Multiple sequence alignment - TraesCS1A01G010000

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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 TraesCS1A01G010000 chr1A 100.000 2258 0 0 1 2258 6225092 6222835 0.000000e+00 4170.0
1 TraesCS1A01G010000 chr1A 86.697 1090 92 20 873 1912 6291342 6290256 0.000000e+00 1160.0
2 TraesCS1A01G010000 chr1A 85.271 1161 99 27 805 1912 6202735 6201594 0.000000e+00 1131.0
3 TraesCS1A01G010000 chr1A 88.249 851 72 5 884 1713 6218512 6217669 0.000000e+00 992.0
4 TraesCS1A01G010000 chr1A 85.510 559 64 3 860 1401 5132356 5132914 3.250000e-158 568.0
5 TraesCS1A01G010000 chr1A 84.448 553 67 9 1709 2258 6209397 6208861 5.520000e-146 527.0
6 TraesCS1A01G010000 chr1A 81.336 434 61 13 806 1230 5332521 5332943 3.590000e-88 335.0
7 TraesCS1A01G010000 chr7B 92.468 770 35 19 50 805 677421957 677422717 0.000000e+00 1079.0
8 TraesCS1A01G010000 chr7B 90.751 519 39 5 49 561 681686954 681687469 0.000000e+00 684.0
9 TraesCS1A01G010000 chr7B 90.580 276 7 10 552 809 681687619 681687893 4.620000e-92 348.0
10 TraesCS1A01G010000 chr1D 91.656 779 33 17 50 805 468135104 468135873 0.000000e+00 1050.0
11 TraesCS1A01G010000 chr1D 81.377 494 62 17 810 1289 3801756 3802233 2.120000e-100 375.0
12 TraesCS1A01G010000 chr3D 82.043 646 57 19 203 804 69039387 69038757 1.560000e-136 496.0
13 TraesCS1A01G010000 chr3D 86.335 161 15 5 2041 2197 25391559 25391716 3.860000e-38 169.0
14 TraesCS1A01G010000 chr3D 78.136 279 41 15 1921 2197 560273849 560274109 2.320000e-35 159.0
15 TraesCS1A01G010000 chr6B 79.693 783 71 30 50 798 624844458 624845186 3.370000e-133 484.0
16 TraesCS1A01G010000 chr6B 78.941 793 72 29 50 806 39310483 39309750 3.420000e-123 451.0
17 TraesCS1A01G010000 chr3B 77.150 814 70 38 46 811 27821746 27821001 1.270000e-97 366.0
18 TraesCS1A01G010000 chr1B 82.477 428 56 10 837 1257 6462627 6463042 7.670000e-95 357.0
19 TraesCS1A01G010000 chr1B 90.955 199 13 3 520 713 626586546 626586744 1.720000e-66 263.0
20 TraesCS1A01G010000 chrUn 80.260 461 71 10 806 1257 85819 85370 1.670000e-86 329.0
21 TraesCS1A01G010000 chrUn 80.260 461 71 10 806 1257 231646097 231645648 1.670000e-86 329.0
22 TraesCS1A01G010000 chr5B 80.645 403 50 17 50 432 175895459 175895065 1.020000e-73 287.0
23 TraesCS1A01G010000 chr5B 77.037 270 43 14 1923 2191 53671486 53671737 1.090000e-28 137.0
24 TraesCS1A01G010000 chr2D 87.879 231 20 5 207 432 549630452 549630225 4.780000e-67 265.0
25 TraesCS1A01G010000 chr2D 87.879 231 20 5 207 432 550095736 550095509 4.780000e-67 265.0
26 TraesCS1A01G010000 chr2D 100.000 28 0 0 2214 2241 15676598 15676625 4.000000e-03 52.8
27 TraesCS1A01G010000 chr7A 89.394 198 16 3 521 713 54727519 54727322 6.230000e-61 244.0
28 TraesCS1A01G010000 chr7A 79.154 331 44 18 1923 2249 664053293 664053602 2.940000e-49 206.0
29 TraesCS1A01G010000 chr7A 76.963 191 30 12 2053 2241 289159447 289159625 1.850000e-16 97.1
30 TraesCS1A01G010000 chr3A 87.117 163 16 4 555 713 600067540 600067379 1.780000e-41 180.0
31 TraesCS1A01G010000 chr3A 78.140 215 31 12 2041 2247 51400810 51401016 3.050000e-24 122.0
32 TraesCS1A01G010000 chr7D 83.168 202 23 8 2004 2197 37807608 37807410 8.290000e-40 174.0
33 TraesCS1A01G010000 chr7D 77.647 170 23 12 217 378 31591733 31591571 3.090000e-14 89.8
34 TraesCS1A01G010000 chr5D 78.832 274 38 15 1923 2195 50784385 50784639 1.390000e-37 167.0
35 TraesCS1A01G010000 chr6A 77.289 273 46 11 1916 2187 3598606 3598349 1.810000e-31 147.0
36 TraesCS1A01G010000 chr6A 81.006 179 29 5 2045 2219 405662310 405662487 1.090000e-28 137.0
37 TraesCS1A01G010000 chr2B 74.224 322 55 17 1932 2250 619697211 619696915 2.370000e-20 110.0
38 TraesCS1A01G010000 chr2A 73.684 323 49 23 1923 2241 510307348 510307638 2.390000e-15 93.5


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 TraesCS1A01G010000 chr1A 6222835 6225092 2257 True 4170 4170 100.0000 1 2258 1 chr1A.!!$R4 2257
1 TraesCS1A01G010000 chr1A 6290256 6291342 1086 True 1160 1160 86.6970 873 1912 1 chr1A.!!$R5 1039
2 TraesCS1A01G010000 chr1A 6201594 6202735 1141 True 1131 1131 85.2710 805 1912 1 chr1A.!!$R1 1107
3 TraesCS1A01G010000 chr1A 6217669 6218512 843 True 992 992 88.2490 884 1713 1 chr1A.!!$R3 829
4 TraesCS1A01G010000 chr1A 5132356 5132914 558 False 568 568 85.5100 860 1401 1 chr1A.!!$F1 541
5 TraesCS1A01G010000 chr1A 6208861 6209397 536 True 527 527 84.4480 1709 2258 1 chr1A.!!$R2 549
6 TraesCS1A01G010000 chr7B 677421957 677422717 760 False 1079 1079 92.4680 50 805 1 chr7B.!!$F1 755
7 TraesCS1A01G010000 chr7B 681686954 681687893 939 False 516 684 90.6655 49 809 2 chr7B.!!$F2 760
8 TraesCS1A01G010000 chr1D 468135104 468135873 769 False 1050 1050 91.6560 50 805 1 chr1D.!!$F2 755
9 TraesCS1A01G010000 chr3D 69038757 69039387 630 True 496 496 82.0430 203 804 1 chr3D.!!$R1 601
10 TraesCS1A01G010000 chr6B 624844458 624845186 728 False 484 484 79.6930 50 798 1 chr6B.!!$F1 748
11 TraesCS1A01G010000 chr6B 39309750 39310483 733 True 451 451 78.9410 50 806 1 chr6B.!!$R1 756
12 TraesCS1A01G010000 chr3B 27821001 27821746 745 True 366 366 77.1500 46 811 1 chr3B.!!$R1 765

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
468 516 1.168714 CTTTGGTGCTGCTTCTACCC 58.831 55.0 0.0 0.0 33.51 3.69 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2035 2368 0.11001 TTTGTGTGTGTGTGTGTGCG 60.11 50.0 0.0 0.0 0.0 5.34 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 6.712241 AAATATTTGAGCGATACGGATCAG 57.288 37.500 8.69 1.74 33.36 2.90
25 26 3.735237 ATTTGAGCGATACGGATCAGT 57.265 42.857 8.69 3.43 33.36 3.41
26 27 2.492019 TTGAGCGATACGGATCAGTG 57.508 50.000 8.69 0.00 33.36 3.66
27 28 1.675552 TGAGCGATACGGATCAGTGA 58.324 50.000 8.69 0.00 31.78 3.41
28 29 2.230660 TGAGCGATACGGATCAGTGAT 58.769 47.619 8.69 4.98 31.78 3.06
29 30 3.408634 TGAGCGATACGGATCAGTGATA 58.591 45.455 8.69 0.00 31.78 2.15
30 31 3.437049 TGAGCGATACGGATCAGTGATAG 59.563 47.826 8.69 6.08 31.78 2.08
31 32 2.162608 AGCGATACGGATCAGTGATAGC 59.837 50.000 8.69 8.70 31.78 2.97
32 33 2.162608 GCGATACGGATCAGTGATAGCT 59.837 50.000 8.69 0.00 31.78 3.32
33 34 3.374367 GCGATACGGATCAGTGATAGCTA 59.626 47.826 8.69 0.00 31.78 3.32
34 35 4.495019 GCGATACGGATCAGTGATAGCTAG 60.495 50.000 8.69 0.00 31.78 3.42
35 36 4.495019 CGATACGGATCAGTGATAGCTAGC 60.495 50.000 6.62 6.62 31.78 3.42
36 37 2.870175 ACGGATCAGTGATAGCTAGCT 58.130 47.619 23.12 23.12 0.00 3.32
37 38 2.556189 ACGGATCAGTGATAGCTAGCTG 59.444 50.000 27.68 10.29 0.00 4.24
38 39 2.094803 CGGATCAGTGATAGCTAGCTGG 60.095 54.545 27.68 9.37 0.00 4.85
39 40 2.896685 GGATCAGTGATAGCTAGCTGGT 59.103 50.000 27.68 15.53 0.00 4.00
40 41 3.323403 GGATCAGTGATAGCTAGCTGGTT 59.677 47.826 27.68 11.77 0.00 3.67
41 42 4.555262 GATCAGTGATAGCTAGCTGGTTC 58.445 47.826 27.68 19.64 0.00 3.62
42 43 3.636679 TCAGTGATAGCTAGCTGGTTCT 58.363 45.455 27.68 16.22 0.00 3.01
43 44 3.634448 TCAGTGATAGCTAGCTGGTTCTC 59.366 47.826 27.68 19.09 0.00 2.87
44 45 3.636300 CAGTGATAGCTAGCTGGTTCTCT 59.364 47.826 27.68 20.72 0.00 3.10
45 46 4.824537 CAGTGATAGCTAGCTGGTTCTCTA 59.175 45.833 27.68 4.61 0.00 2.43
46 47 5.476599 CAGTGATAGCTAGCTGGTTCTCTAT 59.523 44.000 27.68 9.83 0.00 1.98
47 48 6.015519 CAGTGATAGCTAGCTGGTTCTCTATT 60.016 42.308 27.68 0.00 0.00 1.73
96 98 1.529244 GTTCAACTGCACAGGCCCT 60.529 57.895 0.00 0.00 40.13 5.19
291 331 5.212745 TCTCCTCCTTCCTATTCTCTTTCC 58.787 45.833 0.00 0.00 0.00 3.13
308 348 2.297698 TCCCCGTAGTCTCTTTCACA 57.702 50.000 0.00 0.00 0.00 3.58
315 355 2.777832 AGTCTCTTTCACATCCAGCC 57.222 50.000 0.00 0.00 0.00 4.85
449 497 4.647399 AGGTGTCTCCTCTGCTTATTAGAC 59.353 45.833 0.00 0.00 44.42 2.59
454 502 6.045955 GTCTCCTCTGCTTATTAGACTTTGG 58.954 44.000 0.00 0.00 32.51 3.28
468 516 1.168714 CTTTGGTGCTGCTTCTACCC 58.831 55.000 0.00 0.00 33.51 3.69
477 525 2.982130 CTTCTACCCACGCTGCCT 59.018 61.111 0.00 0.00 0.00 4.75
645 876 9.260002 GGAGAAGATTGCTTATGAAAAACAAAA 57.740 29.630 0.00 0.00 33.61 2.44
779 1033 6.739331 TTAATTTTGGATGTTGAACAGGGT 57.261 33.333 3.74 0.00 0.00 4.34
924 1179 5.428253 GGAATGTACCAGTTCATAAGCAGA 58.572 41.667 0.00 0.00 0.00 4.26
1105 1360 0.532115 ATGCGAAAATTGTCTGGGCC 59.468 50.000 0.00 0.00 0.00 5.80
1113 1368 1.549203 ATTGTCTGGGCCATTGTGTC 58.451 50.000 6.72 0.00 0.00 3.67
1236 1491 1.312371 GCGGTGGCACATGTTATGGT 61.312 55.000 20.82 0.00 44.52 3.55
1268 1540 0.459585 TTCTGCTAGCTAAACCGGCG 60.460 55.000 17.23 0.00 34.52 6.46
1311 1583 7.646130 TGTGAATGTTCCTTCGTTTTATTGTTC 59.354 33.333 0.00 0.00 0.00 3.18
1319 1591 8.259049 TCCTTCGTTTTATTGTTCGTTGATAT 57.741 30.769 0.00 0.00 0.00 1.63
1323 1595 8.697846 TCGTTTTATTGTTCGTTGATATCTCT 57.302 30.769 3.98 0.00 0.00 3.10
1356 1629 8.943002 GTTTCTAAGCCAAGTACTAAATAAGCA 58.057 33.333 0.00 0.00 0.00 3.91
1407 1708 6.534793 GGGTACTATGGCAAATGTTTCATTTG 59.465 38.462 22.76 22.76 40.80 2.32
1488 1797 0.457853 ATCATGTGTTCGTCCGACGG 60.458 55.000 20.35 7.84 42.81 4.79
1587 1898 3.433343 TCACGGTAGGGTTTCACATCTA 58.567 45.455 0.00 0.00 0.00 1.98
1607 1918 0.320050 TATGTCGGTGAGTTGCAGCA 59.680 50.000 2.55 0.00 45.15 4.41
1626 1937 2.625737 CATTGCAGAACGAGACTGGAT 58.374 47.619 0.00 0.00 35.82 3.41
1630 1941 0.247460 CAGAACGAGACTGGATGGCA 59.753 55.000 0.00 0.00 0.00 4.92
1646 1957 2.551270 CAGCGTTGGAGCACGAAC 59.449 61.111 0.00 0.00 43.15 3.95
1654 1965 2.743928 GAGCACGAACCCAGCCAG 60.744 66.667 0.00 0.00 0.00 4.85
1656 1967 4.643387 GCACGAACCCAGCCAGGT 62.643 66.667 0.00 0.00 44.00 4.00
1675 1986 2.565841 GTCATTAGACATGGAGGTGGC 58.434 52.381 0.00 0.00 44.34 5.01
1737 2058 4.503991 GGATCACTGACTGAGGTGTCTTTT 60.504 45.833 0.00 0.00 37.79 2.27
1761 2082 3.726517 CGTGCAAAGTGGGCCTCG 61.727 66.667 4.53 0.00 0.00 4.63
1785 2106 1.826487 GGCAACTGGACGTGGGTTT 60.826 57.895 0.00 0.00 0.00 3.27
1801 2122 2.091830 GGGTTTGAGGGCCTAGCTAATT 60.092 50.000 5.73 0.00 0.00 1.40
1834 2155 9.388672 ACTAGTATATGCCCTTAACCTGAAATA 57.611 33.333 0.00 0.00 0.00 1.40
1838 2159 5.535753 ATGCCCTTAACCTGAAATAATGC 57.464 39.130 0.00 0.00 0.00 3.56
1909 2242 3.625764 GGGCTAAATCAATACACTTCGCA 59.374 43.478 0.00 0.00 0.00 5.10
1919 2252 2.550830 ACACTTCGCAGGACATTTCT 57.449 45.000 0.00 0.00 0.00 2.52
1925 2258 4.452455 ACTTCGCAGGACATTTCTACAAAG 59.548 41.667 0.00 0.00 0.00 2.77
1934 2267 8.571336 CAGGACATTTCTACAAAGTCTGAATTT 58.429 33.333 0.00 0.00 0.00 1.82
1966 2299 9.125026 ACTAAAAATAAAGCATCACAGGGATAG 57.875 33.333 0.00 0.00 33.95 2.08
1972 2305 3.878778 AGCATCACAGGGATAGAAACAC 58.121 45.455 0.00 0.00 33.95 3.32
1976 2309 5.449588 GCATCACAGGGATAGAAACACAATG 60.450 44.000 0.00 0.00 33.95 2.82
1979 2312 5.013079 TCACAGGGATAGAAACACAATGAGT 59.987 40.000 0.00 0.00 0.00 3.41
1985 2318 6.823689 GGGATAGAAACACAATGAGTACACAT 59.176 38.462 0.00 0.00 0.00 3.21
1988 2321 8.718102 ATAGAAACACAATGAGTACACATACC 57.282 34.615 6.20 0.00 30.88 2.73
1990 2323 3.857052 ACACAATGAGTACACATACCCG 58.143 45.455 6.20 0.00 30.88 5.28
1994 2327 1.066918 GAGTACACATACCCGGCCG 59.933 63.158 21.04 21.04 30.88 6.13
1996 2329 3.852307 TACACATACCCGGCCGCC 61.852 66.667 22.85 0.00 0.00 6.13
2028 2361 1.317613 TGGACACAGCCAACATCAAC 58.682 50.000 0.00 0.00 34.31 3.18
2030 2363 1.225855 GACACAGCCAACATCAACGA 58.774 50.000 0.00 0.00 0.00 3.85
2031 2364 0.944386 ACACAGCCAACATCAACGAC 59.056 50.000 0.00 0.00 0.00 4.34
2032 2365 0.110688 CACAGCCAACATCAACGACG 60.111 55.000 0.00 0.00 0.00 5.12
2033 2366 1.154413 CAGCCAACATCAACGACGC 60.154 57.895 0.00 0.00 0.00 5.19
2034 2367 2.202171 GCCAACATCAACGACGCG 60.202 61.111 3.53 3.53 0.00 6.01
2035 2368 2.202171 CCAACATCAACGACGCGC 60.202 61.111 5.73 0.00 0.00 6.86
2037 2370 4.424430 AACATCAACGACGCGCGC 62.424 61.111 32.58 23.91 46.04 6.86
2079 2412 4.798387 CACCAACAACTAGCAAAGTCAAAC 59.202 41.667 0.00 0.00 37.50 2.93
2085 2418 5.163652 ACAACTAGCAAAGTCAAACAAGACC 60.164 40.000 0.00 0.00 37.50 3.85
2095 2428 2.742053 TCAAACAAGACCGAAGCTATGC 59.258 45.455 0.00 0.00 0.00 3.14
2102 2435 0.464373 ACCGAAGCTATGCCATGGTG 60.464 55.000 14.67 2.80 0.00 4.17
2103 2436 1.168407 CCGAAGCTATGCCATGGTGG 61.168 60.000 14.67 0.00 41.55 4.61
2107 2440 0.182061 AGCTATGCCATGGTGGACTG 59.818 55.000 14.67 0.61 40.96 3.51
2163 2499 7.400599 ACAATGATCAACAAGCTATGACAAT 57.599 32.000 0.00 0.00 0.00 2.71
2164 2500 7.255569 ACAATGATCAACAAGCTATGACAATG 58.744 34.615 0.00 0.99 0.00 2.82
2167 2503 3.419943 TCAACAAGCTATGACAATGCCA 58.580 40.909 0.00 0.00 0.00 4.92
2184 2520 1.691196 CCAATATCCGCACCAACCAT 58.309 50.000 0.00 0.00 0.00 3.55
2185 2521 1.608590 CCAATATCCGCACCAACCATC 59.391 52.381 0.00 0.00 0.00 3.51
2206 2542 6.990939 CCATCTCTTGACATCACAAGTATCAT 59.009 38.462 0.00 0.00 44.96 2.45
2207 2543 7.041984 CCATCTCTTGACATCACAAGTATCATG 60.042 40.741 0.00 0.00 44.96 3.07
2237 2573 2.354510 TCTTCAACAACAACGCCTTCAG 59.645 45.455 0.00 0.00 0.00 3.02
2247 2583 3.035942 CAACGCCTTCAGAAAAGAAACG 58.964 45.455 0.00 0.00 34.90 3.60
2251 2587 2.542595 GCCTTCAGAAAAGAAACGACGA 59.457 45.455 0.00 0.00 0.00 4.20
2255 2591 6.025280 CCTTCAGAAAAGAAACGACGAAAAA 58.975 36.000 0.00 0.00 0.00 1.94
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
1 2 6.146184 CACTGATCCGTATCGCTCAAATATTT 59.854 38.462 0.00 0.00 34.60 1.40
2 3 5.635280 CACTGATCCGTATCGCTCAAATATT 59.365 40.000 0.00 0.00 34.60 1.28
3 4 5.048013 TCACTGATCCGTATCGCTCAAATAT 60.048 40.000 0.00 0.00 34.60 1.28
4 5 4.277423 TCACTGATCCGTATCGCTCAAATA 59.723 41.667 0.00 0.00 34.60 1.40
5 6 3.068165 TCACTGATCCGTATCGCTCAAAT 59.932 43.478 0.00 0.00 34.60 2.32
6 7 2.425668 TCACTGATCCGTATCGCTCAAA 59.574 45.455 0.00 0.00 34.60 2.69
7 8 2.021457 TCACTGATCCGTATCGCTCAA 58.979 47.619 0.00 0.00 34.60 3.02
8 9 1.675552 TCACTGATCCGTATCGCTCA 58.324 50.000 0.00 0.00 34.60 4.26
9 10 2.999507 ATCACTGATCCGTATCGCTC 57.000 50.000 0.00 0.00 34.60 5.03
10 11 2.162608 GCTATCACTGATCCGTATCGCT 59.837 50.000 0.00 0.00 34.60 4.93
11 12 2.162608 AGCTATCACTGATCCGTATCGC 59.837 50.000 0.00 0.00 34.60 4.58
12 13 4.495019 GCTAGCTATCACTGATCCGTATCG 60.495 50.000 7.70 0.00 34.60 2.92
13 14 4.638421 AGCTAGCTATCACTGATCCGTATC 59.362 45.833 17.69 0.00 0.00 2.24
14 15 4.397730 CAGCTAGCTATCACTGATCCGTAT 59.602 45.833 18.86 0.00 31.67 3.06
15 16 3.753797 CAGCTAGCTATCACTGATCCGTA 59.246 47.826 18.86 0.00 31.67 4.02
16 17 2.556189 CAGCTAGCTATCACTGATCCGT 59.444 50.000 18.86 0.00 31.67 4.69
17 18 2.094803 CCAGCTAGCTATCACTGATCCG 60.095 54.545 18.86 0.00 31.67 4.18
18 19 2.896685 ACCAGCTAGCTATCACTGATCC 59.103 50.000 18.86 0.00 31.67 3.36
19 20 4.280677 AGAACCAGCTAGCTATCACTGATC 59.719 45.833 18.86 7.50 31.67 2.92
20 21 4.222336 AGAACCAGCTAGCTATCACTGAT 58.778 43.478 18.86 0.00 31.67 2.90
21 22 3.634448 GAGAACCAGCTAGCTATCACTGA 59.366 47.826 18.86 0.00 31.67 3.41
22 23 3.636300 AGAGAACCAGCTAGCTATCACTG 59.364 47.826 18.86 4.52 0.00 3.66
23 24 3.909732 AGAGAACCAGCTAGCTATCACT 58.090 45.455 18.86 15.97 0.00 3.41
24 25 5.975693 ATAGAGAACCAGCTAGCTATCAC 57.024 43.478 18.86 14.07 0.00 3.06
25 26 6.551227 TGAAATAGAGAACCAGCTAGCTATCA 59.449 38.462 18.86 0.00 0.00 2.15
26 27 6.987386 TGAAATAGAGAACCAGCTAGCTATC 58.013 40.000 18.86 15.65 0.00 2.08
27 28 6.014669 CCTGAAATAGAGAACCAGCTAGCTAT 60.015 42.308 18.86 5.81 0.00 2.97
28 29 5.303078 CCTGAAATAGAGAACCAGCTAGCTA 59.697 44.000 18.86 0.00 0.00 3.32
29 30 4.100808 CCTGAAATAGAGAACCAGCTAGCT 59.899 45.833 12.68 12.68 0.00 3.32
30 31 4.376146 CCTGAAATAGAGAACCAGCTAGC 58.624 47.826 6.62 6.62 0.00 3.42
31 32 4.376146 GCCTGAAATAGAGAACCAGCTAG 58.624 47.826 0.00 0.00 0.00 3.42
32 33 3.134804 GGCCTGAAATAGAGAACCAGCTA 59.865 47.826 0.00 0.00 0.00 3.32
33 34 2.092699 GGCCTGAAATAGAGAACCAGCT 60.093 50.000 0.00 0.00 0.00 4.24
34 35 2.293170 GGCCTGAAATAGAGAACCAGC 58.707 52.381 0.00 0.00 0.00 4.85
35 36 2.743183 CGGGCCTGAAATAGAGAACCAG 60.743 54.545 5.28 0.00 0.00 4.00
36 37 1.209504 CGGGCCTGAAATAGAGAACCA 59.790 52.381 5.28 0.00 0.00 3.67
37 38 1.209747 ACGGGCCTGAAATAGAGAACC 59.790 52.381 21.41 0.00 0.00 3.62
38 39 2.693267 ACGGGCCTGAAATAGAGAAC 57.307 50.000 21.41 0.00 0.00 3.01
39 40 2.433239 GGTACGGGCCTGAAATAGAGAA 59.567 50.000 21.41 0.00 0.00 2.87
40 41 2.037144 GGTACGGGCCTGAAATAGAGA 58.963 52.381 21.41 0.00 0.00 3.10
41 42 2.528041 GGTACGGGCCTGAAATAGAG 57.472 55.000 21.41 0.00 0.00 2.43
71 72 1.335810 CTGTGCAGTTGAACATGCTGT 59.664 47.619 16.50 0.00 42.98 4.40
96 98 3.256960 GGGGCCCTGGTCACTTGA 61.257 66.667 24.38 0.00 0.00 3.02
215 237 1.982660 TTACCGTGCATGTTCCCAAA 58.017 45.000 4.96 0.00 0.00 3.28
291 331 2.496070 TGGATGTGAAAGAGACTACGGG 59.504 50.000 0.00 0.00 0.00 5.28
308 348 0.325860 ATTTGCATGGGTGGCTGGAT 60.326 50.000 0.00 0.00 0.00 3.41
382 422 6.268158 TGAGGGTGGAGCGTAAATATATGTTA 59.732 38.462 0.00 0.00 0.00 2.41
432 477 5.814705 CACCAAAGTCTAATAAGCAGAGGAG 59.185 44.000 0.00 0.00 0.00 3.69
449 497 1.168714 GGGTAGAAGCAGCACCAAAG 58.831 55.000 0.00 0.00 33.78 2.77
454 502 2.391389 GCGTGGGTAGAAGCAGCAC 61.391 63.158 0.00 0.00 0.00 4.40
468 516 1.518133 GCTCTAGTCAGGCAGCGTG 60.518 63.158 8.91 8.91 0.00 5.34
477 525 6.492429 TGGTAGTCTTGTTAAAGCTCTAGTCA 59.508 38.462 0.00 0.00 33.06 3.41
645 876 6.888632 AGCAGTCCTTGATACAAAATCTTCAT 59.111 34.615 0.00 0.00 0.00 2.57
735 989 5.402054 AAGCCCTTGATATAACCATTGGA 57.598 39.130 10.37 0.00 0.00 3.53
924 1179 4.058417 TGGATGGAGATGAGCTAGCTAT 57.942 45.455 19.38 11.54 0.00 2.97
1035 1290 1.565156 GGACGAGCATGACGCAAACA 61.565 55.000 11.51 0.00 46.13 2.83
1073 1328 3.057548 CGCATTCTGTGGCTGCCA 61.058 61.111 19.30 19.30 32.24 4.92
1113 1368 2.700334 CGTAGGCGATGCAAATGGCG 62.700 60.000 0.00 0.00 43.19 5.69
1230 1485 4.019681 CAGAAGAGGGTACAACCACCATAA 60.020 45.833 0.00 0.00 41.02 1.90
1236 1491 1.729586 AGCAGAAGAGGGTACAACCA 58.270 50.000 0.00 0.00 41.02 3.67
1268 1540 2.358737 ACACGCAGCTTACAGCCC 60.359 61.111 0.00 0.00 43.77 5.19
1311 1583 2.540515 ACAACGCCAGAGATATCAACG 58.459 47.619 5.32 3.69 0.00 4.10
1319 1591 2.413837 GCTTAGAAACAACGCCAGAGA 58.586 47.619 0.00 0.00 0.00 3.10
1342 1614 7.672738 CGACATTCGTTTGCTTATTTAGTACT 58.327 34.615 0.00 0.00 34.72 2.73
1407 1708 9.888878 CACATGTATATTGAAAGATGATGGTTC 57.111 33.333 0.00 0.00 0.00 3.62
1488 1797 4.835199 ATTGTTAAGTATGACGACGTGC 57.165 40.909 4.58 0.00 0.00 5.34
1587 1898 1.066215 TGCTGCAACTCACCGACATAT 60.066 47.619 0.00 0.00 0.00 1.78
1592 1903 2.246841 CAATGCTGCAACTCACCGA 58.753 52.632 6.36 0.00 0.00 4.69
1607 1918 2.625737 CATCCAGTCTCGTTCTGCAAT 58.374 47.619 0.00 0.00 0.00 3.56
1630 1941 2.665185 GGTTCGTGCTCCAACGCT 60.665 61.111 0.00 0.00 43.26 5.07
1643 1954 1.559682 TCTAATGACCTGGCTGGGTTC 59.440 52.381 15.36 4.82 40.06 3.62
1646 1957 0.911769 TGTCTAATGACCTGGCTGGG 59.088 55.000 15.36 5.47 42.28 4.45
1654 1965 2.746472 GCCACCTCCATGTCTAATGACC 60.746 54.545 0.00 0.00 42.28 4.02
1656 1967 1.138859 CGCCACCTCCATGTCTAATGA 59.861 52.381 0.00 0.00 0.00 2.57
1696 2017 4.832608 CCTAAGCACCCCGTCCGC 62.833 72.222 0.00 0.00 0.00 5.54
1744 2065 3.726517 CGAGGCCCACTTTGCACG 61.727 66.667 0.00 0.00 0.00 5.34
1761 2082 1.885850 ACGTCCAGTTGCCGAACAC 60.886 57.895 0.00 0.00 34.17 3.32
1778 2099 1.378646 GCTAGGCCCTCAAACCCAC 60.379 63.158 0.00 0.00 0.00 4.61
1785 2106 7.812306 AGTAATTTTAATTAGCTAGGCCCTCA 58.188 34.615 0.00 0.00 31.94 3.86
1859 2192 1.956477 GCTTCAGTGCTTTCCCAGAAA 59.044 47.619 0.00 0.00 0.00 2.52
1860 2193 1.133823 TGCTTCAGTGCTTTCCCAGAA 60.134 47.619 0.00 0.00 0.00 3.02
1873 2206 3.123620 GCCCGAGCTGTGCTTCAG 61.124 66.667 0.00 5.37 46.12 3.02
1888 2221 4.260784 CCTGCGAAGTGTATTGATTTAGCC 60.261 45.833 0.00 0.00 0.00 3.93
1909 2242 8.697507 AAATTCAGACTTTGTAGAAATGTCCT 57.302 30.769 9.66 0.00 0.00 3.85
1946 2279 7.067494 GTGTTTCTATCCCTGTGATGCTTTATT 59.933 37.037 0.00 0.00 34.76 1.40
1949 2282 4.702131 GTGTTTCTATCCCTGTGATGCTTT 59.298 41.667 0.00 0.00 34.76 3.51
1958 2291 6.313905 GTGTACTCATTGTGTTTCTATCCCTG 59.686 42.308 0.00 0.00 0.00 4.45
1966 2299 5.163893 CGGGTATGTGTACTCATTGTGTTTC 60.164 44.000 15.09 0.30 30.24 2.78
1972 2305 2.210116 GCCGGGTATGTGTACTCATTG 58.790 52.381 15.09 4.51 30.24 2.82
1976 2309 1.066918 CGGCCGGGTATGTGTACTC 59.933 63.158 20.10 0.00 0.00 2.59
1979 2312 3.852307 GGCGGCCGGGTATGTGTA 61.852 66.667 29.38 0.00 0.00 2.90
1994 2327 0.390472 GTCCATCCTAGCTATGCGGC 60.390 60.000 0.00 0.00 0.00 6.53
1996 2329 1.341209 TGTGTCCATCCTAGCTATGCG 59.659 52.381 0.00 0.00 0.00 4.73
2005 2338 0.700564 ATGTTGGCTGTGTCCATCCT 59.299 50.000 0.00 0.00 35.77 3.24
2033 2366 3.858989 TGTGTGTGTGTGTGCGCG 61.859 61.111 0.00 0.00 0.00 6.86
2034 2367 2.277247 GTGTGTGTGTGTGTGCGC 60.277 61.111 0.00 0.00 0.00 6.09
2035 2368 0.110010 TTTGTGTGTGTGTGTGTGCG 60.110 50.000 0.00 0.00 0.00 5.34
2036 2369 1.718711 GTTTTGTGTGTGTGTGTGTGC 59.281 47.619 0.00 0.00 0.00 4.57
2037 2370 2.723658 GTGTTTTGTGTGTGTGTGTGTG 59.276 45.455 0.00 0.00 0.00 3.82
2038 2371 2.287909 GGTGTTTTGTGTGTGTGTGTGT 60.288 45.455 0.00 0.00 0.00 3.72
2039 2372 2.287849 TGGTGTTTTGTGTGTGTGTGTG 60.288 45.455 0.00 0.00 0.00 3.82
2040 2373 1.957177 TGGTGTTTTGTGTGTGTGTGT 59.043 42.857 0.00 0.00 0.00 3.72
2041 2374 2.713895 TGGTGTTTTGTGTGTGTGTG 57.286 45.000 0.00 0.00 0.00 3.82
2042 2375 2.362397 TGTTGGTGTTTTGTGTGTGTGT 59.638 40.909 0.00 0.00 0.00 3.72
2043 2376 3.018598 TGTTGGTGTTTTGTGTGTGTG 57.981 42.857 0.00 0.00 0.00 3.82
2044 2377 3.068873 AGTTGTTGGTGTTTTGTGTGTGT 59.931 39.130 0.00 0.00 0.00 3.72
2079 2412 1.600957 CATGGCATAGCTTCGGTCTTG 59.399 52.381 0.00 0.00 0.00 3.02
2085 2418 0.179048 TCCACCATGGCATAGCTTCG 60.179 55.000 13.04 0.00 37.47 3.79
2095 2428 3.754965 TCTTCTTTTCAGTCCACCATGG 58.245 45.455 11.19 11.19 39.43 3.66
2127 2463 4.582701 TGATCATTGTTTTGACCGCTTT 57.417 36.364 0.00 0.00 0.00 3.51
2133 2469 7.809331 TCATAGCTTGTTGATCATTGTTTTGAC 59.191 33.333 0.00 0.00 0.00 3.18
2163 2499 1.034838 GGTTGGTGCGGATATTGGCA 61.035 55.000 0.00 0.00 36.70 4.92
2164 2500 1.034838 TGGTTGGTGCGGATATTGGC 61.035 55.000 0.00 0.00 0.00 4.52
2167 2503 2.439507 AGAGATGGTTGGTGCGGATATT 59.560 45.455 0.00 0.00 0.00 1.28
2184 2520 7.123247 TCTCATGATACTTGTGATGTCAAGAGA 59.877 37.037 12.38 4.96 45.11 3.10
2185 2521 7.263496 TCTCATGATACTTGTGATGTCAAGAG 58.737 38.462 12.38 0.00 45.11 2.85
2206 2542 4.229304 TGTTGTTGAAGAACCCTTCTCA 57.771 40.909 2.62 4.01 46.84 3.27
2207 2543 4.495844 CGTTGTTGTTGAAGAACCCTTCTC 60.496 45.833 2.62 1.90 46.84 2.87
2220 2556 2.842208 TTCTGAAGGCGTTGTTGTTG 57.158 45.000 0.00 0.00 0.00 3.33


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

AutoCloner maintained by Alex Coulton.