Multiple sequence alignment - TraesCS2B01G389700

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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 TraesCS2B01G389700 chr2B 100.000 5549 0 0 1 5549 553619417 553613869 0.000000e+00 10248.0
1 TraesCS2B01G389700 chr2D 96.960 1875 41 7 1119 2986 473281271 473279406 0.000000e+00 3133.0
2 TraesCS2B01G389700 chr2D 90.681 2350 109 34 3250 5549 473278949 473276660 0.000000e+00 3025.0
3 TraesCS2B01G389700 chr2D 93.717 1130 38 8 2 1119 473282423 473281315 0.000000e+00 1663.0
4 TraesCS2B01G389700 chr2D 95.489 133 6 0 2986 3118 473279339 473279207 4.350000e-51 213.0
5 TraesCS2B01G389700 chr2D 90.511 137 7 2 3117 3248 473279137 473279002 5.710000e-40 176.0
6 TraesCS2B01G389700 chr2A 90.913 2311 117 44 3249 5549 615347259 615345032 0.000000e+00 3018.0
7 TraesCS2B01G389700 chr2A 93.794 1128 46 11 1 1119 615350924 615349812 0.000000e+00 1674.0
8 TraesCS2B01G389700 chr2A 94.166 1097 47 7 1119 2211 615349768 615348685 0.000000e+00 1655.0
9 TraesCS2B01G389700 chr2A 95.000 780 32 6 2211 2986 615348495 615347719 0.000000e+00 1218.0
10 TraesCS2B01G389700 chr2A 93.182 132 8 1 3117 3248 615347438 615347308 5.670000e-45 193.0
11 TraesCS2B01G389700 chr2A 93.162 117 7 1 2986 3102 615347667 615347552 2.660000e-38 171.0
12 TraesCS2B01G389700 chr1B 84.384 365 42 5 4820 5183 599469984 599469634 1.480000e-90 344.0
13 TraesCS2B01G389700 chr5B 97.297 37 1 0 2981 3017 611644218 611644182 4.640000e-06 63.9
14 TraesCS2B01G389700 chr5B 100.000 33 0 0 2987 3019 26443732 26443764 1.670000e-05 62.1
15 TraesCS2B01G389700 chr4A 97.297 37 1 0 2984 3020 590126584 590126548 4.640000e-06 63.9
16 TraesCS2B01G389700 chr4A 94.872 39 2 0 4065 4103 565839565 565839603 1.670000e-05 62.1
17 TraesCS2B01G389700 chr4A 92.500 40 3 0 4064 4103 319828050 319828011 2.160000e-04 58.4
18 TraesCS2B01G389700 chr7B 91.304 46 2 1 2986 3029 478835067 478835022 1.670000e-05 62.1
19 TraesCS2B01G389700 chr6B 91.111 45 4 0 2986 3030 566337897 566337941 1.670000e-05 62.1
20 TraesCS2B01G389700 chr6B 96.970 33 1 0 4071 4103 709216982 709217014 7.770000e-04 56.5
21 TraesCS2B01G389700 chr3A 90.909 44 4 0 2976 3019 459861666 459861623 6.000000e-05 60.2
22 TraesCS2B01G389700 chr3A 92.500 40 3 0 4064 4103 25379238 25379199 2.160000e-04 58.4
23 TraesCS2B01G389700 chr3A 92.308 39 3 0 4064 4102 25394393 25394355 7.770000e-04 56.5
24 TraesCS2B01G389700 chr3A 96.774 31 1 0 4072 4102 25391951 25391921 1.000000e-02 52.8
25 TraesCS2B01G389700 chr3D 85.965 57 5 3 2986 3040 135580081 135580136 2.160000e-04 58.4
26 TraesCS2B01G389700 chr7A 96.970 33 1 0 4071 4103 439794713 439794681 7.770000e-04 56.5
27 TraesCS2B01G389700 chr5D 94.595 37 1 1 4071 4106 334903333 334903369 7.770000e-04 56.5


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 TraesCS2B01G389700 chr2B 553613869 553619417 5548 True 10248.0 10248 100.0000 1 5549 1 chr2B.!!$R1 5548
1 TraesCS2B01G389700 chr2D 473276660 473282423 5763 True 1642.0 3133 93.4716 2 5549 5 chr2D.!!$R1 5547
2 TraesCS2B01G389700 chr2A 615345032 615350924 5892 True 1321.5 3018 93.3695 1 5549 6 chr2A.!!$R1 5548

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
673 683 0.541863 AGATAGCCTGGTTTCCACGG 59.458 55.000 0.00 0.0 0.00 4.94 F
1219 1294 0.250038 CATCATCCGGAAGCCGTCAT 60.250 55.000 9.01 0.0 46.80 3.06 F
1350 1425 1.419387 GATAGATTGTGGGAGGCTGCT 59.581 52.381 5.84 0.0 0.00 4.24 F
2315 2580 3.136260 TCCAGGCAGTCATTATACATGCA 59.864 43.478 0.00 0.0 38.63 3.96 F
3455 3946 1.324134 CTGTGTTTTGTGCTTTTGGCG 59.676 47.619 0.00 0.0 45.43 5.69 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2035 2110 0.104487 TTGTGCCAAGCCATGTGTTG 59.896 50.000 0.0 0.0 0.00 3.33 R
2922 3191 1.126846 CGTGTTTCATCGTCCAAGAGC 59.873 52.381 0.0 0.0 0.00 4.09 R
3318 3809 1.136891 GCACCCCATTTAGCCATGTTC 59.863 52.381 0.0 0.0 0.00 3.18 R
4054 4548 0.450983 AGTAGCTCTTACACGGACGC 59.549 55.000 0.0 0.0 34.56 5.19 R
4835 5359 0.807667 ATCGTGCATCTCTTCGGTGC 60.808 55.000 0.0 0.0 39.26 5.01 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
143 144 1.398799 TCCTTCTCCTTCCTCCTCCT 58.601 55.000 0.00 0.00 0.00 3.69
189 190 1.209383 CGACTCCGACTCGCTTTCA 59.791 57.895 0.00 0.00 38.22 2.69
358 359 3.591835 CGCTCTCCTCCTCCTCGC 61.592 72.222 0.00 0.00 0.00 5.03
366 367 4.435970 TCCTCCTCGCCACGCCTA 62.436 66.667 0.00 0.00 0.00 3.93
670 680 1.568504 ACGAGATAGCCTGGTTTCCA 58.431 50.000 0.00 0.00 28.86 3.53
671 681 1.207329 ACGAGATAGCCTGGTTTCCAC 59.793 52.381 0.00 0.00 28.86 4.02
672 682 1.802880 CGAGATAGCCTGGTTTCCACG 60.803 57.143 0.00 0.00 0.00 4.94
673 683 0.541863 AGATAGCCTGGTTTCCACGG 59.458 55.000 0.00 0.00 0.00 4.94
779 799 1.099689 GTCTGTCTCCCTCTCCTTCG 58.900 60.000 0.00 0.00 0.00 3.79
780 800 0.681564 TCTGTCTCCCTCTCCTTCGC 60.682 60.000 0.00 0.00 0.00 4.70
781 801 0.682855 CTGTCTCCCTCTCCTTCGCT 60.683 60.000 0.00 0.00 0.00 4.93
782 802 0.681564 TGTCTCCCTCTCCTTCGCTC 60.682 60.000 0.00 0.00 0.00 5.03
783 803 1.076632 TCTCCCTCTCCTTCGCTCC 60.077 63.158 0.00 0.00 0.00 4.70
784 804 2.042843 TCCCTCTCCTTCGCTCCC 60.043 66.667 0.00 0.00 0.00 4.30
785 805 2.042435 CCCTCTCCTTCGCTCCCT 60.042 66.667 0.00 0.00 0.00 4.20
786 806 2.131067 CCCTCTCCTTCGCTCCCTC 61.131 68.421 0.00 0.00 0.00 4.30
787 807 1.076339 CCTCTCCTTCGCTCCCTCT 60.076 63.158 0.00 0.00 0.00 3.69
788 808 1.106944 CCTCTCCTTCGCTCCCTCTC 61.107 65.000 0.00 0.00 0.00 3.20
789 809 1.076632 TCTCCTTCGCTCCCTCTCC 60.077 63.158 0.00 0.00 0.00 3.71
790 810 1.076339 CTCCTTCGCTCCCTCTCCT 60.076 63.158 0.00 0.00 0.00 3.69
791 811 0.686112 CTCCTTCGCTCCCTCTCCTT 60.686 60.000 0.00 0.00 0.00 3.36
792 812 0.684805 TCCTTCGCTCCCTCTCCTTC 60.685 60.000 0.00 0.00 0.00 3.46
909 936 1.474330 TGCTCACCTTATCAGCTCGA 58.526 50.000 0.00 0.00 34.03 4.04
1150 1221 7.653311 CAGTCTCATCATTTACGATCCATTGTA 59.347 37.037 0.00 0.00 0.00 2.41
1218 1293 1.143838 CATCATCCGGAAGCCGTCA 59.856 57.895 9.01 0.00 46.80 4.35
1219 1294 0.250038 CATCATCCGGAAGCCGTCAT 60.250 55.000 9.01 0.00 46.80 3.06
1227 1302 1.743772 CGGAAGCCGTCATCCAAATCT 60.744 52.381 0.00 0.00 42.73 2.40
1275 1350 2.263945 GTAGAACTCTGCTCTTTCGCC 58.736 52.381 0.00 0.00 0.00 5.54
1288 1363 4.222114 CTCTTTCGCCATTCTGTTTTGAC 58.778 43.478 0.00 0.00 0.00 3.18
1289 1364 3.882888 TCTTTCGCCATTCTGTTTTGACT 59.117 39.130 0.00 0.00 0.00 3.41
1346 1421 2.050144 TCCTGATAGATTGTGGGAGGC 58.950 52.381 0.00 0.00 0.00 4.70
1350 1425 1.419387 GATAGATTGTGGGAGGCTGCT 59.581 52.381 5.84 0.00 0.00 4.24
1367 1442 3.462021 CTGCTAGTCTAATTGCTGGGTC 58.538 50.000 0.00 0.00 0.00 4.46
1505 1580 8.713271 CATGAAGTAAGTTTCAACCTTACTCTC 58.287 37.037 7.75 8.32 41.37 3.20
1525 1600 5.253330 TCTCCATTGTCTGTTGATTTACCC 58.747 41.667 0.00 0.00 0.00 3.69
1547 1622 4.829492 CCTTTCTCCTTGTTTGAGGATTGT 59.171 41.667 0.00 0.00 44.56 2.71
1600 1675 7.226325 GCTAGATGATTCTTTGTGACAATAGCT 59.774 37.037 12.09 0.00 33.17 3.32
2035 2110 5.304101 TGAAGATGAGAGGAATAGAAGAGCC 59.696 44.000 0.00 0.00 0.00 4.70
2122 2197 3.513912 TGGTATGACTATTATGCTCCCCG 59.486 47.826 0.00 0.00 0.00 5.73
2315 2580 3.136260 TCCAGGCAGTCATTATACATGCA 59.864 43.478 0.00 0.00 38.63 3.96
2364 2629 7.724305 TTTCGGTGGATTATACTGAATAAGC 57.276 36.000 0.00 0.00 41.56 3.09
2418 2683 4.978099 AGGATATGCATACCTTCAGTTGG 58.022 43.478 8.99 0.00 0.00 3.77
2434 2699 3.443681 CAGTTGGTATCATTTGGTGGGAC 59.556 47.826 0.00 0.00 0.00 4.46
2561 2828 6.774673 TGTGGGAAAATACATCACTCTGTTA 58.225 36.000 0.00 0.00 0.00 2.41
2680 2949 8.474025 TCACTTCCAATAAGATGTGTTTTGTTT 58.526 29.630 7.25 0.00 40.78 2.83
2922 3191 3.433615 CGCCCTTAAGAGTTCAAGAACAG 59.566 47.826 14.69 3.54 43.47 3.16
2960 3229 4.726583 ACACGAGCTCTCCAGGTAATATA 58.273 43.478 12.85 0.00 0.00 0.86
2961 3230 5.138276 ACACGAGCTCTCCAGGTAATATAA 58.862 41.667 12.85 0.00 0.00 0.98
2962 3231 5.775701 ACACGAGCTCTCCAGGTAATATAAT 59.224 40.000 12.85 0.00 0.00 1.28
2963 3232 6.946583 ACACGAGCTCTCCAGGTAATATAATA 59.053 38.462 12.85 0.00 0.00 0.98
3094 3430 7.712264 TTGCAAAAACATCACCATTAGAAAG 57.288 32.000 0.00 0.00 0.00 2.62
3125 3559 4.250464 TGTTTGCTAGAATACCGAACCAG 58.750 43.478 0.00 0.00 0.00 4.00
3133 3567 5.112129 AGAATACCGAACCAGGCTATTTT 57.888 39.130 0.00 0.00 33.69 1.82
3161 3600 6.146216 TGATTAAAATAGTGCGTGTTTGTGG 58.854 36.000 0.00 0.00 0.00 4.17
3184 3623 4.613925 ATGTGTAGTGATATCAGCTGGG 57.386 45.455 15.13 0.00 0.00 4.45
3276 3766 7.342581 TGTGGTTATATCAGCTGGTGAATTTA 58.657 34.615 15.13 2.45 39.19 1.40
3334 3825 4.536765 AGGTTAGAACATGGCTAAATGGG 58.463 43.478 10.66 0.00 30.34 4.00
3392 3883 6.414732 TGAGAAATAATGTCCTGAACCGAAT 58.585 36.000 0.00 0.00 0.00 3.34
3408 3899 3.694566 ACCGAATGGCAAATTAGACCTTC 59.305 43.478 0.00 0.00 39.70 3.46
3425 3916 2.289320 CCTTCCAGGTGTGTTCTCTCTG 60.289 54.545 0.00 0.00 0.00 3.35
3455 3946 1.324134 CTGTGTTTTGTGCTTTTGGCG 59.676 47.619 0.00 0.00 45.43 5.69
3544 4035 9.546909 CACAAAATAATGTTGTCTCAGATACAC 57.453 33.333 0.00 0.00 37.09 2.90
3740 4231 5.368145 GACCAGGTATGATATCTGTGCAAA 58.632 41.667 11.48 0.00 35.10 3.68
3926 4420 1.944709 GCAAACTAGGGTTGTTCGTGT 59.055 47.619 9.42 0.00 35.63 4.49
3961 4455 4.764679 TCAAAACGCAGCATATTCTTGT 57.235 36.364 0.00 0.00 0.00 3.16
4054 4548 0.780002 GAGCGCACAACATTTGCTTG 59.220 50.000 11.47 0.00 37.87 4.01
4055 4549 1.202320 GCGCACAACATTTGCTTGC 59.798 52.632 0.30 0.00 37.87 4.01
4060 4554 0.317770 ACAACATTTGCTTGCGTCCG 60.318 50.000 0.00 0.00 0.00 4.79
4061 4555 0.317770 CAACATTTGCTTGCGTCCGT 60.318 50.000 0.00 0.00 0.00 4.69
4062 4556 0.317770 AACATTTGCTTGCGTCCGTG 60.318 50.000 0.00 0.00 0.00 4.94
4069 4563 1.956620 GCTTGCGTCCGTGTAAGAGC 61.957 60.000 2.45 0.00 0.00 4.09
4080 4574 3.433314 CCGTGTAAGAGCTACTCCCTCTA 60.433 52.174 0.00 0.00 38.67 2.43
4081 4575 4.391155 CGTGTAAGAGCTACTCCCTCTAT 58.609 47.826 0.00 0.00 38.67 1.98
4121 4640 6.594159 CGTCTTATGTTTGTTTACAGAGGGAT 59.406 38.462 0.00 0.00 0.00 3.85
4220 4743 5.649395 TGTTTTGGCTGATCTAGGAAATCTG 59.351 40.000 0.00 0.00 0.00 2.90
4229 4752 7.607223 GCTGATCTAGGAAATCTGCAATATCTT 59.393 37.037 13.55 0.00 43.55 2.40
4230 4753 9.504708 CTGATCTAGGAAATCTGCAATATCTTT 57.495 33.333 0.00 0.00 0.00 2.52
4263 4786 2.238521 TCTGCCAAATTCAACAGGACC 58.761 47.619 0.00 0.00 0.00 4.46
4314 4837 8.787852 AGAAAAAGGACACAAAGTTATCTGATC 58.212 33.333 0.00 0.00 0.00 2.92
4354 4878 7.722795 TGAATGACTCGTGATAAGTTTTCAA 57.277 32.000 0.00 0.00 31.68 2.69
4552 5076 7.479980 TCTTGACTGGTACAAAAACTGAATTG 58.520 34.615 0.00 0.00 38.70 2.32
4591 5115 5.965334 CGTACTATTGTGCAAATGGATTGAC 59.035 40.000 10.38 0.00 41.85 3.18
4618 5142 1.079750 GCCTCGTCTCTTGTGGGAC 60.080 63.158 0.00 0.00 0.00 4.46
4650 5174 2.684374 TGTCATGCATATTGGTCAGTGC 59.316 45.455 0.00 0.00 38.05 4.40
4667 5191 6.128254 GGTCAGTGCTACTCTGTTAAAATTCC 60.128 42.308 0.00 0.00 34.86 3.01
4711 5235 9.944376 TGCAAATATAATCAGTATAGTTCCTCC 57.056 33.333 0.00 0.00 32.05 4.30
4786 5310 2.362397 GGCATCTACTACTGTGCTGCTA 59.638 50.000 0.00 0.00 37.70 3.49
4791 5315 0.247736 ACTACTGTGCTGCTACTGCC 59.752 55.000 0.00 0.00 38.71 4.85
4826 5350 3.813596 GCGGAGGCCACAATACTG 58.186 61.111 5.01 0.00 0.00 2.74
4827 5351 1.078426 GCGGAGGCCACAATACTGT 60.078 57.895 5.01 0.00 35.63 3.55
4828 5352 0.676782 GCGGAGGCCACAATACTGTT 60.677 55.000 5.01 0.00 31.64 3.16
4829 5353 1.821216 CGGAGGCCACAATACTGTTT 58.179 50.000 5.01 0.00 31.64 2.83
4830 5354 1.468520 CGGAGGCCACAATACTGTTTG 59.531 52.381 5.01 0.00 31.64 2.93
4831 5355 1.202348 GGAGGCCACAATACTGTTTGC 59.798 52.381 5.01 0.00 31.64 3.68
4832 5356 1.202348 GAGGCCACAATACTGTTTGCC 59.798 52.381 5.01 6.53 45.38 4.52
4833 5357 0.246360 GGCCACAATACTGTTTGCCC 59.754 55.000 0.00 0.00 41.82 5.36
4834 5358 0.109319 GCCACAATACTGTTTGCCCG 60.109 55.000 0.00 0.00 31.64 6.13
4835 5359 0.525761 CCACAATACTGTTTGCCCGG 59.474 55.000 0.00 0.00 31.64 5.73
4836 5360 0.109319 CACAATACTGTTTGCCCGGC 60.109 55.000 1.04 1.04 31.64 6.13
4837 5361 0.538516 ACAATACTGTTTGCCCGGCA 60.539 50.000 8.43 8.43 36.47 5.69
4838 5362 0.109319 CAATACTGTTTGCCCGGCAC 60.109 55.000 13.00 1.73 38.71 5.01
4839 5363 1.248101 AATACTGTTTGCCCGGCACC 61.248 55.000 13.00 6.45 38.71 5.01
4842 5366 4.877619 TGTTTGCCCGGCACCGAA 62.878 61.111 13.00 0.37 38.71 4.30
4843 5367 4.038080 GTTTGCCCGGCACCGAAG 62.038 66.667 13.00 2.54 38.71 3.79
4844 5368 4.257654 TTTGCCCGGCACCGAAGA 62.258 61.111 13.00 0.00 38.71 2.87
4845 5369 4.697756 TTGCCCGGCACCGAAGAG 62.698 66.667 13.00 0.00 38.71 2.85
4877 5426 2.225019 CACATGACTTCTCCTTGCACAC 59.775 50.000 0.00 0.00 0.00 3.82
4891 5440 0.879765 GCACACTGCAGAAAGATGCT 59.120 50.000 23.35 0.00 46.63 3.79
4907 5456 0.459489 TGCTGTTGGGCAAACACTTC 59.541 50.000 2.56 0.00 43.96 3.01
4991 5551 0.441533 CTGATGCGCGATATGCTTCC 59.558 55.000 12.10 0.00 43.27 3.46
4992 5552 0.249826 TGATGCGCGATATGCTTCCA 60.250 50.000 12.10 0.00 43.27 3.53
5014 5574 6.592220 TCCATGTCATTCAATTTGCAAATCTG 59.408 34.615 24.28 21.45 0.00 2.90
5043 5603 6.476380 TGTGCATTTTGAGATGTTCTGAAAAC 59.524 34.615 4.41 0.00 41.11 2.43
5091 5651 7.613146 TGTTAAACACATTAATTGCACAAACG 58.387 30.769 0.00 0.00 35.98 3.60
5107 5667 3.055675 ACAAACGACGAATGGGGAGATTA 60.056 43.478 0.00 0.00 0.00 1.75
5110 5670 3.728845 ACGACGAATGGGGAGATTAATG 58.271 45.455 0.00 0.00 0.00 1.90
5112 5672 3.990469 CGACGAATGGGGAGATTAATGAG 59.010 47.826 0.00 0.00 0.00 2.90
5128 5690 6.578020 TTAATGAGCGTAAATCCAGTAACG 57.422 37.500 0.00 0.00 38.34 3.18
5135 5697 3.434299 CGTAAATCCAGTAACGGCAAACT 59.566 43.478 0.00 0.00 0.00 2.66
5194 5756 8.482852 AAAGAAAATCCAGATTGAGAGGAAAA 57.517 30.769 0.00 0.00 34.62 2.29
5242 5805 0.972883 GGCAAACCAAACAGGCCATA 59.027 50.000 5.01 0.00 44.01 2.74
5263 5826 7.405292 CCATATGTATGGTTCAGGTAATGGAT 58.595 38.462 10.31 0.00 46.42 3.41
5390 5953 8.708883 CGATAGAGACCGTTAAGAGCATTAACG 61.709 44.444 27.00 27.00 46.57 3.18
5399 5962 7.549615 GTTAAGAGCATTAACGGTTCCTTAT 57.450 36.000 0.00 0.00 0.00 1.73
5406 5969 5.298347 CATTAACGGTTCCTTATCCTCTCC 58.702 45.833 0.00 0.00 0.00 3.71
5407 5970 1.790818 ACGGTTCCTTATCCTCTCCC 58.209 55.000 0.00 0.00 0.00 4.30
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
204 205 3.109240 GAGTCGTCCTACTCGGGC 58.891 66.667 0.00 0.00 36.80 6.13
358 359 0.451783 GGCAAGTCAAATAGGCGTGG 59.548 55.000 0.00 0.00 31.61 4.94
426 427 1.448119 GCAAATCCCTAGAAGCCGCC 61.448 60.000 0.00 0.00 0.00 6.13
478 479 4.168291 CAAGGAGGAGGGCGAGGC 62.168 72.222 0.00 0.00 0.00 4.70
479 480 4.168291 GCAAGGAGGAGGGCGAGG 62.168 72.222 0.00 0.00 0.00 4.63
542 543 4.091939 GCGAAACCCTAGGGCGGT 62.092 66.667 28.88 13.20 39.32 5.68
779 799 1.258445 TTGGTCGAAGGAGAGGGAGC 61.258 60.000 0.00 0.00 0.00 4.70
780 800 1.066787 GTTTGGTCGAAGGAGAGGGAG 60.067 57.143 0.00 0.00 0.00 4.30
781 801 0.974383 GTTTGGTCGAAGGAGAGGGA 59.026 55.000 0.00 0.00 0.00 4.20
782 802 0.036294 GGTTTGGTCGAAGGAGAGGG 60.036 60.000 0.00 0.00 0.00 4.30
783 803 0.977395 AGGTTTGGTCGAAGGAGAGG 59.023 55.000 0.00 0.00 0.00 3.69
784 804 1.066787 GGAGGTTTGGTCGAAGGAGAG 60.067 57.143 0.00 0.00 0.00 3.20
785 805 0.974383 GGAGGTTTGGTCGAAGGAGA 59.026 55.000 0.00 0.00 0.00 3.71
786 806 0.036294 GGGAGGTTTGGTCGAAGGAG 60.036 60.000 0.00 0.00 0.00 3.69
787 807 0.765135 TGGGAGGTTTGGTCGAAGGA 60.765 55.000 0.00 0.00 0.00 3.36
788 808 0.605589 GTGGGAGGTTTGGTCGAAGG 60.606 60.000 0.00 0.00 0.00 3.46
789 809 0.605589 GGTGGGAGGTTTGGTCGAAG 60.606 60.000 0.00 0.00 0.00 3.79
790 810 1.057851 AGGTGGGAGGTTTGGTCGAA 61.058 55.000 0.00 0.00 0.00 3.71
791 811 1.460689 AGGTGGGAGGTTTGGTCGA 60.461 57.895 0.00 0.00 0.00 4.20
792 812 1.003718 GAGGTGGGAGGTTTGGTCG 60.004 63.158 0.00 0.00 0.00 4.79
909 936 4.643387 GCGTCAACCCTGCACCCT 62.643 66.667 0.00 0.00 0.00 4.34
995 1022 4.222847 GGACCCTCGACATCGCCC 62.223 72.222 0.00 0.00 39.60 6.13
1150 1221 5.385617 CGACTGCGAAAAGAAGAAATCAAT 58.614 37.500 0.00 0.00 40.82 2.57
1218 1293 5.184864 TGCATTTGTAAACGGAGATTTGGAT 59.815 36.000 0.00 0.00 0.00 3.41
1219 1294 4.520874 TGCATTTGTAAACGGAGATTTGGA 59.479 37.500 0.00 0.00 0.00 3.53
1227 1302 3.254411 TGATTGCTGCATTTGTAAACGGA 59.746 39.130 1.84 0.00 0.00 4.69
1288 1363 0.040067 GCTTTCGGTTCCTGTTGCAG 60.040 55.000 0.00 0.00 0.00 4.41
1289 1364 0.749818 TGCTTTCGGTTCCTGTTGCA 60.750 50.000 0.00 0.00 0.00 4.08
1324 1399 3.312890 CCTCCCACAATCTATCAGGACT 58.687 50.000 0.00 0.00 0.00 3.85
1346 1421 3.462021 GACCCAGCAATTAGACTAGCAG 58.538 50.000 0.00 0.00 0.00 4.24
1350 1425 3.450904 ACAGGACCCAGCAATTAGACTA 58.549 45.455 0.00 0.00 0.00 2.59
1367 1442 0.888619 TCTCAAGCTACACCGACAGG 59.111 55.000 0.00 0.00 45.13 4.00
1505 1580 5.982890 AAGGGTAAATCAACAGACAATGG 57.017 39.130 0.00 0.00 0.00 3.16
2035 2110 0.104487 TTGTGCCAAGCCATGTGTTG 59.896 50.000 0.00 0.00 0.00 3.33
2315 2580 5.027293 TGTGCACATATCAGCTCAGTAAT 57.973 39.130 17.42 0.00 31.49 1.89
2364 2629 8.982723 AGTACTAATCAGGCATAATATACAGGG 58.017 37.037 0.00 0.00 0.00 4.45
2418 2683 5.461032 TGTTTTGTCCCACCAAATGATAC 57.539 39.130 0.00 0.00 34.50 2.24
2922 3191 1.126846 CGTGTTTCATCGTCCAAGAGC 59.873 52.381 0.00 0.00 0.00 4.09
2981 3250 6.128634 CGTCCCAAAATAAGTGTCTCAAGTAC 60.129 42.308 0.00 0.00 0.00 2.73
3094 3430 6.961554 CGGTATTCTAGCAAACAATCTGTTTC 59.038 38.462 1.83 0.00 46.61 2.78
3133 3567 8.561212 ACAAACACGCACTATTTTAATCAACTA 58.439 29.630 0.00 0.00 0.00 2.24
3161 3600 5.473931 CCCAGCTGATATCACTACACATAC 58.526 45.833 17.39 0.00 0.00 2.39
3307 3798 8.950210 CCATTTAGCCATGTTCTAACCTATATG 58.050 37.037 4.68 5.81 0.00 1.78
3318 3809 1.136891 GCACCCCATTTAGCCATGTTC 59.863 52.381 0.00 0.00 0.00 3.18
3334 3825 6.744082 GTGTATCCGTTTATTTTACTTGCACC 59.256 38.462 0.00 0.00 0.00 5.01
3408 3899 0.683973 AGCAGAGAGAACACACCTGG 59.316 55.000 0.00 0.00 0.00 4.45
3425 3916 4.083110 AGCACAAAACACAGTATCATCAGC 60.083 41.667 0.00 0.00 0.00 4.26
3455 3946 2.403698 CGTTACCAAAAGCGTGCAATTC 59.596 45.455 0.00 0.00 0.00 2.17
3865 4359 8.492415 GGATATATCCTATGCCACCTACAATA 57.508 38.462 22.50 0.00 43.73 1.90
3926 4420 5.118990 TGCGTTTTGAAAATTTTGATCCCA 58.881 33.333 8.47 0.00 0.00 4.37
4054 4548 0.450983 AGTAGCTCTTACACGGACGC 59.549 55.000 0.00 0.00 34.56 5.19
4055 4549 1.063764 GGAGTAGCTCTTACACGGACG 59.936 57.143 0.00 0.00 34.56 4.79
4060 4554 7.284944 TGTTTATAGAGGGAGTAGCTCTTACAC 59.715 40.741 0.00 0.00 34.56 2.90
4061 4555 7.351952 TGTTTATAGAGGGAGTAGCTCTTACA 58.648 38.462 0.00 0.00 34.56 2.41
4062 4556 7.820578 TGTTTATAGAGGGAGTAGCTCTTAC 57.179 40.000 0.00 0.00 0.00 2.34
4094 4613 6.128634 CCCTCTGTAAACAAACATAAGACGTC 60.129 42.308 7.70 7.70 0.00 4.34
4104 4623 7.681939 TCATGTAATCCCTCTGTAAACAAAC 57.318 36.000 0.00 0.00 0.00 2.93
4197 4718 5.449725 GCAGATTTCCTAGATCAGCCAAAAC 60.450 44.000 0.00 0.00 31.99 2.43
4203 4726 7.104939 AGATATTGCAGATTTCCTAGATCAGC 58.895 38.462 0.00 0.00 36.79 4.26
4231 4754 9.807649 GTTGAATTTGGCAGATTATCAAGTAAT 57.192 29.630 2.90 0.00 35.71 1.89
4243 4766 2.238521 GGTCCTGTTGAATTTGGCAGA 58.761 47.619 5.89 0.00 0.00 4.26
4269 4792 9.317936 CTTTTTCTTAAGGCAATGACTCTTTTT 57.682 29.630 1.85 0.00 0.00 1.94
4270 4793 7.928167 CCTTTTTCTTAAGGCAATGACTCTTTT 59.072 33.333 1.85 0.00 38.39 2.27
4271 4794 7.287696 TCCTTTTTCTTAAGGCAATGACTCTTT 59.712 33.333 1.85 0.00 43.62 2.52
4272 4795 6.777580 TCCTTTTTCTTAAGGCAATGACTCTT 59.222 34.615 1.85 0.00 43.62 2.85
4273 4796 6.207614 GTCCTTTTTCTTAAGGCAATGACTCT 59.792 38.462 1.85 0.00 43.62 3.24
4274 4797 6.016276 TGTCCTTTTTCTTAAGGCAATGACTC 60.016 38.462 1.85 0.00 43.62 3.36
4552 5076 1.134788 AGTACGGTTACATGAGCTGCC 60.135 52.381 0.00 0.00 0.00 4.85
4618 5142 7.019418 CCAATATGCATGACAAGTGATAATCG 58.981 38.462 10.16 0.00 0.00 3.34
4650 5174 9.760660 CAAAATCTCGGAATTTTAACAGAGTAG 57.239 33.333 7.90 0.00 36.86 2.57
4667 5191 1.065031 CAAACGGCGGCAAAATCTCG 61.065 55.000 13.24 0.00 0.00 4.04
4791 5315 4.135153 CTGTCCGGTGAGAGGGCG 62.135 72.222 0.00 0.00 35.82 6.13
4821 5345 1.677633 GGTGCCGGGCAAACAGTAT 60.678 57.895 25.70 0.00 41.47 2.12
4822 5346 2.281900 GGTGCCGGGCAAACAGTA 60.282 61.111 25.70 0.00 41.47 2.74
4825 5349 4.877619 TTCGGTGCCGGGCAAACA 62.878 61.111 25.70 7.14 41.47 2.83
4826 5350 4.038080 CTTCGGTGCCGGGCAAAC 62.038 66.667 25.70 18.47 41.47 2.93
4827 5351 4.257654 TCTTCGGTGCCGGGCAAA 62.258 61.111 25.70 13.91 41.47 3.68
4828 5352 4.697756 CTCTTCGGTGCCGGGCAA 62.698 66.667 25.70 5.33 41.47 4.52
4830 5354 4.162690 ATCTCTTCGGTGCCGGGC 62.163 66.667 13.32 13.32 40.25 6.13
4831 5355 2.202932 CATCTCTTCGGTGCCGGG 60.203 66.667 10.94 4.70 40.25 5.73
4832 5356 2.892425 GCATCTCTTCGGTGCCGG 60.892 66.667 10.94 0.00 40.25 6.13
4833 5357 2.125552 TGCATCTCTTCGGTGCCG 60.126 61.111 3.94 3.94 38.06 5.69
4834 5358 2.456119 CGTGCATCTCTTCGGTGCC 61.456 63.158 0.00 0.00 38.06 5.01
4835 5359 0.807667 ATCGTGCATCTCTTCGGTGC 60.808 55.000 0.00 0.00 39.26 5.01
4836 5360 0.926155 CATCGTGCATCTCTTCGGTG 59.074 55.000 0.00 0.00 0.00 4.94
4837 5361 0.807667 GCATCGTGCATCTCTTCGGT 60.808 55.000 0.00 0.00 44.26 4.69
4838 5362 1.930100 GCATCGTGCATCTCTTCGG 59.070 57.895 0.00 0.00 44.26 4.30
4877 5426 1.201647 CCCAACAGCATCTTTCTGCAG 59.798 52.381 7.63 7.63 44.77 4.41
4891 5440 6.943146 TGTATAATAGAAGTGTTTGCCCAACA 59.057 34.615 0.00 0.00 43.55 3.33
4907 5456 7.064253 GCCGTGCCCTACTTTATTGTATAATAG 59.936 40.741 0.00 0.00 30.84 1.73
4960 5512 3.058293 TCGCGCATCAGAAAAGAATTGTT 60.058 39.130 8.75 0.00 0.00 2.83
4962 5514 3.121559 TCGCGCATCAGAAAAGAATTG 57.878 42.857 8.75 0.00 0.00 2.32
5014 5574 4.927425 AGAACATCTCAAAATGCACATTGC 59.073 37.500 8.14 0.00 45.29 3.56
5070 5630 5.052040 CGTCGTTTGTGCAATTAATGTGTTT 60.052 36.000 0.00 0.00 0.00 2.83
5091 5651 3.748568 GCTCATTAATCTCCCCATTCGTC 59.251 47.826 0.00 0.00 0.00 4.20
5107 5667 3.869246 CCGTTACTGGATTTACGCTCATT 59.131 43.478 0.00 0.00 32.97 2.57
5110 5670 1.591619 GCCGTTACTGGATTTACGCTC 59.408 52.381 0.00 0.00 32.97 5.03
5112 5672 1.361793 TGCCGTTACTGGATTTACGC 58.638 50.000 0.00 0.00 32.97 4.42
5135 5697 3.747854 TGTTCTTGCATTTGATTGGCA 57.252 38.095 0.00 0.00 35.41 4.92
5183 5745 7.098477 CCATGTAATGCAAATTTTCCTCTCAA 58.902 34.615 0.00 0.00 44.97 3.02
5186 5748 6.610075 ACCATGTAATGCAAATTTTCCTCT 57.390 33.333 0.00 0.00 44.97 3.69
5187 5749 7.489113 CACTACCATGTAATGCAAATTTTCCTC 59.511 37.037 0.00 0.00 44.97 3.71
5194 5756 6.179756 TCTGTCACTACCATGTAATGCAAAT 58.820 36.000 0.00 0.00 44.97 2.32
5242 5805 6.777580 GGAAATCCATTACCTGAACCATACAT 59.222 38.462 0.00 0.00 35.64 2.29
5263 5826 2.038557 GTCTTGCCTCAGTACCAGGAAA 59.961 50.000 11.92 7.10 31.91 3.13
5390 5953 2.191981 TGGGGAGAGGATAAGGAACC 57.808 55.000 0.00 0.00 0.00 3.62
5391 5954 3.071747 GTGATGGGGAGAGGATAAGGAAC 59.928 52.174 0.00 0.00 0.00 3.62
5399 5962 6.485388 ACTTATATAGTGATGGGGAGAGGA 57.515 41.667 0.00 0.00 35.19 3.71


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

AutoCloner maintained by Alex Coulton.