Multiple sequence alignment - TraesCS1B01G138800

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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 TraesCS1B01G138800 chr1B 100.000 2998 0 0 1 2998 180531558 180534555 0.000000e+00 5537.0
1 TraesCS1B01G138800 chr1D 95.531 1835 61 8 379 2201 118803495 118805320 0.000000e+00 2915.0
2 TraesCS1B01G138800 chr1D 82.236 805 88 23 2207 2998 118805651 118806413 0.000000e+00 643.0
3 TraesCS1B01G138800 chr1D 84.543 317 13 7 58 370 118802760 118803044 6.330000e-72 281.0
4 TraesCS1B01G138800 chr1A 95.977 1566 52 4 563 2121 130349255 130350816 0.000000e+00 2532.0
5 TraesCS1B01G138800 chr1A 84.693 797 67 14 2210 2995 130351131 130351883 0.000000e+00 745.0
6 TraesCS1B01G138800 chr1A 95.572 271 11 1 301 571 130348805 130349074 1.650000e-117 433.0
7 TraesCS1B01G138800 chr1A 90.688 247 15 2 59 301 130340168 130340410 3.730000e-84 322.0
8 TraesCS1B01G138800 chr7A 79.088 373 53 19 2646 2998 90483950 90483583 1.800000e-57 233.0
9 TraesCS1B01G138800 chr3A 78.593 327 49 19 2683 2997 684585737 684586054 2.360000e-46 196.0
10 TraesCS1B01G138800 chr3A 81.443 194 27 9 2653 2838 551724072 551724264 1.860000e-32 150.0
11 TraesCS1B01G138800 chr4B 76.267 375 64 23 2640 2998 636509064 636508699 3.070000e-40 176.0
12 TraesCS1B01G138800 chrUn 75.676 370 61 21 2645 2995 65076570 65076929 1.110000e-34 158.0
13 TraesCS1B01G138800 chr2D 78.095 210 33 11 2634 2833 516363134 516362928 1.460000e-23 121.0
14 TraesCS1B01G138800 chr2D 96.970 33 0 1 2373 2404 112340848 112340816 2.000000e-03 54.7
15 TraesCS1B01G138800 chr6D 79.144 187 25 10 2653 2828 332540463 332540646 1.890000e-22 117.0
16 TraesCS1B01G138800 chr6B 77.000 200 33 9 2220 2415 702300554 702300744 5.290000e-18 102.0
17 TraesCS1B01G138800 chr7B 82.927 82 10 2 58 139 15619990 15619913 1.490000e-08 71.3
18 TraesCS1B01G138800 chr5B 73.869 199 28 22 2221 2401 513960720 513960912 1.160000e-04 58.4


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 TraesCS1B01G138800 chr1B 180531558 180534555 2997 False 5537.000000 5537 100.000000 1 2998 1 chr1B.!!$F1 2997
1 TraesCS1B01G138800 chr1D 118802760 118806413 3653 False 1279.666667 2915 87.436667 58 2998 3 chr1D.!!$F1 2940
2 TraesCS1B01G138800 chr1A 130348805 130351883 3078 False 1236.666667 2532 92.080667 301 2995 3 chr1A.!!$F2 2694

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
48 49 0.108615 ATTCTCAACGTCGCCAGAGG 60.109 55.0 8.67 0.0 38.17 3.69 F
250 255 0.178938 TTAGTGTGGGGGTGTACCGA 60.179 55.0 0.00 0.0 41.60 4.69 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1284 1932 1.236616 CCATCAGCGCCACAAGTTCA 61.237 55.0 2.29 0.0 0.00 3.18 R
2208 2858 0.110486 TCAGTCCCTGTTTCCTTGGC 59.890 55.0 0.00 0.0 32.61 4.52 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
40 41 8.851960 AAAAAGAAGGTAAAATTCTCAACGTC 57.148 30.769 0.00 0.00 35.98 4.34
41 42 5.840940 AGAAGGTAAAATTCTCAACGTCG 57.159 39.130 0.00 0.00 31.29 5.12
42 43 4.151867 AGAAGGTAAAATTCTCAACGTCGC 59.848 41.667 0.00 0.00 31.29 5.19
43 44 2.740447 AGGTAAAATTCTCAACGTCGCC 59.260 45.455 0.00 0.00 0.00 5.54
44 45 2.481185 GGTAAAATTCTCAACGTCGCCA 59.519 45.455 0.00 0.00 0.00 5.69
45 46 2.969443 AAAATTCTCAACGTCGCCAG 57.031 45.000 0.00 0.00 0.00 4.85
46 47 2.163818 AAATTCTCAACGTCGCCAGA 57.836 45.000 0.00 0.00 0.00 3.86
47 48 1.714794 AATTCTCAACGTCGCCAGAG 58.285 50.000 0.00 0.00 0.00 3.35
48 49 0.108615 ATTCTCAACGTCGCCAGAGG 60.109 55.000 8.67 0.00 38.17 3.69
49 50 2.765250 TTCTCAACGTCGCCAGAGGC 62.765 60.000 0.00 0.00 46.75 4.70
74 75 2.162408 GAGCAATCCTAAGTGGTGCAAC 59.838 50.000 0.00 0.00 39.48 4.17
139 140 2.092375 AGCCCAGGACAAAGCCTATAAC 60.092 50.000 0.00 0.00 36.22 1.89
142 143 3.545703 CCAGGACAAAGCCTATAACCAG 58.454 50.000 0.00 0.00 36.22 4.00
156 157 6.299141 CCTATAACCAGTGCCAAATATGAGT 58.701 40.000 0.00 0.00 0.00 3.41
172 173 4.608948 ATGAGTTGGGCTACTATACAGC 57.391 45.455 0.00 0.00 38.35 4.40
207 212 4.576463 AGCGGATATGATTTGTGAAAGGTC 59.424 41.667 0.00 0.00 0.00 3.85
208 213 4.576463 GCGGATATGATTTGTGAAAGGTCT 59.424 41.667 0.00 0.00 0.00 3.85
209 214 5.758296 GCGGATATGATTTGTGAAAGGTCTA 59.242 40.000 0.00 0.00 0.00 2.59
210 215 6.073548 GCGGATATGATTTGTGAAAGGTCTAG 60.074 42.308 0.00 0.00 0.00 2.43
211 216 6.073548 CGGATATGATTTGTGAAAGGTCTAGC 60.074 42.308 0.00 0.00 0.00 3.42
247 252 1.070601 ACGTTTAGTGTGGGGGTGTAC 59.929 52.381 0.00 0.00 0.00 2.90
248 253 1.608801 CGTTTAGTGTGGGGGTGTACC 60.609 57.143 0.00 0.00 39.11 3.34
249 254 0.686224 TTTAGTGTGGGGGTGTACCG 59.314 55.000 0.00 0.00 41.60 4.02
250 255 0.178938 TTAGTGTGGGGGTGTACCGA 60.179 55.000 0.00 0.00 41.60 4.69
251 256 0.178938 TAGTGTGGGGGTGTACCGAA 60.179 55.000 0.00 0.00 41.60 4.30
252 257 1.004200 GTGTGGGGGTGTACCGAAG 60.004 63.158 0.00 0.00 41.60 3.79
253 258 2.046604 GTGGGGGTGTACCGAAGC 60.047 66.667 0.00 0.00 41.60 3.86
254 259 3.697747 TGGGGGTGTACCGAAGCG 61.698 66.667 0.00 0.00 41.60 4.68
255 260 3.384532 GGGGGTGTACCGAAGCGA 61.385 66.667 0.00 0.00 41.60 4.93
256 261 2.183555 GGGGTGTACCGAAGCGAG 59.816 66.667 0.00 0.00 41.60 5.03
257 262 2.345760 GGGGTGTACCGAAGCGAGA 61.346 63.158 0.00 0.00 41.60 4.04
258 263 1.153881 GGGTGTACCGAAGCGAGAC 60.154 63.158 0.00 0.00 36.71 3.36
356 361 3.405831 CCTTGCATCTCTGAACTGTTCA 58.594 45.455 20.95 20.95 38.17 3.18
403 850 5.069383 TGCAGCCGTACCTGAAGTAATATAA 59.931 40.000 3.57 0.00 34.77 0.98
426 873 2.613506 CCGGTGGCTCGTTGAAACC 61.614 63.158 0.00 0.00 0.00 3.27
536 983 1.964223 ACGACAGGGACATAGGCATAG 59.036 52.381 0.00 0.00 0.00 2.23
700 1336 1.466167 CAGTTCACGGAATCTGCCTTG 59.534 52.381 0.00 0.00 0.00 3.61
753 1389 4.718940 AACTCCAAGTGACACCTTTTTG 57.281 40.909 0.84 0.12 0.00 2.44
773 1409 1.461091 GCCCCTCGTCACCATCGATA 61.461 60.000 0.00 0.00 36.73 2.92
774 1410 1.257743 CCCCTCGTCACCATCGATAT 58.742 55.000 0.00 0.00 36.73 1.63
831 1471 1.367659 GCATGCAGTGGTCTCTTCTC 58.632 55.000 14.21 0.00 0.00 2.87
882 1522 2.350804 CACATGCAGCTGTACACATCTC 59.649 50.000 16.64 0.00 0.00 2.75
890 1530 0.246360 TGTACACATCTCAGTGCCCG 59.754 55.000 0.00 0.00 43.23 6.13
922 1562 1.278985 TCACAAGGGTATCACTGCCTG 59.721 52.381 0.00 0.00 0.00 4.85
964 1611 5.292765 TGATCGATCTTATCTTGGTGCTTC 58.707 41.667 25.02 0.00 0.00 3.86
981 1628 4.643334 GTGCTTCGGGTTTCCCTATAAATT 59.357 41.667 3.25 0.00 42.67 1.82
1284 1932 1.138247 GTACCACGACTTCGCCGAT 59.862 57.895 0.00 0.00 44.43 4.18
1290 1938 0.038526 ACGACTTCGCCGATGAACTT 60.039 50.000 7.02 0.00 44.43 2.66
1338 1986 1.074951 GGGAACAGTGTTCCTGGGG 59.925 63.158 40.32 0.00 46.06 4.96
1368 2016 1.853114 CTGGCATGATCGGCTGCATC 61.853 60.000 14.33 0.00 40.18 3.91
1469 2119 5.035443 CCAGCTTTCGTACTAGTACATGAC 58.965 45.833 28.03 15.15 35.87 3.06
1546 2196 3.791993 TTAATTGCACGTACGTTGGAC 57.208 42.857 20.23 9.26 0.00 4.02
1962 2612 2.668212 CCGCGCCAAAGGAGTTCA 60.668 61.111 0.00 0.00 0.00 3.18
2017 2667 3.260632 TGAGCTACTACAACCAGCAATGA 59.739 43.478 0.00 0.00 37.78 2.57
2019 2669 4.256920 AGCTACTACAACCAGCAATGAAG 58.743 43.478 0.00 0.00 37.78 3.02
2059 2709 7.616673 TGAATGTGAATTAAAAGTTTGCGTTG 58.383 30.769 0.00 0.00 0.00 4.10
2061 2711 5.105752 TGTGAATTAAAAGTTTGCGTTGCT 58.894 33.333 0.00 0.00 0.00 3.91
2062 2712 5.578727 TGTGAATTAAAAGTTTGCGTTGCTT 59.421 32.000 0.00 0.00 0.00 3.91
2063 2713 6.091441 TGTGAATTAAAAGTTTGCGTTGCTTT 59.909 30.769 0.00 0.00 34.35 3.51
2064 2714 6.407753 GTGAATTAAAAGTTTGCGTTGCTTTG 59.592 34.615 0.00 0.00 33.36 2.77
2069 2719 2.682836 AGTTTGCGTTGCTTTGTTTGT 58.317 38.095 0.00 0.00 0.00 2.83
2096 2746 1.792949 ACTGCTTTCGTCGCTTAGTTG 59.207 47.619 0.00 0.00 0.00 3.16
2100 2750 3.803231 TGCTTTCGTCGCTTAGTTGTTTA 59.197 39.130 0.00 0.00 0.00 2.01
2121 2771 3.623703 ACATGCATGCTTGTAATCCTCA 58.376 40.909 31.27 2.92 33.44 3.86
2122 2772 4.212716 ACATGCATGCTTGTAATCCTCAT 58.787 39.130 31.27 9.13 33.44 2.90
2130 2780 7.095229 GCATGCTTGTAATCCTCATTAATCGTA 60.095 37.037 11.37 0.00 0.00 3.43
2181 2831 6.723298 TTCCAGGTTTTTGTGTGACAATAT 57.277 33.333 0.00 0.00 38.00 1.28
2185 2835 8.138712 TCCAGGTTTTTGTGTGACAATATAAAC 58.861 33.333 0.00 0.00 38.00 2.01
2189 2839 8.964150 GGTTTTTGTGTGACAATATAAACACTC 58.036 33.333 14.21 0.00 42.66 3.51
2201 2851 8.044908 ACAATATAAACACTCGGGTCTTGTAAT 58.955 33.333 0.00 0.00 0.00 1.89
2204 2854 1.346395 ACACTCGGGTCTTGTAATGCA 59.654 47.619 0.00 0.00 0.00 3.96
2206 2856 1.899814 ACTCGGGTCTTGTAATGCAGA 59.100 47.619 0.00 0.00 0.00 4.26
2207 2857 2.501723 ACTCGGGTCTTGTAATGCAGAT 59.498 45.455 0.00 0.00 0.00 2.90
2208 2858 2.868583 CTCGGGTCTTGTAATGCAGATG 59.131 50.000 0.00 0.00 0.00 2.90
2275 3273 5.163561 TGTGATTTGGGTCAGTCACTTTTTC 60.164 40.000 6.01 0.00 41.08 2.29
2278 3282 5.993748 TTTGGGTCAGTCACTTTTTCTTT 57.006 34.783 0.00 0.00 0.00 2.52
2306 3316 1.298157 CGTATGGTGTGCAGTGTGGG 61.298 60.000 0.00 0.00 0.00 4.61
2307 3317 0.960364 GTATGGTGTGCAGTGTGGGG 60.960 60.000 0.00 0.00 0.00 4.96
2318 3328 3.018193 TGTGGGGTGGTGTGGTGT 61.018 61.111 0.00 0.00 0.00 4.16
2319 3329 2.518349 GTGGGGTGGTGTGGTGTG 60.518 66.667 0.00 0.00 0.00 3.82
2320 3330 3.814906 TGGGGTGGTGTGGTGTGG 61.815 66.667 0.00 0.00 0.00 4.17
2321 3331 3.494254 GGGGTGGTGTGGTGTGGA 61.494 66.667 0.00 0.00 0.00 4.02
2322 3332 2.113139 GGGTGGTGTGGTGTGGAG 59.887 66.667 0.00 0.00 0.00 3.86
2323 3333 2.752807 GGGTGGTGTGGTGTGGAGT 61.753 63.158 0.00 0.00 0.00 3.85
2431 3445 1.572085 GCAGCTGAGCGTGATGTGTT 61.572 55.000 20.43 0.00 0.00 3.32
2432 3446 0.165295 CAGCTGAGCGTGATGTGTTG 59.835 55.000 8.42 0.00 0.00 3.33
2433 3447 1.154338 GCTGAGCGTGATGTGTTGC 60.154 57.895 0.00 0.00 0.00 4.17
2434 3448 1.131218 CTGAGCGTGATGTGTTGCG 59.869 57.895 0.00 0.00 0.00 4.85
2435 3449 1.560004 CTGAGCGTGATGTGTTGCGT 61.560 55.000 0.00 0.00 0.00 5.24
2436 3450 1.154599 GAGCGTGATGTGTTGCGTG 60.155 57.895 0.00 0.00 0.00 5.34
2437 3451 2.796617 GCGTGATGTGTTGCGTGC 60.797 61.111 0.00 0.00 0.00 5.34
2438 3452 2.630872 CGTGATGTGTTGCGTGCA 59.369 55.556 0.00 0.00 0.00 4.57
2439 3453 1.207339 CGTGATGTGTTGCGTGCAT 59.793 52.632 0.00 0.00 0.00 3.96
2441 3455 0.518636 GTGATGTGTTGCGTGCATCT 59.481 50.000 0.00 0.00 39.58 2.90
2442 3456 0.518195 TGATGTGTTGCGTGCATCTG 59.482 50.000 0.00 0.00 39.58 2.90
2443 3457 0.518636 GATGTGTTGCGTGCATCTGT 59.481 50.000 0.00 0.00 36.87 3.41
2444 3458 0.518636 ATGTGTTGCGTGCATCTGTC 59.481 50.000 0.00 0.00 0.00 3.51
2448 3463 0.179181 GTTGCGTGCATCTGTCCATG 60.179 55.000 0.00 0.00 0.00 3.66
2458 3473 2.425143 TCTGTCCATGGATTGCTTCC 57.575 50.000 19.62 3.27 45.69 3.46
2491 3506 3.316029 GGTCTGGCCGGTAATGGA 58.684 61.111 12.43 0.00 0.00 3.41
2492 3507 1.146263 GGTCTGGCCGGTAATGGAG 59.854 63.158 12.43 0.00 0.00 3.86
2493 3508 1.523938 GTCTGGCCGGTAATGGAGC 60.524 63.158 12.43 0.00 0.00 4.70
2494 3509 1.992834 TCTGGCCGGTAATGGAGCA 60.993 57.895 12.43 0.00 0.00 4.26
2495 3510 1.524621 CTGGCCGGTAATGGAGCAG 60.525 63.158 2.29 0.00 0.00 4.24
2496 3511 2.902343 GGCCGGTAATGGAGCAGC 60.902 66.667 1.90 0.00 0.00 5.25
2497 3512 2.902343 GCCGGTAATGGAGCAGCC 60.902 66.667 1.90 0.00 37.10 4.85
2498 3513 2.203209 CCGGTAATGGAGCAGCCC 60.203 66.667 0.00 0.00 34.97 5.19
2499 3514 2.588877 CGGTAATGGAGCAGCCCG 60.589 66.667 0.00 0.00 34.97 6.13
2500 3515 2.203209 GGTAATGGAGCAGCCCGG 60.203 66.667 0.00 0.00 34.97 5.73
2501 3516 2.902343 GTAATGGAGCAGCCCGGC 60.902 66.667 0.00 0.00 34.97 6.13
2502 3517 3.407083 TAATGGAGCAGCCCGGCA 61.407 61.111 13.15 0.00 35.83 5.69
2503 3518 3.405093 TAATGGAGCAGCCCGGCAG 62.405 63.158 13.15 4.46 35.83 4.85
2514 3529 4.363990 CCGGCAGAGTCGCAGTGT 62.364 66.667 8.77 0.00 0.00 3.55
2528 3543 1.205655 GCAGTGTGTGGATAGCTCAGA 59.794 52.381 0.00 0.00 0.00 3.27
2576 3591 0.680618 TAGGTCCCACGCGAGAAAAA 59.319 50.000 15.93 0.00 0.00 1.94
2624 3639 1.447317 CCTGACTTTGCGTGCAACCT 61.447 55.000 6.80 0.00 35.46 3.50
2627 3642 1.226746 GACTTTGCGTGCAACCTAGT 58.773 50.000 6.80 8.37 35.46 2.57
2636 3651 1.344763 GTGCAACCTAGTCAGTCACCT 59.655 52.381 0.00 0.00 0.00 4.00
2790 3806 7.219484 TGAGATTTTCCAAGGAAGAATGAAC 57.781 36.000 1.32 1.82 35.38 3.18
2792 3808 7.040201 TGAGATTTTCCAAGGAAGAATGAACTG 60.040 37.037 1.32 0.00 35.38 3.16
2810 3826 3.361786 ACTGGTGGCATTGGTATTAACC 58.638 45.455 0.00 0.00 46.98 2.85
2814 3830 5.580998 TGGTGGCATTGGTATTAACCTTTA 58.419 37.500 0.00 0.00 46.91 1.85
2851 3867 7.775397 ATGAAAACAAATCTGGAACAAACAG 57.225 32.000 0.00 0.00 38.70 3.16
2852 3868 6.105333 TGAAAACAAATCTGGAACAAACAGG 58.895 36.000 0.00 0.00 38.70 4.00
2862 3878 4.187694 TGGAACAAACAGGAACAAATTGC 58.812 39.130 0.00 0.00 31.92 3.56
2863 3879 4.081198 TGGAACAAACAGGAACAAATTGCT 60.081 37.500 0.00 0.00 33.03 3.91
2871 3889 5.348164 ACAGGAACAAATTGCTTACACAAC 58.652 37.500 0.00 0.00 33.54 3.32
2873 3891 5.984926 CAGGAACAAATTGCTTACACAACAT 59.015 36.000 0.00 0.00 33.54 2.71
2875 3893 7.114811 CAGGAACAAATTGCTTACACAACATAC 59.885 37.037 0.00 0.00 33.54 2.39
2876 3894 6.364976 GGAACAAATTGCTTACACAACATACC 59.635 38.462 0.00 0.00 31.03 2.73
2885 3903 7.952671 TGCTTACACAACATACCCAAAAATTA 58.047 30.769 0.00 0.00 0.00 1.40
2926 3944 7.666804 TGCAACAATAAGCATATCATAGTGGAT 59.333 33.333 0.00 0.00 35.51 3.41
2938 3956 9.537192 CATATCATAGTGGATTTTGTGCAAAAT 57.463 29.630 19.11 19.11 43.38 1.82
2971 3989 5.904362 AAGAAGGAATGAATTAGCCACAC 57.096 39.130 0.00 0.00 0.00 3.82
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
15 16 7.642586 CGACGTTGAGAATTTTACCTTCTTTTT 59.357 33.333 0.00 0.00 33.18 1.94
16 17 7.130269 CGACGTTGAGAATTTTACCTTCTTTT 58.870 34.615 0.00 0.00 33.18 2.27
17 18 6.656003 CGACGTTGAGAATTTTACCTTCTTT 58.344 36.000 0.00 0.00 33.18 2.52
18 19 5.333875 GCGACGTTGAGAATTTTACCTTCTT 60.334 40.000 7.08 0.00 33.18 2.52
19 20 4.151867 GCGACGTTGAGAATTTTACCTTCT 59.848 41.667 7.08 0.00 35.69 2.85
20 21 4.392216 GCGACGTTGAGAATTTTACCTTC 58.608 43.478 7.08 0.00 0.00 3.46
21 22 3.187842 GGCGACGTTGAGAATTTTACCTT 59.812 43.478 7.08 0.00 0.00 3.50
22 23 2.740447 GGCGACGTTGAGAATTTTACCT 59.260 45.455 7.08 0.00 0.00 3.08
23 24 2.481185 TGGCGACGTTGAGAATTTTACC 59.519 45.455 7.08 0.00 0.00 2.85
24 25 3.430895 TCTGGCGACGTTGAGAATTTTAC 59.569 43.478 7.08 0.00 0.00 2.01
25 26 3.655486 TCTGGCGACGTTGAGAATTTTA 58.345 40.909 7.08 0.00 0.00 1.52
26 27 2.480419 CTCTGGCGACGTTGAGAATTTT 59.520 45.455 7.08 0.00 0.00 1.82
27 28 2.069273 CTCTGGCGACGTTGAGAATTT 58.931 47.619 7.08 0.00 0.00 1.82
28 29 1.673033 CCTCTGGCGACGTTGAGAATT 60.673 52.381 7.08 0.00 0.00 2.17
29 30 0.108615 CCTCTGGCGACGTTGAGAAT 60.109 55.000 7.08 0.00 0.00 2.40
30 31 1.289066 CCTCTGGCGACGTTGAGAA 59.711 57.895 7.08 0.00 0.00 2.87
31 32 2.962569 CCTCTGGCGACGTTGAGA 59.037 61.111 7.08 0.14 0.00 3.27
32 33 2.811317 GCCTCTGGCGACGTTGAG 60.811 66.667 7.08 0.00 39.62 3.02
42 43 4.845580 ATTGCTCGCCGCCTCTGG 62.846 66.667 0.00 0.00 38.05 3.86
43 44 3.267860 GATTGCTCGCCGCCTCTG 61.268 66.667 0.00 0.00 38.05 3.35
44 45 4.537433 GGATTGCTCGCCGCCTCT 62.537 66.667 0.00 0.00 38.05 3.69
45 46 2.644555 TTAGGATTGCTCGCCGCCTC 62.645 60.000 0.00 0.00 38.05 4.70
46 47 2.650813 CTTAGGATTGCTCGCCGCCT 62.651 60.000 0.00 0.00 38.05 5.52
47 48 2.203015 TTAGGATTGCTCGCCGCC 60.203 61.111 0.00 0.00 38.05 6.13
48 49 1.521681 ACTTAGGATTGCTCGCCGC 60.522 57.895 0.00 0.00 39.77 6.53
49 50 1.154205 CCACTTAGGATTGCTCGCCG 61.154 60.000 0.00 0.00 41.22 6.46
50 51 0.107654 ACCACTTAGGATTGCTCGCC 60.108 55.000 0.00 0.00 41.22 5.54
51 52 1.009829 CACCACTTAGGATTGCTCGC 58.990 55.000 0.00 0.00 41.22 5.03
52 53 1.009829 GCACCACTTAGGATTGCTCG 58.990 55.000 0.00 0.00 41.22 5.03
53 54 2.113860 TGCACCACTTAGGATTGCTC 57.886 50.000 0.00 0.00 39.48 4.26
54 55 2.162681 GTTGCACCACTTAGGATTGCT 58.837 47.619 0.00 0.00 39.48 3.91
55 56 2.162681 AGTTGCACCACTTAGGATTGC 58.837 47.619 0.00 0.00 41.22 3.56
56 57 4.853924 AAAGTTGCACCACTTAGGATTG 57.146 40.909 4.25 0.00 41.22 2.67
122 123 3.941483 CACTGGTTATAGGCTTTGTCCTG 59.059 47.826 0.00 0.00 37.01 3.86
123 124 3.622455 GCACTGGTTATAGGCTTTGTCCT 60.622 47.826 0.00 0.00 40.21 3.85
124 125 2.683362 GCACTGGTTATAGGCTTTGTCC 59.317 50.000 0.00 0.00 0.00 4.02
139 140 2.428171 CCCAACTCATATTTGGCACTGG 59.572 50.000 0.00 0.00 42.06 4.00
142 143 2.102578 AGCCCAACTCATATTTGGCAC 58.897 47.619 0.00 0.00 42.06 5.01
156 157 7.008332 TGTAGATAAGCTGTATAGTAGCCCAA 58.992 38.462 5.52 0.00 42.07 4.12
197 202 6.611642 AGGACAATATAGCTAGACCTTTCACA 59.388 38.462 0.00 0.00 0.00 3.58
198 203 7.056844 AGGACAATATAGCTAGACCTTTCAC 57.943 40.000 0.00 0.00 0.00 3.18
247 252 2.876645 GCACGAGTCTCGCTTCGG 60.877 66.667 22.00 7.94 45.12 4.30
248 253 2.558717 TACGCACGAGTCTCGCTTCG 62.559 60.000 22.00 21.80 45.12 3.79
249 254 1.126996 GTACGCACGAGTCTCGCTTC 61.127 60.000 22.00 10.07 45.12 3.86
250 255 1.154263 GTACGCACGAGTCTCGCTT 60.154 57.895 22.00 6.46 45.12 4.68
251 256 2.479650 GTACGCACGAGTCTCGCT 59.520 61.111 22.00 6.83 45.12 4.93
273 278 1.676014 GCCAAGTCCAGCGTTGTATCT 60.676 52.381 0.00 0.00 0.00 1.98
320 325 4.040936 TGCAAGGCTTTATTACCCTTCA 57.959 40.909 0.00 0.00 36.86 3.02
339 344 3.397482 AGTGTGAACAGTTCAGAGATGC 58.603 45.455 16.68 4.43 41.01 3.91
356 361 6.159988 CAGAGATCCTTCTTTTCGTTAGTGT 58.840 40.000 0.00 0.00 30.30 3.55
403 850 3.857038 AACGAGCCACCGGTGTGT 61.857 61.111 31.80 20.92 41.09 3.72
426 873 3.217599 TCACCAAATCTCTCGACGAAG 57.782 47.619 0.00 0.00 0.00 3.79
523 970 5.234466 AGGATTTGTCTATGCCTATGTCC 57.766 43.478 0.00 0.00 0.00 4.02
618 1254 3.055021 TGACACGGGATAGTTTTATGCCA 60.055 43.478 0.00 0.00 45.39 4.92
753 1389 4.530857 CGATGGTGACGAGGGGCC 62.531 72.222 0.00 0.00 0.00 5.80
773 1409 2.855963 CGGTTGTTTATCGTGCGTCTAT 59.144 45.455 0.00 0.00 0.00 1.98
774 1410 2.252747 CGGTTGTTTATCGTGCGTCTA 58.747 47.619 0.00 0.00 0.00 2.59
882 1522 4.035208 GTGAGAATTATTAACCGGGCACTG 59.965 45.833 6.32 0.00 0.00 3.66
890 1530 8.837389 GTGATACCCTTGTGAGAATTATTAACC 58.163 37.037 0.00 0.00 0.00 2.85
922 1562 2.445654 CCAGAGAGGGAGGAGGGC 60.446 72.222 0.00 0.00 0.00 5.19
1251 1899 1.735559 GTACGAAAACCGCCGCTCT 60.736 57.895 0.00 0.00 43.32 4.09
1284 1932 1.236616 CCATCAGCGCCACAAGTTCA 61.237 55.000 2.29 0.00 0.00 3.18
1290 1938 3.647649 CTCGTCCATCAGCGCCACA 62.648 63.158 2.29 0.00 0.00 4.17
1483 2133 2.988493 TCCTTACGGTCATTTCGTTTCG 59.012 45.455 0.00 0.00 41.38 3.46
1488 2138 3.306166 GTGACATCCTTACGGTCATTTCG 59.694 47.826 0.00 0.00 42.81 3.46
1546 2196 1.625616 GTCGTCGTTGATGTACCTGG 58.374 55.000 0.00 0.00 0.00 4.45
1623 2273 2.106683 CCCACTCGGTGAAATCGGC 61.107 63.158 5.71 0.00 35.23 5.54
1910 2560 1.267574 GGCTGGAGGACTGGATGACA 61.268 60.000 0.00 0.00 0.00 3.58
1962 2612 1.355718 ATGGCCTCAATGACCCGGAT 61.356 55.000 0.73 0.00 0.00 4.18
2017 2667 2.380064 TCAACAAGGCCATGGAACTT 57.620 45.000 18.40 15.93 0.00 2.66
2019 2669 2.299867 ACATTCAACAAGGCCATGGAAC 59.700 45.455 18.40 7.43 0.00 3.62
2077 2727 1.792949 ACAACTAAGCGACGAAAGCAG 59.207 47.619 0.00 0.00 37.01 4.24
2090 2740 6.083098 ACAAGCATGCATGTAAACAACTAA 57.917 33.333 25.90 0.00 0.00 2.24
2096 2746 5.894807 AGGATTACAAGCATGCATGTAAAC 58.105 37.500 37.43 34.32 41.36 2.01
2100 2750 3.623703 TGAGGATTACAAGCATGCATGT 58.376 40.909 29.11 29.11 0.00 3.21
2121 2771 9.193133 CCGATGAAGTAGAAATGTACGATTAAT 57.807 33.333 0.00 0.00 0.00 1.40
2122 2772 8.192774 ACCGATGAAGTAGAAATGTACGATTAA 58.807 33.333 0.00 0.00 0.00 1.40
2130 2780 5.178797 CAAGGACCGATGAAGTAGAAATGT 58.821 41.667 0.00 0.00 0.00 2.71
2138 2788 0.687354 AGCACAAGGACCGATGAAGT 59.313 50.000 7.26 0.00 0.00 3.01
2139 2789 1.813513 AAGCACAAGGACCGATGAAG 58.186 50.000 7.26 1.62 0.00 3.02
2181 2831 3.998341 GCATTACAAGACCCGAGTGTTTA 59.002 43.478 0.00 0.00 0.00 2.01
2185 2835 2.002586 CTGCATTACAAGACCCGAGTG 58.997 52.381 0.00 0.00 0.00 3.51
2189 2839 1.331756 GCATCTGCATTACAAGACCCG 59.668 52.381 0.00 0.00 41.59 5.28
2201 2851 1.250328 CTGTTTCCTTGGCATCTGCA 58.750 50.000 4.33 0.00 44.36 4.41
2204 2854 1.075601 TCCCTGTTTCCTTGGCATCT 58.924 50.000 0.00 0.00 0.00 2.90
2206 2856 0.779997 AGTCCCTGTTTCCTTGGCAT 59.220 50.000 0.00 0.00 0.00 4.40
2207 2857 0.178992 CAGTCCCTGTTTCCTTGGCA 60.179 55.000 0.00 0.00 0.00 4.92
2208 2858 0.110486 TCAGTCCCTGTTTCCTTGGC 59.890 55.000 0.00 0.00 32.61 4.52
2275 3273 0.452987 ACCATACGCTGCATGCAAAG 59.547 50.000 22.88 19.70 43.06 2.77
2278 3282 1.377072 ACACCATACGCTGCATGCA 60.377 52.632 21.29 21.29 43.06 3.96
2292 3302 2.906897 CACCCCACACTGCACACC 60.907 66.667 0.00 0.00 0.00 4.16
2306 3316 1.525995 CACTCCACACCACACCACC 60.526 63.158 0.00 0.00 0.00 4.61
2307 3317 2.186826 GCACTCCACACCACACCAC 61.187 63.158 0.00 0.00 0.00 4.16
2392 3406 3.660111 GAACAGCACACCACGGCC 61.660 66.667 0.00 0.00 0.00 6.13
2417 3431 1.594021 ACGCAACACATCACGCTCA 60.594 52.632 0.00 0.00 0.00 4.26
2421 3435 0.790495 GATGCACGCAACACATCACG 60.790 55.000 0.00 0.00 39.95 4.35
2431 3445 1.746239 CCATGGACAGATGCACGCA 60.746 57.895 5.56 0.00 0.00 5.24
2432 3446 0.816825 ATCCATGGACAGATGCACGC 60.817 55.000 18.99 0.00 0.00 5.34
2433 3447 1.332686 CAATCCATGGACAGATGCACG 59.667 52.381 18.99 0.00 0.00 5.34
2434 3448 1.066605 GCAATCCATGGACAGATGCAC 59.933 52.381 26.46 7.76 0.00 4.57
2435 3449 1.064240 AGCAATCCATGGACAGATGCA 60.064 47.619 29.96 7.09 0.00 3.96
2436 3450 1.688772 AGCAATCCATGGACAGATGC 58.311 50.000 25.09 25.09 0.00 3.91
2437 3451 3.984508 GAAGCAATCCATGGACAGATG 57.015 47.619 18.99 14.67 0.00 2.90
2481 3496 2.203209 GGGCTGCTCCATTACCGG 60.203 66.667 0.00 0.00 36.21 5.28
2482 3497 2.588877 CGGGCTGCTCCATTACCG 60.589 66.667 0.00 0.00 36.21 4.02
2483 3498 2.203209 CCGGGCTGCTCCATTACC 60.203 66.667 0.00 0.00 36.21 2.85
2484 3499 2.902343 GCCGGGCTGCTCCATTAC 60.902 66.667 12.87 0.00 36.21 1.89
2485 3500 3.405093 CTGCCGGGCTGCTCCATTA 62.405 63.158 21.46 0.00 36.21 1.90
2486 3501 4.809496 CTGCCGGGCTGCTCCATT 62.809 66.667 21.46 0.00 36.21 3.16
2490 3505 4.828925 GACTCTGCCGGGCTGCTC 62.829 72.222 21.46 13.07 0.00 4.26
2497 3512 4.363990 ACACTGCGACTCTGCCGG 62.364 66.667 0.00 0.00 0.00 6.13
2498 3513 3.108289 CACACTGCGACTCTGCCG 61.108 66.667 0.00 0.00 0.00 5.69
2499 3514 2.029666 ACACACTGCGACTCTGCC 59.970 61.111 0.00 0.00 0.00 4.85
2500 3515 2.313172 CCACACACTGCGACTCTGC 61.313 63.158 0.00 0.00 0.00 4.26
2501 3516 0.037882 ATCCACACACTGCGACTCTG 60.038 55.000 0.00 0.00 0.00 3.35
2502 3517 1.474478 CTATCCACACACTGCGACTCT 59.526 52.381 0.00 0.00 0.00 3.24
2503 3518 1.914634 CTATCCACACACTGCGACTC 58.085 55.000 0.00 0.00 0.00 3.36
2514 3529 5.053978 TCATCTACTCTGAGCTATCCACA 57.946 43.478 4.19 0.00 0.00 4.17
2592 3607 5.266242 GCAAAGTCAGGTTCGCTATATTTG 58.734 41.667 0.00 0.00 0.00 2.32
2605 3620 1.008538 GGTTGCACGCAAAGTCAGG 60.009 57.895 5.94 0.00 37.70 3.86
2783 3799 1.895131 ACCAATGCCACCAGTTCATTC 59.105 47.619 0.00 0.00 0.00 2.67
2851 3867 6.364976 GGTATGTTGTGTAAGCAATTTGTTCC 59.635 38.462 0.00 0.00 0.00 3.62
2852 3868 6.364976 GGGTATGTTGTGTAAGCAATTTGTTC 59.635 38.462 0.00 0.00 0.00 3.18
2862 3878 8.868916 GCATAATTTTTGGGTATGTTGTGTAAG 58.131 33.333 0.00 0.00 0.00 2.34
2863 3879 8.589338 AGCATAATTTTTGGGTATGTTGTGTAA 58.411 29.630 0.00 0.00 0.00 2.41
2926 3944 5.096443 AGGAAACTCCATTTTGCACAAAA 57.904 34.783 10.70 10.70 39.61 2.44
2930 3948 5.705609 TCTTAGGAAACTCCATTTTGCAC 57.294 39.130 0.00 0.00 43.67 4.57


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

AutoCloner maintained by Alex Coulton.