Multiple sequence alignment - TraesCS1B01G062200

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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 TraesCS1B01G062200 chr1B 100.000 3992 0 0 1 3992 47175704 47179695 0.000000e+00 7372
1 TraesCS1B01G062200 chr1A 93.418 3996 179 41 73 3992 29795641 29799628 0.000000e+00 5845
2 TraesCS1B01G062200 chr1D 94.739 2585 103 15 474 3027 28569599 28572181 0.000000e+00 3989
3 TraesCS1B01G062200 chr1D 91.129 124 8 2 335 458 28569748 28569868 8.880000e-37 165
4 TraesCS1B01G062200 chr1D 87.805 123 8 4 3877 3992 28572685 28572807 1.930000e-28 137
5 TraesCS1B01G062200 chr2B 73.782 431 100 12 2090 2515 26292027 26291605 1.490000e-34 158


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 TraesCS1B01G062200 chr1B 47175704 47179695 3991 False 7372.000000 7372 100.000000 1 3992 1 chr1B.!!$F1 3991
1 TraesCS1B01G062200 chr1A 29795641 29799628 3987 False 5845.000000 5845 93.418000 73 3992 1 chr1A.!!$F1 3919
2 TraesCS1B01G062200 chr1D 28569599 28572807 3208 False 1430.333333 3989 91.224333 335 3992 3 chr1D.!!$F1 3657

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
525 527 0.320374 TGAAATCGGAGTTCGCCACT 59.680 50.0 12.83 0.0 39.07 4.0 F
1593 1655 0.179234 TCCAAAACCTGACACTCGCA 59.821 50.0 0.00 0.0 0.00 5.1 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1827 1889 0.099436 GCTTGGTGATGTCGATTGCC 59.901 55.0 0.0 0.0 0.0 4.52 R
3313 3422 0.307760 GGTTCCACTTGTTGAGCACG 59.692 55.0 0.0 0.0 0.0 5.34 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 6.405278 AAAAACAAATGTAAGGCAGTAGCT 57.595 33.333 0.00 0.00 41.70 3.32
24 25 7.519032 AAAAACAAATGTAAGGCAGTAGCTA 57.481 32.000 0.00 0.00 41.70 3.32
25 26 6.743575 AAACAAATGTAAGGCAGTAGCTAG 57.256 37.500 0.00 0.00 41.70 3.42
26 27 4.770795 ACAAATGTAAGGCAGTAGCTAGG 58.229 43.478 0.00 0.00 41.70 3.02
27 28 4.225267 ACAAATGTAAGGCAGTAGCTAGGT 59.775 41.667 0.00 0.00 41.70 3.08
28 29 4.408182 AATGTAAGGCAGTAGCTAGGTG 57.592 45.455 4.27 0.00 41.70 4.00
29 30 2.108168 TGTAAGGCAGTAGCTAGGTGG 58.892 52.381 4.27 0.00 41.70 4.61
30 31 1.413077 GTAAGGCAGTAGCTAGGTGGG 59.587 57.143 4.27 0.00 41.70 4.61
31 32 1.627297 AAGGCAGTAGCTAGGTGGGC 61.627 60.000 4.27 6.61 41.70 5.36
32 33 2.506472 GCAGTAGCTAGGTGGGCC 59.494 66.667 4.27 0.00 37.91 5.80
34 35 2.034048 GCAGTAGCTAGGTGGGCCTC 62.034 65.000 4.53 0.00 45.64 4.70
35 36 0.397816 CAGTAGCTAGGTGGGCCTCT 60.398 60.000 4.53 5.07 45.64 3.69
36 37 0.397816 AGTAGCTAGGTGGGCCTCTG 60.398 60.000 4.53 0.00 45.64 3.35
37 38 1.762460 TAGCTAGGTGGGCCTCTGC 60.762 63.158 4.53 7.79 45.64 4.26
38 39 2.529930 TAGCTAGGTGGGCCTCTGCA 62.530 60.000 4.53 0.00 45.64 4.41
39 40 2.750657 GCTAGGTGGGCCTCTGCAT 61.751 63.158 4.53 0.00 45.64 3.96
40 41 1.449353 CTAGGTGGGCCTCTGCATC 59.551 63.158 4.53 0.00 45.64 3.91
41 42 1.306911 TAGGTGGGCCTCTGCATCA 60.307 57.895 4.53 0.00 45.64 3.07
42 43 1.340399 TAGGTGGGCCTCTGCATCAG 61.340 60.000 4.53 0.00 45.64 2.90
43 44 2.124403 GTGGGCCTCTGCATCAGG 60.124 66.667 4.53 7.38 40.13 3.86
44 45 2.611800 TGGGCCTCTGCATCAGGT 60.612 61.111 4.53 0.00 40.13 4.00
45 46 1.306911 TGGGCCTCTGCATCAGGTA 60.307 57.895 4.53 0.00 40.13 3.08
46 47 0.695462 TGGGCCTCTGCATCAGGTAT 60.695 55.000 4.53 0.00 40.13 2.73
47 48 1.352083 GGGCCTCTGCATCAGGTATA 58.648 55.000 0.84 0.00 40.13 1.47
48 49 1.912043 GGGCCTCTGCATCAGGTATAT 59.088 52.381 0.84 0.00 40.13 0.86
49 50 3.107601 GGGCCTCTGCATCAGGTATATA 58.892 50.000 0.84 0.00 40.13 0.86
50 51 3.133721 GGGCCTCTGCATCAGGTATATAG 59.866 52.174 0.84 0.00 40.13 1.31
51 52 4.026744 GGCCTCTGCATCAGGTATATAGA 58.973 47.826 12.36 0.00 40.13 1.98
52 53 4.142049 GGCCTCTGCATCAGGTATATAGAC 60.142 50.000 12.36 0.00 40.13 2.59
53 54 4.464244 GCCTCTGCATCAGGTATATAGACA 59.536 45.833 12.36 0.00 37.47 3.41
54 55 5.128499 GCCTCTGCATCAGGTATATAGACAT 59.872 44.000 12.36 0.00 37.47 3.06
55 56 6.322456 GCCTCTGCATCAGGTATATAGACATA 59.678 42.308 12.36 0.00 37.47 2.29
56 57 7.015098 GCCTCTGCATCAGGTATATAGACATAT 59.985 40.741 12.36 0.00 37.47 1.78
57 58 9.579932 CCTCTGCATCAGGTATATAGACATATA 57.420 37.037 0.00 0.00 31.51 0.86
125 126 4.153958 ACAAATCGCGTTCAAGCAATTA 57.846 36.364 5.77 0.00 36.85 1.40
126 127 4.541779 ACAAATCGCGTTCAAGCAATTAA 58.458 34.783 5.77 0.00 36.85 1.40
127 128 4.616802 ACAAATCGCGTTCAAGCAATTAAG 59.383 37.500 5.77 0.00 36.85 1.85
164 165 8.989131 ACACTAACAATGACTAATACCCTACAT 58.011 33.333 0.00 0.00 0.00 2.29
165 166 9.832445 CACTAACAATGACTAATACCCTACATT 57.168 33.333 0.00 0.00 0.00 2.71
169 170 6.984474 ACAATGACTAATACCCTACATTGACG 59.016 38.462 19.52 0.00 43.71 4.35
171 172 6.140303 TGACTAATACCCTACATTGACGAC 57.860 41.667 0.00 0.00 0.00 4.34
172 173 5.889853 TGACTAATACCCTACATTGACGACT 59.110 40.000 0.00 0.00 0.00 4.18
190 191 7.772166 TGACGACTGAGTTATGACTTATGAAT 58.228 34.615 0.00 0.00 35.88 2.57
211 212 6.885918 TGAATCCATGGTTGGCATATGTATAG 59.114 38.462 12.58 0.00 43.29 1.31
262 263 1.956477 ACAACATGAGAACTTGGCCAC 59.044 47.619 3.88 0.00 0.00 5.01
275 276 2.629656 GGCCACATGCACCACACTC 61.630 63.158 0.00 0.00 43.89 3.51
277 278 2.327343 CCACATGCACCACACTCGG 61.327 63.158 0.00 0.00 0.00 4.63
290 291 3.074412 CACACTCGGAGCAAGGTAATTT 58.926 45.455 4.58 0.00 0.00 1.82
309 310 0.685097 TCCACCAGCCACAACTAGAC 59.315 55.000 0.00 0.00 0.00 2.59
350 351 6.471519 GCTCATCAACAAGTCAAAGATTATGC 59.528 38.462 0.00 0.00 0.00 3.14
408 409 4.929819 AGTAATTTCCACCAACCACAAC 57.070 40.909 0.00 0.00 0.00 3.32
492 494 2.158900 AGGTCCACCATCGTTCATGATC 60.159 50.000 0.00 0.00 38.89 2.92
525 527 0.320374 TGAAATCGGAGTTCGCCACT 59.680 50.000 12.83 0.00 39.07 4.00
529 531 1.038130 ATCGGAGTTCGCCACTAGCT 61.038 55.000 0.00 0.00 40.39 3.32
577 579 5.869888 ACAATGACGATTGACTTAGGACTTC 59.130 40.000 4.02 0.00 41.49 3.01
578 580 5.923733 ATGACGATTGACTTAGGACTTCT 57.076 39.130 0.00 0.00 0.00 2.85
658 668 2.576615 ACTTCAGAAGAACTTGGCCAC 58.423 47.619 17.56 0.00 0.00 5.01
659 669 2.173569 ACTTCAGAAGAACTTGGCCACT 59.826 45.455 17.56 0.00 0.00 4.00
694 704 3.385111 GGTAATTTCCACCAACCACAACA 59.615 43.478 0.00 0.00 36.01 3.33
798 820 2.892374 TCCACACGTGCTTCATATGAG 58.108 47.619 17.22 2.00 0.00 2.90
799 821 1.935873 CCACACGTGCTTCATATGAGG 59.064 52.381 17.22 10.38 0.00 3.86
800 822 2.418609 CCACACGTGCTTCATATGAGGA 60.419 50.000 18.34 5.75 0.00 3.71
806 832 3.684305 CGTGCTTCATATGAGGACAACAA 59.316 43.478 18.34 0.00 0.00 2.83
925 954 7.189512 CAGCAAAATACTGCCAAATAGTAGAC 58.810 38.462 0.00 0.00 43.73 2.59
971 1000 5.327732 TGCCTCTCCATCTTTCTTCATTTT 58.672 37.500 0.00 0.00 0.00 1.82
974 1003 6.624642 GCCTCTCCATCTTTCTTCATTTTGTC 60.625 42.308 0.00 0.00 0.00 3.18
975 1004 6.127786 CCTCTCCATCTTTCTTCATTTTGTCC 60.128 42.308 0.00 0.00 0.00 4.02
978 1007 6.306199 TCCATCTTTCTTCATTTTGTCCAGA 58.694 36.000 0.00 0.00 0.00 3.86
979 1008 6.950041 TCCATCTTTCTTCATTTTGTCCAGAT 59.050 34.615 0.00 0.00 0.00 2.90
993 1022 6.358974 TTGTCCAGATACTTCTGTTCATCA 57.641 37.500 2.61 0.00 46.71 3.07
1117 1176 2.501223 CTACTCCGGTTTCGCAGGCA 62.501 60.000 0.00 0.00 34.56 4.75
1159 1218 1.073025 GCCACCATCACACCAGACA 59.927 57.895 0.00 0.00 0.00 3.41
1176 1235 3.154787 AGCCTGCTTGAGCTGACA 58.845 55.556 10.92 0.00 41.71 3.58
1179 1238 0.886563 GCCTGCTTGAGCTGACAAAT 59.113 50.000 10.92 0.00 41.71 2.32
1188 1247 1.615392 GAGCTGACAAATGGCACCTTT 59.385 47.619 0.00 0.00 0.00 3.11
1191 1250 1.608590 CTGACAAATGGCACCTTTCGT 59.391 47.619 0.00 0.00 0.00 3.85
1417 1479 1.745864 AACGACCACAACAACGGCA 60.746 52.632 0.00 0.00 0.00 5.69
1524 1586 2.338500 GACATCAACAACCTCGTCTCC 58.662 52.381 0.00 0.00 0.00 3.71
1593 1655 0.179234 TCCAAAACCTGACACTCGCA 59.821 50.000 0.00 0.00 0.00 5.10
1629 1691 1.066143 CAGGTGTGGGTGGAGTATGAC 60.066 57.143 0.00 0.00 0.00 3.06
1764 1826 3.760035 GGCTTCTCCGCCTCGACA 61.760 66.667 0.00 0.00 46.63 4.35
1827 1889 2.110967 CATCAACAGGCCTGCTCCG 61.111 63.158 33.06 17.86 0.00 4.63
1876 1938 1.076485 CCTCATCAAGGCCCCAAGG 60.076 63.158 0.00 0.00 38.67 3.61
1898 1960 4.443621 GCTAGATCCAAGGTACTGGAAAC 58.556 47.826 7.85 5.96 40.86 2.78
1962 2024 0.804989 CCACCGCCATTCTTCTTGTC 59.195 55.000 0.00 0.00 0.00 3.18
2056 2118 1.278637 GACTTGTTTCACGCCACCG 59.721 57.895 0.00 0.00 41.14 4.94
2235 2297 1.510480 GCCTCCAGCACCGCAATATC 61.510 60.000 0.00 0.00 42.97 1.63
2307 2369 3.531538 TGAATACCTGTCGAATGGAAGC 58.468 45.455 11.36 0.36 0.00 3.86
2352 2414 5.046520 TCAGGAGAAGAAGCCTACTTTAACC 60.047 44.000 0.00 0.00 35.82 2.85
2430 2492 2.821969 CCAGGAATGGGAGAAAGTTGTG 59.178 50.000 0.00 0.00 0.00 3.33
2457 2519 1.135859 CGAGACATCAAGCCAAGCAAC 60.136 52.381 0.00 0.00 0.00 4.17
2481 2543 2.801342 GCTCCTCGATGATGGACTGAAC 60.801 54.545 0.00 0.00 0.00 3.18
2532 2594 3.635373 GGTTATATGACCACGAGACTGGA 59.365 47.826 11.67 0.00 39.57 3.86
2556 2618 2.167281 TCAAACCACACATGTTGTTGGG 59.833 45.455 18.07 11.01 35.67 4.12
2938 3000 2.726821 TGAGCTTCAACATTCCATCCC 58.273 47.619 0.00 0.00 0.00 3.85
3035 3127 3.287312 AGATGCACATTTGTCCAAACG 57.713 42.857 0.00 0.00 32.51 3.60
3192 3300 6.041637 TCAGGAGAACACAACTACACAAGTAT 59.958 38.462 0.00 0.00 37.50 2.12
3240 3349 1.705186 ACTTGTTGGGAGTAGCATGGT 59.295 47.619 1.62 1.62 0.00 3.55
3241 3350 2.086869 CTTGTTGGGAGTAGCATGGTG 58.913 52.381 7.89 0.00 0.00 4.17
3242 3351 0.322456 TGTTGGGAGTAGCATGGTGC 60.322 55.000 7.89 6.22 45.46 5.01
3246 3355 0.106894 GGGAGTAGCATGGTGCCTAC 59.893 60.000 7.89 3.90 46.52 3.18
3347 3456 1.620822 GAACCCATGCCTTCAAGTGT 58.379 50.000 0.00 0.00 0.00 3.55
3365 3474 3.003275 AGTGTTGTGCCACTTAATGAACG 59.997 43.478 0.00 0.00 42.99 3.95
3406 3515 6.009512 CGAACTCATATACACACTTGTTCG 57.990 41.667 9.80 9.80 45.40 3.95
3410 3519 9.297586 GAACTCATATACACACTTGTTCGATAA 57.702 33.333 0.00 0.00 37.15 1.75
3411 3520 8.858003 ACTCATATACACACTTGTTCGATAAG 57.142 34.615 8.03 8.03 37.15 1.73
3443 3552 0.457443 TGAGCGACCAGAGCATAGTG 59.543 55.000 0.00 0.00 37.01 2.74
3527 3636 3.517901 TGGTGATGGTTTAGTCTTCGGAT 59.482 43.478 0.00 0.00 0.00 4.18
3529 3638 4.120589 GTGATGGTTTAGTCTTCGGATCC 58.879 47.826 0.00 0.00 0.00 3.36
3572 3681 1.798813 ACTCTTTTCGTCGAACCATGC 59.201 47.619 7.29 0.00 0.00 4.06
3610 3719 0.943673 TGTGAGTTTGTCATGGTGCG 59.056 50.000 0.00 0.00 37.56 5.34
3631 3740 2.532843 GTGGTGAAGTACTCCCCACTA 58.467 52.381 22.12 14.40 41.83 2.74
3642 3756 0.918983 TCCCCACTAATGCCAAGAGG 59.081 55.000 0.00 0.00 38.23 3.69
3643 3757 0.625849 CCCCACTAATGCCAAGAGGT 59.374 55.000 0.00 0.00 37.19 3.85
3657 3791 1.818642 AGAGGTTCTCTGCATTGCAC 58.181 50.000 7.38 0.00 39.62 4.57
3695 3829 4.889995 GGCTTGCCTTGTATAATCCTTTCT 59.110 41.667 4.11 0.00 0.00 2.52
3698 3832 5.048846 TGCCTTGTATAATCCTTTCTCCC 57.951 43.478 0.00 0.00 0.00 4.30
3702 3836 5.132816 CCTTGTATAATCCTTTCTCCCACCT 59.867 44.000 0.00 0.00 0.00 4.00
3708 3842 0.615850 CCTTTCTCCCACCTCACCTC 59.384 60.000 0.00 0.00 0.00 3.85
3739 3873 4.103311 AGCTTCTAGAACTGGGTTTGTCTT 59.897 41.667 0.00 0.00 0.00 3.01
3776 3910 5.560966 TGAGTTTGTCTTTGTTTGGACTC 57.439 39.130 0.00 0.00 34.01 3.36
3800 3935 4.058124 GTGCATCTTGTTCTGTACAGACA 58.942 43.478 25.13 21.07 38.19 3.41
3822 3957 2.028112 GGGTGTGAACTCTATGCAGTCA 60.028 50.000 0.00 0.00 0.00 3.41
3825 3961 5.453903 GGGTGTGAACTCTATGCAGTCATAT 60.454 44.000 0.00 0.00 34.88 1.78
3828 3964 4.384247 GTGAACTCTATGCAGTCATATCGC 59.616 45.833 0.00 0.00 34.88 4.58
3840 3976 0.436150 CATATCGCCTCGATGCAACG 59.564 55.000 10.48 10.48 46.43 4.10
3850 3986 0.865111 CGATGCAACGTTGGAGTCAA 59.135 50.000 28.33 4.69 30.13 3.18
3859 3995 3.335579 ACGTTGGAGTCAATAAAGCTCC 58.664 45.455 0.00 0.00 46.61 4.70
3876 4018 2.232208 GCTCCCATTGAGAAAAGGGTTG 59.768 50.000 0.00 0.00 44.42 3.77
3900 4042 3.189287 CCTACAACAGTTCCTGACAATGC 59.811 47.826 0.00 0.00 35.18 3.56
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 6.405278 AGCTACTGCCTTACATTTGTTTTT 57.595 33.333 0.00 0.00 40.80 1.94
1 2 6.151144 CCTAGCTACTGCCTTACATTTGTTTT 59.849 38.462 0.00 0.00 40.80 2.43
2 3 5.648092 CCTAGCTACTGCCTTACATTTGTTT 59.352 40.000 0.00 0.00 40.80 2.83
3 4 5.186198 CCTAGCTACTGCCTTACATTTGTT 58.814 41.667 0.00 0.00 40.80 2.83
5 6 4.572389 CACCTAGCTACTGCCTTACATTTG 59.428 45.833 0.00 0.00 40.80 2.32
6 7 4.384208 CCACCTAGCTACTGCCTTACATTT 60.384 45.833 0.00 0.00 40.80 2.32
7 8 3.134804 CCACCTAGCTACTGCCTTACATT 59.865 47.826 0.00 0.00 40.80 2.71
8 9 2.700897 CCACCTAGCTACTGCCTTACAT 59.299 50.000 0.00 0.00 40.80 2.29
9 10 2.108168 CCACCTAGCTACTGCCTTACA 58.892 52.381 0.00 0.00 40.80 2.41
10 11 1.413077 CCCACCTAGCTACTGCCTTAC 59.587 57.143 0.00 0.00 40.80 2.34
11 12 1.789523 CCCACCTAGCTACTGCCTTA 58.210 55.000 0.00 0.00 40.80 2.69
12 13 1.627297 GCCCACCTAGCTACTGCCTT 61.627 60.000 0.00 0.00 40.80 4.35
13 14 2.066999 GCCCACCTAGCTACTGCCT 61.067 63.158 0.00 0.00 40.80 4.75
14 15 2.506472 GCCCACCTAGCTACTGCC 59.494 66.667 0.00 0.00 40.80 4.85
15 16 2.506472 GGCCCACCTAGCTACTGC 59.494 66.667 0.00 0.00 40.05 4.40
25 26 2.124403 CTGATGCAGAGGCCCACC 60.124 66.667 0.00 0.00 40.13 4.61
26 27 1.626356 TACCTGATGCAGAGGCCCAC 61.626 60.000 13.39 0.00 40.13 4.61
27 28 0.695462 ATACCTGATGCAGAGGCCCA 60.695 55.000 13.39 0.00 40.13 5.36
28 29 1.352083 TATACCTGATGCAGAGGCCC 58.648 55.000 13.39 0.00 40.13 5.80
29 30 4.026744 TCTATATACCTGATGCAGAGGCC 58.973 47.826 13.39 0.00 40.13 5.19
30 31 4.464244 TGTCTATATACCTGATGCAGAGGC 59.536 45.833 13.39 0.00 41.68 4.70
31 32 6.788598 ATGTCTATATACCTGATGCAGAGG 57.211 41.667 12.14 12.14 32.44 3.69
61 62 9.952030 TGTTGGTTGTTCTGTCTATCATAATAA 57.048 29.630 0.00 0.00 0.00 1.40
102 103 0.110867 TGCTTGAACGCGATTTGTCG 60.111 50.000 15.93 0.00 0.00 4.35
113 114 4.853743 GCAGCACTACTTAATTGCTTGAAC 59.146 41.667 0.00 0.00 44.26 3.18
118 119 8.724095 TAGTGTCGCAGCACTACTTAATTGCT 62.724 42.308 11.82 0.00 46.68 3.91
164 165 7.153217 TCATAAGTCATAACTCAGTCGTCAA 57.847 36.000 0.00 0.00 33.48 3.18
165 166 6.753107 TCATAAGTCATAACTCAGTCGTCA 57.247 37.500 0.00 0.00 33.48 4.35
169 170 8.986847 CATGGATTCATAAGTCATAACTCAGTC 58.013 37.037 0.00 0.00 33.48 3.51
171 172 7.935755 ACCATGGATTCATAAGTCATAACTCAG 59.064 37.037 21.47 0.00 33.48 3.35
172 173 7.805163 ACCATGGATTCATAAGTCATAACTCA 58.195 34.615 21.47 0.00 33.48 3.41
211 212 0.819259 TGGCTTGCACAAGTCAGTCC 60.819 55.000 13.41 5.47 46.83 3.85
262 263 2.393768 GCTCCGAGTGTGGTGCATG 61.394 63.158 0.00 0.00 45.53 4.06
275 276 1.743394 GGTGGAAATTACCTTGCTCCG 59.257 52.381 0.00 0.00 35.30 4.63
277 278 2.164422 GCTGGTGGAAATTACCTTGCTC 59.836 50.000 0.00 0.00 39.01 4.26
290 291 0.685097 GTCTAGTTGTGGCTGGTGGA 59.315 55.000 0.00 0.00 0.00 4.02
309 310 7.876582 TGTTGATGAGCAGATATATTTCTCTGG 59.123 37.037 10.08 0.00 39.42 3.86
350 351 4.808895 GGCCAAGTTCTTTTTAAGTTGTGG 59.191 41.667 0.00 0.00 37.86 4.17
408 409 8.239998 TGTCGATGTGCAGATATATTTCTCTAG 58.760 37.037 0.00 0.00 0.00 2.43
482 484 3.372206 GGAAGTTGTGGAGATCATGAACG 59.628 47.826 0.00 0.00 0.00 3.95
492 494 3.127548 CCGATTTCATGGAAGTTGTGGAG 59.872 47.826 0.00 0.00 0.00 3.86
525 527 4.089361 TGTGGAGATCACTCAAGAAGCTA 58.911 43.478 0.00 0.00 46.20 3.32
529 531 5.752036 AGATTGTGGAGATCACTCAAGAA 57.248 39.130 0.00 0.00 46.20 2.52
577 579 2.715749 TATGTCAACCATGGCCTCAG 57.284 50.000 13.04 0.00 34.86 3.35
578 580 2.241941 ACATATGTCAACCATGGCCTCA 59.758 45.455 13.04 6.81 34.86 3.86
616 623 8.450578 AAGTTGTGACATAATCTTTGACTTGA 57.549 30.769 0.00 0.00 0.00 3.02
658 668 4.479619 GAAATTACCTTGCTGCAAGTGAG 58.520 43.478 33.16 23.17 39.58 3.51
659 669 3.255642 GGAAATTACCTTGCTGCAAGTGA 59.744 43.478 33.16 21.30 39.58 3.41
694 704 4.184629 GTCGGTGTGCAGATATTTCTCTT 58.815 43.478 0.00 0.00 0.00 2.85
798 820 7.214467 TCTTTGGATCATACTTTTGTTGTCC 57.786 36.000 0.00 0.00 0.00 4.02
799 821 7.327032 GCTTCTTTGGATCATACTTTTGTTGTC 59.673 37.037 0.00 0.00 0.00 3.18
800 822 7.147976 GCTTCTTTGGATCATACTTTTGTTGT 58.852 34.615 0.00 0.00 0.00 3.32
930 959 4.467769 AGGCATAATCACATAAGCAAGCT 58.532 39.130 0.00 0.00 0.00 3.74
950 979 6.127786 GGACAAAATGAAGAAAGATGGAGAGG 60.128 42.308 0.00 0.00 0.00 3.69
993 1022 1.210538 TGATGCTTCTCATGGCTCCT 58.789 50.000 0.88 0.00 35.05 3.69
1159 1218 0.179009 TTTGTCAGCTCAAGCAGGCT 60.179 50.000 4.59 0.00 45.16 4.58
1176 1235 2.154462 CTGAGACGAAAGGTGCCATTT 58.846 47.619 0.00 0.00 0.00 2.32
1179 1238 0.318441 CTCTGAGACGAAAGGTGCCA 59.682 55.000 0.00 0.00 0.00 4.92
1188 1247 1.260538 AAGCATGGCCTCTGAGACGA 61.261 55.000 3.32 0.00 0.00 4.20
1191 1250 0.254178 GGAAAGCATGGCCTCTGAGA 59.746 55.000 3.32 0.00 0.00 3.27
1256 1315 0.990374 AGCAAAGGACTGAGCCTGAT 59.010 50.000 0.00 0.00 38.58 2.90
1524 1586 3.782244 GCGCTGCTGGAGTTCACG 61.782 66.667 0.00 0.00 0.00 4.35
1593 1655 3.828451 ACACCTGCATCATTTTGTAGCTT 59.172 39.130 0.00 0.00 0.00 3.74
1629 1691 3.781770 GATCTGCCTGCGACCTCCG 62.782 68.421 0.00 0.00 42.21 4.63
1669 1731 0.692419 TTGGTGGGTTTGGCCATGTT 60.692 50.000 6.09 0.00 39.65 2.71
1764 1826 2.103143 CGCGAGTCGAATGAGCCT 59.897 61.111 18.61 0.00 41.67 4.58
1827 1889 0.099436 GCTTGGTGATGTCGATTGCC 59.901 55.000 0.00 0.00 0.00 4.52
1876 1938 4.443621 GTTTCCAGTACCTTGGATCTAGC 58.556 47.826 4.78 0.00 46.22 3.42
1898 1960 2.351726 GCAGAAACTATTGGCAGTACGG 59.648 50.000 0.00 0.00 0.00 4.02
1947 2009 1.438651 TTCGGACAAGAAGAATGGCG 58.561 50.000 0.00 0.00 0.00 5.69
2056 2118 9.103861 CAGTAGATTCTTGTTCTTAAATCCCTC 57.896 37.037 0.00 0.00 0.00 4.30
2307 2369 4.338400 TGATCATACAGGTACTTGTCGAGG 59.662 45.833 14.62 0.00 34.60 4.63
2352 2414 2.806945 TTTTGTATCTCTGGGCCCAG 57.193 50.000 41.73 41.73 44.86 4.45
2430 2492 1.063174 GGCTTGATGTCTCGATGCAAC 59.937 52.381 0.00 0.00 0.00 4.17
2457 2519 0.596083 GTCCATCATCGAGGAGCACG 60.596 60.000 5.80 0.00 33.85 5.34
2532 2594 2.733956 ACAACATGTGTGGTTTGAGGT 58.266 42.857 0.00 0.00 39.72 3.85
2556 2618 3.007398 CAGGAGCTAGGTATCCAATGGTC 59.993 52.174 0.00 0.00 38.12 4.02
2670 2732 1.676635 GCCTTGTGATGCTGGCTCA 60.677 57.895 0.00 0.00 41.92 4.26
2870 2932 4.697352 GTGGCATATCACCATTGAGATACC 59.303 45.833 0.00 0.00 37.39 2.73
2938 3000 7.982224 TCTATTGAAACTTCATTCTGCATCAG 58.018 34.615 0.00 0.00 37.00 2.90
3192 3300 1.885887 GCCTTGCAGGACACATGTAAA 59.114 47.619 0.00 0.00 37.67 2.01
3313 3422 0.307760 GGTTCCACTTGTTGAGCACG 59.692 55.000 0.00 0.00 0.00 5.34
3317 3426 1.270550 GCATGGGTTCCACTTGTTGAG 59.729 52.381 0.00 0.00 35.80 3.02
3347 3456 1.950216 TGCGTTCATTAAGTGGCACAA 59.050 42.857 21.41 6.63 44.16 3.33
3384 3493 7.757097 ATCGAACAAGTGTGTATATGAGTTC 57.243 36.000 0.00 0.00 36.80 3.01
3406 3515 4.670221 CGCTCAAAGCAAAGACCACTTATC 60.670 45.833 0.00 0.00 42.58 1.75
3410 3519 0.947244 CGCTCAAAGCAAAGACCACT 59.053 50.000 0.00 0.00 42.58 4.00
3411 3520 0.944386 TCGCTCAAAGCAAAGACCAC 59.056 50.000 0.00 0.00 42.58 4.16
3443 3552 4.874528 TGCCTTTGCAAAAAGCCC 57.125 50.000 23.74 8.61 46.66 5.19
3477 3586 2.299326 AAACATCTCCTTGGCTGCTT 57.701 45.000 0.00 0.00 0.00 3.91
3527 3636 1.420430 CTAAGGTATTGGAGGGCGGA 58.580 55.000 0.00 0.00 0.00 5.54
3529 3638 1.420430 TCCTAAGGTATTGGAGGGCG 58.580 55.000 0.00 0.00 0.00 6.13
3572 3681 7.581476 ACTCACACGTACAAAGATTAAAATGG 58.419 34.615 0.00 0.00 0.00 3.16
3631 3740 1.074405 TGCAGAGAACCTCTTGGCATT 59.926 47.619 5.29 0.00 38.99 3.56
3642 3756 1.467734 CAGAGGTGCAATGCAGAGAAC 59.532 52.381 8.73 0.00 40.08 3.01
3643 3757 1.817357 CAGAGGTGCAATGCAGAGAA 58.183 50.000 8.73 0.00 40.08 2.87
3695 3829 3.311110 GCACGAGGTGAGGTGGGA 61.311 66.667 0.00 0.00 35.23 4.37
3702 3836 2.765250 GAAGCTTCCGCACGAGGTGA 62.765 60.000 15.97 0.00 39.10 4.02
3708 3842 0.992802 GTTCTAGAAGCTTCCGCACG 59.007 55.000 22.81 7.21 39.10 5.34
3753 3887 5.355350 AGAGTCCAAACAAAGACAAACTCAG 59.645 40.000 0.00 0.00 35.49 3.35
3760 3894 2.682856 GCACAGAGTCCAAACAAAGACA 59.317 45.455 0.00 0.00 35.38 3.41
3776 3910 4.151335 GTCTGTACAGAACAAGATGCACAG 59.849 45.833 26.74 0.00 40.62 3.66
3800 3935 2.234908 GACTGCATAGAGTTCACACCCT 59.765 50.000 0.00 0.00 0.00 4.34
3822 3957 0.032130 ACGTTGCATCGAGGCGATAT 59.968 50.000 23.12 3.82 45.19 1.63
3825 3961 2.048597 AACGTTGCATCGAGGCGA 60.049 55.556 23.12 13.46 41.13 5.54
3828 3964 0.670546 ACTCCAACGTTGCATCGAGG 60.671 55.000 25.84 21.25 34.70 4.63
3850 3986 4.958581 CCCTTTTCTCAATGGGAGCTTTAT 59.041 41.667 0.46 0.00 46.43 1.40
3859 3995 3.500343 AGGACAACCCTTTTCTCAATGG 58.500 45.455 0.00 0.00 44.85 3.16
3900 4042 7.227156 AGGAGTATGTAGCATTCTAAATTGGG 58.773 38.462 0.00 0.00 0.00 4.12


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

AutoCloner maintained by Alex Coulton.