Multiple sequence alignment - TraesCS6B01G401500

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 TraesCS6B01G401500 chr6B 100.000 2741 0 0 1 2741 678093813 678091073 0.000000e+00 5062.0
1 TraesCS6B01G401500 chr6B 88.211 1230 77 27 758 1951 678356665 678357862 0.000000e+00 1406.0
2 TraesCS6B01G401500 chr6B 84.304 1236 111 42 768 1951 678174397 678175601 0.000000e+00 1131.0
3 TraesCS6B01G401500 chr6B 84.679 1201 88 44 768 1926 676866138 676864992 0.000000e+00 1110.0
4 TraesCS6B01G401500 chr6B 84.461 1049 84 41 947 1951 677045745 677044732 0.000000e+00 961.0
5 TraesCS6B01G401500 chr6B 88.727 754 57 16 936 1663 677088460 677087709 0.000000e+00 896.0
6 TraesCS6B01G401500 chr6B 84.072 948 72 38 1046 1951 678542623 678543533 0.000000e+00 841.0
7 TraesCS6B01G401500 chr6B 88.397 655 49 15 1997 2638 678175604 678176244 0.000000e+00 763.0
8 TraesCS6B01G401500 chr6B 90.210 572 20 11 146 685 677337979 677337412 0.000000e+00 713.0
9 TraesCS6B01G401500 chr6B 89.662 503 35 12 742 1232 677337176 677336679 2.320000e-175 625.0
10 TraesCS6B01G401500 chr6B 90.024 411 26 6 2008 2405 676864987 676864579 4.050000e-143 518.0
11 TraesCS6B01G401500 chr6B 89.731 409 22 7 2008 2400 677087503 677087099 3.150000e-139 505.0
12 TraesCS6B01G401500 chr6B 88.863 422 26 8 2008 2413 677777704 677777288 1.470000e-137 499.0
13 TraesCS6B01G401500 chr6B 88.998 409 25 7 2008 2400 677909985 677909581 3.170000e-134 488.0
14 TraesCS6B01G401500 chr6B 92.933 283 16 4 2460 2741 676859423 676859144 2.540000e-110 409.0
15 TraesCS6B01G401500 chr6B 92.580 283 17 4 2460 2741 677079706 677079427 1.180000e-108 403.0
16 TraesCS6B01G401500 chr6B 83.120 468 38 19 1497 1947 676730383 676729940 3.310000e-104 388.0
17 TraesCS6B01G401500 chr6B 91.519 283 16 5 2460 2741 677906750 677906475 1.540000e-102 383.0
18 TraesCS6B01G401500 chr6B 91.429 280 16 7 2463 2741 677774639 677774367 7.160000e-101 377.0
19 TraesCS6B01G401500 chr6B 84.404 218 23 6 501 710 678173889 678174103 1.290000e-48 204.0
20 TraesCS6B01G401500 chr6B 89.744 156 14 2 235 390 676869090 676868937 5.990000e-47 198.0
21 TraesCS6B01G401500 chr6B 90.226 133 12 1 1818 1949 677777855 677777723 3.630000e-39 172.0
22 TraesCS6B01G401500 chr6B 90.226 133 12 1 1818 1949 677910136 677910004 3.630000e-39 172.0
23 TraesCS6B01G401500 chr6B 89.922 129 12 1 1822 1949 677087650 677087522 6.070000e-37 165.0
24 TraesCS6B01G401500 chr6B 95.062 81 4 0 146 226 677585599 677585519 7.970000e-26 128.0
25 TraesCS6B01G401500 chr6B 86.179 123 8 5 2559 2676 678178137 678178255 1.030000e-24 124.0
26 TraesCS6B01G401500 chr6B 88.889 99 10 1 3 101 676870777 676870680 1.330000e-23 121.0
27 TraesCS6B01G401500 chr6B 78.000 200 25 9 227 424 676045676 676045858 1.040000e-19 108.0
28 TraesCS6B01G401500 chr6B 87.342 79 7 3 760 837 676730951 676730875 1.350000e-13 87.9
29 TraesCS6B01G401500 chr6B 88.000 75 6 2 226 299 678311542 678311614 4.860000e-13 86.1
30 TraesCS6B01G401500 chr6B 94.340 53 3 0 238 290 678173675 678173727 6.290000e-12 82.4
31 TraesCS6B01G401500 chr6B 85.294 68 9 1 321 388 676035427 676035493 4.900000e-08 69.4
32 TraesCS6B01G401500 chr6B 90.909 44 3 1 1947 1990 678091792 678091750 1.060000e-04 58.4
33 TraesCS6B01G401500 chr6A 80.247 2025 203 107 768 2676 594318906 594320849 0.000000e+00 1341.0
34 TraesCS6B01G401500 chr6A 86.766 1005 99 15 952 1951 594254347 594253372 0.000000e+00 1088.0
35 TraesCS6B01G401500 chr6A 85.812 1022 108 27 940 1950 593992517 593991522 0.000000e+00 1050.0
36 TraesCS6B01G401500 chr6A 87.194 859 67 25 988 1824 594365614 594366451 0.000000e+00 937.0
37 TraesCS6B01G401500 chr6A 86.085 539 49 16 1995 2512 593991516 593990983 8.570000e-155 556.0
38 TraesCS6B01G401500 chr6A 80.791 531 46 31 1459 1951 593929568 593929056 5.580000e-97 364.0
39 TraesCS6B01G401500 chr6A 76.770 551 66 32 1464 1987 569678741 569678226 4.530000e-63 252.0
40 TraesCS6B01G401500 chr6A 82.967 182 12 5 2572 2741 594245310 594245136 2.200000e-31 147.0
41 TraesCS6B01G401500 chr6A 89.655 87 4 1 145 226 594217884 594217798 3.730000e-19 106.0
42 TraesCS6B01G401500 chr6A 87.952 83 6 2 759 837 593930249 593930167 8.080000e-16 95.3
43 TraesCS6B01G401500 chr6A 91.045 67 5 1 226 291 594318109 594318175 3.760000e-14 89.8
44 TraesCS6B01G401500 chr6A 94.545 55 3 0 758 812 594364997 594365051 4.860000e-13 86.1
45 TraesCS6B01G401500 chr6D 88.539 890 63 22 936 1788 447279013 447278126 0.000000e+00 1042.0
46 TraesCS6B01G401500 chr6D 85.248 766 72 17 1999 2739 447277847 447277098 0.000000e+00 750.0
47 TraesCS6B01G401500 chr6D 90.717 474 36 7 2134 2606 447738800 447739266 2.320000e-175 625.0
48 TraesCS6B01G401500 chr6D 81.720 279 39 6 1677 1951 447278122 447277852 3.550000e-54 222.0
49 TraesCS6B01G401500 chr6D 95.122 82 4 0 147 228 447281681 447281600 2.220000e-26 130.0
50 TraesCS6B01G401500 chr6D 83.333 144 12 6 756 887 447279166 447279023 3.710000e-24 122.0
51 TraesCS6B01G401500 chr6D 84.404 109 7 4 341 449 447279821 447279723 6.250000e-17 99.0
52 TraesCS6B01G401500 chr6D 87.879 66 8 0 752 817 447214125 447214060 8.140000e-11 78.7
53 TraesCS6B01G401500 chr7A 80.447 358 35 23 1997 2330 19013055 19013401 9.810000e-60 241.0
54 TraesCS6B01G401500 chr7A 79.144 374 50 16 1464 1824 19012597 19012955 1.640000e-57 233.0
55 TraesCS6B01G401500 chr7A 75.510 147 21 12 1841 1987 19012988 19013119 1.060000e-04 58.4


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 TraesCS6B01G401500 chr6B 678091073 678093813 2740 True 2560.200000 5062 95.454500 1 2741 2 chr6B.!!$R11 2740
1 TraesCS6B01G401500 chr6B 678356665 678357862 1197 False 1406.000000 1406 88.211000 758 1951 1 chr6B.!!$F4 1193
2 TraesCS6B01G401500 chr6B 677044732 677045745 1013 True 961.000000 961 84.461000 947 1951 1 chr6B.!!$R2 1004
3 TraesCS6B01G401500 chr6B 678542623 678543533 910 False 841.000000 841 84.072000 1046 1951 1 chr6B.!!$F5 905
4 TraesCS6B01G401500 chr6B 677336679 677337979 1300 True 669.000000 713 89.936000 146 1232 2 chr6B.!!$R8 1086
5 TraesCS6B01G401500 chr6B 677087099 677088460 1361 True 522.000000 896 89.460000 936 2400 3 chr6B.!!$R7 1464
6 TraesCS6B01G401500 chr6B 676864579 676870777 6198 True 486.750000 1110 88.334000 3 2405 4 chr6B.!!$R6 2402
7 TraesCS6B01G401500 chr6B 678173675 678178255 4580 False 460.880000 1131 87.524800 238 2676 5 chr6B.!!$F6 2438
8 TraesCS6B01G401500 chr6B 677774367 677777855 3488 True 349.333333 499 90.172667 1818 2741 3 chr6B.!!$R9 923
9 TraesCS6B01G401500 chr6B 677906475 677910136 3661 True 347.666667 488 90.247667 1818 2741 3 chr6B.!!$R10 923
10 TraesCS6B01G401500 chr6B 676729940 676730951 1011 True 237.950000 388 85.231000 760 1947 2 chr6B.!!$R5 1187
11 TraesCS6B01G401500 chr6A 594253372 594254347 975 True 1088.000000 1088 86.766000 952 1951 1 chr6A.!!$R4 999
12 TraesCS6B01G401500 chr6A 593990983 593992517 1534 True 803.000000 1050 85.948500 940 2512 2 chr6A.!!$R6 1572
13 TraesCS6B01G401500 chr6A 594318109 594320849 2740 False 715.400000 1341 85.646000 226 2676 2 chr6A.!!$F1 2450
14 TraesCS6B01G401500 chr6A 594364997 594366451 1454 False 511.550000 937 90.869500 758 1824 2 chr6A.!!$F2 1066
15 TraesCS6B01G401500 chr6A 569678226 569678741 515 True 252.000000 252 76.770000 1464 1987 1 chr6A.!!$R1 523
16 TraesCS6B01G401500 chr6A 593929056 593930249 1193 True 229.650000 364 84.371500 759 1951 2 chr6A.!!$R5 1192
17 TraesCS6B01G401500 chr6D 447277098 447281681 4583 True 394.166667 1042 86.394333 147 2739 6 chr6D.!!$R2 2592

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
675 3847 0.178995 TGTGCCAGCTTGACCATCAA 60.179 50.0 0.0 0.0 34.79 2.57 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1895 8898 0.251386 AGCAGAGAGGACGAGGAACA 60.251 55.0 0.0 0.0 0.0 3.18 R

All possible primers

Listed here are all possible primers based on the multiple sequence alignment and SNPs generated previously. A lower penalty score indicates a better primer. If the AutoCloner primers did not work during PCR or sequencing, these could be used as alternatives.

Download all possible primers: (Forward) (Reverse)
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
20 21 1.461888 GGTCGTTTGTTCGATCTTGCG 60.462 52.381 0.00 0.00 41.78 4.85
68 69 4.111016 CTGCGTGCATGTGGCCTG 62.111 66.667 3.32 0.00 43.89 4.85
101 102 2.174060 GCACACGGCTGTAATTAAGC 57.826 50.000 0.00 9.73 40.25 3.09
120 121 9.999660 AATTAAGCCTCTAGTACTAATTTAGCC 57.000 33.333 3.76 0.00 0.00 3.93
121 122 8.543293 TTAAGCCTCTAGTACTAATTTAGCCA 57.457 34.615 3.76 0.00 0.00 4.75
122 123 7.619512 AAGCCTCTAGTACTAATTTAGCCAT 57.380 36.000 3.76 0.00 0.00 4.40
123 124 7.619512 AGCCTCTAGTACTAATTTAGCCATT 57.380 36.000 3.76 0.00 0.00 3.16
124 125 7.445945 AGCCTCTAGTACTAATTTAGCCATTG 58.554 38.462 3.76 0.00 0.00 2.82
125 126 6.147985 GCCTCTAGTACTAATTTAGCCATTGC 59.852 42.308 3.76 0.00 37.95 3.56
126 127 7.217200 CCTCTAGTACTAATTTAGCCATTGCA 58.783 38.462 3.76 0.00 41.13 4.08
127 128 7.386299 CCTCTAGTACTAATTTAGCCATTGCAG 59.614 40.741 3.76 0.00 41.13 4.41
128 129 7.792032 TCTAGTACTAATTTAGCCATTGCAGT 58.208 34.615 3.76 0.00 41.13 4.40
129 130 6.927294 AGTACTAATTTAGCCATTGCAGTC 57.073 37.500 0.00 0.00 41.13 3.51
130 131 6.653989 AGTACTAATTTAGCCATTGCAGTCT 58.346 36.000 0.00 0.00 41.13 3.24
131 132 7.792032 AGTACTAATTTAGCCATTGCAGTCTA 58.208 34.615 0.00 0.00 41.13 2.59
132 133 8.265055 AGTACTAATTTAGCCATTGCAGTCTAA 58.735 33.333 0.00 0.00 41.13 2.10
133 134 7.321745 ACTAATTTAGCCATTGCAGTCTAAC 57.678 36.000 3.28 0.00 41.13 2.34
137 138 0.447801 GCCATTGCAGTCTAACACGG 59.552 55.000 0.00 0.00 37.47 4.94
139 140 2.151202 CCATTGCAGTCTAACACGGTT 58.849 47.619 0.00 0.00 0.00 4.44
141 142 1.873698 TTGCAGTCTAACACGGTTCC 58.126 50.000 0.00 0.00 0.00 3.62
142 143 0.319211 TGCAGTCTAACACGGTTCCG 60.319 55.000 9.81 9.81 0.00 4.30
143 144 1.012486 GCAGTCTAACACGGTTCCGG 61.012 60.000 15.66 0.00 0.00 5.14
144 145 0.316204 CAGTCTAACACGGTTCCGGT 59.684 55.000 15.66 7.71 0.00 5.28
155 1575 4.021544 ACACGGTTCCGGTAGTAATTAACA 60.022 41.667 15.66 0.00 0.00 2.41
228 1648 4.268644 GCTTGTCGATCATCATCTTTCGAA 59.731 41.667 0.00 0.00 41.69 3.71
229 1649 5.556006 GCTTGTCGATCATCATCTTTCGAAG 60.556 44.000 0.00 0.00 41.69 3.79
230 1650 5.248870 TGTCGATCATCATCTTTCGAAGA 57.751 39.130 0.00 0.00 41.69 2.87
233 1653 5.172951 GTCGATCATCATCTTTCGAAGACAG 59.827 44.000 0.00 0.00 41.69 3.51
246 1705 2.353208 CGAAGACAGGAAGACAGGAAGG 60.353 54.545 0.00 0.00 0.00 3.46
295 1754 0.472471 AAAGAGACGCCCACCTTTCA 59.528 50.000 0.00 0.00 0.00 2.69
316 2392 1.338389 ACCACCCGGTCGACTAAAATG 60.338 52.381 16.46 7.81 44.71 2.32
533 3686 4.436584 GGCGATTGATGCTGATGCTATAAC 60.437 45.833 0.00 0.00 40.48 1.89
675 3847 0.178995 TGTGCCAGCTTGACCATCAA 60.179 50.000 0.00 0.00 34.79 2.57
692 3875 1.890510 AACCCGCACTGAACGTTCC 60.891 57.895 24.78 8.87 0.00 3.62
893 7249 4.457496 CAGACGCCCACCGCATCT 62.457 66.667 0.00 0.00 41.76 2.90
906 7264 1.523938 GCATCTCGCTGTAACCCCC 60.524 63.158 0.00 0.00 37.77 5.40
1054 7651 2.677765 TACCCAAACCGGCAGCGAAA 62.678 55.000 0.00 0.00 0.00 3.46
1058 7655 1.901464 AAACCGGCAGCGAAACCAT 60.901 52.632 0.00 0.00 0.00 3.55
1070 7674 1.808411 GAAACCATCGGAGCTCAACA 58.192 50.000 17.19 0.00 0.00 3.33
1071 7675 2.151202 GAAACCATCGGAGCTCAACAA 58.849 47.619 17.19 0.00 0.00 2.83
1092 7708 2.449450 ATACCTAAGCCACCGCCCC 61.449 63.158 0.00 0.00 34.57 5.80
1134 7800 2.414058 ATCTCTCATCATGTCGACGC 57.586 50.000 11.62 0.00 0.00 5.19
1196 7862 0.693622 TTCCCAACTACCAATCCGCA 59.306 50.000 0.00 0.00 0.00 5.69
1224 7890 4.742201 GCGTCAAGCTCTCCGCCA 62.742 66.667 11.47 0.00 44.04 5.69
1245 7962 4.070552 GCTCGCCGGTCAAGTCCT 62.071 66.667 1.90 0.00 0.00 3.85
1328 8054 4.626402 TCCCCGACGAACCACCCT 62.626 66.667 0.00 0.00 0.00 4.34
1340 8066 3.691342 CACCCTGGCTCGTTCCGA 61.691 66.667 0.00 0.00 0.00 4.55
1368 8094 1.370900 CACAAGGAACGCAAGCAGC 60.371 57.895 0.00 0.00 45.62 5.25
1372 8098 2.669569 GGAACGCAAGCAGCAGGA 60.670 61.111 0.00 0.00 46.13 3.86
1720 8637 5.291178 ACGTACATACTGCACAAAGTGTAA 58.709 37.500 0.00 0.00 35.75 2.41
1789 8735 4.581093 GGTGGGGATTAGGCCGGC 62.581 72.222 21.18 21.18 0.00 6.13
1790 8736 4.581093 GTGGGGATTAGGCCGGCC 62.581 72.222 39.29 39.29 0.00 6.13
1793 8739 4.271016 GGGATTAGGCCGGCCCAG 62.271 72.222 41.72 0.00 40.39 4.45
1794 8740 3.168528 GGATTAGGCCGGCCCAGA 61.169 66.667 41.72 27.40 36.58 3.86
1820 8784 5.699097 TTGGAGTTTTAAGACCCAATTCG 57.301 39.130 12.22 0.00 32.51 3.34
1951 8965 1.341778 TGAGCTCTCATCCTCTCTGCA 60.342 52.381 16.19 0.00 34.14 4.41
1957 8971 5.959594 AGCTCTCATCCTCTCTGCATATAAT 59.040 40.000 0.00 0.00 0.00 1.28
1958 8972 7.124721 AGCTCTCATCCTCTCTGCATATAATA 58.875 38.462 0.00 0.00 0.00 0.98
1959 8973 7.785985 AGCTCTCATCCTCTCTGCATATAATAT 59.214 37.037 0.00 0.00 0.00 1.28
1960 8974 8.084073 GCTCTCATCCTCTCTGCATATAATATC 58.916 40.741 0.00 0.00 0.00 1.63
1961 8975 9.134055 CTCTCATCCTCTCTGCATATAATATCA 57.866 37.037 0.00 0.00 0.00 2.15
1962 8976 9.484806 TCTCATCCTCTCTGCATATAATATCAA 57.515 33.333 0.00 0.00 0.00 2.57
1982 8996 7.943079 ATCAATACATGAGTGACAAATTGGA 57.057 32.000 0.00 0.00 42.53 3.53
1983 8997 7.381766 TCAATACATGAGTGACAAATTGGAG 57.618 36.000 0.00 0.00 32.80 3.86
1984 8998 7.167535 TCAATACATGAGTGACAAATTGGAGA 58.832 34.615 0.00 0.00 32.80 3.71
1985 8999 6.992063 ATACATGAGTGACAAATTGGAGAC 57.008 37.500 0.00 0.00 0.00 3.36
1986 9000 4.717877 ACATGAGTGACAAATTGGAGACA 58.282 39.130 0.00 0.00 39.83 3.41
2028 9047 3.368739 GCCCTTGATTTTGGTTCTGGATG 60.369 47.826 0.00 0.00 0.00 3.51
2031 9050 5.658190 CCCTTGATTTTGGTTCTGGATGTAT 59.342 40.000 0.00 0.00 0.00 2.29
2064 9090 4.516321 TGAGTGACAAATTGGAGACACATG 59.484 41.667 13.50 0.00 42.67 3.21
2110 9148 3.181440 GGGAGGCTTATCCATTCACATGA 60.181 47.826 0.00 0.00 41.52 3.07
2129 9167 2.223900 TGAATGATTTGCCGCAACAACA 60.224 40.909 4.98 6.89 0.00 3.33
2130 9168 2.522836 ATGATTTGCCGCAACAACAA 57.477 40.000 4.98 0.00 0.00 2.83
2131 9169 1.565305 TGATTTGCCGCAACAACAAC 58.435 45.000 4.98 0.00 0.00 3.32
2160 9216 5.057149 GCTTCTGTTTCTGTTTCTGGAGTA 58.943 41.667 0.00 0.00 0.00 2.59
2184 9240 1.070786 GTGTCTCGCCCCTGTTTCA 59.929 57.895 0.00 0.00 0.00 2.69
2337 9397 3.119602 CCGACGAGATTTCTGTGGAACTA 60.120 47.826 0.00 0.00 38.04 2.24
2338 9398 4.482386 CGACGAGATTTCTGTGGAACTAA 58.518 43.478 0.00 0.00 38.04 2.24
2368 9428 1.667724 GCAACTGATGAACCGAGGATG 59.332 52.381 0.00 0.00 0.00 3.51
2387 9447 5.073428 GGATGTTTCTTCTTCTTTCCCTGT 58.927 41.667 0.00 0.00 0.00 4.00
2529 12375 3.074412 GGATTTTTCTTCGTCCTGCTCA 58.926 45.455 0.00 0.00 0.00 4.26
2593 12439 7.228507 TGCTATTTTACTGTTCTTTCAGAGCAA 59.771 33.333 0.65 0.00 35.04 3.91
2633 14463 3.146783 CGTAGCGGTTGGGATTTCA 57.853 52.632 0.00 0.00 0.00 2.69
2724 14555 4.308458 TCGTGGGCAGGTGGTTCG 62.308 66.667 0.00 0.00 0.00 3.95
2726 14557 2.203294 GTGGGCAGGTGGTTCGTT 60.203 61.111 0.00 0.00 0.00 3.85
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 1.461888 CGCAAGATCGAACAAACGACC 60.462 52.381 0.00 0.00 44.84 4.79
20 21 0.179145 AATTGCTGCTGCGCTGATTC 60.179 50.000 19.32 5.87 43.34 2.52
24 25 2.506217 CCAATTGCTGCTGCGCTG 60.506 61.111 9.73 10.04 43.34 5.18
25 26 1.243342 TAACCAATTGCTGCTGCGCT 61.243 50.000 9.73 0.00 43.34 5.92
34 35 1.070471 CAGGCGCGTTAACCAATTGC 61.070 55.000 8.43 0.00 0.00 3.56
97 98 8.722622 ATGGCTAAATTAGTACTAGAGGCTTA 57.277 34.615 20.41 9.68 0.00 3.09
101 102 7.217200 TGCAATGGCTAAATTAGTACTAGAGG 58.783 38.462 2.23 0.00 41.91 3.69
102 103 7.928706 ACTGCAATGGCTAAATTAGTACTAGAG 59.071 37.037 2.23 1.49 41.91 2.43
103 104 7.792032 ACTGCAATGGCTAAATTAGTACTAGA 58.208 34.615 2.23 0.00 41.91 2.43
104 105 7.928706 AGACTGCAATGGCTAAATTAGTACTAG 59.071 37.037 2.23 0.00 41.91 2.57
105 106 7.792032 AGACTGCAATGGCTAAATTAGTACTA 58.208 34.615 0.00 0.00 41.91 1.82
106 107 6.653989 AGACTGCAATGGCTAAATTAGTACT 58.346 36.000 0.00 0.00 41.91 2.73
107 108 6.927294 AGACTGCAATGGCTAAATTAGTAC 57.073 37.500 1.68 0.00 41.91 2.73
108 109 8.044309 TGTTAGACTGCAATGGCTAAATTAGTA 58.956 33.333 2.98 0.00 41.91 1.82
109 110 6.884295 TGTTAGACTGCAATGGCTAAATTAGT 59.116 34.615 2.98 0.00 41.91 2.24
110 111 7.189512 GTGTTAGACTGCAATGGCTAAATTAG 58.810 38.462 2.98 0.00 41.91 1.73
112 113 5.391950 CGTGTTAGACTGCAATGGCTAAATT 60.392 40.000 2.98 0.00 41.91 1.82
113 114 4.094887 CGTGTTAGACTGCAATGGCTAAAT 59.905 41.667 2.98 0.00 41.91 1.40
114 115 3.435327 CGTGTTAGACTGCAATGGCTAAA 59.565 43.478 2.98 0.00 41.91 1.85
116 117 2.616960 CGTGTTAGACTGCAATGGCTA 58.383 47.619 0.00 0.00 41.91 3.93
117 118 1.442769 CGTGTTAGACTGCAATGGCT 58.557 50.000 0.00 0.00 41.91 4.75
118 119 0.447801 CCGTGTTAGACTGCAATGGC 59.552 55.000 0.00 0.00 41.68 4.40
120 121 2.159627 GGAACCGTGTTAGACTGCAATG 59.840 50.000 0.00 0.00 0.00 2.82
121 122 2.423577 GGAACCGTGTTAGACTGCAAT 58.576 47.619 0.00 0.00 0.00 3.56
122 123 1.870580 CGGAACCGTGTTAGACTGCAA 60.871 52.381 4.99 0.00 34.35 4.08
123 124 0.319211 CGGAACCGTGTTAGACTGCA 60.319 55.000 4.99 0.00 34.35 4.41
124 125 1.012486 CCGGAACCGTGTTAGACTGC 61.012 60.000 12.23 0.00 37.81 4.40
125 126 0.316204 ACCGGAACCGTGTTAGACTG 59.684 55.000 9.46 0.00 37.81 3.51
126 127 1.815003 CTACCGGAACCGTGTTAGACT 59.185 52.381 9.46 0.00 37.81 3.24
127 128 1.541588 ACTACCGGAACCGTGTTAGAC 59.458 52.381 9.46 0.00 37.81 2.59
128 129 1.909700 ACTACCGGAACCGTGTTAGA 58.090 50.000 9.46 0.00 37.81 2.10
129 130 3.848272 TTACTACCGGAACCGTGTTAG 57.152 47.619 9.46 11.05 37.81 2.34
130 131 4.799564 AATTACTACCGGAACCGTGTTA 57.200 40.909 9.46 3.22 37.81 2.41
131 132 3.683365 AATTACTACCGGAACCGTGTT 57.317 42.857 9.46 0.00 37.81 3.32
132 133 4.021544 TGTTAATTACTACCGGAACCGTGT 60.022 41.667 9.46 11.42 37.81 4.49
133 134 4.493547 TGTTAATTACTACCGGAACCGTG 58.506 43.478 9.46 6.38 37.81 4.94
137 138 6.425577 TGCAATGTTAATTACTACCGGAAC 57.574 37.500 9.46 0.00 0.00 3.62
139 140 5.587043 CCTTGCAATGTTAATTACTACCGGA 59.413 40.000 9.46 0.00 0.00 5.14
141 142 6.671614 TCCTTGCAATGTTAATTACTACCG 57.328 37.500 0.00 0.00 0.00 4.02
155 1575 9.546428 GTTAATGGCTAAATTAATCCTTGCAAT 57.454 29.630 0.00 0.00 35.16 3.56
201 1621 1.530293 GATGATGATCGACAAGCTGCC 59.470 52.381 0.00 0.00 0.00 4.85
228 1648 1.150135 TCCCTTCCTGTCTTCCTGTCT 59.850 52.381 0.00 0.00 0.00 3.41
229 1649 1.645710 TCCCTTCCTGTCTTCCTGTC 58.354 55.000 0.00 0.00 0.00 3.51
230 1650 2.118403 TTCCCTTCCTGTCTTCCTGT 57.882 50.000 0.00 0.00 0.00 4.00
233 1653 1.827681 GCTTTCCCTTCCTGTCTTCC 58.172 55.000 0.00 0.00 0.00 3.46
246 1705 2.073816 TCCGTTTCTCATTCGCTTTCC 58.926 47.619 0.00 0.00 0.00 3.13
310 2386 5.437060 CTTCCTCCGATTCTTCCCATTTTA 58.563 41.667 0.00 0.00 0.00 1.52
312 2388 3.372025 CCTTCCTCCGATTCTTCCCATTT 60.372 47.826 0.00 0.00 0.00 2.32
316 2392 0.179043 GCCTTCCTCCGATTCTTCCC 60.179 60.000 0.00 0.00 0.00 3.97
656 3828 0.178995 TTGATGGTCAAGCTGGCACA 60.179 50.000 0.00 0.00 31.83 4.57
675 3847 2.280592 GGAACGTTCAGTGCGGGT 60.281 61.111 28.24 0.00 0.00 5.28
734 3919 9.292195 GCTAGTTCTACTAATAGTCAAGATCCT 57.708 37.037 0.00 0.00 29.00 3.24
738 3923 9.682465 TCTTGCTAGTTCTACTAATAGTCAAGA 57.318 33.333 10.77 10.77 36.80 3.02
866 7039 4.357947 GGCGTCTGAGCACACCGA 62.358 66.667 3.21 0.00 39.27 4.69
893 7249 1.350071 TAAACTGGGGGTTACAGCGA 58.650 50.000 0.00 0.00 39.55 4.93
1054 7651 1.202758 TGTTTGTTGAGCTCCGATGGT 60.203 47.619 12.15 0.00 0.00 3.55
1058 7655 2.301870 AGGTATGTTTGTTGAGCTCCGA 59.698 45.455 12.15 0.00 0.00 4.55
1070 7674 1.680860 GGCGGTGGCTTAGGTATGTTT 60.681 52.381 0.00 0.00 39.81 2.83
1071 7675 0.107361 GGCGGTGGCTTAGGTATGTT 60.107 55.000 0.00 0.00 39.81 2.71
1097 7724 4.697756 TGGAAAGGTGGAGCGGCG 62.698 66.667 0.51 0.51 0.00 6.46
1098 7725 1.657751 GATTGGAAAGGTGGAGCGGC 61.658 60.000 0.00 0.00 0.00 6.53
1245 7962 2.341101 GGGGAGACGAGACGCTGAA 61.341 63.158 0.00 0.00 0.00 3.02
1289 8015 1.153369 CATGCAGGACCGACGGATT 60.153 57.895 23.38 0.00 0.00 3.01
1340 8066 0.610232 GTTCCTTGTGGAGGCTGCAT 60.610 55.000 13.12 0.00 45.87 3.96
1581 8331 3.059982 CTCCACCACTCGCTTCCA 58.940 61.111 0.00 0.00 0.00 3.53
1789 8735 5.416013 GGTCTTAAAACTCCAATCTTCTGGG 59.584 44.000 0.00 0.00 37.06 4.45
1790 8736 5.416013 GGGTCTTAAAACTCCAATCTTCTGG 59.584 44.000 0.00 0.00 37.87 3.86
1791 8737 6.003950 TGGGTCTTAAAACTCCAATCTTCTG 58.996 40.000 0.00 0.00 0.00 3.02
1792 8738 6.200878 TGGGTCTTAAAACTCCAATCTTCT 57.799 37.500 0.00 0.00 0.00 2.85
1793 8739 6.894339 TTGGGTCTTAAAACTCCAATCTTC 57.106 37.500 0.00 0.00 33.15 2.87
1794 8740 7.309194 CGAATTGGGTCTTAAAACTCCAATCTT 60.309 37.037 12.35 3.04 44.55 2.40
1853 8849 1.822371 GCGGAGAGGAAGAAGAGACTT 59.178 52.381 0.00 0.00 0.00 3.01
1856 8852 1.683629 GGAGCGGAGAGGAAGAAGAGA 60.684 57.143 0.00 0.00 0.00 3.10
1894 8897 0.603569 GCAGAGAGGACGAGGAACAA 59.396 55.000 0.00 0.00 0.00 2.83
1895 8898 0.251386 AGCAGAGAGGACGAGGAACA 60.251 55.000 0.00 0.00 0.00 3.18
1896 8899 0.454196 GAGCAGAGAGGACGAGGAAC 59.546 60.000 0.00 0.00 0.00 3.62
1897 8900 0.681564 GGAGCAGAGAGGACGAGGAA 60.682 60.000 0.00 0.00 0.00 3.36
1898 8901 1.077357 GGAGCAGAGAGGACGAGGA 60.077 63.158 0.00 0.00 0.00 3.71
1899 8902 1.379176 TGGAGCAGAGAGGACGAGG 60.379 63.158 0.00 0.00 0.00 4.63
1957 8971 9.112725 CTCCAATTTGTCACTCATGTATTGATA 57.887 33.333 0.00 0.00 32.72 2.15
1958 8972 7.830697 TCTCCAATTTGTCACTCATGTATTGAT 59.169 33.333 0.00 0.00 32.72 2.57
1959 8973 7.119699 GTCTCCAATTTGTCACTCATGTATTGA 59.880 37.037 0.00 0.00 0.00 2.57
1960 8974 7.094677 TGTCTCCAATTTGTCACTCATGTATTG 60.095 37.037 0.00 0.00 0.00 1.90
1961 8975 6.942005 TGTCTCCAATTTGTCACTCATGTATT 59.058 34.615 0.00 0.00 0.00 1.89
1962 8976 6.475504 TGTCTCCAATTTGTCACTCATGTAT 58.524 36.000 0.00 0.00 0.00 2.29
1963 8977 5.863965 TGTCTCCAATTTGTCACTCATGTA 58.136 37.500 0.00 0.00 0.00 2.29
1964 8978 4.717877 TGTCTCCAATTTGTCACTCATGT 58.282 39.130 0.00 0.00 0.00 3.21
1965 8979 5.694231 TTGTCTCCAATTTGTCACTCATG 57.306 39.130 0.00 0.00 0.00 3.07
1966 8980 6.906157 ATTTGTCTCCAATTTGTCACTCAT 57.094 33.333 0.00 0.00 0.00 2.90
1967 8981 6.461370 CCAATTTGTCTCCAATTTGTCACTCA 60.461 38.462 8.41 0.00 38.98 3.41
1968 8982 5.922544 CCAATTTGTCTCCAATTTGTCACTC 59.077 40.000 8.41 0.00 38.98 3.51
1969 8983 5.598005 TCCAATTTGTCTCCAATTTGTCACT 59.402 36.000 8.41 0.00 38.98 3.41
1970 8984 5.841810 TCCAATTTGTCTCCAATTTGTCAC 58.158 37.500 8.41 0.00 38.98 3.67
1971 8985 6.669125 ATCCAATTTGTCTCCAATTTGTCA 57.331 33.333 8.41 0.00 38.98 3.58
1972 8986 6.753744 GCTATCCAATTTGTCTCCAATTTGTC 59.246 38.462 8.41 0.00 38.98 3.18
1973 8987 6.438425 AGCTATCCAATTTGTCTCCAATTTGT 59.562 34.615 0.00 0.00 38.98 2.83
1974 8988 6.755141 CAGCTATCCAATTTGTCTCCAATTTG 59.245 38.462 0.00 0.00 39.73 2.32
1975 8989 6.438425 ACAGCTATCCAATTTGTCTCCAATTT 59.562 34.615 0.00 0.00 0.00 1.82
1976 8990 5.954150 ACAGCTATCCAATTTGTCTCCAATT 59.046 36.000 0.00 0.00 0.00 2.32
1977 8991 5.359009 CACAGCTATCCAATTTGTCTCCAAT 59.641 40.000 0.00 0.00 0.00 3.16
1978 8992 4.701651 CACAGCTATCCAATTTGTCTCCAA 59.298 41.667 0.00 0.00 0.00 3.53
1979 8993 4.263462 ACACAGCTATCCAATTTGTCTCCA 60.263 41.667 0.00 0.00 0.00 3.86
1980 8994 4.265073 ACACAGCTATCCAATTTGTCTCC 58.735 43.478 0.00 0.00 0.00 3.71
1981 8995 7.095439 GCTATACACAGCTATCCAATTTGTCTC 60.095 40.741 0.00 0.00 38.57 3.36
1982 8996 6.708054 GCTATACACAGCTATCCAATTTGTCT 59.292 38.462 0.00 0.00 38.57 3.41
1983 8997 6.073003 GGCTATACACAGCTATCCAATTTGTC 60.073 42.308 0.00 0.00 41.50 3.18
1984 8998 5.765182 GGCTATACACAGCTATCCAATTTGT 59.235 40.000 0.00 0.00 41.50 2.83
1985 8999 5.182001 GGGCTATACACAGCTATCCAATTTG 59.818 44.000 0.00 0.00 41.50 2.32
1986 9000 5.073691 AGGGCTATACACAGCTATCCAATTT 59.926 40.000 0.00 0.00 41.50 1.82
1987 9001 4.599241 AGGGCTATACACAGCTATCCAATT 59.401 41.667 0.00 0.00 41.50 2.32
1988 9002 4.171234 AGGGCTATACACAGCTATCCAAT 58.829 43.478 0.00 0.00 41.50 3.16
1989 9003 3.587498 AGGGCTATACACAGCTATCCAA 58.413 45.455 0.00 0.00 41.50 3.53
1990 9004 3.260269 AGGGCTATACACAGCTATCCA 57.740 47.619 0.00 0.00 41.50 3.41
1991 9005 3.578716 TCAAGGGCTATACACAGCTATCC 59.421 47.826 0.00 0.00 41.50 2.59
1992 9006 4.873746 TCAAGGGCTATACACAGCTATC 57.126 45.455 0.00 0.00 41.50 2.08
1993 9007 5.832539 AATCAAGGGCTATACACAGCTAT 57.167 39.130 0.00 0.00 41.50 2.97
2031 9050 9.112725 CTCCAATTTGTCACTCATGTATTGATA 57.887 33.333 0.00 0.00 32.72 2.15
2064 9090 4.272018 GTCAACAGATCAGATGCATGTACC 59.728 45.833 2.46 0.00 0.00 3.34
2110 9148 2.522836 TGTTGTTGCGGCAAATCATT 57.477 40.000 18.23 0.00 0.00 2.57
2129 9167 5.904362 AACAGAAACAGAAGCAGAAAGTT 57.096 34.783 0.00 0.00 0.00 2.66
2130 9168 5.649831 AGAAACAGAAACAGAAGCAGAAAGT 59.350 36.000 0.00 0.00 0.00 2.66
2131 9169 5.970023 CAGAAACAGAAACAGAAGCAGAAAG 59.030 40.000 0.00 0.00 0.00 2.62
2160 9216 1.690633 AGGGGCGAGACACATCCAT 60.691 57.895 0.00 0.00 0.00 3.41
2293 9353 0.320374 TCGGAGAATTTCTGCCGTGT 59.680 50.000 23.99 0.00 37.94 4.49
2337 9397 1.911293 ATCAGTTGCGCGCGTCATTT 61.911 50.000 32.35 16.40 0.00 2.32
2338 9398 2.390599 ATCAGTTGCGCGCGTCATT 61.391 52.632 32.35 16.73 0.00 2.57
2368 9428 6.036470 CACAAACAGGGAAAGAAGAAGAAAC 58.964 40.000 0.00 0.00 0.00 2.78
2387 9447 8.426569 ACCACTACCTATTAGTACTTCACAAA 57.573 34.615 0.00 0.00 39.18 2.83
2441 10088 5.423610 TCTTCAGAATCGAGGGATTTCTCTT 59.576 40.000 0.00 0.00 42.86 2.85
2593 12439 3.433173 GCCGTCCCTCAAAATAGTACCAT 60.433 47.826 0.00 0.00 0.00 3.55
2631 14461 4.518970 GTGCAATTTAAGACTTGGAGGTGA 59.481 41.667 0.00 0.00 0.00 4.02
2633 14463 4.469657 TGTGCAATTTAAGACTTGGAGGT 58.530 39.130 0.00 0.00 0.00 3.85
2699 14529 1.672356 CCTGCCCACGAGGTTTCTG 60.672 63.158 0.00 0.00 38.26 3.02


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

AutoCloner maintained by Alex Coulton.