Multiple sequence alignment - TraesCS5D01G372500

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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 TraesCS5D01G372500 chr5D 100.000 4314 0 0 1 4314 446397174 446401487 0.000000e+00 7967.0
1 TraesCS5D01G372500 chr5B 93.408 3216 131 31 185 3349 544325894 544329079 0.000000e+00 4689.0
2 TraesCS5D01G372500 chr5B 85.040 742 50 39 3349 4060 544329437 544330147 0.000000e+00 699.0
3 TraesCS5D01G372500 chr5B 97.268 183 4 1 4089 4270 544330140 544330322 4.190000e-80 309.0
4 TraesCS5D01G372500 chr5B 91.228 114 2 7 3540 3649 658381025 658381134 9.670000e-32 148.0
5 TraesCS5D01G372500 chr5A 94.715 1892 71 11 1479 3349 564072360 564074243 0.000000e+00 2913.0
6 TraesCS5D01G372500 chr5A 93.292 1625 79 16 83 1691 564070747 564072357 0.000000e+00 2370.0
7 TraesCS5D01G372500 chr5A 84.056 784 45 38 3517 4270 564074997 564075730 0.000000e+00 682.0
8 TraesCS5D01G372500 chr5A 94.949 99 2 2 3544 3639 650246612 650246710 7.470000e-33 152.0
9 TraesCS5D01G372500 chr5A 96.667 90 2 1 3544 3633 644821114 644821026 9.670000e-32 148.0
10 TraesCS5D01G372500 chr5A 88.136 59 7 0 1 59 564070690 564070748 2.150000e-08 71.3
11 TraesCS5D01G372500 chr3D 96.809 94 1 2 3544 3637 3302152 3302243 5.780000e-34 156.0
12 TraesCS5D01G372500 chr3D 91.667 108 3 4 3526 3631 3309456 3309559 1.250000e-30 145.0
13 TraesCS5D01G372500 chr7B 96.739 92 1 2 3551 3640 677968307 677968216 7.470000e-33 152.0
14 TraesCS5D01G372500 chr7B 96.739 92 1 2 3551 3640 678012064 678011973 7.470000e-33 152.0


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 TraesCS5D01G372500 chr5D 446397174 446401487 4313 False 7967.000 7967 100.000000 1 4314 1 chr5D.!!$F1 4313
1 TraesCS5D01G372500 chr5B 544325894 544330322 4428 False 1899.000 4689 91.905333 185 4270 3 chr5B.!!$F2 4085
2 TraesCS5D01G372500 chr5A 564070690 564075730 5040 False 1509.075 2913 90.049750 1 4270 4 chr5A.!!$F2 4269

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
607 613 0.179000 AATCTGATCCGGTGGTCTGC 59.821 55.000 0.00 0.0 0.00 4.26 F
1579 1816 0.035881 TGAGAGCCAAGAGGTTGCTG 59.964 55.000 0.00 0.0 37.19 4.41 F
1583 1820 0.329261 AGCCAAGAGGTTGCTGCATA 59.671 50.000 1.84 0.0 37.19 3.14 F
1584 1821 1.064166 AGCCAAGAGGTTGCTGCATAT 60.064 47.619 1.84 0.0 37.19 1.78 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2466 2703 1.375523 GGCGTGATCGACAGGGTTT 60.376 57.895 0.00 0.00 45.53 3.27 R
2486 2723 1.469251 CCCCCAATCCCAGGTTTGT 59.531 57.895 6.72 0.00 0.00 2.83 R
2918 3187 1.475403 GTCAGGGATTCCGTCTGAGA 58.525 55.000 10.82 0.00 38.09 3.27 R
3320 3609 1.542915 AGCAATGTCATTGTCAGGTGC 59.457 47.619 23.27 10.63 42.20 5.01 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
21 22 0.250124 TTGTGGTCGTTGCTAGGTGG 60.250 55.000 0.00 0.00 0.00 4.61
22 23 1.370064 GTGGTCGTTGCTAGGTGGT 59.630 57.895 0.00 0.00 0.00 4.16
26 27 0.669625 GTCGTTGCTAGGTGGTGGTC 60.670 60.000 0.00 0.00 0.00 4.02
29 30 1.135083 CGTTGCTAGGTGGTGGTCTAG 60.135 57.143 0.00 0.00 36.84 2.43
30 31 1.207329 GTTGCTAGGTGGTGGTCTAGG 59.793 57.143 0.00 0.00 34.95 3.02
59 60 9.321562 GATGGATGTAATTTTCGTTACTCCTTA 57.678 33.333 12.26 0.00 35.38 2.69
60 61 9.847224 ATGGATGTAATTTTCGTTACTCCTTAT 57.153 29.630 12.26 0.00 35.38 1.73
71 72 9.768662 TTTCGTTACTCCTTATTTCTTTGTACT 57.231 29.630 0.00 0.00 0.00 2.73
72 73 8.752766 TCGTTACTCCTTATTTCTTTGTACTG 57.247 34.615 0.00 0.00 0.00 2.74
73 74 7.330208 TCGTTACTCCTTATTTCTTTGTACTGC 59.670 37.037 0.00 0.00 0.00 4.40
74 75 7.117236 CGTTACTCCTTATTTCTTTGTACTGCA 59.883 37.037 0.00 0.00 0.00 4.41
75 76 8.947115 GTTACTCCTTATTTCTTTGTACTGCAT 58.053 33.333 0.00 0.00 0.00 3.96
77 78 8.723942 ACTCCTTATTTCTTTGTACTGCATAG 57.276 34.615 0.00 0.00 0.00 2.23
78 79 8.540388 ACTCCTTATTTCTTTGTACTGCATAGA 58.460 33.333 0.00 0.00 34.20 1.98
79 80 9.553064 CTCCTTATTTCTTTGTACTGCATAGAT 57.447 33.333 0.00 0.00 35.61 1.98
80 81 9.330063 TCCTTATTTCTTTGTACTGCATAGATG 57.670 33.333 0.00 0.00 35.61 2.90
81 82 9.113838 CCTTATTTCTTTGTACTGCATAGATGT 57.886 33.333 0.00 0.00 35.61 3.06
85 86 7.977789 TTCTTTGTACTGCATAGATGTTTGA 57.022 32.000 0.00 0.00 35.61 2.69
86 87 8.565896 TTCTTTGTACTGCATAGATGTTTGAT 57.434 30.769 0.00 0.00 35.61 2.57
87 88 7.977904 TCTTTGTACTGCATAGATGTTTGATG 58.022 34.615 0.00 0.00 31.71 3.07
88 89 7.823799 TCTTTGTACTGCATAGATGTTTGATGA 59.176 33.333 0.00 0.00 31.71 2.92
89 90 7.920160 TTGTACTGCATAGATGTTTGATGAA 57.080 32.000 0.00 0.00 0.00 2.57
266 269 2.683968 TCCATTTTCGTCGTCTTCAGG 58.316 47.619 0.00 0.00 0.00 3.86
295 298 0.247934 GAAAAATAACGAGCCGCCCG 60.248 55.000 0.00 0.00 0.00 6.13
429 435 3.024356 TCTCCCCCTCTCTCCGCT 61.024 66.667 0.00 0.00 0.00 5.52
551 557 2.586357 GTTCAGCCGAGGATCCGC 60.586 66.667 5.98 5.59 39.71 5.54
552 558 3.074369 TTCAGCCGAGGATCCGCA 61.074 61.111 16.29 0.00 41.92 5.69
585 591 3.322191 GACCCAGGTCTCCTAGATTCT 57.678 52.381 9.67 0.00 41.57 2.40
607 613 0.179000 AATCTGATCCGGTGGTCTGC 59.821 55.000 0.00 0.00 0.00 4.26
626 632 4.872691 TCTGCTTATCTTTCTGTTAGCTGC 59.127 41.667 0.00 0.00 0.00 5.25
628 634 5.248640 TGCTTATCTTTCTGTTAGCTGCTT 58.751 37.500 7.79 0.00 0.00 3.91
629 635 5.122869 TGCTTATCTTTCTGTTAGCTGCTTG 59.877 40.000 7.79 0.00 0.00 4.01
746 757 1.617947 GGGGGCTGTCTACACTCTGG 61.618 65.000 0.00 0.00 0.00 3.86
884 902 1.137872 GATCCCAGACTGCACGAATCT 59.862 52.381 0.00 0.00 0.00 2.40
903 921 6.259608 CGAATCTCATTTTACTTCTGATGCCT 59.740 38.462 0.00 0.00 0.00 4.75
922 940 5.256474 TGCCTCCTTAATGGAAAAAGAGAG 58.744 41.667 0.00 0.00 45.63 3.20
923 941 5.014123 TGCCTCCTTAATGGAAAAAGAGAGA 59.986 40.000 0.00 0.00 45.63 3.10
927 945 7.667635 CCTCCTTAATGGAAAAAGAGAGACTTT 59.332 37.037 0.00 0.00 45.63 2.66
974 992 7.093988 ACAAACATGAAACCGATTAATCCATGA 60.094 33.333 25.62 4.58 35.32 3.07
990 1009 2.512885 CATGAATCGTGCTGTTTGCTC 58.487 47.619 0.00 0.00 43.37 4.26
1004 1023 4.885413 TGTTTGCTCATTTTTCAGATGGG 58.115 39.130 0.00 0.00 0.00 4.00
1353 1372 3.251004 CCCTAACAGCGGAATTTATGCTC 59.749 47.826 0.00 0.00 36.69 4.26
1363 1382 5.915196 GCGGAATTTATGCTCTGGAATTTAC 59.085 40.000 0.00 0.00 0.00 2.01
1388 1407 2.533266 GCATACACAATTGAGCCAAGC 58.467 47.619 13.59 5.21 0.00 4.01
1513 1715 3.046283 TCCAAGAGAGGCAGGCTAATA 57.954 47.619 0.00 0.00 0.00 0.98
1514 1716 2.700897 TCCAAGAGAGGCAGGCTAATAC 59.299 50.000 0.00 0.00 0.00 1.89
1579 1816 0.035881 TGAGAGCCAAGAGGTTGCTG 59.964 55.000 0.00 0.00 37.19 4.41
1580 1817 1.303155 AGAGCCAAGAGGTTGCTGC 60.303 57.895 0.00 0.00 37.19 5.25
1581 1818 1.601759 GAGCCAAGAGGTTGCTGCA 60.602 57.895 0.00 0.00 37.19 4.41
1582 1819 0.964358 GAGCCAAGAGGTTGCTGCAT 60.964 55.000 1.84 0.00 37.19 3.96
1583 1820 0.329261 AGCCAAGAGGTTGCTGCATA 59.671 50.000 1.84 0.00 37.19 3.14
1584 1821 1.064166 AGCCAAGAGGTTGCTGCATAT 60.064 47.619 1.84 0.00 37.19 1.78
1585 1822 1.336125 GCCAAGAGGTTGCTGCATATC 59.664 52.381 1.84 2.05 37.19 1.63
1599 1836 4.703575 GCTGCATATCACATATGGGATGTT 59.296 41.667 27.42 13.77 42.23 2.71
2130 2367 6.970484 ACCACACAAACATTCACTCTAATTC 58.030 36.000 0.00 0.00 0.00 2.17
2139 2376 7.582435 ACATTCACTCTAATTCGTAACTGTG 57.418 36.000 0.00 0.00 0.00 3.66
2145 2382 7.488150 TCACTCTAATTCGTAACTGTGCTATTG 59.512 37.037 0.00 0.00 0.00 1.90
2430 2667 3.766644 CCACGAGATGGCAGATTCA 57.233 52.632 0.00 0.00 43.24 2.57
2456 2693 1.165907 TCTGCGCAGTTGGTTTCAGG 61.166 55.000 34.70 7.94 0.00 3.86
2486 2723 2.107041 AACCCTGTCGATCACGCCAA 62.107 55.000 0.00 0.00 39.58 4.52
2598 2835 2.358267 CGGTCTCGCCTTCTTGTACTAT 59.642 50.000 0.00 0.00 34.25 2.12
2754 2991 7.345914 GGAGGTATATATGCTTTCTCCTATGGT 59.654 40.741 13.65 0.00 37.08 3.55
2757 2994 8.200792 GGTATATATGCTTTCTCCTATGGTCAG 58.799 40.741 0.62 0.00 0.00 3.51
2782 3051 6.887002 GTCATTTTTCCCAGAGTATCCTTCTT 59.113 38.462 0.00 0.00 33.66 2.52
2787 3056 7.996758 TTTCCCAGAGTATCCTTCTTATTCT 57.003 36.000 0.00 0.00 33.66 2.40
2918 3187 3.036819 TGCATAGCTCCTCTCATGTTCT 58.963 45.455 0.00 0.00 0.00 3.01
3075 3348 0.537653 TGGTCAAACGTCTCACACCA 59.462 50.000 0.00 0.00 0.00 4.17
3250 3538 4.796231 ATGCTCGTGTCGGCCGTC 62.796 66.667 27.15 21.30 0.00 4.79
3304 3592 0.674895 GGAAGCTGAGCGACCACATT 60.675 55.000 15.53 0.00 0.00 2.71
3359 4016 1.001268 CTGCAGCTGCCATCAATCATC 60.001 52.381 34.64 4.39 41.18 2.92
3361 4018 1.589803 CAGCTGCCATCAATCATCGA 58.410 50.000 0.00 0.00 0.00 3.59
3433 4090 2.604912 TGCTCTCTGACTCCTACCAA 57.395 50.000 0.00 0.00 0.00 3.67
3435 4092 3.027412 TGCTCTCTGACTCCTACCAATC 58.973 50.000 0.00 0.00 0.00 2.67
3449 4106 5.013547 CCTACCAATCGATGTATCTCTCCT 58.986 45.833 0.00 0.00 0.00 3.69
3631 4536 1.211457 ACCACCTAGACTACGACGGAT 59.789 52.381 0.00 0.00 0.00 4.18
3651 4556 4.035324 GGATCTTGTTGATACGACTCTCGA 59.965 45.833 0.00 0.00 37.54 4.04
3656 4561 6.315642 TCTTGTTGATACGACTCTCGATTAGT 59.684 38.462 0.00 0.47 43.74 2.24
3657 4562 6.045698 TGTTGATACGACTCTCGATTAGTC 57.954 41.667 14.91 14.91 43.74 2.59
3660 4565 6.288426 TGATACGACTCTCGATTAGTCTTG 57.712 41.667 19.89 11.51 43.74 3.02
3661 4566 5.816258 TGATACGACTCTCGATTAGTCTTGT 59.184 40.000 19.89 15.19 43.74 3.16
3664 4569 5.867166 ACGACTCTCGATTAGTCTTGTTAC 58.133 41.667 19.89 0.69 43.74 2.50
3667 4572 4.025015 TCTCGATTAGTCTTGTTACCGC 57.975 45.455 0.00 0.00 0.00 5.68
3668 4573 3.114065 CTCGATTAGTCTTGTTACCGCC 58.886 50.000 0.00 0.00 0.00 6.13
3669 4574 2.492881 TCGATTAGTCTTGTTACCGCCA 59.507 45.455 0.00 0.00 0.00 5.69
3670 4575 3.131577 TCGATTAGTCTTGTTACCGCCAT 59.868 43.478 0.00 0.00 0.00 4.40
3671 4576 3.489785 CGATTAGTCTTGTTACCGCCATC 59.510 47.826 0.00 0.00 0.00 3.51
3672 4577 2.572191 TAGTCTTGTTACCGCCATCG 57.428 50.000 0.00 0.00 0.00 3.84
3675 4580 1.449601 CTTGTTACCGCCATCGCCT 60.450 57.895 0.00 0.00 0.00 5.52
3676 4581 1.429148 CTTGTTACCGCCATCGCCTC 61.429 60.000 0.00 0.00 0.00 4.70
3697 4618 3.083349 CCGGGCAGGTGAGATGGA 61.083 66.667 0.00 0.00 34.51 3.41
3756 4677 4.918201 CCGGCGCCATCTTCCTCC 62.918 72.222 28.98 0.00 0.00 4.30
3758 4679 4.918201 GGCGCCATCTTCCTCCCG 62.918 72.222 24.80 0.00 0.00 5.14
3760 4681 4.918201 CGCCATCTTCCTCCCGCC 62.918 72.222 0.00 0.00 0.00 6.13
3762 4683 2.770048 CCATCTTCCTCCCGCCCT 60.770 66.667 0.00 0.00 0.00 5.19
3763 4684 2.812619 CCATCTTCCTCCCGCCCTC 61.813 68.421 0.00 0.00 0.00 4.30
3764 4685 2.840102 ATCTTCCTCCCGCCCTCG 60.840 66.667 0.00 0.00 0.00 4.63
3810 4731 1.755395 CCCACATCCACATGCCCAG 60.755 63.158 0.00 0.00 32.57 4.45
3811 4732 1.755395 CCACATCCACATGCCCAGG 60.755 63.158 0.00 0.00 32.57 4.45
3819 4740 4.889112 CATGCCCAGGCGCCATCT 62.889 66.667 31.54 4.59 45.51 2.90
3820 4741 4.575973 ATGCCCAGGCGCCATCTC 62.576 66.667 31.54 15.31 45.51 2.75
4063 4991 4.574674 TCCTGCCTTCAGAACATTACAT 57.425 40.909 0.00 0.00 42.95 2.29
4066 4994 4.418392 CTGCCTTCAGAACATTACATTGC 58.582 43.478 0.00 0.00 42.95 3.56
4067 4995 3.193267 TGCCTTCAGAACATTACATTGCC 59.807 43.478 0.00 0.00 0.00 4.52
4068 4996 3.193267 GCCTTCAGAACATTACATTGCCA 59.807 43.478 0.00 0.00 0.00 4.92
4069 4997 4.676196 GCCTTCAGAACATTACATTGCCAG 60.676 45.833 0.00 0.00 0.00 4.85
4070 4998 4.418392 CTTCAGAACATTACATTGCCAGC 58.582 43.478 0.00 0.00 0.00 4.85
4071 4999 2.754552 TCAGAACATTACATTGCCAGCC 59.245 45.455 0.00 0.00 0.00 4.85
4072 5000 2.102578 AGAACATTACATTGCCAGCCC 58.897 47.619 0.00 0.00 0.00 5.19
4073 5001 1.824230 GAACATTACATTGCCAGCCCA 59.176 47.619 0.00 0.00 0.00 5.36
4074 5002 2.163810 ACATTACATTGCCAGCCCAT 57.836 45.000 0.00 0.00 0.00 4.00
4075 5003 3.311167 ACATTACATTGCCAGCCCATA 57.689 42.857 0.00 0.00 0.00 2.74
4076 5004 2.958355 ACATTACATTGCCAGCCCATAC 59.042 45.455 0.00 0.00 0.00 2.39
4077 5005 1.674359 TTACATTGCCAGCCCATACG 58.326 50.000 0.00 0.00 0.00 3.06
4078 5006 0.544223 TACATTGCCAGCCCATACGT 59.456 50.000 0.00 0.00 0.00 3.57
4079 5007 0.544223 ACATTGCCAGCCCATACGTA 59.456 50.000 0.00 0.00 0.00 3.57
4080 5008 1.229428 CATTGCCAGCCCATACGTAG 58.771 55.000 0.08 0.00 0.00 3.51
4081 5009 0.108585 ATTGCCAGCCCATACGTAGG 59.891 55.000 0.08 0.00 0.00 3.18
4082 5010 1.268992 TTGCCAGCCCATACGTAGGT 61.269 55.000 6.48 0.00 0.00 3.08
4083 5011 1.268992 TGCCAGCCCATACGTAGGTT 61.269 55.000 6.48 0.00 0.00 3.50
4189 5118 2.328099 GCTGGACAACTGGAAGGCG 61.328 63.158 0.00 0.00 39.30 5.52
4270 5199 8.062065 ACAATTCCGTCACCAAAATGTAATAT 57.938 30.769 0.00 0.00 0.00 1.28
4271 5200 8.527810 ACAATTCCGTCACCAAAATGTAATATT 58.472 29.630 0.00 0.00 0.00 1.28
4272 5201 9.364989 CAATTCCGTCACCAAAATGTAATATTT 57.635 29.630 0.00 0.00 0.00 1.40
4273 5202 9.936759 AATTCCGTCACCAAAATGTAATATTTT 57.063 25.926 0.00 0.00 0.00 1.82
4274 5203 9.936759 ATTCCGTCACCAAAATGTAATATTTTT 57.063 25.926 0.00 0.00 0.00 1.94
4306 5235 2.669364 GCTTCTTGCTCAACACCATTG 58.331 47.619 0.00 0.00 38.95 2.82
4307 5236 2.035066 GCTTCTTGCTCAACACCATTGT 59.965 45.455 0.00 0.00 38.95 2.71
4308 5237 4.098770 GCTTCTTGCTCAACACCATTGTG 61.099 47.826 0.00 0.00 42.64 3.33
4309 5238 2.929641 TCTTGCTCAACACCATTGTGA 58.070 42.857 3.55 0.00 45.76 3.58
4310 5239 3.286353 TCTTGCTCAACACCATTGTGAA 58.714 40.909 3.55 0.00 45.76 3.18
4311 5240 3.698539 TCTTGCTCAACACCATTGTGAAA 59.301 39.130 3.55 0.00 45.76 2.69
4312 5241 4.341806 TCTTGCTCAACACCATTGTGAAAT 59.658 37.500 3.55 0.00 45.76 2.17
4313 5242 4.241590 TGCTCAACACCATTGTGAAATC 57.758 40.909 3.55 0.00 45.76 2.17
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
4 5 0.949105 CACCACCTAGCAACGACCAC 60.949 60.000 0.00 0.00 0.00 4.16
6 7 1.375523 CCACCACCTAGCAACGACC 60.376 63.158 0.00 0.00 0.00 4.79
21 22 5.808366 TTACATCCATCATCCTAGACCAC 57.192 43.478 0.00 0.00 0.00 4.16
22 23 7.392766 AAATTACATCCATCATCCTAGACCA 57.607 36.000 0.00 0.00 0.00 4.02
26 27 7.969536 ACGAAAATTACATCCATCATCCTAG 57.030 36.000 0.00 0.00 0.00 3.02
29 30 8.154649 AGTAACGAAAATTACATCCATCATCC 57.845 34.615 0.00 0.00 37.49 3.51
30 31 8.283291 GGAGTAACGAAAATTACATCCATCATC 58.717 37.037 0.00 0.00 37.49 2.92
59 60 9.013229 TCAAACATCTATGCAGTACAAAGAAAT 57.987 29.630 0.00 0.00 0.00 2.17
60 61 8.389779 TCAAACATCTATGCAGTACAAAGAAA 57.610 30.769 0.00 0.00 0.00 2.52
62 63 7.823799 TCATCAAACATCTATGCAGTACAAAGA 59.176 33.333 0.00 0.00 0.00 2.52
63 64 7.977904 TCATCAAACATCTATGCAGTACAAAG 58.022 34.615 0.00 0.00 0.00 2.77
64 65 7.920160 TCATCAAACATCTATGCAGTACAAA 57.080 32.000 0.00 0.00 0.00 2.83
66 67 9.045223 GTATTCATCAAACATCTATGCAGTACA 57.955 33.333 0.00 0.00 0.00 2.90
67 68 9.265901 AGTATTCATCAAACATCTATGCAGTAC 57.734 33.333 0.00 0.00 0.00 2.73
69 70 9.486497 CTAGTATTCATCAAACATCTATGCAGT 57.514 33.333 0.00 0.00 0.00 4.40
70 71 9.702494 TCTAGTATTCATCAAACATCTATGCAG 57.298 33.333 0.00 0.00 0.00 4.41
148 149 9.489084 AAAAGGGCTAGAAAAATGTCAATTTAC 57.511 29.630 0.00 0.00 34.84 2.01
168 169 2.750814 AGGATATTGTGCCCAAAAGGG 58.249 47.619 0.00 0.00 33.44 3.95
229 230 3.678915 TGGAAAGAAAACGTCCGTTTC 57.321 42.857 17.07 11.08 46.22 2.78
418 424 3.535962 GGCTGGAGCGGAGAGAGG 61.536 72.222 0.00 0.00 43.26 3.69
447 453 0.179145 AATCGAGCGTGTTACGAGGG 60.179 55.000 5.44 0.00 46.05 4.30
584 590 4.122776 CAGACCACCGGATCAGATTTAAG 58.877 47.826 9.46 0.00 0.00 1.85
585 591 3.681594 GCAGACCACCGGATCAGATTTAA 60.682 47.826 9.46 0.00 0.00 1.52
607 613 5.567552 GCAAGCAGCTAACAGAAAGATAAG 58.432 41.667 0.00 0.00 41.15 1.73
626 632 4.997395 TCAGTTAGCTTCCTAAACAGCAAG 59.003 41.667 0.00 0.00 38.61 4.01
628 634 4.617253 TCAGTTAGCTTCCTAAACAGCA 57.383 40.909 0.00 0.00 38.61 4.41
629 635 5.941948 TTTCAGTTAGCTTCCTAAACAGC 57.058 39.130 0.00 0.00 35.43 4.40
636 642 4.455877 CCAACGATTTTCAGTTAGCTTCCT 59.544 41.667 0.00 0.00 0.00 3.36
746 757 1.134159 ACTCTCTGGGATTCATGCTGC 60.134 52.381 0.00 0.00 0.00 5.25
884 902 5.441718 AGGAGGCATCAGAAGTAAAATGA 57.558 39.130 0.00 0.00 0.00 2.57
990 1009 1.750778 CCGTCCCCCATCTGAAAAATG 59.249 52.381 0.00 0.00 0.00 2.32
1004 1023 2.073816 CATAAGTTGACACACCGTCCC 58.926 52.381 0.00 0.00 44.71 4.46
1024 1043 2.510238 AAGCGCCTCATCGACAGC 60.510 61.111 2.29 0.00 0.00 4.40
1353 1372 5.680619 TGTGTATGCCTAGGTAAATTCCAG 58.319 41.667 11.31 0.00 0.00 3.86
1363 1382 2.880890 GGCTCAATTGTGTATGCCTAGG 59.119 50.000 3.67 3.67 35.45 3.02
1388 1407 6.978343 ATGAAGCATCATTCCAAAACATTG 57.022 33.333 0.00 0.00 43.89 2.82
1497 1699 3.326297 GGATTGTATTAGCCTGCCTCTCT 59.674 47.826 0.00 0.00 0.00 3.10
1513 1715 3.643792 GCTCTACCATAGACAGGGATTGT 59.356 47.826 0.00 0.00 44.55 2.71
1514 1716 3.900601 AGCTCTACCATAGACAGGGATTG 59.099 47.826 0.00 0.00 0.00 2.67
1579 1816 5.012239 ACCAACATCCCATATGTGATATGC 58.988 41.667 0.00 0.00 40.96 3.14
1580 1817 6.071784 CCAACCAACATCCCATATGTGATATG 60.072 42.308 0.00 3.83 41.75 1.78
1581 1818 6.012113 CCAACCAACATCCCATATGTGATAT 58.988 40.000 0.00 0.00 31.80 1.63
1582 1819 5.384336 CCAACCAACATCCCATATGTGATA 58.616 41.667 0.00 0.00 31.80 2.15
1583 1820 4.217510 CCAACCAACATCCCATATGTGAT 58.782 43.478 1.24 0.00 31.80 3.06
1584 1821 3.626983 CCCAACCAACATCCCATATGTGA 60.627 47.826 1.24 0.00 31.80 3.58
1585 1822 2.694628 CCCAACCAACATCCCATATGTG 59.305 50.000 1.24 0.00 31.80 3.21
1599 1836 3.849574 TCTGGTATGAAGATTCCCAACCA 59.150 43.478 9.22 9.22 33.77 3.67
1677 1914 6.266131 TGTATTTATTTGCCTCTCCCAGAT 57.734 37.500 0.00 0.00 0.00 2.90
2104 2341 4.900635 AGAGTGAATGTTTGTGTGGTTC 57.099 40.909 0.00 0.00 0.00 3.62
2456 2693 3.469739 TCGACAGGGTTTGTTTTCCTAC 58.530 45.455 0.00 0.00 41.05 3.18
2466 2703 1.375523 GGCGTGATCGACAGGGTTT 60.376 57.895 0.00 0.00 45.53 3.27
2486 2723 1.469251 CCCCCAATCCCAGGTTTGT 59.531 57.895 6.72 0.00 0.00 2.83
2598 2835 2.288825 CGAGGTTAGCAGAACAAGACCA 60.289 50.000 4.18 0.00 0.00 4.02
2754 2991 5.745227 GGATACTCTGGGAAAAATGACTGA 58.255 41.667 0.00 0.00 0.00 3.41
2881 3150 2.391469 GCACAGGCAGCTGATGTAG 58.609 57.895 20.43 15.35 40.72 2.74
2918 3187 1.475403 GTCAGGGATTCCGTCTGAGA 58.525 55.000 10.82 0.00 38.09 3.27
3034 3303 7.398024 ACCAAAGAGATTTAGCAGAATACAGT 58.602 34.615 0.00 0.00 0.00 3.55
3229 3517 2.125912 GCCGACACGAGCATCACT 60.126 61.111 0.00 0.00 33.17 3.41
3250 3538 2.183555 GGGAAGTAGGACACGGCG 59.816 66.667 4.80 4.80 0.00 6.46
3320 3609 1.542915 AGCAATGTCATTGTCAGGTGC 59.457 47.619 23.27 10.63 42.20 5.01
3433 4090 5.536538 TGCAAGTAAGGAGAGATACATCGAT 59.463 40.000 0.00 0.00 0.00 3.59
3435 4092 5.188327 TGCAAGTAAGGAGAGATACATCG 57.812 43.478 0.00 0.00 0.00 3.84
3508 4399 9.656040 TGCAGAAATGCAACATTTTCTAATTAT 57.344 25.926 11.63 0.00 42.40 1.28
3542 4433 6.857451 GGCGACGGAATTCTTTTTAGTTTTTA 59.143 34.615 5.23 0.00 0.00 1.52
3545 4436 4.790878 GGCGACGGAATTCTTTTTAGTTT 58.209 39.130 5.23 0.00 0.00 2.66
3546 4437 4.414999 GGCGACGGAATTCTTTTTAGTT 57.585 40.909 5.23 0.00 0.00 2.24
3631 4536 5.562506 AATCGAGAGTCGTATCAACAAGA 57.437 39.130 0.00 0.00 41.35 3.02
3643 4548 5.264712 CGGTAACAAGACTAATCGAGAGTC 58.735 45.833 18.23 18.23 43.12 3.36
3645 4550 4.036352 GCGGTAACAAGACTAATCGAGAG 58.964 47.826 0.00 0.00 0.00 3.20
3649 4554 2.883574 TGGCGGTAACAAGACTAATCG 58.116 47.619 0.00 0.00 0.00 3.34
3651 4556 3.454375 CGATGGCGGTAACAAGACTAAT 58.546 45.455 0.00 0.00 0.00 1.73
3656 4561 1.448893 GGCGATGGCGGTAACAAGA 60.449 57.895 0.00 0.00 41.24 3.02
3657 4562 1.429148 GAGGCGATGGCGGTAACAAG 61.429 60.000 0.00 0.00 41.24 3.16
3660 4565 2.960129 CGAGGCGATGGCGGTAAC 60.960 66.667 0.00 0.00 41.24 2.50
3661 4566 4.215742 CCGAGGCGATGGCGGTAA 62.216 66.667 0.00 0.00 41.24 2.85
3679 4584 4.181010 CCATCTCACCTGCCCGGG 62.181 72.222 19.09 19.09 36.97 5.73
3680 4585 2.669133 TTCCATCTCACCTGCCCGG 61.669 63.158 0.00 0.00 39.35 5.73
3681 4586 1.450312 GTTCCATCTCACCTGCCCG 60.450 63.158 0.00 0.00 0.00 6.13
3682 4587 1.077429 GGTTCCATCTCACCTGCCC 60.077 63.158 0.00 0.00 0.00 5.36
3683 4588 0.329596 AAGGTTCCATCTCACCTGCC 59.670 55.000 0.00 0.00 43.05 4.85
3684 4589 1.003580 TGAAGGTTCCATCTCACCTGC 59.996 52.381 0.00 0.00 43.05 4.85
3685 4590 3.423539 TTGAAGGTTCCATCTCACCTG 57.576 47.619 0.00 0.00 43.05 4.00
3686 4591 4.145052 GTTTTGAAGGTTCCATCTCACCT 58.855 43.478 0.00 0.00 46.04 4.00
3687 4592 3.058224 CGTTTTGAAGGTTCCATCTCACC 60.058 47.826 0.00 0.00 0.00 4.02
3689 4594 4.065088 CTCGTTTTGAAGGTTCCATCTCA 58.935 43.478 0.00 0.00 0.00 3.27
3697 4618 0.185175 AGCCCCTCGTTTTGAAGGTT 59.815 50.000 0.00 0.00 0.00 3.50
3767 4688 3.995506 AAATTGGGAGGGAGGCGCG 62.996 63.158 0.00 0.00 0.00 6.86
3768 4689 0.395173 TAAAATTGGGAGGGAGGCGC 60.395 55.000 0.00 0.00 0.00 6.53
3811 4732 4.916293 TCATGGCGGAGATGGCGC 62.916 66.667 0.00 0.00 37.19 6.53
3822 4743 2.086251 CTCCTCCTCTCGCTCATGGC 62.086 65.000 0.00 0.00 37.64 4.40
3823 4744 0.467106 TCTCCTCCTCTCGCTCATGG 60.467 60.000 0.00 0.00 0.00 3.66
3824 4745 0.953727 CTCTCCTCCTCTCGCTCATG 59.046 60.000 0.00 0.00 0.00 3.07
3867 4788 3.966930 GAGGGAGGGAGGCGTGTCT 62.967 68.421 0.00 0.00 0.00 3.41
4063 4991 1.268992 ACCTACGTATGGGCTGGCAA 61.269 55.000 13.41 0.00 0.00 4.52
4066 4994 1.120530 AGAACCTACGTATGGGCTGG 58.879 55.000 13.41 5.60 0.00 4.85
4067 4995 1.754803 TCAGAACCTACGTATGGGCTG 59.245 52.381 18.79 18.79 34.57 4.85
4068 4996 2.154567 TCAGAACCTACGTATGGGCT 57.845 50.000 13.41 8.54 0.00 5.19
4069 4997 2.429610 TCTTCAGAACCTACGTATGGGC 59.570 50.000 13.41 6.92 0.00 5.36
4070 4998 4.430908 GTTCTTCAGAACCTACGTATGGG 58.569 47.826 8.31 7.49 46.42 4.00
4082 5010 5.811399 ACGTCACAAAATGTTCTTCAGAA 57.189 34.783 0.00 0.00 0.00 3.02
4083 5011 5.811399 AACGTCACAAAATGTTCTTCAGA 57.189 34.783 0.00 0.00 0.00 3.27
4271 5200 5.925907 GCAAGAAGCTTTGTTTGACAAAAA 58.074 33.333 18.00 0.00 46.15 1.94
4272 5201 5.529014 GCAAGAAGCTTTGTTTGACAAAA 57.471 34.783 18.00 0.00 46.15 2.44
4283 5212 7.133334 ACAATGGTGTTGAGCAAGAAGCTTT 62.133 40.000 0.00 0.00 45.56 3.51
4284 5213 5.710638 ACAATGGTGTTGAGCAAGAAGCTT 61.711 41.667 0.00 0.00 45.56 3.74
4286 5215 2.035066 ACAATGGTGTTGAGCAAGAAGC 59.965 45.455 0.00 0.00 38.06 3.86
4287 5216 3.316029 TCACAATGGTGTTGAGCAAGAAG 59.684 43.478 0.00 0.00 45.45 2.85
4288 5217 3.286353 TCACAATGGTGTTGAGCAAGAA 58.714 40.909 0.00 0.00 45.45 2.52
4289 5218 2.929641 TCACAATGGTGTTGAGCAAGA 58.070 42.857 0.00 0.00 45.45 3.02
4290 5219 3.713858 TTCACAATGGTGTTGAGCAAG 57.286 42.857 0.00 0.00 45.45 4.01
4291 5220 4.619973 GATTTCACAATGGTGTTGAGCAA 58.380 39.130 0.00 0.00 45.45 3.91
4292 5221 4.241590 GATTTCACAATGGTGTTGAGCA 57.758 40.909 0.00 0.00 45.45 4.26


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

AutoCloner maintained by Alex Coulton.