Multiple sequence alignment - TraesCS3A01G476100

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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 TraesCS3A01G476100 chr3A 100.000 2820 0 0 1 2820 707466946 707464127 0.000000e+00 5208.0
1 TraesCS3A01G476100 chr3A 92.857 434 28 2 2102 2535 698039229 698039659 6.630000e-176 627.0
2 TraesCS3A01G476100 chr3A 91.630 454 26 7 2374 2820 714514676 714514228 3.990000e-173 617.0
3 TraesCS3A01G476100 chr3A 90.244 287 24 4 2252 2537 290707927 290707644 3.430000e-99 372.0
4 TraesCS3A01G476100 chr4B 92.574 2855 167 26 1 2819 657376940 657374095 0.000000e+00 4056.0
5 TraesCS3A01G476100 chr4B 89.965 289 26 3 2250 2537 649114077 649114363 1.230000e-98 370.0
6 TraesCS3A01G476100 chr6B 87.322 844 83 15 1041 1862 6168831 6167990 0.000000e+00 944.0
7 TraesCS3A01G476100 chr6B 88.382 482 52 4 4 484 716882856 716882378 6.770000e-161 577.0
8 TraesCS3A01G476100 chr6B 88.789 446 42 4 2097 2537 149850160 149850602 8.890000e-150 540.0
9 TraesCS3A01G476100 chr6D 84.551 835 92 21 1041 1862 2958227 2957417 0.000000e+00 793.0
10 TraesCS3A01G476100 chr6D 94.946 277 11 3 2547 2820 384453089 384452813 5.580000e-117 431.0
11 TraesCS3A01G476100 chr6D 87.069 116 5 7 931 1043 2958362 2958254 3.810000e-24 122.0
12 TraesCS3A01G476100 chr6A 83.412 844 86 31 1045 1862 1985232 1986047 0.000000e+00 734.0
13 TraesCS3A01G476100 chr6A 88.296 487 50 5 1 484 16323778 16324260 6.770000e-161 577.0
14 TraesCS3A01G476100 chr6A 89.547 287 26 4 2252 2537 396917535 396917252 7.430000e-96 361.0
15 TraesCS3A01G476100 chr6A 83.721 129 13 6 494 619 558130069 558130192 6.380000e-22 115.0
16 TraesCS3A01G476100 chr3D 88.889 486 50 4 1 484 119679018 119679501 1.870000e-166 595.0
17 TraesCS3A01G476100 chr3D 95.000 280 8 4 2547 2820 256471540 256471819 4.310000e-118 435.0
18 TraesCS3A01G476100 chr3D 93.571 280 12 4 2547 2820 92577547 92577268 2.020000e-111 412.0
19 TraesCS3A01G476100 chr7A 88.706 487 47 8 1 484 494222515 494222034 3.130000e-164 588.0
20 TraesCS3A01G476100 chr7A 88.139 489 50 8 1 486 592762618 592763101 2.440000e-160 575.0
21 TraesCS3A01G476100 chr7A 85.973 221 23 6 1175 1388 23331991 23331772 2.190000e-56 230.0
22 TraesCS3A01G476100 chr2A 88.320 488 49 7 1 484 160095058 160095541 1.880000e-161 579.0
23 TraesCS3A01G476100 chr2A 86.385 213 24 4 1177 1389 689201754 689201961 7.860000e-56 228.0
24 TraesCS3A01G476100 chr7D 88.272 486 52 5 1 484 110225670 110226152 6.770000e-161 577.0
25 TraesCS3A01G476100 chr7D 87.383 214 21 5 1175 1388 22782263 22782056 1.010000e-59 241.0
26 TraesCS3A01G476100 chr7D 79.630 108 17 5 494 598 39860413 39860518 3.900000e-09 73.1
27 TraesCS3A01G476100 chr5D 88.272 486 52 5 1 484 56851393 56851875 6.770000e-161 577.0
28 TraesCS3A01G476100 chr1D 89.013 446 32 5 2097 2537 197244800 197244367 1.150000e-148 536.0
29 TraesCS3A01G476100 chr1D 94.161 274 11 3 2547 2820 263328344 263328612 2.020000e-111 412.0
30 TraesCS3A01G476100 chr1D 89.547 287 25 4 2252 2537 319794593 319794311 2.670000e-95 359.0
31 TraesCS3A01G476100 chr3B 94.585 277 12 3 2547 2820 310607803 310608079 2.600000e-115 425.0
32 TraesCS3A01G476100 chr2B 94.245 278 11 4 2547 2820 621975777 621975501 1.210000e-113 420.0
33 TraesCS3A01G476100 chrUn 94.161 274 11 2 2547 2820 25805942 25805674 2.020000e-111 412.0
34 TraesCS3A01G476100 chr4A 85.973 221 23 6 1175 1388 707036866 707037085 2.190000e-56 230.0


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 TraesCS3A01G476100 chr3A 707464127 707466946 2819 True 5208.0 5208 100.000 1 2820 1 chr3A.!!$R2 2819
1 TraesCS3A01G476100 chr4B 657374095 657376940 2845 True 4056.0 4056 92.574 1 2819 1 chr4B.!!$R1 2818
2 TraesCS3A01G476100 chr6B 6167990 6168831 841 True 944.0 944 87.322 1041 1862 1 chr6B.!!$R1 821
3 TraesCS3A01G476100 chr6D 2957417 2958362 945 True 457.5 793 85.810 931 1862 2 chr6D.!!$R2 931
4 TraesCS3A01G476100 chr6A 1985232 1986047 815 False 734.0 734 83.412 1045 1862 1 chr6A.!!$F1 817

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
140 142 0.100146 GCAAACTATGAGGCAGCTGC 59.9 55.0 30.88 30.88 41.14 5.25 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2097 2186 0.108945 CAGAGCACATGAGAGCACGA 60.109 55.0 0.0 0.0 33.43 4.35 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
40 41 0.525029 GACCGTTCGTAGCTAGTGGC 60.525 60.000 0.00 0.00 42.19 5.01
107 109 7.535139 ACCTATGTACGTGGAAATGATTTTTG 58.465 34.615 0.00 0.00 0.00 2.44
136 138 7.976135 AAATATAGAGCAAACTATGAGGCAG 57.024 36.000 0.00 0.00 35.19 4.85
140 142 0.100146 GCAAACTATGAGGCAGCTGC 59.900 55.000 30.88 30.88 41.14 5.25
142 144 1.400846 CAAACTATGAGGCAGCTGCAG 59.599 52.381 37.63 27.54 44.36 4.41
143 145 0.617413 AACTATGAGGCAGCTGCAGT 59.383 50.000 37.63 28.20 44.36 4.40
164 166 1.885887 TCAAATTTGACCCGCTTCCAG 59.114 47.619 16.91 0.00 31.01 3.86
174 176 1.448540 CGCTTCCAGCTGAATCGGT 60.449 57.895 17.39 0.00 38.57 4.69
176 178 0.391661 GCTTCCAGCTGAATCGGTGA 60.392 55.000 17.39 0.00 38.45 4.02
177 179 1.945819 GCTTCCAGCTGAATCGGTGAA 60.946 52.381 17.39 7.21 38.45 3.18
192 194 6.747659 ATCGGTGAAAATTTGTCTTTTTCG 57.252 33.333 0.00 0.00 43.03 3.46
193 195 5.038033 TCGGTGAAAATTTGTCTTTTTCGG 58.962 37.500 0.00 0.00 43.03 4.30
196 198 5.276820 GGTGAAAATTTGTCTTTTTCGGCAG 60.277 40.000 0.00 0.00 43.03 4.85
209 211 0.911769 TCGGCAGAGGTGGATCAAAT 59.088 50.000 0.00 0.00 0.00 2.32
210 212 1.281867 TCGGCAGAGGTGGATCAAATT 59.718 47.619 0.00 0.00 0.00 1.82
252 254 5.851720 TGGTCAATTGTGCATTAAACATGT 58.148 33.333 5.13 0.00 0.00 3.21
296 298 7.215789 TGAGTATGTCCAATTTTGCAACAAAT 58.784 30.769 0.00 0.00 0.00 2.32
400 403 8.661352 AAAACTCCCTTTGTCAATATTGTTTG 57.339 30.769 14.97 3.30 0.00 2.93
421 424 7.014711 TGTTTGCCAATCCAAGATGTAAACTTA 59.985 33.333 0.00 0.00 0.00 2.24
423 426 8.815565 TTGCCAATCCAAGATGTAAACTTATA 57.184 30.769 0.00 0.00 0.00 0.98
424 427 8.220755 TGCCAATCCAAGATGTAAACTTATAC 57.779 34.615 0.00 0.00 0.00 1.47
530 533 6.017934 GCGTTGTGATTGGTCAATAGACATAT 60.018 38.462 8.11 0.00 46.80 1.78
536 539 4.664150 TGGTCAATAGACATATCACGCA 57.336 40.909 0.00 0.00 46.80 5.24
578 581 3.869272 CTGCGAGCATCCAACGGC 61.869 66.667 0.00 0.00 0.00 5.68
624 627 1.435577 CACGTAACCCTAACACAGCC 58.564 55.000 0.00 0.00 0.00 4.85
661 664 1.608717 CGTCCCCTTCTCTCCCACAG 61.609 65.000 0.00 0.00 0.00 3.66
663 666 2.674220 CCCCTTCTCTCCCACAGCC 61.674 68.421 0.00 0.00 0.00 4.85
664 667 2.581354 CCTTCTCTCCCACAGCCG 59.419 66.667 0.00 0.00 0.00 5.52
666 669 3.672295 CTTCTCTCCCACAGCCGCC 62.672 68.421 0.00 0.00 0.00 6.13
668 671 4.463879 CTCTCCCACAGCCGCCAG 62.464 72.222 0.00 0.00 0.00 4.85
708 728 3.244249 CGATCCACTTCTATCCCTTTCCC 60.244 52.174 0.00 0.00 0.00 3.97
726 746 2.887568 CGATCACACCTCGCTGCC 60.888 66.667 0.00 0.00 0.00 4.85
730 750 1.954362 ATCACACCTCGCTGCCTCTC 61.954 60.000 0.00 0.00 0.00 3.20
796 816 3.488423 CTGCAAGTCCCTCCACCT 58.512 61.111 0.00 0.00 0.00 4.00
798 818 0.111253 CTGCAAGTCCCTCCACCTTT 59.889 55.000 0.00 0.00 0.00 3.11
839 859 1.899437 GCAACGACCATCCCTCTCCA 61.899 60.000 0.00 0.00 0.00 3.86
846 866 1.742768 CATCCCTCTCCACCGTAGC 59.257 63.158 0.00 0.00 0.00 3.58
847 867 1.828660 ATCCCTCTCCACCGTAGCG 60.829 63.158 0.00 0.00 0.00 4.26
863 883 3.151022 CGTGCCCTCCTCCTCCTC 61.151 72.222 0.00 0.00 0.00 3.71
864 884 2.766229 GTGCCCTCCTCCTCCTCC 60.766 72.222 0.00 0.00 0.00 4.30
865 885 2.955246 TGCCCTCCTCCTCCTCCT 60.955 66.667 0.00 0.00 0.00 3.69
886 906 0.660488 CTCGAGTCAGATCCGGACAG 59.340 60.000 6.12 0.00 37.74 3.51
901 921 2.203126 CAGCCCAGCCTCGAATCC 60.203 66.667 0.00 0.00 0.00 3.01
906 926 2.721167 CCAGCCTCGAATCCGTCCA 61.721 63.158 0.00 0.00 37.05 4.02
913 933 1.189524 TCGAATCCGTCCACACCCTT 61.190 55.000 0.00 0.00 37.05 3.95
920 940 2.204090 TCCACACCCTTCCCTCCC 60.204 66.667 0.00 0.00 0.00 4.30
928 948 1.997874 CCTTCCCTCCCCTCCACTG 60.998 68.421 0.00 0.00 0.00 3.66
985 1005 1.145945 GAATTCCCCATTCCCCTCTCC 59.854 57.143 0.00 0.00 36.02 3.71
986 1006 0.702706 ATTCCCCATTCCCCTCTCCC 60.703 60.000 0.00 0.00 0.00 4.30
1119 1171 1.153765 CGACGAAGGAGATGCTGCA 60.154 57.895 4.13 4.13 0.00 4.41
1123 1175 1.452833 GAAGGAGATGCTGCACCCC 60.453 63.158 3.57 6.58 0.00 4.95
1125 1177 4.101448 GGAGATGCTGCACCCCGT 62.101 66.667 3.57 0.00 0.00 5.28
1311 1382 1.210234 TGGCTGATCGTCATGGACAAT 59.790 47.619 0.00 0.00 32.09 2.71
1313 1384 2.484417 GGCTGATCGTCATGGACAATCT 60.484 50.000 0.00 0.00 28.51 2.40
1411 1482 2.851102 CCATCCATCCGGCCTCCT 60.851 66.667 0.00 0.00 0.00 3.69
1533 1609 5.753438 CAGTGTTGCTTTCTGTCAAGTACTA 59.247 40.000 0.00 0.00 0.00 1.82
1540 1616 6.595326 TGCTTTCTGTCAAGTACTATTCATGG 59.405 38.462 0.00 0.00 0.00 3.66
1625 1702 4.201822 GGAAGATTTACAACGTCTCATGCC 60.202 45.833 0.00 0.00 0.00 4.40
1903 1984 7.117379 CACACCATAGAGCATAATACATGACAG 59.883 40.741 0.00 0.00 0.00 3.51
1969 2050 3.104766 GTGGCATCCACGAGCATG 58.895 61.111 0.00 0.00 44.95 4.06
1978 2067 3.829886 TCCACGAGCATGATGTTTTTC 57.170 42.857 0.00 0.00 0.00 2.29
2043 2132 7.219484 AGCCATTGTTGGTATCTATAATTGC 57.781 36.000 0.00 0.00 45.57 3.56
2062 2151 1.604278 GCAGTGGTCAAACTGGAGTTC 59.396 52.381 6.48 0.00 46.34 3.01
2087 2176 5.006844 TGCTGTTTTGATTTTCATGCTTGTG 59.993 36.000 0.00 0.00 0.00 3.33
2097 2186 8.252417 TGATTTTCATGCTTGTGCTATAAATGT 58.748 29.630 0.00 0.00 40.48 2.71
2109 2198 4.746611 TGCTATAAATGTCGTGCTCTCATG 59.253 41.667 0.00 0.00 0.00 3.07
2160 2249 5.048782 TGACATTGGTTCACTAATGCTTGTC 60.049 40.000 14.14 7.86 45.19 3.18
2166 2255 6.007076 TGGTTCACTAATGCTTGTCCATTAA 58.993 36.000 0.00 0.00 37.27 1.40
2169 2258 7.067494 GGTTCACTAATGCTTGTCCATTAATCT 59.933 37.037 0.00 0.00 37.27 2.40
2306 2395 8.932945 TCATGACTGCTATTTAGAACTAAGTG 57.067 34.615 0.00 0.00 0.00 3.16
2334 2423 7.273815 TCCGTAAGTGTTTGTTGAAAATGAAAC 59.726 33.333 0.00 0.00 33.86 2.78
2342 2431 7.600375 TGTTTGTTGAAAATGAAACTGCAGTTA 59.400 29.630 31.31 18.08 37.25 2.24
2382 2471 1.195674 GCTCTCAAACGTCAGAAAGGC 59.804 52.381 0.00 0.00 0.00 4.35
2406 2495 4.160065 TGCTATTGCATTTACATTGCTGGT 59.840 37.500 0.00 0.00 45.31 4.00
2432 2521 1.002257 TGCATTGACCGATGGTGCT 60.002 52.632 0.00 0.00 35.25 4.40
2447 2536 0.474184 GTGCTGCCATATACCCCTGT 59.526 55.000 0.00 0.00 0.00 4.00
2450 2539 1.271054 GCTGCCATATACCCCTGTCAG 60.271 57.143 0.00 0.00 0.00 3.51
2467 2556 4.883083 TGTCAGTACCTGATTGTTCTCAC 58.117 43.478 0.00 0.00 42.73 3.51
2468 2557 4.246458 GTCAGTACCTGATTGTTCTCACC 58.754 47.826 0.00 0.00 42.73 4.02
2479 2568 6.009589 TGATTGTTCTCACCCATTATTGTGT 58.990 36.000 0.00 0.00 34.14 3.72
2505 2594 2.880890 GCGCCTTCTTGTTCATATCCAT 59.119 45.455 0.00 0.00 0.00 3.41
2506 2595 3.316308 GCGCCTTCTTGTTCATATCCATT 59.684 43.478 0.00 0.00 0.00 3.16
2545 2634 4.287067 CCAACATCTACATATACCCCTGCT 59.713 45.833 0.00 0.00 0.00 4.24
2627 2716 2.969628 CATACACATCCCTCCTCCTCT 58.030 52.381 0.00 0.00 0.00 3.69
2638 2733 3.031013 CCTCCTCCTCTTCTCTTCTTCC 58.969 54.545 0.00 0.00 0.00 3.46
2643 2738 2.383683 TCCTCTTCTCTTCTTCCTCCCA 59.616 50.000 0.00 0.00 0.00 4.37
2645 2740 3.779738 CCTCTTCTCTTCTTCCTCCCATT 59.220 47.826 0.00 0.00 0.00 3.16
2654 2749 0.121197 TTCCTCCCATTGTCTCCCCT 59.879 55.000 0.00 0.00 0.00 4.79
2659 2754 3.321950 CTCCCATTGTCTCCCCTAATCT 58.678 50.000 0.00 0.00 0.00 2.40
2707 2802 2.093658 GGTTCGTGAAGAGGCCAATCTA 60.094 50.000 5.01 0.00 0.00 1.98
2736 2831 4.847367 GAAGGGGGCTGGCCATGG 62.847 72.222 22.68 7.63 37.98 3.66
2752 2847 4.610714 GGAGAAGATCCCGCGGCC 62.611 72.222 22.85 9.31 43.01 6.13
2814 2909 3.376546 GGGATGTGAAGATGCAGAACTTC 59.623 47.826 18.06 18.06 41.67 3.01
2819 2914 4.883585 TGTGAAGATGCAGAACTTCTGTTT 59.116 37.500 22.31 7.73 45.94 2.83
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
19 20 1.404391 CCACTAGCTACGAACGGTCAT 59.596 52.381 0.00 0.00 0.00 3.06
84 86 7.757526 TCCAAAAATCATTTCCACGTACATAG 58.242 34.615 0.00 0.00 0.00 2.23
117 119 2.768527 AGCTGCCTCATAGTTTGCTCTA 59.231 45.455 0.00 0.00 0.00 2.43
119 121 1.669779 CAGCTGCCTCATAGTTTGCTC 59.330 52.381 0.00 0.00 0.00 4.26
132 134 1.796459 CAAATTTGAACTGCAGCTGCC 59.204 47.619 34.64 20.02 41.18 4.85
133 135 2.473984 GTCAAATTTGAACTGCAGCTGC 59.526 45.455 31.89 31.89 39.21 5.25
136 138 2.407090 GGGTCAAATTTGAACTGCAGC 58.593 47.619 30.02 13.53 44.25 5.25
142 144 2.035321 TGGAAGCGGGTCAAATTTGAAC 59.965 45.455 25.15 25.15 44.09 3.18
143 145 2.295909 CTGGAAGCGGGTCAAATTTGAA 59.704 45.455 22.07 4.47 39.21 2.69
164 166 4.798574 AGACAAATTTTCACCGATTCAGC 58.201 39.130 0.00 0.00 0.00 4.26
174 176 5.655488 TCTGCCGAAAAAGACAAATTTTCA 58.345 33.333 11.06 0.00 43.61 2.69
176 178 5.049828 CCTCTGCCGAAAAAGACAAATTTT 58.950 37.500 0.00 0.00 33.86 1.82
177 179 4.099419 ACCTCTGCCGAAAAAGACAAATTT 59.901 37.500 0.00 0.00 0.00 1.82
192 194 4.541973 AAAAATTTGATCCACCTCTGCC 57.458 40.909 0.00 0.00 0.00 4.85
224 226 6.765036 TGTTTAATGCACAATTGACCAAATGT 59.235 30.769 13.59 0.00 35.00 2.71
230 232 5.348451 GGACATGTTTAATGCACAATTGACC 59.652 40.000 13.59 2.79 0.00 4.02
276 278 9.887629 TCATATATTTGTTGCAAAATTGGACAT 57.112 25.926 0.00 0.00 32.16 3.06
277 279 9.887629 ATCATATATTTGTTGCAAAATTGGACA 57.112 25.926 0.00 0.00 32.16 4.02
288 290 8.507249 GTGAAGGACCTATCATATATTTGTTGC 58.493 37.037 0.00 0.00 0.00 4.17
321 323 7.877612 CCATTTTTCTAGTGCCCAAAATAAGTT 59.122 33.333 0.00 0.00 29.64 2.66
322 324 7.234577 TCCATTTTTCTAGTGCCCAAAATAAGT 59.765 33.333 0.00 0.00 29.64 2.24
327 329 5.878406 TTCCATTTTTCTAGTGCCCAAAA 57.122 34.783 0.00 0.00 0.00 2.44
400 403 8.220755 TGTATAAGTTTACATCTTGGATTGGC 57.779 34.615 0.00 0.00 0.00 4.52
480 483 8.768019 GCAGCAAAGAATTTAAAGAGTTCAAAT 58.232 29.630 0.00 0.00 35.03 2.32
503 506 2.995466 ATTGACCAATCACAACGCAG 57.005 45.000 0.00 0.00 33.38 5.18
536 539 3.504906 CCAACAGTGTTTGAGCATGATCT 59.495 43.478 12.92 0.00 0.00 2.75
553 556 0.462581 GGATGCTCGCAGATCCAACA 60.463 55.000 6.65 0.00 33.89 3.33
578 581 2.693864 ATGAGGGGGTGAGGGCTG 60.694 66.667 0.00 0.00 0.00 4.85
624 627 3.115556 CGAGGAAGAGGAGAGCCG 58.884 66.667 0.00 0.00 39.96 5.52
689 709 2.488836 GGGGAAAGGGATAGAAGTGGA 58.511 52.381 0.00 0.00 0.00 4.02
708 728 2.887568 GCAGCGAGGTGTGATCGG 60.888 66.667 4.17 0.00 40.50 4.18
794 814 0.105778 GGATCGAGAGGAGGCAAAGG 59.894 60.000 0.00 0.00 0.00 3.11
796 816 0.617535 TGGGATCGAGAGGAGGCAAA 60.618 55.000 0.00 0.00 0.00 3.68
798 818 1.456518 CTGGGATCGAGAGGAGGCA 60.457 63.158 0.00 0.00 0.00 4.75
822 842 1.265454 GGTGGAGAGGGATGGTCGTT 61.265 60.000 0.00 0.00 0.00 3.85
830 850 2.439701 CGCTACGGTGGAGAGGGA 60.440 66.667 0.00 0.00 0.00 4.20
846 866 3.151022 GAGGAGGAGGAGGGCACG 61.151 72.222 0.00 0.00 0.00 5.34
847 867 1.950748 TAGGAGGAGGAGGAGGGCAC 61.951 65.000 0.00 0.00 0.00 5.01
863 883 1.202663 TCCGGATCTGACTCGAGTAGG 60.203 57.143 20.09 14.07 0.00 3.18
864 884 1.868498 GTCCGGATCTGACTCGAGTAG 59.132 57.143 20.09 15.59 0.00 2.57
865 885 1.208776 TGTCCGGATCTGACTCGAGTA 59.791 52.381 20.09 2.97 33.83 2.59
886 906 4.162690 ACGGATTCGAGGCTGGGC 62.163 66.667 0.00 0.00 40.11 5.36
897 917 1.683441 GGAAGGGTGTGGACGGATT 59.317 57.895 0.00 0.00 0.00 3.01
901 921 2.663196 GAGGGAAGGGTGTGGACG 59.337 66.667 0.00 0.00 0.00 4.79
906 926 2.125225 GAGGGGAGGGAAGGGTGT 59.875 66.667 0.00 0.00 0.00 4.16
913 933 1.821966 TTAGCAGTGGAGGGGAGGGA 61.822 60.000 0.00 0.00 0.00 4.20
920 940 0.400213 TGTGGGTTTAGCAGTGGAGG 59.600 55.000 0.00 0.00 0.00 4.30
928 948 3.197983 ACAGAGACCTATGTGGGTTTAGC 59.802 47.826 0.00 0.00 40.06 3.09
985 1005 2.178580 GGCCATGGAGAGAGAGATAGG 58.821 57.143 18.40 0.00 0.00 2.57
986 1006 1.818060 CGGCCATGGAGAGAGAGATAG 59.182 57.143 18.40 0.00 0.00 2.08
1015 1035 4.431131 CCTGCGGGCCATGGAAGT 62.431 66.667 18.40 0.00 0.00 3.01
1043 1064 1.690633 GGTGGGAGATGAGGAGGCA 60.691 63.158 0.00 0.00 0.00 4.75
1091 1140 3.677648 CTTCGTCGACACCGGGGT 61.678 66.667 10.56 10.56 36.24 4.95
1100 1152 1.139734 GCAGCATCTCCTTCGTCGA 59.860 57.895 0.00 0.00 0.00 4.20
1103 1155 1.078848 GGTGCAGCATCTCCTTCGT 60.079 57.895 11.86 0.00 0.00 3.85
1326 1397 3.067320 CGATCATCTGGTGCTTAGAGTCA 59.933 47.826 0.00 0.00 0.00 3.41
1328 1399 3.067461 GTCGATCATCTGGTGCTTAGAGT 59.933 47.826 0.00 0.00 0.00 3.24
1332 1403 2.481969 GCAGTCGATCATCTGGTGCTTA 60.482 50.000 13.56 0.00 32.94 3.09
1411 1482 4.735132 CCGCTCTCGCAACGGGAA 62.735 66.667 0.00 0.00 43.23 3.97
1505 1578 1.265365 GACAGAAAGCAACACTGAGCC 59.735 52.381 0.00 0.00 35.85 4.70
1533 1609 6.135819 TCATATCATCAGGCTTCCATGAAT 57.864 37.500 0.00 0.00 30.43 2.57
1540 1616 4.760715 AGCAACATCATATCATCAGGCTTC 59.239 41.667 0.00 0.00 0.00 3.86
1625 1702 2.158959 CGAACCCGAAGTAGCGCTG 61.159 63.158 22.90 3.15 38.22 5.18
1884 1965 9.948964 AATAATGCTGTCATGTATTATGCTCTA 57.051 29.630 0.00 0.00 36.09 2.43
1903 1984 6.867662 ACCAGCTTCATACACTAATAATGC 57.132 37.500 0.00 0.00 0.00 3.56
1963 2044 2.167075 CCAGGGGAAAAACATCATGCTC 59.833 50.000 0.00 0.00 0.00 4.26
1969 2050 1.691434 TGCAACCAGGGGAAAAACATC 59.309 47.619 0.00 0.00 0.00 3.06
1978 2067 4.550076 TTCATTTAAATGCAACCAGGGG 57.450 40.909 21.15 0.00 36.36 4.79
2043 2132 2.874701 CAGAACTCCAGTTTGACCACTG 59.125 50.000 0.00 0.00 43.46 3.66
2062 2151 5.235616 ACAAGCATGAAAATCAAAACAGCAG 59.764 36.000 0.00 0.00 0.00 4.24
2087 2176 4.747108 ACATGAGAGCACGACATTTATAGC 59.253 41.667 0.00 0.00 0.00 2.97
2097 2186 0.108945 CAGAGCACATGAGAGCACGA 60.109 55.000 0.00 0.00 33.43 4.35
2109 2198 3.059884 TGAGATCGAACAAACAGAGCAC 58.940 45.455 0.00 0.00 0.00 4.40
2160 2249 7.043961 TGCTCACTGTACTCTAGATTAATGG 57.956 40.000 0.00 0.00 0.00 3.16
2166 2255 6.775142 ACATACATGCTCACTGTACTCTAGAT 59.225 38.462 0.00 0.00 32.24 1.98
2169 2258 6.377146 TCAACATACATGCTCACTGTACTCTA 59.623 38.462 0.00 0.00 32.24 2.43
2259 2348 5.835819 TGAAACTAGGAGACCCATCTATCTG 59.164 44.000 0.00 0.00 34.34 2.90
2306 2395 3.955771 TTCAACAAACACTTACGGAGC 57.044 42.857 0.00 0.00 0.00 4.70
2334 2423 5.410924 TCACTGTGCTATAGTTAACTGCAG 58.589 41.667 18.56 13.48 34.15 4.41
2398 2487 0.692476 TGCAGGACACTACCAGCAAT 59.308 50.000 0.00 0.00 46.40 3.56
2402 2491 2.350522 GTCAATGCAGGACACTACCAG 58.649 52.381 14.50 0.00 35.36 4.00
2406 2495 1.262417 TCGGTCAATGCAGGACACTA 58.738 50.000 19.36 5.01 37.00 2.74
2432 2521 2.190398 ACTGACAGGGGTATATGGCA 57.810 50.000 7.51 0.00 32.29 4.92
2450 2539 3.695830 TGGGTGAGAACAATCAGGTAC 57.304 47.619 0.00 0.00 0.00 3.34
2467 2556 1.002468 GCGCTGCTACACAATAATGGG 60.002 52.381 0.00 0.00 35.48 4.00
2468 2557 1.002468 GGCGCTGCTACACAATAATGG 60.002 52.381 7.64 0.00 0.00 3.16
2479 2568 0.034756 TGAACAAGAAGGCGCTGCTA 59.965 50.000 7.64 0.00 0.00 3.49
2627 2716 4.171234 AGACAATGGGAGGAAGAAGAGAA 58.829 43.478 0.00 0.00 0.00 2.87
2638 2733 3.072184 CAGATTAGGGGAGACAATGGGAG 59.928 52.174 0.00 0.00 0.00 4.30
2643 2738 4.723789 ACACATCAGATTAGGGGAGACAAT 59.276 41.667 0.00 0.00 0.00 2.71
2645 2740 3.452264 CACACATCAGATTAGGGGAGACA 59.548 47.826 0.00 0.00 0.00 3.41
2654 2749 5.963176 AAATGCACACACACATCAGATTA 57.037 34.783 0.00 0.00 0.00 1.75
2659 2754 6.292757 GCAAAAATAAATGCACACACACATCA 60.293 34.615 0.00 0.00 42.12 3.07
2707 2802 1.754201 GCCCCCTTCTTTCACAACACT 60.754 52.381 0.00 0.00 0.00 3.55
2736 2831 3.798954 CTGGCCGCGGGATCTTCTC 62.799 68.421 29.38 6.97 0.00 2.87
2752 2847 2.160721 TAACCTACCCTGAGGAGCTG 57.839 55.000 0.00 0.00 39.15 4.24
2761 2856 3.210074 AGATCTGTGGGATAACCTACCCT 59.790 47.826 3.01 0.00 45.30 4.34


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

AutoCloner maintained by Alex Coulton.