Multiple sequence alignment - TraesCS2B01G037000

Loading Multiple Alignment...

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 TraesCS2B01G037000 chr2B 100.000 2645 0 0 1 2645 17443883 17446527 0.000000e+00 4885.0
1 TraesCS2B01G037000 chr2B 92.984 1468 97 3 379 1844 17515105 17513642 0.000000e+00 2135.0
2 TraesCS2B01G037000 chr2B 88.948 1511 145 4 379 1888 17503082 17501593 0.000000e+00 1845.0
3 TraesCS2B01G037000 chr2B 87.490 1279 156 3 379 1653 17440031 17438753 0.000000e+00 1472.0
4 TraesCS2B01G037000 chr2B 90.275 1090 104 2 801 1888 17149599 17150688 0.000000e+00 1424.0
5 TraesCS2B01G037000 chr2B 93.761 593 27 3 2061 2644 17151244 17151835 0.000000e+00 881.0
6 TraesCS2B01G037000 chr2B 88.294 504 46 6 1207 1709 17094640 17094149 2.270000e-165 592.0
7 TraesCS2B01G037000 chr2B 87.119 427 55 0 379 805 17144125 17144551 3.960000e-133 484.0
8 TraesCS2B01G037000 chr2B 78.483 567 77 31 2100 2644 17094502 17093959 1.960000e-86 329.0
9 TraesCS2B01G037000 chr2B 82.353 374 46 9 2100 2454 17514138 17513766 9.200000e-80 307.0
10 TraesCS2B01G037000 chr2B 83.086 337 43 5 2100 2422 17439061 17438725 7.160000e-76 294.0
11 TraesCS2B01G037000 chr2B 81.316 380 41 12 2100 2454 17502115 17501741 5.570000e-72 281.0
12 TraesCS2B01G037000 chr2B 92.857 140 10 0 1911 2050 17150783 17150922 1.240000e-48 204.0
13 TraesCS2B01G037000 chr2B 88.732 71 6 1 155 223 17046706 17046636 4.690000e-13 86.1
14 TraesCS2B01G037000 chr2D 92.336 1344 93 4 379 1720 11327586 11326251 0.000000e+00 1903.0
15 TraesCS2B01G037000 chr2D 82.957 575 67 9 2100 2644 11326619 11326046 8.510000e-135 490.0
16 TraesCS2B01G037000 chr2A 91.227 1345 106 6 379 1720 11983157 11981822 0.000000e+00 1820.0
17 TraesCS2B01G037000 chr2A 89.135 451 40 3 1265 1714 11782637 11782195 1.070000e-153 553.0
18 TraesCS2B01G037000 chr2A 83.452 562 63 9 2100 2644 11782557 11782009 1.830000e-136 496.0
19 TraesCS2B01G037000 chr2A 82.783 575 68 9 2100 2644 11982190 11981617 3.960000e-133 484.0
20 TraesCS2B01G037000 chr2A 79.646 339 24 10 64 381 11983594 11983280 4.460000e-48 202.0
21 TraesCS2B01G037000 chr7D 72.314 1210 241 61 479 1639 21774021 21775185 2.580000e-75 292.0
22 TraesCS2B01G037000 chr4A 73.677 756 163 22 918 1651 687627411 687626670 7.260000e-66 261.0
23 TraesCS2B01G037000 chr3B 71.914 1029 202 52 427 1423 13905413 13904440 4.430000e-53 219.0
24 TraesCS2B01G037000 chr7A 86.538 104 12 2 479 581 22198271 22198373 2.150000e-21 113.0
25 TraesCS2B01G037000 chrUn 97.959 49 1 0 2457 2505 36592576 36592624 4.690000e-13 86.1
26 TraesCS2B01G037000 chr1D 88.333 60 7 0 1816 1875 476593407 476593466 3.650000e-09 73.1
27 TraesCS2B01G037000 chr1B 93.478 46 2 1 1818 1863 460166000 460166044 1.700000e-07 67.6
28 TraesCS2B01G037000 chr5D 87.719 57 5 2 1832 1888 468830995 468830941 6.110000e-07 65.8


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 TraesCS2B01G037000 chr2B 17443883 17446527 2644 False 4885.000000 4885 100.000000 1 2645 1 chr2B.!!$F2 2644
1 TraesCS2B01G037000 chr2B 17513642 17515105 1463 True 1221.000000 2135 87.668500 379 2454 2 chr2B.!!$R5 2075
2 TraesCS2B01G037000 chr2B 17501593 17503082 1489 True 1063.000000 1845 85.132000 379 2454 2 chr2B.!!$R4 2075
3 TraesCS2B01G037000 chr2B 17438725 17440031 1306 True 883.000000 1472 85.288000 379 2422 2 chr2B.!!$R3 2043
4 TraesCS2B01G037000 chr2B 17149599 17151835 2236 False 836.333333 1424 92.297667 801 2644 3 chr2B.!!$F3 1843
5 TraesCS2B01G037000 chr2B 17093959 17094640 681 True 460.500000 592 83.388500 1207 2644 2 chr2B.!!$R2 1437
6 TraesCS2B01G037000 chr2D 11326046 11327586 1540 True 1196.500000 1903 87.646500 379 2644 2 chr2D.!!$R1 2265
7 TraesCS2B01G037000 chr2A 11981617 11983594 1977 True 835.333333 1820 84.552000 64 2644 3 chr2A.!!$R2 2580
8 TraesCS2B01G037000 chr2A 11782009 11782637 628 True 524.500000 553 86.293500 1265 2644 2 chr2A.!!$R1 1379
9 TraesCS2B01G037000 chr7D 21774021 21775185 1164 False 292.000000 292 72.314000 479 1639 1 chr7D.!!$F1 1160
10 TraesCS2B01G037000 chr4A 687626670 687627411 741 True 261.000000 261 73.677000 918 1651 1 chr4A.!!$R1 733
11 TraesCS2B01G037000 chr3B 13904440 13905413 973 True 219.000000 219 71.914000 427 1423 1 chr3B.!!$R1 996

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
235 253 0.170116 CTCGTCACTGAGCCTCTGAC 59.83 60.0 5.53 4.93 0.0 3.51 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1901 2110 0.114364 GGGACCAAAACCCCAGATGT 59.886 55.0 0.0 0.0 42.24 3.06 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
25 26 8.845942 TTATTGCTCATTCTCAAAATGAATCG 57.154 30.769 2.46 0.00 36.35 3.34
26 27 4.665212 TGCTCATTCTCAAAATGAATCGC 58.335 39.130 2.46 3.58 36.35 4.58
27 28 4.397103 TGCTCATTCTCAAAATGAATCGCT 59.603 37.500 10.09 0.00 36.35 4.93
28 29 5.106038 TGCTCATTCTCAAAATGAATCGCTT 60.106 36.000 10.09 0.00 36.35 4.68
29 30 5.454877 GCTCATTCTCAAAATGAATCGCTTC 59.545 40.000 2.46 0.00 36.35 3.86
30 31 6.499234 TCATTCTCAAAATGAATCGCTTCA 57.501 33.333 3.88 3.88 45.15 3.02
31 32 6.912082 TCATTCTCAAAATGAATCGCTTCAA 58.088 32.000 5.70 0.00 44.29 2.69
32 33 7.541162 TCATTCTCAAAATGAATCGCTTCAAT 58.459 30.769 5.70 0.00 44.29 2.57
33 34 8.676401 TCATTCTCAAAATGAATCGCTTCAATA 58.324 29.630 5.70 0.00 44.29 1.90
34 35 8.955002 CATTCTCAAAATGAATCGCTTCAATAG 58.045 33.333 5.70 0.51 44.29 1.73
35 36 7.615582 TCTCAAAATGAATCGCTTCAATAGT 57.384 32.000 5.70 0.00 44.29 2.12
36 37 7.466805 TCTCAAAATGAATCGCTTCAATAGTG 58.533 34.615 5.70 2.99 44.29 2.74
37 38 7.119699 TCTCAAAATGAATCGCTTCAATAGTGT 59.880 33.333 5.70 0.00 44.29 3.55
38 39 7.592938 TCAAAATGAATCGCTTCAATAGTGTT 58.407 30.769 5.70 0.00 44.29 3.32
39 40 8.726068 TCAAAATGAATCGCTTCAATAGTGTTA 58.274 29.630 5.70 0.00 44.29 2.41
40 41 9.507280 CAAAATGAATCGCTTCAATAGTGTTAT 57.493 29.630 5.70 0.00 44.29 1.89
72 73 7.654520 AGACTAACTAGTGCATTAACAAAACGA 59.345 33.333 0.00 0.00 36.50 3.85
97 98 4.005650 TGCTTTTAATGAGAGCACTCCAG 58.994 43.478 8.77 0.00 41.15 3.86
102 103 0.540923 ATGAGAGCACTCCAGAAGGC 59.459 55.000 8.77 0.00 41.99 4.35
111 112 1.238439 CTCCAGAAGGCGAGCAAAAA 58.762 50.000 0.00 0.00 33.74 1.94
118 119 1.680338 AGGCGAGCAAAAAGAACACT 58.320 45.000 0.00 0.00 0.00 3.55
171 189 8.629158 GTTAGTGGATGATACAATAATGGCAAA 58.371 33.333 0.50 0.00 32.09 3.68
207 225 3.904136 GCCATGCCAGTGTTATATCAC 57.096 47.619 5.90 5.90 38.46 3.06
225 243 0.385751 ACACTCACACCTCGTCACTG 59.614 55.000 0.00 0.00 0.00 3.66
226 244 0.668535 CACTCACACCTCGTCACTGA 59.331 55.000 0.00 0.00 0.00 3.41
229 247 1.373497 CACACCTCGTCACTGAGCC 60.373 63.158 0.00 0.00 34.56 4.70
231 249 1.214062 CACCTCGTCACTGAGCCTC 59.786 63.158 0.00 0.00 34.56 4.70
232 250 1.075836 ACCTCGTCACTGAGCCTCT 59.924 57.895 0.00 0.00 34.56 3.69
233 251 1.247419 ACCTCGTCACTGAGCCTCTG 61.247 60.000 0.00 0.00 34.56 3.35
234 252 0.962855 CCTCGTCACTGAGCCTCTGA 60.963 60.000 5.53 0.00 34.56 3.27
235 253 0.170116 CTCGTCACTGAGCCTCTGAC 59.830 60.000 5.53 4.93 0.00 3.51
236 254 1.214062 CGTCACTGAGCCTCTGACC 59.786 63.158 5.53 0.00 32.23 4.02
237 255 1.247419 CGTCACTGAGCCTCTGACCT 61.247 60.000 5.53 0.00 32.23 3.85
238 256 0.972883 GTCACTGAGCCTCTGACCTT 59.027 55.000 5.53 0.00 0.00 3.50
239 257 1.346068 GTCACTGAGCCTCTGACCTTT 59.654 52.381 5.53 0.00 0.00 3.11
240 258 1.620819 TCACTGAGCCTCTGACCTTTC 59.379 52.381 5.53 0.00 0.00 2.62
241 259 1.345741 CACTGAGCCTCTGACCTTTCA 59.654 52.381 5.53 0.00 0.00 2.69
242 260 2.027377 CACTGAGCCTCTGACCTTTCAT 60.027 50.000 5.53 0.00 0.00 2.57
252 270 3.849574 TCTGACCTTTCATATGGTGGGAA 59.150 43.478 2.13 0.00 36.59 3.97
253 271 3.947834 CTGACCTTTCATATGGTGGGAAC 59.052 47.826 2.13 4.15 36.59 3.62
272 290 5.708948 GGAACCAAAACGAATGATCAATCA 58.291 37.500 11.26 0.00 41.70 2.57
273 291 5.572896 GGAACCAAAACGAATGATCAATCAC 59.427 40.000 11.26 0.00 40.03 3.06
274 292 5.059404 ACCAAAACGAATGATCAATCACC 57.941 39.130 11.26 0.00 40.03 4.02
277 295 3.652057 AACGAATGATCAATCACCCCT 57.348 42.857 11.26 0.00 40.03 4.79
282 300 4.444022 CGAATGATCAATCACCCCTCTCTT 60.444 45.833 11.26 0.00 40.03 2.85
343 363 1.597578 GCAGCAGCTATCTCCAGCC 60.598 63.158 0.00 0.00 42.84 4.85
372 392 1.391157 ATCAGCTCCTCGTGCTCCTC 61.391 60.000 0.00 0.00 38.92 3.71
374 394 3.444805 GCTCCTCGTGCTCCTCGT 61.445 66.667 0.00 0.00 0.00 4.18
393 538 2.970639 CTCCTTCTCGAACCGCCA 59.029 61.111 0.00 0.00 0.00 5.69
736 887 0.734889 GCCATGTCATACAGCGCTTT 59.265 50.000 7.50 3.33 0.00 3.51
850 1004 1.043116 TCGATGTCCGGCTCAAGGAT 61.043 55.000 0.00 0.00 40.30 3.24
907 1062 2.282251 AGTCTCCTCGACCACGCA 60.282 61.111 0.00 0.00 43.91 5.24
952 1107 2.843669 GACTCACTCGTCGACCTCT 58.156 57.895 10.58 0.00 0.00 3.69
960 1115 3.371063 GTCGACCTCTGCGTCCCA 61.371 66.667 3.51 0.00 0.00 4.37
1017 1187 3.126831 CGAGATGGTGCAACTAATCTCC 58.873 50.000 20.63 8.25 45.68 3.71
1027 1197 3.131400 GCAACTAATCTCCGAGTTCCTCT 59.869 47.826 0.00 0.00 33.60 3.69
1108 1278 0.107945 GCCGAAGATGCAGGAGAAGT 60.108 55.000 0.00 0.00 0.00 3.01
1191 1385 2.262915 GTCGTGCTGGAGACCCTG 59.737 66.667 0.00 0.00 34.81 4.45
1241 1435 2.520020 CCATGCCCATGCCGATGT 60.520 61.111 2.75 0.00 37.49 3.06
1334 1538 0.883833 GACATTGGCAGGGACAACAG 59.116 55.000 0.00 0.00 31.33 3.16
1348 1552 4.392940 GGACAACAGGATATGGAAGGATG 58.607 47.826 0.00 0.00 0.00 3.51
1714 1923 2.096174 TGTGTTTCTACCGTTGTTGCAC 59.904 45.455 0.00 0.00 0.00 4.57
1715 1924 2.096174 GTGTTTCTACCGTTGTTGCACA 59.904 45.455 0.00 0.00 0.00 4.57
1729 1938 2.103143 CACACGAGCCTAGAGCCG 59.897 66.667 0.00 2.37 45.47 5.52
1731 1940 3.826754 CACGAGCCTAGAGCCGCA 61.827 66.667 0.00 0.00 45.47 5.69
1742 1951 0.390998 AGAGCCGCAGAAAGCTTCTC 60.391 55.000 0.00 0.00 40.11 2.87
1758 1967 4.018960 AGCTTCTCCTTCTGCCATTTTCTA 60.019 41.667 0.00 0.00 0.00 2.10
1759 1968 4.886489 GCTTCTCCTTCTGCCATTTTCTAT 59.114 41.667 0.00 0.00 0.00 1.98
1768 1977 4.635765 TCTGCCATTTTCTATCGGTTTCAG 59.364 41.667 0.00 0.00 0.00 3.02
1770 1979 3.489229 GCCATTTTCTATCGGTTTCAGCC 60.489 47.826 0.00 0.00 0.00 4.85
1804 2013 2.563702 GAACCCCGGATTTATACGCAA 58.436 47.619 0.73 0.00 31.29 4.85
1818 2027 9.746711 GATTTATACGCAATGCTATCTAGTTTG 57.253 33.333 2.94 0.00 0.00 2.93
1823 2032 3.243201 GCAATGCTATCTAGTTTGGGTGC 60.243 47.826 0.00 0.00 0.00 5.01
1824 2033 3.931907 ATGCTATCTAGTTTGGGTGCA 57.068 42.857 0.00 0.00 0.00 4.57
1826 2035 1.943340 GCTATCTAGTTTGGGTGCAGC 59.057 52.381 7.55 7.55 0.00 5.25
1836 2045 1.260538 TGGGTGCAGCTAGGTCTCAG 61.261 60.000 16.65 0.00 0.00 3.35
1898 2107 9.890629 ATATAACATATAAGAATGCGACATGGT 57.109 29.630 0.00 0.00 0.00 3.55
1899 2108 6.942532 AACATATAAGAATGCGACATGGTT 57.057 33.333 0.00 0.00 0.00 3.67
1900 2109 6.304356 ACATATAAGAATGCGACATGGTTG 57.696 37.500 0.00 0.00 0.00 3.77
1901 2110 6.054941 ACATATAAGAATGCGACATGGTTGA 58.945 36.000 0.00 0.00 0.00 3.18
1902 2111 4.882671 ATAAGAATGCGACATGGTTGAC 57.117 40.909 0.00 0.00 0.00 3.18
1903 2112 2.183478 AGAATGCGACATGGTTGACA 57.817 45.000 0.00 0.00 0.00 3.58
1904 2113 2.715046 AGAATGCGACATGGTTGACAT 58.285 42.857 0.00 0.00 41.57 3.06
1905 2114 2.679837 AGAATGCGACATGGTTGACATC 59.320 45.455 0.00 0.00 37.84 3.06
1906 2115 2.408271 ATGCGACATGGTTGACATCT 57.592 45.000 0.00 0.00 37.84 2.90
1907 2116 1.441738 TGCGACATGGTTGACATCTG 58.558 50.000 0.00 0.00 37.84 2.90
1908 2117 0.729116 GCGACATGGTTGACATCTGG 59.271 55.000 0.00 0.00 37.84 3.86
1909 2118 1.372582 CGACATGGTTGACATCTGGG 58.627 55.000 0.00 0.00 37.84 4.45
1927 2208 1.071542 GGGGTTTTGGTCCCACAAATG 59.928 52.381 3.37 0.00 46.26 2.32
1931 2212 2.432510 GTTTTGGTCCCACAAATGGTCA 59.567 45.455 0.00 0.00 45.66 4.02
1933 2214 0.112218 TGGTCCCACAAATGGTCAGG 59.888 55.000 0.00 0.00 45.66 3.86
1952 2233 3.739300 CAGGTCACCAGTGTAAACTAACG 59.261 47.826 0.00 0.00 0.00 3.18
1953 2234 3.062042 GGTCACCAGTGTAAACTAACGG 58.938 50.000 0.00 0.00 0.00 4.44
1982 2263 1.402613 ACACTTACGGGTTGTTTGTGC 59.597 47.619 0.00 0.00 36.60 4.57
1985 2266 2.061182 TTACGGGTTGTTTGTGCGCC 62.061 55.000 4.18 0.00 0.00 6.53
1987 2268 4.639171 GGGTTGTTTGTGCGCCGG 62.639 66.667 4.18 0.00 0.00 6.13
1997 2278 1.870901 GTGCGCCGGAGTAGTTACG 60.871 63.158 5.05 0.00 0.00 3.18
2040 2321 4.077184 TTAGTGGTGGGCGCCTCG 62.077 66.667 28.56 0.00 0.00 4.63
2050 2331 2.437716 GCGCCTCGGGGAAATTCA 60.438 61.111 4.80 0.00 33.58 2.57
2051 2332 1.823899 GCGCCTCGGGGAAATTCAT 60.824 57.895 4.80 0.00 33.58 2.57
2052 2333 2.024918 CGCCTCGGGGAAATTCATG 58.975 57.895 4.80 0.00 33.58 3.07
2053 2334 1.447317 CGCCTCGGGGAAATTCATGG 61.447 60.000 4.80 0.00 33.58 3.66
2054 2335 0.395724 GCCTCGGGGAAATTCATGGT 60.396 55.000 4.80 0.00 33.58 3.55
2055 2336 1.392589 CCTCGGGGAAATTCATGGTG 58.607 55.000 0.00 0.00 33.58 4.17
2056 2337 1.392589 CTCGGGGAAATTCATGGTGG 58.607 55.000 0.00 0.00 0.00 4.61
2057 2338 0.033601 TCGGGGAAATTCATGGTGGG 60.034 55.000 0.00 0.00 0.00 4.61
2058 2339 0.033601 CGGGGAAATTCATGGTGGGA 60.034 55.000 0.00 0.00 0.00 4.37
2059 2340 1.780503 GGGGAAATTCATGGTGGGAG 58.219 55.000 0.00 0.00 0.00 4.30
2096 2688 2.125952 ACGTTAGCCCGTTACCGC 60.126 61.111 0.00 0.00 37.96 5.68
2144 2736 2.363795 TTCCTGTCCGGCGGAGAT 60.364 61.111 31.98 0.00 29.39 2.75
2246 2838 0.255604 TGGGCATGACGATGGTGAAT 59.744 50.000 0.00 0.00 0.00 2.57
2294 2893 2.034687 GGCACCACTGACAGGCAT 59.965 61.111 7.51 0.00 0.00 4.40
2357 2956 0.605319 AAGAAGCCGAATTCCACGCA 60.605 50.000 0.00 0.00 0.00 5.24
2481 3093 3.282021 GGTGGATTAATGAGCTGCTCAA 58.718 45.455 33.31 19.44 44.04 3.02
2537 3199 4.321008 GCTTAACAAGTAGAAAACCCTGCC 60.321 45.833 0.00 0.00 0.00 4.85
2559 3221 4.119136 CCGGCTTTGTTCATTTGAAACTT 58.881 39.130 0.00 0.00 35.58 2.66
2606 3268 0.611200 ACTACAATGTGCTACGGCCA 59.389 50.000 2.24 0.00 37.74 5.36
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 7.433131 GCGATTCATTTTGAGAATGAGCAATAA 59.567 33.333 0.00 0.00 37.86 1.40
1 2 6.914215 GCGATTCATTTTGAGAATGAGCAATA 59.086 34.615 0.00 0.00 37.86 1.90
2 3 5.747197 GCGATTCATTTTGAGAATGAGCAAT 59.253 36.000 0.00 0.00 37.86 3.56
3 4 5.097529 GCGATTCATTTTGAGAATGAGCAA 58.902 37.500 0.00 0.00 37.86 3.91
4 5 4.397103 AGCGATTCATTTTGAGAATGAGCA 59.603 37.500 9.82 0.00 37.79 4.26
5 6 4.918037 AGCGATTCATTTTGAGAATGAGC 58.082 39.130 0.00 0.34 37.86 4.26
6 7 6.549061 TGAAGCGATTCATTTTGAGAATGAG 58.451 36.000 12.91 0.00 37.86 2.90
7 8 6.499234 TGAAGCGATTCATTTTGAGAATGA 57.501 33.333 12.91 0.00 35.93 2.57
8 9 7.751047 ATTGAAGCGATTCATTTTGAGAATG 57.249 32.000 17.94 0.00 35.93 2.67
9 10 8.680903 ACTATTGAAGCGATTCATTTTGAGAAT 58.319 29.630 17.94 7.51 38.35 2.40
10 11 7.964559 CACTATTGAAGCGATTCATTTTGAGAA 59.035 33.333 17.94 0.00 0.00 2.87
11 12 7.119699 ACACTATTGAAGCGATTCATTTTGAGA 59.880 33.333 17.94 0.00 0.00 3.27
12 13 7.246311 ACACTATTGAAGCGATTCATTTTGAG 58.754 34.615 17.94 10.38 0.00 3.02
13 14 7.144722 ACACTATTGAAGCGATTCATTTTGA 57.855 32.000 17.94 1.59 0.00 2.69
14 15 7.801547 AACACTATTGAAGCGATTCATTTTG 57.198 32.000 17.94 15.15 0.00 2.44
45 46 8.918658 CGTTTTGTTAATGCACTAGTTAGTCTA 58.081 33.333 0.00 0.00 33.46 2.59
46 47 7.654520 TCGTTTTGTTAATGCACTAGTTAGTCT 59.345 33.333 0.00 0.00 33.46 3.24
47 48 7.790000 TCGTTTTGTTAATGCACTAGTTAGTC 58.210 34.615 0.00 0.00 33.46 2.59
48 49 7.654520 TCTCGTTTTGTTAATGCACTAGTTAGT 59.345 33.333 0.00 0.00 36.90 2.24
49 50 8.014322 TCTCGTTTTGTTAATGCACTAGTTAG 57.986 34.615 0.00 0.00 0.00 2.34
50 51 7.949903 TCTCGTTTTGTTAATGCACTAGTTA 57.050 32.000 0.00 0.00 0.00 2.24
51 52 6.854496 TCTCGTTTTGTTAATGCACTAGTT 57.146 33.333 0.00 0.00 0.00 2.24
52 53 6.620733 GCATCTCGTTTTGTTAATGCACTAGT 60.621 38.462 0.00 0.00 39.36 2.57
53 54 5.734498 GCATCTCGTTTTGTTAATGCACTAG 59.266 40.000 0.00 0.00 39.36 2.57
54 55 5.411361 AGCATCTCGTTTTGTTAATGCACTA 59.589 36.000 7.75 0.00 41.42 2.74
55 56 4.216257 AGCATCTCGTTTTGTTAATGCACT 59.784 37.500 7.75 0.00 41.42 4.40
56 57 4.475944 AGCATCTCGTTTTGTTAATGCAC 58.524 39.130 7.75 0.00 41.42 4.57
57 58 4.764679 AGCATCTCGTTTTGTTAATGCA 57.235 36.364 7.75 0.00 41.42 3.96
58 59 6.452244 AAAAGCATCTCGTTTTGTTAATGC 57.548 33.333 0.00 0.00 39.74 3.56
59 60 9.941991 CATTAAAAGCATCTCGTTTTGTTAATG 57.058 29.630 0.00 0.00 29.71 1.90
60 61 9.906660 TCATTAAAAGCATCTCGTTTTGTTAAT 57.093 25.926 0.00 0.00 0.00 1.40
61 62 9.393249 CTCATTAAAAGCATCTCGTTTTGTTAA 57.607 29.630 0.00 0.00 0.00 2.01
62 63 8.779303 TCTCATTAAAAGCATCTCGTTTTGTTA 58.221 29.630 0.00 0.00 0.00 2.41
63 64 7.648142 TCTCATTAAAAGCATCTCGTTTTGTT 58.352 30.769 0.00 0.00 0.00 2.83
64 65 7.202016 TCTCATTAAAAGCATCTCGTTTTGT 57.798 32.000 0.00 0.00 0.00 2.83
65 66 6.250104 GCTCTCATTAAAAGCATCTCGTTTTG 59.750 38.462 0.00 0.00 36.06 2.44
66 67 6.072508 TGCTCTCATTAAAAGCATCTCGTTTT 60.073 34.615 0.00 0.00 40.91 2.43
67 68 5.412594 TGCTCTCATTAAAAGCATCTCGTTT 59.587 36.000 0.00 0.00 40.91 3.60
68 69 4.937620 TGCTCTCATTAAAAGCATCTCGTT 59.062 37.500 0.00 0.00 40.91 3.85
72 73 4.880696 GGAGTGCTCTCATTAAAAGCATCT 59.119 41.667 17.04 0.00 46.73 2.90
97 98 2.033424 AGTGTTCTTTTTGCTCGCCTTC 59.967 45.455 0.00 0.00 0.00 3.46
102 103 6.255215 TCTTTGTTAGTGTTCTTTTTGCTCG 58.745 36.000 0.00 0.00 0.00 5.03
147 165 8.795513 CATTTGCCATTATTGTATCATCCACTA 58.204 33.333 0.00 0.00 0.00 2.74
171 189 1.064003 TGGCCACTCACACCTAACAT 58.936 50.000 0.00 0.00 0.00 2.71
207 225 0.668535 TCAGTGACGAGGTGTGAGTG 59.331 55.000 0.00 0.00 36.57 3.51
211 229 1.373497 GGCTCAGTGACGAGGTGTG 60.373 63.158 0.00 0.00 33.36 3.82
212 230 1.528292 GAGGCTCAGTGACGAGGTGT 61.528 60.000 10.25 0.00 33.36 4.16
217 235 1.244697 GGTCAGAGGCTCAGTGACGA 61.245 60.000 22.90 6.71 41.33 4.20
218 236 1.214062 GGTCAGAGGCTCAGTGACG 59.786 63.158 22.90 4.80 41.33 4.35
225 243 3.135530 ACCATATGAAAGGTCAGAGGCTC 59.864 47.826 6.34 6.34 37.14 4.70
226 244 3.118112 CACCATATGAAAGGTCAGAGGCT 60.118 47.826 3.65 0.00 37.14 4.58
229 247 3.455910 TCCCACCATATGAAAGGTCAGAG 59.544 47.826 3.65 0.00 37.14 3.35
231 249 3.931907 TCCCACCATATGAAAGGTCAG 57.068 47.619 3.65 0.00 37.14 3.51
232 250 3.308832 GGTTCCCACCATATGAAAGGTCA 60.309 47.826 3.65 0.00 43.61 4.02
233 251 3.288092 GGTTCCCACCATATGAAAGGTC 58.712 50.000 3.65 0.63 43.61 3.85
234 252 3.382083 GGTTCCCACCATATGAAAGGT 57.618 47.619 3.65 0.00 43.61 3.50
252 270 4.082245 GGGTGATTGATCATTCGTTTTGGT 60.082 41.667 11.83 0.00 39.30 3.67
253 271 4.423732 GGGTGATTGATCATTCGTTTTGG 58.576 43.478 11.83 0.00 39.30 3.28
254 272 4.158394 AGGGGTGATTGATCATTCGTTTTG 59.842 41.667 11.83 0.00 39.30 2.44
255 273 4.344104 AGGGGTGATTGATCATTCGTTTT 58.656 39.130 11.83 0.00 39.30 2.43
256 274 3.947834 GAGGGGTGATTGATCATTCGTTT 59.052 43.478 11.83 0.00 39.30 3.60
257 275 3.200825 AGAGGGGTGATTGATCATTCGTT 59.799 43.478 11.83 0.00 39.30 3.85
258 276 2.774234 AGAGGGGTGATTGATCATTCGT 59.226 45.455 11.83 0.00 39.30 3.85
259 277 3.070734 AGAGAGGGGTGATTGATCATTCG 59.929 47.826 11.83 0.00 39.30 3.34
260 278 4.703379 AGAGAGGGGTGATTGATCATTC 57.297 45.455 10.10 10.10 39.30 2.67
261 279 5.193325 AGAAAGAGAGGGGTGATTGATCATT 59.807 40.000 0.00 0.00 39.30 2.57
262 280 4.725810 AGAAAGAGAGGGGTGATTGATCAT 59.274 41.667 0.00 0.00 39.30 2.45
263 281 4.107072 AGAAAGAGAGGGGTGATTGATCA 58.893 43.478 0.00 0.00 0.00 2.92
264 282 4.163078 TGAGAAAGAGAGGGGTGATTGATC 59.837 45.833 0.00 0.00 0.00 2.92
265 283 4.080638 GTGAGAAAGAGAGGGGTGATTGAT 60.081 45.833 0.00 0.00 0.00 2.57
266 284 3.261897 GTGAGAAAGAGAGGGGTGATTGA 59.738 47.826 0.00 0.00 0.00 2.57
267 285 3.262915 AGTGAGAAAGAGAGGGGTGATTG 59.737 47.826 0.00 0.00 0.00 2.67
268 286 3.517500 GAGTGAGAAAGAGAGGGGTGATT 59.482 47.826 0.00 0.00 0.00 2.57
269 287 3.103742 GAGTGAGAAAGAGAGGGGTGAT 58.896 50.000 0.00 0.00 0.00 3.06
270 288 2.530701 GAGTGAGAAAGAGAGGGGTGA 58.469 52.381 0.00 0.00 0.00 4.02
271 289 1.552792 GGAGTGAGAAAGAGAGGGGTG 59.447 57.143 0.00 0.00 0.00 4.61
272 290 1.435168 AGGAGTGAGAAAGAGAGGGGT 59.565 52.381 0.00 0.00 0.00 4.95
273 291 2.246091 AGGAGTGAGAAAGAGAGGGG 57.754 55.000 0.00 0.00 0.00 4.79
274 292 6.133356 ACTTATAGGAGTGAGAAAGAGAGGG 58.867 44.000 0.00 0.00 0.00 4.30
277 295 8.503573 TGGATACTTATAGGAGTGAGAAAGAGA 58.496 37.037 0.00 0.00 37.61 3.10
282 300 8.475639 GTGTTTGGATACTTATAGGAGTGAGAA 58.524 37.037 0.00 0.00 37.61 2.87
332 352 2.564504 TCCATTGATCGGCTGGAGATAG 59.435 50.000 6.62 0.00 34.17 2.08
335 355 1.345741 GATCCATTGATCGGCTGGAGA 59.654 52.381 13.95 0.00 42.10 3.71
372 392 1.801913 CGGTTCGAGAAGGAGCACG 60.802 63.158 0.00 0.00 0.00 5.34
374 394 2.261671 GCGGTTCGAGAAGGAGCA 59.738 61.111 0.00 0.00 0.00 4.26
437 582 1.068055 GTTGAGGTTCTCGTTCCGCTA 60.068 52.381 0.00 0.00 32.35 4.26
692 843 2.672996 GTGCACGTGGGCCTCATT 60.673 61.111 18.88 0.00 0.00 2.57
721 872 2.741759 TCTGAAAGCGCTGTATGACA 57.258 45.000 12.58 0.00 0.00 3.58
850 1004 0.338467 TCGATGGGAGGGAGGAAAGA 59.662 55.000 0.00 0.00 0.00 2.52
1093 1263 1.677217 GCGGAACTTCTCCTGCATCTT 60.677 52.381 0.00 0.00 42.85 2.40
1108 1278 4.047059 GTCGACCTCACCGCGGAA 62.047 66.667 35.90 18.67 0.00 4.30
1191 1385 3.673484 AACTGTGGGTGCATGCGC 61.673 61.111 23.05 23.05 39.24 6.09
1287 1490 5.333035 CGCAGAGAAATTCACGTAAAAGTCA 60.333 40.000 0.00 0.00 0.00 3.41
1334 1538 1.673033 CGTCGGCATCCTTCCATATCC 60.673 57.143 0.00 0.00 0.00 2.59
1348 1552 4.373116 TGGCAGGAACTCGTCGGC 62.373 66.667 0.00 0.00 34.60 5.54
1625 1833 4.331968 TCTTTAGATGGATTTGGTGCGTT 58.668 39.130 0.00 0.00 0.00 4.84
1714 1923 3.764810 CTGCGGCTCTAGGCTCGTG 62.765 68.421 0.00 0.00 41.46 4.35
1715 1924 3.522731 CTGCGGCTCTAGGCTCGT 61.523 66.667 0.00 0.00 41.46 4.18
1731 1940 1.701847 TGGCAGAAGGAGAAGCTTTCT 59.298 47.619 0.00 0.00 42.99 2.52
1742 1951 3.545703 ACCGATAGAAAATGGCAGAAGG 58.454 45.455 0.00 0.00 39.76 3.46
1781 1990 1.695788 CGTATAAATCCGGGGTTCCCT 59.304 52.381 0.00 0.00 42.67 4.20
1791 2000 8.480643 AACTAGATAGCATTGCGTATAAATCC 57.519 34.615 2.38 0.00 0.00 3.01
1795 2004 6.649141 CCCAAACTAGATAGCATTGCGTATAA 59.351 38.462 2.38 0.00 0.00 0.98
1801 2010 3.243201 GCACCCAAACTAGATAGCATTGC 60.243 47.826 0.00 0.00 0.00 3.56
1804 2013 3.813443 CTGCACCCAAACTAGATAGCAT 58.187 45.455 0.00 0.00 0.00 3.79
1818 2027 1.261238 ACTGAGACCTAGCTGCACCC 61.261 60.000 1.02 0.00 0.00 4.61
1823 2032 4.702612 TCTTAGTCAACTGAGACCTAGCTG 59.297 45.833 0.00 0.00 39.34 4.24
1824 2033 4.924625 TCTTAGTCAACTGAGACCTAGCT 58.075 43.478 0.84 0.00 39.34 3.32
1888 2097 1.441738 CAGATGTCAACCATGTCGCA 58.558 50.000 0.00 0.00 32.56 5.10
1890 2099 1.372582 CCCAGATGTCAACCATGTCG 58.627 55.000 0.00 0.00 32.56 4.35
1891 2100 1.004745 ACCCCAGATGTCAACCATGTC 59.995 52.381 0.00 0.00 32.56 3.06
1893 2102 2.220653 AACCCCAGATGTCAACCATG 57.779 50.000 0.00 0.00 32.56 3.66
1895 2104 2.315176 CAAAACCCCAGATGTCAACCA 58.685 47.619 0.00 0.00 0.00 3.67
1897 2106 2.296190 GACCAAAACCCCAGATGTCAAC 59.704 50.000 0.00 0.00 0.00 3.18
1898 2107 2.593026 GACCAAAACCCCAGATGTCAA 58.407 47.619 0.00 0.00 0.00 3.18
1899 2108 1.203001 GGACCAAAACCCCAGATGTCA 60.203 52.381 0.00 0.00 0.00 3.58
1900 2109 1.545841 GGACCAAAACCCCAGATGTC 58.454 55.000 0.00 0.00 0.00 3.06
1901 2110 0.114364 GGGACCAAAACCCCAGATGT 59.886 55.000 0.00 0.00 42.24 3.06
1902 2111 2.976099 GGGACCAAAACCCCAGATG 58.024 57.895 0.00 0.00 42.24 2.90
1907 2116 1.071542 CATTTGTGGGACCAAAACCCC 59.928 52.381 0.00 0.00 46.21 4.95
1908 2117 1.071542 CCATTTGTGGGACCAAAACCC 59.928 52.381 0.00 0.00 46.87 4.11
1909 2118 1.765904 ACCATTTGTGGGACCAAAACC 59.234 47.619 0.00 0.00 37.81 3.27
1927 2208 2.104281 AGTTTACACTGGTGACCTGACC 59.896 50.000 15.78 0.00 36.43 4.02
1931 2212 3.243975 CCGTTAGTTTACACTGGTGACCT 60.244 47.826 2.11 0.84 34.06 3.85
1933 2214 3.981211 TCCGTTAGTTTACACTGGTGAC 58.019 45.455 7.78 0.00 34.06 3.67
1952 2233 2.167900 ACCCGTAAGTGTAGCATTCTCC 59.832 50.000 0.00 0.00 0.00 3.71
1953 2234 3.521947 ACCCGTAAGTGTAGCATTCTC 57.478 47.619 0.00 0.00 0.00 2.87
1982 2263 2.410469 CCCGTAACTACTCCGGCG 59.590 66.667 0.00 0.00 40.38 6.46
1985 2266 0.813184 TTCAGCCCGTAACTACTCCG 59.187 55.000 0.00 0.00 0.00 4.63
1987 2268 3.858247 ACAATTCAGCCCGTAACTACTC 58.142 45.455 0.00 0.00 0.00 2.59
1997 2278 2.354821 CCGTAGCTTTACAATTCAGCCC 59.645 50.000 0.00 0.00 33.73 5.19
2040 2321 1.287739 TCTCCCACCATGAATTTCCCC 59.712 52.381 0.00 0.00 0.00 4.81
2050 2331 4.263068 CGCCTTATTAATCTCTCCCACCAT 60.263 45.833 0.00 0.00 0.00 3.55
2051 2332 3.071023 CGCCTTATTAATCTCTCCCACCA 59.929 47.826 0.00 0.00 0.00 4.17
2052 2333 3.665190 CGCCTTATTAATCTCTCCCACC 58.335 50.000 0.00 0.00 0.00 4.61
2053 2334 3.067833 GCGCCTTATTAATCTCTCCCAC 58.932 50.000 0.00 0.00 0.00 4.61
2054 2335 2.703536 TGCGCCTTATTAATCTCTCCCA 59.296 45.455 4.18 0.00 0.00 4.37
2055 2336 3.006967 TCTGCGCCTTATTAATCTCTCCC 59.993 47.826 4.18 0.00 0.00 4.30
2056 2337 3.991121 GTCTGCGCCTTATTAATCTCTCC 59.009 47.826 4.18 0.00 0.00 3.71
2057 2338 4.446051 GTGTCTGCGCCTTATTAATCTCTC 59.554 45.833 4.18 0.00 0.00 3.20
2058 2339 4.372656 GTGTCTGCGCCTTATTAATCTCT 58.627 43.478 4.18 0.00 0.00 3.10
2059 2340 3.182572 CGTGTCTGCGCCTTATTAATCTC 59.817 47.826 4.18 0.00 0.00 2.75
2096 2688 2.028112 TCAGAACTCGTTGGGATCCAAG 60.028 50.000 15.23 5.04 44.82 3.61
2139 2731 2.851071 CGACGCTCTCCCCATCTCC 61.851 68.421 0.00 0.00 0.00 3.71
2140 2732 2.725008 CGACGCTCTCCCCATCTC 59.275 66.667 0.00 0.00 0.00 2.75
2151 2743 3.665675 CTAGCAAAGGGCCGACGCT 62.666 63.158 18.31 18.31 46.50 5.07
2167 2759 1.008327 TCCTGATCTGCTTGGGTCCTA 59.992 52.381 0.00 0.00 0.00 2.94
2294 2893 1.891919 GTGAGGTCAACAGCGGCAA 60.892 57.895 1.45 0.00 0.00 4.52
2347 2946 0.516877 CGTGTGACATGCGTGGAATT 59.483 50.000 11.36 0.00 0.00 2.17
2357 2956 0.812014 TTTGGTGCGTCGTGTGACAT 60.812 50.000 0.00 0.00 45.80 3.06
2537 3199 3.716601 AGTTTCAAATGAACAAAGCCGG 58.283 40.909 0.00 0.00 33.13 6.13
2559 3221 2.333926 CGAGCATTCACGACCTTAACA 58.666 47.619 0.00 0.00 0.00 2.41


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

AutoCloner maintained by Alex Coulton.