Multiple sequence alignment - TraesCS4A01G164500

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 TraesCS4A01G164500 chr4A 100.000 4818 0 0 1 4818 380148377 380143560 0 8898
1 TraesCS4A01G164500 chr4A 95.618 753 32 1 4066 4818 437503672 437502921 0 1206
2 TraesCS4A01G164500 chr4D 93.694 3457 170 26 67 3493 149072707 149069269 0 5132
3 TraesCS4A01G164500 chr1B 93.400 3197 166 26 901 4059 90710747 90713936 0 4693
4 TraesCS4A01G164500 chr1D 93.174 1963 105 17 1994 3929 55210096 55212056 0 2856
5 TraesCS4A01G164500 chr1D 95.868 1089 36 3 913 1997 55208891 55209974 0 1753
6 TraesCS4A01G164500 chr7A 95.618 753 32 1 4066 4818 466210303 466209552 0 1206
7 TraesCS4A01G164500 chr7A 95.352 753 34 1 4066 4818 81551393 81552144 0 1195
8 TraesCS4A01G164500 chr3A 95.485 753 33 1 4066 4818 36754545 36755296 0 1201
9 TraesCS4A01G164500 chr3A 95.219 753 33 3 4066 4818 733279764 733280513 0 1188
10 TraesCS4A01G164500 chr3A 94.688 753 38 2 4066 4818 534188101 534188851 0 1168
11 TraesCS4A01G164500 chr5A 95.340 751 34 1 4068 4818 680192366 680191617 0 1192
12 TraesCS4A01G164500 chr5A 95.086 753 36 1 4066 4818 18536419 18537170 0 1184
13 TraesCS4A01G164500 chr6A 95.086 753 35 2 4066 4818 594459307 594460057 0 1184


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 TraesCS4A01G164500 chr4A 380143560 380148377 4817 True 8898.0 8898 100.000 1 4818 1 chr4A.!!$R1 4817
1 TraesCS4A01G164500 chr4A 437502921 437503672 751 True 1206.0 1206 95.618 4066 4818 1 chr4A.!!$R2 752
2 TraesCS4A01G164500 chr4D 149069269 149072707 3438 True 5132.0 5132 93.694 67 3493 1 chr4D.!!$R1 3426
3 TraesCS4A01G164500 chr1B 90710747 90713936 3189 False 4693.0 4693 93.400 901 4059 1 chr1B.!!$F1 3158
4 TraesCS4A01G164500 chr1D 55208891 55212056 3165 False 2304.5 2856 94.521 913 3929 2 chr1D.!!$F1 3016
5 TraesCS4A01G164500 chr7A 466209552 466210303 751 True 1206.0 1206 95.618 4066 4818 1 chr7A.!!$R1 752
6 TraesCS4A01G164500 chr7A 81551393 81552144 751 False 1195.0 1195 95.352 4066 4818 1 chr7A.!!$F1 752
7 TraesCS4A01G164500 chr3A 36754545 36755296 751 False 1201.0 1201 95.485 4066 4818 1 chr3A.!!$F1 752
8 TraesCS4A01G164500 chr3A 733279764 733280513 749 False 1188.0 1188 95.219 4066 4818 1 chr3A.!!$F3 752
9 TraesCS4A01G164500 chr3A 534188101 534188851 750 False 1168.0 1168 94.688 4066 4818 1 chr3A.!!$F2 752
10 TraesCS4A01G164500 chr5A 680191617 680192366 749 True 1192.0 1192 95.340 4068 4818 1 chr5A.!!$R1 750
11 TraesCS4A01G164500 chr5A 18536419 18537170 751 False 1184.0 1184 95.086 4066 4818 1 chr5A.!!$F1 752
12 TraesCS4A01G164500 chr6A 594459307 594460057 750 False 1184.0 1184 95.086 4066 4818 1 chr6A.!!$F1 752

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
256 269 0.108233 CCTCCTTCTCTCAGCAGCAC 60.108 60.000 0.00 0.0 0.00 4.40 F
591 609 1.006832 CGCTGGTTTTCTATCCACCG 58.993 55.000 0.00 0.0 32.71 4.94 F
893 912 1.023513 ATGCTCTTCCTTCGCTGTGC 61.024 55.000 0.00 0.0 0.00 4.57 F
1240 1263 2.149973 AATTCCCCTTCCATGTCTGC 57.850 50.000 0.00 0.0 0.00 4.26 F
2246 2395 3.241067 TGTTATAACGTGGTCTGAGCC 57.759 47.619 10.92 0.0 0.00 4.70 F
3553 3719 0.034059 CGTCCACCTCTTGTCTGCTT 59.966 55.000 0.00 0.0 0.00 3.91 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1253 1276 0.998727 GCTTTTCCGCTGTTTCGCTG 60.999 55.000 0.0 0.0 0.00 5.18 R
1434 1457 1.194218 GTGCAACCCCAGCCAAATAT 58.806 50.000 0.0 0.0 0.00 1.28 R
2732 2885 0.239347 CCTGCCACAGCGAAAAAGAG 59.761 55.000 0.0 0.0 44.31 2.85 R
2733 2886 0.465460 ACCTGCCACAGCGAAAAAGA 60.465 50.000 0.0 0.0 44.31 2.52 R
3790 3963 0.536006 AGCCCAGCGATTGCCTTATC 60.536 55.000 0.0 0.0 44.31 1.75 R
4384 4577 1.061657 TGATCTAGGATTTCCCCCGGT 60.062 52.381 0.0 0.0 36.42 5.28 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
29 30 9.970243 TTGCAAATTAAAATGATATTTTGCTCG 57.030 25.926 19.92 0.00 44.49 5.03
30 31 8.602328 TGCAAATTAAAATGATATTTTGCTCGG 58.398 29.630 19.92 0.06 44.49 4.63
31 32 8.603181 GCAAATTAAAATGATATTTTGCTCGGT 58.397 29.630 15.85 0.00 42.79 4.69
32 33 9.904647 CAAATTAAAATGATATTTTGCTCGGTG 57.095 29.630 9.19 0.00 0.00 4.94
33 34 9.651913 AAATTAAAATGATATTTTGCTCGGTGT 57.348 25.926 9.19 0.00 0.00 4.16
36 37 9.944663 TTAAAATGATATTTTGCTCGGTGTATC 57.055 29.630 9.19 0.00 0.00 2.24
37 38 7.807977 AAATGATATTTTGCTCGGTGTATCT 57.192 32.000 0.00 0.00 0.00 1.98
38 39 8.902540 AAATGATATTTTGCTCGGTGTATCTA 57.097 30.769 0.00 0.00 0.00 1.98
39 40 9.507329 AAATGATATTTTGCTCGGTGTATCTAT 57.493 29.630 0.00 0.00 0.00 1.98
42 43 9.803315 TGATATTTTGCTCGGTGTATCTATATC 57.197 33.333 0.00 0.00 0.00 1.63
46 47 6.438259 TTGCTCGGTGTATCTATATCTAGC 57.562 41.667 0.00 0.00 0.00 3.42
47 48 5.497474 TGCTCGGTGTATCTATATCTAGCA 58.503 41.667 0.00 0.00 34.14 3.49
48 49 6.122964 TGCTCGGTGTATCTATATCTAGCAT 58.877 40.000 0.00 0.00 31.78 3.79
49 50 7.280356 TGCTCGGTGTATCTATATCTAGCATA 58.720 38.462 0.00 0.00 31.78 3.14
50 51 7.773690 TGCTCGGTGTATCTATATCTAGCATAA 59.226 37.037 0.00 0.00 31.78 1.90
51 52 8.788806 GCTCGGTGTATCTATATCTAGCATAAT 58.211 37.037 0.00 0.00 0.00 1.28
81 82 2.105477 ACGATGGATGAGGCTATTGCTT 59.895 45.455 0.00 0.00 39.59 3.91
84 85 2.564771 TGGATGAGGCTATTGCTTTCG 58.435 47.619 0.00 0.00 39.59 3.46
115 117 6.595326 GGAATAATCCCAAGCAAAAGGAAAAG 59.405 38.462 0.00 0.00 40.10 2.27
117 119 2.758130 TCCCAAGCAAAAGGAAAAGGT 58.242 42.857 0.00 0.00 0.00 3.50
122 124 4.511454 CCAAGCAAAAGGAAAAGGTAAAGC 59.489 41.667 0.00 0.00 0.00 3.51
130 132 1.272490 GAAAAGGTAAAGCAGGCCCAC 59.728 52.381 0.00 0.00 0.00 4.61
153 155 3.520862 CGCCCATGCCATGTCCAC 61.521 66.667 3.63 0.00 0.00 4.02
176 178 3.949113 AGAAATAGACTCACTCCTCGTCC 59.051 47.826 0.00 0.00 0.00 4.79
181 183 0.402504 ACTCACTCCTCGTCCTCACT 59.597 55.000 0.00 0.00 0.00 3.41
189 197 1.534175 CCTCGTCCTCACTGATAACGC 60.534 57.143 7.96 0.00 33.58 4.84
201 209 3.068873 ACTGATAACGCTTCCTCATCCTC 59.931 47.826 0.00 0.00 0.00 3.71
239 248 1.078710 ACCTTGGAGCGTAGACCCT 59.921 57.895 0.00 0.00 0.00 4.34
242 251 0.684805 CTTGGAGCGTAGACCCTCCT 60.685 60.000 13.26 0.00 46.23 3.69
256 269 0.108233 CCTCCTTCTCTCAGCAGCAC 60.108 60.000 0.00 0.00 0.00 4.40
304 322 1.025647 GTAGACCGACCGCACTCTCT 61.026 60.000 0.00 0.00 0.00 3.10
353 371 1.986378 GTCGCTGTTGTGCTAGTACTG 59.014 52.381 12.42 0.00 0.00 2.74
400 418 8.794335 AGGAATAATTCGAGGGATAAATTAGC 57.206 34.615 0.00 0.00 30.71 3.09
423 441 2.808543 GGCACCATTAGAATCATCGACC 59.191 50.000 0.00 0.00 0.00 4.79
455 473 4.715222 GGAATCAGTTCTAGGCTGGGCC 62.715 59.091 12.90 0.00 40.62 5.80
503 521 1.227853 AACCTGCGGTTGGAGTGTC 60.228 57.895 11.39 0.00 45.07 3.67
514 532 2.433318 GAGTGTCGTGCTGCCTCC 60.433 66.667 0.00 0.00 0.00 4.30
573 591 1.665442 CCCCCTTGTTTTCTTGGCG 59.335 57.895 0.00 0.00 0.00 5.69
587 605 1.401905 CTTGGCGCTGGTTTTCTATCC 59.598 52.381 7.64 0.00 0.00 2.59
591 609 1.006832 CGCTGGTTTTCTATCCACCG 58.993 55.000 0.00 0.00 32.71 4.94
637 656 6.018180 TGTTTCGTTTCTCTAAGAAGCCTTTC 60.018 38.462 0.00 0.00 35.37 2.62
648 667 1.398390 GAAGCCTTTCGATCATTGCGT 59.602 47.619 0.00 0.00 0.00 5.24
688 707 7.669089 TTTCCCTTAGGATTCTTGTTTTTGT 57.331 32.000 0.00 0.00 43.54 2.83
770 789 1.455822 AGACCTGTTGGGATTTGGGA 58.544 50.000 0.00 0.00 38.76 4.37
826 845 4.368543 GCAGTGCCCAGCTTTGCC 62.369 66.667 2.85 0.00 34.44 4.52
882 901 2.929531 TGTCGACTGAGATGCTCTTC 57.070 50.000 17.92 0.00 0.00 2.87
886 905 2.425312 TCGACTGAGATGCTCTTCCTTC 59.575 50.000 0.00 0.00 0.00 3.46
888 907 1.134848 ACTGAGATGCTCTTCCTTCGC 60.135 52.381 0.00 0.00 0.00 4.70
893 912 1.023513 ATGCTCTTCCTTCGCTGTGC 61.024 55.000 0.00 0.00 0.00 4.57
933 952 6.899393 ATTATCCTTGCTTTGTTGTTCAGA 57.101 33.333 0.00 0.00 0.00 3.27
1240 1263 2.149973 AATTCCCCTTCCATGTCTGC 57.850 50.000 0.00 0.00 0.00 4.26
1253 1276 5.976458 TCCATGTCTGCCCAAATTTAATTC 58.024 37.500 0.00 0.00 0.00 2.17
1398 1421 4.943705 TCACCAAATCTAATGTTGCTCTCC 59.056 41.667 0.00 0.00 0.00 3.71
1434 1457 4.311606 TGACTATCAGCGTAGTTTTTGCA 58.688 39.130 1.89 0.00 35.14 4.08
1576 1599 9.737427 TTTAATGTCGCTTTTAGATGTCAAAAA 57.263 25.926 0.00 0.00 0.00 1.94
1740 1764 5.590259 GCCTTAGAAGCAAATGGTCAAGATA 59.410 40.000 0.00 0.00 0.00 1.98
1855 1879 5.048504 GGCTTCTTCTGATCACATTTCAACA 60.049 40.000 0.00 0.00 0.00 3.33
1978 2002 6.205076 CGAGTTTAGATAAGCTAGTAGGCAGA 59.795 42.308 0.00 0.00 34.17 4.26
2189 2338 5.389859 TCAAGTAGCATTTGACCCAATTG 57.610 39.130 0.00 0.00 30.03 2.32
2246 2395 3.241067 TGTTATAACGTGGTCTGAGCC 57.759 47.619 10.92 0.00 0.00 4.70
2278 2427 5.917447 GCAAGAAATGTCTCTGGAAGTTTTC 59.083 40.000 0.00 0.00 30.70 2.29
2405 2554 3.391506 TGGCAAGATCGATGAGGTATG 57.608 47.619 0.54 0.00 0.00 2.39
2435 2584 3.795688 TGAACTGCCTTCCATTTCTCT 57.204 42.857 0.00 0.00 35.01 3.10
2453 2606 7.872061 TTTCTCTATATTGGCTATCCTCCAA 57.128 36.000 0.00 0.00 46.44 3.53
2454 2607 6.859112 TCTCTATATTGGCTATCCTCCAAC 57.141 41.667 0.00 0.00 45.35 3.77
2455 2608 6.565974 TCTCTATATTGGCTATCCTCCAACT 58.434 40.000 0.00 0.00 45.35 3.16
2456 2609 7.709601 TCTCTATATTGGCTATCCTCCAACTA 58.290 38.462 0.00 0.00 45.35 2.24
2647 2800 4.394300 CCCTTCTTGATGCTTAGTCTTGTG 59.606 45.833 0.00 0.00 0.00 3.33
2663 2816 4.978580 GTCTTGTGCTGTTCAATTTCTTCC 59.021 41.667 0.00 0.00 0.00 3.46
2670 2823 4.808895 GCTGTTCAATTTCTTCCCGTTTTT 59.191 37.500 0.00 0.00 0.00 1.94
2732 2885 9.408069 CGTAAGGTCCATAGTTACATCTTTATC 57.592 37.037 0.00 0.00 0.00 1.75
2743 2897 8.779354 AGTTACATCTTTATCTCTTTTTCGCT 57.221 30.769 0.00 0.00 0.00 4.93
2911 3065 0.401738 TGTTGGCTCCAGCTTAGCTT 59.598 50.000 3.00 0.00 36.40 3.74
2962 3116 2.838736 AGCAGCGTAATGAGGTAATGG 58.161 47.619 0.00 0.00 0.00 3.16
2967 3121 4.034048 CAGCGTAATGAGGTAATGGTTGTC 59.966 45.833 0.00 0.00 0.00 3.18
2974 3128 0.802494 GGTAATGGTTGTCGGCTGTG 59.198 55.000 0.00 0.00 0.00 3.66
3187 3352 8.147058 AGATTCTCATGTTATGATGTGTCCTAC 58.853 37.037 0.00 0.00 38.85 3.18
3189 3354 7.423844 TCTCATGTTATGATGTGTCCTACTT 57.576 36.000 0.00 0.00 38.85 2.24
3206 3371 8.755028 TGTCCTACTTAGCAATTTGATACTGTA 58.245 33.333 0.00 4.06 0.00 2.74
3208 3373 9.817809 TCCTACTTAGCAATTTGATACTGTAAG 57.182 33.333 0.00 0.00 42.29 2.34
3422 3588 7.462571 ACCTGATAAAACTAATTGGTTGACC 57.537 36.000 8.06 0.00 0.00 4.02
3518 3684 2.260822 AGGACAAAGGAGCTAAGAGCA 58.739 47.619 0.64 0.00 45.56 4.26
3553 3719 0.034059 CGTCCACCTCTTGTCTGCTT 59.966 55.000 0.00 0.00 0.00 3.91
3570 3738 7.741198 TGTCTGCTTTTTGTTTCATGAAAAAG 58.259 30.769 22.07 20.46 45.68 2.27
3610 3778 5.545658 TGTGCGACTTGGATTAAGATTTC 57.454 39.130 0.00 0.00 39.76 2.17
3612 3780 5.647658 TGTGCGACTTGGATTAAGATTTCAT 59.352 36.000 0.00 0.00 39.76 2.57
3613 3781 6.150976 TGTGCGACTTGGATTAAGATTTCATT 59.849 34.615 0.00 0.00 39.76 2.57
3615 3783 7.542130 GTGCGACTTGGATTAAGATTTCATTTT 59.458 33.333 0.00 0.00 39.76 1.82
3616 3784 8.087750 TGCGACTTGGATTAAGATTTCATTTTT 58.912 29.630 0.00 0.00 39.76 1.94
3617 3785 8.587111 GCGACTTGGATTAAGATTTCATTTTTC 58.413 33.333 0.00 0.00 39.76 2.29
3618 3786 9.846248 CGACTTGGATTAAGATTTCATTTTTCT 57.154 29.630 0.00 0.00 39.76 2.52
3643 3816 4.543590 AACATTCTTCTCCGTCATCTGT 57.456 40.909 0.00 0.00 0.00 3.41
3770 3943 3.513515 GGTGTCCATGATAGGGAGATCTC 59.486 52.174 14.75 14.75 34.44 2.75
3775 3948 3.245911 CCATGATAGGGAGATCTCTGGGA 60.246 52.174 21.81 6.20 31.21 4.37
3778 3951 3.181424 TGATAGGGAGATCTCTGGGACTG 60.181 52.174 21.81 0.00 0.00 3.51
3856 4036 8.412456 TCAGCTTTCATTTTGACAAATTCAGTA 58.588 29.630 0.50 0.00 34.94 2.74
3899 4080 7.445096 TCAAAGATGATTGTCTTGTGCTCTTTA 59.555 33.333 0.00 0.00 38.41 1.85
3915 4096 8.075574 TGTGCTCTTTATTGTAGTGTTTCATTG 58.924 33.333 0.00 0.00 0.00 2.82
3992 4178 9.899226 AACTCAAAGACATTGCTACTTATTTTC 57.101 29.630 0.00 0.00 38.98 2.29
4038 4231 6.358762 CAGTCAAGTTGAGTCGAAAGATTTC 58.641 40.000 10.37 0.00 45.19 2.17
4059 4252 4.664188 TCGCCTAGACAACAAAACAAAAC 58.336 39.130 0.00 0.00 0.00 2.43
4060 4253 3.794564 CGCCTAGACAACAAAACAAAACC 59.205 43.478 0.00 0.00 0.00 3.27
4061 4254 3.794564 GCCTAGACAACAAAACAAAACCG 59.205 43.478 0.00 0.00 0.00 4.44
4062 4255 4.356289 CCTAGACAACAAAACAAAACCGG 58.644 43.478 0.00 0.00 0.00 5.28
4063 4256 4.096682 CCTAGACAACAAAACAAAACCGGA 59.903 41.667 9.46 0.00 0.00 5.14
4064 4257 4.729227 AGACAACAAAACAAAACCGGAT 57.271 36.364 9.46 0.00 0.00 4.18
4100 4293 1.005037 GCGACACACCATCTGACCA 60.005 57.895 0.00 0.00 0.00 4.02
4193 4386 4.783621 GATCTGGCTGGTGCGGCA 62.784 66.667 0.00 0.00 40.82 5.69
4255 4448 4.574828 GCACATAATACGTGATGGAGGTTT 59.425 41.667 0.00 0.00 36.43 3.27
4362 4555 2.125512 GCATCGCCGTGGAGAAGT 60.126 61.111 0.00 0.00 0.00 3.01
4384 4577 2.977580 TCTAGACCTCTATCCGCTACCA 59.022 50.000 0.00 0.00 0.00 3.25
4411 4604 5.163045 GGGGGAAATCCTAGATCAGTTGATT 60.163 44.000 0.00 0.00 33.62 2.57
4537 4730 6.259608 GGTACTTCATCCTTCACATTGATGAG 59.740 42.308 0.00 0.00 43.98 2.90
4601 4794 4.498520 CGCGGTGATGGACTCGCT 62.499 66.667 0.00 0.00 45.11 4.93
4706 4899 3.375699 AGACGGACCTATGAAAGATGGT 58.624 45.455 0.00 0.00 35.23 3.55
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
6 7 9.904647 CACCGAGCAAAATATCATTTTAATTTG 57.095 29.630 0.00 0.00 0.00 2.32
7 8 9.651913 ACACCGAGCAAAATATCATTTTAATTT 57.348 25.926 0.00 0.00 0.00 1.82
10 11 9.944663 GATACACCGAGCAAAATATCATTTTAA 57.055 29.630 0.00 0.00 0.00 1.52
11 12 9.337396 AGATACACCGAGCAAAATATCATTTTA 57.663 29.630 0.00 0.00 0.00 1.52
12 13 8.225603 AGATACACCGAGCAAAATATCATTTT 57.774 30.769 0.00 0.00 0.00 1.82
13 14 7.807977 AGATACACCGAGCAAAATATCATTT 57.192 32.000 0.00 0.00 0.00 2.32
16 17 9.803315 GATATAGATACACCGAGCAAAATATCA 57.197 33.333 0.00 0.00 0.00 2.15
20 21 7.976734 GCTAGATATAGATACACCGAGCAAAAT 59.023 37.037 0.00 0.00 0.00 1.82
21 22 7.039993 TGCTAGATATAGATACACCGAGCAAAA 60.040 37.037 0.00 0.00 33.55 2.44
22 23 6.433093 TGCTAGATATAGATACACCGAGCAAA 59.567 38.462 0.00 0.00 33.55 3.68
23 24 5.944007 TGCTAGATATAGATACACCGAGCAA 59.056 40.000 0.00 0.00 33.55 3.91
24 25 5.497474 TGCTAGATATAGATACACCGAGCA 58.503 41.667 0.00 0.00 34.04 4.26
25 26 6.627395 ATGCTAGATATAGATACACCGAGC 57.373 41.667 0.00 0.00 0.00 5.03
47 48 9.547753 GCCTCATCCATCGTACAATAATATTAT 57.452 33.333 1.91 1.91 0.00 1.28
48 49 8.758829 AGCCTCATCCATCGTACAATAATATTA 58.241 33.333 0.00 0.00 0.00 0.98
49 50 7.624549 AGCCTCATCCATCGTACAATAATATT 58.375 34.615 0.00 0.00 0.00 1.28
50 51 7.187824 AGCCTCATCCATCGTACAATAATAT 57.812 36.000 0.00 0.00 0.00 1.28
51 52 6.605471 AGCCTCATCCATCGTACAATAATA 57.395 37.500 0.00 0.00 0.00 0.98
52 53 5.489792 AGCCTCATCCATCGTACAATAAT 57.510 39.130 0.00 0.00 0.00 1.28
53 54 4.955811 AGCCTCATCCATCGTACAATAA 57.044 40.909 0.00 0.00 0.00 1.40
54 55 6.398095 CAATAGCCTCATCCATCGTACAATA 58.602 40.000 0.00 0.00 0.00 1.90
55 56 5.240891 CAATAGCCTCATCCATCGTACAAT 58.759 41.667 0.00 0.00 0.00 2.71
56 57 4.631131 CAATAGCCTCATCCATCGTACAA 58.369 43.478 0.00 0.00 0.00 2.41
57 58 3.554960 GCAATAGCCTCATCCATCGTACA 60.555 47.826 0.00 0.00 33.58 2.90
58 59 2.996621 GCAATAGCCTCATCCATCGTAC 59.003 50.000 0.00 0.00 33.58 3.67
59 60 2.899900 AGCAATAGCCTCATCCATCGTA 59.100 45.455 0.00 0.00 43.56 3.43
60 61 1.696336 AGCAATAGCCTCATCCATCGT 59.304 47.619 0.00 0.00 43.56 3.73
61 62 2.469274 AGCAATAGCCTCATCCATCG 57.531 50.000 0.00 0.00 43.56 3.84
62 63 3.188048 CGAAAGCAATAGCCTCATCCATC 59.812 47.826 0.00 0.00 43.56 3.51
63 64 3.144506 CGAAAGCAATAGCCTCATCCAT 58.855 45.455 0.00 0.00 43.56 3.41
64 65 2.564771 CGAAAGCAATAGCCTCATCCA 58.435 47.619 0.00 0.00 43.56 3.41
65 66 1.876156 CCGAAAGCAATAGCCTCATCC 59.124 52.381 0.00 0.00 43.56 3.51
81 82 1.566703 TGGGATTATTCCTTGGCCGAA 59.433 47.619 0.00 0.00 42.20 4.30
84 85 1.688735 GCTTGGGATTATTCCTTGGCC 59.311 52.381 0.00 0.00 42.20 5.36
106 108 2.632996 GGCCTGCTTTACCTTTTCCTTT 59.367 45.455 0.00 0.00 0.00 3.11
115 117 2.033602 ACGTGGGCCTGCTTTACC 59.966 61.111 4.53 0.00 0.00 2.85
117 119 2.047655 CGACGTGGGCCTGCTTTA 60.048 61.111 4.53 0.00 0.00 1.85
139 141 1.548081 TTTCTGTGGACATGGCATGG 58.452 50.000 29.49 12.05 33.60 3.66
140 142 4.036027 GTCTATTTCTGTGGACATGGCATG 59.964 45.833 25.31 25.31 0.00 4.06
141 143 4.080129 AGTCTATTTCTGTGGACATGGCAT 60.080 41.667 0.00 0.00 0.00 4.40
142 144 3.264193 AGTCTATTTCTGTGGACATGGCA 59.736 43.478 0.00 0.00 0.00 4.92
143 145 3.873952 GAGTCTATTTCTGTGGACATGGC 59.126 47.826 0.00 0.00 0.00 4.40
153 155 4.201970 GGACGAGGAGTGAGTCTATTTCTG 60.202 50.000 0.00 0.00 35.42 3.02
176 178 3.510388 TGAGGAAGCGTTATCAGTGAG 57.490 47.619 0.00 0.00 0.00 3.51
181 183 2.034685 CGAGGATGAGGAAGCGTTATCA 59.965 50.000 0.00 0.00 0.00 2.15
189 197 1.227089 CCACGCGAGGATGAGGAAG 60.227 63.158 18.51 0.00 0.00 3.46
221 229 0.971447 GAGGGTCTACGCTCCAAGGT 60.971 60.000 14.45 0.00 46.45 3.50
239 248 1.588597 CGTGCTGCTGAGAGAAGGA 59.411 57.895 0.00 0.00 0.00 3.36
256 269 4.680237 TGAACCGTGGAGCCAGCG 62.680 66.667 0.00 0.00 0.00 5.18
259 272 4.680237 CGCTGAACCGTGGAGCCA 62.680 66.667 0.00 0.00 0.00 4.75
269 282 1.189403 CTACCGAATCGTCGCTGAAC 58.811 55.000 0.82 0.00 46.28 3.18
284 297 1.991099 GAGAGTGCGGTCGGTCTACC 61.991 65.000 0.00 0.00 36.08 3.18
294 307 1.173043 AACTGAGAGAGAGAGTGCGG 58.827 55.000 0.00 0.00 0.00 5.69
295 308 2.985809 CAAAACTGAGAGAGAGAGTGCG 59.014 50.000 0.00 0.00 0.00 5.34
304 322 7.509141 TTATGCAAACATCAAAACTGAGAGA 57.491 32.000 0.00 0.00 37.74 3.10
372 390 6.415206 TTTATCCCTCGAATTATTCCTCGT 57.585 37.500 0.00 0.00 36.46 4.18
378 396 6.598064 CCCGCTAATTTATCCCTCGAATTATT 59.402 38.462 0.00 0.00 0.00 1.40
400 418 1.800586 CGATGATTCTAATGGTGCCCG 59.199 52.381 0.00 0.00 0.00 6.13
423 441 1.523258 CTGATTCCTGGCAGGAGCG 60.523 63.158 33.14 19.53 46.73 5.03
455 473 3.490793 ATCTGCCTCGCACGGATCG 62.491 63.158 0.00 0.00 33.79 3.69
461 479 1.086634 GTTCAGGATCTGCCTCGCAC 61.087 60.000 0.00 0.00 46.97 5.34
501 519 3.363844 GAGGAGGAGGCAGCACGAC 62.364 68.421 0.00 0.00 0.00 4.34
503 521 4.154347 GGAGGAGGAGGCAGCACG 62.154 72.222 0.00 0.00 0.00 5.34
514 532 1.497161 ATCAACTTACGGGGGAGGAG 58.503 55.000 0.00 0.00 0.00 3.69
573 591 2.396590 TCGGTGGATAGAAAACCAGC 57.603 50.000 0.00 0.00 46.87 4.85
618 637 5.869888 TGATCGAAAGGCTTCTTAGAGAAAC 59.130 40.000 0.00 0.00 33.19 2.78
637 656 4.326205 CACTAAACAAGACGCAATGATCG 58.674 43.478 0.00 0.00 0.00 3.69
688 707 7.165485 ACCACATACATTTGCAGACTACTAAA 58.835 34.615 0.00 0.00 0.00 1.85
725 744 1.077787 CACACCACACCACACCAGT 60.078 57.895 0.00 0.00 0.00 4.00
739 758 2.549754 CAACAGGTCTTCCACATCACAC 59.450 50.000 0.00 0.00 35.89 3.82
770 789 8.514504 AGTCCCCAATTTCTCCATCTAATAATT 58.485 33.333 0.00 0.00 0.00 1.40
789 808 2.742116 GGCGGCATCTAAGTCCCCA 61.742 63.158 3.07 0.00 0.00 4.96
823 842 3.126879 CATTTCTCGCTGGCGGCA 61.127 61.111 19.92 12.58 41.91 5.69
826 845 1.298157 TGTTCCATTTCTCGCTGGCG 61.298 55.000 8.80 8.80 41.35 5.69
829 848 3.070018 AGAACTGTTCCATTTCTCGCTG 58.930 45.455 16.48 0.00 29.47 5.18
853 872 1.884464 CAGTCGACATGCCCGGATG 60.884 63.158 19.50 1.32 0.00 3.51
854 873 2.021068 CTCAGTCGACATGCCCGGAT 62.021 60.000 19.50 0.00 0.00 4.18
882 901 1.571460 GACAACAGCACAGCGAAGG 59.429 57.895 0.00 0.00 0.00 3.46
886 905 0.602638 TTAGGGACAACAGCACAGCG 60.603 55.000 0.00 0.00 0.00 5.18
888 907 2.839486 TCTTAGGGACAACAGCACAG 57.161 50.000 0.00 0.00 0.00 3.66
893 912 9.277783 CAAGGATAATAATCTTAGGGACAACAG 57.722 37.037 0.00 0.00 32.29 3.16
929 948 1.888512 GGAAACAAGCATGCCTTCTGA 59.111 47.619 15.66 0.00 0.00 3.27
933 952 0.178924 AGGGGAAACAAGCATGCCTT 60.179 50.000 15.66 5.27 0.00 4.35
1024 1043 1.410850 CCACGATACTGGCCTCCCAT 61.411 60.000 3.32 0.00 41.21 4.00
1240 1263 5.163963 GCTGTTTCGCTGAATTAAATTTGGG 60.164 40.000 0.00 0.00 0.00 4.12
1253 1276 0.998727 GCTTTTCCGCTGTTTCGCTG 60.999 55.000 0.00 0.00 0.00 5.18
1275 1298 8.902806 CCATGAAACTTATAAGAGGTAAATGCA 58.097 33.333 19.38 0.00 0.00 3.96
1398 1421 2.194800 TAGTCAGAAGCGCTTCATCG 57.805 50.000 42.14 31.32 41.84 3.84
1434 1457 1.194218 GTGCAACCCCAGCCAAATAT 58.806 50.000 0.00 0.00 0.00 1.28
1855 1879 5.626116 GCATTTCTTGCCTCCATTTCAAGAT 60.626 40.000 4.97 0.00 46.15 2.40
1978 2002 7.013655 CCATTTTGGTACATAATAGCTCAGCTT 59.986 37.037 3.31 0.00 37.88 3.74
2228 2377 2.181125 TGGGCTCAGACCACGTTATAA 58.819 47.619 0.00 0.00 34.69 0.98
2246 2395 1.822990 AGACATTTCTTGCCTGCATGG 59.177 47.619 5.34 0.00 39.35 3.66
2278 2427 4.444022 CCACCTGATCCCATCTAGAAGTTG 60.444 50.000 0.00 0.00 0.00 3.16
2435 2584 8.917414 AAGATAGTTGGAGGATAGCCAATATA 57.083 34.615 0.00 0.00 46.21 0.86
2478 2631 5.378230 TCACCATCATAAGCTTCTGGAAT 57.622 39.130 18.74 3.14 0.00 3.01
2647 2800 3.643159 AACGGGAAGAAATTGAACAGC 57.357 42.857 0.00 0.00 0.00 4.40
2732 2885 0.239347 CCTGCCACAGCGAAAAAGAG 59.761 55.000 0.00 0.00 44.31 2.85
2733 2886 0.465460 ACCTGCCACAGCGAAAAAGA 60.465 50.000 0.00 0.00 44.31 2.52
2743 2897 2.159179 TAGCTATCAGACCTGCCACA 57.841 50.000 0.00 0.00 0.00 4.17
3095 3249 9.566432 AAATGGATCCAGAATTAGACTATTCAC 57.434 33.333 21.33 0.00 37.06 3.18
3162 3327 8.147058 AGTAGGACACATCATAACATGAGAATC 58.853 37.037 0.00 0.00 43.53 2.52
3206 3371 9.860898 GCATGAAAGTTGGAATATTTAAGACTT 57.139 29.630 0.00 0.00 0.00 3.01
3208 3373 9.076596 GTGCATGAAAGTTGGAATATTTAAGAC 57.923 33.333 0.00 0.00 0.00 3.01
3209 3374 9.023962 AGTGCATGAAAGTTGGAATATTTAAGA 57.976 29.630 0.00 0.00 0.00 2.10
3210 3375 9.643693 AAGTGCATGAAAGTTGGAATATTTAAG 57.356 29.630 0.00 0.00 0.00 1.85
3211 3376 9.995003 AAAGTGCATGAAAGTTGGAATATTTAA 57.005 25.926 0.00 0.00 0.00 1.52
3213 3378 8.907222 AAAAGTGCATGAAAGTTGGAATATTT 57.093 26.923 0.00 0.00 0.00 1.40
3422 3588 4.563976 GTGGAAGGATTTCGAAATGCAATG 59.436 41.667 34.37 0.00 38.95 2.82
3518 3684 2.032620 GGACGATACCATCCAGTCAGT 58.967 52.381 0.00 0.00 34.87 3.41
3539 3705 4.462483 TGAAACAAAAAGCAGACAAGAGGT 59.538 37.500 0.00 0.00 0.00 3.85
3610 3778 8.076178 ACGGAGAAGAATGTTACAAGAAAAATG 58.924 33.333 0.00 0.00 0.00 2.32
3612 3780 7.281324 TGACGGAGAAGAATGTTACAAGAAAAA 59.719 33.333 0.00 0.00 0.00 1.94
3613 3781 6.764085 TGACGGAGAAGAATGTTACAAGAAAA 59.236 34.615 0.00 0.00 0.00 2.29
3615 3783 5.849510 TGACGGAGAAGAATGTTACAAGAA 58.150 37.500 0.00 0.00 0.00 2.52
3616 3784 5.462530 TGACGGAGAAGAATGTTACAAGA 57.537 39.130 0.00 0.00 0.00 3.02
3617 3785 6.035435 CAGATGACGGAGAAGAATGTTACAAG 59.965 42.308 0.00 0.00 0.00 3.16
3618 3786 5.869344 CAGATGACGGAGAAGAATGTTACAA 59.131 40.000 0.00 0.00 0.00 2.41
3643 3816 3.134081 GGCTGTAGTAATACCTCCTGCAA 59.866 47.826 0.00 0.00 0.00 4.08
3790 3963 0.536006 AGCCCAGCGATTGCCTTATC 60.536 55.000 0.00 0.00 44.31 1.75
3856 4036 6.174720 TCTTTGAGAGTAACAGGTGACAAT 57.825 37.500 0.00 0.00 0.00 2.71
3863 4043 7.102346 AGACAATCATCTTTGAGAGTAACAGG 58.898 38.462 0.00 0.00 34.73 4.00
3899 4080 3.153919 ACCCGCAATGAAACACTACAAT 58.846 40.909 0.00 0.00 0.00 2.71
3915 4096 8.788325 AAATAATCTCCTTATACATAACCCGC 57.212 34.615 0.00 0.00 29.63 6.13
3949 4130 6.636454 TTGAGTTGGTAAGATTAGGATGGT 57.364 37.500 0.00 0.00 0.00 3.55
3952 4133 7.918076 TGTCTTTGAGTTGGTAAGATTAGGAT 58.082 34.615 0.00 0.00 31.25 3.24
3992 4178 4.638421 TGCCGGTGTATTTATCTCTTTTGG 59.362 41.667 1.90 0.00 0.00 3.28
4003 4189 2.552315 CAACTTGACTGCCGGTGTATTT 59.448 45.455 1.90 0.00 0.00 1.40
4038 4231 3.794564 GGTTTTGTTTTGTTGTCTAGGCG 59.205 43.478 0.00 0.00 0.00 5.52
4040 4233 4.096682 TCCGGTTTTGTTTTGTTGTCTAGG 59.903 41.667 0.00 0.00 0.00 3.02
4237 4430 5.722263 TCGAAAAACCTCCATCACGTATTA 58.278 37.500 0.00 0.00 0.00 0.98
4255 4448 3.072468 ACCCGGATCCGCTCGAAA 61.072 61.111 29.12 0.00 38.24 3.46
4362 4555 3.393609 TGGTAGCGGATAGAGGTCTAGAA 59.606 47.826 0.00 0.00 0.00 2.10
4384 4577 1.061657 TGATCTAGGATTTCCCCCGGT 60.062 52.381 0.00 0.00 36.42 5.28
4511 4704 5.497464 TCAATGTGAAGGATGAAGTACCA 57.503 39.130 0.00 0.00 0.00 3.25
4601 4794 2.571653 CCAGACAATTACCTCCACCTGA 59.428 50.000 0.00 0.00 0.00 3.86
4706 4899 1.372872 CTCACATGTGTCGTCGCCA 60.373 57.895 24.63 2.63 0.00 5.69


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

AutoCloner maintained by Alex Coulton.