Multiple sequence alignment - TraesCS1B01G347100

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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 TraesCS1B01G347100 chr1B 100.000 3560 0 0 1 3560 576204415 576207974 0.000000e+00 6575.0
1 TraesCS1B01G347100 chr1D 92.618 3102 147 41 477 3546 426586356 426589407 0.000000e+00 4385.0
2 TraesCS1B01G347100 chr1D 90.760 487 42 2 1 487 426584809 426585292 0.000000e+00 647.0
3 TraesCS1B01G347100 chr1A 93.306 2659 116 25 938 3560 521628958 521631590 0.000000e+00 3868.0
4 TraesCS1B01G347100 chr1A 90.330 879 69 12 1 868 521628075 521628948 0.000000e+00 1138.0
5 TraesCS1B01G347100 chr3B 81.056 1420 233 29 1116 2517 534965470 534964069 0.000000e+00 1099.0
6 TraesCS1B01G347100 chr3B 81.583 695 120 8 1120 1810 146183121 146182431 5.160000e-158 568.0
7 TraesCS1B01G347100 chr3B 80.220 273 50 4 1474 1744 729415080 729415350 6.030000e-48 202.0
8 TraesCS1B01G347100 chr3D 80.862 1416 243 22 1116 2517 409022003 409020602 0.000000e+00 1088.0
9 TraesCS1B01G347100 chr3D 83.103 651 104 6 1163 1810 95246449 95245802 3.960000e-164 588.0
10 TraesCS1B01G347100 chr3D 78.603 229 33 11 1 222 522200494 522200275 1.720000e-28 137.0
11 TraesCS1B01G347100 chr3A 79.508 1586 265 51 970 2517 542202607 542204170 0.000000e+00 1074.0
12 TraesCS1B01G347100 chr3A 82.565 694 115 6 1120 1810 113342383 113341693 1.090000e-169 606.0
13 TraesCS1B01G347100 chr3A 80.473 169 28 4 3 168 8600164 8599998 1.340000e-24 124.0
14 TraesCS1B01G347100 chr4B 81.865 193 33 2 1 192 575045076 575045267 1.020000e-35 161.0
15 TraesCS1B01G347100 chr2D 82.424 165 25 4 1 163 19634552 19634714 1.330000e-29 141.0
16 TraesCS1B01G347100 chr2D 79.630 162 31 2 2 162 187528528 187528368 8.080000e-22 115.0
17 TraesCS1B01G347100 chr4D 78.659 164 33 2 1 163 443221313 443221475 1.350000e-19 108.0
18 TraesCS1B01G347100 chr2B 77.381 168 34 4 3 168 555852230 555852065 2.930000e-16 97.1


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 TraesCS1B01G347100 chr1B 576204415 576207974 3559 False 6575 6575 100.000 1 3560 1 chr1B.!!$F1 3559
1 TraesCS1B01G347100 chr1D 426584809 426589407 4598 False 2516 4385 91.689 1 3546 2 chr1D.!!$F1 3545
2 TraesCS1B01G347100 chr1A 521628075 521631590 3515 False 2503 3868 91.818 1 3560 2 chr1A.!!$F1 3559
3 TraesCS1B01G347100 chr3B 534964069 534965470 1401 True 1099 1099 81.056 1116 2517 1 chr3B.!!$R2 1401
4 TraesCS1B01G347100 chr3B 146182431 146183121 690 True 568 568 81.583 1120 1810 1 chr3B.!!$R1 690
5 TraesCS1B01G347100 chr3D 409020602 409022003 1401 True 1088 1088 80.862 1116 2517 1 chr3D.!!$R2 1401
6 TraesCS1B01G347100 chr3D 95245802 95246449 647 True 588 588 83.103 1163 1810 1 chr3D.!!$R1 647
7 TraesCS1B01G347100 chr3A 542202607 542204170 1563 False 1074 1074 79.508 970 2517 1 chr3A.!!$F1 1547
8 TraesCS1B01G347100 chr3A 113341693 113342383 690 True 606 606 82.565 1120 1810 1 chr3A.!!$R2 690

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
932 2019 0.179048 AAAGCCAAAGCCAAGCCAAC 60.179 50.0 0.00 0.0 41.25 3.77 F
2088 3242 0.688087 GGTGGGAGTCGGATTCCTCT 60.688 60.0 17.73 0.0 35.01 3.69 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2521 3675 0.320374 ACATTTCGAGCCGAACCAGA 59.680 50.0 9.15 0.0 45.64 3.86 R
3029 4193 0.904649 ATCACGGAAGCTGGACATCA 59.095 50.0 0.00 0.0 0.00 3.07 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
44 45 1.437625 GCAGTCTTGTCTTCCTGAGC 58.562 55.000 0.00 0.00 0.00 4.26
66 67 5.064441 CAGGATGCAAACCCTAAGAAAAG 57.936 43.478 9.25 0.00 0.00 2.27
103 104 2.681778 CAGAGTCCCTCCCGCTGT 60.682 66.667 0.00 0.00 0.00 4.40
163 164 2.435586 GGAGACGAGACGGACCGA 60.436 66.667 23.38 0.00 0.00 4.69
164 165 1.818785 GGAGACGAGACGGACCGAT 60.819 63.158 23.38 8.67 0.00 4.18
183 184 2.437359 GCCACGCCTGCAGAAGAT 60.437 61.111 17.39 0.00 0.00 2.40
225 232 4.792804 GGGAGGAGGCAGCTGCAC 62.793 72.222 37.63 28.79 44.36 4.57
352 359 1.523711 ATGGAGTTGGCGTATGGCG 60.524 57.895 3.80 0.00 44.92 5.69
444 451 3.059188 CGACGTGCCAAGATTGTTAGTTT 60.059 43.478 0.00 0.00 0.00 2.66
445 452 4.464112 GACGTGCCAAGATTGTTAGTTTC 58.536 43.478 0.00 0.00 0.00 2.78
515 1596 2.776312 TCGATTGCTAGCTCGGTAAG 57.224 50.000 21.82 6.24 35.64 2.34
530 1613 5.289917 GCTCGGTAAGAAGACTGATCTTTTC 59.710 44.000 0.00 0.00 45.60 2.29
531 1614 6.591750 TCGGTAAGAAGACTGATCTTTTCT 57.408 37.500 0.00 0.00 45.60 2.52
532 1615 6.622549 TCGGTAAGAAGACTGATCTTTTCTC 58.377 40.000 0.00 0.00 45.60 2.87
533 1616 6.208797 TCGGTAAGAAGACTGATCTTTTCTCA 59.791 38.462 0.00 0.00 45.60 3.27
534 1617 7.038659 CGGTAAGAAGACTGATCTTTTCTCAT 58.961 38.462 0.00 0.00 45.60 2.90
557 1640 9.042008 TCATTTTTAGAGTTACATATTCGAGCC 57.958 33.333 0.00 0.00 0.00 4.70
627 1713 7.153985 ACTTGAATTTATGTCACCCAATTGTG 58.846 34.615 4.43 0.00 37.59 3.33
631 1717 7.989741 TGAATTTATGTCACCCAATTGTGTTTT 59.010 29.630 4.43 0.00 37.51 2.43
639 1725 1.765314 CCAATTGTGTTTTCCCCACCA 59.235 47.619 4.43 0.00 31.71 4.17
665 1751 3.375299 CCAGCAGAACCCTAGAAAATTCG 59.625 47.826 0.00 0.00 0.00 3.34
905 1992 6.038825 TCAAATAGAGCGAAACAACAGGAAAA 59.961 34.615 0.00 0.00 0.00 2.29
914 2001 5.656480 GAAACAACAGGAAAACTAAGCCAA 58.344 37.500 0.00 0.00 0.00 4.52
915 2002 5.669164 AACAACAGGAAAACTAAGCCAAA 57.331 34.783 0.00 0.00 0.00 3.28
916 2003 5.262588 ACAACAGGAAAACTAAGCCAAAG 57.737 39.130 0.00 0.00 0.00 2.77
917 2004 4.051237 CAACAGGAAAACTAAGCCAAAGC 58.949 43.478 0.00 0.00 40.32 3.51
918 2005 2.628178 ACAGGAAAACTAAGCCAAAGCC 59.372 45.455 0.00 0.00 41.25 4.35
919 2006 2.627699 CAGGAAAACTAAGCCAAAGCCA 59.372 45.455 0.00 0.00 41.25 4.75
920 2007 3.069443 CAGGAAAACTAAGCCAAAGCCAA 59.931 43.478 0.00 0.00 41.25 4.52
921 2008 3.709141 AGGAAAACTAAGCCAAAGCCAAA 59.291 39.130 0.00 0.00 41.25 3.28
922 2009 4.058124 GGAAAACTAAGCCAAAGCCAAAG 58.942 43.478 0.00 0.00 41.25 2.77
923 2010 2.820059 AACTAAGCCAAAGCCAAAGC 57.180 45.000 0.00 0.00 41.25 3.51
924 2011 0.969149 ACTAAGCCAAAGCCAAAGCC 59.031 50.000 0.00 0.00 41.25 4.35
932 2019 0.179048 AAAGCCAAAGCCAAGCCAAC 60.179 50.000 0.00 0.00 41.25 3.77
951 2038 1.370064 CTGTTCCCGTTCCGTTCCT 59.630 57.895 0.00 0.00 0.00 3.36
1188 2324 2.436115 GCCAAGGTCTACCACGCC 60.436 66.667 1.26 0.00 38.89 5.68
1998 3134 2.183555 GGGCTGGTCGAACCTACG 59.816 66.667 0.00 0.00 39.58 3.51
2004 3140 2.050934 GGTCGAACCTACGGAGCCT 61.051 63.158 0.00 0.00 34.73 4.58
2019 3155 3.015332 GCCTCCTCCTCCTCCTCCA 62.015 68.421 0.00 0.00 0.00 3.86
2088 3242 0.688087 GGTGGGAGTCGGATTCCTCT 60.688 60.000 17.73 0.00 35.01 3.69
2322 3476 2.015736 TGAAGAGCTTCTCCATTCGC 57.984 50.000 11.16 0.00 40.14 4.70
2521 3675 1.003355 CCTCTCGTGCACCACCAAT 60.003 57.895 12.15 0.00 0.00 3.16
2523 3677 0.036952 CTCTCGTGCACCACCAATCT 60.037 55.000 12.15 0.00 0.00 2.40
2596 3750 7.498570 AGCTCTCTTGCTTGAAAGGAATATAAG 59.501 37.037 0.00 0.00 40.93 1.73
2619 3773 6.175471 AGGAAATTTTGGATTGAAAGGATGC 58.825 36.000 0.00 0.00 0.00 3.91
2662 3816 1.981256 TGGGACCTGAGCAGAAAAAC 58.019 50.000 0.00 0.00 0.00 2.43
2665 3819 1.230324 GACCTGAGCAGAAAAACGCT 58.770 50.000 0.00 0.00 42.42 5.07
2685 3839 5.780793 ACGCTATTCATATTCCTTAGTCCCT 59.219 40.000 0.00 0.00 0.00 4.20
2726 3880 9.902196 ATTCATTTTTGCAATCCAGAATTTTTC 57.098 25.926 0.00 0.00 0.00 2.29
2736 3890 3.378112 TCCAGAATTTTTCATGCTAGCGG 59.622 43.478 10.77 4.96 0.00 5.52
2775 3933 9.634163 TTGTAGTTGTTACATACATACAGTCTG 57.366 33.333 0.00 0.00 41.72 3.51
2931 4095 3.246619 GGAACTTTCGTGAGTGCTAGAG 58.753 50.000 0.00 0.00 0.00 2.43
2932 4096 3.057456 GGAACTTTCGTGAGTGCTAGAGA 60.057 47.826 0.00 0.00 0.00 3.10
2964 4128 9.367444 GAGTATTATAGCTGTTGTGTAACTTGT 57.633 33.333 0.00 0.00 38.04 3.16
2966 4130 6.795098 TTATAGCTGTTGTGTAACTTGTGG 57.205 37.500 0.00 0.00 38.04 4.17
2967 4131 3.275617 AGCTGTTGTGTAACTTGTGGA 57.724 42.857 0.00 0.00 38.04 4.02
2968 4132 3.820557 AGCTGTTGTGTAACTTGTGGAT 58.179 40.909 0.00 0.00 38.04 3.41
2970 4134 5.373222 AGCTGTTGTGTAACTTGTGGATTA 58.627 37.500 0.00 0.00 38.04 1.75
2972 4136 6.490040 AGCTGTTGTGTAACTTGTGGATTATT 59.510 34.615 0.00 0.00 38.04 1.40
2973 4137 7.014230 AGCTGTTGTGTAACTTGTGGATTATTT 59.986 33.333 0.00 0.00 38.04 1.40
2974 4138 7.651704 GCTGTTGTGTAACTTGTGGATTATTTT 59.348 33.333 0.00 0.00 38.04 1.82
2975 4139 9.180678 CTGTTGTGTAACTTGTGGATTATTTTC 57.819 33.333 0.00 0.00 38.04 2.29
2976 4140 8.908903 TGTTGTGTAACTTGTGGATTATTTTCT 58.091 29.630 0.00 0.00 38.04 2.52
2977 4141 9.744468 GTTGTGTAACTTGTGGATTATTTTCTT 57.256 29.630 0.00 0.00 38.04 2.52
3055 4219 4.891168 TGTCCAGCTTCCGTGATATACTAA 59.109 41.667 0.00 0.00 0.00 2.24
3056 4220 5.538813 TGTCCAGCTTCCGTGATATACTAAT 59.461 40.000 0.00 0.00 0.00 1.73
3057 4221 6.041637 TGTCCAGCTTCCGTGATATACTAATT 59.958 38.462 0.00 0.00 0.00 1.40
3058 4222 6.586844 GTCCAGCTTCCGTGATATACTAATTC 59.413 42.308 0.00 0.00 0.00 2.17
3059 4223 6.266786 TCCAGCTTCCGTGATATACTAATTCA 59.733 38.462 0.00 0.00 0.00 2.57
3061 4225 7.371159 CAGCTTCCGTGATATACTAATTCAGA 58.629 38.462 0.00 0.00 0.00 3.27
3062 4226 7.327275 CAGCTTCCGTGATATACTAATTCAGAC 59.673 40.741 0.00 0.00 0.00 3.51
3063 4227 6.586844 GCTTCCGTGATATACTAATTCAGACC 59.413 42.308 0.00 0.00 0.00 3.85
3064 4228 7.591421 TTCCGTGATATACTAATTCAGACCA 57.409 36.000 0.00 0.00 0.00 4.02
3067 4231 6.311445 CCGTGATATACTAATTCAGACCATGC 59.689 42.308 0.00 0.00 0.00 4.06
3069 4233 7.062722 CGTGATATACTAATTCAGACCATGCTG 59.937 40.741 0.00 0.00 37.24 4.41
3070 4234 7.875041 GTGATATACTAATTCAGACCATGCTGT 59.125 37.037 0.98 0.00 37.20 4.40
3071 4235 8.432013 TGATATACTAATTCAGACCATGCTGTT 58.568 33.333 0.98 0.00 37.20 3.16
3076 4240 8.668510 ACTAATTCAGACCATGCTGTTATTAG 57.331 34.615 20.32 20.32 41.18 1.73
3077 4241 6.949352 AATTCAGACCATGCTGTTATTAGG 57.051 37.500 0.98 0.00 37.20 2.69
3078 4242 5.435686 TTCAGACCATGCTGTTATTAGGT 57.564 39.130 0.98 0.00 37.20 3.08
3079 4243 5.023533 TCAGACCATGCTGTTATTAGGTC 57.976 43.478 0.00 0.00 44.43 3.85
3080 4244 4.469586 TCAGACCATGCTGTTATTAGGTCA 59.530 41.667 11.48 0.00 46.03 4.02
3081 4245 5.045942 TCAGACCATGCTGTTATTAGGTCAA 60.046 40.000 11.48 0.00 46.03 3.18
3082 4246 5.647658 CAGACCATGCTGTTATTAGGTCAAA 59.352 40.000 11.48 0.00 46.03 2.69
3083 4247 5.882557 AGACCATGCTGTTATTAGGTCAAAG 59.117 40.000 11.48 0.00 46.03 2.77
3099 4263 7.472334 AGGTCAAAGCAAAATAAGATGTGAT 57.528 32.000 0.00 0.00 0.00 3.06
3126 4291 5.104610 AGTGATGCTCTACTGATGATGGTTT 60.105 40.000 0.00 0.00 0.00 3.27
3138 4303 8.006298 ACTGATGATGGTTTAGTTGAACAAAA 57.994 30.769 0.00 0.00 0.00 2.44
3141 4306 8.474025 TGATGATGGTTTAGTTGAACAAAACTT 58.526 29.630 0.00 0.00 40.77 2.66
3179 4344 5.837437 ACTCTATAGATCAACTCGGCTTTG 58.163 41.667 2.11 0.00 0.00 2.77
3187 4352 5.582665 AGATCAACTCGGCTTTGTTATCTTC 59.417 40.000 0.00 0.00 0.00 2.87
3188 4353 4.894784 TCAACTCGGCTTTGTTATCTTCT 58.105 39.130 0.00 0.00 0.00 2.85
3189 4354 4.690748 TCAACTCGGCTTTGTTATCTTCTG 59.309 41.667 0.00 0.00 0.00 3.02
3214 4379 9.661563 TGAATTAGTACAAAATCGTGTTATCCT 57.338 29.630 0.00 0.00 32.75 3.24
3220 4385 6.287589 ACAAAATCGTGTTATCCTCTCTCT 57.712 37.500 0.00 0.00 0.00 3.10
3256 4421 2.234300 TGGTCTTGACAGAAACCGAC 57.766 50.000 3.08 0.00 34.39 4.79
3270 4435 2.815647 CGACCAGAAGCGAAGGGC 60.816 66.667 0.00 0.00 44.05 5.19
3300 4465 5.163322 ACAATTCAATTCCTGTTCCTGCAAA 60.163 36.000 0.00 0.00 0.00 3.68
3314 4479 6.183360 TGTTCCTGCAAAGTCACAAACATATT 60.183 34.615 0.00 0.00 0.00 1.28
3315 4480 5.771469 TCCTGCAAAGTCACAAACATATTG 58.229 37.500 0.00 0.00 0.00 1.90
3316 4481 4.386652 CCTGCAAAGTCACAAACATATTGC 59.613 41.667 0.00 0.00 41.10 3.56
3425 4602 5.316987 ACAAACTGAAGCTTAGTGCCTATT 58.683 37.500 0.00 0.00 44.23 1.73
3426 4603 5.182001 ACAAACTGAAGCTTAGTGCCTATTG 59.818 40.000 0.00 7.26 44.23 1.90
3552 4731 1.978580 GGAGTTGGGATGGGACGATAT 59.021 52.381 0.00 0.00 0.00 1.63
3554 4733 2.632996 GAGTTGGGATGGGACGATATGA 59.367 50.000 0.00 0.00 0.00 2.15
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
44 45 4.524328 ACTTTTCTTAGGGTTTGCATCCTG 59.476 41.667 12.36 0.00 34.75 3.86
50 51 5.068591 TCCTTTGACTTTTCTTAGGGTTTGC 59.931 40.000 0.00 0.00 0.00 3.68
66 67 9.827411 GACTCTGTTTTTATATGTTCCTTTGAC 57.173 33.333 0.00 0.00 0.00 3.18
177 178 6.619329 AAGCCAAGAGTTTCTCTATCTTCT 57.381 37.500 0.00 0.00 40.28 2.85
183 184 6.263168 CCAAAGAAAAGCCAAGAGTTTCTCTA 59.737 38.462 0.00 0.00 40.28 2.43
224 231 3.052455 TCAAACATACATGTGCCTCGT 57.948 42.857 9.11 0.00 41.61 4.18
225 232 4.811024 AGTATCAAACATACATGTGCCTCG 59.189 41.667 9.11 0.00 41.61 4.63
323 330 2.372264 CCAACTCCATGGAACAGGATG 58.628 52.381 17.00 8.80 46.40 3.51
444 451 3.571828 TGGCAAAATTTCACAGGAATCGA 59.428 39.130 0.00 0.00 31.93 3.59
445 452 3.674753 GTGGCAAAATTTCACAGGAATCG 59.325 43.478 0.00 0.00 31.93 3.34
531 1614 9.042008 GGCTCGAATATGTAACTCTAAAAATGA 57.958 33.333 0.00 0.00 0.00 2.57
532 1615 8.826710 TGGCTCGAATATGTAACTCTAAAAATG 58.173 33.333 0.00 0.00 0.00 2.32
533 1616 8.827677 GTGGCTCGAATATGTAACTCTAAAAAT 58.172 33.333 0.00 0.00 0.00 1.82
534 1617 7.820386 TGTGGCTCGAATATGTAACTCTAAAAA 59.180 33.333 0.00 0.00 0.00 1.94
538 1621 5.221185 GGTGTGGCTCGAATATGTAACTCTA 60.221 44.000 0.00 0.00 0.00 2.43
557 1640 3.799281 AGACAAAAATGTGGTGGTGTG 57.201 42.857 0.00 0.00 0.00 3.82
627 1713 1.474320 GCTGGTTTTGGTGGGGAAAAC 60.474 52.381 0.00 0.00 40.89 2.43
631 1717 1.152567 CTGCTGGTTTTGGTGGGGA 60.153 57.895 0.00 0.00 0.00 4.81
639 1725 3.876309 TTCTAGGGTTCTGCTGGTTTT 57.124 42.857 0.00 0.00 0.00 2.43
665 1751 4.932200 ACTCGGAGTGTGATGAAATTTCTC 59.068 41.667 18.64 13.38 30.90 2.87
750 1837 4.099266 TGTTTACAGCTCAATGCCAACTTT 59.901 37.500 0.00 0.00 44.23 2.66
856 1943 2.520741 CTTGGTTGCGGTTGGGGT 60.521 61.111 0.00 0.00 0.00 4.95
905 1992 0.969149 GGCTTTGGCTTTGGCTTAGT 59.031 50.000 0.00 0.00 38.73 2.24
914 2001 1.447217 GTTGGCTTGGCTTTGGCTT 59.553 52.632 0.00 0.00 38.73 4.35
915 2002 2.510551 GGTTGGCTTGGCTTTGGCT 61.511 57.895 0.00 0.00 38.73 4.75
916 2003 2.031012 GGTTGGCTTGGCTTTGGC 59.969 61.111 0.00 0.00 37.82 4.52
917 2004 1.368579 CAGGTTGGCTTGGCTTTGG 59.631 57.895 0.00 0.00 0.00 3.28
918 2005 0.465287 AACAGGTTGGCTTGGCTTTG 59.535 50.000 0.00 0.00 0.00 2.77
919 2006 0.752658 GAACAGGTTGGCTTGGCTTT 59.247 50.000 0.00 0.00 0.00 3.51
920 2007 1.115326 GGAACAGGTTGGCTTGGCTT 61.115 55.000 0.00 0.00 0.00 4.35
921 2008 1.531602 GGAACAGGTTGGCTTGGCT 60.532 57.895 0.00 0.00 0.00 4.75
922 2009 2.574018 GGGAACAGGTTGGCTTGGC 61.574 63.158 0.00 0.00 0.00 4.52
923 2010 2.268076 CGGGAACAGGTTGGCTTGG 61.268 63.158 0.00 0.00 0.00 3.61
924 2011 1.106944 AACGGGAACAGGTTGGCTTG 61.107 55.000 0.00 0.00 0.00 4.01
1087 2223 2.045340 GTTGCCTATGGTGCCGGT 60.045 61.111 1.90 0.00 0.00 5.28
1093 2229 2.046285 GCTTGCCGTTGCCTATGGT 61.046 57.895 0.00 0.00 35.16 3.55
1998 3134 2.123033 GGAGGAGGAGGAGGCTCC 60.123 72.222 26.42 26.42 43.65 4.70
2004 3140 0.336737 GAAGTGGAGGAGGAGGAGGA 59.663 60.000 0.00 0.00 0.00 3.71
2521 3675 0.320374 ACATTTCGAGCCGAACCAGA 59.680 50.000 9.15 0.00 45.64 3.86
2523 3677 1.673626 GGTACATTTCGAGCCGAACCA 60.674 52.381 9.15 0.00 45.64 3.67
2526 3680 2.232941 AGAAGGTACATTTCGAGCCGAA 59.767 45.455 6.01 6.01 44.28 4.30
2596 3750 5.063817 CGCATCCTTTCAATCCAAAATTTCC 59.936 40.000 0.00 0.00 0.00 3.13
2636 3790 0.991146 TGCTCAGGTCCCATGCTTAA 59.009 50.000 0.00 0.00 0.00 1.85
2637 3791 0.543277 CTGCTCAGGTCCCATGCTTA 59.457 55.000 0.00 0.00 0.00 3.09
2638 3792 1.203441 TCTGCTCAGGTCCCATGCTT 61.203 55.000 0.00 0.00 0.00 3.91
2662 3816 6.287589 AGGGACTAAGGAATATGAATAGCG 57.712 41.667 0.00 0.00 36.02 4.26
2665 3819 9.627123 CACAAAAGGGACTAAGGAATATGAATA 57.373 33.333 0.00 0.00 38.49 1.75
2726 3880 2.010145 ACACAGTAACCGCTAGCATG 57.990 50.000 16.45 7.65 0.00 4.06
2736 3890 8.229137 TGTAACAACTACAACAAACACAGTAAC 58.771 33.333 0.00 0.00 37.58 2.50
2775 3933 0.727398 CGAAATCCGCAACTCCCTTC 59.273 55.000 0.00 0.00 0.00 3.46
2895 4059 7.484641 CACGAAAGTTCCAATGGTACATTTATG 59.515 37.037 11.58 4.88 44.73 1.90
2931 4095 7.914346 ACACAACAGCTATAATACTCGTAAGTC 59.086 37.037 0.00 0.00 36.92 3.01
2932 4096 7.769220 ACACAACAGCTATAATACTCGTAAGT 58.231 34.615 0.00 0.00 39.66 2.24
2991 4155 7.255381 GCCATTCTGCTTATGATGTGATACTTT 60.255 37.037 0.00 0.00 0.00 2.66
2994 4158 5.106396 GGCCATTCTGCTTATGATGTGATAC 60.106 44.000 0.00 0.00 0.00 2.24
2995 4159 5.005740 GGCCATTCTGCTTATGATGTGATA 58.994 41.667 0.00 0.00 0.00 2.15
3029 4193 0.904649 ATCACGGAAGCTGGACATCA 59.095 50.000 0.00 0.00 0.00 3.07
3030 4194 2.890808 TATCACGGAAGCTGGACATC 57.109 50.000 0.00 0.00 0.00 3.06
3043 4207 7.062722 CAGCATGGTCTGAATTAGTATATCACG 59.937 40.741 0.00 0.00 36.19 4.35
3045 4209 7.966812 ACAGCATGGTCTGAATTAGTATATCA 58.033 34.615 7.27 0.00 43.62 2.15
3055 4219 6.006275 ACCTAATAACAGCATGGTCTGAAT 57.994 37.500 7.27 0.00 43.62 2.57
3056 4220 5.045942 TGACCTAATAACAGCATGGTCTGAA 60.046 40.000 7.27 0.00 43.62 3.02
3057 4221 4.469586 TGACCTAATAACAGCATGGTCTGA 59.530 41.667 7.27 0.00 43.62 3.27
3058 4222 4.769688 TGACCTAATAACAGCATGGTCTG 58.230 43.478 10.65 0.00 43.62 3.51
3059 4223 5.435686 TTGACCTAATAACAGCATGGTCT 57.564 39.130 10.65 0.00 43.62 3.85
3061 4225 4.399303 GCTTTGACCTAATAACAGCATGGT 59.601 41.667 0.00 0.00 43.62 3.55
3062 4226 4.398988 TGCTTTGACCTAATAACAGCATGG 59.601 41.667 0.00 0.00 43.62 3.66
3063 4227 5.565592 TGCTTTGACCTAATAACAGCATG 57.434 39.130 0.00 0.00 46.00 4.06
3064 4228 6.588719 TTTGCTTTGACCTAATAACAGCAT 57.411 33.333 0.00 0.00 0.00 3.79
3073 4237 8.402798 TCACATCTTATTTTGCTTTGACCTAA 57.597 30.769 0.00 0.00 0.00 2.69
3074 4238 7.994425 TCACATCTTATTTTGCTTTGACCTA 57.006 32.000 0.00 0.00 0.00 3.08
3075 4239 6.899393 TCACATCTTATTTTGCTTTGACCT 57.101 33.333 0.00 0.00 0.00 3.85
3076 4240 7.315142 TCATCACATCTTATTTTGCTTTGACC 58.685 34.615 0.00 0.00 0.00 4.02
3077 4241 8.746922 TTCATCACATCTTATTTTGCTTTGAC 57.253 30.769 0.00 0.00 0.00 3.18
3078 4242 8.579006 ACTTCATCACATCTTATTTTGCTTTGA 58.421 29.630 0.00 0.00 0.00 2.69
3079 4243 8.644619 CACTTCATCACATCTTATTTTGCTTTG 58.355 33.333 0.00 0.00 0.00 2.77
3080 4244 8.579006 TCACTTCATCACATCTTATTTTGCTTT 58.421 29.630 0.00 0.00 0.00 3.51
3081 4245 8.114331 TCACTTCATCACATCTTATTTTGCTT 57.886 30.769 0.00 0.00 0.00 3.91
3082 4246 7.692460 TCACTTCATCACATCTTATTTTGCT 57.308 32.000 0.00 0.00 0.00 3.91
3083 4247 7.043590 GCATCACTTCATCACATCTTATTTTGC 60.044 37.037 0.00 0.00 0.00 3.68
3095 4259 5.003692 TCAGTAGAGCATCACTTCATCAC 57.996 43.478 0.00 0.00 37.82 3.06
3099 4263 5.452917 CCATCATCAGTAGAGCATCACTTCA 60.453 44.000 0.00 0.00 37.82 3.02
3172 4337 7.308782 ACTAATTCAGAAGATAACAAAGCCG 57.691 36.000 0.00 0.00 0.00 5.52
3187 4352 9.916397 GGATAACACGATTTTGTACTAATTCAG 57.084 33.333 10.89 6.40 0.00 3.02
3188 4353 9.661563 AGGATAACACGATTTTGTACTAATTCA 57.338 29.630 10.89 0.00 0.00 2.57
3212 4377 5.243730 ACTTGACTCAGAAGAAAGAGAGAGG 59.756 44.000 0.00 0.00 35.83 3.69
3214 4379 6.462207 CCAACTTGACTCAGAAGAAAGAGAGA 60.462 42.308 0.00 0.00 35.83 3.10
3220 4385 5.359194 AGACCAACTTGACTCAGAAGAAA 57.641 39.130 0.00 0.00 0.00 2.52
3270 4435 5.178067 GGAACAGGAATTGAATTGTTTGCAG 59.822 40.000 0.00 0.00 34.18 4.41
3300 4465 8.565896 TTCTGAATAGCAATATGTTTGTGACT 57.434 30.769 0.00 0.00 0.00 3.41
3314 4479 2.621338 CGCACCTCTTTCTGAATAGCA 58.379 47.619 0.00 0.00 0.00 3.49
3315 4480 1.936547 CCGCACCTCTTTCTGAATAGC 59.063 52.381 0.00 0.00 0.00 2.97
3316 4481 3.252974 ACCGCACCTCTTTCTGAATAG 57.747 47.619 0.00 0.00 0.00 1.73
3378 4555 3.943671 TCCTTTTTCTGGACCAACAGA 57.056 42.857 0.00 0.00 45.22 3.41
3441 4618 2.231964 TGGTCCTCTTCATTTGCAATGC 59.768 45.455 0.00 0.00 0.00 3.56


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

AutoCloner maintained by Alex Coulton.