Multiple sequence alignment - TraesCS6D01G099700

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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 TraesCS6D01G099700 chr6D 100.000 4957 0 0 1 4957 62881488 62876532 0.000000e+00 9154.0
1 TraesCS6D01G099700 chr6D 100.000 35 0 0 1502 1536 62879955 62879921 1.150000e-06 65.8
2 TraesCS6D01G099700 chr6D 100.000 35 0 0 1534 1568 62879987 62879953 1.150000e-06 65.8
3 TraesCS6D01G099700 chr6A 93.273 3984 156 41 919 4847 80647815 80643889 0.000000e+00 5770.0
4 TraesCS6D01G099700 chr6A 97.143 35 1 0 1502 1536 80647201 80647167 5.360000e-05 60.2
5 TraesCS6D01G099700 chr6B 96.012 2257 59 11 975 3218 136460547 136458309 0.000000e+00 3640.0
6 TraesCS6D01G099700 chr6B 94.965 993 41 2 3217 4207 136458205 136457220 0.000000e+00 1548.0
7 TraesCS6D01G099700 chr6B 86.677 653 34 14 4332 4957 136456954 136456328 0.000000e+00 675.0
8 TraesCS6D01G099700 chr6B 100.000 35 0 0 1502 1536 136459992 136459958 1.150000e-06 65.8
9 TraesCS6D01G099700 chr6B 100.000 35 0 0 1534 1568 136460024 136459990 1.150000e-06 65.8
10 TraesCS6D01G099700 chr5D 91.459 761 62 1 112 869 27818302 27817542 0.000000e+00 1042.0
11 TraesCS6D01G099700 chr5A 89.096 752 77 3 121 869 436905498 436906247 0.000000e+00 929.0
12 TraesCS6D01G099700 chr5A 88.732 710 71 7 174 875 578843320 578842612 0.000000e+00 859.0
13 TraesCS6D01G099700 chr5A 88.868 539 55 2 341 876 671349234 671349770 0.000000e+00 658.0
14 TraesCS6D01G099700 chr7B 88.482 764 76 2 109 869 45185515 45184761 0.000000e+00 913.0
15 TraesCS6D01G099700 chr1A 88.177 702 74 3 174 873 562722670 562723364 0.000000e+00 828.0
16 TraesCS6D01G099700 chr2A 87.729 709 79 6 174 875 5182942 5183649 0.000000e+00 821.0
17 TraesCS6D01G099700 chr4B 86.745 762 66 15 109 866 10745850 10746580 0.000000e+00 815.0
18 TraesCS6D01G099700 chr3D 89.547 574 49 2 298 869 330909271 330909835 0.000000e+00 717.0
19 TraesCS6D01G099700 chr3D 97.059 34 1 0 41 74 330908958 330908991 1.930000e-04 58.4
20 TraesCS6D01G099700 chr2B 86.007 536 69 4 342 873 760112492 760111959 2.000000e-158 569.0
21 TraesCS6D01G099700 chr2D 91.239 331 23 3 342 671 548270381 548270706 3.520000e-121 446.0
22 TraesCS6D01G099700 chr7A 90.640 203 19 0 181 383 287006944 287007146 2.270000e-68 270.0
23 TraesCS6D01G099700 chr7A 100.000 36 0 0 109 144 287006917 287006952 3.200000e-07 67.6
24 TraesCS6D01G099700 chr1D 81.731 104 7 1 211 314 375205271 375205362 5.320000e-10 76.8


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 TraesCS6D01G099700 chr6D 62876532 62881488 4956 True 3095.20 9154 100.0000 1 4957 3 chr6D.!!$R1 4956
1 TraesCS6D01G099700 chr6A 80643889 80647815 3926 True 2915.10 5770 95.2080 919 4847 2 chr6A.!!$R1 3928
2 TraesCS6D01G099700 chr6B 136456328 136460547 4219 True 1198.92 3640 95.5308 975 4957 5 chr6B.!!$R1 3982
3 TraesCS6D01G099700 chr5D 27817542 27818302 760 True 1042.00 1042 91.4590 112 869 1 chr5D.!!$R1 757
4 TraesCS6D01G099700 chr5A 436905498 436906247 749 False 929.00 929 89.0960 121 869 1 chr5A.!!$F1 748
5 TraesCS6D01G099700 chr5A 578842612 578843320 708 True 859.00 859 88.7320 174 875 1 chr5A.!!$R1 701
6 TraesCS6D01G099700 chr5A 671349234 671349770 536 False 658.00 658 88.8680 341 876 1 chr5A.!!$F2 535
7 TraesCS6D01G099700 chr7B 45184761 45185515 754 True 913.00 913 88.4820 109 869 1 chr7B.!!$R1 760
8 TraesCS6D01G099700 chr1A 562722670 562723364 694 False 828.00 828 88.1770 174 873 1 chr1A.!!$F1 699
9 TraesCS6D01G099700 chr2A 5182942 5183649 707 False 821.00 821 87.7290 174 875 1 chr2A.!!$F1 701
10 TraesCS6D01G099700 chr4B 10745850 10746580 730 False 815.00 815 86.7450 109 866 1 chr4B.!!$F1 757
11 TraesCS6D01G099700 chr3D 330908958 330909835 877 False 387.70 717 93.3030 41 869 2 chr3D.!!$F1 828
12 TraesCS6D01G099700 chr2B 760111959 760112492 533 True 569.00 569 86.0070 342 873 1 chr2B.!!$R1 531

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
869 933 1.077787 CGCCCCATTGGAGTTGCTA 60.078 57.895 3.62 0.0 35.39 3.49 F
945 1009 1.142748 AGAATGAGCGCTCCTTCCG 59.857 57.895 36.42 0.0 35.65 4.30 F
952 1016 1.227263 GCGCTCCTTCCGATAGCAA 60.227 57.895 0.00 0.0 35.98 3.91 F
956 1020 1.576356 CTCCTTCCGATAGCAAGTGC 58.424 55.000 0.00 0.0 42.49 4.40 F
1021 1090 1.742761 CACGGCATCTCATCCTTGTT 58.257 50.000 0.00 0.0 0.00 2.83 F
1030 1099 2.045047 TCTCATCCTTGTTCCTCCCTCT 59.955 50.000 0.00 0.0 0.00 3.69 F
2660 2738 2.170166 CCTTGTCTATGGCTTTGGCAA 58.830 47.619 0.00 0.0 42.43 4.52 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2140 2218 0.826715 GAGCAGGGCACATGACTCTA 59.173 55.000 0.00 0.00 0.00 2.43 R
2179 2257 1.170919 ATGAGAAGCGCCATGATGCC 61.171 55.000 2.29 0.00 0.00 4.40 R
2605 2683 6.104665 TCATGTCACAGCAAAAATGAACAAA 58.895 32.000 0.00 0.00 0.00 2.83 R
2660 2738 6.706716 GGTCAACTTTTAGCTTCTCTTACTGT 59.293 38.462 0.00 0.00 0.00 3.55 R
2974 3052 9.661563 TCCATATACACTGGTTACTACAAAAAG 57.338 33.333 0.00 0.00 35.19 2.27 R
3292 3476 8.620416 TGGATACATGTGCTCATATGTTTTAAC 58.380 33.333 15.54 5.89 46.17 2.01 R
4207 4399 0.035056 GCATAGAACACAGCAGGGGT 60.035 55.000 0.00 0.00 0.00 4.95 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
25 26 4.760047 CACCCCGCCTCCTTCGTG 62.760 72.222 0.00 0.00 0.00 4.35
27 28 4.452733 CCCCGCCTCCTTCGTGTC 62.453 72.222 0.00 0.00 0.00 3.67
28 29 4.796231 CCCGCCTCCTTCGTGTCG 62.796 72.222 0.00 0.00 0.00 4.35
29 30 4.796231 CCGCCTCCTTCGTGTCGG 62.796 72.222 0.00 0.00 0.00 4.79
32 33 4.796231 CCTCCTTCGTGTCGGCCG 62.796 72.222 22.12 22.12 0.00 6.13
33 34 4.796231 CTCCTTCGTGTCGGCCGG 62.796 72.222 27.83 9.38 0.00 6.13
74 75 2.112815 ATTTTGCTACCCCTCGCGC 61.113 57.895 0.00 0.00 0.00 6.86
107 108 4.463879 CTCCCCCTCGCACTGCTG 62.464 72.222 0.00 0.00 0.00 4.41
211 212 4.285790 TGCTTCCCCCTCCCCTGT 62.286 66.667 0.00 0.00 0.00 4.00
220 221 1.920325 CCTCCCCTGTCCTGCTTCA 60.920 63.158 0.00 0.00 0.00 3.02
276 280 4.834453 CAGAGCAGCGCCTCCTGG 62.834 72.222 2.29 0.00 33.44 4.45
375 432 1.599171 CCGATGACGAGATCTGCAGTC 60.599 57.143 14.67 10.66 42.66 3.51
483 540 3.299977 CCGTCGTCCTGGACCACA 61.300 66.667 21.75 4.76 33.30 4.17
764 826 2.243994 GGGCTAAGTTTGGGTTAGGGAT 59.756 50.000 0.00 0.00 0.00 3.85
779 841 2.202932 GATGGACAGCACGCGGAT 60.203 61.111 12.47 0.00 0.00 4.18
869 933 1.077787 CGCCCCATTGGAGTTGCTA 60.078 57.895 3.62 0.00 35.39 3.49
876 940 5.388654 CCCCATTGGAGTTGCTATAAGATT 58.611 41.667 3.62 0.00 35.39 2.40
877 941 5.835280 CCCCATTGGAGTTGCTATAAGATTT 59.165 40.000 3.62 0.00 35.39 2.17
878 942 6.015940 CCCCATTGGAGTTGCTATAAGATTTC 60.016 42.308 3.62 0.00 35.39 2.17
879 943 6.293626 CCCATTGGAGTTGCTATAAGATTTCG 60.294 42.308 3.62 0.00 0.00 3.46
880 944 6.260936 CCATTGGAGTTGCTATAAGATTTCGT 59.739 38.462 0.00 0.00 0.00 3.85
881 945 7.441157 CCATTGGAGTTGCTATAAGATTTCGTA 59.559 37.037 0.00 0.00 0.00 3.43
882 946 8.993121 CATTGGAGTTGCTATAAGATTTCGTAT 58.007 33.333 0.00 0.00 0.00 3.06
883 947 8.958119 TTGGAGTTGCTATAAGATTTCGTATT 57.042 30.769 0.00 0.00 0.00 1.89
915 979 4.459390 AAAAAGGTTTTGCGTGGTACTT 57.541 36.364 0.00 0.00 0.00 2.24
916 980 5.579564 AAAAAGGTTTTGCGTGGTACTTA 57.420 34.783 0.00 0.00 0.00 2.24
917 981 5.777850 AAAAGGTTTTGCGTGGTACTTAT 57.222 34.783 0.00 0.00 0.00 1.73
925 989 7.695201 GGTTTTGCGTGGTACTTATATTCTTTC 59.305 37.037 0.00 0.00 0.00 2.62
945 1009 1.142748 AGAATGAGCGCTCCTTCCG 59.857 57.895 36.42 0.00 35.65 4.30
951 1015 2.076622 GAGCGCTCCTTCCGATAGCA 62.077 60.000 27.22 0.00 35.98 3.49
952 1016 1.227263 GCGCTCCTTCCGATAGCAA 60.227 57.895 0.00 0.00 35.98 3.91
956 1020 1.576356 CTCCTTCCGATAGCAAGTGC 58.424 55.000 0.00 0.00 42.49 4.40
983 1047 2.640346 AAACCGCGTTGAAAAACTGT 57.360 40.000 4.92 0.00 0.00 3.55
1021 1090 1.742761 CACGGCATCTCATCCTTGTT 58.257 50.000 0.00 0.00 0.00 2.83
1030 1099 2.045047 TCTCATCCTTGTTCCTCCCTCT 59.955 50.000 0.00 0.00 0.00 3.69
1085 1154 2.676822 TCTCTCCGGCAGCGTCTT 60.677 61.111 0.00 0.00 0.00 3.01
1609 1678 8.988064 TCTTAGCTTAGTGAGTACATTTTCAG 57.012 34.615 0.00 0.00 0.00 3.02
1612 1681 9.555727 TTAGCTTAGTGAGTACATTTTCAGTTT 57.444 29.630 0.00 0.00 0.00 2.66
1613 1682 8.089115 AGCTTAGTGAGTACATTTTCAGTTTC 57.911 34.615 0.00 0.00 0.00 2.78
1614 1683 7.715249 AGCTTAGTGAGTACATTTTCAGTTTCA 59.285 33.333 0.00 0.00 0.00 2.69
1668 1737 2.171003 GGTTTTAGCAGATGCCCAGTT 58.829 47.619 0.14 0.00 43.38 3.16
1707 1776 5.300034 TCTCATTGTGTGCATTATGATTCCC 59.700 40.000 0.00 0.00 0.00 3.97
1756 1825 6.741358 GTCAAAACTCAACAGTTGTTACACTC 59.259 38.462 13.14 0.00 42.45 3.51
1766 1835 8.491152 CAACAGTTGTTACACTCTTCTGATAAG 58.509 37.037 4.99 0.00 36.32 1.73
1779 1848 4.574674 TCTGATAAGATTTGGCACTGGT 57.425 40.909 0.00 0.00 0.00 4.00
1859 1936 6.211384 GCTCATAGGTTTTTAATGGGCCATAT 59.789 38.462 21.54 12.53 40.51 1.78
2045 2122 5.829924 AGGATACAGTTGCAATTAAGGGATG 59.170 40.000 0.59 0.00 41.41 3.51
2611 2689 6.385649 TCAGGTTGGTTACTGATTTTGTTC 57.614 37.500 0.00 0.00 38.71 3.18
2660 2738 2.170166 CCTTGTCTATGGCTTTGGCAA 58.830 47.619 0.00 0.00 42.43 4.52
2747 2825 6.433093 ACCTGAGTGTTTAACTTGTTCAGTTT 59.567 34.615 13.16 3.35 43.89 2.66
2748 2826 6.747280 CCTGAGTGTTTAACTTGTTCAGTTTG 59.253 38.462 13.16 1.77 43.89 2.93
2974 3052 7.408132 TCATATACTGCTGATAACGCTTTTC 57.592 36.000 0.00 0.00 0.00 2.29
3208 3287 4.862902 ACTCCATTCTGTATCCATCTCG 57.137 45.455 0.00 0.00 0.00 4.04
3323 3507 3.808466 TGAGCACATGTATCCAGTCTC 57.192 47.619 0.00 0.00 0.00 3.36
3330 3514 3.132824 ACATGTATCCAGTCTCGCAATCA 59.867 43.478 0.00 0.00 0.00 2.57
3332 3516 5.011023 ACATGTATCCAGTCTCGCAATCATA 59.989 40.000 0.00 0.00 0.00 2.15
3333 3517 5.728637 TGTATCCAGTCTCGCAATCATAT 57.271 39.130 0.00 0.00 0.00 1.78
3697 3881 2.927004 CCTTTGGCAACTCGTAGCA 58.073 52.632 0.00 0.00 37.61 3.49
3718 3904 3.325135 CACAGTGGGTTAGGAGAAGACTT 59.675 47.826 0.00 0.00 0.00 3.01
3742 3928 1.924320 ATATCTAGACCGAGGCGCGC 61.924 60.000 25.94 25.94 39.11 6.86
3773 3959 5.536916 CCTTTTTGTCCTGTAAATACCCACA 59.463 40.000 0.00 0.00 0.00 4.17
3849 4037 6.648725 GGATGATTTGTAAGTATCTCCTCTGC 59.351 42.308 0.00 0.00 0.00 4.26
3931 4120 1.243902 ACGGATTCAAACACGGCAAT 58.756 45.000 0.00 0.00 0.00 3.56
4126 4318 1.600957 CATACAAGCAATGGAGAGGCG 59.399 52.381 0.00 0.00 0.00 5.52
4198 4390 1.645402 AACCACCCCTGCTGTGTTCT 61.645 55.000 0.00 0.00 31.71 3.01
4199 4391 0.766674 ACCACCCCTGCTGTGTTCTA 60.767 55.000 0.00 0.00 31.71 2.10
4200 4392 0.620556 CCACCCCTGCTGTGTTCTAT 59.379 55.000 0.00 0.00 31.71 1.98
4201 4393 1.679944 CCACCCCTGCTGTGTTCTATG 60.680 57.143 0.00 0.00 31.71 2.23
4202 4394 0.035056 ACCCCTGCTGTGTTCTATGC 60.035 55.000 0.00 0.00 0.00 3.14
4203 4395 0.749454 CCCCTGCTGTGTTCTATGCC 60.749 60.000 0.00 0.00 0.00 4.40
4204 4396 0.254178 CCCTGCTGTGTTCTATGCCT 59.746 55.000 0.00 0.00 0.00 4.75
4205 4397 1.340405 CCCTGCTGTGTTCTATGCCTT 60.340 52.381 0.00 0.00 0.00 4.35
4206 4398 2.440409 CCTGCTGTGTTCTATGCCTTT 58.560 47.619 0.00 0.00 0.00 3.11
4207 4399 3.609853 CCTGCTGTGTTCTATGCCTTTA 58.390 45.455 0.00 0.00 0.00 1.85
4208 4400 3.375299 CCTGCTGTGTTCTATGCCTTTAC 59.625 47.826 0.00 0.00 0.00 2.01
4209 4401 3.343617 TGCTGTGTTCTATGCCTTTACC 58.656 45.455 0.00 0.00 0.00 2.85
4210 4402 2.683362 GCTGTGTTCTATGCCTTTACCC 59.317 50.000 0.00 0.00 0.00 3.69
4211 4403 3.279434 CTGTGTTCTATGCCTTTACCCC 58.721 50.000 0.00 0.00 0.00 4.95
4212 4404 2.916934 TGTGTTCTATGCCTTTACCCCT 59.083 45.455 0.00 0.00 0.00 4.79
4213 4405 3.279434 GTGTTCTATGCCTTTACCCCTG 58.721 50.000 0.00 0.00 0.00 4.45
4214 4406 2.298610 GTTCTATGCCTTTACCCCTGC 58.701 52.381 0.00 0.00 0.00 4.85
4215 4407 1.893315 TCTATGCCTTTACCCCTGCT 58.107 50.000 0.00 0.00 0.00 4.24
4216 4408 1.490490 TCTATGCCTTTACCCCTGCTG 59.510 52.381 0.00 0.00 0.00 4.41
4217 4409 1.212935 CTATGCCTTTACCCCTGCTGT 59.787 52.381 0.00 0.00 0.00 4.40
4218 4410 0.323725 ATGCCTTTACCCCTGCTGTG 60.324 55.000 0.00 0.00 0.00 3.66
4219 4411 1.074951 GCCTTTACCCCTGCTGTGT 59.925 57.895 0.00 0.00 0.00 3.72
4220 4412 0.539669 GCCTTTACCCCTGCTGTGTT 60.540 55.000 0.00 0.00 0.00 3.32
4221 4413 1.534729 CCTTTACCCCTGCTGTGTTC 58.465 55.000 0.00 0.00 0.00 3.18
4239 4431 6.634805 TGTGTTCTATGCCTTTGTTTTTCAA 58.365 32.000 0.00 0.00 0.00 2.69
4288 4480 7.568349 ACTGCTCAGGTCTAAAATATTCATCA 58.432 34.615 1.66 0.00 0.00 3.07
4294 4486 9.904198 TCAGGTCTAAAATATTCATCATGTTCA 57.096 29.630 0.00 0.00 0.00 3.18
4341 4700 5.475909 TGCCCTAAGTCTATAATACGGAGTG 59.524 44.000 0.00 0.00 45.73 3.51
4488 4849 7.551035 AGATCATGCTGTAGAAAGCTTTTAG 57.449 36.000 14.05 10.56 43.90 1.85
4489 4850 7.334090 AGATCATGCTGTAGAAAGCTTTTAGA 58.666 34.615 14.05 5.75 43.90 2.10
4492 4853 7.584987 TCATGCTGTAGAAAGCTTTTAGAAAC 58.415 34.615 14.05 8.02 43.90 2.78
4493 4854 7.445402 TCATGCTGTAGAAAGCTTTTAGAAACT 59.555 33.333 14.05 7.09 43.90 2.66
4494 4855 7.568199 TGCTGTAGAAAGCTTTTAGAAACTT 57.432 32.000 14.05 0.00 43.90 2.66
4497 4858 7.800847 GCTGTAGAAAGCTTTTAGAAACTTCTG 59.199 37.037 14.05 7.59 40.20 3.02
4499 4860 6.078202 AGAAAGCTTTTAGAAACTTCTGCC 57.922 37.500 14.05 0.00 38.19 4.85
4532 4894 9.174166 GAACCCATTAGAGTTAAAAGAAGCATA 57.826 33.333 0.00 0.00 0.00 3.14
4554 4931 1.814248 AACGGAGTGTTTCCAGAAGCC 60.814 52.381 0.00 0.00 45.00 4.35
4589 4966 6.892485 TGATGAGGTGAGATGTTTATGTCAT 58.108 36.000 0.00 0.00 38.64 3.06
4663 5061 1.550524 CGGTTCAGTCAAGGGAGATCA 59.449 52.381 0.00 0.00 0.00 2.92
4697 5102 1.249407 AACCAAAATTCCGGCGCTTA 58.751 45.000 7.64 0.00 0.00 3.09
4701 5106 3.258228 CCAAAATTCCGGCGCTTATTTT 58.742 40.909 7.64 9.87 32.14 1.82
4752 5160 4.080299 AGGAACTGAAAAGGACAGACAAGT 60.080 41.667 0.00 0.00 37.18 3.16
4918 5342 1.751351 CAGAACGAGGCTCCTATGACA 59.249 52.381 9.32 0.00 0.00 3.58
4928 5352 4.414846 AGGCTCCTATGACATTCTTGGAAT 59.585 41.667 0.00 0.00 0.00 3.01
4937 5361 4.588106 TGACATTCTTGGAATGAAGCCAAA 59.412 37.500 22.02 2.49 44.23 3.28
4942 5366 8.156165 ACATTCTTGGAATGAAGCCAAAATTTA 58.844 29.630 22.02 0.00 44.23 1.40
4944 5368 7.537596 TCTTGGAATGAAGCCAAAATTTAGA 57.462 32.000 0.00 0.00 44.23 2.10
4945 5369 8.137745 TCTTGGAATGAAGCCAAAATTTAGAT 57.862 30.769 0.00 0.00 44.23 1.98
4946 5370 8.253113 TCTTGGAATGAAGCCAAAATTTAGATC 58.747 33.333 0.00 0.00 44.23 2.75
4947 5371 7.722949 TGGAATGAAGCCAAAATTTAGATCT 57.277 32.000 0.00 0.00 31.13 2.75
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
8 9 4.760047 CACGAAGGAGGCGGGGTG 62.760 72.222 0.00 0.00 0.00 4.61
10 11 4.452733 GACACGAAGGAGGCGGGG 62.453 72.222 0.00 0.00 36.25 5.73
11 12 4.796231 CGACACGAAGGAGGCGGG 62.796 72.222 0.00 0.00 34.62 6.13
15 16 4.796231 CGGCCGACACGAAGGAGG 62.796 72.222 24.07 0.00 0.00 4.30
16 17 4.796231 CCGGCCGACACGAAGGAG 62.796 72.222 30.73 0.44 0.00 3.69
90 91 4.463879 CAGCAGTGCGAGGGGGAG 62.464 72.222 10.00 0.00 0.00 4.30
276 280 3.152937 CTTCGCGCTGCAGCAGATC 62.153 63.158 36.03 20.55 42.21 2.75
359 416 1.323271 GGGGACTGCAGATCTCGTCA 61.323 60.000 23.35 4.37 0.00 4.35
483 540 2.749044 CAAGCTGCATCCCACGCT 60.749 61.111 1.02 0.00 31.95 5.07
546 604 1.229658 CCCACCCAGTCCTCCTTCT 60.230 63.158 0.00 0.00 0.00 2.85
583 641 2.099652 CTCCACCGTCCTGCTCACAA 62.100 60.000 0.00 0.00 0.00 3.33
764 826 2.183300 GTATCCGCGTGCTGTCCA 59.817 61.111 4.92 0.00 0.00 4.02
894 958 4.459390 AAGTACCACGCAAAACCTTTTT 57.541 36.364 0.00 0.00 0.00 1.94
895 959 5.777850 ATAAGTACCACGCAAAACCTTTT 57.222 34.783 0.00 0.00 0.00 2.27
896 960 7.392393 AGAATATAAGTACCACGCAAAACCTTT 59.608 33.333 0.00 0.00 0.00 3.11
897 961 6.882678 AGAATATAAGTACCACGCAAAACCTT 59.117 34.615 0.00 0.00 0.00 3.50
898 962 6.412214 AGAATATAAGTACCACGCAAAACCT 58.588 36.000 0.00 0.00 0.00 3.50
899 963 6.673154 AGAATATAAGTACCACGCAAAACC 57.327 37.500 0.00 0.00 0.00 3.27
900 964 7.695201 GGAAAGAATATAAGTACCACGCAAAAC 59.305 37.037 0.00 0.00 0.00 2.43
901 965 7.390996 TGGAAAGAATATAAGTACCACGCAAAA 59.609 33.333 0.00 0.00 0.00 2.44
902 966 6.879993 TGGAAAGAATATAAGTACCACGCAAA 59.120 34.615 0.00 0.00 0.00 3.68
903 967 6.408035 TGGAAAGAATATAAGTACCACGCAA 58.592 36.000 0.00 0.00 0.00 4.85
904 968 5.979993 TGGAAAGAATATAAGTACCACGCA 58.020 37.500 0.00 0.00 0.00 5.24
905 969 6.278363 TCTGGAAAGAATATAAGTACCACGC 58.722 40.000 0.00 0.00 0.00 5.34
906 970 8.765219 CATTCTGGAAAGAATATAAGTACCACG 58.235 37.037 0.85 0.00 36.82 4.94
907 971 9.832445 TCATTCTGGAAAGAATATAAGTACCAC 57.168 33.333 0.85 0.00 36.82 4.16
909 973 8.994170 GCTCATTCTGGAAAGAATATAAGTACC 58.006 37.037 0.85 0.00 36.82 3.34
910 974 8.704234 CGCTCATTCTGGAAAGAATATAAGTAC 58.296 37.037 0.85 0.00 36.82 2.73
911 975 7.385205 GCGCTCATTCTGGAAAGAATATAAGTA 59.615 37.037 0.00 0.00 36.82 2.24
912 976 6.203723 GCGCTCATTCTGGAAAGAATATAAGT 59.796 38.462 0.00 0.00 36.82 2.24
913 977 6.426328 AGCGCTCATTCTGGAAAGAATATAAG 59.574 38.462 2.64 1.92 36.82 1.73
914 978 6.291377 AGCGCTCATTCTGGAAAGAATATAA 58.709 36.000 2.64 0.00 36.82 0.98
915 979 5.858381 AGCGCTCATTCTGGAAAGAATATA 58.142 37.500 2.64 0.00 36.82 0.86
916 980 4.712476 AGCGCTCATTCTGGAAAGAATAT 58.288 39.130 2.64 0.00 36.82 1.28
917 981 4.122776 GAGCGCTCATTCTGGAAAGAATA 58.877 43.478 31.91 0.00 36.82 1.75
925 989 0.813210 GGAAGGAGCGCTCATTCTGG 60.813 60.000 44.45 0.00 46.17 3.86
934 998 1.218230 CTTGCTATCGGAAGGAGCGC 61.218 60.000 0.00 0.00 41.48 5.92
1021 1090 4.779733 GGTGCGGGAGAGGGAGGA 62.780 72.222 0.00 0.00 0.00 3.71
1420 1489 2.283529 GGACACCTCTTCCGGAGCA 61.284 63.158 3.34 0.00 40.57 4.26
1609 1678 8.031277 ACCTCATTTGAGCTAATTTGATGAAAC 58.969 33.333 1.90 0.00 40.75 2.78
1612 1681 7.613022 AGAACCTCATTTGAGCTAATTTGATGA 59.387 33.333 1.90 0.00 40.75 2.92
1613 1682 7.769220 AGAACCTCATTTGAGCTAATTTGATG 58.231 34.615 1.90 0.00 40.75 3.07
1614 1683 7.613022 TGAGAACCTCATTTGAGCTAATTTGAT 59.387 33.333 1.90 0.00 40.75 2.57
1668 1737 5.050159 CACAATGAGAAGACAATGTTCACGA 60.050 40.000 0.00 0.00 32.53 4.35
1756 1825 4.946157 ACCAGTGCCAAATCTTATCAGAAG 59.054 41.667 0.00 0.00 30.76 2.85
1779 1848 1.355381 ACAAGACCTCCAATCCATGCA 59.645 47.619 0.00 0.00 0.00 3.96
2045 2122 7.556275 TCCTAATTTGATTGAACTGTGATACCC 59.444 37.037 0.00 0.00 0.00 3.69
2140 2218 0.826715 GAGCAGGGCACATGACTCTA 59.173 55.000 0.00 0.00 0.00 2.43
2178 2256 1.820906 GAGAAGCGCCATGATGCCA 60.821 57.895 2.29 0.00 0.00 4.92
2179 2257 1.170919 ATGAGAAGCGCCATGATGCC 61.171 55.000 2.29 0.00 0.00 4.40
2605 2683 6.104665 TCATGTCACAGCAAAAATGAACAAA 58.895 32.000 0.00 0.00 0.00 2.83
2611 2689 7.671827 CATGTAATCATGTCACAGCAAAAATG 58.328 34.615 0.00 0.00 44.37 2.32
2660 2738 6.706716 GGTCAACTTTTAGCTTCTCTTACTGT 59.293 38.462 0.00 0.00 0.00 3.55
2974 3052 9.661563 TCCATATACACTGGTTACTACAAAAAG 57.338 33.333 0.00 0.00 35.19 2.27
3292 3476 8.620416 TGGATACATGTGCTCATATGTTTTAAC 58.380 33.333 15.54 5.89 46.17 2.01
3293 3477 8.744568 TGGATACATGTGCTCATATGTTTTAA 57.255 30.769 15.54 1.12 46.17 1.52
3323 3507 6.859508 ACAATTTGCAGTATGATATGATTGCG 59.140 34.615 0.00 0.00 39.69 4.85
3330 3514 9.060347 CAAGGACTACAATTTGCAGTATGATAT 57.940 33.333 2.23 0.00 39.69 1.63
3332 3516 6.886459 ACAAGGACTACAATTTGCAGTATGAT 59.114 34.615 2.23 0.00 39.69 2.45
3333 3517 6.237901 ACAAGGACTACAATTTGCAGTATGA 58.762 36.000 2.23 0.00 39.69 2.15
3696 3880 2.900546 AGTCTTCTCCTAACCCACTGTG 59.099 50.000 0.00 0.00 0.00 3.66
3697 3881 3.261818 AGTCTTCTCCTAACCCACTGT 57.738 47.619 0.00 0.00 0.00 3.55
3718 3904 3.075148 CGCCTCGGTCTAGATATTCAGA 58.925 50.000 0.00 0.00 0.00 3.27
3742 3928 1.074951 AGGACAAAAAGGGGAGGCG 59.925 57.895 0.00 0.00 0.00 5.52
3813 4001 6.604795 ACTTACAAATCATCCAGCTGCTTTAT 59.395 34.615 8.66 0.00 0.00 1.40
3819 4007 6.426328 GGAGATACTTACAAATCATCCAGCTG 59.574 42.308 6.78 6.78 0.00 4.24
3849 4037 6.459024 GGTTCTCTACAGCTACTGTACTCATG 60.459 46.154 3.37 0.00 43.46 3.07
3908 4097 2.070783 GCCGTGTTTGAATCCGTTCTA 58.929 47.619 0.00 0.00 35.33 2.10
3947 4136 4.449743 TGAAGTACGCATTTAGTGACCAAC 59.550 41.667 0.00 0.00 0.00 3.77
3996 4185 3.121030 CTTCCCTTCACTGCCGCG 61.121 66.667 0.00 0.00 0.00 6.46
4087 4278 3.694043 TGCTATAAGCTGTGTTCCACA 57.306 42.857 0.03 0.00 42.97 4.17
4126 4318 0.882042 CACACACTGGCAGACACTCC 60.882 60.000 23.66 0.00 0.00 3.85
4198 4390 1.064758 CACAGCAGGGGTAAAGGCATA 60.065 52.381 0.00 0.00 0.00 3.14
4199 4391 0.323725 CACAGCAGGGGTAAAGGCAT 60.324 55.000 0.00 0.00 0.00 4.40
4200 4392 1.074775 CACAGCAGGGGTAAAGGCA 59.925 57.895 0.00 0.00 0.00 4.75
4201 4393 0.539669 AACACAGCAGGGGTAAAGGC 60.540 55.000 0.00 0.00 0.00 4.35
4202 4394 1.073923 AGAACACAGCAGGGGTAAAGG 59.926 52.381 0.00 0.00 0.00 3.11
4203 4395 2.568623 AGAACACAGCAGGGGTAAAG 57.431 50.000 0.00 0.00 0.00 1.85
4204 4396 3.872240 GCATAGAACACAGCAGGGGTAAA 60.872 47.826 0.00 0.00 0.00 2.01
4205 4397 2.355716 GCATAGAACACAGCAGGGGTAA 60.356 50.000 0.00 0.00 0.00 2.85
4206 4398 1.209504 GCATAGAACACAGCAGGGGTA 59.790 52.381 0.00 0.00 0.00 3.69
4207 4399 0.035056 GCATAGAACACAGCAGGGGT 60.035 55.000 0.00 0.00 0.00 4.95
4208 4400 0.749454 GGCATAGAACACAGCAGGGG 60.749 60.000 0.00 0.00 0.00 4.79
4209 4401 0.254178 AGGCATAGAACACAGCAGGG 59.746 55.000 0.00 0.00 0.00 4.45
4210 4402 2.119801 AAGGCATAGAACACAGCAGG 57.880 50.000 0.00 0.00 0.00 4.85
4211 4403 2.816087 ACAAAGGCATAGAACACAGCAG 59.184 45.455 0.00 0.00 0.00 4.24
4212 4404 2.862541 ACAAAGGCATAGAACACAGCA 58.137 42.857 0.00 0.00 0.00 4.41
4213 4405 3.923017 AACAAAGGCATAGAACACAGC 57.077 42.857 0.00 0.00 0.00 4.40
4214 4406 6.272318 TGAAAAACAAAGGCATAGAACACAG 58.728 36.000 0.00 0.00 0.00 3.66
4215 4407 6.214191 TGAAAAACAAAGGCATAGAACACA 57.786 33.333 0.00 0.00 0.00 3.72
4216 4408 6.200854 CCTTGAAAAACAAAGGCATAGAACAC 59.799 38.462 0.00 0.00 38.08 3.32
4217 4409 6.279882 CCTTGAAAAACAAAGGCATAGAACA 58.720 36.000 0.00 0.00 38.08 3.18
4218 4410 5.696270 CCCTTGAAAAACAAAGGCATAGAAC 59.304 40.000 0.00 0.00 38.08 3.01
4219 4411 5.600484 TCCCTTGAAAAACAAAGGCATAGAA 59.400 36.000 0.00 0.00 39.29 2.10
4220 4412 5.144100 TCCCTTGAAAAACAAAGGCATAGA 58.856 37.500 0.00 0.00 39.29 1.98
4221 4413 5.243730 TCTCCCTTGAAAAACAAAGGCATAG 59.756 40.000 0.00 0.00 39.29 2.23
4262 4454 7.712639 TGATGAATATTTTAGACCTGAGCAGTC 59.287 37.037 0.00 0.00 0.00 3.51
4401 4760 1.336440 TGCTCCAACAACATTTCACCG 59.664 47.619 0.00 0.00 0.00 4.94
4436 4795 6.430925 TGCTTGAGAAGTACATGCATTAAAGT 59.569 34.615 0.00 0.00 41.20 2.66
4488 4849 3.500299 GGTTCAAGAGAGGCAGAAGTTTC 59.500 47.826 0.00 0.00 0.00 2.78
4489 4850 3.481453 GGTTCAAGAGAGGCAGAAGTTT 58.519 45.455 0.00 0.00 0.00 2.66
4492 4853 1.349026 TGGGTTCAAGAGAGGCAGAAG 59.651 52.381 0.00 0.00 0.00 2.85
4493 4854 1.434188 TGGGTTCAAGAGAGGCAGAA 58.566 50.000 0.00 0.00 0.00 3.02
4494 4855 1.661463 ATGGGTTCAAGAGAGGCAGA 58.339 50.000 0.00 0.00 0.00 4.26
4497 4858 3.198853 ACTCTAATGGGTTCAAGAGAGGC 59.801 47.826 5.27 0.00 38.80 4.70
4499 4860 8.848474 TTTTAACTCTAATGGGTTCAAGAGAG 57.152 34.615 5.27 0.00 38.16 3.20
4554 4931 5.545588 TCTCACCTCATCAGAGAACAAAAG 58.454 41.667 0.00 0.00 44.98 2.27
4589 4966 4.127171 GACAAACACTTGGCTGTCTTCTA 58.873 43.478 5.96 0.00 37.61 2.10
4619 5008 2.813172 TCGAATGACTGATTGCAAAGCA 59.187 40.909 1.71 4.05 41.67 3.91
4663 5061 8.306761 GGAATTTTGGTTATCTGATTTGACTGT 58.693 33.333 0.00 0.00 0.00 3.55
4701 5106 2.045561 TCGCAGACAACCCAAAGAAA 57.954 45.000 0.00 0.00 0.00 2.52
4744 5152 1.443194 GCCGCATGCAACTTGTCTG 60.443 57.895 19.57 0.00 40.77 3.51
4752 5160 1.615165 ATTTCCATGGCCGCATGCAA 61.615 50.000 19.57 0.70 43.89 4.08
4825 5234 1.411246 GTACACATCGCCTACCATGGA 59.589 52.381 21.47 0.67 0.00 3.41
4877 5286 3.200605 TGATTATGCCTGAAGAGGAGCAA 59.799 43.478 0.00 0.00 42.93 3.91
4918 5342 8.596293 TCTAAATTTTGGCTTCATTCCAAGAAT 58.404 29.630 0.00 0.00 43.67 2.40
4928 5352 7.233348 ACTTGGAAGATCTAAATTTTGGCTTCA 59.767 33.333 23.05 14.18 33.74 3.02


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

AutoCloner maintained by Alex Coulton.