Multiple sequence alignment - TraesCS3D01G286800

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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 TraesCS3D01G286800 chr3D 100.000 2655 0 0 1 2655 395651652 395648998 0.000000e+00 4903.0
1 TraesCS3D01G286800 chr3A 90.648 2577 126 39 129 2630 515736556 515734020 0.000000e+00 3317.0
2 TraesCS3D01G286800 chr3B 92.098 1101 63 12 1066 2155 520465212 520464125 0.000000e+00 1530.0
3 TraesCS3D01G286800 chr3B 88.276 725 48 19 211 907 520471959 520471244 0.000000e+00 833.0
4 TraesCS3D01G286800 chr3B 82.096 229 24 10 2414 2630 520463786 520463563 2.100000e-41 180.0
5 TraesCS3D01G286800 chr3B 94.444 72 2 2 1004 1074 520471188 520471118 2.790000e-20 110.0
6 TraesCS3D01G286800 chr3B 81.250 128 11 7 5 119 520472363 520472236 1.010000e-14 91.6
7 TraesCS3D01G286800 chr4A 88.073 109 9 3 804 908 615448195 615448087 2.770000e-25 126.0
8 TraesCS3D01G286800 chr5B 85.833 120 11 4 804 917 697861223 697861104 3.590000e-24 122.0
9 TraesCS3D01G286800 chr5D 100.000 29 0 0 799 827 290067139 290067167 1.000000e-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 TraesCS3D01G286800 chr3D 395648998 395651652 2654 True 4903.000000 4903 100.000 1 2655 1 chr3D.!!$R1 2654
1 TraesCS3D01G286800 chr3A 515734020 515736556 2536 True 3317.000000 3317 90.648 129 2630 1 chr3A.!!$R1 2501
2 TraesCS3D01G286800 chr3B 520463563 520465212 1649 True 855.000000 1530 87.097 1066 2630 2 chr3B.!!$R1 1564
3 TraesCS3D01G286800 chr3B 520471118 520472363 1245 True 344.866667 833 87.990 5 1074 3 chr3B.!!$R2 1069

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
641 875 0.108329 ATACCTGCCGTCTTGGTTCG 60.108 55.0 0.0 0.0 41.21 3.95 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2455 2840 0.944386 GACACACACGCCAAGAACAT 59.056 50.0 0.0 0.0 0.0 2.71 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
20 21 1.617322 TTGGTACAGAGCAGTCGACT 58.383 50.000 13.58 13.58 42.39 4.18
21 22 2.484742 TGGTACAGAGCAGTCGACTA 57.515 50.000 19.57 0.00 0.00 2.59
60 61 3.831911 TGTGACATGTCATCTGTCTACCA 59.168 43.478 30.10 17.15 42.78 3.25
63 64 5.125578 GTGACATGTCATCTGTCTACCACTA 59.874 44.000 30.10 0.00 42.78 2.74
92 106 6.691388 CAGTGTCATTCTTCGATGATAACGTA 59.309 38.462 1.37 0.00 38.25 3.57
105 119 5.428496 TGATAACGTATCAGTAACCTCCG 57.572 43.478 0.00 0.00 40.09 4.63
107 121 2.425143 ACGTATCAGTAACCTCCGGA 57.575 50.000 2.93 2.93 0.00 5.14
119 133 1.206371 ACCTCCGGAAGATGTAAACCG 59.794 52.381 7.17 0.00 44.16 4.44
121 135 2.268298 CTCCGGAAGATGTAAACCGTG 58.732 52.381 5.23 0.00 43.22 4.94
124 138 2.607635 CCGGAAGATGTAAACCGTGATG 59.392 50.000 0.00 0.00 43.22 3.07
127 297 4.504858 GGAAGATGTAAACCGTGATGTCT 58.495 43.478 0.00 0.00 0.00 3.41
137 307 6.663944 AAACCGTGATGTCTATTAGCTTTC 57.336 37.500 0.00 0.00 0.00 2.62
147 317 5.523916 TGTCTATTAGCTTTCGATTTGAGCC 59.476 40.000 0.00 0.00 37.11 4.70
151 321 2.284190 AGCTTTCGATTTGAGCCTAGC 58.716 47.619 6.89 0.00 37.11 3.42
176 346 0.527565 CGGGCAGCTGCTACATTTTT 59.472 50.000 35.82 0.00 41.70 1.94
178 348 2.477863 CGGGCAGCTGCTACATTTTTAC 60.478 50.000 35.82 16.27 41.70 2.01
179 349 2.491693 GGGCAGCTGCTACATTTTTACA 59.508 45.455 35.82 0.00 41.70 2.41
190 360 8.969121 TGCTACATTTTTACAAGATTGATGTG 57.031 30.769 0.00 0.00 32.27 3.21
195 365 7.596248 ACATTTTTACAAGATTGATGTGAGTGC 59.404 33.333 0.00 0.00 32.27 4.40
196 366 6.882610 TTTTACAAGATTGATGTGAGTGCT 57.117 33.333 0.00 0.00 32.27 4.40
197 367 5.868043 TTACAAGATTGATGTGAGTGCTG 57.132 39.130 0.00 0.00 32.27 4.41
200 370 3.977134 AGATTGATGTGAGTGCTGAGT 57.023 42.857 0.00 0.00 0.00 3.41
202 372 5.411831 AGATTGATGTGAGTGCTGAGTAA 57.588 39.130 0.00 0.00 0.00 2.24
204 374 6.233434 AGATTGATGTGAGTGCTGAGTAAAA 58.767 36.000 0.00 0.00 0.00 1.52
233 433 4.098196 AGGTCTTTTATGCGTAGAGGACTC 59.902 45.833 15.48 8.21 0.00 3.36
248 451 7.873505 CGTAGAGGACTCGATATATGATGGATA 59.126 40.741 0.00 0.00 34.09 2.59
256 459 7.039853 ACTCGATATATGATGGATATCTGGCTG 60.040 40.741 2.05 0.00 35.13 4.85
278 484 6.071896 GCTGCTTATTTCACTTCCTAGGTTTT 60.072 38.462 9.08 0.00 0.00 2.43
295 520 0.812014 TTTGCGCCTTCTTGACGTGA 60.812 50.000 4.18 0.00 0.00 4.35
304 529 5.593010 GCCTTCTTGACGTGATCTTATAGT 58.407 41.667 0.00 0.00 0.00 2.12
305 530 6.512903 CGCCTTCTTGACGTGATCTTATAGTA 60.513 42.308 0.00 0.00 0.00 1.82
306 531 6.637658 GCCTTCTTGACGTGATCTTATAGTAC 59.362 42.308 0.00 0.00 0.00 2.73
307 532 7.681304 GCCTTCTTGACGTGATCTTATAGTACA 60.681 40.741 0.00 0.00 0.00 2.90
308 533 8.188799 CCTTCTTGACGTGATCTTATAGTACAA 58.811 37.037 0.00 0.00 0.00 2.41
309 534 9.227490 CTTCTTGACGTGATCTTATAGTACAAG 57.773 37.037 0.00 0.00 34.38 3.16
332 557 6.855836 AGTACAAAACCAGCATGTATGATTG 58.144 36.000 0.00 3.79 32.65 2.67
360 585 6.708054 AGGATCTATGTTAATTTCTTCTGGCG 59.292 38.462 0.00 0.00 0.00 5.69
438 670 0.908180 ATCCTTCCCCTTTCCGACGT 60.908 55.000 0.00 0.00 0.00 4.34
453 685 1.381327 ACGTCGATCCATCCACCCT 60.381 57.895 0.00 0.00 0.00 4.34
641 875 0.108329 ATACCTGCCGTCTTGGTTCG 60.108 55.000 0.00 0.00 41.21 3.95
704 938 4.453136 TCGGTAATAAGACAAACAGGCAAC 59.547 41.667 0.00 0.00 0.00 4.17
731 965 3.498397 ACATCCAAGACAACGCTACTTTG 59.502 43.478 0.00 0.00 0.00 2.77
760 996 4.095036 GGAGTTTATTCTTTCTTGGAGGCG 59.905 45.833 0.00 0.00 0.00 5.52
778 1014 1.120147 CGTTGCCGCGAAAGAAATCG 61.120 55.000 8.23 0.00 45.41 3.34
785 1021 2.726760 CCGCGAAAGAAATCGATCTAGG 59.273 50.000 8.23 0.00 45.48 3.02
786 1022 3.372954 CGCGAAAGAAATCGATCTAGGT 58.627 45.455 0.00 0.00 45.48 3.08
838 1074 1.456705 ACCGTGGTTGCCCATGTTT 60.457 52.632 1.19 0.00 44.96 2.83
930 1166 3.581101 TCAATGATTGGGGGTTTCAACA 58.419 40.909 5.20 0.00 0.00 3.33
940 1176 2.888414 GGGGTTTCAACATCCTTTTCGA 59.112 45.455 0.00 0.00 0.00 3.71
943 1179 5.353111 GGGTTTCAACATCCTTTTCGAAAA 58.647 37.500 21.35 21.35 0.00 2.29
945 1181 6.270064 GGTTTCAACATCCTTTTCGAAAAGA 58.730 36.000 39.33 28.33 46.39 2.52
946 1182 6.754675 GGTTTCAACATCCTTTTCGAAAAGAA 59.245 34.615 39.33 28.16 46.39 2.52
947 1183 7.276878 GGTTTCAACATCCTTTTCGAAAAGAAA 59.723 33.333 39.33 28.64 46.39 2.52
982 1218 1.975680 TGGTTCTGGGACTCTACCAAC 59.024 52.381 0.00 0.00 37.59 3.77
1096 1333 5.346181 AAGACTAGAGAAACCTGGCATAC 57.654 43.478 0.00 0.00 0.00 2.39
1100 1337 5.767670 ACTAGAGAAACCTGGCATACTAGA 58.232 41.667 16.46 0.00 33.00 2.43
1101 1338 5.595133 ACTAGAGAAACCTGGCATACTAGAC 59.405 44.000 16.46 0.00 33.00 2.59
1102 1339 3.707102 AGAGAAACCTGGCATACTAGACC 59.293 47.826 0.00 0.00 0.00 3.85
1150 1387 2.114056 CATTTCATTTCATCGCGGCAG 58.886 47.619 6.13 0.00 0.00 4.85
1253 1490 1.965643 AGAAATGCTTGCAGCTTCCAA 59.034 42.857 13.26 0.00 42.97 3.53
1321 1558 1.464376 ATACCATCACCGAGGAGGCG 61.464 60.000 0.00 0.00 46.52 5.52
1543 1780 3.005155 ACAGAAAATCAGTGCTCTTTGGC 59.995 43.478 0.00 0.00 0.00 4.52
1744 1981 3.971245 ACAGAAGCTCTTGGGTTAGAG 57.029 47.619 0.00 0.00 43.66 2.43
1966 2212 4.934001 GTGGATATCTGATGGCATACACAG 59.066 45.833 0.00 3.98 32.79 3.66
1994 2240 1.264288 GCTCCTTCTGTTTGGTGAACG 59.736 52.381 0.00 0.00 41.29 3.95
2002 2248 0.386731 GTTTGGTGAACGCCCGAATG 60.387 55.000 1.86 0.00 0.00 2.67
2101 2347 2.045045 TCCATGGCGCTTTCCAGG 60.045 61.111 6.96 0.00 39.89 4.45
2133 2379 2.909006 TCCTCCAAGAGCAAGATCACTT 59.091 45.455 0.00 0.00 36.73 3.16
2192 2442 4.862018 GCCTATACGAGAGATTTGATGCTC 59.138 45.833 0.00 0.00 0.00 4.26
2193 2443 5.406649 CCTATACGAGAGATTTGATGCTCC 58.593 45.833 0.00 0.00 0.00 4.70
2194 2444 4.944619 ATACGAGAGATTTGATGCTCCA 57.055 40.909 0.00 0.00 0.00 3.86
2195 2445 3.176552 ACGAGAGATTTGATGCTCCAG 57.823 47.619 0.00 0.00 0.00 3.86
2196 2446 2.158986 ACGAGAGATTTGATGCTCCAGG 60.159 50.000 0.00 0.00 0.00 4.45
2197 2447 2.220313 GAGAGATTTGATGCTCCAGGC 58.780 52.381 0.00 0.00 42.22 4.85
2198 2448 1.133853 AGAGATTTGATGCTCCAGGCC 60.134 52.381 0.00 0.00 40.92 5.19
2199 2449 0.627451 AGATTTGATGCTCCAGGCCA 59.373 50.000 5.01 0.00 40.92 5.36
2200 2450 0.743097 GATTTGATGCTCCAGGCCAC 59.257 55.000 5.01 0.00 40.92 5.01
2201 2451 1.033746 ATTTGATGCTCCAGGCCACG 61.034 55.000 5.01 0.00 40.92 4.94
2202 2452 3.626996 TTGATGCTCCAGGCCACGG 62.627 63.158 5.01 4.90 40.92 4.94
2203 2453 4.864334 GATGCTCCAGGCCACGGG 62.864 72.222 5.01 3.12 40.92 5.28
2266 2516 3.259374 CAGGAACAGGAAGAAGAGCAGTA 59.741 47.826 0.00 0.00 0.00 2.74
2288 2538 9.049523 CAGTATAAAAGCTGCATTTGATCTCTA 57.950 33.333 12.62 0.00 0.00 2.43
2289 2539 9.790344 AGTATAAAAGCTGCATTTGATCTCTAT 57.210 29.630 12.62 0.00 0.00 1.98
2303 2553 6.668541 TGATCTCTATTGTAAAAGCTGCAC 57.331 37.500 1.02 0.00 0.00 4.57
2314 2564 2.486472 AAGCTGCACTTGCTGAGTAT 57.514 45.000 11.87 0.00 41.03 2.12
2371 2622 8.440833 GTTGTGTGAGTAGTAAATGGTGATTAC 58.559 37.037 0.00 0.00 34.24 1.89
2435 2817 6.736110 ATATATCTGTGGCATTTTGGCTTT 57.264 33.333 0.00 0.00 44.10 3.51
2447 2829 5.346822 GCATTTTGGCTTTGTTCTATGTCTG 59.653 40.000 0.00 0.00 0.00 3.51
2449 2834 5.437289 TTTGGCTTTGTTCTATGTCTGTG 57.563 39.130 0.00 0.00 0.00 3.66
2452 2837 4.887071 TGGCTTTGTTCTATGTCTGTGTTT 59.113 37.500 0.00 0.00 0.00 2.83
2455 2840 6.426937 GGCTTTGTTCTATGTCTGTGTTTCTA 59.573 38.462 0.00 0.00 0.00 2.10
2467 2852 3.472652 TGTGTTTCTATGTTCTTGGCGT 58.527 40.909 0.00 0.00 0.00 5.68
2470 2855 3.249799 TGTTTCTATGTTCTTGGCGTGTG 59.750 43.478 0.00 0.00 0.00 3.82
2472 2857 2.412870 TCTATGTTCTTGGCGTGTGTG 58.587 47.619 0.00 0.00 0.00 3.82
2473 2858 2.143122 CTATGTTCTTGGCGTGTGTGT 58.857 47.619 0.00 0.00 0.00 3.72
2474 2859 0.944386 ATGTTCTTGGCGTGTGTGTC 59.056 50.000 0.00 0.00 0.00 3.67
2475 2860 0.391793 TGTTCTTGGCGTGTGTGTCA 60.392 50.000 0.00 0.00 0.00 3.58
2476 2861 0.027586 GTTCTTGGCGTGTGTGTCAC 59.972 55.000 0.00 0.00 43.03 3.67
2490 2900 5.008613 GTGTGTGTCACCTCATAATTTGTGT 59.991 40.000 0.00 0.00 40.84 3.72
2553 2969 3.846754 GCAAAACAGCCATCGCAC 58.153 55.556 0.00 0.00 37.52 5.34
2554 2970 1.286880 GCAAAACAGCCATCGCACT 59.713 52.632 0.00 0.00 37.52 4.40
2593 3012 0.809241 CTTCTCTGATGGCGCCAGTC 60.809 60.000 35.36 28.41 33.57 3.51
2630 3049 3.665675 AATCCTGAGCGCACCCGAC 62.666 63.158 11.47 0.00 36.29 4.79
2638 3057 4.680237 CGCACCCGACCTGCAGAA 62.680 66.667 17.39 0.00 36.29 3.02
2639 3058 2.281484 GCACCCGACCTGCAGAAA 60.281 61.111 17.39 0.00 34.56 2.52
2640 3059 1.675641 GCACCCGACCTGCAGAAAT 60.676 57.895 17.39 0.00 34.56 2.17
2641 3060 1.926511 GCACCCGACCTGCAGAAATG 61.927 60.000 17.39 0.00 34.56 2.32
2642 3061 1.675641 ACCCGACCTGCAGAAATGC 60.676 57.895 17.39 0.00 0.00 3.56
2643 3062 1.675310 CCCGACCTGCAGAAATGCA 60.675 57.895 17.39 2.57 43.22 3.96
2644 3063 1.503542 CCGACCTGCAGAAATGCAC 59.496 57.895 17.39 0.00 40.23 4.57
2645 3064 1.503542 CGACCTGCAGAAATGCACC 59.496 57.895 17.39 0.00 40.23 5.01
2646 3065 1.236616 CGACCTGCAGAAATGCACCA 61.237 55.000 17.39 0.00 40.23 4.17
2647 3066 0.961019 GACCTGCAGAAATGCACCAA 59.039 50.000 17.39 0.00 40.23 3.67
2648 3067 0.675633 ACCTGCAGAAATGCACCAAC 59.324 50.000 17.39 0.00 40.23 3.77
2649 3068 0.675083 CCTGCAGAAATGCACCAACA 59.325 50.000 17.39 0.00 40.23 3.33
2650 3069 1.336517 CCTGCAGAAATGCACCAACAG 60.337 52.381 17.39 0.00 40.23 3.16
2651 3070 0.032403 TGCAGAAATGCACCAACAGC 59.968 50.000 0.00 0.00 40.23 4.40
2652 3071 1.005294 GCAGAAATGCACCAACAGCG 61.005 55.000 0.00 0.00 33.85 5.18
2653 3072 1.005294 CAGAAATGCACCAACAGCGC 61.005 55.000 0.00 0.00 33.85 5.92
2654 3073 1.734117 GAAATGCACCAACAGCGCC 60.734 57.895 2.29 0.00 33.85 6.53
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 2.171840 AGTCGACTGCTCTGTACCAAT 58.828 47.619 19.30 0.00 0.00 3.16
1 2 1.617322 AGTCGACTGCTCTGTACCAA 58.383 50.000 19.30 0.00 0.00 3.67
2 3 2.290134 ACTAGTCGACTGCTCTGTACCA 60.290 50.000 28.12 2.62 0.00 3.25
3 4 2.352342 GACTAGTCGACTGCTCTGTACC 59.648 54.545 28.12 4.82 0.00 3.34
20 21 2.771639 ATCTTGCCGCGCTCGACTA 61.772 57.895 5.56 0.00 38.10 2.59
21 22 4.135153 ATCTTGCCGCGCTCGACT 62.135 61.111 5.56 0.00 38.10 4.18
28 29 1.061411 CATGTCACATCTTGCCGCG 59.939 57.895 0.00 0.00 0.00 6.46
30 31 1.441738 TGACATGTCACATCTTGCCG 58.558 50.000 24.56 0.00 34.14 5.69
60 61 6.319911 TCATCGAAGAATGACACTGAGATAGT 59.680 38.462 0.00 0.00 43.58 2.12
63 64 5.588958 TCATCGAAGAATGACACTGAGAT 57.411 39.130 0.00 0.00 43.58 2.75
80 94 6.084925 GGAGGTTACTGATACGTTATCATCG 58.915 44.000 0.00 0.00 43.66 3.84
105 119 4.504858 AGACATCACGGTTTACATCTTCC 58.495 43.478 0.00 0.00 0.00 3.46
107 121 7.438459 GCTAATAGACATCACGGTTTACATCTT 59.562 37.037 0.00 0.00 0.00 2.40
119 133 8.131455 TCAAATCGAAAGCTAATAGACATCAC 57.869 34.615 0.00 0.00 0.00 3.06
121 135 7.287229 GCTCAAATCGAAAGCTAATAGACATC 58.713 38.462 0.00 0.00 33.23 3.06
124 138 5.755861 AGGCTCAAATCGAAAGCTAATAGAC 59.244 40.000 10.85 0.00 36.29 2.59
127 297 5.696724 GCTAGGCTCAAATCGAAAGCTAATA 59.303 40.000 10.85 3.89 36.29 0.98
137 307 2.131183 GTAGCTGCTAGGCTCAAATCG 58.869 52.381 10.13 0.00 42.97 3.34
176 346 5.151297 TCAGCACTCACATCAATCTTGTA 57.849 39.130 0.00 0.00 0.00 2.41
178 348 4.001652 ACTCAGCACTCACATCAATCTTG 58.998 43.478 0.00 0.00 0.00 3.02
179 349 4.283363 ACTCAGCACTCACATCAATCTT 57.717 40.909 0.00 0.00 0.00 2.40
202 372 8.556213 TCTACGCATAAAAGACCTGTATTTTT 57.444 30.769 7.81 3.41 35.81 1.94
204 374 6.761714 CCTCTACGCATAAAAGACCTGTATTT 59.238 38.462 0.00 0.00 0.00 1.40
222 422 6.049790 TCCATCATATATCGAGTCCTCTACG 58.950 44.000 0.00 0.00 0.00 3.51
233 433 5.868258 GCAGCCAGATATCCATCATATATCG 59.132 44.000 0.00 0.00 40.01 2.92
248 451 3.950395 GGAAGTGAAATAAGCAGCCAGAT 59.050 43.478 0.00 0.00 0.00 2.90
256 459 6.093404 GCAAAACCTAGGAAGTGAAATAAGC 58.907 40.000 17.98 0.26 0.00 3.09
295 520 9.379791 GCTGGTTTTGTACTTGTACTATAAGAT 57.620 33.333 11.53 0.00 0.00 2.40
304 529 6.937465 TCATACATGCTGGTTTTGTACTTGTA 59.063 34.615 0.00 0.00 0.00 2.41
305 530 5.767665 TCATACATGCTGGTTTTGTACTTGT 59.232 36.000 0.00 0.00 0.00 3.16
306 531 6.252967 TCATACATGCTGGTTTTGTACTTG 57.747 37.500 0.00 0.00 0.00 3.16
307 532 7.039784 ACAATCATACATGCTGGTTTTGTACTT 60.040 33.333 0.00 0.00 0.00 2.24
308 533 6.434028 ACAATCATACATGCTGGTTTTGTACT 59.566 34.615 0.00 0.00 0.00 2.73
309 534 6.620678 ACAATCATACATGCTGGTTTTGTAC 58.379 36.000 0.00 0.00 0.00 2.90
320 545 8.783833 ACATAGATCCTAACAATCATACATGC 57.216 34.615 0.00 0.00 0.00 4.06
360 585 1.739667 GGCAGTTGGTGGTTTGGAC 59.260 57.895 0.00 0.00 0.00 4.02
438 670 1.486310 CTTTCAGGGTGGATGGATCGA 59.514 52.381 0.00 0.00 0.00 3.59
453 685 1.895131 GAGCTTTGCCAATCCCTTTCA 59.105 47.619 0.00 0.00 0.00 2.69
470 702 0.948678 CTCCTACGGTCTAGCAGAGC 59.051 60.000 5.58 5.58 39.24 4.09
545 777 7.576287 GCAGTGTCAGTGTACTTACCACTATTA 60.576 40.741 9.41 0.00 0.00 0.98
641 875 3.935828 AGCTGCTTTTATTTCGAGGAGAC 59.064 43.478 0.00 0.00 31.36 3.36
704 938 1.875963 GTTGTCTTGGATGTGGCGG 59.124 57.895 0.00 0.00 0.00 6.13
731 965 5.390991 CCAAGAAAGAATAAACTCCTCGTGC 60.391 44.000 0.00 0.00 0.00 5.34
760 996 0.165079 TCGATTTCTTTCGCGGCAAC 59.835 50.000 6.13 0.00 38.97 4.17
765 1001 3.180584 CACCTAGATCGATTTCTTTCGCG 59.819 47.826 0.00 0.00 38.97 5.87
769 1005 6.154706 ACACCTACACCTAGATCGATTTCTTT 59.845 38.462 0.00 0.00 0.00 2.52
778 1014 6.640518 TGAAATGAACACCTACACCTAGATC 58.359 40.000 0.00 0.00 0.00 2.75
785 1021 8.268850 ACAAGATATGAAATGAACACCTACAC 57.731 34.615 0.00 0.00 0.00 2.90
786 1022 9.952030 TTACAAGATATGAAATGAACACCTACA 57.048 29.630 0.00 0.00 0.00 2.74
838 1074 8.081633 CCAAAAACATCAACAAGCAGAGTATAA 58.918 33.333 0.00 0.00 0.00 0.98
947 1183 5.163416 CCCAGAACCAAGATCAACTGTTTTT 60.163 40.000 0.00 0.00 0.00 1.94
968 1204 2.042569 TCTGCTAGTTGGTAGAGTCCCA 59.957 50.000 0.00 0.00 0.00 4.37
982 1218 8.830201 ATTAACATCAATAGCTCTTCTGCTAG 57.170 34.615 0.00 0.00 46.89 3.42
1096 1333 1.056660 AAGTGGTGGTGGTGGTCTAG 58.943 55.000 0.00 0.00 0.00 2.43
1100 1337 1.440618 TATCAAGTGGTGGTGGTGGT 58.559 50.000 0.00 0.00 0.00 4.16
1101 1338 2.239654 AGATATCAAGTGGTGGTGGTGG 59.760 50.000 5.32 0.00 0.00 4.61
1102 1339 3.535561 GAGATATCAAGTGGTGGTGGTG 58.464 50.000 5.32 0.00 0.00 4.17
1150 1387 0.599204 TTGTGAACCTCCGTCGAAGC 60.599 55.000 0.00 0.00 0.00 3.86
1253 1490 2.927014 GCTCCAGATTCTTGTCGACGTT 60.927 50.000 11.62 0.00 0.00 3.99
1321 1558 3.366052 TTGTTGATAAGCCTTCCCTCC 57.634 47.619 0.00 0.00 0.00 4.30
1543 1780 9.307121 CCTTGTAGATCTTCTATGTTGTTACTG 57.693 37.037 0.00 0.00 30.76 2.74
1744 1981 3.022607 AGCTTCTTGATGCAAGCAAAC 57.977 42.857 8.43 0.00 44.21 2.93
1994 2240 2.151202 TCAACAGAAGTTCATTCGGGC 58.849 47.619 5.50 0.00 43.16 6.13
2077 2323 2.474816 GAAAGCGCCATGGAGTAGTAG 58.525 52.381 18.40 0.00 0.00 2.57
2101 2347 1.072331 TCTTGGAGGAGTTGGTTCTGC 59.928 52.381 0.00 0.00 0.00 4.26
2133 2379 4.939439 CACATCCTGACATGAATCTGACAA 59.061 41.667 0.00 0.00 0.00 3.18
2163 2413 7.526142 TCAAATCTCTCGTATAGGCAATAGT 57.474 36.000 0.00 0.00 0.00 2.12
2176 2426 2.481854 CCTGGAGCATCAAATCTCTCG 58.518 52.381 0.00 0.00 36.25 4.04
2193 2443 4.641645 TTCAGCACCCGTGGCCTG 62.642 66.667 3.32 0.00 0.00 4.85
2194 2444 3.850098 CTTTCAGCACCCGTGGCCT 62.850 63.158 3.32 0.00 0.00 5.19
2195 2445 3.365265 CTTTCAGCACCCGTGGCC 61.365 66.667 0.00 0.00 0.00 5.36
2196 2446 3.365265 CCTTTCAGCACCCGTGGC 61.365 66.667 0.00 0.00 0.00 5.01
2197 2447 3.365265 GCCTTTCAGCACCCGTGG 61.365 66.667 0.00 0.00 0.00 4.94
2198 2448 3.726517 CGCCTTTCAGCACCCGTG 61.727 66.667 0.00 0.00 0.00 4.94
2199 2449 3.883744 CTCGCCTTTCAGCACCCGT 62.884 63.158 0.00 0.00 0.00 5.28
2200 2450 3.121030 CTCGCCTTTCAGCACCCG 61.121 66.667 0.00 0.00 0.00 5.28
2201 2451 2.747855 CCTCGCCTTTCAGCACCC 60.748 66.667 0.00 0.00 0.00 4.61
2202 2452 2.747855 CCCTCGCCTTTCAGCACC 60.748 66.667 0.00 0.00 0.00 5.01
2203 2453 2.032681 ACCCTCGCCTTTCAGCAC 59.967 61.111 0.00 0.00 0.00 4.40
2204 2454 2.032528 CACCCTCGCCTTTCAGCA 59.967 61.111 0.00 0.00 0.00 4.41
2205 2455 2.747855 CCACCCTCGCCTTTCAGC 60.748 66.667 0.00 0.00 0.00 4.26
2249 2499 5.877564 GCTTTTATACTGCTCTTCTTCCTGT 59.122 40.000 0.00 0.00 0.00 4.00
2266 2516 8.910944 ACAATAGAGATCAAATGCAGCTTTTAT 58.089 29.630 5.97 1.90 0.00 1.40
2288 2538 3.318839 TCAGCAAGTGCAGCTTTTACAAT 59.681 39.130 6.00 0.00 45.16 2.71
2289 2539 2.687425 TCAGCAAGTGCAGCTTTTACAA 59.313 40.909 6.00 0.00 45.16 2.41
2303 2553 5.122869 TGCAGCTTTTAGAATACTCAGCAAG 59.877 40.000 0.00 0.00 0.00 4.01
2314 2564 6.430925 ACATACATCAACTGCAGCTTTTAGAA 59.569 34.615 15.27 0.00 0.00 2.10
2359 2610 7.707624 ACATCACAATCAGTAATCACCATTT 57.292 32.000 0.00 0.00 0.00 2.32
2362 2613 6.260714 GCATACATCACAATCAGTAATCACCA 59.739 38.462 0.00 0.00 0.00 4.17
2363 2614 6.484643 AGCATACATCACAATCAGTAATCACC 59.515 38.462 0.00 0.00 0.00 4.02
2371 2622 7.175073 CTTGAGTAGCATACATCACAATCAG 57.825 40.000 0.00 0.00 46.26 2.90
2435 2817 8.367911 AGAACATAGAAACACAGACATAGAACA 58.632 33.333 0.00 0.00 0.00 3.18
2447 2829 3.250040 ACACGCCAAGAACATAGAAACAC 59.750 43.478 0.00 0.00 0.00 3.32
2449 2834 3.250040 ACACACGCCAAGAACATAGAAAC 59.750 43.478 0.00 0.00 0.00 2.78
2452 2837 2.224185 ACACACACGCCAAGAACATAGA 60.224 45.455 0.00 0.00 0.00 1.98
2455 2840 0.944386 GACACACACGCCAAGAACAT 59.056 50.000 0.00 0.00 0.00 2.71
2467 2852 5.129634 ACACAAATTATGAGGTGACACACA 58.870 37.500 8.08 7.49 35.86 3.72
2470 2855 6.128282 CCAGTACACAAATTATGAGGTGACAC 60.128 42.308 0.00 0.00 35.33 3.67
2472 2857 5.354234 CCCAGTACACAAATTATGAGGTGAC 59.646 44.000 0.00 0.00 35.33 3.67
2473 2858 5.496556 CCCAGTACACAAATTATGAGGTGA 58.503 41.667 0.00 0.00 35.33 4.02
2474 2859 4.096382 GCCCAGTACACAAATTATGAGGTG 59.904 45.833 0.00 0.00 37.29 4.00
2475 2860 4.270008 GCCCAGTACACAAATTATGAGGT 58.730 43.478 0.00 0.00 0.00 3.85
2476 2861 3.632145 GGCCCAGTACACAAATTATGAGG 59.368 47.826 0.00 0.00 0.00 3.86
2593 3012 3.799281 TTTTTGGCTGTGTTTCTCCTG 57.201 42.857 0.00 0.00 0.00 3.86
2634 3053 3.096541 CGCTGTTGGTGCATTTCTG 57.903 52.632 0.00 0.00 0.00 3.02


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

AutoCloner maintained by Alex Coulton.