Multiple sequence alignment - TraesCS6D01G123100

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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 TraesCS6D01G123100 chr6D 100.000 3638 0 0 1 3638 87595447 87599084 0.000000e+00 6719.0
1 TraesCS6D01G123100 chr6B 93.464 2953 90 36 641 3545 166593206 166596103 0.000000e+00 4289.0
2 TraesCS6D01G123100 chr6B 89.787 470 34 9 145 605 166591353 166591817 1.130000e-164 590.0
3 TraesCS6D01G123100 chr6A 93.727 2758 81 36 442 3153 105870493 105873204 0.000000e+00 4050.0
4 TraesCS6D01G123100 chr6A 94.947 376 19 0 3263 3638 105873201 105873576 1.130000e-164 590.0
5 TraesCS6D01G123100 chr6A 89.078 293 27 3 146 436 105869879 105870168 3.450000e-95 359.0
6 TraesCS6D01G123100 chrUn 85.449 323 33 5 2724 3038 243363640 243363956 1.260000e-84 324.0
7 TraesCS6D01G123100 chr5D 86.174 311 29 5 2736 3038 552097010 552096706 1.260000e-84 324.0
8 TraesCS6D01G123100 chr5D 86.174 311 29 5 2736 3038 552097567 552097263 1.260000e-84 324.0
9 TraesCS6D01G123100 chr5D 84.259 108 12 5 24 127 437615490 437615384 2.310000e-17 100.0
10 TraesCS6D01G123100 chr3D 85.449 323 33 5 2724 3038 561758416 561758732 1.260000e-84 324.0
11 TraesCS6D01G123100 chr4A 85.852 311 29 6 2736 3038 611226706 611226403 2.110000e-82 316.0
12 TraesCS6D01G123100 chr4A 90.909 132 8 2 3150 3278 467246602 467246472 1.340000e-39 174.0
13 TraesCS6D01G123100 chr7B 88.725 204 21 1 2837 3038 211940718 211940921 7.800000e-62 248.0
14 TraesCS6D01G123100 chr7B 90.909 99 8 1 41 138 21719391 21719489 8.200000e-27 132.0
15 TraesCS6D01G123100 chr7B 86.957 115 15 0 38 152 512761205 512761091 2.950000e-26 130.0
16 TraesCS6D01G123100 chr7B 83.654 104 17 0 40 143 705970497 705970600 8.310000e-17 99.0
17 TraesCS6D01G123100 chr1B 90.588 170 16 0 2869 3038 36351745 36351914 3.660000e-55 226.0
18 TraesCS6D01G123100 chr4D 90.152 132 9 2 3150 3278 109274972 109275102 6.250000e-38 169.0
19 TraesCS6D01G123100 chr1D 91.736 121 7 1 3149 3266 216329003 216328883 8.080000e-37 165.0
20 TraesCS6D01G123100 chr1D 90.323 124 9 2 3150 3270 465887144 465887267 3.760000e-35 159.0
21 TraesCS6D01G123100 chr2B 90.678 118 11 0 3150 3267 358048117 358048000 1.350000e-34 158.0
22 TraesCS6D01G123100 chr2D 89.147 129 9 3 3139 3264 58812086 58812212 4.860000e-34 156.0
23 TraesCS6D01G123100 chr5B 88.976 127 11 1 3142 3265 661308683 661308809 1.750000e-33 154.0
24 TraesCS6D01G123100 chr4B 87.879 132 12 4 3150 3278 167350082 167349952 6.290000e-33 152.0
25 TraesCS6D01G123100 chr7A 85.714 112 16 0 32 143 642938653 642938764 6.380000e-23 119.0
26 TraesCS6D01G123100 chr7A 84.404 109 14 3 36 143 135631057 135631163 1.790000e-18 104.0
27 TraesCS6D01G123100 chr1A 83.333 108 17 1 26 132 486335284 486335177 8.310000e-17 99.0
28 TraesCS6D01G123100 chr1A 83.178 107 14 3 39 143 587358197 587358301 1.080000e-15 95.3
29 TraesCS6D01G123100 chr7D 80.000 115 16 6 32 143 1472250 1472360 1.080000e-10 78.7


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 TraesCS6D01G123100 chr6D 87595447 87599084 3637 False 6719.000000 6719 100.0000 1 3638 1 chr6D.!!$F1 3637
1 TraesCS6D01G123100 chr6B 166591353 166596103 4750 False 2439.500000 4289 91.6255 145 3545 2 chr6B.!!$F1 3400
2 TraesCS6D01G123100 chr6A 105869879 105873576 3697 False 1666.333333 4050 92.5840 146 3638 3 chr6A.!!$F1 3492
3 TraesCS6D01G123100 chr5D 552096706 552097567 861 True 324.000000 324 86.1740 2736 3038 2 chr5D.!!$R2 302

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
994 2709 0.759060 GAAGAGGAGGAGGAGGAGGC 60.759 65.0 0.0 0.0 0.0 4.70 F
1937 3667 0.804989 CAGGTTCGTCTTTGGCATCC 59.195 55.0 0.0 0.0 0.0 3.51 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2601 4334 0.674581 CTTCCGAGTGCAATGGCTGA 60.675 55.000 0.0 0.0 41.91 4.26 R
2810 4543 2.497675 AGAGGCAAAGACGCAGATCTTA 59.502 45.455 0.0 0.0 37.99 2.10 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 8.593945 AATGATGTACCACAACCTAATCAAAT 57.406 30.769 0.00 0.00 0.00 2.32
26 27 9.693739 AATGATGTACCACAACCTAATCAAATA 57.306 29.630 0.00 0.00 0.00 1.40
27 28 8.500753 TGATGTACCACAACCTAATCAAATAC 57.499 34.615 0.00 0.00 0.00 1.89
28 29 8.325787 TGATGTACCACAACCTAATCAAATACT 58.674 33.333 0.00 0.00 0.00 2.12
31 32 9.826574 TGTACCACAACCTAATCAAATACTATC 57.173 33.333 0.00 0.00 0.00 2.08
34 35 9.614792 ACCACAACCTAATCAAATACTATCTTC 57.385 33.333 0.00 0.00 0.00 2.87
35 36 8.765219 CCACAACCTAATCAAATACTATCTTCG 58.235 37.037 0.00 0.00 0.00 3.79
37 38 9.530633 ACAACCTAATCAAATACTATCTTCGTC 57.469 33.333 0.00 0.00 0.00 4.20
39 40 9.751542 AACCTAATCAAATACTATCTTCGTCTG 57.248 33.333 0.00 0.00 0.00 3.51
41 42 9.967346 CCTAATCAAATACTATCTTCGTCTGAA 57.033 33.333 0.00 0.00 0.00 3.02
50 51 7.787725 ACTATCTTCGTCTGAAAAAGTTTGT 57.212 32.000 0.00 0.00 32.66 2.83
51 52 8.209917 ACTATCTTCGTCTGAAAAAGTTTGTT 57.790 30.769 0.00 0.00 32.66 2.83
52 53 8.336080 ACTATCTTCGTCTGAAAAAGTTTGTTC 58.664 33.333 0.00 0.00 32.66 3.18
53 54 5.875930 TCTTCGTCTGAAAAAGTTTGTTCC 58.124 37.500 0.00 0.00 32.66 3.62
54 55 5.646360 TCTTCGTCTGAAAAAGTTTGTTCCT 59.354 36.000 0.00 0.00 32.66 3.36
55 56 5.479716 TCGTCTGAAAAAGTTTGTTCCTC 57.520 39.130 0.00 0.00 0.00 3.71
56 57 4.938832 TCGTCTGAAAAAGTTTGTTCCTCA 59.061 37.500 0.00 0.00 0.00 3.86
57 58 5.413213 TCGTCTGAAAAAGTTTGTTCCTCAA 59.587 36.000 0.00 0.00 0.00 3.02
58 59 6.072397 TCGTCTGAAAAAGTTTGTTCCTCAAA 60.072 34.615 0.00 0.00 42.79 2.69
60 61 7.253750 CGTCTGAAAAAGTTTGTTCCTCAAATG 60.254 37.037 0.00 0.00 45.88 2.32
61 62 7.010460 GTCTGAAAAAGTTTGTTCCTCAAATGG 59.990 37.037 0.00 0.00 45.88 3.16
63 64 7.563906 TGAAAAAGTTTGTTCCTCAAATGGAT 58.436 30.769 0.00 0.00 45.88 3.41
66 67 7.595819 AAAGTTTGTTCCTCAAATGGATGTA 57.404 32.000 0.00 0.00 45.88 2.29
69 70 7.177878 AGTTTGTTCCTCAAATGGATGTATCT 58.822 34.615 0.00 0.00 45.88 1.98
70 71 8.328758 AGTTTGTTCCTCAAATGGATGTATCTA 58.671 33.333 0.00 0.00 45.88 1.98
73 74 8.547481 TGTTCCTCAAATGGATGTATCTAGTA 57.453 34.615 0.00 0.00 35.83 1.82
85 86 9.642343 TGGATGTATCTAGTATCAAGTTAGTGT 57.358 33.333 0.00 0.00 0.00 3.55
116 117 8.141835 ACATTTATTTGAGAAACAAGTTTGGC 57.858 30.769 2.45 0.00 39.77 4.52
117 118 7.768120 ACATTTATTTGAGAAACAAGTTTGGCA 59.232 29.630 2.45 0.00 39.77 4.92
118 119 8.776470 CATTTATTTGAGAAACAAGTTTGGCAT 58.224 29.630 2.45 0.00 39.77 4.40
119 120 9.995003 ATTTATTTGAGAAACAAGTTTGGCATA 57.005 25.926 2.45 0.00 39.77 3.14
120 121 9.823647 TTTATTTGAGAAACAAGTTTGGCATAA 57.176 25.926 2.45 0.00 39.77 1.90
121 122 7.951530 ATTTGAGAAACAAGTTTGGCATAAG 57.048 32.000 2.45 0.00 39.77 1.73
122 123 6.463995 TTGAGAAACAAGTTTGGCATAAGT 57.536 33.333 2.45 0.00 34.20 2.24
123 124 6.463995 TGAGAAACAAGTTTGGCATAAGTT 57.536 33.333 2.45 0.00 32.11 2.66
125 126 7.327214 TGAGAAACAAGTTTGGCATAAGTTTT 58.673 30.769 2.45 0.00 32.11 2.43
126 127 7.821846 TGAGAAACAAGTTTGGCATAAGTTTTT 59.178 29.630 2.45 0.00 32.11 1.94
143 144 3.955650 TTTTTCGGACAGAGGGAGTAG 57.044 47.619 0.00 0.00 0.00 2.57
154 156 3.385111 CAGAGGGAGTAGGAAATAACGCT 59.615 47.826 0.00 0.00 0.00 5.07
185 188 2.585247 GGTATGGCTCGTCGTGGC 60.585 66.667 13.32 13.32 0.00 5.01
222 225 4.021102 AGATACTTGGGGTCACAACTTG 57.979 45.455 0.00 0.00 0.00 3.16
290 294 2.681344 CCCGGACTAAACACAATTAGCC 59.319 50.000 0.73 0.00 36.54 3.93
319 323 1.522130 AACGGGTCACACGAACACC 60.522 57.895 6.37 0.00 34.93 4.16
333 337 1.636003 GAACACCAAAGGATCTCCCCT 59.364 52.381 0.00 0.00 38.42 4.79
406 410 1.190323 GTGTGAAACGAACGCAGAGAG 59.810 52.381 0.00 0.00 42.39 3.20
449 773 9.129532 GAGAGAAATGATTCATTACTCCCAAAT 57.870 33.333 12.15 0.00 38.06 2.32
479 803 1.819288 GGAAAAGAAGCTACAAGGCCC 59.181 52.381 0.00 0.00 0.00 5.80
647 2340 1.226717 GAACCAAACGCAACGGCAA 60.227 52.632 0.00 0.00 41.24 4.52
648 2341 1.476235 GAACCAAACGCAACGGCAAC 61.476 55.000 0.00 0.00 41.24 4.17
704 2397 4.862823 GAGGGAGGGAGGGACGGG 62.863 77.778 0.00 0.00 0.00 5.28
746 2439 5.986501 ACAAAGGTAGAAGAGTGGTAGAG 57.013 43.478 0.00 0.00 0.00 2.43
747 2440 4.773149 ACAAAGGTAGAAGAGTGGTAGAGG 59.227 45.833 0.00 0.00 0.00 3.69
748 2441 4.949966 AAGGTAGAAGAGTGGTAGAGGA 57.050 45.455 0.00 0.00 0.00 3.71
749 2442 4.513406 AGGTAGAAGAGTGGTAGAGGAG 57.487 50.000 0.00 0.00 0.00 3.69
750 2443 3.203487 AGGTAGAAGAGTGGTAGAGGAGG 59.797 52.174 0.00 0.00 0.00 4.30
751 2444 3.202595 GGTAGAAGAGTGGTAGAGGAGGA 59.797 52.174 0.00 0.00 0.00 3.71
752 2445 3.662759 AGAAGAGTGGTAGAGGAGGAG 57.337 52.381 0.00 0.00 0.00 3.69
994 2709 0.759060 GAAGAGGAGGAGGAGGAGGC 60.759 65.000 0.00 0.00 0.00 4.70
995 2710 2.123033 GAGGAGGAGGAGGAGGCC 60.123 72.222 0.00 0.00 0.00 5.19
1374 3104 4.218578 CTGCAGCTCCGCCTCGAT 62.219 66.667 0.00 0.00 0.00 3.59
1791 3521 1.004918 CCTTTTCTCTGGCGTCGGT 60.005 57.895 0.00 0.00 0.00 4.69
1929 3659 1.415672 TTGCCCTCCAGGTTCGTCTT 61.416 55.000 0.00 0.00 38.26 3.01
1930 3660 1.375326 GCCCTCCAGGTTCGTCTTT 59.625 57.895 0.00 0.00 38.26 2.52
1937 3667 0.804989 CAGGTTCGTCTTTGGCATCC 59.195 55.000 0.00 0.00 0.00 3.51
1956 3686 5.569227 GCATCCATTCCATTTCCTTGTGAAA 60.569 40.000 0.00 0.00 46.54 2.69
1974 3704 5.163513 GTGAAACACTTTCCATTGGCTATG 58.836 41.667 1.70 1.70 38.90 2.23
2033 3763 2.436646 CGTCACTGGCCACCATCC 60.437 66.667 0.00 0.00 30.82 3.51
2101 3831 1.076777 CGGGATGGCCAACTCCAAT 60.077 57.895 23.85 0.00 39.96 3.16
2181 3911 5.407387 TCTTCGTGCAGGTTGTTATCTTTAC 59.593 40.000 6.26 0.00 0.00 2.01
2182 3912 3.676172 TCGTGCAGGTTGTTATCTTTACG 59.324 43.478 6.26 0.00 0.00 3.18
2298 4031 3.303938 ACCAACAAACACCCATGATTCA 58.696 40.909 0.00 0.00 0.00 2.57
2506 4239 4.013050 ACAAGGGCTAAGAAAGATTCAGC 58.987 43.478 0.00 0.00 0.00 4.26
2598 4331 1.834263 AGTGGGCCTGATAGTTCTCAC 59.166 52.381 4.53 0.00 0.00 3.51
2601 4334 0.461961 GGCCTGATAGTTCTCACGCT 59.538 55.000 0.00 0.00 30.75 5.07
2810 4543 6.738453 GCAAGATGGTTAAAATGTGAGGTGTT 60.738 38.462 0.00 0.00 0.00 3.32
2843 4584 5.354792 CGTCTTTGCCTCTTCTACTACTACT 59.645 44.000 0.00 0.00 0.00 2.57
2844 4585 6.538021 CGTCTTTGCCTCTTCTACTACTACTA 59.462 42.308 0.00 0.00 0.00 1.82
2845 4586 7.465781 CGTCTTTGCCTCTTCTACTACTACTAC 60.466 44.444 0.00 0.00 0.00 2.73
2846 4587 7.553760 GTCTTTGCCTCTTCTACTACTACTACT 59.446 40.741 0.00 0.00 0.00 2.57
2847 4588 8.766476 TCTTTGCCTCTTCTACTACTACTACTA 58.234 37.037 0.00 0.00 0.00 1.82
2848 4589 8.729805 TTTGCCTCTTCTACTACTACTACTAC 57.270 38.462 0.00 0.00 0.00 2.73
2849 4590 6.825610 TGCCTCTTCTACTACTACTACTACC 58.174 44.000 0.00 0.00 0.00 3.18
2850 4591 5.925969 GCCTCTTCTACTACTACTACTACCG 59.074 48.000 0.00 0.00 0.00 4.02
2859 4600 6.413892 ACTACTACTACTACCGCTTTTCTCT 58.586 40.000 0.00 0.00 0.00 3.10
2972 4713 8.466798 ACAAATATGCTTACACCATAGGAAAAC 58.533 33.333 0.00 0.00 0.00 2.43
2975 4716 4.643463 TGCTTACACCATAGGAAAACGAA 58.357 39.130 0.00 0.00 0.00 3.85
2981 4722 5.313712 ACACCATAGGAAAACGAATGACTT 58.686 37.500 0.00 0.00 0.00 3.01
3047 4806 3.938963 ACCGTGCATAGATTGGTAAGTTG 59.061 43.478 0.00 0.00 0.00 3.16
3048 4807 3.938963 CCGTGCATAGATTGGTAAGTTGT 59.061 43.478 0.00 0.00 0.00 3.32
3114 4880 5.560724 CTCCCTTGGTTAGTCTCAAAATCA 58.439 41.667 0.00 0.00 0.00 2.57
3127 4893 8.443953 AGTCTCAAAATCACTATTGCCTTATC 57.556 34.615 0.00 0.00 0.00 1.75
3163 4929 1.054978 ATTTCTACTCCCTCCGCCCC 61.055 60.000 0.00 0.00 0.00 5.80
3164 4930 2.465010 TTTCTACTCCCTCCGCCCCA 62.465 60.000 0.00 0.00 0.00 4.96
3169 4935 0.917333 ACTCCCTCCGCCCCAAATTA 60.917 55.000 0.00 0.00 0.00 1.40
3170 4936 0.465642 CTCCCTCCGCCCCAAATTAC 60.466 60.000 0.00 0.00 0.00 1.89
3172 4938 0.465642 CCCTCCGCCCCAAATTACTC 60.466 60.000 0.00 0.00 0.00 2.59
3173 4939 0.814010 CCTCCGCCCCAAATTACTCG 60.814 60.000 0.00 0.00 0.00 4.18
3174 4940 1.436983 CTCCGCCCCAAATTACTCGC 61.437 60.000 0.00 0.00 0.00 5.03
3175 4941 1.747367 CCGCCCCAAATTACTCGCA 60.747 57.895 0.00 0.00 0.00 5.10
3176 4942 1.309499 CCGCCCCAAATTACTCGCAA 61.309 55.000 0.00 0.00 0.00 4.85
3188 4954 7.973388 CCAAATTACTCGCAAAAATGGATAGAA 59.027 33.333 0.00 0.00 0.00 2.10
3261 5027 0.388294 GTAATTCCGGACGGAGGGAG 59.612 60.000 13.64 0.00 46.06 4.30
3300 5066 3.548745 TGTACAGGAGCATTCTGATGG 57.451 47.619 7.75 0.00 33.72 3.51
3380 5149 4.467198 AAGCCGTATAAACTACAGCTGT 57.533 40.909 25.12 25.12 0.00 4.40
3459 5231 6.529829 GCTTAGATAGTACTACATGCAGCATC 59.470 42.308 4.38 0.00 0.00 3.91
3480 5252 7.172190 AGCATCGAAATGTACTTTCCTATCATG 59.828 37.037 0.00 0.00 40.19 3.07
3541 5313 4.899352 ATAGCCACTCTTTCAGACTGTT 57.101 40.909 1.59 0.00 0.00 3.16
3567 5339 6.488817 CAATGATGTATGTGCAATCTTTCGA 58.511 36.000 0.00 0.00 0.00 3.71
3585 5357 7.930217 TCTTTCGAAGATGATGTTTTCTTGTT 58.070 30.769 0.00 0.00 35.04 2.83
3589 5361 5.117592 CGAAGATGATGTTTTCTTGTTTGGC 59.882 40.000 0.00 0.00 32.46 4.52
3613 5385 6.673316 GCGAATCTTCCTTCAAGTATGTGTTC 60.673 42.308 0.00 0.00 33.27 3.18
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
1 2 9.120538 GTATTTGATTAGGTTGTGGTACATCAT 57.879 33.333 0.00 0.00 44.52 2.45
2 3 8.325787 AGTATTTGATTAGGTTGTGGTACATCA 58.674 33.333 0.00 0.00 44.52 3.07
3 4 8.732746 AGTATTTGATTAGGTTGTGGTACATC 57.267 34.615 0.00 0.00 44.52 3.06
5 6 9.826574 GATAGTATTTGATTAGGTTGTGGTACA 57.173 33.333 0.00 0.00 0.00 2.90
8 9 9.614792 GAAGATAGTATTTGATTAGGTTGTGGT 57.385 33.333 0.00 0.00 0.00 4.16
9 10 8.765219 CGAAGATAGTATTTGATTAGGTTGTGG 58.235 37.037 0.00 0.00 0.00 4.17
10 11 9.314321 ACGAAGATAGTATTTGATTAGGTTGTG 57.686 33.333 0.00 0.00 0.00 3.33
11 12 9.530633 GACGAAGATAGTATTTGATTAGGTTGT 57.469 33.333 0.00 0.00 0.00 3.32
12 13 9.751542 AGACGAAGATAGTATTTGATTAGGTTG 57.248 33.333 0.00 0.00 0.00 3.77
13 14 9.751542 CAGACGAAGATAGTATTTGATTAGGTT 57.248 33.333 0.00 0.00 0.00 3.50
15 16 9.967346 TTCAGACGAAGATAGTATTTGATTAGG 57.033 33.333 0.00 0.00 0.00 2.69
24 25 9.490379 ACAAACTTTTTCAGACGAAGATAGTAT 57.510 29.630 0.00 0.00 31.28 2.12
25 26 8.882415 ACAAACTTTTTCAGACGAAGATAGTA 57.118 30.769 0.00 0.00 31.28 1.82
26 27 7.787725 ACAAACTTTTTCAGACGAAGATAGT 57.212 32.000 0.00 0.00 31.28 2.12
27 28 7.798982 GGAACAAACTTTTTCAGACGAAGATAG 59.201 37.037 0.00 0.00 31.28 2.08
28 29 7.497909 AGGAACAAACTTTTTCAGACGAAGATA 59.502 33.333 0.00 0.00 31.28 1.98
31 32 5.880341 AGGAACAAACTTTTTCAGACGAAG 58.120 37.500 0.00 0.00 31.28 3.79
32 33 5.413213 TGAGGAACAAACTTTTTCAGACGAA 59.587 36.000 0.00 0.00 0.00 3.85
33 34 4.938832 TGAGGAACAAACTTTTTCAGACGA 59.061 37.500 0.00 0.00 0.00 4.20
34 35 5.229921 TGAGGAACAAACTTTTTCAGACG 57.770 39.130 0.00 0.00 0.00 4.18
50 51 9.379770 TGATACTAGATACATCCATTTGAGGAA 57.620 33.333 0.00 0.00 41.92 3.36
51 52 8.956446 TGATACTAGATACATCCATTTGAGGA 57.044 34.615 0.00 0.00 43.01 3.71
52 53 9.650539 CTTGATACTAGATACATCCATTTGAGG 57.349 37.037 0.00 0.00 0.00 3.86
91 92 7.768120 TGCCAAACTTGTTTCTCAAATAAATGT 59.232 29.630 0.00 0.00 35.48 2.71
93 94 8.907222 ATGCCAAACTTGTTTCTCAAATAAAT 57.093 26.923 0.00 0.00 35.48 1.40
95 96 9.474920 CTTATGCCAAACTTGTTTCTCAAATAA 57.525 29.630 0.00 0.00 35.48 1.40
97 98 7.500141 ACTTATGCCAAACTTGTTTCTCAAAT 58.500 30.769 0.00 0.00 35.48 2.32
100 101 6.463995 AACTTATGCCAAACTTGTTTCTCA 57.536 33.333 0.00 0.00 0.00 3.27
101 102 7.770801 AAAACTTATGCCAAACTTGTTTCTC 57.229 32.000 0.00 0.00 0.00 2.87
123 124 2.565834 CCTACTCCCTCTGTCCGAAAAA 59.434 50.000 0.00 0.00 0.00 1.94
125 126 1.356738 TCCTACTCCCTCTGTCCGAAA 59.643 52.381 0.00 0.00 0.00 3.46
126 127 0.997363 TCCTACTCCCTCTGTCCGAA 59.003 55.000 0.00 0.00 0.00 4.30
127 128 0.997363 TTCCTACTCCCTCTGTCCGA 59.003 55.000 0.00 0.00 0.00 4.55
128 129 1.848652 TTTCCTACTCCCTCTGTCCG 58.151 55.000 0.00 0.00 0.00 4.79
130 131 4.737055 GCGTTATTTCCTACTCCCTCTGTC 60.737 50.000 0.00 0.00 0.00 3.51
132 133 3.385111 AGCGTTATTTCCTACTCCCTCTG 59.615 47.826 0.00 0.00 0.00 3.35
135 136 4.031611 AGAAGCGTTATTTCCTACTCCCT 58.968 43.478 0.00 0.00 0.00 4.20
136 137 4.403585 AGAAGCGTTATTTCCTACTCCC 57.596 45.455 0.00 0.00 0.00 4.30
137 138 5.416947 TCAAGAAGCGTTATTTCCTACTCC 58.583 41.667 0.00 0.00 0.00 3.85
138 139 6.035112 CACTCAAGAAGCGTTATTTCCTACTC 59.965 42.308 0.00 0.00 0.00 2.59
139 140 5.869888 CACTCAAGAAGCGTTATTTCCTACT 59.130 40.000 0.00 0.00 0.00 2.57
140 141 5.638234 ACACTCAAGAAGCGTTATTTCCTAC 59.362 40.000 0.00 0.00 0.00 3.18
141 142 5.790593 ACACTCAAGAAGCGTTATTTCCTA 58.209 37.500 0.00 0.00 0.00 2.94
143 144 4.451096 TGACACTCAAGAAGCGTTATTTCC 59.549 41.667 0.00 0.00 0.00 3.13
154 156 2.611971 GCCATACCGTGACACTCAAGAA 60.612 50.000 3.68 0.00 0.00 2.52
185 188 2.638556 ATCTTGGAGACGTGACGAAG 57.361 50.000 13.70 4.34 0.00 3.79
248 252 2.636830 CTAATTGAGCTGACCCACCTG 58.363 52.381 0.00 0.00 0.00 4.00
290 294 2.140717 GTGACCCGTTGTTTAGTCAGG 58.859 52.381 0.00 0.00 39.76 3.86
333 337 6.884280 TGTTTTTCTTGCCCTTTTTGAAAA 57.116 29.167 0.00 0.00 35.63 2.29
449 773 7.176589 TGTAGCTTCTTTTCCAAAAGGAAAA 57.823 32.000 18.31 18.31 44.22 2.29
470 794 2.353573 GCTTTCCGGGGCCTTGTA 59.646 61.111 0.84 0.00 0.00 2.41
501 825 2.223803 TTCCTTCTCCTTCTCTCGCT 57.776 50.000 0.00 0.00 0.00 4.93
526 851 3.656045 CGTTCGCCCTGCCGTTTT 61.656 61.111 0.00 0.00 0.00 2.43
746 2439 4.862823 CCCGTCCCTCCCTCCTCC 62.863 77.778 0.00 0.00 0.00 4.30
994 2709 3.610669 CTCCCGCTCCATCCTCGG 61.611 72.222 0.00 0.00 42.58 4.63
995 2710 4.292178 GCTCCCGCTCCATCCTCG 62.292 72.222 0.00 0.00 0.00 4.63
1755 3485 1.676967 GTTGCTGCAGAGGAAGGGG 60.677 63.158 20.43 0.00 28.76 4.79
1791 3521 4.017037 AGGTAGAGATCCTGGAAAGAGTCA 60.017 45.833 0.00 0.00 33.62 3.41
1929 3659 3.119009 AGGAAATGGAATGGATGCCAA 57.881 42.857 0.00 0.00 36.95 4.52
1930 3660 2.767394 CAAGGAAATGGAATGGATGCCA 59.233 45.455 0.00 0.00 38.19 4.92
1937 3667 5.846203 AGTGTTTCACAAGGAAATGGAATG 58.154 37.500 2.80 0.00 46.55 2.67
1956 3686 1.745087 CGCATAGCCAATGGAAAGTGT 59.255 47.619 2.05 0.00 35.99 3.55
1974 3704 5.349809 AGAGGTAGAACAAAGTATAAGCGC 58.650 41.667 0.00 0.00 0.00 5.92
2047 3777 1.975327 CTCCTTCAACCTGCGGAGA 59.025 57.895 5.10 0.00 44.56 3.71
2101 3831 3.684788 GGAAGCTAAAAATGTCTGCGAGA 59.315 43.478 0.00 0.00 0.00 4.04
2181 3911 2.473530 ATGACCAAATACATTGCGCG 57.526 45.000 0.00 0.00 37.73 6.86
2182 3912 4.527564 GACTATGACCAAATACATTGCGC 58.472 43.478 0.00 0.00 37.73 6.09
2298 4031 4.181578 CGTCCAAGTAATTCCTCGTGAAT 58.818 43.478 0.00 0.00 45.75 2.57
2494 4227 3.015327 GCACATCTGGCTGAATCTTTCT 58.985 45.455 0.00 0.00 0.00 2.52
2506 4239 1.304713 AAAGGGGCAGCACATCTGG 60.305 57.895 0.00 0.00 43.06 3.86
2598 4331 2.789917 GAGTGCAATGGCTGAGCG 59.210 61.111 0.00 0.00 41.91 5.03
2601 4334 0.674581 CTTCCGAGTGCAATGGCTGA 60.675 55.000 0.00 0.00 41.91 4.26
2810 4543 2.497675 AGAGGCAAAGACGCAGATCTTA 59.502 45.455 0.00 0.00 37.99 2.10
2843 4584 7.284944 AGCTATTTAGAGAGAAAAGCGGTAGTA 59.715 37.037 0.00 0.00 32.48 1.82
2844 4585 6.097129 AGCTATTTAGAGAGAAAAGCGGTAGT 59.903 38.462 0.00 0.00 32.48 2.73
2845 4586 6.508777 AGCTATTTAGAGAGAAAAGCGGTAG 58.491 40.000 0.00 0.00 32.48 3.18
2846 4587 6.466885 AGCTATTTAGAGAGAAAAGCGGTA 57.533 37.500 0.00 0.00 32.48 4.02
2847 4588 5.346181 AGCTATTTAGAGAGAAAAGCGGT 57.654 39.130 0.00 0.00 32.48 5.68
2848 4589 6.481984 CAAAGCTATTTAGAGAGAAAAGCGG 58.518 40.000 0.00 0.00 32.48 5.52
2849 4590 5.962423 GCAAAGCTATTTAGAGAGAAAAGCG 59.038 40.000 0.00 0.00 32.48 4.68
2850 4591 5.962423 CGCAAAGCTATTTAGAGAGAAAAGC 59.038 40.000 0.00 0.00 0.00 3.51
2859 4600 5.466728 CAGGCTAATCGCAAAGCTATTTAGA 59.533 40.000 0.00 0.00 41.67 2.10
2889 4630 9.988815 ATACATAAGCTAACTACAAAGAGATGG 57.011 33.333 0.00 0.00 0.00 3.51
2975 4716 5.246981 TGTCCCTCAAAGAATGAAGTCAT 57.753 39.130 0.00 0.00 37.67 3.06
2981 4722 4.141274 TCCAGTTTGTCCCTCAAAGAATGA 60.141 41.667 0.00 0.00 45.15 2.57
3047 4806 6.428159 CACCAAGGTATCTTATATCAGGCAAC 59.572 42.308 0.00 0.00 0.00 4.17
3048 4807 6.101150 ACACCAAGGTATCTTATATCAGGCAA 59.899 38.462 0.00 0.00 0.00 4.52
3114 4880 5.386924 ACCTAGACGAGATAAGGCAATAGT 58.613 41.667 0.00 0.00 31.98 2.12
3127 4893 7.540299 AGTAGAAATCAAGAAACCTAGACGAG 58.460 38.462 0.00 0.00 0.00 4.18
3163 4929 8.909708 TTCTATCCATTTTTGCGAGTAATTTG 57.090 30.769 0.00 0.00 0.00 2.32
3169 4935 6.757897 TCATTTCTATCCATTTTTGCGAGT 57.242 33.333 0.00 0.00 0.00 4.18
3170 4936 7.703621 ACATTCATTTCTATCCATTTTTGCGAG 59.296 33.333 0.00 0.00 0.00 5.03
3172 4938 7.760131 ACATTCATTTCTATCCATTTTTGCG 57.240 32.000 0.00 0.00 0.00 4.85
3362 5131 4.745125 CCATGACAGCTGTAGTTTATACGG 59.255 45.833 21.73 6.50 0.00 4.02
3459 5231 9.265901 ATCTTCATGATAGGAAAGTACATTTCG 57.734 33.333 0.00 0.00 39.91 3.46
3541 5313 5.585820 AAGATTGCACATACATCATTGCA 57.414 34.783 0.00 0.00 43.11 4.08
3567 5339 4.984161 CGCCAAACAAGAAAACATCATCTT 59.016 37.500 0.00 0.00 36.35 2.40
3578 5350 3.486383 AGGAAGATTCGCCAAACAAGAA 58.514 40.909 0.00 0.00 0.00 2.52
3585 5357 3.140325 ACTTGAAGGAAGATTCGCCAA 57.860 42.857 0.00 0.00 35.42 4.52
3589 5361 6.591834 AGAACACATACTTGAAGGAAGATTCG 59.408 38.462 0.00 0.00 35.42 3.34
3613 5385 3.698040 ACAAGATAGCATTGCAAAGGGAG 59.302 43.478 11.91 0.00 0.00 4.30


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

AutoCloner maintained by Alex Coulton.