Multiple sequence alignment - TraesCS3B01G500400

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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 TraesCS3B01G500400 chr3B 100.000 3880 0 0 1 3880 744600262 744596383 0.000000e+00 7166.0
1 TraesCS3B01G500400 chr3B 94.426 2135 68 19 789 2897 746846559 746848668 0.000000e+00 3236.0
2 TraesCS3B01G500400 chr3B 98.837 602 7 0 2894 3495 746848779 746849380 0.000000e+00 1074.0
3 TraesCS3B01G500400 chr3B 82.288 1259 170 34 1109 2331 745540226 745541467 0.000000e+00 1040.0
4 TraesCS3B01G500400 chr3B 86.017 801 106 6 1116 1912 744512807 744512009 0.000000e+00 854.0
5 TraesCS3B01G500400 chr3B 85.609 813 107 10 1109 1915 745450361 745449553 0.000000e+00 845.0
6 TraesCS3B01G500400 chr3B 95.396 391 14 4 3493 3880 746849629 746850018 1.530000e-173 619.0
7 TraesCS3B01G500400 chr3B 78.807 637 93 23 2144 2754 745202226 745201606 1.310000e-104 390.0
8 TraesCS3B01G500400 chr3B 78.425 635 99 23 2144 2758 746286246 746286862 2.830000e-101 379.0
9 TraesCS3B01G500400 chr3B 78.370 638 94 32 2144 2758 744729772 744730388 1.320000e-99 374.0
10 TraesCS3B01G500400 chr3B 88.158 304 34 2 3 304 399651156 399650853 1.020000e-95 361.0
11 TraesCS3B01G500400 chr3B 84.314 357 50 6 2403 2754 747095217 747095572 1.030000e-90 344.0
12 TraesCS3B01G500400 chr3B 84.615 325 42 3 2399 2718 744216762 744216441 2.250000e-82 316.0
13 TraesCS3B01G500400 chr3B 84.878 205 16 6 2112 2302 744418698 744418495 3.960000e-45 193.0
14 TraesCS3B01G500400 chr3B 84.390 205 17 6 2112 2302 747494202 747494405 1.840000e-43 187.0
15 TraesCS3B01G500400 chr3B 89.855 138 11 2 396 530 104330735 104330872 1.430000e-39 174.0
16 TraesCS3B01G500400 chr3B 92.727 110 7 1 681 789 104330880 104330989 1.440000e-34 158.0
17 TraesCS3B01G500400 chr3B 80.676 207 21 10 3214 3416 744730765 744730956 4.040000e-30 143.0
18 TraesCS3B01G500400 chr3B 77.073 205 33 11 3208 3408 744593130 744593324 5.300000e-19 106.0
19 TraesCS3B01G500400 chr3B 77.073 205 33 11 3208 3408 746853833 746853639 5.300000e-19 106.0
20 TraesCS3B01G500400 chr3B 82.609 92 10 4 3217 3304 747332599 747332688 4.160000e-10 76.8
21 TraesCS3B01G500400 chr3B 100.000 35 0 0 3390 3424 744596823 744596789 9.000000e-07 65.8
22 TraesCS3B01G500400 chr3B 100.000 35 0 0 3440 3474 744596873 744596839 9.000000e-07 65.8
23 TraesCS3B01G500400 chr3B 97.143 35 1 0 3390 3424 746849325 746849359 4.190000e-05 60.2
24 TraesCS3B01G500400 chr3B 100.000 28 0 0 368 395 744599852 744599825 7.000000e-03 52.8
25 TraesCS3B01G500400 chr3B 100.000 28 0 0 411 438 744599895 744599868 7.000000e-03 52.8
26 TraesCS3B01G500400 chr3A 88.626 2743 179 51 801 3491 696478224 696475563 0.000000e+00 3214.0
27 TraesCS3B01G500400 chr3A 86.946 812 100 6 1109 1916 696637319 696638128 0.000000e+00 907.0
28 TraesCS3B01G500400 chr3A 86.514 786 101 5 1135 1917 696290089 696289306 0.000000e+00 859.0
29 TraesCS3B01G500400 chr3A 92.366 393 23 5 3493 3880 696475303 696474913 1.580000e-153 553.0
30 TraesCS3B01G500400 chr3A 79.562 685 97 14 2111 2753 696269654 696268971 2.130000e-122 449.0
31 TraesCS3B01G500400 chr3A 83.420 193 26 5 2144 2331 696599319 696599128 1.430000e-39 174.0
32 TraesCS3B01G500400 chr2B 95.807 787 13 4 2 787 601432744 601433511 0.000000e+00 1253.0
33 TraesCS3B01G500400 chr2B 90.580 138 10 2 396 530 794931045 794931182 3.080000e-41 180.0
34 TraesCS3B01G500400 chr2B 90.909 110 9 1 681 789 794931190 794931299 3.120000e-31 147.0
35 TraesCS3B01G500400 chr2B 94.000 50 2 1 325 373 142545846 142545895 1.500000e-09 75.0
36 TraesCS3B01G500400 chr2B 100.000 28 0 0 411 438 601433091 601433118 7.000000e-03 52.8
37 TraesCS3B01G500400 chr3D 87.500 800 96 4 1116 1912 560269488 560268690 0.000000e+00 920.0
38 TraesCS3B01G500400 chr3D 87.069 812 101 4 1109 1917 560640212 560641022 0.000000e+00 915.0
39 TraesCS3B01G500400 chr3D 86.823 812 101 6 1109 1916 560826977 560827786 0.000000e+00 902.0
40 TraesCS3B01G500400 chr3D 86.398 794 106 2 1126 1917 560198840 560198047 0.000000e+00 867.0
41 TraesCS3B01G500400 chr3D 80.288 624 90 19 2144 2756 560784582 560783981 1.280000e-119 440.0
42 TraesCS3B01G500400 chr3D 78.752 673 86 26 2112 2758 560641261 560641902 7.810000e-107 398.0
43 TraesCS3B01G500400 chr3D 82.908 392 51 7 2383 2758 560553062 560553453 4.800000e-89 339.0
44 TraesCS3B01G500400 chr3D 82.216 388 61 6 2381 2761 560703105 560702719 1.040000e-85 327.0
45 TraesCS3B01G500400 chr3D 86.926 283 33 2 2435 2713 560111649 560111367 8.090000e-82 315.0
46 TraesCS3B01G500400 chr3D 85.366 164 19 3 2144 2302 560285606 560285443 8.620000e-37 165.0
47 TraesCS3B01G500400 chr3D 84.756 164 20 3 2144 2302 560233918 560233755 4.010000e-35 159.0
48 TraesCS3B01G500400 chr3D 81.564 179 19 8 3214 3389 560642276 560642443 6.760000e-28 135.0
49 TraesCS3B01G500400 chr3D 78.261 207 25 13 3214 3419 560754899 560755086 8.810000e-22 115.0
50 TraesCS3B01G500400 chr3D 80.531 113 7 10 3196 3299 560267349 560267243 5.380000e-09 73.1
51 TraesCS3B01G500400 chr3D 85.484 62 6 3 3354 3415 560333912 560333970 1.160000e-05 62.1
52 TraesCS3B01G500400 chrUn 88.636 308 28 3 3 305 11619620 11619315 6.120000e-98 368.0
53 TraesCS3B01G500400 chr2D 88.562 306 31 3 3 305 640367417 640367721 6.120000e-98 368.0
54 TraesCS3B01G500400 chr2A 88.667 300 30 4 2 300 469791608 469791904 2.850000e-96 363.0
55 TraesCS3B01G500400 chr2A 90.741 54 3 1 314 365 771514889 771514836 1.930000e-08 71.3
56 TraesCS3B01G500400 chr5D 88.158 304 32 3 4 304 397021295 397021597 3.690000e-95 359.0
57 TraesCS3B01G500400 chr5D 92.000 50 4 0 321 370 381563829 381563878 1.930000e-08 71.3
58 TraesCS3B01G500400 chr5A 88.294 299 31 3 3 298 184259316 184259613 4.770000e-94 355.0
59 TraesCS3B01G500400 chr6B 84.916 358 41 9 3 349 49952656 49953011 2.220000e-92 350.0
60 TraesCS3B01G500400 chr4D 87.582 306 33 3 3 304 509505670 509505366 2.220000e-92 350.0
61 TraesCS3B01G500400 chr5B 82.310 407 23 15 409 787 543286285 543286670 1.350000e-79 307.0
62 TraesCS3B01G500400 chr5B 95.833 48 2 0 319 366 462886722 462886769 1.160000e-10 78.7
63 TraesCS3B01G500400 chr5B 91.071 56 4 1 315 370 561068778 561068832 1.500000e-09 75.0
64 TraesCS3B01G500400 chr5B 96.774 31 1 0 365 395 543286284 543286314 7.000000e-03 52.8
65 TraesCS3B01G500400 chr4B 86.842 266 26 5 396 655 95455492 95455230 4.900000e-74 289.0
66 TraesCS3B01G500400 chr4B 84.810 158 12 5 642 787 95448150 95447993 8.690000e-32 148.0
67 TraesCS3B01G500400 chr4B 89.655 58 4 2 318 373 568720134 568720191 5.380000e-09 73.1
68 TraesCS3B01G500400 chr7B 92.308 52 3 1 323 373 14062809 14062860 5.380000e-09 73.1
69 TraesCS3B01G500400 chr1A 87.097 62 7 1 309 370 554524423 554524483 6.960000e-08 69.4


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 TraesCS3B01G500400 chr3B 744596383 744600262 3879 True 1480.640000 7166 100.000000 1 3880 5 chr3B.!!$R8 3879
1 TraesCS3B01G500400 chr3B 746846559 746850018 3459 False 1247.300000 3236 96.450500 789 3880 4 chr3B.!!$F9 3091
2 TraesCS3B01G500400 chr3B 745540226 745541467 1241 False 1040.000000 1040 82.288000 1109 2331 1 chr3B.!!$F2 1222
3 TraesCS3B01G500400 chr3B 744512009 744512807 798 True 854.000000 854 86.017000 1116 1912 1 chr3B.!!$R4 796
4 TraesCS3B01G500400 chr3B 745449553 745450361 808 True 845.000000 845 85.609000 1109 1915 1 chr3B.!!$R6 806
5 TraesCS3B01G500400 chr3B 745201606 745202226 620 True 390.000000 390 78.807000 2144 2754 1 chr3B.!!$R5 610
6 TraesCS3B01G500400 chr3B 746286246 746286862 616 False 379.000000 379 78.425000 2144 2758 1 chr3B.!!$F3 614
7 TraesCS3B01G500400 chr3B 744729772 744730956 1184 False 258.500000 374 79.523000 2144 3416 2 chr3B.!!$F8 1272
8 TraesCS3B01G500400 chr3A 696474913 696478224 3311 True 1883.500000 3214 90.496000 801 3880 2 chr3A.!!$R4 3079
9 TraesCS3B01G500400 chr3A 696637319 696638128 809 False 907.000000 907 86.946000 1109 1916 1 chr3A.!!$F1 807
10 TraesCS3B01G500400 chr3A 696289306 696290089 783 True 859.000000 859 86.514000 1135 1917 1 chr3A.!!$R2 782
11 TraesCS3B01G500400 chr3A 696268971 696269654 683 True 449.000000 449 79.562000 2111 2753 1 chr3A.!!$R1 642
12 TraesCS3B01G500400 chr2B 601432744 601433511 767 False 652.900000 1253 97.903500 2 787 2 chr2B.!!$F2 785
13 TraesCS3B01G500400 chr3D 560826977 560827786 809 False 902.000000 902 86.823000 1109 1916 1 chr3D.!!$F4 807
14 TraesCS3B01G500400 chr3D 560198047 560198840 793 True 867.000000 867 86.398000 1126 1917 1 chr3D.!!$R2 791
15 TraesCS3B01G500400 chr3D 560267243 560269488 2245 True 496.550000 920 84.015500 1116 3299 2 chr3D.!!$R7 2183
16 TraesCS3B01G500400 chr3D 560640212 560642443 2231 False 482.666667 915 82.461667 1109 3389 3 chr3D.!!$F5 2280
17 TraesCS3B01G500400 chr3D 560783981 560784582 601 True 440.000000 440 80.288000 2144 2756 1 chr3D.!!$R6 612

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
952 956 1.29478 CTCAGCCACTCCACTCCAC 59.705 63.158 0.0 0.0 0.00 4.02 F
1558 1577 0.76706 AGGGGGTCCAAGAACTCGTT 60.767 55.000 0.0 0.0 34.83 3.85 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1970 2034 0.107654 ATTCGCAGGTTAGGTGCTCC 60.108 55.000 0.0 0.0 38.88 4.70 R
3535 4282 1.850755 TCACCCCACCTTCCCTTCC 60.851 63.158 0.0 0.0 0.00 3.46 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 8.490291 GTCTAGATACATAATGTACACGTGTG 57.510 38.462 30.83 14.57 35.42 3.82
40 41 4.208355 CACGTGTGTAAATTTTCTGGTCG 58.792 43.478 7.58 0.00 0.00 4.79
124 125 7.294017 ACTGTTCATTTTCAAAGTCCATGAT 57.706 32.000 0.00 0.00 0.00 2.45
129 130 9.868389 GTTCATTTTCAAAGTCCATGATTTTTC 57.132 29.630 0.00 0.00 0.00 2.29
139 140 6.527423 AGTCCATGATTTTTCTTTTGTGCAT 58.473 32.000 0.00 0.00 0.00 3.96
203 204 9.845740 ATATACACTTTACATCCTTGCATACAA 57.154 29.630 0.00 0.00 0.00 2.41
348 349 6.115448 ACTCCCTCCGATCCAAAATATAAG 57.885 41.667 0.00 0.00 0.00 1.73
349 350 5.844516 ACTCCCTCCGATCCAAAATATAAGA 59.155 40.000 0.00 0.00 0.00 2.10
350 351 6.329197 ACTCCCTCCGATCCAAAATATAAGAA 59.671 38.462 0.00 0.00 0.00 2.52
351 352 6.531021 TCCCTCCGATCCAAAATATAAGAAC 58.469 40.000 0.00 0.00 0.00 3.01
352 353 5.408604 CCCTCCGATCCAAAATATAAGAACG 59.591 44.000 0.00 0.00 0.00 3.95
353 354 5.989777 CCTCCGATCCAAAATATAAGAACGT 59.010 40.000 0.00 0.00 0.00 3.99
354 355 6.482308 CCTCCGATCCAAAATATAAGAACGTT 59.518 38.462 0.00 0.00 0.00 3.99
355 356 7.012044 CCTCCGATCCAAAATATAAGAACGTTT 59.988 37.037 0.46 0.00 0.00 3.60
356 357 8.271312 TCCGATCCAAAATATAAGAACGTTTT 57.729 30.769 0.46 0.00 0.00 2.43
357 358 8.732531 TCCGATCCAAAATATAAGAACGTTTTT 58.267 29.630 9.22 9.22 0.00 1.94
492 493 6.903883 TTCTGGCTACTTACGATGATTTTC 57.096 37.500 0.00 0.00 0.00 2.29
781 782 8.556213 TGGCTTCTATTAGAAAATACAACGTT 57.444 30.769 7.51 0.00 33.19 3.99
782 783 8.662141 TGGCTTCTATTAGAAAATACAACGTTC 58.338 33.333 0.00 0.00 33.19 3.95
865 866 2.823758 GCCCAGCCCAGGAGATACC 61.824 68.421 0.00 0.00 39.35 2.73
908 909 3.933332 ACATCTTGCTAGCGAAACCTAAC 59.067 43.478 10.77 0.00 0.00 2.34
909 910 3.955650 TCTTGCTAGCGAAACCTAACT 57.044 42.857 10.77 0.00 0.00 2.24
919 923 2.599082 CGAAACCTAACTAAGCAGCTCG 59.401 50.000 0.00 0.00 0.00 5.03
952 956 1.294780 CTCAGCCACTCCACTCCAC 59.705 63.158 0.00 0.00 0.00 4.02
1558 1577 0.767060 AGGGGGTCCAAGAACTCGTT 60.767 55.000 0.00 0.00 34.83 3.85
1587 1606 2.427753 CCCTTGGCCGCTAGATCC 59.572 66.667 0.00 0.00 0.00 3.36
1660 1679 2.066393 CATCTGGAGGCTCCCGGAA 61.066 63.158 30.03 11.11 44.18 4.30
1922 1941 9.660180 GTCTGGAGAGACTTTTTCAGTATTATT 57.340 33.333 0.00 0.00 44.73 1.40
1947 2011 4.798387 CACTTACACCAACAAAAACTGCTC 59.202 41.667 0.00 0.00 0.00 4.26
1969 2033 3.308688 CCACTTCCAGGATCAAGATTGGT 60.309 47.826 0.00 0.00 32.51 3.67
1970 2034 3.693085 CACTTCCAGGATCAAGATTGGTG 59.307 47.826 0.00 0.00 32.51 4.17
1988 2052 1.295423 GGAGCACCTAACCTGCGAA 59.705 57.895 0.00 0.00 39.79 4.70
2023 2087 4.995594 CCAGGAGGGCAGGAATTC 57.004 61.111 0.00 0.00 0.00 2.17
2026 2090 1.063417 CCAGGAGGGCAGGAATTCAAT 60.063 52.381 7.93 0.00 0.00 2.57
2027 2091 2.625087 CCAGGAGGGCAGGAATTCAATT 60.625 50.000 7.93 0.00 0.00 2.32
2043 2129 0.378257 AATTTGGTATGCAGCTCGCG 59.622 50.000 0.00 0.00 46.97 5.87
2045 2131 1.358725 TTTGGTATGCAGCTCGCGAC 61.359 55.000 3.71 2.10 46.97 5.19
2086 2172 1.675483 TGTGTGCCTGTGCTGTTTAAG 59.325 47.619 0.00 0.00 38.71 1.85
2093 2179 4.994852 TGCCTGTGCTGTTTAAGTTAGTAG 59.005 41.667 0.00 0.00 38.71 2.57
2095 2181 6.161381 GCCTGTGCTGTTTAAGTTAGTAGTA 58.839 40.000 0.00 0.00 33.53 1.82
2096 2182 6.647895 GCCTGTGCTGTTTAAGTTAGTAGTAA 59.352 38.462 0.00 0.00 33.53 2.24
2097 2183 7.359849 GCCTGTGCTGTTTAAGTTAGTAGTAAC 60.360 40.741 11.84 11.84 35.57 2.50
2098 2184 7.117379 CCTGTGCTGTTTAAGTTAGTAGTAACC 59.883 40.741 15.43 2.56 39.65 2.85
2100 2186 8.206189 TGTGCTGTTTAAGTTAGTAGTAACCTT 58.794 33.333 15.43 11.67 39.65 3.50
2101 2187 8.493547 GTGCTGTTTAAGTTAGTAGTAACCTTG 58.506 37.037 15.43 3.02 39.65 3.61
2102 2188 7.658575 TGCTGTTTAAGTTAGTAGTAACCTTGG 59.341 37.037 15.43 3.46 39.65 3.61
2103 2189 7.118825 GCTGTTTAAGTTAGTAGTAACCTTGGG 59.881 40.741 15.43 3.87 39.65 4.12
2104 2190 8.033178 TGTTTAAGTTAGTAGTAACCTTGGGT 57.967 34.615 15.43 0.00 39.65 4.51
2105 2191 7.933033 TGTTTAAGTTAGTAGTAACCTTGGGTG 59.067 37.037 15.43 0.00 39.65 4.61
2106 2192 4.548451 AGTTAGTAGTAACCTTGGGTGC 57.452 45.455 15.43 0.00 39.65 5.01
2107 2193 3.905591 AGTTAGTAGTAACCTTGGGTGCA 59.094 43.478 15.43 0.00 39.65 4.57
2109 2195 5.722923 AGTTAGTAGTAACCTTGGGTGCATA 59.277 40.000 15.43 0.00 39.65 3.14
2110 2196 6.386050 AGTTAGTAGTAACCTTGGGTGCATAT 59.614 38.462 15.43 0.00 39.65 1.78
2111 2197 5.710409 AGTAGTAACCTTGGGTGCATATT 57.290 39.130 0.00 0.00 35.34 1.28
2112 2198 5.437060 AGTAGTAACCTTGGGTGCATATTG 58.563 41.667 0.00 0.00 35.34 1.90
2113 2199 3.023832 AGTAACCTTGGGTGCATATTGC 58.976 45.455 0.00 0.00 45.29 3.56
2142 2347 0.179051 CTGGGAGCAAGGAGAGCATC 60.179 60.000 0.00 0.00 0.00 3.91
2307 2544 7.066525 TGGTAATTTTGCAATACTAGTGCCTAC 59.933 37.037 5.39 1.31 41.49 3.18
2308 2545 7.282450 GGTAATTTTGCAATACTAGTGCCTACT 59.718 37.037 5.39 0.00 41.49 2.57
2309 2546 9.321562 GTAATTTTGCAATACTAGTGCCTACTA 57.678 33.333 5.39 0.00 41.49 1.82
2310 2547 7.787725 ATTTTGCAATACTAGTGCCTACTAC 57.212 36.000 5.39 0.00 41.49 2.73
2338 2586 7.581213 ATCTAGTATGGTCAGAAGTCAGAAG 57.419 40.000 0.00 0.00 0.00 2.85
2352 2601 4.667262 AGTCAGAAGAGTGAATCGAATCG 58.333 43.478 0.00 0.00 0.00 3.34
2837 3161 3.749609 CGGACCCTTTTAACGTCAAAGAT 59.250 43.478 17.65 8.45 33.69 2.40
2868 3192 3.927142 AGAAAGAATCGCCGAGTTAACTG 59.073 43.478 14.14 5.51 0.00 3.16
3350 3828 9.712305 ATGAGTATACTGTAATTGATTACTGCC 57.288 33.333 10.90 6.51 42.42 4.85
3531 4278 4.740822 GCCCCGTTCATGGCCACT 62.741 66.667 8.16 0.00 41.97 4.00
3535 4282 2.334946 CCGTTCATGGCCACTGGTG 61.335 63.158 8.16 1.52 0.00 4.17
3595 4342 2.670148 GGGTGAGGAATGGAGGCGT 61.670 63.158 0.00 0.00 0.00 5.68
3677 4424 2.511659 TGTCGGCAGTAGTAGTGTCTT 58.488 47.619 7.94 0.00 0.00 3.01
3682 4429 5.005740 TCGGCAGTAGTAGTGTCTTTCTTA 58.994 41.667 7.94 0.00 0.00 2.10
3705 4452 4.779489 AGGCCCATTGAATAGCTTTTTCTT 59.221 37.500 0.00 0.00 0.00 2.52
3735 4482 9.836076 TCGAACGACATCCTATATTAAATACTG 57.164 33.333 0.00 0.00 0.00 2.74
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 8.127327 ACACACGTGTACATTATGTATCTAGAC 58.873 37.037 22.90 0.00 42.90 2.59
20 21 4.718858 TCGACCAGAAAATTTACACACG 57.281 40.909 0.00 0.00 0.00 4.49
139 140 8.733458 CAGGATGAAATACTTTGAATTGTGAGA 58.267 33.333 0.00 0.00 27.86 3.27
354 355 7.093068 TGAGAGGCACATATCCTAGTGTAAAAA 60.093 37.037 0.00 0.00 38.02 1.94
355 356 6.382859 TGAGAGGCACATATCCTAGTGTAAAA 59.617 38.462 0.00 0.00 38.02 1.52
356 357 5.897250 TGAGAGGCACATATCCTAGTGTAAA 59.103 40.000 0.00 0.00 38.02 2.01
357 358 5.454966 TGAGAGGCACATATCCTAGTGTAA 58.545 41.667 0.00 0.00 38.02 2.41
358 359 5.061721 TGAGAGGCACATATCCTAGTGTA 57.938 43.478 0.00 0.00 38.02 2.90
359 360 3.916035 TGAGAGGCACATATCCTAGTGT 58.084 45.455 0.00 0.00 38.02 3.55
360 361 6.788598 ATATGAGAGGCACATATCCTAGTG 57.211 41.667 0.00 0.00 36.58 2.74
416 417 0.390860 ACACGCAGGATATGAGAGGC 59.609 55.000 0.00 0.00 32.27 4.70
473 474 5.049405 CCATGGAAAATCATCGTAAGTAGCC 60.049 44.000 5.56 0.00 39.48 3.93
577 578 2.673833 CCGAGTTAACAGAAGCGAACT 58.326 47.619 8.61 0.00 34.88 3.01
723 724 5.051039 CGGCGTATATGCATGTTGTATATCC 60.051 44.000 18.41 4.02 37.03 2.59
801 802 9.396022 AGGTGATCAAAGTTATGAACGATATTT 57.604 29.630 0.00 0.00 36.23 1.40
802 803 8.964476 AGGTGATCAAAGTTATGAACGATATT 57.036 30.769 0.00 0.00 36.23 1.28
803 804 7.382488 CGAGGTGATCAAAGTTATGAACGATAT 59.618 37.037 0.00 0.00 36.23 1.63
804 805 6.695713 CGAGGTGATCAAAGTTATGAACGATA 59.304 38.462 0.00 0.00 36.23 2.92
865 866 1.508088 GGCCAAATGTCGGAAGCAG 59.492 57.895 0.00 0.00 0.00 4.24
908 909 2.103042 GTGGTGGCGAGCTGCTTAG 61.103 63.158 2.53 2.41 45.43 2.18
909 910 2.047274 GTGGTGGCGAGCTGCTTA 60.047 61.111 2.53 0.00 45.43 3.09
919 923 0.882042 CTGAGTGAGTGTGTGGTGGC 60.882 60.000 0.00 0.00 0.00 5.01
952 956 3.952628 GAAGGGGGTTGACGGCGAG 62.953 68.421 16.62 0.00 0.00 5.03
1088 1105 0.959553 ATAGTAGTCGCCCATGTCGG 59.040 55.000 5.03 0.00 0.00 4.79
1558 1577 2.022240 GCCAAGGGCGGTTGACAAAA 62.022 55.000 0.00 0.00 39.62 2.44
1919 1938 7.916450 GCAGTTTTTGTTGGTGTAAGTGTAATA 59.084 33.333 0.00 0.00 0.00 0.98
1921 1940 6.071840 AGCAGTTTTTGTTGGTGTAAGTGTAA 60.072 34.615 0.00 0.00 0.00 2.41
1922 1941 5.416326 AGCAGTTTTTGTTGGTGTAAGTGTA 59.584 36.000 0.00 0.00 0.00 2.90
1925 1944 4.142249 GGAGCAGTTTTTGTTGGTGTAAGT 60.142 41.667 0.00 0.00 0.00 2.24
1928 1947 3.129638 GTGGAGCAGTTTTTGTTGGTGTA 59.870 43.478 0.00 0.00 0.00 2.90
1939 2003 1.140312 TCCTGGAAGTGGAGCAGTTT 58.860 50.000 0.00 0.00 0.00 2.66
1947 2011 3.285484 CCAATCTTGATCCTGGAAGTGG 58.715 50.000 0.00 0.00 0.00 4.00
1969 2033 1.476845 TTCGCAGGTTAGGTGCTCCA 61.477 55.000 7.70 0.00 38.88 3.86
1970 2034 0.107654 ATTCGCAGGTTAGGTGCTCC 60.108 55.000 0.00 0.00 38.88 4.70
1988 2052 0.475906 GGCTCAAGGTATCCCAGCAT 59.524 55.000 0.00 0.00 0.00 3.79
2023 2087 1.831343 GCGAGCTGCATACCAAATTG 58.169 50.000 1.02 0.00 45.45 2.32
2026 2090 1.079474 TCGCGAGCTGCATACCAAA 60.079 52.632 3.71 0.00 46.97 3.28
2027 2091 1.809619 GTCGCGAGCTGCATACCAA 60.810 57.895 10.24 0.00 46.97 3.67
2043 2129 7.434307 CACATGCAAATTGAATTAGGATGAGTC 59.566 37.037 0.00 0.00 0.00 3.36
2045 2131 7.222031 CACACATGCAAATTGAATTAGGATGAG 59.778 37.037 0.00 0.00 0.00 2.90
2086 2172 4.276058 TGCACCCAAGGTTACTACTAAC 57.724 45.455 0.00 0.00 31.02 2.34
2093 2179 3.436700 GCAATATGCACCCAAGGTTAC 57.563 47.619 0.00 0.00 44.26 2.50
2112 2198 3.060615 CTCCCAGCCTGCAAGTGC 61.061 66.667 0.00 0.00 42.50 4.40
2113 2199 3.060615 GCTCCCAGCCTGCAAGTG 61.061 66.667 0.00 0.00 34.48 3.16
2115 2201 2.282674 TTGCTCCCAGCCTGCAAG 60.283 61.111 0.00 0.00 41.51 4.01
2274 2497 9.316730 CTAGTATTGCAAAATTACCAATGCATT 57.683 29.630 5.99 5.99 46.97 3.56
2275 2498 8.477256 ACTAGTATTGCAAAATTACCAATGCAT 58.523 29.630 1.71 0.00 46.97 3.96
2308 2545 9.916360 TGACTTCTGACCATACTAGATAAAGTA 57.084 33.333 0.00 0.00 36.44 2.24
2309 2546 8.824756 TGACTTCTGACCATACTAGATAAAGT 57.175 34.615 0.00 0.00 0.00 2.66
2310 2547 9.126151 TCTGACTTCTGACCATACTAGATAAAG 57.874 37.037 0.00 0.00 0.00 1.85
2338 2586 1.846782 CGTGACCGATTCGATTCACTC 59.153 52.381 25.25 11.04 37.46 3.51
2352 2601 4.034048 CAGCAGGACATAAATTACGTGACC 59.966 45.833 0.00 0.00 0.00 4.02
2837 3161 3.678072 CGGCGATTCTTTCTTCACAGTAA 59.322 43.478 0.00 0.00 0.00 2.24
2868 3192 3.354467 AGTCAGGGTGCTACTGTACTAC 58.646 50.000 0.00 0.00 37.25 2.73
3068 3540 5.001232 TGGAGAAATTGGTAGCACTAACAC 58.999 41.667 0.00 0.00 31.56 3.32
3531 4278 2.160171 CCCACCTTCCCTTCCACCA 61.160 63.158 0.00 0.00 0.00 4.17
3535 4282 1.850755 TCACCCCACCTTCCCTTCC 60.851 63.158 0.00 0.00 0.00 3.46
3595 4342 5.067936 CGAAACCTAGCTCTCCAGAGAATAA 59.932 44.000 7.84 0.00 44.74 1.40
3677 4424 4.796110 AGCTATTCAATGGGCCTAAGAA 57.204 40.909 4.53 6.24 0.00 2.52
3682 4429 4.356436 AGAAAAAGCTATTCAATGGGCCT 58.644 39.130 4.53 0.00 0.00 5.19
3735 4482 1.909700 TTTGGTGAGTGGGAGAATGC 58.090 50.000 0.00 0.00 0.00 3.56


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

AutoCloner maintained by Alex Coulton.