Multiple sequence alignment - TraesCS4D01G106000

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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 TraesCS4D01G106000 chr4D 100.000 4367 0 0 1 4367 84548712 84544346 0.000000e+00 8065
1 TraesCS4D01G106000 chr4A 92.647 4393 208 56 1 4342 497443545 497439217 0.000000e+00 6216
2 TraesCS4D01G106000 chr4B 93.546 3672 133 51 718 4342 119825178 119821564 0.000000e+00 5373
3 TraesCS4D01G106000 chr4B 89.474 551 26 10 190 719 119825754 119825215 0.000000e+00 667
4 TraesCS4D01G106000 chr5D 88.032 376 45 0 2924 3299 5816881 5816506 3.100000e-121 446
5 TraesCS4D01G106000 chr5D 87.853 354 43 0 2488 2841 5817278 5816925 2.430000e-112 416
6 TraesCS4D01G106000 chr5D 90.000 140 14 0 2304 2443 5817426 5817287 9.650000e-42 182
7 TraesCS4D01G106000 chr2A 74.927 1025 174 62 2284 3277 530380363 530381335 4.090000e-105 392
8 TraesCS4D01G106000 chr2D 74.339 1021 187 54 2284 3277 392525697 392526669 8.930000e-97 364
9 TraesCS4D01G106000 chr2B 75.575 565 103 28 2284 2826 464466316 464466867 3.370000e-61 246
10 TraesCS4D01G106000 chr2B 79.580 333 51 13 2920 3243 464466933 464467257 5.680000e-54 222
11 TraesCS4D01G106000 chr7A 73.817 676 112 42 2365 3027 464573277 464572654 1.590000e-49 207
12 TraesCS4D01G106000 chr7D 74.948 483 90 24 2365 2833 407072271 407071806 4.460000e-45 193
13 TraesCS4D01G106000 chr7D 88.073 109 12 1 2920 3027 407071756 407071648 1.270000e-25 128
14 TraesCS4D01G106000 chr7B 74.534 483 92 24 2365 2833 418049671 418049206 9.650000e-42 182
15 TraesCS4D01G106000 chr7B 88.073 109 12 1 2920 3027 418049156 418049048 1.270000e-25 128


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 TraesCS4D01G106000 chr4D 84544346 84548712 4366 True 8065 8065 100.000000 1 4367 1 chr4D.!!$R1 4366
1 TraesCS4D01G106000 chr4A 497439217 497443545 4328 True 6216 6216 92.647000 1 4342 1 chr4A.!!$R1 4341
2 TraesCS4D01G106000 chr4B 119821564 119825754 4190 True 3020 5373 91.510000 190 4342 2 chr4B.!!$R1 4152
3 TraesCS4D01G106000 chr5D 5816506 5817426 920 True 348 446 88.628333 2304 3299 3 chr5D.!!$R1 995
4 TraesCS4D01G106000 chr2A 530380363 530381335 972 False 392 392 74.927000 2284 3277 1 chr2A.!!$F1 993
5 TraesCS4D01G106000 chr2D 392525697 392526669 972 False 364 364 74.339000 2284 3277 1 chr2D.!!$F1 993
6 TraesCS4D01G106000 chr2B 464466316 464467257 941 False 234 246 77.577500 2284 3243 2 chr2B.!!$F1 959
7 TraesCS4D01G106000 chr7A 464572654 464573277 623 True 207 207 73.817000 2365 3027 1 chr7A.!!$R1 662

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
325 334 0.105039 CCTTGATCGAGCCTACACCC 59.895 60.0 4.21 0.0 0.0 4.61 F
1550 1639 0.036010 ATCAGGTGCTTCGGGAACAG 60.036 55.0 0.00 0.0 0.0 3.16 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2213 2302 0.606401 CTCATCCGGGCTGTTGTTGT 60.606 55.0 0.0 0.0 0.0 3.32 R
3478 3604 1.169661 TGTGTGTTCCAATGGCGACC 61.170 55.0 0.0 0.0 0.0 4.79 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
46 47 3.691049 AATTATGTTTGCCGACGATGG 57.309 42.857 0.00 0.00 0.00 3.51
59 60 2.423577 GACGATGGCAGGTTTAGTTGT 58.576 47.619 0.00 0.00 0.00 3.32
63 64 3.120199 CGATGGCAGGTTTAGTTGTTGAG 60.120 47.826 0.00 0.00 0.00 3.02
64 65 1.953686 TGGCAGGTTTAGTTGTTGAGC 59.046 47.619 0.00 0.00 0.00 4.26
67 68 3.366374 GGCAGGTTTAGTTGTTGAGCATC 60.366 47.826 0.00 0.00 0.00 3.91
82 83 5.813080 TGAGCATCACAAATTCATCTCAG 57.187 39.130 0.00 0.00 42.56 3.35
83 84 5.493809 TGAGCATCACAAATTCATCTCAGA 58.506 37.500 0.00 0.00 42.56 3.27
90 91 9.803315 CATCACAAATTCATCTCAGATCATTTT 57.197 29.630 0.00 0.00 0.00 1.82
124 125 7.475137 AATTACCCTGCTTGCAAACTAAATA 57.525 32.000 0.00 0.00 0.00 1.40
127 128 4.772100 ACCCTGCTTGCAAACTAAATATGT 59.228 37.500 0.00 0.00 0.00 2.29
133 134 7.035004 TGCTTGCAAACTAAATATGTCATTCC 58.965 34.615 0.00 0.00 0.00 3.01
134 135 6.197096 GCTTGCAAACTAAATATGTCATTCCG 59.803 38.462 0.00 0.00 0.00 4.30
137 139 4.468095 AACTAAATATGTCATTCCGCGC 57.532 40.909 0.00 0.00 0.00 6.86
146 148 2.805671 TGTCATTCCGCGCCAATATAAG 59.194 45.455 0.00 0.00 0.00 1.73
150 152 2.319136 TCCGCGCCAATATAAGTTGT 57.681 45.000 0.00 0.00 0.00 3.32
155 157 4.212425 CCGCGCCAATATAAGTTGTCATAA 59.788 41.667 0.00 0.00 0.00 1.90
157 159 5.845953 CGCGCCAATATAAGTTGTCATAAAG 59.154 40.000 0.00 0.00 0.00 1.85
174 176 7.930325 TGTCATAAAGAAATGTTTGATTTGGCA 59.070 29.630 0.00 0.00 0.00 4.92
187 189 3.195396 TGATTTGGCATGCCTAAAAGTCC 59.805 43.478 35.53 20.17 34.78 3.85
188 190 2.300956 TTGGCATGCCTAAAAGTCCA 57.699 45.000 35.53 11.01 36.94 4.02
199 201 5.774690 TGCCTAAAAGTCCAACATCAGATTT 59.225 36.000 0.00 0.00 0.00 2.17
209 211 8.370182 AGTCCAACATCAGATTTTTAGCATTTT 58.630 29.630 0.00 0.00 0.00 1.82
215 217 9.906660 ACATCAGATTTTTAGCATTTTCGTAAA 57.093 25.926 0.00 0.00 0.00 2.01
287 296 2.723273 GGACCCGTTCCATTCAAAGAT 58.277 47.619 0.00 0.00 45.10 2.40
309 318 2.128771 ATTAACCACGCAGCATCCTT 57.871 45.000 0.00 0.00 0.00 3.36
325 334 0.105039 CCTTGATCGAGCCTACACCC 59.895 60.000 4.21 0.00 0.00 4.61
419 429 2.102588 TCGTTAGCAAAGGCCTATCCTC 59.897 50.000 5.16 0.00 46.94 3.71
536 549 5.295787 GCACTATCATTTGTCCGGAATTGTA 59.704 40.000 5.23 0.00 0.00 2.41
539 552 2.675844 TCATTTGTCCGGAATTGTAGCG 59.324 45.455 5.23 0.00 0.00 4.26
540 553 2.459060 TTTGTCCGGAATTGTAGCGA 57.541 45.000 5.23 0.00 0.00 4.93
541 554 2.684001 TTGTCCGGAATTGTAGCGAT 57.316 45.000 5.23 0.00 0.00 4.58
542 555 2.684001 TGTCCGGAATTGTAGCGATT 57.316 45.000 5.23 0.00 0.00 3.34
543 556 2.980568 TGTCCGGAATTGTAGCGATTT 58.019 42.857 5.23 0.00 0.00 2.17
544 557 2.675844 TGTCCGGAATTGTAGCGATTTG 59.324 45.455 5.23 0.00 0.00 2.32
545 558 2.031683 GTCCGGAATTGTAGCGATTTGG 59.968 50.000 5.23 0.00 0.00 3.28
665 697 1.632018 TTCCCCGGATGACACATCCC 61.632 60.000 20.49 7.39 34.76 3.85
700 732 2.282462 CGGGAAGCAAGCAACCCT 60.282 61.111 18.92 0.00 40.12 4.34
737 807 3.449018 ACCATGATAAGCAACTCGTCTCT 59.551 43.478 0.00 0.00 0.00 3.10
745 815 3.070018 AGCAACTCGTCTCTCATTTTGG 58.930 45.455 0.00 0.00 0.00 3.28
808 878 2.847449 TCTAGAGTCTAGACCAGTGGCT 59.153 50.000 23.38 10.16 0.00 4.75
809 879 2.614134 AGAGTCTAGACCAGTGGCTT 57.386 50.000 19.38 0.00 0.00 4.35
810 880 2.452505 AGAGTCTAGACCAGTGGCTTC 58.547 52.381 19.38 7.73 0.00 3.86
811 881 1.478916 GAGTCTAGACCAGTGGCTTCC 59.521 57.143 19.38 0.00 0.00 3.46
885 958 4.554036 GCGGCTAAGCTGGAGGGG 62.554 72.222 0.00 0.00 35.15 4.79
954 1028 1.486310 GCTCTACCATGTCCATGTCCA 59.514 52.381 6.53 0.00 37.11 4.02
960 1034 0.181114 CATGTCCATGTCCATCCGGT 59.819 55.000 0.00 0.00 34.23 5.28
1036 1113 4.742201 TCCTCGCCTTGCTCGTGC 62.742 66.667 1.71 1.71 40.20 5.34
1167 1256 0.819259 TGCTTGACCTCAACTGCACC 60.819 55.000 0.00 0.00 33.81 5.01
1550 1639 0.036010 ATCAGGTGCTTCGGGAACAG 60.036 55.000 0.00 0.00 0.00 3.16
1767 1856 4.988598 CTGCGGACCAACGGCACT 62.989 66.667 0.00 0.00 46.85 4.40
2868 2972 3.112709 GGCGACTGCGAGGACAAC 61.113 66.667 0.00 0.00 44.10 3.32
2870 2974 2.805353 CGACTGCGAGGACAACGG 60.805 66.667 0.00 0.00 40.82 4.44
3410 3532 4.030452 GCAACCCACGCTGCTGAC 62.030 66.667 0.00 0.00 35.62 3.51
3498 3624 0.665835 GTCGCCATTGGAACACACAA 59.334 50.000 6.95 0.00 39.29 3.33
3654 3781 2.421424 GTCAAAATCAAGGAGCAGCGAT 59.579 45.455 0.00 0.00 0.00 4.58
3737 3868 0.526211 GAACCGGGGCAAAATGAGAC 59.474 55.000 6.32 0.00 0.00 3.36
3843 3975 1.602377 ACGCCTGCACTTGTTCTTTAC 59.398 47.619 0.00 0.00 0.00 2.01
3844 3976 1.873591 CGCCTGCACTTGTTCTTTACT 59.126 47.619 0.00 0.00 0.00 2.24
3845 3977 2.096218 CGCCTGCACTTGTTCTTTACTC 60.096 50.000 0.00 0.00 0.00 2.59
3846 3978 3.142174 GCCTGCACTTGTTCTTTACTCT 58.858 45.455 0.00 0.00 0.00 3.24
3847 3979 3.565902 GCCTGCACTTGTTCTTTACTCTT 59.434 43.478 0.00 0.00 0.00 2.85
3848 3980 4.036852 GCCTGCACTTGTTCTTTACTCTTT 59.963 41.667 0.00 0.00 0.00 2.52
3849 3981 5.514279 CCTGCACTTGTTCTTTACTCTTTG 58.486 41.667 0.00 0.00 0.00 2.77
3850 3982 5.499139 TGCACTTGTTCTTTACTCTTTGG 57.501 39.130 0.00 0.00 0.00 3.28
3851 3983 4.947388 TGCACTTGTTCTTTACTCTTTGGT 59.053 37.500 0.00 0.00 0.00 3.67
3852 3984 5.417580 TGCACTTGTTCTTTACTCTTTGGTT 59.582 36.000 0.00 0.00 0.00 3.67
3853 3985 6.600032 TGCACTTGTTCTTTACTCTTTGGTTA 59.400 34.615 0.00 0.00 0.00 2.85
3854 3986 7.284489 TGCACTTGTTCTTTACTCTTTGGTTAT 59.716 33.333 0.00 0.00 0.00 1.89
3855 3987 8.135529 GCACTTGTTCTTTACTCTTTGGTTATT 58.864 33.333 0.00 0.00 0.00 1.40
3895 4028 1.337118 GGTTGTTTCATTGGGCTGGA 58.663 50.000 0.00 0.00 0.00 3.86
3987 4123 8.000780 ACAAGATCAAGATTATTACAAAGGGC 57.999 34.615 0.00 0.00 0.00 5.19
3991 4127 4.879545 TCAAGATTATTACAAAGGGCGGAC 59.120 41.667 0.00 0.00 0.00 4.79
4025 4165 8.696410 TTTTGTTCATGGTTCTGTTTTACTTC 57.304 30.769 0.00 0.00 0.00 3.01
4026 4166 7.639113 TTGTTCATGGTTCTGTTTTACTTCT 57.361 32.000 0.00 0.00 0.00 2.85
4027 4167 8.740123 TTGTTCATGGTTCTGTTTTACTTCTA 57.260 30.769 0.00 0.00 0.00 2.10
4029 4169 9.349713 TGTTCATGGTTCTGTTTTACTTCTATT 57.650 29.630 0.00 0.00 0.00 1.73
4106 4255 1.285950 CACACGGCAGAACGAGAGA 59.714 57.895 0.00 0.00 37.61 3.10
4107 4256 1.004277 CACACGGCAGAACGAGAGAC 61.004 60.000 0.00 0.00 37.61 3.36
4301 4456 3.710209 AGTGATTCTCCCTTTCACAGG 57.290 47.619 5.23 0.00 41.71 4.00
4321 4476 1.073722 CACTTTGCCTGCCTCCTCA 59.926 57.895 0.00 0.00 0.00 3.86
4342 4497 4.721776 TCAAGATGCAAGGGGAGTAGTTAT 59.278 41.667 0.00 0.00 0.00 1.89
4343 4498 5.191722 TCAAGATGCAAGGGGAGTAGTTATT 59.808 40.000 0.00 0.00 0.00 1.40
4344 4499 6.385759 TCAAGATGCAAGGGGAGTAGTTATTA 59.614 38.462 0.00 0.00 0.00 0.98
4345 4500 7.072454 TCAAGATGCAAGGGGAGTAGTTATTAT 59.928 37.037 0.00 0.00 0.00 1.28
4346 4501 6.773638 AGATGCAAGGGGAGTAGTTATTATG 58.226 40.000 0.00 0.00 0.00 1.90
4347 4502 5.304686 TGCAAGGGGAGTAGTTATTATGG 57.695 43.478 0.00 0.00 0.00 2.74
4348 4503 4.104102 TGCAAGGGGAGTAGTTATTATGGG 59.896 45.833 0.00 0.00 0.00 4.00
4349 4504 4.652822 CAAGGGGAGTAGTTATTATGGGC 58.347 47.826 0.00 0.00 0.00 5.36
4350 4505 2.904434 AGGGGAGTAGTTATTATGGGCG 59.096 50.000 0.00 0.00 0.00 6.13
4351 4506 2.901839 GGGGAGTAGTTATTATGGGCGA 59.098 50.000 0.00 0.00 0.00 5.54
4352 4507 3.518303 GGGGAGTAGTTATTATGGGCGAT 59.482 47.826 0.00 0.00 0.00 4.58
4353 4508 4.504858 GGGAGTAGTTATTATGGGCGATG 58.495 47.826 0.00 0.00 0.00 3.84
4354 4509 3.933332 GGAGTAGTTATTATGGGCGATGC 59.067 47.826 0.00 0.00 0.00 3.91
4355 4510 4.322801 GGAGTAGTTATTATGGGCGATGCT 60.323 45.833 0.00 0.00 0.00 3.79
4356 4511 5.105473 GGAGTAGTTATTATGGGCGATGCTA 60.105 44.000 0.00 0.00 0.00 3.49
4357 4512 5.967088 AGTAGTTATTATGGGCGATGCTAG 58.033 41.667 0.00 0.00 0.00 3.42
4358 4513 4.207891 AGTTATTATGGGCGATGCTAGG 57.792 45.455 0.00 0.00 0.00 3.02
4359 4514 2.678336 GTTATTATGGGCGATGCTAGGC 59.322 50.000 0.00 0.00 0.00 3.93
4360 4515 0.391661 ATTATGGGCGATGCTAGGCG 60.392 55.000 0.00 0.00 34.74 5.52
4361 4516 1.754380 TTATGGGCGATGCTAGGCGT 61.754 55.000 0.00 0.00 34.74 5.68
4362 4517 2.154798 TATGGGCGATGCTAGGCGTC 62.155 60.000 2.03 2.03 40.75 5.19
4363 4518 4.221422 GGGCGATGCTAGGCGTCA 62.221 66.667 11.47 0.00 43.95 4.35
4364 4519 2.202878 GGCGATGCTAGGCGTCAA 60.203 61.111 11.47 0.00 43.95 3.18
4365 4520 2.526120 GGCGATGCTAGGCGTCAAC 61.526 63.158 11.47 3.63 43.95 3.18
4366 4521 2.526120 GCGATGCTAGGCGTCAACC 61.526 63.158 11.47 0.00 43.95 3.77
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
38 39 1.393539 CAACTAAACCTGCCATCGTCG 59.606 52.381 0.00 0.00 0.00 5.12
41 42 2.811431 TCAACAACTAAACCTGCCATCG 59.189 45.455 0.00 0.00 0.00 3.84
46 47 3.253188 TGATGCTCAACAACTAAACCTGC 59.747 43.478 0.00 0.00 0.00 4.85
49 50 4.829064 TGTGATGCTCAACAACTAAACC 57.171 40.909 0.00 0.00 0.00 3.27
59 60 5.941647 TCTGAGATGAATTTGTGATGCTCAA 59.058 36.000 0.00 0.00 31.59 3.02
63 64 6.373186 TGATCTGAGATGAATTTGTGATGC 57.627 37.500 0.00 0.00 0.00 3.91
64 65 9.803315 AAAATGATCTGAGATGAATTTGTGATG 57.197 29.630 0.00 0.00 0.00 3.07
97 98 5.034852 AGTTTGCAAGCAGGGTAATTTTT 57.965 34.783 16.04 0.00 0.00 1.94
104 105 4.772100 ACATATTTAGTTTGCAAGCAGGGT 59.228 37.500 16.04 1.76 0.00 4.34
106 107 5.953183 TGACATATTTAGTTTGCAAGCAGG 58.047 37.500 16.04 0.00 0.00 4.85
109 110 6.197096 CGGAATGACATATTTAGTTTGCAAGC 59.803 38.462 4.95 4.95 0.00 4.01
113 114 4.670621 CGCGGAATGACATATTTAGTTTGC 59.329 41.667 0.00 0.00 0.00 3.68
124 125 1.896220 ATATTGGCGCGGAATGACAT 58.104 45.000 8.83 0.00 0.00 3.06
127 128 3.120321 ACTTATATTGGCGCGGAATGA 57.880 42.857 8.83 0.00 0.00 2.57
133 134 3.878086 ATGACAACTTATATTGGCGCG 57.122 42.857 0.00 0.00 40.83 6.86
134 135 6.954944 TCTTTATGACAACTTATATTGGCGC 58.045 36.000 0.00 0.00 40.83 6.53
150 152 8.937884 CATGCCAAATCAAACATTTCTTTATGA 58.062 29.630 0.00 0.00 0.00 2.15
155 157 4.456566 GGCATGCCAAATCAAACATTTCTT 59.543 37.500 32.08 0.00 35.81 2.52
157 159 4.004982 AGGCATGCCAAATCAAACATTTC 58.995 39.130 37.18 5.40 38.92 2.17
162 164 4.996758 ACTTTTAGGCATGCCAAATCAAAC 59.003 37.500 37.18 8.13 38.92 2.93
163 165 5.226194 ACTTTTAGGCATGCCAAATCAAA 57.774 34.783 37.18 23.73 38.92 2.69
164 166 4.322650 GGACTTTTAGGCATGCCAAATCAA 60.323 41.667 37.18 20.19 38.92 2.57
165 167 3.195396 GGACTTTTAGGCATGCCAAATCA 59.805 43.478 37.18 18.77 38.92 2.57
174 176 4.922206 TCTGATGTTGGACTTTTAGGCAT 58.078 39.130 0.00 0.00 0.00 4.40
187 189 8.231304 ACGAAAATGCTAAAAATCTGATGTTG 57.769 30.769 0.00 0.00 0.00 3.33
188 190 9.906660 TTACGAAAATGCTAAAAATCTGATGTT 57.093 25.926 0.00 0.00 0.00 2.71
215 217 9.563748 CTCCCATATGCCATTTTCATTAAAAAT 57.436 29.630 0.00 0.00 46.23 1.82
287 296 1.742831 GGATGCTGCGTGGTTAATTCA 59.257 47.619 0.00 0.00 0.00 2.57
309 318 0.681887 TTCGGGTGTAGGCTCGATCA 60.682 55.000 0.00 0.00 0.00 2.92
325 334 5.848207 CAATAATTGGTTGCATACGTTCG 57.152 39.130 0.00 0.00 0.00 3.95
419 429 4.313282 AGCGATCATCCATCACTAATGTG 58.687 43.478 0.00 0.00 45.07 3.21
431 441 1.695813 CGAGTGATGAGCGATCATCC 58.304 55.000 33.79 25.63 43.20 3.51
536 549 2.438254 TCCGCATGCCAAATCGCT 60.438 55.556 13.15 0.00 0.00 4.93
539 552 0.659957 GTCTCTCCGCATGCCAAATC 59.340 55.000 13.15 0.00 0.00 2.17
540 553 1.091771 CGTCTCTCCGCATGCCAAAT 61.092 55.000 13.15 0.00 0.00 2.32
541 554 1.741401 CGTCTCTCCGCATGCCAAA 60.741 57.895 13.15 0.00 0.00 3.28
542 555 2.125552 CGTCTCTCCGCATGCCAA 60.126 61.111 13.15 0.00 0.00 4.52
543 556 2.166130 TTTCGTCTCTCCGCATGCCA 62.166 55.000 13.15 0.00 0.00 4.92
544 557 1.447838 TTTCGTCTCTCCGCATGCC 60.448 57.895 13.15 0.00 0.00 4.40
545 558 1.696832 GGTTTCGTCTCTCCGCATGC 61.697 60.000 7.91 7.91 0.00 4.06
665 697 0.318107 CGGCTTGTTTGCTTCCTGTG 60.318 55.000 0.00 0.00 0.00 3.66
700 732 0.615261 ATGGTGCATGTGGGCATTGA 60.615 50.000 0.00 0.00 46.92 2.57
737 807 4.211125 TGGCTAAGTGTGAACCAAAATGA 58.789 39.130 0.00 0.00 0.00 2.57
745 815 6.258947 GGAGAAGATAATGGCTAAGTGTGAAC 59.741 42.308 0.00 0.00 0.00 3.18
780 850 3.118186 TGGTCTAGACTCTAGAGTGCCTC 60.118 52.174 29.84 15.00 42.66 4.70
783 853 3.625764 CACTGGTCTAGACTCTAGAGTGC 59.374 52.174 29.84 19.44 42.66 4.40
792 862 1.562783 GGAAGCCACTGGTCTAGACT 58.437 55.000 21.88 0.00 0.00 3.24
793 863 0.537653 GGGAAGCCACTGGTCTAGAC 59.462 60.000 14.87 14.87 0.00 2.59
794 864 0.116342 TGGGAAGCCACTGGTCTAGA 59.884 55.000 0.00 0.00 0.00 2.43
795 865 0.984230 TTGGGAAGCCACTGGTCTAG 59.016 55.000 0.00 0.00 0.00 2.43
796 866 1.351017 CTTTGGGAAGCCACTGGTCTA 59.649 52.381 0.00 0.00 0.00 2.59
811 881 3.947834 CCAACTATTCCCACTAGCTTTGG 59.052 47.826 7.02 7.02 0.00 3.28
819 889 1.065126 GCTCTGCCAACTATTCCCACT 60.065 52.381 0.00 0.00 0.00 4.00
885 958 0.739112 GCTCTGTCAGCCACACTAGC 60.739 60.000 0.00 0.00 43.17 3.42
960 1034 2.050350 CGGTGGAGCGGAGTAGGAA 61.050 63.158 0.00 0.00 0.00 3.36
1550 1639 1.596895 GGCCTCGATATCCTCCGTCC 61.597 65.000 0.00 0.00 0.00 4.79
2213 2302 0.606401 CTCATCCGGGCTGTTGTTGT 60.606 55.000 0.00 0.00 0.00 3.32
3330 3440 1.525077 GTCAAACTGGTCCGTGCCA 60.525 57.895 0.00 0.00 36.97 4.92
3410 3532 3.032609 GCGGATCCAGACATCGCG 61.033 66.667 13.41 0.00 37.12 5.87
3478 3604 1.169661 TGTGTGTTCCAATGGCGACC 61.170 55.000 0.00 0.00 0.00 4.79
3498 3624 2.069273 CATTGCTTTCCGTCTCGACTT 58.931 47.619 0.00 0.00 0.00 3.01
3654 3781 3.713288 CTGTGGAGTTGTTAACGAGTGA 58.287 45.455 7.97 0.00 36.23 3.41
3737 3868 1.079819 ATGGTGCCGTGTCTTCTCG 60.080 57.895 0.00 0.00 0.00 4.04
3857 3989 7.654022 ACAACCAAAGAGAAGTATCCAAAAA 57.346 32.000 0.00 0.00 0.00 1.94
3858 3990 7.654022 AACAACCAAAGAGAAGTATCCAAAA 57.346 32.000 0.00 0.00 0.00 2.44
3859 3991 7.340743 TGAAACAACCAAAGAGAAGTATCCAAA 59.659 33.333 0.00 0.00 0.00 3.28
3860 3992 6.831353 TGAAACAACCAAAGAGAAGTATCCAA 59.169 34.615 0.00 0.00 0.00 3.53
3861 3993 6.361433 TGAAACAACCAAAGAGAAGTATCCA 58.639 36.000 0.00 0.00 0.00 3.41
3862 3994 6.877611 TGAAACAACCAAAGAGAAGTATCC 57.122 37.500 0.00 0.00 0.00 2.59
3863 3995 7.809806 CCAATGAAACAACCAAAGAGAAGTATC 59.190 37.037 0.00 0.00 0.00 2.24
3864 3996 7.255942 CCCAATGAAACAACCAAAGAGAAGTAT 60.256 37.037 0.00 0.00 0.00 2.12
3865 3997 6.040391 CCCAATGAAACAACCAAAGAGAAGTA 59.960 38.462 0.00 0.00 0.00 2.24
3866 3998 5.163416 CCCAATGAAACAACCAAAGAGAAGT 60.163 40.000 0.00 0.00 0.00 3.01
3867 3999 5.291971 CCCAATGAAACAACCAAAGAGAAG 58.708 41.667 0.00 0.00 0.00 2.85
3868 4000 4.442753 GCCCAATGAAACAACCAAAGAGAA 60.443 41.667 0.00 0.00 0.00 2.87
3869 4001 3.069443 GCCCAATGAAACAACCAAAGAGA 59.931 43.478 0.00 0.00 0.00 3.10
3932 4065 4.310022 ACACAATTATCCCCGGAAAGAA 57.690 40.909 0.73 0.00 0.00 2.52
3934 4067 6.765403 TCTATACACAATTATCCCCGGAAAG 58.235 40.000 0.73 0.00 0.00 2.62
3936 4069 6.945636 ATCTATACACAATTATCCCCGGAA 57.054 37.500 0.73 0.00 0.00 4.30
3937 4070 9.139734 GTATATCTATACACAATTATCCCCGGA 57.860 37.037 0.73 0.00 38.66 5.14
3938 4071 8.920174 TGTATATCTATACACAATTATCCCCGG 58.080 37.037 6.05 0.00 42.47 5.73
4035 4175 9.952030 TGAGATATTTATATCCCGTTGCAATTA 57.048 29.630 0.59 0.00 39.94 1.40
4036 4176 8.862325 TGAGATATTTATATCCCGTTGCAATT 57.138 30.769 0.59 0.00 39.94 2.32
4037 4177 8.862325 TTGAGATATTTATATCCCGTTGCAAT 57.138 30.769 0.59 0.00 39.94 3.56
4073 4222 2.719046 CCGTGTGCGAAACTTCAAAATC 59.281 45.455 0.00 0.00 41.33 2.17
4106 4255 0.392998 GGCATCAGACATGTTCCCGT 60.393 55.000 0.00 0.00 0.00 5.28
4107 4256 1.431488 CGGCATCAGACATGTTCCCG 61.431 60.000 0.00 2.78 0.00 5.14
4240 4394 5.294552 GCGAAGATAGCACTACCAAGAAAAT 59.705 40.000 0.00 0.00 34.19 1.82
4301 4456 0.957888 GAGGAGGCAGGCAAAGTGAC 60.958 60.000 0.00 0.00 0.00 3.67
4321 4476 5.717119 AATAACTACTCCCCTTGCATCTT 57.283 39.130 0.00 0.00 0.00 2.40
4342 4497 1.005037 CGCCTAGCATCGCCCATAA 60.005 57.895 0.00 0.00 0.00 1.90
4343 4498 2.154798 GACGCCTAGCATCGCCCATA 62.155 60.000 0.00 0.00 0.00 2.74
4344 4499 3.521529 GACGCCTAGCATCGCCCAT 62.522 63.158 0.00 0.00 0.00 4.00
4345 4500 4.221422 GACGCCTAGCATCGCCCA 62.221 66.667 0.00 0.00 0.00 5.36
4346 4501 3.733344 TTGACGCCTAGCATCGCCC 62.733 63.158 0.00 0.00 0.00 6.13
4347 4502 2.202878 TTGACGCCTAGCATCGCC 60.203 61.111 0.00 0.00 0.00 5.54
4348 4503 2.526120 GGTTGACGCCTAGCATCGC 61.526 63.158 0.00 0.00 0.00 4.58
4349 4504 3.706140 GGTTGACGCCTAGCATCG 58.294 61.111 0.00 0.00 0.00 3.84


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

AutoCloner maintained by Alex Coulton.