Multiple sequence alignment - TraesCS7A01G259500

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 TraesCS7A01G259500 chr7A 100.000 4224 0 0 1 4224 251286978 251282755 0.000000e+00 7801.0
1 TraesCS7A01G259500 chr7A 77.642 246 55 0 403 648 667920991 667920746 2.630000e-32 150.0
2 TraesCS7A01G259500 chr7A 91.892 37 3 0 3578 3614 105168444 105168408 8.000000e-03 52.8
3 TraesCS7A01G259500 chr7B 92.381 3688 183 32 1 3675 212480005 212476403 0.000000e+00 5164.0
4 TraesCS7A01G259500 chr7B 86.826 334 24 10 3904 4221 212476144 212475815 5.190000e-94 355.0
5 TraesCS7A01G259500 chr7B 83.721 86 10 2 563 648 639147405 639147324 1.260000e-10 78.7
6 TraesCS7A01G259500 chr7D 92.036 3403 159 31 830 4141 236185059 236181678 0.000000e+00 4680.0
7 TraesCS7A01G259500 chr7D 89.410 576 60 1 1 575 236187825 236187250 0.000000e+00 725.0
8 TraesCS7A01G259500 chr7D 93.548 124 8 0 4098 4221 236181678 236181555 7.210000e-43 185.0
9 TraesCS7A01G259500 chr7D 74.105 475 95 23 100 557 525360184 525360647 2.020000e-38 171.0
10 TraesCS7A01G259500 chr7D 94.286 35 2 0 3575 3609 10510650 10510684 2.000000e-03 54.7
11 TraesCS7A01G259500 chr2D 76.768 594 129 9 58 645 317879258 317878668 1.460000e-84 324.0
12 TraesCS7A01G259500 chr2D 81.503 173 29 3 4032 4203 638410932 638411102 5.690000e-29 139.0
13 TraesCS7A01G259500 chr6B 75.276 453 98 10 57 499 71151952 71152400 1.990000e-48 204.0
14 TraesCS7A01G259500 chr3A 73.134 603 129 23 54 648 69961550 69962127 7.210000e-43 185.0
15 TraesCS7A01G259500 chr4D 75.385 325 67 8 329 648 121472628 121472944 1.220000e-30 145.0
16 TraesCS7A01G259500 chrUn 71.672 586 138 18 72 648 275048377 275048943 2.050000e-28 137.0
17 TraesCS7A01G259500 chrUn 71.672 586 138 18 72 648 275056040 275056606 2.050000e-28 137.0
18 TraesCS7A01G259500 chrUn 71.701 576 137 17 80 648 282338132 282337576 2.050000e-28 137.0
19 TraesCS7A01G259500 chr6D 72.934 484 97 27 55 514 470029227 470029700 2.050000e-28 137.0
20 TraesCS7A01G259500 chr2A 75.424 236 34 14 286 508 711519881 711519657 4.500000e-15 93.5
21 TraesCS7A01G259500 chr1D 79.048 105 21 1 410 514 442154078 442154181 2.110000e-08 71.3
22 TraesCS7A01G259500 chr5A 92.500 40 3 0 3578 3617 132095767 132095728 1.640000e-04 58.4
23 TraesCS7A01G259500 chr3B 89.130 46 5 0 383 428 752036074 752036029 1.640000e-04 58.4
24 TraesCS7A01G259500 chr5B 100.000 29 0 0 3538 3566 322271633 322271661 2.000000e-03 54.7


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 TraesCS7A01G259500 chr7A 251282755 251286978 4223 True 7801.000000 7801 100.000000 1 4224 1 chr7A.!!$R2 4223
1 TraesCS7A01G259500 chr7B 212475815 212480005 4190 True 2759.500000 5164 89.603500 1 4221 2 chr7B.!!$R2 4220
2 TraesCS7A01G259500 chr7D 236181555 236187825 6270 True 1863.333333 4680 91.664667 1 4221 3 chr7D.!!$R1 4220
3 TraesCS7A01G259500 chr2D 317878668 317879258 590 True 324.000000 324 76.768000 58 645 1 chr2D.!!$R1 587

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
289 295 0.036388 TCGCGGCTTTGATCTTCCTT 60.036 50.0 6.13 0.0 0.0 3.36 F
1642 3612 0.109132 CCAAAATCTGCCCAGTTCGC 60.109 55.0 0.00 0.0 0.0 4.70 F
2323 4311 0.819259 TGCCAGCACAGTTGTTCCTC 60.819 55.0 0.00 0.0 0.0 3.71 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1671 3641 0.366871 CAGCAGCGTACTTAAGCGTG 59.633 55.0 1.29 2.36 38.61 5.34 R
2492 4488 0.036732 AGGGAATCGCTTGCTTGTGA 59.963 50.0 0.00 0.00 0.00 3.58 R
3963 6059 1.084370 CATCCCGAACTTGTCTCCGC 61.084 60.0 0.00 0.00 0.00 5.54 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
92 94 0.840288 TGGCTAGGCAAACTCTCCCA 60.840 55.000 17.92 0.00 0.00 4.37
104 106 1.306141 TCTCCCATCCAGGCTTCGT 60.306 57.895 0.00 0.00 35.39 3.85
148 151 1.293498 CTCTGCTTGCCGTACTGGT 59.707 57.895 5.79 0.00 41.21 4.00
234 240 0.321653 GTCATCTTGGGGCGACACTT 60.322 55.000 0.00 0.00 31.84 3.16
289 295 0.036388 TCGCGGCTTTGATCTTCCTT 60.036 50.000 6.13 0.00 0.00 3.36
295 301 3.503748 CGGCTTTGATCTTCCTTGACTTT 59.496 43.478 0.00 0.00 0.00 2.66
374 380 2.678336 CAATGAGGTTAGGGTTTCTCGC 59.322 50.000 0.00 0.00 0.00 5.03
395 401 0.238289 GTGTGGCGAGATTTGGTGTG 59.762 55.000 0.00 0.00 0.00 3.82
447 453 4.435970 TCCACCGCGGCTCTAGGA 62.436 66.667 28.58 21.30 33.14 2.94
515 521 0.821711 CAAGGTCAAGCCGGTTCCAA 60.822 55.000 1.90 0.00 43.70 3.53
523 529 2.840576 CCGGTTCCAACAGGGGAA 59.159 61.111 0.00 0.00 44.50 3.97
533 539 1.001974 CAACAGGGGAACGATGACAGA 59.998 52.381 0.00 0.00 0.00 3.41
534 540 1.348064 ACAGGGGAACGATGACAGAA 58.652 50.000 0.00 0.00 0.00 3.02
571 577 3.365969 CGTTTTGGCTTCAATAGTGGTCC 60.366 47.826 0.00 0.00 0.00 4.46
576 582 3.073798 TGGCTTCAATAGTGGTCCTTTGA 59.926 43.478 0.00 0.00 0.00 2.69
763 2700 5.063312 ACAAAAGATTTGTTTTTGAGCGGTG 59.937 36.000 15.05 0.00 44.37 4.94
767 2704 1.919918 TTGTTTTTGAGCGGTGCAAG 58.080 45.000 0.00 0.00 0.00 4.01
875 2844 3.390280 AGCTGTGAAGCTCTAGGGT 57.610 52.632 0.00 0.00 42.12 4.34
900 2869 0.468214 CGCCTCCTCATAGACCTCCA 60.468 60.000 0.00 0.00 0.00 3.86
906 2875 0.757188 CTCATAGACCTCCACCGCCT 60.757 60.000 0.00 0.00 0.00 5.52
917 2886 0.955919 CCACCGCCTCCTCAGTTTTC 60.956 60.000 0.00 0.00 0.00 2.29
1029 2998 0.681564 TCGTCCCTCTCTTCTCAGGC 60.682 60.000 0.00 0.00 0.00 4.85
1036 3005 2.500910 CCTCTCTTCTCAGGCACAATCT 59.499 50.000 0.00 0.00 0.00 2.40
1050 3019 2.417933 CACAATCTTCTGCCTGCTGTAC 59.582 50.000 0.00 0.00 0.00 2.90
1138 3107 3.705051 ACCCGACCAAGTGTAAGATCTA 58.295 45.455 0.00 0.00 0.00 1.98
1162 3131 1.203428 TCCCTCTGTCCCCTCAATGAA 60.203 52.381 0.00 0.00 0.00 2.57
1191 3161 1.280206 GCTTTGCGCTTTGCCTTCTG 61.280 55.000 9.73 0.00 45.60 3.02
1205 3175 0.954452 CTTCTGCTTGTGGTGGGTTC 59.046 55.000 0.00 0.00 0.00 3.62
1413 3383 3.014623 GTTAGGGAGTGTACAAATGGCC 58.985 50.000 0.00 0.00 0.00 5.36
1429 3399 4.931661 ATGGCCTCATGAATGATTGAAC 57.068 40.909 3.32 0.00 36.02 3.18
1435 3405 5.675575 GCCTCATGAATGATTGAACTGTGAC 60.676 44.000 0.00 0.00 36.02 3.67
1451 3421 7.990886 TGAACTGTGACAAACCTAAAGAGTAAT 59.009 33.333 0.00 0.00 0.00 1.89
1482 3452 3.882288 TCTGTTCTTTGCATGCACAGTTA 59.118 39.130 28.14 17.26 36.91 2.24
1520 3490 5.106157 GGGATATCAATGCATTCTTTACCGG 60.106 44.000 9.53 0.00 0.00 5.28
1538 3508 1.372499 GCGTTAGTCACAGTCGCCA 60.372 57.895 0.00 0.00 40.83 5.69
1555 3525 2.223572 CGCCAATGGTTCTTAGGCAATC 60.224 50.000 0.00 0.00 45.47 2.67
1556 3526 3.026694 GCCAATGGTTCTTAGGCAATCT 58.973 45.455 0.00 0.00 44.59 2.40
1573 3543 4.093998 GCAATCTGAACGTGACATCATCTT 59.906 41.667 0.00 0.00 0.00 2.40
1576 3546 7.624134 GCAATCTGAACGTGACATCATCTTTAA 60.624 37.037 0.00 0.00 0.00 1.52
1624 3594 6.149474 ACATAGCTAATGTCCGCATTTAATCC 59.851 38.462 0.00 0.00 46.15 3.01
1642 3612 0.109132 CCAAAATCTGCCCAGTTCGC 60.109 55.000 0.00 0.00 0.00 4.70
1658 3628 4.549599 CAGTTCGCGTTGTATTTGCTAAAG 59.450 41.667 5.77 0.00 0.00 1.85
1659 3629 4.449743 AGTTCGCGTTGTATTTGCTAAAGA 59.550 37.500 5.77 0.00 0.00 2.52
1660 3630 4.994220 TCGCGTTGTATTTGCTAAAGAA 57.006 36.364 5.77 0.00 0.00 2.52
1671 3641 2.947852 TGCTAAAGAACGCTGAGAGTC 58.052 47.619 0.00 0.00 0.00 3.36
1683 3653 3.172824 GCTGAGAGTCACGCTTAAGTAC 58.827 50.000 4.02 0.00 0.00 2.73
1712 3682 6.765512 GCTGCTACTTTATCCTTCTCATTTCT 59.234 38.462 0.00 0.00 0.00 2.52
1713 3683 7.254727 GCTGCTACTTTATCCTTCTCATTTCTG 60.255 40.741 0.00 0.00 0.00 3.02
1714 3684 7.624549 TGCTACTTTATCCTTCTCATTTCTGT 58.375 34.615 0.00 0.00 0.00 3.41
1715 3685 8.758829 TGCTACTTTATCCTTCTCATTTCTGTA 58.241 33.333 0.00 0.00 0.00 2.74
1716 3686 9.036671 GCTACTTTATCCTTCTCATTTCTGTAC 57.963 37.037 0.00 0.00 0.00 2.90
1717 3687 9.535878 CTACTTTATCCTTCTCATTTCTGTACC 57.464 37.037 0.00 0.00 0.00 3.34
1718 3688 8.152023 ACTTTATCCTTCTCATTTCTGTACCT 57.848 34.615 0.00 0.00 0.00 3.08
1719 3689 9.268282 ACTTTATCCTTCTCATTTCTGTACCTA 57.732 33.333 0.00 0.00 0.00 3.08
1816 3797 8.714179 CATTGAATATTGTTGTGTTCATTGCTT 58.286 29.630 0.00 0.00 31.39 3.91
1850 3831 2.033675 TCACTTTGTGATGTTGCTGCAG 59.966 45.455 10.11 10.11 37.67 4.41
1854 3835 1.401761 TGTGATGTTGCTGCAGGTTT 58.598 45.000 17.12 0.00 0.00 3.27
1856 3837 1.610522 GTGATGTTGCTGCAGGTTTCT 59.389 47.619 17.12 0.00 0.00 2.52
1959 3941 5.932303 CGATGTATCCAAGTCGGGATTAATT 59.068 40.000 0.00 0.00 45.42 1.40
1967 3949 7.343357 TCCAAGTCGGGATTAATTGTTTAGAT 58.657 34.615 0.00 0.00 34.36 1.98
2023 4007 7.041030 TCGTTTATGTTGTTTGATAGCTTTCCA 60.041 33.333 0.00 0.00 0.00 3.53
2030 4014 5.245531 TGTTTGATAGCTTTCCATCGTCTT 58.754 37.500 0.00 0.00 0.00 3.01
2085 4069 6.604735 ATCATTAGTTATGAAGACGCCAAC 57.395 37.500 0.00 0.00 45.99 3.77
2177 4165 7.385267 TGAACTTGGTGAAAAATATCCCAATG 58.615 34.615 0.00 0.00 34.85 2.82
2185 4173 7.255001 GGTGAAAAATATCCCAATGTAGTACCG 60.255 40.741 0.00 0.00 0.00 4.02
2196 4184 5.640357 CCAATGTAGTACCGTTGCTTCTTAA 59.360 40.000 9.05 0.00 31.37 1.85
2220 4208 5.070685 GGCTAATAATGTGTAAGGGAAGGG 58.929 45.833 0.00 0.00 0.00 3.95
2238 4226 1.598701 GGAATGGTCTGTTGGCCTGC 61.599 60.000 3.32 0.00 0.00 4.85
2255 4243 2.559668 CCTGCAATCTTTTTCTGCCAGA 59.440 45.455 0.00 0.00 35.13 3.86
2276 4264 7.598493 GCCAGATTTTGCATCTGTAAAACTAAA 59.402 33.333 13.37 0.00 42.88 1.85
2323 4311 0.819259 TGCCAGCACAGTTGTTCCTC 60.819 55.000 0.00 0.00 0.00 3.71
2346 4337 8.184192 CCTCGTTTTTGTGCTAGATTGATAATT 58.816 33.333 0.00 0.00 0.00 1.40
2355 4346 9.109393 TGTGCTAGATTGATAATTTTGTAGTCC 57.891 33.333 0.00 0.00 0.00 3.85
2370 4361 6.513806 TTGTAGTCCCATCATTGTCAAATG 57.486 37.500 0.00 0.00 43.94 2.32
2492 4488 1.270907 ACCTTGAGGATGTTCTCGCT 58.729 50.000 3.59 0.00 38.94 4.93
2543 4539 1.590147 CAGAGGTGTGGGTCGTACC 59.410 63.158 0.00 0.00 37.60 3.34
2560 4556 0.533308 ACCGCGCAAGTAAAGAACCA 60.533 50.000 8.75 0.00 41.68 3.67
2653 4649 3.552875 AGAGTAACGCTGAGGTATGCTA 58.447 45.455 0.00 0.00 0.00 3.49
2654 4650 3.315749 AGAGTAACGCTGAGGTATGCTAC 59.684 47.826 0.00 0.00 0.00 3.58
2655 4651 3.288964 AGTAACGCTGAGGTATGCTACT 58.711 45.455 0.00 0.00 0.00 2.57
2727 4729 8.637986 TCTGAGCATTTGTTTTGGTTAACTTAT 58.362 29.630 5.42 0.00 0.00 1.73
2858 4860 4.142337 TGGACGCATCAATCGTAAGTTCTA 60.142 41.667 0.00 0.00 40.59 2.10
2916 4918 6.942532 TTGGACATGGTGCTAATATTTCTC 57.057 37.500 0.00 0.00 0.00 2.87
3099 5102 8.478877 TCTTAAGATTCACCTTCTAATCAGTCC 58.521 37.037 0.00 0.00 35.07 3.85
3367 5382 4.712476 AGGTTGATGCTATCCTTGTGATC 58.288 43.478 0.00 0.00 34.76 2.92
3420 5435 5.884322 TCAGATATTTGAGCATTAGCCCAT 58.116 37.500 0.00 0.00 43.56 4.00
3457 5472 0.909610 AGATGCTGGTCCTTTCGGGA 60.910 55.000 0.00 0.00 42.77 5.14
3668 5685 4.260170 ACTGCTTTGCAATTTTTGGTTGA 58.740 34.783 0.00 0.00 38.41 3.18
3693 5736 1.967319 TTTCTGTTCCTGCCACTGAC 58.033 50.000 0.00 0.00 0.00 3.51
3694 5737 0.108585 TTCTGTTCCTGCCACTGACC 59.891 55.000 0.00 0.00 0.00 4.02
3695 5738 1.053835 TCTGTTCCTGCCACTGACCA 61.054 55.000 0.00 0.00 0.00 4.02
3722 5765 5.711976 AGCTCATTAAAGTTGTTATGTGCCT 59.288 36.000 12.03 2.95 31.39 4.75
3723 5766 6.209391 AGCTCATTAAAGTTGTTATGTGCCTT 59.791 34.615 12.03 0.00 31.39 4.35
3743 5786 8.860128 GTGCCTTACATTTTCTTTAATTACTGC 58.140 33.333 0.00 0.00 0.00 4.40
3745 5788 7.966204 GCCTTACATTTTCTTTAATTACTGCGA 59.034 33.333 0.00 0.00 0.00 5.10
3746 5789 9.834628 CCTTACATTTTCTTTAATTACTGCGAA 57.165 29.630 0.00 0.00 0.00 4.70
3749 5792 8.601243 ACATTTTCTTTAATTACTGCGAATCG 57.399 30.769 0.00 0.00 0.00 3.34
3817 5860 1.752833 GGACCTTCACCGGTGTTCT 59.247 57.895 32.74 14.66 37.42 3.01
3826 5869 1.117150 ACCGGTGTTCTGTGTACTGT 58.883 50.000 6.12 0.00 0.00 3.55
3831 5874 1.597663 GTGTTCTGTGTACTGTGTGGC 59.402 52.381 0.00 0.00 0.00 5.01
3835 5878 2.358247 GTGTACTGTGTGGCGGGG 60.358 66.667 0.00 0.00 0.00 5.73
3853 5897 1.304381 GAAGGCAACCATCCAGGCA 60.304 57.895 0.00 0.00 43.14 4.75
3910 5986 6.017109 GGCTGTATACGGTCAAATCAAATCAT 60.017 38.462 11.51 0.00 0.00 2.45
3912 5988 7.041780 GCTGTATACGGTCAAATCAAATCATCT 60.042 37.037 13.23 0.00 0.00 2.90
3932 6028 0.470766 AAGTTTGTAGTGGGCGTCCA 59.529 50.000 3.51 3.51 41.58 4.02
3963 6059 7.651304 TGTACTAACAAATTGTCAGCAAAATGG 59.349 33.333 0.00 0.00 33.47 3.16
3965 6061 2.801679 ACAAATTGTCAGCAAAATGGCG 59.198 40.909 0.00 0.00 38.21 5.69
4063 6180 3.424861 TCGATGTTTGCAAAATTTCAGCG 59.575 39.130 23.84 23.84 36.34 5.18
4081 6198 2.095059 AGCGTGAAATGACATTCTTGGC 60.095 45.455 0.05 3.95 0.00 4.52
4178 6337 8.532186 TTATTTTGCCATGGCTTCTAGAAATA 57.468 30.769 35.53 26.33 42.51 1.40
4206 6365 6.450845 TTCACGATGAAAATTTGCAATCAC 57.549 33.333 2.14 0.00 32.71 3.06
4213 6372 6.831727 TGAAAATTTGCAATCACTGACAAG 57.168 33.333 0.00 0.00 0.00 3.16
4221 6380 5.904941 TGCAATCACTGACAAGATTTGTTT 58.095 33.333 0.00 0.00 45.52 2.83
4222 6381 6.339730 TGCAATCACTGACAAGATTTGTTTT 58.660 32.000 0.00 0.00 45.52 2.43
4223 6382 6.256104 TGCAATCACTGACAAGATTTGTTTTG 59.744 34.615 0.00 0.00 45.52 2.44
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
36 37 7.342581 AGGAGGAAGAGTTAAAGATGGAAATC 58.657 38.462 0.00 0.00 0.00 2.17
92 94 1.949847 CTCACCGACGAAGCCTGGAT 61.950 60.000 0.00 0.00 0.00 3.41
221 226 4.966787 GCCCAAGTGTCGCCCCAA 62.967 66.667 0.00 0.00 0.00 4.12
289 295 1.883926 TCGTCGAGATGGACAAAGTCA 59.116 47.619 0.00 0.00 36.73 3.41
295 301 0.171231 CAGCTTCGTCGAGATGGACA 59.829 55.000 0.00 0.00 36.73 4.02
374 380 0.518636 CACCAAATCTCGCCACACAG 59.481 55.000 0.00 0.00 0.00 3.66
395 401 0.659957 GAATGGATCTGAAGCACCGC 59.340 55.000 0.00 0.00 0.00 5.68
457 463 1.078497 TTCGTGCATGTGCCCCTAG 60.078 57.895 5.68 0.00 41.18 3.02
515 521 1.348064 TTCTGTCATCGTTCCCCTGT 58.652 50.000 0.00 0.00 0.00 4.00
523 529 0.170339 TGACGCGATTCTGTCATCGT 59.830 50.000 15.93 0.00 46.50 3.73
571 577 5.003692 TCGAGATTCTGAGACCATCAAAG 57.996 43.478 0.00 0.00 37.52 2.77
604 2541 3.367607 TGCAAAGCACGTCAAACATAAC 58.632 40.909 0.00 0.00 31.71 1.89
700 2637 6.294397 GGGAAAGCCATCATGATGACTTTATC 60.294 42.308 35.43 29.73 46.56 1.75
763 2700 5.190342 GCGTTTCATCTTTTGTTTTCTTGC 58.810 37.500 0.00 0.00 0.00 4.01
767 2704 5.173854 CCTCTGCGTTTCATCTTTTGTTTTC 59.826 40.000 0.00 0.00 0.00 2.29
872 2841 0.253327 ATGAGGAGGCGAGAAAACCC 59.747 55.000 0.00 0.00 0.00 4.11
875 2844 2.431057 GGTCTATGAGGAGGCGAGAAAA 59.569 50.000 0.00 0.00 0.00 2.29
900 2869 1.375326 GGAAAACTGAGGAGGCGGT 59.625 57.895 0.00 0.00 0.00 5.68
906 2875 1.144913 CAACAGGGGGAAAACTGAGGA 59.855 52.381 0.00 0.00 38.09 3.71
917 2886 0.321653 CGAACTCTTCCAACAGGGGG 60.322 60.000 0.00 0.00 37.22 5.40
1029 2998 1.531423 ACAGCAGGCAGAAGATTGTG 58.469 50.000 0.00 0.00 0.00 3.33
1036 3005 1.667830 GCACGTACAGCAGGCAGAA 60.668 57.895 2.66 0.00 0.00 3.02
1138 3107 0.719015 TGAGGGGACAGAGGGAAGAT 59.281 55.000 0.00 0.00 0.00 2.40
1191 3161 1.168714 GATCAGAACCCACCACAAGC 58.831 55.000 0.00 0.00 0.00 4.01
1205 3175 1.645034 AGCACGAAACATCGGATCAG 58.355 50.000 3.12 0.00 37.45 2.90
1413 3383 6.490566 TGTCACAGTTCAATCATTCATGAG 57.509 37.500 0.00 0.00 40.64 2.90
1429 3399 6.710744 ACCATTACTCTTTAGGTTTGTCACAG 59.289 38.462 0.00 0.00 0.00 3.66
1435 3405 7.979444 TCAGAACCATTACTCTTTAGGTTTG 57.021 36.000 0.00 0.00 42.26 2.93
1451 3421 3.819368 TGCAAAGAACAGATCAGAACCA 58.181 40.909 0.00 0.00 0.00 3.67
1482 3452 7.518188 CATTGATATCCCTAAAGTAACCTGGT 58.482 38.462 0.00 0.00 0.00 4.00
1520 3490 0.942410 TTGGCGACTGTGACTAACGC 60.942 55.000 0.00 0.00 46.79 4.84
1538 3508 4.396166 CGTTCAGATTGCCTAAGAACCATT 59.604 41.667 0.00 0.00 36.20 3.16
1555 3525 5.408299 TGGTTAAAGATGATGTCACGTTCAG 59.592 40.000 0.00 0.00 0.00 3.02
1556 3526 5.301555 TGGTTAAAGATGATGTCACGTTCA 58.698 37.500 0.00 0.00 0.00 3.18
1573 3543 6.605594 ACTTCCTCAAAACAAGACATGGTTAA 59.394 34.615 0.00 0.00 38.24 2.01
1576 3546 4.536765 ACTTCCTCAAAACAAGACATGGT 58.463 39.130 0.00 0.00 0.00 3.55
1624 3594 0.454957 CGCGAACTGGGCAGATTTTG 60.455 55.000 0.00 0.00 0.00 2.44
1642 3612 4.549599 CAGCGTTCTTTAGCAAATACAACG 59.450 41.667 0.00 0.00 38.48 4.10
1658 3628 0.664767 AAGCGTGACTCTCAGCGTTC 60.665 55.000 0.00 0.00 34.34 3.95
1659 3629 0.596577 TAAGCGTGACTCTCAGCGTT 59.403 50.000 0.00 0.00 34.34 4.84
1660 3630 0.596577 TTAAGCGTGACTCTCAGCGT 59.403 50.000 0.00 0.00 34.34 5.07
1671 3641 0.366871 CAGCAGCGTACTTAAGCGTG 59.633 55.000 1.29 2.36 38.61 5.34
1712 3682 7.230510 ACTTCAAAATTGCAGACATTAGGTACA 59.769 33.333 0.00 0.00 0.00 2.90
1713 3683 7.593825 ACTTCAAAATTGCAGACATTAGGTAC 58.406 34.615 0.00 0.00 0.00 3.34
1714 3684 7.094377 GGACTTCAAAATTGCAGACATTAGGTA 60.094 37.037 0.00 0.00 0.00 3.08
1715 3685 6.294731 GGACTTCAAAATTGCAGACATTAGGT 60.295 38.462 0.00 0.00 0.00 3.08
1716 3686 6.095377 GGACTTCAAAATTGCAGACATTAGG 58.905 40.000 0.00 0.00 0.00 2.69
1717 3687 5.796935 CGGACTTCAAAATTGCAGACATTAG 59.203 40.000 0.00 0.00 0.00 1.73
1718 3688 5.240623 ACGGACTTCAAAATTGCAGACATTA 59.759 36.000 0.00 0.00 0.00 1.90
1719 3689 4.037923 ACGGACTTCAAAATTGCAGACATT 59.962 37.500 0.00 0.00 0.00 2.71
1720 3690 3.569701 ACGGACTTCAAAATTGCAGACAT 59.430 39.130 0.00 0.00 0.00 3.06
1721 3691 2.948979 ACGGACTTCAAAATTGCAGACA 59.051 40.909 0.00 0.00 0.00 3.41
1722 3692 3.243068 ACACGGACTTCAAAATTGCAGAC 60.243 43.478 0.00 0.00 0.00 3.51
1791 3772 8.714179 CAAGCAATGAACACAACAATATTCAAT 58.286 29.630 0.00 0.00 34.88 2.57
1802 3783 1.403323 TGACGCAAGCAATGAACACAA 59.597 42.857 0.00 0.00 45.62 3.33
1816 3797 5.474825 TCACAAAGTGATAACTATGACGCA 58.525 37.500 0.00 0.00 37.67 5.24
1850 3831 3.133141 AGGAGTTTGAGCAGAGAAACC 57.867 47.619 0.00 0.00 33.34 3.27
1854 3835 4.411927 AGACTTAGGAGTTTGAGCAGAGA 58.588 43.478 0.00 0.00 35.88 3.10
1856 3837 4.152647 TGAGACTTAGGAGTTTGAGCAGA 58.847 43.478 0.00 0.00 35.88 4.26
2010 3994 4.832248 ACAAGACGATGGAAAGCTATCAA 58.168 39.130 0.00 0.00 32.02 2.57
2065 4049 7.448748 AAAAGTTGGCGTCTTCATAACTAAT 57.551 32.000 0.00 0.00 31.85 1.73
2085 4069 5.382618 AAATAGAGCAGGCTGACAAAAAG 57.617 39.130 20.86 0.00 0.00 2.27
2129 4113 3.276857 AGAGTGAGCAATGCTTGGTATG 58.723 45.455 9.91 0.00 42.23 2.39
2177 4165 3.615937 GCCTTAAGAAGCAACGGTACTAC 59.384 47.826 3.36 0.00 0.00 2.73
2185 4173 7.762382 ACACATTATTAGCCTTAAGAAGCAAC 58.238 34.615 3.36 0.00 0.00 4.17
2196 4184 5.163088 CCCTTCCCTTACACATTATTAGCCT 60.163 44.000 0.00 0.00 0.00 4.58
2220 4208 0.895100 TGCAGGCCAACAGACCATTC 60.895 55.000 5.01 0.00 0.00 2.67
2238 4226 5.467399 TGCAAAATCTGGCAGAAAAAGATTG 59.533 36.000 22.84 18.50 39.86 2.67
2276 4264 9.799106 CAGGGTCCTATGATAAAATAACTGAAT 57.201 33.333 0.00 0.00 0.00 2.57
2299 4287 2.203394 AACTGTGCTGGCACCAGG 60.203 61.111 20.80 13.73 45.63 4.45
2323 4311 9.941991 CAAAATTATCAATCTAGCACAAAAACG 57.058 29.630 0.00 0.00 0.00 3.60
2346 4337 6.071447 CCATTTGACAATGATGGGACTACAAA 60.071 38.462 10.07 0.00 42.35 2.83
2355 4346 9.687210 CAAGATATAACCATTTGACAATGATGG 57.313 33.333 14.75 14.75 42.35 3.51
2370 4361 8.448615 AGTTAGCGAAACAAACAAGATATAACC 58.551 33.333 7.58 0.00 40.83 2.85
2492 4488 0.036732 AGGGAATCGCTTGCTTGTGA 59.963 50.000 0.00 0.00 0.00 3.58
2543 4539 0.110373 GGTGGTTCTTTACTTGCGCG 60.110 55.000 0.00 0.00 0.00 6.86
2653 4649 4.133078 GAGGATAAAATAGCAGCAGCAGT 58.867 43.478 3.17 0.00 45.49 4.40
2654 4650 4.132336 TGAGGATAAAATAGCAGCAGCAG 58.868 43.478 3.17 0.00 45.49 4.24
2655 4651 4.155063 TGAGGATAAAATAGCAGCAGCA 57.845 40.909 3.17 0.00 45.49 4.41
2727 4729 7.064847 CCTTTAACCTATGTACGCAACACATAA 59.935 37.037 4.26 0.00 42.09 1.90
2916 4918 3.198409 TGGACATGTAAGCTGCCATAG 57.802 47.619 0.00 0.00 0.00 2.23
3024 5026 7.094205 ACAAATTTACAAGTTCCAGATAGGCAG 60.094 37.037 0.00 0.00 37.29 4.85
3063 5065 9.225436 GAAGGTGAATCTTAAGAATCTTGAAGT 57.775 33.333 18.94 2.94 0.00 3.01
3099 5102 4.037565 AGCATGGCAATGTGATTGATGTAG 59.962 41.667 2.31 0.00 42.83 2.74
3279 5294 3.583806 CAACAAACACTGCCAACAAAGA 58.416 40.909 0.00 0.00 0.00 2.52
3367 5382 2.743938 AGCATATAAAGACCACTCGCG 58.256 47.619 0.00 0.00 0.00 5.87
3531 5546 8.366671 ACATCTTATATTTAAGAACAGACGGC 57.633 34.615 9.31 0.00 45.24 5.68
3605 5622 9.590451 TTTTATGACCAATAGAAAGTACTACCG 57.410 33.333 0.00 0.00 0.00 4.02
3668 5685 2.365293 GTGGCAGGAACAGAAAACCATT 59.635 45.455 0.00 0.00 0.00 3.16
3693 5736 7.752239 CACATAACAACTTTAATGAGCTTCTGG 59.248 37.037 0.00 0.00 0.00 3.86
3694 5737 7.272084 GCACATAACAACTTTAATGAGCTTCTG 59.728 37.037 0.00 0.00 0.00 3.02
3695 5738 7.308435 GCACATAACAACTTTAATGAGCTTCT 58.692 34.615 0.00 0.00 0.00 2.85
3723 5766 9.697250 CGATTCGCAGTAATTAAAGAAAATGTA 57.303 29.630 0.00 0.00 0.00 2.29
3749 5792 4.319549 GGCTGCAATATCGGTAAAAGTAGC 60.320 45.833 0.50 6.85 0.00 3.58
3750 5793 4.814234 TGGCTGCAATATCGGTAAAAGTAG 59.186 41.667 0.50 0.00 0.00 2.57
3751 5794 4.771903 TGGCTGCAATATCGGTAAAAGTA 58.228 39.130 0.50 0.00 0.00 2.24
3752 5795 3.616219 TGGCTGCAATATCGGTAAAAGT 58.384 40.909 0.50 0.00 0.00 2.66
3817 5860 2.423874 CCCGCCACACAGTACACA 59.576 61.111 0.00 0.00 0.00 3.72
3826 5869 4.966787 GTTGCCTTCCCCGCCACA 62.967 66.667 0.00 0.00 0.00 4.17
3831 5874 2.440247 GGATGGTTGCCTTCCCCG 60.440 66.667 8.44 0.00 40.65 5.73
3835 5878 1.304381 TGCCTGGATGGTTGCCTTC 60.304 57.895 0.00 0.00 38.35 3.46
3910 5986 2.028748 GGACGCCCACTACAAACTTAGA 60.029 50.000 0.00 0.00 0.00 2.10
3912 5988 1.693062 TGGACGCCCACTACAAACTTA 59.307 47.619 0.00 0.00 37.58 2.24
3932 6028 7.767261 TGCTGACAATTTGTTAGTACAACTTT 58.233 30.769 19.01 0.00 43.66 2.66
3963 6059 1.084370 CATCCCGAACTTGTCTCCGC 61.084 60.000 0.00 0.00 0.00 5.54
3965 6061 2.762535 TTCATCCCGAACTTGTCTCC 57.237 50.000 0.00 0.00 0.00 3.71
4028 6132 4.326009 GCAAACATCGAAAACTGTTGTTGT 59.674 37.500 3.04 0.00 35.82 3.32
4029 6133 4.325741 TGCAAACATCGAAAACTGTTGTTG 59.674 37.500 3.04 0.98 35.82 3.33
4030 6134 4.489810 TGCAAACATCGAAAACTGTTGTT 58.510 34.783 3.04 0.00 35.82 2.83
4042 6159 3.182173 ACGCTGAAATTTTGCAAACATCG 59.818 39.130 12.39 15.39 0.00 3.84
4063 6180 4.232221 CACTGCCAAGAATGTCATTTCAC 58.768 43.478 0.00 0.00 0.00 3.18
4101 6260 3.446442 AAGGCATCTTGGAGTGATGTT 57.554 42.857 0.00 0.00 42.21 2.71
4102 6261 3.087031 CAAAGGCATCTTGGAGTGATGT 58.913 45.455 0.00 0.00 42.21 3.06


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

AutoCloner maintained by Alex Coulton.