Multiple sequence alignment - TraesCS3A01G102700

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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 TraesCS3A01G102700 chr3A 100.000 1947 0 0 681 2627 66297634 66299580 0.000000e+00 3596
1 TraesCS3A01G102700 chr3A 95.945 1948 69 5 681 2627 620631046 620632984 0.000000e+00 3151
2 TraesCS3A01G102700 chr3A 100.000 376 0 0 1 376 66296954 66297329 0.000000e+00 695
3 TraesCS3A01G102700 chr3A 93.258 267 14 4 113 376 620630714 620630979 8.820000e-105 390
4 TraesCS3A01G102700 chr5A 95.893 1948 72 5 681 2627 306451088 306453028 0.000000e+00 3147
5 TraesCS3A01G102700 chr5A 93.909 788 41 4 1841 2627 255510493 255509712 0.000000e+00 1182
6 TraesCS3A01G102700 chr5A 90.496 242 11 1 135 376 306450792 306451021 2.540000e-80 309
7 TraesCS3A01G102700 chr7A 95.747 1834 72 3 795 2627 184080294 184082122 0.000000e+00 2950
8 TraesCS3A01G102700 chr7A 91.713 543 34 6 2085 2627 129444789 129445320 0.000000e+00 743
9 TraesCS3A01G102700 chr7A 95.473 243 10 1 135 376 184079585 184079827 1.140000e-103 387
10 TraesCS3A01G102700 chr7A 89.231 195 20 1 839 1033 688936909 688936716 2.610000e-60 243
11 TraesCS3A01G102700 chr7A 98.936 94 1 0 681 774 184079894 184079987 4.500000e-38 169
12 TraesCS3A01G102700 chr2A 94.401 1679 65 5 681 2337 210329791 210328120 0.000000e+00 2553
13 TraesCS3A01G102700 chr2A 96.708 243 7 1 135 376 210330100 210329858 1.130000e-108 403
14 TraesCS3A01G102700 chr7D 94.961 1548 60 6 1081 2627 627570484 627568954 0.000000e+00 2410
15 TraesCS3A01G102700 chr7D 92.097 329 18 2 681 1001 627570812 627570484 8.570000e-125 457
16 TraesCS3A01G102700 chr7D 92.827 237 15 2 135 370 627571127 627570892 2.500000e-90 342
17 TraesCS3A01G102700 chr4B 92.950 1461 93 8 1079 2537 327120211 327121663 0.000000e+00 2119
18 TraesCS3A01G102700 chr4B 91.139 237 20 1 135 370 327119557 327119793 1.170000e-83 320
19 TraesCS3A01G102700 chr5B 92.397 1460 90 8 1079 2537 488455756 488454317 0.000000e+00 2061
20 TraesCS3A01G102700 chr5B 92.562 242 16 2 135 375 488456407 488456167 1.940000e-91 346
21 TraesCS3A01G102700 chr6A 85.658 1018 103 22 1037 2041 30434390 30435377 0.000000e+00 1031
22 TraesCS3A01G102700 chr6A 90.993 544 44 1 2084 2627 173604931 173604393 0.000000e+00 728
23 TraesCS3A01G102700 chr6B 85.861 877 88 12 1037 1904 51425527 51424678 0.000000e+00 900
24 TraesCS3A01G102700 chr6D 85.568 880 81 20 1037 1910 27673767 27672928 0.000000e+00 880
25 TraesCS3A01G102700 chr1B 87.649 251 28 3 787 1036 291874291 291874043 3.310000e-74 289


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 TraesCS3A01G102700 chr3A 66296954 66299580 2626 False 2145.500000 3596 100.000000 1 2627 2 chr3A.!!$F1 2626
1 TraesCS3A01G102700 chr3A 620630714 620632984 2270 False 1770.500000 3151 94.601500 113 2627 2 chr3A.!!$F2 2514
2 TraesCS3A01G102700 chr5A 306450792 306453028 2236 False 1728.000000 3147 93.194500 135 2627 2 chr5A.!!$F1 2492
3 TraesCS3A01G102700 chr5A 255509712 255510493 781 True 1182.000000 1182 93.909000 1841 2627 1 chr5A.!!$R1 786
4 TraesCS3A01G102700 chr7A 184079585 184082122 2537 False 1168.666667 2950 96.718667 135 2627 3 chr7A.!!$F2 2492
5 TraesCS3A01G102700 chr7A 129444789 129445320 531 False 743.000000 743 91.713000 2085 2627 1 chr7A.!!$F1 542
6 TraesCS3A01G102700 chr2A 210328120 210330100 1980 True 1478.000000 2553 95.554500 135 2337 2 chr2A.!!$R1 2202
7 TraesCS3A01G102700 chr7D 627568954 627571127 2173 True 1069.666667 2410 93.295000 135 2627 3 chr7D.!!$R1 2492
8 TraesCS3A01G102700 chr4B 327119557 327121663 2106 False 1219.500000 2119 92.044500 135 2537 2 chr4B.!!$F1 2402
9 TraesCS3A01G102700 chr5B 488454317 488456407 2090 True 1203.500000 2061 92.479500 135 2537 2 chr5B.!!$R1 2402
10 TraesCS3A01G102700 chr6A 30434390 30435377 987 False 1031.000000 1031 85.658000 1037 2041 1 chr6A.!!$F1 1004
11 TraesCS3A01G102700 chr6A 173604393 173604931 538 True 728.000000 728 90.993000 2084 2627 1 chr6A.!!$R1 543
12 TraesCS3A01G102700 chr6B 51424678 51425527 849 True 900.000000 900 85.861000 1037 1904 1 chr6B.!!$R1 867
13 TraesCS3A01G102700 chr6D 27672928 27673767 839 True 880.000000 880 85.568000 1037 1910 1 chr6D.!!$R1 873

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
187 189 0.038159 GGGCTCGATCATAGGTTCCG 60.038 60.0 0.0 0.0 0.00 4.30 F
1185 1515 0.793478 CGCCTGACTACGACAACGAG 60.793 60.0 0.0 0.0 42.66 4.18 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1415 1747 1.153127 CCTACCTCTCGCTCGTCCT 60.153 63.158 0.0 0.0 0.0 3.85 R
2475 2827 1.679153 GTCCTCCTTCAAACCGCAAAA 59.321 47.619 0.0 0.0 0.0 2.44 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
24 25 7.448748 AATTACATAGTCTTCGCTTTTGGTT 57.551 32.000 0.00 0.00 0.00 3.67
25 26 6.870971 TTACATAGTCTTCGCTTTTGGTTT 57.129 33.333 0.00 0.00 0.00 3.27
26 27 5.767816 ACATAGTCTTCGCTTTTGGTTTT 57.232 34.783 0.00 0.00 0.00 2.43
27 28 5.519722 ACATAGTCTTCGCTTTTGGTTTTG 58.480 37.500 0.00 0.00 0.00 2.44
28 29 5.067283 ACATAGTCTTCGCTTTTGGTTTTGT 59.933 36.000 0.00 0.00 0.00 2.83
29 30 4.028852 AGTCTTCGCTTTTGGTTTTGTC 57.971 40.909 0.00 0.00 0.00 3.18
30 31 3.694566 AGTCTTCGCTTTTGGTTTTGTCT 59.305 39.130 0.00 0.00 0.00 3.41
31 32 4.157840 AGTCTTCGCTTTTGGTTTTGTCTT 59.842 37.500 0.00 0.00 0.00 3.01
32 33 4.499399 GTCTTCGCTTTTGGTTTTGTCTTC 59.501 41.667 0.00 0.00 0.00 2.87
33 34 4.156922 TCTTCGCTTTTGGTTTTGTCTTCA 59.843 37.500 0.00 0.00 0.00 3.02
34 35 4.442375 TCGCTTTTGGTTTTGTCTTCAA 57.558 36.364 0.00 0.00 0.00 2.69
35 36 4.170256 TCGCTTTTGGTTTTGTCTTCAAC 58.830 39.130 0.00 0.00 32.93 3.18
36 37 3.001168 CGCTTTTGGTTTTGTCTTCAACG 60.001 43.478 0.00 0.00 32.93 4.10
37 38 3.924073 GCTTTTGGTTTTGTCTTCAACGT 59.076 39.130 0.00 0.00 32.93 3.99
38 39 4.387559 GCTTTTGGTTTTGTCTTCAACGTT 59.612 37.500 0.00 0.00 32.93 3.99
39 40 5.667644 GCTTTTGGTTTTGTCTTCAACGTTG 60.668 40.000 22.35 22.35 32.93 4.10
40 41 4.768130 TTGGTTTTGTCTTCAACGTTGA 57.232 36.364 26.53 26.53 32.93 3.18
41 42 4.974368 TGGTTTTGTCTTCAACGTTGAT 57.026 36.364 30.10 0.00 37.00 2.57
42 43 5.317733 TGGTTTTGTCTTCAACGTTGATT 57.682 34.783 30.10 0.00 37.00 2.57
43 44 5.715070 TGGTTTTGTCTTCAACGTTGATTT 58.285 33.333 30.10 0.00 37.00 2.17
44 45 5.574830 TGGTTTTGTCTTCAACGTTGATTTG 59.425 36.000 30.10 21.73 37.00 2.32
45 46 5.802956 GGTTTTGTCTTCAACGTTGATTTGA 59.197 36.000 30.10 23.38 37.00 2.69
46 47 6.475402 GGTTTTGTCTTCAACGTTGATTTGAT 59.525 34.615 30.10 0.00 37.00 2.57
47 48 7.010091 GGTTTTGTCTTCAACGTTGATTTGATT 59.990 33.333 30.10 0.00 37.00 2.57
48 49 8.379902 GTTTTGTCTTCAACGTTGATTTGATTT 58.620 29.630 30.10 0.00 37.00 2.17
49 50 7.448588 TTGTCTTCAACGTTGATTTGATTTG 57.551 32.000 30.10 13.18 37.00 2.32
50 51 6.790282 TGTCTTCAACGTTGATTTGATTTGA 58.210 32.000 30.10 12.04 37.00 2.69
51 52 6.690957 TGTCTTCAACGTTGATTTGATTTGAC 59.309 34.615 30.10 22.95 37.00 3.18
52 53 6.912591 GTCTTCAACGTTGATTTGATTTGACT 59.087 34.615 30.10 0.00 37.00 3.41
53 54 7.432252 GTCTTCAACGTTGATTTGATTTGACTT 59.568 33.333 30.10 0.00 37.00 3.01
54 55 7.643764 TCTTCAACGTTGATTTGATTTGACTTC 59.356 33.333 30.10 0.00 37.00 3.01
55 56 6.790282 TCAACGTTGATTTGATTTGACTTCA 58.210 32.000 26.53 0.00 31.01 3.02
56 57 7.254137 TCAACGTTGATTTGATTTGACTTCAA 58.746 30.769 26.53 0.00 31.01 2.69
57 58 7.431960 TCAACGTTGATTTGATTTGACTTCAAG 59.568 33.333 26.53 0.00 32.87 3.02
58 59 6.208644 ACGTTGATTTGATTTGACTTCAAGG 58.791 36.000 0.00 0.00 37.15 3.61
59 60 6.183360 ACGTTGATTTGATTTGACTTCAAGGT 60.183 34.615 0.00 0.00 37.37 3.50
60 61 6.697019 CGTTGATTTGATTTGACTTCAAGGTT 59.303 34.615 0.00 0.00 37.15 3.50
61 62 7.222611 CGTTGATTTGATTTGACTTCAAGGTTT 59.777 33.333 0.00 0.00 37.15 3.27
62 63 9.528018 GTTGATTTGATTTGACTTCAAGGTTTA 57.472 29.630 0.00 0.00 37.15 2.01
64 65 9.912634 TGATTTGATTTGACTTCAAGGTTTATC 57.087 29.630 0.00 0.00 37.15 1.75
67 68 9.965824 TTTGATTTGACTTCAAGGTTTATCTTC 57.034 29.630 0.00 0.00 37.15 2.87
68 69 7.806690 TGATTTGACTTCAAGGTTTATCTTCG 58.193 34.615 0.00 0.00 37.15 3.79
69 70 7.659799 TGATTTGACTTCAAGGTTTATCTTCGA 59.340 33.333 0.00 0.00 37.15 3.71
70 71 7.795482 TTTGACTTCAAGGTTTATCTTCGAA 57.205 32.000 0.00 0.00 37.15 3.71
71 72 7.795482 TTGACTTCAAGGTTTATCTTCGAAA 57.205 32.000 0.00 0.00 0.00 3.46
72 73 7.979444 TGACTTCAAGGTTTATCTTCGAAAT 57.021 32.000 0.00 0.00 0.00 2.17
73 74 7.806690 TGACTTCAAGGTTTATCTTCGAAATG 58.193 34.615 0.00 0.00 0.00 2.32
74 75 7.444183 TGACTTCAAGGTTTATCTTCGAAATGT 59.556 33.333 0.00 0.00 0.00 2.71
75 76 8.166422 ACTTCAAGGTTTATCTTCGAAATGTT 57.834 30.769 0.00 0.00 0.00 2.71
76 77 8.076178 ACTTCAAGGTTTATCTTCGAAATGTTG 58.924 33.333 0.00 0.00 0.00 3.33
77 78 7.737972 TCAAGGTTTATCTTCGAAATGTTGA 57.262 32.000 0.00 0.00 0.00 3.18
78 79 7.806690 TCAAGGTTTATCTTCGAAATGTTGAG 58.193 34.615 0.00 0.00 0.00 3.02
79 80 7.444183 TCAAGGTTTATCTTCGAAATGTTGAGT 59.556 33.333 0.00 0.00 0.00 3.41
80 81 7.745620 AGGTTTATCTTCGAAATGTTGAGTT 57.254 32.000 0.00 0.00 0.00 3.01
81 82 7.584987 AGGTTTATCTTCGAAATGTTGAGTTG 58.415 34.615 0.00 0.00 0.00 3.16
82 83 6.801862 GGTTTATCTTCGAAATGTTGAGTTGG 59.198 38.462 0.00 0.00 0.00 3.77
83 84 7.360361 GTTTATCTTCGAAATGTTGAGTTGGT 58.640 34.615 0.00 0.00 0.00 3.67
84 85 5.613358 ATCTTCGAAATGTTGAGTTGGTC 57.387 39.130 0.00 0.00 0.00 4.02
85 86 4.703897 TCTTCGAAATGTTGAGTTGGTCT 58.296 39.130 0.00 0.00 0.00 3.85
86 87 4.511454 TCTTCGAAATGTTGAGTTGGTCTG 59.489 41.667 0.00 0.00 0.00 3.51
87 88 4.066646 TCGAAATGTTGAGTTGGTCTGA 57.933 40.909 0.00 0.00 0.00 3.27
88 89 4.641396 TCGAAATGTTGAGTTGGTCTGAT 58.359 39.130 0.00 0.00 0.00 2.90
89 90 5.789521 TCGAAATGTTGAGTTGGTCTGATA 58.210 37.500 0.00 0.00 0.00 2.15
90 91 5.637810 TCGAAATGTTGAGTTGGTCTGATAC 59.362 40.000 0.00 0.00 0.00 2.24
91 92 5.408299 CGAAATGTTGAGTTGGTCTGATACA 59.592 40.000 0.00 0.00 0.00 2.29
92 93 6.092670 CGAAATGTTGAGTTGGTCTGATACAT 59.907 38.462 0.00 0.00 0.00 2.29
93 94 7.277760 CGAAATGTTGAGTTGGTCTGATACATA 59.722 37.037 0.00 0.00 0.00 2.29
94 95 7.849804 AATGTTGAGTTGGTCTGATACATAC 57.150 36.000 0.00 0.00 0.00 2.39
95 96 6.353404 TGTTGAGTTGGTCTGATACATACA 57.647 37.500 0.00 0.00 0.00 2.29
96 97 6.946340 TGTTGAGTTGGTCTGATACATACAT 58.054 36.000 0.00 0.00 0.00 2.29
97 98 8.073467 TGTTGAGTTGGTCTGATACATACATA 57.927 34.615 0.00 0.00 0.00 2.29
98 99 7.979537 TGTTGAGTTGGTCTGATACATACATAC 59.020 37.037 0.00 0.00 0.00 2.39
99 100 7.654022 TGAGTTGGTCTGATACATACATACA 57.346 36.000 0.00 0.00 0.00 2.29
100 101 8.250143 TGAGTTGGTCTGATACATACATACAT 57.750 34.615 0.00 0.00 0.00 2.29
101 102 9.362151 TGAGTTGGTCTGATACATACATACATA 57.638 33.333 0.00 0.00 0.00 2.29
102 103 9.627395 GAGTTGGTCTGATACATACATACATAC 57.373 37.037 0.00 0.00 0.00 2.39
103 104 9.143155 AGTTGGTCTGATACATACATACATACA 57.857 33.333 0.00 0.00 0.00 2.29
104 105 9.929180 GTTGGTCTGATACATACATACATACAT 57.071 33.333 0.00 0.00 0.00 2.29
187 189 0.038159 GGGCTCGATCATAGGTTCCG 60.038 60.000 0.00 0.00 0.00 4.30
312 315 1.616921 CACCATCAGCCCCCAGAAT 59.383 57.895 0.00 0.00 0.00 2.40
819 1108 2.037847 GCCCTTGCCTCCAACCAT 59.962 61.111 0.00 0.00 0.00 3.55
881 1178 4.060667 CTTCCACCCGCCCCCAAT 62.061 66.667 0.00 0.00 0.00 3.16
934 1253 2.364961 CGACCTTCCCTCCCCTCT 59.635 66.667 0.00 0.00 0.00 3.69
975 1294 1.535028 CATGTTTCTTGCACCGTGCTA 59.465 47.619 23.52 15.63 45.31 3.49
1007 1327 1.819208 CAAATCGAGCCATGGCCGA 60.819 57.895 36.00 36.00 43.58 5.54
1185 1515 0.793478 CGCCTGACTACGACAACGAG 60.793 60.000 0.00 0.00 42.66 4.18
1374 1706 1.135373 CGTCGTCAGAGTGCAGGTTAT 60.135 52.381 0.00 0.00 0.00 1.89
1649 1982 2.115911 GTGGCGGTGGTGTTGACAA 61.116 57.895 0.00 0.00 0.00 3.18
1736 2071 8.415950 AGCAGAGCATAGTACTGAATTACTAT 57.584 34.615 5.39 0.00 43.28 2.12
2015 2354 1.628340 TCTGAAATGGAAGGCCGAAGA 59.372 47.619 0.00 0.00 36.79 2.87
2058 2398 5.646793 ACACAAACTTGGATGATCTGATCTG 59.353 40.000 17.82 7.52 0.00 2.90
2059 2399 5.878669 CACAAACTTGGATGATCTGATCTGA 59.121 40.000 17.82 4.63 0.00 3.27
2060 2400 6.542735 CACAAACTTGGATGATCTGATCTGAT 59.457 38.462 17.82 14.33 0.00 2.90
2061 2401 6.766944 ACAAACTTGGATGATCTGATCTGATC 59.233 38.462 27.10 27.10 42.19 2.92
2062 2402 6.750660 AACTTGGATGATCTGATCTGATCT 57.249 37.500 30.92 21.23 42.30 2.75
2113 2453 4.870363 TGCTGCAACTTTCATTTAGTTCC 58.130 39.130 0.00 0.00 33.73 3.62
2246 2598 3.125316 GGTCAAAGAGTATGTTGCTTCGG 59.875 47.826 0.00 0.00 0.00 4.30
2403 2755 6.811253 TTGTATGTTAGGAAAATTGACGCT 57.189 33.333 0.00 0.00 0.00 5.07
2472 2824 4.721776 AGGTCACATATGTGTACCAGGAAT 59.278 41.667 34.29 22.41 45.76 3.01
2473 2825 5.191722 AGGTCACATATGTGTACCAGGAATT 59.808 40.000 34.29 21.97 45.76 2.17
2474 2826 5.885912 GGTCACATATGTGTACCAGGAATTT 59.114 40.000 31.43 1.14 45.76 1.82
2475 2827 6.377146 GGTCACATATGTGTACCAGGAATTTT 59.623 38.462 31.43 0.61 45.76 1.82
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 7.448748 AACCAAAAGCGAAGACTATGTAATT 57.551 32.000 0.00 0.00 0.00 1.40
1 2 7.448748 AAACCAAAAGCGAAGACTATGTAAT 57.551 32.000 0.00 0.00 0.00 1.89
3 4 6.261381 ACAAAACCAAAAGCGAAGACTATGTA 59.739 34.615 0.00 0.00 0.00 2.29
4 5 5.067283 ACAAAACCAAAAGCGAAGACTATGT 59.933 36.000 0.00 0.00 0.00 2.29
5 6 5.519722 ACAAAACCAAAAGCGAAGACTATG 58.480 37.500 0.00 0.00 0.00 2.23
6 7 5.531287 AGACAAAACCAAAAGCGAAGACTAT 59.469 36.000 0.00 0.00 0.00 2.12
7 8 4.879545 AGACAAAACCAAAAGCGAAGACTA 59.120 37.500 0.00 0.00 0.00 2.59
8 9 3.694566 AGACAAAACCAAAAGCGAAGACT 59.305 39.130 0.00 0.00 0.00 3.24
9 10 4.028852 AGACAAAACCAAAAGCGAAGAC 57.971 40.909 0.00 0.00 0.00 3.01
10 11 4.156922 TGAAGACAAAACCAAAAGCGAAGA 59.843 37.500 0.00 0.00 0.00 2.87
11 12 4.420168 TGAAGACAAAACCAAAAGCGAAG 58.580 39.130 0.00 0.00 0.00 3.79
12 13 4.442375 TGAAGACAAAACCAAAAGCGAA 57.558 36.364 0.00 0.00 0.00 4.70
13 14 4.170256 GTTGAAGACAAAACCAAAAGCGA 58.830 39.130 0.00 0.00 37.77 4.93
14 15 3.001168 CGTTGAAGACAAAACCAAAAGCG 60.001 43.478 0.00 0.00 37.77 4.68
15 16 3.924073 ACGTTGAAGACAAAACCAAAAGC 59.076 39.130 0.00 0.00 37.77 3.51
16 17 5.631512 TCAACGTTGAAGACAAAACCAAAAG 59.368 36.000 27.94 0.00 37.77 2.27
17 18 5.529791 TCAACGTTGAAGACAAAACCAAAA 58.470 33.333 27.94 0.00 37.77 2.44
18 19 5.122512 TCAACGTTGAAGACAAAACCAAA 57.877 34.783 27.94 0.25 37.77 3.28
19 20 4.768130 TCAACGTTGAAGACAAAACCAA 57.232 36.364 27.94 0.72 37.77 3.67
20 21 4.974368 ATCAACGTTGAAGACAAAACCA 57.026 36.364 32.69 7.69 41.13 3.67
21 22 5.802956 TCAAATCAACGTTGAAGACAAAACC 59.197 36.000 32.69 0.00 41.13 3.27
22 23 6.862944 TCAAATCAACGTTGAAGACAAAAC 57.137 33.333 32.69 0.00 41.13 2.43
23 24 8.379161 CAAATCAAATCAACGTTGAAGACAAAA 58.621 29.630 32.69 15.67 41.13 2.44
24 25 7.757173 TCAAATCAAATCAACGTTGAAGACAAA 59.243 29.630 32.69 17.11 41.13 2.83
25 26 7.219917 GTCAAATCAAATCAACGTTGAAGACAA 59.780 33.333 32.69 18.08 41.13 3.18
26 27 6.690957 GTCAAATCAAATCAACGTTGAAGACA 59.309 34.615 32.69 18.20 41.13 3.41
27 28 6.912591 AGTCAAATCAAATCAACGTTGAAGAC 59.087 34.615 32.69 24.72 41.13 3.01
28 29 7.026631 AGTCAAATCAAATCAACGTTGAAGA 57.973 32.000 32.69 27.70 41.13 2.87
29 30 7.431960 TGAAGTCAAATCAAATCAACGTTGAAG 59.568 33.333 32.69 24.06 41.13 3.02
30 31 7.254137 TGAAGTCAAATCAAATCAACGTTGAA 58.746 30.769 32.69 18.11 41.13 2.69
31 32 6.790282 TGAAGTCAAATCAAATCAACGTTGA 58.210 32.000 31.41 31.41 42.14 3.18
32 33 7.306167 CCTTGAAGTCAAATCAAATCAACGTTG 60.306 37.037 22.35 22.35 36.43 4.10
33 34 6.697019 CCTTGAAGTCAAATCAAATCAACGTT 59.303 34.615 0.00 0.00 36.43 3.99
34 35 6.183360 ACCTTGAAGTCAAATCAAATCAACGT 60.183 34.615 0.00 0.00 36.43 3.99
35 36 6.208644 ACCTTGAAGTCAAATCAAATCAACG 58.791 36.000 0.00 0.00 36.43 4.10
36 37 8.424274 AAACCTTGAAGTCAAATCAAATCAAC 57.576 30.769 0.00 0.00 36.43 3.18
38 39 9.912634 GATAAACCTTGAAGTCAAATCAAATCA 57.087 29.630 0.00 0.00 36.43 2.57
41 42 9.965824 GAAGATAAACCTTGAAGTCAAATCAAA 57.034 29.630 0.00 0.00 36.43 2.69
42 43 8.289618 CGAAGATAAACCTTGAAGTCAAATCAA 58.710 33.333 0.00 0.00 35.15 2.57
43 44 7.659799 TCGAAGATAAACCTTGAAGTCAAATCA 59.340 33.333 0.00 0.00 35.15 2.57
44 45 8.029642 TCGAAGATAAACCTTGAAGTCAAATC 57.970 34.615 0.00 0.00 35.15 2.17
45 46 7.979444 TCGAAGATAAACCTTGAAGTCAAAT 57.021 32.000 0.00 0.00 35.15 2.32
46 47 7.795482 TTCGAAGATAAACCTTGAAGTCAAA 57.205 32.000 0.00 0.00 35.04 2.69
47 48 7.795482 TTTCGAAGATAAACCTTGAAGTCAA 57.205 32.000 0.00 0.00 35.04 3.18
48 49 7.444183 ACATTTCGAAGATAAACCTTGAAGTCA 59.556 33.333 0.00 0.00 35.04 3.41
49 50 7.807680 ACATTTCGAAGATAAACCTTGAAGTC 58.192 34.615 0.00 0.00 35.04 3.01
50 51 7.745620 ACATTTCGAAGATAAACCTTGAAGT 57.254 32.000 0.00 0.00 35.04 3.01
51 52 8.289618 TCAACATTTCGAAGATAAACCTTGAAG 58.710 33.333 0.00 0.00 35.04 3.02
52 53 8.160521 TCAACATTTCGAAGATAAACCTTGAA 57.839 30.769 0.00 0.00 35.04 2.69
53 54 7.444183 ACTCAACATTTCGAAGATAAACCTTGA 59.556 33.333 0.00 0.00 35.04 3.02
54 55 7.584987 ACTCAACATTTCGAAGATAAACCTTG 58.415 34.615 0.00 0.00 35.04 3.61
55 56 7.745620 ACTCAACATTTCGAAGATAAACCTT 57.254 32.000 0.00 0.00 35.04 3.50
56 57 7.308589 CCAACTCAACATTTCGAAGATAAACCT 60.309 37.037 0.00 0.00 35.04 3.50
57 58 6.801862 CCAACTCAACATTTCGAAGATAAACC 59.198 38.462 0.00 0.00 35.04 3.27
58 59 7.360361 ACCAACTCAACATTTCGAAGATAAAC 58.640 34.615 0.00 0.00 35.04 2.01
59 60 7.444183 AGACCAACTCAACATTTCGAAGATAAA 59.556 33.333 0.00 0.00 35.04 1.40
60 61 6.934645 AGACCAACTCAACATTTCGAAGATAA 59.065 34.615 0.00 0.00 35.04 1.75
61 62 6.368791 CAGACCAACTCAACATTTCGAAGATA 59.631 38.462 0.00 0.00 35.04 1.98
62 63 5.180117 CAGACCAACTCAACATTTCGAAGAT 59.820 40.000 0.00 0.00 35.04 2.40
63 64 4.511454 CAGACCAACTCAACATTTCGAAGA 59.489 41.667 0.00 0.00 0.00 2.87
64 65 4.511454 TCAGACCAACTCAACATTTCGAAG 59.489 41.667 0.00 0.00 0.00 3.79
65 66 4.447290 TCAGACCAACTCAACATTTCGAA 58.553 39.130 0.00 0.00 0.00 3.71
66 67 4.066646 TCAGACCAACTCAACATTTCGA 57.933 40.909 0.00 0.00 0.00 3.71
67 68 5.408299 TGTATCAGACCAACTCAACATTTCG 59.592 40.000 0.00 0.00 0.00 3.46
68 69 6.801539 TGTATCAGACCAACTCAACATTTC 57.198 37.500 0.00 0.00 0.00 2.17
69 70 7.882791 TGTATGTATCAGACCAACTCAACATTT 59.117 33.333 0.00 0.00 0.00 2.32
70 71 7.394016 TGTATGTATCAGACCAACTCAACATT 58.606 34.615 0.00 0.00 0.00 2.71
71 72 6.946340 TGTATGTATCAGACCAACTCAACAT 58.054 36.000 0.00 0.00 0.00 2.71
72 73 6.353404 TGTATGTATCAGACCAACTCAACA 57.647 37.500 0.00 0.00 0.00 3.33
73 74 7.979537 TGTATGTATGTATCAGACCAACTCAAC 59.020 37.037 0.00 0.00 0.00 3.18
74 75 8.073467 TGTATGTATGTATCAGACCAACTCAA 57.927 34.615 0.00 0.00 0.00 3.02
75 76 7.654022 TGTATGTATGTATCAGACCAACTCA 57.346 36.000 0.00 0.00 0.00 3.41
76 77 9.627395 GTATGTATGTATGTATCAGACCAACTC 57.373 37.037 0.00 0.00 0.00 3.01
77 78 9.143155 TGTATGTATGTATGTATCAGACCAACT 57.857 33.333 0.00 0.00 0.00 3.16
78 79 9.929180 ATGTATGTATGTATGTATCAGACCAAC 57.071 33.333 0.00 0.00 0.00 3.77
132 133 9.923143 CGGTGTGATCCAAATAGTTATTCTATA 57.077 33.333 0.00 0.00 38.29 1.31
187 189 2.741211 GCACGGTTCGGGAGTTCC 60.741 66.667 0.00 0.00 28.17 3.62
318 321 2.103538 GGTTAGATGCGACGGCGA 59.896 61.111 18.90 0.00 44.10 5.54
881 1178 2.747686 GTCACGCTGGAGGGGAAA 59.252 61.111 0.00 0.00 0.00 3.13
950 1269 1.523154 GGTGCAAGAAACATGGGCGA 61.523 55.000 0.00 0.00 0.00 5.54
975 1294 0.462047 GATTTGCGAGTGGGGACGAT 60.462 55.000 0.00 0.00 0.00 3.73
1185 1515 2.034221 GTGAGGGTCCCTTGCACC 59.966 66.667 13.13 0.00 31.76 5.01
1217 1547 4.830765 TGGCGCCCACATACTCGC 62.831 66.667 26.77 0.00 45.99 5.03
1224 1554 4.854924 CCGATGATGGCGCCCACA 62.855 66.667 26.77 23.61 35.80 4.17
1374 1706 2.618241 GAGATATTGATTTGCACGCCCA 59.382 45.455 0.00 0.00 0.00 5.36
1415 1747 1.153127 CCTACCTCTCGCTCGTCCT 60.153 63.158 0.00 0.00 0.00 3.85
1608 1941 2.311124 GCTACCGGCAGTGACTATTT 57.689 50.000 0.00 0.00 41.35 1.40
1649 1982 2.348998 CTTCCTTGACAGGCCGCT 59.651 61.111 0.00 0.00 40.58 5.52
1736 2071 1.837439 CTGCCCTACTACCACCATCAA 59.163 52.381 0.00 0.00 0.00 2.57
1856 2191 1.402720 CCAAAACTAACCATGCAGCCG 60.403 52.381 0.00 0.00 0.00 5.52
2062 2402 4.081807 CACAGTGGAAGTCTGATCAGATCA 60.082 45.833 27.51 19.14 39.97 2.92
2067 2407 2.608623 TCCACAGTGGAAGTCTGATCA 58.391 47.619 20.84 0.00 45.00 2.92
2113 2453 8.522178 ACTAAACTGACAAAATTAGAGTCTCG 57.478 34.615 0.00 0.00 33.56 4.04
2382 2734 7.766219 TCTAGCGTCAATTTTCCTAACATAC 57.234 36.000 0.00 0.00 0.00 2.39
2474 2826 2.100087 GTCCTCCTTCAAACCGCAAAAA 59.900 45.455 0.00 0.00 0.00 1.94
2475 2827 1.679153 GTCCTCCTTCAAACCGCAAAA 59.321 47.619 0.00 0.00 0.00 2.44
2550 2902 7.509546 AGAACAAGAGAGGAAAAACATGTCTA 58.490 34.615 0.00 0.00 31.95 2.59


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

AutoCloner maintained by Alex Coulton.