Multiple sequence alignment - TraesCS4A01G172200

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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 TraesCS4A01G172200 chr4A 100.000 2320 0 0 940 3259 437484141 437481822 0.000000e+00 4285.0
1 TraesCS4A01G172200 chr4A 100.000 625 0 0 1 625 437485080 437484456 0.000000e+00 1155.0
2 TraesCS4A01G172200 chr4D 93.316 1900 56 22 964 2806 129776337 129778222 0.000000e+00 2739.0
3 TraesCS4A01G172200 chr4D 91.374 626 28 6 1 625 129775413 129776013 0.000000e+00 833.0
4 TraesCS4A01G172200 chr4D 87.054 448 49 7 2813 3259 129778308 129778747 6.280000e-137 497.0
5 TraesCS4A01G172200 chrUn 92.604 1636 49 17 946 2540 58871050 58869446 0.000000e+00 2285.0
6 TraesCS4A01G172200 chrUn 91.534 626 28 5 1 625 319831869 319831268 0.000000e+00 839.0
7 TraesCS4A01G172200 chrUn 91.534 626 28 5 1 625 332180600 332181201 0.000000e+00 839.0
8 TraesCS4A01G172200 chrUn 91.534 626 28 5 1 625 380953832 380954433 0.000000e+00 839.0
9 TraesCS4A01G172200 chrUn 97.710 262 6 0 951 1212 319831212 319830951 4.960000e-123 451.0
10 TraesCS4A01G172200 chrUn 97.710 262 6 0 951 1212 332181257 332181518 4.960000e-123 451.0
11 TraesCS4A01G172200 chrUn 91.909 309 18 2 2536 2837 58869382 58869074 3.010000e-115 425.0
12 TraesCS4A01G172200 chrUn 90.435 230 19 1 3030 3259 58955862 58955636 1.900000e-77 300.0
13 TraesCS4A01G172200 chr3D 82.520 246 39 4 1053 1296 525917798 525917555 2.550000e-51 213.0
14 TraesCS4A01G172200 chr3D 85.083 181 25 2 1687 1866 525917553 525917374 2.000000e-42 183.0
15 TraesCS4A01G172200 chr5D 93.617 141 9 0 1163 1303 110794092 110794232 9.160000e-51 211.0
16 TraesCS4A01G172200 chr5B 94.815 135 7 0 1169 1303 122101437 122101303 9.160000e-51 211.0
17 TraesCS4A01G172200 chr5A 94.615 130 7 0 1174 1303 116034549 116034420 5.510000e-48 202.0
18 TraesCS4A01G172200 chr3B 81.356 236 40 4 1063 1296 694263467 694263700 4.290000e-44 189.0
19 TraesCS4A01G172200 chr3A 84.066 182 27 2 1687 1867 660196184 660196364 1.200000e-39 174.0
20 TraesCS4A01G172200 chr1A 88.806 134 13 2 1166 1298 58946920 58947052 2.600000e-36 163.0
21 TraesCS4A01G172200 chr1D 87.121 132 15 2 1166 1296 60317506 60317636 7.290000e-32 148.0
22 TraesCS4A01G172200 chr2D 90.000 70 5 2 1683 1751 466723987 466723919 4.480000e-14 89.8
23 TraesCS4A01G172200 chr2B 90.000 70 5 2 1683 1751 545366056 545365988 4.480000e-14 89.8
24 TraesCS4A01G172200 chr2A 90.000 70 5 2 1683 1751 607841870 607841802 4.480000e-14 89.8
25 TraesCS4A01G172200 chr6D 87.838 74 6 3 1680 1751 292737755 292737683 2.080000e-12 84.2
26 TraesCS4A01G172200 chr6B 87.838 74 6 3 1680 1751 457216782 457216710 2.080000e-12 84.2


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 TraesCS4A01G172200 chr4A 437481822 437485080 3258 True 2720.000000 4285 100.000000 1 3259 2 chr4A.!!$R1 3258
1 TraesCS4A01G172200 chr4D 129775413 129778747 3334 False 1356.333333 2739 90.581333 1 3259 3 chr4D.!!$F1 3258
2 TraesCS4A01G172200 chrUn 58869074 58871050 1976 True 1355.000000 2285 92.256500 946 2837 2 chrUn.!!$R2 1891
3 TraesCS4A01G172200 chrUn 380953832 380954433 601 False 839.000000 839 91.534000 1 625 1 chrUn.!!$F1 624
4 TraesCS4A01G172200 chrUn 319830951 319831869 918 True 645.000000 839 94.622000 1 1212 2 chrUn.!!$R3 1211
5 TraesCS4A01G172200 chrUn 332180600 332181518 918 False 645.000000 839 94.622000 1 1212 2 chrUn.!!$F2 1211

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
540 542 0.313987 TGTAGGCGAGTGTGTGTGAG 59.686 55.000 0.0 0.0 0.00 3.51 F
546 548 0.665670 CGAGTGTGTGTGAGCCTGAG 60.666 60.000 0.0 0.0 0.00 3.35 F
547 549 0.948141 GAGTGTGTGTGAGCCTGAGC 60.948 60.000 0.0 0.0 40.32 4.26 F
1446 1733 1.076777 ATTTGGCCGGTGATGGGAG 60.077 57.895 1.9 0.0 0.00 4.30 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1572 1861 0.752743 CCATGCACCCATCATTCGGT 60.753 55.0 0.00 0.0 0.0 4.69 R
1573 1862 0.752743 ACCATGCACCCATCATTCGG 60.753 55.0 0.00 0.0 0.0 4.30 R
1592 1881 1.012086 CTAGTACAGCGCCGTCAGTA 58.988 55.0 2.29 0.0 0.0 2.74 R
3061 3579 0.388907 GTTGTCGTTAGGGTGCGCTA 60.389 55.0 9.73 0.0 0.0 4.26 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
41 42 0.455815 TGACGACAGATGGTGGATCG 59.544 55.000 0.00 0.00 36.04 3.69
47 48 1.224075 CAGATGGTGGATCGATGCAC 58.776 55.000 34.25 34.25 46.73 4.57
57 58 1.976728 GATCGATGCACGGTATACACG 59.023 52.381 0.54 8.52 42.82 4.49
82 83 5.803461 GTGCATAAATGACTCACACTACGTA 59.197 40.000 0.00 0.00 0.00 3.57
83 84 5.803461 TGCATAAATGACTCACACTACGTAC 59.197 40.000 0.00 0.00 0.00 3.67
85 86 3.482722 AATGACTCACACTACGTACGG 57.517 47.619 21.06 5.00 0.00 4.02
89 90 3.229552 GACTCACACTACGTACGGTTTC 58.770 50.000 21.06 0.73 0.00 2.78
100 101 7.062138 CACTACGTACGGTTTCTTAATTTAGCA 59.938 37.037 21.06 0.00 0.00 3.49
101 102 6.783892 ACGTACGGTTTCTTAATTTAGCAA 57.216 33.333 21.06 0.00 0.00 3.91
102 103 7.188468 ACGTACGGTTTCTTAATTTAGCAAA 57.812 32.000 21.06 0.00 0.00 3.68
103 104 7.071414 ACGTACGGTTTCTTAATTTAGCAAAC 58.929 34.615 21.06 9.25 0.00 2.93
104 105 7.041848 ACGTACGGTTTCTTAATTTAGCAAACT 60.042 33.333 21.06 0.00 0.00 2.66
105 106 8.434661 CGTACGGTTTCTTAATTTAGCAAACTA 58.565 33.333 7.57 3.94 0.00 2.24
106 107 9.533983 GTACGGTTTCTTAATTTAGCAAACTAC 57.466 33.333 13.84 9.13 0.00 2.73
107 108 8.156994 ACGGTTTCTTAATTTAGCAAACTACA 57.843 30.769 13.84 0.00 0.00 2.74
200 201 5.011635 TGTTTTTCTTAAAGGAGGAATGCCC 59.988 40.000 0.00 0.00 33.31 5.36
223 224 4.520179 CCGGCCTTTTAGTAGTAACCATT 58.480 43.478 0.00 0.00 0.00 3.16
242 243 6.999950 ACCATTTATTCCAGGTAAAACAACC 58.000 36.000 0.00 0.00 40.06 3.77
306 307 5.648572 TGCAAATGAATATCGAATTGTGCA 58.351 33.333 0.00 1.38 36.03 4.57
341 343 2.977914 AGTTTGAGCAGTGCATCGTAT 58.022 42.857 19.20 0.00 0.00 3.06
342 344 2.674852 AGTTTGAGCAGTGCATCGTATG 59.325 45.455 19.20 0.00 0.00 2.39
352 354 4.813161 CAGTGCATCGTATGATTTCTTCCT 59.187 41.667 0.00 0.00 30.49 3.36
373 375 7.050970 TCCTGAATAAAGTACTATGCGTCAT 57.949 36.000 0.00 0.00 0.00 3.06
540 542 0.313987 TGTAGGCGAGTGTGTGTGAG 59.686 55.000 0.00 0.00 0.00 3.51
541 543 1.009389 GTAGGCGAGTGTGTGTGAGC 61.009 60.000 0.00 0.00 0.00 4.26
542 544 2.154798 TAGGCGAGTGTGTGTGAGCC 62.155 60.000 0.00 0.00 44.45 4.70
543 545 2.029666 GCGAGTGTGTGTGAGCCT 59.970 61.111 0.00 0.00 0.00 4.58
544 546 2.313172 GCGAGTGTGTGTGAGCCTG 61.313 63.158 0.00 0.00 0.00 4.85
545 547 1.363807 CGAGTGTGTGTGAGCCTGA 59.636 57.895 0.00 0.00 0.00 3.86
546 548 0.665670 CGAGTGTGTGTGAGCCTGAG 60.666 60.000 0.00 0.00 0.00 3.35
547 549 0.948141 GAGTGTGTGTGAGCCTGAGC 60.948 60.000 0.00 0.00 40.32 4.26
548 550 1.963338 GTGTGTGTGAGCCTGAGCC 60.963 63.158 0.00 0.00 41.25 4.70
549 551 2.427320 GTGTGTGAGCCTGAGCCA 59.573 61.111 0.00 0.00 41.25 4.75
550 552 1.670406 GTGTGTGAGCCTGAGCCAG 60.670 63.158 0.00 0.00 41.25 4.85
551 553 2.142761 TGTGTGAGCCTGAGCCAGT 61.143 57.895 2.18 0.00 41.25 4.00
552 554 1.670406 GTGTGAGCCTGAGCCAGTG 60.670 63.158 2.18 0.00 41.25 3.66
553 555 1.838396 TGTGAGCCTGAGCCAGTGA 60.838 57.895 0.00 0.00 41.25 3.41
568 570 4.033251 TGATCCCTCCCCCGGGTT 62.033 66.667 21.85 0.00 44.95 4.11
612 614 2.036346 CTCCACTTTCCCTTTTGCCTTG 59.964 50.000 0.00 0.00 0.00 3.61
970 1257 3.913799 CCCTCTCTCCCTCTCTACATCTA 59.086 52.174 0.00 0.00 0.00 1.98
971 1258 4.263331 CCCTCTCTCCCTCTCTACATCTAC 60.263 54.167 0.00 0.00 0.00 2.59
1361 1648 3.015095 CATCGCGCTGCAAATCGC 61.015 61.111 5.56 15.06 46.98 4.58
1431 1718 1.893137 GAAAGTTTGAGGGGCCGATTT 59.107 47.619 0.00 0.00 0.00 2.17
1446 1733 1.076777 ATTTGGCCGGTGATGGGAG 60.077 57.895 1.90 0.00 0.00 4.30
1553 1842 3.322466 CCCGGCTCTTCACCCACT 61.322 66.667 0.00 0.00 0.00 4.00
1555 1844 2.266055 CGGCTCTTCACCCACTCC 59.734 66.667 0.00 0.00 0.00 3.85
1559 1848 2.606519 TCTTCACCCACTCCCCGG 60.607 66.667 0.00 0.00 0.00 5.73
1560 1849 4.410400 CTTCACCCACTCCCCGGC 62.410 72.222 0.00 0.00 0.00 6.13
1592 1881 0.752743 CCGAATGATGGGTGCATGGT 60.753 55.000 0.00 0.00 0.00 3.55
1655 1968 0.899720 TTGTCGACCTCCATGGGTAC 59.100 55.000 14.12 0.00 40.06 3.34
1909 2246 2.807045 GTGCGCGTCAGGAGTCAG 60.807 66.667 8.43 0.00 0.00 3.51
1917 2254 0.457851 GTCAGGAGTCAGGTCGATGG 59.542 60.000 0.00 0.00 0.00 3.51
1918 2255 1.142748 CAGGAGTCAGGTCGATGGC 59.857 63.158 0.00 0.00 0.00 4.40
1919 2256 1.000993 AGGAGTCAGGTCGATGGCT 59.999 57.895 0.00 0.00 38.00 4.75
1920 2257 0.259065 AGGAGTCAGGTCGATGGCTA 59.741 55.000 0.00 0.00 34.61 3.93
1921 2258 0.386113 GGAGTCAGGTCGATGGCTAC 59.614 60.000 0.00 0.00 34.61 3.58
1922 2259 0.386113 GAGTCAGGTCGATGGCTACC 59.614 60.000 0.00 0.00 34.61 3.18
1923 2260 0.324368 AGTCAGGTCGATGGCTACCA 60.324 55.000 0.00 0.00 38.30 3.25
1924 2261 0.179108 GTCAGGTCGATGGCTACCAC 60.179 60.000 0.00 0.00 38.30 4.16
1925 2262 1.144057 CAGGTCGATGGCTACCACC 59.856 63.158 0.00 0.00 38.30 4.61
1962 2308 4.115516 CACATATCCCGAGAACAACTCTG 58.884 47.826 0.00 0.00 42.92 3.35
2078 2424 1.209383 CGAGAAGACAACGAGCGGA 59.791 57.895 0.00 0.00 0.00 5.54
2096 2442 1.229951 AGGGGACTGGATGCAGGAA 60.230 57.895 19.22 0.00 41.13 3.36
2141 2487 2.701107 CATATGCAGATCCAGCCTGAG 58.299 52.381 0.00 0.00 33.65 3.35
2150 2496 4.767255 CAGCCTGAGGACGGTGGC 62.767 72.222 0.65 0.00 45.21 5.01
2265 2611 7.341256 ACATATGGAAGATGCAATGAGTTTTCT 59.659 33.333 7.80 0.00 0.00 2.52
2272 2618 9.928236 GAAGATGCAATGAGTTTTCTAGTTATC 57.072 33.333 0.00 0.00 0.00 1.75
2356 2715 2.024414 GAGGATGGCGGCAAACTTAAT 58.976 47.619 18.31 0.00 0.00 1.40
2526 2889 8.319881 AGGAGAGATGATGACAATGTTATATGG 58.680 37.037 0.00 0.00 0.00 2.74
2532 2895 9.836076 GATGATGACAATGTTATATGGTTGATG 57.164 33.333 0.00 0.00 0.00 3.07
2548 2980 5.985530 TGGTTGATGCATATCTACGAAGAAG 59.014 40.000 0.00 0.00 39.13 2.85
2555 2987 4.747108 GCATATCTACGAAGAAGTGCACAT 59.253 41.667 21.04 7.05 41.85 3.21
2762 3201 0.451957 TGCGTTTAATCAGTTGCGCG 60.452 50.000 0.00 0.00 46.55 6.86
2831 3349 5.413499 TCCTTAACCGTAAGTGAATGCTAC 58.587 41.667 0.00 0.00 35.82 3.58
2840 3358 4.410492 AAGTGAATGCTACGCTCTTTTG 57.590 40.909 0.00 0.00 0.00 2.44
2841 3359 2.160417 AGTGAATGCTACGCTCTTTTGC 59.840 45.455 0.00 0.00 0.00 3.68
2842 3360 2.160417 GTGAATGCTACGCTCTTTTGCT 59.840 45.455 0.00 0.00 0.00 3.91
2845 3363 2.969443 TGCTACGCTCTTTTGCTTTC 57.031 45.000 0.00 0.00 0.00 2.62
2848 3366 2.159639 GCTACGCTCTTTTGCTTTCTCC 60.160 50.000 0.00 0.00 0.00 3.71
2894 3412 3.700538 ACCATGGCAGTACAATCAACAT 58.299 40.909 13.04 0.00 0.00 2.71
2937 3455 6.177310 ATCTAGATCTGTAGACCACGTAGT 57.823 41.667 5.18 0.00 34.07 2.73
2940 3458 7.473653 ATCTAGATCTGTAGACCACGTAGTGAT 60.474 40.741 5.18 0.00 46.05 3.06
2962 3480 2.163815 GGCTACAAGTACTGAAGCGAGA 59.836 50.000 14.65 0.00 33.96 4.04
2964 3482 3.366070 GCTACAAGTACTGAAGCGAGACA 60.366 47.826 0.00 0.00 0.00 3.41
2976 3494 2.946762 GAGACAAAGGCACGCCAC 59.053 61.111 11.35 0.00 38.92 5.01
2985 3503 2.819595 GCACGCCACCGTCATCAT 60.820 61.111 0.00 0.00 46.39 2.45
2991 3509 0.179000 GCCACCGTCATCATCCTTCT 59.821 55.000 0.00 0.00 0.00 2.85
2998 3516 1.672881 GTCATCATCCTTCTTTGCCGG 59.327 52.381 0.00 0.00 0.00 6.13
3001 3519 0.984230 TCATCCTTCTTTGCCGGAGT 59.016 50.000 5.05 0.00 0.00 3.85
3009 3527 1.275291 TCTTTGCCGGAGTAGGACAAG 59.725 52.381 5.05 0.00 32.16 3.16
3012 3530 0.251653 TGCCGGAGTAGGACAAGACT 60.252 55.000 5.05 0.00 0.00 3.24
3017 3535 3.429547 CCGGAGTAGGACAAGACTGATTG 60.430 52.174 0.00 0.00 36.22 2.67
3020 3538 5.449314 CGGAGTAGGACAAGACTGATTGTAG 60.449 48.000 3.66 0.00 43.32 2.74
3024 3542 5.312120 AGGACAAGACTGATTGTAGTACG 57.688 43.478 0.00 0.00 43.32 3.67
3028 3546 3.152261 AGACTGATTGTAGTACGCAGC 57.848 47.619 14.10 9.21 0.00 5.25
3048 3566 2.860062 CCGAGAAGTCGTCGTGTTAAT 58.140 47.619 0.00 0.00 45.30 1.40
3050 3568 3.231965 CGAGAAGTCGTCGTGTTAATGT 58.768 45.455 0.00 0.00 41.57 2.71
3051 3569 3.667261 CGAGAAGTCGTCGTGTTAATGTT 59.333 43.478 0.00 0.00 41.57 2.71
3052 3570 4.147653 CGAGAAGTCGTCGTGTTAATGTTT 59.852 41.667 0.00 0.00 41.57 2.83
3057 3575 8.857216 AGAAGTCGTCGTGTTAATGTTTTATAG 58.143 33.333 0.00 0.00 0.00 1.31
3058 3576 7.515957 AGTCGTCGTGTTAATGTTTTATAGG 57.484 36.000 0.00 0.00 0.00 2.57
3061 3579 7.274250 GTCGTCGTGTTAATGTTTTATAGGACT 59.726 37.037 0.00 0.00 0.00 3.85
3075 3593 1.226888 GGACTAGCGCACCCTAACG 60.227 63.158 11.47 0.00 0.00 3.18
3081 3599 1.666872 GCGCACCCTAACGACAACT 60.667 57.895 0.30 0.00 0.00 3.16
3093 3611 0.948623 CGACAACTGCCGAATGACCA 60.949 55.000 0.00 0.00 0.00 4.02
3095 3613 0.179032 ACAACTGCCGAATGACCACA 60.179 50.000 0.00 0.00 0.00 4.17
3106 3624 4.024893 CCGAATGACCACATATTGCTACAC 60.025 45.833 0.00 0.00 35.50 2.90
3186 3704 2.944129 ACATGGGTTGCACTAACTTGT 58.056 42.857 0.00 0.00 39.31 3.16
3232 3750 0.179048 AAGCTTGCTTTGGGTTTGGC 60.179 50.000 0.00 0.00 0.00 4.52
3237 3755 2.339712 CTTTGGGTTTGGCTGGCG 59.660 61.111 0.00 0.00 0.00 5.69
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
12 13 1.852942 TCTGTCGTCACAAGACTTGC 58.147 50.000 15.24 0.00 42.73 4.01
17 18 1.000843 CCACCATCTGTCGTCACAAGA 59.999 52.381 0.00 0.00 29.82 3.02
41 42 1.205657 CACCGTGTATACCGTGCATC 58.794 55.000 0.00 0.00 31.24 3.91
47 48 4.052608 TCATTTATGCACCGTGTATACCG 58.947 43.478 8.66 3.74 0.00 4.02
57 58 4.032900 CGTAGTGTGAGTCATTTATGCACC 59.967 45.833 0.00 0.00 0.00 5.01
82 83 8.156994 TGTAGTTTGCTAAATTAAGAAACCGT 57.843 30.769 0.00 0.00 0.00 4.83
83 84 9.453325 TTTGTAGTTTGCTAAATTAAGAAACCG 57.547 29.630 0.00 0.00 0.00 4.44
100 101 7.703058 ATTCCGAAAGATGGATTTGTAGTTT 57.297 32.000 0.00 0.00 34.91 2.66
101 102 8.980481 ATATTCCGAAAGATGGATTTGTAGTT 57.020 30.769 0.00 0.00 34.91 2.24
102 103 9.712305 CTATATTCCGAAAGATGGATTTGTAGT 57.288 33.333 0.00 0.00 34.91 2.73
103 104 9.929180 TCTATATTCCGAAAGATGGATTTGTAG 57.071 33.333 0.00 0.00 34.91 2.74
105 106 9.627123 TTTCTATATTCCGAAAGATGGATTTGT 57.373 29.630 0.00 0.00 34.91 2.83
107 108 9.853177 ACTTTCTATATTCCGAAAGATGGATTT 57.147 29.630 19.86 3.03 45.51 2.17
200 201 2.236893 TGGTTACTACTAAAAGGCCGGG 59.763 50.000 2.18 0.00 0.00 5.73
223 224 9.016438 GTCTTATGGTTGTTTTACCTGGAATAA 57.984 33.333 0.00 0.00 39.04 1.40
236 237 8.512138 GCAAAGTTAGTATGTCTTATGGTTGTT 58.488 33.333 0.00 0.00 0.00 2.83
286 287 8.786937 GTGTATGCACAATTCGATATTCATTT 57.213 30.769 9.26 0.00 44.64 2.32
352 354 8.748582 CGTAAATGACGCATAGTACTTTATTCA 58.251 33.333 0.00 0.00 46.27 2.57
373 375 8.937884 TGATTTTCGACCAAGAAATATCGTAAA 58.062 29.630 0.00 0.00 39.52 2.01
433 435 2.084546 ACGAACCTGCCTTTTATCTGC 58.915 47.619 0.00 0.00 0.00 4.26
540 542 2.191641 GGGATCACTGGCTCAGGC 59.808 66.667 7.06 0.00 35.51 4.85
541 543 1.694133 GGAGGGATCACTGGCTCAGG 61.694 65.000 0.00 0.00 35.51 3.86
542 544 1.694133 GGGAGGGATCACTGGCTCAG 61.694 65.000 0.00 1.16 37.52 3.35
543 545 1.690633 GGGAGGGATCACTGGCTCA 60.691 63.158 0.00 0.00 0.00 4.26
544 546 2.447714 GGGGAGGGATCACTGGCTC 61.448 68.421 0.00 0.00 0.00 4.70
545 547 2.367512 GGGGAGGGATCACTGGCT 60.368 66.667 0.00 0.00 0.00 4.75
546 548 3.493303 GGGGGAGGGATCACTGGC 61.493 72.222 0.00 0.00 0.00 4.85
547 549 3.164269 CGGGGGAGGGATCACTGG 61.164 72.222 0.00 0.00 0.00 4.00
548 550 3.164269 CCGGGGGAGGGATCACTG 61.164 72.222 0.00 0.00 0.00 3.66
949 991 4.263331 GGTAGATGTAGAGAGGGAGAGAGG 60.263 54.167 0.00 0.00 0.00 3.69
957 999 4.770010 GGATCCAAGGTAGATGTAGAGAGG 59.230 50.000 6.95 0.00 0.00 3.69
1431 1718 2.366837 ATCTCCCATCACCGGCCA 60.367 61.111 0.00 0.00 0.00 5.36
1446 1733 4.496183 GTGTTCACACGAGTCTAATCGATC 59.504 45.833 6.84 0.00 45.56 3.69
1572 1861 0.752743 CCATGCACCCATCATTCGGT 60.753 55.000 0.00 0.00 0.00 4.69
1573 1862 0.752743 ACCATGCACCCATCATTCGG 60.753 55.000 0.00 0.00 0.00 4.30
1574 1863 1.603802 GTACCATGCACCCATCATTCG 59.396 52.381 0.00 0.00 0.00 3.34
1575 1864 2.620115 CAGTACCATGCACCCATCATTC 59.380 50.000 0.00 0.00 0.00 2.67
1592 1881 1.012086 CTAGTACAGCGCCGTCAGTA 58.988 55.000 2.29 0.00 0.00 2.74
1655 1968 9.533253 CAGCCATTAATCCCAAAAGTAATTAAG 57.467 33.333 0.00 0.00 29.79 1.85
1871 2208 2.047655 GTGTCGCCGATTGTGGGA 60.048 61.111 0.00 0.00 0.00 4.37
1934 2280 1.071471 CTCGGGATATGTGGTGGCC 59.929 63.158 0.00 0.00 0.00 5.36
2078 2424 1.229951 TTCCTGCATCCAGTCCCCT 60.230 57.895 0.00 0.00 37.38 4.79
2096 2442 1.674057 CCAGAACTCTTGGTCCGCT 59.326 57.895 0.00 0.00 0.00 5.52
2141 2487 2.114411 TGGAAAAGGCCACCGTCC 59.886 61.111 5.01 6.68 31.66 4.79
2150 2496 1.554042 CGTGGTCGACGTGGAAAAGG 61.554 60.000 9.92 0.00 43.50 3.11
2272 2618 8.738199 TGTATAAGTATAAAAATCGCTCCTCG 57.262 34.615 0.00 0.00 40.15 4.63
2336 2695 1.459450 TTAAGTTTGCCGCCATCCTC 58.541 50.000 0.00 0.00 0.00 3.71
2415 2778 7.230712 AGGTAAAACAAGATCCAACGAAGAAAT 59.769 33.333 0.00 0.00 0.00 2.17
2516 2879 9.317936 CGTAGATATGCATCAACCATATAACAT 57.682 33.333 0.19 0.00 36.34 2.71
2526 2889 6.563010 GCACTTCTTCGTAGATATGCATCAAC 60.563 42.308 17.62 0.00 39.58 3.18
2532 2895 4.112634 TGTGCACTTCTTCGTAGATATGC 58.887 43.478 19.41 16.39 39.93 3.14
2541 2973 4.408993 TCATCAAATGTGCACTTCTTCG 57.591 40.909 19.41 1.90 0.00 3.79
2548 2980 5.334260 CCAAAACCAATCATCAAATGTGCAC 60.334 40.000 10.75 10.75 0.00 4.57
2555 2987 3.135348 TGGCACCAAAACCAATCATCAAA 59.865 39.130 0.00 0.00 31.46 2.69
2627 3066 7.394816 ACTTGTCATAGCAAACTATACTTGGT 58.605 34.615 0.00 0.00 36.96 3.67
2667 3106 3.049206 CGTGGAAATGTCAAATGCGTTT 58.951 40.909 0.00 0.00 0.00 3.60
2762 3201 6.509418 TGTGCTGGATAAATTTAGTGGAAC 57.491 37.500 3.94 0.49 0.00 3.62
2831 3349 3.632855 AAAGGAGAAAGCAAAAGAGCG 57.367 42.857 0.00 0.00 40.15 5.03
2855 3373 7.230309 TGCCATGGTTGATGATAATAAATCGAA 59.770 33.333 14.67 0.00 33.31 3.71
2856 3374 6.714356 TGCCATGGTTGATGATAATAAATCGA 59.286 34.615 14.67 0.00 33.31 3.59
2857 3375 6.912082 TGCCATGGTTGATGATAATAAATCG 58.088 36.000 14.67 0.00 33.31 3.34
2869 3387 3.966979 TGATTGTACTGCCATGGTTGAT 58.033 40.909 14.67 0.00 0.00 2.57
2873 3391 3.153369 TGTTGATTGTACTGCCATGGT 57.847 42.857 14.67 0.00 0.00 3.55
2876 3394 4.847198 TCTGATGTTGATTGTACTGCCAT 58.153 39.130 0.00 0.00 0.00 4.40
2908 3426 9.570468 ACGTGGTCTACAGATCTAGATTTAATA 57.430 33.333 6.70 0.00 0.00 0.98
2913 3431 6.483974 CACTACGTGGTCTACAGATCTAGATT 59.516 42.308 6.70 0.00 0.00 2.40
2919 3437 4.261238 CCATCACTACGTGGTCTACAGATC 60.261 50.000 0.00 0.00 33.87 2.75
2923 3441 1.475280 GCCATCACTACGTGGTCTACA 59.525 52.381 0.00 0.00 37.81 2.74
2924 3442 1.749634 AGCCATCACTACGTGGTCTAC 59.250 52.381 0.00 0.00 37.81 2.59
2930 3448 3.232213 ACTTGTAGCCATCACTACGTG 57.768 47.619 0.00 0.00 44.55 4.49
2931 3449 4.015084 AGTACTTGTAGCCATCACTACGT 58.985 43.478 0.00 0.00 44.55 3.57
2932 3450 4.095932 TCAGTACTTGTAGCCATCACTACG 59.904 45.833 0.00 0.00 44.55 3.51
2937 3455 3.676049 CGCTTCAGTACTTGTAGCCATCA 60.676 47.826 12.57 0.00 44.63 3.07
2940 3458 1.890489 TCGCTTCAGTACTTGTAGCCA 59.110 47.619 12.57 0.97 44.63 4.75
2941 3459 2.163815 TCTCGCTTCAGTACTTGTAGCC 59.836 50.000 12.57 0.31 44.63 3.93
2950 3468 1.343142 TGCCTTTGTCTCGCTTCAGTA 59.657 47.619 0.00 0.00 0.00 2.74
2962 3480 4.868116 ACGGTGGCGTGCCTTTGT 62.868 61.111 12.84 4.65 36.94 2.83
2964 3482 3.842925 ATGACGGTGGCGTGCCTTT 62.843 57.895 12.84 0.00 36.94 3.11
2976 3494 1.672881 GGCAAAGAAGGATGATGACGG 59.327 52.381 0.00 0.00 0.00 4.79
2985 3503 0.902531 CCTACTCCGGCAAAGAAGGA 59.097 55.000 0.00 0.00 0.00 3.36
2991 3509 1.001633 GTCTTGTCCTACTCCGGCAAA 59.998 52.381 0.00 0.00 0.00 3.68
2998 3516 6.518208 ACTACAATCAGTCTTGTCCTACTC 57.482 41.667 0.00 0.00 39.88 2.59
3001 3519 5.163683 GCGTACTACAATCAGTCTTGTCCTA 60.164 44.000 0.00 0.00 39.88 2.94
3009 3527 2.194271 GGCTGCGTACTACAATCAGTC 58.806 52.381 0.00 0.00 0.00 3.51
3012 3530 0.812549 TCGGCTGCGTACTACAATCA 59.187 50.000 0.00 0.00 0.00 2.57
3017 3535 0.450983 ACTTCTCGGCTGCGTACTAC 59.549 55.000 0.00 0.00 0.00 2.73
3020 3538 1.868251 CGACTTCTCGGCTGCGTAC 60.868 63.158 0.00 0.00 36.16 3.67
3024 3542 2.876645 CGACGACTTCTCGGCTGC 60.877 66.667 0.00 0.00 46.79 5.25
3028 3546 2.320805 TTAACACGACGACTTCTCGG 57.679 50.000 0.00 0.00 44.80 4.63
3048 3566 3.431207 GGGTGCGCTAGTCCTATAAAACA 60.431 47.826 9.73 0.00 0.00 2.83
3050 3568 3.036091 AGGGTGCGCTAGTCCTATAAAA 58.964 45.455 9.73 0.00 0.00 1.52
3051 3569 2.674420 AGGGTGCGCTAGTCCTATAAA 58.326 47.619 9.73 0.00 0.00 1.40
3052 3570 2.376695 AGGGTGCGCTAGTCCTATAA 57.623 50.000 9.73 0.00 0.00 0.98
3057 3575 1.226888 CGTTAGGGTGCGCTAGTCC 60.227 63.158 9.73 5.95 0.00 3.85
3058 3576 0.525029 GTCGTTAGGGTGCGCTAGTC 60.525 60.000 9.73 0.00 0.00 2.59
3061 3579 0.388907 GTTGTCGTTAGGGTGCGCTA 60.389 55.000 9.73 0.00 0.00 4.26
3075 3593 0.517316 GTGGTCATTCGGCAGTTGTC 59.483 55.000 0.00 0.00 0.00 3.18
3081 3599 1.675483 GCAATATGTGGTCATTCGGCA 59.325 47.619 0.00 0.00 35.70 5.69
3093 3611 8.615878 TTTCTTTGTACAGTGTAGCAATATGT 57.384 30.769 2.39 0.00 0.00 2.29
3095 3613 9.502091 TCTTTTCTTTGTACAGTGTAGCAATAT 57.498 29.630 2.39 0.00 0.00 1.28
3106 3624 5.437289 TGTGCCATCTTTTCTTTGTACAG 57.563 39.130 0.00 0.00 0.00 2.74
3153 3671 5.884792 TGCAACCCATGTTCTTTTTCATTTT 59.115 32.000 0.00 0.00 30.42 1.82
3157 3675 3.450457 AGTGCAACCCATGTTCTTTTTCA 59.550 39.130 0.00 0.00 37.80 2.69
3186 3704 3.059257 CGTTCCACATTTGTTGATCGTGA 60.059 43.478 6.94 0.00 32.03 4.35
3232 3750 1.523258 AGCTAGATTGCTGCGCCAG 60.523 57.895 4.18 3.40 42.33 4.85


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

AutoCloner maintained by Alex Coulton.