Multiple sequence alignment - TraesCS1A01G381600

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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 TraesCS1A01G381600 chr1A 100.000 2756 0 0 1 2756 552183083 552180328 0.000000e+00 5090.0
1 TraesCS1A01G381600 chr1A 94.169 1715 72 9 95 1793 552203425 552201723 0.000000e+00 2588.0
2 TraesCS1A01G381600 chr1A 77.253 233 36 13 324 554 552203632 552203415 1.340000e-23 121.0
3 TraesCS1A01G381600 chr1D 94.016 1972 79 14 50 1985 461118654 461116686 0.000000e+00 2952.0
4 TraesCS1A01G381600 chr1B 93.655 1702 77 18 1082 2756 633320936 633319239 0.000000e+00 2516.0
5 TraesCS1A01G381600 chr1B 92.177 997 61 9 95 1076 633321974 633320980 0.000000e+00 1393.0
6 TraesCS1A01G381600 chr7D 77.684 475 69 19 136 594 392642215 392641762 3.520000e-64 255.0
7 TraesCS1A01G381600 chr7D 82.390 159 27 1 123 280 481179815 481179973 1.330000e-28 137.0
8 TraesCS1A01G381600 chr5B 82.857 245 35 5 151 394 692280627 692280865 2.150000e-51 213.0
9 TraesCS1A01G381600 chr5B 81.061 264 42 6 133 394 692255838 692256095 1.290000e-48 204.0
10 TraesCS1A01G381600 chr2A 79.623 265 44 10 136 394 680101605 680101865 6.060000e-42 182.0
11 TraesCS1A01G381600 chr7B 82.803 157 26 1 123 278 506757893 506758049 3.700000e-29 139.0
12 TraesCS1A01G381600 chr5A 81.212 165 21 9 431 588 520669258 520669097 1.040000e-24 124.0
13 TraesCS1A01G381600 chr4D 84.874 119 13 5 399 514 337938238 337938354 6.240000e-22 115.0
14 TraesCS1A01G381600 chr3A 78.977 176 30 6 132 300 444536726 444536551 2.240000e-21 113.0
15 TraesCS1A01G381600 chr4A 98.113 53 1 0 1 53 600882756 600882808 2.920000e-15 93.5
16 TraesCS1A01G381600 chr2B 80.000 110 21 1 284 393 650481778 650481886 2.280000e-11 80.5
17 TraesCS1A01G381600 chr4B 94.231 52 2 1 1 52 613443236 613443286 8.180000e-11 78.7


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 TraesCS1A01G381600 chr1A 552180328 552183083 2755 True 5090.0 5090 100.000 1 2756 1 chr1A.!!$R1 2755
1 TraesCS1A01G381600 chr1A 552201723 552203632 1909 True 1354.5 2588 85.711 95 1793 2 chr1A.!!$R2 1698
2 TraesCS1A01G381600 chr1D 461116686 461118654 1968 True 2952.0 2952 94.016 50 1985 1 chr1D.!!$R1 1935
3 TraesCS1A01G381600 chr1B 633319239 633321974 2735 True 1954.5 2516 92.916 95 2756 2 chr1B.!!$R1 2661

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
56 57 1.072266 TCCCCAACAACAGCATAGGT 58.928 50.000 0.00 0.0 0.0 3.08 F
100 214 1.985895 AGAAATTTCGGTGAGGAGGGT 59.014 47.619 12.42 0.0 0.0 4.34 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1583 1756 1.538276 GCAACGGATCTTGCATTTCG 58.462 50.0 13.27 0.0 45.07 3.46 R
1997 2170 2.169352 ACTATGCTGTGGCTAGAACCAG 59.831 50.0 0.00 0.0 41.46 4.00 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
45 46 7.841282 TTTGAAATTACTACATTCCCCAACA 57.159 32.000 0.00 0.00 0.00 3.33
46 47 7.841282 TTGAAATTACTACATTCCCCAACAA 57.159 32.000 0.00 0.00 0.00 2.83
47 48 7.222000 TGAAATTACTACATTCCCCAACAAC 57.778 36.000 0.00 0.00 0.00 3.32
48 49 6.778069 TGAAATTACTACATTCCCCAACAACA 59.222 34.615 0.00 0.00 0.00 3.33
49 50 6.834168 AATTACTACATTCCCCAACAACAG 57.166 37.500 0.00 0.00 0.00 3.16
50 51 2.514803 ACTACATTCCCCAACAACAGC 58.485 47.619 0.00 0.00 0.00 4.40
51 52 2.158534 ACTACATTCCCCAACAACAGCA 60.159 45.455 0.00 0.00 0.00 4.41
52 53 2.014010 ACATTCCCCAACAACAGCAT 57.986 45.000 0.00 0.00 0.00 3.79
53 54 3.168035 ACATTCCCCAACAACAGCATA 57.832 42.857 0.00 0.00 0.00 3.14
55 56 2.214376 TTCCCCAACAACAGCATAGG 57.786 50.000 0.00 0.00 0.00 2.57
56 57 1.072266 TCCCCAACAACAGCATAGGT 58.928 50.000 0.00 0.00 0.00 3.08
60 61 2.489329 CCCAACAACAGCATAGGTTGAG 59.511 50.000 11.76 4.45 46.56 3.02
61 62 3.411446 CCAACAACAGCATAGGTTGAGA 58.589 45.455 11.76 0.00 46.56 3.27
62 63 4.012374 CCAACAACAGCATAGGTTGAGAT 58.988 43.478 11.76 0.00 46.56 2.75
64 65 5.396484 CAACAACAGCATAGGTTGAGATTG 58.604 41.667 11.76 3.24 46.56 2.67
65 66 4.655963 ACAACAGCATAGGTTGAGATTGT 58.344 39.130 11.76 0.00 46.56 2.71
66 67 5.804639 ACAACAGCATAGGTTGAGATTGTA 58.195 37.500 11.76 0.00 46.56 2.41
68 69 6.714810 ACAACAGCATAGGTTGAGATTGTAAA 59.285 34.615 11.76 0.00 46.56 2.01
69 70 7.230510 ACAACAGCATAGGTTGAGATTGTAAAA 59.769 33.333 11.76 0.00 46.56 1.52
70 71 7.759489 ACAGCATAGGTTGAGATTGTAAAAA 57.241 32.000 0.00 0.00 0.00 1.94
99 213 2.789409 AGAAATTTCGGTGAGGAGGG 57.211 50.000 12.42 0.00 0.00 4.30
100 214 1.985895 AGAAATTTCGGTGAGGAGGGT 59.014 47.619 12.42 0.00 0.00 4.34
130 244 3.118223 GGACCTACTAGGCAAGCTCATTT 60.118 47.826 1.55 0.00 39.63 2.32
269 383 9.939802 GTTTGGATAGGAGAAGACTAGTAAAAA 57.060 33.333 0.00 0.00 0.00 1.94
313 427 6.240894 TGGTAAGATTTGATCTGATATGGGC 58.759 40.000 0.00 0.00 40.13 5.36
477 593 4.130118 TGGTTTTTATTTTGTGCGGCATT 58.870 34.783 5.72 0.00 0.00 3.56
659 776 4.960469 TCTTTGGATACTGACCGTATTCCT 59.040 41.667 0.00 0.00 38.90 3.36
967 1096 3.434309 CAACAGGTTTCCCCAAGATCAT 58.566 45.455 0.00 0.00 34.66 2.45
977 1106 5.509832 TCCCCAAGATCATATCCTCATTG 57.490 43.478 0.00 0.00 0.00 2.82
983 1112 6.882678 CCAAGATCATATCCTCATTGCATACA 59.117 38.462 0.00 0.00 0.00 2.29
1076 1205 3.199071 GTGGTACCTCTCTCTCTCTCTCA 59.801 52.174 14.36 0.00 0.00 3.27
1077 1206 3.847184 TGGTACCTCTCTCTCTCTCTCAA 59.153 47.826 14.36 0.00 0.00 3.02
1131 1299 6.757237 TGTTTAACCATGAGTTGCAATCATT 58.243 32.000 16.73 9.77 39.67 2.57
1219 1387 2.267351 CCATGGCGCTGGTGAAACA 61.267 57.895 7.64 0.00 39.98 2.83
1231 1399 5.437289 CTGGTGAAACAGCAAATAAGTCA 57.563 39.130 5.24 0.00 41.37 3.41
1236 1404 6.459573 GGTGAAACAGCAAATAAGTCACAAGA 60.460 38.462 0.00 0.00 39.98 3.02
1264 1432 9.911138 TTATGTCGTACTTGTATCAAAACACTA 57.089 29.630 0.00 0.00 0.00 2.74
1383 1554 5.413499 ACAAAATTCTAAGTCCATGCATGC 58.587 37.500 21.69 11.82 0.00 4.06
1583 1756 0.379669 CGATGAACAGAATGCCCAGC 59.620 55.000 0.00 0.00 42.53 4.85
1761 1934 1.512926 CTAAGTGCCCGTGATATGCC 58.487 55.000 0.00 0.00 0.00 4.40
1890 2063 8.502738 AGACAAAATAGGAGATAGGCCAAAATA 58.497 33.333 5.01 0.00 0.00 1.40
1997 2170 2.037251 TCTGGCAAGTTAGGTCACTGTC 59.963 50.000 0.00 0.00 0.00 3.51
2027 2200 3.077359 GCCACAGCATAGTCAAGTTCTT 58.923 45.455 0.00 0.00 39.53 2.52
2064 2245 6.685527 TTGGACAAATAAGCGCAATATGTA 57.314 33.333 11.47 0.00 0.00 2.29
2065 2246 6.055231 TGGACAAATAAGCGCAATATGTAC 57.945 37.500 11.47 9.37 0.00 2.90
2107 2294 8.015087 CCATATGCCATATGTACTTAAAACGTG 58.985 37.037 20.35 0.48 40.76 4.49
2122 2309 7.977293 ACTTAAAACGTGTAAGAGGCAAATTTT 59.023 29.630 20.46 2.64 33.57 1.82
2123 2310 6.582437 AAAACGTGTAAGAGGCAAATTTTG 57.418 33.333 4.72 4.72 0.00 2.44
2242 2429 3.582647 TGAAGGCATACTGAAACAGAGGA 59.417 43.478 5.76 0.00 35.18 3.71
2250 2437 6.767902 GCATACTGAAACAGAGGATGGATTAA 59.232 38.462 5.76 0.00 35.18 1.40
2251 2438 7.446625 GCATACTGAAACAGAGGATGGATTAAT 59.553 37.037 5.76 0.00 35.18 1.40
2256 2443 9.347240 CTGAAACAGAGGATGGATTAATATTGT 57.653 33.333 0.00 0.00 32.44 2.71
2260 2447 7.062322 ACAGAGGATGGATTAATATTGTTGCA 58.938 34.615 0.00 0.00 0.00 4.08
2277 2464 4.849310 AGCGCGGGTGTGTGTGTT 62.849 61.111 8.83 0.00 0.00 3.32
2278 2465 4.605967 GCGCGGGTGTGTGTGTTG 62.606 66.667 8.83 0.00 0.00 3.33
2280 2467 2.713154 GCGGGTGTGTGTGTTGTC 59.287 61.111 0.00 0.00 0.00 3.18
2281 2468 2.109739 GCGGGTGTGTGTGTTGTCA 61.110 57.895 0.00 0.00 0.00 3.58
2282 2469 1.444119 GCGGGTGTGTGTGTTGTCAT 61.444 55.000 0.00 0.00 0.00 3.06
2290 2479 0.602638 GTGTGTTGTCATGCGGGAGA 60.603 55.000 0.00 0.00 0.00 3.71
2319 2508 2.263077 GTGCACCAAGTAGAGACATCG 58.737 52.381 5.22 0.00 0.00 3.84
2356 2545 1.672881 GTTGACATGCTATGTGCCTCC 59.327 52.381 6.52 0.00 45.03 4.30
2400 2589 4.222124 AGGGAAGCATCTAAAATGACGT 57.778 40.909 0.00 0.00 0.00 4.34
2401 2590 3.941483 AGGGAAGCATCTAAAATGACGTG 59.059 43.478 0.00 0.00 0.00 4.49
2404 2593 5.106317 GGGAAGCATCTAAAATGACGTGAAA 60.106 40.000 0.00 0.00 0.00 2.69
2410 2599 9.906660 AGCATCTAAAATGACGTGAAAATTTAA 57.093 25.926 0.00 0.00 0.00 1.52
2417 2606 6.709018 ATGACGTGAAAATTTAATAGGGGG 57.291 37.500 0.00 0.00 0.00 5.40
2422 2611 7.580007 ACGTGAAAATTTAATAGGGGGATACT 58.420 34.615 0.00 0.00 0.00 2.12
2423 2612 7.501225 ACGTGAAAATTTAATAGGGGGATACTG 59.499 37.037 0.00 0.00 0.00 2.74
2575 2764 3.728718 GTCGTGCACAAAAATTCATCGTT 59.271 39.130 18.64 0.00 0.00 3.85
2583 2772 5.868801 CACAAAAATTCATCGTTTAGGGCAT 59.131 36.000 0.00 0.00 0.00 4.40
2607 2803 3.577389 GCCAAAGGCCAGTAGATGT 57.423 52.632 5.01 0.00 44.06 3.06
2611 2807 2.161855 CAAAGGCCAGTAGATGTTGCA 58.838 47.619 5.01 0.00 0.00 4.08
2633 2829 0.110295 AAAAATTGGCCAGCCCCAAC 59.890 50.000 5.11 0.00 46.85 3.77
2647 2843 3.509967 AGCCCCAACTGCTACAAATTTAC 59.490 43.478 0.00 0.00 37.28 2.01
2705 2901 3.666253 GGAAACCCAACCGCCACG 61.666 66.667 0.00 0.00 0.00 4.94
2708 2904 3.479127 AAACCCAACCGCCACGCTA 62.479 57.895 0.00 0.00 0.00 4.26
2720 2916 1.666023 GCCACGCTAAAACTTCCTTGC 60.666 52.381 0.00 0.00 0.00 4.01
2725 2921 1.889170 GCTAAAACTTCCTTGCAGCCT 59.111 47.619 0.00 0.00 0.00 4.58
2729 2925 0.475906 AACTTCCTTGCAGCCTGACT 59.524 50.000 0.00 0.00 0.00 3.41
2742 2938 4.712476 CAGCCTGACTATTGCCTAATTCT 58.288 43.478 0.00 0.00 0.00 2.40
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 1.231221 AAATTCCTACGCACACGCAA 58.769 45.000 0.00 0.00 45.53 4.85
1 2 1.231221 AAAATTCCTACGCACACGCA 58.769 45.000 0.00 0.00 45.53 5.24
2 3 2.325509 AAAAATTCCTACGCACACGC 57.674 45.000 0.00 0.00 45.53 5.34
19 20 8.705594 TGTTGGGGAATGTAGTAATTTCAAAAA 58.294 29.630 0.00 0.00 0.00 1.94
24 25 7.222000 TGTTGTTGGGGAATGTAGTAATTTC 57.778 36.000 0.00 0.00 0.00 2.17
25 26 6.295067 GCTGTTGTTGGGGAATGTAGTAATTT 60.295 38.462 0.00 0.00 0.00 1.82
26 27 5.185056 GCTGTTGTTGGGGAATGTAGTAATT 59.815 40.000 0.00 0.00 0.00 1.40
27 28 4.705023 GCTGTTGTTGGGGAATGTAGTAAT 59.295 41.667 0.00 0.00 0.00 1.89
28 29 4.076394 GCTGTTGTTGGGGAATGTAGTAA 58.924 43.478 0.00 0.00 0.00 2.24
29 30 3.073209 TGCTGTTGTTGGGGAATGTAGTA 59.927 43.478 0.00 0.00 0.00 1.82
30 31 2.158534 TGCTGTTGTTGGGGAATGTAGT 60.159 45.455 0.00 0.00 0.00 2.73
31 32 2.513753 TGCTGTTGTTGGGGAATGTAG 58.486 47.619 0.00 0.00 0.00 2.74
33 34 2.014010 ATGCTGTTGTTGGGGAATGT 57.986 45.000 0.00 0.00 0.00 2.71
34 35 2.428171 CCTATGCTGTTGTTGGGGAATG 59.572 50.000 0.00 0.00 0.00 2.67
35 36 2.042979 ACCTATGCTGTTGTTGGGGAAT 59.957 45.455 0.00 0.00 0.00 3.01
36 37 1.427368 ACCTATGCTGTTGTTGGGGAA 59.573 47.619 0.00 0.00 0.00 3.97
37 38 1.072266 ACCTATGCTGTTGTTGGGGA 58.928 50.000 0.00 0.00 0.00 4.81
38 39 1.545582 CAACCTATGCTGTTGTTGGGG 59.454 52.381 0.00 0.00 38.58 4.96
39 40 2.489329 CTCAACCTATGCTGTTGTTGGG 59.511 50.000 0.00 0.00 42.82 4.12
40 41 3.411446 TCTCAACCTATGCTGTTGTTGG 58.589 45.455 0.00 0.00 42.82 3.77
41 42 5.048504 ACAATCTCAACCTATGCTGTTGTTG 60.049 40.000 0.00 0.00 42.82 3.33
43 44 4.655963 ACAATCTCAACCTATGCTGTTGT 58.344 39.130 0.00 0.00 42.82 3.32
44 45 6.741992 TTACAATCTCAACCTATGCTGTTG 57.258 37.500 0.00 0.00 43.46 3.33
45 46 7.759489 TTTTACAATCTCAACCTATGCTGTT 57.241 32.000 0.00 0.00 0.00 3.16
46 47 7.759489 TTTTTACAATCTCAACCTATGCTGT 57.241 32.000 0.00 0.00 0.00 4.40
69 70 8.082242 CCTCACCGAAATTTCTATTGACTTTTT 58.918 33.333 15.92 0.00 0.00 1.94
70 71 7.447238 TCCTCACCGAAATTTCTATTGACTTTT 59.553 33.333 15.92 0.00 0.00 2.27
71 72 6.940298 TCCTCACCGAAATTTCTATTGACTTT 59.060 34.615 15.92 0.00 0.00 2.66
73 74 6.049955 TCCTCACCGAAATTTCTATTGACT 57.950 37.500 15.92 0.00 0.00 3.41
74 75 5.294552 CCTCCTCACCGAAATTTCTATTGAC 59.705 44.000 15.92 0.00 0.00 3.18
76 77 4.576463 CCCTCCTCACCGAAATTTCTATTG 59.424 45.833 15.92 9.73 0.00 1.90
77 78 4.227527 ACCCTCCTCACCGAAATTTCTATT 59.772 41.667 15.92 0.00 0.00 1.73
78 79 3.780850 ACCCTCCTCACCGAAATTTCTAT 59.219 43.478 15.92 1.18 0.00 1.98
79 80 3.055385 CACCCTCCTCACCGAAATTTCTA 60.055 47.826 15.92 0.00 0.00 2.10
81 82 2.084546 CACCCTCCTCACCGAAATTTC 58.915 52.381 8.20 8.20 0.00 2.17
83 84 1.064825 ACACCCTCCTCACCGAAATT 58.935 50.000 0.00 0.00 0.00 1.82
84 85 0.324943 CACACCCTCCTCACCGAAAT 59.675 55.000 0.00 0.00 0.00 2.17
85 86 0.761323 TCACACCCTCCTCACCGAAA 60.761 55.000 0.00 0.00 0.00 3.46
88 89 2.650116 CCTCACACCCTCCTCACCG 61.650 68.421 0.00 0.00 0.00 4.94
89 90 1.536662 ACCTCACACCCTCCTCACC 60.537 63.158 0.00 0.00 0.00 4.02
90 91 1.674057 CACCTCACACCCTCCTCAC 59.326 63.158 0.00 0.00 0.00 3.51
92 93 1.229209 TCCACCTCACACCCTCCTC 60.229 63.158 0.00 0.00 0.00 3.71
99 213 2.100989 CCTAGTAGGTCCACCTCACAC 58.899 57.143 8.17 0.00 44.77 3.82
100 214 1.618888 GCCTAGTAGGTCCACCTCACA 60.619 57.143 17.69 0.00 44.77 3.58
130 244 0.888736 CCTCATTGCAACACACGGGA 60.889 55.000 0.00 0.00 0.00 5.14
237 351 5.480772 AGTCTTCTCCTATCCAAACTCGAAA 59.519 40.000 0.00 0.00 0.00 3.46
239 353 4.601084 AGTCTTCTCCTATCCAAACTCGA 58.399 43.478 0.00 0.00 0.00 4.04
269 383 6.670695 ACCAAAACCTCAGCTAAATCAAAT 57.329 33.333 0.00 0.00 0.00 2.32
280 394 7.391554 TCAGATCAAATCTTACCAAAACCTCAG 59.608 37.037 0.00 0.00 37.58 3.35
313 427 1.771255 CCTTCCCTTCCTCTACCCATG 59.229 57.143 0.00 0.00 0.00 3.66
451 565 4.024472 GCCGCACAAAATAAAAACCAATGT 60.024 37.500 0.00 0.00 0.00 2.71
452 566 4.024556 TGCCGCACAAAATAAAAACCAATG 60.025 37.500 0.00 0.00 0.00 2.82
453 567 4.130118 TGCCGCACAAAATAAAAACCAAT 58.870 34.783 0.00 0.00 0.00 3.16
454 568 3.531538 TGCCGCACAAAATAAAAACCAA 58.468 36.364 0.00 0.00 0.00 3.67
456 570 4.462307 CAATGCCGCACAAAATAAAAACC 58.538 39.130 0.00 0.00 0.00 3.27
462 578 2.297315 TCAACCAATGCCGCACAAAATA 59.703 40.909 0.00 0.00 0.00 1.40
540 657 4.699994 AGATTCTCTTCACCCCCTTTCTA 58.300 43.478 0.00 0.00 0.00 2.10
543 660 3.523972 GGTAGATTCTCTTCACCCCCTTT 59.476 47.826 0.00 0.00 0.00 3.11
548 665 4.383226 GGAGTTGGTAGATTCTCTTCACCC 60.383 50.000 1.74 0.00 0.00 4.61
549 666 4.383226 GGGAGTTGGTAGATTCTCTTCACC 60.383 50.000 0.00 0.00 0.00 4.02
734 863 7.600752 GTCTGGTATGGAGTAGAAGATAATTGC 59.399 40.741 0.00 0.00 0.00 3.56
735 864 8.865090 AGTCTGGTATGGAGTAGAAGATAATTG 58.135 37.037 0.00 0.00 0.00 2.32
920 1049 9.988815 GCTGACCTTGGTATATATAATATCCAG 57.011 37.037 0.00 0.00 0.00 3.86
977 1106 4.142622 TGCTTCTTAGTTGCACATGTATGC 60.143 41.667 0.00 0.00 46.32 3.14
983 1112 2.165030 GCCATGCTTCTTAGTTGCACAT 59.835 45.455 4.46 0.00 39.63 3.21
1219 1387 8.177663 CGACATAATTCTTGTGACTTATTTGCT 58.822 33.333 0.00 0.00 29.30 3.91
1231 1399 9.647797 TTGATACAAGTACGACATAATTCTTGT 57.352 29.630 11.88 11.88 44.51 3.16
1583 1756 1.538276 GCAACGGATCTTGCATTTCG 58.462 50.000 13.27 0.00 45.07 3.46
1761 1934 2.633657 GCCACACACGACTTGCAG 59.366 61.111 0.00 0.00 0.00 4.41
1997 2170 2.169352 ACTATGCTGTGGCTAGAACCAG 59.831 50.000 0.00 0.00 41.46 4.00
2039 2220 6.572519 ACATATTGCGCTTATTTGTCCAAAT 58.427 32.000 9.73 9.92 42.95 2.32
2147 2334 5.415221 TGTTTGGTTGGAACTTTGCTTTAG 58.585 37.500 0.00 0.00 0.00 1.85
2196 2383 4.196971 AGATGGTAAAAATGTAGTCCGCC 58.803 43.478 0.00 0.00 0.00 6.13
2197 2384 6.704493 TCATAGATGGTAAAAATGTAGTCCGC 59.296 38.462 0.00 0.00 0.00 5.54
2242 2429 4.549458 GCGCTGCAACAATATTAATCCAT 58.451 39.130 0.00 0.00 0.00 3.41
2250 2437 1.748879 ACCCGCGCTGCAACAATAT 60.749 52.632 5.56 0.00 0.00 1.28
2251 2438 2.359354 ACCCGCGCTGCAACAATA 60.359 55.556 5.56 0.00 0.00 1.90
2260 2447 4.849310 AACACACACACCCGCGCT 62.849 61.111 5.56 0.00 0.00 5.92
2277 2464 3.083349 CCCCTCTCCCGCATGACA 61.083 66.667 0.00 0.00 0.00 3.58
2278 2465 2.764128 TCCCCTCTCCCGCATGAC 60.764 66.667 0.00 0.00 0.00 3.06
2280 2467 3.554342 CCTCCCCTCTCCCGCATG 61.554 72.222 0.00 0.00 0.00 4.06
2281 2468 4.888325 CCCTCCCCTCTCCCGCAT 62.888 72.222 0.00 0.00 0.00 4.73
2290 2479 4.938756 TTGGTGCACCCCTCCCCT 62.939 66.667 32.62 0.00 34.29 4.79
2319 2508 3.067106 TCAACTTGTTGCTCGGATCTTC 58.933 45.455 8.48 0.00 0.00 2.87
2356 2545 2.422597 TGTGGGTGTGCTTTATCGAAG 58.577 47.619 0.00 0.00 38.45 3.79
2391 2580 8.038351 CCCCCTATTAAATTTTCACGTCATTTT 58.962 33.333 0.00 0.00 0.00 1.82
2400 2589 8.561769 TGACAGTATCCCCCTATTAAATTTTCA 58.438 33.333 0.00 0.00 0.00 2.69
2401 2590 8.990163 TGACAGTATCCCCCTATTAAATTTTC 57.010 34.615 0.00 0.00 0.00 2.29
2404 2593 9.951866 AAAATGACAGTATCCCCCTATTAAATT 57.048 29.630 0.00 0.00 0.00 1.82
2410 2599 7.421382 CCAACTAAAATGACAGTATCCCCCTAT 60.421 40.741 0.00 0.00 0.00 2.57
2451 2640 4.447290 GCACCAAGTTTTGTAAACCCAAT 58.553 39.130 0.00 0.00 0.00 3.16
2461 2650 3.634568 TTATCACCGCACCAAGTTTTG 57.365 42.857 0.00 0.00 0.00 2.44
2505 2694 7.093112 GGAGATGTCTAAGGCAAGATATACCAT 60.093 40.741 12.46 4.66 30.94 3.55
2509 2698 7.855784 TTGGAGATGTCTAAGGCAAGATATA 57.144 36.000 0.29 0.00 28.56 0.86
2512 2701 5.643421 ATTGGAGATGTCTAAGGCAAGAT 57.357 39.130 0.00 0.00 0.00 2.40
2549 2738 3.838120 TGAATTTTTGTGCACGACAACA 58.162 36.364 13.13 2.41 44.53 3.33
2550 2739 4.373914 CGATGAATTTTTGTGCACGACAAC 60.374 41.667 13.13 2.35 44.53 3.32
2595 2784 3.658757 TTTTTGCAACATCTACTGGCC 57.341 42.857 0.00 0.00 0.00 5.36
2633 2829 4.697352 AGAGGTGCTGTAAATTTGTAGCAG 59.303 41.667 23.28 15.83 45.74 4.24
2688 2884 3.666253 CGTGGCGGTTGGGTTTCC 61.666 66.667 0.00 0.00 0.00 3.13
2705 2901 1.889170 AGGCTGCAAGGAAGTTTTAGC 59.111 47.619 0.50 0.00 0.00 3.09
2708 2904 1.683385 GTCAGGCTGCAAGGAAGTTTT 59.317 47.619 10.34 0.00 0.00 2.43
2720 2916 4.514441 CAGAATTAGGCAATAGTCAGGCTG 59.486 45.833 8.58 8.58 41.13 4.85
2725 2921 5.815581 ACAACCAGAATTAGGCAATAGTCA 58.184 37.500 0.00 0.00 0.00 3.41
2729 2925 6.945435 TGAGAAACAACCAGAATTAGGCAATA 59.055 34.615 0.00 0.00 0.00 1.90


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

AutoCloner maintained by Alex Coulton.