Multiple sequence alignment - TraesCS1B01G226800

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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 TraesCS1B01G226800 chr1B 100.000 4667 0 0 1 4667 407547997 407543331 0.000000e+00 8619.0
1 TraesCS1B01G226800 chr1D 96.539 2629 66 10 1 2619 301951409 301948796 0.000000e+00 4327.0
2 TraesCS1B01G226800 chr1D 94.091 1337 34 15 2618 3915 301948635 301947305 0.000000e+00 1989.0
3 TraesCS1B01G226800 chr1D 83.333 768 76 25 3918 4667 301947271 301946538 0.000000e+00 662.0
4 TraesCS1B01G226800 chr1A 94.430 2621 98 27 1 2592 376674208 376671607 0.000000e+00 3988.0
5 TraesCS1B01G226800 chr1A 90.273 843 46 6 3197 4008 376671069 376670232 0.000000e+00 1070.0
6 TraesCS1B01G226800 chr1A 95.552 562 18 6 2623 3182 376671609 376671053 0.000000e+00 893.0
7 TraesCS1B01G226800 chr1A 89.871 464 35 9 4211 4667 376670099 376669641 1.870000e-163 586.0
8 TraesCS1B01G226800 chr5B 85.632 348 27 14 4326 4667 36613550 36613220 1.240000e-90 344.0
9 TraesCS1B01G226800 chr5B 82.000 350 33 20 4326 4667 36798489 36798816 2.140000e-68 270.0
10 TraesCS1B01G226800 chr5B 82.000 350 33 20 4326 4667 36829264 36829591 2.140000e-68 270.0
11 TraesCS1B01G226800 chr5A 84.548 343 45 8 4326 4665 30558509 30558846 2.690000e-87 333.0
12 TraesCS1B01G226800 chr5A 83.390 295 37 8 4326 4614 30559672 30559960 3.580000e-66 263.0
13 TraesCS1B01G226800 chr5A 87.200 125 16 0 1937 2061 621546088 621545964 4.870000e-30 143.0
14 TraesCS1B01G226800 chrUn 82.000 350 33 20 4326 4667 65829701 65829374 2.140000e-68 270.0
15 TraesCS1B01G226800 chr5D 81.792 346 42 8 4326 4667 42066025 42066353 2.140000e-68 270.0
16 TraesCS1B01G226800 chr3D 83.884 242 19 13 4431 4667 42368061 42368287 3.660000e-51 213.0
17 TraesCS1B01G226800 chr3B 83.200 250 21 16 4431 4667 65361757 65361516 4.730000e-50 209.0
18 TraesCS1B01G226800 chr3B 92.857 42 3 0 2265 2306 14152267 14152308 1.400000e-05 62.1
19 TraesCS1B01G226800 chr3A 83.471 242 20 15 4431 4667 53335515 53335289 1.700000e-49 207.0


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 TraesCS1B01G226800 chr1B 407543331 407547997 4666 True 8619.00 8619 100.0000 1 4667 1 chr1B.!!$R1 4666
1 TraesCS1B01G226800 chr1D 301946538 301951409 4871 True 2326.00 4327 91.3210 1 4667 3 chr1D.!!$R1 4666
2 TraesCS1B01G226800 chr1A 376669641 376674208 4567 True 1634.25 3988 92.5315 1 4667 4 chr1A.!!$R1 4666
3 TraesCS1B01G226800 chr5A 30558509 30559960 1451 False 298.00 333 83.9690 4326 4665 2 chr5A.!!$F1 339

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
460 473 0.395311 TAGCCCCTACTGTCTGTCGG 60.395 60.000 0.0 0.0 0.00 4.79 F
1398 1447 0.251165 TCCCAGCACCAAAAGGCTAC 60.251 55.000 0.0 0.0 38.56 3.58 F
3058 3270 1.126113 GTCATGAACGTTGTGCCTACG 59.874 52.381 5.0 7.4 44.20 3.51 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1515 1564 0.749454 CGCCTCCTGGGAAATGGAAG 60.749 60.0 0.00 0.0 37.23 3.46 R
3213 3456 0.958822 AGGAATGGTTTCAACGCACC 59.041 50.0 0.00 0.0 33.23 5.01 R
4154 4483 0.539986 GTTACCAGGGAAGATCGCCA 59.460 55.0 9.44 0.0 0.00 5.69 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
164 165 1.682849 CTGGTGGAATTCCGACCCA 59.317 57.895 28.59 25.55 39.43 4.51
201 202 0.820871 TGTTGCTTTTGTTCCGCCTT 59.179 45.000 0.00 0.00 0.00 4.35
412 424 2.100916 GGTCGATTGGCTAGTGCTTCTA 59.899 50.000 0.00 0.00 39.59 2.10
417 429 4.500545 CGATTGGCTAGTGCTTCTATGAGT 60.501 45.833 0.00 0.00 39.59 3.41
445 458 3.438297 TCTAGAATGTTGTCGCTAGCC 57.562 47.619 9.66 0.00 32.41 3.93
455 468 0.752376 GTCGCTAGCCCCTACTGTCT 60.752 60.000 9.66 0.00 0.00 3.41
458 471 0.747852 GCTAGCCCCTACTGTCTGTC 59.252 60.000 2.29 0.00 0.00 3.51
459 472 1.025812 CTAGCCCCTACTGTCTGTCG 58.974 60.000 0.00 0.00 0.00 4.35
460 473 0.395311 TAGCCCCTACTGTCTGTCGG 60.395 60.000 0.00 0.00 0.00 4.79
461 474 1.982938 GCCCCTACTGTCTGTCGGT 60.983 63.158 0.65 0.00 39.26 4.69
550 563 9.197306 TCTGTAAATAGACATCTAAAGGCTACA 57.803 33.333 0.00 0.00 31.39 2.74
551 564 9.988815 CTGTAAATAGACATCTAAAGGCTACAT 57.011 33.333 0.00 0.00 31.39 2.29
555 568 9.950496 AAATAGACATCTAAAGGCTACATATGG 57.050 33.333 7.80 0.00 31.39 2.74
556 569 8.671987 ATAGACATCTAAAGGCTACATATGGT 57.328 34.615 7.80 0.00 31.39 3.55
605 618 6.317893 CCTTAATAAACTGGGTCGCACTATTT 59.682 38.462 0.00 0.00 0.00 1.40
720 769 4.832266 TGCATGAGGGTTTGTAAATCTTGT 59.168 37.500 0.00 0.00 0.00 3.16
728 777 6.382859 AGGGTTTGTAAATCTTGTCTGGTTTT 59.617 34.615 0.00 0.00 0.00 2.43
841 890 7.552459 TCAATTGTGATCATCTGATGCAATTT 58.448 30.769 21.15 11.08 40.56 1.82
1203 1252 2.101582 GCACTTCGAGACCCATCATAGT 59.898 50.000 0.00 0.00 0.00 2.12
1353 1402 0.809241 GAGAGAGGCATTGTCCTGCG 60.809 60.000 4.63 0.00 43.23 5.18
1398 1447 0.251165 TCCCAGCACCAAAAGGCTAC 60.251 55.000 0.00 0.00 38.56 3.58
1479 1528 7.307632 CCATACAAGAGTCTGACAGTTGAAAAG 60.308 40.741 21.79 11.91 0.00 2.27
1515 1564 1.222936 CCAGCACCAGGGAGATGTC 59.777 63.158 0.61 0.00 0.00 3.06
1597 1646 4.910195 ACTTGCATCAGTCATTCCACTTA 58.090 39.130 0.00 0.00 0.00 2.24
1825 1875 9.014297 CATATCTTAGTTCTTGGTCCAACTTTT 57.986 33.333 0.00 0.00 34.60 2.27
1917 1967 6.884280 AAGACTTGGGAGTAACATTTTGAG 57.116 37.500 0.00 0.00 35.88 3.02
2583 2633 3.293311 AACATGCACATCAACTTGAGC 57.707 42.857 0.00 0.00 34.31 4.26
2589 2639 2.350197 GCACATCAACTTGAGCACTCAC 60.350 50.000 0.00 0.00 39.66 3.51
2651 2863 9.793259 TCAAGGTCTGAGATTGTTATAGTTTTT 57.207 29.630 0.00 0.00 0.00 1.94
3058 3270 1.126113 GTCATGAACGTTGTGCCTACG 59.874 52.381 5.00 7.40 44.20 3.51
3182 3425 8.932610 TGGTATCAATGGGCAAATAATATGTTT 58.067 29.630 0.00 0.00 0.00 2.83
3183 3426 9.206870 GGTATCAATGGGCAAATAATATGTTTG 57.793 33.333 8.68 8.68 39.08 2.93
3187 3430 9.160496 TCAATGGGCAAATAATATGTTTGTTTC 57.840 29.630 12.69 6.22 38.49 2.78
3188 3431 9.165035 CAATGGGCAAATAATATGTTTGTTTCT 57.835 29.630 12.69 0.00 38.49 2.52
3189 3432 9.737844 AATGGGCAAATAATATGTTTGTTTCTT 57.262 25.926 12.69 3.66 38.49 2.52
3190 3433 9.737844 ATGGGCAAATAATATGTTTGTTTCTTT 57.262 25.926 12.69 0.00 38.49 2.52
3191 3434 8.997323 TGGGCAAATAATATGTTTGTTTCTTTG 58.003 29.630 12.69 0.00 38.49 2.77
3192 3435 9.213799 GGGCAAATAATATGTTTGTTTCTTTGA 57.786 29.630 12.69 0.00 38.49 2.69
3200 3443 9.949174 AATATGTTTGTTTCTTTGAATTTTGGC 57.051 25.926 0.00 0.00 0.00 4.52
3201 3444 6.808008 TGTTTGTTTCTTTGAATTTTGGCA 57.192 29.167 0.00 0.00 0.00 4.92
3202 3445 7.206981 TGTTTGTTTCTTTGAATTTTGGCAA 57.793 28.000 0.00 0.00 0.00 4.52
3203 3446 7.651808 TGTTTGTTTCTTTGAATTTTGGCAAA 58.348 26.923 8.93 8.93 33.41 3.68
3204 3447 8.302438 TGTTTGTTTCTTTGAATTTTGGCAAAT 58.698 25.926 14.29 0.00 33.94 2.32
3205 3448 9.780413 GTTTGTTTCTTTGAATTTTGGCAAATA 57.220 25.926 14.29 5.46 33.94 1.40
3215 3458 9.512588 TTGAATTTTGGCAAATAATATGTTGGT 57.487 25.926 14.29 0.00 31.89 3.67
3216 3459 8.944029 TGAATTTTGGCAAATAATATGTTGGTG 58.056 29.630 14.29 0.00 31.89 4.17
3217 3460 6.734104 TTTTGGCAAATAATATGTTGGTGC 57.266 33.333 14.29 0.00 0.00 5.01
3245 3488 8.837099 TGAAACCATTCCTGAATTACCATTAT 57.163 30.769 0.00 0.00 34.49 1.28
3316 3559 1.146930 CCTGATACATGCCAGCGGT 59.853 57.895 0.00 0.00 0.00 5.68
3382 3625 9.415008 CTCCTGGTGATACAGCTATATTATACT 57.585 37.037 0.00 0.00 37.16 2.12
3477 3721 8.043429 ACATTCTTCTTGAGATGGATAGGATT 57.957 34.615 0.00 0.00 33.49 3.01
3486 3730 2.341846 TGGATAGGATTTTGCGTCCC 57.658 50.000 0.00 0.00 36.36 4.46
3516 3760 2.290008 TGTCATACTGCGGGACAATGTT 60.290 45.455 0.00 0.00 38.50 2.71
3540 3784 1.131638 TGCTGAACAAGGTCAGGAGT 58.868 50.000 16.22 0.00 44.43 3.85
3594 3838 0.461870 TTGATCACGAAGATGGCCCG 60.462 55.000 0.00 0.00 37.00 6.13
3661 3905 1.068679 GCAGCAAAGAAGGAAGCAGTC 60.069 52.381 0.00 0.00 0.00 3.51
3723 3967 2.666862 CTGTTGGGTGCCGCGTTA 60.667 61.111 4.92 0.00 0.00 3.18
3739 3994 3.306166 CGCGTTAGGAAACAGTTCATAGG 59.694 47.826 0.00 0.00 32.02 2.57
3742 3997 5.180680 GCGTTAGGAAACAGTTCATAGGTTT 59.819 40.000 0.00 0.00 37.44 3.27
3744 3999 7.075741 CGTTAGGAAACAGTTCATAGGTTTTG 58.924 38.462 0.00 0.00 35.08 2.44
3778 4054 4.358851 TGATTTTGGACAGCGAAAAAGTG 58.641 39.130 0.00 0.00 35.74 3.16
3781 4057 0.934496 TGGACAGCGAAAAAGTGACG 59.066 50.000 0.00 0.00 0.00 4.35
3803 4079 5.221541 ACGGTTCATAGATTCTTGATCCCTC 60.222 44.000 14.05 0.00 35.21 4.30
3804 4080 5.555966 GGTTCATAGATTCTTGATCCCTCC 58.444 45.833 0.00 0.00 35.21 4.30
3805 4081 5.072329 GGTTCATAGATTCTTGATCCCTCCA 59.928 44.000 0.00 0.00 35.21 3.86
3819 4095 5.780282 TGATCCCTCCACATCGATTAATAGT 59.220 40.000 0.00 0.00 0.00 2.12
3877 4159 8.620416 TGGTATAGTTGACAAACATTCATATGC 58.380 33.333 0.00 0.00 38.88 3.14
3891 4173 5.665381 TTCATATGCGCATGTCGATAAAA 57.335 34.783 32.48 9.79 41.67 1.52
3933 4245 6.773976 TTTTCCAATAGGCTGTTAATCCAG 57.226 37.500 0.00 0.00 35.49 3.86
4005 4317 7.502561 GGCAGTAATCCTTAATGTACTGGAATT 59.497 37.037 10.69 0.00 42.36 2.17
4040 4368 7.424803 TCAAACCAAACAATATTCTGACAGTG 58.575 34.615 1.59 0.00 0.00 3.66
4045 4373 3.262420 ACAATATTCTGACAGTGCCGTC 58.738 45.455 1.59 0.00 36.40 4.79
4074 4402 4.394300 CCATGTACAGCTTTCTCCAAAGAG 59.606 45.833 0.33 0.00 41.60 2.85
4118 4447 0.035739 TTTACAACGTGGAGGAGGGC 59.964 55.000 0.00 0.00 0.00 5.19
4130 4459 3.351416 GAGGGCGCCGTTTCGTTT 61.351 61.111 24.48 0.00 0.00 3.60
4142 4471 1.801178 GTTTCGTTTCTCTCCCTGCTG 59.199 52.381 0.00 0.00 0.00 4.41
4145 4474 1.000955 TCGTTTCTCTCCCTGCTGTTC 59.999 52.381 0.00 0.00 0.00 3.18
4153 4482 2.309755 TCTCCCTGCTGTTCCATTGATT 59.690 45.455 0.00 0.00 0.00 2.57
4154 4483 3.094572 CTCCCTGCTGTTCCATTGATTT 58.905 45.455 0.00 0.00 0.00 2.17
4155 4484 2.827322 TCCCTGCTGTTCCATTGATTTG 59.173 45.455 0.00 0.00 0.00 2.32
4156 4485 2.093869 CCCTGCTGTTCCATTGATTTGG 60.094 50.000 0.00 0.00 38.18 3.28
4168 4497 2.042686 TGATTTGGCGATCTTCCCTG 57.957 50.000 0.00 0.00 0.00 4.45
4170 4499 0.625849 ATTTGGCGATCTTCCCTGGT 59.374 50.000 0.00 0.00 0.00 4.00
4206 4553 0.250209 AAGGCTATGGCGCAGATCTG 60.250 55.000 18.84 18.84 39.81 2.90
4207 4554 1.670406 GGCTATGGCGCAGATCTGG 60.670 63.158 23.89 14.64 39.81 3.86
4208 4555 1.368950 GCTATGGCGCAGATCTGGA 59.631 57.895 23.89 0.59 0.00 3.86
4209 4556 0.669932 GCTATGGCGCAGATCTGGAG 60.670 60.000 23.89 8.02 0.00 3.86
4224 4571 1.375268 GGAGGCTATGGCGCAGATC 60.375 63.158 10.83 0.01 39.81 2.75
4225 4572 1.670590 GAGGCTATGGCGCAGATCT 59.329 57.895 10.83 0.00 39.81 2.75
4255 4602 1.739466 CACACGCCACATAATCAAGCT 59.261 47.619 0.00 0.00 0.00 3.74
4261 4608 3.282021 GCCACATAATCAAGCTCCTGAA 58.718 45.455 0.00 0.00 0.00 3.02
4264 4611 5.163478 GCCACATAATCAAGCTCCTGAATTT 60.163 40.000 0.00 0.00 0.00 1.82
4271 4618 5.200368 TCAAGCTCCTGAATTTGGTTTTC 57.800 39.130 0.00 0.00 0.00 2.29
4306 4654 8.826710 GTGCAGCTGTACTATGTTTTATTGATA 58.173 33.333 25.57 0.00 0.00 2.15
4340 4688 9.461312 TGAGAATGTTAAGCATATTTTACTGGT 57.539 29.630 0.00 0.00 36.67 4.00
4355 4703 6.707440 TTTACTGGTTTGATGAAAGAAGCA 57.293 33.333 0.00 0.00 0.00 3.91
4364 5876 3.058708 TGATGAAAGAAGCAACAGAAGCG 60.059 43.478 0.00 0.00 37.01 4.68
4390 5902 4.499183 TGAAAACCAAACGAAATTGCAGT 58.501 34.783 0.00 0.00 0.00 4.40
4537 6070 2.810274 CCTCGCATCGAAATCAATCCAT 59.190 45.455 0.00 0.00 34.74 3.41
4539 6072 2.807967 TCGCATCGAAATCAATCCATCC 59.192 45.455 0.00 0.00 31.06 3.51
4587 6122 5.521735 CACTCGGAAGAATAAACATCCAGAG 59.478 44.000 0.00 0.00 41.32 3.35
4592 6127 6.183360 CGGAAGAATAAACATCCAGAGAACAC 60.183 42.308 0.00 0.00 32.08 3.32
4593 6128 6.655003 GGAAGAATAAACATCCAGAGAACACA 59.345 38.462 0.00 0.00 32.08 3.72
4595 6130 5.645497 AGAATAAACATCCAGAGAACACAGC 59.355 40.000 0.00 0.00 0.00 4.40
4597 6132 0.036952 ACATCCAGAGAACACAGCGG 60.037 55.000 0.00 0.00 0.00 5.52
4601 6136 1.140052 TCCAGAGAACACAGCGGAAAA 59.860 47.619 0.00 0.00 0.00 2.29
4603 6138 1.264288 CAGAGAACACAGCGGAAAACC 59.736 52.381 0.00 0.00 0.00 3.27
4605 6140 0.463116 AGAACACAGCGGAAAACCGT 60.463 50.000 10.25 0.00 35.43 4.83
4609 6144 0.368907 CACAGCGGAAAACCGTATCG 59.631 55.000 10.25 0.15 35.43 2.92
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
164 165 2.259439 ACGCGACGAACAGAGAGGT 61.259 57.895 15.93 0.00 0.00 3.85
229 230 2.279252 AATTCCGATCCCGCGACG 60.279 61.111 8.23 7.85 0.00 5.12
230 231 1.954651 GGAATTCCGATCCCGCGAC 60.955 63.158 8.23 0.00 0.00 5.19
231 232 2.420043 GGAATTCCGATCCCGCGA 59.580 61.111 8.23 0.00 0.00 5.87
412 424 3.119459 ACATTCTAGAACGACGCACTCAT 60.119 43.478 7.48 0.00 0.00 2.90
417 429 2.984471 GACAACATTCTAGAACGACGCA 59.016 45.455 7.48 0.00 0.00 5.24
445 458 3.057456 GCATATACCGACAGACAGTAGGG 60.057 52.174 2.35 0.00 46.27 3.53
455 468 4.689071 CCTAGTTTGTGCATATACCGACA 58.311 43.478 0.57 0.00 0.00 4.35
458 471 2.806244 GGCCTAGTTTGTGCATATACCG 59.194 50.000 0.00 0.00 0.00 4.02
459 472 2.806244 CGGCCTAGTTTGTGCATATACC 59.194 50.000 0.00 0.00 0.00 2.73
460 473 3.463944 ACGGCCTAGTTTGTGCATATAC 58.536 45.455 0.00 0.00 0.00 1.47
461 474 3.830744 ACGGCCTAGTTTGTGCATATA 57.169 42.857 0.00 0.00 0.00 0.86
605 618 2.609244 GCGCTGGCCTTCAATTTAACAA 60.609 45.455 3.32 0.00 0.00 2.83
688 701 8.588290 TTACAAACCCTCATGCATACTTTAAT 57.412 30.769 0.00 0.00 0.00 1.40
694 743 6.699575 AGATTTACAAACCCTCATGCATAC 57.300 37.500 0.00 0.00 0.00 2.39
905 954 8.339714 GCTTATAGATAGGACATCTACATCGAC 58.660 40.741 0.00 0.00 33.91 4.20
949 998 4.308899 AGGATTCACTCTAAACGGATCG 57.691 45.455 0.00 0.00 0.00 3.69
1203 1252 3.263681 TCAACGGATTAACACCACCCATA 59.736 43.478 0.00 0.00 0.00 2.74
1353 1402 2.555757 ACAGTGCAGCTTCTCATTTTCC 59.444 45.455 0.00 0.00 0.00 3.13
1398 1447 1.659794 CCAAGCAAAAGGGGTGACG 59.340 57.895 0.00 0.00 0.00 4.35
1515 1564 0.749454 CGCCTCCTGGGAAATGGAAG 60.749 60.000 0.00 0.00 37.23 3.46
1597 1646 2.092753 CAGTCCTAATGGTGCCATCAGT 60.093 50.000 3.96 0.00 35.31 3.41
1852 1902 6.629291 CGGCACCACCATAAGGAAAAATTAAT 60.629 38.462 0.00 0.00 39.03 1.40
1856 1906 2.495669 CGGCACCACCATAAGGAAAAAT 59.504 45.455 0.00 0.00 39.03 1.82
1917 1967 0.883833 AGCTTGCAACCTACACATGC 59.116 50.000 0.00 0.00 40.45 4.06
1959 2009 7.596248 GGTGCAAATGACATGGTCAATATATTC 59.404 37.037 2.87 0.00 45.96 1.75
2589 2639 7.961351 TCATTATTTTTATTATGCCACCCAGG 58.039 34.615 0.00 0.00 41.84 4.45
3189 3432 9.512588 ACCAACATATTATTTGCCAAAATTCAA 57.487 25.926 0.00 0.00 37.23 2.69
3190 3433 8.944029 CACCAACATATTATTTGCCAAAATTCA 58.056 29.630 0.00 0.00 37.23 2.57
3191 3434 7.909641 GCACCAACATATTATTTGCCAAAATTC 59.090 33.333 0.00 0.00 37.23 2.17
3192 3435 7.413877 CGCACCAACATATTATTTGCCAAAATT 60.414 33.333 0.00 0.00 37.23 1.82
3193 3436 6.036953 CGCACCAACATATTATTTGCCAAAAT 59.963 34.615 0.00 0.00 39.38 1.82
3194 3437 5.349817 CGCACCAACATATTATTTGCCAAAA 59.650 36.000 0.00 0.00 0.00 2.44
3195 3438 4.867047 CGCACCAACATATTATTTGCCAAA 59.133 37.500 0.00 0.00 0.00 3.28
3196 3439 4.081972 ACGCACCAACATATTATTTGCCAA 60.082 37.500 0.00 0.00 0.00 4.52
3197 3440 3.445450 ACGCACCAACATATTATTTGCCA 59.555 39.130 0.00 0.00 0.00 4.92
3198 3441 4.040445 ACGCACCAACATATTATTTGCC 57.960 40.909 0.00 0.00 0.00 4.52
3199 3442 5.098893 TCAACGCACCAACATATTATTTGC 58.901 37.500 0.00 0.00 0.00 3.68
3200 3443 7.411372 GGTTTCAACGCACCAACATATTATTTG 60.411 37.037 0.00 0.00 32.74 2.32
3201 3444 6.588373 GGTTTCAACGCACCAACATATTATTT 59.412 34.615 0.00 0.00 32.74 1.40
3202 3445 6.096695 GGTTTCAACGCACCAACATATTATT 58.903 36.000 0.00 0.00 32.74 1.40
3203 3446 5.184096 TGGTTTCAACGCACCAACATATTAT 59.816 36.000 0.00 0.00 40.26 1.28
3204 3447 4.519350 TGGTTTCAACGCACCAACATATTA 59.481 37.500 0.00 0.00 40.26 0.98
3205 3448 3.319405 TGGTTTCAACGCACCAACATATT 59.681 39.130 0.00 0.00 40.26 1.28
3206 3449 2.887783 TGGTTTCAACGCACCAACATAT 59.112 40.909 0.00 0.00 40.26 1.78
3207 3450 2.298610 TGGTTTCAACGCACCAACATA 58.701 42.857 0.00 0.00 40.26 2.29
3208 3451 1.107114 TGGTTTCAACGCACCAACAT 58.893 45.000 0.00 0.00 40.26 2.71
3209 3452 1.107114 ATGGTTTCAACGCACCAACA 58.893 45.000 0.00 0.00 46.29 3.33
3210 3453 2.124122 GAATGGTTTCAACGCACCAAC 58.876 47.619 0.00 0.00 46.29 3.77
3211 3454 1.067821 GGAATGGTTTCAACGCACCAA 59.932 47.619 0.00 0.00 46.29 3.67
3213 3456 0.958822 AGGAATGGTTTCAACGCACC 59.041 50.000 0.00 0.00 33.23 5.01
3214 3457 1.606668 TCAGGAATGGTTTCAACGCAC 59.393 47.619 0.00 0.00 33.23 5.34
3215 3458 1.974265 TCAGGAATGGTTTCAACGCA 58.026 45.000 0.00 0.00 33.23 5.24
3216 3459 3.575965 ATTCAGGAATGGTTTCAACGC 57.424 42.857 0.00 0.00 33.23 4.84
3217 3460 5.048364 TGGTAATTCAGGAATGGTTTCAACG 60.048 40.000 0.00 0.00 33.23 4.10
3245 3488 2.031245 CGCACCTGATAACAGCACAAAA 60.031 45.455 0.00 0.00 42.25 2.44
3316 3559 7.047891 ACTTGTTCTCATACAAACTGAAGACA 58.952 34.615 0.00 0.00 37.55 3.41
3382 3625 8.232412 AGGTCATGGATTTCCTATGTAGTACTA 58.768 37.037 0.00 0.00 36.82 1.82
3383 3626 7.076446 AGGTCATGGATTTCCTATGTAGTACT 58.924 38.462 0.00 0.00 36.82 2.73
3384 3627 7.233757 AGAGGTCATGGATTTCCTATGTAGTAC 59.766 40.741 0.00 0.00 36.82 2.73
3486 3730 1.589993 CAGTATGACAGCGCCCTCG 60.590 63.158 2.29 0.00 39.69 4.63
3493 3737 0.391130 TTGTCCCGCAGTATGACAGC 60.391 55.000 0.00 0.00 39.89 4.40
3516 3760 0.836606 TGACCTTGTTCAGCACCTCA 59.163 50.000 0.00 0.00 0.00 3.86
3540 3784 1.669049 ATCGCATTCCCGTCACCGTA 61.669 55.000 0.00 0.00 0.00 4.02
3594 3838 1.604278 AGAAGTTTTTCAGGCACGAGC 59.396 47.619 0.00 0.00 35.70 5.03
3661 3905 1.202627 GCAGGGCAAGAGAGTCTATGG 60.203 57.143 0.00 0.00 0.00 2.74
3723 3967 5.535030 GGACAAAACCTATGAACTGTTTCCT 59.465 40.000 0.00 0.00 31.37 3.36
3739 3994 4.460948 AATCATGATGCAGGGACAAAAC 57.539 40.909 9.46 0.00 0.00 2.43
3742 3997 3.196039 CCAAAATCATGATGCAGGGACAA 59.804 43.478 9.46 0.00 0.00 3.18
3744 3999 3.025978 TCCAAAATCATGATGCAGGGAC 58.974 45.455 9.46 0.00 0.00 4.46
3778 4054 4.991687 GGGATCAAGAATCTATGAACCGTC 59.008 45.833 12.04 2.71 38.87 4.79
3781 4057 5.072329 TGGAGGGATCAAGAATCTATGAACC 59.928 44.000 10.78 10.78 37.67 3.62
3803 4079 5.991328 ACAAGCACTATTAATCGATGTGG 57.009 39.130 12.97 2.24 0.00 4.17
3804 4080 7.003939 TGAACAAGCACTATTAATCGATGTG 57.996 36.000 0.00 3.36 0.00 3.21
3805 4081 7.792374 ATGAACAAGCACTATTAATCGATGT 57.208 32.000 0.00 0.00 0.00 3.06
3819 4095 7.594351 AGAGATCTGTATCTATGAACAAGCA 57.406 36.000 0.00 0.00 42.73 3.91
3877 4159 7.946918 TTAATGTTTCTTTTATCGACATGCG 57.053 32.000 0.00 0.00 42.69 4.73
3908 4190 7.068716 ACTGGATTAACAGCCTATTGGAAAATC 59.931 37.037 0.00 0.00 42.21 2.17
3920 4202 3.947834 AGCACAATACTGGATTAACAGCC 59.052 43.478 0.00 0.00 42.21 4.85
3922 4204 8.668510 ATCTAAGCACAATACTGGATTAACAG 57.331 34.615 0.00 0.00 44.03 3.16
3927 4209 9.632638 AATGTAATCTAAGCACAATACTGGATT 57.367 29.630 0.00 0.00 0.00 3.01
3973 4285 4.342092 ACATTAAGGATTACTGCCAATGCC 59.658 41.667 0.00 0.00 34.92 4.40
4013 4325 7.920682 ACTGTCAGAATATTGTTTGGTTTGAAC 59.079 33.333 6.91 0.00 0.00 3.18
4016 4328 6.144402 GCACTGTCAGAATATTGTTTGGTTTG 59.856 38.462 6.91 0.00 0.00 2.93
4040 4368 1.732259 CTGTACATGGACTTTGACGGC 59.268 52.381 10.05 0.00 0.00 5.68
4045 4373 4.154918 GGAGAAAGCTGTACATGGACTTTG 59.845 45.833 10.05 0.88 31.04 2.77
4091 4420 4.281435 TCCTCCACGTTGTAAATACTGTCA 59.719 41.667 0.00 0.00 0.00 3.58
4096 4425 3.528532 CCCTCCTCCACGTTGTAAATAC 58.471 50.000 0.00 0.00 0.00 1.89
4098 4427 1.339727 GCCCTCCTCCACGTTGTAAAT 60.340 52.381 0.00 0.00 0.00 1.40
4118 4447 1.623973 GGGAGAGAAACGAAACGGCG 61.624 60.000 4.80 4.80 37.29 6.46
4121 4450 0.790814 GCAGGGAGAGAAACGAAACG 59.209 55.000 0.00 0.00 0.00 3.60
4122 4451 1.801178 CAGCAGGGAGAGAAACGAAAC 59.199 52.381 0.00 0.00 0.00 2.78
4124 4453 1.048601 ACAGCAGGGAGAGAAACGAA 58.951 50.000 0.00 0.00 0.00 3.85
4130 4459 4.975490 TGGAACAGCAGGGAGAGA 57.025 55.556 0.00 0.00 0.00 3.10
4142 4471 4.354587 GAAGATCGCCAAATCAATGGAAC 58.645 43.478 0.00 0.00 43.54 3.62
4145 4474 2.035066 GGGAAGATCGCCAAATCAATGG 59.965 50.000 9.44 0.00 43.70 3.16
4153 4482 1.065709 GTTACCAGGGAAGATCGCCAA 60.066 52.381 9.44 0.00 0.00 4.52
4154 4483 0.539986 GTTACCAGGGAAGATCGCCA 59.460 55.000 9.44 0.00 0.00 5.69
4155 4484 0.539986 TGTTACCAGGGAAGATCGCC 59.460 55.000 0.00 0.00 0.00 5.54
4156 4485 2.007608 GTTGTTACCAGGGAAGATCGC 58.992 52.381 0.00 0.00 0.00 4.58
4168 4497 3.425227 CCTTGTATTTCGCCGTTGTTACC 60.425 47.826 0.00 0.00 0.00 2.85
4170 4499 2.160022 GCCTTGTATTTCGCCGTTGTTA 59.840 45.455 0.00 0.00 0.00 2.41
4179 4508 1.069906 GCGCCATAGCCTTGTATTTCG 60.070 52.381 0.00 0.00 34.57 3.46
4180 4509 1.946768 TGCGCCATAGCCTTGTATTTC 59.053 47.619 4.18 0.00 36.02 2.17
4181 4510 1.949525 CTGCGCCATAGCCTTGTATTT 59.050 47.619 4.18 0.00 36.02 1.40
4182 4511 1.140852 TCTGCGCCATAGCCTTGTATT 59.859 47.619 4.18 0.00 36.02 1.89
4183 4512 0.758734 TCTGCGCCATAGCCTTGTAT 59.241 50.000 4.18 0.00 36.02 2.29
4206 4553 1.375268 GATCTGCGCCATAGCCTCC 60.375 63.158 4.18 0.00 36.02 4.30
4207 4554 0.669932 CAGATCTGCGCCATAGCCTC 60.670 60.000 10.38 0.00 36.02 4.70
4208 4555 1.370437 CAGATCTGCGCCATAGCCT 59.630 57.895 10.38 0.00 36.02 4.58
4209 4556 1.670406 CCAGATCTGCGCCATAGCC 60.670 63.158 17.76 0.00 36.02 3.93
4255 4602 7.831691 TGAATGTAGAAAACCAAATTCAGGA 57.168 32.000 4.06 0.00 32.05 3.86
4261 4608 6.403866 TGCACTGAATGTAGAAAACCAAAT 57.596 33.333 0.00 0.00 0.00 2.32
4264 4611 3.253188 GCTGCACTGAATGTAGAAAACCA 59.747 43.478 0.00 0.00 43.37 3.67
4324 4672 9.643693 CTTTCATCAAACCAGTAAAATATGCTT 57.356 29.630 0.00 0.00 0.00 3.91
4336 4684 4.935702 TGTTGCTTCTTTCATCAAACCAG 58.064 39.130 0.00 0.00 0.00 4.00
4340 4688 5.284079 GCTTCTGTTGCTTCTTTCATCAAA 58.716 37.500 0.00 0.00 0.00 2.69
4355 4703 5.508200 TTGGTTTTCAATACGCTTCTGTT 57.492 34.783 0.00 0.00 0.00 3.16
4364 5876 6.938542 TGCAATTTCGTTTGGTTTTCAATAC 58.061 32.000 0.00 0.00 34.98 1.89
4390 5902 6.430000 GCGATTCCCTTCTTATTTTAGCCATA 59.570 38.462 0.00 0.00 0.00 2.74
4537 6070 5.951148 TGATATGCTGGATTTGTTTTGAGGA 59.049 36.000 0.00 0.00 0.00 3.71
4539 6072 7.062605 GTGTTGATATGCTGGATTTGTTTTGAG 59.937 37.037 0.00 0.00 0.00 3.02
4597 6132 1.660167 CCCCCTTCGATACGGTTTTC 58.340 55.000 0.00 0.00 0.00 2.29
4601 6136 2.042230 AGCCCCCTTCGATACGGT 60.042 61.111 0.00 0.00 0.00 4.83
4603 6138 1.107538 TCTGAGCCCCCTTCGATACG 61.108 60.000 0.00 0.00 0.00 3.06
4605 6140 1.120530 GTTCTGAGCCCCCTTCGATA 58.879 55.000 0.00 0.00 0.00 2.92
4609 6144 0.988063 AGAAGTTCTGAGCCCCCTTC 59.012 55.000 4.10 0.00 33.40 3.46


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

AutoCloner maintained by Alex Coulton.