Multiple sequence alignment - TraesCS7D01G442600

Loading Multiple Alignment...

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 TraesCS7D01G442600 chr7D 100.000 4173 0 0 327 4499 562120797 562124969 0.000000e+00 7707
1 TraesCS7D01G442600 chr7D 100.000 117 0 0 1 117 562120471 562120587 2.730000e-52 217
2 TraesCS7D01G442600 chr7A 96.662 2337 72 5 1428 3759 647296458 647298793 0.000000e+00 3879
3 TraesCS7D01G442600 chr7A 90.472 1123 48 9 327 1430 647295253 647296335 0.000000e+00 1426
4 TraesCS7D01G442600 chr7A 91.407 675 27 11 3832 4485 647299628 647300292 0.000000e+00 896
5 TraesCS7D01G442600 chr7B 96.724 1618 50 2 2142 3759 611720336 611721950 0.000000e+00 2691
6 TraesCS7D01G442600 chr7B 91.098 1831 110 17 327 2145 611718467 611720256 0.000000e+00 2429
7 TraesCS7D01G442600 chr7B 94.815 675 29 2 3819 4493 611722821 611723489 0.000000e+00 1048
8 TraesCS7D01G442600 chr3D 81.833 1855 239 63 1569 3366 324386570 324388383 0.000000e+00 1469
9 TraesCS7D01G442600 chr3B 80.837 1936 265 62 1568 3436 424792427 424790531 0.000000e+00 1423
10 TraesCS7D01G442600 chr3B 90.354 311 29 1 941 1250 424792761 424792451 1.510000e-109 407
11 TraesCS7D01G442600 chr3A 84.152 1527 164 44 1957 3436 437863778 437865273 0.000000e+00 1408
12 TraesCS7D01G442600 chr3A 81.825 1414 186 39 1586 2963 437635635 437637013 0.000000e+00 1122
13 TraesCS7D01G442600 chr3A 84.018 438 65 5 932 1365 437862400 437862836 2.500000e-112 416
14 TraesCS7D01G442600 chr3A 88.554 166 19 0 1085 1250 437635420 437635585 7.630000e-48 202
15 TraesCS7D01G442600 chr3A 83.744 203 26 4 3002 3198 437643479 437643680 7.690000e-43 185
16 TraesCS7D01G442600 chr2A 78.322 429 61 15 501 923 722521614 722522016 9.660000e-62 248
17 TraesCS7D01G442600 chr2D 77.622 429 63 16 501 923 587699638 587700039 3.500000e-56 230
18 TraesCS7D01G442600 chr2B 74.495 396 69 15 501 890 710283823 710284192 4.690000e-30 143


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 TraesCS7D01G442600 chr7D 562120471 562124969 4498 False 3962 7707 100.000000 1 4499 2 chr7D.!!$F1 4498
1 TraesCS7D01G442600 chr7A 647295253 647300292 5039 False 2067 3879 92.847000 327 4485 3 chr7A.!!$F1 4158
2 TraesCS7D01G442600 chr7B 611718467 611723489 5022 False 2056 2691 94.212333 327 4493 3 chr7B.!!$F1 4166
3 TraesCS7D01G442600 chr3D 324386570 324388383 1813 False 1469 1469 81.833000 1569 3366 1 chr3D.!!$F1 1797
4 TraesCS7D01G442600 chr3B 424790531 424792761 2230 True 915 1423 85.595500 941 3436 2 chr3B.!!$R1 2495
5 TraesCS7D01G442600 chr3A 437862400 437865273 2873 False 912 1408 84.085000 932 3436 2 chr3A.!!$F3 2504
6 TraesCS7D01G442600 chr3A 437635420 437637013 1593 False 662 1122 85.189500 1085 2963 2 chr3A.!!$F2 1878

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
55 56 0.178068 TCTAGGCGGATTTCCACTGC 59.822 55.000 0.00 0.00 38.72 4.40 F
56 57 0.179000 CTAGGCGGATTTCCACTGCT 59.821 55.000 0.00 0.00 39.31 4.24 F
58 59 0.251341 AGGCGGATTTCCACTGCTTT 60.251 50.000 0.00 0.00 39.31 3.51 F
787 796 0.897863 AAACCGGGCTGCAAATGCTA 60.898 50.000 6.32 0.00 42.66 3.49 F
800 809 3.003068 GCAAATGCTATAGGACTGCTGTG 59.997 47.826 17.85 1.74 38.21 3.66 F
2243 2897 3.084039 TGATGGAAGAAGTGGCACATTC 58.916 45.455 21.41 18.75 44.52 2.67 F
2662 3319 1.598130 GGCAGAGCTTGTTCACCGT 60.598 57.895 0.00 0.00 0.00 4.83 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1210 1220 0.800012 TCTACAACAATTTCCCGCGC 59.200 50.000 0.00 0.0 0.00 6.86 R
1302 1316 4.800471 GCCAGCAAACTATCTAACAAATGC 59.200 41.667 0.00 0.0 0.00 3.56 R
2243 2897 5.416952 AGGAAAGCTCTTGTTACCAATCATG 59.583 40.000 0.00 0.0 0.00 3.07 R
2256 2910 2.839425 AGAGAGATGCAGGAAAGCTCTT 59.161 45.455 0.00 0.0 36.17 2.85 R
2461 3117 5.645497 AGTCCATGCTTGTATTCAACTTCTC 59.355 40.000 0.00 0.0 0.00 2.87 R
3244 3935 0.390472 GCCCACTTCAGTTCTCCGAG 60.390 60.000 0.00 0.0 0.00 4.63 R
3826 4552 0.393537 AAAGGCCGAGCTCCAATGAG 60.394 55.000 8.47 0.0 41.84 2.90 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
20 21 3.996150 CACACCACTGCAAATCTCTTT 57.004 42.857 0.00 0.00 0.00 2.52
21 22 3.635331 CACACCACTGCAAATCTCTTTG 58.365 45.455 0.00 0.00 43.81 2.77
31 32 4.012319 CAAATCTCTTTGCCTCACATCG 57.988 45.455 0.00 0.00 35.69 3.84
32 33 1.661341 ATCTCTTTGCCTCACATCGC 58.339 50.000 0.00 0.00 0.00 4.58
33 34 0.391661 TCTCTTTGCCTCACATCGCC 60.392 55.000 0.00 0.00 0.00 5.54
34 35 0.392193 CTCTTTGCCTCACATCGCCT 60.392 55.000 0.00 0.00 0.00 5.52
35 36 0.901827 TCTTTGCCTCACATCGCCTA 59.098 50.000 0.00 0.00 0.00 3.93
36 37 1.486310 TCTTTGCCTCACATCGCCTAT 59.514 47.619 0.00 0.00 0.00 2.57
37 38 1.869767 CTTTGCCTCACATCGCCTATC 59.130 52.381 0.00 0.00 0.00 2.08
38 39 1.123077 TTGCCTCACATCGCCTATCT 58.877 50.000 0.00 0.00 0.00 1.98
39 40 1.995376 TGCCTCACATCGCCTATCTA 58.005 50.000 0.00 0.00 0.00 1.98
40 41 1.889170 TGCCTCACATCGCCTATCTAG 59.111 52.381 0.00 0.00 0.00 2.43
41 42 1.203523 GCCTCACATCGCCTATCTAGG 59.796 57.143 0.00 0.00 46.42 3.02
52 53 3.320673 CCTATCTAGGCGGATTTCCAC 57.679 52.381 0.00 0.00 36.53 4.02
53 54 2.900546 CCTATCTAGGCGGATTTCCACT 59.099 50.000 0.00 0.00 36.53 4.00
54 55 2.918712 ATCTAGGCGGATTTCCACTG 57.081 50.000 0.00 0.00 35.14 3.66
55 56 0.178068 TCTAGGCGGATTTCCACTGC 59.822 55.000 0.00 0.00 38.72 4.40
56 57 0.179000 CTAGGCGGATTTCCACTGCT 59.821 55.000 0.00 0.00 39.31 4.24
57 58 0.618458 TAGGCGGATTTCCACTGCTT 59.382 50.000 0.00 0.00 39.31 3.91
58 59 0.251341 AGGCGGATTTCCACTGCTTT 60.251 50.000 0.00 0.00 39.31 3.51
59 60 1.004277 AGGCGGATTTCCACTGCTTTA 59.996 47.619 0.00 0.00 39.31 1.85
60 61 2.024414 GGCGGATTTCCACTGCTTTAT 58.976 47.619 0.00 0.00 39.31 1.40
61 62 2.427095 GGCGGATTTCCACTGCTTTATT 59.573 45.455 0.00 0.00 39.31 1.40
62 63 3.630312 GGCGGATTTCCACTGCTTTATTA 59.370 43.478 0.00 0.00 39.31 0.98
63 64 4.097286 GGCGGATTTCCACTGCTTTATTAA 59.903 41.667 0.00 0.00 39.31 1.40
64 65 5.273944 GCGGATTTCCACTGCTTTATTAAG 58.726 41.667 0.00 0.00 36.79 1.85
65 66 5.163652 GCGGATTTCCACTGCTTTATTAAGT 60.164 40.000 0.00 0.00 36.79 2.24
66 67 6.625081 GCGGATTTCCACTGCTTTATTAAGTT 60.625 38.462 0.00 0.00 36.79 2.66
67 68 7.414762 GCGGATTTCCACTGCTTTATTAAGTTA 60.415 37.037 0.00 0.00 36.79 2.24
68 69 8.122952 CGGATTTCCACTGCTTTATTAAGTTAG 58.877 37.037 0.00 0.00 35.14 2.34
69 70 8.406297 GGATTTCCACTGCTTTATTAAGTTAGG 58.594 37.037 0.00 0.00 33.18 2.69
70 71 6.753107 TTCCACTGCTTTATTAAGTTAGGC 57.247 37.500 0.00 0.00 33.74 3.93
71 72 5.190677 TCCACTGCTTTATTAAGTTAGGCC 58.809 41.667 0.00 0.00 33.74 5.19
72 73 5.045140 TCCACTGCTTTATTAAGTTAGGCCT 60.045 40.000 11.78 11.78 33.74 5.19
73 74 5.297029 CCACTGCTTTATTAAGTTAGGCCTC 59.703 44.000 9.68 0.00 33.74 4.70
74 75 5.880332 CACTGCTTTATTAAGTTAGGCCTCA 59.120 40.000 9.68 0.00 33.74 3.86
75 76 6.037610 CACTGCTTTATTAAGTTAGGCCTCAG 59.962 42.308 9.68 8.23 33.74 3.35
76 77 4.881850 TGCTTTATTAAGTTAGGCCTCAGC 59.118 41.667 9.68 0.00 33.74 4.26
77 78 4.881850 GCTTTATTAAGTTAGGCCTCAGCA 59.118 41.667 9.68 0.00 35.64 4.41
78 79 5.357032 GCTTTATTAAGTTAGGCCTCAGCAA 59.643 40.000 9.68 0.00 35.64 3.91
79 80 6.039829 GCTTTATTAAGTTAGGCCTCAGCAAT 59.960 38.462 9.68 6.64 35.64 3.56
80 81 6.942532 TTATTAAGTTAGGCCTCAGCAATG 57.057 37.500 9.68 0.00 42.56 2.82
81 82 2.887151 AAGTTAGGCCTCAGCAATGT 57.113 45.000 9.68 0.00 42.56 2.71
82 83 2.887151 AGTTAGGCCTCAGCAATGTT 57.113 45.000 9.68 0.00 42.56 2.71
83 84 4.301072 AAGTTAGGCCTCAGCAATGTTA 57.699 40.909 9.68 0.00 42.56 2.41
84 85 4.510167 AGTTAGGCCTCAGCAATGTTAT 57.490 40.909 9.68 0.00 42.56 1.89
85 86 4.455606 AGTTAGGCCTCAGCAATGTTATC 58.544 43.478 9.68 0.00 42.56 1.75
86 87 4.080356 AGTTAGGCCTCAGCAATGTTATCA 60.080 41.667 9.68 0.00 42.56 2.15
87 88 2.648059 AGGCCTCAGCAATGTTATCAC 58.352 47.619 0.00 0.00 42.56 3.06
88 89 1.678101 GGCCTCAGCAATGTTATCACC 59.322 52.381 0.00 0.00 42.56 4.02
89 90 2.368439 GCCTCAGCAATGTTATCACCA 58.632 47.619 0.00 0.00 39.53 4.17
90 91 2.754552 GCCTCAGCAATGTTATCACCAA 59.245 45.455 0.00 0.00 39.53 3.67
91 92 3.181493 GCCTCAGCAATGTTATCACCAAG 60.181 47.826 0.00 0.00 39.53 3.61
92 93 4.012374 CCTCAGCAATGTTATCACCAAGT 58.988 43.478 0.00 0.00 0.00 3.16
93 94 5.185454 CCTCAGCAATGTTATCACCAAGTA 58.815 41.667 0.00 0.00 0.00 2.24
94 95 5.824624 CCTCAGCAATGTTATCACCAAGTAT 59.175 40.000 0.00 0.00 0.00 2.12
95 96 6.992123 CCTCAGCAATGTTATCACCAAGTATA 59.008 38.462 0.00 0.00 0.00 1.47
96 97 7.498900 CCTCAGCAATGTTATCACCAAGTATAA 59.501 37.037 0.00 0.00 0.00 0.98
97 98 8.978874 TCAGCAATGTTATCACCAAGTATAAT 57.021 30.769 0.00 0.00 0.00 1.28
109 110 8.743085 TCACCAAGTATAATAACTACGAGACT 57.257 34.615 0.00 0.00 0.00 3.24
110 111 9.182214 TCACCAAGTATAATAACTACGAGACTT 57.818 33.333 0.00 0.00 0.00 3.01
111 112 9.234384 CACCAAGTATAATAACTACGAGACTTG 57.766 37.037 0.00 0.00 41.27 3.16
112 113 8.964772 ACCAAGTATAATAACTACGAGACTTGT 58.035 33.333 0.00 0.00 40.44 3.16
388 389 4.039973 AGACTTGTTGAGTTCGGTGGAATA 59.960 41.667 0.00 0.00 39.19 1.75
549 558 3.774066 GGTGACCTGCAAGAAAATATGC 58.226 45.455 0.00 0.00 42.86 3.14
631 640 8.924691 CACCACACCATGTAAAGATAAATTTTG 58.075 33.333 0.00 0.00 0.00 2.44
650 659 8.647143 AATTTTGACAAACCATGTAACTTCAG 57.353 30.769 0.00 0.00 44.12 3.02
691 700 9.536510 AGTAAGGAGAACTCTAATTTCAGTAGT 57.463 33.333 1.86 0.00 0.00 2.73
695 704 9.536510 AGGAGAACTCTAATTTCAGTAGTAAGT 57.463 33.333 1.86 0.00 0.00 2.24
696 705 9.791820 GGAGAACTCTAATTTCAGTAGTAAGTC 57.208 37.037 1.86 0.00 0.00 3.01
697 706 9.791820 GAGAACTCTAATTTCAGTAGTAAGTCC 57.208 37.037 0.00 0.00 0.00 3.85
698 707 9.310449 AGAACTCTAATTTCAGTAGTAAGTCCA 57.690 33.333 0.00 0.00 0.00 4.02
701 710 9.877178 ACTCTAATTTCAGTAGTAAGTCCATTG 57.123 33.333 0.00 0.00 0.00 2.82
702 711 9.877178 CTCTAATTTCAGTAGTAAGTCCATTGT 57.123 33.333 0.00 0.00 0.00 2.71
703 712 9.653287 TCTAATTTCAGTAGTAAGTCCATTGTG 57.347 33.333 0.00 0.00 0.00 3.33
704 713 9.653287 CTAATTTCAGTAGTAAGTCCATTGTGA 57.347 33.333 0.00 0.00 0.00 3.58
787 796 0.897863 AAACCGGGCTGCAAATGCTA 60.898 50.000 6.32 0.00 42.66 3.49
800 809 3.003068 GCAAATGCTATAGGACTGCTGTG 59.997 47.826 17.85 1.74 38.21 3.66
859 868 6.566197 AGGATGATCTGAAAAGTGAAACAC 57.434 37.500 0.00 0.00 41.43 3.32
867 876 8.856490 ATCTGAAAAGTGAAACACATGTTAAC 57.144 30.769 0.00 0.00 41.43 2.01
937 946 5.879223 AGAAATGATGATGCGAGTTCTTCTT 59.121 36.000 0.00 0.00 0.00 2.52
943 952 5.344743 TGATGCGAGTTCTTCTTTAGGAT 57.655 39.130 0.00 0.00 0.00 3.24
1210 1220 4.475944 CCGCAAATTCTACTTCCTGTTTG 58.524 43.478 0.00 0.00 0.00 2.93
1302 1316 3.594603 ATACACTGAAACAGAGACGGG 57.405 47.619 5.76 0.00 35.18 5.28
1466 1700 4.086706 AGTGTTCTTGGTAGTTTGGAGG 57.913 45.455 0.00 0.00 0.00 4.30
1641 1889 8.150945 AGTCTGTTGTAACTGTCTCATTAACAT 58.849 33.333 0.00 0.00 0.00 2.71
2101 2671 6.858993 GCGTTTCATTTCCTGTAATTACAACA 59.141 34.615 18.55 5.98 35.50 3.33
2243 2897 3.084039 TGATGGAAGAAGTGGCACATTC 58.916 45.455 21.41 18.75 44.52 2.67
2256 2910 4.082300 GTGGCACATTCATGATTGGTAACA 60.082 41.667 13.86 10.81 45.90 2.41
2662 3319 1.598130 GGCAGAGCTTGTTCACCGT 60.598 57.895 0.00 0.00 0.00 4.83
2768 3427 6.766944 CCTTATTGCAATGGAATAAATGGCAA 59.233 34.615 22.27 0.00 42.97 4.52
3009 3694 3.989167 CACCGACGTCATAGGTTTTGTAA 59.011 43.478 17.16 0.00 33.22 2.41
3262 3953 0.969894 ACTCGGAGAACTGAAGTGGG 59.030 55.000 12.86 0.00 34.09 4.61
3278 3977 3.658725 AGTGGGCCAGAATAGATAGTGT 58.341 45.455 6.40 0.00 0.00 3.55
3522 4230 5.230097 CGACGAATTGGATGATATATCACCG 59.770 44.000 17.60 13.35 40.03 4.94
3558 4266 4.560128 GCCAATGTGCGAGAAGATATAGA 58.440 43.478 0.00 0.00 0.00 1.98
3566 4274 3.727673 GCGAGAAGATATAGAGCAGCTCG 60.728 52.174 16.99 11.20 44.67 5.03
3794 4512 6.072112 TCAAAAGTAACAGAATTGGAGTGC 57.928 37.500 0.00 0.00 0.00 4.40
3795 4513 5.592282 TCAAAAGTAACAGAATTGGAGTGCA 59.408 36.000 0.00 0.00 0.00 4.57
3796 4514 6.096141 TCAAAAGTAACAGAATTGGAGTGCAA 59.904 34.615 0.00 0.00 0.00 4.08
3806 4532 7.385752 ACAGAATTGGAGTGCAATTATGTTTTG 59.614 33.333 32.11 20.14 46.01 2.44
3808 4534 8.316214 AGAATTGGAGTGCAATTATGTTTTGAT 58.684 29.630 20.94 0.00 32.98 2.57
3918 5759 5.399152 GGGTATCTTCCTCCTTGGCTTTTAT 60.399 44.000 0.00 0.00 35.26 1.40
4031 5894 1.486310 TGTCCTAGGGTGATGTGCATC 59.514 52.381 9.46 5.30 38.29 3.91
4065 5928 5.630680 GCCAAATATAGAAAATCACCATGCG 59.369 40.000 0.00 0.00 0.00 4.73
4104 5967 2.295629 TCGCTCTATGATGCAAGAGGAG 59.704 50.000 13.64 8.45 39.73 3.69
4225 6088 9.151471 ACATACATACTCACAAGTCATAAACAC 57.849 33.333 0.00 0.00 36.92 3.32
4324 6187 3.763897 GGTATGGAGCACACAAAGGATTT 59.236 43.478 0.00 0.00 40.26 2.17
4357 6220 8.958060 ACCTAACTGCAGGAGAAGATATATAA 57.042 34.615 19.93 0.00 39.18 0.98
4358 6221 9.381038 ACCTAACTGCAGGAGAAGATATATAAA 57.619 33.333 19.93 0.00 39.18 1.40
4359 6222 9.868277 CCTAACTGCAGGAGAAGATATATAAAG 57.132 37.037 19.93 0.00 38.00 1.85
4485 6348 4.202738 ACCCTTTCTTTTTACCATAGCCCA 60.203 41.667 0.00 0.00 0.00 5.36
4493 6356 7.555087 TCTTTTTACCATAGCCCATCATTTTG 58.445 34.615 0.00 0.00 0.00 2.44
4494 6357 7.398618 TCTTTTTACCATAGCCCATCATTTTGA 59.601 33.333 0.00 0.00 0.00 2.69
4495 6358 6.713762 TTTACCATAGCCCATCATTTTGAG 57.286 37.500 0.00 0.00 0.00 3.02
4496 6359 3.569491 ACCATAGCCCATCATTTTGAGG 58.431 45.455 0.00 0.00 0.00 3.86
4497 6360 3.205056 ACCATAGCCCATCATTTTGAGGA 59.795 43.478 0.00 0.00 27.97 3.71
4498 6361 4.217510 CCATAGCCCATCATTTTGAGGAA 58.782 43.478 0.00 0.00 27.97 3.36
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 3.635331 CAAAGAGATTTGCAGTGGTGTG 58.365 45.455 0.00 0.00 0.00 3.82
10 11 3.730061 GCGATGTGAGGCAAAGAGATTTG 60.730 47.826 0.00 0.00 35.15 2.32
11 12 2.421424 GCGATGTGAGGCAAAGAGATTT 59.579 45.455 0.00 0.00 0.00 2.17
12 13 2.012673 GCGATGTGAGGCAAAGAGATT 58.987 47.619 0.00 0.00 0.00 2.40
13 14 1.661341 GCGATGTGAGGCAAAGAGAT 58.339 50.000 0.00 0.00 0.00 2.75
14 15 0.391661 GGCGATGTGAGGCAAAGAGA 60.392 55.000 0.00 0.00 0.00 3.10
15 16 0.392193 AGGCGATGTGAGGCAAAGAG 60.392 55.000 0.00 0.00 36.55 2.85
16 17 0.901827 TAGGCGATGTGAGGCAAAGA 59.098 50.000 0.00 0.00 36.55 2.52
17 18 1.869767 GATAGGCGATGTGAGGCAAAG 59.130 52.381 0.00 0.00 36.55 2.77
18 19 1.486310 AGATAGGCGATGTGAGGCAAA 59.514 47.619 0.00 0.00 36.55 3.68
19 20 1.123077 AGATAGGCGATGTGAGGCAA 58.877 50.000 0.00 0.00 36.55 4.52
20 21 1.889170 CTAGATAGGCGATGTGAGGCA 59.111 52.381 0.00 0.00 36.55 4.75
21 22 1.203523 CCTAGATAGGCGATGTGAGGC 59.796 57.143 0.00 0.00 36.53 4.70
32 33 3.320673 GTGGAAATCCGCCTAGATAGG 57.679 52.381 1.40 1.23 46.42 2.57
40 41 8.067852 ACTTAATAAAGCAGTGGAAATCCGCC 62.068 42.308 9.33 0.00 40.68 6.13
41 42 3.782889 AATAAAGCAGTGGAAATCCGC 57.217 42.857 4.82 4.82 46.57 5.54
42 43 6.436843 ACTTAATAAAGCAGTGGAAATCCG 57.563 37.500 0.00 0.00 35.94 4.18
43 44 8.406297 CCTAACTTAATAAAGCAGTGGAAATCC 58.594 37.037 0.00 0.00 36.05 3.01
44 45 7.915923 GCCTAACTTAATAAAGCAGTGGAAATC 59.084 37.037 0.00 0.00 36.05 2.17
45 46 7.147897 GGCCTAACTTAATAAAGCAGTGGAAAT 60.148 37.037 0.00 0.00 36.05 2.17
46 47 6.152154 GGCCTAACTTAATAAAGCAGTGGAAA 59.848 38.462 0.00 0.00 36.05 3.13
47 48 5.650703 GGCCTAACTTAATAAAGCAGTGGAA 59.349 40.000 0.00 0.00 36.05 3.53
48 49 5.045140 AGGCCTAACTTAATAAAGCAGTGGA 60.045 40.000 1.29 0.00 36.05 4.02
49 50 5.193679 AGGCCTAACTTAATAAAGCAGTGG 58.806 41.667 1.29 0.00 36.05 4.00
50 51 5.880332 TGAGGCCTAACTTAATAAAGCAGTG 59.120 40.000 4.42 0.00 36.05 3.66
51 52 6.062258 TGAGGCCTAACTTAATAAAGCAGT 57.938 37.500 4.42 0.00 36.05 4.40
52 53 5.008118 GCTGAGGCCTAACTTAATAAAGCAG 59.992 44.000 4.42 4.93 36.05 4.24
53 54 4.881850 GCTGAGGCCTAACTTAATAAAGCA 59.118 41.667 4.42 0.00 36.05 3.91
54 55 4.881850 TGCTGAGGCCTAACTTAATAAAGC 59.118 41.667 4.42 3.03 35.30 3.51
55 56 7.067494 ACATTGCTGAGGCCTAACTTAATAAAG 59.933 37.037 4.42 0.00 36.85 1.85
56 57 6.889722 ACATTGCTGAGGCCTAACTTAATAAA 59.110 34.615 4.42 0.00 37.74 1.40
57 58 6.423182 ACATTGCTGAGGCCTAACTTAATAA 58.577 36.000 4.42 0.00 37.74 1.40
58 59 6.001449 ACATTGCTGAGGCCTAACTTAATA 57.999 37.500 4.42 0.00 37.74 0.98
59 60 4.860022 ACATTGCTGAGGCCTAACTTAAT 58.140 39.130 4.42 0.10 37.74 1.40
60 61 4.301072 ACATTGCTGAGGCCTAACTTAA 57.699 40.909 4.42 0.00 37.74 1.85
61 62 4.301072 AACATTGCTGAGGCCTAACTTA 57.699 40.909 4.42 0.00 37.74 2.24
62 63 2.887151 ACATTGCTGAGGCCTAACTT 57.113 45.000 4.42 0.00 37.74 2.66
63 64 2.887151 AACATTGCTGAGGCCTAACT 57.113 45.000 4.42 0.00 37.74 2.24
64 65 4.035675 GTGATAACATTGCTGAGGCCTAAC 59.964 45.833 4.42 0.00 37.74 2.34
65 66 4.199310 GTGATAACATTGCTGAGGCCTAA 58.801 43.478 4.42 0.00 37.74 2.69
66 67 3.433598 GGTGATAACATTGCTGAGGCCTA 60.434 47.826 4.42 0.00 37.74 3.93
67 68 2.648059 GTGATAACATTGCTGAGGCCT 58.352 47.619 3.86 3.86 37.74 5.19
68 69 1.678101 GGTGATAACATTGCTGAGGCC 59.322 52.381 0.00 0.00 37.74 5.19
69 70 2.368439 TGGTGATAACATTGCTGAGGC 58.632 47.619 0.00 0.00 39.26 4.70
70 71 4.012374 ACTTGGTGATAACATTGCTGAGG 58.988 43.478 0.00 0.00 0.00 3.86
71 72 6.932356 ATACTTGGTGATAACATTGCTGAG 57.068 37.500 0.00 0.00 0.00 3.35
72 73 8.978874 ATTATACTTGGTGATAACATTGCTGA 57.021 30.769 0.00 0.00 0.00 4.26
83 84 9.352191 AGTCTCGTAGTTATTATACTTGGTGAT 57.648 33.333 0.00 0.00 0.00 3.06
84 85 8.743085 AGTCTCGTAGTTATTATACTTGGTGA 57.257 34.615 0.00 0.00 0.00 4.02
85 86 9.234384 CAAGTCTCGTAGTTATTATACTTGGTG 57.766 37.037 0.00 0.00 39.09 4.17
86 87 8.964772 ACAAGTCTCGTAGTTATTATACTTGGT 58.035 33.333 14.28 0.90 44.19 3.67
353 354 7.624360 ACTCAACAAGTCTTAAAACACATGA 57.376 32.000 0.00 0.00 30.02 3.07
354 355 7.164171 CGAACTCAACAAGTCTTAAAACACATG 59.836 37.037 0.00 0.00 37.17 3.21
355 356 7.186804 CGAACTCAACAAGTCTTAAAACACAT 58.813 34.615 0.00 0.00 37.17 3.21
364 365 2.169769 TCCACCGAACTCAACAAGTCTT 59.830 45.455 0.00 0.00 37.17 3.01
388 389 8.121305 TCAACCTCAATATGTTTAACTGCATT 57.879 30.769 0.00 0.00 0.00 3.56
411 412 6.303054 TCATGTGTTTCTTGGATTTACCTCA 58.697 36.000 0.00 0.00 39.86 3.86
495 502 4.082463 CGCAAAATTTACAGGGCTTTCCTA 60.082 41.667 0.00 0.00 46.12 2.94
549 558 6.862608 TGCAAAAATGTGTATCACTTAGCAAG 59.137 34.615 1.72 0.00 35.11 4.01
631 640 5.758296 TGAGACTGAAGTTACATGGTTTGTC 59.242 40.000 0.00 0.00 39.87 3.18
650 659 9.308318 GTTCTCCTTACTTTATTCTCATGAGAC 57.692 37.037 25.07 4.33 37.14 3.36
707 716 9.429109 TCACAATGGACTTACTACTGGATATTA 57.571 33.333 0.00 0.00 0.00 0.98
708 717 8.319057 TCACAATGGACTTACTACTGGATATT 57.681 34.615 0.00 0.00 0.00 1.28
709 718 7.914427 TCACAATGGACTTACTACTGGATAT 57.086 36.000 0.00 0.00 0.00 1.63
710 719 7.914427 ATCACAATGGACTTACTACTGGATA 57.086 36.000 0.00 0.00 0.00 2.59
711 720 6.814954 ATCACAATGGACTTACTACTGGAT 57.185 37.500 0.00 0.00 0.00 3.41
712 721 7.914427 ATATCACAATGGACTTACTACTGGA 57.086 36.000 0.00 0.00 0.00 3.86
787 796 2.290323 GGTTTGGTCACAGCAGTCCTAT 60.290 50.000 0.00 0.00 0.00 2.57
800 809 4.599047 TGGAACATTGAATGGTTTGGTC 57.401 40.909 10.27 0.00 33.60 4.02
839 848 7.281040 ACATGTGTTTCACTTTTCAGATCAT 57.719 32.000 0.00 0.00 35.11 2.45
859 868 5.290885 TCGTTGATCCTCATTCGTTAACATG 59.709 40.000 6.39 3.10 0.00 3.21
867 876 4.568359 AGACATTTCGTTGATCCTCATTCG 59.432 41.667 0.00 0.00 0.00 3.34
926 935 7.813148 TGTCTGTTTATCCTAAAGAAGAACTCG 59.187 37.037 0.00 0.00 0.00 4.18
937 946 5.853572 ACCCCTTTGTCTGTTTATCCTAA 57.146 39.130 0.00 0.00 0.00 2.69
943 952 2.645797 CCCCTACCCCTTTGTCTGTTTA 59.354 50.000 0.00 0.00 0.00 2.01
1083 1093 4.105486 CAGATTCGTTCATAAGACGCTCA 58.895 43.478 0.00 0.00 0.00 4.26
1210 1220 0.800012 TCTACAACAATTTCCCGCGC 59.200 50.000 0.00 0.00 0.00 6.86
1302 1316 4.800471 GCCAGCAAACTATCTAACAAATGC 59.200 41.667 0.00 0.00 0.00 3.56
2243 2897 5.416952 AGGAAAGCTCTTGTTACCAATCATG 59.583 40.000 0.00 0.00 0.00 3.07
2256 2910 2.839425 AGAGAGATGCAGGAAAGCTCTT 59.161 45.455 0.00 0.00 36.17 2.85
2461 3117 5.645497 AGTCCATGCTTGTATTCAACTTCTC 59.355 40.000 0.00 0.00 0.00 2.87
3009 3694 4.932799 CCAATGAACACAATGCAATCATGT 59.067 37.500 0.00 0.00 31.49 3.21
3113 3798 2.038762 ACCCCCACCTTCACCACT 60.039 61.111 0.00 0.00 0.00 4.00
3244 3935 0.390472 GCCCACTTCAGTTCTCCGAG 60.390 60.000 0.00 0.00 0.00 4.63
3262 3953 6.090483 TGAAGCTACACTATCTATTCTGGC 57.910 41.667 0.00 0.00 0.00 4.85
3278 3977 1.079127 GCTCGGCCAACTGAAGCTA 60.079 57.895 2.24 0.00 0.00 3.32
3513 4221 7.156673 GGCCAGACTAAAATTACGGTGATATA 58.843 38.462 0.00 0.00 0.00 0.86
3522 4230 5.102313 GCACATTGGCCAGACTAAAATTAC 58.898 41.667 5.11 0.00 0.00 1.89
3558 4266 1.476007 GGATATCACCCCGAGCTGCT 61.476 60.000 0.00 0.00 0.00 4.24
3771 4489 5.592282 TGCACTCCAATTCTGTTACTTTTGA 59.408 36.000 0.00 0.00 0.00 2.69
3772 4490 5.830912 TGCACTCCAATTCTGTTACTTTTG 58.169 37.500 0.00 0.00 0.00 2.44
3773 4491 6.463995 TTGCACTCCAATTCTGTTACTTTT 57.536 33.333 0.00 0.00 0.00 2.27
3774 4492 6.655078 ATTGCACTCCAATTCTGTTACTTT 57.345 33.333 0.00 0.00 41.29 2.66
3785 4503 8.723311 CAAATCAAAACATAATTGCACTCCAAT 58.277 29.630 0.00 0.00 45.90 3.16
3787 4505 7.215789 ACAAATCAAAACATAATTGCACTCCA 58.784 30.769 0.00 0.00 0.00 3.86
3788 4506 7.656707 ACAAATCAAAACATAATTGCACTCC 57.343 32.000 0.00 0.00 0.00 3.85
3826 4552 0.393537 AAAGGCCGAGCTCCAATGAG 60.394 55.000 8.47 0.00 41.84 2.90
3827 4553 0.677731 CAAAGGCCGAGCTCCAATGA 60.678 55.000 8.47 0.00 0.00 2.57
3828 4554 1.805254 CAAAGGCCGAGCTCCAATG 59.195 57.895 8.47 0.00 0.00 2.82
3830 4556 2.672996 GCAAAGGCCGAGCTCCAA 60.673 61.111 8.47 0.00 0.00 3.53
4225 6088 9.179909 TCTTATCACTCTTCTCTAGTTACCAAG 57.820 37.037 0.00 0.00 0.00 3.61
4324 6187 1.272490 CCTGCAGTTAGGTCTCGAACA 59.728 52.381 13.81 0.00 32.08 3.18
4357 6220 8.567948 CCAAATGTTTATCACTTGTGAGTACTT 58.432 33.333 9.39 3.46 32.24 2.24
4358 6221 7.174946 CCCAAATGTTTATCACTTGTGAGTACT 59.825 37.037 9.39 0.00 32.24 2.73
4359 6222 7.174253 TCCCAAATGTTTATCACTTGTGAGTAC 59.826 37.037 9.39 7.43 32.24 2.73
4360 6223 7.227873 TCCCAAATGTTTATCACTTGTGAGTA 58.772 34.615 9.39 0.00 32.24 2.59
4361 6224 6.068010 TCCCAAATGTTTATCACTTGTGAGT 58.932 36.000 9.39 1.40 32.24 3.41


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

AutoCloner maintained by Alex Coulton.