Multiple sequence alignment - TraesCS1B01G195800

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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 TraesCS1B01G195800 chr1B 100.000 3218 0 0 1 3218 351438758 351441975 0.000000e+00 5943
1 TraesCS1B01G195800 chr1D 93.821 2800 88 28 236 2976 260980154 260977381 0.000000e+00 4133
2 TraesCS1B01G195800 chr1D 89.575 259 13 8 2960 3218 260972078 260971834 1.860000e-82 316
3 TraesCS1B01G195800 chr1A 90.662 2977 92 63 326 3218 339482623 339485497 0.000000e+00 3786
4 TraesCS1B01G195800 chr6D 96.591 88 3 0 120 207 403969209 403969122 2.590000e-31 147
5 TraesCS1B01G195800 chr5A 96.591 88 3 0 119 206 65549801 65549714 2.590000e-31 147
6 TraesCS1B01G195800 chr6B 93.617 94 6 0 114 207 646750151 646750058 1.200000e-29 141
7 TraesCS1B01G195800 chr3B 94.382 89 5 0 119 207 485691489 485691401 1.560000e-28 137
8 TraesCS1B01G195800 chr2D 94.186 86 5 0 122 207 128890639 128890724 7.240000e-27 132
9 TraesCS1B01G195800 chr2D 90.816 98 7 2 112 207 588514066 588514163 2.610000e-26 130
10 TraesCS1B01G195800 chr7D 93.103 87 6 0 120 206 351587192 351587106 9.370000e-26 128
11 TraesCS1B01G195800 chr4D 92.222 90 6 1 118 207 303079345 303079257 3.370000e-25 126
12 TraesCS1B01G195800 chr2A 88.462 104 9 3 117 218 70101473 70101371 4.360000e-24 122


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 TraesCS1B01G195800 chr1B 351438758 351441975 3217 False 5943 5943 100.000 1 3218 1 chr1B.!!$F1 3217
1 TraesCS1B01G195800 chr1D 260977381 260980154 2773 True 4133 4133 93.821 236 2976 1 chr1D.!!$R2 2740
2 TraesCS1B01G195800 chr1A 339482623 339485497 2874 False 3786 3786 90.662 326 3218 1 chr1A.!!$F1 2892

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
802 816 0.03759 TAAGCATGCAAGAACCCGGT 59.962 50.0 21.98 0.0 0.0 5.28 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2396 2440 1.196354 GCACACAGCTAAACAGCAGAG 59.804 52.381 0.0 0.0 41.15 3.35 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
17 18 4.540153 AAATGGGTGCGGAGATCG 57.460 55.556 0.00 0.00 42.76 3.69
18 19 1.153168 AAATGGGTGCGGAGATCGG 60.153 57.895 0.00 0.00 39.69 4.18
19 20 3.757248 AATGGGTGCGGAGATCGGC 62.757 63.158 5.51 5.51 41.78 5.54
21 22 3.224324 GGGTGCGGAGATCGGCTA 61.224 66.667 12.74 0.00 41.92 3.93
22 23 2.792947 GGGTGCGGAGATCGGCTAA 61.793 63.158 12.74 0.00 41.92 3.09
23 24 1.367840 GGTGCGGAGATCGGCTAAT 59.632 57.895 12.74 0.00 41.92 1.73
24 25 0.946221 GGTGCGGAGATCGGCTAATG 60.946 60.000 12.74 0.00 41.92 1.90
25 26 0.946221 GTGCGGAGATCGGCTAATGG 60.946 60.000 12.74 0.00 41.92 3.16
26 27 1.374758 GCGGAGATCGGCTAATGGG 60.375 63.158 5.24 0.00 38.87 4.00
27 28 1.293498 CGGAGATCGGCTAATGGGG 59.707 63.158 0.00 0.00 34.75 4.96
28 29 1.003233 GGAGATCGGCTAATGGGGC 60.003 63.158 0.00 0.00 0.00 5.80
29 30 1.484444 GGAGATCGGCTAATGGGGCT 61.484 60.000 0.00 0.00 0.00 5.19
30 31 0.321122 GAGATCGGCTAATGGGGCTG 60.321 60.000 0.00 0.00 37.41 4.85
31 32 1.968540 GATCGGCTAATGGGGCTGC 60.969 63.158 0.00 0.00 36.16 5.25
32 33 3.497884 ATCGGCTAATGGGGCTGCC 62.498 63.158 11.05 11.05 41.76 4.85
45 46 3.733443 GGGCTGCCCACATTATAAAAG 57.267 47.619 32.46 0.00 44.65 2.27
46 47 3.295973 GGGCTGCCCACATTATAAAAGA 58.704 45.455 32.46 0.00 44.65 2.52
47 48 3.897505 GGGCTGCCCACATTATAAAAGAT 59.102 43.478 32.46 0.00 44.65 2.40
48 49 4.262164 GGGCTGCCCACATTATAAAAGATG 60.262 45.833 32.46 0.00 44.65 2.90
49 50 4.584325 GGCTGCCCACATTATAAAAGATGA 59.416 41.667 7.66 0.00 0.00 2.92
50 51 5.244626 GGCTGCCCACATTATAAAAGATGAT 59.755 40.000 7.66 0.00 0.00 2.45
51 52 6.239402 GGCTGCCCACATTATAAAAGATGATT 60.239 38.462 7.66 0.00 0.00 2.57
52 53 7.212274 GCTGCCCACATTATAAAAGATGATTT 58.788 34.615 0.00 0.00 0.00 2.17
53 54 7.383300 GCTGCCCACATTATAAAAGATGATTTC 59.617 37.037 0.00 0.00 0.00 2.17
54 55 8.303780 TGCCCACATTATAAAAGATGATTTCA 57.696 30.769 0.00 0.00 0.00 2.69
55 56 8.926374 TGCCCACATTATAAAAGATGATTTCAT 58.074 29.630 0.00 0.00 39.70 2.57
56 57 9.199982 GCCCACATTATAAAAGATGATTTCATG 57.800 33.333 0.00 0.00 36.57 3.07
64 65 6.939551 AAAAGATGATTTCATGTTTCGCTG 57.060 33.333 13.95 0.00 45.36 5.18
65 66 4.627611 AGATGATTTCATGTTTCGCTGG 57.372 40.909 0.00 0.00 36.57 4.85
66 67 4.264253 AGATGATTTCATGTTTCGCTGGA 58.736 39.130 0.00 0.00 36.57 3.86
67 68 4.885907 AGATGATTTCATGTTTCGCTGGAT 59.114 37.500 0.00 0.00 36.57 3.41
68 69 5.359009 AGATGATTTCATGTTTCGCTGGATT 59.641 36.000 0.00 0.00 36.57 3.01
69 70 4.735985 TGATTTCATGTTTCGCTGGATTG 58.264 39.130 0.00 0.00 0.00 2.67
70 71 2.634982 TTCATGTTTCGCTGGATTGC 57.365 45.000 0.00 0.00 0.00 3.56
71 72 1.532523 TCATGTTTCGCTGGATTGCA 58.467 45.000 0.00 0.00 0.00 4.08
72 73 2.093890 TCATGTTTCGCTGGATTGCAT 58.906 42.857 0.00 0.00 0.00 3.96
73 74 2.492881 TCATGTTTCGCTGGATTGCATT 59.507 40.909 0.00 0.00 0.00 3.56
74 75 2.634982 TGTTTCGCTGGATTGCATTC 57.365 45.000 0.00 0.00 0.00 2.67
75 76 1.885233 TGTTTCGCTGGATTGCATTCA 59.115 42.857 10.55 0.00 0.00 2.57
76 77 2.295629 TGTTTCGCTGGATTGCATTCAA 59.704 40.909 10.55 0.00 36.51 2.69
77 78 2.634982 TTCGCTGGATTGCATTCAAC 57.365 45.000 10.55 0.00 34.60 3.18
78 79 1.532523 TCGCTGGATTGCATTCAACA 58.467 45.000 10.55 0.11 34.60 3.33
79 80 2.093890 TCGCTGGATTGCATTCAACAT 58.906 42.857 10.55 0.00 34.60 2.71
80 81 2.159352 TCGCTGGATTGCATTCAACATG 60.159 45.455 10.55 0.00 34.60 3.21
81 82 2.416296 CGCTGGATTGCATTCAACATGT 60.416 45.455 10.55 0.00 34.60 3.21
82 83 3.592059 GCTGGATTGCATTCAACATGTT 58.408 40.909 4.92 4.92 34.60 2.71
83 84 3.369756 GCTGGATTGCATTCAACATGTTG 59.630 43.478 29.01 29.01 41.71 3.33
84 85 4.562082 CTGGATTGCATTCAACATGTTGT 58.438 39.130 31.99 15.90 41.16 3.32
85 86 4.958509 TGGATTGCATTCAACATGTTGTT 58.041 34.783 31.99 20.62 42.08 2.83
95 96 3.773860 AACATGTTGTTGCGTCAGAAA 57.226 38.095 11.07 0.00 39.45 2.52
96 97 3.988379 ACATGTTGTTGCGTCAGAAAT 57.012 38.095 0.00 0.00 0.00 2.17
97 98 4.305989 ACATGTTGTTGCGTCAGAAATT 57.694 36.364 0.00 0.00 0.00 1.82
98 99 4.681744 ACATGTTGTTGCGTCAGAAATTT 58.318 34.783 0.00 0.00 0.00 1.82
99 100 4.739716 ACATGTTGTTGCGTCAGAAATTTC 59.260 37.500 10.33 10.33 0.00 2.17
100 101 4.630894 TGTTGTTGCGTCAGAAATTTCT 57.369 36.364 15.11 15.11 38.25 2.52
101 102 8.830328 AACATGTTGTTGCGTCAGAAATTTCTG 61.830 37.037 33.28 33.28 45.90 3.02
147 148 8.622948 ACTCCCTCTGTAAAGAAATACAAAAG 57.377 34.615 0.00 0.00 35.48 2.27
148 149 8.218488 ACTCCCTCTGTAAAGAAATACAAAAGT 58.782 33.333 0.00 0.00 35.48 2.66
149 150 8.391075 TCCCTCTGTAAAGAAATACAAAAGTG 57.609 34.615 0.00 0.00 35.48 3.16
150 151 7.996644 TCCCTCTGTAAAGAAATACAAAAGTGT 59.003 33.333 0.00 0.00 42.09 3.55
151 152 8.630037 CCCTCTGTAAAGAAATACAAAAGTGTT 58.370 33.333 0.00 0.00 39.30 3.32
201 202 9.774413 AACACTCTTATATTTATTTACGGAGGG 57.226 33.333 0.00 0.00 0.00 4.30
202 203 9.151177 ACACTCTTATATTTATTTACGGAGGGA 57.849 33.333 0.00 0.00 0.00 4.20
203 204 9.640963 CACTCTTATATTTATTTACGGAGGGAG 57.359 37.037 0.00 0.00 0.00 4.30
204 205 9.377238 ACTCTTATATTTATTTACGGAGGGAGT 57.623 33.333 0.00 0.00 0.00 3.85
267 268 4.816925 GCCTTAATCAATAGAAACTCGCCT 59.183 41.667 0.00 0.00 0.00 5.52
269 270 5.237344 CCTTAATCAATAGAAACTCGCCTGG 59.763 44.000 0.00 0.00 0.00 4.45
270 271 4.487714 AATCAATAGAAACTCGCCTGGA 57.512 40.909 0.00 0.00 0.00 3.86
343 344 6.500684 ACTTCGCTGTCATCATTTTTGTAT 57.499 33.333 0.00 0.00 0.00 2.29
403 410 4.537135 TGACTTTTCGAGCTTATCACCT 57.463 40.909 0.00 0.00 0.00 4.00
802 816 0.037590 TAAGCATGCAAGAACCCGGT 59.962 50.000 21.98 0.00 0.00 5.28
848 862 1.228003 TTCGGAGAAAAGGCGGCAA 60.228 52.632 13.08 0.00 45.90 4.52
849 863 1.234615 TTCGGAGAAAAGGCGGCAAG 61.235 55.000 13.08 0.00 45.90 4.01
901 915 2.753029 GCCAAGCCACTCTGGAGT 59.247 61.111 0.00 0.00 40.96 3.85
962 982 0.167470 TCTCGACGCTTGTTACTCCG 59.833 55.000 0.00 0.00 0.00 4.63
964 984 0.806868 TCGACGCTTGTTACTCCGAT 59.193 50.000 0.00 0.00 0.00 4.18
995 1015 4.011517 GACCTCACCGCCCGGAAA 62.012 66.667 14.44 0.00 38.96 3.13
996 1016 3.540367 GACCTCACCGCCCGGAAAA 62.540 63.158 14.44 0.00 38.96 2.29
1054 1074 3.950861 CTCCTCCTCCCCAAGCCCA 62.951 68.421 0.00 0.00 0.00 5.36
1149 1169 0.181587 TCAACGGGCACTCCAAGAAA 59.818 50.000 0.00 0.00 34.36 2.52
1154 1174 2.260869 GGCACTCCAAGAAAGCGCA 61.261 57.895 11.47 0.00 0.00 6.09
1566 1601 1.153745 CGTGCACTACTGCCTCCTC 60.154 63.158 16.19 0.00 43.51 3.71
1997 2032 1.464997 GGAGGTCATCAACAACGAAGC 59.535 52.381 0.00 0.00 0.00 3.86
2247 2282 0.914644 ACAGTGATCCTCCCACCATG 59.085 55.000 0.00 0.00 35.23 3.66
2254 2289 2.471815 TCCTCCCACCATGGTACTAG 57.528 55.000 19.28 14.14 35.17 2.57
2259 2294 4.028131 CTCCCACCATGGTACTAGTACAA 58.972 47.826 29.38 21.96 37.78 2.41
2278 2313 7.827701 AGTACAAGTGAAGTGATCGAATTAGA 58.172 34.615 0.00 0.00 0.00 2.10
2390 2434 6.054295 ACAGATGCAATAAGGCTCTTTCTAG 58.946 40.000 0.00 0.00 34.04 2.43
2395 2439 7.655521 TGCAATAAGGCTCTTTCTAGTACTA 57.344 36.000 1.89 1.89 34.04 1.82
2396 2440 7.490000 TGCAATAAGGCTCTTTCTAGTACTAC 58.510 38.462 0.00 0.00 34.04 2.73
2397 2441 7.342284 TGCAATAAGGCTCTTTCTAGTACTACT 59.658 37.037 0.00 0.00 34.04 2.57
2401 2445 4.885325 AGGCTCTTTCTAGTACTACTCTGC 59.115 45.833 0.00 0.00 0.00 4.26
2402 2446 4.885325 GGCTCTTTCTAGTACTACTCTGCT 59.115 45.833 0.00 0.00 0.00 4.24
2527 2571 5.646360 GTGCTAGATCTGAGGGTAGAGTATC 59.354 48.000 5.18 0.00 0.00 2.24
2528 2572 4.873827 GCTAGATCTGAGGGTAGAGTATCG 59.126 50.000 5.18 0.00 42.67 2.92
2531 2575 4.532916 AGATCTGAGGGTAGAGTATCGCTA 59.467 45.833 0.00 0.00 42.67 4.26
2532 2576 4.005487 TCTGAGGGTAGAGTATCGCTAC 57.995 50.000 0.00 0.00 42.67 3.58
2629 2698 6.294176 GCTGTTCTTTCCAATAGCAGAAGAAA 60.294 38.462 0.00 0.00 39.60 2.52
2633 2702 8.784043 GTTCTTTCCAATAGCAGAAGAAAACTA 58.216 33.333 0.00 0.00 0.00 2.24
2678 2752 3.054434 TGCAATACTAGGATGGTGTGCTT 60.054 43.478 10.08 0.00 40.73 3.91
2695 2769 3.927142 GTGCTTTGTATACGAGCTGAACT 59.073 43.478 23.40 0.00 37.32 3.01
2701 2775 5.128992 TGTATACGAGCTGAACTGTGAAA 57.871 39.130 0.00 0.00 0.00 2.69
2706 2780 2.975851 CGAGCTGAACTGTGAAATTTGC 59.024 45.455 0.00 0.00 0.00 3.68
2707 2781 2.975851 GAGCTGAACTGTGAAATTTGCG 59.024 45.455 0.00 0.00 0.00 4.85
2724 2798 7.484035 AATTTGCGGTGCTTTTATACAAAAA 57.516 28.000 0.00 0.00 33.33 1.94
2809 2898 9.161684 GAATTTGAATCATTTTGTTCTGTTTGC 57.838 29.630 0.00 0.00 0.00 3.68
2841 2930 1.371183 TTGGCCTCGTCCAAGACTG 59.629 57.895 3.32 0.00 40.92 3.51
2904 2993 1.557832 TCCGACAAGGGAATCCGAATT 59.442 47.619 0.00 0.00 41.52 2.17
2920 3009 1.814394 GAATTCATGTGGAGCACTGCA 59.186 47.619 3.30 0.00 35.11 4.41
2979 3068 5.238214 GGTTGAATTGCCATTTTTGCAGTTA 59.762 36.000 0.00 0.00 38.56 2.24
2988 3077 4.024977 CCATTTTTGCAGTTACAAGTTGCC 60.025 41.667 1.81 0.00 37.03 4.52
2990 3079 2.861462 TTGCAGTTACAAGTTGCCAC 57.139 45.000 1.81 0.00 37.03 5.01
2991 3080 2.051334 TGCAGTTACAAGTTGCCACT 57.949 45.000 1.81 2.13 37.03 4.00
2992 3081 1.675483 TGCAGTTACAAGTTGCCACTG 59.325 47.619 22.41 22.41 37.03 3.66
2993 3082 1.001378 GCAGTTACAAGTTGCCACTGG 60.001 52.381 25.50 14.01 33.58 4.00
2994 3083 2.297701 CAGTTACAAGTTGCCACTGGT 58.702 47.619 20.31 3.09 40.64 4.00
2995 3084 3.472652 CAGTTACAAGTTGCCACTGGTA 58.527 45.455 20.31 1.00 38.29 3.25
2996 3085 3.498397 CAGTTACAAGTTGCCACTGGTAG 59.502 47.826 20.31 2.82 40.08 3.18
2997 3086 2.178912 TACAAGTTGCCACTGGTAGC 57.821 50.000 1.81 0.00 38.29 3.58
2998 3087 0.182537 ACAAGTTGCCACTGGTAGCA 59.817 50.000 1.81 0.00 35.13 3.49
3000 3089 0.884704 AAGTTGCCACTGGTAGCACG 60.885 55.000 2.93 0.00 39.10 5.34
3076 3171 7.449247 AGAAAGATCTGAGCAGACTTAACTTT 58.551 34.615 1.71 9.33 40.75 2.66
3077 3172 7.602265 AGAAAGATCTGAGCAGACTTAACTTTC 59.398 37.037 21.27 21.27 40.75 2.62
3105 3200 1.901085 CGAGGGCCCTGATATAGCC 59.099 63.158 34.59 11.46 46.37 3.93
3110 3205 1.952621 GGCCCTGATATAGCCCTACA 58.047 55.000 0.00 0.00 41.00 2.74
3111 3206 2.266279 GGCCCTGATATAGCCCTACAA 58.734 52.381 0.00 0.00 41.00 2.41
3112 3207 2.846827 GGCCCTGATATAGCCCTACAAT 59.153 50.000 0.00 0.00 41.00 2.71
3114 3209 3.118223 GCCCTGATATAGCCCTACAATCC 60.118 52.174 0.00 0.00 0.00 3.01
3115 3210 4.366267 CCCTGATATAGCCCTACAATCCT 58.634 47.826 0.00 0.00 0.00 3.24
3140 3247 4.800023 TGAACCGGGAGAGATACTATCAA 58.200 43.478 6.32 0.00 0.00 2.57
3151 3258 7.655328 GGAGAGATACTATCAAATTCACCTGTG 59.345 40.741 0.00 0.00 0.00 3.66
3152 3259 7.504403 AGAGATACTATCAAATTCACCTGTGG 58.496 38.462 0.00 0.00 0.00 4.17
3153 3260 6.595682 AGATACTATCAAATTCACCTGTGGG 58.404 40.000 0.00 0.00 38.88 4.61
3154 3261 3.356290 ACTATCAAATTCACCTGTGGGC 58.644 45.455 0.00 0.00 35.63 5.36
3155 3262 2.610438 ATCAAATTCACCTGTGGGCT 57.390 45.000 0.00 0.00 35.63 5.19
3156 3263 1.619654 TCAAATTCACCTGTGGGCTG 58.380 50.000 0.00 0.00 35.63 4.85
3157 3264 1.133513 TCAAATTCACCTGTGGGCTGT 60.134 47.619 0.00 0.00 35.63 4.40
3165 3272 2.203337 TGTGGGCTGTGGCTGAAC 60.203 61.111 0.00 0.00 38.73 3.18
3187 3294 1.296727 GGCCTATTTGTACGACTGGC 58.703 55.000 0.00 10.28 38.28 4.85
3208 3318 1.012486 GTACGCCCCAGAAGTGAACG 61.012 60.000 0.00 0.00 0.00 3.95
3209 3319 2.162338 TACGCCCCAGAAGTGAACGG 62.162 60.000 0.00 0.00 0.00 4.44
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 1.153168 CCGATCTCCGCACCCATTT 60.153 57.895 0.00 0.00 36.84 2.32
1 2 2.505982 CCGATCTCCGCACCCATT 59.494 61.111 0.00 0.00 36.84 3.16
2 3 4.241555 GCCGATCTCCGCACCCAT 62.242 66.667 0.00 0.00 36.84 4.00
4 5 2.100879 ATTAGCCGATCTCCGCACCC 62.101 60.000 0.00 0.00 36.84 4.61
5 6 0.946221 CATTAGCCGATCTCCGCACC 60.946 60.000 0.00 0.00 36.84 5.01
6 7 0.946221 CCATTAGCCGATCTCCGCAC 60.946 60.000 0.00 0.00 36.84 5.34
7 8 1.367471 CCATTAGCCGATCTCCGCA 59.633 57.895 0.00 0.00 36.84 5.69
8 9 1.374758 CCCATTAGCCGATCTCCGC 60.375 63.158 0.00 0.00 36.84 5.54
9 10 1.293498 CCCCATTAGCCGATCTCCG 59.707 63.158 0.00 0.00 38.18 4.63
10 11 1.003233 GCCCCATTAGCCGATCTCC 60.003 63.158 0.00 0.00 0.00 3.71
11 12 0.321122 CAGCCCCATTAGCCGATCTC 60.321 60.000 0.00 0.00 0.00 2.75
12 13 1.757306 CAGCCCCATTAGCCGATCT 59.243 57.895 0.00 0.00 0.00 2.75
13 14 1.968540 GCAGCCCCATTAGCCGATC 60.969 63.158 0.00 0.00 0.00 3.69
14 15 2.113986 GCAGCCCCATTAGCCGAT 59.886 61.111 0.00 0.00 0.00 4.18
15 16 4.189580 GGCAGCCCCATTAGCCGA 62.190 66.667 0.00 0.00 37.41 5.54
25 26 3.295973 TCTTTTATAATGTGGGCAGCCC 58.704 45.455 25.54 25.54 45.71 5.19
26 27 4.584325 TCATCTTTTATAATGTGGGCAGCC 59.416 41.667 1.26 1.26 0.00 4.85
27 28 5.772825 TCATCTTTTATAATGTGGGCAGC 57.227 39.130 0.00 0.00 0.00 5.25
28 29 8.415553 TGAAATCATCTTTTATAATGTGGGCAG 58.584 33.333 0.00 0.00 0.00 4.85
29 30 8.303780 TGAAATCATCTTTTATAATGTGGGCA 57.696 30.769 0.00 0.00 0.00 5.36
30 31 9.199982 CATGAAATCATCTTTTATAATGTGGGC 57.800 33.333 0.00 0.00 33.61 5.36
38 39 9.720667 CAGCGAAACATGAAATCATCTTTTATA 57.279 29.630 0.00 0.00 33.61 0.98
39 40 7.703621 CCAGCGAAACATGAAATCATCTTTTAT 59.296 33.333 0.00 0.00 33.61 1.40
40 41 7.028962 CCAGCGAAACATGAAATCATCTTTTA 58.971 34.615 0.00 0.00 33.61 1.52
41 42 5.865552 CCAGCGAAACATGAAATCATCTTTT 59.134 36.000 0.00 0.00 33.61 2.27
42 43 5.183713 TCCAGCGAAACATGAAATCATCTTT 59.816 36.000 0.00 0.00 33.61 2.52
43 44 4.701651 TCCAGCGAAACATGAAATCATCTT 59.298 37.500 0.00 0.00 33.61 2.40
44 45 4.264253 TCCAGCGAAACATGAAATCATCT 58.736 39.130 0.00 0.00 33.61 2.90
45 46 4.621068 TCCAGCGAAACATGAAATCATC 57.379 40.909 0.00 0.00 33.61 2.92
46 47 5.345702 CAATCCAGCGAAACATGAAATCAT 58.654 37.500 0.00 0.00 36.96 2.45
47 48 4.735985 CAATCCAGCGAAACATGAAATCA 58.264 39.130 0.00 0.00 0.00 2.57
48 49 3.549070 GCAATCCAGCGAAACATGAAATC 59.451 43.478 0.00 0.00 0.00 2.17
49 50 3.056678 TGCAATCCAGCGAAACATGAAAT 60.057 39.130 0.00 0.00 37.31 2.17
50 51 2.295629 TGCAATCCAGCGAAACATGAAA 59.704 40.909 0.00 0.00 37.31 2.69
51 52 1.885233 TGCAATCCAGCGAAACATGAA 59.115 42.857 0.00 0.00 37.31 2.57
52 53 1.532523 TGCAATCCAGCGAAACATGA 58.467 45.000 0.00 0.00 37.31 3.07
53 54 2.572191 ATGCAATCCAGCGAAACATG 57.428 45.000 0.00 0.00 37.31 3.21
54 55 2.492881 TGAATGCAATCCAGCGAAACAT 59.507 40.909 0.00 0.00 37.31 2.71
55 56 1.885233 TGAATGCAATCCAGCGAAACA 59.115 42.857 0.00 0.00 37.31 2.83
56 57 2.634982 TGAATGCAATCCAGCGAAAC 57.365 45.000 0.00 0.00 37.31 2.78
57 58 2.295629 TGTTGAATGCAATCCAGCGAAA 59.704 40.909 0.00 0.00 36.22 3.46
58 59 1.885233 TGTTGAATGCAATCCAGCGAA 59.115 42.857 0.00 0.00 36.22 4.70
59 60 1.532523 TGTTGAATGCAATCCAGCGA 58.467 45.000 0.00 0.00 36.22 4.93
60 61 2.190161 CATGTTGAATGCAATCCAGCG 58.810 47.619 0.00 0.00 36.22 5.18
61 62 3.241067 ACATGTTGAATGCAATCCAGC 57.759 42.857 0.00 0.00 36.22 4.85
62 63 4.562082 ACAACATGTTGAATGCAATCCAG 58.438 39.130 38.30 12.93 42.93 3.86
63 64 4.603989 ACAACATGTTGAATGCAATCCA 57.396 36.364 38.30 0.00 42.93 3.41
74 75 8.830328 AGAAATTTCTGACGCAACAACATGTTG 61.830 37.037 32.03 32.03 46.53 3.33
75 76 3.773860 TTTCTGACGCAACAACATGTT 57.226 38.095 4.92 4.92 42.08 2.71
76 77 3.988379 ATTTCTGACGCAACAACATGT 57.012 38.095 0.00 0.00 0.00 3.21
77 78 4.977963 AGAAATTTCTGACGCAACAACATG 59.022 37.500 19.86 0.00 35.89 3.21
78 79 5.186996 AGAAATTTCTGACGCAACAACAT 57.813 34.783 19.86 0.00 35.89 2.71
79 80 4.630894 AGAAATTTCTGACGCAACAACA 57.369 36.364 19.86 0.00 35.89 3.33
121 122 9.720769 CTTTTGTATTTCTTTACAGAGGGAGTA 57.279 33.333 0.00 0.00 33.81 2.59
122 123 8.218488 ACTTTTGTATTTCTTTACAGAGGGAGT 58.782 33.333 0.00 0.00 33.81 3.85
123 124 8.507249 CACTTTTGTATTTCTTTACAGAGGGAG 58.493 37.037 0.00 0.00 33.81 4.30
124 125 7.996644 ACACTTTTGTATTTCTTTACAGAGGGA 59.003 33.333 0.00 0.00 33.81 4.20
125 126 8.166422 ACACTTTTGTATTTCTTTACAGAGGG 57.834 34.615 0.00 0.00 33.81 4.30
175 176 9.774413 CCCTCCGTAAATAAATATAAGAGTGTT 57.226 33.333 0.00 0.00 0.00 3.32
176 177 9.151177 TCCCTCCGTAAATAAATATAAGAGTGT 57.849 33.333 0.00 0.00 0.00 3.55
177 178 9.640963 CTCCCTCCGTAAATAAATATAAGAGTG 57.359 37.037 0.00 0.00 0.00 3.51
178 179 9.377238 ACTCCCTCCGTAAATAAATATAAGAGT 57.623 33.333 0.00 0.00 0.00 3.24
247 248 5.984725 TCCAGGCGAGTTTCTATTGATTAA 58.015 37.500 0.00 0.00 0.00 1.40
267 268 1.827344 TGGTTGCATGTGTGTTTTCCA 59.173 42.857 0.00 0.00 0.00 3.53
269 270 1.860326 GCTGGTTGCATGTGTGTTTTC 59.140 47.619 0.00 0.00 42.31 2.29
270 271 1.802136 CGCTGGTTGCATGTGTGTTTT 60.802 47.619 0.00 0.00 43.06 2.43
302 303 3.116096 AGTATCCTGCTACTTGGACCA 57.884 47.619 0.00 0.00 34.90 4.02
335 336 8.500753 AGAACGTGCCAGATATAATACAAAAA 57.499 30.769 0.00 0.00 0.00 1.94
343 344 4.921515 GCGATAAGAACGTGCCAGATATAA 59.078 41.667 0.00 0.00 0.00 0.98
403 410 1.559682 GGATCCAGGAGGCTGTACAAA 59.440 52.381 6.95 0.00 33.74 2.83
533 540 3.179048 GCTCGCTCTTTTCTCTTCTCTC 58.821 50.000 0.00 0.00 0.00 3.20
848 862 8.148351 TGCTTATATAATTCTACCGCAAGTTCT 58.852 33.333 0.00 0.00 0.00 3.01
849 863 8.306680 TGCTTATATAATTCTACCGCAAGTTC 57.693 34.615 0.00 0.00 0.00 3.01
901 915 5.512753 TTATACACGCGGAAATGGTACTA 57.487 39.130 12.47 0.00 0.00 1.82
962 982 2.046700 TCGGCGGTGGTTGGAATC 60.047 61.111 7.21 0.00 0.00 2.52
964 984 4.629523 GGTCGGCGGTGGTTGGAA 62.630 66.667 7.21 0.00 0.00 3.53
995 1015 3.243724 GAGGAGGTGTAGGCCATAGATT 58.756 50.000 5.01 0.00 0.00 2.40
996 1016 2.493687 GGAGGAGGTGTAGGCCATAGAT 60.494 54.545 5.01 0.00 0.00 1.98
1149 1169 3.818121 TACCTTGCCGTTGTGCGCT 62.818 57.895 9.73 0.00 39.71 5.92
1154 1174 1.346395 TGATCTGTACCTTGCCGTTGT 59.654 47.619 0.00 0.00 0.00 3.32
1187 1207 2.746277 CCCCTTTCTTGCCGTCGG 60.746 66.667 6.99 6.99 0.00 4.79
1188 1208 3.431725 GCCCCTTTCTTGCCGTCG 61.432 66.667 0.00 0.00 0.00 5.12
1189 1209 3.062466 GGCCCCTTTCTTGCCGTC 61.062 66.667 0.00 0.00 35.08 4.79
1192 1212 0.904394 TTGATGGCCCCTTTCTTGCC 60.904 55.000 0.00 0.00 45.56 4.52
1193 1213 0.247460 GTTGATGGCCCCTTTCTTGC 59.753 55.000 0.00 0.00 0.00 4.01
1194 1214 0.527565 CGTTGATGGCCCCTTTCTTG 59.472 55.000 0.00 0.00 0.00 3.02
1195 1215 0.611896 CCGTTGATGGCCCCTTTCTT 60.612 55.000 0.00 0.00 0.00 2.52
1227 1262 2.027897 ACGTGCGTCTTGCCGTTA 59.972 55.556 0.00 0.00 44.40 3.18
1233 1268 2.544359 CCGTTCACGTGCGTCTTG 59.456 61.111 11.67 0.00 37.74 3.02
2247 2282 6.093219 TCGATCACTTCACTTGTACTAGTACC 59.907 42.308 26.41 11.84 35.26 3.34
2254 2289 8.635877 ATCTAATTCGATCACTTCACTTGTAC 57.364 34.615 0.00 0.00 0.00 2.90
2278 2313 4.201910 CCAAATTCGATTGTGCCGAACTAT 60.202 41.667 0.00 0.00 46.77 2.12
2390 2434 4.859798 CACAGCTAAACAGCAGAGTAGTAC 59.140 45.833 0.00 0.00 37.25 2.73
2395 2439 2.487934 CACACAGCTAAACAGCAGAGT 58.512 47.619 0.00 0.00 37.25 3.24
2396 2440 1.196354 GCACACAGCTAAACAGCAGAG 59.804 52.381 0.00 0.00 41.15 3.35
2397 2441 1.229428 GCACACAGCTAAACAGCAGA 58.771 50.000 0.00 0.00 41.15 4.26
2401 2445 3.125829 CACCTATGCACACAGCTAAACAG 59.874 47.826 0.00 0.00 45.94 3.16
2402 2446 3.073678 CACCTATGCACACAGCTAAACA 58.926 45.455 0.00 0.00 45.94 2.83
2498 2542 2.906389 ACCCTCAGATCTAGCACAACAA 59.094 45.455 0.00 0.00 0.00 2.83
2499 2543 2.540383 ACCCTCAGATCTAGCACAACA 58.460 47.619 0.00 0.00 0.00 3.33
2548 2601 2.724690 CGTACAAGTTGAACACCGAGAG 59.275 50.000 10.54 0.00 0.00 3.20
2585 2638 1.547372 GCCAGTCTTCAATGTGCCAAT 59.453 47.619 0.00 0.00 0.00 3.16
2629 2698 8.879759 CAAATTCCAGTATCGTTACACATAGTT 58.120 33.333 6.43 0.00 0.00 2.24
2633 2702 6.403200 GCACAAATTCCAGTATCGTTACACAT 60.403 38.462 6.43 0.00 0.00 3.21
2678 2752 4.776795 TCACAGTTCAGCTCGTATACAA 57.223 40.909 3.32 0.00 0.00 2.41
2695 2769 2.593346 AAAGCACCGCAAATTTCACA 57.407 40.000 0.00 0.00 0.00 3.58
2753 2827 6.531948 GTCGTTGAGTACTGAAGATTAGCAAT 59.468 38.462 0.00 0.00 0.00 3.56
2809 2898 1.101331 GGCCAATGCTCCAAGAGAAG 58.899 55.000 0.00 0.00 37.74 2.85
2841 2930 5.582269 TCGAATCACAATCATGGTTCTCTTC 59.418 40.000 0.00 0.00 0.00 2.87
2904 2993 0.604511 CTGTGCAGTGCTCCACATGA 60.605 55.000 17.60 0.00 40.76 3.07
2920 3009 1.203441 TGCAGATTCTCTGGGCCTGT 61.203 55.000 4.53 0.00 44.43 4.00
2979 3068 0.182537 TGCTACCAGTGGCAACTTGT 59.817 50.000 9.78 3.09 44.11 3.16
2988 3077 1.412710 ACATATCCCGTGCTACCAGTG 59.587 52.381 0.00 0.00 0.00 3.66
2990 3079 1.270305 CCACATATCCCGTGCTACCAG 60.270 57.143 0.00 0.00 32.85 4.00
2991 3080 0.756294 CCACATATCCCGTGCTACCA 59.244 55.000 0.00 0.00 32.85 3.25
2992 3081 1.000955 CTCCACATATCCCGTGCTACC 59.999 57.143 0.00 0.00 32.85 3.18
2993 3082 1.000955 CCTCCACATATCCCGTGCTAC 59.999 57.143 0.00 0.00 32.85 3.58
2994 3083 1.338107 CCTCCACATATCCCGTGCTA 58.662 55.000 0.00 0.00 32.85 3.49
2995 3084 2.044806 GCCTCCACATATCCCGTGCT 62.045 60.000 0.00 0.00 32.85 4.40
2996 3085 1.598130 GCCTCCACATATCCCGTGC 60.598 63.158 0.00 0.00 32.85 5.34
2997 3086 1.071471 GGCCTCCACATATCCCGTG 59.929 63.158 0.00 0.00 0.00 4.94
2998 3087 2.147387 GGGCCTCCACATATCCCGT 61.147 63.158 0.84 0.00 0.00 5.28
3000 3089 1.763770 CAGGGCCTCCACATATCCC 59.236 63.158 0.95 0.00 37.24 3.85
3039 3131 2.481952 AGATCTTTCTGCTGCGAAACAC 59.518 45.455 13.03 8.92 0.00 3.32
3062 3157 6.816140 GCTTATCAGAGAAAGTTAAGTCTGCT 59.184 38.462 4.79 0.00 37.04 4.24
3068 3163 5.751028 CCCTCGCTTATCAGAGAAAGTTAAG 59.249 44.000 0.00 0.00 36.65 1.85
3076 3171 1.115930 GGGCCCTCGCTTATCAGAGA 61.116 60.000 17.04 0.00 36.65 3.10
3077 3172 1.118356 AGGGCCCTCGCTTATCAGAG 61.118 60.000 22.28 0.00 34.44 3.35
3105 3200 2.485479 CCCGGTTCATGAGGATTGTAGG 60.485 54.545 0.00 0.00 0.00 3.18
3106 3201 2.434336 TCCCGGTTCATGAGGATTGTAG 59.566 50.000 0.00 0.00 0.00 2.74
3107 3202 2.434336 CTCCCGGTTCATGAGGATTGTA 59.566 50.000 0.00 0.00 0.00 2.41
3108 3203 1.210478 CTCCCGGTTCATGAGGATTGT 59.790 52.381 0.00 0.00 0.00 2.71
3110 3205 1.765314 CTCTCCCGGTTCATGAGGATT 59.235 52.381 0.00 0.00 0.00 3.01
3111 3206 1.062886 TCTCTCCCGGTTCATGAGGAT 60.063 52.381 0.00 0.00 0.00 3.24
3112 3207 0.335019 TCTCTCCCGGTTCATGAGGA 59.665 55.000 0.00 1.45 0.00 3.71
3114 3209 3.226777 AGTATCTCTCCCGGTTCATGAG 58.773 50.000 0.00 0.00 0.00 2.90
3115 3210 3.314307 AGTATCTCTCCCGGTTCATGA 57.686 47.619 0.00 0.00 0.00 3.07
3165 3272 0.462789 AGTCGTACAAATAGGCCCGG 59.537 55.000 0.00 0.00 0.00 5.73
3169 3276 1.933853 CAGCCAGTCGTACAAATAGGC 59.066 52.381 0.00 0.00 40.85 3.93
3187 3294 0.320374 TTCACTTCTGGGGCGTACAG 59.680 55.000 0.00 0.00 37.30 2.74


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

AutoCloner maintained by Alex Coulton.