Multiple sequence alignment - TraesCS6D01G091600

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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 TraesCS6D01G091600 chr6D 100.000 6601 0 0 1 6601 57223757 57217157 0.000000e+00 12190.0
1 TraesCS6D01G091600 chr6A 95.662 3642 92 27 2991 6601 72434822 72431216 0.000000e+00 5790.0
2 TraesCS6D01G091600 chr6A 92.170 2848 133 31 192 3002 72437652 72434858 0.000000e+00 3941.0
3 TraesCS6D01G091600 chr6A 93.711 159 9 1 1 158 72437811 72437653 3.080000e-58 237.0
4 TraesCS6D01G091600 chr6B 93.316 3456 148 35 2991 6416 129274082 129270680 0.000000e+00 5025.0
5 TraesCS6D01G091600 chr6B 92.635 3028 143 38 10 3002 129277100 129274118 0.000000e+00 4283.0
6 TraesCS6D01G091600 chr6B 85.735 694 64 15 1963 2631 618113036 618113719 0.000000e+00 701.0
7 TraesCS6D01G091600 chr6B 97.902 143 3 0 6415 6557 129270641 129270499 1.420000e-61 248.0
8 TraesCS6D01G091600 chr6B 82.946 258 22 18 2742 2995 618113719 618113958 5.190000e-51 213.0
9 TraesCS6D01G091600 chr6B 89.655 116 12 0 1795 1910 618112901 618113016 1.480000e-31 148.0
10 TraesCS6D01G091600 chr5A 79.971 2062 303 69 3089 5090 591092299 591090288 0.000000e+00 1419.0
11 TraesCS6D01G091600 chr5A 80.035 571 89 17 1069 1632 591094689 591094137 3.710000e-107 399.0
12 TraesCS6D01G091600 chr5D 82.298 1384 188 36 3741 5090 470386859 470385499 0.000000e+00 1146.0
13 TraesCS6D01G091600 chr5D 81.162 568 90 13 1069 1632 470389789 470389235 2.180000e-119 440.0
14 TraesCS6D01G091600 chr5D 76.389 864 145 38 1757 2589 470389172 470388337 1.710000e-110 411.0
15 TraesCS6D01G091600 chr5D 81.137 387 68 5 3075 3460 470387568 470387186 8.320000e-79 305.0
16 TraesCS6D01G091600 chr5B 81.825 1381 198 33 3741 5090 577695264 577693906 0.000000e+00 1110.0
17 TraesCS6D01G091600 chr5B 76.532 865 142 40 1757 2589 577697443 577696608 3.680000e-112 416.0
18 TraesCS6D01G091600 chr5B 79.512 615 97 17 1025 1632 577698098 577697506 1.710000e-110 411.0
19 TraesCS6D01G091600 chr5B 81.867 375 60 7 3089 3460 577695960 577695591 6.430000e-80 309.0
20 TraesCS6D01G091600 chr4B 86.364 682 51 15 1976 2631 251278206 251278871 0.000000e+00 706.0
21 TraesCS6D01G091600 chr4B 86.152 686 52 19 1976 2635 251664866 251665534 0.000000e+00 701.0
22 TraesCS6D01G091600 chr4B 84.047 257 25 14 2742 2995 251278871 251279114 3.980000e-57 233.0
23 TraesCS6D01G091600 chr7B 93.878 49 2 1 3979 4026 282303385 282303337 9.180000e-09 73.1


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 TraesCS6D01G091600 chr6D 57217157 57223757 6600 True 12190.000000 12190 100.000000 1 6601 1 chr6D.!!$R1 6600
1 TraesCS6D01G091600 chr6A 72431216 72437811 6595 True 3322.666667 5790 93.847667 1 6601 3 chr6A.!!$R1 6600
2 TraesCS6D01G091600 chr6B 129270499 129277100 6601 True 3185.333333 5025 94.617667 10 6557 3 chr6B.!!$R1 6547
3 TraesCS6D01G091600 chr6B 618112901 618113958 1057 False 354.000000 701 86.112000 1795 2995 3 chr6B.!!$F1 1200
4 TraesCS6D01G091600 chr5A 591090288 591094689 4401 True 909.000000 1419 80.003000 1069 5090 2 chr5A.!!$R1 4021
5 TraesCS6D01G091600 chr5D 470385499 470389789 4290 True 575.500000 1146 80.246500 1069 5090 4 chr5D.!!$R1 4021
6 TraesCS6D01G091600 chr5B 577693906 577698098 4192 True 561.500000 1110 79.934000 1025 5090 4 chr5B.!!$R1 4065
7 TraesCS6D01G091600 chr4B 251664866 251665534 668 False 701.000000 701 86.152000 1976 2635 1 chr4B.!!$F1 659
8 TraesCS6D01G091600 chr4B 251278206 251279114 908 False 469.500000 706 85.205500 1976 2995 2 chr4B.!!$F2 1019

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
82 88 1.253593 ATCGCTGCTCTGGTGAGTGA 61.254 55.000 0.0 0.0 42.13 3.41 F
598 651 1.586422 TCTGTGCTTGAACTGCTGTC 58.414 50.000 0.0 0.0 0.00 3.51 F
1064 1124 1.922135 ATTCAACGCACACCGATGGC 61.922 55.000 0.0 0.0 39.81 4.40 F
2070 2142 2.095059 GGCATTTGTGAAGGTACTGCTG 60.095 50.000 0.0 0.0 40.86 4.41 F
2833 2953 3.858247 TCATGAACTGCATCAGACAGAG 58.142 45.455 0.0 0.0 38.55 3.35 F
4314 5054 2.238646 TCCACTGGGTATAAGCAACAGG 59.761 50.000 0.0 0.0 33.63 4.00 F
5139 5887 0.386838 GGTGATATTGCTGCCTTGCC 59.613 55.000 0.0 0.0 0.00 4.52 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1350 1415 1.272425 TGGCCCAAACACCTTATCTGG 60.272 52.381 0.00 0.00 0.00 3.86 R
2322 2415 1.215647 CGCTTCACGGAGCCTACTT 59.784 57.895 0.00 0.00 39.51 2.24 R
2735 2854 1.688735 TGCTGAGAGGCGCTACATATT 59.311 47.619 7.64 0.00 34.52 1.28 R
3107 3755 0.468648 GGTAGGGTATGTGGCCACTC 59.531 60.000 34.75 23.52 0.00 3.51 R
4581 5327 0.247736 CCACCCTCTCCTTCAGTTCG 59.752 60.000 0.00 0.00 0.00 3.95 R
5276 6025 0.033699 GCCTTGAGCCCATCCTTCTT 60.034 55.000 0.00 0.00 34.35 2.52 R
6247 7027 0.255604 TCGCCATGTTCATCCACCAT 59.744 50.000 0.00 0.00 0.00 3.55 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
82 88 1.253593 ATCGCTGCTCTGGTGAGTGA 61.254 55.000 0.00 0.00 42.13 3.41
88 94 3.672808 CTGCTCTGGTGAGTGATTTCTT 58.327 45.455 0.00 0.00 42.13 2.52
289 305 4.512961 TGCGCTCGACCGATGCAT 62.513 61.111 9.73 0.00 32.86 3.96
377 394 5.511571 GGAAGTGCTTTTCTGTTTCTGTAC 58.488 41.667 0.00 0.00 0.00 2.90
388 412 2.031560 TGTTTCTGTACAAGCGTTGCTG 59.968 45.455 0.00 0.00 39.62 4.41
553 606 4.051922 GGATTCGCTTCATGTAATCGTCT 58.948 43.478 0.00 0.00 30.67 4.18
559 612 4.439449 CGCTTCATGTAATCGTCTCTCTTC 59.561 45.833 0.00 0.00 0.00 2.87
598 651 1.586422 TCTGTGCTTGAACTGCTGTC 58.414 50.000 0.00 0.00 0.00 3.51
717 772 5.718130 TCCGGAAGTAAAGTATTTCTCAGGA 59.282 40.000 0.00 0.00 40.09 3.86
753 808 6.928492 GTCTTCAATTTCCTTGGCAATTTGTA 59.072 34.615 0.00 0.00 35.43 2.41
756 811 8.511604 TTCAATTTCCTTGGCAATTTGTAAAA 57.488 26.923 0.00 0.00 35.43 1.52
757 812 8.688747 TCAATTTCCTTGGCAATTTGTAAAAT 57.311 26.923 0.00 0.00 35.43 1.82
805 864 8.874744 ATGAGCTGCCACTTCATTTTATATAT 57.125 30.769 0.00 0.00 0.00 0.86
806 865 9.964354 ATGAGCTGCCACTTCATTTTATATATA 57.036 29.630 0.00 0.00 0.00 0.86
875 935 4.554036 GCAGATCCTGGCGTCCCC 62.554 72.222 0.00 0.00 31.21 4.81
878 938 2.764128 GATCCTGGCGTCCCCTCA 60.764 66.667 0.00 0.00 0.00 3.86
881 941 3.402681 CCTGGCGTCCCCTCACAT 61.403 66.667 0.00 0.00 0.00 3.21
889 949 2.354821 GCGTCCCCTCACATAACAATTC 59.645 50.000 0.00 0.00 0.00 2.17
932 992 4.088634 TGCTATTTTGCACATCCTTCCTT 58.911 39.130 0.00 0.00 38.12 3.36
968 1028 3.813150 GGCCTGAAGGACCTCTGT 58.187 61.111 0.00 0.00 37.19 3.41
978 1038 4.597507 TGAAGGACCTCTGTAGTTTTCCAT 59.402 41.667 0.00 0.00 0.00 3.41
980 1040 6.443849 TGAAGGACCTCTGTAGTTTTCCATAT 59.556 38.462 0.00 0.00 0.00 1.78
985 1045 7.362802 ACCTCTGTAGTTTTCCATATACCTC 57.637 40.000 0.00 0.00 0.00 3.85
991 1051 5.532664 AGTTTTCCATATACCTCGAGGAC 57.467 43.478 37.69 20.03 38.94 3.85
994 1054 5.786264 TTTCCATATACCTCGAGGACTTC 57.214 43.478 37.69 0.00 38.94 3.01
1006 1066 4.058124 TCGAGGACTTCACAAAATGAGTG 58.942 43.478 0.00 0.00 38.99 3.51
1011 1071 4.022935 GGACTTCACAAAATGAGTGCATCA 60.023 41.667 0.00 0.00 43.70 3.07
1017 1077 3.058016 ACAAAATGAGTGCATCAAGACCG 60.058 43.478 0.00 0.00 42.53 4.79
1064 1124 1.922135 ATTCAACGCACACCGATGGC 61.922 55.000 0.00 0.00 39.81 4.40
1123 1183 2.999355 GAGAAGATCCTTGTCACTGTGC 59.001 50.000 2.12 0.00 0.00 4.57
1261 1321 5.313712 CCACCTCTTACACTTTTGGTACAT 58.686 41.667 0.00 0.00 39.30 2.29
1320 1384 9.739276 AATTCTGTATCATAAAAGTGACCTTCA 57.261 29.630 0.00 0.00 0.00 3.02
1535 1600 2.224018 TGGTTTTGCAGCCACAATCTTC 60.224 45.455 3.08 0.00 0.00 2.87
1643 1708 5.587289 GAAAATGTGAGTAGTGGCAAAACA 58.413 37.500 0.00 0.00 0.00 2.83
1645 1710 5.376854 AATGTGAGTAGTGGCAAAACATC 57.623 39.130 0.00 0.00 0.00 3.06
2070 2142 2.095059 GGCATTTGTGAAGGTACTGCTG 60.095 50.000 0.00 0.00 40.86 4.41
2085 2169 3.935315 ACTGCTGCATATGTATAGCCTG 58.065 45.455 19.16 15.51 35.36 4.85
2833 2953 3.858247 TCATGAACTGCATCAGACAGAG 58.142 45.455 0.00 0.00 38.55 3.35
2888 3462 7.497909 TGAAACACTAAGGTTTTGACCTTCTAG 59.502 37.037 13.68 9.67 46.41 2.43
2995 3569 7.137426 GGCTACATCTTCTTTTAGAATGCATG 58.863 38.462 0.00 0.00 33.13 4.06
2997 3571 7.854916 GCTACATCTTCTTTTAGAATGCATGTC 59.145 37.037 0.00 0.01 33.13 3.06
3002 3576 8.339344 TCTTCTTTTAGAATGCATGTCATTGA 57.661 30.769 16.66 6.99 44.95 2.57
3008 3582 5.874895 AGAATGCATGTCATTGATATCGG 57.125 39.130 16.66 0.00 44.95 4.18
3013 3636 5.852827 TGCATGTCATTGATATCGGTTCTA 58.147 37.500 0.00 0.00 0.00 2.10
3048 3671 7.606349 AGCAAAAATCTAATGAGAAAAGACCC 58.394 34.615 0.00 0.00 34.61 4.46
3049 3672 7.233348 AGCAAAAATCTAATGAGAAAAGACCCA 59.767 33.333 0.00 0.00 34.61 4.51
3050 3673 8.037166 GCAAAAATCTAATGAGAAAAGACCCAT 58.963 33.333 0.00 0.00 34.61 4.00
3052 3675 7.888250 AAATCTAATGAGAAAAGACCCATCC 57.112 36.000 0.00 0.00 34.61 3.51
3054 3677 6.642733 TCTAATGAGAAAAGACCCATCCTT 57.357 37.500 0.00 0.00 0.00 3.36
3055 3678 7.749377 TCTAATGAGAAAAGACCCATCCTTA 57.251 36.000 0.00 0.00 0.00 2.69
3057 3680 8.781951 TCTAATGAGAAAAGACCCATCCTTATT 58.218 33.333 0.00 0.00 0.00 1.40
3107 3755 2.281517 CATTGCAGCTCAGAGAAGAGG 58.718 52.381 0.00 0.00 36.15 3.69
3152 3800 5.122396 GGATTCAAAGCTCACACGTATTCTT 59.878 40.000 0.00 0.00 0.00 2.52
3176 3824 2.676076 CTTTCTTTGGGTGGAAATGCG 58.324 47.619 0.00 0.00 32.15 4.73
3210 3858 4.746309 GCACCATGAGCCCAGCCA 62.746 66.667 0.00 0.00 0.00 4.75
3359 4009 4.009675 TGCTGAAGTCAACTCAACACTTT 58.990 39.130 0.00 0.00 30.32 2.66
3393 4043 7.182817 ACAGGTTGTATCTGATAAGCAACTA 57.817 36.000 20.98 1.14 39.28 2.24
3421 4071 3.616379 GCATCTACAGACAGAAGTTGCTC 59.384 47.826 0.00 0.00 34.57 4.26
3468 4118 2.726351 CCGTGCCTCCTCTTCCTCC 61.726 68.421 0.00 0.00 0.00 4.30
3569 4248 9.638239 TTGAATAAGAATCATTTTGTAACTGGC 57.362 29.630 0.00 0.00 0.00 4.85
3654 4344 7.293745 CACAGTTAGCACTTGAAGAAATACAG 58.706 38.462 0.00 0.00 0.00 2.74
3713 4403 6.253946 TCTTCCTTTCTTCTTCCAGAACTT 57.746 37.500 0.00 0.00 32.28 2.66
3715 4405 6.543831 TCTTCCTTTCTTCTTCCAGAACTTTG 59.456 38.462 0.00 0.00 32.28 2.77
3716 4406 6.001449 TCCTTTCTTCTTCCAGAACTTTGA 57.999 37.500 0.00 0.00 32.28 2.69
3717 4407 6.423182 TCCTTTCTTCTTCCAGAACTTTGAA 58.577 36.000 0.00 0.00 32.28 2.69
3718 4408 6.318900 TCCTTTCTTCTTCCAGAACTTTGAAC 59.681 38.462 0.00 0.00 32.28 3.18
3719 4409 6.319911 CCTTTCTTCTTCCAGAACTTTGAACT 59.680 38.462 0.00 0.00 32.28 3.01
4314 5054 2.238646 TCCACTGGGTATAAGCAACAGG 59.761 50.000 0.00 0.00 33.63 4.00
4469 5209 4.478317 TGGAGACACTGGGGATTTATCATT 59.522 41.667 0.00 0.00 33.40 2.57
4581 5327 7.873505 GTGAGAAGTATTAGGGATTATGTCACC 59.126 40.741 0.00 0.00 0.00 4.02
4689 5435 8.355913 TCTTGCACACACATTCAATTTGTTATA 58.644 29.630 0.00 0.00 0.00 0.98
4690 5436 9.142515 CTTGCACACACATTCAATTTGTTATAT 57.857 29.630 0.00 0.00 0.00 0.86
5104 5850 0.889994 TGATGACAAGCCAACATGCC 59.110 50.000 0.00 0.00 0.00 4.40
5108 5854 1.228245 ACAAGCCAACATGCCGTCT 60.228 52.632 0.00 0.00 0.00 4.18
5132 5880 4.460382 AGTGTCCTTTTGGTGATATTGCTG 59.540 41.667 0.00 0.00 41.38 4.41
5135 5883 2.762327 CCTTTTGGTGATATTGCTGCCT 59.238 45.455 0.00 0.00 34.07 4.75
5139 5887 0.386838 GGTGATATTGCTGCCTTGCC 59.613 55.000 0.00 0.00 0.00 4.52
5143 5891 0.462789 ATATTGCTGCCTTGCCTTGC 59.537 50.000 0.00 0.00 0.00 4.01
5173 5921 5.048504 GCATCATTCAATTCGTCCCATGTAT 60.049 40.000 0.00 0.00 0.00 2.29
5351 6100 3.003173 CAAGTCCCCCTCGAGGCA 61.003 66.667 26.87 8.96 0.00 4.75
5364 6113 1.968540 GAGGCAAAGCAGCGGAAGT 60.969 57.895 0.00 0.00 34.64 3.01
5432 6181 1.888436 TTGAGGAGAGCGCCGACATT 61.888 55.000 2.29 0.00 0.00 2.71
5729 6478 1.746615 TCATCAAGGAAGGCTGCGC 60.747 57.895 0.00 0.00 0.00 6.09
5740 6489 2.385091 GGCTGCGCAATTTGCTTGG 61.385 57.895 13.05 9.27 42.25 3.61
5861 6611 7.482743 CAGTGATTGTTGGATGAAAATAACTCG 59.517 37.037 0.00 0.00 0.00 4.18
5872 6622 3.782889 AAATAACTCGGAGGCAATTGC 57.217 42.857 22.47 22.47 41.14 3.56
5889 6642 4.535526 ATTGCCGGTGCTTAAGATTTTT 57.464 36.364 6.67 0.00 38.71 1.94
5914 6667 3.576078 TGTTCAGTCAGGTGGTTGATT 57.424 42.857 0.00 0.00 0.00 2.57
5915 6668 3.897239 TGTTCAGTCAGGTGGTTGATTT 58.103 40.909 0.00 0.00 0.00 2.17
5916 6669 3.882888 TGTTCAGTCAGGTGGTTGATTTC 59.117 43.478 0.00 0.00 0.00 2.17
5959 6713 7.596494 TCAGGTTCAGATGCAAAATTTTAGAG 58.404 34.615 2.44 0.00 0.00 2.43
5970 6724 7.195646 TGCAAAATTTTAGAGTGTTCACAGAG 58.804 34.615 2.44 0.00 0.00 3.35
5979 6733 6.771188 AGAGTGTTCACAGAGTTTTTATCG 57.229 37.500 5.74 0.00 0.00 2.92
6024 6778 4.752146 TGTCATCAAATGCAACACACAAA 58.248 34.783 0.00 0.00 0.00 2.83
6046 6800 6.530019 AATTAATACTTTTGGCAGAGTGGG 57.470 37.500 13.78 0.00 0.00 4.61
6245 7025 4.635699 ATCATCAGATGCATGGAAGCTA 57.364 40.909 2.46 0.00 31.91 3.32
6246 7026 4.004196 TCATCAGATGCATGGAAGCTAG 57.996 45.455 2.46 0.00 34.99 3.42
6247 7027 3.644738 TCATCAGATGCATGGAAGCTAGA 59.355 43.478 2.46 0.00 34.99 2.43
6248 7028 4.286291 TCATCAGATGCATGGAAGCTAGAT 59.714 41.667 2.46 0.00 34.99 1.98
6249 7029 4.004196 TCAGATGCATGGAAGCTAGATG 57.996 45.455 2.46 0.00 34.99 2.90
6250 7030 3.075148 CAGATGCATGGAAGCTAGATGG 58.925 50.000 2.46 0.00 34.99 3.51
6251 7031 2.709934 AGATGCATGGAAGCTAGATGGT 59.290 45.455 2.46 0.00 34.99 3.55
6275 7055 1.703438 GAACATGGCGAGCAGAGCAG 61.703 60.000 0.00 0.00 36.08 4.24
6294 7074 3.979495 GCAGAGCATAGCATATTGTTTGC 59.021 43.478 0.00 0.00 40.45 3.68
6532 7364 7.516209 AGTTCCTGATAAATAATACCAGGGCTA 59.484 37.037 0.00 0.00 43.34 3.93
6558 7390 9.349713 AGAGTACTATATCTAGCCAGCATATTC 57.650 37.037 0.00 0.00 0.00 1.75
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
82 88 1.078426 CCGCCACGAGGGAAGAAAT 60.078 57.895 0.00 0.00 40.01 2.17
287 303 1.315257 AAAGCCGGCAGCCACTTATG 61.315 55.000 31.54 0.00 45.47 1.90
289 305 1.674322 GAAAGCCGGCAGCCACTTA 60.674 57.895 31.54 0.00 45.47 2.24
324 341 0.178967 TTCCAAATCTGCAGCACCCA 60.179 50.000 9.47 0.00 0.00 4.51
328 345 5.472148 CAACTAATTTCCAAATCTGCAGCA 58.528 37.500 9.47 0.00 0.00 4.41
377 394 4.419522 ACCTAATTAACAGCAACGCTTG 57.580 40.909 0.00 0.00 36.40 4.01
388 412 5.105635 CGGGGGAAAAGGAAACCTAATTAAC 60.106 44.000 0.00 0.00 31.13 2.01
553 606 4.003648 GGCTTTTCTCCATTTCGAAGAGA 58.996 43.478 10.60 10.60 38.43 3.10
559 612 1.448985 TCCGGCTTTTCTCCATTTCG 58.551 50.000 0.00 0.00 0.00 3.46
598 651 2.093447 AGGGAACGCCAGATTCAACTAG 60.093 50.000 0.00 0.00 35.15 2.57
644 698 5.788450 AGCTAGCAGCAGTTCGATATATTT 58.212 37.500 18.83 0.00 45.56 1.40
645 699 5.398603 AGCTAGCAGCAGTTCGATATATT 57.601 39.130 18.83 0.00 45.56 1.28
647 701 5.553290 CTAGCTAGCAGCAGTTCGATATA 57.447 43.478 18.83 0.00 45.56 0.86
717 772 3.328535 AATTGAAGACCTTGTTGGGGT 57.671 42.857 0.00 0.00 41.11 4.95
875 935 7.961827 GCTTTCTCAAGAGAATTGTTATGTGAG 59.038 37.037 12.84 5.23 45.78 3.51
878 938 7.094463 CCAGCTTTCTCAAGAGAATTGTTATGT 60.094 37.037 12.84 0.00 45.78 2.29
881 941 6.533730 TCCAGCTTTCTCAAGAGAATTGTTA 58.466 36.000 12.84 0.00 45.78 2.41
889 949 5.589452 AGCAATTATCCAGCTTTCTCAAGAG 59.411 40.000 0.00 0.00 34.37 2.85
954 1014 4.040461 TGGAAAACTACAGAGGTCCTTCAG 59.960 45.833 0.00 0.00 0.00 3.02
968 1028 6.371278 AGTCCTCGAGGTATATGGAAAACTA 58.629 40.000 30.17 3.35 36.34 2.24
978 1038 5.988310 TTTTGTGAAGTCCTCGAGGTATA 57.012 39.130 30.17 9.49 36.34 1.47
980 1040 4.282449 TCATTTTGTGAAGTCCTCGAGGTA 59.718 41.667 30.17 14.85 32.78 3.08
985 1045 3.364366 GCACTCATTTTGTGAAGTCCTCG 60.364 47.826 0.00 0.00 37.60 4.63
991 1051 5.628193 GTCTTGATGCACTCATTTTGTGAAG 59.372 40.000 0.00 0.00 37.60 3.02
994 1054 4.232221 GGTCTTGATGCACTCATTTTGTG 58.768 43.478 0.00 0.00 38.36 3.33
1006 1066 2.480555 CGTTGGCGGTCTTGATGC 59.519 61.111 0.00 0.00 0.00 3.91
1011 1071 2.978010 CTTGGCGTTGGCGGTCTT 60.978 61.111 0.00 0.00 41.24 3.01
1066 1126 4.442454 GCCACCAGGGGTAAGGCC 62.442 72.222 0.00 0.00 38.40 5.19
1067 1127 3.645268 CTGCCACCAGGGGTAAGGC 62.645 68.421 9.23 9.23 42.79 4.35
1123 1183 3.499737 GCTCAATGGTCGCACCCG 61.500 66.667 3.33 0.00 37.50 5.28
1186 1246 7.468141 TGTATAAGATTGTCTGACTGTCAGT 57.532 36.000 30.74 16.27 44.58 3.41
1261 1321 4.545208 TCAGTAATGGATCGTTGGACAA 57.455 40.909 0.00 0.00 0.00 3.18
1350 1415 1.272425 TGGCCCAAACACCTTATCTGG 60.272 52.381 0.00 0.00 0.00 3.86
1379 1444 4.700213 CCATCTTCATAAACCAAGTCCGTT 59.300 41.667 0.00 0.00 0.00 4.44
1535 1600 3.859961 CACTACTTGTCTGACCATAAGCG 59.140 47.826 5.17 1.10 0.00 4.68
1671 1736 1.341209 TCGACAGATGTGCACAACTCT 59.659 47.619 25.07 20.21 0.00 3.24
1672 1737 1.783284 TCGACAGATGTGCACAACTC 58.217 50.000 25.07 18.29 0.00 3.01
1755 1820 5.723492 AGCAATCAACAAAAGCAAGAAAC 57.277 34.783 0.00 0.00 0.00 2.78
2070 2142 3.875727 CAGATGGCAGGCTATACATATGC 59.124 47.826 1.58 0.00 36.16 3.14
2085 2169 5.066246 CCATCTTCTTCTTTTCTCAGATGGC 59.934 44.000 11.98 0.00 46.67 4.40
2322 2415 1.215647 CGCTTCACGGAGCCTACTT 59.784 57.895 0.00 0.00 39.51 2.24
2725 2843 5.611374 AGGCGCTACATATTCAACAGTAAT 58.389 37.500 7.64 0.00 0.00 1.89
2735 2854 1.688735 TGCTGAGAGGCGCTACATATT 59.311 47.619 7.64 0.00 34.52 1.28
2833 2953 7.489574 AAAGAGTAGCTTAGCAAGAATATGC 57.510 36.000 7.07 0.00 40.38 3.14
2915 3489 7.194607 AGCACGAATATGTTCCATCTTAATG 57.805 36.000 0.00 0.00 0.00 1.90
2924 3498 4.119862 TCTGCTTAGCACGAATATGTTCC 58.880 43.478 1.39 0.00 33.79 3.62
2935 3509 9.956720 AACATGAAAAATATATCTGCTTAGCAC 57.043 29.630 1.39 0.00 33.79 4.40
2968 3542 6.830324 TGCATTCTAAAAGAAGATGTAGCCAT 59.170 34.615 0.00 0.00 37.69 4.40
3005 3579 8.836268 TTTTTGCTAGTTAAATCTAGAACCGA 57.164 30.769 0.00 0.00 39.57 4.69
3006 3580 9.704098 GATTTTTGCTAGTTAAATCTAGAACCG 57.296 33.333 0.00 0.00 39.57 4.44
3021 3644 9.780413 GGTCTTTTCTCATTAGATTTTTGCTAG 57.220 33.333 0.00 0.00 0.00 3.42
3035 3658 6.973642 TCAATAAGGATGGGTCTTTTCTCAT 58.026 36.000 0.00 0.00 0.00 2.90
3042 3665 4.540099 TGGAGTTCAATAAGGATGGGTCTT 59.460 41.667 0.00 0.00 0.00 3.01
3045 3668 4.946160 TTGGAGTTCAATAAGGATGGGT 57.054 40.909 0.00 0.00 0.00 4.51
3078 3701 4.005650 TCTGAGCTGCAATGGAAGTTTAG 58.994 43.478 1.02 0.00 0.00 1.85
3086 3734 2.281517 CTCTTCTCTGAGCTGCAATGG 58.718 52.381 1.02 0.00 0.00 3.16
3107 3755 0.468648 GGTAGGGTATGTGGCCACTC 59.531 60.000 34.75 23.52 0.00 3.51
3152 3800 2.746279 TTCCACCCAAAGAAAGCTGA 57.254 45.000 0.00 0.00 0.00 4.26
3176 3824 1.669779 GTGCAGATGATGGCTGTTCTC 59.330 52.381 0.00 0.00 35.81 2.87
3210 3858 6.653020 TCCTAGATTGTTCTGCATGTGTTAT 58.347 36.000 0.00 0.00 33.17 1.89
3353 4003 6.303839 ACAACCTGTATGGACAATAAAGTGT 58.696 36.000 0.00 0.00 39.71 3.55
3359 4009 7.669089 TCAGATACAACCTGTATGGACAATA 57.331 36.000 4.08 0.00 43.08 1.90
3393 4043 6.597832 ACTTCTGTCTGTAGATGCTTAACT 57.402 37.500 0.00 0.00 0.00 2.24
3421 4071 1.470632 CCTCAGTTCTGCTTCTAGCCG 60.471 57.143 0.00 0.00 41.51 5.52
3569 4248 3.788333 CCATCTGCATGGTTGTTTAGG 57.212 47.619 0.00 0.00 44.46 2.69
3654 4344 3.007635 CTGGTTATCACCCGTCCTTTTC 58.992 50.000 0.00 0.00 43.49 2.29
3717 4407 5.183904 AGTTGCAAGTCAGAACTTCAAAAGT 59.816 36.000 0.00 0.00 43.99 2.66
3718 4408 5.514204 CAGTTGCAAGTCAGAACTTCAAAAG 59.486 40.000 3.08 0.00 43.99 2.27
3719 4409 5.048083 ACAGTTGCAAGTCAGAACTTCAAAA 60.048 36.000 3.08 0.00 43.99 2.44
4314 5054 3.549794 AGGTGCTCTTATCAGATTTGGC 58.450 45.455 0.00 0.00 0.00 4.52
4581 5327 0.247736 CCACCCTCTCCTTCAGTTCG 59.752 60.000 0.00 0.00 0.00 3.95
4690 5436 9.534565 CAGGAGAATAAAGATAATTTCTCGACA 57.465 33.333 0.00 0.00 43.14 4.35
5104 5850 3.380479 TCACCAAAAGGACACTAGACG 57.620 47.619 0.00 0.00 0.00 4.18
5108 5854 5.647658 CAGCAATATCACCAAAAGGACACTA 59.352 40.000 0.00 0.00 0.00 2.74
5132 5880 1.732308 GCAGATAGCAAGGCAAGGC 59.268 57.895 0.00 0.00 44.79 4.35
5143 5891 5.106791 GGGACGAATTGAATGATGCAGATAG 60.107 44.000 0.00 0.00 0.00 2.08
5160 5908 5.941058 ACAAATAACACATACATGGGACGAA 59.059 36.000 0.00 0.00 34.60 3.85
5276 6025 0.033699 GCCTTGAGCCCATCCTTCTT 60.034 55.000 0.00 0.00 34.35 2.52
5321 6070 2.566724 GGGGACTTGCCATTTGATGAAA 59.433 45.455 0.00 0.00 38.95 2.69
5351 6100 1.656441 CTGCAACTTCCGCTGCTTT 59.344 52.632 0.00 0.00 39.38 3.51
5432 6181 4.641645 CCAACCAGCCGAGCCACA 62.642 66.667 0.00 0.00 0.00 4.17
5438 6187 2.032528 CAGAAGCCAACCAGCCGA 59.967 61.111 0.00 0.00 0.00 5.54
5729 6478 7.392673 AGCTATCTACATATCCCAAGCAAATTG 59.607 37.037 0.00 0.00 38.74 2.32
5889 6642 4.080807 TCAACCACCTGACTGAACAAGTAA 60.081 41.667 0.00 0.00 40.07 2.24
5890 6643 3.452990 TCAACCACCTGACTGAACAAGTA 59.547 43.478 0.00 0.00 40.07 2.24
5900 6653 4.938226 CCTAGAAGAAATCAACCACCTGAC 59.062 45.833 0.00 0.00 0.00 3.51
5914 6667 5.217978 TGAAACGTTAAGCCCTAGAAGAA 57.782 39.130 0.00 0.00 0.00 2.52
5915 6668 4.322499 CCTGAAACGTTAAGCCCTAGAAGA 60.322 45.833 0.00 0.00 0.00 2.87
5916 6669 3.933332 CCTGAAACGTTAAGCCCTAGAAG 59.067 47.826 0.00 0.00 0.00 2.85
5959 6713 5.907391 CCAACGATAAAAACTCTGTGAACAC 59.093 40.000 0.00 0.00 0.00 3.32
5970 6724 5.516090 TGCAGAAGTTCCAACGATAAAAAC 58.484 37.500 0.00 0.00 0.00 2.43
5979 6733 3.375782 AGCAAATGCAGAAGTTCCAAC 57.624 42.857 8.28 0.00 45.16 3.77
6024 6778 4.956075 CCCCACTCTGCCAAAAGTATTAAT 59.044 41.667 0.00 0.00 0.00 1.40
6046 6800 4.943705 TCATTGTCACTCTGATTTTAGGCC 59.056 41.667 0.00 0.00 0.00 5.19
6113 6880 4.219070 TCAGAGTCAGGAATGCAAATTTGG 59.781 41.667 19.47 1.46 0.00 3.28
6245 7025 1.748244 CGCCATGTTCATCCACCATCT 60.748 52.381 0.00 0.00 0.00 2.90
6246 7026 0.664761 CGCCATGTTCATCCACCATC 59.335 55.000 0.00 0.00 0.00 3.51
6247 7027 0.255604 TCGCCATGTTCATCCACCAT 59.744 50.000 0.00 0.00 0.00 3.55
6248 7028 0.392863 CTCGCCATGTTCATCCACCA 60.393 55.000 0.00 0.00 0.00 4.17
6249 7029 1.718757 GCTCGCCATGTTCATCCACC 61.719 60.000 0.00 0.00 0.00 4.61
6250 7030 1.026182 TGCTCGCCATGTTCATCCAC 61.026 55.000 0.00 0.00 0.00 4.02
6251 7031 0.745486 CTGCTCGCCATGTTCATCCA 60.745 55.000 0.00 0.00 0.00 3.41
6275 7055 3.558505 CCGCAAACAATATGCTATGCTC 58.441 45.455 0.00 0.00 41.64 4.26
6294 7074 1.577328 CCTAGTTGTGGTTGCAGCCG 61.577 60.000 15.43 0.00 0.00 5.52
6532 7364 9.349713 GAATATGCTGGCTAGATATAGTACTCT 57.650 37.037 0.00 0.00 0.00 3.24
6558 7390 4.825422 AGGATATACAAGATGGTGATGCG 58.175 43.478 0.00 0.00 0.00 4.73


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

AutoCloner maintained by Alex Coulton.