Multiple sequence alignment - TraesCS6D01G166100

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 TraesCS6D01G166100 chr6D 100.000 8430 0 0 1 8430 147157280 147148851 0.000000e+00 15568.0
1 TraesCS6D01G166100 chr6B 96.534 5973 142 29 219 6176 258005482 258011404 0.000000e+00 9823.0
2 TraesCS6D01G166100 chr6B 97.978 1533 24 5 6171 7696 258011427 258012959 0.000000e+00 2652.0
3 TraesCS6D01G166100 chr6B 94.631 447 17 4 7691 8135 258013042 258013483 0.000000e+00 686.0
4 TraesCS6D01G166100 chr6B 93.617 235 11 3 8199 8430 258013488 258013721 1.740000e-91 348.0
5 TraesCS6D01G166100 chr6A 95.386 5006 175 26 3196 8180 200249801 200254771 0.000000e+00 7914.0
6 TraesCS6D01G166100 chr6A 94.186 3199 98 37 1 3176 200246681 200249814 0.000000e+00 4796.0
7 TraesCS6D01G166100 chr6A 91.139 237 7 6 8199 8430 200254761 200254988 8.220000e-80 309.0
8 TraesCS6D01G166100 chr3A 75.083 301 56 13 1075 1359 399580097 399579800 1.150000e-23 122.0
9 TraesCS6D01G166100 chr3A 97.778 45 1 0 7887 7931 119479828 119479872 2.520000e-10 78.7
10 TraesCS6D01G166100 chr3D 75.175 286 54 10 1090 1359 323327721 323328005 1.490000e-22 119.0
11 TraesCS6D01G166100 chr3D 72.549 255 57 12 1113 1359 394195030 394194781 4.220000e-08 71.3
12 TraesCS6D01G166100 chr3B 75.547 274 50 11 1102 1359 395858788 395858516 1.490000e-22 119.0
13 TraesCS6D01G166100 chr3B 72.308 260 59 12 1108 1359 513814959 513814705 1.520000e-07 69.4
14 TraesCS6D01G166100 chr2D 100.000 45 0 0 7887 7931 469737367 469737323 5.420000e-12 84.2
15 TraesCS6D01G166100 chr2A 97.778 45 1 0 7887 7931 611104669 611104625 2.520000e-10 78.7
16 TraesCS6D01G166100 chr7D 95.455 44 2 0 7888 7931 135361527 135361484 4.220000e-08 71.3
17 TraesCS6D01G166100 chr7D 93.617 47 3 0 7887 7933 452969839 452969885 4.220000e-08 71.3
18 TraesCS6D01G166100 chr7B 93.617 47 3 0 7887 7933 476199897 476199943 4.220000e-08 71.3
19 TraesCS6D01G166100 chr1A 89.091 55 4 1 7886 7938 347323161 347323107 5.460000e-07 67.6


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 TraesCS6D01G166100 chr6D 147148851 147157280 8429 True 15568.000000 15568 100.000000 1 8430 1 chr6D.!!$R1 8429
1 TraesCS6D01G166100 chr6B 258005482 258013721 8239 False 3377.250000 9823 95.690000 219 8430 4 chr6B.!!$F1 8211
2 TraesCS6D01G166100 chr6A 200246681 200254988 8307 False 4339.666667 7914 93.570333 1 8430 3 chr6A.!!$F1 8429

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
863 869 0.952280 GACAGTCCGTCAGTCAGTCA 59.048 55.000 0.00 0.0 44.69 3.41 F
1664 1682 0.249911 ACGCTGAGTGGTTCCAACTC 60.250 55.000 0.00 11.6 0.00 3.01 F
2990 3021 1.366111 TAATCGCGTTGCTTCAGCCC 61.366 55.000 5.77 0.0 41.18 5.19 F
3887 3921 1.621317 TCATTTCTGGAGTGTGCCGTA 59.379 47.619 0.00 0.0 0.00 4.02 F
4273 4316 1.276622 ACGAGTTCCTTGGGCATAGT 58.723 50.000 0.00 0.0 0.00 2.12 F
6107 6150 0.620556 TCAGGAAGATGCCTTGGGTC 59.379 55.000 0.00 0.0 35.66 4.46 F
6733 6806 0.391130 TGCACAGGTATTGCTCGTCC 60.391 55.000 0.00 0.0 40.86 4.79 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2614 2645 0.394216 TGTGTCAGGGGCATATGCAC 60.394 55.000 28.07 25.33 45.53 4.57 R
3398 3430 0.323629 GGTGGTTCCTGGTTCGATCA 59.676 55.000 0.00 0.00 0.00 2.92 R
4273 4316 1.746861 CGCTGCATTACCATCCTCCAA 60.747 52.381 0.00 0.00 0.00 3.53 R
5264 5307 1.347707 ACGGTGACATGTGGAGAATGT 59.652 47.619 1.15 0.00 40.93 2.71 R
6251 6324 0.687354 CAGGTGGAGGTGTGCTTAGT 59.313 55.000 0.00 0.00 0.00 2.24 R
6975 7051 1.017177 TGTTTGGCGTCATAGCGACC 61.017 55.000 0.00 0.00 42.07 4.79 R
8348 8524 0.748005 GTGGTGGGATCGATTGGGTG 60.748 60.000 0.00 0.00 0.00 4.61 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
23 24 1.473258 GCATCAATGGCCCACTTACA 58.527 50.000 0.00 0.00 0.00 2.41
73 74 2.286418 GGAATACTAGCAATGCACGTGC 60.286 50.000 33.11 33.11 42.55 5.34
94 95 3.036091 CCGAGGAGGATAAGTTTACCCA 58.964 50.000 0.00 0.00 45.00 4.51
170 172 9.832445 TCAATAATAGGTTGTATGTCTCCTTTC 57.168 33.333 0.00 0.00 0.00 2.62
237 239 0.955919 GGGAAGGAGCCAAGTTGACG 60.956 60.000 3.87 0.00 0.00 4.35
245 247 1.940613 AGCCAAGTTGACGACAGAAAC 59.059 47.619 3.87 0.00 0.00 2.78
247 249 2.561569 CCAAGTTGACGACAGAAACCT 58.438 47.619 3.87 0.00 0.00 3.50
248 250 3.724374 CCAAGTTGACGACAGAAACCTA 58.276 45.455 3.87 0.00 0.00 3.08
250 252 4.369182 CAAGTTGACGACAGAAACCTAGT 58.631 43.478 0.00 0.00 0.00 2.57
251 253 5.508489 CCAAGTTGACGACAGAAACCTAGTA 60.508 44.000 3.87 0.00 0.00 1.82
252 254 5.779529 AGTTGACGACAGAAACCTAGTAA 57.220 39.130 0.00 0.00 0.00 2.24
254 256 6.214399 AGTTGACGACAGAAACCTAGTAAAG 58.786 40.000 0.00 0.00 0.00 1.85
255 257 4.553323 TGACGACAGAAACCTAGTAAAGC 58.447 43.478 0.00 0.00 0.00 3.51
256 258 4.038282 TGACGACAGAAACCTAGTAAAGCA 59.962 41.667 0.00 0.00 0.00 3.91
257 259 4.952460 ACGACAGAAACCTAGTAAAGCAA 58.048 39.130 0.00 0.00 0.00 3.91
258 260 4.748600 ACGACAGAAACCTAGTAAAGCAAC 59.251 41.667 0.00 0.00 0.00 4.17
259 261 4.989168 CGACAGAAACCTAGTAAAGCAACT 59.011 41.667 0.00 0.00 0.00 3.16
260 262 6.154445 CGACAGAAACCTAGTAAAGCAACTA 58.846 40.000 0.00 0.00 0.00 2.24
261 263 6.308282 CGACAGAAACCTAGTAAAGCAACTAG 59.692 42.308 11.83 11.83 45.71 2.57
304 306 5.899547 TCTACATGAATAGTGTGAGGGTCAT 59.100 40.000 0.00 0.00 0.00 3.06
509 515 1.065701 CAGTTCCCTGATCTCCGTACG 59.934 57.143 8.69 8.69 41.50 3.67
510 516 1.101331 GTTCCCTGATCTCCGTACGT 58.899 55.000 15.21 0.00 0.00 3.57
660 666 2.418910 ATGCACGCTCGAGCCTAGT 61.419 57.895 30.66 20.13 37.91 2.57
862 868 3.777016 GACAGTCCGTCAGTCAGTC 57.223 57.895 0.00 0.00 44.69 3.51
863 869 0.952280 GACAGTCCGTCAGTCAGTCA 59.048 55.000 0.00 0.00 44.69 3.41
903 909 1.065709 GCCATTTCCAACCCTCTCGTA 60.066 52.381 0.00 0.00 0.00 3.43
984 999 2.107953 GGCTAGCGGCTGAAGGAG 59.892 66.667 13.86 2.19 41.46 3.69
985 1000 2.107953 GCTAGCGGCTGAAGGAGG 59.892 66.667 13.86 0.00 38.06 4.30
986 1001 2.427245 GCTAGCGGCTGAAGGAGGA 61.427 63.158 13.86 0.00 38.06 3.71
987 1002 1.739049 CTAGCGGCTGAAGGAGGAG 59.261 63.158 13.86 0.00 0.00 3.69
988 1003 1.743321 CTAGCGGCTGAAGGAGGAGG 61.743 65.000 13.86 0.00 0.00 4.30
989 1004 2.224805 TAGCGGCTGAAGGAGGAGGA 62.225 60.000 13.86 0.00 0.00 3.71
990 1005 3.087666 GCGGCTGAAGGAGGAGGAG 62.088 68.421 0.00 0.00 0.00 3.69
991 1006 2.430610 CGGCTGAAGGAGGAGGAGG 61.431 68.421 0.00 0.00 0.00 4.30
992 1007 1.002274 GGCTGAAGGAGGAGGAGGA 59.998 63.158 0.00 0.00 0.00 3.71
1020 1035 0.261696 TGGAGATCGTGAGGATGGGA 59.738 55.000 0.00 0.00 34.82 4.37
1362 1377 4.498520 ATGGAGCGGTGCGTCTCG 62.499 66.667 0.61 0.00 33.41 4.04
1385 1400 2.611292 CTCAATTCATCACCTCGCTTCC 59.389 50.000 0.00 0.00 0.00 3.46
1412 1427 4.810491 GCTCTGTTCATCCATTTCTCTCTC 59.190 45.833 0.00 0.00 0.00 3.20
1413 1428 5.350504 TCTGTTCATCCATTTCTCTCTCC 57.649 43.478 0.00 0.00 0.00 3.71
1579 1594 5.657745 TCTCCAACAAAATCATGGTATGCAT 59.342 36.000 3.79 3.79 35.66 3.96
1580 1595 5.904941 TCCAACAAAATCATGGTATGCATC 58.095 37.500 0.19 0.00 35.66 3.91
1581 1596 5.657745 TCCAACAAAATCATGGTATGCATCT 59.342 36.000 0.19 0.00 35.66 2.90
1582 1597 6.154877 TCCAACAAAATCATGGTATGCATCTT 59.845 34.615 0.19 0.00 35.66 2.40
1583 1598 7.341512 TCCAACAAAATCATGGTATGCATCTTA 59.658 33.333 0.19 0.00 35.66 2.10
1584 1599 8.145767 CCAACAAAATCATGGTATGCATCTTAT 58.854 33.333 0.19 0.00 0.00 1.73
1615 1630 2.355132 CAGCAGCTTCATGATCCTTCAC 59.645 50.000 0.00 0.00 33.85 3.18
1664 1682 0.249911 ACGCTGAGTGGTTCCAACTC 60.250 55.000 0.00 11.60 0.00 3.01
1688 1706 4.980434 CAGCTTCTGATCCTTGTTTGTTTG 59.020 41.667 0.00 0.00 32.44 2.93
1779 1797 2.128035 GACATCAGCGGAATCGTAAGG 58.872 52.381 0.00 0.00 38.89 2.69
1906 1929 2.437413 CCTGGGTCTGGAAAAACTAGC 58.563 52.381 0.00 0.00 0.00 3.42
2018 2041 4.092821 TCGTTCGGATACAGAAATTTGCAG 59.907 41.667 0.00 0.00 32.47 4.41
2179 2202 2.558378 CAGCATGATCTTCACATCGGT 58.442 47.619 0.00 0.00 39.69 4.69
2421 2445 5.428253 TGAAGGTGAGCTGTTATTCCATAC 58.572 41.667 0.00 0.00 0.00 2.39
2453 2484 5.425630 ACCCCAGCTTATTTAGAAGTAACG 58.574 41.667 0.00 0.00 0.00 3.18
2669 2700 4.462483 GTGCAGATTTTGGGTCTGGAAATA 59.538 41.667 5.41 0.00 44.04 1.40
2894 2925 6.600822 CACTGTTTATGGATGAAATCTCCACT 59.399 38.462 0.00 0.00 45.27 4.00
2957 2988 1.637553 AGGCAATCTGTCCACATCCTT 59.362 47.619 0.00 0.00 0.00 3.36
2972 3003 2.666862 CTTGGTGGCACGGCGTTA 60.667 61.111 11.19 0.00 0.00 3.18
2990 3021 1.366111 TAATCGCGTTGCTTCAGCCC 61.366 55.000 5.77 0.00 41.18 5.19
3230 3261 6.465084 ACATGTTAGGACTAGGAACTCAAAC 58.535 40.000 0.00 0.00 41.75 2.93
3252 3284 9.428363 CAAACTTGACATTTTTCATTGTGAATG 57.572 29.630 0.00 0.00 36.11 2.67
3398 3430 2.032681 GAGCTCAGGGTGCCGTTT 59.967 61.111 9.40 0.00 0.00 3.60
3431 3463 4.694233 CACCCTGCTGCGCTCACT 62.694 66.667 9.73 0.00 0.00 3.41
3550 3582 3.118531 AGATAGTCCAGGTTTGCATCCT 58.881 45.455 5.29 5.29 35.45 3.24
3657 3691 2.027745 ACCATCGCAATGACTGTCTTCT 60.028 45.455 9.51 0.00 34.61 2.85
3740 3774 1.743623 CGGCCTGGTCACGCATTTA 60.744 57.895 0.00 0.00 0.00 1.40
3887 3921 1.621317 TCATTTCTGGAGTGTGCCGTA 59.379 47.619 0.00 0.00 0.00 4.02
4076 4110 4.133078 CTCAGCTTGTTCTTCTGGTTCTT 58.867 43.478 0.00 0.00 0.00 2.52
4117 4151 3.139397 AGAGGTATGTCGAATCTCCCTCT 59.861 47.826 13.31 13.31 41.84 3.69
4273 4316 1.276622 ACGAGTTCCTTGGGCATAGT 58.723 50.000 0.00 0.00 0.00 2.12
4310 4353 1.592223 CGTCTCCTGGACCCTTGAC 59.408 63.158 0.00 0.00 41.64 3.18
4889 4932 5.009631 CCATTTACTCCCTTGTCAATCACA 58.990 41.667 0.00 0.00 0.00 3.58
5264 5307 7.360113 TGGTTACTGTGAGCAGAATGATATA 57.640 36.000 0.00 0.00 45.28 0.86
5436 5479 4.929479 ACTGATCTCTGGAGTACTGAACT 58.071 43.478 0.00 0.00 42.80 3.01
5949 5992 4.590647 TGAGGCTCCTTACTGATCTATTGG 59.409 45.833 12.86 0.00 0.00 3.16
5951 5994 5.410602 AGGCTCCTTACTGATCTATTGGAT 58.589 41.667 0.00 0.00 37.37 3.41
5975 6018 8.918202 ATAGAGCAACCGATTTCCAATTTATA 57.082 30.769 0.00 0.00 0.00 0.98
6107 6150 0.620556 TCAGGAAGATGCCTTGGGTC 59.379 55.000 0.00 0.00 35.66 4.46
6251 6324 6.016276 GGAGGAACAAAGCTTTGATAAGTGAA 60.016 38.462 38.78 0.00 40.55 3.18
6410 6483 5.341617 AGAATCTTCTTCACGACGGTTATC 58.658 41.667 0.00 0.00 32.55 1.75
6591 6664 5.975693 TCAATTCTTTGGGTTCCATGTAC 57.024 39.130 0.00 0.00 31.53 2.90
6733 6806 0.391130 TGCACAGGTATTGCTCGTCC 60.391 55.000 0.00 0.00 40.86 4.79
6756 6830 9.014297 GTCCCAGAAGATTTGAAAGAAAAGATA 57.986 33.333 0.00 0.00 0.00 1.98
6915 6991 6.127366 TGGACTGGGCATTTATGAAATTCTTC 60.127 38.462 0.00 0.00 0.00 2.87
6975 7051 3.569277 TCACATTTTATGGGATGATGGCG 59.431 43.478 0.00 0.00 37.88 5.69
6981 7057 4.241555 GGGATGATGGCGGTCGCT 62.242 66.667 15.04 0.00 41.60 4.93
7099 7175 5.648092 AGTGTCCTATGACTGGTTTATTTGC 59.352 40.000 0.00 0.00 42.28 3.68
7460 7536 1.806542 TGAAAACAGCTTCAGATCGCC 59.193 47.619 0.00 0.00 31.67 5.54
7543 7623 8.405531 CACAAATATTTGGTATCCGTTTCTCAT 58.594 33.333 27.43 2.70 42.34 2.90
7733 7901 2.420827 CCATTACCGACTAACATGGCCA 60.421 50.000 8.56 8.56 0.00 5.36
7850 8019 2.159338 AGATTTGTGAATGGTGATGCGC 60.159 45.455 0.00 0.00 0.00 6.09
7871 8040 3.544651 CTGTGTTTGTGTTCAGCATACG 58.455 45.455 0.00 0.00 0.00 3.06
7876 8045 5.115472 GTGTTTGTGTTCAGCATACGAATTG 59.885 40.000 0.00 0.00 0.00 2.32
7938 8107 8.303876 AGACGTTTTGGCAGTTTAAATATCATT 58.696 29.630 0.00 0.00 0.00 2.57
7948 8117 9.013490 GCAGTTTAAATATCATTGTAGCACTTG 57.987 33.333 0.00 0.00 0.00 3.16
7969 8138 7.970614 CACTTGGAAAATAGAGCCTTAATGAAC 59.029 37.037 0.00 0.00 0.00 3.18
8058 8227 7.718272 ATTCACATTTTCAATTGTTGAGGTG 57.282 32.000 5.13 10.00 41.38 4.00
8102 8271 6.488683 TCTTATTTCAACAACTAACAGGGTGG 59.511 38.462 0.00 0.00 0.00 4.61
8132 8301 9.243637 GCTATTGTGTCTCAAATTGTTTTGTTA 57.756 29.630 0.00 0.00 42.37 2.41
8184 8356 5.378230 TGATTTCATCATAGCCCTGAGTT 57.622 39.130 0.00 0.00 33.59 3.01
8185 8357 5.759059 TGATTTCATCATAGCCCTGAGTTT 58.241 37.500 0.00 0.00 33.59 2.66
8186 8358 6.189859 TGATTTCATCATAGCCCTGAGTTTT 58.810 36.000 0.00 0.00 33.59 2.43
8187 8359 6.664816 TGATTTCATCATAGCCCTGAGTTTTT 59.335 34.615 0.00 0.00 33.59 1.94
8221 8393 6.931840 AGATTATAGCCCTGAGAATTCGAAAC 59.068 38.462 0.00 0.00 0.00 2.78
8309 8485 1.065102 CCGCCAGATTCTGCAGATTTG 59.935 52.381 19.04 15.27 0.00 2.32
8366 8542 1.204786 ACACCCAATCGATCCCACCA 61.205 55.000 0.00 0.00 0.00 4.17
8382 8558 1.393539 CACCACCGAATCAACATCGAC 59.606 52.381 0.00 0.00 42.76 4.20
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
4 5 1.473258 TGTAAGTGGGCCATTGATGC 58.527 50.000 10.70 0.50 0.00 3.91
10 11 3.571590 TGAAGTTTTGTAAGTGGGCCAT 58.428 40.909 10.70 0.00 0.00 4.40
73 74 3.036091 TGGGTAAACTTATCCTCCTCGG 58.964 50.000 0.62 0.00 34.91 4.63
185 187 1.931635 GGTGTGCCCCTTCCATTTTA 58.068 50.000 0.00 0.00 0.00 1.52
187 189 4.539235 GGTGTGCCCCTTCCATTT 57.461 55.556 0.00 0.00 0.00 2.32
237 239 6.091034 GCTAGTTGCTTTACTAGGTTTCTGTC 59.909 42.308 17.18 1.92 45.01 3.51
261 263 5.408909 TGTAGACGATGATGTAGCTACTAGC 59.591 44.000 23.84 13.63 42.84 3.42
279 281 5.127194 TGACCCTCACACTATTCATGTAGAC 59.873 44.000 0.00 0.00 0.00 2.59
324 326 7.974675 TGTGACGAAAATTAATTCTCTGGATC 58.025 34.615 0.10 0.00 0.00 3.36
329 331 7.592938 TGCATTGTGACGAAAATTAATTCTCT 58.407 30.769 0.10 0.00 0.00 3.10
330 332 7.795431 TGCATTGTGACGAAAATTAATTCTC 57.205 32.000 0.10 0.00 0.00 2.87
331 333 7.814107 ACATGCATTGTGACGAAAATTAATTCT 59.186 29.630 0.00 0.00 37.11 2.40
332 334 7.952339 ACATGCATTGTGACGAAAATTAATTC 58.048 30.769 0.00 0.00 37.11 2.17
333 335 7.887996 ACATGCATTGTGACGAAAATTAATT 57.112 28.000 0.00 0.00 37.11 1.40
509 515 0.317479 CGGTGGATCGGAGGGATTAC 59.683 60.000 0.00 0.00 34.82 1.89
510 516 0.186630 TCGGTGGATCGGAGGGATTA 59.813 55.000 0.00 0.00 34.82 1.75
625 631 4.966787 TGGTTTGACCCGCCCAGC 62.967 66.667 0.00 0.00 37.50 4.85
626 632 2.035626 ATGGTTTGACCCGCCCAG 59.964 61.111 0.00 0.00 37.50 4.45
627 633 2.282816 CATGGTTTGACCCGCCCA 60.283 61.111 0.00 0.00 37.50 5.36
628 634 3.758931 GCATGGTTTGACCCGCCC 61.759 66.667 0.00 0.00 37.50 6.13
629 635 2.988684 TGCATGGTTTGACCCGCC 60.989 61.111 0.00 0.00 37.50 6.13
630 636 2.258286 GTGCATGGTTTGACCCGC 59.742 61.111 0.00 0.00 37.50 6.13
660 666 2.484065 GCTCTACTGCTCTCTAGTCGGA 60.484 54.545 0.00 0.00 0.00 4.55
673 679 1.618861 CTTGTCGTTCGGCTCTACTG 58.381 55.000 0.00 0.00 0.00 2.74
861 867 0.244721 CGTCAGTGGCTGATGACTGA 59.755 55.000 11.70 7.82 46.87 3.41
862 868 2.746997 CGTCAGTGGCTGATGACTG 58.253 57.895 11.70 5.84 46.87 3.51
903 909 1.153745 GCTCTCGTGGAAGATGCGT 60.154 57.895 0.00 0.00 0.00 5.24
984 999 4.565850 ATCGGCCCCTCCTCCTCC 62.566 72.222 0.00 0.00 0.00 4.30
985 1000 3.237741 CATCGGCCCCTCCTCCTC 61.238 72.222 0.00 0.00 0.00 3.71
986 1001 4.888325 CCATCGGCCCCTCCTCCT 62.888 72.222 0.00 0.00 0.00 3.69
987 1002 4.880426 TCCATCGGCCCCTCCTCC 62.880 72.222 0.00 0.00 0.00 4.30
988 1003 3.237741 CTCCATCGGCCCCTCCTC 61.238 72.222 0.00 0.00 0.00 3.71
989 1004 3.106859 ATCTCCATCGGCCCCTCCT 62.107 63.158 0.00 0.00 0.00 3.69
990 1005 2.527875 ATCTCCATCGGCCCCTCC 60.528 66.667 0.00 0.00 0.00 4.30
991 1006 3.064416 GATCTCCATCGGCCCCTC 58.936 66.667 0.00 0.00 0.00 4.30
1362 1377 0.659957 GCGAGGTGATGAATTGAGCC 59.340 55.000 0.00 0.00 0.00 4.70
1385 1400 4.437239 AGAAATGGATGAACAGAGCTACG 58.563 43.478 0.00 0.00 0.00 3.51
1579 1594 2.621338 CTGCTGTGCCGAAGAATAAGA 58.379 47.619 0.00 0.00 0.00 2.10
1580 1595 1.063174 GCTGCTGTGCCGAAGAATAAG 59.937 52.381 0.00 0.00 0.00 1.73
1581 1596 1.086696 GCTGCTGTGCCGAAGAATAA 58.913 50.000 0.00 0.00 0.00 1.40
1582 1597 0.250234 AGCTGCTGTGCCGAAGAATA 59.750 50.000 0.00 0.00 0.00 1.75
1583 1598 0.607489 AAGCTGCTGTGCCGAAGAAT 60.607 50.000 1.35 0.00 0.00 2.40
1584 1599 1.227943 AAGCTGCTGTGCCGAAGAA 60.228 52.632 1.35 0.00 0.00 2.52
1615 1630 1.486310 TCGGTTCTCCCATTCCATGAG 59.514 52.381 0.00 0.00 0.00 2.90
1660 1678 2.641815 ACAAGGATCAGAAGCTGGAGTT 59.358 45.455 0.00 0.00 31.51 3.01
1664 1682 3.152341 ACAAACAAGGATCAGAAGCTGG 58.848 45.455 0.00 0.00 31.51 4.85
1688 1706 7.378008 GCACTCAGCACATTCTGAAGGATTC 62.378 48.000 9.26 0.00 44.63 2.52
1906 1929 2.249413 CTGCCAGTGCCAGGAGTAGG 62.249 65.000 0.00 0.00 36.33 3.18
1918 1941 2.530151 TCCAGCTTCCCTGCCAGT 60.530 61.111 0.00 0.00 40.36 4.00
2018 2041 9.420118 ACATCTCTATATCTTCCCTGATCATAC 57.580 37.037 0.00 0.00 0.00 2.39
2179 2202 1.275291 GTCTCCCTCACCGTCATTTCA 59.725 52.381 0.00 0.00 0.00 2.69
2295 2319 6.480524 TTGAAACCACGATAAGAATCACTG 57.519 37.500 0.00 0.00 31.93 3.66
2421 2445 2.122783 TAAGCTGGGGTTTTGATCCG 57.877 50.000 0.00 0.00 0.00 4.18
2453 2484 8.184192 TCGATTCTCTTCAAAAAGGCAAATATC 58.816 33.333 0.00 0.00 33.03 1.63
2614 2645 0.394216 TGTGTCAGGGGCATATGCAC 60.394 55.000 28.07 25.33 45.53 4.57
2669 2700 2.428171 GCCAACCATTGTATCTGCACAT 59.572 45.455 0.00 0.00 0.00 3.21
2957 2988 2.032834 ATTAACGCCGTGCCACCA 59.967 55.556 0.00 0.00 0.00 4.17
2972 3003 2.690778 GGGCTGAAGCAACGCGATT 61.691 57.895 15.93 0.00 44.36 3.34
2990 3021 1.631072 CTCGTATGTTTCAGGCGCG 59.369 57.895 0.00 0.00 0.00 6.86
3186 3217 5.755409 TGTAGCATAGGGAGTTTCTTTCA 57.245 39.130 0.00 0.00 0.00 2.69
3198 3229 6.010850 TCCTAGTCCTAACATGTAGCATAGG 58.989 44.000 13.20 13.20 36.96 2.57
3230 3261 7.067116 GTGCATTCACAATGAAAAATGTCAAG 58.933 34.615 0.00 0.00 40.12 3.02
3252 3284 3.451178 TCCTTCCTAGATGTTACCTGTGC 59.549 47.826 0.00 0.00 0.00 4.57
3380 3412 2.520536 AAACGGCACCCTGAGCTCT 61.521 57.895 16.19 0.00 0.00 4.09
3398 3430 0.323629 GGTGGTTCCTGGTTCGATCA 59.676 55.000 0.00 0.00 0.00 2.92
3431 3463 3.512329 TGCTGATACCGAACTTGGAAGTA 59.488 43.478 0.00 0.00 38.57 2.24
3550 3582 6.409524 AATTGAGGAAGATTTCAACAAGCA 57.590 33.333 0.00 0.00 36.26 3.91
3657 3691 1.447140 GGTGCATCTCCGTACGCAA 60.447 57.895 10.49 0.00 35.87 4.85
3678 3712 1.821753 CACTCCATCCTCGACTGAGTT 59.178 52.381 0.00 0.00 40.85 3.01
3740 3774 0.029834 GCTCGGCGAATGCATTGAAT 59.970 50.000 18.59 0.00 45.35 2.57
3887 3921 6.042437 TGACATAGTAAGTCATGCAGATCCAT 59.958 38.462 4.13 0.00 40.80 3.41
4076 4110 3.374764 TCTAGCTATCAAGAAGCCACCA 58.625 45.455 0.00 0.00 41.02 4.17
4117 4151 6.877236 TGACTACATGAACAGATGCTGAATA 58.123 36.000 0.00 0.00 35.18 1.75
4168 4211 6.121590 TGCCTTGATGTTATCTGCAGAAATA 58.878 36.000 22.50 14.27 0.00 1.40
4273 4316 1.746861 CGCTGCATTACCATCCTCCAA 60.747 52.381 0.00 0.00 0.00 3.53
4310 4353 3.584406 ATCTGTCTGAAAGTCGACTGG 57.416 47.619 20.85 10.02 33.76 4.00
4716 4759 4.335416 TGACCATTGGAAGGTGAATTCTC 58.665 43.478 10.37 2.70 40.09 2.87
5075 5118 2.437359 CCTGGCCTGAAAGCTCCG 60.437 66.667 11.88 0.00 0.00 4.63
5194 5237 3.314307 TCTTCGGGTATCCAGAGATGT 57.686 47.619 0.00 0.00 33.67 3.06
5264 5307 1.347707 ACGGTGACATGTGGAGAATGT 59.652 47.619 1.15 0.00 40.93 2.71
5499 5542 1.383799 CCACCAATGCTCCCCTCAA 59.616 57.895 0.00 0.00 0.00 3.02
5702 5745 2.679342 GCTGGGCTGGTGGATGGTA 61.679 63.158 0.00 0.00 0.00 3.25
5841 5884 1.422024 TCCCCGTTTCATCAGGAACAA 59.578 47.619 0.00 0.00 34.56 2.83
5949 5992 5.757850 AATTGGAAATCGGTTGCTCTATC 57.242 39.130 0.00 0.00 0.00 2.08
5951 5994 7.041372 GCTATAAATTGGAAATCGGTTGCTCTA 60.041 37.037 0.00 0.00 0.00 2.43
5958 6001 5.301551 TGCATGCTATAAATTGGAAATCGGT 59.698 36.000 20.33 0.00 0.00 4.69
5975 6018 1.136305 GCAAGGTTCATCATGCATGCT 59.864 47.619 22.25 9.87 38.63 3.79
6011 6054 2.086869 CTTCACACCTTGTATGCCCTG 58.913 52.381 0.00 0.00 0.00 4.45
6107 6150 5.580691 TCATGTATACTTCGGCAAAGTTGAG 59.419 40.000 8.78 0.00 46.26 3.02
6251 6324 0.687354 CAGGTGGAGGTGTGCTTAGT 59.313 55.000 0.00 0.00 0.00 2.24
6591 6664 4.095410 TCCAATGAAAATAACTGCTGCG 57.905 40.909 0.00 0.00 0.00 5.18
6733 6806 8.517878 TGCTATCTTTTCTTTCAAATCTTCTGG 58.482 33.333 0.00 0.00 0.00 3.86
6756 6830 5.859205 AATGTTGAAGGAAGAAAAGTGCT 57.141 34.783 0.00 0.00 0.00 4.40
6975 7051 1.017177 TGTTTGGCGTCATAGCGACC 61.017 55.000 0.00 0.00 42.07 4.79
6981 7057 2.535012 TGTCACTGTTTGGCGTCATA 57.465 45.000 0.00 0.00 29.36 2.15
7099 7175 5.765182 AGAAAATGTAGAGGTTGGTTCACTG 59.235 40.000 0.00 0.00 0.00 3.66
7458 7534 3.748568 GCCAACACTCTATTAGCTATGGC 59.251 47.826 12.14 12.14 40.72 4.40
7460 7536 5.468072 CCAAGCCAACACTCTATTAGCTATG 59.532 44.000 0.00 0.00 0.00 2.23
7597 7677 3.070302 GGGCCCTTCTCTGATAGTTACAG 59.930 52.174 17.04 0.00 36.80 2.74
7756 7924 5.414765 AGTTTCCCACAATATTCTTCGGAAC 59.585 40.000 3.44 0.00 36.72 3.62
7850 8019 3.247411 TCGTATGCTGAACACAAACACAG 59.753 43.478 0.00 0.00 0.00 3.66
7871 8040 4.143094 GGAGTACTTGTGAACGAGCAATTC 60.143 45.833 0.00 0.00 0.00 2.17
7876 8045 1.272769 AGGGAGTACTTGTGAACGAGC 59.727 52.381 0.00 0.00 0.00 5.03
7938 8107 4.019321 AGGCTCTATTTTCCAAGTGCTACA 60.019 41.667 0.00 0.00 33.76 2.74
7948 8117 7.646548 AAGGTTCATTAAGGCTCTATTTTCC 57.353 36.000 0.00 0.00 0.00 3.13
7969 8138 5.120986 GCGAGTTCCTTCTTCTTCTTTAAGG 59.879 44.000 0.00 0.00 39.93 2.69
8102 8271 8.579682 AAACAATTTGAGACACAATAGCTTTC 57.420 30.769 2.79 0.00 38.36 2.62
8132 8301 5.979517 GCTGCTCCAAAATTATCGCTTTTAT 59.020 36.000 0.00 0.00 0.00 1.40
8133 8302 5.105957 TGCTGCTCCAAAATTATCGCTTTTA 60.106 36.000 0.00 0.00 0.00 1.52
8134 8303 4.176271 GCTGCTCCAAAATTATCGCTTTT 58.824 39.130 0.00 0.00 0.00 2.27
8135 8304 3.193267 TGCTGCTCCAAAATTATCGCTTT 59.807 39.130 0.00 0.00 0.00 3.51
8138 8307 2.849880 TGCTGCTCCAAAATTATCGC 57.150 45.000 0.00 0.00 0.00 4.58
8185 8357 8.877864 TCAGGGCTATAATCTCAAAAGAAAAA 57.122 30.769 0.00 0.00 34.49 1.94
8186 8358 8.328758 TCTCAGGGCTATAATCTCAAAAGAAAA 58.671 33.333 0.00 0.00 34.49 2.29
8187 8359 7.861629 TCTCAGGGCTATAATCTCAAAAGAAA 58.138 34.615 0.00 0.00 34.49 2.52
8188 8360 7.437713 TCTCAGGGCTATAATCTCAAAAGAA 57.562 36.000 0.00 0.00 34.49 2.52
8189 8361 7.437713 TTCTCAGGGCTATAATCTCAAAAGA 57.562 36.000 0.00 0.00 35.54 2.52
8190 8362 8.688747 AATTCTCAGGGCTATAATCTCAAAAG 57.311 34.615 0.00 0.00 0.00 2.27
8191 8363 7.442364 CGAATTCTCAGGGCTATAATCTCAAAA 59.558 37.037 3.52 0.00 0.00 2.44
8192 8364 6.931281 CGAATTCTCAGGGCTATAATCTCAAA 59.069 38.462 3.52 0.00 0.00 2.69
8193 8365 6.267699 TCGAATTCTCAGGGCTATAATCTCAA 59.732 38.462 3.52 0.00 0.00 3.02
8194 8366 5.775195 TCGAATTCTCAGGGCTATAATCTCA 59.225 40.000 3.52 0.00 0.00 3.27
8195 8367 6.274157 TCGAATTCTCAGGGCTATAATCTC 57.726 41.667 3.52 0.00 0.00 2.75
8196 8368 6.672266 TTCGAATTCTCAGGGCTATAATCT 57.328 37.500 3.52 0.00 0.00 2.40
8197 8369 6.706270 TGTTTCGAATTCTCAGGGCTATAATC 59.294 38.462 0.00 0.00 0.00 1.75
8198 8370 6.591935 TGTTTCGAATTCTCAGGGCTATAAT 58.408 36.000 0.00 0.00 0.00 1.28
8199 8371 5.984725 TGTTTCGAATTCTCAGGGCTATAA 58.015 37.500 0.00 0.00 0.00 0.98
8200 8372 5.128827 ACTGTTTCGAATTCTCAGGGCTATA 59.871 40.000 17.64 0.00 0.00 1.31
8201 8373 4.080863 ACTGTTTCGAATTCTCAGGGCTAT 60.081 41.667 17.64 2.18 0.00 2.97
8202 8374 3.260884 ACTGTTTCGAATTCTCAGGGCTA 59.739 43.478 17.64 0.00 0.00 3.93
8203 8375 2.039084 ACTGTTTCGAATTCTCAGGGCT 59.961 45.455 17.64 2.68 0.00 5.19
8204 8376 2.427506 ACTGTTTCGAATTCTCAGGGC 58.572 47.619 17.64 0.00 0.00 5.19
8205 8377 3.619038 GCTACTGTTTCGAATTCTCAGGG 59.381 47.826 17.64 12.99 0.00 4.45
8206 8378 4.245660 TGCTACTGTTTCGAATTCTCAGG 58.754 43.478 17.64 7.80 0.00 3.86
8207 8379 7.489435 TCTTATGCTACTGTTTCGAATTCTCAG 59.511 37.037 0.00 8.41 0.00 3.35
8208 8380 7.275779 GTCTTATGCTACTGTTTCGAATTCTCA 59.724 37.037 0.00 0.00 0.00 3.27
8209 8381 7.489757 AGTCTTATGCTACTGTTTCGAATTCTC 59.510 37.037 0.00 0.00 0.00 2.87
8309 8485 2.944349 CTCCTTCAGGTAGTCCGTACTC 59.056 54.545 0.00 0.00 37.15 2.59
8348 8524 0.748005 GTGGTGGGATCGATTGGGTG 60.748 60.000 0.00 0.00 0.00 4.61
8366 8542 1.825474 AGGAGTCGATGTTGATTCGGT 59.175 47.619 0.00 0.00 37.22 4.69
8382 8558 1.440893 CGTGATGGAGGCAGAGGAG 59.559 63.158 0.00 0.00 0.00 3.69


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

AutoCloner maintained by Alex Coulton.