Multiple sequence alignment - TraesCS7A01G552900

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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 TraesCS7A01G552900 chr7A 100.000 2675 0 0 604 3278 725720073 725722747 0.000000e+00 4940.0
1 TraesCS7A01G552900 chr7A 100.000 327 0 0 1 327 725719470 725719796 3.620000e-169 604.0
2 TraesCS7A01G552900 chr7A 79.186 221 39 6 108 321 725701347 725701567 2.640000e-31 147.0
3 TraesCS7A01G552900 chr7D 95.908 2346 83 3 934 3278 629638628 629640961 0.000000e+00 3788.0
4 TraesCS7A01G552900 chr7D 82.326 215 37 1 108 321 629635419 629635633 5.590000e-43 185.0
5 TraesCS7A01G552900 chr7D 81.250 96 10 7 3189 3278 166480636 166480543 1.630000e-08 71.3
6 TraesCS7A01G552900 chr7B 86.758 1095 123 14 2099 3176 732600642 732601731 0.000000e+00 1199.0
7 TraesCS7A01G552900 chr7B 91.264 435 33 3 1578 2007 732600211 732600645 3.640000e-164 588.0
8 TraesCS7A01G552900 chr7B 88.715 319 28 4 670 988 732599096 732599406 1.850000e-102 383.0
9 TraesCS7A01G552900 chr7B 89.767 215 21 1 108 321 732594708 732594922 1.160000e-69 274.0
10 TraesCS7A01G552900 chr2D 93.846 65 3 1 604 667 24449886 24449950 2.690000e-16 97.1
11 TraesCS7A01G552900 chr4D 96.429 56 2 0 604 659 485682205 485682260 3.480000e-15 93.5
12 TraesCS7A01G552900 chr4A 93.548 62 4 0 604 665 326004983 326004922 3.480000e-15 93.5
13 TraesCS7A01G552900 chr2B 90.476 63 5 1 604 665 68607904 68607842 7.540000e-12 82.4
14 TraesCS7A01G552900 chr6B 82.979 94 8 7 3191 3278 5888887 5888796 9.750000e-11 78.7
15 TraesCS7A01G552900 chr6B 82.979 94 8 7 3191 3278 5892968 5892877 9.750000e-11 78.7
16 TraesCS7A01G552900 chr6A 86.486 74 6 4 3207 3278 587974744 587974673 9.750000e-11 78.7
17 TraesCS7A01G552900 chr2A 82.979 94 8 7 3191 3278 508446698 508446607 9.750000e-11 78.7
18 TraesCS7A01G552900 chr1B 84.524 84 8 5 3198 3278 59007223 59007142 9.750000e-11 78.7
19 TraesCS7A01G552900 chr3B 91.071 56 4 1 3221 3275 823321870 823321925 1.260000e-09 75.0
20 TraesCS7A01G552900 chr3A 94.000 50 2 1 3230 3278 704105933 704105982 1.260000e-09 75.0
21 TraesCS7A01G552900 chr4B 80.460 87 15 1 2904 2990 646862148 646862064 7.590000e-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 TraesCS7A01G552900 chr7A 725719470 725722747 3277 False 2772.000000 4940 100.000000 1 3278 2 chr7A.!!$F2 3277
1 TraesCS7A01G552900 chr7D 629635419 629640961 5542 False 1986.500000 3788 89.117000 108 3278 2 chr7D.!!$F1 3170
2 TraesCS7A01G552900 chr7B 732599096 732601731 2635 False 723.333333 1199 88.912333 670 3176 3 chr7B.!!$F2 2506

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
307 308 0.107066 CCCTATGCACAGACATGCCA 60.107 55.0 0.0 0.0 45.5 4.92 F
1221 3626 0.321653 GACGGTGCCAAGGAGAACAT 60.322 55.0 0.0 0.0 0.0 2.71 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1893 4838 0.389948 GAAGATGAGTGTCGGCGGTT 60.390 55.000 7.21 0.0 0.0 4.44 R
2922 5877 1.229400 TTAGGCGAGGGGTGGTCTT 60.229 57.895 0.00 0.0 0.0 3.01 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
60 61 3.555917 AACGTACTATAGCCTCGATGC 57.444 47.619 4.31 4.31 0.00 3.91
61 62 1.811359 ACGTACTATAGCCTCGATGCC 59.189 52.381 9.21 0.00 0.00 4.40
62 63 2.085320 CGTACTATAGCCTCGATGCCT 58.915 52.381 9.21 0.03 0.00 4.75
63 64 2.488545 CGTACTATAGCCTCGATGCCTT 59.511 50.000 9.21 0.00 0.00 4.35
64 65 3.670895 CGTACTATAGCCTCGATGCCTTG 60.671 52.174 9.21 1.54 0.00 3.61
65 66 1.001406 ACTATAGCCTCGATGCCTTGC 59.999 52.381 9.21 0.00 0.00 4.01
66 67 1.274728 CTATAGCCTCGATGCCTTGCT 59.725 52.381 9.21 2.49 36.11 3.91
67 68 0.250209 ATAGCCTCGATGCCTTGCTG 60.250 55.000 9.21 0.00 33.63 4.41
68 69 1.329913 TAGCCTCGATGCCTTGCTGA 61.330 55.000 9.21 0.00 33.63 4.26
69 70 1.525535 GCCTCGATGCCTTGCTGAT 60.526 57.895 0.58 0.00 0.00 2.90
70 71 0.250038 GCCTCGATGCCTTGCTGATA 60.250 55.000 0.58 0.00 0.00 2.15
71 72 1.811558 GCCTCGATGCCTTGCTGATAA 60.812 52.381 0.58 0.00 0.00 1.75
72 73 2.564771 CCTCGATGCCTTGCTGATAAA 58.435 47.619 0.00 0.00 0.00 1.40
73 74 2.945008 CCTCGATGCCTTGCTGATAAAA 59.055 45.455 0.00 0.00 0.00 1.52
74 75 3.378112 CCTCGATGCCTTGCTGATAAAAA 59.622 43.478 0.00 0.00 0.00 1.94
102 103 3.555917 AACGTACTATAGCCTCGATGC 57.444 47.619 4.31 4.31 0.00 3.91
103 104 1.811359 ACGTACTATAGCCTCGATGCC 59.189 52.381 9.21 0.00 0.00 4.40
104 105 1.132643 CGTACTATAGCCTCGATGCCC 59.867 57.143 9.21 0.00 0.00 5.36
105 106 2.168496 GTACTATAGCCTCGATGCCCA 58.832 52.381 9.21 0.00 0.00 5.36
106 107 1.261480 ACTATAGCCTCGATGCCCAG 58.739 55.000 9.21 6.65 0.00 4.45
107 108 1.203063 ACTATAGCCTCGATGCCCAGA 60.203 52.381 9.21 0.00 0.00 3.86
108 109 1.895798 CTATAGCCTCGATGCCCAGAA 59.104 52.381 9.21 0.00 0.00 3.02
109 110 1.131638 ATAGCCTCGATGCCCAGAAA 58.868 50.000 9.21 0.00 0.00 2.52
110 111 0.908910 TAGCCTCGATGCCCAGAAAA 59.091 50.000 9.21 0.00 0.00 2.29
111 112 0.257039 AGCCTCGATGCCCAGAAAAT 59.743 50.000 9.21 0.00 0.00 1.82
112 113 0.383231 GCCTCGATGCCCAGAAAATG 59.617 55.000 0.58 0.00 0.00 2.32
113 114 1.755179 CCTCGATGCCCAGAAAATGT 58.245 50.000 0.00 0.00 0.00 2.71
114 115 1.672881 CCTCGATGCCCAGAAAATGTC 59.327 52.381 0.00 0.00 0.00 3.06
115 116 2.358957 CTCGATGCCCAGAAAATGTCA 58.641 47.619 0.00 0.00 0.00 3.58
116 117 2.353889 CTCGATGCCCAGAAAATGTCAG 59.646 50.000 0.00 0.00 0.00 3.51
117 118 1.402968 CGATGCCCAGAAAATGTCAGG 59.597 52.381 0.00 0.00 32.62 3.86
118 119 2.726821 GATGCCCAGAAAATGTCAGGA 58.273 47.619 0.00 0.00 34.81 3.86
119 120 2.673775 TGCCCAGAAAATGTCAGGAA 57.326 45.000 0.00 0.00 34.81 3.36
120 121 3.173953 TGCCCAGAAAATGTCAGGAAT 57.826 42.857 0.00 0.00 34.81 3.01
121 122 3.091545 TGCCCAGAAAATGTCAGGAATC 58.908 45.455 0.00 0.00 34.81 2.52
122 123 3.245371 TGCCCAGAAAATGTCAGGAATCT 60.245 43.478 0.00 0.00 34.81 2.40
123 124 3.379688 GCCCAGAAAATGTCAGGAATCTC 59.620 47.826 0.00 0.00 34.81 2.75
124 125 3.624861 CCCAGAAAATGTCAGGAATCTCG 59.375 47.826 0.00 0.00 34.81 4.04
125 126 4.507710 CCAGAAAATGTCAGGAATCTCGA 58.492 43.478 0.00 0.00 34.81 4.04
129 130 1.418334 ATGTCAGGAATCTCGAGGGG 58.582 55.000 13.56 0.00 0.00 4.79
130 131 1.330655 TGTCAGGAATCTCGAGGGGC 61.331 60.000 13.56 1.64 0.00 5.80
134 135 2.501610 GAATCTCGAGGGGCGCTT 59.498 61.111 13.56 0.00 40.61 4.68
148 149 0.721718 GCGCTTCTCGTTGCTACAAT 59.278 50.000 0.00 0.00 41.07 2.71
149 150 1.527793 GCGCTTCTCGTTGCTACAATG 60.528 52.381 0.00 0.00 41.07 2.82
150 151 1.061131 CGCTTCTCGTTGCTACAATGG 59.939 52.381 0.00 0.00 0.00 3.16
152 153 2.094417 GCTTCTCGTTGCTACAATGGAC 59.906 50.000 0.00 0.00 0.00 4.02
154 155 3.610040 TCTCGTTGCTACAATGGACAT 57.390 42.857 0.00 0.00 0.00 3.06
159 160 5.610398 TCGTTGCTACAATGGACATATGAT 58.390 37.500 10.38 0.00 0.00 2.45
162 163 7.877612 TCGTTGCTACAATGGACATATGATAAT 59.122 33.333 10.38 0.00 0.00 1.28
163 164 7.959109 CGTTGCTACAATGGACATATGATAATG 59.041 37.037 10.38 4.46 0.00 1.90
164 165 8.786898 GTTGCTACAATGGACATATGATAATGT 58.213 33.333 10.38 9.82 42.75 2.71
165 166 8.922931 TGCTACAATGGACATATGATAATGTT 57.077 30.769 10.38 0.00 40.17 2.71
169 170 8.985315 ACAATGGACATATGATAATGTTGTCT 57.015 30.769 10.38 0.00 40.17 3.41
186 187 4.840005 TTGTGTCGTGGCGTGGCA 62.840 61.111 0.00 0.00 0.00 4.92
213 214 2.479901 GCTCGCCTGGTACTTAGAAGTC 60.480 54.545 0.00 0.00 40.37 3.01
218 219 1.136500 CTGGTACTTAGAAGTCGGGGC 59.864 57.143 0.00 0.00 40.37 5.80
220 221 1.482954 GTACTTAGAAGTCGGGGCCT 58.517 55.000 0.84 0.00 40.37 5.19
224 225 0.543410 TTAGAAGTCGGGGCCTCACA 60.543 55.000 1.96 0.00 0.00 3.58
228 229 0.822121 AAGTCGGGGCCTCACAAAAC 60.822 55.000 1.96 0.00 0.00 2.43
236 237 3.442625 GGGGCCTCACAAAACTATTACAC 59.557 47.826 0.84 0.00 0.00 2.90
244 245 7.876068 CCTCACAAAACTATTACACCTTAGACA 59.124 37.037 0.00 0.00 0.00 3.41
250 251 6.791867 ACTATTACACCTTAGACATGAGCA 57.208 37.500 0.00 0.00 0.00 4.26
255 256 1.899814 ACCTTAGACATGAGCACCGAA 59.100 47.619 0.00 0.00 0.00 4.30
292 293 0.178987 GACGGAGATCTCAGGCCCTA 60.179 60.000 24.07 0.00 0.00 3.53
301 302 0.179062 CTCAGGCCCTATGCACAGAC 60.179 60.000 0.00 0.00 43.89 3.51
307 308 0.107066 CCCTATGCACAGACATGCCA 60.107 55.000 0.00 0.00 45.50 4.92
309 310 1.402968 CCTATGCACAGACATGCCAAC 59.597 52.381 0.00 0.00 45.50 3.77
312 313 1.330234 TGCACAGACATGCCAACAAT 58.670 45.000 0.00 0.00 45.50 2.71
324 325 2.298411 CCAACAATGGTAGCATTGCC 57.702 50.000 35.76 2.72 44.10 4.52
624 625 3.966979 TCATTAAGCCAAATCTCAGCCA 58.033 40.909 0.00 0.00 0.00 4.75
626 627 4.957954 TCATTAAGCCAAATCTCAGCCAAT 59.042 37.500 0.00 0.00 0.00 3.16
627 628 4.989279 TTAAGCCAAATCTCAGCCAATC 57.011 40.909 0.00 0.00 0.00 2.67
628 629 2.519771 AGCCAAATCTCAGCCAATCA 57.480 45.000 0.00 0.00 0.00 2.57
629 630 2.811410 AGCCAAATCTCAGCCAATCAA 58.189 42.857 0.00 0.00 0.00 2.57
630 631 3.371965 AGCCAAATCTCAGCCAATCAAT 58.628 40.909 0.00 0.00 0.00 2.57
633 634 3.132289 CCAAATCTCAGCCAATCAATGCT 59.868 43.478 0.00 0.00 38.67 3.79
634 635 4.340097 CCAAATCTCAGCCAATCAATGCTA 59.660 41.667 0.00 0.00 35.69 3.49
635 636 5.163488 CCAAATCTCAGCCAATCAATGCTAA 60.163 40.000 0.00 0.00 35.69 3.09
636 637 5.511234 AATCTCAGCCAATCAATGCTAAC 57.489 39.130 0.00 0.00 35.69 2.34
637 638 3.282021 TCTCAGCCAATCAATGCTAACC 58.718 45.455 0.00 0.00 35.69 2.85
638 639 3.018856 CTCAGCCAATCAATGCTAACCA 58.981 45.455 0.00 0.00 35.69 3.67
651 1385 1.799544 CTAACCAGCCCGTTAAACGT 58.200 50.000 0.00 0.00 40.58 3.99
652 1386 1.728425 CTAACCAGCCCGTTAAACGTC 59.272 52.381 0.00 0.00 40.58 4.34
653 1387 0.886043 AACCAGCCCGTTAAACGTCC 60.886 55.000 0.00 0.00 40.58 4.79
660 1394 2.131183 CCCGTTAAACGTCCGTAAACA 58.869 47.619 14.39 0.00 40.58 2.83
662 1396 2.794350 CCGTTAAACGTCCGTAAACAGT 59.206 45.455 14.39 0.00 40.58 3.55
665 1399 1.490621 AAACGTCCGTAAACAGTCCG 58.509 50.000 0.00 0.00 0.00 4.79
666 1400 0.385390 AACGTCCGTAAACAGTCCGT 59.615 50.000 0.00 0.00 0.00 4.69
667 1401 1.234821 ACGTCCGTAAACAGTCCGTA 58.765 50.000 0.00 0.00 0.00 4.02
695 1860 5.975693 TGACCAATCAAATTAACCCACTC 57.024 39.130 0.00 0.00 0.00 3.51
711 1876 4.352893 ACCCACTCTGTAAAACCCTGTAAT 59.647 41.667 0.00 0.00 0.00 1.89
715 1880 7.094506 CCCACTCTGTAAAACCCTGTAATTTAC 60.095 40.741 0.00 0.00 39.06 2.01
848 3203 4.084287 ACGAGTCCATGGTAGAAAGTACA 58.916 43.478 12.58 0.00 0.00 2.90
849 3204 4.158025 ACGAGTCCATGGTAGAAAGTACAG 59.842 45.833 12.58 1.29 0.00 2.74
850 3205 4.434520 GAGTCCATGGTAGAAAGTACAGC 58.565 47.826 12.58 0.00 0.00 4.40
903 3278 5.923204 ACTCCAGATCCAATAACATCTGAC 58.077 41.667 9.96 0.00 46.23 3.51
909 3284 5.536538 AGATCCAATAACATCTGACGCTAGA 59.463 40.000 0.00 0.00 0.00 2.43
921 3298 6.502136 TCTGACGCTAGATATGTATTCTGG 57.498 41.667 0.00 0.00 0.00 3.86
1016 3421 1.405821 GAAGATGGACGAGATCACGGT 59.594 52.381 16.88 2.70 37.61 4.83
1021 3426 1.141881 GACGAGATCACGGTGGCAT 59.858 57.895 16.88 0.00 37.61 4.40
1060 3465 1.376942 GTCGTCCTCGAGGTCCTCA 60.377 63.158 30.17 8.66 46.96 3.86
1131 3536 2.441348 TGGCGAGGGCTCATCGTA 60.441 61.111 10.15 0.00 42.13 3.43
1132 3537 2.336809 GGCGAGGGCTCATCGTAG 59.663 66.667 10.15 0.00 42.13 3.51
1180 3585 2.483745 CGAGCGCGTCCTACTTCA 59.516 61.111 8.43 0.00 0.00 3.02
1215 3620 4.373116 GAGCGACGGTGCCAAGGA 62.373 66.667 3.31 0.00 34.65 3.36
1221 3626 0.321653 GACGGTGCCAAGGAGAACAT 60.322 55.000 0.00 0.00 0.00 2.71
1261 3666 4.951963 GCTCCCCGCCGATCTTCG 62.952 72.222 0.00 0.00 40.07 3.79
1271 3676 2.202892 GATCTTCGTCCCGGTGCC 60.203 66.667 0.00 0.00 0.00 5.01
1404 3809 4.162690 CTGGTACGCCTCAGCCCC 62.163 72.222 0.00 0.00 34.57 5.80
1496 3901 3.302347 CTCCACTGGACAGCGGGTC 62.302 68.421 6.54 3.28 46.20 4.46
1575 3980 3.106986 ATCGCCTGCGCCCAACTAT 62.107 57.895 4.18 0.00 39.59 2.12
1686 4630 0.383590 CATCATCGTCGAGCTGGAGT 59.616 55.000 0.00 0.00 0.00 3.85
1776 4721 1.381928 ATAGCATCGTCGTGGACCGT 61.382 55.000 0.00 0.00 37.94 4.83
1852 4797 1.143684 ACACTGTTGACATGAAGGGCT 59.856 47.619 0.00 0.00 0.00 5.19
1954 4899 3.084278 CGCTCGCTCTTTTTAATGTTCG 58.916 45.455 0.00 0.00 0.00 3.95
2007 4952 3.587797 TTTAGAGGTGACGATGGACAC 57.412 47.619 1.91 1.91 37.97 3.67
2088 5033 2.022764 TTGATGACGTGCTATGGGTG 57.977 50.000 0.00 0.00 0.00 4.61
2093 5038 0.321298 GACGTGCTATGGGTGTGGTT 60.321 55.000 0.00 0.00 0.00 3.67
2259 5204 2.102588 GGCTTTATTCAGGACTCGGCTA 59.897 50.000 0.00 0.00 0.00 3.93
2274 5219 2.557056 TCGGCTAGGTAGACACATATGC 59.443 50.000 1.58 0.00 0.00 3.14
2282 5227 8.358148 GCTAGGTAGACACATATGCTAAACTTA 58.642 37.037 1.58 0.00 0.00 2.24
2361 5316 5.593679 TTAGAGAAGAATTAGGACCACCG 57.406 43.478 0.00 0.00 41.83 4.94
2518 5473 4.271533 CCGTATTTATGCAACGCCTTTCTA 59.728 41.667 2.35 0.00 35.36 2.10
2574 5529 0.462937 TTATGGCCACATTACGCGCT 60.463 50.000 8.16 0.00 38.53 5.92
2624 5579 4.574892 TGAAGTTCTGTCATATTTCGCCA 58.425 39.130 4.17 0.00 0.00 5.69
2887 5842 0.321298 GGGAAAGTTGTAGCTCGCCA 60.321 55.000 0.00 0.00 0.00 5.69
2922 5877 5.120399 CGTTTATAAGATAGGCAACCACCA 58.880 41.667 0.00 0.00 37.17 4.17
2933 5893 1.699930 AACCACCAAGACCACCCCT 60.700 57.895 0.00 0.00 0.00 4.79
3075 6037 4.065281 CCGAACCGGGAGCTTCGT 62.065 66.667 19.67 0.00 44.15 3.85
3086 6048 4.505217 GCTTCGTCGCGCACCATG 62.505 66.667 8.75 0.00 0.00 3.66
3110 6073 4.101790 CCGCCGTTGTGCCATCAC 62.102 66.667 0.00 0.00 43.40 3.06
3182 6145 2.271800 CCTAAAGTGCTTCGCGAAGAT 58.728 47.619 43.98 28.53 40.79 2.40
3183 6146 2.029728 CCTAAAGTGCTTCGCGAAGATG 59.970 50.000 43.98 24.89 40.79 2.90
3184 6147 0.166814 AAAGTGCTTCGCGAAGATGC 59.833 50.000 43.98 32.27 46.58 3.91
3185 6148 1.639298 AAGTGCTTCGCGAAGATGCC 61.639 55.000 43.98 29.05 46.05 4.40
3186 6149 2.047370 TGCTTCGCGAAGATGCCA 60.047 55.556 43.98 31.02 46.05 4.92
3187 6150 2.390599 TGCTTCGCGAAGATGCCAC 61.391 57.895 43.98 28.08 46.05 5.01
3188 6151 2.103042 GCTTCGCGAAGATGCCACT 61.103 57.895 43.98 0.00 42.29 4.00
3189 6152 1.712081 CTTCGCGAAGATGCCACTG 59.288 57.895 39.00 13.48 40.79 3.66
3190 6153 1.005037 TTCGCGAAGATGCCACTGT 60.005 52.632 19.38 0.00 0.00 3.55
3191 6154 1.291184 TTCGCGAAGATGCCACTGTG 61.291 55.000 19.38 0.00 0.00 3.66
3192 6155 2.743752 CGCGAAGATGCCACTGTGG 61.744 63.158 22.46 22.46 41.55 4.17
3247 6210 5.505181 ACTGTTGTATTGATCTGACCCTT 57.495 39.130 0.00 0.00 0.00 3.95
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
37 38 4.743644 GCATCGAGGCTATAGTACGTTTTT 59.256 41.667 16.00 0.00 0.00 1.94
38 39 4.296690 GCATCGAGGCTATAGTACGTTTT 58.703 43.478 16.00 0.00 0.00 2.43
39 40 3.305199 GGCATCGAGGCTATAGTACGTTT 60.305 47.826 22.57 0.00 40.24 3.60
40 41 2.228343 GGCATCGAGGCTATAGTACGTT 59.772 50.000 22.57 0.00 40.24 3.99
41 42 1.811359 GGCATCGAGGCTATAGTACGT 59.189 52.381 22.57 0.00 40.24 3.57
42 43 2.546195 GGCATCGAGGCTATAGTACG 57.454 55.000 22.57 5.47 40.24 3.67
51 52 0.250038 TATCAGCAAGGCATCGAGGC 60.250 55.000 14.84 14.84 44.61 4.70
52 53 2.245159 TTATCAGCAAGGCATCGAGG 57.755 50.000 0.00 0.00 0.00 4.63
53 54 4.621068 TTTTTATCAGCAAGGCATCGAG 57.379 40.909 0.00 0.00 0.00 4.04
79 80 4.743644 GCATCGAGGCTATAGTACGTTTTT 59.256 41.667 16.00 0.00 0.00 1.94
80 81 4.296690 GCATCGAGGCTATAGTACGTTTT 58.703 43.478 16.00 0.00 0.00 2.43
81 82 3.305199 GGCATCGAGGCTATAGTACGTTT 60.305 47.826 22.57 0.00 40.24 3.60
82 83 2.228343 GGCATCGAGGCTATAGTACGTT 59.772 50.000 22.57 0.00 40.24 3.99
83 84 1.811359 GGCATCGAGGCTATAGTACGT 59.189 52.381 22.57 0.00 40.24 3.57
84 85 1.132643 GGGCATCGAGGCTATAGTACG 59.867 57.143 22.57 5.47 43.56 3.67
85 86 2.164624 CTGGGCATCGAGGCTATAGTAC 59.835 54.545 22.57 2.67 43.56 2.73
86 87 2.041216 TCTGGGCATCGAGGCTATAGTA 59.959 50.000 22.57 0.21 43.56 1.82
87 88 1.203063 TCTGGGCATCGAGGCTATAGT 60.203 52.381 22.57 0.00 43.56 2.12
88 89 1.550327 TCTGGGCATCGAGGCTATAG 58.450 55.000 22.57 16.45 43.56 1.31
89 90 2.009681 TTCTGGGCATCGAGGCTATA 57.990 50.000 22.57 7.58 43.56 1.31
90 91 1.131638 TTTCTGGGCATCGAGGCTAT 58.868 50.000 22.57 0.00 43.56 2.97
91 92 0.908910 TTTTCTGGGCATCGAGGCTA 59.091 50.000 22.57 10.48 43.56 3.93
92 93 0.257039 ATTTTCTGGGCATCGAGGCT 59.743 50.000 22.57 0.00 43.56 4.58
93 94 0.383231 CATTTTCTGGGCATCGAGGC 59.617 55.000 14.84 14.84 43.27 4.70
94 95 1.672881 GACATTTTCTGGGCATCGAGG 59.327 52.381 0.00 0.00 0.00 4.63
95 96 2.353889 CTGACATTTTCTGGGCATCGAG 59.646 50.000 0.00 0.00 0.00 4.04
96 97 2.358957 CTGACATTTTCTGGGCATCGA 58.641 47.619 0.00 0.00 0.00 3.59
97 98 1.402968 CCTGACATTTTCTGGGCATCG 59.597 52.381 0.00 0.00 39.23 3.84
98 99 2.726821 TCCTGACATTTTCTGGGCATC 58.273 47.619 0.00 0.00 42.43 3.91
99 100 2.905415 TCCTGACATTTTCTGGGCAT 57.095 45.000 0.00 0.00 42.43 4.40
100 101 2.673775 TTCCTGACATTTTCTGGGCA 57.326 45.000 0.00 0.00 42.43 5.36
101 102 3.359950 AGATTCCTGACATTTTCTGGGC 58.640 45.455 0.00 0.00 42.43 5.36
102 103 3.624861 CGAGATTCCTGACATTTTCTGGG 59.375 47.826 0.00 0.00 42.43 4.45
103 104 4.507710 TCGAGATTCCTGACATTTTCTGG 58.492 43.478 0.00 0.00 43.32 3.86
104 105 4.569966 CCTCGAGATTCCTGACATTTTCTG 59.430 45.833 15.71 0.00 0.00 3.02
105 106 4.383552 CCCTCGAGATTCCTGACATTTTCT 60.384 45.833 15.71 0.00 0.00 2.52
106 107 3.873952 CCCTCGAGATTCCTGACATTTTC 59.126 47.826 15.71 0.00 0.00 2.29
107 108 3.370953 CCCCTCGAGATTCCTGACATTTT 60.371 47.826 15.71 0.00 0.00 1.82
108 109 2.171448 CCCCTCGAGATTCCTGACATTT 59.829 50.000 15.71 0.00 0.00 2.32
109 110 1.765314 CCCCTCGAGATTCCTGACATT 59.235 52.381 15.71 0.00 0.00 2.71
110 111 1.418334 CCCCTCGAGATTCCTGACAT 58.582 55.000 15.71 0.00 0.00 3.06
111 112 1.330655 GCCCCTCGAGATTCCTGACA 61.331 60.000 15.71 0.00 0.00 3.58
112 113 1.443828 GCCCCTCGAGATTCCTGAC 59.556 63.158 15.71 0.00 0.00 3.51
113 114 2.127869 CGCCCCTCGAGATTCCTGA 61.128 63.158 15.71 0.00 41.67 3.86
114 115 2.419198 CGCCCCTCGAGATTCCTG 59.581 66.667 15.71 0.00 41.67 3.86
115 116 3.541713 GCGCCCCTCGAGATTCCT 61.542 66.667 15.71 0.00 41.67 3.36
116 117 2.980213 GAAGCGCCCCTCGAGATTCC 62.980 65.000 15.71 0.00 41.67 3.01
117 118 1.592939 GAAGCGCCCCTCGAGATTC 60.593 63.158 15.71 0.00 41.67 2.52
118 119 2.022240 GAGAAGCGCCCCTCGAGATT 62.022 60.000 15.71 0.00 41.67 2.40
119 120 2.443016 AGAAGCGCCCCTCGAGAT 60.443 61.111 15.71 0.00 41.67 2.75
120 121 3.141488 GAGAAGCGCCCCTCGAGA 61.141 66.667 15.71 0.00 41.67 4.04
124 125 2.815647 CAACGAGAAGCGCCCCTC 60.816 66.667 2.29 10.34 46.04 4.30
129 130 0.721718 ATTGTAGCAACGAGAAGCGC 59.278 50.000 0.00 0.00 46.04 5.92
134 135 3.610040 ATGTCCATTGTAGCAACGAGA 57.390 42.857 0.00 0.00 0.00 4.04
139 140 8.922931 ACATTATCATATGTCCATTGTAGCAA 57.077 30.769 1.90 0.00 33.58 3.91
148 149 7.828717 ACACAAGACAACATTATCATATGTCCA 59.171 33.333 1.90 0.00 40.92 4.02
149 150 8.213518 ACACAAGACAACATTATCATATGTCC 57.786 34.615 1.90 0.00 40.92 4.02
150 151 8.058328 CGACACAAGACAACATTATCATATGTC 58.942 37.037 1.90 0.00 37.76 3.06
152 153 7.847564 CACGACACAAGACAACATTATCATATG 59.152 37.037 0.00 0.00 0.00 1.78
154 155 6.312672 CCACGACACAAGACAACATTATCATA 59.687 38.462 0.00 0.00 0.00 2.15
159 160 2.546368 GCCACGACACAAGACAACATTA 59.454 45.455 0.00 0.00 0.00 1.90
162 163 1.425267 CGCCACGACACAAGACAACA 61.425 55.000 0.00 0.00 0.00 3.33
163 164 1.275657 CGCCACGACACAAGACAAC 59.724 57.895 0.00 0.00 0.00 3.32
164 165 1.153529 ACGCCACGACACAAGACAA 60.154 52.632 0.00 0.00 0.00 3.18
165 166 1.880796 CACGCCACGACACAAGACA 60.881 57.895 0.00 0.00 0.00 3.41
169 170 4.840005 TGCCACGCCACGACACAA 62.840 61.111 0.00 0.00 0.00 3.33
190 191 1.065928 CTAAGTACCAGGCGAGCCG 59.934 63.158 8.63 3.89 41.95 5.52
213 214 1.834188 AATAGTTTTGTGAGGCCCCG 58.166 50.000 0.00 0.00 0.00 5.73
218 219 7.876068 TGTCTAAGGTGTAATAGTTTTGTGAGG 59.124 37.037 0.00 0.00 0.00 3.86
220 221 9.214957 CATGTCTAAGGTGTAATAGTTTTGTGA 57.785 33.333 0.00 0.00 0.00 3.58
224 225 8.100791 TGCTCATGTCTAAGGTGTAATAGTTTT 58.899 33.333 0.00 0.00 0.00 2.43
228 229 5.986135 GGTGCTCATGTCTAAGGTGTAATAG 59.014 44.000 0.00 0.00 0.00 1.73
236 237 2.672961 TTCGGTGCTCATGTCTAAGG 57.327 50.000 0.00 0.00 0.00 2.69
244 245 0.537188 AGATCGGTTTCGGTGCTCAT 59.463 50.000 0.00 0.00 36.95 2.90
250 251 1.067071 GGAGACAAGATCGGTTTCGGT 60.067 52.381 5.46 0.00 36.95 4.69
255 256 3.320673 GTCAAGGAGACAAGATCGGTT 57.679 47.619 0.00 0.00 46.77 4.44
285 286 0.182061 CATGTCTGTGCATAGGGCCT 59.818 55.000 12.58 12.58 43.89 5.19
292 293 1.330234 TTGTTGGCATGTCTGTGCAT 58.670 45.000 0.00 0.00 46.81 3.96
604 605 4.724074 TTGGCTGAGATTTGGCTTAATG 57.276 40.909 0.00 0.00 0.00 1.90
605 606 4.957954 TGATTGGCTGAGATTTGGCTTAAT 59.042 37.500 0.00 0.00 0.00 1.40
606 607 4.343231 TGATTGGCTGAGATTTGGCTTAA 58.657 39.130 0.00 0.00 0.00 1.85
607 608 3.966979 TGATTGGCTGAGATTTGGCTTA 58.033 40.909 0.00 0.00 0.00 3.09
608 609 2.811410 TGATTGGCTGAGATTTGGCTT 58.189 42.857 0.00 0.00 0.00 4.35
609 610 2.519771 TGATTGGCTGAGATTTGGCT 57.480 45.000 0.00 0.00 0.00 4.75
610 611 3.454375 CATTGATTGGCTGAGATTTGGC 58.546 45.455 0.00 0.00 0.00 4.52
611 612 3.132289 AGCATTGATTGGCTGAGATTTGG 59.868 43.478 0.00 0.00 39.30 3.28
612 613 4.386867 AGCATTGATTGGCTGAGATTTG 57.613 40.909 0.00 0.00 39.30 2.32
613 614 5.163478 GGTTAGCATTGATTGGCTGAGATTT 60.163 40.000 0.00 0.00 41.25 2.17
614 615 4.340381 GGTTAGCATTGATTGGCTGAGATT 59.660 41.667 0.00 0.00 41.25 2.40
615 616 3.887716 GGTTAGCATTGATTGGCTGAGAT 59.112 43.478 0.00 0.00 41.25 2.75
616 617 3.282021 GGTTAGCATTGATTGGCTGAGA 58.718 45.455 0.00 0.00 41.25 3.27
617 618 3.018856 TGGTTAGCATTGATTGGCTGAG 58.981 45.455 0.00 0.00 41.25 3.35
619 620 3.431922 CTGGTTAGCATTGATTGGCTG 57.568 47.619 0.00 0.00 41.25 4.85
627 628 6.944068 CGTTTAACGGGCTGGTTAGCATTG 62.944 50.000 9.88 0.00 42.91 2.82
628 629 4.968303 CGTTTAACGGGCTGGTTAGCATT 61.968 47.826 9.88 0.00 42.91 3.56
629 630 3.510317 CGTTTAACGGGCTGGTTAGCAT 61.510 50.000 9.88 0.00 42.91 3.79
630 631 2.208227 CGTTTAACGGGCTGGTTAGCA 61.208 52.381 9.88 0.00 42.91 3.49
643 1377 3.121362 CGGACTGTTTACGGACGTTTAAC 60.121 47.826 1.57 8.81 0.00 2.01
651 1385 5.589855 TCAATAGATACGGACTGTTTACGGA 59.410 40.000 0.00 0.00 0.00 4.69
652 1386 5.684626 GTCAATAGATACGGACTGTTTACGG 59.315 44.000 0.00 0.00 0.00 4.02
653 1387 5.684626 GGTCAATAGATACGGACTGTTTACG 59.315 44.000 0.00 0.00 0.00 3.18
660 1394 6.479972 TTGATTGGTCAATAGATACGGACT 57.520 37.500 0.00 0.00 39.36 3.85
662 1396 9.839817 TTAATTTGATTGGTCAATAGATACGGA 57.160 29.630 0.00 0.00 43.49 4.69
666 1400 9.928618 TGGGTTAATTTGATTGGTCAATAGATA 57.071 29.630 0.00 0.00 43.49 1.98
667 1401 8.695456 GTGGGTTAATTTGATTGGTCAATAGAT 58.305 33.333 0.00 0.00 43.49 1.98
690 1855 6.894339 AAATTACAGGGTTTTACAGAGTGG 57.106 37.500 0.00 0.00 0.00 4.00
711 1876 8.192774 AGCAGTAATGCTACACGTATAAGTAAA 58.807 33.333 17.43 0.00 44.28 2.01
715 1880 7.464830 AAAGCAGTAATGCTACACGTATAAG 57.535 36.000 19.32 0.00 45.54 1.73
745 3100 5.288712 CCAAAGTACAGTACATCACATCGAC 59.711 44.000 13.37 0.00 0.00 4.20
748 3103 8.542497 TTAACCAAAGTACAGTACATCACATC 57.458 34.615 13.37 0.00 0.00 3.06
749 3104 9.515226 AATTAACCAAAGTACAGTACATCACAT 57.485 29.630 13.37 0.00 0.00 3.21
789 3144 3.952323 TCGGTTCAAACTCGGATCTATCT 59.048 43.478 0.00 0.00 0.00 1.98
804 3159 4.098044 GTCTTGAGAGTCCATATCGGTTCA 59.902 45.833 0.00 0.00 35.57 3.18
836 3191 5.761165 TTTGGTTTGCTGTACTTTCTACC 57.239 39.130 0.00 0.00 0.00 3.18
848 3203 4.864704 ATTATCCACGTTTTGGTTTGCT 57.135 36.364 0.00 0.00 46.97 3.91
849 3204 6.864165 TCTTAATTATCCACGTTTTGGTTTGC 59.136 34.615 0.00 0.00 46.97 3.68
850 3205 7.327518 GGTCTTAATTATCCACGTTTTGGTTTG 59.672 37.037 0.00 0.00 46.97 2.93
875 3230 5.102953 TGTTATTGGATCTGGAGTTCTGG 57.897 43.478 0.00 0.00 0.00 3.86
903 3278 5.689514 GCATAGCCAGAATACATATCTAGCG 59.310 44.000 0.00 0.00 36.77 4.26
1131 3536 2.362632 CGGAGGAAGGACCGGTCT 60.363 66.667 32.52 15.67 44.59 3.85
1180 3585 0.532573 TCTCGAGCAAAGAATCCGCT 59.467 50.000 7.81 0.00 39.12 5.52
1203 3608 0.606401 CATGTTCTCCTTGGCACCGT 60.606 55.000 0.00 0.00 0.00 4.83
1303 3708 2.544844 AGAAACGAGGTGAGGGGATA 57.455 50.000 0.00 0.00 0.00 2.59
1371 3776 2.282958 AGGAGGAGACCGTTGCGA 60.283 61.111 0.00 0.00 34.73 5.10
1507 3912 2.035576 CGGTTAGGATGGTGTAGCCTAC 59.964 54.545 0.00 0.00 46.70 3.18
1518 3923 0.460311 AGTCTTCGCCGGTTAGGATG 59.540 55.000 1.90 0.00 45.00 3.51
1686 4630 3.745332 TCGTCAAACTCTATACGCGAA 57.255 42.857 15.93 0.00 35.40 4.70
1776 4721 3.234630 GAGGTAGTGTGCCACGCCA 62.235 63.158 4.46 0.00 39.64 5.69
1893 4838 0.389948 GAAGATGAGTGTCGGCGGTT 60.390 55.000 7.21 0.00 0.00 4.44
2007 4952 6.090898 CCTTGTAAATCCAGTCTAAGTTGTCG 59.909 42.308 0.00 0.00 0.00 4.35
2088 5033 1.981256 TGCTCTTTTCTCCCAACCAC 58.019 50.000 0.00 0.00 0.00 4.16
2093 5038 1.494721 AGGTGTTGCTCTTTTCTCCCA 59.505 47.619 0.00 0.00 0.00 4.37
2259 5204 9.953565 TTTTAAGTTTAGCATATGTGTCTACCT 57.046 29.630 4.29 0.00 0.00 3.08
2322 5268 9.537192 TCTTCTCTAAAAGTTTCAATTCGTACA 57.463 29.630 0.00 0.00 0.00 2.90
2445 5400 8.646900 TCATATAGCTATATGTTTGGTCACACA 58.353 33.333 36.04 19.82 43.68 3.72
2574 5529 1.669760 GCGGTGGACGATTCAACCA 60.670 57.895 0.90 0.00 45.59 3.67
2887 5842 7.707035 CCTATCTTATAAACGTGTCAGAAAGCT 59.293 37.037 0.00 0.00 0.00 3.74
2894 5849 5.813672 GGTTGCCTATCTTATAAACGTGTCA 59.186 40.000 0.00 0.00 0.00 3.58
2922 5877 1.229400 TTAGGCGAGGGGTGGTCTT 60.229 57.895 0.00 0.00 0.00 3.01
2933 5893 3.194755 TGTAGCATTCTTGACTTAGGCGA 59.805 43.478 0.00 0.00 0.00 5.54
3014 5975 5.511031 CGACATCCTCATGAAGATTCTGGAT 60.511 44.000 3.96 4.49 33.72 3.41
3182 6145 4.853468 TCCTATAAATTCCACAGTGGCA 57.147 40.909 15.64 4.10 37.47 4.92
3183 6146 5.376625 TCATCCTATAAATTCCACAGTGGC 58.623 41.667 15.64 0.00 37.47 5.01
3184 6147 7.720957 TCAATCATCCTATAAATTCCACAGTGG 59.279 37.037 14.19 14.19 39.43 4.00
3185 6148 8.681486 TCAATCATCCTATAAATTCCACAGTG 57.319 34.615 0.00 0.00 0.00 3.66
3186 6149 9.872684 ATTCAATCATCCTATAAATTCCACAGT 57.127 29.630 0.00 0.00 0.00 3.55
3225 6188 5.221925 ACAAGGGTCAGATCAATACAACAGT 60.222 40.000 0.00 0.00 0.00 3.55
3226 6189 5.248640 ACAAGGGTCAGATCAATACAACAG 58.751 41.667 0.00 0.00 0.00 3.16


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

AutoCloner maintained by Alex Coulton.