Multiple sequence alignment - TraesCS3A01G149100

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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 TraesCS3A01G149100 chr3A 100.000 4297 0 0 1 4297 134238202 134233906 0.000000e+00 7936.0
1 TraesCS3A01G149100 chr3D 93.810 3990 141 41 1 3942 125482798 125478867 0.000000e+00 5903.0
2 TraesCS3A01G149100 chr3B 95.134 1788 64 11 1788 3571 179368359 179366591 0.000000e+00 2798.0
3 TraesCS3A01G149100 chr3B 93.235 1700 51 24 1 1686 179370055 179368406 0.000000e+00 2444.0
4 TraesCS3A01G149100 chr3B 86.921 367 32 12 3608 3960 179366587 179366223 8.660000e-107 398.0
5 TraesCS3A01G149100 chr3B 96.078 51 1 1 4248 4297 179365788 179365738 9.900000e-12 82.4
6 TraesCS3A01G149100 chr7D 88.889 54 6 0 1204 1257 427631636 427631583 2.770000e-07 67.6
7 TraesCS3A01G149100 chr7B 90.000 50 5 0 1204 1253 445423214 445423165 9.970000e-07 65.8


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 TraesCS3A01G149100 chr3A 134233906 134238202 4296 True 7936.0 7936 100.000 1 4297 1 chr3A.!!$R1 4296
1 TraesCS3A01G149100 chr3D 125478867 125482798 3931 True 5903.0 5903 93.810 1 3942 1 chr3D.!!$R1 3941
2 TraesCS3A01G149100 chr3B 179365738 179370055 4317 True 1430.6 2798 92.842 1 4297 4 chr3B.!!$R1 4296

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
535 545 0.177604 GGAGAGATGTGTGGCTCTGG 59.822 60.0 0.0 0.0 41.33 3.86 F
1674 1693 0.457035 GGCCATGTCGATGTTTGCAT 59.543 50.0 0.0 0.0 38.18 3.96 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1816 1836 0.321671 TCCTGCTCTTTCGAGGTTGG 59.678 55.0 0.0 0.0 37.75 3.77 R
3606 3630 0.887933 ATGAACGGGGCAACAATGTC 59.112 50.0 0.0 0.0 39.74 3.06 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
25 26 8.958119 TCTACCATCCAACAAAAGTATGTATC 57.042 34.615 0.00 0.00 32.02 2.24
39 40 5.940617 AGTATGTATCCCTTTAGCATGCAA 58.059 37.500 21.98 9.44 0.00 4.08
160 165 1.995542 AGTCCCACAATTGTCCATCCT 59.004 47.619 8.48 0.00 0.00 3.24
203 208 6.441222 AGATAAGATTACTCAGTGGTGGGTA 58.559 40.000 0.00 0.00 38.75 3.69
258 265 4.160329 AGACCTTCAGTACAGGATCACAA 58.840 43.478 4.80 0.00 35.14 3.33
259 266 4.593206 AGACCTTCAGTACAGGATCACAAA 59.407 41.667 4.80 0.00 35.14 2.83
260 267 5.249393 AGACCTTCAGTACAGGATCACAAAT 59.751 40.000 4.80 0.00 35.14 2.32
261 268 5.491982 ACCTTCAGTACAGGATCACAAATC 58.508 41.667 4.80 0.00 35.14 2.17
262 269 5.013079 ACCTTCAGTACAGGATCACAAATCA 59.987 40.000 4.80 0.00 35.14 2.57
263 270 6.118170 CCTTCAGTACAGGATCACAAATCAT 58.882 40.000 0.00 0.00 32.41 2.45
264 271 7.092891 ACCTTCAGTACAGGATCACAAATCATA 60.093 37.037 4.80 0.00 35.14 2.15
265 272 7.440556 CCTTCAGTACAGGATCACAAATCATAG 59.559 40.741 0.00 0.00 32.41 2.23
266 273 7.423844 TCAGTACAGGATCACAAATCATAGT 57.576 36.000 0.00 0.00 0.00 2.12
267 274 7.851228 TCAGTACAGGATCACAAATCATAGTT 58.149 34.615 0.00 0.00 0.00 2.24
268 275 8.321353 TCAGTACAGGATCACAAATCATAGTTT 58.679 33.333 0.00 0.00 0.00 2.66
269 276 8.393366 CAGTACAGGATCACAAATCATAGTTTG 58.607 37.037 0.00 0.00 43.11 2.93
320 327 2.825975 AAACGGTCCACCAAACGCG 61.826 57.895 3.53 3.53 35.14 6.01
322 329 2.740826 CGGTCCACCAAACGCGAT 60.741 61.111 15.93 0.00 35.14 4.58
325 332 2.281139 TCCACCAAACGCGATGCA 60.281 55.556 15.93 0.00 0.00 3.96
330 340 1.442520 CCAAACGCGATGCACTTGG 60.443 57.895 15.93 11.36 34.93 3.61
514 524 1.662438 CCAACCAACCAACAGCACGT 61.662 55.000 0.00 0.00 0.00 4.49
515 525 1.018148 CAACCAACCAACAGCACGTA 58.982 50.000 0.00 0.00 0.00 3.57
527 537 1.474478 CAGCACGTAGGAGAGATGTGT 59.526 52.381 0.00 0.00 36.40 3.72
528 538 1.474478 AGCACGTAGGAGAGATGTGTG 59.526 52.381 0.00 0.00 36.40 3.82
529 539 1.469940 GCACGTAGGAGAGATGTGTGG 60.470 57.143 0.00 0.00 36.40 4.17
531 541 1.107114 CGTAGGAGAGATGTGTGGCT 58.893 55.000 0.00 0.00 0.00 4.75
532 542 1.066303 CGTAGGAGAGATGTGTGGCTC 59.934 57.143 0.00 0.00 0.00 4.70
533 543 2.383855 GTAGGAGAGATGTGTGGCTCT 58.616 52.381 0.00 0.00 43.78 4.09
534 544 1.193323 AGGAGAGATGTGTGGCTCTG 58.807 55.000 0.00 0.00 41.33 3.35
535 545 0.177604 GGAGAGATGTGTGGCTCTGG 59.822 60.000 0.00 0.00 41.33 3.86
562 572 1.035932 TGCTACTACCTGGAGACCGC 61.036 60.000 0.00 0.00 0.00 5.68
628 638 3.030652 CTGCCGGTTTGGTGTGTC 58.969 61.111 1.90 0.00 41.21 3.67
629 639 2.892334 CTGCCGGTTTGGTGTGTCG 61.892 63.158 1.90 0.00 41.21 4.35
630 640 3.656045 GCCGGTTTGGTGTGTCGG 61.656 66.667 1.90 0.00 43.13 4.79
705 715 4.978099 TGATGGCATAGAAGGAAGGATTC 58.022 43.478 0.00 0.00 46.67 2.52
706 716 4.662179 TGATGGCATAGAAGGAAGGATTCT 59.338 41.667 0.00 0.00 46.56 2.40
724 734 5.180304 GGATTCTGAAAGCTCTCGAGTTTTT 59.820 40.000 13.13 11.18 41.00 1.94
813 825 0.623723 AGAATTTAAGAGGGCCGCCA 59.376 50.000 12.58 0.00 0.00 5.69
852 864 1.148273 GCCGATGGCCCATGTCTTA 59.852 57.895 0.00 0.00 44.06 2.10
864 876 3.257393 CCATGTCTTAGTCACTGTCAGC 58.743 50.000 0.00 0.00 0.00 4.26
865 877 3.306294 CCATGTCTTAGTCACTGTCAGCA 60.306 47.826 0.00 0.00 0.00 4.41
866 878 3.371102 TGTCTTAGTCACTGTCAGCAC 57.629 47.619 0.00 0.00 0.00 4.40
899 914 3.588955 CTCAGCAAAATTTTACCTGCCC 58.411 45.455 18.77 0.14 35.33 5.36
905 920 4.089361 CAAAATTTTACCTGCCCCTCTCT 58.911 43.478 2.44 0.00 0.00 3.10
906 921 3.653835 AATTTTACCTGCCCCTCTCTC 57.346 47.619 0.00 0.00 0.00 3.20
907 922 2.344093 TTTTACCTGCCCCTCTCTCT 57.656 50.000 0.00 0.00 0.00 3.10
908 923 1.867363 TTTACCTGCCCCTCTCTCTC 58.133 55.000 0.00 0.00 0.00 3.20
909 924 1.011595 TTACCTGCCCCTCTCTCTCT 58.988 55.000 0.00 0.00 0.00 3.10
1317 1332 1.895886 ATCCCCTGCTCAGACCCTCT 61.896 60.000 0.00 0.00 0.00 3.69
1359 1374 2.731721 TACTGTGTTCCGCGCGTG 60.732 61.111 29.95 19.95 0.00 5.34
1460 1475 2.010582 GAGGCTCGCTGTGGGTAGAG 62.011 65.000 0.00 0.00 0.00 2.43
1613 1629 5.952347 GGGAAATCACCCTGAACTAAATCTT 59.048 40.000 0.00 0.00 45.90 2.40
1630 1646 9.796120 ACTAAATCTTCAGATAGTTCTTTCGAG 57.204 33.333 0.00 0.00 33.73 4.04
1674 1693 0.457035 GGCCATGTCGATGTTTGCAT 59.543 50.000 0.00 0.00 38.18 3.96
1753 1773 4.024809 GGTTTTCTCTGAAGGTTCAACTCG 60.025 45.833 0.00 0.00 36.64 4.18
1778 1798 5.417266 TCTCGAATTATGGGAAACAAATGCA 59.583 36.000 0.00 0.00 0.00 3.96
2069 2089 1.524393 TATCTGCCGCTGCACCATG 60.524 57.895 0.00 0.00 44.23 3.66
2191 2211 6.868622 AGGCGATATCTTTGTGATAGGATAC 58.131 40.000 0.34 0.00 40.58 2.24
2200 2220 7.497595 TCTTTGTGATAGGATACGTTATTGCT 58.502 34.615 0.00 0.00 46.39 3.91
2246 2266 4.881273 TGTGTTTCTGCATGTTGTAGTTCT 59.119 37.500 0.00 0.00 31.74 3.01
2280 2300 2.363680 AGACCGCTAGATCACAATCTGG 59.636 50.000 0.00 0.00 42.36 3.86
2437 2457 6.223351 TCTGGAATTTCATAATGCATGCAA 57.777 33.333 26.68 9.94 34.35 4.08
2632 2652 1.740585 CAACCACTGAACGTTTGGACA 59.259 47.619 21.42 5.93 34.24 4.02
2711 2732 6.656902 AGATTCTCTTTATGTTCAGGCATCA 58.343 36.000 0.00 0.00 0.00 3.07
2714 2735 8.985315 ATTCTCTTTATGTTCAGGCATCAATA 57.015 30.769 0.00 0.00 0.00 1.90
2723 2744 5.414454 TGTTCAGGCATCAATAAAGTACCAC 59.586 40.000 0.00 0.00 0.00 4.16
2903 2924 6.669154 ACCATGGGAATAATCACAAAGTCATT 59.331 34.615 18.09 0.00 43.63 2.57
3017 3038 2.230508 CGCTAACAGTACCAAGGAGACA 59.769 50.000 0.00 0.00 0.00 3.41
3067 3088 5.295540 GGATGGTTTCTTCTAGTCTTGATGC 59.704 44.000 0.00 0.00 0.00 3.91
3096 3117 8.040132 TCAGGAACAGTTTCAATGTGAAAAATT 58.960 29.630 5.04 1.20 46.53 1.82
3238 3259 3.520569 TCAATCGCGATGATTCTTCACA 58.479 40.909 24.47 0.00 45.59 3.58
3261 3282 0.106167 TCTGGCAGGGCGTAGTAGAT 60.106 55.000 15.73 0.00 0.00 1.98
3262 3283 0.315568 CTGGCAGGGCGTAGTAGATC 59.684 60.000 6.61 0.00 0.00 2.75
3365 3387 6.624352 TTGTTAGCATCTTATCTGCCATTC 57.376 37.500 0.00 0.00 40.56 2.67
3423 3445 4.955811 TTGCATTCTAGGTATGGATCGT 57.044 40.909 0.00 0.00 0.00 3.73
3438 3460 3.147629 GGATCGTGTTAGCTAGGCTAGA 58.852 50.000 25.37 1.94 42.34 2.43
3458 3480 6.477360 GCTAGATTACCTCTGCTACTTTCAAC 59.523 42.308 0.00 0.00 35.28 3.18
3500 3522 3.923017 ATCCTTGTTGTAAGCAGCAAC 57.077 42.857 9.97 9.97 40.14 4.17
3508 3530 3.624326 TGTAAGCAGCAACATGTTGTC 57.376 42.857 33.01 25.64 42.31 3.18
3529 3551 7.984422 TGTCTTCATGTGAATCTATTGTGTT 57.016 32.000 0.00 0.00 33.01 3.32
3588 3612 8.617809 GTTGTACAAAGTCTTGGTTCTGAAATA 58.382 33.333 10.51 0.00 36.82 1.40
3603 3627 6.462073 TCTGAAATAAGTTTGCGTACTCAC 57.538 37.500 0.00 0.00 0.00 3.51
3606 3630 7.541091 TCTGAAATAAGTTTGCGTACTCACTAG 59.459 37.037 0.00 0.00 0.00 2.57
3635 3659 3.013921 TGCCCCGTTCATTAGATTGTTC 58.986 45.455 0.00 0.00 0.00 3.18
3667 3691 4.341806 TCTGTTTTCATGCTTGTGATGGTT 59.658 37.500 0.00 0.00 0.00 3.67
3668 3692 4.619973 TGTTTTCATGCTTGTGATGGTTC 58.380 39.130 0.00 0.00 0.00 3.62
3669 3693 4.099113 TGTTTTCATGCTTGTGATGGTTCA 59.901 37.500 0.00 0.00 0.00 3.18
3671 3695 5.471556 TTTCATGCTTGTGATGGTTCATT 57.528 34.783 0.00 0.00 33.56 2.57
3786 3828 9.927668 AAACCAGATTATGTTGGATTTTTGTAG 57.072 29.630 0.00 0.00 37.89 2.74
3789 3831 7.147846 CCAGATTATGTTGGATTTTTGTAGCCT 60.148 37.037 0.00 0.00 36.55 4.58
3792 3834 3.988819 TGTTGGATTTTTGTAGCCTTGC 58.011 40.909 0.00 0.00 0.00 4.01
3793 3835 3.386078 TGTTGGATTTTTGTAGCCTTGCA 59.614 39.130 0.00 0.00 0.00 4.08
3809 3851 5.589452 AGCCTTGCAAATTCAAATCAAAACA 59.411 32.000 0.00 0.00 0.00 2.83
3815 3874 7.416022 TGCAAATTCAAATCAAAACATCAACC 58.584 30.769 0.00 0.00 0.00 3.77
3828 3887 7.726291 TCAAAACATCAACCCAGGAACTATTTA 59.274 33.333 0.00 0.00 36.02 1.40
3829 3888 7.462571 AAACATCAACCCAGGAACTATTTAC 57.537 36.000 0.00 0.00 36.02 2.01
3849 3908 3.214328 ACTGTCAGGTTTTGTCCATGTC 58.786 45.455 4.53 0.00 0.00 3.06
3850 3909 3.213506 CTGTCAGGTTTTGTCCATGTCA 58.786 45.455 0.00 0.00 0.00 3.58
3863 3923 6.968263 TGTCCATGTCAAATTTTACTTGGA 57.032 33.333 25.21 25.21 43.68 3.53
3917 3977 2.875296 TGCATTAGGGTGCTGAGTTTT 58.125 42.857 0.34 0.00 45.27 2.43
3924 3984 0.595095 GGTGCTGAGTTTTGGCTGAG 59.405 55.000 0.00 0.00 0.00 3.35
3951 4011 3.556817 TGCAATCTAGGTGCAGTGG 57.443 52.632 15.47 0.00 46.76 4.00
3952 4012 0.983467 TGCAATCTAGGTGCAGTGGA 59.017 50.000 15.47 0.00 46.76 4.02
3953 4013 1.339055 TGCAATCTAGGTGCAGTGGAC 60.339 52.381 15.47 6.17 46.76 4.02
3955 4015 2.681976 GCAATCTAGGTGCAGTGGACAT 60.682 50.000 17.16 12.39 41.80 3.06
3956 4016 2.941064 CAATCTAGGTGCAGTGGACATG 59.059 50.000 17.16 5.91 0.00 3.21
3958 4018 2.815158 TCTAGGTGCAGTGGACATGTA 58.185 47.619 17.16 4.11 0.00 2.29
3959 4019 2.496070 TCTAGGTGCAGTGGACATGTAC 59.504 50.000 17.16 0.00 33.11 2.90
3960 4020 0.037326 AGGTGCAGTGGACATGTACG 60.037 55.000 17.16 0.00 34.50 3.67
3961 4021 0.037697 GGTGCAGTGGACATGTACGA 60.038 55.000 17.16 0.00 34.50 3.43
3962 4022 1.405526 GGTGCAGTGGACATGTACGAT 60.406 52.381 17.16 0.00 34.50 3.73
3963 4023 1.660607 GTGCAGTGGACATGTACGATG 59.339 52.381 10.26 5.78 0.00 3.84
3964 4024 1.275010 TGCAGTGGACATGTACGATGT 59.725 47.619 12.49 9.71 34.52 3.06
3965 4025 2.494073 TGCAGTGGACATGTACGATGTA 59.506 45.455 12.49 6.60 31.52 2.29
3966 4026 2.858344 GCAGTGGACATGTACGATGTAC 59.142 50.000 12.49 11.56 33.54 2.90
3967 4027 3.444916 CAGTGGACATGTACGATGTACC 58.555 50.000 3.00 13.87 31.94 3.34
3968 4028 3.130516 CAGTGGACATGTACGATGTACCT 59.869 47.826 3.00 9.96 31.94 3.08
3969 4029 4.337274 CAGTGGACATGTACGATGTACCTA 59.663 45.833 3.00 0.00 31.94 3.08
3970 4030 4.579340 AGTGGACATGTACGATGTACCTAG 59.421 45.833 3.00 0.00 31.94 3.02
3971 4031 4.337555 GTGGACATGTACGATGTACCTAGT 59.662 45.833 3.00 1.32 31.94 2.57
3972 4032 4.951715 TGGACATGTACGATGTACCTAGTT 59.048 41.667 3.00 0.00 31.94 2.24
3973 4033 5.066893 TGGACATGTACGATGTACCTAGTTC 59.933 44.000 3.00 1.24 31.94 3.01
3974 4034 5.066893 GGACATGTACGATGTACCTAGTTCA 59.933 44.000 0.00 0.00 31.52 3.18
3975 4035 6.238953 GGACATGTACGATGTACCTAGTTCAT 60.239 42.308 0.00 0.00 31.52 2.57
3976 4036 7.108841 ACATGTACGATGTACCTAGTTCATT 57.891 36.000 0.00 0.00 0.00 2.57
3977 4037 7.553334 ACATGTACGATGTACCTAGTTCATTT 58.447 34.615 0.00 0.00 0.00 2.32
3978 4038 8.689061 ACATGTACGATGTACCTAGTTCATTTA 58.311 33.333 0.00 0.00 0.00 1.40
3979 4039 9.524106 CATGTACGATGTACCTAGTTCATTTAA 57.476 33.333 4.78 0.00 0.00 1.52
3981 4041 9.926158 TGTACGATGTACCTAGTTCATTTAAAA 57.074 29.630 4.78 0.00 0.00 1.52
4037 4097 5.443693 GCTTCACGCTAAAAATGCTCAATTG 60.444 40.000 0.00 0.00 35.14 2.32
4057 4117 1.661509 GGGCTTTGCTCGTTTGTGC 60.662 57.895 0.00 0.00 35.20 4.57
4058 4118 1.065600 GGCTTTGCTCGTTTGTGCA 59.934 52.632 0.00 0.00 42.42 4.57
4160 4397 0.326264 GACACCATGCCAGGAGAGTT 59.674 55.000 0.00 0.00 0.00 3.01
4168 4405 4.491676 CATGCCAGGAGAGTTTTCATTTG 58.508 43.478 0.00 0.00 0.00 2.32
4171 4408 3.319122 GCCAGGAGAGTTTTCATTTGTGT 59.681 43.478 0.00 0.00 0.00 3.72
4172 4409 4.557496 GCCAGGAGAGTTTTCATTTGTGTC 60.557 45.833 0.00 0.00 0.00 3.67
4173 4410 4.823989 CCAGGAGAGTTTTCATTTGTGTCT 59.176 41.667 0.00 0.00 0.00 3.41
4174 4411 5.997746 CCAGGAGAGTTTTCATTTGTGTCTA 59.002 40.000 0.00 0.00 0.00 2.59
4175 4412 6.486657 CCAGGAGAGTTTTCATTTGTGTCTAA 59.513 38.462 0.00 0.00 0.00 2.10
4176 4413 7.013274 CCAGGAGAGTTTTCATTTGTGTCTAAA 59.987 37.037 0.00 0.00 0.00 1.85
4177 4414 8.405531 CAGGAGAGTTTTCATTTGTGTCTAAAA 58.594 33.333 0.00 0.00 0.00 1.52
4178 4415 8.966868 AGGAGAGTTTTCATTTGTGTCTAAAAA 58.033 29.630 0.00 0.00 0.00 1.94
4241 4478 2.795121 GTGTCATGCACGACTGAATC 57.205 50.000 14.75 0.00 38.45 2.52
4242 4479 2.341257 GTGTCATGCACGACTGAATCT 58.659 47.619 14.75 0.00 38.45 2.40
4243 4480 3.511699 GTGTCATGCACGACTGAATCTA 58.488 45.455 14.75 0.00 38.45 1.98
4244 4481 4.115516 GTGTCATGCACGACTGAATCTAT 58.884 43.478 14.75 0.00 38.45 1.98
4245 4482 5.281727 GTGTCATGCACGACTGAATCTATA 58.718 41.667 14.75 0.00 38.45 1.31
4246 4483 5.174035 GTGTCATGCACGACTGAATCTATAC 59.826 44.000 14.75 0.00 38.45 1.47
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
25 26 4.427312 GAACAATCTTGCATGCTAAAGGG 58.573 43.478 20.33 10.43 0.00 3.95
160 165 7.663905 TCTTATCTTTGTGCCTAGCTGTTTTTA 59.336 33.333 0.00 0.00 0.00 1.52
264 271 9.261180 CCGATACAACTATGATTGATACAAACT 57.739 33.333 0.00 0.00 33.57 2.66
265 272 8.009974 GCCGATACAACTATGATTGATACAAAC 58.990 37.037 0.00 0.00 33.57 2.93
266 273 7.713073 TGCCGATACAACTATGATTGATACAAA 59.287 33.333 0.00 0.00 33.57 2.83
267 274 7.213678 TGCCGATACAACTATGATTGATACAA 58.786 34.615 0.00 0.00 33.57 2.41
268 275 6.754193 TGCCGATACAACTATGATTGATACA 58.246 36.000 0.00 0.00 33.57 2.29
269 276 7.598869 TCTTGCCGATACAACTATGATTGATAC 59.401 37.037 0.00 0.00 33.57 2.24
270 277 7.666623 TCTTGCCGATACAACTATGATTGATA 58.333 34.615 0.00 0.00 33.57 2.15
271 278 6.524734 TCTTGCCGATACAACTATGATTGAT 58.475 36.000 0.00 0.00 33.57 2.57
272 279 5.912892 TCTTGCCGATACAACTATGATTGA 58.087 37.500 0.00 0.00 33.57 2.57
273 280 6.603237 TTCTTGCCGATACAACTATGATTG 57.397 37.500 0.00 0.00 35.59 2.67
320 327 4.459337 GGTAATTATAGGCCCAAGTGCATC 59.541 45.833 0.00 0.00 0.00 3.91
322 329 3.461831 AGGTAATTATAGGCCCAAGTGCA 59.538 43.478 0.00 0.00 0.00 4.57
325 332 5.897250 CCAAAAGGTAATTATAGGCCCAAGT 59.103 40.000 0.00 0.00 0.00 3.16
330 340 3.254903 CGCCCAAAAGGTAATTATAGGCC 59.745 47.826 0.00 0.00 38.26 5.19
514 524 2.382882 CAGAGCCACACATCTCTCCTA 58.617 52.381 0.00 0.00 37.56 2.94
515 525 1.193323 CAGAGCCACACATCTCTCCT 58.807 55.000 0.00 0.00 37.56 3.69
535 545 1.075151 AGGTAGTAGCAGCTCCCCC 60.075 63.158 0.00 0.00 0.00 5.40
562 572 0.648441 TAAATTACGAAGCAGCGCCG 59.352 50.000 2.29 1.74 33.86 6.46
705 715 3.187432 GGGAAAAACTCGAGAGCTTTCAG 59.813 47.826 21.68 3.99 36.26 3.02
706 716 3.139077 GGGAAAAACTCGAGAGCTTTCA 58.861 45.455 21.68 0.00 36.26 2.69
740 751 3.233259 GATCTGGGCTCTAGCGGGC 62.233 68.421 0.00 1.54 43.26 6.13
813 825 4.423732 GCCGTCTGCAACATTCATTAAAT 58.576 39.130 0.00 0.00 40.77 1.40
852 864 1.051008 TGATGGTGCTGACAGTGACT 58.949 50.000 3.99 0.00 0.00 3.41
864 876 2.021457 TGCTGAGCAATGATGATGGTG 58.979 47.619 3.81 0.00 34.76 4.17
865 877 2.430248 TGCTGAGCAATGATGATGGT 57.570 45.000 3.81 0.00 34.76 3.55
896 911 1.152546 GGGAGAGAGAGAGAGGGGC 60.153 68.421 0.00 0.00 0.00 5.80
899 914 1.221635 TGGAGGGAGAGAGAGAGAGG 58.778 60.000 0.00 0.00 0.00 3.69
905 920 0.411452 ACTGCTTGGAGGGAGAGAGA 59.589 55.000 0.00 0.00 0.00 3.10
906 921 1.206849 GAACTGCTTGGAGGGAGAGAG 59.793 57.143 0.00 0.00 0.00 3.20
907 922 1.270907 GAACTGCTTGGAGGGAGAGA 58.729 55.000 0.00 0.00 0.00 3.10
908 923 0.108424 CGAACTGCTTGGAGGGAGAG 60.108 60.000 0.00 0.00 0.00 3.20
909 924 1.544825 CCGAACTGCTTGGAGGGAGA 61.545 60.000 0.00 0.00 0.00 3.71
1317 1332 0.934496 CAAACCACGCGAACAAGAGA 59.066 50.000 15.93 0.00 0.00 3.10
1359 1374 3.189287 CCAATCAACATATAGCGAAGGCC 59.811 47.826 0.00 0.00 41.24 5.19
1460 1475 5.390613 CAGTCGGTTGAATTTACCAACATC 58.609 41.667 9.83 1.82 44.07 3.06
1613 1629 7.101652 ACTAATGCTCGAAAGAACTATCTGA 57.898 36.000 0.00 0.00 41.32 3.27
1674 1693 5.127194 ACGCACTAATTCTTATCTCACCAGA 59.873 40.000 0.00 0.00 0.00 3.86
1753 1773 5.743872 GCATTTGTTTCCCATAATTCGAGAC 59.256 40.000 0.00 0.00 0.00 3.36
1816 1836 0.321671 TCCTGCTCTTTCGAGGTTGG 59.678 55.000 0.00 0.00 37.75 3.77
1951 1971 5.535030 ACAGAAAACAAGGTTATCCAGTTCC 59.465 40.000 2.36 0.00 34.68 3.62
2069 2089 5.380043 ACAAGGATATGAATGTCCATGTCC 58.620 41.667 10.15 10.45 43.41 4.02
2191 2211 1.667724 CCCTGCTGAGAAGCAATAACG 59.332 52.381 1.61 0.00 44.88 3.18
2200 2220 3.370840 ACAATATTGCCCTGCTGAGAA 57.629 42.857 15.48 0.00 0.00 2.87
2280 2300 1.064758 TGGGTGATAGATGTGCCCAAC 60.065 52.381 0.00 0.00 45.43 3.77
2320 2340 1.203137 TCGGAGGGGAGACTTCTGAAA 60.203 52.381 0.00 0.00 0.00 2.69
2415 2435 6.704050 TCATTGCATGCATTATGAAATTCCAG 59.296 34.615 25.66 7.06 41.42 3.86
2437 2457 8.093307 GTCAGACACTCCATGAATATACATCAT 58.907 37.037 0.00 0.00 38.02 2.45
2652 2672 8.189119 AGTTTCCAACTTATTAAATTCAGCCA 57.811 30.769 0.00 0.00 39.04 4.75
2711 2732 8.500753 TCAAGCATTAATCGTGGTACTTTATT 57.499 30.769 0.00 0.00 0.00 1.40
2714 2735 6.811253 TTCAAGCATTAATCGTGGTACTTT 57.189 33.333 0.00 0.00 0.00 2.66
2723 2744 7.305820 GCAGACATGAAATTCAAGCATTAATCG 60.306 37.037 0.00 0.00 0.00 3.34
2903 2924 1.338674 ACGAAATCCAACGCCTCATCA 60.339 47.619 0.00 0.00 0.00 3.07
3017 3038 6.190587 CCCTAAGAAATTTGAACCATCTCCT 58.809 40.000 0.00 0.00 0.00 3.69
3067 3088 5.066375 TTCACATTGAAACTGTTCCTGACAG 59.934 40.000 4.73 4.73 45.06 3.51
3087 3108 7.011950 CCCTAGAAAACCACCAAAATTTTTCAC 59.988 37.037 0.00 0.00 39.42 3.18
3096 3117 4.211920 CTGTTCCCTAGAAAACCACCAAA 58.788 43.478 0.00 0.00 32.58 3.28
3238 3259 2.037367 TACGCCCTGCCAGAGACT 59.963 61.111 0.00 0.00 0.00 3.24
3365 3387 6.717084 ACCCAGAAAATAGAAACTTCCTTCAG 59.283 38.462 0.00 0.00 0.00 3.02
3423 3445 5.770663 CAGAGGTAATCTAGCCTAGCTAACA 59.229 44.000 0.00 0.00 40.82 2.41
3438 3460 5.485708 AGGAGTTGAAAGTAGCAGAGGTAAT 59.514 40.000 0.00 0.00 0.00 1.89
3458 3480 7.995488 AGGATTACAATAGTCCATTTCAAGGAG 59.005 37.037 0.85 0.00 37.06 3.69
3500 3522 8.456471 ACAATAGATTCACATGAAGACAACATG 58.544 33.333 0.00 0.00 46.96 3.21
3508 3530 8.037382 ACAGAACACAATAGATTCACATGAAG 57.963 34.615 0.00 0.00 37.48 3.02
3577 3601 6.073440 TGAGTACGCAAACTTATTTCAGAACC 60.073 38.462 0.00 0.00 0.00 3.62
3588 3612 4.579454 TGTCTAGTGAGTACGCAAACTT 57.421 40.909 0.00 0.00 0.00 2.66
3603 3627 1.737793 GAACGGGGCAACAATGTCTAG 59.262 52.381 0.00 0.00 39.74 2.43
3606 3630 0.887933 ATGAACGGGGCAACAATGTC 59.112 50.000 0.00 0.00 39.74 3.06
3635 3659 8.270799 CACAAGCATGAAAACAGAAAACATTAG 58.729 33.333 0.00 0.00 0.00 1.73
3648 3672 4.933505 TGAACCATCACAAGCATGAAAA 57.066 36.364 0.00 0.00 30.82 2.29
3667 3691 7.595819 AACAGGGAACAAACAAATCTAATGA 57.404 32.000 0.00 0.00 0.00 2.57
3668 3692 7.307337 GCAAACAGGGAACAAACAAATCTAATG 60.307 37.037 0.00 0.00 0.00 1.90
3669 3693 6.705825 GCAAACAGGGAACAAACAAATCTAAT 59.294 34.615 0.00 0.00 0.00 1.73
3671 3695 5.362430 AGCAAACAGGGAACAAACAAATCTA 59.638 36.000 0.00 0.00 0.00 1.98
3714 3756 4.280677 CCAACAAAATCCTCACCTGCTTAA 59.719 41.667 0.00 0.00 0.00 1.85
3786 3828 5.819059 TGTTTTGATTTGAATTTGCAAGGC 58.181 33.333 0.00 0.00 0.00 4.35
3789 3831 7.914346 GGTTGATGTTTTGATTTGAATTTGCAA 59.086 29.630 0.00 0.00 0.00 4.08
3792 3834 7.928103 TGGGTTGATGTTTTGATTTGAATTTG 58.072 30.769 0.00 0.00 0.00 2.32
3793 3835 7.229106 CCTGGGTTGATGTTTTGATTTGAATTT 59.771 33.333 0.00 0.00 0.00 1.82
3809 3851 6.012858 TGACAGTAAATAGTTCCTGGGTTGAT 60.013 38.462 0.54 0.00 0.00 2.57
3815 3874 5.422214 ACCTGACAGTAAATAGTTCCTGG 57.578 43.478 0.93 0.00 0.00 4.45
3828 3887 3.214328 GACATGGACAAAACCTGACAGT 58.786 45.455 0.93 0.00 0.00 3.55
3829 3888 3.213506 TGACATGGACAAAACCTGACAG 58.786 45.455 0.00 0.00 0.00 3.51
3849 3908 8.911662 CCTATGAAAACGTCCAAGTAAAATTTG 58.088 33.333 0.00 0.00 0.00 2.32
3850 3909 8.635328 ACCTATGAAAACGTCCAAGTAAAATTT 58.365 29.630 0.00 0.00 0.00 1.82
3890 3950 0.897621 GCACCCTAATGCAAAAGGCT 59.102 50.000 11.37 0.00 45.39 4.58
3917 3977 1.601759 GCAAGCTCAACCTCAGCCA 60.602 57.895 0.00 0.00 37.63 4.75
3924 3984 2.421424 CACCTAGATTGCAAGCTCAACC 59.579 50.000 22.43 0.00 0.00 3.77
3949 4009 4.529897 ACTAGGTACATCGTACATGTCCA 58.470 43.478 0.00 0.00 33.76 4.02
3951 4011 6.127810 TGAACTAGGTACATCGTACATGTC 57.872 41.667 0.00 0.00 33.76 3.06
3952 4012 6.710597 ATGAACTAGGTACATCGTACATGT 57.289 37.500 2.69 2.69 36.13 3.21
3953 4013 9.524106 TTAAATGAACTAGGTACATCGTACATG 57.476 33.333 6.62 0.00 0.00 3.21
3955 4015 9.926158 TTTTAAATGAACTAGGTACATCGTACA 57.074 29.630 6.62 0.00 0.00 2.90
3980 4040 5.333566 TGAACTAGGTTCCCCTCATTTTT 57.666 39.130 7.77 0.00 41.35 1.94
3981 4041 5.015178 TGATGAACTAGGTTCCCCTCATTTT 59.985 40.000 7.77 0.00 41.35 1.82
3982 4042 4.540099 TGATGAACTAGGTTCCCCTCATTT 59.460 41.667 7.77 0.00 41.35 2.32
3983 4043 4.111577 TGATGAACTAGGTTCCCCTCATT 58.888 43.478 7.77 0.00 41.35 2.57
3984 4044 3.736094 TGATGAACTAGGTTCCCCTCAT 58.264 45.455 7.77 0.00 41.35 2.90
3985 4045 3.199442 TGATGAACTAGGTTCCCCTCA 57.801 47.619 7.77 5.90 41.35 3.86
3986 4046 4.569719 TTTGATGAACTAGGTTCCCCTC 57.430 45.455 7.77 3.84 41.35 4.30
3987 4047 4.540099 TCATTTGATGAACTAGGTTCCCCT 59.460 41.667 7.77 0.00 41.35 4.79
3988 4048 4.855340 TCATTTGATGAACTAGGTTCCCC 58.145 43.478 7.77 1.48 41.35 4.81
3989 4049 5.745227 TCTCATTTGATGAACTAGGTTCCC 58.255 41.667 7.77 1.78 41.35 3.97
3990 4050 5.295540 GCTCTCATTTGATGAACTAGGTTCC 59.704 44.000 7.77 0.00 41.35 3.62
3991 4051 6.112058 AGCTCTCATTTGATGAACTAGGTTC 58.888 40.000 0.00 3.75 42.26 3.62
3992 4052 6.059787 AGCTCTCATTTGATGAACTAGGTT 57.940 37.500 0.00 0.00 39.11 3.50
4027 4087 1.338389 GCAAAGCCCACAATTGAGCAT 60.338 47.619 13.59 2.20 0.00 3.79
4037 4097 0.594796 CACAAACGAGCAAAGCCCAC 60.595 55.000 0.00 0.00 0.00 4.61
4047 4107 1.600413 GCTCCCTTTTGCACAAACGAG 60.600 52.381 1.53 5.71 0.00 4.18
4057 4117 4.501071 CCATCAATTCTTGCTCCCTTTTG 58.499 43.478 0.00 0.00 0.00 2.44
4058 4118 3.516700 CCCATCAATTCTTGCTCCCTTTT 59.483 43.478 0.00 0.00 0.00 2.27
4062 4122 0.749049 GCCCATCAATTCTTGCTCCC 59.251 55.000 0.00 0.00 0.00 4.30
4138 4211 0.325933 TCTCCTGGCATGGTGTCAAG 59.674 55.000 0.00 0.00 28.17 3.02
4140 4213 0.837691 ACTCTCCTGGCATGGTGTCA 60.838 55.000 0.00 0.00 0.00 3.58
4224 4461 5.524284 AGTATAGATTCAGTCGTGCATGAC 58.476 41.667 28.14 28.14 39.21 3.06
4226 4463 6.903419 TCTAGTATAGATTCAGTCGTGCATG 58.097 40.000 0.00 0.00 44.15 4.06
4241 4478 8.858003 TCGAACAAGCTCAAATTCTAGTATAG 57.142 34.615 0.00 0.00 41.04 1.31
4242 4479 7.435488 GCTCGAACAAGCTCAAATTCTAGTATA 59.565 37.037 0.00 0.00 39.27 1.47
4243 4480 6.256757 GCTCGAACAAGCTCAAATTCTAGTAT 59.743 38.462 0.00 0.00 39.27 2.12
4244 4481 5.577164 GCTCGAACAAGCTCAAATTCTAGTA 59.423 40.000 0.00 0.00 39.27 1.82
4245 4482 4.390297 GCTCGAACAAGCTCAAATTCTAGT 59.610 41.667 0.00 0.00 39.27 2.57
4246 4483 4.891516 GCTCGAACAAGCTCAAATTCTAG 58.108 43.478 0.00 0.00 39.27 2.43
4264 4535 2.030717 AGCTCCGATACATGTTAGCTCG 60.031 50.000 2.30 8.14 35.47 5.03


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

AutoCloner maintained by Alex Coulton.