGATAGGGACAAGCGC 59.611 55.000 0.00 0.00 0.00 5.92
3643 3763 2.802816 GCAAGTGTCAGATATAAGGCCG 59.197 50.000 0.00 0.00 0.00 6.13
3657 3777 5.852282 ACTTAATGAACCAAAGCAAGTGT 57.148 34.783 0.00 0.00 0.00 3.55
3661 3781 6.208402 TGCATCTACTTAATGAACCAAAGCAA 59.792 34.615 0.00 0.00 0.00 3.91
3718 3838 3.070018 CCGAGATCATGGGAATAGCAAC 58.930 50.000 0.00 0.00 0.00 4.17
3760 3880 5.987098 AGTCACTAGTTAGTCCAGTCGATA 58.013 41.667 0.00 0.00 33.46 2.92
3764 3884 6.642430 TCTCTAGTCACTAGTTAGTCCAGTC 58.358 44.000 11.77 0.00 35.72 3.51
3807 3927 9.807649 GAAAGACAATGCCACATTTTCTAATAT 57.192 29.630 8.86 0.00 0.00 1.28
3808 3928 8.250332 GGAAAGACAATGCCACATTTTCTAATA 58.750 33.333 8.86 0.00 0.00 0.98
3809 3929 7.099120 GGAAAGACAATGCCACATTTTCTAAT 58.901 34.615 8.86 3.07 0.00 1.73
3810 3930 6.454795 GGAAAGACAATGCCACATTTTCTAA 58.545 36.000 8.86 0.00 0.00 2.10
3811 3931 5.047377 GGGAAAGACAATGCCACATTTTCTA 60.047 40.000 8.86 0.00 0.00 2.10
3812 3932 4.262592 GGGAAAGACAATGCCACATTTTCT 60.263 41.667 3.70 3.70 0.00 2.52
3813 3933 3.996363 GGGAAAGACAATGCCACATTTTC 59.004 43.478 0.00 0.00 0.00 2.29
3814 3934 3.244526 GGGGAAAGACAATGCCACATTTT 60.245 43.478 0.00 0.00 0.00 1.82
3815 3935 2.302733 GGGGAAAGACAATGCCACATTT 59.697 45.455 0.00 0.00 0.00 2.32
3816 3936 1.901833 GGGGAAAGACAATGCCACATT 59.098 47.619 0.00 0.00 0.00 2.71
3817 3937 1.077663 AGGGGAAAGACAATGCCACAT 59.922 47.619 0.00 0.00 0.00 3.21
3818 3938 0.482446 AGGGGAAAGACAATGCCACA 59.518 50.000 0.00 0.00 0.00 4.17
3819 3939 1.632589 AAGGGGAAAGACAATGCCAC 58.367 50.000 0.00 0.00 0.00 5.01
3820 3940 2.397044 AAAGGGGAAAGACAATGCCA 57.603 45.000 0.00 0.00 0.00 4.92
3821 3941 3.070878 TCAAAAAGGGGAAAGACAATGCC 59.929 43.478 0.00 0.00 0.00 4.40
3822 3942 4.335400 TCAAAAAGGGGAAAGACAATGC 57.665 40.909 0.00 0.00 0.00 3.56
3823 3943 7.622893 TTTTTCAAAAAGGGGAAAGACAATG 57.377 32.000 0.00 0.00 34.77 2.82
3872 3992 1.466558 GCACAAGAGTTTCTAGCCAGC 59.533 52.381 0.00 0.00 0.00 4.85
3927 4065 5.335661 GGAATCTACACACAATGTTCCCAAC 60.336 44.000 0.00 0.00 43.19 3.77
3997 4135 5.132897 ACAATATTGACAACAATGGCGTT 57.867 34.783 22.16 0.00 44.97 4.84
4000 4138 7.485913 CAGACTTACAATATTGACAACAATGGC 59.514 37.037 22.16 6.01 44.97 4.40
4003 4163 9.897744 CAACAGACTTACAATATTGACAACAAT 57.102 29.630 22.16 0.14 46.64 2.71
4057 4217 6.706716 TCGTCATCGACTGTCTAAGATTCTAT 59.293 38.462 6.21 0.00 41.35 1.98
4059 4219 4.876679 TCGTCATCGACTGTCTAAGATTCT 59.123 41.667 6.21 0.00 41.35 2.40
4154 4319 7.643569 TTCCAAAGTCATGTAATGTATGCAT 57.356 32.000 3.79 3.79 46.80 3.96
4216 4381 7.080099 AGTATGCATGCGTAAATCATGATTTC 58.920 34.615 31.70 22.21 42.84 2.17
4223 4388 4.813697 TGCTAAGTATGCATGCGTAAATCA 59.186 37.500 20.95 11.61 35.31 2.57
4224 4389 5.342806 TGCTAAGTATGCATGCGTAAATC 57.657 39.130 20.95 9.32 35.31 2.17
4260 4425 4.682589 TGGAACAATTGCATTTTGCAGACA 60.683 37.500 5.05 2.85 46.88 3.41
4261 4426 3.808726 TGGAACAATTGCATTTTGCAGAC 59.191 39.130 5.05 0.79 46.88 3.51
4285 4450 4.344104 GAATCCCTGAATTTTGGACCAGA 58.656 43.478 0.00 0.00 0.00 3.86
4286 4451 3.448660 GGAATCCCTGAATTTTGGACCAG 59.551 47.826 0.00 0.00 0.00 4.00
4287 4452 3.181413 TGGAATCCCTGAATTTTGGACCA 60.181 43.478 0.00 0.00 0.00 4.02
4288 4453 3.440127 TGGAATCCCTGAATTTTGGACC 58.560 45.455 0.00 0.00 0.00 4.46
4289 4454 4.528206 AGTTGGAATCCCTGAATTTTGGAC 59.472 41.667 0.00 0.00 0.00 4.02
4290 4455 4.527816 CAGTTGGAATCCCTGAATTTTGGA 59.472 41.667 0.00 0.00 0.00 3.53
4291 4456 4.284234 ACAGTTGGAATCCCTGAATTTTGG 59.716 41.667 11.66 0.00 0.00 3.28
4292 4457 5.473066 ACAGTTGGAATCCCTGAATTTTG 57.527 39.130 11.66 0.00 0.00 2.44
4293 4458 6.553100 TGTAACAGTTGGAATCCCTGAATTTT 59.447 34.615 11.66 0.14 0.00 1.82
4337 4502 4.280819 CAAGGGCCCTTAATGAAGATCAA 58.719 43.478 36.69 0.00 34.25 2.57
4339 4504 2.625314 GCAAGGGCCCTTAATGAAGATC 59.375 50.000 36.69 8.66 34.25 2.75
4475 4656 6.723977 AGCTGTGATCCATAAAACCCTAAAAA 59.276 34.615 0.00 0.00 0.00 1.94
4480 4661 4.019174 CAAGCTGTGATCCATAAAACCCT 58.981 43.478 0.00 0.00 0.00 4.34
4481 4662 3.763897 ACAAGCTGTGATCCATAAAACCC 59.236 43.478 0.00 0.00 0.00 4.11
4484 4665 6.096705 CCCAATACAAGCTGTGATCCATAAAA 59.903 38.462 0.00 0.00 0.00 1.52
4488 4669 3.053395 ACCCAATACAAGCTGTGATCCAT 60.053 43.478 0.00 0.00 0.00 3.41
4490 4671 2.684881 CACCCAATACAAGCTGTGATCC 59.315 50.000 0.00 0.00 0.00 3.36
4516 4725 3.065371 CGGCACAATCTAAACCATTCCTC 59.935 47.826 0.00 0.00 0.00 3.71
4517 4726 3.016736 CGGCACAATCTAAACCATTCCT 58.983 45.455 0.00 0.00 0.00 3.36
4518 4727 2.479560 GCGGCACAATCTAAACCATTCC 60.480 50.000 0.00 0.00 0.00 3.01
4519 4728 2.791158 CGCGGCACAATCTAAACCATTC 60.791 50.000 0.00 0.00 0.00 2.67
4540 4749 1.003718 AAGCCTTGGACGGTACAGC 60.004 57.895 0.00 0.00 0.00 4.40


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

AutoCloner maintained by Alex Coulton.