Multiple sequence alignment - TraesCS2A01G260700

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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 TraesCS2A01G260700 chr2A 100.000 4538 0 0 1 4538 410863969 410859432 0.000000e+00 8381.0
1 TraesCS2A01G260700 chr2A 86.486 222 21 4 2452 2668 410861299 410861082 7.590000e-58 235.0
2 TraesCS2A01G260700 chr2A 86.486 222 21 4 2671 2888 410861518 410861302 7.590000e-58 235.0
3 TraesCS2A01G260700 chr2A 85.185 189 25 3 2673 2860 410861030 410860844 1.670000e-44 191.0
4 TraesCS2A01G260700 chr2A 85.185 189 25 3 2940 3126 410861297 410861110 1.670000e-44 191.0
5 TraesCS2A01G260700 chr2A 76.923 156 25 6 42 186 152312035 152312190 1.350000e-10 78.7
6 TraesCS2A01G260700 chr2A 81.579 76 10 4 436 510 593902459 593902387 4.900000e-05 60.2
7 TraesCS2A01G260700 chr2A 97.143 35 1 0 432 466 593902909 593902875 4.900000e-05 60.2
8 TraesCS2A01G260700 chr2B 90.399 2333 153 33 25 2303 388500405 388502720 0.000000e+00 3001.0
9 TraesCS2A01G260700 chr2B 93.043 1538 70 21 2304 3819 388502777 388504299 0.000000e+00 2213.0
10 TraesCS2A01G260700 chr2B 90.719 334 29 2 4205 4538 388505438 388505769 1.160000e-120 444.0
11 TraesCS2A01G260700 chr2B 81.903 431 54 14 2669 3089 388502655 388503071 4.350000e-90 342.0
12 TraesCS2A01G260700 chr2B 90.909 187 15 2 2449 2635 388503134 388503318 2.710000e-62 250.0
13 TraesCS2A01G260700 chr2B 87.845 181 19 3 2940 3118 388503139 388503318 4.600000e-50 209.0
14 TraesCS2A01G260700 chr2B 83.636 220 21 6 2673 2888 388502926 388503134 4.630000e-45 193.0
15 TraesCS2A01G260700 chr2B 82.857 210 11 8 3879 4085 388504460 388504647 1.010000e-36 165.0
16 TraesCS2A01G260700 chr2B 89.655 87 9 0 4120 4206 388504648 388504734 1.330000e-20 111.0
17 TraesCS2A01G260700 chr2D 94.595 1554 68 10 760 2303 320251266 320252813 0.000000e+00 2390.0
18 TraesCS2A01G260700 chr2D 92.759 1160 55 17 2668 3819 320252984 320254122 0.000000e+00 1650.0
19 TraesCS2A01G260700 chr2D 83.333 612 58 29 175 758 320250632 320251227 4.020000e-145 525.0
20 TraesCS2A01G260700 chr2D 88.642 405 16 4 3821 4204 320254265 320254660 2.470000e-127 466.0
21 TraesCS2A01G260700 chr2D 91.642 335 27 1 4204 4538 320254722 320255055 3.200000e-126 462.0
22 TraesCS2A01G260700 chr2D 88.489 278 16 6 2359 2635 320252906 320253168 5.660000e-84 322.0
23 TraesCS2A01G260700 chr2D 87.634 186 20 3 2668 2852 320253251 320253434 3.560000e-51 213.0
24 TraesCS2A01G260700 chr2D 85.787 197 25 3 2932 3126 320252981 320253176 5.950000e-49 206.0
25 TraesCS2A01G260700 chr5A 90.984 244 21 1 1000 1243 588852153 588852395 1.220000e-85 327.0
26 TraesCS2A01G260700 chr5D 88.000 275 29 3 1000 1272 468651741 468652013 5.660000e-84 322.0
27 TraesCS2A01G260700 chr5B 90.574 244 22 1 1000 1243 575253007 575253249 5.660000e-84 322.0


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 TraesCS2A01G260700 chr2A 410859432 410863969 4537 True 1846.600000 8381 88.668400 1 4538 5 chr2A.!!$R1 4537
1 TraesCS2A01G260700 chr2B 388500405 388505769 5364 False 769.777778 3001 87.885111 25 4538 9 chr2B.!!$F1 4513
2 TraesCS2A01G260700 chr2D 320250632 320255055 4423 False 779.250000 2390 89.110125 175 4538 8 chr2D.!!$F1 4363

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
134 135 0.247185 ACCATGGAAATTTGCCGCTG 59.753 50.000 21.47 2.63 0.00 5.18 F
171 172 0.890996 CTTGGTGGCCCAACAGAGTC 60.891 60.000 0.00 0.00 45.93 3.36 F
990 1085 1.073923 GAGGAAGGGAGAAGCCAACAA 59.926 52.381 0.00 0.00 38.95 2.83 F
991 1086 1.202940 AGGAAGGGAGAAGCCAACAAC 60.203 52.381 0.00 0.00 38.95 3.32 F
992 1087 1.478654 GGAAGGGAGAAGCCAACAACA 60.479 52.381 0.00 0.00 38.95 3.33 F
2353 2519 1.553248 AGGCGTATCTAACAACCAGCA 59.447 47.619 0.00 0.00 0.00 4.41 F
3063 3231 0.178767 TGCTCCCCAGTTGATGATCG 59.821 55.000 0.00 0.00 0.00 3.69 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1374 1469 1.137404 GTACTTTAGCGCGTCGGGA 59.863 57.895 14.18 0.00 0.00 5.14 R
2127 2233 1.903877 ATCAGGCACGAGGGAACAGG 61.904 60.000 0.00 0.00 0.00 4.00 R
2560 2726 0.036164 TGGTCATCAACTGGGGAACG 59.964 55.000 0.00 0.00 0.00 3.95 R
2778 2944 0.994247 TGGTCATCAACTGGGAGCAT 59.006 50.000 0.00 0.00 34.47 3.79 R
2896 3063 5.813672 CCAATCCCAGTTTTATGATTTGCTG 59.186 40.000 0.00 0.00 0.00 4.41 R
3435 3616 0.397941 CCAGTTGCTTCCTCCTGTCA 59.602 55.000 0.00 0.00 0.00 3.58 R
4101 4462 0.750850 AAGCATGCCCTTGATGCATC 59.249 50.000 20.14 20.14 46.04 3.91 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
22 23 3.885724 AACAACTTTGAGTGTTTGGGG 57.114 42.857 0.00 0.00 0.00 4.96
23 24 2.107366 ACAACTTTGAGTGTTTGGGGG 58.893 47.619 0.00 0.00 0.00 5.40
51 52 6.977213 GGCTTAAAAGACCACTTGTATTTGA 58.023 36.000 0.00 0.00 37.40 2.69
52 53 6.861572 GGCTTAAAAGACCACTTGTATTTGAC 59.138 38.462 0.00 0.00 37.40 3.18
55 56 8.740123 TTAAAAGACCACTTGTATTTGACTGA 57.260 30.769 0.00 0.00 37.40 3.41
57 58 7.823745 AAAGACCACTTGTATTTGACTGAAT 57.176 32.000 0.00 0.00 37.03 2.57
62 63 6.151691 CCACTTGTATTTGACTGAATGGTTG 58.848 40.000 0.00 0.00 0.00 3.77
70 71 5.499139 TTGACTGAATGGTTGTTTGAGAC 57.501 39.130 0.00 0.00 0.00 3.36
72 73 4.946772 TGACTGAATGGTTGTTTGAGACAA 59.053 37.500 0.00 0.00 45.70 3.18
82 83 5.514274 TTGTTTGAGACAAACCATCTTCC 57.486 39.130 19.76 0.00 44.95 3.46
90 91 2.112998 CAAACCATCTTCCCCATGCAT 58.887 47.619 0.00 0.00 0.00 3.96
93 94 1.144503 ACCATCTTCCCCATGCATCTC 59.855 52.381 0.00 0.00 0.00 2.75
97 98 1.918262 TCTTCCCCATGCATCTCTTGT 59.082 47.619 0.00 0.00 0.00 3.16
121 122 7.093552 TGTGGATTGATAAACCTTAAACCATGG 60.094 37.037 11.19 11.19 29.58 3.66
129 130 6.875948 AAACCTTAAACCATGGAAATTTGC 57.124 33.333 21.47 2.22 0.00 3.68
132 133 1.807139 AAACCATGGAAATTTGCCGC 58.193 45.000 21.47 0.00 0.00 6.53
134 135 0.247185 ACCATGGAAATTTGCCGCTG 59.753 50.000 21.47 2.63 0.00 5.18
147 148 2.841215 TGCCGCTGTACTACAAAACTT 58.159 42.857 0.00 0.00 0.00 2.66
149 150 3.002862 TGCCGCTGTACTACAAAACTTTG 59.997 43.478 0.60 0.60 43.62 2.77
160 161 1.665169 CAAAACTTTGTGCTTGGTGGC 59.335 47.619 0.00 0.00 33.59 5.01
171 172 0.890996 CTTGGTGGCCCAACAGAGTC 60.891 60.000 0.00 0.00 45.93 3.36
172 173 1.352622 TTGGTGGCCCAACAGAGTCT 61.353 55.000 0.00 0.00 45.93 3.24
182 184 5.112686 GCCCAACAGAGTCTACAAGATAAG 58.887 45.833 0.00 0.00 0.00 1.73
242 244 1.600636 CCCATATGCGCAACGGGAT 60.601 57.895 28.99 10.02 39.44 3.85
255 257 2.961424 CGGGATGCCTCCTGTTTTT 58.039 52.632 8.63 0.00 42.27 1.94
348 365 5.948742 TCAAGGTTTCCAAAAACTTCCAT 57.051 34.783 0.00 0.00 43.55 3.41
573 610 6.304208 GCGAATTTCAAAAACTGTTTGCAAAA 59.696 30.769 14.67 7.85 0.00 2.44
808 903 3.627395 TGTGGAGTACAGCCCATTAAG 57.373 47.619 0.00 0.00 33.42 1.85
810 905 3.197766 TGTGGAGTACAGCCCATTAAGAG 59.802 47.826 0.00 0.00 33.42 2.85
861 956 2.232298 GAGAGCACTAGCAACCGCCT 62.232 60.000 0.00 0.00 45.49 5.52
990 1085 1.073923 GAGGAAGGGAGAAGCCAACAA 59.926 52.381 0.00 0.00 38.95 2.83
991 1086 1.202940 AGGAAGGGAGAAGCCAACAAC 60.203 52.381 0.00 0.00 38.95 3.32
992 1087 1.478654 GGAAGGGAGAAGCCAACAACA 60.479 52.381 0.00 0.00 38.95 3.33
1008 1103 2.367567 ACAACAGGTAACGATGGTGTCT 59.632 45.455 0.00 0.00 43.78 3.41
1239 1334 4.473520 CCCATCCACTTCCGCGCT 62.474 66.667 5.56 0.00 0.00 5.92
1386 1481 2.103538 GTCATTCCCGACGCGCTA 59.896 61.111 5.73 0.00 0.00 4.26
1402 1497 2.653890 CGCTAAAGTACGCGCCTTATA 58.346 47.619 5.73 3.89 43.01 0.98
1415 1510 3.489059 GCGCCTTATATTTCTTGCTTGCA 60.489 43.478 0.00 0.00 0.00 4.08
1433 1528 3.466836 TGCACTCTAATGGCGGATTTAG 58.533 45.455 0.00 0.00 0.00 1.85
1459 1554 6.748333 AGTTATGTGGTGATGATCTTTGTG 57.252 37.500 0.00 0.00 0.00 3.33
1466 1561 4.516321 TGGTGATGATCTTTGTGTGACTTG 59.484 41.667 0.00 0.00 0.00 3.16
1694 1794 6.270463 TGTCCTGTGGGTTTAGTTTGTAGATA 59.730 38.462 0.00 0.00 0.00 1.98
1792 1892 5.296813 GCTGAAACACAGGTTAGGTTATG 57.703 43.478 0.00 0.00 45.82 1.90
1798 1898 2.498481 CACAGGTTAGGTTATGGGTCGA 59.502 50.000 0.00 0.00 0.00 4.20
1815 1915 5.048364 TGGGTCGACATGAAATAAGGTTTTG 60.048 40.000 18.91 0.00 0.00 2.44
1904 2006 4.644685 TCAAGTTTCCTTTTGTGCTTAGCT 59.355 37.500 5.60 0.00 0.00 3.32
1924 2026 4.123506 GCTTAGTAGCTTCCATCAGTTCC 58.876 47.826 0.00 0.00 44.27 3.62
1925 2027 4.141824 GCTTAGTAGCTTCCATCAGTTCCT 60.142 45.833 0.00 0.00 44.27 3.36
1926 2028 5.627968 GCTTAGTAGCTTCCATCAGTTCCTT 60.628 44.000 0.00 0.00 44.27 3.36
2087 2193 6.628398 GCTTACAACCAGCTACTTCTGACTAT 60.628 42.308 0.00 0.00 36.19 2.12
2096 2202 7.205992 CAGCTACTTCTGACTATTCATGCTAA 58.794 38.462 0.00 0.00 36.19 3.09
2127 2233 6.307800 TGACAGCAAAAGCTATTTTAATTCGC 59.692 34.615 0.00 0.00 36.47 4.70
2141 2247 3.876589 TTCGCCTGTTCCCTCGTGC 62.877 63.158 0.00 0.00 0.00 5.34
2152 2262 2.329267 TCCCTCGTGCCTGATGATATT 58.671 47.619 0.00 0.00 0.00 1.28
2156 2266 5.063204 CCCTCGTGCCTGATGATATTTTTA 58.937 41.667 0.00 0.00 0.00 1.52
2341 2507 2.625790 ACCAAGATCTCTGAGGCGTATC 59.374 50.000 4.59 0.59 0.00 2.24
2353 2519 1.553248 AGGCGTATCTAACAACCAGCA 59.447 47.619 0.00 0.00 0.00 4.41
2434 2600 9.888878 AGATATCAAATCATAAAACTGCGATTG 57.111 29.630 5.32 0.00 0.00 2.67
2441 2607 4.394920 TCATAAAACTGCGATTGGGACTTC 59.605 41.667 0.00 0.00 0.00 3.01
2499 2665 8.763049 GCTTTTAGCCTGTTCTTTTATTTGAT 57.237 30.769 0.00 0.00 34.48 2.57
2500 2666 9.208022 GCTTTTAGCCTGTTCTTTTATTTGATT 57.792 29.630 0.00 0.00 34.48 2.57
2504 2670 7.163001 AGCCTGTTCTTTTATTTGATTCTCC 57.837 36.000 0.00 0.00 0.00 3.71
2541 2707 7.741027 ATAAGCCTGTGATGTGAGATTAATG 57.259 36.000 0.00 0.00 0.00 1.90
2560 2726 2.436417 TGTTTGCTACTCTTGATGGGC 58.564 47.619 0.00 0.00 0.00 5.36
2615 2781 4.020128 TCTCTGAGGCCTCTTTTAACTTCC 60.020 45.833 32.28 3.37 0.00 3.46
2618 2784 3.244911 TGAGGCCTCTTTTAACTTCCAGG 60.245 47.826 32.28 0.00 0.00 4.45
2694 2860 7.537596 TTCTCATTTAACATTTGGATGTGGT 57.462 32.000 0.00 0.00 45.58 4.16
2740 2906 7.568349 TGATTCTCCTGTGCTTGAGTTATAAT 58.432 34.615 0.00 0.00 0.00 1.28
2926 3093 4.290985 TCATAAAACTGGGATTGGGTCTCA 59.709 41.667 0.00 0.00 35.55 3.27
3001 3169 5.947228 TTGATTCTCCTGTGCTTTAGTTG 57.053 39.130 0.00 0.00 0.00 3.16
3021 3189 7.959689 AGTTGTAAGCATATGATGTGAGATC 57.040 36.000 6.97 0.00 0.00 2.75
3063 3231 0.178767 TGCTCCCCAGTTGATGATCG 59.821 55.000 0.00 0.00 0.00 3.69
3121 3290 5.469760 GCCATGGCTTGTTTTCTTATTGTTT 59.530 36.000 29.98 0.00 38.26 2.83
3123 3292 7.468494 GCCATGGCTTGTTTTCTTATTGTTTTT 60.468 33.333 29.98 0.00 38.26 1.94
3194 3363 8.831715 TTGCACATATCGTAATGATGTTAGAT 57.168 30.769 6.73 0.00 37.99 1.98
3216 3394 0.886043 ATGTGCGCTGCTCTTGTTGA 60.886 50.000 9.73 0.00 0.00 3.18
3246 3426 5.593909 TCAATAGTTAATGGCCATTGACCAG 59.406 40.000 36.66 26.66 41.46 4.00
3262 3442 2.178890 CAGCAAGATCTCCAGCGCC 61.179 63.158 2.29 0.00 0.00 6.53
3300 3481 8.028652 TGATTGGGGACTGTTTTTAATTCTTT 57.971 30.769 0.00 0.00 0.00 2.52
3327 3508 2.159338 AGCGCATGCCTTGAAAACATAG 60.159 45.455 13.15 0.00 44.31 2.23
3423 3604 2.183679 GAGAAGAGGAAGGAGAAGGCA 58.816 52.381 0.00 0.00 0.00 4.75
3435 3616 2.354805 GGAGAAGGCAAAGGTGTCGTAT 60.355 50.000 0.00 0.00 33.27 3.06
3466 3647 4.962836 AACTGGCCAAGCTGCGCT 62.963 61.111 7.01 0.00 42.56 5.92
3513 3694 1.366319 AGCTGGGTTCTCAGTTGGAT 58.634 50.000 1.58 0.00 37.12 3.41
3546 3727 2.018542 TCAAATACTAGTGTGCCGCC 57.981 50.000 5.39 0.00 0.00 6.13
3558 3739 3.896133 GCCGCCCAGTCATGCATG 61.896 66.667 21.07 21.07 0.00 4.06
3589 3770 3.636300 TGCTGGATAATGGTGGTTATTGC 59.364 43.478 0.00 0.00 0.00 3.56
3746 3934 2.685388 TCATGTTTTTGTTGTCGCCAGA 59.315 40.909 0.00 0.00 0.00 3.86
3753 3941 5.508200 TTTTGTTGTCGCCAGAAACTTAT 57.492 34.783 0.00 0.00 0.00 1.73
3757 3945 2.695359 TGTCGCCAGAAACTTATGACC 58.305 47.619 0.00 0.00 0.00 4.02
3782 3970 4.089361 TCTAGATCCAGCTCTCACACAAA 58.911 43.478 0.00 0.00 0.00 2.83
3806 3994 0.511221 GCGTGCAAGCGAGTTAAAGA 59.489 50.000 9.33 0.00 0.00 2.52
3819 4008 4.578601 GAGTTAAAGAACATTGATCCGCG 58.421 43.478 0.00 0.00 38.10 6.46
3874 4214 0.106521 AGGTGTTTGCCAACATTGCC 59.893 50.000 6.64 3.84 44.85 4.52
3875 4215 0.884259 GGTGTTTGCCAACATTGCCC 60.884 55.000 6.64 0.00 44.85 5.36
3876 4216 0.179062 GTGTTTGCCAACATTGCCCA 60.179 50.000 6.64 0.00 44.85 5.36
3877 4217 0.106335 TGTTTGCCAACATTGCCCAG 59.894 50.000 0.00 0.00 38.03 4.45
3878 4218 1.071128 TTTGCCAACATTGCCCAGC 59.929 52.632 0.00 0.00 0.00 4.85
3879 4219 1.693152 TTTGCCAACATTGCCCAGCA 61.693 50.000 0.00 0.00 36.47 4.41
3880 4220 2.047939 GCCAACATTGCCCAGCAC 60.048 61.111 0.00 0.00 38.71 4.40
3881 4221 2.576832 GCCAACATTGCCCAGCACT 61.577 57.895 0.00 0.00 38.71 4.40
3882 4222 1.290955 CCAACATTGCCCAGCACTG 59.709 57.895 5.49 5.49 43.30 3.66
3883 4223 1.373748 CAACATTGCCCAGCACTGC 60.374 57.895 6.81 0.00 41.79 4.40
4033 4391 5.221803 ACAGATCGGCCATCAGAATATCTTT 60.222 40.000 2.24 0.00 33.29 2.52
4089 4450 1.707632 CGAGCTGTCCAGAAACTCTG 58.292 55.000 0.00 0.00 43.91 3.35
4134 4495 1.406539 CATGCTTGGTAGGTTGCATCC 59.593 52.381 5.61 5.61 43.24 3.51
4172 4533 3.238788 TCTGTGACTCAGTTGGACCTA 57.761 47.619 4.54 0.00 43.97 3.08
4213 5279 0.743688 AACGCATGCTTGTTTGGTGA 59.256 45.000 17.13 0.00 0.00 4.02
4218 5284 2.679450 CATGCTTGTTTGGTGACATGG 58.321 47.619 0.00 0.00 42.32 3.66
4234 5300 2.828549 GGGTTGGGCATGGCGTAG 60.829 66.667 13.76 0.00 0.00 3.51
4261 5327 2.381752 TCACCTCTTCTCACCAGTGA 57.618 50.000 0.00 0.00 38.06 3.41
4271 5337 3.779444 TCTCACCAGTGATGACCTTACT 58.221 45.455 0.04 0.00 39.13 2.24
4302 5368 7.390440 ACGATCAAAACATCATTTCAGTCCTAA 59.610 33.333 0.00 0.00 0.00 2.69
4306 5372 9.567776 TCAAAACATCATTTCAGTCCTAACTAA 57.432 29.630 0.00 0.00 33.25 2.24
4404 5470 0.968901 TCACCGATGCCGAACTAGGT 60.969 55.000 0.00 0.00 38.22 3.08
4417 5483 3.679083 CGAACTAGGTGAAAGTCCATCCC 60.679 52.174 0.00 0.00 0.00 3.85
4426 5492 5.423886 GTGAAAGTCCATCCCTCTTCTTAG 58.576 45.833 0.00 0.00 0.00 2.18
4427 5493 5.046231 GTGAAAGTCCATCCCTCTTCTTAGT 60.046 44.000 0.00 0.00 0.00 2.24
4473 5539 3.252701 CAGCATCTCAAAGAAGCACTTGT 59.747 43.478 6.90 0.00 41.05 3.16
4499 5565 4.342378 CAGCTCCAATACTAGCTCTACCAA 59.658 45.833 0.00 0.00 45.92 3.67
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
1 2 3.702045 CCCCCAAACACTCAAAGTTGTTA 59.298 43.478 0.00 0.00 0.00 2.41
3 4 2.107366 CCCCCAAACACTCAAAGTTGT 58.893 47.619 0.00 0.00 0.00 3.32
4 5 2.888834 CCCCCAAACACTCAAAGTTG 57.111 50.000 0.00 0.00 0.00 3.16
30 31 8.740123 TCAGTCAAATACAAGTGGTCTTTTAA 57.260 30.769 0.00 0.00 0.00 1.52
31 32 8.740123 TTCAGTCAAATACAAGTGGTCTTTTA 57.260 30.769 0.00 0.00 0.00 1.52
34 35 6.207417 CCATTCAGTCAAATACAAGTGGTCTT 59.793 38.462 0.00 0.00 0.00 3.01
62 63 3.255888 GGGGAAGATGGTTTGTCTCAAAC 59.744 47.826 14.50 14.50 0.00 2.93
70 71 1.559368 TGCATGGGGAAGATGGTTTG 58.441 50.000 0.00 0.00 0.00 2.93
72 73 1.572415 AGATGCATGGGGAAGATGGTT 59.428 47.619 2.46 0.00 0.00 3.67
78 79 2.022195 CACAAGAGATGCATGGGGAAG 58.978 52.381 2.46 0.00 0.00 3.46
82 83 2.359981 ATCCACAAGAGATGCATGGG 57.640 50.000 2.46 0.00 0.00 4.00
90 91 9.010029 GTTTAAGGTTTATCAATCCACAAGAGA 57.990 33.333 0.00 0.00 0.00 3.10
93 94 7.891561 TGGTTTAAGGTTTATCAATCCACAAG 58.108 34.615 0.00 0.00 0.00 3.16
97 98 7.185565 TCCATGGTTTAAGGTTTATCAATCCA 58.814 34.615 12.58 0.00 0.00 3.41
121 122 4.413495 TTGTAGTACAGCGGCAAATTTC 57.587 40.909 1.45 0.00 0.00 2.17
160 161 5.187967 ACCTTATCTTGTAGACTCTGTTGGG 59.812 44.000 0.00 0.00 0.00 4.12
191 193 1.441729 CGCACGGGGTGATGTCTAT 59.558 57.895 0.00 0.00 35.23 1.98
312 329 8.533569 TGGAAACCTTGAATTCTTAAAGAAGT 57.466 30.769 7.05 0.00 37.69 3.01
319 336 9.594478 GAAGTTTTTGGAAACCTTGAATTCTTA 57.406 29.630 7.05 0.00 44.97 2.10
322 339 6.821160 TGGAAGTTTTTGGAAACCTTGAATTC 59.179 34.615 0.00 0.00 44.97 2.17
427 462 8.909708 TGAACATTTTATGATTTCCGAACATC 57.090 30.769 0.00 0.00 0.00 3.06
657 714 9.810545 TTTTTGGAATCGAGTAACATTTTCTTT 57.189 25.926 0.00 0.00 0.00 2.52
666 723 6.128929 GGCAAACATTTTTGGAATCGAGTAAC 60.129 38.462 6.47 0.00 42.22 2.50
669 726 4.306600 GGCAAACATTTTTGGAATCGAGT 58.693 39.130 6.47 0.00 42.22 4.18
670 727 3.364621 CGGCAAACATTTTTGGAATCGAG 59.635 43.478 6.47 0.00 42.22 4.04
673 730 5.407995 TGAATCGGCAAACATTTTTGGAATC 59.592 36.000 6.47 0.54 42.22 2.52
722 780 1.554392 GTGCGCATGTTGTGAACAAA 58.446 45.000 15.91 0.00 45.86 2.83
758 816 7.231722 AGTCCTAATAGGCTTACACTATGTCAG 59.768 40.741 0.34 0.00 34.61 3.51
808 903 5.273674 AGGCCTCGTTACCTAATAAACTC 57.726 43.478 0.00 0.00 33.38 3.01
810 905 6.988580 ACAATAGGCCTCGTTACCTAATAAAC 59.011 38.462 9.68 0.00 41.76 2.01
861 956 1.635817 GGAGGTAGCAGATTGGGCCA 61.636 60.000 0.00 0.00 0.00 5.36
915 1010 3.394836 GGCGAAGGAGGGAGCAGT 61.395 66.667 0.00 0.00 0.00 4.40
990 1085 1.275291 CCAGACACCATCGTTACCTGT 59.725 52.381 0.00 0.00 0.00 4.00
991 1086 2.007049 GCCAGACACCATCGTTACCTG 61.007 57.143 0.00 0.00 0.00 4.00
992 1087 0.249398 GCCAGACACCATCGTTACCT 59.751 55.000 0.00 0.00 0.00 3.08
1239 1334 1.745115 CCAGAAAATGCGCGAGGGA 60.745 57.895 12.10 0.00 0.00 4.20
1308 1403 4.400961 GCCTTGAGCCTGGCGAGT 62.401 66.667 13.96 0.00 39.71 4.18
1374 1469 1.137404 GTACTTTAGCGCGTCGGGA 59.863 57.895 14.18 0.00 0.00 5.14
1386 1481 5.503520 GCAAGAAATATAAGGCGCGTACTTT 60.504 40.000 20.09 12.09 0.00 2.66
1402 1497 4.381292 GCCATTAGAGTGCAAGCAAGAAAT 60.381 41.667 0.00 0.00 0.00 2.17
1415 1510 6.481434 ACTAACTAAATCCGCCATTAGAGT 57.519 37.500 6.40 0.00 34.11 3.24
1433 1528 8.177663 CACAAAGATCATCACCACATAACTAAC 58.822 37.037 0.00 0.00 0.00 2.34
1459 1554 3.751518 ACCCTATCCAACAACAAGTCAC 58.248 45.455 0.00 0.00 0.00 3.67
1466 1561 3.610911 CCTCAGAACCCTATCCAACAAC 58.389 50.000 0.00 0.00 0.00 3.32
1792 1892 5.399013 CAAAACCTTATTTCATGTCGACCC 58.601 41.667 14.12 0.00 0.00 4.46
1798 1898 8.877864 TCACTATCCAAAACCTTATTTCATGT 57.122 30.769 0.00 0.00 0.00 3.21
1815 1915 6.753180 TCAGCATTTCACTCTATCACTATCC 58.247 40.000 0.00 0.00 0.00 2.59
1827 1927 5.464168 GCTTACACAATTCAGCATTTCACT 58.536 37.500 0.00 0.00 32.17 3.41
1904 2006 5.104900 GGAAGGAACTGATGGAAGCTACTAA 60.105 44.000 0.00 0.00 40.86 2.24
1924 2026 5.947228 TCTCAATGCACTTAACAAGGAAG 57.053 39.130 0.00 0.00 0.00 3.46
1925 2027 5.827797 AGTTCTCAATGCACTTAACAAGGAA 59.172 36.000 0.00 0.00 0.00 3.36
1926 2028 5.376625 AGTTCTCAATGCACTTAACAAGGA 58.623 37.500 0.00 0.00 0.00 3.36
1987 2090 5.105797 CCCAGTCATGCTAAATTTGCACTTA 60.106 40.000 14.67 4.34 43.59 2.24
2127 2233 1.903877 ATCAGGCACGAGGGAACAGG 61.904 60.000 0.00 0.00 0.00 4.00
2165 2275 9.703892 TCATTGACAAAATTAATCAAAATCGGT 57.296 25.926 0.00 0.00 36.03 4.69
2256 2366 3.548770 ACATGATGATAACCACAGCCAG 58.451 45.455 0.00 0.00 0.00 4.85
2381 2547 9.355215 GAGTTCAAATAATTGAGACGAACTAGA 57.645 33.333 0.00 0.00 45.82 2.43
2434 2600 1.228154 AAACAGGTGCCGAAGTCCC 60.228 57.895 0.00 0.00 0.00 4.46
2441 2607 1.522668 TGAATGAGAAACAGGTGCCG 58.477 50.000 0.00 0.00 0.00 5.69
2541 2707 1.398390 CGCCCATCAAGAGTAGCAAAC 59.602 52.381 0.00 0.00 0.00 2.93
2560 2726 0.036164 TGGTCATCAACTGGGGAACG 59.964 55.000 0.00 0.00 0.00 3.95
2679 2845 4.588528 AGCTAAACACCACATCCAAATGTT 59.411 37.500 0.00 0.00 43.74 2.71
2688 2854 5.852282 AAAGAACAAGCTAAACACCACAT 57.148 34.783 0.00 0.00 0.00 3.21
2694 2860 8.770438 AATCAAACAAAAGAACAAGCTAAACA 57.230 26.923 0.00 0.00 0.00 2.83
2778 2944 0.994247 TGGTCATCAACTGGGAGCAT 59.006 50.000 0.00 0.00 34.47 3.79
2896 3063 5.813672 CCAATCCCAGTTTTATGATTTGCTG 59.186 40.000 0.00 0.00 0.00 4.41
2926 3093 9.342308 CAAATGTACATGAGGAACAGGTATTAT 57.658 33.333 9.63 0.00 45.23 1.28
3021 3189 6.148480 GCACCCATCAAGAGTAGCAAATATAG 59.852 42.308 0.00 0.00 0.00 1.31
3063 3231 3.680196 GCCTCAGAGATCTTGGTGGTTAC 60.680 52.174 0.00 0.00 0.00 2.50
3157 3326 7.268199 ACGATATGTGCAATCTGATTTTGAT 57.732 32.000 0.00 0.00 0.00 2.57
3194 3363 1.522668 ACAAGAGCAGCGCACATTTA 58.477 45.000 11.47 0.00 0.00 1.40
3216 3394 6.736110 ATGGCCATTAACTATTGAAATGCT 57.264 33.333 14.09 0.00 30.81 3.79
3246 3426 1.525535 ATGGCGCTGGAGATCTTGC 60.526 57.895 7.64 1.39 0.00 4.01
3262 3442 4.399303 GTCCCCAATCAAGAACCTAACATG 59.601 45.833 0.00 0.00 0.00 3.21
3300 3481 1.748950 TCAAGGCATGCGCTCAAATA 58.251 45.000 12.44 0.00 38.60 1.40
3329 3510 3.801698 ACATCTAGTTGCAGCAGGTATG 58.198 45.455 2.55 3.77 0.00 2.39
3334 3515 5.355071 TCCAAATAACATCTAGTTGCAGCAG 59.645 40.000 2.55 0.00 41.50 4.24
3335 3516 5.252547 TCCAAATAACATCTAGTTGCAGCA 58.747 37.500 2.55 0.00 41.50 4.41
3336 3517 5.818136 TCCAAATAACATCTAGTTGCAGC 57.182 39.130 0.51 0.00 41.50 5.25
3435 3616 0.397941 CCAGTTGCTTCCTCCTGTCA 59.602 55.000 0.00 0.00 0.00 3.58
3466 3647 0.607489 GCAGCCTTCTCAGCCTTGAA 60.607 55.000 0.00 0.00 31.69 2.69
3513 3694 5.387113 AGTATTTGATTGGTGCCAGGATA 57.613 39.130 0.00 0.00 0.00 2.59
3546 3727 1.830279 AACAGACCATGCATGACTGG 58.170 50.000 34.25 23.41 36.82 4.00
3558 3739 3.763897 ACCATTATCCAGCAAAACAGACC 59.236 43.478 0.00 0.00 0.00 3.85
3746 3934 6.408662 GCTGGATCTAGAAGGGTCATAAGTTT 60.409 42.308 10.75 0.00 0.00 2.66
3753 3941 2.246067 AGAGCTGGATCTAGAAGGGTCA 59.754 50.000 10.75 0.00 0.00 4.02
3757 3945 3.068024 GTGTGAGAGCTGGATCTAGAAGG 59.932 52.174 10.75 0.00 0.00 3.46
3782 3970 1.230635 AACTCGCTTGCACGCTTGAT 61.231 50.000 13.78 0.00 0.00 2.57
3806 3994 1.240641 TGTTGCCGCGGATCAATGTT 61.241 50.000 33.48 0.00 0.00 2.71
3874 4214 0.953727 TGCTTAAACTGCAGTGCTGG 59.046 50.000 22.49 12.44 35.31 4.85
3875 4215 2.780065 TTGCTTAAACTGCAGTGCTG 57.220 45.000 22.49 19.32 41.71 4.41
3876 4216 2.951642 TCTTTGCTTAAACTGCAGTGCT 59.048 40.909 22.49 13.51 41.71 4.40
3877 4217 3.045688 GTCTTTGCTTAAACTGCAGTGC 58.954 45.455 22.49 19.55 41.71 4.40
3878 4218 3.002246 TCGTCTTTGCTTAAACTGCAGTG 59.998 43.478 22.49 9.00 41.71 3.66
3879 4219 3.202906 TCGTCTTTGCTTAAACTGCAGT 58.797 40.909 15.25 15.25 41.71 4.40
3880 4220 3.364366 CCTCGTCTTTGCTTAAACTGCAG 60.364 47.826 13.48 13.48 41.71 4.41
3881 4221 2.548057 CCTCGTCTTTGCTTAAACTGCA 59.452 45.455 0.00 0.00 38.80 4.41
3882 4222 2.548480 ACCTCGTCTTTGCTTAAACTGC 59.452 45.455 0.00 0.00 0.00 4.40
3883 4223 4.813296 AACCTCGTCTTTGCTTAAACTG 57.187 40.909 0.00 0.00 0.00 3.16
4046 4404 6.624204 CGCCATCGGTTTAAACTAAAAATCCT 60.624 38.462 17.50 0.00 0.00 3.24
4101 4462 0.750850 AAGCATGCCCTTGATGCATC 59.249 50.000 20.14 20.14 46.04 3.91
4172 4533 6.861055 CGTTTTTGGCATACATTTACTCAGTT 59.139 34.615 0.00 0.00 0.00 3.16
4213 5279 2.684655 GCCATGCCCAACCCATGT 60.685 61.111 0.00 0.00 38.67 3.21
4218 5284 3.518068 GCTACGCCATGCCCAACC 61.518 66.667 0.00 0.00 0.00 3.77
4234 5300 2.999355 GTGAGAAGAGGTGATCACAAGC 59.001 50.000 26.47 14.65 41.32 4.01
4247 5313 2.894731 AGGTCATCACTGGTGAGAAGA 58.105 47.619 9.33 4.81 43.61 2.87
4261 5327 2.233676 TGATCGTGTGCAGTAAGGTCAT 59.766 45.455 0.00 0.00 0.00 3.06
4271 5337 4.502171 AATGATGTTTTGATCGTGTGCA 57.498 36.364 0.00 0.00 0.00 4.57
4374 5440 2.814336 GGCATCGGTGAACTTTTCTCTT 59.186 45.455 0.00 0.00 0.00 2.85
4377 5443 1.156736 CGGCATCGGTGAACTTTTCT 58.843 50.000 0.00 0.00 0.00 2.52
4404 5470 5.094387 ACTAAGAAGAGGGATGGACTTTCA 58.906 41.667 0.00 0.00 0.00 2.69
4426 5492 7.389607 TGAAAGGCAATTTTAGTAGTAGGTGAC 59.610 37.037 0.00 0.00 0.00 3.67
4427 5493 7.455058 TGAAAGGCAATTTTAGTAGTAGGTGA 58.545 34.615 0.00 0.00 0.00 4.02
4486 5552 6.420913 TTCTTGAAGTTTGGTAGAGCTAGT 57.579 37.500 0.00 0.00 0.00 2.57
4499 5565 9.921637 TTCTACAACAAAATGTTTCTTGAAGTT 57.078 25.926 0.00 0.00 38.77 2.66


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

AutoCloner maintained by Alex Coulton.