Multiple sequence alignment - TraesCS1A01G377000

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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 TraesCS1A01G377000 chr1A 100.000 2216 0 0 1 2216 550668384 550670599 0.000000e+00 4093.0
1 TraesCS1A01G377000 chr1A 95.827 1222 41 9 1001 2214 550824680 550825899 0.000000e+00 1965.0
2 TraesCS1A01G377000 chr1A 93.339 1261 35 8 1003 2214 550655563 550656823 0.000000e+00 1818.0
3 TraesCS1A01G377000 chr1A 91.615 811 42 7 135 942 550682181 550682968 0.000000e+00 1098.0
4 TraesCS1A01G377000 chr1A 91.369 811 44 7 135 942 550691810 550692597 0.000000e+00 1086.0
5 TraesCS1A01G377000 chr1A 90.424 825 42 16 1233 2023 550695933 550696754 0.000000e+00 1051.0
6 TraesCS1A01G377000 chr1A 89.626 829 56 14 135 942 550823742 550824561 0.000000e+00 1027.0
7 TraesCS1A01G377000 chr1A 85.680 412 43 9 1811 2211 550708280 550708686 9.460000e-114 420.0
8 TraesCS1A01G377000 chr1A 89.458 332 16 13 937 1249 550695589 550695920 3.430000e-108 401.0
9 TraesCS1A01G377000 chr1A 78.667 675 78 40 1355 1992 550705168 550705813 2.670000e-104 388.0
10 TraesCS1A01G377000 chr1A 80.762 525 76 16 1001 1511 550661330 550661843 9.600000e-104 387.0
11 TraesCS1A01G377000 chr1A 93.478 138 9 0 1 138 398835904 398836041 2.880000e-49 206.0
12 TraesCS1A01G377000 chr1A 93.478 138 9 0 1 138 398884313 398884450 2.880000e-49 206.0
13 TraesCS1A01G377000 chr1A 91.489 141 11 1 1 141 585232484 585232623 2.250000e-45 193.0
14 TraesCS1A01G377000 chr1A 97.015 67 2 0 937 1003 550655470 550655536 1.800000e-21 113.0
15 TraesCS1A01G377000 chr1A 94.030 67 2 1 937 1003 550824591 550824655 1.400000e-17 100.0
16 TraesCS1A01G377000 chr1A 92.537 67 5 0 937 1003 550692627 550692693 1.810000e-16 97.1
17 TraesCS1A01G377000 chr1D 86.943 965 54 29 1002 1905 458273161 458274114 0.000000e+00 1018.0
18 TraesCS1A01G377000 chr1D 88.378 826 51 17 135 942 458166145 458166943 0.000000e+00 952.0
19 TraesCS1A01G377000 chr1D 94.203 621 19 2 1611 2214 458239155 458239775 0.000000e+00 931.0
20 TraesCS1A01G377000 chr1D 91.289 574 19 10 1002 1566 458167065 458167616 0.000000e+00 754.0
21 TraesCS1A01G377000 chr1D 83.431 851 89 28 132 942 458177688 458178526 0.000000e+00 743.0
22 TraesCS1A01G377000 chr1D 81.987 755 88 23 1492 2214 458201098 458201836 4.070000e-167 597.0
23 TraesCS1A01G377000 chr1D 91.142 429 29 3 515 942 458238130 458238550 6.860000e-160 573.0
24 TraesCS1A01G377000 chr1D 91.176 408 23 5 1002 1400 458238677 458239080 1.940000e-150 542.0
25 TraesCS1A01G377000 chr1D 83.702 497 58 14 1001 1485 458257327 458257812 4.340000e-122 448.0
26 TraesCS1A01G377000 chr1D 97.211 251 6 1 1965 2214 458276249 458276499 7.310000e-115 424.0
27 TraesCS1A01G377000 chr1D 78.581 747 74 42 608 1290 458272733 458273457 4.400000e-112 414.0
28 TraesCS1A01G377000 chr1D 82.200 500 54 19 1002 1485 458230223 458230703 4.430000e-107 398.0
29 TraesCS1A01G377000 chr1D 95.522 67 3 0 937 1003 458166973 458167039 8.370000e-20 108.0
30 TraesCS1A01G377000 chr1B 91.252 743 42 8 1300 2021 628811960 628812700 0.000000e+00 990.0
31 TraesCS1A01G377000 chr1B 87.393 817 61 19 135 942 628987256 628988039 0.000000e+00 900.0
32 TraesCS1A01G377000 chr1B 86.041 831 60 20 135 942 628911250 628912047 0.000000e+00 841.0
33 TraesCS1A01G377000 chr1B 90.476 630 39 6 1300 1909 628976031 628976659 0.000000e+00 811.0
34 TraesCS1A01G377000 chr1B 90.159 630 41 6 1300 1909 628899858 628900486 0.000000e+00 800.0
35 TraesCS1A01G377000 chr1B 85.130 807 68 21 154 942 628939787 628940559 0.000000e+00 778.0
36 TraesCS1A01G377000 chr1B 89.432 634 39 10 1300 1909 628856962 628857591 0.000000e+00 774.0
37 TraesCS1A01G377000 chr1B 84.634 807 67 22 154 942 628874187 628874954 0.000000e+00 750.0
38 TraesCS1A01G377000 chr1B 91.028 457 36 4 1300 1753 629092692 629093146 1.450000e-171 612.0
39 TraesCS1A01G377000 chr1B 89.485 466 35 7 213 673 628985084 628985540 5.310000e-161 577.0
40 TraesCS1A01G377000 chr1B 79.376 834 112 35 135 942 628810677 628811476 1.160000e-147 532.0
41 TraesCS1A01G377000 chr1B 83.144 528 52 18 1714 2211 629097556 629098076 4.340000e-122 448.0
42 TraesCS1A01G377000 chr1B 80.741 540 82 16 1002 1530 628784008 628784536 3.430000e-108 401.0
43 TraesCS1A01G377000 chr1B 86.919 344 31 8 1879 2214 628918853 628919190 7.470000e-100 374.0
44 TraesCS1A01G377000 chr1B 86.919 344 31 8 1879 2214 628995188 628995525 7.470000e-100 374.0
45 TraesCS1A01G377000 chr1B 80.965 373 45 19 578 942 628898978 628899332 2.800000e-69 272.0
46 TraesCS1A01G377000 chr1B 80.593 371 46 20 580 942 628975198 628975550 1.690000e-66 263.0
47 TraesCS1A01G377000 chr1B 80.161 373 48 19 578 942 628856125 628856479 2.820000e-64 255.0
48 TraesCS1A01G377000 chr1B 87.586 145 12 4 1796 1936 628673594 628673736 1.760000e-36 163.0
49 TraesCS1A01G377000 chr4A 95.620 137 6 0 1 137 541018868 541019004 1.030000e-53 220.0
50 TraesCS1A01G377000 chr4D 92.754 138 9 1 1 138 399419322 399419186 4.830000e-47 198.0
51 TraesCS1A01G377000 chrUn 91.912 136 11 0 1 136 406827454 406827589 8.080000e-45 191.0
52 TraesCS1A01G377000 chr7A 91.912 136 11 0 1 136 403183741 403183606 8.080000e-45 191.0
53 TraesCS1A01G377000 chr7A 91.912 136 11 0 1 136 403185175 403185040 8.080000e-45 191.0
54 TraesCS1A01G377000 chr7A 91.912 136 11 0 1 136 403186609 403186474 8.080000e-45 191.0


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 TraesCS1A01G377000 chr1A 550668384 550670599 2215 False 4093.000000 4093 100.000000 1 2216 1 chr1A.!!$F4 2215
1 TraesCS1A01G377000 chr1A 550682181 550682968 787 False 1098.000000 1098 91.615000 135 942 1 chr1A.!!$F5 807
2 TraesCS1A01G377000 chr1A 550823742 550825899 2157 False 1030.666667 1965 93.161000 135 2214 3 chr1A.!!$F10 2079
3 TraesCS1A01G377000 chr1A 550655470 550656823 1353 False 965.500000 1818 95.177000 937 2214 2 chr1A.!!$F7 1277
4 TraesCS1A01G377000 chr1A 550691810 550696754 4944 False 658.775000 1086 90.947000 135 2023 4 chr1A.!!$F8 1888
5 TraesCS1A01G377000 chr1A 550705168 550708686 3518 False 404.000000 420 82.173500 1355 2211 2 chr1A.!!$F9 856
6 TraesCS1A01G377000 chr1A 550661330 550661843 513 False 387.000000 387 80.762000 1001 1511 1 chr1A.!!$F3 510
7 TraesCS1A01G377000 chr1D 458177688 458178526 838 False 743.000000 743 83.431000 132 942 1 chr1D.!!$F1 810
8 TraesCS1A01G377000 chr1D 458238130 458239775 1645 False 682.000000 931 92.173667 515 2214 3 chr1D.!!$F6 1699
9 TraesCS1A01G377000 chr1D 458272733 458276499 3766 False 618.666667 1018 87.578333 608 2214 3 chr1D.!!$F7 1606
10 TraesCS1A01G377000 chr1D 458166145 458167616 1471 False 604.666667 952 91.729667 135 1566 3 chr1D.!!$F5 1431
11 TraesCS1A01G377000 chr1D 458201098 458201836 738 False 597.000000 597 81.987000 1492 2214 1 chr1D.!!$F2 722
12 TraesCS1A01G377000 chr1B 628911250 628912047 797 False 841.000000 841 86.041000 135 942 1 chr1B.!!$F4 807
13 TraesCS1A01G377000 chr1B 628939787 628940559 772 False 778.000000 778 85.130000 154 942 1 chr1B.!!$F6 788
14 TraesCS1A01G377000 chr1B 628810677 628812700 2023 False 761.000000 990 85.314000 135 2021 2 chr1B.!!$F10 1886
15 TraesCS1A01G377000 chr1B 628874187 628874954 767 False 750.000000 750 84.634000 154 942 1 chr1B.!!$F3 788
16 TraesCS1A01G377000 chr1B 628985084 628988039 2955 False 738.500000 900 88.439000 135 942 2 chr1B.!!$F14 807
17 TraesCS1A01G377000 chr1B 628975198 628976659 1461 False 537.000000 811 85.534500 580 1909 2 chr1B.!!$F13 1329
18 TraesCS1A01G377000 chr1B 628898978 628900486 1508 False 536.000000 800 85.562000 578 1909 2 chr1B.!!$F12 1331
19 TraesCS1A01G377000 chr1B 628856125 628857591 1466 False 514.500000 774 84.796500 578 1909 2 chr1B.!!$F11 1331
20 TraesCS1A01G377000 chr1B 629097556 629098076 520 False 448.000000 448 83.144000 1714 2211 1 chr1B.!!$F9 497
21 TraesCS1A01G377000 chr1B 628784008 628784536 528 False 401.000000 401 80.741000 1002 1530 1 chr1B.!!$F2 528

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
43 44 0.106149 AGCGAGTTTGTCCGGTCTTT 59.894 50.0 0.0 0.0 0.0 2.52 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1801 9814 1.001406 GTAAGGATGGATCTCGGCCTG 59.999 57.143 0.0 0.0 0.0 4.85 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 2.677228 AAATGGGGTAGCAGCGCT 59.323 55.556 2.64 2.64 43.41 5.92
35 36 2.127609 GCGTGCAGCGAGTTTGTC 60.128 61.111 11.94 0.00 44.77 3.18
36 37 2.551270 CGTGCAGCGAGTTTGTCC 59.449 61.111 3.04 0.00 44.77 4.02
37 38 2.551270 GTGCAGCGAGTTTGTCCG 59.449 61.111 0.00 0.00 0.00 4.79
39 40 2.665185 GCAGCGAGTTTGTCCGGT 60.665 61.111 0.00 0.00 36.94 5.28
40 41 2.668280 GCAGCGAGTTTGTCCGGTC 61.668 63.158 0.00 0.00 34.04 4.79
41 42 1.006102 CAGCGAGTTTGTCCGGTCT 60.006 57.895 0.00 0.00 34.04 3.85
42 43 0.600255 CAGCGAGTTTGTCCGGTCTT 60.600 55.000 0.00 0.00 34.04 3.01
43 44 0.106149 AGCGAGTTTGTCCGGTCTTT 59.894 50.000 0.00 0.00 0.00 2.52
44 45 0.234884 GCGAGTTTGTCCGGTCTTTG 59.765 55.000 0.00 0.00 0.00 2.77
45 46 1.578583 CGAGTTTGTCCGGTCTTTGT 58.421 50.000 0.00 0.00 0.00 2.83
46 47 1.525619 CGAGTTTGTCCGGTCTTTGTC 59.474 52.381 0.00 0.00 0.00 3.18
47 48 1.871676 GAGTTTGTCCGGTCTTTGTCC 59.128 52.381 0.00 0.00 0.00 4.02
48 49 0.584876 GTTTGTCCGGTCTTTGTCCG 59.415 55.000 0.00 0.00 46.49 4.79
53 54 2.663852 CGGTCTTTGTCCGGCGTT 60.664 61.111 6.01 0.00 43.68 4.84
54 55 2.248835 CGGTCTTTGTCCGGCGTTT 61.249 57.895 6.01 0.00 43.68 3.60
55 56 1.778027 CGGTCTTTGTCCGGCGTTTT 61.778 55.000 6.01 0.00 43.68 2.43
56 57 0.382873 GGTCTTTGTCCGGCGTTTTT 59.617 50.000 6.01 0.00 0.00 1.94
79 80 5.984695 TCTCTCTATTTCCATCCCATACG 57.015 43.478 0.00 0.00 0.00 3.06
80 81 4.772624 TCTCTCTATTTCCATCCCATACGG 59.227 45.833 0.00 0.00 0.00 4.02
82 83 4.527038 TCTCTATTTCCATCCCATACGGAC 59.473 45.833 0.00 0.00 46.09 4.79
83 84 4.228010 TCTATTTCCATCCCATACGGACA 58.772 43.478 0.00 0.00 46.09 4.02
84 85 3.943671 ATTTCCATCCCATACGGACAA 57.056 42.857 0.00 0.00 46.09 3.18
85 86 3.722908 TTTCCATCCCATACGGACAAA 57.277 42.857 0.00 0.00 46.09 2.83
86 87 3.722908 TTCCATCCCATACGGACAAAA 57.277 42.857 0.00 0.00 46.09 2.44
87 88 3.943671 TCCATCCCATACGGACAAAAT 57.056 42.857 0.00 0.00 46.09 1.82
89 90 2.884639 CCATCCCATACGGACAAAATCC 59.115 50.000 0.00 0.00 46.09 3.01
100 101 3.584834 GGACAAAATCCGGACAAAATGG 58.415 45.455 6.12 0.00 37.88 3.16
101 102 3.584834 GACAAAATCCGGACAAAATGGG 58.415 45.455 6.12 0.00 0.00 4.00
102 103 2.969262 ACAAAATCCGGACAAAATGGGT 59.031 40.909 6.12 0.00 0.00 4.51
103 104 4.153411 ACAAAATCCGGACAAAATGGGTA 58.847 39.130 6.12 0.00 0.00 3.69
104 105 4.775253 ACAAAATCCGGACAAAATGGGTAT 59.225 37.500 6.12 0.00 0.00 2.73
105 106 5.952947 ACAAAATCCGGACAAAATGGGTATA 59.047 36.000 6.12 0.00 0.00 1.47
106 107 6.437793 ACAAAATCCGGACAAAATGGGTATAA 59.562 34.615 6.12 0.00 0.00 0.98
108 109 7.669089 AAATCCGGACAAAATGGGTATAAAT 57.331 32.000 6.12 0.00 0.00 1.40
109 110 7.669089 AATCCGGACAAAATGGGTATAAATT 57.331 32.000 6.12 0.00 0.00 1.82
110 111 7.669089 ATCCGGACAAAATGGGTATAAATTT 57.331 32.000 6.12 0.00 0.00 1.82
111 112 8.770010 ATCCGGACAAAATGGGTATAAATTTA 57.230 30.769 6.12 0.00 0.00 1.40
112 113 8.228035 TCCGGACAAAATGGGTATAAATTTAG 57.772 34.615 0.00 0.00 0.00 1.85
113 114 7.285858 TCCGGACAAAATGGGTATAAATTTAGG 59.714 37.037 0.00 0.00 0.00 2.69
117 118 8.002984 ACAAAATGGGTATAAATTTAGGGTCG 57.997 34.615 3.94 0.00 0.00 4.79
118 119 7.616542 ACAAAATGGGTATAAATTTAGGGTCGT 59.383 33.333 3.94 0.00 0.00 4.34
119 120 7.576861 AAATGGGTATAAATTTAGGGTCGTG 57.423 36.000 3.94 0.00 0.00 4.35
120 121 4.453751 TGGGTATAAATTTAGGGTCGTGC 58.546 43.478 3.94 0.00 0.00 5.34
121 122 3.495753 GGGTATAAATTTAGGGTCGTGCG 59.504 47.826 3.94 0.00 0.00 5.34
123 124 2.766345 TAAATTTAGGGTCGTGCGGT 57.234 45.000 0.00 0.00 0.00 5.68
124 125 1.161843 AAATTTAGGGTCGTGCGGTG 58.838 50.000 0.00 0.00 0.00 4.94
125 126 0.675522 AATTTAGGGTCGTGCGGTGG 60.676 55.000 0.00 0.00 0.00 4.61
126 127 1.546589 ATTTAGGGTCGTGCGGTGGA 61.547 55.000 0.00 0.00 0.00 4.02
127 128 2.162338 TTTAGGGTCGTGCGGTGGAG 62.162 60.000 0.00 0.00 0.00 3.86
129 130 4.309950 GGGTCGTGCGGTGGAGTT 62.310 66.667 0.00 0.00 0.00 3.01
130 131 3.041940 GGTCGTGCGGTGGAGTTG 61.042 66.667 0.00 0.00 0.00 3.16
131 132 3.041940 GTCGTGCGGTGGAGTTGG 61.042 66.667 0.00 0.00 0.00 3.77
132 133 4.980805 TCGTGCGGTGGAGTTGGC 62.981 66.667 0.00 0.00 0.00 4.52
178 2219 7.497595 TGTCGATTGCTAGGTCTATACAAAAT 58.502 34.615 0.00 0.00 0.00 1.82
318 2405 6.300703 TCCTCCCTTTGTTTCTTTTTCGATA 58.699 36.000 0.00 0.00 0.00 2.92
350 2440 8.742125 ATGTCCCAAAGAACTATATCATCCTA 57.258 34.615 0.00 0.00 0.00 2.94
408 2502 6.990349 ACATGGTTCCACCGTATCTTTATTAG 59.010 38.462 0.00 0.00 42.58 1.73
444 2538 7.890655 AGTATTTTCCTAGTTGCCAATCTTTCT 59.109 33.333 0.00 0.00 0.00 2.52
506 2615 0.879400 CTGAGACCATGCGATCCAGC 60.879 60.000 0.00 0.00 37.71 4.85
528 2638 3.304057 CGCTTCTTCCTTGTGACCTTTTC 60.304 47.826 0.00 0.00 0.00 2.29
573 2683 2.922740 AAACACTGGTCGTGGTATGT 57.077 45.000 0.00 0.00 44.52 2.29
628 2747 4.617223 GCCTCAAGCGAAATTACTTTTGAC 59.383 41.667 0.00 0.00 0.00 3.18
640 2766 9.495754 GAAATTACTTTTGACTATGCATCTGTC 57.504 33.333 19.73 19.73 0.00 3.51
677 2803 3.382832 CCACCGACCCTCTCGCTT 61.383 66.667 0.00 0.00 41.46 4.68
802 5880 2.986479 GTCCGAAATGTGATTTTGCCAC 59.014 45.455 0.00 0.00 33.25 5.01
855 5933 1.153489 CAGCTAGCCATGAGTGCGT 60.153 57.895 12.13 0.00 0.00 5.24
963 6105 4.683320 GCAACCAAATCAAGAAAGAAGAGC 59.317 41.667 0.00 0.00 0.00 4.09
964 6106 5.508657 GCAACCAAATCAAGAAAGAAGAGCT 60.509 40.000 0.00 0.00 0.00 4.09
1019 6190 1.739466 GATGACGAGAAGCATTGGCAA 59.261 47.619 0.68 0.68 44.61 4.52
1240 6518 0.108804 CCCGCAGCGTCTTCTTCTTA 60.109 55.000 15.05 0.00 0.00 2.10
1243 6521 3.444916 CCGCAGCGTCTTCTTCTTATTA 58.555 45.455 15.05 0.00 0.00 0.98
1325 6666 8.767478 TCAGCTACCAGTGTATTAGTAAAAAC 57.233 34.615 0.00 0.00 0.00 2.43
1486 6845 2.481795 GCCACAATGGAATGGGATTTCG 60.482 50.000 0.00 0.00 40.96 3.46
1671 7053 3.744940 TCAGGAGGCAAGATTTGGAAT 57.255 42.857 0.00 0.00 0.00 3.01
1731 7114 7.566760 TCAGCAGTGAGATTAAAACTTTTCA 57.433 32.000 0.00 0.00 0.00 2.69
1801 9814 1.468914 GTCCTCGAAACTCCCATTTGC 59.531 52.381 0.00 0.00 0.00 3.68
2060 12177 2.557317 ACTCAACGTCCGAAACAACAT 58.443 42.857 0.00 0.00 0.00 2.71
2214 12337 8.481314 ACATACAGAACATAGAACTCATGTGAT 58.519 33.333 0.94 0.00 36.74 3.06
2215 12338 8.762426 CATACAGAACATAGAACTCATGTGATG 58.238 37.037 0.94 0.00 36.74 3.07
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
1 2 2.124570 CAGCGCTGCTACCCCATT 60.125 61.111 26.68 0.00 36.40 3.16
16 17 2.127496 CAAACTCGCTGCACGCAG 60.127 61.111 14.73 14.73 46.15 5.18
17 18 2.881266 GACAAACTCGCTGCACGCA 61.881 57.895 0.00 0.00 43.23 5.24
19 20 2.551270 GGACAAACTCGCTGCACG 59.449 61.111 0.00 2.79 45.62 5.34
20 21 2.551270 CGGACAAACTCGCTGCAC 59.449 61.111 0.00 0.00 0.00 4.57
21 22 2.664851 CCGGACAAACTCGCTGCA 60.665 61.111 0.00 0.00 0.00 4.41
22 23 2.665185 ACCGGACAAACTCGCTGC 60.665 61.111 9.46 0.00 0.00 5.25
23 24 0.600255 AAGACCGGACAAACTCGCTG 60.600 55.000 9.46 0.00 0.00 5.18
24 25 0.106149 AAAGACCGGACAAACTCGCT 59.894 50.000 9.46 0.00 0.00 4.93
25 26 0.234884 CAAAGACCGGACAAACTCGC 59.765 55.000 9.46 0.00 0.00 5.03
26 27 1.525619 GACAAAGACCGGACAAACTCG 59.474 52.381 9.46 0.00 0.00 4.18
29 30 0.584876 CGGACAAAGACCGGACAAAC 59.415 55.000 9.46 0.00 45.65 2.93
30 31 2.994990 CGGACAAAGACCGGACAAA 58.005 52.632 9.46 0.00 45.65 2.83
37 38 0.382873 AAAAACGCCGGACAAAGACC 59.617 50.000 5.05 0.00 0.00 3.85
53 54 7.715249 CGTATGGGATGGAAATAGAGAGAAAAA 59.285 37.037 0.00 0.00 0.00 1.94
54 55 7.217200 CGTATGGGATGGAAATAGAGAGAAAA 58.783 38.462 0.00 0.00 0.00 2.29
55 56 6.239600 CCGTATGGGATGGAAATAGAGAGAAA 60.240 42.308 0.00 0.00 38.47 2.52
56 57 5.246203 CCGTATGGGATGGAAATAGAGAGAA 59.754 44.000 0.00 0.00 38.47 2.87
57 58 4.772624 CCGTATGGGATGGAAATAGAGAGA 59.227 45.833 0.00 0.00 38.47 3.10
58 59 4.772624 TCCGTATGGGATGGAAATAGAGAG 59.227 45.833 0.00 0.00 40.55 3.20
79 80 3.584834 CCATTTTGTCCGGATTTTGTCC 58.415 45.455 7.81 0.00 44.10 4.02
80 81 3.006430 ACCCATTTTGTCCGGATTTTGTC 59.994 43.478 7.81 0.00 0.00 3.18
81 82 2.969262 ACCCATTTTGTCCGGATTTTGT 59.031 40.909 7.81 0.00 0.00 2.83
82 83 3.676291 ACCCATTTTGTCCGGATTTTG 57.324 42.857 7.81 1.49 0.00 2.44
83 84 7.483580 TTTATACCCATTTTGTCCGGATTTT 57.516 32.000 7.81 0.00 0.00 1.82
84 85 7.669089 ATTTATACCCATTTTGTCCGGATTT 57.331 32.000 7.81 0.00 0.00 2.17
85 86 7.669089 AATTTATACCCATTTTGTCCGGATT 57.331 32.000 7.81 0.00 0.00 3.01
86 87 7.669089 AAATTTATACCCATTTTGTCCGGAT 57.331 32.000 7.81 0.00 0.00 4.18
87 88 7.285858 CCTAAATTTATACCCATTTTGTCCGGA 59.714 37.037 0.00 0.00 0.00 5.14
89 90 7.068962 ACCCTAAATTTATACCCATTTTGTCCG 59.931 37.037 0.00 0.00 0.00 4.79
90 91 8.313944 ACCCTAAATTTATACCCATTTTGTCC 57.686 34.615 0.00 0.00 0.00 4.02
91 92 8.132995 CGACCCTAAATTTATACCCATTTTGTC 58.867 37.037 0.00 0.00 0.00 3.18
92 93 7.616542 ACGACCCTAAATTTATACCCATTTTGT 59.383 33.333 0.00 0.00 0.00 2.83
93 94 7.918562 CACGACCCTAAATTTATACCCATTTTG 59.081 37.037 0.00 0.00 0.00 2.44
94 95 7.417003 GCACGACCCTAAATTTATACCCATTTT 60.417 37.037 0.00 0.00 0.00 1.82
95 96 6.040054 GCACGACCCTAAATTTATACCCATTT 59.960 38.462 0.00 0.00 0.00 2.32
96 97 5.533528 GCACGACCCTAAATTTATACCCATT 59.466 40.000 0.00 0.00 0.00 3.16
97 98 5.067954 GCACGACCCTAAATTTATACCCAT 58.932 41.667 0.00 0.00 0.00 4.00
99 100 3.495753 CGCACGACCCTAAATTTATACCC 59.504 47.826 0.00 0.00 0.00 3.69
100 101 3.495753 CCGCACGACCCTAAATTTATACC 59.504 47.826 0.00 0.00 0.00 2.73
101 102 4.025480 CACCGCACGACCCTAAATTTATAC 60.025 45.833 0.00 0.00 0.00 1.47
102 103 4.121317 CACCGCACGACCCTAAATTTATA 58.879 43.478 0.00 0.00 0.00 0.98
103 104 2.940410 CACCGCACGACCCTAAATTTAT 59.060 45.455 0.00 0.00 0.00 1.40
104 105 2.348660 CACCGCACGACCCTAAATTTA 58.651 47.619 0.00 0.00 0.00 1.40
105 106 1.161843 CACCGCACGACCCTAAATTT 58.838 50.000 0.00 0.00 0.00 1.82
106 107 0.675522 CCACCGCACGACCCTAAATT 60.676 55.000 0.00 0.00 0.00 1.82
108 109 2.162338 CTCCACCGCACGACCCTAAA 62.162 60.000 0.00 0.00 0.00 1.85
109 110 2.601067 TCCACCGCACGACCCTAA 60.601 61.111 0.00 0.00 0.00 2.69
110 111 3.066190 CTCCACCGCACGACCCTA 61.066 66.667 0.00 0.00 0.00 3.53
112 113 4.309950 AACTCCACCGCACGACCC 62.310 66.667 0.00 0.00 0.00 4.46
113 114 3.041940 CAACTCCACCGCACGACC 61.042 66.667 0.00 0.00 0.00 4.79
117 118 2.741486 TAAGGCCAACTCCACCGCAC 62.741 60.000 5.01 0.00 0.00 5.34
118 119 2.463589 CTAAGGCCAACTCCACCGCA 62.464 60.000 5.01 0.00 0.00 5.69
119 120 1.745489 CTAAGGCCAACTCCACCGC 60.745 63.158 5.01 0.00 0.00 5.68
120 121 0.323629 TTCTAAGGCCAACTCCACCG 59.676 55.000 5.01 0.00 0.00 4.94
121 122 2.808906 ATTCTAAGGCCAACTCCACC 57.191 50.000 5.01 0.00 0.00 4.61
123 124 4.202567 ACAGAAATTCTAAGGCCAACTCCA 60.203 41.667 5.01 0.00 0.00 3.86
124 125 4.336280 ACAGAAATTCTAAGGCCAACTCC 58.664 43.478 5.01 0.00 0.00 3.85
125 126 5.966742 AACAGAAATTCTAAGGCCAACTC 57.033 39.130 5.01 0.00 0.00 3.01
126 127 6.731292 AAAACAGAAATTCTAAGGCCAACT 57.269 33.333 5.01 0.00 0.00 3.16
170 2211 8.073768 CAGACGTACCACTTTCAAATTTTGTAT 58.926 33.333 8.89 0.00 0.00 2.29
178 2219 2.610374 GTGCAGACGTACCACTTTCAAA 59.390 45.455 0.00 0.00 0.00 2.69
350 2440 5.825593 AGTGACAACCCATATATCCGATT 57.174 39.130 0.00 0.00 0.00 3.34
408 2502 7.910683 GCAACTAGGAAAATACTCTTTATGTGC 59.089 37.037 0.00 0.00 0.00 4.57
430 2524 6.374333 TCCACATTACTAGAAAGATTGGCAAC 59.626 38.462 0.00 0.00 0.00 4.17
431 2525 6.374333 GTCCACATTACTAGAAAGATTGGCAA 59.626 38.462 0.68 0.68 0.00 4.52
444 2538 3.637911 ATTTGGCCGTCCACATTACTA 57.362 42.857 0.00 0.00 43.33 1.82
506 2615 1.884235 AAGGTCACAAGGAAGAAGCG 58.116 50.000 0.00 0.00 0.00 4.68
573 2683 1.861542 GCGTTGGTGCTTGCCATACA 61.862 55.000 0.00 0.00 38.48 2.29
628 2747 2.379732 CGTGTCGAGACAGATGCATAG 58.620 52.381 13.65 0.00 42.74 2.23
677 2803 3.965347 GGGCAAAGGTACAGTATCCTAGA 59.035 47.826 0.00 0.00 33.27 2.43
699 2825 5.477510 CGATGGAATCTCTCTCCCATAAAG 58.522 45.833 0.00 0.00 42.58 1.85
802 5880 1.393539 CTTTACACAACGATCAGCCCG 59.606 52.381 0.00 0.00 0.00 6.13
901 5996 4.814294 GCTCGCGGATTGGACGGT 62.814 66.667 6.13 0.00 0.00 4.83
963 6105 1.795768 TTAAACACGGCTCTGCTGAG 58.204 50.000 15.76 15.76 42.96 3.35
964 6106 2.289382 TGATTAAACACGGCTCTGCTGA 60.289 45.455 5.31 0.00 38.46 4.26
1019 6190 2.058595 CCCTCCGTCATCTTCCCGT 61.059 63.158 0.00 0.00 0.00 5.28
1240 6518 6.315144 GGGCGGCAAGTAAAATTGAAAATAAT 59.685 34.615 12.47 0.00 31.55 1.28
1243 6521 4.000325 GGGCGGCAAGTAAAATTGAAAAT 59.000 39.130 12.47 0.00 31.55 1.82
1276 6554 2.543067 AAATCACCAGCCTCGAGCCC 62.543 60.000 6.99 0.00 45.47 5.19
1325 6666 6.158598 CACTGGGTATTTTCCAACTCAATTG 58.841 40.000 0.00 0.00 38.12 2.32
1705 7087 9.283768 TGAAAAGTTTTAATCTCACTGCTGATA 57.716 29.630 0.00 0.00 0.00 2.15
1782 7168 1.073125 TGCAAATGGGAGTTTCGAGGA 59.927 47.619 0.00 0.00 0.00 3.71
1801 9814 1.001406 GTAAGGATGGATCTCGGCCTG 59.999 57.143 0.00 0.00 0.00 4.85
2060 12177 2.177394 TGCTTGTATGTGCGAAAGGA 57.823 45.000 0.00 0.00 0.00 3.36


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

AutoCloner maintained by Alex Coulton.