Multiple sequence alignment - TraesCS3D01G471200

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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 TraesCS3D01G471200 chr3D 100.000 3151 0 0 1 3151 573689248 573692398 0.000000e+00 5819.0
1 TraesCS3D01G471200 chr3D 93.046 417 27 2 1341 1756 305580070 305580485 2.690000e-170 608.0
2 TraesCS3D01G471200 chr3D 80.541 370 40 19 1970 2338 305581334 305581672 4.030000e-64 255.0
3 TraesCS3D01G471200 chr3D 91.489 141 11 1 989 1128 305579654 305579794 3.210000e-45 193.0
4 TraesCS3D01G471200 chr3D 92.523 107 8 0 1164 1270 305579863 305579969 1.510000e-33 154.0
5 TraesCS3D01G471200 chr3D 94.565 92 5 0 1753 1844 305580597 305580688 3.280000e-30 143.0
6 TraesCS3D01G471200 chr3A 92.550 3114 152 30 84 3148 708321515 708324597 0.000000e+00 4392.0
7 TraesCS3D01G471200 chr3A 94.598 722 34 2 1710 2426 708325248 708325969 0.000000e+00 1112.0
8 TraesCS3D01G471200 chr3A 90.203 541 20 11 2418 2955 708330360 708330870 0.000000e+00 675.0
9 TraesCS3D01G471200 chr3A 93.012 415 29 0 1342 1756 423619438 423619852 9.670000e-170 606.0
10 TraesCS3D01G471200 chr3A 79.888 537 60 26 775 1271 423618819 423619347 1.800000e-92 350.0
11 TraesCS3D01G471200 chr3A 81.250 432 49 16 1970 2399 423620973 423621374 1.410000e-83 320.0
12 TraesCS3D01G471200 chr3A 88.304 171 14 3 2984 3148 708330864 708331034 1.920000e-47 200.0
13 TraesCS3D01G471200 chr3A 94.565 92 5 0 1753 1844 423619975 423620066 3.280000e-30 143.0
14 TraesCS3D01G471200 chr3B 90.156 2753 177 31 348 3033 763775091 763772366 0.000000e+00 3496.0
15 TraesCS3D01G471200 chr3B 93.269 416 26 2 1342 1756 416151854 416151440 2.080000e-171 612.0
16 TraesCS3D01G471200 chr3B 81.977 344 38 13 1995 2338 416150234 416149915 1.440000e-68 270.0
17 TraesCS3D01G471200 chr3B 90.741 162 14 1 992 1152 416152272 416152111 6.840000e-52 215.0
18 TraesCS3D01G471200 chr3B 94.000 100 6 0 124 223 763780623 763780524 5.440000e-33 152.0
19 TraesCS3D01G471200 chr3B 91.589 107 9 0 1164 1270 416152057 416151951 7.040000e-32 148.0
20 TraesCS3D01G471200 chr3B 100.000 45 0 0 26 70 118791944 118791988 2.010000e-12 84.2
21 TraesCS3D01G471200 chr7A 84.086 465 58 10 2578 3026 287491446 287490982 4.830000e-118 435.0
22 TraesCS3D01G471200 chr6B 81.356 531 54 21 2581 3070 707717009 707716483 1.060000e-104 390.0
23 TraesCS3D01G471200 chr6B 97.826 46 1 0 28 73 452817860 452817815 2.610000e-11 80.5
24 TraesCS3D01G471200 chr6B 97.826 46 1 0 28 73 452930819 452930774 2.610000e-11 80.5
25 TraesCS3D01G471200 chr7D 80.979 531 55 24 2581 3070 2491627 2491102 2.290000e-101 379.0
26 TraesCS3D01G471200 chr5B 81.172 478 49 19 2582 3025 434430830 434431300 2.330000e-91 346.0
27 TraesCS3D01G471200 chr5B 96.000 50 1 1 26 75 532347377 532347329 2.610000e-11 80.5
28 TraesCS3D01G471200 chr5B 94.000 50 3 0 26 75 146913806 146913855 3.370000e-10 76.8
29 TraesCS3D01G471200 chr5B 97.727 44 1 0 26 69 319352838 319352881 3.370000e-10 76.8
30 TraesCS3D01G471200 chr7B 79.463 521 60 23 2581 3060 747120079 747120593 3.030000e-85 326.0
31 TraesCS3D01G471200 chr7B 78.838 241 29 10 2837 3065 568003633 568003863 3.280000e-30 143.0
32 TraesCS3D01G471200 chr2A 80.043 461 54 15 2582 3026 30823628 30824066 1.100000e-79 307.0
33 TraesCS3D01G471200 chr1B 80.328 427 49 22 2576 2996 278633487 278633884 1.110000e-74 291.0
34 TraesCS3D01G471200 chr1A 79.487 429 52 27 2576 2989 249148946 249149353 4.000000e-69 272.0
35 TraesCS3D01G471200 chr1A 91.139 79 7 0 3073 3151 377012879 377012801 1.200000e-19 108.0
36 TraesCS3D01G471200 chr1A 96.154 52 2 0 26 77 33227937 33227886 5.600000e-13 86.1
37 TraesCS3D01G471200 chr1D 89.697 165 13 2 2578 2738 198756174 198756338 1.150000e-49 207.0
38 TraesCS3D01G471200 chr4B 96.296 54 0 1 21 72 584587256 584587309 1.560000e-13 87.9
39 TraesCS3D01G471200 chr2B 97.826 46 0 1 26 70 752488112 752488067 9.370000e-11 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 TraesCS3D01G471200 chr3D 573689248 573692398 3150 False 5819.00 5819 100.00000 1 3151 1 chr3D.!!$F1 3150
1 TraesCS3D01G471200 chr3D 305579654 305581672 2018 False 270.60 608 90.43280 989 2338 5 chr3D.!!$F2 1349
2 TraesCS3D01G471200 chr3A 708321515 708325969 4454 False 2752.00 4392 93.57400 84 3148 2 chr3A.!!$F2 3064
3 TraesCS3D01G471200 chr3A 708330360 708331034 674 False 437.50 675 89.25350 2418 3148 2 chr3A.!!$F3 730
4 TraesCS3D01G471200 chr3A 423618819 423621374 2555 False 354.75 606 87.17875 775 2399 4 chr3A.!!$F1 1624
5 TraesCS3D01G471200 chr3B 763772366 763775091 2725 True 3496.00 3496 90.15600 348 3033 1 chr3B.!!$R1 2685
6 TraesCS3D01G471200 chr3B 416149915 416152272 2357 True 311.25 612 89.39400 992 2338 4 chr3B.!!$R3 1346
7 TraesCS3D01G471200 chr6B 707716483 707717009 526 True 390.00 390 81.35600 2581 3070 1 chr6B.!!$R3 489
8 TraesCS3D01G471200 chr7D 2491102 2491627 525 True 379.00 379 80.97900 2581 3070 1 chr7D.!!$R1 489
9 TraesCS3D01G471200 chr7B 747120079 747120593 514 False 326.00 326 79.46300 2581 3060 1 chr7B.!!$F2 479

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
518 524 0.096454 GGCGTGGAATTAACTCGTGC 59.904 55.0 6.13 0.0 0.0 5.34 F
985 1037 0.321671 GCAGTCAAGGAGCACAGGTA 59.678 55.0 0.00 0.0 0.0 3.08 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1852 2991 1.302832 GTTGTGTCCCCAGAGCAGG 60.303 63.158 0.00 0.0 0.00 4.85 R
2295 3480 2.806198 CAAATTGCGCGGTGCTGG 60.806 61.111 15.31 0.0 46.63 4.85 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
26 27 6.192970 ACTCCCTCTGTCCCATAATAAATG 57.807 41.667 0.00 0.00 0.00 2.32
27 28 5.672194 ACTCCCTCTGTCCCATAATAAATGT 59.328 40.000 0.00 0.00 0.00 2.71
28 29 6.849697 ACTCCCTCTGTCCCATAATAAATGTA 59.150 38.462 0.00 0.00 0.00 2.29
29 30 7.074653 TCCCTCTGTCCCATAATAAATGTAC 57.925 40.000 0.00 0.00 0.00 2.90
30 31 6.849697 TCCCTCTGTCCCATAATAAATGTACT 59.150 38.462 0.00 0.00 0.00 2.73
31 32 8.014263 TCCCTCTGTCCCATAATAAATGTACTA 58.986 37.037 0.00 0.00 0.00 1.82
32 33 8.656806 CCCTCTGTCCCATAATAAATGTACTAA 58.343 37.037 0.00 0.00 0.00 2.24
33 34 9.712305 CCTCTGTCCCATAATAAATGTACTAAG 57.288 37.037 0.00 0.00 0.00 2.18
34 35 9.209175 CTCTGTCCCATAATAAATGTACTAAGC 57.791 37.037 0.00 0.00 0.00 3.09
35 36 8.934697 TCTGTCCCATAATAAATGTACTAAGCT 58.065 33.333 0.00 0.00 0.00 3.74
36 37 9.209175 CTGTCCCATAATAAATGTACTAAGCTC 57.791 37.037 0.00 0.00 0.00 4.09
37 38 8.710239 TGTCCCATAATAAATGTACTAAGCTCA 58.290 33.333 0.00 0.00 0.00 4.26
38 39 9.555727 GTCCCATAATAAATGTACTAAGCTCAA 57.444 33.333 0.00 0.00 0.00 3.02
39 40 9.778741 TCCCATAATAAATGTACTAAGCTCAAG 57.221 33.333 0.00 0.00 0.00 3.02
40 41 9.778741 CCCATAATAAATGTACTAAGCTCAAGA 57.221 33.333 3.19 0.00 0.00 3.02
45 46 9.726438 AATAAATGTACTAAGCTCAAGACACTT 57.274 29.630 3.19 0.00 0.00 3.16
48 49 9.726438 AAATGTACTAAGCTCAAGACACTTATT 57.274 29.630 3.19 0.00 0.00 1.40
49 50 9.726438 AATGTACTAAGCTCAAGACACTTATTT 57.274 29.630 3.19 0.00 0.00 1.40
50 51 9.726438 ATGTACTAAGCTCAAGACACTTATTTT 57.274 29.630 3.19 0.00 0.00 1.82
53 54 8.779354 ACTAAGCTCAAGACACTTATTTTAGG 57.221 34.615 3.19 0.00 0.00 2.69
54 55 8.594550 ACTAAGCTCAAGACACTTATTTTAGGA 58.405 33.333 3.19 0.00 0.00 2.94
55 56 7.674471 AAGCTCAAGACACTTATTTTAGGAC 57.326 36.000 0.00 0.00 0.00 3.85
56 57 5.869888 AGCTCAAGACACTTATTTTAGGACG 59.130 40.000 0.00 0.00 0.00 4.79
57 58 5.063564 GCTCAAGACACTTATTTTAGGACGG 59.936 44.000 0.00 0.00 0.00 4.79
58 59 6.349243 TCAAGACACTTATTTTAGGACGGA 57.651 37.500 0.00 0.00 0.00 4.69
59 60 6.395629 TCAAGACACTTATTTTAGGACGGAG 58.604 40.000 0.00 0.00 0.00 4.63
60 61 5.340439 AGACACTTATTTTAGGACGGAGG 57.660 43.478 0.00 0.00 0.00 4.30
61 62 4.161754 AGACACTTATTTTAGGACGGAGGG 59.838 45.833 0.00 0.00 0.00 4.30
62 63 4.098894 ACACTTATTTTAGGACGGAGGGA 58.901 43.478 0.00 0.00 0.00 4.20
63 64 4.161754 ACACTTATTTTAGGACGGAGGGAG 59.838 45.833 0.00 0.00 0.00 4.30
64 65 4.161754 CACTTATTTTAGGACGGAGGGAGT 59.838 45.833 0.00 0.00 0.00 3.85
65 66 5.361857 CACTTATTTTAGGACGGAGGGAGTA 59.638 44.000 0.00 0.00 0.00 2.59
66 67 6.041751 CACTTATTTTAGGACGGAGGGAGTAT 59.958 42.308 0.00 0.00 0.00 2.12
67 68 6.614496 ACTTATTTTAGGACGGAGGGAGTATT 59.386 38.462 0.00 0.00 0.00 1.89
68 69 7.786464 ACTTATTTTAGGACGGAGGGAGTATTA 59.214 37.037 0.00 0.00 0.00 0.98
69 70 8.731591 TTATTTTAGGACGGAGGGAGTATTAT 57.268 34.615 0.00 0.00 0.00 1.28
70 71 7.628501 ATTTTAGGACGGAGGGAGTATTATT 57.371 36.000 0.00 0.00 0.00 1.40
71 72 7.441903 TTTTAGGACGGAGGGAGTATTATTT 57.558 36.000 0.00 0.00 0.00 1.40
72 73 7.441903 TTTAGGACGGAGGGAGTATTATTTT 57.558 36.000 0.00 0.00 0.00 1.82
73 74 8.551682 TTTAGGACGGAGGGAGTATTATTTTA 57.448 34.615 0.00 0.00 0.00 1.52
74 75 6.416631 AGGACGGAGGGAGTATTATTTTAC 57.583 41.667 0.00 0.00 0.00 2.01
75 76 5.901276 AGGACGGAGGGAGTATTATTTTACA 59.099 40.000 0.00 0.00 0.00 2.41
76 77 6.384886 AGGACGGAGGGAGTATTATTTTACAA 59.615 38.462 0.00 0.00 0.00 2.41
77 78 7.049754 GGACGGAGGGAGTATTATTTTACAAA 58.950 38.462 0.00 0.00 0.00 2.83
78 79 7.226128 GGACGGAGGGAGTATTATTTTACAAAG 59.774 40.741 0.00 0.00 0.00 2.77
79 80 7.052248 ACGGAGGGAGTATTATTTTACAAAGG 58.948 38.462 0.00 0.00 0.00 3.11
80 81 7.052248 CGGAGGGAGTATTATTTTACAAAGGT 58.948 38.462 0.00 0.00 0.00 3.50
81 82 7.555195 CGGAGGGAGTATTATTTTACAAAGGTT 59.445 37.037 0.00 0.00 0.00 3.50
82 83 8.683615 GGAGGGAGTATTATTTTACAAAGGTTG 58.316 37.037 0.00 0.00 0.00 3.77
97 98 6.677913 ACAAAGGTTGTACTATTGATTGTGC 58.322 36.000 0.00 0.00 43.27 4.57
102 103 6.374333 AGGTTGTACTATTGATTGTGCGAATT 59.626 34.615 0.00 0.00 0.00 2.17
122 123 1.795768 TCAAGTCGAGGTTGCATGTC 58.204 50.000 0.00 0.00 0.00 3.06
145 146 0.866427 GTCGAGCATCATGCCATCTG 59.134 55.000 5.84 0.00 46.52 2.90
161 162 2.281484 TGGCCAAAGCGTCAGGAC 60.281 61.111 0.61 0.00 41.24 3.85
187 188 6.948589 AGGTTCCTCTACCAGTTAAAATCTC 58.051 40.000 0.00 0.00 40.82 2.75
188 189 6.500751 AGGTTCCTCTACCAGTTAAAATCTCA 59.499 38.462 0.00 0.00 40.82 3.27
198 199 4.159135 CAGTTAAAATCTCATGGCTGGCTT 59.841 41.667 2.00 0.00 0.00 4.35
224 225 8.886719 TGAGTTGATGAATCTAATGACAATCAC 58.113 33.333 0.00 0.00 0.00 3.06
234 235 5.872617 TCTAATGACAATCACGAAAACCGAT 59.127 36.000 0.00 0.00 41.76 4.18
251 252 2.358957 CGATCATTTGCTTGGAGTCCA 58.641 47.619 8.12 8.12 0.00 4.02
255 256 4.789012 TCATTTGCTTGGAGTCCATTTC 57.211 40.909 14.00 5.81 31.53 2.17
256 257 3.191162 TCATTTGCTTGGAGTCCATTTCG 59.809 43.478 14.00 3.39 31.53 3.46
266 267 7.148804 GCTTGGAGTCCATTTCGTTTTATTTTC 60.149 37.037 14.00 0.00 31.53 2.29
268 269 6.265649 TGGAGTCCATTTCGTTTTATTTTCCA 59.734 34.615 8.12 0.00 0.00 3.53
280 281 6.183359 CGTTTTATTTTCCAAAGGATCAAGCG 60.183 38.462 0.00 0.00 0.00 4.68
311 312 6.183359 CGTAAACTGCAGATCAAACAAATTCG 60.183 38.462 23.35 0.00 0.00 3.34
322 323 4.013728 CAAACAAATTCGGTGAGGGGATA 58.986 43.478 0.00 0.00 0.00 2.59
408 409 0.521735 GGGTTTGGACATCGCTTCAC 59.478 55.000 0.00 0.00 0.00 3.18
496 502 1.482182 CATGAGGATGTCGTCTTCCCA 59.518 52.381 10.27 8.80 38.27 4.37
512 518 0.808755 CCCAGTGGCGTGGAATTAAC 59.191 55.000 2.61 0.00 40.44 2.01
516 522 1.001633 AGTGGCGTGGAATTAACTCGT 59.998 47.619 6.13 0.00 0.00 4.18
518 524 0.096454 GGCGTGGAATTAACTCGTGC 59.904 55.000 6.13 0.00 0.00 5.34
548 554 1.244019 ATTCCACGCCAAAGTGAGCC 61.244 55.000 0.00 0.00 44.43 4.70
551 557 1.898574 CACGCCAAAGTGAGCCCTT 60.899 57.895 0.00 0.00 44.43 3.95
672 684 5.760253 CGATGGTGATAGGTTAGCAAAAGAT 59.240 40.000 0.00 0.00 0.00 2.40
696 708 1.492319 TTCCGTTCGGTGCGTGAAAG 61.492 55.000 11.04 0.00 0.00 2.62
717 733 5.913137 AGCATTTTTATTTCACCCATCGA 57.087 34.783 0.00 0.00 0.00 3.59
740 756 6.034683 CGATAGTAGAACAACTTGCAACTACC 59.965 42.308 15.29 4.25 33.18 3.18
763 782 4.706476 CACCAGAAGGAAATGAATGCCTTA 59.294 41.667 0.00 0.00 41.85 2.69
799 821 3.314541 TCGGTAGAAGAAGAACTTGCC 57.685 47.619 0.00 0.00 39.13 4.52
826 849 2.691409 CGGAAGGAGTTGAATGCCTA 57.309 50.000 0.00 0.00 0.00 3.93
888 918 3.005539 AGCCAGGTCGTCTGCCAT 61.006 61.111 3.61 0.00 42.05 4.40
900 930 5.869888 GGTCGTCTGCCATTCTTATATAAGG 59.130 44.000 19.98 8.12 34.14 2.69
916 949 2.038863 AAGGTCACCACCCATACTGA 57.961 50.000 0.00 0.00 45.12 3.41
920 953 1.207329 GTCACCACCCATACTGACTCC 59.793 57.143 0.00 0.00 31.99 3.85
984 1036 1.072159 GCAGTCAAGGAGCACAGGT 59.928 57.895 0.00 0.00 0.00 4.00
985 1037 0.321671 GCAGTCAAGGAGCACAGGTA 59.678 55.000 0.00 0.00 0.00 3.08
1142 1194 2.672996 CAAGGTGCCCGGGAACAG 60.673 66.667 33.33 18.14 0.00 3.16
1153 1205 2.741092 GGAACAGCTCCACCGTCA 59.259 61.111 0.00 0.00 44.67 4.35
1189 1289 0.667792 GAGCGAGACGAAAGCCAACT 60.668 55.000 0.00 0.00 0.00 3.16
1279 1385 2.490328 TTGCACTTTGTACTTGCAGC 57.510 45.000 10.47 0.00 46.46 5.25
1280 1386 1.387539 TGCACTTTGTACTTGCAGCA 58.612 45.000 0.00 0.00 41.29 4.41
1282 1388 1.927710 GCACTTTGTACTTGCAGCAGC 60.928 52.381 0.00 0.00 42.57 5.25
1687 1844 2.759795 GTCAAGGGGCTCAAGGCT 59.240 61.111 3.42 0.00 41.46 4.58
1852 2991 2.908626 CGTTTTGCCGCAGAAAATACTC 59.091 45.455 0.00 0.00 0.00 2.59
2295 3480 2.040278 TGCATAATACCATGGAGGGAGC 59.960 50.000 21.47 14.91 43.89 4.70
2313 3498 3.472298 CAGCACCGCGCAATTTGC 61.472 61.111 8.75 11.42 46.13 3.68
2573 3787 2.361230 GAAAACAGCCCCTCCCCG 60.361 66.667 0.00 0.00 0.00 5.73
2574 3788 2.856988 AAAACAGCCCCTCCCCGA 60.857 61.111 0.00 0.00 0.00 5.14
3052 4342 2.923035 ACACGCCCCTGTAGCTGT 60.923 61.111 0.00 0.00 0.00 4.40
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
12 13 9.555727 TTGAGCTTAGTACATTTATTATGGGAC 57.444 33.333 0.00 0.00 0.00 4.46
13 14 9.778741 CTTGAGCTTAGTACATTTATTATGGGA 57.221 33.333 0.00 0.00 0.00 4.37
14 15 9.778741 TCTTGAGCTTAGTACATTTATTATGGG 57.221 33.333 0.00 0.00 0.00 4.00
19 20 9.726438 AAGTGTCTTGAGCTTAGTACATTTATT 57.274 29.630 0.00 0.00 0.00 1.40
22 23 9.726438 AATAAGTGTCTTGAGCTTAGTACATTT 57.274 29.630 0.00 0.00 0.00 2.32
23 24 9.726438 AAATAAGTGTCTTGAGCTTAGTACATT 57.274 29.630 0.00 0.00 0.00 2.71
24 25 9.726438 AAAATAAGTGTCTTGAGCTTAGTACAT 57.274 29.630 0.00 0.00 0.00 2.29
27 28 9.871238 CCTAAAATAAGTGTCTTGAGCTTAGTA 57.129 33.333 0.00 0.00 0.00 1.82
28 29 8.594550 TCCTAAAATAAGTGTCTTGAGCTTAGT 58.405 33.333 0.00 0.00 0.00 2.24
29 30 8.874816 GTCCTAAAATAAGTGTCTTGAGCTTAG 58.125 37.037 0.00 0.00 0.00 2.18
30 31 7.544566 CGTCCTAAAATAAGTGTCTTGAGCTTA 59.455 37.037 0.00 0.00 0.00 3.09
31 32 6.369065 CGTCCTAAAATAAGTGTCTTGAGCTT 59.631 38.462 0.00 0.00 0.00 3.74
32 33 5.869888 CGTCCTAAAATAAGTGTCTTGAGCT 59.130 40.000 0.00 0.00 0.00 4.09
33 34 5.063564 CCGTCCTAAAATAAGTGTCTTGAGC 59.936 44.000 0.00 0.00 0.00 4.26
34 35 6.395629 TCCGTCCTAAAATAAGTGTCTTGAG 58.604 40.000 0.00 0.00 0.00 3.02
35 36 6.349243 TCCGTCCTAAAATAAGTGTCTTGA 57.651 37.500 0.00 0.00 0.00 3.02
36 37 5.581085 CCTCCGTCCTAAAATAAGTGTCTTG 59.419 44.000 0.00 0.00 0.00 3.02
37 38 5.338137 CCCTCCGTCCTAAAATAAGTGTCTT 60.338 44.000 0.00 0.00 0.00 3.01
38 39 4.161754 CCCTCCGTCCTAAAATAAGTGTCT 59.838 45.833 0.00 0.00 0.00 3.41
39 40 4.161001 TCCCTCCGTCCTAAAATAAGTGTC 59.839 45.833 0.00 0.00 0.00 3.67
40 41 4.098894 TCCCTCCGTCCTAAAATAAGTGT 58.901 43.478 0.00 0.00 0.00 3.55
41 42 4.161754 ACTCCCTCCGTCCTAAAATAAGTG 59.838 45.833 0.00 0.00 0.00 3.16
42 43 4.359996 ACTCCCTCCGTCCTAAAATAAGT 58.640 43.478 0.00 0.00 0.00 2.24
43 44 6.667558 ATACTCCCTCCGTCCTAAAATAAG 57.332 41.667 0.00 0.00 0.00 1.73
44 45 8.731591 ATAATACTCCCTCCGTCCTAAAATAA 57.268 34.615 0.00 0.00 0.00 1.40
45 46 8.731591 AATAATACTCCCTCCGTCCTAAAATA 57.268 34.615 0.00 0.00 0.00 1.40
46 47 7.628501 AATAATACTCCCTCCGTCCTAAAAT 57.371 36.000 0.00 0.00 0.00 1.82
47 48 7.441903 AAATAATACTCCCTCCGTCCTAAAA 57.558 36.000 0.00 0.00 0.00 1.52
48 49 7.441903 AAAATAATACTCCCTCCGTCCTAAA 57.558 36.000 0.00 0.00 0.00 1.85
49 50 7.564660 TGTAAAATAATACTCCCTCCGTCCTAA 59.435 37.037 0.00 0.00 0.00 2.69
50 51 7.068702 TGTAAAATAATACTCCCTCCGTCCTA 58.931 38.462 0.00 0.00 0.00 2.94
51 52 5.901276 TGTAAAATAATACTCCCTCCGTCCT 59.099 40.000 0.00 0.00 0.00 3.85
52 53 6.165700 TGTAAAATAATACTCCCTCCGTCC 57.834 41.667 0.00 0.00 0.00 4.79
53 54 7.226128 CCTTTGTAAAATAATACTCCCTCCGTC 59.774 40.741 0.00 0.00 0.00 4.79
54 55 7.052248 CCTTTGTAAAATAATACTCCCTCCGT 58.948 38.462 0.00 0.00 0.00 4.69
55 56 7.052248 ACCTTTGTAAAATAATACTCCCTCCG 58.948 38.462 0.00 0.00 0.00 4.63
56 57 8.683615 CAACCTTTGTAAAATAATACTCCCTCC 58.316 37.037 0.00 0.00 0.00 4.30
57 58 9.239551 ACAACCTTTGTAAAATAATACTCCCTC 57.760 33.333 0.00 0.00 43.27 4.30
71 72 8.293867 GCACAATCAATAGTACAACCTTTGTAA 58.706 33.333 0.38 0.00 46.72 2.41
72 73 7.360522 CGCACAATCAATAGTACAACCTTTGTA 60.361 37.037 0.00 0.00 43.27 2.41
74 75 5.794945 CGCACAATCAATAGTACAACCTTTG 59.205 40.000 0.00 0.00 0.00 2.77
75 76 5.703592 TCGCACAATCAATAGTACAACCTTT 59.296 36.000 0.00 0.00 0.00 3.11
76 77 5.242434 TCGCACAATCAATAGTACAACCTT 58.758 37.500 0.00 0.00 0.00 3.50
77 78 4.827692 TCGCACAATCAATAGTACAACCT 58.172 39.130 0.00 0.00 0.00 3.50
78 79 5.539582 TTCGCACAATCAATAGTACAACC 57.460 39.130 0.00 0.00 0.00 3.77
79 80 7.748683 TGAAATTCGCACAATCAATAGTACAAC 59.251 33.333 0.00 0.00 0.00 3.32
80 81 7.811653 TGAAATTCGCACAATCAATAGTACAA 58.188 30.769 0.00 0.00 0.00 2.41
81 82 7.371126 TGAAATTCGCACAATCAATAGTACA 57.629 32.000 0.00 0.00 0.00 2.90
82 83 7.962918 ACTTGAAATTCGCACAATCAATAGTAC 59.037 33.333 0.00 0.00 30.39 2.73
97 98 2.223144 TGCAACCTCGACTTGAAATTCG 59.777 45.455 2.81 0.00 36.55 3.34
102 103 2.143122 GACATGCAACCTCGACTTGAA 58.857 47.619 0.00 0.00 0.00 2.69
110 111 0.792640 CGACAGTGACATGCAACCTC 59.207 55.000 0.00 0.00 0.00 3.85
122 123 0.741927 TGGCATGATGCTCGACAGTG 60.742 55.000 17.84 0.00 44.28 3.66
161 162 4.796038 TTTAACTGGTAGAGGAACCTCG 57.204 45.455 14.13 3.70 46.90 4.63
168 169 5.529060 GCCATGAGATTTTAACTGGTAGAGG 59.471 44.000 0.00 0.00 0.00 3.69
187 188 1.134367 CATCAACTCAAGCCAGCCATG 59.866 52.381 0.00 0.00 0.00 3.66
188 189 1.005097 TCATCAACTCAAGCCAGCCAT 59.995 47.619 0.00 0.00 0.00 4.40
198 199 8.886719 GTGATTGTCATTAGATTCATCAACTCA 58.113 33.333 0.00 0.00 0.00 3.41
224 225 2.916716 CCAAGCAAATGATCGGTTTTCG 59.083 45.455 0.00 0.00 40.90 3.46
234 235 3.191162 CGAAATGGACTCCAAGCAAATGA 59.809 43.478 0.66 0.00 36.95 2.57
251 252 9.771534 TTGATCCTTTGGAAAATAAAACGAAAT 57.228 25.926 0.00 0.00 34.34 2.17
255 256 6.183359 CGCTTGATCCTTTGGAAAATAAAACG 60.183 38.462 0.00 0.00 34.34 3.60
256 257 6.866248 TCGCTTGATCCTTTGGAAAATAAAAC 59.134 34.615 0.00 0.00 34.34 2.43
266 267 1.709147 CGCCTCGCTTGATCCTTTGG 61.709 60.000 0.00 0.00 0.00 3.28
268 269 4.208632 CGCCTCGCTTGATCCTTT 57.791 55.556 0.00 0.00 0.00 3.11
280 281 1.084370 ATCTGCAGTTTACGCGCCTC 61.084 55.000 14.67 0.00 0.00 4.70
290 291 4.037923 ACCGAATTTGTTTGATCTGCAGTT 59.962 37.500 14.67 5.03 0.00 3.16
293 294 3.567585 TCACCGAATTTGTTTGATCTGCA 59.432 39.130 0.00 0.00 0.00 4.41
322 323 1.496429 CTGCCATATCCCTTTGGAGGT 59.504 52.381 0.00 0.00 46.08 3.85
330 331 4.796110 AACATGTAACTGCCATATCCCT 57.204 40.909 0.00 0.00 0.00 4.20
493 499 0.808755 GTTAATTCCACGCCACTGGG 59.191 55.000 0.00 0.00 37.18 4.45
496 502 1.001633 ACGAGTTAATTCCACGCCACT 59.998 47.619 0.00 0.00 0.00 4.00
518 524 3.530260 GTGGAATGCCGCCATGGG 61.530 66.667 15.13 3.37 38.80 4.00
532 538 3.365265 GGGCTCACTTTGGCGTGG 61.365 66.667 0.00 0.00 35.63 4.94
551 557 1.591703 CCTACTCAGAGCAACCGCA 59.408 57.895 0.00 0.00 42.27 5.69
652 664 7.048512 ACACTATCTTTTGCTAACCTATCACC 58.951 38.462 0.00 0.00 0.00 4.02
672 684 1.372004 CGCACCGAACGGAACACTA 60.372 57.895 20.14 0.00 38.96 2.74
696 708 7.425606 ACTATCGATGGGTGAAATAAAAATGC 58.574 34.615 13.75 0.00 0.00 3.56
717 733 6.649557 GTGGTAGTTGCAAGTTGTTCTACTAT 59.350 38.462 12.95 2.21 0.00 2.12
740 756 3.094572 AGGCATTCATTTCCTTCTGGTG 58.905 45.455 0.00 0.00 34.23 4.17
763 782 7.883311 TCTTCTACCGATCTGGAAATTTTCTTT 59.117 33.333 8.93 0.00 42.00 2.52
799 821 0.249398 CAACTCCTTCCGGTGGTAGG 59.751 60.000 14.11 10.97 40.94 3.18
826 849 5.425630 ACTATTCGGGCGAACTTTTCTTAT 58.574 37.500 0.00 0.00 36.91 1.73
888 918 7.792736 AGTATGGGTGGTGACCTTATATAAGAA 59.207 37.037 21.75 6.29 42.66 2.52
900 930 1.207329 GGAGTCAGTATGGGTGGTGAC 59.793 57.143 0.00 0.00 39.74 3.67
920 953 4.124351 CAATGCTGCTGCGTGGGG 62.124 66.667 11.37 0.89 43.34 4.96
938 971 2.602257 TCCTGGATCTACGCACAATG 57.398 50.000 0.00 0.00 0.00 2.82
984 1036 6.246919 GTTCACCATCCTATCCTAGCTACTA 58.753 44.000 0.00 0.00 0.00 1.82
985 1037 5.081032 GTTCACCATCCTATCCTAGCTACT 58.919 45.833 0.00 0.00 0.00 2.57
1153 1205 3.764466 CTGCTTCTCCTCGGGCGT 61.764 66.667 0.00 0.00 0.00 5.68
1161 1261 1.226547 CGTCTCGCTCTGCTTCTCC 60.227 63.158 0.00 0.00 0.00 3.71
1282 1388 6.475207 GGAATGTACGTAGCATAACAAAGTG 58.525 40.000 0.00 0.00 0.00 3.16
1285 1391 5.170021 ACGGAATGTACGTAGCATAACAAA 58.830 37.500 0.00 0.00 43.60 2.83
1687 1844 4.212913 GCGGCGATGGAGAGCAGA 62.213 66.667 12.98 0.00 34.54 4.26
1852 2991 1.302832 GTTGTGTCCCCAGAGCAGG 60.303 63.158 0.00 0.00 0.00 4.85
2295 3480 2.806198 CAAATTGCGCGGTGCTGG 60.806 61.111 15.31 0.00 46.63 4.85
2705 3927 3.540367 GAAAGAACCCCACCGCCGA 62.540 63.158 0.00 0.00 0.00 5.54
3037 4327 3.706373 CCACAGCTACAGGGGCGT 61.706 66.667 0.00 0.00 34.52 5.68


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

AutoCloner maintained by Alex Coulton.