Multiple sequence alignment - TraesCS5D01G413900

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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 TraesCS5D01G413900 chr5D 100.000 2845 0 0 1 2845 476695770 476698614 0.000000e+00 5254.0
1 TraesCS5D01G413900 chr5B 89.163 2713 160 66 174 2821 584112887 584115530 0.000000e+00 3258.0
2 TraesCS5D01G413900 chr5A 88.294 1606 102 43 1260 2821 596020075 596021638 0.000000e+00 1845.0
3 TraesCS5D01G413900 chr5A 92.935 1005 44 11 174 1158 596018935 596019932 0.000000e+00 1437.0
4 TraesCS5D01G413900 chr4B 81.061 132 21 4 2315 2444 598915035 598914906 5.010000e-18 102.0
5 TraesCS5D01G413900 chr4B 78.947 133 23 5 2315 2444 598604385 598604255 5.050000e-13 86.1


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 TraesCS5D01G413900 chr5D 476695770 476698614 2844 False 5254 5254 100.0000 1 2845 1 chr5D.!!$F1 2844
1 TraesCS5D01G413900 chr5B 584112887 584115530 2643 False 3258 3258 89.1630 174 2821 1 chr5B.!!$F1 2647
2 TraesCS5D01G413900 chr5A 596018935 596021638 2703 False 1641 1845 90.6145 174 2821 2 chr5A.!!$F1 2647

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
792 831 0.039618 TTTTCATCCTGTCCCCCTGC 59.96 55.0 0.0 0.0 0.0 4.85 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2551 2745 0.323816 AGATGAGCTCGGTGAGGTGA 60.324 55.0 9.64 0.0 40.67 4.02 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
17 18 4.104183 GGGCCGGAAATGGGTCGA 62.104 66.667 5.05 0.00 0.00 4.20
18 19 2.822701 GGCCGGAAATGGGTCGAC 60.823 66.667 5.05 7.13 0.00 4.20
19 20 2.046700 GCCGGAAATGGGTCGACA 60.047 61.111 18.91 0.00 0.00 4.35
20 21 2.106683 GCCGGAAATGGGTCGACAG 61.107 63.158 18.91 0.00 0.00 3.51
21 22 1.449601 CCGGAAATGGGTCGACAGG 60.450 63.158 18.91 3.33 0.00 4.00
22 23 2.106683 CGGAAATGGGTCGACAGGC 61.107 63.158 18.91 0.00 0.00 4.85
23 24 2.106683 GGAAATGGGTCGACAGGCG 61.107 63.158 18.91 0.00 42.69 5.52
33 34 1.154654 CGACAGGCGAACGAAAAGC 60.155 57.895 0.00 0.00 44.57 3.51
34 35 2.796020 CGACAGGCGAACGAAAAGCG 62.796 60.000 0.00 0.00 44.57 4.68
35 36 2.173382 CAGGCGAACGAAAAGCGG 59.827 61.111 0.00 0.00 46.49 5.52
36 37 3.047877 AGGCGAACGAAAAGCGGG 61.048 61.111 0.00 0.00 46.49 6.13
37 38 4.753877 GGCGAACGAAAAGCGGGC 62.754 66.667 0.00 0.00 46.49 6.13
54 55 3.539107 CGCGCGTCCGTTTAGGTC 61.539 66.667 24.19 0.00 41.99 3.85
60 61 2.285154 GTCCGTTTAGGTCGATGCG 58.715 57.895 0.00 0.00 41.99 4.73
61 62 0.457337 GTCCGTTTAGGTCGATGCGT 60.457 55.000 0.00 0.00 41.99 5.24
62 63 0.244450 TCCGTTTAGGTCGATGCGTT 59.756 50.000 0.00 0.00 41.99 4.84
63 64 0.368907 CCGTTTAGGTCGATGCGTTG 59.631 55.000 0.00 0.00 34.51 4.10
64 65 0.368907 CGTTTAGGTCGATGCGTTGG 59.631 55.000 0.00 0.00 0.00 3.77
65 66 0.725117 GTTTAGGTCGATGCGTTGGG 59.275 55.000 0.00 0.00 0.00 4.12
66 67 1.022451 TTTAGGTCGATGCGTTGGGC 61.022 55.000 0.00 0.00 43.96 5.36
67 68 2.862674 TTAGGTCGATGCGTTGGGCC 62.863 60.000 0.00 0.00 42.61 5.80
72 73 2.746277 GATGCGTTGGGCCGACTT 60.746 61.111 21.44 6.47 42.61 3.01
73 74 2.282180 ATGCGTTGGGCCGACTTT 60.282 55.556 21.44 3.48 42.61 2.66
74 75 1.862602 GATGCGTTGGGCCGACTTTT 61.863 55.000 21.44 5.75 42.61 2.27
75 76 1.460273 ATGCGTTGGGCCGACTTTTT 61.460 50.000 21.44 1.34 42.61 1.94
90 91 1.728672 TTTTTGTTGACCGCGACCC 59.271 52.632 8.23 0.00 0.00 4.46
91 92 1.030488 TTTTTGTTGACCGCGACCCA 61.030 50.000 8.23 0.00 0.00 4.51
92 93 1.030488 TTTTGTTGACCGCGACCCAA 61.030 50.000 8.23 5.62 0.00 4.12
93 94 1.030488 TTTGTTGACCGCGACCCAAA 61.030 50.000 8.23 10.25 0.00 3.28
94 95 1.716826 TTGTTGACCGCGACCCAAAC 61.717 55.000 8.23 5.43 0.00 2.93
95 96 2.968156 TTGACCGCGACCCAAACG 60.968 61.111 8.23 0.00 0.00 3.60
107 108 3.990806 CAAACGGACGCGCGTGAA 61.991 61.111 42.90 0.00 0.00 3.18
108 109 3.992019 AAACGGACGCGCGTGAAC 61.992 61.111 42.90 27.36 0.00 3.18
112 113 3.694394 GGACGCGCGTGAACGAAA 61.694 61.111 42.90 0.00 43.02 3.46
113 114 2.468532 GACGCGCGTGAACGAAAT 59.531 55.556 42.90 12.81 43.02 2.17
114 115 1.853192 GACGCGCGTGAACGAAATG 60.853 57.895 42.90 4.22 43.02 2.32
115 116 2.205595 GACGCGCGTGAACGAAATGA 62.206 55.000 42.90 0.00 43.02 2.57
116 117 1.575132 CGCGCGTGAACGAAATGAG 60.575 57.895 24.19 0.00 43.02 2.90
117 118 1.491563 GCGCGTGAACGAAATGAGT 59.508 52.632 8.43 0.00 43.02 3.41
118 119 0.516524 GCGCGTGAACGAAATGAGTC 60.517 55.000 8.43 0.00 43.02 3.36
119 120 0.246374 CGCGTGAACGAAATGAGTCG 60.246 55.000 7.10 0.00 46.54 4.18
120 121 0.093026 GCGTGAACGAAATGAGTCGG 59.907 55.000 7.10 0.00 45.40 4.79
121 122 0.093026 CGTGAACGAAATGAGTCGGC 59.907 55.000 0.00 0.00 45.40 5.54
122 123 1.144969 GTGAACGAAATGAGTCGGCA 58.855 50.000 0.00 0.00 45.40 5.69
123 124 1.732259 GTGAACGAAATGAGTCGGCAT 59.268 47.619 0.00 0.00 45.40 4.40
124 125 2.927477 GTGAACGAAATGAGTCGGCATA 59.073 45.455 0.00 0.00 45.40 3.14
125 126 3.555956 GTGAACGAAATGAGTCGGCATAT 59.444 43.478 0.00 0.00 45.40 1.78
126 127 4.034048 GTGAACGAAATGAGTCGGCATATT 59.966 41.667 0.00 0.00 45.40 1.28
127 128 4.033932 TGAACGAAATGAGTCGGCATATTG 59.966 41.667 0.00 0.00 45.40 1.90
128 129 2.872245 ACGAAATGAGTCGGCATATTGG 59.128 45.455 0.00 0.00 45.40 3.16
129 130 3.130633 CGAAATGAGTCGGCATATTGGA 58.869 45.455 0.00 0.00 37.37 3.53
130 131 3.185188 CGAAATGAGTCGGCATATTGGAG 59.815 47.826 0.00 0.00 37.37 3.86
131 132 3.845781 AATGAGTCGGCATATTGGAGT 57.154 42.857 0.00 0.00 0.00 3.85
132 133 3.845781 ATGAGTCGGCATATTGGAGTT 57.154 42.857 0.00 0.00 0.00 3.01
133 134 2.905075 TGAGTCGGCATATTGGAGTTG 58.095 47.619 0.00 0.00 0.00 3.16
134 135 1.599542 GAGTCGGCATATTGGAGTTGC 59.400 52.381 0.00 0.00 35.64 4.17
135 136 1.210478 AGTCGGCATATTGGAGTTGCT 59.790 47.619 0.00 0.00 36.62 3.91
136 137 1.599542 GTCGGCATATTGGAGTTGCTC 59.400 52.381 0.00 0.00 36.62 4.26
137 138 1.486310 TCGGCATATTGGAGTTGCTCT 59.514 47.619 0.00 0.00 36.62 4.09
138 139 2.698274 TCGGCATATTGGAGTTGCTCTA 59.302 45.455 0.00 0.00 36.62 2.43
139 140 3.133901 TCGGCATATTGGAGTTGCTCTAA 59.866 43.478 0.00 0.00 35.57 2.10
140 141 3.248602 CGGCATATTGGAGTTGCTCTAAC 59.751 47.826 0.00 0.00 34.03 2.34
308 311 4.074970 AGATATTGTCGGATTCCATTGCC 58.925 43.478 3.09 0.00 0.00 4.52
338 343 4.753516 TTCTCCTCTCAACACAACTTGA 57.246 40.909 0.00 0.00 0.00 3.02
406 415 1.080705 CCACCGGAAGACACGAGAC 60.081 63.158 9.46 0.00 0.00 3.36
412 421 1.080705 GAAGACACGAGACCCACCG 60.081 63.158 0.00 0.00 0.00 4.94
413 422 3.222354 AAGACACGAGACCCACCGC 62.222 63.158 0.00 0.00 0.00 5.68
480 497 2.107141 CCCGATCTCGCACCTTCC 59.893 66.667 0.00 0.00 38.18 3.46
568 600 0.318107 AGACGTGTGGTTTACCGACG 60.318 55.000 17.04 17.04 44.94 5.12
572 604 0.877213 GTGTGGTTTACCGACGCTGT 60.877 55.000 0.00 0.00 39.43 4.40
597 629 3.257375 TCACCAATAGTCTACGCAGTGTT 59.743 43.478 0.00 0.00 45.73 3.32
603 635 3.720949 AGTCTACGCAGTGTTGTGTAA 57.279 42.857 0.00 0.00 46.44 2.41
607 639 1.361793 ACGCAGTGTTGTGTAAACGT 58.638 45.000 0.00 0.00 45.76 3.99
719 751 6.209391 GGAGAATCTAGAGGAAGAGGAATCAG 59.791 46.154 0.00 0.00 33.73 2.90
790 829 0.332972 GCTTTTCATCCTGTCCCCCT 59.667 55.000 0.00 0.00 0.00 4.79
791 830 1.957113 GCTTTTCATCCTGTCCCCCTG 60.957 57.143 0.00 0.00 0.00 4.45
792 831 0.039618 TTTTCATCCTGTCCCCCTGC 59.960 55.000 0.00 0.00 0.00 4.85
794 833 2.693864 CATCCTGTCCCCCTGCCT 60.694 66.667 0.00 0.00 0.00 4.75
798 837 1.607467 CCTGTCCCCCTGCCTTTTG 60.607 63.158 0.00 0.00 0.00 2.44
799 838 1.153756 CTGTCCCCCTGCCTTTTGT 59.846 57.895 0.00 0.00 0.00 2.83
857 896 6.514863 TCATCATTCCCTCCATATATCTCCA 58.485 40.000 0.00 0.00 0.00 3.86
886 925 2.024871 CACGATCGAGCCGGAGAC 59.975 66.667 24.34 0.00 0.00 3.36
1110 1153 1.950484 GCCCTCATGTTCATGTCCGTT 60.950 52.381 11.73 0.00 0.00 4.44
1134 1177 2.597520 GTCGAGTTCTTCAGCTACACC 58.402 52.381 0.00 0.00 0.00 4.16
1181 1306 4.342378 CCCTCTCTGATCTTCGGTTTATGA 59.658 45.833 0.00 0.00 0.00 2.15
1193 1318 4.191544 TCGGTTTATGATTCAGCCTTCAG 58.808 43.478 0.00 0.00 0.00 3.02
1218 1343 1.068055 GCAGTGATCAGCAAGTTTGGG 60.068 52.381 0.00 0.00 0.00 4.12
1279 1420 8.540507 TGCATAGTACTATCTTTCTTTCTCCT 57.459 34.615 12.62 0.00 0.00 3.69
1312 1453 7.287927 TGGAAATATAGACCTCTCGTTGATCTT 59.712 37.037 0.00 0.00 0.00 2.40
1579 1720 2.093537 CTAGCATCTCCCCCTCGTGC 62.094 65.000 0.00 0.00 36.11 5.34
1586 1727 1.306654 TCCCCCTCGTGCCAATACT 60.307 57.895 0.00 0.00 0.00 2.12
1589 1730 1.227263 CCCTCGTGCCAATACTCGG 60.227 63.158 0.00 0.00 0.00 4.63
1634 1775 9.107177 GCTATAAGAAGCATGCTGAACATATAT 57.893 33.333 23.48 14.44 42.30 0.86
1724 1867 2.711922 CCTCCTCGAGTTCCACGGG 61.712 68.421 12.31 0.00 0.00 5.28
1904 2060 2.938451 TGCAGCATCTCTAAATTCCGTG 59.062 45.455 0.00 0.00 0.00 4.94
2035 2202 4.038642 TGCCCAACTGGTAAAGATTGTTTC 59.961 41.667 0.00 0.00 36.04 2.78
2041 2208 7.222611 CCAACTGGTAAAGATTGTTTCAAGTTG 59.777 37.037 14.90 14.90 0.00 3.16
2045 2212 7.254852 TGGTAAAGATTGTTTCAAGTTGACAC 58.745 34.615 14.05 14.05 0.00 3.67
2078 2245 3.372206 ACACGATCAGCTCTTTGCATAAC 59.628 43.478 0.00 0.00 45.94 1.89
2094 2261 9.998106 CTTTGCATAACAGGGTACTATTATAGT 57.002 33.333 9.96 9.96 42.68 2.12
2180 2347 4.500499 AATACAAGAGGCTGCTGAAGAT 57.500 40.909 0.00 0.00 0.00 2.40
2185 2352 1.065564 AGAGGCTGCTGAAGATGGAAC 60.066 52.381 0.00 0.00 0.00 3.62
2220 2390 5.846714 AGGTAGTAGGCTGATGGATGTTATT 59.153 40.000 0.00 0.00 0.00 1.40
2221 2391 6.330250 AGGTAGTAGGCTGATGGATGTTATTT 59.670 38.462 0.00 0.00 0.00 1.40
2264 2435 5.197224 TCATTTTCTGAGGGAATGGTGAT 57.803 39.130 8.21 0.00 33.53 3.06
2268 2439 4.428294 TTCTGAGGGAATGGTGATCATC 57.572 45.455 0.00 0.00 34.44 2.92
2277 2448 4.264253 GAATGGTGATCATCTGTTGGTGA 58.736 43.478 7.64 0.00 34.44 4.02
2278 2449 3.339253 TGGTGATCATCTGTTGGTGAG 57.661 47.619 7.64 0.00 0.00 3.51
2309 2480 0.373716 GCAAAGTAGACATTCCGGCG 59.626 55.000 0.00 0.00 0.00 6.46
2353 2524 2.797074 TGTCACGTCGGACAAATGTA 57.203 45.000 9.10 0.00 44.34 2.29
2375 2546 5.888982 AGAGGTGTAGGAAAGAGAAACAA 57.111 39.130 0.00 0.00 0.00 2.83
2376 2547 6.248569 AGAGGTGTAGGAAAGAGAAACAAA 57.751 37.500 0.00 0.00 0.00 2.83
2377 2548 6.659824 AGAGGTGTAGGAAAGAGAAACAAAA 58.340 36.000 0.00 0.00 0.00 2.44
2384 2555 8.466798 TGTAGGAAAGAGAAACAAAAGAAAAGG 58.533 33.333 0.00 0.00 0.00 3.11
2405 2576 4.105486 GGCTTTGCCTTCGCTTAATTAAG 58.895 43.478 19.08 19.08 46.69 1.85
2407 2578 5.030936 GCTTTGCCTTCGCTTAATTAAGAG 58.969 41.667 26.00 22.66 35.33 2.85
2480 2651 6.636454 AAGATTAAGAGACCACCCATTGTA 57.364 37.500 0.00 0.00 0.00 2.41
2487 2658 4.228210 AGAGACCACCCATTGTACATCATT 59.772 41.667 0.00 0.00 0.00 2.57
2496 2667 7.329226 CACCCATTGTACATCATTTTCTTTGTC 59.671 37.037 0.00 0.00 0.00 3.18
2521 2692 4.316205 TCTACATTACGATGGCACGATT 57.684 40.909 14.63 0.00 37.60 3.34
2557 2751 6.098409 TGTCTTATAACCTCAATCCTCACCTC 59.902 42.308 0.00 0.00 0.00 3.85
2561 2755 0.176680 CCTCAATCCTCACCTCACCG 59.823 60.000 0.00 0.00 0.00 4.94
2592 2786 2.131854 CCACCACCTACCCATGGATAA 58.868 52.381 15.22 0.00 39.46 1.75
2605 2799 3.440173 CCATGGATAACTTTGCGTCAAGT 59.560 43.478 5.56 0.00 0.00 3.16
2612 2806 7.120579 TGGATAACTTTGCGTCAAGTTGATAAT 59.879 33.333 18.82 8.50 0.00 1.28
2626 2820 8.519526 TCAAGTTGATAATTAGTTCCGCAATTT 58.480 29.630 0.08 0.00 0.00 1.82
2787 2985 9.825972 AAGTTCATGAGTATAAATGTTTGTTCG 57.174 29.630 0.00 0.00 0.00 3.95
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 4.104183 TCGACCCATTTCCGGCCC 62.104 66.667 0.00 0.00 0.00 5.80
1 2 2.822701 GTCGACCCATTTCCGGCC 60.823 66.667 3.51 0.00 0.00 6.13
2 3 2.046700 TGTCGACCCATTTCCGGC 60.047 61.111 14.12 0.00 0.00 6.13
3 4 1.449601 CCTGTCGACCCATTTCCGG 60.450 63.158 14.12 0.00 0.00 5.14
4 5 2.106683 GCCTGTCGACCCATTTCCG 61.107 63.158 14.12 0.00 0.00 4.30
5 6 2.106683 CGCCTGTCGACCCATTTCC 61.107 63.158 14.12 0.00 41.67 3.13
6 7 1.079405 TCGCCTGTCGACCCATTTC 60.079 57.895 14.12 0.00 43.16 2.17
7 8 3.065306 TCGCCTGTCGACCCATTT 58.935 55.556 14.12 0.00 43.16 2.32
14 15 1.554042 GCTTTTCGTTCGCCTGTCGA 61.554 55.000 0.00 0.00 46.88 4.20
15 16 1.154654 GCTTTTCGTTCGCCTGTCG 60.155 57.895 0.00 0.00 40.15 4.35
16 17 1.154654 CGCTTTTCGTTCGCCTGTC 60.155 57.895 0.00 0.00 0.00 3.51
17 18 2.604174 CCGCTTTTCGTTCGCCTGT 61.604 57.895 0.00 0.00 36.19 4.00
18 19 2.173382 CCGCTTTTCGTTCGCCTG 59.827 61.111 0.00 0.00 36.19 4.85
19 20 3.047877 CCCGCTTTTCGTTCGCCT 61.048 61.111 0.00 0.00 36.19 5.52
20 21 4.753877 GCCCGCTTTTCGTTCGCC 62.754 66.667 0.00 0.00 36.19 5.54
37 38 3.539107 GACCTAAACGGACGCGCG 61.539 66.667 30.96 30.96 36.31 6.86
38 39 3.539107 CGACCTAAACGGACGCGC 61.539 66.667 5.73 0.00 43.39 6.86
42 43 0.457337 ACGCATCGACCTAAACGGAC 60.457 55.000 0.00 0.00 36.31 4.79
43 44 0.244450 AACGCATCGACCTAAACGGA 59.756 50.000 0.00 0.00 36.31 4.69
44 45 0.368907 CAACGCATCGACCTAAACGG 59.631 55.000 0.00 0.00 39.35 4.44
45 46 0.368907 CCAACGCATCGACCTAAACG 59.631 55.000 0.00 0.00 0.00 3.60
46 47 0.725117 CCCAACGCATCGACCTAAAC 59.275 55.000 0.00 0.00 0.00 2.01
47 48 1.022451 GCCCAACGCATCGACCTAAA 61.022 55.000 0.00 0.00 37.47 1.85
48 49 1.448893 GCCCAACGCATCGACCTAA 60.449 57.895 0.00 0.00 37.47 2.69
49 50 2.185867 GCCCAACGCATCGACCTA 59.814 61.111 0.00 0.00 37.47 3.08
50 51 4.778143 GGCCCAACGCATCGACCT 62.778 66.667 0.00 0.00 40.31 3.85
55 56 1.862602 AAAAGTCGGCCCAACGCATC 61.863 55.000 0.00 0.00 40.31 3.91
56 57 1.460273 AAAAAGTCGGCCCAACGCAT 61.460 50.000 0.00 0.00 40.31 4.73
57 58 2.122167 AAAAAGTCGGCCCAACGCA 61.122 52.632 0.00 0.00 40.31 5.24
58 59 2.725641 AAAAAGTCGGCCCAACGC 59.274 55.556 0.00 0.00 0.00 4.84
72 73 1.030488 TGGGTCGCGGTCAACAAAAA 61.030 50.000 6.13 0.00 0.00 1.94
73 74 1.030488 TTGGGTCGCGGTCAACAAAA 61.030 50.000 6.13 0.00 0.00 2.44
74 75 1.030488 TTTGGGTCGCGGTCAACAAA 61.030 50.000 6.13 12.03 0.00 2.83
75 76 1.451567 TTTGGGTCGCGGTCAACAA 60.452 52.632 6.13 6.84 0.00 2.83
76 77 2.181521 GTTTGGGTCGCGGTCAACA 61.182 57.895 6.13 0.69 0.00 3.33
77 78 2.635338 GTTTGGGTCGCGGTCAAC 59.365 61.111 6.13 0.00 0.00 3.18
78 79 2.968156 CGTTTGGGTCGCGGTCAA 60.968 61.111 6.13 5.91 0.00 3.18
79 80 4.973055 CCGTTTGGGTCGCGGTCA 62.973 66.667 6.13 0.00 40.53 4.02
80 81 4.668118 TCCGTTTGGGTCGCGGTC 62.668 66.667 6.13 0.00 45.11 4.79
81 82 4.974989 GTCCGTTTGGGTCGCGGT 62.975 66.667 6.13 0.00 45.11 5.68
90 91 3.990806 TTCACGCGCGTCCGTTTG 61.991 61.111 35.61 21.21 39.83 2.93
91 92 3.992019 GTTCACGCGCGTCCGTTT 61.992 61.111 35.61 7.71 39.83 3.60
95 96 3.007070 ATTTCGTTCACGCGCGTCC 62.007 57.895 35.61 22.09 39.60 4.79
96 97 1.853192 CATTTCGTTCACGCGCGTC 60.853 57.895 35.61 21.53 39.60 5.19
97 98 2.170036 CATTTCGTTCACGCGCGT 59.830 55.556 32.73 32.73 39.60 6.01
98 99 1.575132 CTCATTTCGTTCACGCGCG 60.575 57.895 30.96 30.96 39.60 6.86
99 100 0.516524 GACTCATTTCGTTCACGCGC 60.517 55.000 5.73 0.00 39.60 6.86
100 101 0.246374 CGACTCATTTCGTTCACGCG 60.246 55.000 3.53 3.53 39.60 6.01
101 102 0.093026 CCGACTCATTTCGTTCACGC 59.907 55.000 0.00 0.00 37.29 5.34
102 103 0.093026 GCCGACTCATTTCGTTCACG 59.907 55.000 0.00 0.00 37.29 4.35
103 104 1.144969 TGCCGACTCATTTCGTTCAC 58.855 50.000 0.00 0.00 37.29 3.18
104 105 2.093306 ATGCCGACTCATTTCGTTCA 57.907 45.000 0.00 0.00 37.29 3.18
105 106 4.518217 CAATATGCCGACTCATTTCGTTC 58.482 43.478 0.00 0.00 37.29 3.95
106 107 3.312421 CCAATATGCCGACTCATTTCGTT 59.688 43.478 0.00 0.00 37.29 3.85
107 108 2.872245 CCAATATGCCGACTCATTTCGT 59.128 45.455 0.00 0.00 37.29 3.85
108 109 3.130633 TCCAATATGCCGACTCATTTCG 58.869 45.455 0.00 0.00 38.80 3.46
109 110 4.130118 ACTCCAATATGCCGACTCATTTC 58.870 43.478 0.00 0.00 0.00 2.17
110 111 4.156455 ACTCCAATATGCCGACTCATTT 57.844 40.909 0.00 0.00 0.00 2.32
111 112 3.845781 ACTCCAATATGCCGACTCATT 57.154 42.857 0.00 0.00 0.00 2.57
112 113 3.470709 CAACTCCAATATGCCGACTCAT 58.529 45.455 0.00 0.00 0.00 2.90
113 114 2.905075 CAACTCCAATATGCCGACTCA 58.095 47.619 0.00 0.00 0.00 3.41
114 115 1.599542 GCAACTCCAATATGCCGACTC 59.400 52.381 0.00 0.00 34.03 3.36
115 116 1.210478 AGCAACTCCAATATGCCGACT 59.790 47.619 0.00 0.00 40.93 4.18
116 117 1.599542 GAGCAACTCCAATATGCCGAC 59.400 52.381 0.00 0.00 40.93 4.79
117 118 1.486310 AGAGCAACTCCAATATGCCGA 59.514 47.619 0.00 0.00 40.93 5.54
118 119 1.959042 AGAGCAACTCCAATATGCCG 58.041 50.000 0.00 0.00 40.93 5.69
119 120 4.455606 AGTTAGAGCAACTCCAATATGCC 58.544 43.478 0.00 0.00 44.48 4.40
120 121 7.065803 TGTTTAGTTAGAGCAACTCCAATATGC 59.934 37.037 0.00 0.00 44.48 3.14
121 122 8.492673 TGTTTAGTTAGAGCAACTCCAATATG 57.507 34.615 0.00 0.00 44.48 1.78
122 123 9.113838 CATGTTTAGTTAGAGCAACTCCAATAT 57.886 33.333 0.00 0.00 44.48 1.28
123 124 8.318412 TCATGTTTAGTTAGAGCAACTCCAATA 58.682 33.333 0.00 0.00 44.48 1.90
124 125 7.168219 TCATGTTTAGTTAGAGCAACTCCAAT 58.832 34.615 0.00 0.00 44.48 3.16
125 126 6.530120 TCATGTTTAGTTAGAGCAACTCCAA 58.470 36.000 0.00 0.00 44.48 3.53
126 127 6.014584 TCTCATGTTTAGTTAGAGCAACTCCA 60.015 38.462 0.00 0.00 44.48 3.86
127 128 6.398918 TCTCATGTTTAGTTAGAGCAACTCC 58.601 40.000 0.00 0.00 44.48 3.85
128 129 7.518731 CTCTCATGTTTAGTTAGAGCAACTC 57.481 40.000 0.00 0.00 44.48 3.01
159 160 3.390311 AGACAGGAACTCCCTACGTTTTT 59.610 43.478 0.00 0.00 45.60 1.94
160 161 2.970640 AGACAGGAACTCCCTACGTTTT 59.029 45.455 0.00 0.00 45.60 2.43
161 162 2.606378 AGACAGGAACTCCCTACGTTT 58.394 47.619 0.00 0.00 45.60 3.60
162 163 2.305858 AGACAGGAACTCCCTACGTT 57.694 50.000 0.00 0.00 45.60 3.99
163 164 2.305858 AAGACAGGAACTCCCTACGT 57.694 50.000 0.00 0.00 45.60 3.57
164 165 5.340439 AAATAAGACAGGAACTCCCTACG 57.660 43.478 0.00 0.00 45.60 3.51
165 166 6.070136 AGGAAAATAAGACAGGAACTCCCTAC 60.070 42.308 0.00 0.00 45.60 3.18
166 167 6.030082 AGGAAAATAAGACAGGAACTCCCTA 58.970 40.000 0.00 0.00 45.60 3.53
168 169 5.180810 AGGAAAATAAGACAGGAACTCCC 57.819 43.478 0.00 0.00 34.60 4.30
169 170 4.870991 CGAGGAAAATAAGACAGGAACTCC 59.129 45.833 0.00 0.00 34.60 3.85
170 171 5.480205 ACGAGGAAAATAAGACAGGAACTC 58.520 41.667 0.00 0.00 34.60 3.01
171 172 5.480205 GACGAGGAAAATAAGACAGGAACT 58.520 41.667 0.00 0.00 43.88 3.01
172 173 4.630505 GGACGAGGAAAATAAGACAGGAAC 59.369 45.833 0.00 0.00 0.00 3.62
183 184 1.804326 CGCGACGGACGAGGAAAAT 60.804 57.895 0.00 0.00 45.77 1.82
328 333 3.555956 GTCACTGTTCGATCAAGTTGTGT 59.444 43.478 2.11 0.00 0.00 3.72
338 343 0.809385 ACGATCGGTCACTGTTCGAT 59.191 50.000 21.36 5.29 44.83 3.59
393 402 1.292541 GGTGGGTCTCGTGTCTTCC 59.707 63.158 0.00 0.00 0.00 3.46
538 570 2.355126 CACGTCTGTGCACGCTCT 60.355 61.111 13.13 0.00 43.93 4.09
568 600 4.435651 GCGTAGACTATTGGTGAAAACAGC 60.436 45.833 0.00 0.00 0.00 4.40
572 604 4.688879 CACTGCGTAGACTATTGGTGAAAA 59.311 41.667 7.78 0.00 0.00 2.29
597 629 3.127589 CTGGATCACACACGTTTACACA 58.872 45.455 0.00 0.00 0.00 3.72
603 635 0.250295 CCACCTGGATCACACACGTT 60.250 55.000 0.00 0.00 37.39 3.99
607 639 0.976641 GTCTCCACCTGGATCACACA 59.023 55.000 0.00 0.00 44.46 3.72
719 751 3.775654 CGTGGGAGGGGAGCAGAC 61.776 72.222 0.00 0.00 0.00 3.51
871 910 2.329690 CTGTCTCCGGCTCGATCG 59.670 66.667 9.36 9.36 0.00 3.69
903 942 4.742201 CACACCTGTCGGCCTCGG 62.742 72.222 0.00 0.00 36.95 4.63
1110 1153 1.372997 GCTGAAGAACTCGACGCCA 60.373 57.895 0.00 0.00 0.00 5.69
1134 1177 1.754803 TGGAGTACATACCAGAAGGCG 59.245 52.381 0.00 0.00 39.06 5.52
1159 1274 5.521906 TCATAAACCGAAGATCAGAGAGG 57.478 43.478 0.00 0.00 0.00 3.69
1181 1306 1.000396 GCACCCCTGAAGGCTGAAT 60.000 57.895 0.00 0.00 0.00 2.57
1193 1318 2.352422 TGCTGATCACTGCACCCC 59.648 61.111 5.58 0.00 43.83 4.95
1218 1343 7.743520 TTCAAATGTTTCGTTTTACACTTCC 57.256 32.000 0.00 0.00 0.00 3.46
1279 1420 7.724506 ACGAGAGGTCTATATTTCCATGTCTTA 59.275 37.037 0.00 0.00 0.00 2.10
1358 1499 6.366332 AGAACAAACGACAGACTTTAGCATAG 59.634 38.462 0.00 0.00 0.00 2.23
1365 1506 4.935808 AGTTCAGAACAAACGACAGACTTT 59.064 37.500 15.85 0.00 0.00 2.66
1579 1720 1.737793 GGTTGAAGTGCCGAGTATTGG 59.262 52.381 0.00 0.00 45.02 3.16
1586 1727 2.895404 ACTAGTAAGGTTGAAGTGCCGA 59.105 45.455 0.00 0.00 0.00 5.54
1590 1731 8.467598 TCTTATAGCACTAGTAAGGTTGAAGTG 58.532 37.037 0.00 0.00 40.38 3.16
1591 1732 8.591114 TCTTATAGCACTAGTAAGGTTGAAGT 57.409 34.615 0.00 0.00 0.00 3.01
1634 1775 5.163764 CGACAGCACCTGCAAATTTATTCTA 60.164 40.000 0.00 0.00 45.16 2.10
1712 1855 3.307906 TGGGACCCGTGGAACTCG 61.308 66.667 5.91 0.00 45.50 4.18
1904 2060 3.070302 CCTTCCTTCCAGCTATACAGACC 59.930 52.174 0.00 0.00 0.00 3.85
2016 2183 7.973388 TCAACTTGAAACAATCTTTACCAGTTG 59.027 33.333 0.00 0.00 33.83 3.16
2035 2202 3.065371 GTGGAAAGTGGAGTGTCAACTTG 59.935 47.826 0.00 0.00 36.52 3.16
2041 2208 1.202486 TCGTGTGGAAAGTGGAGTGTC 60.202 52.381 0.00 0.00 0.00 3.67
2045 2212 2.341257 CTGATCGTGTGGAAAGTGGAG 58.659 52.381 0.00 0.00 0.00 3.86
2093 2260 6.569780 ACTGACCAGAAACCAAAACAAATAC 58.430 36.000 3.76 0.00 0.00 1.89
2094 2261 6.783708 ACTGACCAGAAACCAAAACAAATA 57.216 33.333 3.76 0.00 0.00 1.40
2095 2262 5.675684 ACTGACCAGAAACCAAAACAAAT 57.324 34.783 3.76 0.00 0.00 2.32
2104 2271 5.767816 AAATGTTGTACTGACCAGAAACC 57.232 39.130 3.76 0.00 0.00 3.27
2185 2352 5.538813 TCAGCCTACTACCTACATATGGTTG 59.461 44.000 7.80 0.00 38.88 3.77
2186 2353 5.712752 TCAGCCTACTACCTACATATGGTT 58.287 41.667 7.80 0.00 38.88 3.67
2187 2354 5.335028 TCAGCCTACTACCTACATATGGT 57.665 43.478 7.80 0.00 41.28 3.55
2188 2355 5.127845 CCATCAGCCTACTACCTACATATGG 59.872 48.000 7.80 0.00 0.00 2.74
2237 2407 7.016465 TCACCATTCCCTCAGAAAATGAAAAAT 59.984 33.333 1.62 0.00 38.21 1.82
2264 2435 5.359756 CGATAAATCCTCACCAACAGATGA 58.640 41.667 0.00 0.00 0.00 2.92
2268 2439 3.623060 CACCGATAAATCCTCACCAACAG 59.377 47.826 0.00 0.00 0.00 3.16
2277 2448 5.116882 GTCTACTTTGCACCGATAAATCCT 58.883 41.667 0.00 0.00 0.00 3.24
2278 2449 4.873827 TGTCTACTTTGCACCGATAAATCC 59.126 41.667 0.00 0.00 0.00 3.01
2327 2498 2.503375 CCGACGTGACACCGCTAC 60.503 66.667 0.00 0.00 0.00 3.58
2353 2524 5.888982 TTGTTTCTCTTTCCTACACCTCT 57.111 39.130 0.00 0.00 0.00 3.69
2384 2555 4.981794 TCTTAATTAAGCGAAGGCAAAGC 58.018 39.130 18.68 0.00 43.41 3.51
2405 2576 9.160496 AGACATTTGTTGTTAAGAGATCATCTC 57.840 33.333 6.55 6.55 40.31 2.75
2407 2578 8.939929 TGAGACATTTGTTGTTAAGAGATCATC 58.060 33.333 0.00 0.00 39.18 2.92
2429 2600 8.593679 TCTCTAGTTCATAAAAATGTGGTGAGA 58.406 33.333 0.00 0.00 0.00 3.27
2496 2667 4.506288 TCGTGCCATCGTAATGTAGAAATG 59.494 41.667 0.00 0.00 0.00 2.32
2504 2675 5.845985 ATCTTAATCGTGCCATCGTAATG 57.154 39.130 0.00 0.00 0.00 1.90
2510 2681 7.386299 AGACAATCTTATCTTAATCGTGCCATC 59.614 37.037 0.00 0.00 0.00 3.51
2551 2745 0.323816 AGATGAGCTCGGTGAGGTGA 60.324 55.000 9.64 0.00 40.67 4.02
2557 2751 0.460987 GGTGGAAGATGAGCTCGGTG 60.461 60.000 9.64 0.00 0.00 4.94
2561 2755 0.908198 AGGTGGTGGAAGATGAGCTC 59.092 55.000 6.82 6.82 0.00 4.09
2592 2786 7.435068 ACTAATTATCAACTTGACGCAAAGT 57.565 32.000 0.00 0.00 42.21 2.66


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

AutoCloner maintained by Alex Coulton.