Multiple sequence alignment - TraesCS6A01G273100

Loading Multiple Alignment...

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 TraesCS6A01G273100 chr6A 100.000 5142 0 0 1 5142 499595019 499589878 0.000000e+00 9496.0
1 TraesCS6A01G273100 chr6D 96.273 4588 144 15 569 5142 357349177 357344603 0.000000e+00 7500.0
2 TraesCS6A01G273100 chr6D 87.943 564 37 14 1 552 357349778 357349234 2.020000e-178 636.0
3 TraesCS6A01G273100 chr6D 85.448 268 35 4 4598 4862 78794105 78793839 5.070000e-70 276.0
4 TraesCS6A01G273100 chr6B 95.310 4392 153 28 81 4452 538951658 538947300 0.000000e+00 6920.0
5 TraesCS6A01G273100 chr6B 94.891 137 7 0 4443 4579 538946871 538946735 1.120000e-51 215.0
6 TraesCS6A01G273100 chr2D 83.784 481 67 7 4641 5111 633268171 633268650 3.650000e-121 446.0
7 TraesCS6A01G273100 chr2D 81.042 480 61 13 4641 5111 633246320 633246778 6.330000e-94 355.0
8 TraesCS6A01G273100 chr2D 81.092 476 58 13 4641 5085 633299395 633298921 8.190000e-93 351.0
9 TraesCS6A01G273100 chr7A 100.000 29 0 0 5047 5075 538249387 538249415 3.000000e-03 54.7


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 TraesCS6A01G273100 chr6A 499589878 499595019 5141 True 9496.0 9496 100.0000 1 5142 1 chr6A.!!$R1 5141
1 TraesCS6A01G273100 chr6D 357344603 357349778 5175 True 4068.0 7500 92.1080 1 5142 2 chr6D.!!$R2 5141
2 TraesCS6A01G273100 chr6B 538946735 538951658 4923 True 3567.5 6920 95.1005 81 4579 2 chr6B.!!$R1 4498

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
327 337 0.034477 AATTGTGTAAGGCGGAGGGG 60.034 55.0 0.0 0.0 0.00 4.79 F
526 538 1.067295 TTGGGCTAGGGCATATCCTG 58.933 55.0 0.0 0.0 40.87 3.86 F
1171 1225 0.532115 GCGGGGAAATCATGCTGTTT 59.468 50.0 0.0 0.0 0.00 2.83 F
2033 2088 2.093288 TGCTGAGGTCCACAATGATCTC 60.093 50.0 0.0 0.0 41.89 2.75 F
2840 2895 0.033920 ACAGCAGTTCATCTGTCGCA 59.966 50.0 0.0 0.0 45.23 5.10 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1147 1201 1.076024 AGCATGATTTCCCCGCCATAT 59.924 47.619 0.00 0.0 0.00 1.78 R
1631 1685 1.616865 CTCTGACCCTTTCACACCGTA 59.383 52.381 0.00 0.0 0.00 4.02 R
2786 2841 0.396139 TCCTGCCATTCCCAGCAATC 60.396 55.000 0.00 0.0 38.82 2.67 R
3964 4019 1.022982 TGAGCTCGCTTTGCCTCATG 61.023 55.000 9.64 0.0 0.00 3.07 R
4370 4429 0.813184 GCCACACAAGACATGGATGG 59.187 55.000 0.00 0.0 39.80 3.51 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 1.032014 TCCACTGCTTTCCACTTTGC 58.968 50.000 0.00 0.00 0.00 3.68
22 23 0.318107 CCACTGCTTTCCACTTTGCG 60.318 55.000 0.00 0.00 0.00 4.85
32 33 1.226379 CACTTTGCGCTAATGGCCG 60.226 57.895 9.73 0.00 37.74 6.13
42 43 2.624674 CTAATGGCCGGGGAGGTTGG 62.625 65.000 2.18 0.00 43.70 3.77
64 65 3.803082 CGTGCCTCATGCGGGTTG 61.803 66.667 3.43 0.00 45.60 3.77
66 67 4.738998 TGCCTCATGCGGGTTGGG 62.739 66.667 3.43 0.00 45.60 4.12
68 69 2.438434 CCTCATGCGGGTTGGGTC 60.438 66.667 0.00 0.00 0.00 4.46
73 74 0.250295 CATGCGGGTTGGGTCGATAT 60.250 55.000 0.00 0.00 0.00 1.63
75 76 0.462937 TGCGGGTTGGGTCGATATTG 60.463 55.000 0.00 0.00 0.00 1.90
76 77 0.179067 GCGGGTTGGGTCGATATTGA 60.179 55.000 0.00 0.00 0.00 2.57
77 78 1.542547 GCGGGTTGGGTCGATATTGAT 60.543 52.381 0.00 0.00 0.00 2.57
78 79 2.289195 GCGGGTTGGGTCGATATTGATA 60.289 50.000 0.00 0.00 0.00 2.15
79 80 3.323243 CGGGTTGGGTCGATATTGATAC 58.677 50.000 0.00 0.00 0.00 2.24
80 81 3.006537 CGGGTTGGGTCGATATTGATACT 59.993 47.826 0.00 0.00 0.00 2.12
81 82 4.502604 CGGGTTGGGTCGATATTGATACTT 60.503 45.833 0.00 0.00 0.00 2.24
82 83 4.755123 GGGTTGGGTCGATATTGATACTTG 59.245 45.833 0.00 0.00 0.00 3.16
83 84 5.454187 GGGTTGGGTCGATATTGATACTTGA 60.454 44.000 0.00 0.00 0.00 3.02
84 85 6.231211 GGTTGGGTCGATATTGATACTTGAT 58.769 40.000 0.00 0.00 0.00 2.57
85 86 7.383687 GGTTGGGTCGATATTGATACTTGATA 58.616 38.462 0.00 0.00 0.00 2.15
86 87 7.331193 GGTTGGGTCGATATTGATACTTGATAC 59.669 40.741 0.00 0.00 0.00 2.24
87 88 7.776618 TGGGTCGATATTGATACTTGATACT 57.223 36.000 0.00 0.00 0.00 2.12
88 89 8.873186 TGGGTCGATATTGATACTTGATACTA 57.127 34.615 0.00 0.00 0.00 1.82
89 90 8.957466 TGGGTCGATATTGATACTTGATACTAG 58.043 37.037 0.00 0.00 0.00 2.57
145 146 3.056536 GCAAAACTCCATTCTCCTTTCCC 60.057 47.826 0.00 0.00 0.00 3.97
147 148 2.059756 ACTCCATTCTCCTTTCCCCA 57.940 50.000 0.00 0.00 0.00 4.96
148 149 2.577970 ACTCCATTCTCCTTTCCCCAT 58.422 47.619 0.00 0.00 0.00 4.00
150 151 3.053320 ACTCCATTCTCCTTTCCCCATTC 60.053 47.826 0.00 0.00 0.00 2.67
151 152 3.201363 TCCATTCTCCTTTCCCCATTCT 58.799 45.455 0.00 0.00 0.00 2.40
152 153 3.597868 TCCATTCTCCTTTCCCCATTCTT 59.402 43.478 0.00 0.00 0.00 2.52
153 154 3.703052 CCATTCTCCTTTCCCCATTCTTG 59.297 47.826 0.00 0.00 0.00 3.02
154 155 2.514458 TCTCCTTTCCCCATTCTTGC 57.486 50.000 0.00 0.00 0.00 4.01
155 156 1.098050 CTCCTTTCCCCATTCTTGCG 58.902 55.000 0.00 0.00 0.00 4.85
158 159 1.228706 TTTCCCCATTCTTGCGGCA 60.229 52.632 0.00 0.00 0.00 5.69
159 160 0.829602 TTTCCCCATTCTTGCGGCAA 60.830 50.000 15.55 15.55 0.00 4.52
160 161 1.250154 TTCCCCATTCTTGCGGCAAG 61.250 55.000 31.64 31.64 42.25 4.01
176 186 1.788886 GCAAGCTTTAGCAGTTGCAAC 59.211 47.619 22.17 22.17 45.63 4.17
199 209 7.545362 ACAAGTATGTTTGCTTAGCTGATAG 57.455 36.000 5.60 0.00 35.91 2.08
200 210 7.331026 ACAAGTATGTTTGCTTAGCTGATAGA 58.669 34.615 5.60 0.00 35.91 1.98
201 211 7.989741 ACAAGTATGTTTGCTTAGCTGATAGAT 59.010 33.333 5.60 0.00 35.91 1.98
202 212 9.481340 CAAGTATGTTTGCTTAGCTGATAGATA 57.519 33.333 5.60 0.00 0.00 1.98
233 243 1.732941 TTGTCATGTACGCACCCATC 58.267 50.000 0.00 0.00 0.00 3.51
262 272 7.175641 CACCCTTTGAAATTCAGACTATGTCTT 59.824 37.037 0.00 0.00 41.37 3.01
267 277 9.734620 TTTGAAATTCAGACTATGTCTTGTTTG 57.265 29.630 0.00 0.00 41.37 2.93
285 295 8.730680 TCTTGTTTGTTTATTCCTGCTCTTATC 58.269 33.333 0.00 0.00 0.00 1.75
314 324 8.277713 GTGATTTGATTTCTTCAACCAATTGTG 58.722 33.333 4.43 0.00 43.99 3.33
327 337 0.034477 AATTGTGTAAGGCGGAGGGG 60.034 55.000 0.00 0.00 0.00 4.79
348 358 1.822990 TGAAACGGTCTACTGGCCTAG 59.177 52.381 3.32 2.01 0.00 3.02
357 367 4.162509 GGTCTACTGGCCTAGAATCAACTT 59.837 45.833 3.32 0.00 0.00 2.66
363 373 2.678336 GGCCTAGAATCAACTTGGTTCG 59.322 50.000 8.78 0.00 42.12 3.95
377 387 9.672086 TCAACTTGGTTCGTTCTTATTTTATTG 57.328 29.630 0.00 0.00 0.00 1.90
391 401 9.421806 TCTTATTTTATTGCATGGTTGTTGAAG 57.578 29.630 0.00 0.00 0.00 3.02
444 454 6.549364 TCTGTTGACTTTCAATAATGGTGGTT 59.451 34.615 0.00 0.00 38.79 3.67
526 538 1.067295 TTGGGCTAGGGCATATCCTG 58.933 55.000 0.00 0.00 40.87 3.86
553 565 6.163476 TGTTACTGATGACATGTCTTGGTAC 58.837 40.000 25.55 14.67 0.00 3.34
559 571 3.181329 TGACATGTCTTGGTACCCTGAT 58.819 45.455 25.55 0.00 0.00 2.90
562 574 3.055094 ACATGTCTTGGTACCCTGATGAC 60.055 47.826 10.07 9.31 0.00 3.06
610 662 6.349280 GCTTTGATAGTTTTGACCATAGCACA 60.349 38.462 0.00 0.00 33.88 4.57
613 665 1.535462 AGTTTTGACCATAGCACACGC 59.465 47.619 0.00 0.00 38.99 5.34
618 670 2.268920 CCATAGCACACGCACCCT 59.731 61.111 0.00 0.00 42.27 4.34
737 789 4.895668 ATGCATGGTGAAAAATGTTCCT 57.104 36.364 0.00 0.00 0.00 3.36
769 821 6.126863 ACAATCCACCACCATACCATATAG 57.873 41.667 0.00 0.00 0.00 1.31
783 835 7.825761 CCATACCATATAGATTTGACATCTGCA 59.174 37.037 0.00 0.00 0.00 4.41
809 861 5.995282 TGACTGGACTATTGTTTCGTTTGAT 59.005 36.000 0.00 0.00 0.00 2.57
1088 1142 7.440856 TCCATTTTTGCAACCATTCTACTTTTC 59.559 33.333 0.00 0.00 0.00 2.29
1147 1201 1.945819 GCAAGATGAAACCCTCTCGCA 60.946 52.381 0.00 0.00 0.00 5.10
1169 1223 1.754234 GGCGGGGAAATCATGCTGT 60.754 57.895 0.00 0.00 0.00 4.40
1170 1224 1.322538 GGCGGGGAAATCATGCTGTT 61.323 55.000 0.00 0.00 0.00 3.16
1171 1225 0.532115 GCGGGGAAATCATGCTGTTT 59.468 50.000 0.00 0.00 0.00 2.83
1203 1257 4.160439 GTCATAGAAGTCATGTGAGGGTGA 59.840 45.833 0.00 0.00 0.00 4.02
1215 1269 3.820467 TGTGAGGGTGACATTCATTGTTC 59.180 43.478 0.00 0.00 39.18 3.18
1244 1298 7.544566 TCAGTTTCATCTTCGTGTACCTAAATC 59.455 37.037 0.00 0.00 0.00 2.17
1250 1304 5.950883 TCTTCGTGTACCTAAATCTCTGTG 58.049 41.667 0.00 0.00 0.00 3.66
1631 1685 6.238759 GCAATTACTGGAGAGGCGATTTTATT 60.239 38.462 0.00 0.00 0.00 1.40
1935 1990 7.665559 TCCCTATTGGTATTGCTTATCACAATC 59.334 37.037 0.00 0.00 38.62 2.67
1965 2020 5.291371 CACTCTTATGACAGCATCTTCACTG 59.709 44.000 0.00 0.00 39.86 3.66
2033 2088 2.093288 TGCTGAGGTCCACAATGATCTC 60.093 50.000 0.00 0.00 41.89 2.75
2348 2403 8.375465 CGGAATGAAAATTTACAATCTGAAAGC 58.625 33.333 0.00 0.00 0.00 3.51
2543 2598 9.988815 GTGATAATAACATCTGGACAGACTTAT 57.011 33.333 3.82 6.28 40.75 1.73
2633 2688 5.163713 GCTAGAAAACTTTGCGATGATTCCT 60.164 40.000 0.00 0.00 0.00 3.36
2699 2754 5.803967 GCATGGTTTCACAATCTCAGATTTC 59.196 40.000 0.00 0.00 0.00 2.17
2774 2829 5.761003 TCTATGTCAAGTTTGCACAATGTG 58.239 37.500 9.36 9.36 36.51 3.21
2786 2841 1.534163 CACAATGTGTCAGTGCCTCTG 59.466 52.381 5.00 0.33 44.85 3.35
2800 2855 1.688772 CCTCTGATTGCTGGGAATGG 58.311 55.000 0.00 0.00 0.00 3.16
2840 2895 0.033920 ACAGCAGTTCATCTGTCGCA 59.966 50.000 0.00 0.00 45.23 5.10
3321 3376 3.402628 AGTTTTGTGCGTATCTCAGGT 57.597 42.857 0.00 0.00 0.00 4.00
3324 3379 3.678056 TTTGTGCGTATCTCAGGTCTT 57.322 42.857 0.00 0.00 0.00 3.01
3419 3474 2.539142 CGTCTTATCACGTCCTTCCTCG 60.539 54.545 0.00 0.00 34.95 4.63
3520 3575 1.342074 CCTCTGTTGTCACTCCTCCA 58.658 55.000 0.00 0.00 0.00 3.86
3529 3584 0.110486 TCACTCCTCCAGTTTTGGCC 59.890 55.000 0.00 0.00 44.63 5.36
3856 3911 1.515954 CCGTAGCGTGGAGGATTGT 59.484 57.895 0.00 0.00 0.00 2.71
3964 4019 3.704061 AGCTACTGAATCTTCTGAGGGAC 59.296 47.826 4.12 0.00 0.00 4.46
3991 4046 1.069636 CAAAGCGAGCTCAACAACTCC 60.070 52.381 15.40 0.00 0.00 3.85
4160 4215 2.582978 GACCGAGGTTGTAGGCCC 59.417 66.667 0.00 0.00 0.00 5.80
4340 4399 6.536224 TCTTGCTGATTGTAGATGTGTGTATG 59.464 38.462 0.00 0.00 0.00 2.39
4370 4429 8.035984 AGTAAAGAAAGACAGCTGGTATAGTTC 58.964 37.037 19.93 11.81 0.00 3.01
4445 4504 2.376808 CTGTTCCACAGTAGCTGGAG 57.623 55.000 0.00 0.00 41.19 3.86
4587 5084 9.396022 TCTAAATGGAACTTTATCATTGACTCC 57.604 33.333 0.00 0.00 32.24 3.85
4588 5085 9.177608 CTAAATGGAACTTTATCATTGACTCCA 57.822 33.333 0.00 0.00 36.23 3.86
4593 5090 7.090808 GGAACTTTATCATTGACTCCAAAACC 58.909 38.462 0.00 0.00 35.67 3.27
4597 5094 7.451255 ACTTTATCATTGACTCCAAAACCATCA 59.549 33.333 0.00 0.00 35.67 3.07
4689 5186 2.725008 CATCTCCCTCGTCGCCTC 59.275 66.667 0.00 0.00 0.00 4.70
4758 5255 2.420722 CGAGGATCTACCCTATTCGCTC 59.579 54.545 0.00 0.00 40.05 5.03
4762 5259 3.422796 GATCTACCCTATTCGCTCCTGA 58.577 50.000 0.00 0.00 0.00 3.86
4769 5266 2.546795 CCTATTCGCTCCTGATGGTGAC 60.547 54.545 0.00 0.00 34.23 3.67
4789 5287 1.735376 GATAGGTCGGCTTCGAGGCA 61.735 60.000 21.86 0.00 44.17 4.75
4809 5307 2.893398 GGCTTCGACGATGAGGGT 59.107 61.111 14.34 0.00 0.00 4.34
4811 5309 1.511305 GCTTCGACGATGAGGGTGA 59.489 57.895 14.34 0.00 0.00 4.02
4875 5374 2.678934 CCTTGCAGCATGGGCAGT 60.679 61.111 17.99 0.00 43.05 4.40
4901 5400 1.908793 CAGAGGAGGTGGTCACGGT 60.909 63.158 0.00 0.00 0.00 4.83
4907 5406 3.552384 GGTGGTCACGGTGTGGGA 61.552 66.667 8.17 0.00 33.87 4.37
4908 5407 2.747686 GTGGTCACGGTGTGGGAT 59.252 61.111 8.17 0.00 33.87 3.85
4909 5408 1.546589 GGTGGTCACGGTGTGGGATA 61.547 60.000 8.17 0.00 33.87 2.59
4910 5409 0.390735 GTGGTCACGGTGTGGGATAC 60.391 60.000 8.17 0.00 33.87 2.24
4989 5488 4.547367 GGCTGGTTCGATCCCCCG 62.547 72.222 10.02 0.38 0.00 5.73
5009 5508 1.139853 GCGAGTTCCTCTTCATGGGAT 59.860 52.381 0.00 0.00 0.00 3.85
5012 5511 3.891977 CGAGTTCCTCTTCATGGGATCTA 59.108 47.826 0.00 0.00 33.38 1.98
5041 5540 1.385347 TGGTGGGAGTTGGACTGGT 60.385 57.895 0.00 0.00 0.00 4.00
5051 5555 0.768622 TTGGACTGGTTGTACAGGGG 59.231 55.000 0.00 0.00 41.17 4.79
5093 5597 4.681421 CACGACATCTGTGGTGCT 57.319 55.556 11.65 0.00 45.12 4.40
5094 5598 2.156542 CACGACATCTGTGGTGCTG 58.843 57.895 11.65 0.00 45.12 4.41
5116 5620 3.550431 CGCCGGATCCCCAGTGAT 61.550 66.667 5.05 0.00 0.00 3.06
5124 5628 1.351080 ATCCCCAGTGATGGAGCCAG 61.351 60.000 7.34 0.00 33.27 4.85
5138 5642 6.772716 TGATGGAGCCAGGAATTAAAGATTAC 59.227 38.462 0.00 0.00 0.00 1.89
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
21 22 4.626081 CCTCCCCGGCCATTAGCG 62.626 72.222 2.24 0.00 45.17 4.26
22 23 3.056754 AACCTCCCCGGCCATTAGC 62.057 63.158 2.24 0.00 42.60 3.09
37 38 4.717313 GAGGCACGGACCCCAACC 62.717 72.222 0.00 0.00 0.00 3.77
47 48 3.803082 CAACCCGCATGAGGCACG 61.803 66.667 10.45 0.00 45.17 5.34
48 49 3.443045 CCAACCCGCATGAGGCAC 61.443 66.667 10.45 0.00 45.17 5.01
64 65 8.958506 ACTAGTATCAAGTATCAATATCGACCC 58.041 37.037 0.00 0.00 0.00 4.46
87 88 9.470399 TTGATCAGTTGGTCTAGTATTGTACTA 57.530 33.333 0.00 0.00 40.14 1.82
88 89 7.956328 TGATCAGTTGGTCTAGTATTGTACT 57.044 36.000 0.00 0.00 42.68 2.73
89 90 9.035607 CATTGATCAGTTGGTCTAGTATTGTAC 57.964 37.037 0.00 0.00 0.00 2.90
145 146 0.037975 AAAGCTTGCCGCAAGAATGG 60.038 50.000 32.61 10.74 43.42 3.16
147 148 1.135286 GCTAAAGCTTGCCGCAAGAAT 60.135 47.619 32.61 18.93 43.42 2.40
148 149 0.240945 GCTAAAGCTTGCCGCAAGAA 59.759 50.000 32.61 15.17 43.42 2.52
150 151 0.455633 CTGCTAAAGCTTGCCGCAAG 60.456 55.000 25.91 25.91 43.57 4.01
151 152 1.172180 ACTGCTAAAGCTTGCCGCAA 61.172 50.000 15.52 5.52 42.61 4.85
152 153 1.172180 AACTGCTAAAGCTTGCCGCA 61.172 50.000 14.40 14.40 42.61 5.69
153 154 0.730494 CAACTGCTAAAGCTTGCCGC 60.730 55.000 0.00 3.69 42.66 6.53
154 155 0.730494 GCAACTGCTAAAGCTTGCCG 60.730 55.000 14.67 0.00 42.66 5.69
155 156 0.314935 TGCAACTGCTAAAGCTTGCC 59.685 50.000 19.95 8.16 39.84 4.52
158 159 3.131046 ACTTGTTGCAACTGCTAAAGCTT 59.869 39.130 28.61 7.38 42.66 3.74
159 160 2.689983 ACTTGTTGCAACTGCTAAAGCT 59.310 40.909 28.61 11.82 42.66 3.74
160 161 3.084070 ACTTGTTGCAACTGCTAAAGC 57.916 42.857 28.61 0.95 42.66 3.51
161 162 5.762045 ACATACTTGTTGCAACTGCTAAAG 58.238 37.500 28.61 23.50 42.66 1.85
176 186 7.776933 TCTATCAGCTAAGCAAACATACTTG 57.223 36.000 0.00 0.00 0.00 3.16
199 209 5.408356 ACATGACAAACTACCAGTCGTATC 58.592 41.667 0.00 0.00 35.09 2.24
200 210 5.401531 ACATGACAAACTACCAGTCGTAT 57.598 39.130 0.00 0.00 35.09 3.06
201 211 4.859304 ACATGACAAACTACCAGTCGTA 57.141 40.909 0.00 0.00 35.09 3.43
202 212 3.746045 ACATGACAAACTACCAGTCGT 57.254 42.857 0.00 0.00 35.09 4.34
233 243 1.885887 TCTGAATTTCAAAGGGTGCCG 59.114 47.619 0.01 0.00 0.00 5.69
262 272 6.377146 GGGATAAGAGCAGGAATAAACAAACA 59.623 38.462 0.00 0.00 0.00 2.83
267 277 4.511826 CACGGGATAAGAGCAGGAATAAAC 59.488 45.833 0.00 0.00 0.00 2.01
314 324 0.675837 GTTTCACCCCTCCGCCTTAC 60.676 60.000 0.00 0.00 0.00 2.34
327 337 0.320697 AGGCCAGTAGACCGTTTCAC 59.679 55.000 5.01 0.00 0.00 3.18
348 358 8.797266 AAAATAAGAACGAACCAAGTTGATTC 57.203 30.769 3.87 1.37 31.14 2.52
357 367 7.032580 CCATGCAATAAAATAAGAACGAACCA 58.967 34.615 0.00 0.00 0.00 3.67
363 373 9.202273 TCAACAACCATGCAATAAAATAAGAAC 57.798 29.630 0.00 0.00 0.00 3.01
444 454 3.215151 TGGTCAAAATACGGCTTGAACA 58.785 40.909 0.51 0.51 44.83 3.18
490 501 2.529744 AACTCCCAGTGTCCCAGCC 61.530 63.158 0.00 0.00 0.00 4.85
526 538 5.349817 CCAAGACATGTCATCAGTAACAGAC 59.650 44.000 27.02 0.00 0.00 3.51
553 565 1.012086 CACTTCGCATGTCATCAGGG 58.988 55.000 0.00 0.00 0.00 4.45
559 571 1.338674 CCCCTTACACTTCGCATGTCA 60.339 52.381 0.00 0.00 0.00 3.58
562 574 1.066143 ACTCCCCTTACACTTCGCATG 60.066 52.381 0.00 0.00 0.00 4.06
613 665 5.593909 TCCATTTTCATAACTATGCAGGGTG 59.406 40.000 0.00 0.00 33.76 4.61
618 670 9.219603 GTAGCTATCCATTTTCATAACTATGCA 57.780 33.333 0.00 0.00 33.76 3.96
716 768 4.895668 AGGAACATTTTTCACCATGCAT 57.104 36.364 0.00 0.00 0.00 3.96
737 789 2.036992 GGTGGTGGATTGTTGCATCAAA 59.963 45.455 13.88 0.00 35.93 2.69
769 821 4.397103 TCCAGTCAATGCAGATGTCAAATC 59.603 41.667 0.00 0.00 0.00 2.17
783 835 6.485313 TCAAACGAAACAATAGTCCAGTCAAT 59.515 34.615 0.00 0.00 0.00 2.57
809 861 7.121907 TGTGATGTATGCAATTTACCAAAGCTA 59.878 33.333 0.00 0.00 0.00 3.32
883 936 6.375945 TGGAAATTCAACCATATCATGACG 57.624 37.500 0.00 0.00 0.00 4.35
1088 1142 0.834612 AAATGCCCCATGCCTGAATG 59.165 50.000 0.00 0.00 40.16 2.67
1147 1201 1.076024 AGCATGATTTCCCCGCCATAT 59.924 47.619 0.00 0.00 0.00 1.78
1203 1257 8.636213 AGATGAAACTGAAAGAACAATGAATGT 58.364 29.630 0.00 0.00 40.56 2.71
1215 1269 5.696724 AGGTACACGAAGATGAAACTGAAAG 59.303 40.000 0.00 0.00 42.29 2.62
1539 1593 5.304101 AGCACCAAATAATCACAACAAAGGA 59.696 36.000 0.00 0.00 0.00 3.36
1631 1685 1.616865 CTCTGACCCTTTCACACCGTA 59.383 52.381 0.00 0.00 0.00 4.02
1790 1844 3.776969 TGATAAGCAACACTGAGAGGGAT 59.223 43.478 0.00 0.00 0.00 3.85
1935 1990 2.093816 TGCTGTCATAAGAGTGCCTGAG 60.094 50.000 0.00 0.00 0.00 3.35
2033 2088 7.698130 GGATCAACAGAAAATTTTACATCTCGG 59.302 37.037 2.75 0.00 0.00 4.63
2348 2403 5.529060 ACTTAAGCTTGGACTCAAAGACTTG 59.471 40.000 9.86 2.26 31.77 3.16
2699 2754 4.335416 TGTAGGAATCTTTGCTTGGAAGG 58.665 43.478 0.00 0.00 31.99 3.46
2786 2841 0.396139 TCCTGCCATTCCCAGCAATC 60.396 55.000 0.00 0.00 38.82 2.67
2800 2855 3.989817 GTGGTCAATCACAAAATTCCTGC 59.010 43.478 0.00 0.00 37.57 4.85
2840 2895 6.182627 TGAGACATAACTGGCATCAGAAAAT 58.817 36.000 0.00 0.00 43.49 1.82
2983 3038 1.347817 GGACAGCTCGCAGAAGAACG 61.348 60.000 0.00 0.00 34.09 3.95
3321 3376 6.369890 GTGTCTTTGAGAATGCTATCACAAGA 59.630 38.462 3.43 0.00 32.72 3.02
3324 3379 5.798132 AGTGTCTTTGAGAATGCTATCACA 58.202 37.500 0.00 0.00 0.00 3.58
3419 3474 3.365064 GCTTCAGTTTTTAGCTCCGAACC 60.365 47.826 0.00 0.00 32.26 3.62
3529 3584 5.482006 TCGATATCTTCAGGTGCCAATATG 58.518 41.667 0.34 0.00 0.00 1.78
3856 3911 1.289160 CCTCCTTCATCACCTGGGAA 58.711 55.000 0.00 0.00 0.00 3.97
3964 4019 1.022982 TGAGCTCGCTTTGCCTCATG 61.023 55.000 9.64 0.00 0.00 3.07
4160 4215 7.759886 AGTGTTGTATACTGCTAACATGTACAG 59.240 37.037 17.38 17.38 35.72 2.74
4340 4399 5.301555 ACCAGCTGTCTTTCTTTACTTCTC 58.698 41.667 13.81 0.00 0.00 2.87
4370 4429 0.813184 GCCACACAAGACATGGATGG 59.187 55.000 0.00 0.00 39.80 3.51
4445 4504 8.478066 AGTAAAATCTTCATTTATTTGGGGCTC 58.522 33.333 0.00 0.00 31.51 4.70
4566 5063 8.306761 GTTTTGGAGTCAATGATAAAGTTCCAT 58.693 33.333 0.00 0.00 33.83 3.41
4580 5077 2.238521 GCCTGATGGTTTTGGAGTCAA 58.761 47.619 0.00 0.00 35.27 3.18
4582 5079 1.177401 GGCCTGATGGTTTTGGAGTC 58.823 55.000 0.00 0.00 35.27 3.36
4587 5084 1.891722 GCAGGGGCCTGATGGTTTTG 61.892 60.000 0.84 0.00 46.30 2.44
4588 5085 1.610379 GCAGGGGCCTGATGGTTTT 60.610 57.895 0.84 0.00 46.30 2.43
4653 5150 2.454941 GGAGGAGGGGAAGGGACA 59.545 66.667 0.00 0.00 0.00 4.02
4655 5152 3.707189 GGGGAGGAGGGGAAGGGA 61.707 72.222 0.00 0.00 0.00 4.20
4713 5210 1.591703 CTCTTCACCAGCGGCTACA 59.408 57.895 0.26 0.00 0.00 2.74
4758 5255 1.001268 CGACCTATCGTCACCATCAGG 60.001 57.143 0.00 0.00 43.66 3.86
4780 5277 3.191539 GAAGCCGCTGCCTCGAAG 61.192 66.667 0.00 0.00 38.69 3.79
4789 5287 2.103143 CTCATCGTCGAAGCCGCT 59.897 61.111 0.00 0.00 35.37 5.52
4791 5289 2.278857 CCCTCATCGTCGAAGCCG 60.279 66.667 0.00 0.00 37.07 5.52
4798 5296 4.787999 GACGTCACCCTCATCGTC 57.212 61.111 11.55 0.00 43.81 4.20
4809 5307 2.357034 GCCGCAAGAAGGACGTCA 60.357 61.111 18.91 0.00 43.02 4.35
4863 5361 2.439701 CCCTCACTGCCCATGCTG 60.440 66.667 0.00 0.00 41.75 4.41
4864 5362 4.437587 GCCCTCACTGCCCATGCT 62.438 66.667 0.00 0.00 38.71 3.79
4865 5363 4.746309 TGCCCTCACTGCCCATGC 62.746 66.667 0.00 0.00 38.26 4.06
4866 5364 2.753043 GTGCCCTCACTGCCCATG 60.753 66.667 0.00 0.00 40.03 3.66
4867 5365 3.259314 TGTGCCCTCACTGCCCAT 61.259 61.111 0.00 0.00 43.49 4.00
4875 5374 1.915266 CACCTCCTCTGTGCCCTCA 60.915 63.158 0.00 0.00 0.00 3.86
4907 5406 0.843984 CATGGGGAAGAACGGGGTAT 59.156 55.000 0.00 0.00 0.00 2.73
4908 5407 1.276140 CCATGGGGAAGAACGGGGTA 61.276 60.000 2.85 0.00 35.59 3.69
4909 5408 2.612493 CCATGGGGAAGAACGGGGT 61.612 63.158 2.85 0.00 35.59 4.95
4910 5409 2.275418 CCATGGGGAAGAACGGGG 59.725 66.667 2.85 0.00 35.59 5.73
4914 5413 0.259938 ATCTGGCCATGGGGAAGAAC 59.740 55.000 15.13 0.00 33.63 3.01
5009 5508 0.384309 CCACCACGCTAATCGCTAGA 59.616 55.000 0.00 0.00 43.23 2.43
5012 5511 2.186903 CCCACCACGCTAATCGCT 59.813 61.111 0.00 0.00 43.23 4.93
5051 5555 2.322830 GCCGACGACCAAGGGTTTC 61.323 63.158 0.00 0.00 35.25 2.78
5116 5620 5.123227 CGTAATCTTTAATTCCTGGCTCCA 58.877 41.667 0.00 0.00 0.00 3.86


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

AutoCloner maintained by Alex Coulton.