Multiple sequence alignment - TraesCS4A01G480200

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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 TraesCS4A01G480200 chr4A 100.000 5204 0 0 1 5204 736882978 736888181 0.000000e+00 9611.0
1 TraesCS4A01G480200 chr4A 94.868 3527 143 10 131 3652 735766282 735769775 0.000000e+00 5476.0
2 TraesCS4A01G480200 chr4A 89.740 3499 323 18 131 3618 736055083 736058556 0.000000e+00 4440.0
3 TraesCS4A01G480200 chr4A 86.829 3910 458 28 1029 4913 735316354 735320231 0.000000e+00 4314.0
4 TraesCS4A01G480200 chr4A 85.205 3954 522 31 1029 4949 735562666 735558743 0.000000e+00 4002.0
5 TraesCS4A01G480200 chr4A 83.731 4186 590 50 998 5135 736570747 736574889 0.000000e+00 3873.0
6 TraesCS4A01G480200 chr4A 83.656 4185 597 46 998 5135 734730670 734734814 0.000000e+00 3858.0
7 TraesCS4A01G480200 chr4A 83.857 4076 570 49 1029 5060 734385222 734389253 0.000000e+00 3801.0
8 TraesCS4A01G480200 chr4A 84.063 3953 571 39 1029 4958 736413256 736409340 0.000000e+00 3755.0
9 TraesCS4A01G480200 chr4A 84.054 3957 550 49 1029 4958 736756368 736760270 0.000000e+00 3736.0
10 TraesCS4A01G480200 chr4A 82.807 4240 637 59 1029 5193 735776448 735780670 0.000000e+00 3707.0
11 TraesCS4A01G480200 chr4A 83.793 3955 569 40 1032 4954 735747182 735751096 0.000000e+00 3687.0
12 TraesCS4A01G480200 chr4A 83.683 3959 562 44 1029 4954 734585182 734589089 0.000000e+00 3655.0
13 TraesCS4A01G480200 chr4A 84.092 3539 506 32 1436 4949 735689506 735693012 0.000000e+00 3363.0
14 TraesCS4A01G480200 chr4A 84.420 3421 477 46 1526 4912 736724764 736728162 0.000000e+00 3314.0
15 TraesCS4A01G480200 chr4A 87.594 1999 210 19 1029 3018 735487909 735485940 0.000000e+00 2283.0
16 TraesCS4A01G480200 chr4A 87.350 2000 213 20 1029 3018 735003467 735005436 0.000000e+00 2255.0
17 TraesCS4A01G480200 chr4A 97.649 1106 22 3 4100 5204 736475524 736474422 0.000000e+00 1895.0
18 TraesCS4A01G480200 chr4A 82.454 1915 305 29 3052 4954 735022315 735024210 0.000000e+00 1646.0
19 TraesCS4A01G480200 chr4A 83.648 1749 257 13 3214 4947 734482988 734484722 0.000000e+00 1618.0
20 TraesCS4A01G480200 chr4A 95.923 981 38 1 3917 4895 735770929 735771909 0.000000e+00 1589.0
21 TraesCS4A01G480200 chr4A 74.400 750 134 39 168 878 736755421 736756151 8.590000e-68 268.0
22 TraesCS4A01G480200 chr4A 74.844 481 85 28 167 633 736895686 736896144 8.900000e-43 185.0
23 TraesCS4A01G480200 chr4A 73.862 593 97 38 167 731 736610888 736611450 3.200000e-42 183.0
24 TraesCS4A01G480200 chr4A 87.200 125 10 4 143 265 735765109 735765229 2.530000e-28 137.0
25 TraesCS4A01G480200 chr4A 72.973 444 66 33 180 594 734872817 734873235 7.130000e-19 106.0
26 TraesCS4A01G480200 chr4A 72.973 444 66 33 180 594 736111112 736111530 7.130000e-19 106.0
27 TraesCS4A01G480200 chr4A 94.737 38 2 0 66 103 735664567 735664530 5.630000e-05 60.2
28 TraesCS4A01G480200 chr7A 86.783 4827 539 54 131 4912 7323190 7318418 0.000000e+00 5288.0
29 TraesCS4A01G480200 chr7A 85.063 4057 521 50 1029 5039 7045456 7041439 0.000000e+00 4056.0
30 TraesCS4A01G480200 chr7A 83.888 4239 573 57 1030 5204 6928615 6924423 0.000000e+00 3943.0
31 TraesCS4A01G480200 chr7A 97.248 109 2 1 1 109 7323555 7323448 3.200000e-42 183.0
32 TraesCS4A01G480200 chr7A 73.261 460 79 31 185 609 6595191 6595641 1.520000e-25 128.0
33 TraesCS4A01G480200 chr7D 84.118 4055 555 43 1029 5039 5649342 5645333 0.000000e+00 3838.0
34 TraesCS4A01G480200 chr7D 83.440 4221 596 61 1038 5201 5638037 5633863 0.000000e+00 3827.0
35 TraesCS4A01G480200 chr7D 83.833 3866 537 47 1321 5138 5486536 5482711 0.000000e+00 3596.0
36 TraesCS4A01G480200 chr7D 82.390 1431 227 23 3534 4954 5798444 5797029 0.000000e+00 1223.0
37 TraesCS4A01G480200 chr7D 76.628 522 90 23 167 670 5449765 5449258 5.170000e-65 259.0
38 TraesCS4A01G480200 chr7D 75.425 529 102 21 165 670 5557925 5557402 1.130000e-56 231.0


These results show the homologous regions that are presented in the multiple sequence alignment. HSPs from the BLAST search that are within 2000 bases of each other have been grouped together. Homologous regions that are purely upstream or downstream may be removed if they don't overlap both primers.

query scaffold start end length rev.comp avg.bitscore max.bitscore avg.percent.identical query.start query.end num_hsp groupid homo_length
0 TraesCS4A01G480200 chr4A 736882978 736888181 5203 False 9611.000000 9611 100.000000 1 5204 1 chr4A.!!$F17 5203
1 TraesCS4A01G480200 chr4A 736055083 736058556 3473 False 4440.000000 4440 89.740000 131 3618 1 chr4A.!!$F12 3487
2 TraesCS4A01G480200 chr4A 735316354 735320231 3877 False 4314.000000 4314 86.829000 1029 4913 1 chr4A.!!$F8 3884
3 TraesCS4A01G480200 chr4A 735558743 735562666 3923 True 4002.000000 4002 85.205000 1029 4949 1 chr4A.!!$R2 3920
4 TraesCS4A01G480200 chr4A 736570747 736574889 4142 False 3873.000000 3873 83.731000 998 5135 1 chr4A.!!$F14 4137
5 TraesCS4A01G480200 chr4A 734730670 734734814 4144 False 3858.000000 3858 83.656000 998 5135 1 chr4A.!!$F4 4137
6 TraesCS4A01G480200 chr4A 734385222 734389253 4031 False 3801.000000 3801 83.857000 1029 5060 1 chr4A.!!$F1 4031
7 TraesCS4A01G480200 chr4A 736409340 736413256 3916 True 3755.000000 3755 84.063000 1029 4958 1 chr4A.!!$R4 3929
8 TraesCS4A01G480200 chr4A 735776448 735780670 4222 False 3707.000000 3707 82.807000 1029 5193 1 chr4A.!!$F11 4164
9 TraesCS4A01G480200 chr4A 735747182 735751096 3914 False 3687.000000 3687 83.793000 1032 4954 1 chr4A.!!$F10 3922
10 TraesCS4A01G480200 chr4A 734585182 734589089 3907 False 3655.000000 3655 83.683000 1029 4954 1 chr4A.!!$F3 3925
11 TraesCS4A01G480200 chr4A 735689506 735693012 3506 False 3363.000000 3363 84.092000 1436 4949 1 chr4A.!!$F9 3513
12 TraesCS4A01G480200 chr4A 736724764 736728162 3398 False 3314.000000 3314 84.420000 1526 4912 1 chr4A.!!$F16 3386
13 TraesCS4A01G480200 chr4A 735765109 735771909 6800 False 2400.666667 5476 92.663667 131 4895 3 chr4A.!!$F19 4764
14 TraesCS4A01G480200 chr4A 735485940 735487909 1969 True 2283.000000 2283 87.594000 1029 3018 1 chr4A.!!$R1 1989
15 TraesCS4A01G480200 chr4A 735003467 735005436 1969 False 2255.000000 2255 87.350000 1029 3018 1 chr4A.!!$F6 1989
16 TraesCS4A01G480200 chr4A 736755421 736760270 4849 False 2002.000000 3736 79.227000 168 4958 2 chr4A.!!$F20 4790
17 TraesCS4A01G480200 chr4A 736474422 736475524 1102 True 1895.000000 1895 97.649000 4100 5204 1 chr4A.!!$R5 1104
18 TraesCS4A01G480200 chr4A 735022315 735024210 1895 False 1646.000000 1646 82.454000 3052 4954 1 chr4A.!!$F7 1902
19 TraesCS4A01G480200 chr4A 734482988 734484722 1734 False 1618.000000 1618 83.648000 3214 4947 1 chr4A.!!$F2 1733
20 TraesCS4A01G480200 chr7A 7041439 7045456 4017 True 4056.000000 4056 85.063000 1029 5039 1 chr7A.!!$R2 4010
21 TraesCS4A01G480200 chr7A 6924423 6928615 4192 True 3943.000000 3943 83.888000 1030 5204 1 chr7A.!!$R1 4174
22 TraesCS4A01G480200 chr7A 7318418 7323555 5137 True 2735.500000 5288 92.015500 1 4912 2 chr7A.!!$R3 4911
23 TraesCS4A01G480200 chr7D 5645333 5649342 4009 True 3838.000000 3838 84.118000 1029 5039 1 chr7D.!!$R5 4010
24 TraesCS4A01G480200 chr7D 5633863 5638037 4174 True 3827.000000 3827 83.440000 1038 5201 1 chr7D.!!$R4 4163
25 TraesCS4A01G480200 chr7D 5482711 5486536 3825 True 3596.000000 3596 83.833000 1321 5138 1 chr7D.!!$R2 3817
26 TraesCS4A01G480200 chr7D 5797029 5798444 1415 True 1223.000000 1223 82.390000 3534 4954 1 chr7D.!!$R6 1420
27 TraesCS4A01G480200 chr7D 5449258 5449765 507 True 259.000000 259 76.628000 167 670 1 chr7D.!!$R1 503
28 TraesCS4A01G480200 chr7D 5557402 5557925 523 True 231.000000 231 75.425000 165 670 1 chr7D.!!$R3 505

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
691 1769 0.104120 TATCCCCATTGCAGTCGACG 59.896 55.000 10.46 6.47 0.00 5.12 F
1860 3043 1.151668 AGCGCAAGTTGACAGACATC 58.848 50.000 11.47 0.00 41.68 3.06 F
2869 4120 2.432444 TGAAGCACCTTCGGTATTTGG 58.568 47.619 1.07 0.00 42.78 3.28 F
3657 4948 1.000274 GGAAACCACTTGGCATCACAC 60.000 52.381 0.00 0.00 39.32 3.82 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2171 3376 3.766545 ACTTTTGCTGCCAAAGGAGATA 58.233 40.909 24.46 0.00 41.58 1.98 R
3537 4801 0.393132 GGCCTAGTGGAAGACAAGGC 60.393 60.000 0.00 3.04 39.97 4.35 R
4129 6619 0.328592 TCTGAGAGACAGGTAGCGGT 59.671 55.000 0.00 0.00 45.76 5.68 R
5039 7580 1.028868 GCTGGAGGGCACACATCTTC 61.029 60.000 0.00 0.00 0.00 2.87 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
72 73 7.398829 TGGTGTATTTGACTTAAAGAGGCATA 58.601 34.615 0.00 0.00 44.78 3.14
93 94 6.149474 GCATAGTTTCCTGTTTTCTGCTTCTA 59.851 38.462 0.00 0.00 0.00 2.10
109 110 1.376424 CTAGGTGTGCAGTGCAGGG 60.376 63.158 20.42 1.39 40.08 4.45
110 111 1.830587 CTAGGTGTGCAGTGCAGGGA 61.831 60.000 20.42 2.25 40.08 4.20
114 115 2.431683 GTGCAGTGCAGGGAAGGA 59.568 61.111 20.42 0.00 40.08 3.36
115 116 1.968540 GTGCAGTGCAGGGAAGGAC 60.969 63.158 20.42 0.00 40.08 3.85
116 117 2.360475 GCAGTGCAGGGAAGGACC 60.360 66.667 11.09 0.00 38.08 4.46
117 118 2.046892 CAGTGCAGGGAAGGACCG 60.047 66.667 0.00 0.00 40.11 4.79
118 119 3.322466 AGTGCAGGGAAGGACCGG 61.322 66.667 0.00 0.00 40.11 5.28
121 122 1.002403 TGCAGGGAAGGACCGGATA 59.998 57.895 9.46 0.00 40.11 2.59
123 124 2.041206 GCAGGGAAGGACCGGATACC 62.041 65.000 9.46 8.86 40.11 2.73
124 125 1.074699 AGGGAAGGACCGGATACCC 60.075 63.158 9.46 13.36 40.11 3.69
125 126 1.383525 GGGAAGGACCGGATACCCA 60.384 63.158 9.46 0.00 40.11 4.51
127 128 1.137697 GGAAGGACCGGATACCCATT 58.862 55.000 9.46 0.00 0.00 3.16
163 1207 7.843490 TGCCTAGCTTACTTTATGTACTTTG 57.157 36.000 0.00 0.00 0.00 2.77
268 1314 2.114616 CAGGTAGCTGGATCAGACCTT 58.885 52.381 14.29 0.00 36.83 3.50
449 1516 7.835682 TGTTTTCCTCATCAAATCTGGATGTAT 59.164 33.333 0.00 0.00 42.16 2.29
519 1586 6.877611 TGATTTTCTACTCCAACAGGTTTC 57.122 37.500 0.00 0.00 0.00 2.78
537 1604 9.936329 ACAGGTTTCCTATCCATTGTTATATTT 57.064 29.630 0.00 0.00 29.64 1.40
565 1632 5.125739 AGTTGTTTCTACTACCTCCGATCTG 59.874 44.000 0.00 0.00 31.47 2.90
691 1769 0.104120 TATCCCCATTGCAGTCGACG 59.896 55.000 10.46 6.47 0.00 5.12
734 1812 5.050837 GCACTCCAACATGTTTTTCATCAAC 60.051 40.000 8.77 0.00 34.09 3.18
754 1836 3.370104 ACCACAAGTCCAACAATTCCAA 58.630 40.909 0.00 0.00 0.00 3.53
757 1839 4.202243 CCACAAGTCCAACAATTCCAATGT 60.202 41.667 0.00 0.00 0.00 2.71
763 1845 3.254657 TCCAACAATTCCAATGTTCGTCC 59.745 43.478 0.00 0.00 38.90 4.79
779 1861 4.730949 TCGTCCTTCGATTTATTCAGGT 57.269 40.909 0.00 0.00 44.01 4.00
819 1901 6.201615 CACCAAGAAAAATCAAGGAAAAGAGC 59.798 38.462 0.00 0.00 0.00 4.09
820 1902 6.127083 ACCAAGAAAAATCAAGGAAAAGAGCA 60.127 34.615 0.00 0.00 0.00 4.26
828 1910 8.599055 AAATCAAGGAAAAGAGCAGAAATTTC 57.401 30.769 10.33 10.33 0.00 2.17
857 1939 3.150848 GCTTTTGCTCCTATTTTCCCG 57.849 47.619 0.00 0.00 43.35 5.14
858 1940 2.159240 GCTTTTGCTCCTATTTTCCCGG 60.159 50.000 0.00 0.00 43.35 5.73
860 1942 2.122783 TTGCTCCTATTTTCCCGGTG 57.877 50.000 0.00 0.00 0.00 4.94
864 1947 2.744166 GCTCCTATTTTCCCGGTGTACC 60.744 54.545 0.00 0.00 0.00 3.34
878 1961 3.535561 GGTGTACCTGTTCATCTCCATG 58.464 50.000 0.00 0.00 0.00 3.66
934 2020 9.408648 TGATAGAATTTGTTCTCTTATTTCCCC 57.591 33.333 0.00 0.00 32.72 4.81
1087 2236 6.516194 GCTCCATGCTAATGCTTCAACATATT 60.516 38.462 0.00 0.00 40.48 1.28
1279 2428 3.192844 TGAGTACAACCTCCTTAAGCTCG 59.807 47.826 0.00 0.00 0.00 5.03
1618 2799 4.457603 AGACAACTGCTACTACTGAGTCTG 59.542 45.833 0.00 0.00 37.10 3.51
1809 2991 2.063378 GTCTGCCTCTCAGGGGGAG 61.063 68.421 5.51 5.51 45.49 4.30
1860 3043 1.151668 AGCGCAAGTTGACAGACATC 58.848 50.000 11.47 0.00 41.68 3.06
2121 3326 5.221581 ACCAGAAATCAAAAATCTGCAGCTT 60.222 36.000 9.47 1.96 39.36 3.74
2171 3376 5.013599 AGAGGATTGCTAAAAGACTTGGACT 59.986 40.000 0.00 0.00 0.00 3.85
2869 4120 2.432444 TGAAGCACCTTCGGTATTTGG 58.568 47.619 1.07 0.00 42.78 3.28
2903 4154 7.147976 AGAACACTAATTTCTGAATTGCCAAC 58.852 34.615 0.00 0.00 36.22 3.77
3250 4513 6.971184 GCTACATCAGAAAATTCATCTTGGTG 59.029 38.462 0.00 0.00 0.00 4.17
3537 4801 1.197721 GTGCCGAACCTGAAGACATTG 59.802 52.381 0.00 0.00 0.00 2.82
3657 4948 1.000274 GGAAACCACTTGGCATCACAC 60.000 52.381 0.00 0.00 39.32 3.82
3688 4979 2.561187 TCTGGGATGTGGATTCAGGAA 58.439 47.619 0.00 0.00 0.00 3.36
3689 4980 2.918934 TCTGGGATGTGGATTCAGGAAA 59.081 45.455 0.00 0.00 0.00 3.13
3733 5024 6.927416 TCATTGGAACATTCATTTCTGAAGG 58.073 36.000 0.00 0.00 46.11 3.46
3738 5029 5.163673 GGAACATTCATTTCTGAAGGAGCTC 60.164 44.000 4.71 4.71 44.04 4.09
3847 6115 6.099990 AGAGGATATCATCAAGGCATGGATAG 59.900 42.308 18.86 0.00 0.00 2.08
3858 6126 2.159099 GGCATGGATAGACTGTCACGAA 60.159 50.000 10.88 0.00 0.00 3.85
4129 6619 2.093553 CGGTCATTAGGGGGTTTACGAA 60.094 50.000 0.00 0.00 0.00 3.85
4139 6629 1.353076 GGTTTACGAACCGCTACCTG 58.647 55.000 0.00 0.00 45.43 4.00
4202 6694 1.135199 GGCATGTGGAGCAGAATGTTG 60.135 52.381 0.00 0.00 39.31 3.33
4921 7438 2.496470 AGGTAAACTAGCTTCAGTCGGG 59.504 50.000 0.00 0.00 31.36 5.14
5039 7580 2.166254 ACTTCAAATTAATGGCAGGCCG 59.834 45.455 5.74 0.00 39.42 6.13
5064 7605 2.282745 GTGCCCTCCAGCAAGCTT 60.283 61.111 0.00 0.00 46.19 3.74
5065 7606 1.905354 GTGCCCTCCAGCAAGCTTT 60.905 57.895 0.00 0.00 46.19 3.51
5120 7678 5.848406 AGTTCAAACTCTGTCTCCTACTTG 58.152 41.667 0.00 0.00 32.86 3.16
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
72 73 5.066593 CCTAGAAGCAGAAAACAGGAAACT 58.933 41.667 0.00 0.00 46.44 2.66
93 94 2.687418 CTTCCCTGCACTGCACACCT 62.687 60.000 0.00 0.00 33.79 4.00
109 110 1.814248 GCAATGGGTATCCGGTCCTTC 60.814 57.143 0.00 0.00 35.24 3.46
110 111 0.182775 GCAATGGGTATCCGGTCCTT 59.817 55.000 0.00 0.00 35.24 3.36
114 115 1.140312 AGATGCAATGGGTATCCGGT 58.860 50.000 0.00 0.00 39.21 5.28
115 116 2.276732 AAGATGCAATGGGTATCCGG 57.723 50.000 0.00 0.00 39.21 5.14
116 117 7.019774 CATTATAAGATGCAATGGGTATCCG 57.980 40.000 0.00 0.00 39.21 4.18
162 1206 8.360390 ACATAGCTCACTGATCGATAATTAACA 58.640 33.333 0.00 0.00 0.00 2.41
163 1207 8.749841 ACATAGCTCACTGATCGATAATTAAC 57.250 34.615 0.00 0.00 0.00 2.01
268 1314 0.103755 CAGCTCAGCGAGGCAATAGA 59.896 55.000 0.00 0.00 0.00 1.98
449 1516 5.470098 GCAACAGAGAAGATAAACAGAACCA 59.530 40.000 0.00 0.00 0.00 3.67
537 1604 6.182627 TCGGAGGTAGTAGAAACAACTGATA 58.817 40.000 0.00 0.00 0.00 2.15
539 1606 4.401022 TCGGAGGTAGTAGAAACAACTGA 58.599 43.478 0.00 0.00 0.00 3.41
541 1608 5.125739 CAGATCGGAGGTAGTAGAAACAACT 59.874 44.000 0.00 0.00 0.00 3.16
636 1704 3.309954 GCAGATCGGTAGACAATGGAAAC 59.690 47.826 0.00 0.00 0.00 2.78
691 1769 7.148018 TGGAGTGCAAAATGAGGAGATAAATTC 60.148 37.037 0.00 0.00 0.00 2.17
734 1812 4.202243 ACATTGGAATTGTTGGACTTGTGG 60.202 41.667 0.00 0.00 0.00 4.17
763 1845 6.316140 TGTGGAATGACCTGAATAAATCGAAG 59.684 38.462 0.00 0.00 39.86 3.79
779 1861 1.135960 TGGTGTGGACTGTGGAATGA 58.864 50.000 0.00 0.00 0.00 2.57
819 1901 9.852091 AGCAAAAGCTATAAAGAGAAATTTCTG 57.148 29.630 25.12 9.90 37.73 3.02
828 1910 9.943163 GAAAATAGGAGCAAAAGCTATAAAGAG 57.057 33.333 0.00 0.00 0.00 2.85
857 1939 3.535561 CATGGAGATGAACAGGTACACC 58.464 50.000 0.00 0.00 0.00 4.16
858 1940 2.939103 GCATGGAGATGAACAGGTACAC 59.061 50.000 0.00 0.00 0.00 2.90
860 1942 3.550437 AGCATGGAGATGAACAGGTAC 57.450 47.619 0.00 0.00 0.00 3.34
864 1947 3.118482 ACACCTAGCATGGAGATGAACAG 60.118 47.826 0.00 0.00 0.00 3.16
928 2014 3.279771 AGGGGTTGTTTATAGGGGGAAA 58.720 45.455 0.00 0.00 0.00 3.13
930 2016 2.692122 AGGGGTTGTTTATAGGGGGA 57.308 50.000 0.00 0.00 0.00 4.81
931 2017 4.884887 TTAAGGGGTTGTTTATAGGGGG 57.115 45.455 0.00 0.00 0.00 5.40
934 2020 7.631007 AGAGAGTTTAAGGGGTTGTTTATAGG 58.369 38.462 0.00 0.00 0.00 2.57
1087 2236 1.971167 GCGCCATGTCCACTCCAAA 60.971 57.895 0.00 0.00 0.00 3.28
1233 2382 1.493311 GTTCAGCAAGTCTTCGGCG 59.507 57.895 0.00 0.00 0.00 6.46
1319 2471 6.015180 AGGCTTCATAAAAGTGCTTTTGATGA 60.015 34.615 17.27 16.71 42.18 2.92
2121 3326 7.980662 TCTGCAAAATCTTCAAGTTTTTCATGA 59.019 29.630 3.58 0.00 27.88 3.07
2171 3376 3.766545 ACTTTTGCTGCCAAAGGAGATA 58.233 40.909 24.46 0.00 41.58 1.98
2903 4154 5.784177 AGTGGTAAAGAGTACACAGTGATG 58.216 41.667 7.81 0.00 36.35 3.07
3045 4308 3.764885 ATGTTACGAATTTGAGGCAGC 57.235 42.857 0.00 0.00 0.00 5.25
3250 4513 3.493767 ACTCCAGAGAAGTTTCAACCC 57.506 47.619 0.70 0.00 0.00 4.11
3470 4734 6.292168 GCAATTCTCAAATAGACATGCATTGC 60.292 38.462 0.00 0.46 42.10 3.56
3537 4801 0.393132 GGCCTAGTGGAAGACAAGGC 60.393 60.000 0.00 3.04 39.97 4.35
3657 4948 3.701040 CCACATCCCAGATTAAACCAAGG 59.299 47.826 0.00 0.00 0.00 3.61
3688 4979 5.219739 TGAGAGTGCCCTCCTAATATTCTT 58.780 41.667 0.00 0.00 38.58 2.52
3689 4980 4.820775 TGAGAGTGCCCTCCTAATATTCT 58.179 43.478 0.00 0.00 38.58 2.40
3733 5024 3.424565 GCATGCATCAATATCACGAGCTC 60.425 47.826 14.21 2.73 0.00 4.09
3738 5029 4.083484 ACATCAGCATGCATCAATATCACG 60.083 41.667 21.98 0.00 34.76 4.35
3858 6126 4.442052 CCATACACGAGTCCAATCATCTGT 60.442 45.833 0.00 0.00 0.00 3.41
3867 6135 2.100197 CTCCTTCCATACACGAGTCCA 58.900 52.381 0.00 0.00 0.00 4.02
4129 6619 0.328592 TCTGAGAGACAGGTAGCGGT 59.671 55.000 0.00 0.00 45.76 5.68
4139 6629 6.479660 GGAATTCAATCTGACATCTGAGAGAC 59.520 42.308 7.93 0.00 0.00 3.36
4202 6694 2.708325 AGGCTCTCAAGGGATAATGGTC 59.292 50.000 0.00 0.00 0.00 4.02
5016 7557 4.682787 GGCCTGCCATTAATTTGAAGTAC 58.317 43.478 2.58 0.00 35.81 2.73
5039 7580 1.028868 GCTGGAGGGCACACATCTTC 61.029 60.000 0.00 0.00 0.00 2.87
5064 7605 1.374947 CCCGAGGCACCTCAGAAAA 59.625 57.895 16.68 0.00 42.86 2.29
5065 7606 3.068881 CCCGAGGCACCTCAGAAA 58.931 61.111 16.68 0.00 42.86 2.52
5120 7678 4.699522 GACCAGCACCACCCGGTC 62.700 72.222 0.00 0.00 44.71 4.79


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

AutoCloner maintained by Alex Coulton.