Multiple sequence alignment - TraesCS7D01G327000

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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 TraesCS7D01G327000 chr7D 100.000 6486 0 0 1 6486 417623410 417616925 0.000000e+00 11978.0
1 TraesCS7D01G327000 chr7D 90.323 124 10 2 1 123 480698559 480698681 1.870000e-35 161.0
2 TraesCS7D01G327000 chr7D 85.859 99 10 4 119 213 101769911 101769813 1.150000e-17 102.0
3 TraesCS7D01G327000 chr7B 96.427 6410 143 38 119 6486 433352546 433346181 0.000000e+00 10490.0
4 TraesCS7D01G327000 chr7A 96.511 5474 147 19 579 6036 482490123 482484678 0.000000e+00 9010.0
5 TraesCS7D01G327000 chr7A 91.844 282 20 2 203 483 482569262 482568983 2.190000e-104 390.0
6 TraesCS7D01G327000 chr7A 86.869 99 9 4 119 213 673242660 673242562 2.470000e-19 108.0
7 TraesCS7D01G327000 chr2D 86.935 199 22 3 203 398 476691889 476691692 3.040000e-53 220.0
8 TraesCS7D01G327000 chr2D 91.667 60 5 0 6404 6463 534963690 534963749 4.170000e-12 84.2
9 TraesCS7D01G327000 chr2D 91.525 59 5 0 6405 6463 630539950 630539892 1.500000e-11 82.4
10 TraesCS7D01G327000 chr5A 91.935 124 8 2 2 123 195578204 195578081 8.650000e-39 172.0
11 TraesCS7D01G327000 chr5A 83.133 83 9 5 6405 6484 265540027 265540107 3.240000e-08 71.3
12 TraesCS7D01G327000 chr6D 92.562 121 6 2 1 118 10173042 10172922 3.110000e-38 171.0
13 TraesCS7D01G327000 chr6D 85.859 99 10 4 119 213 131933915 131934013 1.150000e-17 102.0
14 TraesCS7D01G327000 chr6D 85.859 99 10 4 119 213 303614549 303614647 1.150000e-17 102.0
15 TraesCS7D01G327000 chr6D 85.859 99 11 3 118 213 464274138 464274236 1.150000e-17 102.0
16 TraesCS7D01G327000 chr5B 92.437 119 7 2 2 118 64633771 64633889 1.120000e-37 169.0
17 TraesCS7D01G327000 chr3B 90.551 127 10 2 1 125 243610604 243610478 4.020000e-37 167.0
18 TraesCS7D01G327000 chr1D 90.000 130 10 3 1 128 24212571 24212699 1.450000e-36 165.0
19 TraesCS7D01G327000 chr1D 85.859 99 10 4 119 213 272538833 272538931 1.150000e-17 102.0
20 TraesCS7D01G327000 chr4A 91.597 119 9 1 1 118 485573750 485573868 5.200000e-36 163.0
21 TraesCS7D01G327000 chr4A 89.764 127 11 2 1 125 5423069 5422943 1.870000e-35 161.0
22 TraesCS7D01G327000 chr6A 89.844 128 10 3 1 126 556709304 556709178 1.870000e-35 161.0
23 TraesCS7D01G327000 chr5D 85.859 99 10 4 119 213 482814538 482814440 1.150000e-17 102.0
24 TraesCS7D01G327000 chr4D 85.859 99 10 4 119 213 486776998 486777096 1.150000e-17 102.0
25 TraesCS7D01G327000 chr2B 100.000 40 0 0 6416 6455 715608089 715608050 2.510000e-09 75.0


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 TraesCS7D01G327000 chr7D 417616925 417623410 6485 True 11978 11978 100.000 1 6486 1 chr7D.!!$R2 6485
1 TraesCS7D01G327000 chr7B 433346181 433352546 6365 True 10490 10490 96.427 119 6486 1 chr7B.!!$R1 6367
2 TraesCS7D01G327000 chr7A 482484678 482490123 5445 True 9010 9010 96.511 579 6036 1 chr7A.!!$R1 5457

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
390 393 0.036952 CCTCACCAGCACGATCAACT 60.037 55.000 0.00 0.0 0.00 3.16 F
405 408 0.317269 CAACTTCGCAAGTGCCACTG 60.317 55.000 0.00 0.0 41.91 3.66 F
433 440 1.092921 TTGCGCCGCTAAGTATTGGG 61.093 55.000 11.67 0.0 0.00 4.12 F
854 862 1.381928 TACCTAGGTTCTGCTCGGCG 61.382 60.000 22.11 0.0 0.00 6.46 F
1760 1773 1.450312 GCCTGCGAGCCAGTATGTT 60.450 57.895 0.00 0.0 40.06 2.71 F
2348 2369 1.535204 GGAGGCATGTTGGTTGGTGG 61.535 60.000 0.00 0.0 0.00 4.61 F
4211 4237 2.260844 TTCTCAAACCAGTGCTCCAG 57.739 50.000 0.00 0.0 0.00 3.86 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1298 1306 1.393603 TGGACGGAGAGCACTAGATG 58.606 55.000 0.00 0.00 0.00 2.90 R
1436 1448 2.676748 TGCAAAGTCCTGTTTCCCATT 58.323 42.857 0.00 0.00 0.00 3.16 R
1601 1613 4.575885 TGCAGGGTTCTACTGTTAATGAC 58.424 43.478 0.00 0.00 38.22 3.06 R
2360 2381 5.907197 ACGAGAGCATATAATTGTTTCGG 57.093 39.130 0.00 0.00 0.00 4.30 R
3048 3072 4.093556 GTGCTTCTGTCTACAATAGCCAAC 59.906 45.833 11.42 3.67 33.79 3.77 R
4247 4273 2.546373 GCAGCTGCAAAGAATTGTTGGA 60.546 45.455 33.36 0.00 41.59 3.53 R
5514 5540 0.321671 CTCCTCCTTTCGAGCCAACA 59.678 55.000 0.00 0.00 37.27 3.33 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
33 34 8.836268 ATTGATTTTGTGTCAATGTGCTAATT 57.164 26.923 0.95 0.00 42.87 1.40
34 35 8.659925 TTGATTTTGTGTCAATGTGCTAATTT 57.340 26.923 0.00 0.00 31.07 1.82
35 36 8.659925 TGATTTTGTGTCAATGTGCTAATTTT 57.340 26.923 0.00 0.00 0.00 1.82
36 37 9.107177 TGATTTTGTGTCAATGTGCTAATTTTT 57.893 25.926 0.00 0.00 0.00 1.94
77 78 9.825972 ACATTCTAAAAACATAATGTGAGTTCG 57.174 29.630 0.00 0.00 40.18 3.95
78 79 9.277565 CATTCTAAAAACATAATGTGAGTTCGG 57.722 33.333 0.00 0.00 0.00 4.30
79 80 7.972832 TCTAAAAACATAATGTGAGTTCGGT 57.027 32.000 0.00 0.00 0.00 4.69
80 81 7.802738 TCTAAAAACATAATGTGAGTTCGGTG 58.197 34.615 0.00 0.00 0.00 4.94
81 82 4.419522 AAACATAATGTGAGTTCGGTGC 57.580 40.909 0.00 0.00 0.00 5.01
82 83 3.052455 ACATAATGTGAGTTCGGTGCA 57.948 42.857 0.00 0.00 0.00 4.57
83 84 2.742053 ACATAATGTGAGTTCGGTGCAC 59.258 45.455 8.80 8.80 0.00 4.57
84 85 1.803334 TAATGTGAGTTCGGTGCACC 58.197 50.000 26.78 26.78 0.00 5.01
96 97 3.551407 TGCACCGGTAGCACCACA 61.551 61.111 22.47 5.12 38.47 4.17
97 98 2.281208 GCACCGGTAGCACCACAA 60.281 61.111 19.85 0.00 38.47 3.33
98 99 2.325082 GCACCGGTAGCACCACAAG 61.325 63.158 19.85 0.99 38.47 3.16
99 100 2.032071 ACCGGTAGCACCACAAGC 59.968 61.111 4.49 0.00 38.47 4.01
100 101 2.347490 CCGGTAGCACCACAAGCT 59.653 61.111 0.00 0.00 45.77 3.74
101 102 1.741770 CCGGTAGCACCACAAGCTC 60.742 63.158 0.00 0.00 42.32 4.09
102 103 1.741770 CGGTAGCACCACAAGCTCC 60.742 63.158 6.21 0.00 42.32 4.70
103 104 1.741770 GGTAGCACCACAAGCTCCG 60.742 63.158 0.00 0.00 42.32 4.63
104 105 1.741770 GTAGCACCACAAGCTCCGG 60.742 63.158 0.00 0.00 42.32 5.14
105 106 2.214216 TAGCACCACAAGCTCCGGT 61.214 57.895 0.00 0.00 42.32 5.28
107 108 3.357079 CACCACAAGCTCCGGTGC 61.357 66.667 20.71 20.71 43.43 5.01
108 109 3.872603 ACCACAAGCTCCGGTGCA 61.873 61.111 28.68 0.00 33.72 4.57
109 110 3.357079 CCACAAGCTCCGGTGCAC 61.357 66.667 28.68 8.80 33.72 4.57
110 111 3.357079 CACAAGCTCCGGTGCACC 61.357 66.667 28.68 26.78 34.99 5.01
111 112 3.872603 ACAAGCTCCGGTGCACCA 61.873 61.111 34.16 16.11 35.14 4.17
112 113 3.052082 CAAGCTCCGGTGCACCAG 61.052 66.667 34.16 25.24 35.14 4.00
113 114 3.241530 AAGCTCCGGTGCACCAGA 61.242 61.111 34.16 27.41 35.14 3.86
114 115 2.596851 AAGCTCCGGTGCACCAGAT 61.597 57.895 34.16 21.47 35.14 2.90
115 116 1.264749 AAGCTCCGGTGCACCAGATA 61.265 55.000 34.16 15.43 35.14 1.98
116 117 1.050988 AGCTCCGGTGCACCAGATAT 61.051 55.000 34.16 17.14 35.14 1.63
117 118 0.179045 GCTCCGGTGCACCAGATATT 60.179 55.000 34.16 0.00 35.14 1.28
118 119 1.871080 CTCCGGTGCACCAGATATTC 58.129 55.000 34.16 6.04 35.14 1.75
119 120 0.468226 TCCGGTGCACCAGATATTCC 59.532 55.000 34.16 5.35 35.14 3.01
120 121 0.535102 CCGGTGCACCAGATATTCCC 60.535 60.000 34.16 4.55 35.14 3.97
121 122 0.535102 CGGTGCACCAGATATTCCCC 60.535 60.000 34.16 3.99 35.14 4.81
122 123 0.178990 GGTGCACCAGATATTCCCCC 60.179 60.000 31.23 0.00 35.64 5.40
214 217 5.771153 TGTTTGACATCTTGAATGCTCAA 57.229 34.783 0.00 0.00 39.30 3.02
222 225 7.391275 TGACATCTTGAATGCTCAATGAAACTA 59.609 33.333 0.00 0.00 40.78 2.24
261 264 5.551233 TGCTCTTCTTATGCACTAGTTTGT 58.449 37.500 0.00 0.00 0.00 2.83
262 265 5.409520 TGCTCTTCTTATGCACTAGTTTGTG 59.590 40.000 0.00 0.00 40.62 3.33
273 276 1.886542 CTAGTTTGTGCCTTTCCCACC 59.113 52.381 0.00 0.00 32.30 4.61
275 278 0.104120 GTTTGTGCCTTTCCCACCAC 59.896 55.000 0.00 0.00 32.30 4.16
288 291 4.771114 TCCCACCACAAATACTAGGATG 57.229 45.455 0.00 0.00 0.00 3.51
363 366 8.196771 TCATCTGGCATATGTAACAAAAATTCC 58.803 33.333 11.98 0.00 0.00 3.01
377 380 6.230472 ACAAAAATTCCAAAATAGCCTCACC 58.770 36.000 0.00 0.00 0.00 4.02
378 381 6.183361 ACAAAAATTCCAAAATAGCCTCACCA 60.183 34.615 0.00 0.00 0.00 4.17
379 382 5.665916 AAATTCCAAAATAGCCTCACCAG 57.334 39.130 0.00 0.00 0.00 4.00
380 383 2.128771 TCCAAAATAGCCTCACCAGC 57.871 50.000 0.00 0.00 0.00 4.85
381 384 1.354031 TCCAAAATAGCCTCACCAGCA 59.646 47.619 0.00 0.00 0.00 4.41
382 385 1.474077 CCAAAATAGCCTCACCAGCAC 59.526 52.381 0.00 0.00 0.00 4.40
383 386 1.131126 CAAAATAGCCTCACCAGCACG 59.869 52.381 0.00 0.00 0.00 5.34
384 387 0.613260 AAATAGCCTCACCAGCACGA 59.387 50.000 0.00 0.00 0.00 4.35
385 388 0.833287 AATAGCCTCACCAGCACGAT 59.167 50.000 0.00 0.00 0.00 3.73
386 389 0.390860 ATAGCCTCACCAGCACGATC 59.609 55.000 0.00 0.00 0.00 3.69
387 390 0.970427 TAGCCTCACCAGCACGATCA 60.970 55.000 0.00 0.00 0.00 2.92
388 391 1.375908 GCCTCACCAGCACGATCAA 60.376 57.895 0.00 0.00 0.00 2.57
389 392 1.639298 GCCTCACCAGCACGATCAAC 61.639 60.000 0.00 0.00 0.00 3.18
390 393 0.036952 CCTCACCAGCACGATCAACT 60.037 55.000 0.00 0.00 0.00 3.16
391 394 1.609061 CCTCACCAGCACGATCAACTT 60.609 52.381 0.00 0.00 0.00 2.66
392 395 1.728971 CTCACCAGCACGATCAACTTC 59.271 52.381 0.00 0.00 0.00 3.01
393 396 0.439985 CACCAGCACGATCAACTTCG 59.560 55.000 0.00 0.00 44.56 3.79
394 397 1.291877 ACCAGCACGATCAACTTCGC 61.292 55.000 0.00 0.00 42.82 4.70
403 406 0.593128 ATCAACTTCGCAAGTGCCAC 59.407 50.000 0.00 0.00 41.91 5.01
405 408 0.317269 CAACTTCGCAAGTGCCACTG 60.317 55.000 0.00 0.00 41.91 3.66
433 440 1.092921 TTGCGCCGCTAAGTATTGGG 61.093 55.000 11.67 0.00 0.00 4.12
441 448 2.619590 CGCTAAGTATTGGGGGTTGGTT 60.620 50.000 0.00 0.00 35.87 3.67
443 450 4.204799 GCTAAGTATTGGGGGTTGGTTAG 58.795 47.826 0.00 0.00 0.00 2.34
497 504 7.524717 AATGCTCTAAATGGTACTTTGTTGT 57.475 32.000 0.00 0.00 0.00 3.32
498 505 8.630054 AATGCTCTAAATGGTACTTTGTTGTA 57.370 30.769 0.00 0.00 0.00 2.41
499 506 7.429636 TGCTCTAAATGGTACTTTGTTGTAC 57.570 36.000 0.00 0.00 41.31 2.90
551 558 9.760926 ATTAGAGGTGCTCTTATACATCATCTA 57.239 33.333 0.00 0.00 41.50 1.98
661 669 2.344500 CCAACCTGCCGACCGTAA 59.656 61.111 0.00 0.00 0.00 3.18
854 862 1.381928 TACCTAGGTTCTGCTCGGCG 61.382 60.000 22.11 0.00 0.00 6.46
1298 1306 5.638234 AGTAACCGTTTTGAGCTCAAGTATC 59.362 40.000 27.02 17.22 37.15 2.24
1601 1613 7.130917 GCTCATAGTTGCATTTCTACATTCAG 58.869 38.462 0.00 0.00 0.00 3.02
1750 1763 2.863137 GTTTCTCTTCATAGCCTGCGAG 59.137 50.000 0.00 0.00 0.00 5.03
1760 1773 1.450312 GCCTGCGAGCCAGTATGTT 60.450 57.895 0.00 0.00 40.06 2.71
1804 1817 8.476657 TCAACGATGTGGATACGTTTATTTAA 57.523 30.769 0.00 0.00 45.58 1.52
2147 2168 2.443255 AGGGTTCAAGTTCTGATGGTGT 59.557 45.455 0.00 0.00 32.78 4.16
2348 2369 1.535204 GGAGGCATGTTGGTTGGTGG 61.535 60.000 0.00 0.00 0.00 4.61
2360 2381 3.093057 TGGTTGGTGGTTATGGTTATGC 58.907 45.455 0.00 0.00 0.00 3.14
3047 3071 4.570369 GTGTTGCATTTACCTTTTGCTGTT 59.430 37.500 0.00 0.00 37.28 3.16
3048 3072 4.569966 TGTTGCATTTACCTTTTGCTGTTG 59.430 37.500 0.00 0.00 37.28 3.33
3049 3073 4.399004 TGCATTTACCTTTTGCTGTTGT 57.601 36.364 0.00 0.00 37.28 3.32
3475 3499 4.243007 AGCTTTGTATTTGGTGCTGTTC 57.757 40.909 0.00 0.00 0.00 3.18
3805 3831 3.366440 ACTACGTCAACTGAACACCTC 57.634 47.619 0.00 0.00 0.00 3.85
4066 4092 9.220767 GTAAATTCAACAGATACTCCAGAAACT 57.779 33.333 0.00 0.00 0.00 2.66
4211 4237 2.260844 TTCTCAAACCAGTGCTCCAG 57.739 50.000 0.00 0.00 0.00 3.86
4247 4273 1.344763 GGCCTACACCGAGCTCATTAT 59.655 52.381 15.40 0.00 0.00 1.28
4350 4376 1.039856 ATGCCAAGAAACACACCACC 58.960 50.000 0.00 0.00 0.00 4.61
4641 4667 2.202932 CTCGCCAGTTCCATCGGG 60.203 66.667 0.00 0.00 0.00 5.14
4642 4668 2.682136 TCGCCAGTTCCATCGGGA 60.682 61.111 0.00 0.00 43.03 5.14
4708 4734 1.532868 CCAAGAGCAAACTTCACTCCG 59.467 52.381 0.00 0.00 0.00 4.63
4839 4865 0.887933 CAGCAAACTTACCCGCCATT 59.112 50.000 0.00 0.00 0.00 3.16
5514 5540 2.692024 ACTGAGGATCTCATGGCATCT 58.308 47.619 0.00 0.00 39.92 2.90
5687 5713 1.994779 GACATTTCTTGCATTTGCGGG 59.005 47.619 0.00 0.00 45.83 6.13
5806 5835 8.626576 CGTTTGTTTACAGCAATTTATGTACTG 58.373 33.333 0.00 0.00 31.83 2.74
5952 5982 2.453521 TCCCGAGTAGCTAAAAGCAGA 58.546 47.619 0.00 0.00 45.56 4.26
5955 5985 4.647853 TCCCGAGTAGCTAAAAGCAGAATA 59.352 41.667 0.00 0.00 45.56 1.75
5969 5999 8.910351 AAAAGCAGAATATCCTATCCACTAAC 57.090 34.615 0.00 0.00 0.00 2.34
6001 6031 1.242076 CCAAGCCTTCTGTGGTTCAG 58.758 55.000 0.00 0.00 44.85 3.02
6025 6055 1.076332 GTGGAGTCCGGTTTTGATCG 58.924 55.000 4.30 0.00 0.00 3.69
6030 6060 1.142474 GTCCGGTTTTGATCGTCGTT 58.858 50.000 0.00 0.00 0.00 3.85
6031 6061 1.528161 GTCCGGTTTTGATCGTCGTTT 59.472 47.619 0.00 0.00 0.00 3.60
6032 6062 1.527736 TCCGGTTTTGATCGTCGTTTG 59.472 47.619 0.00 0.00 0.00 2.93
6033 6063 1.262151 CCGGTTTTGATCGTCGTTTGT 59.738 47.619 0.00 0.00 0.00 2.83
6034 6064 2.556806 CGGTTTTGATCGTCGTTTGTC 58.443 47.619 0.00 0.00 0.00 3.18
6035 6065 2.033577 CGGTTTTGATCGTCGTTTGTCA 60.034 45.455 0.00 0.00 0.00 3.58
6036 6066 3.544440 CGGTTTTGATCGTCGTTTGTCAA 60.544 43.478 0.00 0.00 0.00 3.18
6053 6083 7.096885 CGTTTGTCAATTGTCATGACTTCTTTC 60.097 37.037 25.55 12.85 45.81 2.62
6137 6167 2.415168 AGTTCATGTATGCCGTGTTTCG 59.585 45.455 0.00 0.00 39.52 3.46
6144 6174 4.996344 TGTATGCCGTGTTTCGATTACTA 58.004 39.130 0.00 0.00 42.86 1.82
6194 6225 2.337583 CTCGAACGTCACATGGTTCAT 58.662 47.619 11.51 0.00 41.97 2.57
6221 6252 1.069568 CGTTAGCGGTTCAAACATGCA 60.070 47.619 0.00 0.00 35.20 3.96
6243 6274 5.114780 CAGAGTCTCGTTCCAATCATCATT 58.885 41.667 0.00 0.00 0.00 2.57
6250 6281 7.439356 GTCTCGTTCCAATCATCATTTATCAGA 59.561 37.037 0.00 0.00 0.00 3.27
6310 6355 6.428083 TGGGTAAGTTAGTGTTTCATCTCA 57.572 37.500 0.00 0.00 0.00 3.27
6316 6361 7.823745 AAGTTAGTGTTTCATCTCATGGTTT 57.176 32.000 0.00 0.00 0.00 3.27
6326 6371 5.818887 TCATCTCATGGTTTGAAAGGATCA 58.181 37.500 0.00 0.00 32.78 2.92
6345 6390 2.307980 TCAAGAGTTCGACTAGAGGGGA 59.692 50.000 0.00 0.00 0.00 4.81
6353 6398 1.133761 CGACTAGAGGGGATGGAGTGA 60.134 57.143 0.00 0.00 0.00 3.41
6372 6417 5.026121 AGTGAGGGTGAATATGAGACTGAA 58.974 41.667 0.00 0.00 0.00 3.02
6411 6464 5.277857 TCTAAAGGCGAAGAGGATAAAGG 57.722 43.478 0.00 0.00 0.00 3.11
6422 6475 6.512091 CGAAGAGGATAAAGGACGTTCTCTAG 60.512 46.154 0.00 0.00 30.94 2.43
6423 6476 6.003859 AGAGGATAAAGGACGTTCTCTAGA 57.996 41.667 0.00 0.00 0.00 2.43
6424 6477 6.607019 AGAGGATAAAGGACGTTCTCTAGAT 58.393 40.000 0.00 0.00 0.00 1.98
6425 6478 7.747690 AGAGGATAAAGGACGTTCTCTAGATA 58.252 38.462 0.00 0.00 0.00 1.98
6437 6490 6.024664 CGTTCTCTAGATATGCAATCTACGG 58.975 44.000 15.62 11.18 0.00 4.02
6438 6491 6.348622 CGTTCTCTAGATATGCAATCTACGGT 60.349 42.308 15.62 0.00 0.00 4.83
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
9 10 8.659925 AAATTAGCACATTGACACAAAATCAA 57.340 26.923 0.00 0.00 40.25 2.57
10 11 8.659925 AAAATTAGCACATTGACACAAAATCA 57.340 26.923 0.00 0.00 0.00 2.57
51 52 9.825972 CGAACTCACATTATGTTTTTAGAATGT 57.174 29.630 0.00 0.00 41.63 2.71
52 53 9.277565 CCGAACTCACATTATGTTTTTAGAATG 57.722 33.333 0.00 0.00 35.84 2.67
53 54 9.010029 ACCGAACTCACATTATGTTTTTAGAAT 57.990 29.630 0.00 0.00 0.00 2.40
54 55 8.286800 CACCGAACTCACATTATGTTTTTAGAA 58.713 33.333 0.00 0.00 0.00 2.10
55 56 7.572353 GCACCGAACTCACATTATGTTTTTAGA 60.572 37.037 0.00 0.00 0.00 2.10
56 57 6.523201 GCACCGAACTCACATTATGTTTTTAG 59.477 38.462 0.00 0.00 0.00 1.85
57 58 6.017026 TGCACCGAACTCACATTATGTTTTTA 60.017 34.615 0.00 0.00 0.00 1.52
58 59 5.219633 GCACCGAACTCACATTATGTTTTT 58.780 37.500 0.00 0.00 0.00 1.94
59 60 4.277174 TGCACCGAACTCACATTATGTTTT 59.723 37.500 0.00 0.00 0.00 2.43
60 61 3.818210 TGCACCGAACTCACATTATGTTT 59.182 39.130 0.00 0.00 0.00 2.83
61 62 3.188460 GTGCACCGAACTCACATTATGTT 59.812 43.478 5.22 0.00 0.00 2.71
62 63 2.742053 GTGCACCGAACTCACATTATGT 59.258 45.455 5.22 0.00 0.00 2.29
63 64 2.095853 GGTGCACCGAACTCACATTATG 59.904 50.000 22.49 0.00 32.69 1.90
64 65 2.356135 GGTGCACCGAACTCACATTAT 58.644 47.619 22.49 0.00 32.69 1.28
65 66 1.803334 GGTGCACCGAACTCACATTA 58.197 50.000 22.49 0.00 32.69 1.90
66 67 2.629002 GGTGCACCGAACTCACATT 58.371 52.632 22.49 0.00 32.69 2.71
67 68 4.379174 GGTGCACCGAACTCACAT 57.621 55.556 22.49 0.00 32.69 3.21
79 80 3.108288 TTGTGGTGCTACCGGTGCA 62.108 57.895 19.93 21.51 42.58 4.57
80 81 2.281208 TTGTGGTGCTACCGGTGC 60.281 61.111 19.93 19.04 42.58 5.01
81 82 2.325082 GCTTGTGGTGCTACCGGTG 61.325 63.158 19.93 8.61 42.58 4.94
82 83 2.032071 GCTTGTGGTGCTACCGGT 59.968 61.111 13.98 13.98 42.58 5.28
83 84 1.741770 GAGCTTGTGGTGCTACCGG 60.742 63.158 0.00 0.00 42.58 5.28
84 85 1.741770 GGAGCTTGTGGTGCTACCG 60.742 63.158 0.00 0.00 42.58 4.02
85 86 1.741770 CGGAGCTTGTGGTGCTACC 60.742 63.158 0.00 0.00 41.30 3.18
86 87 1.741770 CCGGAGCTTGTGGTGCTAC 60.742 63.158 0.00 0.00 41.30 3.58
87 88 2.214216 ACCGGAGCTTGTGGTGCTA 61.214 57.895 9.46 0.00 41.30 3.49
88 89 3.560251 ACCGGAGCTTGTGGTGCT 61.560 61.111 9.46 0.00 44.24 4.40
89 90 3.357079 CACCGGAGCTTGTGGTGC 61.357 66.667 9.46 0.00 45.85 5.01
91 92 3.872603 TGCACCGGAGCTTGTGGT 61.873 61.111 24.52 6.83 36.10 4.16
92 93 3.357079 GTGCACCGGAGCTTGTGG 61.357 66.667 24.52 6.27 34.99 4.17
93 94 3.357079 GGTGCACCGGAGCTTGTG 61.357 66.667 22.49 4.12 34.99 3.33
94 95 3.832237 CTGGTGCACCGGAGCTTGT 62.832 63.158 37.13 0.00 45.36 3.16
95 96 3.052082 CTGGTGCACCGGAGCTTG 61.052 66.667 37.13 13.64 45.36 4.01
96 97 3.241530 TCTGGTGCACCGGAGCTT 61.242 61.111 38.27 0.00 46.04 3.74
101 102 0.535102 GGGAATATCTGGTGCACCGG 60.535 60.000 35.06 35.06 43.86 5.28
102 103 0.535102 GGGGAATATCTGGTGCACCG 60.535 60.000 30.07 23.48 39.43 4.94
103 104 0.178990 GGGGGAATATCTGGTGCACC 60.179 60.000 29.67 29.67 0.00 5.01
104 105 3.421567 GGGGGAATATCTGGTGCAC 57.578 57.895 8.80 8.80 0.00 4.57
120 121 3.720002 TCCAAAGGCTACTATAAAGGGGG 59.280 47.826 0.00 0.00 0.00 5.40
121 122 4.658901 TCTCCAAAGGCTACTATAAAGGGG 59.341 45.833 0.00 0.00 0.00 4.79
122 123 5.888982 TCTCCAAAGGCTACTATAAAGGG 57.111 43.478 0.00 0.00 0.00 3.95
123 124 7.067496 TCATCTCCAAAGGCTACTATAAAGG 57.933 40.000 0.00 0.00 0.00 3.11
124 125 7.172361 GCTTCATCTCCAAAGGCTACTATAAAG 59.828 40.741 0.00 0.00 0.00 1.85
125 126 6.992715 GCTTCATCTCCAAAGGCTACTATAAA 59.007 38.462 0.00 0.00 0.00 1.40
214 217 6.899393 TTCAAGATGCCAAACTAGTTTCAT 57.101 33.333 18.00 17.89 0.00 2.57
222 225 3.428532 AGAGCATTCAAGATGCCAAACT 58.571 40.909 7.33 0.97 45.59 2.66
261 264 2.158385 AGTATTTGTGGTGGGAAAGGCA 60.158 45.455 0.00 0.00 0.00 4.75
262 265 2.525368 AGTATTTGTGGTGGGAAAGGC 58.475 47.619 0.00 0.00 0.00 4.35
268 271 4.503714 ACATCCTAGTATTTGTGGTGGG 57.496 45.455 0.00 0.00 0.00 4.61
338 341 7.980662 TGGAATTTTTGTTACATATGCCAGATG 59.019 33.333 1.58 0.00 0.00 2.90
363 366 1.131126 CGTGCTGGTGAGGCTATTTTG 59.869 52.381 0.00 0.00 0.00 2.44
371 374 0.036952 AGTTGATCGTGCTGGTGAGG 60.037 55.000 0.00 0.00 0.00 3.86
377 380 0.512518 TTGCGAAGTTGATCGTGCTG 59.487 50.000 0.00 0.00 44.49 4.41
378 381 0.792640 CTTGCGAAGTTGATCGTGCT 59.207 50.000 0.00 0.00 44.49 4.40
379 382 0.512952 ACTTGCGAAGTTGATCGTGC 59.487 50.000 0.00 0.00 44.49 5.34
380 383 1.722751 GCACTTGCGAAGTTGATCGTG 60.723 52.381 0.00 0.00 44.49 4.35
381 384 0.512952 GCACTTGCGAAGTTGATCGT 59.487 50.000 0.00 0.00 44.49 3.73
382 385 0.179215 GGCACTTGCGAAGTTGATCG 60.179 55.000 0.00 0.00 45.41 3.69
383 386 0.874390 TGGCACTTGCGAAGTTGATC 59.126 50.000 0.00 0.00 40.46 2.92
384 387 0.593128 GTGGCACTTGCGAAGTTGAT 59.407 50.000 11.13 0.00 40.46 2.57
385 388 0.463654 AGTGGCACTTGCGAAGTTGA 60.464 50.000 15.88 0.00 40.46 3.18
386 389 0.317269 CAGTGGCACTTGCGAAGTTG 60.317 55.000 19.43 0.00 40.46 3.16
387 390 0.463654 TCAGTGGCACTTGCGAAGTT 60.464 50.000 19.43 0.00 40.46 2.66
388 391 0.250467 ATCAGTGGCACTTGCGAAGT 60.250 50.000 19.43 0.00 44.06 3.01
389 392 0.877071 AATCAGTGGCACTTGCGAAG 59.123 50.000 19.43 5.68 43.26 3.79
390 393 1.317613 AAATCAGTGGCACTTGCGAA 58.682 45.000 19.43 1.57 43.26 4.70
391 394 1.317613 AAAATCAGTGGCACTTGCGA 58.682 45.000 19.43 13.13 43.26 5.10
392 395 2.138596 AAAAATCAGTGGCACTTGCG 57.861 45.000 19.43 7.32 43.26 4.85
420 427 1.064979 ACCAACCCCCAATACTTAGCG 60.065 52.381 0.00 0.00 0.00 4.26
433 440 5.738619 AAATGATTGTTCCTAACCAACCC 57.261 39.130 0.00 0.00 0.00 4.11
491 498 7.654022 AAAATTCAGAGAAAGGGTACAACAA 57.346 32.000 0.00 0.00 0.00 2.83
492 499 8.754991 TTAAAATTCAGAGAAAGGGTACAACA 57.245 30.769 0.00 0.00 0.00 3.33
494 501 9.284968 CTCTTAAAATTCAGAGAAAGGGTACAA 57.715 33.333 0.00 0.00 39.21 2.41
495 502 8.656806 TCTCTTAAAATTCAGAGAAAGGGTACA 58.343 33.333 4.91 0.00 42.14 2.90
496 503 9.674068 ATCTCTTAAAATTCAGAGAAAGGGTAC 57.326 33.333 10.23 0.00 46.78 3.34
497 504 9.892130 GATCTCTTAAAATTCAGAGAAAGGGTA 57.108 33.333 10.23 0.00 46.78 3.69
498 505 8.386264 TGATCTCTTAAAATTCAGAGAAAGGGT 58.614 33.333 10.23 0.00 46.78 4.34
499 506 8.798859 TGATCTCTTAAAATTCAGAGAAAGGG 57.201 34.615 10.23 0.00 46.78 3.95
564 571 6.879458 AGAGTACCTCCAAACAAATGATGTAC 59.121 38.462 0.00 0.00 42.99 2.90
565 572 7.016153 AGAGTACCTCCAAACAAATGATGTA 57.984 36.000 0.00 0.00 42.99 2.29
566 573 5.880901 AGAGTACCTCCAAACAAATGATGT 58.119 37.500 0.00 0.00 46.82 3.06
567 574 7.148239 GGTTAGAGTACCTCCAAACAAATGATG 60.148 40.741 0.00 0.00 35.23 3.07
568 575 6.884836 GGTTAGAGTACCTCCAAACAAATGAT 59.115 38.462 0.00 0.00 35.23 2.45
569 576 6.235664 GGTTAGAGTACCTCCAAACAAATGA 58.764 40.000 0.00 0.00 35.23 2.57
570 577 5.414765 GGGTTAGAGTACCTCCAAACAAATG 59.585 44.000 0.00 0.00 38.30 2.32
830 838 0.105039 AGCAGAACCTAGGTATGCGC 59.895 55.000 31.29 23.61 42.26 6.09
1119 1127 7.579531 CGGATAATCATTGAGCCTGGTATCTTA 60.580 40.741 0.00 0.00 0.00 2.10
1298 1306 1.393603 TGGACGGAGAGCACTAGATG 58.606 55.000 0.00 0.00 0.00 2.90
1436 1448 2.676748 TGCAAAGTCCTGTTTCCCATT 58.323 42.857 0.00 0.00 0.00 3.16
1601 1613 4.575885 TGCAGGGTTCTACTGTTAATGAC 58.424 43.478 0.00 0.00 38.22 3.06
1804 1817 6.318900 GCTGGTTCTATGGTTGCTAAAGTAAT 59.681 38.462 0.00 0.00 0.00 1.89
2147 2168 6.070656 ACCTCATTCTCTTTTGGATTGTCAA 58.929 36.000 0.00 0.00 0.00 3.18
2360 2381 5.907197 ACGAGAGCATATAATTGTTTCGG 57.093 39.130 0.00 0.00 0.00 4.30
3047 3071 4.253685 GCTTCTGTCTACAATAGCCAACA 58.746 43.478 5.30 0.00 0.00 3.33
3048 3072 4.093556 GTGCTTCTGTCTACAATAGCCAAC 59.906 45.833 11.42 3.67 33.79 3.77
3049 3073 4.253685 GTGCTTCTGTCTACAATAGCCAA 58.746 43.478 11.42 0.00 33.79 4.52
3805 3831 5.518847 CAGCCTGAGCATGAATAACAAATTG 59.481 40.000 0.00 0.00 43.56 2.32
3930 3956 6.766944 CAGGAGTAAGAAGCATCTCAATCAAT 59.233 38.462 0.00 0.00 33.77 2.57
4066 4092 2.778299 ACTGCCGAAGAAACAATAGCA 58.222 42.857 0.00 0.00 0.00 3.49
4247 4273 2.546373 GCAGCTGCAAAGAATTGTTGGA 60.546 45.455 33.36 0.00 41.59 3.53
4350 4376 3.765511 TGATGGCTGAAATCCAGGAAAAG 59.234 43.478 0.00 0.00 43.13 2.27
4641 4667 5.582665 GTGGACATATTTGACTGAGAAGGTC 59.417 44.000 0.00 0.00 0.00 3.85
4642 4668 5.491982 GTGGACATATTTGACTGAGAAGGT 58.508 41.667 0.00 0.00 0.00 3.50
4708 4734 3.428045 GCCTGGAATGTAATGTTGCTGAC 60.428 47.826 0.00 0.00 0.00 3.51
4839 4865 1.031571 GGGAGGACGCATTTGCATCA 61.032 55.000 0.78 0.00 42.21 3.07
5514 5540 0.321671 CTCCTCCTTTCGAGCCAACA 59.678 55.000 0.00 0.00 37.27 3.33
5687 5713 5.622770 AATGGAGGATTTGAACGTACAAC 57.377 39.130 0.00 0.00 0.00 3.32
5757 5786 3.543680 AGTGATCCGGGTATGAGTTTG 57.456 47.619 0.00 0.00 0.00 2.93
5806 5835 2.960170 CACTGGAAGCAAGGCAGC 59.040 61.111 0.00 0.00 37.60 5.25
5952 5982 6.044404 CACTTGGGGTTAGTGGATAGGATATT 59.956 42.308 0.00 0.00 39.42 1.28
5955 5985 3.716872 CACTTGGGGTTAGTGGATAGGAT 59.283 47.826 0.00 0.00 39.42 3.24
5969 5999 1.471829 GGCTTGGTTTCCACTTGGGG 61.472 60.000 0.00 0.00 37.22 4.96
6001 6031 1.003223 CAAAACCGGACTCCACGTTTC 60.003 52.381 9.46 0.00 29.23 2.78
6025 6055 5.095691 AGTCATGACAATTGACAAACGAC 57.904 39.130 27.02 18.11 44.73 4.34
6030 6060 7.572523 AGAAAGAAGTCATGACAATTGACAA 57.427 32.000 27.02 0.00 44.73 3.18
6031 6061 8.675705 TTAGAAAGAAGTCATGACAATTGACA 57.324 30.769 27.02 13.18 44.73 3.58
6032 6062 8.778358 ACTTAGAAAGAAGTCATGACAATTGAC 58.222 33.333 27.02 13.71 43.05 3.18
6033 6063 8.908786 ACTTAGAAAGAAGTCATGACAATTGA 57.091 30.769 27.02 6.03 34.48 2.57
6064 6094 9.719355 ACAAACTTACCAAAAGAAAAGTTGATT 57.281 25.926 0.51 0.00 40.35 2.57
6076 6106 5.794894 TCCAAGCAAACAAACTTACCAAAA 58.205 33.333 0.00 0.00 0.00 2.44
6159 6190 6.037423 ACGTTCGAGCAAATTAGATGATTC 57.963 37.500 0.00 0.00 0.00 2.52
6168 6199 2.095768 CCATGTGACGTTCGAGCAAATT 60.096 45.455 0.00 0.00 0.00 1.82
6194 6225 1.448893 GAACCGCTAACGCCATCCA 60.449 57.895 0.00 0.00 38.22 3.41
6221 6252 5.350504 AATGATGATTGGAACGAGACTCT 57.649 39.130 0.03 0.00 0.00 3.24
6286 6331 6.833041 TGAGATGAAACACTAACTTACCCAA 58.167 36.000 0.00 0.00 0.00 4.12
6287 6332 6.428083 TGAGATGAAACACTAACTTACCCA 57.572 37.500 0.00 0.00 0.00 4.51
6290 6335 7.907214 ACCATGAGATGAAACACTAACTTAC 57.093 36.000 0.00 0.00 0.00 2.34
6291 6336 8.783093 CAAACCATGAGATGAAACACTAACTTA 58.217 33.333 0.00 0.00 0.00 2.24
6310 6355 5.182001 CGAACTCTTGATCCTTTCAAACCAT 59.818 40.000 0.00 0.00 43.64 3.55
6316 6361 4.873746 AGTCGAACTCTTGATCCTTTCA 57.126 40.909 0.00 0.00 0.00 2.69
6326 6371 3.292460 CATCCCCTCTAGTCGAACTCTT 58.708 50.000 0.00 0.00 0.00 2.85
6333 6378 1.133761 TCACTCCATCCCCTCTAGTCG 60.134 57.143 0.00 0.00 0.00 4.18
6334 6379 2.593026 CTCACTCCATCCCCTCTAGTC 58.407 57.143 0.00 0.00 0.00 2.59
6345 6390 4.346418 GTCTCATATTCACCCTCACTCCAT 59.654 45.833 0.00 0.00 0.00 3.41
6380 6426 7.166167 TCCTCTTCGCCTTTAGAAATTAAACT 58.834 34.615 0.00 0.00 0.00 2.66
6398 6451 5.585820 AGAGAACGTCCTTTATCCTCTTC 57.414 43.478 0.00 0.00 0.00 2.87
6411 6464 6.739100 CGTAGATTGCATATCTAGAGAACGTC 59.261 42.308 14.85 4.86 31.90 4.34
6422 6475 5.289595 TGTTCTCACCGTAGATTGCATATC 58.710 41.667 0.00 0.00 0.00 1.63
6423 6476 5.276461 TGTTCTCACCGTAGATTGCATAT 57.724 39.130 0.00 0.00 0.00 1.78
6424 6477 4.729227 TGTTCTCACCGTAGATTGCATA 57.271 40.909 0.00 0.00 0.00 3.14
6425 6478 3.610040 TGTTCTCACCGTAGATTGCAT 57.390 42.857 0.00 0.00 0.00 3.96
6437 6490 8.662781 TTGCTTATCATATAGGTTGTTCTCAC 57.337 34.615 0.00 0.00 0.00 3.51
6438 6491 9.330063 CTTTGCTTATCATATAGGTTGTTCTCA 57.670 33.333 0.00 0.00 0.00 3.27


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

AutoCloner maintained by Alex Coulton.