Multiple sequence alignment - TraesCS7A01G059600

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 TraesCS7A01G059600 chr7A 100.000 3930 0 0 1 3930 29031045 29034974 0.000000e+00 7258.0
1 TraesCS7A01G059600 chr7A 85.837 3029 342 52 1 2993 29108361 29111338 0.000000e+00 3136.0
2 TraesCS7A01G059600 chr7A 86.216 399 54 1 3319 3716 225059299 225059697 7.800000e-117 431.0
3 TraesCS7A01G059600 chr7A 88.816 304 23 6 2981 3281 29108544 29108839 2.890000e-96 363.0
4 TraesCS7A01G059600 chr7A 86.792 212 28 0 3718 3929 225059732 225059943 1.830000e-58 237.0
5 TraesCS7A01G059600 chr7D 90.483 2091 170 18 916 2993 28673552 28675626 0.000000e+00 2732.0
6 TraesCS7A01G059600 chr7D 87.554 2065 239 14 936 2993 28695548 28697601 0.000000e+00 2374.0
7 TraesCS7A01G059600 chr7D 90.382 655 52 6 243 888 28672552 28673204 0.000000e+00 850.0
8 TraesCS7A01G059600 chr7D 83.854 929 94 17 1 894 28694407 28695314 0.000000e+00 833.0
9 TraesCS7A01G059600 chr7D 88.351 661 57 7 3281 3930 28684000 28684651 0.000000e+00 776.0
10 TraesCS7A01G059600 chr7D 86.216 399 54 1 3319 3716 213514130 213514528 7.800000e-117 431.0
11 TraesCS7A01G059600 chr7D 89.037 301 28 4 2981 3278 28694589 28694887 6.200000e-98 368.0
12 TraesCS7A01G059600 chr7D 92.460 252 13 5 3028 3275 28672552 28672801 4.830000e-94 355.0
13 TraesCS7A01G059600 chr7D 88.679 212 24 0 3718 3929 213514563 213514774 3.900000e-65 259.0
14 TraesCS7A01G059600 chr7D 89.305 187 19 1 27 212 28672364 28672550 2.360000e-57 233.0
15 TraesCS7A01G059600 chr4A 89.570 1582 141 12 608 2187 702379402 702380961 0.000000e+00 1986.0
16 TraesCS7A01G059600 chr4A 91.261 1316 105 6 1673 2987 702398795 702400101 0.000000e+00 1784.0
17 TraesCS7A01G059600 chr4A 86.654 1551 193 10 1452 2993 701313074 701311529 0.000000e+00 1705.0
18 TraesCS7A01G059600 chr4A 89.436 1259 98 18 1 1249 702397573 702398806 0.000000e+00 1555.0
19 TraesCS7A01G059600 chr4A 83.897 1360 182 29 695 2033 702503709 702505052 0.000000e+00 1264.0
20 TraesCS7A01G059600 chr4A 86.467 835 75 16 2175 2993 702381007 702381819 0.000000e+00 881.0
21 TraesCS7A01G059600 chr4A 86.100 777 105 3 2218 2993 702339889 702340663 0.000000e+00 833.0
22 TraesCS7A01G059600 chr4A 85.623 779 107 3 2218 2993 702505157 702505933 0.000000e+00 813.0
23 TraesCS7A01G059600 chr4A 84.894 662 72 16 1 651 702337613 702338257 0.000000e+00 643.0
24 TraesCS7A01G059600 chr4A 88.499 513 49 9 390 899 701314422 701313917 2.600000e-171 612.0
25 TraesCS7A01G059600 chr4A 83.409 663 80 15 1 648 702503066 702503713 4.370000e-164 588.0
26 TraesCS7A01G059600 chr4A 88.696 460 50 2 927 1384 701313533 701313074 9.540000e-156 560.0
27 TraesCS7A01G059600 chr4A 84.337 581 65 12 1 571 702383531 702384095 2.670000e-151 545.0
28 TraesCS7A01G059600 chr4A 85.837 466 43 17 2986 3445 702402231 702402679 1.280000e-129 473.0
29 TraesCS7A01G059600 chr4A 91.246 297 20 4 2987 3281 702383720 702384012 2.200000e-107 399.0
30 TraesCS7A01G059600 chr4A 90.136 294 22 5 2986 3275 702397773 702398063 3.710000e-100 375.0
31 TraesCS7A01G059600 chr4A 85.294 374 36 10 243 607 702378994 702379357 6.200000e-98 368.0
32 TraesCS7A01G059600 chr4A 88.814 295 28 4 2986 3278 702337800 702338091 1.340000e-94 357.0
33 TraesCS7A01G059600 chr4A 88.255 298 28 5 2986 3278 702503254 702503549 2.250000e-92 350.0
34 TraesCS7A01G059600 chr4A 91.080 213 19 0 3718 3930 702384525 702384737 4.970000e-74 289.0
35 TraesCS7A01G059600 chr4A 90.610 213 19 1 1 212 702378780 702378992 8.310000e-72 281.0
36 TraesCS7A01G059600 chr4A 87.302 252 17 8 3028 3275 702378994 702379234 1.390000e-69 274.0
37 TraesCS7A01G059600 chr4A 85.185 216 24 3 3718 3925 702404387 702404602 8.550000e-52 215.0
38 TraesCS7A01G059600 chr4A 86.387 191 19 4 697 882 702338251 702338439 6.660000e-48 202.0
39 TraesCS7A01G059600 chr4A 80.702 114 22 0 58 171 701309848 701309735 5.410000e-14 89.8
40 TraesCS7A01G059600 chr5A 85.714 399 55 2 3319 3716 683132957 683133354 1.690000e-113 420.0
41 TraesCS7A01G059600 chr5A 83.886 211 30 4 3718 3926 683133389 683133597 8.610000e-47 198.0
42 TraesCS7A01G059600 chr7B 85.213 399 58 1 3319 3716 188394910 188394512 3.660000e-110 409.0
43 TraesCS7A01G059600 chr7B 88.679 212 24 0 3718 3929 188394477 188394266 3.900000e-65 259.0
44 TraesCS7A01G059600 chr4D 84.826 402 57 2 3319 3716 501168377 501167976 6.120000e-108 401.0
45 TraesCS7A01G059600 chr4D 85.849 212 24 5 3721 3929 501167938 501167730 1.840000e-53 220.0


These results show the homologous regions that are presented in the multiple sequence alignment. HSPs from the BLAST search that are within 2000 bases of each other have been grouped together. Homologous regions that are purely upstream or downstream may be removed if they don't overlap both primers.

query scaffold start end length rev.comp avg.bitscore max.bitscore avg.percent.identical query.start query.end num_hsp groupid homo_length
0 TraesCS7A01G059600 chr7A 29031045 29034974 3929 False 7258.000000 7258 100.00000 1 3930 1 chr7A.!!$F1 3929
1 TraesCS7A01G059600 chr7A 29108361 29111338 2977 False 1749.500000 3136 87.32650 1 3281 2 chr7A.!!$F2 3280
2 TraesCS7A01G059600 chr7A 225059299 225059943 644 False 334.000000 431 86.50400 3319 3929 2 chr7A.!!$F3 610
3 TraesCS7A01G059600 chr7D 28694407 28697601 3194 False 1191.666667 2374 86.81500 1 3278 3 chr7D.!!$F3 3277
4 TraesCS7A01G059600 chr7D 28672364 28675626 3262 False 1042.500000 2732 90.65750 27 3275 4 chr7D.!!$F2 3248
5 TraesCS7A01G059600 chr7D 28684000 28684651 651 False 776.000000 776 88.35100 3281 3930 1 chr7D.!!$F1 649
6 TraesCS7A01G059600 chr7D 213514130 213514774 644 False 345.000000 431 87.44750 3319 3929 2 chr7D.!!$F4 610
7 TraesCS7A01G059600 chr4A 702397573 702404602 7029 False 880.400000 1784 88.37100 1 3925 5 chr4A.!!$F3 3924
8 TraesCS7A01G059600 chr4A 702503066 702505933 2867 False 753.750000 1264 85.29600 1 3278 4 chr4A.!!$F4 3277
9 TraesCS7A01G059600 chr4A 701309735 701314422 4687 True 741.700000 1705 86.13775 58 2993 4 chr4A.!!$R1 2935
10 TraesCS7A01G059600 chr4A 702378780 702384737 5957 False 627.875000 1986 88.23825 1 3930 8 chr4A.!!$F2 3929
11 TraesCS7A01G059600 chr4A 702337613 702340663 3050 False 508.750000 833 86.54875 1 3278 4 chr4A.!!$F1 3277
12 TraesCS7A01G059600 chr5A 683132957 683133597 640 False 309.000000 420 84.80000 3319 3926 2 chr5A.!!$F1 607
13 TraesCS7A01G059600 chr7B 188394266 188394910 644 True 334.000000 409 86.94600 3319 3929 2 chr7B.!!$R1 610
14 TraesCS7A01G059600 chr4D 501167730 501168377 647 True 310.500000 401 85.33750 3319 3929 2 chr4D.!!$R1 610

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
692 820 1.289231 TGAGATGGTGGCCTCTACTCT 59.711 52.381 3.32 4.21 0.0 3.24 F
2043 2593 0.723981 GAGATGACGCTTGCAACCTC 59.276 55.000 0.00 0.00 0.0 3.85 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2205 2815 1.130561 GGAGAGCACGTTGTATTTGCC 59.869 52.381 0.00 0.00 36.91 4.52 R
3482 7851 0.108138 CCTTCCAGAACGCCTGTAGG 60.108 60.000 4.95 6.93 41.33 3.18 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
48 49 5.346551 TGAAACAACTATTGGACGATGTACG 59.653 40.000 0.00 0.00 40.69 3.67
83 85 6.745450 ACATTTTTCTTGACAAGTAACGTGTG 59.255 34.615 14.75 9.52 0.00 3.82
84 86 4.868450 TTTCTTGACAAGTAACGTGTGG 57.132 40.909 14.75 0.00 0.00 4.17
95 97 4.742201 CGTGTGGAGGCGAGTGGG 62.742 72.222 0.00 0.00 0.00 4.61
147 149 9.771534 GAGTCAGCAAACTAATCCTAGATTATT 57.228 33.333 0.00 0.00 0.00 1.40
213 215 4.165372 TGGTTGTACCTTTTCCAAGACTCT 59.835 41.667 0.00 0.00 39.58 3.24
286 289 6.481954 AGAAAACAATCTCGTGTACATTCC 57.518 37.500 0.00 0.00 0.00 3.01
308 311 4.262549 CCACCATTGATTCAACACCAACAT 60.263 41.667 0.15 0.00 0.00 2.71
338 347 5.133941 TGCACAAACTATTTTACCAGTGGA 58.866 37.500 18.40 0.00 0.00 4.02
537 558 6.426646 AATGTGCTTTTACCCCAACAATAA 57.573 33.333 0.00 0.00 0.00 1.40
541 562 8.140112 TGTGCTTTTACCCCAACAATAATTAT 57.860 30.769 0.00 0.00 0.00 1.28
542 563 8.254508 TGTGCTTTTACCCCAACAATAATTATC 58.745 33.333 0.00 0.00 0.00 1.75
543 564 7.434013 GTGCTTTTACCCCAACAATAATTATCG 59.566 37.037 0.00 0.00 0.00 2.92
544 565 7.339721 TGCTTTTACCCCAACAATAATTATCGA 59.660 33.333 0.00 0.00 0.00 3.59
545 566 8.357402 GCTTTTACCCCAACAATAATTATCGAT 58.643 33.333 2.16 2.16 0.00 3.59
546 567 9.677567 CTTTTACCCCAACAATAATTATCGATG 57.322 33.333 8.54 0.00 0.00 3.84
547 568 8.754991 TTTACCCCAACAATAATTATCGATGT 57.245 30.769 8.54 0.00 0.00 3.06
548 569 9.848710 TTTACCCCAACAATAATTATCGATGTA 57.151 29.630 8.54 0.00 0.00 2.29
549 570 7.979444 ACCCCAACAATAATTATCGATGTAG 57.021 36.000 8.54 0.00 0.00 2.74
575 608 1.768275 AGATGGTTACCGATGGATGCA 59.232 47.619 0.00 0.00 0.00 3.96
579 612 3.360867 TGGTTACCGATGGATGCATTTT 58.639 40.909 0.00 0.00 0.00 1.82
584 617 2.824936 ACCGATGGATGCATTTTGACAA 59.175 40.909 0.00 0.00 0.00 3.18
669 797 2.486191 GCAGAAATCCTGATCATCCGGT 60.486 50.000 0.00 0.00 45.78 5.28
688 816 2.042464 GTCATGAGATGGTGGCCTCTA 58.958 52.381 3.32 0.00 0.00 2.43
692 820 1.289231 TGAGATGGTGGCCTCTACTCT 59.711 52.381 3.32 4.21 0.00 3.24
709 837 4.899352 ACTCTCACTTTAGCAACTCCAT 57.101 40.909 0.00 0.00 0.00 3.41
772 925 5.047188 CACTCACCAACACAAAATTAACCC 58.953 41.667 0.00 0.00 0.00 4.11
966 1479 8.538409 ACAACCTAAATACAAGTAAGGTAACG 57.462 34.615 3.27 0.00 39.64 3.18
989 1502 5.451937 CGAAATATCCTAGGTGTGCTCTCAA 60.452 44.000 9.08 0.00 0.00 3.02
1131 1651 9.941325 TTACAAATTTGTTCTCATGCCATTAAT 57.059 25.926 27.66 0.53 42.35 1.40
1208 1728 1.153549 GCTCAAGGTCTAGCCGTGG 60.154 63.158 15.22 9.56 45.14 4.94
1223 1743 2.680841 GCCGTGGATTTATTGTGTGCTA 59.319 45.455 0.00 0.00 0.00 3.49
1235 1755 1.336424 TGTGTGCTACAATCGCTCGAA 60.336 47.619 0.00 0.00 36.06 3.71
1300 1820 6.499350 TGGTTCAGAACTAGTTACCCACTTAT 59.501 38.462 18.46 0.00 36.88 1.73
1317 1837 7.120726 ACCCACTTATTAGCAATTGTTAGTGTC 59.879 37.037 16.78 0.00 32.07 3.67
1417 1937 9.603921 AATGAATGAAAGAAACACTCAAATTGT 57.396 25.926 0.00 0.00 27.98 2.71
1450 1972 9.924650 TTTCCTTATGAAGTAGAAGTAGACAAC 57.075 33.333 0.00 0.00 33.63 3.32
1473 1995 5.529800 ACGGTGTGAATATATTTAGTTGGCC 59.470 40.000 0.00 0.00 0.00 5.36
1489 2011 1.810151 TGGCCGTTTGAGTTAATGAGC 59.190 47.619 0.00 0.00 0.00 4.26
1501 2023 7.263100 TGAGTTAATGAGCGCAAATGAATAT 57.737 32.000 11.47 0.00 0.00 1.28
1542 2064 2.009774 CGACTGAAAATAGGCCAGTGG 58.990 52.381 5.01 4.20 40.80 4.00
1555 2077 1.946283 GCCAGTGGTGCTTAAGAGGAC 60.946 57.143 11.74 0.00 42.90 3.85
1569 2091 8.924303 TGCTTAAGAGGACTATAAGAATAGCAA 58.076 33.333 6.67 0.00 39.01 3.91
1668 2195 9.444668 TCCCAAAATGGAATGATTGGAATAATA 57.555 29.630 5.01 0.00 43.24 0.98
1669 2196 9.492973 CCCAAAATGGAATGATTGGAATAATAC 57.507 33.333 5.01 0.00 43.24 1.89
1761 2288 8.548877 TGAGTTAAAACTAGCCATCTTAATCCT 58.451 33.333 0.00 0.00 39.88 3.24
1796 2323 7.665559 TCCTCATGAAACAATTTAGCTGTACTT 59.334 33.333 0.00 0.00 0.00 2.24
1801 2328 8.014322 TGAAACAATTTAGCTGTACTTCTACG 57.986 34.615 0.00 0.00 0.00 3.51
1802 2329 6.963049 AACAATTTAGCTGTACTTCTACGG 57.037 37.500 0.00 0.00 32.89 4.02
1866 2394 8.018677 ACATAAGTACTCTTGAAAACATCACG 57.981 34.615 10.96 0.00 37.92 4.35
1988 2516 7.468357 GCAATATCACTGGAATTTGAGAGGAAG 60.468 40.741 0.00 0.00 0.00 3.46
1998 2526 6.375455 GGAATTTGAGAGGAAGCAGTTCAATA 59.625 38.462 0.00 0.00 33.93 1.90
2010 2538 3.345714 CAGTTCAATATTCGCTTGTCGC 58.654 45.455 0.00 0.00 38.27 5.19
2043 2593 0.723981 GAGATGACGCTTGCAACCTC 59.276 55.000 0.00 0.00 0.00 3.85
2111 2665 4.284829 TCCCCAAAAGCAAAATCCATTC 57.715 40.909 0.00 0.00 0.00 2.67
2121 2675 4.520492 AGCAAAATCCATTCGAAGTTCTGT 59.480 37.500 3.35 0.00 0.00 3.41
2160 2714 3.864921 GCCAGCACTATATTAACCCCTCG 60.865 52.174 0.00 0.00 0.00 4.63
2164 2718 2.904434 CACTATATTAACCCCTCGCCCT 59.096 50.000 0.00 0.00 0.00 5.19
2205 2815 8.594687 CACACACAAAGAGATTAAAAAGGTTTG 58.405 33.333 0.00 0.00 0.00 2.93
2266 2883 1.571457 CCTCCTCCTCCTCCTCTACAA 59.429 57.143 0.00 0.00 0.00 2.41
2359 2977 2.309755 TGATATTCCAGGGGCATCATCC 59.690 50.000 0.00 0.00 0.00 3.51
2489 3107 1.207089 TCTCGGCTGTTATGGAACCAG 59.793 52.381 0.00 0.00 34.38 4.00
2493 3111 0.676782 GCTGTTATGGAACCAGCCGT 60.677 55.000 0.00 0.00 35.45 5.68
2525 3143 1.455773 ATCGTCGGGCCTCTCATCA 60.456 57.895 0.84 0.00 0.00 3.07
2552 3170 1.499688 CGCGCGTGAGATCCTAGAGA 61.500 60.000 24.19 0.00 0.00 3.10
2684 3302 7.229306 TCAAGTAAGCAATTGATTGTCAAGTCT 59.771 33.333 18.87 3.57 40.05 3.24
2794 3416 6.605594 TGGGATTTTGTAAACAAGAGTGTCTT 59.394 34.615 0.00 0.00 36.80 3.01
2808 3430 5.583495 AGAGTGTCTTTGCGACTATATCAC 58.417 41.667 0.00 0.00 43.25 3.06
2809 3431 5.358442 AGAGTGTCTTTGCGACTATATCACT 59.642 40.000 0.00 0.00 43.25 3.41
2824 3446 8.218338 ACTATATCACTGAGCAATTGGAAAAG 57.782 34.615 7.72 0.00 0.00 2.27
2831 3453 3.822735 TGAGCAATTGGAAAAGGAGACAG 59.177 43.478 7.72 0.00 0.00 3.51
2873 3495 3.299503 AGAGAAAAGGTGCCAACAATGT 58.700 40.909 0.00 0.00 0.00 2.71
2874 3496 3.706086 AGAGAAAAGGTGCCAACAATGTT 59.294 39.130 0.00 0.00 0.00 2.71
2939 3577 1.788258 CAGCCTATGATGCACCTACG 58.212 55.000 0.00 0.00 0.00 3.51
2974 3612 3.648545 AGATGTATGGGCTTAGAAGGACC 59.351 47.826 0.00 0.00 0.00 4.46
3040 5940 3.959449 ACGTAATTAACCCCTCCTCTCTC 59.041 47.826 0.00 0.00 0.00 3.20
3044 5944 5.443230 AATTAACCCCTCCTCTCTCTTTG 57.557 43.478 0.00 0.00 0.00 2.77
3172 6074 9.211485 AGGAAATTTAGAAAAATGCAATCACTG 57.789 29.630 0.00 0.00 35.46 3.66
3257 6160 6.870895 TTTTTGTAACCCATATAAACCCCC 57.129 37.500 0.00 0.00 0.00 5.40
3294 6239 9.745880 AATACACACTCTAACAATAGTTATCCG 57.254 33.333 0.00 0.00 39.36 4.18
3377 6322 2.619074 GCTTGCCATCAAAGACTACCCT 60.619 50.000 0.00 0.00 0.00 4.34
3393 6338 0.177141 CCCTTTCGCTAATGACGGGA 59.823 55.000 0.00 0.00 32.91 5.14
3406 6351 1.460305 ACGGGATCCTCATCTGGGG 60.460 63.158 12.58 0.00 0.00 4.96
3410 6355 3.873026 GATCCTCATCTGGGGCGCG 62.873 68.421 0.00 0.00 0.00 6.86
3441 7803 1.517832 GTGCTGGCATACGTCTCCT 59.482 57.895 0.00 0.00 0.00 3.69
3450 7812 3.573110 GGCATACGTCTCCTGGTATTACT 59.427 47.826 0.00 0.00 0.00 2.24
3457 7824 2.024655 TCTCCTGGTATTACTGGGACGT 60.025 50.000 0.00 0.00 0.00 4.34
3507 7876 1.371558 GCGTTCTGGAAGGAGGTGT 59.628 57.895 7.14 0.00 27.59 4.16
3526 7896 4.082523 CACCTGGGACACGGCGAT 62.083 66.667 16.62 0.00 31.39 4.58
3533 7903 1.152383 GGGACACGGCGATAAGAAGC 61.152 60.000 16.62 0.00 0.00 3.86
3635 8005 2.280592 ACACGGCGGTCAACTTCC 60.281 61.111 13.24 0.00 0.00 3.46
3638 8008 4.675029 CGGCGGTCAACTTCCGGT 62.675 66.667 0.00 0.00 46.90 5.28
3763 8201 2.864471 GCAGGTGCAGGCAAAGCTT 61.864 57.895 0.00 0.00 41.59 3.74
3775 8213 1.001378 GCAAAGCTTGTGATGACGGTT 60.001 47.619 0.00 0.00 0.00 4.44
3837 8283 2.685017 AGGGATGGAGAGCGCACA 60.685 61.111 11.47 2.95 0.00 4.57
3838 8284 2.037620 GAGGGATGGAGAGCGCACAT 62.038 60.000 11.47 8.49 0.00 3.21
3904 8350 2.761208 CGAGTGTCTTAAGGAGGTGGAT 59.239 50.000 1.85 0.00 0.00 3.41
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
15 16 8.073768 CGTCCAATAGTTGTTTCAACTTTATGT 58.926 33.333 18.02 0.00 0.00 2.29
64 66 4.116961 CTCCACACGTTACTTGTCAAGAA 58.883 43.478 19.53 6.49 0.00 2.52
83 85 0.175989 CTTTAGTCCCACTCGCCTCC 59.824 60.000 0.00 0.00 0.00 4.30
84 86 0.896226 ACTTTAGTCCCACTCGCCTC 59.104 55.000 0.00 0.00 0.00 4.70
95 97 8.660373 CAACATCTACATCTTCCAACTTTAGTC 58.340 37.037 0.00 0.00 0.00 2.59
147 149 5.888724 AGAGAGAGAACCGTATCAAATCTCA 59.111 40.000 0.00 0.00 39.14 3.27
213 215 8.774890 TTACGTAGAATGCTATTACCAAAACA 57.225 30.769 0.00 0.00 0.00 2.83
264 267 6.077838 GTGGAATGTACACGAGATTGTTTTC 58.922 40.000 0.00 0.00 0.00 2.29
269 272 3.595173 TGGTGGAATGTACACGAGATTG 58.405 45.455 0.00 0.00 39.69 2.67
278 281 6.092748 GTGTTGAATCAATGGTGGAATGTAC 58.907 40.000 0.00 0.00 0.00 2.90
279 282 5.184864 GGTGTTGAATCAATGGTGGAATGTA 59.815 40.000 0.00 0.00 0.00 2.29
280 283 4.021192 GGTGTTGAATCAATGGTGGAATGT 60.021 41.667 0.00 0.00 0.00 2.71
286 289 4.319139 TGTTGGTGTTGAATCAATGGTG 57.681 40.909 0.00 0.00 0.00 4.17
523 544 9.496873 CTACATCGATAATTATTGTTGGGGTAA 57.503 33.333 20.59 0.65 0.00 2.85
543 564 4.738740 CGGTAACCATCTTTCGACTACATC 59.261 45.833 0.00 0.00 0.00 3.06
544 565 4.400251 TCGGTAACCATCTTTCGACTACAT 59.600 41.667 0.00 0.00 0.00 2.29
545 566 3.758023 TCGGTAACCATCTTTCGACTACA 59.242 43.478 0.00 0.00 0.00 2.74
546 567 4.361451 TCGGTAACCATCTTTCGACTAC 57.639 45.455 0.00 0.00 0.00 2.73
547 568 4.202080 CCATCGGTAACCATCTTTCGACTA 60.202 45.833 0.00 0.00 0.00 2.59
548 569 3.430374 CCATCGGTAACCATCTTTCGACT 60.430 47.826 0.00 0.00 0.00 4.18
549 570 2.864343 CCATCGGTAACCATCTTTCGAC 59.136 50.000 0.00 0.00 0.00 4.20
557 590 2.957402 ATGCATCCATCGGTAACCAT 57.043 45.000 0.00 0.00 0.00 3.55
575 608 5.870978 GGCTTAGCATTCACATTGTCAAAAT 59.129 36.000 6.53 0.00 0.00 1.82
579 612 3.419943 TGGCTTAGCATTCACATTGTCA 58.580 40.909 6.53 0.00 0.00 3.58
584 617 4.440525 CGGATTTTGGCTTAGCATTCACAT 60.441 41.667 6.53 0.00 0.00 3.21
595 628 1.676014 CCTCTCGACGGATTTTGGCTT 60.676 52.381 0.00 0.00 0.00 4.35
669 797 2.042464 GTAGAGGCCACCATCTCATGA 58.958 52.381 5.01 0.00 32.76 3.07
688 816 4.040952 ACATGGAGTTGCTAAAGTGAGAGT 59.959 41.667 0.00 0.00 0.00 3.24
709 837 3.963129 AGAGTCCAACAAAGGAACAACA 58.037 40.909 0.00 0.00 39.92 3.33
721 851 6.674760 GCACATTTACCGAAATAGAGTCCAAC 60.675 42.308 0.00 0.00 33.33 3.77
918 1394 1.274703 GGGGGATCTGCACCTCTTCA 61.275 60.000 0.00 0.00 41.14 3.02
966 1479 5.537300 TGAGAGCACACCTAGGATATTTC 57.463 43.478 17.98 7.46 0.00 2.17
989 1502 1.130749 CGACTCTCATCGGAAGTTCGT 59.869 52.381 0.00 0.00 38.47 3.85
1067 1587 6.206829 GTGCCATTACCCAAATAATCTACCTC 59.793 42.308 0.00 0.00 0.00 3.85
1223 1743 0.179073 CCCCATCTTCGAGCGATTGT 60.179 55.000 0.00 0.00 0.00 2.71
1235 1755 5.697067 TGTAGTAAAACACAAACCCCATCT 58.303 37.500 0.00 0.00 0.00 2.90
1317 1837 9.877178 GTTCCTTGGTCCATCTAATATAGTATG 57.123 37.037 0.00 0.00 0.00 2.39
1368 1888 9.894783 CATTATAGCTACATAACGACACTTACT 57.105 33.333 0.00 0.00 0.00 2.24
1431 1953 5.243283 ACACCGTTGTCTACTTCTACTTCAT 59.757 40.000 0.00 0.00 0.00 2.57
1450 1972 5.333798 CGGCCAACTAAATATATTCACACCG 60.334 44.000 2.24 3.20 0.00 4.94
1473 1995 2.873170 TGCGCTCATTAACTCAAACG 57.127 45.000 9.73 0.00 0.00 3.60
1489 2011 8.022550 TCCAATAGCACATAATATTCATTTGCG 58.977 33.333 0.00 0.00 32.84 4.85
1501 2023 4.081365 TCGTTCTGGTCCAATAGCACATAA 60.081 41.667 0.00 0.00 0.00 1.90
1542 2064 8.361139 TGCTATTCTTATAGTCCTCTTAAGCAC 58.639 37.037 0.00 0.00 36.82 4.40
1590 2112 6.525629 ACCAATATGTAGTTCTCCATACTGC 58.474 40.000 0.00 0.00 0.00 4.40
1640 2167 4.686891 TCCAATCATTCCATTTTGGGACT 58.313 39.130 0.00 0.00 39.27 3.85
1668 2195 4.277174 TGGTTTTGCACATATCTTCAACGT 59.723 37.500 0.00 0.00 0.00 3.99
1669 2196 4.793071 TGGTTTTGCACATATCTTCAACG 58.207 39.130 0.00 0.00 0.00 4.10
1796 2323 9.184523 ACCATATGAATTCAATTTTTCCGTAGA 57.815 29.630 13.09 0.00 0.00 2.59
1855 2383 5.839262 TGTAGACATGACGTGATGTTTTC 57.161 39.130 21.61 14.13 36.67 2.29
1988 2516 3.345714 CGACAAGCGAATATTGAACTGC 58.654 45.455 0.00 0.00 44.57 4.40
2010 2538 3.983988 CGTCATCTCCTCCATACGAATTG 59.016 47.826 0.00 0.00 32.35 2.32
2111 2665 5.728049 CGCATGTTGTAATTACAGAACTTCG 59.272 40.000 17.36 13.62 37.52 3.79
2121 2675 2.087646 TGGCAGCGCATGTTGTAATTA 58.912 42.857 11.47 0.00 0.00 1.40
2164 2718 3.936203 GTGTGTGCACGGGAGGGA 61.936 66.667 13.13 0.00 35.75 4.20
2173 2727 2.106477 TCTCTTTGTGTGTGTGTGCA 57.894 45.000 0.00 0.00 0.00 4.57
2205 2815 1.130561 GGAGAGCACGTTGTATTTGCC 59.869 52.381 0.00 0.00 36.91 4.52
2266 2883 5.158141 TGAGAGGATATCAACTGCCCTATT 58.842 41.667 4.83 0.00 0.00 1.73
2318 2936 2.697147 ATTGCAGGCACGGTCAGGTT 62.697 55.000 0.00 0.00 0.00 3.50
2359 2977 2.125326 CATGGCCATGGAGCACTGG 61.125 63.158 34.31 8.65 35.24 4.00
2435 3053 2.111384 GGATCTCTCTGGGTTGTAGCA 58.889 52.381 0.00 0.00 0.00 3.49
2493 3111 3.185365 CGATGCGTAGGCGTGCAA 61.185 61.111 6.90 0.00 45.45 4.08
2525 3143 3.636043 CTCACGCGCGTTGGTGTT 61.636 61.111 35.90 6.91 35.67 3.32
2552 3170 4.322499 CCAACAGAGGTTCGGTAGTGTAAT 60.322 45.833 0.00 0.00 34.21 1.89
2684 3302 2.840511 TGGATGCTAAGGGGAAGTGTA 58.159 47.619 0.00 0.00 0.00 2.90
2764 3386 6.149474 ACTCTTGTTTACAAAATCCCATCTCG 59.851 38.462 0.00 0.00 35.15 4.04
2794 3416 4.385358 TTGCTCAGTGATATAGTCGCAA 57.615 40.909 9.01 9.01 39.86 4.85
2808 3430 3.822735 TGTCTCCTTTTCCAATTGCTCAG 59.177 43.478 0.00 0.00 0.00 3.35
2809 3431 3.822735 CTGTCTCCTTTTCCAATTGCTCA 59.177 43.478 0.00 0.00 0.00 4.26
2824 3446 2.031120 CATCTCACCCTCTCTGTCTCC 58.969 57.143 0.00 0.00 0.00 3.71
2831 3453 0.539051 CCACACCATCTCACCCTCTC 59.461 60.000 0.00 0.00 0.00 3.20
2873 3495 1.072505 GGTCGCCTTCCTTGTCCAA 59.927 57.895 0.00 0.00 0.00 3.53
2874 3496 2.111999 CTGGTCGCCTTCCTTGTCCA 62.112 60.000 0.00 0.00 0.00 4.02
2939 3577 5.336372 GCCCATACATCTCTCAGACATAGAC 60.336 48.000 0.00 0.00 0.00 2.59
2988 3626 5.870978 GCTATTACCAAAACCGAGTCTTGTA 59.129 40.000 0.00 0.00 0.00 2.41
2993 3631 5.220796 GGAATGCTATTACCAAAACCGAGTC 60.221 44.000 0.00 0.00 0.00 3.36
2994 3632 4.638865 GGAATGCTATTACCAAAACCGAGT 59.361 41.667 0.00 0.00 0.00 4.18
2995 3633 4.638421 TGGAATGCTATTACCAAAACCGAG 59.362 41.667 0.00 0.00 0.00 4.63
2997 3635 4.668289 GTGGAATGCTATTACCAAAACCG 58.332 43.478 0.00 0.00 34.11 4.44
2998 3636 4.157105 ACGTGGAATGCTATTACCAAAACC 59.843 41.667 0.00 0.00 34.11 3.27
3117 6019 7.281324 CACCGTATTATGATTTTTCCACTGGTA 59.719 37.037 0.00 0.00 0.00 3.25
3126 6028 7.948034 TTCCTTCCACCGTATTATGATTTTT 57.052 32.000 0.00 0.00 0.00 1.94
3138 6040 6.718522 TTTTTCTAAATTTCCTTCCACCGT 57.281 33.333 0.00 0.00 0.00 4.83
3294 6239 4.478699 GGTAACCAACTTTTCCATTACGC 58.521 43.478 0.00 0.00 0.00 4.42
3377 6322 1.760613 AGGATCCCGTCATTAGCGAAA 59.239 47.619 8.55 0.00 0.00 3.46
3393 6338 3.933722 CGCGCCCCAGATGAGGAT 61.934 66.667 0.00 0.00 0.00 3.24
3410 6355 1.903404 CAGCACCCACCCCTTGAAC 60.903 63.158 0.00 0.00 0.00 3.18
3411 6356 2.520458 CAGCACCCACCCCTTGAA 59.480 61.111 0.00 0.00 0.00 2.69
3441 7803 1.065998 GGCAACGTCCCAGTAATACCA 60.066 52.381 0.00 0.00 0.00 3.25
3482 7851 0.108138 CCTTCCAGAACGCCTGTAGG 60.108 60.000 4.95 6.93 41.33 3.18
3513 7882 0.174845 CTTCTTATCGCCGTGTCCCA 59.825 55.000 0.00 0.00 0.00 4.37
3526 7896 1.451927 CCAGGGCGCATGCTTCTTA 60.452 57.895 17.13 0.00 42.25 2.10
3533 7903 2.324014 TTAGGCTACCAGGGCGCATG 62.324 60.000 10.83 7.39 36.85 4.06
3616 7986 3.236618 GAAGTTGACCGCCGTGTGC 62.237 63.158 0.00 0.00 0.00 4.57
3635 8005 0.672342 CCCCCGAAGTCATACTACCG 59.328 60.000 0.00 0.00 0.00 4.02
3638 8008 2.024655 AGTGTCCCCCGAAGTCATACTA 60.025 50.000 0.00 0.00 0.00 1.82
3682 8052 4.634703 ACCGGCATGTTGGTGCGA 62.635 61.111 0.00 0.00 45.97 5.10
3763 8201 1.222300 CGTCCAAAACCGTCATCACA 58.778 50.000 0.00 0.00 0.00 3.58
3837 8283 2.966732 ATGGTGTCGTCGCCCCAAT 61.967 57.895 9.77 0.00 43.03 3.16
3838 8284 3.632080 ATGGTGTCGTCGCCCCAA 61.632 61.111 9.77 0.00 43.03 4.12
3871 8317 2.032620 AGACACTCGTTGAACCTCAGT 58.967 47.619 0.00 0.00 0.00 3.41
3904 8350 0.396556 TCCTTCCGTCGATGATCCCA 60.397 55.000 6.11 0.00 0.00 4.37


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

AutoCloner maintained by Alex Coulton.