Multiple sequence alignment - TraesCS6D01G120600

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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 TraesCS6D01G120600 chr6D 100.000 3454 0 0 1 3454 85553010 85556463 0.000000e+00 6379.0
1 TraesCS6D01G120600 chr6D 90.608 1874 111 33 2 1838 84679328 84677483 0.000000e+00 2425.0
2 TraesCS6D01G120600 chr6D 91.989 749 39 9 1836 2563 84677447 84676699 0.000000e+00 1031.0
3 TraesCS6D01G120600 chr6D 84.793 434 64 2 2739 3171 448504633 448505065 5.290000e-118 435.0
4 TraesCS6D01G120600 chr6D 82.563 476 69 4 2698 3159 13150302 13150777 1.150000e-109 407.0
5 TraesCS6D01G120600 chr6D 76.190 567 111 13 1863 2405 430243634 430243068 9.440000e-71 278.0
6 TraesCS6D01G120600 chr6D 84.277 159 25 0 2247 2405 430367460 430367618 4.620000e-34 156.0
7 TraesCS6D01G120600 chr6B 89.509 1935 126 35 768 2643 161344253 161342337 0.000000e+00 2377.0
8 TraesCS6D01G120600 chr6B 79.204 452 51 20 1 442 161345648 161345230 1.220000e-69 274.0
9 TraesCS6D01G120600 chr6B 89.423 208 15 6 3243 3444 161334695 161334489 4.420000e-64 255.0
10 TraesCS6D01G120600 chr6B 84.674 261 23 12 479 737 161345239 161344994 9.580000e-61 244.0
11 TraesCS6D01G120600 chr6B 95.522 67 2 1 2626 2691 161342320 161342254 4.710000e-19 106.0
12 TraesCS6D01G120600 chr6A 94.242 990 49 5 795 1778 101896986 101895999 0.000000e+00 1506.0
13 TraesCS6D01G120600 chr6A 91.930 855 29 12 1826 2643 101895929 101895078 0.000000e+00 1160.0
14 TraesCS6D01G120600 chr6A 86.017 801 56 25 7 779 101903149 101902377 0.000000e+00 808.0
15 TraesCS6D01G120600 chr6A 89.453 256 25 2 3189 3444 101894711 101894458 4.300000e-84 322.0
16 TraesCS6D01G120600 chr6A 87.179 273 30 4 1567 1835 215047251 215047522 4.330000e-79 305.0
17 TraesCS6D01G120600 chr6A 91.724 145 10 2 2170 2314 215047660 215047802 2.100000e-47 200.0
18 TraesCS6D01G120600 chr6A 89.815 108 10 1 1300 1407 215047139 215047245 1.670000e-28 137.0
19 TraesCS6D01G120600 chr6A 93.651 63 1 1 2630 2692 101895053 101894994 1.320000e-14 91.6
20 TraesCS6D01G120600 chr3B 84.501 471 68 5 2719 3185 586858121 586858590 8.730000e-126 460.0
21 TraesCS6D01G120600 chr3B 82.840 507 72 9 2698 3189 389787870 389787364 1.140000e-119 440.0
22 TraesCS6D01G120600 chr1D 85.235 447 65 1 2738 3183 346016182 346016628 3.140000e-125 459.0
23 TraesCS6D01G120600 chr1D 83.516 455 69 6 2738 3189 420001378 420000927 1.480000e-113 420.0
24 TraesCS6D01G120600 chr4D 84.270 445 65 5 2731 3171 380465714 380465271 2.460000e-116 429.0
25 TraesCS6D01G120600 chr7D 83.592 451 69 5 2736 3181 80712822 80712372 5.330000e-113 418.0
26 TraesCS6D01G120600 chr7D 82.046 479 81 3 2712 3185 42803945 42803467 1.490000e-108 403.0
27 TraesCS6D01G120600 chr7B 83.705 448 66 5 2742 3185 173330956 173331400 1.920000e-112 416.0
28 TraesCS6D01G120600 chr2B 92.053 151 9 3 2170 2320 108247446 108247299 3.490000e-50 209.0


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 TraesCS6D01G120600 chr6D 85553010 85556463 3453 False 6379.00 6379 100.000000 1 3454 1 chr6D.!!$F2 3453
1 TraesCS6D01G120600 chr6D 84676699 84679328 2629 True 1728.00 2425 91.298500 2 2563 2 chr6D.!!$R2 2561
2 TraesCS6D01G120600 chr6D 430243068 430243634 566 True 278.00 278 76.190000 1863 2405 1 chr6D.!!$R1 542
3 TraesCS6D01G120600 chr6B 161342254 161345648 3394 True 750.25 2377 87.227250 1 2691 4 chr6B.!!$R2 2690
4 TraesCS6D01G120600 chr6A 101902377 101903149 772 True 808.00 808 86.017000 7 779 1 chr6A.!!$R1 772
5 TraesCS6D01G120600 chr6A 101894458 101896986 2528 True 769.90 1506 92.319000 795 3444 4 chr6A.!!$R2 2649
6 TraesCS6D01G120600 chr6A 215047139 215047802 663 False 214.00 305 89.572667 1300 2314 3 chr6A.!!$F1 1014
7 TraesCS6D01G120600 chr3B 389787364 389787870 506 True 440.00 440 82.840000 2698 3189 1 chr3B.!!$R1 491

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
184 186 0.744281 ACAACTTTTCCCCGCAACTG 59.256 50.000 0.0 0.0 0.00 3.16 F
202 204 1.415289 CTGCCTCATGGTCATAGCTCA 59.585 52.381 0.0 0.0 35.27 4.26 F
1496 2246 0.176449 ACGTGTAAGTTATCCGGGGC 59.824 55.000 0.0 0.0 0.00 5.80 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1315 2063 1.082561 CGACCTCGACGAACGTGAA 60.083 57.895 4.19 0.0 43.02 3.18 R
1735 2485 2.476534 ATTTGCCGCAAGAACAGCCG 62.477 55.000 5.83 0.0 43.02 5.52 R
3172 4065 0.036306 GGACGTTGTCATCACCCCTT 59.964 55.000 0.00 0.0 33.68 3.95 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
70 71 4.517453 GTCAGGTATAGTGACTCTGCTAGG 59.483 50.000 7.61 0.00 41.05 3.02
73 74 3.570550 GGTATAGTGACTCTGCTAGGGTG 59.429 52.174 0.00 0.00 0.00 4.61
74 75 2.901338 TAGTGACTCTGCTAGGGTGT 57.099 50.000 0.00 0.00 0.00 4.16
75 76 1.551452 AGTGACTCTGCTAGGGTGTC 58.449 55.000 0.00 0.00 0.00 3.67
76 77 1.203063 AGTGACTCTGCTAGGGTGTCA 60.203 52.381 0.00 0.00 35.68 3.58
105 106 9.902684 TTTTTGCCAAATGGTCATAATAATGAT 57.097 25.926 0.71 0.00 43.87 2.45
107 108 9.902684 TTTGCCAAATGGTCATAATAATGATTT 57.097 25.926 0.71 0.00 43.87 2.17
108 109 9.902684 TTGCCAAATGGTCATAATAATGATTTT 57.097 25.926 0.71 0.00 43.87 1.82
184 186 0.744281 ACAACTTTTCCCCGCAACTG 59.256 50.000 0.00 0.00 0.00 3.16
202 204 1.415289 CTGCCTCATGGTCATAGCTCA 59.585 52.381 0.00 0.00 35.27 4.26
203 205 1.839354 TGCCTCATGGTCATAGCTCAA 59.161 47.619 0.00 0.00 35.27 3.02
205 207 2.877168 GCCTCATGGTCATAGCTCAAAG 59.123 50.000 0.00 0.00 35.27 2.77
206 208 2.877168 CCTCATGGTCATAGCTCAAAGC 59.123 50.000 0.00 0.00 42.84 3.51
207 209 2.877168 CTCATGGTCATAGCTCAAAGCC 59.123 50.000 0.00 0.00 43.77 4.35
208 210 2.507058 TCATGGTCATAGCTCAAAGCCT 59.493 45.455 0.00 0.00 43.77 4.58
209 211 2.698855 TGGTCATAGCTCAAAGCCTC 57.301 50.000 0.00 0.00 43.77 4.70
236 238 2.550978 ACAAGACCTGTGTTGTTCGAG 58.449 47.619 6.96 0.00 43.34 4.04
245 247 2.147958 GTGTTGTTCGAGGTGGCATAA 58.852 47.619 0.00 0.00 0.00 1.90
336 358 7.843490 TGTCTAGCTCCACAATACATTTTAC 57.157 36.000 0.00 0.00 0.00 2.01
675 700 9.959749 TCATGTTTTCCAAAACTATGTTTCTAC 57.040 29.630 14.43 0.00 46.37 2.59
827 1571 8.498054 TCAGAAATAAATCAGATGAAGACACC 57.502 34.615 0.00 0.00 0.00 4.16
1250 1998 2.481919 CGGCGCACTCACGTACTA 59.518 61.111 10.83 0.00 34.88 1.82
1331 2079 1.371389 GCTTCACGTTCGTCGAGGT 60.371 57.895 4.85 0.00 42.86 3.85
1496 2246 0.176449 ACGTGTAAGTTATCCGGGGC 59.824 55.000 0.00 0.00 0.00 5.80
1661 2411 2.112297 GGCCGGTGTTGAGGTTGA 59.888 61.111 1.90 0.00 0.00 3.18
1668 2418 0.393820 GTGTTGAGGTTGACCGGGTA 59.606 55.000 6.32 0.00 42.08 3.69
2447 3274 4.483683 CGCGACGTGTTCATGGCG 62.484 66.667 14.88 14.88 37.56 5.69
2480 3307 1.006102 GACCGTCCTGTGGTGACTG 60.006 63.158 0.00 0.00 40.63 3.51
2539 3372 9.838339 AAATAATCGATAGTTTCAGGTGAAGAT 57.162 29.630 0.00 0.00 35.21 2.40
2542 3375 6.968131 TCGATAGTTTCAGGTGAAGATTTG 57.032 37.500 0.00 0.00 35.21 2.32
2547 3381 2.496899 TCAGGTGAAGATTTGGCCTC 57.503 50.000 3.32 0.00 0.00 4.70
2593 3433 3.119673 CCTCTCTGAACCATATCCGATCG 60.120 52.174 8.51 8.51 0.00 3.69
2692 3570 5.354792 TGGTACAGAAACCGCCATAATAAAC 59.645 40.000 0.00 0.00 42.91 2.01
2693 3571 5.354792 GGTACAGAAACCGCCATAATAAACA 59.645 40.000 0.00 0.00 0.00 2.83
2694 3572 5.968528 ACAGAAACCGCCATAATAAACAA 57.031 34.783 0.00 0.00 0.00 2.83
2695 3573 6.334102 ACAGAAACCGCCATAATAAACAAA 57.666 33.333 0.00 0.00 0.00 2.83
2696 3574 6.750148 ACAGAAACCGCCATAATAAACAAAA 58.250 32.000 0.00 0.00 0.00 2.44
2697 3575 6.643360 ACAGAAACCGCCATAATAAACAAAAC 59.357 34.615 0.00 0.00 0.00 2.43
2698 3576 6.866248 CAGAAACCGCCATAATAAACAAAACT 59.134 34.615 0.00 0.00 0.00 2.66
2699 3577 7.061789 CAGAAACCGCCATAATAAACAAAACTC 59.938 37.037 0.00 0.00 0.00 3.01
2700 3578 5.319140 ACCGCCATAATAAACAAAACTCC 57.681 39.130 0.00 0.00 0.00 3.85
2701 3579 5.014202 ACCGCCATAATAAACAAAACTCCT 58.986 37.500 0.00 0.00 0.00 3.69
2705 3583 5.163447 GCCATAATAAACAAAACTCCTCCCC 60.163 44.000 0.00 0.00 0.00 4.81
2728 3606 6.266786 CCCAAGAAAAGAAAAGGCTAGGTTTA 59.733 38.462 0.00 0.00 0.00 2.01
2729 3607 7.039011 CCCAAGAAAAGAAAAGGCTAGGTTTAT 60.039 37.037 0.00 0.00 0.00 1.40
2730 3608 8.029522 CCAAGAAAAGAAAAGGCTAGGTTTATC 58.970 37.037 0.00 0.00 0.00 1.75
2731 3609 8.797438 CAAGAAAAGAAAAGGCTAGGTTTATCT 58.203 33.333 0.00 0.00 0.00 1.98
2732 3610 8.341892 AGAAAAGAAAAGGCTAGGTTTATCTG 57.658 34.615 0.00 0.00 0.00 2.90
2735 3626 6.628644 AGAAAAGGCTAGGTTTATCTGTCT 57.371 37.500 0.00 0.00 0.00 3.41
2736 3627 7.021998 AGAAAAGGCTAGGTTTATCTGTCTT 57.978 36.000 0.00 0.00 0.00 3.01
2739 3630 3.385111 AGGCTAGGTTTATCTGTCTTCCG 59.615 47.826 0.00 0.00 0.00 4.30
2747 3638 3.691342 CTGTCTTCCGCCGGTCCA 61.691 66.667 1.63 0.00 0.00 4.02
2751 3642 4.452733 CTTCCGCCGGTCCACCTC 62.453 72.222 1.63 0.00 0.00 3.85
2756 3647 2.579738 GCCGGTCCACCTCTTCTC 59.420 66.667 1.90 0.00 0.00 2.87
2815 3707 4.284550 TTGCTGGCGGGAAGGCTT 62.285 61.111 0.00 0.00 46.88 4.35
2830 3722 4.695928 GGAAGGCTTCGTCTTTAGATGTTT 59.304 41.667 20.26 0.00 33.00 2.83
2837 3729 7.352739 GCTTCGTCTTTAGATGTTTCTTCAAA 58.647 34.615 0.00 0.00 33.17 2.69
2852 3744 8.940952 TGTTTCTTCAAATTTTGTTAGGGTTTG 58.059 29.630 8.89 0.00 0.00 2.93
2860 3752 1.975660 TGTTAGGGTTTGTGTCCTGC 58.024 50.000 0.00 0.00 34.75 4.85
2875 3767 3.114558 CTGCTCAGGAAGACGACAC 57.885 57.895 0.00 0.00 0.00 3.67
2877 3769 1.170290 TGCTCAGGAAGACGACACGA 61.170 55.000 0.00 0.00 0.00 4.35
2878 3770 0.171455 GCTCAGGAAGACGACACGAT 59.829 55.000 0.00 0.00 0.00 3.73
2883 3775 0.167470 GGAAGACGACACGATGACGA 59.833 55.000 14.02 0.00 42.66 4.20
2889 3781 1.002142 ACGACACGATGACGACTTTCA 60.002 47.619 14.02 0.00 42.66 2.69
2896 3789 3.679980 ACGATGACGACTTTCAAAGATGG 59.320 43.478 3.49 0.00 42.66 3.51
2923 3816 1.821966 TTCTCCCTGCCTAGTCCCCA 61.822 60.000 0.00 0.00 0.00 4.96
2926 3819 0.645496 TCCCTGCCTAGTCCCCATTA 59.355 55.000 0.00 0.00 0.00 1.90
2928 3821 0.765510 CCTGCCTAGTCCCCATTACC 59.234 60.000 0.00 0.00 0.00 2.85
2955 3848 1.379443 TCTAGCATCGTCGGTGGGT 60.379 57.895 7.76 0.00 0.00 4.51
2961 3854 2.204461 ATCGTCGGTGGGTGTGTGA 61.204 57.895 0.00 0.00 0.00 3.58
3038 3931 3.561503 TCGTCTACGTTCATGTGTCTTG 58.438 45.455 0.00 0.00 40.80 3.02
3046 3939 3.214328 GTTCATGTGTCTTGAGGTTGGT 58.786 45.455 0.00 0.00 0.00 3.67
3052 3945 3.288092 GTGTCTTGAGGTTGGTTCCTTT 58.712 45.455 0.00 0.00 38.02 3.11
3053 3946 3.315470 GTGTCTTGAGGTTGGTTCCTTTC 59.685 47.826 0.00 0.00 38.02 2.62
3057 3950 3.053831 TGAGGTTGGTTCCTTTCGATC 57.946 47.619 0.00 0.00 38.02 3.69
3059 3952 3.263261 GAGGTTGGTTCCTTTCGATCTC 58.737 50.000 0.00 0.00 38.02 2.75
3067 3960 4.382147 GGTTCCTTTCGATCTCTGCTACTT 60.382 45.833 0.00 0.00 0.00 2.24
3069 3962 5.407407 TCCTTTCGATCTCTGCTACTTTT 57.593 39.130 0.00 0.00 0.00 2.27
3075 3968 3.304559 CGATCTCTGCTACTTTTCAACGG 59.695 47.826 0.00 0.00 0.00 4.44
3080 3973 1.847890 GCTACTTTTCAACGGCGGCA 61.848 55.000 13.24 0.00 0.00 5.69
3081 3974 0.589223 CTACTTTTCAACGGCGGCAA 59.411 50.000 13.24 0.00 0.00 4.52
3082 3975 1.002251 CTACTTTTCAACGGCGGCAAA 60.002 47.619 13.24 3.82 0.00 3.68
3090 3983 0.596341 AACGGCGGCAAATGTTGTTC 60.596 50.000 13.24 0.00 0.00 3.18
3092 3985 0.519519 CGGCGGCAAATGTTGTTCTA 59.480 50.000 10.53 0.00 0.00 2.10
3093 3986 1.068885 CGGCGGCAAATGTTGTTCTAA 60.069 47.619 10.53 0.00 0.00 2.10
3095 3988 3.181505 CGGCGGCAAATGTTGTTCTAATA 60.182 43.478 10.53 0.00 0.00 0.98
3097 3990 4.380023 GGCGGCAAATGTTGTTCTAATACA 60.380 41.667 3.07 0.00 0.00 2.29
3102 3995 7.096551 GGCAAATGTTGTTCTAATACATTGGT 58.903 34.615 0.00 0.00 40.54 3.67
3120 4013 1.068121 GTCCTATGGGGCCTTAGCAT 58.932 55.000 0.84 0.14 42.56 3.79
3126 4019 1.151760 TGGGGCCTTAGCATGATGAT 58.848 50.000 0.84 0.00 42.56 2.45
3129 4022 2.967887 GGGGCCTTAGCATGATGATTTT 59.032 45.455 0.84 0.00 42.56 1.82
3130 4023 3.389002 GGGGCCTTAGCATGATGATTTTT 59.611 43.478 0.84 0.00 42.56 1.94
3161 4054 9.914834 TGTCTACTATAATAAAATTTGCCTGGT 57.085 29.630 0.00 0.00 0.00 4.00
3172 4065 0.179032 TTGCCTGGTTTCAGCGAGAA 60.179 50.000 0.00 0.00 39.61 2.87
3178 4071 0.250770 GGTTTCAGCGAGAAAGGGGT 60.251 55.000 7.49 0.00 46.34 4.95
3185 4078 0.036388 GCGAGAAAGGGGTGATGACA 60.036 55.000 0.00 0.00 0.00 3.58
3193 4151 0.953960 GGGGTGATGACAACGTCCAC 60.954 60.000 0.00 0.00 34.03 4.02
3197 4155 1.263217 GTGATGACAACGTCCACAACC 59.737 52.381 0.00 0.00 0.00 3.77
3204 4162 2.292292 ACAACGTCCACAACCAATAAGC 59.708 45.455 0.00 0.00 0.00 3.09
3210 4168 4.634004 CGTCCACAACCAATAAGCAATCTA 59.366 41.667 0.00 0.00 0.00 1.98
3234 4192 1.197721 CAACCTCGACTGAATTGCACC 59.802 52.381 0.00 0.00 0.00 5.01
3238 4196 1.399440 CTCGACTGAATTGCACCATGG 59.601 52.381 11.19 11.19 0.00 3.66
3254 4212 5.747565 CACCATGGCATTGTTAATACTACG 58.252 41.667 13.04 0.00 0.00 3.51
3256 4214 5.526111 ACCATGGCATTGTTAATACTACGTC 59.474 40.000 13.04 0.00 0.00 4.34
3257 4215 5.049680 CCATGGCATTGTTAATACTACGTCC 60.050 44.000 0.00 0.00 0.00 4.79
3262 4220 5.172771 GCATTGTTAATACTACGTCCGAGAC 59.827 44.000 0.00 0.00 0.00 3.36
3280 4238 7.806487 GTCCGAGACGTATAAATATGAACATGA 59.194 37.037 0.00 0.00 0.00 3.07
3283 4241 8.630840 CGAGACGTATAAATATGAACATGACAG 58.369 37.037 0.00 0.00 0.00 3.51
3285 4243 9.249457 AGACGTATAAATATGAACATGACAGTG 57.751 33.333 0.00 0.00 0.00 3.66
3288 4246 9.636965 CGTATAAATATGAACATGACAGTGTTG 57.363 33.333 0.00 0.00 42.08 3.33
3295 4253 5.777802 TGAACATGACAGTGTTGTTTTTGT 58.222 33.333 13.24 2.43 42.08 2.83
3296 4254 5.632764 TGAACATGACAGTGTTGTTTTTGTG 59.367 36.000 13.24 0.86 42.08 3.33
3305 4263 5.567534 CAGTGTTGTTTTTGTGTGTGTAGAC 59.432 40.000 0.00 0.00 0.00 2.59
3337 4295 5.882557 TGCCCAAAACAAACAACATACAAAT 59.117 32.000 0.00 0.00 0.00 2.32
3349 4307 5.882557 ACAACATACAAATAGGCCTCAAGAG 59.117 40.000 9.68 0.00 0.00 2.85
3358 4316 4.479993 CCTCAAGAGCCCGGCCTG 62.480 72.222 5.55 1.33 0.00 4.85
3379 4337 3.131933 TGGTTGATTTTGGTTGTGACCTG 59.868 43.478 0.00 0.00 46.66 4.00
3387 4345 0.655733 GGTTGTGACCTGACACGTTG 59.344 55.000 0.00 0.00 42.99 4.10
3411 4369 8.657074 TGACCGTTTTATCGATTTTATCTGAT 57.343 30.769 1.71 0.00 0.00 2.90
3444 4402 2.965831 TCGATCTACTTATGGGCAGCTT 59.034 45.455 0.00 0.00 0.00 3.74
3445 4403 3.062763 CGATCTACTTATGGGCAGCTTG 58.937 50.000 0.00 0.00 0.00 4.01
3446 4404 3.493350 CGATCTACTTATGGGCAGCTTGT 60.493 47.826 0.00 0.00 0.00 3.16
3447 4405 3.543680 TCTACTTATGGGCAGCTTGTC 57.456 47.619 0.00 0.00 0.00 3.18
3448 4406 2.837591 TCTACTTATGGGCAGCTTGTCA 59.162 45.455 0.00 0.00 0.00 3.58
3449 4407 2.119801 ACTTATGGGCAGCTTGTCAG 57.880 50.000 0.00 0.00 0.00 3.51
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
105 106 9.884636 ATCGGTCCGATCATCATAATAATAAAA 57.115 29.630 21.31 0.00 43.45 1.52
107 108 9.961265 GTATCGGTCCGATCATCATAATAATAA 57.039 33.333 29.61 4.78 43.45 1.40
108 109 9.127277 TGTATCGGTCCGATCATCATAATAATA 57.873 33.333 29.61 5.24 43.45 0.98
109 110 8.007405 TGTATCGGTCCGATCATCATAATAAT 57.993 34.615 29.61 5.23 43.45 1.28
110 111 7.399245 TGTATCGGTCCGATCATCATAATAA 57.601 36.000 29.61 5.99 43.45 1.40
152 153 5.067283 GGGAAAAGTTGTTGTGCTAAGAGAA 59.933 40.000 0.00 0.00 0.00 2.87
153 154 4.578928 GGGAAAAGTTGTTGTGCTAAGAGA 59.421 41.667 0.00 0.00 0.00 3.10
184 186 2.627515 TTGAGCTATGACCATGAGGC 57.372 50.000 0.00 0.00 39.06 4.70
202 204 3.769300 AGGTCTTGTTTGTTTGAGGCTTT 59.231 39.130 0.00 0.00 0.00 3.51
203 205 3.131046 CAGGTCTTGTTTGTTTGAGGCTT 59.869 43.478 0.00 0.00 0.00 4.35
205 207 2.427095 ACAGGTCTTGTTTGTTTGAGGC 59.573 45.455 0.00 0.00 36.31 4.70
206 208 3.443681 ACACAGGTCTTGTTTGTTTGAGG 59.556 43.478 0.00 0.00 38.16 3.86
207 209 4.701956 ACACAGGTCTTGTTTGTTTGAG 57.298 40.909 0.00 0.00 38.16 3.02
208 210 4.279671 ACAACACAGGTCTTGTTTGTTTGA 59.720 37.500 8.70 0.00 37.55 2.69
209 211 4.555262 ACAACACAGGTCTTGTTTGTTTG 58.445 39.130 8.70 3.41 37.55 2.93
231 233 3.680937 CGTTACTTTTATGCCACCTCGAA 59.319 43.478 0.00 0.00 0.00 3.71
236 238 4.142838 GGTGTACGTTACTTTTATGCCACC 60.143 45.833 0.00 0.00 32.73 4.61
290 293 7.236432 AGACAAACACTAGCCCATATATGATCT 59.764 37.037 14.54 11.96 0.00 2.75
379 401 8.495148 GGGTTTTTATAGCACAAGACATTTTTG 58.505 33.333 0.00 0.00 0.00 2.44
492 515 9.443283 TTTTGCAAACATTTTTAACATACATGC 57.557 25.926 12.39 0.00 0.00 4.06
610 635 7.171167 TCCACAAACATTTTTCTTGCATATGTG 59.829 33.333 4.29 0.00 34.58 3.21
675 700 8.807948 TCTTTTCTTAAGACCAATTCCCTATG 57.192 34.615 4.18 0.00 0.00 2.23
827 1571 2.947852 AGACTCGTGTCCGATTTCAAG 58.052 47.619 13.70 0.00 43.27 3.02
1131 1879 1.258445 GGGAGCGGAAGAGGAAGACA 61.258 60.000 0.00 0.00 0.00 3.41
1218 1966 4.109675 CCGGCGAAGGGGTGGAAT 62.110 66.667 9.30 0.00 0.00 3.01
1315 2063 1.082561 CGACCTCGACGAACGTGAA 60.083 57.895 4.19 0.00 43.02 3.18
1723 2473 4.767255 CAGCCGGGCGAGCTCTTT 62.767 66.667 14.39 0.00 38.95 2.52
1735 2485 2.476534 ATTTGCCGCAAGAACAGCCG 62.477 55.000 5.83 0.00 43.02 5.52
2168 2974 4.988716 TCCCTGACGGCCACGAGT 62.989 66.667 2.24 0.00 44.60 4.18
2280 3107 2.334946 CGAAGTCCACCCCGTACGA 61.335 63.158 18.76 0.00 0.00 3.43
2539 3372 1.228245 GCAGGTGTCTGAGGCCAAA 60.228 57.895 5.01 0.00 43.49 3.28
2542 3375 1.748122 CATGCAGGTGTCTGAGGCC 60.748 63.158 0.00 0.00 43.49 5.19
2593 3433 3.966218 GTGCGCGTTATATCATTTGTTCC 59.034 43.478 8.43 0.00 0.00 3.62
2595 3435 3.603379 CGTGCGCGTTATATCATTTGTT 58.397 40.909 12.43 0.00 0.00 2.83
2597 3437 1.962547 GCGTGCGCGTTATATCATTTG 59.037 47.619 22.18 0.00 40.81 2.32
2604 3444 1.059681 GCTTTGCGTGCGCGTTATA 59.940 52.632 22.18 5.39 45.51 0.98
2627 3467 7.067494 GGTGATTCTACCAAGTGCAGATTATTT 59.933 37.037 0.00 0.00 40.54 1.40
2692 3570 4.215109 TCTTTTCTTGGGGAGGAGTTTTG 58.785 43.478 0.00 0.00 0.00 2.44
2693 3571 4.536295 TCTTTTCTTGGGGAGGAGTTTT 57.464 40.909 0.00 0.00 0.00 2.43
2694 3572 4.536295 TTCTTTTCTTGGGGAGGAGTTT 57.464 40.909 0.00 0.00 0.00 2.66
2695 3573 4.536295 TTTCTTTTCTTGGGGAGGAGTT 57.464 40.909 0.00 0.00 0.00 3.01
2696 3574 4.474394 CTTTTCTTTTCTTGGGGAGGAGT 58.526 43.478 0.00 0.00 0.00 3.85
2697 3575 3.829026 CCTTTTCTTTTCTTGGGGAGGAG 59.171 47.826 0.00 0.00 0.00 3.69
2698 3576 3.844640 CCTTTTCTTTTCTTGGGGAGGA 58.155 45.455 0.00 0.00 0.00 3.71
2699 3577 2.300152 GCCTTTTCTTTTCTTGGGGAGG 59.700 50.000 0.00 0.00 0.00 4.30
2700 3578 3.234353 AGCCTTTTCTTTTCTTGGGGAG 58.766 45.455 0.00 0.00 0.00 4.30
2701 3579 3.328535 AGCCTTTTCTTTTCTTGGGGA 57.671 42.857 0.00 0.00 0.00 4.81
2705 3583 8.797438 AGATAAACCTAGCCTTTTCTTTTCTTG 58.203 33.333 0.00 0.00 0.00 3.02
2728 3606 2.722201 GGACCGGCGGAAGACAGAT 61.722 63.158 35.78 7.12 41.50 2.90
2729 3607 3.379445 GGACCGGCGGAAGACAGA 61.379 66.667 35.78 0.00 41.50 3.41
2730 3608 3.691342 TGGACCGGCGGAAGACAG 61.691 66.667 35.78 3.81 41.50 3.51
2731 3609 3.998672 GTGGACCGGCGGAAGACA 61.999 66.667 35.78 21.29 41.50 3.41
2732 3610 4.754667 GGTGGACCGGCGGAAGAC 62.755 72.222 35.78 23.09 0.00 3.01
2739 3630 2.579738 GAGAAGAGGTGGACCGGC 59.420 66.667 0.00 0.00 42.08 6.13
2747 3638 0.041386 AAGGCTACCGGAGAAGAGGT 59.959 55.000 9.46 0.00 44.08 3.85
2751 3642 1.041437 CCCTAAGGCTACCGGAGAAG 58.959 60.000 9.46 3.30 0.00 2.85
2752 3643 3.218974 CCCTAAGGCTACCGGAGAA 57.781 57.895 9.46 0.00 0.00 2.87
2802 3694 4.388499 GACGAAGCCTTCCCGCCA 62.388 66.667 0.00 0.00 0.00 5.69
2804 3696 0.390735 TAAAGACGAAGCCTTCCCGC 60.391 55.000 0.00 0.00 0.00 6.13
2809 3701 5.552178 AGAAACATCTAAAGACGAAGCCTT 58.448 37.500 0.00 0.00 0.00 4.35
2810 3702 5.153950 AGAAACATCTAAAGACGAAGCCT 57.846 39.130 0.00 0.00 0.00 4.58
2830 3722 7.616313 ACACAAACCCTAACAAAATTTGAAGA 58.384 30.769 13.19 0.00 34.93 2.87
2837 3729 4.202212 GCAGGACACAAACCCTAACAAAAT 60.202 41.667 0.00 0.00 0.00 1.82
2860 3752 1.468914 TCATCGTGTCGTCTTCCTGAG 59.531 52.381 0.00 0.00 0.00 3.35
2873 3765 4.434725 CCATCTTTGAAAGTCGTCATCGTG 60.435 45.833 4.68 0.00 38.33 4.35
2875 3767 3.926527 TCCATCTTTGAAAGTCGTCATCG 59.073 43.478 4.68 0.00 38.55 3.84
2877 3769 7.066284 CCTTATTCCATCTTTGAAAGTCGTCAT 59.934 37.037 4.68 0.00 0.00 3.06
2878 3770 6.371548 CCTTATTCCATCTTTGAAAGTCGTCA 59.628 38.462 4.68 0.00 0.00 4.35
2883 3775 7.394641 GGAGAACCTTATTCCATCTTTGAAAGT 59.605 37.037 4.68 0.00 0.00 2.66
2911 3804 0.325860 ACGGTAATGGGGACTAGGCA 60.326 55.000 0.00 0.00 0.00 4.75
2945 3838 1.954146 CTTCACACACCCACCGACG 60.954 63.158 0.00 0.00 0.00 5.12
2955 3848 0.104120 CGGAGACACACCTTCACACA 59.896 55.000 0.00 0.00 0.00 3.72
2961 3854 0.836400 ATCCACCGGAGACACACCTT 60.836 55.000 9.46 0.00 34.05 3.50
3029 3922 2.443255 AGGAACCAACCTCAAGACACAT 59.557 45.455 0.00 0.00 34.98 3.21
3032 3925 3.551846 GAAAGGAACCAACCTCAAGACA 58.448 45.455 0.00 0.00 39.62 3.41
3038 3931 3.055747 AGAGATCGAAAGGAACCAACCTC 60.056 47.826 0.00 0.00 39.62 3.85
3046 3939 5.407407 AAAGTAGCAGAGATCGAAAGGAA 57.593 39.130 0.00 0.00 0.00 3.36
3052 3945 4.166523 CGTTGAAAAGTAGCAGAGATCGA 58.833 43.478 0.00 0.00 0.00 3.59
3053 3946 3.304559 CCGTTGAAAAGTAGCAGAGATCG 59.695 47.826 0.00 0.00 0.00 3.69
3057 3950 1.126846 CGCCGTTGAAAAGTAGCAGAG 59.873 52.381 0.00 0.00 0.00 3.35
3059 3952 0.165944 CCGCCGTTGAAAAGTAGCAG 59.834 55.000 0.00 0.00 0.00 4.24
3067 3960 0.103208 AACATTTGCCGCCGTTGAAA 59.897 45.000 0.00 0.00 0.00 2.69
3069 3962 1.007964 CAACATTTGCCGCCGTTGA 60.008 52.632 0.00 0.00 40.92 3.18
3075 3968 4.728534 TGTATTAGAACAACATTTGCCGC 58.271 39.130 0.00 0.00 0.00 6.53
3080 3973 8.650143 AGGACCAATGTATTAGAACAACATTT 57.350 30.769 0.00 0.00 40.83 2.32
3081 3974 9.920946 ATAGGACCAATGTATTAGAACAACATT 57.079 29.630 0.00 0.00 42.91 2.71
3082 3975 9.342308 CATAGGACCAATGTATTAGAACAACAT 57.658 33.333 0.00 0.00 35.40 2.71
3090 3983 4.567747 GGCCCCATAGGACCAATGTATTAG 60.568 50.000 0.00 0.00 37.96 1.73
3092 3985 2.110011 GGCCCCATAGGACCAATGTATT 59.890 50.000 0.00 0.00 37.96 1.89
3093 3986 1.710809 GGCCCCATAGGACCAATGTAT 59.289 52.381 0.00 0.00 37.96 2.29
3095 3988 1.930520 GGCCCCATAGGACCAATGT 59.069 57.895 0.00 0.00 37.96 2.71
3102 3995 1.067295 CATGCTAAGGCCCCATAGGA 58.933 55.000 0.00 1.23 38.24 2.94
3147 4040 3.319405 TCGCTGAAACCAGGCAAATTTTA 59.681 39.130 0.00 0.00 32.40 1.52
3150 4043 1.270550 CTCGCTGAAACCAGGCAAATT 59.729 47.619 0.00 0.00 32.40 1.82
3151 4044 0.883833 CTCGCTGAAACCAGGCAAAT 59.116 50.000 0.00 0.00 32.40 2.32
3156 4049 1.160137 CCTTTCTCGCTGAAACCAGG 58.840 55.000 0.00 0.00 39.50 4.45
3157 4050 1.160137 CCCTTTCTCGCTGAAACCAG 58.840 55.000 0.00 0.00 39.50 4.00
3158 4051 0.250727 CCCCTTTCTCGCTGAAACCA 60.251 55.000 0.42 0.00 39.50 3.67
3161 4054 0.762418 TCACCCCTTTCTCGCTGAAA 59.238 50.000 4.00 4.00 41.85 2.69
3172 4065 0.036306 GGACGTTGTCATCACCCCTT 59.964 55.000 0.00 0.00 33.68 3.95
3178 4071 1.134371 TGGTTGTGGACGTTGTCATCA 60.134 47.619 0.00 0.00 33.68 3.07
3185 4078 2.577700 TGCTTATTGGTTGTGGACGTT 58.422 42.857 0.00 0.00 0.00 3.99
3193 4151 8.253113 AGGTTGAATTAGATTGCTTATTGGTTG 58.747 33.333 0.00 0.00 0.00 3.77
3197 4155 7.852945 GTCGAGGTTGAATTAGATTGCTTATTG 59.147 37.037 0.00 0.00 0.00 1.90
3204 4162 6.968131 TTCAGTCGAGGTTGAATTAGATTG 57.032 37.500 3.54 0.00 0.00 2.67
3254 4212 7.806487 TCATGTTCATATTTATACGTCTCGGAC 59.194 37.037 0.00 0.00 0.00 4.79
3256 4214 7.593644 TGTCATGTTCATATTTATACGTCTCGG 59.406 37.037 0.00 0.00 0.00 4.63
3257 4215 8.502161 TGTCATGTTCATATTTATACGTCTCG 57.498 34.615 0.00 0.00 0.00 4.04
3262 4220 9.636965 CAACACTGTCATGTTCATATTTATACG 57.363 33.333 0.00 0.00 40.89 3.06
3271 4229 6.310956 CACAAAAACAACACTGTCATGTTCAT 59.689 34.615 7.85 0.23 40.89 2.57
3280 4238 4.314740 ACACACACAAAAACAACACTGT 57.685 36.364 0.00 0.00 37.39 3.55
3283 4241 4.551892 CGTCTACACACACAAAAACAACAC 59.448 41.667 0.00 0.00 0.00 3.32
3285 4243 4.960329 TCGTCTACACACACAAAAACAAC 58.040 39.130 0.00 0.00 0.00 3.32
3288 4246 5.852229 TGTTTTCGTCTACACACACAAAAAC 59.148 36.000 0.00 0.00 36.43 2.43
3290 4248 5.608676 TGTTTTCGTCTACACACACAAAA 57.391 34.783 0.00 0.00 0.00 2.44
3295 4253 2.546368 GGCATGTTTTCGTCTACACACA 59.454 45.455 0.00 0.00 0.00 3.72
3296 4254 2.095919 GGGCATGTTTTCGTCTACACAC 60.096 50.000 0.00 0.00 0.00 3.82
3305 4263 3.372206 TGTTTGTTTTGGGCATGTTTTCG 59.628 39.130 0.00 0.00 0.00 3.46
3349 4307 2.282783 AAAATCAACCAGGCCGGGC 61.283 57.895 23.25 22.67 40.22 6.13
3352 4310 0.678950 AACCAAAATCAACCAGGCCG 59.321 50.000 0.00 0.00 0.00 6.13
3355 4313 3.492482 GGTCACAACCAAAATCAACCAGG 60.492 47.826 0.00 0.00 45.68 4.45
3387 4345 8.761497 TCATCAGATAAAATCGATAAAACGGTC 58.239 33.333 0.00 0.00 0.00 4.79
3411 4369 5.723672 AAGTAGATCGAACCAAAGACTCA 57.276 39.130 0.00 0.00 0.00 3.41
3417 4375 4.080807 TGCCCATAAGTAGATCGAACCAAA 60.081 41.667 0.00 0.00 0.00 3.28


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

AutoCloner maintained by Alex Coulton.