Multiple sequence alignment - TraesCS7A01G495500

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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 TraesCS7A01G495500 chr7A 100.000 4436 0 0 1 4436 685834175 685829740 0.000000e+00 8192.0
1 TraesCS7A01G495500 chr7A 99.209 506 3 1 3932 4436 685751519 685751014 0.000000e+00 911.0
2 TraesCS7A01G495500 chr7A 99.012 506 4 1 3932 4436 685797283 685796778 0.000000e+00 905.0
3 TraesCS7A01G495500 chr7A 98.814 506 5 1 3932 4436 685734927 685734422 0.000000e+00 900.0
4 TraesCS7A01G495500 chr7A 98.814 506 5 1 3932 4436 685781286 685780781 0.000000e+00 900.0
5 TraesCS7A01G495500 chr7A 98.814 506 5 1 3932 4436 685814320 685813815 0.000000e+00 900.0
6 TraesCS7A01G495500 chr7D 93.529 3755 145 37 1 3714 593122506 593118809 0.000000e+00 5498.0
7 TraesCS7A01G495500 chr7D 87.847 288 22 7 3701 3985 593118789 593118512 4.280000e-85 326.0
8 TraesCS7A01G495500 chr7D 91.150 226 12 5 4201 4419 593118282 593118058 2.590000e-77 300.0
9 TraesCS7A01G495500 chr7D 85.204 196 18 7 4027 4212 593118498 593118304 1.630000e-44 191.0
10 TraesCS7A01G495500 chr7B 91.853 2455 103 53 284 2718 668029278 668031655 0.000000e+00 3336.0
11 TraesCS7A01G495500 chr7B 93.346 1052 48 8 2715 3748 668031735 668032782 0.000000e+00 1535.0
12 TraesCS7A01G495500 chr7B 92.339 248 19 0 1 248 668029032 668029279 1.960000e-93 353.0
13 TraesCS7A01G495500 chr7B 87.709 179 17 2 4198 4373 668033191 668033367 2.090000e-48 204.0
14 TraesCS7A01G495500 chr5D 91.610 441 17 3 1065 1505 3523869 3523449 3.820000e-165 592.0
15 TraesCS7A01G495500 chr5D 96.689 302 10 0 1529 1830 3523057 3522756 1.840000e-138 503.0
16 TraesCS7A01G495500 chr3D 96.774 31 1 0 3752 3782 523834376 523834406 8.000000e-03 52.8


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 TraesCS7A01G495500 chr7A 685829740 685834175 4435 True 8192.00 8192 100.00000 1 4436 1 chr7A.!!$R6 4435
1 TraesCS7A01G495500 chr7A 685751014 685751519 505 True 911.00 911 99.20900 3932 4436 1 chr7A.!!$R2 504
2 TraesCS7A01G495500 chr7A 685796778 685797283 505 True 905.00 905 99.01200 3932 4436 1 chr7A.!!$R4 504
3 TraesCS7A01G495500 chr7A 685734422 685734927 505 True 900.00 900 98.81400 3932 4436 1 chr7A.!!$R1 504
4 TraesCS7A01G495500 chr7A 685780781 685781286 505 True 900.00 900 98.81400 3932 4436 1 chr7A.!!$R3 504
5 TraesCS7A01G495500 chr7A 685813815 685814320 505 True 900.00 900 98.81400 3932 4436 1 chr7A.!!$R5 504
6 TraesCS7A01G495500 chr7D 593118058 593122506 4448 True 1578.75 5498 89.43250 1 4419 4 chr7D.!!$R1 4418
7 TraesCS7A01G495500 chr7B 668029032 668033367 4335 False 1357.00 3336 91.31175 1 4373 4 chr7B.!!$F1 4372
8 TraesCS7A01G495500 chr5D 3522756 3523869 1113 True 547.50 592 94.14950 1065 1830 2 chr5D.!!$R1 765

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
249 250 0.034337 TTACCGTTGGTCCTGACTGC 59.966 55.0 0.00 0.00 37.09 4.40 F
588 659 0.035725 TGCTTCTCTCATGGTGCAGG 60.036 55.0 0.00 0.00 0.00 4.85 F
612 683 0.037326 TTCTGACACGGTCTCATGCC 60.037 55.0 5.77 0.00 33.15 4.40 F
623 695 0.038599 TCTCATGCCCATGTGCTGTT 59.961 50.0 0.86 0.00 39.72 3.16 F
2025 2465 0.111061 ACAATGAGCTTGCTGGGTCA 59.889 50.0 12.14 12.14 45.67 4.02 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2055 2495 0.032815 TCGTGTCGAGACATTTGGCA 59.967 50.000 13.65 0.0 43.97 4.92 R
2064 2504 1.355563 GCCGATCATCGTGTCGAGA 59.644 57.895 6.25 0.0 39.91 4.04 R
2257 2697 1.735920 GCATCTCTAGCATCGCCGG 60.736 63.158 0.00 0.0 0.00 6.13 R
2699 3139 2.543635 TGGTACCTTGGTAGACTTCCC 58.456 52.381 14.36 0.0 0.00 3.97 R
3441 3971 0.033601 AACAAGCACCTTGGTCACCA 60.034 50.000 0.00 0.0 44.81 4.17 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
100 101 2.594962 CCACGCCGATAACGATGGC 61.595 63.158 0.00 0.00 45.39 4.40
197 198 5.513267 GGATCCTGTTCATGGGTATACTTCC 60.513 48.000 3.84 0.00 0.00 3.46
239 240 1.609841 GGAGGACCTTGTTACCGTTGG 60.610 57.143 0.00 0.00 0.00 3.77
246 247 2.140717 CTTGTTACCGTTGGTCCTGAC 58.859 52.381 0.00 0.00 37.09 3.51
247 248 1.416243 TGTTACCGTTGGTCCTGACT 58.584 50.000 0.00 0.00 37.09 3.41
248 249 1.069513 TGTTACCGTTGGTCCTGACTG 59.930 52.381 0.00 0.00 37.09 3.51
249 250 0.034337 TTACCGTTGGTCCTGACTGC 59.966 55.000 0.00 0.00 37.09 4.40
250 251 1.116536 TACCGTTGGTCCTGACTGCA 61.117 55.000 0.00 0.00 37.09 4.41
251 252 1.003355 CCGTTGGTCCTGACTGCAT 60.003 57.895 0.00 0.00 0.00 3.96
252 253 0.249120 CCGTTGGTCCTGACTGCATA 59.751 55.000 0.00 0.00 0.00 3.14
253 254 1.134401 CCGTTGGTCCTGACTGCATAT 60.134 52.381 0.00 0.00 0.00 1.78
254 255 2.632377 CGTTGGTCCTGACTGCATATT 58.368 47.619 0.00 0.00 0.00 1.28
255 256 3.009723 CGTTGGTCCTGACTGCATATTT 58.990 45.455 0.00 0.00 0.00 1.40
256 257 3.063997 CGTTGGTCCTGACTGCATATTTC 59.936 47.826 0.00 0.00 0.00 2.17
257 258 4.265073 GTTGGTCCTGACTGCATATTTCT 58.735 43.478 0.00 0.00 0.00 2.52
258 259 4.142609 TGGTCCTGACTGCATATTTCTC 57.857 45.455 0.00 0.00 0.00 2.87
259 260 3.126831 GGTCCTGACTGCATATTTCTCG 58.873 50.000 0.00 0.00 0.00 4.04
260 261 2.541762 GTCCTGACTGCATATTTCTCGC 59.458 50.000 0.00 0.00 0.00 5.03
261 262 2.432146 TCCTGACTGCATATTTCTCGCT 59.568 45.455 0.00 0.00 0.00 4.93
262 263 2.543012 CCTGACTGCATATTTCTCGCTG 59.457 50.000 0.00 0.00 0.00 5.18
263 264 1.935873 TGACTGCATATTTCTCGCTGC 59.064 47.619 0.00 0.00 35.21 5.25
264 265 1.262683 GACTGCATATTTCTCGCTGCC 59.737 52.381 0.00 0.00 33.70 4.85
265 266 1.302366 CTGCATATTTCTCGCTGCCA 58.698 50.000 0.00 0.00 33.70 4.92
266 267 1.878088 CTGCATATTTCTCGCTGCCAT 59.122 47.619 0.00 0.00 33.70 4.40
267 268 2.292569 CTGCATATTTCTCGCTGCCATT 59.707 45.455 0.00 0.00 33.70 3.16
268 269 2.291465 TGCATATTTCTCGCTGCCATTC 59.709 45.455 0.00 0.00 33.70 2.67
269 270 2.291465 GCATATTTCTCGCTGCCATTCA 59.709 45.455 0.00 0.00 0.00 2.57
270 271 3.608707 GCATATTTCTCGCTGCCATTCAG 60.609 47.826 0.00 0.00 45.62 3.02
271 272 2.119801 ATTTCTCGCTGCCATTCAGT 57.880 45.000 0.00 0.00 44.66 3.41
272 273 1.442769 TTTCTCGCTGCCATTCAGTC 58.557 50.000 0.00 0.00 44.66 3.51
273 274 0.610174 TTCTCGCTGCCATTCAGTCT 59.390 50.000 0.00 0.00 44.66 3.24
274 275 0.610174 TCTCGCTGCCATTCAGTCTT 59.390 50.000 0.00 0.00 44.66 3.01
275 276 0.725686 CTCGCTGCCATTCAGTCTTG 59.274 55.000 0.00 0.00 44.66 3.02
276 277 1.136147 CGCTGCCATTCAGTCTTGC 59.864 57.895 0.00 0.00 44.66 4.01
277 278 1.509923 GCTGCCATTCAGTCTTGCC 59.490 57.895 0.00 0.00 44.66 4.52
278 279 1.798735 CTGCCATTCAGTCTTGCCG 59.201 57.895 0.00 0.00 38.02 5.69
279 280 0.957395 CTGCCATTCAGTCTTGCCGT 60.957 55.000 0.00 0.00 38.02 5.68
280 281 0.955428 TGCCATTCAGTCTTGCCGTC 60.955 55.000 0.00 0.00 0.00 4.79
281 282 1.970917 GCCATTCAGTCTTGCCGTCG 61.971 60.000 0.00 0.00 0.00 5.12
282 283 1.421485 CATTCAGTCTTGCCGTCGC 59.579 57.895 0.00 0.00 0.00 5.19
323 356 3.065925 GCAAGAAATCTGCAGTATGGGAC 59.934 47.826 14.67 0.70 35.86 4.46
350 383 1.407656 AACTGACAGGGCGACAGGAA 61.408 55.000 7.51 0.00 41.10 3.36
369 402 3.196254 GGAATGCCATGGAATTTCAGTGT 59.804 43.478 19.57 0.00 0.00 3.55
370 403 4.322953 GGAATGCCATGGAATTTCAGTGTT 60.323 41.667 19.57 0.00 0.00 3.32
371 404 4.895668 ATGCCATGGAATTTCAGTGTTT 57.104 36.364 18.40 0.00 0.00 2.83
376 420 5.622233 GCCATGGAATTTCAGTGTTTACTCC 60.622 44.000 18.40 0.00 34.07 3.85
386 430 5.632118 TCAGTGTTTACTCCTGTAGAGACT 58.368 41.667 0.00 0.00 46.50 3.24
460 504 2.575108 CATGCCTGCCATGTCACTT 58.425 52.632 0.00 0.00 45.05 3.16
502 546 7.701501 GGTTTAGTCAGACTAATGTGCTAGTAC 59.298 40.741 21.41 13.51 40.08 2.73
503 547 7.933215 TTAGTCAGACTAATGTGCTAGTACA 57.067 36.000 17.71 16.34 35.89 2.90
504 548 8.521170 TTAGTCAGACTAATGTGCTAGTACAT 57.479 34.615 19.46 19.46 42.82 2.29
505 549 6.800543 AGTCAGACTAATGTGCTAGTACATG 58.199 40.000 24.68 16.25 40.24 3.21
548 600 6.458751 GGTGCACTGTAAATCATAGTTCCATG 60.459 42.308 17.98 0.00 0.00 3.66
568 620 6.885918 TCCATGTTATTCATCTTGTGTGACAT 59.114 34.615 0.00 0.00 34.09 3.06
588 659 0.035725 TGCTTCTCTCATGGTGCAGG 60.036 55.000 0.00 0.00 0.00 4.85
612 683 0.037326 TTCTGACACGGTCTCATGCC 60.037 55.000 5.77 0.00 33.15 4.40
623 695 0.038599 TCTCATGCCCATGTGCTGTT 59.961 50.000 0.86 0.00 39.72 3.16
668 740 7.704271 TGTCAGTACTGATAGAAGAATAACCG 58.296 38.462 27.54 0.00 42.18 4.44
669 741 7.140048 GTCAGTACTGATAGAAGAATAACCGG 58.860 42.308 27.54 0.00 42.18 5.28
670 742 6.264744 TCAGTACTGATAGAAGAATAACCGGG 59.735 42.308 21.74 0.00 34.14 5.73
673 745 4.058817 CTGATAGAAGAATAACCGGGCAC 58.941 47.826 6.32 0.00 0.00 5.01
675 747 0.743345 AGAAGAATAACCGGGCACGC 60.743 55.000 0.58 0.00 39.22 5.34
676 748 1.003112 AAGAATAACCGGGCACGCA 60.003 52.632 0.58 0.00 39.22 5.24
677 749 1.024579 AAGAATAACCGGGCACGCAG 61.025 55.000 0.58 0.00 39.22 5.18
678 750 2.437716 AATAACCGGGCACGCAGG 60.438 61.111 0.58 0.00 39.22 4.85
679 751 2.862674 GAATAACCGGGCACGCAGGA 62.863 60.000 0.58 0.00 39.22 3.86
680 752 2.869503 AATAACCGGGCACGCAGGAG 62.870 60.000 0.58 0.00 39.22 3.69
707 779 1.302112 TGGATCTTTTGACGCGCCA 60.302 52.632 5.73 0.00 0.00 5.69
708 780 0.676466 TGGATCTTTTGACGCGCCAT 60.676 50.000 5.73 0.00 0.00 4.40
731 803 7.337689 CCATTGGTAGTTCAGATTCAGATCAAA 59.662 37.037 0.00 0.00 34.60 2.69
734 806 7.397221 TGGTAGTTCAGATTCAGATCAAATGT 58.603 34.615 0.00 0.00 34.60 2.71
746 818 1.089481 TCAAATGTCGATCTGGCGCC 61.089 55.000 22.73 22.73 0.00 6.53
748 820 2.852495 AAATGTCGATCTGGCGCCGT 62.852 55.000 23.90 10.63 0.00 5.68
749 821 4.794439 TGTCGATCTGGCGCCGTG 62.794 66.667 23.90 17.53 0.00 4.94
837 909 2.587194 ATCAGATGGCGCTCGTGC 60.587 61.111 7.64 0.00 0.00 5.34
915 987 2.074948 CCCCATCTCCCCTGACTGG 61.075 68.421 0.00 0.00 0.00 4.00
921 993 3.249189 TCCCCTGACTGGCACACC 61.249 66.667 0.00 0.00 0.00 4.16
1389 1461 3.003173 CCGTCCCTCCTCAAGGCA 61.003 66.667 0.00 0.00 44.71 4.75
1551 1991 2.998667 CTCGACGAAATGCCGCTC 59.001 61.111 0.00 0.00 0.00 5.03
1920 2360 1.751927 CAATGCCCTCCTGCAGGTC 60.752 63.158 31.58 18.76 45.93 3.85
1974 2414 2.159043 GCGAGTGATCAAGGAGATGGAA 60.159 50.000 0.00 0.00 37.00 3.53
1980 2420 0.537188 TCAAGGAGATGGAAGACGCC 59.463 55.000 0.00 0.00 0.00 5.68
2004 2444 2.045926 AAGCCTGATGCCGTCACC 60.046 61.111 0.00 0.00 42.71 4.02
2016 2456 1.676014 GCCGTCACCTACAATGAGCTT 60.676 52.381 0.00 0.00 0.00 3.74
2025 2465 0.111061 ACAATGAGCTTGCTGGGTCA 59.889 50.000 12.14 12.14 45.67 4.02
2064 2504 1.304713 CCAGGAGGCTGCCAAATGT 60.305 57.895 22.65 0.00 0.00 2.71
2163 2603 3.591254 GAAGGTGGACGAGGCGCTT 62.591 63.158 7.64 0.00 0.00 4.68
2196 2636 2.945668 CCGGATGAAGAAGAATGGGTTC 59.054 50.000 0.00 0.00 34.46 3.62
2257 2697 3.092301 CTGGGGAAGAAATCAAGGTTCC 58.908 50.000 0.00 0.00 38.21 3.62
2382 2822 0.528684 GCTATGTCACTCGGGTGCTC 60.529 60.000 11.61 7.03 42.72 4.26
2581 3021 4.778143 GGGATTGGACCGCTGCGT 62.778 66.667 21.59 9.06 0.00 5.24
2748 3271 1.980765 AGCTGGGTCATCTTGAGAACA 59.019 47.619 0.00 0.00 0.00 3.18
2751 3274 3.808618 GCTGGGTCATCTTGAGAACACTT 60.809 47.826 0.00 0.00 0.00 3.16
2772 3295 1.873591 GTGATCGCCAACTTCAAGTGT 59.126 47.619 0.00 0.00 0.00 3.55
2857 3380 2.167281 CTCGTCATCCTCAACTCCATGT 59.833 50.000 0.00 0.00 0.00 3.21
2877 3400 6.852853 CCATGTTGTCAATATATGCGAAGAAC 59.147 38.462 0.00 0.00 0.00 3.01
2895 3418 1.019278 ACGGAATGTACAGCAAGGCG 61.019 55.000 0.33 0.00 0.00 5.52
2907 3430 1.098050 GCAAGGCGATGGAGATGTTT 58.902 50.000 0.00 0.00 0.00 2.83
2973 3496 3.054139 ACAACAGCCTGATGGACATGTAT 60.054 43.478 6.92 0.00 34.57 2.29
3072 3601 1.227438 CAAACCCGACGTGGTGTCT 60.227 57.895 8.51 0.00 45.87 3.41
3141 3670 2.262915 CAGAGGGTGCTGTCGGAC 59.737 66.667 0.00 0.00 0.00 4.79
3240 3769 3.003763 GAGGCGAGGGAGGTGGTT 61.004 66.667 0.00 0.00 0.00 3.67
3241 3770 3.003763 AGGCGAGGGAGGTGGTTC 61.004 66.667 0.00 0.00 0.00 3.62
3312 3841 0.831711 TGGTGGACAGCTACTGCAGA 60.832 55.000 23.35 2.95 42.74 4.26
3439 3969 2.522836 CCAGTTCGGGAGATGAGATG 57.477 55.000 0.00 0.00 39.57 2.90
3440 3970 2.034878 CCAGTTCGGGAGATGAGATGA 58.965 52.381 0.00 0.00 39.57 2.92
3441 3971 2.632028 CCAGTTCGGGAGATGAGATGAT 59.368 50.000 0.00 0.00 39.57 2.45
3500 4030 2.604914 CGTGTTCTGTGGCAGATATGTC 59.395 50.000 0.00 0.00 40.39 3.06
3509 4039 2.146342 GGCAGATATGTCGGGTGATTG 58.854 52.381 0.00 0.00 0.00 2.67
3523 4053 3.383761 GGTGATTGCCAAGTTTTGACAG 58.616 45.455 0.00 0.00 0.00 3.51
3566 4102 5.016051 TGTGAAGAAGATGAGATAGTGCC 57.984 43.478 0.00 0.00 0.00 5.01
3570 4106 2.131183 GAAGATGAGATAGTGCCGCAC 58.869 52.381 16.04 16.04 34.10 5.34
3683 4222 5.136105 AGAGTCTGAATTTTGAGGTGCTTT 58.864 37.500 0.00 0.00 0.00 3.51
3693 4232 3.998913 TGAGGTGCTTTGGATGTATCA 57.001 42.857 0.00 0.00 0.00 2.15
3699 4238 4.114794 GTGCTTTGGATGTATCATTTGGC 58.885 43.478 0.00 0.00 0.00 4.52
3728 4300 6.567321 GCAGAATATACATAAGCAGCAAGGTG 60.567 42.308 0.00 0.00 0.00 4.00
3730 4302 3.652057 ATACATAAGCAGCAAGGTGGT 57.348 42.857 0.00 0.00 0.00 4.16
3830 4402 3.927142 CCTTACCTTACTTCTCAGTTGCG 59.073 47.826 0.00 0.00 34.06 4.85
3863 4436 2.977914 CAACCTATGCAGTAGCTGTGT 58.022 47.619 0.00 0.00 42.74 3.72
3864 4437 2.932614 CAACCTATGCAGTAGCTGTGTC 59.067 50.000 0.00 0.00 42.74 3.67
3865 4438 2.461695 ACCTATGCAGTAGCTGTGTCT 58.538 47.619 0.00 0.00 42.74 3.41
3866 4439 2.167281 ACCTATGCAGTAGCTGTGTCTG 59.833 50.000 0.00 1.04 42.74 3.51
3910 4483 1.072331 GGGGAGCTCAAACTCTGTCAA 59.928 52.381 17.19 0.00 36.87 3.18
3912 4485 1.803555 GGAGCTCAAACTCTGTCAAGC 59.196 52.381 17.19 0.00 36.87 4.01
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
47 48 1.847328 TGATCTCTGCCTTGACCGTA 58.153 50.000 0.00 0.00 0.00 4.02
83 84 2.928361 GCCATCGTTATCGGCGTG 59.072 61.111 6.85 0.00 35.79 5.34
100 101 4.125703 GACATAGTCTGGATCTTGCTTGG 58.874 47.826 0.00 0.00 0.00 3.61
197 198 1.225475 CGCGTGAAGCTAGTTTGCG 60.225 57.895 7.85 7.85 45.59 4.85
239 240 2.541762 GCGAGAAATATGCAGTCAGGAC 59.458 50.000 0.00 0.00 0.00 3.85
246 247 1.302366 TGGCAGCGAGAAATATGCAG 58.698 50.000 0.00 0.00 40.46 4.41
247 248 1.971481 ATGGCAGCGAGAAATATGCA 58.029 45.000 0.00 0.00 40.46 3.96
248 249 2.291465 TGAATGGCAGCGAGAAATATGC 59.709 45.455 0.00 0.00 37.95 3.14
249 250 4.143194 CTGAATGGCAGCGAGAAATATG 57.857 45.455 0.00 0.00 37.90 1.78
261 262 0.955428 GACGGCAAGACTGAATGGCA 60.955 55.000 0.00 0.00 41.79 4.92
262 263 1.796796 GACGGCAAGACTGAATGGC 59.203 57.895 0.00 0.00 38.62 4.40
263 264 1.970917 GCGACGGCAAGACTGAATGG 61.971 60.000 0.00 0.00 39.62 3.16
264 265 1.421485 GCGACGGCAAGACTGAATG 59.579 57.895 0.00 0.00 39.62 2.67
265 266 1.741770 GGCGACGGCAAGACTGAAT 60.742 57.895 17.49 0.00 42.47 2.57
266 267 2.357034 GGCGACGGCAAGACTGAA 60.357 61.111 17.49 0.00 42.47 3.02
267 268 3.282745 GAGGCGACGGCAAGACTGA 62.283 63.158 24.23 0.00 42.47 3.41
268 269 2.811317 GAGGCGACGGCAAGACTG 60.811 66.667 24.23 0.00 42.47 3.51
269 270 2.992114 AGAGGCGACGGCAAGACT 60.992 61.111 24.23 13.33 42.47 3.24
270 271 2.765250 TTCAGAGGCGACGGCAAGAC 62.765 60.000 24.23 11.34 42.47 3.01
271 272 2.492449 CTTCAGAGGCGACGGCAAGA 62.492 60.000 24.23 14.45 42.47 3.02
272 273 2.048222 TTCAGAGGCGACGGCAAG 60.048 61.111 24.23 12.33 42.47 4.01
273 274 2.048222 CTTCAGAGGCGACGGCAA 60.048 61.111 24.23 7.92 42.47 4.52
274 275 4.069232 CCTTCAGAGGCGACGGCA 62.069 66.667 24.23 0.00 42.47 5.69
323 356 1.293924 GCCCTGTCAGTTCATCATCG 58.706 55.000 0.00 0.00 0.00 3.84
350 383 4.895668 AAACACTGAAATTCCATGGCAT 57.104 36.364 6.96 0.00 0.00 4.40
369 402 6.096987 CAGGCATAAGTCTCTACAGGAGTAAA 59.903 42.308 0.00 0.00 42.40 2.01
370 403 5.594725 CAGGCATAAGTCTCTACAGGAGTAA 59.405 44.000 0.00 0.00 42.40 2.24
371 404 5.133941 CAGGCATAAGTCTCTACAGGAGTA 58.866 45.833 0.00 0.00 42.40 2.59
376 420 3.492309 CCAGCAGGCATAAGTCTCTACAG 60.492 52.174 0.00 0.00 0.00 2.74
386 430 0.106569 CCCATGTCCAGCAGGCATAA 60.107 55.000 5.08 0.00 32.66 1.90
485 529 5.598416 TGCATGTACTAGCACATTAGTCT 57.402 39.130 5.81 0.00 37.02 3.24
548 600 6.615088 AGCAATGTCACACAAGATGAATAAC 58.385 36.000 0.00 0.00 0.00 1.89
568 620 1.612462 CCTGCACCATGAGAGAAGCAA 60.612 52.381 0.00 0.00 0.00 3.91
588 659 2.546778 TGAGACCGTGTCAGAAAACAC 58.453 47.619 0.00 0.00 44.87 3.32
623 695 5.238432 TGACAGAGCAAATCGAAGCTAAAAA 59.762 36.000 9.89 0.00 42.04 1.94
660 732 2.469516 CCTGCGTGCCCGGTTATTC 61.470 63.158 0.00 0.00 33.68 1.75
663 735 4.077184 CTCCTGCGTGCCCGGTTA 62.077 66.667 0.00 0.00 33.68 2.85
677 749 4.554036 GATCCACCTGCCCGCTCC 62.554 72.222 0.00 0.00 0.00 4.70
678 750 2.543067 AAAGATCCACCTGCCCGCTC 62.543 60.000 0.00 0.00 0.00 5.03
679 751 2.142292 AAAAGATCCACCTGCCCGCT 62.142 55.000 0.00 0.00 0.00 5.52
680 752 1.678970 AAAAGATCCACCTGCCCGC 60.679 57.895 0.00 0.00 0.00 6.13
707 779 8.900781 CATTTGATCTGAATCTGAACTACCAAT 58.099 33.333 0.00 0.00 32.75 3.16
708 780 7.884877 ACATTTGATCTGAATCTGAACTACCAA 59.115 33.333 0.00 0.00 32.75 3.67
731 803 3.838271 ACGGCGCCAGATCGACAT 61.838 61.111 28.98 0.00 37.32 3.06
748 820 1.179174 ATATCTGTCTAGCCGCGCCA 61.179 55.000 0.00 0.00 0.00 5.69
749 821 0.038159 AATATCTGTCTAGCCGCGCC 60.038 55.000 0.00 0.00 0.00 6.53
750 822 1.341606 GAATATCTGTCTAGCCGCGC 58.658 55.000 0.00 0.00 0.00 6.86
751 823 1.729472 CGGAATATCTGTCTAGCCGCG 60.729 57.143 0.00 0.00 0.00 6.46
752 824 1.540267 TCGGAATATCTGTCTAGCCGC 59.460 52.381 0.00 0.00 37.36 6.53
753 825 2.414824 GCTCGGAATATCTGTCTAGCCG 60.415 54.545 0.00 0.00 38.68 5.52
754 826 2.414824 CGCTCGGAATATCTGTCTAGCC 60.415 54.545 0.00 0.00 0.00 3.93
755 827 2.484651 TCGCTCGGAATATCTGTCTAGC 59.515 50.000 0.00 0.00 0.00 3.42
756 828 4.750952 TTCGCTCGGAATATCTGTCTAG 57.249 45.455 0.00 0.00 0.00 2.43
939 1011 0.456312 CAGGAAGCAGACGTACGGAC 60.456 60.000 21.06 13.04 0.00 4.79
974 1046 4.579384 CGGTGGGTGGTTGGCAGT 62.579 66.667 0.00 0.00 0.00 4.40
1389 1461 4.742649 TGGCCGGAGAGCTCGAGT 62.743 66.667 15.13 0.23 0.00 4.18
1785 2225 4.947147 GTGCTGGCGGTGAACCCA 62.947 66.667 0.00 0.00 0.00 4.51
2004 2444 2.012673 GACCCAGCAAGCTCATTGTAG 58.987 52.381 0.00 0.00 41.29 2.74
2016 2456 1.533219 CCTGGCATATGACCCAGCA 59.467 57.895 18.97 0.00 45.75 4.41
2040 2480 0.621571 TGGCAGCCTCCTGGTAGAAT 60.622 55.000 14.15 0.00 39.54 2.40
2055 2495 0.032815 TCGTGTCGAGACATTTGGCA 59.967 50.000 13.65 0.00 43.97 4.92
2064 2504 1.355563 GCCGATCATCGTGTCGAGA 59.644 57.895 6.25 0.00 39.91 4.04
2163 2603 3.000819 ATCCGGTCGAACAGGGCA 61.001 61.111 0.00 0.00 34.05 5.36
2196 2636 2.178912 AGGTGTTTGTGTATGGGACG 57.821 50.000 0.00 0.00 0.00 4.79
2208 2648 4.315803 CGAGGACAAGATTGTAGGTGTTT 58.684 43.478 0.00 0.00 42.43 2.83
2257 2697 1.735920 GCATCTCTAGCATCGCCGG 60.736 63.158 0.00 0.00 0.00 6.13
2699 3139 2.543635 TGGTACCTTGGTAGACTTCCC 58.456 52.381 14.36 0.00 0.00 3.97
2739 3262 2.158449 GGCGATCACAAGTGTTCTCAAG 59.842 50.000 8.99 0.00 0.00 3.02
2740 3263 2.143122 GGCGATCACAAGTGTTCTCAA 58.857 47.619 8.99 0.00 0.00 3.02
2748 3271 2.254546 TGAAGTTGGCGATCACAAGT 57.745 45.000 0.44 1.54 33.13 3.16
2751 3274 1.872952 CACTTGAAGTTGGCGATCACA 59.127 47.619 0.00 0.00 0.00 3.58
2823 3346 3.934391 GACGAGGTCCGGCTTGTGG 62.934 68.421 6.69 0.00 44.62 4.17
2857 3380 5.353111 TCCGTTCTTCGCATATATTGACAA 58.647 37.500 0.00 0.00 38.35 3.18
2877 3400 0.739462 TCGCCTTGCTGTACATTCCG 60.739 55.000 0.00 0.00 0.00 4.30
2880 3403 1.065491 TCCATCGCCTTGCTGTACATT 60.065 47.619 0.00 0.00 0.00 2.71
2895 3418 3.733224 CGATCGACTCAAACATCTCCATC 59.267 47.826 10.26 0.00 0.00 3.51
2907 3430 1.706287 CGGACTGCTCGATCGACTCA 61.706 60.000 15.15 13.75 0.00 3.41
3000 3523 0.873743 GCCGCTTCAGGATCTTCTCG 60.874 60.000 0.00 0.00 0.00 4.04
3072 3601 2.136728 CCGTTGATGACCGTGTTGTAA 58.863 47.619 0.00 0.00 0.00 2.41
3240 3769 1.067416 GCGCTGGATCATGTACCGA 59.933 57.895 0.00 0.00 0.00 4.69
3241 3770 0.809636 TTGCGCTGGATCATGTACCG 60.810 55.000 9.73 0.00 0.00 4.02
3312 3841 2.678934 TCCTCGTACCGCTTGGCT 60.679 61.111 0.00 0.00 35.53 4.75
3409 3938 1.736586 CGAACTGGGCGCTCTCTAT 59.263 57.895 9.62 0.00 0.00 1.98
3411 3940 3.764466 CCGAACTGGGCGCTCTCT 61.764 66.667 9.62 0.00 0.00 3.10
3438 3968 0.478072 AAGCACCTTGGTCACCATCA 59.522 50.000 0.00 0.00 31.53 3.07
3439 3969 0.883833 CAAGCACCTTGGTCACCATC 59.116 55.000 0.00 0.00 37.77 3.51
3440 3970 0.185901 ACAAGCACCTTGGTCACCAT 59.814 50.000 0.00 0.00 44.81 3.55
3441 3971 0.033601 AACAAGCACCTTGGTCACCA 60.034 50.000 0.00 0.00 44.81 4.17
3500 4030 1.339610 TCAAAACTTGGCAATCACCCG 59.660 47.619 0.00 0.00 0.00 5.28
3509 4039 0.961753 CTCCCCTGTCAAAACTTGGC 59.038 55.000 0.00 0.00 35.37 4.52
3523 4053 3.679824 AGTAAATATGCTACGCTCCCC 57.320 47.619 0.00 0.00 0.00 4.81
3556 4092 0.940126 CCATTGTGCGGCACTATCTC 59.060 55.000 30.81 6.86 35.11 2.75
3566 4102 0.386352 CTGTTCTGTGCCATTGTGCG 60.386 55.000 0.00 0.00 0.00 5.34
3570 4106 4.067896 ACTAGTTCTGTTCTGTGCCATTG 58.932 43.478 0.00 0.00 0.00 2.82
3581 4117 4.067972 TGCGAGGAAAACTAGTTCTGTT 57.932 40.909 8.95 0.00 0.00 3.16
3588 4124 6.721571 TTGTAAGAATGCGAGGAAAACTAG 57.278 37.500 0.00 0.00 0.00 2.57
3589 4125 6.708949 ACTTTGTAAGAATGCGAGGAAAACTA 59.291 34.615 0.00 0.00 0.00 2.24
3683 4222 3.768215 TGCAAAGCCAAATGATACATCCA 59.232 39.130 0.00 0.00 0.00 3.41
3693 4232 7.869429 GCTTATGTATATTCTGCAAAGCCAAAT 59.131 33.333 1.84 0.00 32.71 2.32
3699 4238 6.962686 TGCTGCTTATGTATATTCTGCAAAG 58.037 36.000 0.00 0.00 0.00 2.77
3728 4300 0.393808 TAGAATTTGGGAGCGGCACC 60.394 55.000 8.03 8.03 0.00 5.01
3730 4302 2.435372 AATAGAATTTGGGAGCGGCA 57.565 45.000 1.45 0.00 0.00 5.69
3733 4305 4.273480 CAGTGGTAATAGAATTTGGGAGCG 59.727 45.833 0.00 0.00 0.00 5.03
3772 4344 9.117183 ACACTGTCATACATAGACTATAAACGA 57.883 33.333 0.00 0.00 36.94 3.85
3773 4345 9.383462 GACACTGTCATACATAGACTATAAACG 57.617 37.037 4.17 0.00 36.94 3.60
3802 4374 4.964593 TGAGAAGTAAGGTAAGGCGTTTT 58.035 39.130 0.00 0.00 0.00 2.43
3806 4378 3.870633 ACTGAGAAGTAAGGTAAGGCG 57.129 47.619 0.00 0.00 0.00 5.52
3808 4380 3.927142 CGCAACTGAGAAGTAAGGTAAGG 59.073 47.826 0.00 0.00 0.00 2.69
3812 4384 1.968493 TCCGCAACTGAGAAGTAAGGT 59.032 47.619 0.00 0.00 0.00 3.50
3818 4390 0.321122 AGGCTTCCGCAACTGAGAAG 60.321 55.000 0.00 0.00 39.99 2.85
3830 4402 0.321298 TAGGTTGCGTTCAGGCTTCC 60.321 55.000 0.00 0.00 0.00 3.46
3863 4436 2.114625 ACGGACGGGTCAGACAGA 59.885 61.111 2.17 0.00 0.00 3.41
3864 4437 2.258591 CACGGACGGGTCAGACAG 59.741 66.667 2.17 0.00 0.00 3.51
3865 4438 3.299977 CCACGGACGGGTCAGACA 61.300 66.667 2.17 0.00 0.00 3.41
3866 4439 1.885163 ATTCCACGGACGGGTCAGAC 61.885 60.000 5.97 0.00 0.00 3.51
3912 4485 1.070758 AGTGTGTAGCCAAGTGAGTGG 59.929 52.381 0.00 0.00 42.05 4.00
3948 4528 0.748005 AACACACAGCCAGGTGACAC 60.748 55.000 3.46 0.00 41.32 3.67


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

AutoCloner maintained by Alex Coulton.