Multiple sequence alignment - TraesCS3B01G559700

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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 TraesCS3B01G559700 chr3B 100.000 3215 0 0 1 3215 793370293 793367079 0.000000e+00 5938.0
1 TraesCS3B01G559700 chr3B 91.321 3134 158 38 100 3207 792300181 792303226 0.000000e+00 4176.0
2 TraesCS3B01G559700 chr3B 92.070 2585 128 28 644 3207 792386817 792389345 0.000000e+00 3567.0
3 TraesCS3B01G559700 chr3B 92.848 2251 124 11 965 3207 793439092 793436871 0.000000e+00 3230.0
4 TraesCS3B01G559700 chr3B 92.211 475 25 4 92 562 792386352 792386818 0.000000e+00 662.0
5 TraesCS3B01G559700 chr3B 79.778 450 61 15 2448 2880 792268211 792268647 1.870000e-77 300.0
6 TraesCS3B01G559700 chrUn 92.031 2585 129 28 644 3207 154993534 154991006 0.000000e+00 3561.0
7 TraesCS3B01G559700 chrUn 91.876 2585 132 29 644 3207 155075707 155073180 0.000000e+00 3539.0
8 TraesCS3B01G559700 chrUn 94.030 1675 79 2 965 2639 308788219 308789872 0.000000e+00 2519.0
9 TraesCS3B01G559700 chrUn 91.579 475 28 4 92 562 154993999 154993533 0.000000e+00 645.0
10 TraesCS3B01G559700 chrUn 91.579 475 28 4 92 562 155076172 155075706 0.000000e+00 645.0
11 TraesCS3B01G559700 chrUn 91.579 475 28 4 92 562 405500338 405499872 0.000000e+00 645.0
12 TraesCS3B01G559700 chrUn 88.312 308 6 13 644 948 405499873 405499593 3.070000e-90 342.0
13 TraesCS3B01G559700 chrUn 78.947 456 58 25 2444 2880 155023778 155023342 3.160000e-70 276.0
14 TraesCS3B01G559700 chrUn 82.270 141 22 3 1 139 108394033 108393894 5.630000e-23 119.0
15 TraesCS3B01G559700 chr3A 94.744 2283 99 9 944 3215 721565510 721567782 0.000000e+00 3531.0
16 TraesCS3B01G559700 chr3A 90.761 368 21 5 202 562 721561414 721561775 2.240000e-131 479.0
17 TraesCS3B01G559700 chr3A 94.510 255 6 6 644 894 721561774 721562024 1.400000e-103 387.0
18 TraesCS3B01G559700 chr3A 94.059 101 6 0 100 200 721559494 721559394 1.540000e-33 154.0
19 TraesCS3B01G559700 chr3A 100.000 65 0 0 884 948 721565121 721565185 1.570000e-23 121.0
20 TraesCS3B01G559700 chr3A 80.292 137 25 2 1 135 717299566 717299702 5.670000e-18 102.0
21 TraesCS3B01G559700 chr3D 94.793 1498 50 12 644 2120 591176642 591178132 0.000000e+00 2309.0
22 TraesCS3B01G559700 chr3D 97.130 1115 25 4 2105 3215 591178985 591180096 0.000000e+00 1875.0
23 TraesCS3B01G559700 chr3D 86.478 1516 160 28 913 2407 591124158 591125649 0.000000e+00 1622.0
24 TraesCS3B01G559700 chr3D 92.575 431 25 4 136 562 591176216 591176643 2.120000e-171 612.0
25 TraesCS3B01G559700 chr3D 79.021 143 28 2 1 141 114078789 114078647 2.640000e-16 97.1
26 TraesCS3B01G559700 chr6B 93.182 88 6 0 561 648 18238281 18238194 2.600000e-26 130.0
27 TraesCS3B01G559700 chr6B 92.045 88 6 1 560 647 374144307 374144393 4.360000e-24 122.0
28 TraesCS3B01G559700 chr6B 91.954 87 7 0 561 647 408760635 408760549 4.360000e-24 122.0
29 TraesCS3B01G559700 chr6B 79.021 143 24 6 1 139 643815905 643816045 3.420000e-15 93.5
30 TraesCS3B01G559700 chr5B 93.182 88 6 0 561 648 311079283 311079370 2.600000e-26 130.0
31 TraesCS3B01G559700 chr7B 92.045 88 7 0 561 648 399888246 399888159 1.210000e-24 124.0
32 TraesCS3B01G559700 chr7B 89.362 94 10 0 554 647 712096344 712096437 5.630000e-23 119.0
33 TraesCS3B01G559700 chr1A 91.011 89 8 0 561 649 561070468 561070556 1.570000e-23 121.0
34 TraesCS3B01G559700 chr6A 88.000 100 12 0 561 660 1090368 1090269 5.630000e-23 119.0
35 TraesCS3B01G559700 chr4B 81.159 138 24 2 4 139 168913420 168913283 3.390000e-20 110.0
36 TraesCS3B01G559700 chr1B 80.667 150 22 7 1 148 573853461 573853317 3.390000e-20 110.0
37 TraesCS3B01G559700 chr7D 79.137 139 27 2 1 137 454069636 454069774 9.500000e-16 95.3
38 TraesCS3B01G559700 chr4A 78.947 133 24 4 10 139 539304108 539303977 1.590000e-13 87.9
39 TraesCS3B01G559700 chr2B 78.261 138 20 8 6 137 217303795 217303928 2.660000e-11 80.5


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 TraesCS3B01G559700 chr3B 793367079 793370293 3214 True 5938.000000 5938 100.000000 1 3215 1 chr3B.!!$R1 3214
1 TraesCS3B01G559700 chr3B 792300181 792303226 3045 False 4176.000000 4176 91.321000 100 3207 1 chr3B.!!$F2 3107
2 TraesCS3B01G559700 chr3B 793436871 793439092 2221 True 3230.000000 3230 92.848000 965 3207 1 chr3B.!!$R2 2242
3 TraesCS3B01G559700 chr3B 792386352 792389345 2993 False 2114.500000 3567 92.140500 92 3207 2 chr3B.!!$F3 3115
4 TraesCS3B01G559700 chrUn 308788219 308789872 1653 False 2519.000000 2519 94.030000 965 2639 1 chrUn.!!$F1 1674
5 TraesCS3B01G559700 chrUn 154991006 154993999 2993 True 2103.000000 3561 91.805000 92 3207 2 chrUn.!!$R3 3115
6 TraesCS3B01G559700 chrUn 155073180 155076172 2992 True 2092.000000 3539 91.727500 92 3207 2 chrUn.!!$R4 3115
7 TraesCS3B01G559700 chrUn 405499593 405500338 745 True 493.500000 645 89.945500 92 948 2 chrUn.!!$R5 856
8 TraesCS3B01G559700 chr3A 721561414 721567782 6368 False 1129.500000 3531 95.003750 202 3215 4 chr3A.!!$F2 3013
9 TraesCS3B01G559700 chr3D 591124158 591125649 1491 False 1622.000000 1622 86.478000 913 2407 1 chr3D.!!$F1 1494
10 TraesCS3B01G559700 chr3D 591176216 591180096 3880 False 1598.666667 2309 94.832667 136 3215 3 chr3D.!!$F2 3079

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
44 45 0.094046 CGTCCGAACGCACCATAAAC 59.906 55.0 0.00 0.0 42.82 2.01 F
107 108 0.174845 CGTTCCGGACTTATGCTGGA 59.825 55.0 1.83 0.0 39.00 3.86 F
431 440 0.391927 CCTTATTCCAACCCGTCGCA 60.392 55.0 0.00 0.0 0.00 5.10 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1297 4757 0.811915 TACTCTGCTTGCTCCTCGTC 59.188 55.0 0.0 0.0 0.00 4.20 R
1452 4915 1.169661 TGTTGTTGGTGATGACGGCC 61.170 55.0 0.0 0.0 0.00 6.13 R
2422 6784 1.350706 GCTGAGACGAGCAAGCAGAC 61.351 60.0 0.0 0.0 38.95 3.51 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 4.473643 TTGTCTCCAGTTTGCGGG 57.526 55.556 0.00 0.00 0.00 6.13
18 19 1.833606 TTGTCTCCAGTTTGCGGGA 59.166 52.632 0.00 0.00 37.42 5.14
23 24 3.015516 TCCAGTTTGCGGGAGAAAC 57.984 52.632 0.00 0.00 34.05 2.78
24 25 0.882927 TCCAGTTTGCGGGAGAAACG 60.883 55.000 0.00 0.00 38.18 3.60
32 33 2.048877 GGGAGAAACGCGTCCGAA 60.049 61.111 14.44 0.00 38.29 4.30
33 34 2.378084 GGGAGAAACGCGTCCGAAC 61.378 63.158 14.44 3.12 38.29 3.95
42 43 4.172346 CGTCCGAACGCACCATAA 57.828 55.556 0.00 0.00 42.82 1.90
43 44 2.447408 CGTCCGAACGCACCATAAA 58.553 52.632 0.00 0.00 42.82 1.40
44 45 0.094046 CGTCCGAACGCACCATAAAC 59.906 55.000 0.00 0.00 42.82 2.01
45 46 0.445043 GTCCGAACGCACCATAAACC 59.555 55.000 0.00 0.00 0.00 3.27
46 47 1.015085 TCCGAACGCACCATAAACCG 61.015 55.000 0.00 0.00 0.00 4.44
47 48 1.015085 CCGAACGCACCATAAACCGA 61.015 55.000 0.00 0.00 0.00 4.69
48 49 1.003851 CGAACGCACCATAAACCGAT 58.996 50.000 0.00 0.00 0.00 4.18
49 50 2.195096 CGAACGCACCATAAACCGATA 58.805 47.619 0.00 0.00 0.00 2.92
50 51 2.034339 CGAACGCACCATAAACCGATAC 60.034 50.000 0.00 0.00 0.00 2.24
51 52 2.676632 ACGCACCATAAACCGATACA 57.323 45.000 0.00 0.00 0.00 2.29
52 53 2.546778 ACGCACCATAAACCGATACAG 58.453 47.619 0.00 0.00 0.00 2.74
53 54 1.864711 CGCACCATAAACCGATACAGG 59.135 52.381 0.00 0.00 37.30 4.00
54 55 2.482316 CGCACCATAAACCGATACAGGA 60.482 50.000 0.00 0.00 34.73 3.86
55 56 2.870411 GCACCATAAACCGATACAGGAC 59.130 50.000 0.00 0.00 34.73 3.85
56 57 3.463944 CACCATAAACCGATACAGGACC 58.536 50.000 0.00 0.00 34.73 4.46
57 58 2.101917 ACCATAAACCGATACAGGACCG 59.898 50.000 0.00 0.00 34.73 4.79
58 59 2.101917 CCATAAACCGATACAGGACCGT 59.898 50.000 0.00 0.00 34.73 4.83
59 60 2.945447 TAAACCGATACAGGACCGTG 57.055 50.000 0.00 0.00 34.73 4.94
60 61 0.971386 AAACCGATACAGGACCGTGT 59.029 50.000 0.96 0.96 34.73 4.49
61 62 0.971386 AACCGATACAGGACCGTGTT 59.029 50.000 0.54 0.00 34.73 3.32
62 63 0.245539 ACCGATACAGGACCGTGTTG 59.754 55.000 0.54 0.00 34.73 3.33
63 64 0.459585 CCGATACAGGACCGTGTTGG 60.460 60.000 0.54 4.16 46.41 3.77
64 65 0.528924 CGATACAGGACCGTGTTGGA 59.471 55.000 0.54 0.00 42.00 3.53
65 66 1.136305 CGATACAGGACCGTGTTGGAT 59.864 52.381 0.54 0.00 42.00 3.41
66 67 2.550978 GATACAGGACCGTGTTGGATG 58.449 52.381 0.54 0.00 42.00 3.51
67 68 0.611200 TACAGGACCGTGTTGGATGG 59.389 55.000 0.54 0.00 42.00 3.51
68 69 1.377202 CAGGACCGTGTTGGATGGG 60.377 63.158 0.00 0.00 42.00 4.00
69 70 1.846124 AGGACCGTGTTGGATGGGT 60.846 57.895 0.00 0.00 42.00 4.51
70 71 1.074248 GGACCGTGTTGGATGGGTT 59.926 57.895 0.00 0.00 42.00 4.11
71 72 0.958876 GGACCGTGTTGGATGGGTTC 60.959 60.000 0.00 0.00 42.00 3.62
72 73 0.958876 GACCGTGTTGGATGGGTTCC 60.959 60.000 0.00 0.00 45.69 3.62
79 80 2.271173 GGATGGGTTCCACGGTCC 59.729 66.667 0.00 0.00 44.74 4.46
80 81 2.125269 GATGGGTTCCACGGTCCG 60.125 66.667 10.48 10.48 35.80 4.79
81 82 3.675619 GATGGGTTCCACGGTCCGG 62.676 68.421 17.28 0.00 35.80 5.14
82 83 4.938074 TGGGTTCCACGGTCCGGA 62.938 66.667 17.28 0.00 0.00 5.14
83 84 4.383861 GGGTTCCACGGTCCGGAC 62.384 72.222 27.04 27.04 30.29 4.79
84 85 4.729856 GGTTCCACGGTCCGGACG 62.730 72.222 27.68 23.43 30.29 4.79
85 86 4.729856 GTTCCACGGTCCGGACGG 62.730 72.222 33.41 33.41 37.61 4.79
87 88 3.859118 TTCCACGGTCCGGACGGTA 62.859 63.158 37.79 25.48 41.94 4.02
88 89 4.120331 CCACGGTCCGGACGGTAC 62.120 72.222 37.79 20.47 41.94 3.34
104 105 1.135721 GGTACGTTCCGGACTTATGCT 59.864 52.381 1.83 0.00 40.97 3.79
107 108 0.174845 CGTTCCGGACTTATGCTGGA 59.825 55.000 1.83 0.00 39.00 3.86
119 120 3.056328 GCTGGAGGTTTGCGGGTC 61.056 66.667 0.00 0.00 0.00 4.46
132 133 2.511600 GGGTCGGCGTTGGAGATG 60.512 66.667 6.85 0.00 0.00 2.90
196 205 1.135199 GCATGCAATCCTTCACCACAG 60.135 52.381 14.21 0.00 0.00 3.66
221 230 7.950124 AGATCTAGAGGGTTGGAAAATTTTGAA 59.050 33.333 8.47 0.00 0.00 2.69
379 388 1.153706 CCTTCGTATGCGTCGGGTT 60.154 57.895 2.37 0.00 39.49 4.11
430 439 0.392060 ACCTTATTCCAACCCGTCGC 60.392 55.000 0.00 0.00 0.00 5.19
431 440 0.391927 CCTTATTCCAACCCGTCGCA 60.392 55.000 0.00 0.00 0.00 5.10
519 532 8.606830 ACTTAATGGGAGAAATAGACTCTGTTT 58.393 33.333 0.65 0.65 35.10 2.83
577 594 3.497332 CAGATACTCCTTCCGTCCCATA 58.503 50.000 0.00 0.00 0.00 2.74
578 595 3.895656 CAGATACTCCTTCCGTCCCATAA 59.104 47.826 0.00 0.00 0.00 1.90
580 597 5.715279 CAGATACTCCTTCCGTCCCATAATA 59.285 44.000 0.00 0.00 0.00 0.98
581 598 6.381420 CAGATACTCCTTCCGTCCCATAATAT 59.619 42.308 0.00 0.00 0.00 1.28
582 599 7.560262 CAGATACTCCTTCCGTCCCATAATATA 59.440 40.741 0.00 0.00 0.00 0.86
583 600 8.120538 AGATACTCCTTCCGTCCCATAATATAA 58.879 37.037 0.00 0.00 0.00 0.98
584 601 6.607004 ACTCCTTCCGTCCCATAATATAAG 57.393 41.667 0.00 0.00 0.00 1.73
585 602 6.320518 ACTCCTTCCGTCCCATAATATAAGA 58.679 40.000 0.00 0.00 0.00 2.10
586 603 6.785963 ACTCCTTCCGTCCCATAATATAAGAA 59.214 38.462 0.00 0.00 0.00 2.52
587 604 7.001099 TCCTTCCGTCCCATAATATAAGAAC 57.999 40.000 0.00 0.00 0.00 3.01
588 605 5.867716 CCTTCCGTCCCATAATATAAGAACG 59.132 44.000 0.00 0.00 0.00 3.95
589 606 6.409524 TTCCGTCCCATAATATAAGAACGT 57.590 37.500 0.00 0.00 0.00 3.99
590 607 6.409524 TCCGTCCCATAATATAAGAACGTT 57.590 37.500 0.00 0.00 0.00 3.99
591 608 6.819284 TCCGTCCCATAATATAAGAACGTTT 58.181 36.000 0.46 0.00 0.00 3.60
592 609 7.274447 TCCGTCCCATAATATAAGAACGTTTT 58.726 34.615 0.46 0.00 0.00 2.43
593 610 7.769970 TCCGTCCCATAATATAAGAACGTTTTT 59.230 33.333 9.22 9.22 0.00 1.94
594 611 9.044150 CCGTCCCATAATATAAGAACGTTTTTA 57.956 33.333 13.02 13.02 0.00 1.52
822 844 0.759346 AACGAGTCTTGGCTTGGACT 59.241 50.000 7.15 7.15 44.29 3.85
958 4416 1.614996 CAAGGCACACCACCAATACA 58.385 50.000 0.00 0.00 39.06 2.29
1014 4474 0.846015 CCAATATGGGCCTCCTGTCA 59.154 55.000 4.53 0.00 32.67 3.58
1297 4757 4.680237 TCGGCCAGAAGCACACCG 62.680 66.667 2.24 0.00 46.50 4.94
1402 4865 0.608308 TGATGTCGTCGTCCAGGAGT 60.608 55.000 0.00 0.00 0.00 3.85
1452 4915 1.792632 TCGACGGTCGACGATTTCATG 60.793 52.381 27.66 0.00 44.82 3.07
1473 4936 1.877637 CCGTCATCACCAACAACAGA 58.122 50.000 0.00 0.00 0.00 3.41
1668 5138 2.258286 GTTGCAATGGGACCACGC 59.742 61.111 0.59 7.46 0.00 5.34
1669 5139 2.203408 TTGCAATGGGACCACGCA 60.203 55.556 11.94 11.94 42.77 5.24
1686 5156 5.589855 ACCACGCATCATCAAGAAATCAATA 59.410 36.000 0.00 0.00 0.00 1.90
1770 5243 4.369872 AGGATGGAGAGGAAGAAGACAAT 58.630 43.478 0.00 0.00 0.00 2.71
1827 5303 5.985530 TGATTTGACCTATATCAACTGCTCG 59.014 40.000 0.00 0.00 38.31 5.03
1830 5306 1.000163 ACCTATATCAACTGCTCGGCG 60.000 52.381 0.00 0.00 0.00 6.46
2124 6467 7.151999 TGCAATTTATTTTATGGACACGAGT 57.848 32.000 0.00 0.00 0.00 4.18
2380 6724 4.442192 GGTCAGATTATATGGGCTCGATCC 60.442 50.000 0.00 0.00 0.00 3.36
2422 6784 0.395311 AGCACCCATGGCATCTCTTG 60.395 55.000 6.09 0.00 0.00 3.02
2443 6805 3.184683 GCTTGCTCGTCTCAGCGG 61.185 66.667 0.00 0.00 42.92 5.52
2513 6875 9.278734 GAAGATTTTAGCTTTAACCTTGATTCG 57.721 33.333 0.00 0.00 0.00 3.34
2524 6886 3.525537 ACCTTGATTCGTGTATCTGCAG 58.474 45.455 7.63 7.63 0.00 4.41
2553 6915 7.381408 TGTCTTCGTTCTTCATGTAGTTTAGTG 59.619 37.037 0.00 0.00 0.00 2.74
2907 7279 2.721167 CGACAGCTTCCCCGATCCA 61.721 63.158 0.00 0.00 0.00 3.41
2982 7357 3.589988 AGATGAAACCGCTCTACACTTG 58.410 45.455 0.00 0.00 0.00 3.16
3109 7484 2.434185 GAGCGCCATCACCAACGA 60.434 61.111 2.29 0.00 0.00 3.85
3177 7556 0.252761 TCAAATGGATGAGCTCGCCA 59.747 50.000 24.90 24.90 35.91 5.69
3207 7586 2.203422 CCCCCACCGAGCACAAAA 60.203 61.111 0.00 0.00 0.00 2.44
3208 7587 2.561037 CCCCCACCGAGCACAAAAC 61.561 63.158 0.00 0.00 0.00 2.43
3209 7588 1.528309 CCCCACCGAGCACAAAACT 60.528 57.895 0.00 0.00 0.00 2.66
3210 7589 1.515521 CCCCACCGAGCACAAAACTC 61.516 60.000 0.00 0.00 0.00 3.01
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 1.833606 TCCCGCAAACTGGAGACAA 59.166 52.632 0.00 0.00 42.06 3.18
1 2 3.557220 TCCCGCAAACTGGAGACA 58.443 55.556 0.00 0.00 39.59 3.41
4 5 0.875059 GTTTCTCCCGCAAACTGGAG 59.125 55.000 0.00 0.00 45.97 3.86
5 6 0.882927 CGTTTCTCCCGCAAACTGGA 60.883 55.000 0.00 0.00 32.46 3.86
6 7 1.574428 CGTTTCTCCCGCAAACTGG 59.426 57.895 0.00 0.00 32.46 4.00
14 15 3.902162 TTCGGACGCGTTTCTCCCG 62.902 63.158 25.23 25.23 41.36 5.14
15 16 2.048877 TTCGGACGCGTTTCTCCC 60.049 61.111 15.53 8.78 0.00 4.30
16 17 2.713894 CGTTCGGACGCGTTTCTCC 61.714 63.158 15.53 9.23 43.03 3.71
17 18 2.761354 CGTTCGGACGCGTTTCTC 59.239 61.111 15.53 0.00 43.03 2.87
26 27 0.445043 GGTTTATGGTGCGTTCGGAC 59.555 55.000 8.24 8.24 0.00 4.79
27 28 1.015085 CGGTTTATGGTGCGTTCGGA 61.015 55.000 0.00 0.00 0.00 4.55
28 29 1.015085 TCGGTTTATGGTGCGTTCGG 61.015 55.000 0.00 0.00 0.00 4.30
29 30 1.003851 ATCGGTTTATGGTGCGTTCG 58.996 50.000 0.00 0.00 0.00 3.95
30 31 2.931325 TGTATCGGTTTATGGTGCGTTC 59.069 45.455 0.00 0.00 0.00 3.95
31 32 2.933906 CTGTATCGGTTTATGGTGCGTT 59.066 45.455 0.00 0.00 0.00 4.84
32 33 2.546778 CTGTATCGGTTTATGGTGCGT 58.453 47.619 0.00 0.00 0.00 5.24
33 34 1.864711 CCTGTATCGGTTTATGGTGCG 59.135 52.381 0.00 0.00 0.00 5.34
34 35 2.870411 GTCCTGTATCGGTTTATGGTGC 59.130 50.000 0.00 0.00 0.00 5.01
35 36 3.463944 GGTCCTGTATCGGTTTATGGTG 58.536 50.000 0.00 0.00 0.00 4.17
36 37 2.101917 CGGTCCTGTATCGGTTTATGGT 59.898 50.000 0.00 0.00 0.00 3.55
37 38 2.101917 ACGGTCCTGTATCGGTTTATGG 59.898 50.000 0.00 0.00 35.41 2.74
38 39 3.120792 CACGGTCCTGTATCGGTTTATG 58.879 50.000 0.00 0.00 35.41 1.90
39 40 2.762327 ACACGGTCCTGTATCGGTTTAT 59.238 45.455 0.00 0.00 35.41 1.40
40 41 2.170166 ACACGGTCCTGTATCGGTTTA 58.830 47.619 0.00 0.00 35.41 2.01
41 42 0.971386 ACACGGTCCTGTATCGGTTT 59.029 50.000 0.00 0.00 35.41 3.27
42 43 0.971386 AACACGGTCCTGTATCGGTT 59.029 50.000 0.00 0.00 35.41 4.44
43 44 0.245539 CAACACGGTCCTGTATCGGT 59.754 55.000 0.00 0.00 35.41 4.69
44 45 0.459585 CCAACACGGTCCTGTATCGG 60.460 60.000 0.00 0.00 35.41 4.18
45 46 0.528924 TCCAACACGGTCCTGTATCG 59.471 55.000 0.00 0.00 37.86 2.92
46 47 2.550978 CATCCAACACGGTCCTGTATC 58.449 52.381 0.00 0.00 35.57 2.24
47 48 1.209504 CCATCCAACACGGTCCTGTAT 59.790 52.381 0.00 0.00 35.57 2.29
48 49 0.611200 CCATCCAACACGGTCCTGTA 59.389 55.000 0.00 0.00 35.57 2.74
49 50 1.374947 CCATCCAACACGGTCCTGT 59.625 57.895 0.00 0.00 35.57 4.00
50 51 1.377202 CCCATCCAACACGGTCCTG 60.377 63.158 0.00 0.00 35.57 3.86
51 52 1.423794 AACCCATCCAACACGGTCCT 61.424 55.000 0.00 0.00 35.57 3.85
52 53 0.958876 GAACCCATCCAACACGGTCC 60.959 60.000 0.00 0.00 35.57 4.46
53 54 2.551644 GAACCCATCCAACACGGTC 58.448 57.895 0.00 0.00 35.57 4.79
54 55 4.813346 GAACCCATCCAACACGGT 57.187 55.556 0.00 0.00 35.57 4.83
63 64 2.125269 CGGACCGTGGAACCCATC 60.125 66.667 5.48 0.00 35.28 3.51
64 65 3.712907 CCGGACCGTGGAACCCAT 61.713 66.667 13.94 0.00 35.28 4.00
65 66 4.938074 TCCGGACCGTGGAACCCA 62.938 66.667 13.94 0.00 30.98 4.51
66 67 4.383861 GTCCGGACCGTGGAACCC 62.384 72.222 24.75 0.00 37.23 4.11
67 68 4.729856 CGTCCGGACCGTGGAACC 62.730 72.222 28.52 0.46 37.23 3.62
68 69 4.729856 CCGTCCGGACCGTGGAAC 62.730 72.222 28.52 1.93 37.23 3.62
69 70 3.859118 TACCGTCCGGACCGTGGAA 62.859 63.158 30.96 14.27 37.23 3.53
70 71 4.343323 TACCGTCCGGACCGTGGA 62.343 66.667 30.96 15.14 38.96 4.02
71 72 4.120331 GTACCGTCCGGACCGTGG 62.120 72.222 30.96 26.32 38.96 4.94
72 73 4.465512 CGTACCGTCCGGACCGTG 62.466 72.222 30.96 21.27 38.96 4.94
74 75 3.667429 GAACGTACCGTCCGGACCG 62.667 68.421 28.52 25.81 39.99 4.79
75 76 2.179267 GAACGTACCGTCCGGACC 59.821 66.667 28.52 13.50 39.99 4.46
76 77 2.179267 GGAACGTACCGTCCGGAC 59.821 66.667 25.28 25.28 39.99 4.79
89 90 1.473434 CCTCCAGCATAAGTCCGGAAC 60.473 57.143 5.23 0.00 0.00 3.62
90 91 0.830648 CCTCCAGCATAAGTCCGGAA 59.169 55.000 5.23 0.00 0.00 4.30
97 98 0.734889 CCGCAAACCTCCAGCATAAG 59.265 55.000 0.00 0.00 0.00 1.73
98 99 0.679640 CCCGCAAACCTCCAGCATAA 60.680 55.000 0.00 0.00 0.00 1.90
101 102 3.842925 GACCCGCAAACCTCCAGCA 62.843 63.158 0.00 0.00 0.00 4.41
104 105 4.323477 CCGACCCGCAAACCTCCA 62.323 66.667 0.00 0.00 0.00 3.86
132 133 1.894282 GGCGATGCTCCTTTAGGGC 60.894 63.158 0.00 0.00 35.41 5.19
168 169 1.225373 AGGATTGCATGCCTTCCCTA 58.775 50.000 24.77 0.23 0.00 3.53
173 182 1.188863 GGTGAAGGATTGCATGCCTT 58.811 50.000 16.68 17.65 46.74 4.35
174 183 0.040058 TGGTGAAGGATTGCATGCCT 59.960 50.000 16.68 1.69 35.61 4.75
175 184 0.174162 GTGGTGAAGGATTGCATGCC 59.826 55.000 16.68 0.00 0.00 4.40
176 185 0.889994 TGTGGTGAAGGATTGCATGC 59.110 50.000 11.82 11.82 0.00 4.06
177 186 2.439409 TCTGTGGTGAAGGATTGCATG 58.561 47.619 0.00 0.00 0.00 4.06
178 187 2.885135 TCTGTGGTGAAGGATTGCAT 57.115 45.000 0.00 0.00 0.00 3.96
179 188 2.306805 AGATCTGTGGTGAAGGATTGCA 59.693 45.455 0.00 0.00 0.00 4.08
180 189 2.996631 AGATCTGTGGTGAAGGATTGC 58.003 47.619 0.00 0.00 0.00 3.56
196 205 7.703058 TCAAAATTTTCCAACCCTCTAGATC 57.297 36.000 0.00 0.00 0.00 2.75
221 230 4.521130 TTCAGTTCGATCTACAGCAAGT 57.479 40.909 0.00 0.00 0.00 3.16
379 388 3.994317 TCTCCCACCTTGATGACATCTA 58.006 45.455 16.25 8.11 0.00 1.98
519 532 7.741785 TCAGAGATTTCACTTACCTAAACCAA 58.258 34.615 0.00 0.00 0.00 3.67
582 599 9.925268 CATTACACTAGTGTTAAAAACGTTCTT 57.075 29.630 32.15 5.99 41.83 2.52
583 600 9.101655 ACATTACACTAGTGTTAAAAACGTTCT 57.898 29.630 32.15 6.43 41.83 3.01
584 601 9.361712 GACATTACACTAGTGTTAAAAACGTTC 57.638 33.333 32.15 13.59 41.83 3.95
585 602 8.881743 TGACATTACACTAGTGTTAAAAACGTT 58.118 29.630 32.15 9.27 41.83 3.99
586 603 8.422973 TGACATTACACTAGTGTTAAAAACGT 57.577 30.769 32.15 19.02 41.83 3.99
587 604 9.365311 CTTGACATTACACTAGTGTTAAAAACG 57.635 33.333 32.15 16.01 41.83 3.60
588 605 9.659830 CCTTGACATTACACTAGTGTTAAAAAC 57.340 33.333 32.15 18.89 41.83 2.43
589 606 9.616156 TCCTTGACATTACACTAGTGTTAAAAA 57.384 29.630 32.15 20.62 41.83 1.94
590 607 9.048446 GTCCTTGACATTACACTAGTGTTAAAA 57.952 33.333 32.15 20.97 37.47 1.52
591 608 8.205512 TGTCCTTGACATTACACTAGTGTTAAA 58.794 33.333 32.15 21.67 40.02 1.52
592 609 7.728148 TGTCCTTGACATTACACTAGTGTTAA 58.272 34.615 32.15 22.35 40.02 2.01
593 610 7.292713 TGTCCTTGACATTACACTAGTGTTA 57.707 36.000 32.15 24.22 40.02 2.41
594 611 6.169557 TGTCCTTGACATTACACTAGTGTT 57.830 37.500 32.15 15.56 40.02 3.32
595 612 5.801531 TGTCCTTGACATTACACTAGTGT 57.198 39.130 30.13 30.13 41.32 3.55
637 654 1.883084 GCCGCATGAACTACTCCCG 60.883 63.158 0.00 0.00 0.00 5.14
729 750 3.112580 CAAAAATAATGTTAGCGGCCCG 58.887 45.455 0.00 0.00 0.00 6.13
768 790 2.049802 TCGACCGGCAGAAACGTC 60.050 61.111 0.00 0.00 0.00 4.34
958 4416 5.419542 TCCTCTTGTTGATTCGATTCGATT 58.580 37.500 9.96 6.37 35.23 3.34
1297 4757 0.811915 TACTCTGCTTGCTCCTCGTC 59.188 55.000 0.00 0.00 0.00 4.20
1402 4865 1.461091 AACTTGCGGACGAGAGACCA 61.461 55.000 0.00 0.00 46.53 4.02
1452 4915 1.169661 TGTTGTTGGTGATGACGGCC 61.170 55.000 0.00 0.00 0.00 6.13
1489 4952 1.913419 ACCTTTCCCTCGCTGGAATAA 59.087 47.619 6.35 0.00 43.72 1.40
1770 5243 4.283467 TCCTCTTCCTTCTTTTCATCGTCA 59.717 41.667 0.00 0.00 0.00 4.35
1821 5297 3.793144 GCAAACTCCGCCGAGCAG 61.793 66.667 1.65 0.00 40.03 4.24
1830 5306 2.665185 ACGTCTGGCGCAAACTCC 60.665 61.111 10.83 0.00 46.11 3.85
2124 6467 3.501828 CGGATTTCATGTTGAACACCTCA 59.498 43.478 0.00 0.00 35.89 3.86
2422 6784 1.350706 GCTGAGACGAGCAAGCAGAC 61.351 60.000 0.00 0.00 38.95 3.51
2443 6805 3.004106 CCACGTACCAGCCACTATACTAC 59.996 52.174 0.00 0.00 0.00 2.73
2513 6875 4.673441 ACGAAGACATACTGCAGATACAC 58.327 43.478 23.35 8.67 0.00 2.90
2524 6886 7.813852 AACTACATGAAGAACGAAGACATAC 57.186 36.000 0.00 0.00 0.00 2.39
2553 6915 3.509575 TCATTGGACAAACAATACCCTGC 59.490 43.478 0.00 0.00 38.94 4.85
2799 7168 9.984590 AGTACAACCCCATAATACACTAATTTT 57.015 29.630 0.00 0.00 0.00 1.82
2807 7176 6.419791 CCTCAAAGTACAACCCCATAATACA 58.580 40.000 0.00 0.00 0.00 2.29
2907 7279 2.378547 AGACTGAGAGAGGACCTTGTCT 59.621 50.000 6.97 6.97 32.47 3.41
2982 7357 7.206687 TGTTGATTAATTTGTTCACCTCCAAC 58.793 34.615 0.00 0.00 0.00 3.77
3109 7484 1.006102 CGAGGGTGAGACGCAAACT 60.006 57.895 0.00 0.00 32.95 2.66


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

AutoCloner maintained by Alex Coulton.