Multiple sequence alignment - TraesCS2A01G181200

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 TraesCS2A01G181200 chr2A 100.000 3599 0 0 1 3599 140367152 140363554 0.000000e+00 6647.0
1 TraesCS2A01G181200 chr2A 83.333 90 13 2 2009 2096 670314622 670314533 8.280000e-12 82.4
2 TraesCS2A01G181200 chr2D 90.917 3523 132 64 1 3443 132705741 132702327 0.000000e+00 4560.0
3 TraesCS2A01G181200 chr2D 95.122 123 6 0 3477 3599 132702265 132702143 1.020000e-45 195.0
4 TraesCS2A01G181200 chr2B 92.880 3118 103 52 524 3598 188471292 188468251 0.000000e+00 4418.0
5 TraesCS2A01G181200 chr2B 85.327 443 41 5 2 444 188471712 188471294 1.530000e-118 436.0
6 TraesCS2A01G181200 chr2B 84.946 372 33 15 2981 3341 53460955 53461314 4.420000e-94 355.0
7 TraesCS2A01G181200 chr2B 77.475 404 41 17 3067 3443 519434563 519434183 2.830000e-46 196.0
8 TraesCS2A01G181200 chr2B 90.244 82 6 2 448 527 195678231 195678150 4.910000e-19 106.0
9 TraesCS2A01G181200 chr1A 85.465 344 25 12 2981 3310 565150100 565150432 5.760000e-88 335.0
10 TraesCS2A01G181200 chr5B 83.003 353 26 13 2981 3310 262567867 262567526 1.260000e-74 291.0
11 TraesCS2A01G181200 chr5B 76.093 389 58 17 3074 3443 71162337 71161965 1.720000e-38 171.0
12 TraesCS2A01G181200 chr5B 86.897 145 7 5 3059 3203 708404475 708404343 6.220000e-33 152.0
13 TraesCS2A01G181200 chr3B 83.003 353 26 13 2981 3310 735974086 735974427 1.260000e-74 291.0
14 TraesCS2A01G181200 chr3B 87.786 131 4 5 3063 3193 413565306 413565424 3.750000e-30 143.0
15 TraesCS2A01G181200 chr3B 84.828 145 10 5 3059 3203 461803126 461802994 6.270000e-28 135.0
16 TraesCS2A01G181200 chr7D 81.553 309 24 20 947 1250 28069200 28069480 1.300000e-54 224.0
17 TraesCS2A01G181200 chr4A 91.781 73 6 0 448 520 57167263 57167335 6.360000e-18 102.0
18 TraesCS2A01G181200 chr4A 96.970 33 1 0 2316 2348 544397633 544397665 5.020000e-04 56.5
19 TraesCS2A01G181200 chr4D 88.312 77 5 4 446 518 399535194 399535270 4.950000e-14 89.8
20 TraesCS2A01G181200 chr4D 96.970 33 1 0 2316 2348 52215648 52215680 5.020000e-04 56.5
21 TraesCS2A01G181200 chr7B 89.552 67 5 2 1748 1812 312434120 312434054 2.300000e-12 84.2
22 TraesCS2A01G181200 chr6B 89.655 58 6 0 1752 1809 126525658 126525715 1.390000e-09 75.0
23 TraesCS2A01G181200 chr4B 96.970 33 1 0 2316 2348 76565482 76565450 5.020000e-04 56.5


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 TraesCS2A01G181200 chr2A 140363554 140367152 3598 True 6647.0 6647 100.0000 1 3599 1 chr2A.!!$R1 3598
1 TraesCS2A01G181200 chr2D 132702143 132705741 3598 True 2377.5 4560 93.0195 1 3599 2 chr2D.!!$R1 3598
2 TraesCS2A01G181200 chr2B 188468251 188471712 3461 True 2427.0 4418 89.1035 2 3598 2 chr2B.!!$R3 3596

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
156 157 1.00225 CGTCGTCGAAGTCCTTGTGG 61.002 60.000 0.0 0.0 39.71 4.17 F
1507 1564 1.00990 CGATGAGTACGACGAGGCC 60.010 63.158 0.0 0.0 0.00 5.19 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1585 1648 0.105709 CCTCCTCCTCCTCCTTCTCC 60.106 65.0 0.00 0.00 0.00 3.71 R
3212 3297 0.105709 TCACCCTGTCAGTCAGTGGA 60.106 55.0 12.44 1.47 42.19 4.02 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
62 63 8.076178 CAGTTATTACACACCAAAAGAAGAAGG 58.924 37.037 0.00 0.00 0.00 3.46
71 72 4.079730 ACCAAAAGAAGAAGGAACCTCACT 60.080 41.667 0.00 0.00 0.00 3.41
125 126 9.500785 AATTAACACCATTTGTATTTTTCCTGG 57.499 29.630 0.00 0.00 37.51 4.45
156 157 1.002250 CGTCGTCGAAGTCCTTGTGG 61.002 60.000 0.00 0.00 39.71 4.17
192 193 2.596452 CTCGCTAAAGAAACTCGCTCA 58.404 47.619 0.00 0.00 0.00 4.26
212 214 6.512903 CGCTCAAGCTCAAATCATTATGTGAT 60.513 38.462 0.00 0.00 43.46 3.06
262 264 8.764524 TTACACAACAAAACATTTACAAGCTT 57.235 26.923 0.00 0.00 0.00 3.74
263 265 7.289587 ACACAACAAAACATTTACAAGCTTC 57.710 32.000 0.00 0.00 0.00 3.86
264 266 6.312672 ACACAACAAAACATTTACAAGCTTCC 59.687 34.615 0.00 0.00 0.00 3.46
265 267 5.815222 ACAACAAAACATTTACAAGCTTCCC 59.185 36.000 0.00 0.00 0.00 3.97
266 268 4.956085 ACAAAACATTTACAAGCTTCCCC 58.044 39.130 0.00 0.00 0.00 4.81
267 269 4.653801 ACAAAACATTTACAAGCTTCCCCT 59.346 37.500 0.00 0.00 0.00 4.79
268 270 5.836358 ACAAAACATTTACAAGCTTCCCCTA 59.164 36.000 0.00 0.00 0.00 3.53
269 271 6.325286 ACAAAACATTTACAAGCTTCCCCTAA 59.675 34.615 0.00 0.00 0.00 2.69
270 272 6.987403 AAACATTTACAAGCTTCCCCTAAA 57.013 33.333 0.00 0.00 0.00 1.85
271 273 6.987403 AACATTTACAAGCTTCCCCTAAAA 57.013 33.333 0.00 0.00 0.00 1.52
272 274 6.987403 ACATTTACAAGCTTCCCCTAAAAA 57.013 33.333 0.00 0.00 0.00 1.94
335 337 3.490761 GCAACACCACTTTATGTGCAAGT 60.491 43.478 0.00 0.00 44.92 3.16
348 350 2.263077 GTGCAAGTGAGACCATCTACG 58.737 52.381 0.00 0.00 0.00 3.51
349 351 1.893137 TGCAAGTGAGACCATCTACGT 59.107 47.619 0.00 0.00 0.00 3.57
350 352 2.094700 TGCAAGTGAGACCATCTACGTC 60.095 50.000 0.00 0.00 0.00 4.34
378 381 6.477053 TTCCTTTCAAATTGACCATCAACA 57.523 33.333 0.00 0.00 39.45 3.33
411 414 3.822735 TCAATTTGCTCTGTTCCTTCCAG 59.177 43.478 0.00 0.00 0.00 3.86
427 430 1.626321 TCCAGCCCGAAGAATTGTGTA 59.374 47.619 0.00 0.00 0.00 2.90
447 450 7.450074 TGTGTAGGCTATCCGAATAAAATGAT 58.550 34.615 0.00 0.00 37.47 2.45
448 451 7.936847 TGTGTAGGCTATCCGAATAAAATGATT 59.063 33.333 0.00 0.00 37.47 2.57
449 452 8.784043 GTGTAGGCTATCCGAATAAAATGATTT 58.216 33.333 0.00 0.00 37.47 2.17
450 453 9.349713 TGTAGGCTATCCGAATAAAATGATTTT 57.650 29.630 8.35 8.35 37.47 1.82
507 510 3.342377 TCACAGGATTACAATCGGCAA 57.658 42.857 0.00 0.00 36.27 4.52
508 511 3.006940 TCACAGGATTACAATCGGCAAC 58.993 45.455 0.00 0.00 36.27 4.17
735 779 1.537889 CTCTGGGTGGGTGTGGGTA 60.538 63.158 0.00 0.00 0.00 3.69
772 816 7.041984 GGGTGTCAGTTTGTTTGTTTTGTTTAA 60.042 33.333 0.00 0.00 0.00 1.52
773 817 8.336080 GGTGTCAGTTTGTTTGTTTTGTTTAAA 58.664 29.630 0.00 0.00 0.00 1.52
774 818 9.704098 GTGTCAGTTTGTTTGTTTTGTTTAAAA 57.296 25.926 0.00 0.00 33.57 1.52
775 819 9.922305 TGTCAGTTTGTTTGTTTTGTTTAAAAG 57.078 25.926 0.00 0.00 36.51 2.27
928 972 2.012236 ACCTTTCCTCCCCTCTACTCT 58.988 52.381 0.00 0.00 0.00 3.24
1071 1116 2.402388 CGCATCGCTGCTTCTTGG 59.598 61.111 9.85 0.00 46.65 3.61
1129 1186 2.360191 GGGATGCACCACCACCAT 59.640 61.111 7.49 0.00 41.20 3.55
1255 1312 2.652496 GCCGACGACGAGCTGATC 60.652 66.667 9.28 0.00 42.66 2.92
1372 1429 3.519930 GCCGACGAGGAGGAGGAC 61.520 72.222 0.00 0.00 45.00 3.85
1507 1564 1.009900 CGATGAGTACGACGAGGCC 60.010 63.158 0.00 0.00 0.00 5.19
1528 1591 4.681978 GGCGACGTGGACCTGCTT 62.682 66.667 0.11 0.00 0.00 3.91
1554 1617 2.104530 GGAGTACTCCTTCGCCGC 59.895 66.667 31.12 5.27 46.16 6.53
1555 1618 2.278013 GAGTACTCCTTCGCCGCG 60.278 66.667 12.13 6.39 0.00 6.46
1556 1619 3.753070 GAGTACTCCTTCGCCGCGG 62.753 68.421 24.05 24.05 0.00 6.46
1557 1620 3.818787 GTACTCCTTCGCCGCGGA 61.819 66.667 33.48 5.65 0.00 5.54
1603 1666 0.467290 CGGAGAAGGAGGAGGAGGAG 60.467 65.000 0.00 0.00 0.00 3.69
1604 1667 0.105709 GGAGAAGGAGGAGGAGGAGG 60.106 65.000 0.00 0.00 0.00 4.30
1605 1668 0.930726 GAGAAGGAGGAGGAGGAGGA 59.069 60.000 0.00 0.00 0.00 3.71
1606 1669 0.933700 AGAAGGAGGAGGAGGAGGAG 59.066 60.000 0.00 0.00 0.00 3.69
1607 1670 0.105709 GAAGGAGGAGGAGGAGGAGG 60.106 65.000 0.00 0.00 0.00 4.30
1608 1671 0.556380 AAGGAGGAGGAGGAGGAGGA 60.556 60.000 0.00 0.00 0.00 3.71
1622 1685 1.047801 GGAGGAAGAGGAGATGGAGC 58.952 60.000 0.00 0.00 0.00 4.70
1873 1936 1.080435 GGAACGGCTACGGCTACAAC 61.080 60.000 0.00 0.00 46.48 3.32
1888 1951 1.509370 CAACTCCGACGACGACTCG 60.509 63.158 9.28 0.59 46.06 4.18
2374 2443 4.856607 GACGCCGCCTTCTCCTCG 62.857 72.222 0.00 0.00 0.00 4.63
2498 2573 3.522731 CGTCGGAGGAGGCCTGAG 61.523 72.222 12.00 0.00 31.76 3.35
2720 2800 1.606189 TCAGAGAAGCCATCGATCTCG 59.394 52.381 0.00 0.00 43.40 4.04
2726 2806 3.514777 GCCATCGATCTCGGCATTA 57.485 52.632 17.83 0.00 45.52 1.90
2770 2852 9.657419 AAAAGAAAGAAAGAAAGAAAGAATGCA 57.343 25.926 0.00 0.00 0.00 3.96
2771 2853 9.828039 AAAGAAAGAAAGAAAGAAAGAATGCAT 57.172 25.926 0.00 0.00 0.00 3.96
2772 2854 9.828039 AAGAAAGAAAGAAAGAAAGAATGCATT 57.172 25.926 12.83 12.83 0.00 3.56
2773 2855 9.828039 AGAAAGAAAGAAAGAAAGAATGCATTT 57.172 25.926 14.33 0.00 0.00 2.32
2775 2857 9.828039 AAAGAAAGAAAGAAAGAATGCATTTCT 57.172 25.926 14.33 10.60 46.37 2.52
2968 3051 4.664536 TGGATGGATGGAGATTTGGTCATA 59.335 41.667 0.00 0.00 0.00 2.15
2970 3053 4.071961 TGGATGGAGATTTGGTCATACG 57.928 45.455 0.00 0.00 0.00 3.06
2971 3054 2.808543 GGATGGAGATTTGGTCATACGC 59.191 50.000 0.00 0.00 0.00 4.42
2974 3057 3.884895 TGGAGATTTGGTCATACGCATT 58.115 40.909 0.00 0.00 0.00 3.56
3017 3100 4.325472 GCTGTTAAGCTTTGCTAATTGCTG 59.675 41.667 3.20 0.00 46.60 4.41
3025 3108 0.818938 TGCTAATTGCTGCCCATGTG 59.181 50.000 0.00 0.00 43.37 3.21
3026 3109 0.103572 GCTAATTGCTGCCCATGTGG 59.896 55.000 0.00 0.00 38.95 4.17
3027 3110 1.477553 CTAATTGCTGCCCATGTGGT 58.522 50.000 0.00 0.00 36.04 4.16
3028 3111 1.135527 CTAATTGCTGCCCATGTGGTG 59.864 52.381 0.00 0.00 36.04 4.17
3150 3233 1.339438 TGAGATCTCCAGCAACCAAGC 60.339 52.381 20.03 0.00 0.00 4.01
3151 3234 0.694771 AGATCTCCAGCAACCAAGCA 59.305 50.000 0.00 0.00 36.85 3.91
3152 3235 1.074405 AGATCTCCAGCAACCAAGCAA 59.926 47.619 0.00 0.00 36.85 3.91
3153 3236 1.200948 GATCTCCAGCAACCAAGCAAC 59.799 52.381 0.00 0.00 36.85 4.17
3162 3245 0.539518 AACCAAGCAACCAACCAACC 59.460 50.000 0.00 0.00 0.00 3.77
3182 3265 1.208614 CTTTGCTTCAGTCGCTGCC 59.791 57.895 0.00 0.00 0.00 4.85
3236 3321 2.693069 CTGACTGACAGGGTGACAATC 58.307 52.381 7.51 0.00 42.39 2.67
3237 3322 2.037641 CTGACTGACAGGGTGACAATCA 59.962 50.000 7.51 0.00 42.39 2.57
3238 3323 2.037641 TGACTGACAGGGTGACAATCAG 59.962 50.000 7.51 0.00 39.59 2.90
3239 3324 1.271054 ACTGACAGGGTGACAATCAGC 60.271 52.381 7.51 0.00 43.63 4.26
3270 3355 2.503895 AGCTAAGCCATCAAGCAAGT 57.496 45.000 0.00 0.00 38.75 3.16
3271 3356 2.800250 AGCTAAGCCATCAAGCAAGTT 58.200 42.857 0.00 0.00 38.75 2.66
3272 3357 3.160269 AGCTAAGCCATCAAGCAAGTTT 58.840 40.909 0.00 0.00 38.75 2.66
3273 3358 3.575687 AGCTAAGCCATCAAGCAAGTTTT 59.424 39.130 0.00 0.00 38.75 2.43
3274 3359 3.922850 GCTAAGCCATCAAGCAAGTTTTC 59.077 43.478 0.00 0.00 36.26 2.29
3275 3360 3.391506 AAGCCATCAAGCAAGTTTTCC 57.608 42.857 0.00 0.00 34.23 3.13
3276 3361 1.620323 AGCCATCAAGCAAGTTTTCCC 59.380 47.619 0.00 0.00 34.23 3.97
3277 3362 1.344114 GCCATCAAGCAAGTTTTCCCA 59.656 47.619 0.00 0.00 0.00 4.37
3278 3363 2.224257 GCCATCAAGCAAGTTTTCCCAA 60.224 45.455 0.00 0.00 0.00 4.12
3279 3364 3.392882 CCATCAAGCAAGTTTTCCCAAC 58.607 45.455 0.00 0.00 0.00 3.77
3280 3365 3.181467 CCATCAAGCAAGTTTTCCCAACA 60.181 43.478 0.00 0.00 0.00 3.33
3281 3366 4.440880 CATCAAGCAAGTTTTCCCAACAA 58.559 39.130 0.00 0.00 0.00 2.83
3282 3367 4.751767 TCAAGCAAGTTTTCCCAACAAT 57.248 36.364 0.00 0.00 0.00 2.71
3283 3368 4.440880 TCAAGCAAGTTTTCCCAACAATG 58.559 39.130 0.00 0.00 0.00 2.82
3284 3369 2.837498 AGCAAGTTTTCCCAACAATGC 58.163 42.857 7.18 7.18 36.29 3.56
3285 3370 2.170187 AGCAAGTTTTCCCAACAATGCA 59.830 40.909 14.19 0.00 37.56 3.96
3403 3491 3.758554 ACTGTACTGGTGAAATGATTGGC 59.241 43.478 4.66 0.00 0.00 4.52
3425 3513 1.338973 AGCACAGTGGAGCAACAAATG 59.661 47.619 11.67 0.00 32.55 2.32
3433 3521 5.860182 CAGTGGAGCAACAAATGTTTATGAG 59.140 40.000 0.00 0.00 35.83 2.90
3471 3563 1.714899 GCGTGGTGGCATGTGGTATC 61.715 60.000 0.00 0.00 0.00 2.24
3577 3698 1.742831 TGCAGCGGCCAAAATAGTTAG 59.257 47.619 6.32 0.00 40.13 2.34
3587 3708 6.202954 CGGCCAAAATAGTTAGAGATTAGTGG 59.797 42.308 2.24 0.00 0.00 4.00
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
10 11 1.618837 AGCAACGTGTAGACATCCTGT 59.381 47.619 0.00 0.00 0.00 4.00
46 47 4.207955 GAGGTTCCTTCTTCTTTTGGTGT 58.792 43.478 0.00 0.00 0.00 4.16
62 63 3.117046 GCGAGTAATAGCAGTGAGGTTC 58.883 50.000 0.00 0.00 0.00 3.62
71 72 3.740141 GCTTTACCCAGCGAGTAATAGCA 60.740 47.826 16.23 0.00 35.82 3.49
125 126 0.840729 CGACGACGAATCAAGCTAGC 59.159 55.000 6.62 6.62 42.66 3.42
156 157 1.281899 CGAGGAGAAATGAAGACCGC 58.718 55.000 0.00 0.00 0.00 5.68
192 193 7.287005 ACCATCATCACATAATGATTTGAGCTT 59.713 33.333 0.00 0.00 46.54 3.74
212 214 8.922931 ATGCATTGTTATATCTACAACCATCA 57.077 30.769 0.00 3.49 38.23 3.07
272 274 9.054969 AGCGATGCGTATAGCTTGTAAATGTTT 62.055 37.037 14.89 0.00 41.68 2.83
273 275 7.667039 AGCGATGCGTATAGCTTGTAAATGTT 61.667 38.462 14.89 0.00 41.68 2.71
274 276 6.248719 AGCGATGCGTATAGCTTGTAAATGT 61.249 40.000 14.89 0.00 41.68 2.71
275 277 4.150627 AGCGATGCGTATAGCTTGTAAATG 59.849 41.667 14.89 0.00 41.68 2.32
276 278 4.307432 AGCGATGCGTATAGCTTGTAAAT 58.693 39.130 14.89 0.00 41.68 1.40
277 279 3.713288 AGCGATGCGTATAGCTTGTAAA 58.287 40.909 14.89 0.00 41.68 2.01
278 280 3.364889 AGCGATGCGTATAGCTTGTAA 57.635 42.857 14.89 0.00 41.68 2.41
279 281 4.696899 ATAGCGATGCGTATAGCTTGTA 57.303 40.909 24.16 8.97 41.68 2.41
280 282 3.577649 ATAGCGATGCGTATAGCTTGT 57.422 42.857 24.16 12.19 41.68 3.16
281 283 6.575083 AATTATAGCGATGCGTATAGCTTG 57.425 37.500 24.16 0.00 41.68 4.01
282 284 6.811665 TGAAATTATAGCGATGCGTATAGCTT 59.188 34.615 24.16 14.81 41.68 3.74
285 287 7.649705 AGGATGAAATTATAGCGATGCGTATAG 59.350 37.037 0.00 0.00 0.00 1.31
291 293 5.091431 GCAAGGATGAAATTATAGCGATGC 58.909 41.667 0.00 0.00 0.00 3.91
378 381 5.068198 ACAGAGCAAATTGACATTGTGAAGT 59.932 36.000 0.00 0.00 0.00 3.01
411 414 0.733150 GCCTACACAATTCTTCGGGC 59.267 55.000 0.00 0.00 0.00 6.13
481 484 5.118990 CCGATTGTAATCCTGTGAATCTGT 58.881 41.667 0.00 0.00 31.68 3.41
482 485 4.024556 GCCGATTGTAATCCTGTGAATCTG 60.025 45.833 0.00 0.00 31.68 2.90
490 493 2.030457 GTCGTTGCCGATTGTAATCCTG 59.970 50.000 0.00 0.00 46.30 3.86
507 510 7.095899 GGTTTCGTTTTATTCTGAACTAGTCGT 60.096 37.037 0.00 0.00 0.00 4.34
508 511 7.115947 AGGTTTCGTTTTATTCTGAACTAGTCG 59.884 37.037 0.00 0.00 0.00 4.18
519 522 9.155053 CAGCGATTAATAGGTTTCGTTTTATTC 57.845 33.333 0.00 0.00 34.24 1.75
595 603 7.275341 TGCCGAATATTTGTTTCAATTCATGAC 59.725 33.333 0.00 0.00 37.92 3.06
707 725 1.680651 CACCCAGAGAGAGAGCCGT 60.681 63.158 0.00 0.00 0.00 5.68
710 728 1.305718 ACCCACCCAGAGAGAGAGC 60.306 63.158 0.00 0.00 0.00 4.09
962 1006 1.889105 CGCGACCATTGGGGATCTG 60.889 63.158 0.00 0.00 41.15 2.90
1071 1116 2.658593 CGTCCATGATCGACCGGC 60.659 66.667 0.00 0.00 0.00 6.13
1075 1120 2.104331 ACGGCGTCCATGATCGAC 59.896 61.111 6.77 8.96 0.00 4.20
1118 1175 1.603455 GGTGGTGATGGTGGTGGTG 60.603 63.158 0.00 0.00 0.00 4.17
1119 1176 2.081787 TGGTGGTGATGGTGGTGGT 61.082 57.895 0.00 0.00 0.00 4.16
1120 1177 1.603455 GTGGTGGTGATGGTGGTGG 60.603 63.158 0.00 0.00 0.00 4.61
1129 1186 2.751731 CCTGTGGTGGTGGTGGTGA 61.752 63.158 0.00 0.00 0.00 4.02
1512 1569 3.414700 CAAGCAGGTCCACGTCGC 61.415 66.667 0.00 0.00 0.00 5.19
1585 1648 0.105709 CCTCCTCCTCCTCCTTCTCC 60.106 65.000 0.00 0.00 0.00 3.71
1603 1666 1.047801 GCTCCATCTCCTCTTCCTCC 58.952 60.000 0.00 0.00 0.00 4.30
1604 1667 1.047801 GGCTCCATCTCCTCTTCCTC 58.952 60.000 0.00 0.00 0.00 3.71
1605 1668 0.758685 CGGCTCCATCTCCTCTTCCT 60.759 60.000 0.00 0.00 0.00 3.36
1606 1669 1.745264 CGGCTCCATCTCCTCTTCC 59.255 63.158 0.00 0.00 0.00 3.46
1607 1670 1.745264 CCGGCTCCATCTCCTCTTC 59.255 63.158 0.00 0.00 0.00 2.87
1608 1671 2.439104 GCCGGCTCCATCTCCTCTT 61.439 63.158 22.15 0.00 0.00 2.85
2167 2236 0.109412 CGAACGAGGTGTAGGTGTCC 60.109 60.000 0.00 0.00 0.00 4.02
2374 2443 4.253257 CCGTAGAGCTCGCCGTCC 62.253 72.222 21.24 3.22 0.00 4.79
2482 2557 3.844090 GCTCAGGCCTCCTCCGAC 61.844 72.222 0.00 0.00 0.00 4.79
2541 2616 1.635663 CGGTTTGCGGATCGAGCTTT 61.636 55.000 0.00 0.00 35.28 3.51
2720 2800 7.404671 TTTCCTAATCAAGAACCTTAATGCC 57.595 36.000 0.00 0.00 0.00 4.40
2902 2985 5.176958 GGAAATAAACTATGACGACCCGATG 59.823 44.000 0.00 0.00 0.00 3.84
2968 3051 5.183140 AGGCTAAAAATAACACTGAATGCGT 59.817 36.000 0.00 0.00 0.00 5.24
2970 3053 6.183360 GCAAGGCTAAAAATAACACTGAATGC 60.183 38.462 0.00 0.00 0.00 3.56
2971 3054 7.062605 CAGCAAGGCTAAAAATAACACTGAATG 59.937 37.037 0.00 0.00 36.40 2.67
2974 3057 5.534654 ACAGCAAGGCTAAAAATAACACTGA 59.465 36.000 0.00 0.00 36.40 3.41
3025 3108 1.142262 ACTTCAGTTACCACCACCACC 59.858 52.381 0.00 0.00 0.00 4.61
3026 3109 2.632987 ACTTCAGTTACCACCACCAC 57.367 50.000 0.00 0.00 0.00 4.16
3027 3110 3.070446 CAGTACTTCAGTTACCACCACCA 59.930 47.826 0.00 0.00 0.00 4.17
3028 3111 3.322828 TCAGTACTTCAGTTACCACCACC 59.677 47.826 0.00 0.00 0.00 4.61
3150 3233 1.151172 GCAAAGCGGTTGGTTGGTTG 61.151 55.000 0.00 0.00 37.73 3.77
3151 3234 1.142965 GCAAAGCGGTTGGTTGGTT 59.857 52.632 0.00 0.00 37.73 3.67
3152 3235 1.756561 AGCAAAGCGGTTGGTTGGT 60.757 52.632 0.00 0.00 45.71 3.67
3153 3236 3.128375 AGCAAAGCGGTTGGTTGG 58.872 55.556 0.00 0.00 45.71 3.77
3162 3245 1.154525 CAGCGACTGAAGCAAAGCG 60.155 57.895 1.18 0.00 37.01 4.68
3212 3297 0.105709 TCACCCTGTCAGTCAGTGGA 60.106 55.000 12.44 1.47 42.19 4.02
3215 3300 1.496060 TTGTCACCCTGTCAGTCAGT 58.504 50.000 0.00 0.00 42.19 3.41
3236 3321 1.620739 TAGCTTCTCCTGGCTGGCTG 61.621 60.000 5.39 1.43 39.31 4.85
3237 3322 0.911525 TTAGCTTCTCCTGGCTGGCT 60.912 55.000 5.39 1.60 39.31 4.75
3238 3323 0.463474 CTTAGCTTCTCCTGGCTGGC 60.463 60.000 5.39 0.00 39.31 4.85
3239 3324 0.463474 GCTTAGCTTCTCCTGGCTGG 60.463 60.000 3.65 3.65 39.31 4.85
3270 3355 2.433604 TGCTCTTGCATTGTTGGGAAAA 59.566 40.909 0.00 0.00 45.31 2.29
3271 3356 2.037901 TGCTCTTGCATTGTTGGGAAA 58.962 42.857 0.00 0.00 45.31 3.13
3272 3357 1.702182 TGCTCTTGCATTGTTGGGAA 58.298 45.000 0.00 0.00 45.31 3.97
3273 3358 3.435846 TGCTCTTGCATTGTTGGGA 57.564 47.368 0.00 0.00 45.31 4.37
3283 3368 0.109412 GTCCAGTGCAATGCTCTTGC 60.109 55.000 9.04 15.07 45.11 4.01
3284 3369 0.524862 GGTCCAGTGCAATGCTCTTG 59.475 55.000 9.04 4.58 29.56 3.02
3285 3370 0.610232 GGGTCCAGTGCAATGCTCTT 60.610 55.000 9.04 0.00 29.56 2.85
3344 3429 1.663135 GCTTCCATCGCTCTGAAGAAC 59.337 52.381 0.00 0.00 38.16 3.01
3347 3432 3.756739 AGCTTCCATCGCTCTGAAG 57.243 52.632 0.00 0.00 38.77 3.02
3374 3459 5.650266 TCATTTCACCAGTACAGTGTGTTTT 59.350 36.000 5.88 0.00 36.58 2.43
3403 3491 1.882912 TTGTTGCTCCACTGTGCTAG 58.117 50.000 1.29 3.26 32.27 3.42
3425 3513 3.075866 GCATGCTTGCTCCTCATAAAC 57.924 47.619 16.80 0.00 45.77 2.01
3471 3563 2.169789 CAAGGCTCGTCCTGCATCG 61.170 63.158 0.00 0.00 46.94 3.84
3524 3645 2.433838 CAGCAGGACAGTGGCTCG 60.434 66.667 0.00 0.00 35.27 5.03


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

AutoCloner maintained by Alex Coulton.