Multiple sequence alignment - TraesCS1B01G169100

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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 TraesCS1B01G169100 chr1B 100.000 3538 0 0 1 3538 300327776 300331313 0.000000e+00 6534.0
1 TraesCS1B01G169100 chr1A 95.389 2646 82 17 774 3383 260833890 260836531 0.000000e+00 4174.0
2 TraesCS1B01G169100 chr1A 86.835 790 65 22 1 775 260824835 260825600 0.000000e+00 846.0
3 TraesCS1B01G169100 chr1A 94.595 74 4 0 3465 3538 260836529 260836602 8.030000e-22 115.0
4 TraesCS1B01G169100 chr1A 100.000 40 0 0 774 813 260833850 260833889 1.360000e-09 75.0
5 TraesCS1B01G169100 chr1D 91.804 2977 157 35 1 2947 204476061 204478980 0.000000e+00 4065.0
6 TraesCS1B01G169100 chr1D 88.957 326 15 9 2960 3271 204479525 204479843 1.990000e-102 383.0
7 TraesCS1B01G169100 chr1D 91.089 101 6 3 3372 3470 243753288 243753387 2.220000e-27 134.0
8 TraesCS1B01G169100 chr1D 87.342 79 5 1 3465 3538 204479953 204480031 6.290000e-13 86.1
9 TraesCS1B01G169100 chr3B 80.719 612 88 20 72 659 35133427 35134032 1.940000e-122 449.0
10 TraesCS1B01G169100 chr3B 79.935 613 89 23 72 659 35049427 35050030 1.520000e-113 420.0
11 TraesCS1B01G169100 chr3B 77.679 224 25 13 1 200 600909862 600910084 2.890000e-21 113.0
12 TraesCS1B01G169100 chr3B 90.000 80 8 0 1 80 35049335 35049414 1.740000e-18 104.0
13 TraesCS1B01G169100 chr3B 88.750 80 9 0 1 80 35133335 35133414 8.080000e-17 99.0
14 TraesCS1B01G169100 chr3D 82.895 380 42 11 311 670 46527716 46527340 1.580000e-83 320.0
15 TraesCS1B01G169100 chr3D 92.473 93 5 2 3376 3468 336539268 336539178 7.970000e-27 132.0
16 TraesCS1B01G169100 chr3D 93.333 90 5 1 3377 3466 583869077 583868989 7.970000e-27 132.0
17 TraesCS1B01G169100 chr3D 91.579 95 5 3 3377 3470 484628973 484629065 1.030000e-25 128.0
18 TraesCS1B01G169100 chr7B 92.632 95 5 2 3374 3467 48190912 48190819 6.160000e-28 135.0
19 TraesCS1B01G169100 chr4B 92.391 92 6 1 3377 3468 507357776 507357686 2.870000e-26 130.0
20 TraesCS1B01G169100 chr4B 89.423 104 8 3 3375 3477 342857069 342857170 1.030000e-25 128.0
21 TraesCS1B01G169100 chr3A 89.000 100 10 1 3375 3474 168540325 168540423 4.800000e-24 122.0
22 TraesCS1B01G169100 chr6B 87.156 109 10 4 3360 3467 20980033 20980138 1.730000e-23 121.0
23 TraesCS1B01G169100 chr6D 77.528 178 20 11 182 349 473287954 473287787 4.860000e-14 89.8
24 TraesCS1B01G169100 chr5A 88.136 59 5 2 373 429 554351501 554351443 6.340000e-08 69.4


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 TraesCS1B01G169100 chr1B 300327776 300331313 3537 False 6534.000000 6534 100.000000 1 3538 1 chr1B.!!$F1 3537
1 TraesCS1B01G169100 chr1A 260833850 260836602 2752 False 1454.666667 4174 96.661333 774 3538 3 chr1A.!!$F2 2764
2 TraesCS1B01G169100 chr1A 260824835 260825600 765 False 846.000000 846 86.835000 1 775 1 chr1A.!!$F1 774
3 TraesCS1B01G169100 chr1D 204476061 204480031 3970 False 1511.366667 4065 89.367667 1 3538 3 chr1D.!!$F2 3537
4 TraesCS1B01G169100 chr3B 35133335 35134032 697 False 274.000000 449 84.734500 1 659 2 chr3B.!!$F3 658
5 TraesCS1B01G169100 chr3B 35049335 35050030 695 False 262.000000 420 84.967500 1 659 2 chr3B.!!$F2 658

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
473 506 0.110295 TGAGATGTTGGTGGTGGGTG 59.890 55.0 0.00 0.0 0.00 4.61 F
974 1092 0.249657 CAACAGCTCGAGGCCCTATC 60.250 60.0 15.58 0.0 43.05 2.08 F
975 1093 0.687757 AACAGCTCGAGGCCCTATCA 60.688 55.0 15.58 0.0 43.05 2.15 F
1979 2100 0.915364 GAAAGACAGAGGATGGGGCT 59.085 55.0 0.00 0.0 0.00 5.19 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1970 2091 0.480252 AGAGCCAAATAGCCCCATCC 59.520 55.000 0.00 0.0 0.00 3.51 R
2147 2268 1.143684 TCTGCAAGCCTCCTTTGAACT 59.856 47.619 0.00 0.0 0.00 3.01 R
2477 2598 1.565390 ATAGCAGCAGCACCTTCCCA 61.565 55.000 3.17 0.0 45.49 4.37 R
3447 4168 0.179000 GTACTCCCTCTCGTCCCGTA 59.821 60.000 0.00 0.0 0.00 4.02 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
138 160 0.250124 AACGACGAAGGATGCAACCA 60.250 50.000 16.21 0.00 0.00 3.67
169 195 6.748132 ACAAATACAACCCTTTGACAAGATG 58.252 36.000 2.33 0.00 36.19 2.90
173 199 8.650143 AATACAACCCTTTGACAAGATGTTAT 57.350 30.769 0.00 0.00 36.48 1.89
175 201 7.687941 ACAACCCTTTGACAAGATGTTATAG 57.312 36.000 0.00 0.00 36.48 1.31
176 202 7.231467 ACAACCCTTTGACAAGATGTTATAGT 58.769 34.615 0.00 0.00 36.48 2.12
270 296 1.830279 CAACTGGCACCATCAGATGT 58.170 50.000 9.64 0.00 36.22 3.06
309 335 4.555709 TTGCAACCCACGACGCCT 62.556 61.111 0.00 0.00 0.00 5.52
327 354 2.210961 CCTAGAGACGACGATGCTACA 58.789 52.381 0.00 0.00 0.00 2.74
352 380 1.808411 CATGGCGAGTTACAACCAGT 58.192 50.000 0.00 0.00 35.20 4.00
367 397 2.049063 AGTGACGACGGCAGAAGC 60.049 61.111 1.99 0.00 41.10 3.86
454 487 2.140792 ACAGTGCTTCACGGGAGGT 61.141 57.895 0.00 0.00 39.64 3.85
473 506 0.110295 TGAGATGTTGGTGGTGGGTG 59.890 55.000 0.00 0.00 0.00 4.61
521 578 2.619177 GCAGGACGACTATCTAGCTTGA 59.381 50.000 0.00 0.00 0.00 3.02
585 642 2.125512 GCCGCACATTCGAGGAGT 60.126 61.111 0.00 0.00 0.00 3.85
595 652 4.872485 CGAGGAGTCGCGCGAGAC 62.872 72.222 35.75 31.86 39.88 3.36
723 795 2.201022 CGCCTAGTACCGCCCATCT 61.201 63.158 0.00 0.00 0.00 2.90
724 796 1.745320 CGCCTAGTACCGCCCATCTT 61.745 60.000 0.00 0.00 0.00 2.40
825 941 3.064408 CCTGTGATGACAATCCATGAACG 59.936 47.826 0.00 0.00 31.15 3.95
923 1039 2.324330 CGTTGCTCATGCGGAACCA 61.324 57.895 13.54 0.00 43.34 3.67
924 1040 1.647545 CGTTGCTCATGCGGAACCAT 61.648 55.000 13.54 0.00 43.34 3.55
925 1041 0.527565 GTTGCTCATGCGGAACCATT 59.472 50.000 8.73 0.00 43.34 3.16
926 1042 0.810648 TTGCTCATGCGGAACCATTC 59.189 50.000 0.00 0.00 43.34 2.67
971 1089 0.687757 TATCAACAGCTCGAGGCCCT 60.688 55.000 15.58 0.00 43.05 5.19
972 1090 0.687757 ATCAACAGCTCGAGGCCCTA 60.688 55.000 15.58 0.00 43.05 3.53
973 1091 0.687757 TCAACAGCTCGAGGCCCTAT 60.688 55.000 15.58 0.00 43.05 2.57
974 1092 0.249657 CAACAGCTCGAGGCCCTATC 60.250 60.000 15.58 0.00 43.05 2.08
975 1093 0.687757 AACAGCTCGAGGCCCTATCA 60.688 55.000 15.58 0.00 43.05 2.15
976 1094 0.687757 ACAGCTCGAGGCCCTATCAA 60.688 55.000 15.58 0.00 43.05 2.57
1581 1701 6.227298 TCTGACCAGGATTTATCAGAGAAC 57.773 41.667 3.10 0.00 41.99 3.01
1742 1863 2.479566 AGAAGCGGCTCAATTCAGAA 57.520 45.000 1.45 0.00 0.00 3.02
1955 2076 2.005451 CTGAAGAGCGATGGAACCAAG 58.995 52.381 0.00 0.00 0.00 3.61
1979 2100 0.915364 GAAAGACAGAGGATGGGGCT 59.085 55.000 0.00 0.00 0.00 5.19
2018 2139 3.589288 AGATGCTCTCCCCTTACAAGTTT 59.411 43.478 0.00 0.00 0.00 2.66
2327 2448 7.546667 TGTTCTTTACCATACGACCAAGTATTC 59.453 37.037 0.00 0.00 35.32 1.75
2428 2549 4.694037 GGGTGGTCTGTACTTGAATAACAC 59.306 45.833 0.00 0.00 0.00 3.32
2433 2554 5.347907 GGTCTGTACTTGAATAACACGAAGG 59.652 44.000 0.00 0.00 0.00 3.46
2436 2557 5.845103 TGTACTTGAATAACACGAAGGTCA 58.155 37.500 0.00 0.00 0.00 4.02
2477 2598 5.244178 GGTCGAGGAAGGTGATATAGTTGAT 59.756 44.000 0.00 0.00 0.00 2.57
2507 2628 0.035534 TGCTGCTATCTGCCGGAAAA 60.036 50.000 5.05 0.00 42.00 2.29
2528 2649 2.254546 AGAACAAGATGGTTGTGCGA 57.745 45.000 0.00 0.00 33.20 5.10
2540 2661 8.902540 AGATGGTTGTGCGAATATCTTAATTA 57.097 30.769 0.00 0.00 0.00 1.40
2604 2732 4.910458 AAAGTAACAGCCCTGTACTCAT 57.090 40.909 0.72 0.00 44.13 2.90
2735 2864 7.880713 TGTACTGGTCATTTTGCTTTAGTATCA 59.119 33.333 0.00 0.00 0.00 2.15
2737 2868 6.714810 ACTGGTCATTTTGCTTTAGTATCACA 59.285 34.615 0.00 0.00 0.00 3.58
2848 2979 7.816031 CAGTTTTTATGTCAGCATCTTTGGATT 59.184 33.333 0.00 0.00 36.58 3.01
2883 3014 7.977789 TGCACATTCAGTATCTCTAAACAAA 57.022 32.000 0.00 0.00 0.00 2.83
2948 3079 4.674281 AGCATAGGTAGCAAACTAGACC 57.326 45.455 0.00 0.00 0.00 3.85
2952 3083 5.395324 GCATAGGTAGCAAACTAGACCAGAA 60.395 44.000 0.00 0.00 0.00 3.02
2999 3663 2.224079 CGTGATATGTGCCCATGTAAGC 59.776 50.000 0.00 0.00 32.29 3.09
3005 3669 1.628340 TGTGCCCATGTAAGCTGTAGT 59.372 47.619 0.00 0.00 0.00 2.73
3221 3905 5.355910 TGCGTTAACTTTGGAGAGTTTTTCT 59.644 36.000 3.71 0.00 40.24 2.52
3222 3906 5.681543 GCGTTAACTTTGGAGAGTTTTTCTG 59.318 40.000 3.71 0.00 40.24 3.02
3230 3914 7.931407 ACTTTGGAGAGTTTTTCTGTTGTTTTT 59.069 29.630 0.00 0.00 35.87 1.94
3231 3915 7.650834 TTGGAGAGTTTTTCTGTTGTTTTTG 57.349 32.000 0.00 0.00 35.87 2.44
3232 3916 6.162777 TGGAGAGTTTTTCTGTTGTTTTTGG 58.837 36.000 0.00 0.00 35.87 3.28
3242 3926 2.703007 TGTTGTTTTTGGGGGATTCTGG 59.297 45.455 0.00 0.00 0.00 3.86
3248 3932 0.783206 TTGGGGGATTCTGGAAGCAA 59.217 50.000 1.14 0.00 0.00 3.91
3264 3953 5.066375 TGGAAGCAAAGATACGATGGAAATG 59.934 40.000 0.00 0.00 0.00 2.32
3295 3984 3.365472 ACTTGGCTGGTTTCAGTTTTCT 58.635 40.909 0.00 0.00 42.78 2.52
3331 4020 1.153168 AAGAGTTGCAGTGCACGGT 60.153 52.632 19.58 4.86 38.71 4.83
3335 4024 2.124529 TTGCAGTGCACGGTTGGA 60.125 55.556 19.58 6.77 38.71 3.53
3360 4049 3.117888 TGGATCCCTGCAGAATTTAGTCC 60.118 47.826 17.39 12.36 0.00 3.85
3378 4099 5.924475 AGTCCGAGTGATTTGTACAAAAG 57.076 39.130 23.97 11.32 33.56 2.27
3380 4101 4.213482 GTCCGAGTGATTTGTACAAAAGCT 59.787 41.667 23.97 19.89 33.56 3.74
3381 4102 5.407387 GTCCGAGTGATTTGTACAAAAGCTA 59.593 40.000 23.97 8.73 33.56 3.32
3382 4103 5.407387 TCCGAGTGATTTGTACAAAAGCTAC 59.593 40.000 23.97 18.27 33.56 3.58
3383 4104 5.408604 CCGAGTGATTTGTACAAAAGCTACT 59.591 40.000 23.97 21.80 33.56 2.57
3384 4105 6.401153 CCGAGTGATTTGTACAAAAGCTACTC 60.401 42.308 26.87 26.87 33.56 2.59
3385 4106 6.401153 CGAGTGATTTGTACAAAAGCTACTCC 60.401 42.308 28.41 19.86 33.56 3.85
3386 4107 6.534634 AGTGATTTGTACAAAAGCTACTCCT 58.465 36.000 23.97 11.95 33.56 3.69
3387 4108 6.998673 AGTGATTTGTACAAAAGCTACTCCTT 59.001 34.615 23.97 4.38 33.56 3.36
3388 4109 7.173390 AGTGATTTGTACAAAAGCTACTCCTTC 59.827 37.037 23.97 13.27 33.56 3.46
3389 4110 7.173390 GTGATTTGTACAAAAGCTACTCCTTCT 59.827 37.037 23.97 3.66 33.56 2.85
3390 4111 6.861065 TTTGTACAAAAGCTACTCCTTCTG 57.139 37.500 18.54 0.00 0.00 3.02
3391 4112 5.546621 TGTACAAAAGCTACTCCTTCTGT 57.453 39.130 0.00 0.00 31.47 3.41
3392 4113 5.539048 TGTACAAAAGCTACTCCTTCTGTC 58.461 41.667 0.00 0.00 29.50 3.51
3393 4114 4.009370 ACAAAAGCTACTCCTTCTGTCC 57.991 45.455 0.00 0.00 0.00 4.02
3394 4115 3.244596 ACAAAAGCTACTCCTTCTGTCCC 60.245 47.826 0.00 0.00 0.00 4.46
3395 4116 2.327325 AAGCTACTCCTTCTGTCCCA 57.673 50.000 0.00 0.00 0.00 4.37
3396 4117 2.559381 AGCTACTCCTTCTGTCCCAT 57.441 50.000 0.00 0.00 0.00 4.00
3397 4118 3.689872 AGCTACTCCTTCTGTCCCATA 57.310 47.619 0.00 0.00 0.00 2.74
3398 4119 3.995636 AGCTACTCCTTCTGTCCCATAA 58.004 45.455 0.00 0.00 0.00 1.90
3399 4120 4.561752 AGCTACTCCTTCTGTCCCATAAT 58.438 43.478 0.00 0.00 0.00 1.28
3400 4121 5.716979 AGCTACTCCTTCTGTCCCATAATA 58.283 41.667 0.00 0.00 0.00 0.98
3401 4122 6.326970 AGCTACTCCTTCTGTCCCATAATAT 58.673 40.000 0.00 0.00 0.00 1.28
3402 4123 7.479579 AGCTACTCCTTCTGTCCCATAATATA 58.520 38.462 0.00 0.00 0.00 0.86
3403 4124 7.956315 AGCTACTCCTTCTGTCCCATAATATAA 59.044 37.037 0.00 0.00 0.00 0.98
3404 4125 8.254508 GCTACTCCTTCTGTCCCATAATATAAG 58.745 40.741 0.00 0.00 0.00 1.73
3405 4126 9.535170 CTACTCCTTCTGTCCCATAATATAAGA 57.465 37.037 0.00 0.00 0.00 2.10
3406 4127 8.798975 ACTCCTTCTGTCCCATAATATAAGAA 57.201 34.615 0.00 0.00 0.00 2.52
3407 4128 8.652290 ACTCCTTCTGTCCCATAATATAAGAAC 58.348 37.037 0.00 0.00 0.00 3.01
3408 4129 7.667557 TCCTTCTGTCCCATAATATAAGAACG 58.332 38.462 0.00 0.00 0.00 3.95
3409 4130 7.289317 TCCTTCTGTCCCATAATATAAGAACGT 59.711 37.037 0.00 0.00 0.00 3.99
3410 4131 7.931948 CCTTCTGTCCCATAATATAAGAACGTT 59.068 37.037 0.00 0.00 0.00 3.99
3411 4132 9.326413 CTTCTGTCCCATAATATAAGAACGTTT 57.674 33.333 0.46 0.00 0.00 3.60
3412 4133 9.675464 TTCTGTCCCATAATATAAGAACGTTTT 57.325 29.630 0.46 0.00 0.00 2.43
3413 4134 9.675464 TCTGTCCCATAATATAAGAACGTTTTT 57.325 29.630 9.22 9.22 0.00 1.94
3414 4135 9.716507 CTGTCCCATAATATAAGAACGTTTTTG 57.283 33.333 13.87 0.00 0.00 2.44
3415 4136 9.451002 TGTCCCATAATATAAGAACGTTTTTGA 57.549 29.630 13.87 2.81 0.00 2.69
3416 4137 9.712359 GTCCCATAATATAAGAACGTTTTTGAC 57.288 33.333 13.87 5.89 0.00 3.18
3417 4138 9.451002 TCCCATAATATAAGAACGTTTTTGACA 57.549 29.630 13.87 0.01 0.00 3.58
3418 4139 9.498307 CCCATAATATAAGAACGTTTTTGACAC 57.502 33.333 13.87 0.00 0.00 3.67
3425 4146 8.876275 ATAAGAACGTTTTTGACACTAGTGTA 57.124 30.769 27.98 11.50 45.05 2.90
3426 4147 6.823678 AGAACGTTTTTGACACTAGTGTAG 57.176 37.500 27.98 14.79 45.05 2.74
3427 4148 6.335777 AGAACGTTTTTGACACTAGTGTAGT 58.664 36.000 27.98 15.35 45.05 2.73
3428 4149 6.815142 AGAACGTTTTTGACACTAGTGTAGTT 59.185 34.615 27.98 21.29 45.05 2.24
3429 4150 6.973229 ACGTTTTTGACACTAGTGTAGTTT 57.027 33.333 27.98 5.50 45.05 2.66
3430 4151 6.997222 ACGTTTTTGACACTAGTGTAGTTTC 58.003 36.000 27.98 15.61 45.05 2.78
3431 4152 6.591062 ACGTTTTTGACACTAGTGTAGTTTCA 59.409 34.615 27.98 17.99 45.05 2.69
3437 4158 6.996106 TGACACTAGTGTAGTTTCAAAAACG 58.004 36.000 27.98 0.00 45.05 3.60
3438 4159 6.591062 TGACACTAGTGTAGTTTCAAAAACGT 59.409 34.615 27.98 0.00 45.05 3.99
3439 4160 7.118101 TGACACTAGTGTAGTTTCAAAAACGTT 59.882 33.333 27.98 0.00 45.05 3.99
3440 4161 7.809665 ACACTAGTGTAGTTTCAAAAACGTTT 58.190 30.769 26.91 7.96 42.90 3.60
3441 4162 7.747357 ACACTAGTGTAGTTTCAAAAACGTTTG 59.253 33.333 26.91 3.70 42.90 2.93
3442 4163 7.747357 CACTAGTGTAGTTTCAAAAACGTTTGT 59.253 33.333 15.46 5.99 40.08 2.83
3443 4164 8.934825 ACTAGTGTAGTTTCAAAAACGTTTGTA 58.065 29.630 15.46 0.00 39.60 2.41
3444 4165 9.925268 CTAGTGTAGTTTCAAAAACGTTTGTAT 57.075 29.630 15.46 1.15 43.90 2.29
3451 4172 9.384682 AGTTTCAAAAACGTTTGTATATTACGG 57.615 29.630 15.46 0.00 43.90 4.02
3452 4173 8.629132 GTTTCAAAAACGTTTGTATATTACGGG 58.371 33.333 15.46 0.00 43.90 5.28
3453 4174 7.664082 TCAAAAACGTTTGTATATTACGGGA 57.336 32.000 15.46 0.00 43.90 5.14
3454 4175 7.517321 TCAAAAACGTTTGTATATTACGGGAC 58.483 34.615 15.46 0.00 43.90 4.46
3456 4177 7.621013 CAAAAACGTTTGTATATTACGGGACGA 60.621 37.037 15.46 0.00 46.79 4.20
3470 4191 1.204231 GGGACGAGAGGGAGTACAAAC 59.796 57.143 0.00 0.00 0.00 2.93
3522 4248 5.521735 TCAATATGGTTTTGTTTGTGTGTGC 59.478 36.000 0.00 0.00 0.00 4.57
3523 4249 2.820059 TGGTTTTGTTTGTGTGTGCA 57.180 40.000 0.00 0.00 0.00 4.57
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
37 38 1.067071 GGTTGTAGCTCCTAACTGCGT 60.067 52.381 0.00 0.00 0.00 5.24
138 160 5.105146 TCAAAGGGTTGTATTTGTTGTTGCT 60.105 36.000 0.00 0.00 37.60 3.91
148 170 6.976934 AACATCTTGTCAAAGGGTTGTATT 57.023 33.333 0.00 0.00 36.07 1.89
176 202 5.772169 TGGTTGTAACATTTGTCATCCATGA 59.228 36.000 0.00 0.00 0.00 3.07
192 218 1.608542 CGGGGTCGTTCATGGTTGTAA 60.609 52.381 0.00 0.00 0.00 2.41
220 246 4.941263 TGTTGTCCATAGTTGTAGCATTCC 59.059 41.667 0.00 0.00 0.00 3.01
260 286 5.063438 ACAAAACGATCGTAACATCTGATGG 59.937 40.000 23.04 4.18 33.60 3.51
270 296 6.415702 CAACTTCTTGACAAAACGATCGTAA 58.584 36.000 23.04 9.93 0.00 3.18
309 335 1.938577 GGTGTAGCATCGTCGTCTCTA 59.061 52.381 0.00 0.00 0.00 2.43
327 354 1.078426 GTAACTCGCCATGCAGGGT 60.078 57.895 20.22 0.28 38.09 4.34
335 363 0.753867 TCACTGGTTGTAACTCGCCA 59.246 50.000 0.00 0.00 0.00 5.69
352 380 0.531974 AAAAGCTTCTGCCGTCGTCA 60.532 50.000 0.00 0.00 40.80 4.35
367 397 1.463056 TCGATACGGTTGCAGCAAAAG 59.537 47.619 10.11 9.43 0.00 2.27
454 487 0.110295 CACCCACCACCAACATCTCA 59.890 55.000 0.00 0.00 0.00 3.27
671 743 1.068585 AAAGTTTCGGTCGGTCGCT 59.931 52.632 0.00 0.00 0.00 4.93
679 751 2.596338 CCGGCCCAAAGTTTCGGT 60.596 61.111 0.00 0.00 36.38 4.69
723 795 5.628797 TCATGGTATGTGAGGCATAAGAA 57.371 39.130 0.00 0.00 41.29 2.52
724 796 5.104569 TGTTCATGGTATGTGAGGCATAAGA 60.105 40.000 0.00 0.00 41.29 2.10
825 941 2.540515 CCGTCATACACTCATGTCCAC 58.459 52.381 0.00 0.00 40.48 4.02
923 1039 0.107654 GGGTTAGCCAGACGCAGAAT 60.108 55.000 0.00 0.00 41.38 2.40
924 1040 1.295423 GGGTTAGCCAGACGCAGAA 59.705 57.895 0.00 0.00 41.38 3.02
925 1041 2.978824 GGGTTAGCCAGACGCAGA 59.021 61.111 0.00 0.00 41.38 4.26
926 1042 2.509336 CGGGTTAGCCAGACGCAG 60.509 66.667 0.15 0.00 41.38 5.18
971 1089 0.325296 AGGAGGCGGAGGTGTTGATA 60.325 55.000 0.00 0.00 0.00 2.15
972 1090 1.613630 AGGAGGCGGAGGTGTTGAT 60.614 57.895 0.00 0.00 0.00 2.57
973 1091 2.203788 AGGAGGCGGAGGTGTTGA 60.204 61.111 0.00 0.00 0.00 3.18
974 1092 2.232298 GAGAGGAGGCGGAGGTGTTG 62.232 65.000 0.00 0.00 0.00 3.33
975 1093 1.985116 GAGAGGAGGCGGAGGTGTT 60.985 63.158 0.00 0.00 0.00 3.32
976 1094 2.363147 GAGAGGAGGCGGAGGTGT 60.363 66.667 0.00 0.00 0.00 4.16
1742 1863 4.541705 ACTCAGTGTAGCTCATACCATCT 58.458 43.478 0.00 0.00 33.01 2.90
1955 2076 3.084786 CCCATCCTCTGTCTTTCCAAAC 58.915 50.000 0.00 0.00 0.00 2.93
1961 2082 2.270434 TAGCCCCATCCTCTGTCTTT 57.730 50.000 0.00 0.00 0.00 2.52
1970 2091 0.480252 AGAGCCAAATAGCCCCATCC 59.520 55.000 0.00 0.00 0.00 3.51
1979 2100 5.443283 AGCATCTTTGATGAGAGCCAAATA 58.557 37.500 11.25 0.00 32.60 1.40
2018 2139 5.510179 CGGGACTGAGAAAAAGTACTGGTAA 60.510 44.000 0.00 0.00 32.04 2.85
2147 2268 1.143684 TCTGCAAGCCTCCTTTGAACT 59.856 47.619 0.00 0.00 0.00 3.01
2256 2377 3.254166 CCCTCAATTGTTTGTGAGTCCAG 59.746 47.826 5.13 0.00 39.76 3.86
2327 2448 1.912043 AGATCAACCAGGGGAGACTTG 59.088 52.381 0.00 0.00 0.00 3.16
2414 2535 6.774354 TTGACCTTCGTGTTATTCAAGTAC 57.226 37.500 0.00 0.00 0.00 2.73
2428 2549 6.150396 ACTTATCCTCACTATTGACCTTCG 57.850 41.667 0.00 0.00 0.00 3.79
2433 2554 5.749109 CGACCAACTTATCCTCACTATTGAC 59.251 44.000 0.00 0.00 0.00 3.18
2436 2557 5.069251 CCTCGACCAACTTATCCTCACTATT 59.931 44.000 0.00 0.00 0.00 1.73
2477 2598 1.565390 ATAGCAGCAGCACCTTCCCA 61.565 55.000 3.17 0.00 45.49 4.37
2507 2628 2.948979 TCGCACAACCATCTTGTTCTTT 59.051 40.909 0.00 0.00 0.00 2.52
2604 2732 6.538945 TGTGTATGTTCAGGACAGCTAATA 57.461 37.500 0.00 0.00 42.62 0.98
2735 2864 6.557110 ACTTACAAACAAATAGCAAACGTGT 58.443 32.000 0.00 0.00 0.00 4.49
2737 2868 7.221259 GGAAACTTACAAACAAATAGCAAACGT 59.779 33.333 0.00 0.00 0.00 3.99
2883 3014 8.109634 AGTCCTTTCAGTAATGTCACCAAATAT 58.890 33.333 0.00 0.00 0.00 1.28
2952 3083 9.445786 GCGCATATTAGTTTACACATAATTTGT 57.554 29.630 0.30 0.00 39.91 2.83
2973 3637 2.253758 GGGCACATATCACGCGCAT 61.254 57.895 5.73 0.04 38.38 4.73
2999 3663 4.238514 GTCTCAGCAACCTACAACTACAG 58.761 47.826 0.00 0.00 0.00 2.74
3005 3669 4.020307 TGATGATGTCTCAGCAACCTACAA 60.020 41.667 0.00 0.00 44.39 2.41
3221 3905 2.703007 CCAGAATCCCCCAAAAACAACA 59.297 45.455 0.00 0.00 0.00 3.33
3222 3906 2.969262 TCCAGAATCCCCCAAAAACAAC 59.031 45.455 0.00 0.00 0.00 3.32
3230 3914 0.783206 TTTGCTTCCAGAATCCCCCA 59.217 50.000 0.00 0.00 0.00 4.96
3231 3915 1.005924 TCTTTGCTTCCAGAATCCCCC 59.994 52.381 0.00 0.00 0.00 5.40
3232 3916 2.514458 TCTTTGCTTCCAGAATCCCC 57.486 50.000 0.00 0.00 0.00 4.81
3242 3926 4.972440 GCATTTCCATCGTATCTTTGCTTC 59.028 41.667 0.00 0.00 0.00 3.86
3248 3932 3.884693 TGCATGCATTTCCATCGTATCTT 59.115 39.130 18.46 0.00 0.00 2.40
3264 3953 2.362120 AGCCAAGTCCCTGCATGC 60.362 61.111 11.82 11.82 0.00 4.06
3295 3984 4.159506 ACTCTTGCTTGCTTTTACACCAAA 59.840 37.500 0.00 0.00 0.00 3.28
3331 4020 0.329261 CTGCAGGGATCCAAGTCCAA 59.671 55.000 15.23 0.00 40.17 3.53
3335 4024 3.463048 AAATTCTGCAGGGATCCAAGT 57.537 42.857 15.13 0.00 0.00 3.16
3360 4049 6.401153 GGAGTAGCTTTTGTACAAATCACTCG 60.401 42.308 25.83 14.16 31.62 4.18
3378 4099 4.965200 ATTATGGGACAGAAGGAGTAGC 57.035 45.455 0.00 0.00 45.00 3.58
3380 4101 9.892444 TTCTTATATTATGGGACAGAAGGAGTA 57.108 33.333 0.00 0.00 45.00 2.59
3381 4102 8.652290 GTTCTTATATTATGGGACAGAAGGAGT 58.348 37.037 0.00 0.00 45.00 3.85
3382 4103 7.815068 CGTTCTTATATTATGGGACAGAAGGAG 59.185 40.741 0.00 0.00 45.00 3.69
3383 4104 7.289317 ACGTTCTTATATTATGGGACAGAAGGA 59.711 37.037 0.00 0.00 45.00 3.36
3384 4105 7.442656 ACGTTCTTATATTATGGGACAGAAGG 58.557 38.462 0.00 0.00 45.00 3.46
3385 4106 8.888579 AACGTTCTTATATTATGGGACAGAAG 57.111 34.615 0.00 0.00 45.00 2.85
3390 4111 9.712359 GTCAAAAACGTTCTTATATTATGGGAC 57.288 33.333 0.00 0.00 0.00 4.46
3391 4112 9.451002 TGTCAAAAACGTTCTTATATTATGGGA 57.549 29.630 0.00 0.00 0.00 4.37
3392 4113 9.498307 GTGTCAAAAACGTTCTTATATTATGGG 57.502 33.333 0.00 0.00 0.00 4.00
3398 4119 9.485206 ACACTAGTGTCAAAAACGTTCTTATAT 57.515 29.630 22.95 0.00 40.24 0.86
3399 4120 8.876275 ACACTAGTGTCAAAAACGTTCTTATA 57.124 30.769 22.95 0.00 40.24 0.98
3400 4121 7.781548 ACACTAGTGTCAAAAACGTTCTTAT 57.218 32.000 22.95 0.00 40.24 1.73
3401 4122 7.975616 ACTACACTAGTGTCAAAAACGTTCTTA 59.024 33.333 31.11 8.36 43.74 2.10
3402 4123 6.815142 ACTACACTAGTGTCAAAAACGTTCTT 59.185 34.615 31.11 4.99 43.74 2.52
3403 4124 6.335777 ACTACACTAGTGTCAAAAACGTTCT 58.664 36.000 31.11 5.44 43.74 3.01
3404 4125 6.579491 ACTACACTAGTGTCAAAAACGTTC 57.421 37.500 31.11 0.00 43.74 3.95
3405 4126 6.973229 AACTACACTAGTGTCAAAAACGTT 57.027 33.333 31.11 18.57 43.74 3.99
3406 4127 6.973229 AAACTACACTAGTGTCAAAAACGT 57.027 33.333 31.11 14.47 43.74 3.99
3414 4135 6.997222 ACGTTTTTGAAACTACACTAGTGTC 58.003 36.000 31.11 17.07 43.74 3.67
3415 4136 6.973229 ACGTTTTTGAAACTACACTAGTGT 57.027 33.333 30.13 30.13 46.87 3.55
3416 4137 7.747357 ACAAACGTTTTTGAAACTACACTAGTG 59.253 33.333 21.44 21.44 44.38 2.74
3417 4138 7.809665 ACAAACGTTTTTGAAACTACACTAGT 58.190 30.769 11.66 0.00 44.38 2.57
3418 4139 9.925268 ATACAAACGTTTTTGAAACTACACTAG 57.075 29.630 11.66 0.00 44.38 2.57
3425 4146 9.384682 CCGTAATATACAAACGTTTTTGAAACT 57.615 29.630 11.66 0.00 44.38 2.66
3426 4147 8.629132 CCCGTAATATACAAACGTTTTTGAAAC 58.371 33.333 11.66 3.57 44.38 2.78
3427 4148 8.562892 TCCCGTAATATACAAACGTTTTTGAAA 58.437 29.630 11.66 0.00 44.38 2.69
3428 4149 8.014517 GTCCCGTAATATACAAACGTTTTTGAA 58.985 33.333 11.66 0.00 44.38 2.69
3429 4150 7.517321 GTCCCGTAATATACAAACGTTTTTGA 58.483 34.615 11.66 0.00 44.38 2.69
3430 4151 6.462323 CGTCCCGTAATATACAAACGTTTTTG 59.538 38.462 11.66 4.42 46.61 2.44
3431 4152 6.367422 TCGTCCCGTAATATACAAACGTTTTT 59.633 34.615 11.66 7.99 34.90 1.94
3432 4153 5.866633 TCGTCCCGTAATATACAAACGTTTT 59.133 36.000 11.66 5.92 34.90 2.43
3433 4154 5.406649 TCGTCCCGTAATATACAAACGTTT 58.593 37.500 7.96 7.96 34.90 3.60
3434 4155 4.992688 TCGTCCCGTAATATACAAACGTT 58.007 39.130 0.00 0.00 34.90 3.99
3435 4156 4.335315 TCTCGTCCCGTAATATACAAACGT 59.665 41.667 0.00 0.00 34.90 3.99
3436 4157 4.847633 TCTCGTCCCGTAATATACAAACG 58.152 43.478 0.00 0.00 36.42 3.60
3437 4158 5.218139 CCTCTCGTCCCGTAATATACAAAC 58.782 45.833 0.00 0.00 0.00 2.93
3438 4159 4.279169 CCCTCTCGTCCCGTAATATACAAA 59.721 45.833 0.00 0.00 0.00 2.83
3439 4160 3.822735 CCCTCTCGTCCCGTAATATACAA 59.177 47.826 0.00 0.00 0.00 2.41
3440 4161 3.072915 TCCCTCTCGTCCCGTAATATACA 59.927 47.826 0.00 0.00 0.00 2.29
3441 4162 3.679389 TCCCTCTCGTCCCGTAATATAC 58.321 50.000 0.00 0.00 0.00 1.47
3442 4163 3.328931 ACTCCCTCTCGTCCCGTAATATA 59.671 47.826 0.00 0.00 0.00 0.86
3443 4164 2.107901 ACTCCCTCTCGTCCCGTAATAT 59.892 50.000 0.00 0.00 0.00 1.28
3444 4165 1.492176 ACTCCCTCTCGTCCCGTAATA 59.508 52.381 0.00 0.00 0.00 0.98
3445 4166 0.258194 ACTCCCTCTCGTCCCGTAAT 59.742 55.000 0.00 0.00 0.00 1.89
3446 4167 0.911769 TACTCCCTCTCGTCCCGTAA 59.088 55.000 0.00 0.00 0.00 3.18
3447 4168 0.179000 GTACTCCCTCTCGTCCCGTA 59.821 60.000 0.00 0.00 0.00 4.02
3448 4169 1.077858 GTACTCCCTCTCGTCCCGT 60.078 63.158 0.00 0.00 0.00 5.28
3449 4170 0.679002 TTGTACTCCCTCTCGTCCCG 60.679 60.000 0.00 0.00 0.00 5.14
3450 4171 1.204231 GTTTGTACTCCCTCTCGTCCC 59.796 57.143 0.00 0.00 0.00 4.46
3451 4172 1.135460 CGTTTGTACTCCCTCTCGTCC 60.135 57.143 0.00 0.00 0.00 4.79
3452 4173 1.808945 TCGTTTGTACTCCCTCTCGTC 59.191 52.381 0.00 0.00 0.00 4.20
3453 4174 1.901591 TCGTTTGTACTCCCTCTCGT 58.098 50.000 0.00 0.00 0.00 4.18
3454 4175 2.985139 GTTTCGTTTGTACTCCCTCTCG 59.015 50.000 0.00 0.00 0.00 4.04
3455 4176 3.986277 TGTTTCGTTTGTACTCCCTCTC 58.014 45.455 0.00 0.00 0.00 3.20
3456 4177 4.411256 TTGTTTCGTTTGTACTCCCTCT 57.589 40.909 0.00 0.00 0.00 3.69
3457 4178 4.514066 ACATTGTTTCGTTTGTACTCCCTC 59.486 41.667 0.00 0.00 0.00 4.30
3458 4179 4.457466 ACATTGTTTCGTTTGTACTCCCT 58.543 39.130 0.00 0.00 0.00 4.20
3459 4180 4.823790 ACATTGTTTCGTTTGTACTCCC 57.176 40.909 0.00 0.00 0.00 4.30
3460 4181 6.535274 ACTACATTGTTTCGTTTGTACTCC 57.465 37.500 0.00 0.00 0.00 3.85
3463 4184 9.962759 CCTTATACTACATTGTTTCGTTTGTAC 57.037 33.333 0.00 0.00 0.00 2.90
3470 4191 6.764877 ATCGCCTTATACTACATTGTTTCG 57.235 37.500 0.00 0.00 0.00 3.46


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

AutoCloner maintained by Alex Coulton.