Multiple sequence alignment - TraesCS2B01G090800

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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 TraesCS2B01G090800 chr2B 100.000 4105 0 0 1 4105 52222196 52226300 0.000000e+00 7581.0
1 TraesCS2B01G090800 chr2B 94.571 4034 156 12 1 3992 52513505 52509493 0.000000e+00 6178.0
2 TraesCS2B01G090800 chr2D 93.409 2109 110 16 1602 3686 31896803 31898906 0.000000e+00 3097.0
3 TraesCS2B01G090800 chr2D 91.927 1375 109 2 230 1604 31895385 31896757 0.000000e+00 1923.0
4 TraesCS2B01G090800 chr2D 90.598 351 32 1 198 547 561897736 561897386 8.040000e-127 464.0
5 TraesCS2B01G090800 chr2A 91.837 2107 135 18 1602 3684 33952700 33954793 0.000000e+00 2904.0
6 TraesCS2B01G090800 chr2A 91.491 1375 116 1 230 1604 33785500 33786873 0.000000e+00 1890.0
7 TraesCS2B01G090800 chr2A 91.127 1375 120 2 230 1604 33951282 33952654 0.000000e+00 1862.0
8 TraesCS2B01G090800 chr2A 91.325 1268 69 13 2446 3684 33790456 33791711 0.000000e+00 1694.0
9 TraesCS2B01G090800 chr2A 93.772 851 51 2 1602 2452 33786919 33787767 0.000000e+00 1277.0
10 TraesCS2B01G090800 chr5D 86.471 2114 232 27 1602 3683 227545131 227547222 0.000000e+00 2270.0
11 TraesCS2B01G090800 chr5D 87.367 942 109 9 666 1604 227544151 227545085 0.000000e+00 1072.0
12 TraesCS2B01G090800 chr5D 92.949 312 22 0 3681 3992 452983081 452983392 4.840000e-124 455.0
13 TraesCS2B01G090800 chr5D 93.092 304 21 0 3689 3992 38930146 38929843 2.910000e-121 446.0
14 TraesCS2B01G090800 chr5B 85.607 2126 249 37 1602 3683 250952496 250954608 0.000000e+00 2178.0
15 TraesCS2B01G090800 chr5B 85.963 1033 119 15 577 1604 250951439 250952450 0.000000e+00 1081.0
16 TraesCS2B01G090800 chr5B 98.319 119 1 1 3987 4105 134200106 134199989 1.500000e-49 207.0
17 TraesCS2B01G090800 chr5B 85.915 142 16 4 40 179 602847225 602847364 9.190000e-32 148.0
18 TraesCS2B01G090800 chr5A 86.591 1857 215 19 1602 3434 305279058 305280904 0.000000e+00 2019.0
19 TraesCS2B01G090800 chr5A 87.197 1031 120 11 577 1604 305277991 305279012 0.000000e+00 1162.0
20 TraesCS2B01G090800 chr5A 91.746 315 25 1 3678 3992 323768889 323769202 1.750000e-118 436.0
21 TraesCS2B01G090800 chr5A 86.166 253 29 4 3434 3683 305280968 305281217 6.760000e-68 268.0
22 TraesCS2B01G090800 chr5A 80.755 265 44 5 3847 4105 109856896 109856633 2.500000e-47 200.0
23 TraesCS2B01G090800 chr6D 81.645 1994 302 31 1604 3544 441713516 441711534 0.000000e+00 1596.0
24 TraesCS2B01G090800 chr6A 81.459 1974 299 43 1604 3518 590895549 590893584 0.000000e+00 1555.0
25 TraesCS2B01G090800 chr6B 81.097 2005 296 50 1604 3544 667247696 667245711 0.000000e+00 1526.0
26 TraesCS2B01G090800 chr6B 79.561 1003 168 26 567 1546 667248794 667247806 0.000000e+00 682.0
27 TraesCS2B01G090800 chr6B 94.074 135 5 3 3973 4105 543679600 543679467 6.960000e-48 202.0
28 TraesCS2B01G090800 chr3D 91.014 345 31 0 203 547 36911340 36911684 2.230000e-127 466.0
29 TraesCS2B01G090800 chr3D 89.859 355 33 3 195 547 348130948 348130595 1.740000e-123 453.0
30 TraesCS2B01G090800 chr3D 92.605 311 23 0 3682 3992 137338244 137337934 8.090000e-122 448.0
31 TraesCS2B01G090800 chr3D 92.834 307 22 0 3686 3992 305145543 305145849 2.910000e-121 446.0
32 TraesCS2B01G090800 chr3D 99.160 119 1 0 3987 4105 13137787 13137669 8.940000e-52 215.0
33 TraesCS2B01G090800 chr4A 90.544 349 33 0 199 547 697565930 697565582 2.890000e-126 462.0
34 TraesCS2B01G090800 chr3A 90.571 350 31 1 200 547 466817424 466817075 2.890000e-126 462.0
35 TraesCS2B01G090800 chr7A 92.605 311 22 1 3682 3992 537761805 537761496 2.910000e-121 446.0
36 TraesCS2B01G090800 chr7A 95.385 130 5 1 3977 4105 383358477 383358606 5.380000e-49 206.0
37 TraesCS2B01G090800 chr4D 92.532 308 23 0 3685 3992 52864126 52863819 3.770000e-120 442.0
38 TraesCS2B01G090800 chr4D 81.119 143 23 4 40 179 46473127 46472986 1.210000e-20 111.0
39 TraesCS2B01G090800 chr7D 85.349 430 54 8 3680 4104 142607478 142607053 1.750000e-118 436.0
40 TraesCS2B01G090800 chr4B 87.245 196 16 8 3913 4105 165483191 165483380 8.940000e-52 215.0
41 TraesCS2B01G090800 chr4B 99.160 119 1 0 3987 4105 666923468 666923350 8.940000e-52 215.0
42 TraesCS2B01G090800 chr4B 79.577 142 24 5 40 179 67877289 67877151 3.380000e-16 97.1
43 TraesCS2B01G090800 chr1B 96.063 127 5 0 3979 4105 663289520 663289646 1.500000e-49 207.0
44 TraesCS2B01G090800 chr1B 88.732 142 15 1 40 180 482750574 482750715 5.460000e-39 172.0
45 TraesCS2B01G090800 chr1B 88.028 142 16 1 40 180 482719414 482719555 2.540000e-37 167.0


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 TraesCS2B01G090800 chr2B 52222196 52226300 4104 False 7581.000000 7581 100.000000 1 4105 1 chr2B.!!$F1 4104
1 TraesCS2B01G090800 chr2B 52509493 52513505 4012 True 6178.000000 6178 94.571000 1 3992 1 chr2B.!!$R1 3991
2 TraesCS2B01G090800 chr2D 31895385 31898906 3521 False 2510.000000 3097 92.668000 230 3686 2 chr2D.!!$F1 3456
3 TraesCS2B01G090800 chr2A 33951282 33954793 3511 False 2383.000000 2904 91.482000 230 3684 2 chr2A.!!$F2 3454
4 TraesCS2B01G090800 chr2A 33785500 33791711 6211 False 1620.333333 1890 92.196000 230 3684 3 chr2A.!!$F1 3454
5 TraesCS2B01G090800 chr5D 227544151 227547222 3071 False 1671.000000 2270 86.919000 666 3683 2 chr5D.!!$F2 3017
6 TraesCS2B01G090800 chr5B 250951439 250954608 3169 False 1629.500000 2178 85.785000 577 3683 2 chr5B.!!$F2 3106
7 TraesCS2B01G090800 chr5A 305277991 305281217 3226 False 1149.666667 2019 86.651333 577 3683 3 chr5A.!!$F2 3106
8 TraesCS2B01G090800 chr6D 441711534 441713516 1982 True 1596.000000 1596 81.645000 1604 3544 1 chr6D.!!$R1 1940
9 TraesCS2B01G090800 chr6A 590893584 590895549 1965 True 1555.000000 1555 81.459000 1604 3518 1 chr6A.!!$R1 1914
10 TraesCS2B01G090800 chr6B 667245711 667248794 3083 True 1104.000000 1526 80.329000 567 3544 2 chr6B.!!$R2 2977

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
340 343 0.578683 CTCATATGCACGCGTGGAAG 59.421 55.000 36.42 26.86 33.77 3.46 F
1095 1114 0.526662 GGTGTGTCGGACGAGAAGAT 59.473 55.000 3.34 0.00 0.00 2.40 F
1593 1616 2.301346 GGTATGGTCATCAAGCAAGGG 58.699 52.381 0.00 0.00 39.21 3.95 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1579 1602 2.352127 GCAGTTTCCCTTGCTTGATGAC 60.352 50.000 0.0 0.0 37.35 3.06 R
3067 5907 1.136961 TGGACCATAAGCCACCCACA 61.137 55.000 0.0 0.0 0.00 4.17 R
3350 6194 2.172505 TCCATCAACATAACCCATCGCT 59.827 45.455 0.0 0.0 0.00 4.93 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
90 93 4.650588 TCCCATTCCTGCAATTCCAAATAG 59.349 41.667 0.00 0.00 0.00 1.73
104 107 4.804108 TCCAAATAGTCCAAAACATTGCG 58.196 39.130 0.00 0.00 0.00 4.85
187 190 6.877322 CCAAAGCAATCTTCAATCTTCCAAAT 59.123 34.615 0.00 0.00 0.00 2.32
297 300 7.773489 TCTATGCTATATCTGCTATGATCCC 57.227 40.000 0.00 0.00 0.00 3.85
333 336 2.420022 AGTGGAAAACTCATATGCACGC 59.580 45.455 0.00 0.00 39.94 5.34
340 343 0.578683 CTCATATGCACGCGTGGAAG 59.421 55.000 36.42 26.86 33.77 3.46
386 389 6.268855 TCTTAGTCTTGCCTCTAGGACTAT 57.731 41.667 0.00 0.00 39.83 2.12
400 403 9.186837 CCTCTAGGACTATCTAAAGTGTTGTTA 57.813 37.037 0.00 0.00 37.39 2.41
416 419 8.902540 AGTGTTGTTAGTGATCATGTTTTCTA 57.097 30.769 0.00 0.00 0.00 2.10
431 434 8.981659 TCATGTTTTCTAGATCTTAGGATGTCA 58.018 33.333 0.00 0.00 31.46 3.58
472 475 8.960591 AGTCCTAAAACAACATTGAGATTATGG 58.039 33.333 0.00 0.00 0.00 2.74
484 487 7.716998 ACATTGAGATTATGGCGTTAGAAGAAT 59.283 33.333 0.00 0.00 0.00 2.40
512 515 3.980646 TTGAATCGACCCAAACTTGTG 57.019 42.857 0.00 0.00 0.00 3.33
711 714 7.589081 TGTATCCTATCTACTGTAAGGGTGAA 58.411 38.462 4.62 0.00 39.30 3.18
819 823 8.088365 GGGCATTAGTACTTCAAGATTTTTGTT 58.912 33.333 0.00 0.00 0.00 2.83
1081 1100 3.146847 GGTGGAAAGGAAGTAAGGTGTG 58.853 50.000 0.00 0.00 0.00 3.82
1084 1103 3.064931 GGAAAGGAAGTAAGGTGTGTCG 58.935 50.000 0.00 0.00 0.00 4.35
1095 1114 0.526662 GGTGTGTCGGACGAGAAGAT 59.473 55.000 3.34 0.00 0.00 2.40
1099 1118 3.791887 GTGTGTCGGACGAGAAGATAATG 59.208 47.826 3.34 0.00 0.00 1.90
1108 1127 3.961408 ACGAGAAGATAATGCTAGTGGGT 59.039 43.478 0.00 0.00 0.00 4.51
1213 1233 2.725221 ATGAAGTTGAGGAGATGCCC 57.275 50.000 0.00 0.00 37.37 5.36
1225 1245 3.269381 AGGAGATGCCCAAATAGGTTGAA 59.731 43.478 0.00 0.00 39.87 2.69
1253 1273 7.385267 AGGAGATGTTTATGACTGCATCTATC 58.615 38.462 5.97 3.12 45.37 2.08
1593 1616 2.301346 GGTATGGTCATCAAGCAAGGG 58.699 52.381 0.00 0.00 39.21 3.95
1712 1791 6.587273 GCTGAGTATTTCTACCAAATCTCCT 58.413 40.000 0.00 0.00 0.00 3.69
2029 2117 5.916883 CGCATTAAATTCAGCCTTTAGATGG 59.083 40.000 0.00 0.00 0.00 3.51
2052 2140 6.792473 TGGAATATATGGTCCAAGGTAGTCAT 59.208 38.462 3.98 0.00 41.02 3.06
2579 5404 7.877003 TGACGTTGGAACACATTTATGTAAAT 58.123 30.769 0.00 0.00 39.29 1.40
2841 5675 7.648039 ACCAAACTTATAGGTGTCAAAACAA 57.352 32.000 0.00 0.00 37.08 2.83
2967 5807 8.189119 TGGAACACAATTAAAAGGATAGCTTT 57.811 30.769 0.00 0.00 0.00 3.51
3067 5907 9.927081 ATTTTAGGATCCAATGACTAGACATTT 57.073 29.630 15.82 4.32 38.25 2.32
3350 6194 6.773200 TCGCCACCAATTTATCCAAATATACA 59.227 34.615 0.00 0.00 33.09 2.29
3355 6199 8.514594 CACCAATTTATCCAAATATACAGCGAT 58.485 33.333 0.00 0.00 33.09 4.58
3388 6232 2.930950 TGGATATAGCCACTTTGGTGC 58.069 47.619 5.37 0.00 40.46 5.01
3646 6583 8.821686 TTTGATGCCAAATAAGAATAGGAGAA 57.178 30.769 0.00 0.00 37.36 2.87
3687 6624 0.531974 TGTGCGGACTTCACTTCCAC 60.532 55.000 8.99 0.00 35.58 4.02
3717 6654 3.062234 GGATGCTGCTAACGTGAAACTAC 59.938 47.826 0.00 0.00 31.75 2.73
3721 6658 3.367025 GCTGCTAACGTGAAACTACGATT 59.633 43.478 5.23 0.00 46.46 3.34
3732 6669 6.396450 GTGAAACTACGATTAGAGACCCTTT 58.604 40.000 0.00 0.00 0.00 3.11
3747 6684 2.023673 CCCTTTGAGAAACTGTGTGCA 58.976 47.619 0.00 0.00 0.00 4.57
3765 6702 2.094338 TGCAATGCCATAATCGCAAACA 60.094 40.909 1.53 0.00 40.22 2.83
3766 6703 3.125316 GCAATGCCATAATCGCAAACAT 58.875 40.909 0.00 0.00 40.22 2.71
3768 6705 4.318263 GCAATGCCATAATCGCAAACATTC 60.318 41.667 0.00 0.00 40.22 2.67
3769 6706 4.652421 ATGCCATAATCGCAAACATTCA 57.348 36.364 0.00 0.00 40.22 2.57
3800 6737 7.799447 TGAAAACCGTCAGAAATGTATAAAACG 59.201 33.333 0.00 0.00 0.00 3.60
3826 6763 2.286008 CGATGACGGATGCATCAAACAG 60.286 50.000 27.25 14.60 41.66 3.16
3829 6766 1.315257 ACGGATGCATCAAACAGGGC 61.315 55.000 27.25 7.10 0.00 5.19
3831 6768 0.743097 GGATGCATCAAACAGGGCTC 59.257 55.000 27.25 2.88 0.00 4.70
3834 6771 1.246056 TGCATCAAACAGGGCTCAGC 61.246 55.000 0.00 0.00 0.00 4.26
3845 6782 1.202927 AGGGCTCAGCTTTTAGTTGCA 60.203 47.619 0.00 0.00 0.00 4.08
3865 6802 0.809636 TGTGCGATGAAGGGCATACG 60.810 55.000 0.00 0.00 41.83 3.06
3914 6851 2.092049 AGGAGGAACAAAAGAAACGGGT 60.092 45.455 0.00 0.00 0.00 5.28
3915 6852 2.034179 GGAGGAACAAAAGAAACGGGTG 59.966 50.000 0.00 0.00 0.00 4.61
3916 6853 2.028876 AGGAACAAAAGAAACGGGTGG 58.971 47.619 0.00 0.00 0.00 4.61
3934 6871 0.250901 GGCCAGATGAAGGTGTGTGT 60.251 55.000 0.00 0.00 0.00 3.72
3941 6878 6.528321 CCAGATGAAGGTGTGTGTGATATAT 58.472 40.000 0.00 0.00 0.00 0.86
3943 6880 7.816513 CCAGATGAAGGTGTGTGTGATATATAG 59.183 40.741 0.00 0.00 0.00 1.31
3948 6885 8.646900 TGAAGGTGTGTGTGATATATAGCATAA 58.353 33.333 3.63 0.00 0.00 1.90
3950 6887 7.615403 AGGTGTGTGTGATATATAGCATAAGG 58.385 38.462 3.63 0.00 0.00 2.69
3978 6915 6.092670 CACTCGGATGAACTGTTTGTGATTAT 59.907 38.462 0.00 0.00 0.00 1.28
3993 6930 7.640616 TTGTGATTATGCAACACAAAAGATG 57.359 32.000 20.89 0.00 46.56 2.90
3994 6931 6.979465 TGTGATTATGCAACACAAAAGATGA 58.021 32.000 13.87 0.00 40.72 2.92
3995 6932 7.432059 TGTGATTATGCAACACAAAAGATGAA 58.568 30.769 13.87 0.00 40.72 2.57
3996 6933 7.595875 TGTGATTATGCAACACAAAAGATGAAG 59.404 33.333 13.87 0.00 40.72 3.02
3997 6934 7.062605 GTGATTATGCAACACAAAAGATGAAGG 59.937 37.037 0.00 0.00 35.06 3.46
3998 6935 6.647334 TTATGCAACACAAAAGATGAAGGA 57.353 33.333 0.00 0.00 0.00 3.36
3999 6936 4.998671 TGCAACACAAAAGATGAAGGAA 57.001 36.364 0.00 0.00 0.00 3.36
4000 6937 5.336150 TGCAACACAAAAGATGAAGGAAA 57.664 34.783 0.00 0.00 0.00 3.13
4001 6938 5.916318 TGCAACACAAAAGATGAAGGAAAT 58.084 33.333 0.00 0.00 0.00 2.17
4002 6939 7.048629 TGCAACACAAAAGATGAAGGAAATA 57.951 32.000 0.00 0.00 0.00 1.40
4003 6940 7.669427 TGCAACACAAAAGATGAAGGAAATAT 58.331 30.769 0.00 0.00 0.00 1.28
4004 6941 7.599621 TGCAACACAAAAGATGAAGGAAATATG 59.400 33.333 0.00 0.00 0.00 1.78
4005 6942 7.412237 GCAACACAAAAGATGAAGGAAATATGC 60.412 37.037 0.00 0.00 0.00 3.14
4006 6943 6.633856 ACACAAAAGATGAAGGAAATATGCC 58.366 36.000 0.00 0.00 0.00 4.40
4007 6944 6.044682 CACAAAAGATGAAGGAAATATGCCC 58.955 40.000 0.00 0.00 0.00 5.36
4008 6945 5.960202 ACAAAAGATGAAGGAAATATGCCCT 59.040 36.000 0.00 0.00 0.00 5.19
4009 6946 7.068593 CACAAAAGATGAAGGAAATATGCCCTA 59.931 37.037 0.00 0.00 31.36 3.53
4010 6947 7.286316 ACAAAAGATGAAGGAAATATGCCCTAG 59.714 37.037 0.00 0.00 31.36 3.02
4011 6948 6.770286 AAGATGAAGGAAATATGCCCTAGA 57.230 37.500 0.00 0.00 31.36 2.43
4012 6949 6.371595 AGATGAAGGAAATATGCCCTAGAG 57.628 41.667 0.00 0.00 31.36 2.43
4013 6950 4.982241 TGAAGGAAATATGCCCTAGAGG 57.018 45.455 0.00 0.00 39.47 3.69
4087 7024 5.749596 TCATGCCAGAATTGTATTAACCG 57.250 39.130 0.00 0.00 0.00 4.44
4088 7025 4.578516 TCATGCCAGAATTGTATTAACCGG 59.421 41.667 0.00 0.00 0.00 5.28
4089 7026 4.223556 TGCCAGAATTGTATTAACCGGA 57.776 40.909 9.46 0.00 0.00 5.14
4090 7027 4.590918 TGCCAGAATTGTATTAACCGGAA 58.409 39.130 9.46 0.00 0.00 4.30
4091 7028 5.010933 TGCCAGAATTGTATTAACCGGAAA 58.989 37.500 9.46 1.61 0.00 3.13
4092 7029 5.106078 TGCCAGAATTGTATTAACCGGAAAC 60.106 40.000 9.46 0.00 0.00 2.78
4093 7030 5.124936 GCCAGAATTGTATTAACCGGAAACT 59.875 40.000 9.46 0.00 0.00 2.66
4094 7031 6.349860 GCCAGAATTGTATTAACCGGAAACTT 60.350 38.462 9.46 0.00 0.00 2.66
4095 7032 7.148205 GCCAGAATTGTATTAACCGGAAACTTA 60.148 37.037 9.46 0.00 0.00 2.24
4096 7033 8.395633 CCAGAATTGTATTAACCGGAAACTTAG 58.604 37.037 9.46 0.00 0.00 2.18
4097 7034 8.943002 CAGAATTGTATTAACCGGAAACTTAGT 58.057 33.333 9.46 0.00 0.00 2.24
4100 7037 9.723601 AATTGTATTAACCGGAAACTTAGTACA 57.276 29.630 9.46 10.88 28.23 2.90
4101 7038 9.895138 ATTGTATTAACCGGAAACTTAGTACAT 57.105 29.630 9.46 2.28 29.53 2.29
4102 7039 8.706492 TGTATTAACCGGAAACTTAGTACATG 57.294 34.615 9.46 0.00 0.00 3.21
4103 7040 8.313292 TGTATTAACCGGAAACTTAGTACATGT 58.687 33.333 9.46 2.69 0.00 3.21
4104 7041 7.605410 ATTAACCGGAAACTTAGTACATGTG 57.395 36.000 9.46 0.00 0.00 3.21
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
77 80 7.520686 CAATGTTTTGGACTATTTGGAATTGC 58.479 34.615 0.00 0.00 0.00 3.56
90 93 0.943835 GTGGCCGCAATGTTTTGGAC 60.944 55.000 12.58 0.00 33.22 4.02
104 107 1.279025 TAGTCCTGATTGGGGTGGCC 61.279 60.000 0.00 0.00 36.20 5.36
139 142 6.187682 GGGAGATGGATCAAAACCTTTAGAA 58.812 40.000 0.00 0.00 0.00 2.10
187 190 8.247562 GGCATATTTCCAACACTTAAATGTACA 58.752 33.333 0.00 0.00 30.75 2.90
284 287 4.081476 CACATATTCCGGGATCATAGCAGA 60.081 45.833 0.00 0.00 0.00 4.26
297 300 6.094048 AGTTTTCCACTGAATCACATATTCCG 59.906 38.462 0.00 0.00 32.83 4.30
386 389 8.902540 AACATGATCACTAACAACACTTTAGA 57.097 30.769 0.00 0.00 31.92 2.10
400 403 9.206690 TCCTAAGATCTAGAAAACATGATCACT 57.793 33.333 0.00 0.00 38.13 3.41
472 475 9.752274 GATTCAATATGATCATTCTTCTAACGC 57.248 33.333 14.65 0.00 0.00 4.84
484 487 6.356556 AGTTTGGGTCGATTCAATATGATCA 58.643 36.000 0.00 0.00 0.00 2.92
711 714 6.828785 GGATAATGTTGACCCTAGTTGATTGT 59.171 38.462 0.00 0.00 0.00 2.71
792 796 7.451566 ACAAAAATCTTGAAGTACTAATGCCCT 59.548 33.333 0.00 0.00 0.00 5.19
819 823 9.841295 ATAATTGACCGCCTCTTAGTTTTTATA 57.159 29.630 0.00 0.00 0.00 0.98
964 982 8.489990 TGAAATGTTCAATTTGTTGATGTGTT 57.510 26.923 0.00 0.00 36.59 3.32
1076 1095 0.526662 ATCTTCTCGTCCGACACACC 59.473 55.000 0.00 0.00 0.00 4.16
1081 1100 3.357166 AGCATTATCTTCTCGTCCGAC 57.643 47.619 0.00 0.00 0.00 4.79
1084 1103 4.551388 CCACTAGCATTATCTTCTCGTCC 58.449 47.826 0.00 0.00 0.00 4.79
1108 1127 9.709495 CTTATTGACTTTTTGATTCAATGGGAA 57.291 29.630 0.00 0.00 37.93 3.97
1213 1233 5.749462 ACATCTCCTCCTTCAACCTATTTG 58.251 41.667 0.00 0.00 36.42 2.32
1225 1245 3.776969 TGCAGTCATAAACATCTCCTCCT 59.223 43.478 0.00 0.00 0.00 3.69
1250 1270 5.425217 TCAAGGCTGGTTGTAGATTCAGATA 59.575 40.000 0.00 0.00 0.00 1.98
1253 1273 3.937706 CTCAAGGCTGGTTGTAGATTCAG 59.062 47.826 0.00 0.00 0.00 3.02
1579 1602 2.352127 GCAGTTTCCCTTGCTTGATGAC 60.352 50.000 0.00 0.00 37.35 3.06
1748 1827 2.375174 TGTTCCTGTAGGGCACTCAATT 59.625 45.455 0.00 0.00 35.41 2.32
2018 2106 6.721318 TGGACCATATATTCCATCTAAAGGC 58.279 40.000 2.48 0.00 36.96 4.35
2362 2471 4.038042 TCCACGATGCACTTAGATCCTTAG 59.962 45.833 0.00 0.00 0.00 2.18
2412 2521 2.624029 CCCCTATCCCATTTGCAACACT 60.624 50.000 0.00 0.00 0.00 3.55
2579 5404 3.255642 GGCAAGTCTTTAAGCCATCAACA 59.744 43.478 7.40 0.00 46.26 3.33
2790 5623 7.472334 AGCCAATGTCTTCAAGTTTTCATAT 57.528 32.000 0.00 0.00 0.00 1.78
2926 5766 8.415950 TTGTGTTCCATATTACCAAGAACATT 57.584 30.769 7.10 0.00 45.95 2.71
2947 5787 8.122952 CGAGGTAAAGCTATCCTTTTAATTGTG 58.877 37.037 5.87 0.00 40.85 3.33
2967 5807 2.852449 TCAAATGTTTGTGGCGAGGTA 58.148 42.857 5.48 0.00 39.18 3.08
3067 5907 1.136961 TGGACCATAAGCCACCCACA 61.137 55.000 0.00 0.00 0.00 4.17
3102 5942 5.104569 GGAAAATTTCCCTTGGCCAATATCA 60.105 40.000 20.85 2.63 44.30 2.15
3303 6147 5.820423 CGACATACCCAAATTTCCTGTCATA 59.180 40.000 12.08 0.00 32.98 2.15
3350 6194 2.172505 TCCATCAACATAACCCATCGCT 59.827 45.455 0.00 0.00 0.00 4.93
3355 6199 5.311913 TGGCTATATCCATCAACATAACCCA 59.688 40.000 0.00 0.00 0.00 4.51
3388 6232 3.321111 AGGTCCACCATAGTAAGTATGCG 59.679 47.826 0.00 0.00 37.76 4.73
3672 6609 2.927014 GCAGTAGTGGAAGTGAAGTCCG 60.927 54.545 0.00 0.00 38.06 4.79
3674 6611 3.321497 CTGCAGTAGTGGAAGTGAAGTC 58.679 50.000 5.25 0.00 0.00 3.01
3708 6645 5.579564 AGGGTCTCTAATCGTAGTTTCAC 57.420 43.478 0.00 0.00 0.00 3.18
3709 6646 6.209986 TCAAAGGGTCTCTAATCGTAGTTTCA 59.790 38.462 0.00 0.00 0.00 2.69
3717 6654 5.578727 CAGTTTCTCAAAGGGTCTCTAATCG 59.421 44.000 0.00 0.00 0.00 3.34
3721 6658 4.654262 ACACAGTTTCTCAAAGGGTCTCTA 59.346 41.667 0.00 0.00 0.00 2.43
3732 6669 1.337703 GGCATTGCACACAGTTTCTCA 59.662 47.619 11.39 0.00 0.00 3.27
3747 6684 5.008619 TGAATGTTTGCGATTATGGCATT 57.991 34.783 4.78 0.00 40.62 3.56
3765 6702 7.447374 TTTCTGACGGTTTTCATACATGAAT 57.553 32.000 0.00 0.00 45.30 2.57
3766 6703 6.869315 TTTCTGACGGTTTTCATACATGAA 57.131 33.333 0.00 0.45 44.42 2.57
3768 6705 6.611381 ACATTTCTGACGGTTTTCATACATG 58.389 36.000 0.00 0.00 0.00 3.21
3769 6706 6.817765 ACATTTCTGACGGTTTTCATACAT 57.182 33.333 0.00 0.00 0.00 2.29
3800 6737 0.378257 ATGCATCCGTCATCGCAAAC 59.622 50.000 0.00 0.00 38.01 2.93
3826 6763 1.247567 TGCAACTAAAAGCTGAGCCC 58.752 50.000 0.00 0.00 0.00 5.19
3829 6766 3.240069 GCACATGCAACTAAAAGCTGAG 58.760 45.455 0.00 0.00 41.59 3.35
3831 6768 1.980844 CGCACATGCAACTAAAAGCTG 59.019 47.619 4.49 0.00 42.21 4.24
3834 6771 4.082274 TCATCGCACATGCAACTAAAAG 57.918 40.909 4.49 0.00 42.21 2.27
3845 6782 1.597742 GTATGCCCTTCATCGCACAT 58.402 50.000 0.00 0.00 37.93 3.21
3891 6828 3.211045 CCGTTTCTTTTGTTCCTCCTCA 58.789 45.455 0.00 0.00 0.00 3.86
3892 6829 2.552743 CCCGTTTCTTTTGTTCCTCCTC 59.447 50.000 0.00 0.00 0.00 3.71
3914 6851 0.250858 CACACACCTTCATCTGGCCA 60.251 55.000 4.71 4.71 0.00 5.36
3915 6852 0.250901 ACACACACCTTCATCTGGCC 60.251 55.000 0.00 0.00 0.00 5.36
3916 6853 0.877071 CACACACACCTTCATCTGGC 59.123 55.000 0.00 0.00 0.00 4.85
3934 6871 7.614192 TCCGAGTGAACCTTATGCTATATATCA 59.386 37.037 0.00 0.00 0.00 2.15
3941 6878 3.958147 TCATCCGAGTGAACCTTATGCTA 59.042 43.478 0.00 0.00 0.00 3.49
3943 6880 3.179443 TCATCCGAGTGAACCTTATGC 57.821 47.619 0.00 0.00 0.00 3.14
3978 6915 4.998671 TTCCTTCATCTTTTGTGTTGCA 57.001 36.364 0.00 0.00 0.00 4.08
3992 6929 4.982241 CCTCTAGGGCATATTTCCTTCA 57.018 45.455 0.00 0.00 34.75 3.02
4004 6941 8.637196 AATAACTTTATTATTGCCTCTAGGGC 57.363 34.615 13.60 13.60 44.71 5.19
4061 6998 8.349245 CGGTTAATACAATTCTGGCATGAATAA 58.651 33.333 0.00 3.63 35.82 1.40
4062 6999 7.040755 CCGGTTAATACAATTCTGGCATGAATA 60.041 37.037 0.00 0.16 35.82 1.75
4063 7000 6.239008 CCGGTTAATACAATTCTGGCATGAAT 60.239 38.462 0.00 6.42 38.19 2.57
4064 7001 5.067153 CCGGTTAATACAATTCTGGCATGAA 59.933 40.000 0.00 0.00 0.00 2.57
4065 7002 4.578516 CCGGTTAATACAATTCTGGCATGA 59.421 41.667 0.00 0.00 0.00 3.07
4066 7003 4.578516 TCCGGTTAATACAATTCTGGCATG 59.421 41.667 0.00 0.00 0.00 4.06
4067 7004 4.787551 TCCGGTTAATACAATTCTGGCAT 58.212 39.130 0.00 0.00 0.00 4.40
4068 7005 4.223556 TCCGGTTAATACAATTCTGGCA 57.776 40.909 0.00 0.00 0.00 4.92
4069 7006 5.124936 AGTTTCCGGTTAATACAATTCTGGC 59.875 40.000 0.00 0.00 0.00 4.85
4070 7007 6.753107 AGTTTCCGGTTAATACAATTCTGG 57.247 37.500 0.00 0.00 0.00 3.86
4071 7008 8.943002 ACTAAGTTTCCGGTTAATACAATTCTG 58.057 33.333 0.00 0.00 0.00 3.02
4074 7011 9.723601 TGTACTAAGTTTCCGGTTAATACAATT 57.276 29.630 0.00 0.00 0.00 2.32
4075 7012 9.895138 ATGTACTAAGTTTCCGGTTAATACAAT 57.105 29.630 0.00 0.00 28.05 2.71
4076 7013 9.153721 CATGTACTAAGTTTCCGGTTAATACAA 57.846 33.333 0.00 0.00 28.05 2.41
4077 7014 8.313292 ACATGTACTAAGTTTCCGGTTAATACA 58.687 33.333 0.00 3.81 28.60 2.29
4078 7015 8.598075 CACATGTACTAAGTTTCCGGTTAATAC 58.402 37.037 0.00 0.00 0.00 1.89
4079 7016 8.706492 CACATGTACTAAGTTTCCGGTTAATA 57.294 34.615 0.00 0.00 0.00 0.98
4080 7017 7.605410 CACATGTACTAAGTTTCCGGTTAAT 57.395 36.000 0.00 0.00 0.00 1.40


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

AutoCloner maintained by Alex Coulton.