Multiple sequence alignment - TraesCS7A01G013300

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 TraesCS7A01G013300 chr7A 100.000 3123 0 0 1 3123 5909671 5912793 0.000000e+00 5768.0
1 TraesCS7A01G013300 chr7A 99.466 1686 8 1 146 1831 6065280 6063596 0.000000e+00 3062.0
2 TraesCS7A01G013300 chr7A 100.000 958 0 0 2166 3123 6063337 6062380 0.000000e+00 1770.0
3 TraesCS7A01G013300 chr7A 80.325 1230 196 20 934 2133 4993605 4992392 0.000000e+00 889.0
4 TraesCS7A01G013300 chr7A 78.451 1072 190 24 1051 2108 5430032 5428988 0.000000e+00 662.0
5 TraesCS7A01G013300 chr7A 77.736 1069 204 22 1050 2106 5599663 5600709 2.640000e-175 625.0
6 TraesCS7A01G013300 chr7A 78.423 964 162 31 947 1889 5434598 5435536 1.250000e-163 586.0
7 TraesCS7A01G013300 chr7A 76.083 1108 219 27 1021 2112 5419358 5420435 1.270000e-148 536.0
8 TraesCS7A01G013300 chr7A 84.841 409 61 1 1731 2138 5051931 5051523 8.060000e-111 411.0
9 TraesCS7A01G013300 chr7A 76.479 693 147 11 969 1658 4974491 4973812 2.290000e-96 363.0
10 TraesCS7A01G013300 chr7A 83.624 287 41 4 1883 2167 5440833 5441115 6.640000e-67 265.0
11 TraesCS7A01G013300 chr7A 96.491 114 2 2 2945 3057 60794641 60794753 1.480000e-43 187.0
12 TraesCS7A01G013300 chr7A 93.878 98 6 0 146 243 6020476 6020379 6.980000e-32 148.0
13 TraesCS7A01G013300 chr4A 80.906 1236 198 19 934 2138 738669916 738671144 0.000000e+00 941.0
14 TraesCS7A01G013300 chr4A 78.781 1362 208 42 1042 2352 737738456 737737125 0.000000e+00 839.0
15 TraesCS7A01G013300 chr4A 79.617 1202 210 31 893 2082 738094201 738093023 0.000000e+00 830.0
16 TraesCS7A01G013300 chr4A 77.717 1472 238 49 934 2352 737944622 737946056 0.000000e+00 819.0
17 TraesCS7A01G013300 chr4A 77.758 1142 213 18 1015 2123 738719349 738718216 0.000000e+00 664.0
18 TraesCS7A01G013300 chr4A 75.000 1092 244 20 1010 2089 738710754 738711828 7.840000e-131 477.0
19 TraesCS7A01G013300 chr4A 76.398 805 163 22 1319 2108 738034534 738035326 2.900000e-110 409.0
20 TraesCS7A01G013300 chr4A 76.260 615 120 18 1459 2067 738080874 738080280 1.410000e-78 303.0
21 TraesCS7A01G013300 chr4A 98.198 111 1 1 2947 3057 131245830 131245721 3.180000e-45 193.0
22 TraesCS7A01G013300 chr4A 97.368 114 2 1 2944 3057 168005710 168005598 3.180000e-45 193.0
23 TraesCS7A01G013300 chr4A 92.035 113 8 1 2945 3057 711518202 711518091 1.160000e-34 158.0
24 TraesCS7A01G013300 chr4A 91.150 113 9 1 2945 3057 711481002 711480891 5.390000e-33 152.0
25 TraesCS7A01G013300 chr4A 89.655 116 12 0 1990 2105 738533322 738533207 6.980000e-32 148.0
26 TraesCS7A01G013300 chr4A 90.385 52 4 1 214 264 485227521 485227572 2.010000e-07 67.6
27 TraesCS7A01G013300 chr4A 90.385 52 4 1 214 264 485256501 485256552 2.010000e-07 67.6
28 TraesCS7A01G013300 chrUn 78.528 652 114 18 1463 2106 334640591 334641224 3.750000e-109 405.0
29 TraesCS7A01G013300 chrUn 98.592 71 1 0 3053 3123 32470661 32470591 3.270000e-25 126.0
30 TraesCS7A01G013300 chrUn 98.592 71 1 0 3053 3123 32474296 32474226 3.270000e-25 126.0
31 TraesCS7A01G013300 chrUn 98.592 71 1 0 3053 3123 371256793 371256863 3.270000e-25 126.0
32 TraesCS7A01G013300 chrUn 98.592 71 1 0 3053 3123 371323327 371323397 3.270000e-25 126.0
33 TraesCS7A01G013300 chrUn 98.592 71 1 0 3053 3123 377384879 377384809 3.270000e-25 126.0
34 TraesCS7A01G013300 chrUn 98.592 71 1 0 3053 3123 412072552 412072622 3.270000e-25 126.0
35 TraesCS7A01G013300 chrUn 98.592 71 1 0 3053 3123 447877861 447877791 3.270000e-25 126.0
36 TraesCS7A01G013300 chrUn 96.875 32 0 1 233 263 76583444 76583475 6.000000e-03 52.8
37 TraesCS7A01G013300 chr2B 97.015 134 4 0 884 1017 311794 311927 3.130000e-55 226.0
38 TraesCS7A01G013300 chr5A 98.198 111 1 1 2947 3057 614249206 614249315 3.180000e-45 193.0
39 TraesCS7A01G013300 chr5A 95.690 116 4 1 2942 3057 14026885 14026771 5.320000e-43 185.0
40 TraesCS7A01G013300 chr5A 85.938 64 4 4 203 264 616354823 616354883 2.600000e-06 63.9
41 TraesCS7A01G013300 chr3A 98.198 111 1 1 2947 3057 685470887 685470996 3.180000e-45 193.0
42 TraesCS7A01G013300 chr3A 97.321 112 2 1 2949 3060 33126452 33126342 4.110000e-44 189.0
43 TraesCS7A01G013300 chr3A 97.333 75 1 1 3050 3123 11033475 11033401 3.270000e-25 126.0
44 TraesCS7A01G013300 chr2A 98.182 110 1 1 2948 3057 765388730 765388838 1.140000e-44 191.0
45 TraesCS7A01G013300 chr6B 80.714 140 19 5 2923 3057 10123838 10123974 5.510000e-18 102.0
46 TraesCS7A01G013300 chr3B 80.992 121 17 6 3005 3122 801703047 801703164 1.190000e-14 91.6
47 TraesCS7A01G013300 chr3B 92.157 51 4 0 219 269 719909767 719909717 4.320000e-09 73.1
48 TraesCS7A01G013300 chr3B 91.304 46 4 0 212 257 676971162 676971207 2.600000e-06 63.9
49 TraesCS7A01G013300 chr1D 93.878 49 2 1 217 264 452830258 452830306 4.320000e-09 73.1
50 TraesCS7A01G013300 chr1D 92.500 40 3 0 230 269 298599817 298599778 1.210000e-04 58.4
51 TraesCS7A01G013300 chr1D 94.595 37 1 1 229 264 436719065 436719029 4.350000e-04 56.5
52 TraesCS7A01G013300 chr1D 87.755 49 5 1 217 264 466395370 466395418 4.350000e-04 56.5
53 TraesCS7A01G013300 chr6D 89.474 57 5 1 207 263 397637826 397637771 1.550000e-08 71.3
54 TraesCS7A01G013300 chr6D 89.362 47 5 0 214 260 463091082 463091128 3.360000e-05 60.2
55 TraesCS7A01G013300 chr6D 85.185 54 7 1 217 269 2829941 2829888 2.000000e-03 54.7
56 TraesCS7A01G013300 chr5D 90.566 53 5 0 217 269 456684280 456684228 1.550000e-08 71.3
57 TraesCS7A01G013300 chr5D 88.679 53 6 0 217 269 350900120 350900068 7.230000e-07 65.8
58 TraesCS7A01G013300 chr5B 93.750 48 2 1 213 260 219059000 219059046 1.550000e-08 71.3
59 TraesCS7A01G013300 chr5B 86.207 58 7 1 214 270 570645510 570645567 9.350000e-06 62.1
60 TraesCS7A01G013300 chr3D 91.837 49 3 1 217 264 64866708 64866660 2.010000e-07 67.6
61 TraesCS7A01G013300 chr3D 90.196 51 5 0 219 269 543996902 543996852 2.010000e-07 67.6
62 TraesCS7A01G013300 chr3D 88.889 54 5 1 217 269 25147476 25147423 7.230000e-07 65.8
63 TraesCS7A01G013300 chr3D 87.755 49 5 1 212 260 514684051 514684098 4.350000e-04 56.5
64 TraesCS7A01G013300 chr1A 100.000 34 0 0 230 263 371243571 371243604 2.600000e-06 63.9
65 TraesCS7A01G013300 chr1A 90.909 44 4 0 226 269 520920606 520920649 3.360000e-05 60.2
66 TraesCS7A01G013300 chr4B 86.792 53 7 0 217 269 77022816 77022764 3.360000e-05 60.2
67 TraesCS7A01G013300 chr4D 87.234 47 6 0 214 260 5032924 5032970 2.000000e-03 54.7


These results show the homologous regions that are presented in the multiple sequence alignment. HSPs from the BLAST search that are within 2000 bases of each other have been grouped together. Homologous regions that are purely upstream or downstream may be removed if they don't overlap both primers.

query scaffold start end length rev.comp avg.bitscore max.bitscore avg.percent.identical query.start query.end num_hsp groupid homo_length
0 TraesCS7A01G013300 chr7A 5909671 5912793 3122 False 5768 5768 100.000 1 3123 1 chr7A.!!$F5 3122
1 TraesCS7A01G013300 chr7A 6062380 6065280 2900 True 2416 3062 99.733 146 3123 2 chr7A.!!$R6 2977
2 TraesCS7A01G013300 chr7A 4992392 4993605 1213 True 889 889 80.325 934 2133 1 chr7A.!!$R2 1199
3 TraesCS7A01G013300 chr7A 5428988 5430032 1044 True 662 662 78.451 1051 2108 1 chr7A.!!$R4 1057
4 TraesCS7A01G013300 chr7A 5599663 5600709 1046 False 625 625 77.736 1050 2106 1 chr7A.!!$F4 1056
5 TraesCS7A01G013300 chr7A 5434598 5435536 938 False 586 586 78.423 947 1889 1 chr7A.!!$F2 942
6 TraesCS7A01G013300 chr7A 5419358 5420435 1077 False 536 536 76.083 1021 2112 1 chr7A.!!$F1 1091
7 TraesCS7A01G013300 chr7A 4973812 4974491 679 True 363 363 76.479 969 1658 1 chr7A.!!$R1 689
8 TraesCS7A01G013300 chr4A 738669916 738671144 1228 False 941 941 80.906 934 2138 1 chr4A.!!$F5 1204
9 TraesCS7A01G013300 chr4A 737737125 737738456 1331 True 839 839 78.781 1042 2352 1 chr4A.!!$R5 1310
10 TraesCS7A01G013300 chr4A 738093023 738094201 1178 True 830 830 79.617 893 2082 1 chr4A.!!$R7 1189
11 TraesCS7A01G013300 chr4A 737944622 737946056 1434 False 819 819 77.717 934 2352 1 chr4A.!!$F3 1418
12 TraesCS7A01G013300 chr4A 738718216 738719349 1133 True 664 664 77.758 1015 2123 1 chr4A.!!$R9 1108
13 TraesCS7A01G013300 chr4A 738710754 738711828 1074 False 477 477 75.000 1010 2089 1 chr4A.!!$F6 1079
14 TraesCS7A01G013300 chr4A 738034534 738035326 792 False 409 409 76.398 1319 2108 1 chr4A.!!$F4 789
15 TraesCS7A01G013300 chr4A 738080280 738080874 594 True 303 303 76.260 1459 2067 1 chr4A.!!$R6 608
16 TraesCS7A01G013300 chrUn 334640591 334641224 633 False 405 405 78.528 1463 2106 1 chrUn.!!$F2 643

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
98 99 0.251165 TTAGTTGTCTGCCTTGCCCC 60.251 55.0 0.0 0.0 0.00 5.80 F
102 103 0.398381 TTGTCTGCCTTGCCCCTTTT 60.398 50.0 0.0 0.0 0.00 2.27 F
103 104 0.398381 TGTCTGCCTTGCCCCTTTTT 60.398 50.0 0.0 0.0 0.00 1.94 F
472 473 0.800631 CGCAGCATTCAGAGCTTTCA 59.199 50.0 0.0 0.0 41.14 2.69 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1895 1988 0.389296 TGGTTCGCCATCAGTGTACG 60.389 55.0 0.00 0.00 43.56 3.67 R
1971 2064 0.393537 CACAGTTGCCATCTCCTCCC 60.394 60.0 0.00 0.00 0.00 4.30 R
2108 2201 0.723981 GAGCGTCACATCAGAAAGCC 59.276 55.0 0.00 0.00 0.00 4.35 R
2156 2249 0.107263 TGGTCCATACATGCATGCGT 60.107 50.0 26.53 10.53 0.00 5.24 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
23 24 6.391227 CCATCTTTGTTGTTTGTCTTACCT 57.609 37.500 0.00 0.00 0.00 3.08
24 25 6.805713 CCATCTTTGTTGTTTGTCTTACCTT 58.194 36.000 0.00 0.00 0.00 3.50
25 26 7.264947 CCATCTTTGTTGTTTGTCTTACCTTT 58.735 34.615 0.00 0.00 0.00 3.11
26 27 7.763985 CCATCTTTGTTGTTTGTCTTACCTTTT 59.236 33.333 0.00 0.00 0.00 2.27
27 28 9.150348 CATCTTTGTTGTTTGTCTTACCTTTTT 57.850 29.630 0.00 0.00 0.00 1.94
50 51 8.934507 TTTTTCTTTTTGTACCGTCATCATTT 57.065 26.923 0.00 0.00 0.00 2.32
51 52 8.568732 TTTTCTTTTTGTACCGTCATCATTTC 57.431 30.769 0.00 0.00 0.00 2.17
52 53 6.869315 TCTTTTTGTACCGTCATCATTTCA 57.131 33.333 0.00 0.00 0.00 2.69
53 54 6.898041 TCTTTTTGTACCGTCATCATTTCAG 58.102 36.000 0.00 0.00 0.00 3.02
54 55 6.485313 TCTTTTTGTACCGTCATCATTTCAGT 59.515 34.615 0.00 0.00 0.00 3.41
55 56 7.658167 TCTTTTTGTACCGTCATCATTTCAGTA 59.342 33.333 0.00 0.00 0.00 2.74
56 57 7.731882 TTTTGTACCGTCATCATTTCAGTAA 57.268 32.000 0.00 0.00 0.00 2.24
57 58 7.915293 TTTGTACCGTCATCATTTCAGTAAT 57.085 32.000 0.00 0.00 0.00 1.89
58 59 9.438228 TTTTGTACCGTCATCATTTCAGTAATA 57.562 29.630 0.00 0.00 0.00 0.98
59 60 9.607988 TTTGTACCGTCATCATTTCAGTAATAT 57.392 29.630 0.00 0.00 0.00 1.28
60 61 8.812147 TGTACCGTCATCATTTCAGTAATATC 57.188 34.615 0.00 0.00 0.00 1.63
61 62 8.417884 TGTACCGTCATCATTTCAGTAATATCA 58.582 33.333 0.00 0.00 0.00 2.15
62 63 9.424319 GTACCGTCATCATTTCAGTAATATCAT 57.576 33.333 0.00 0.00 0.00 2.45
63 64 8.539770 ACCGTCATCATTTCAGTAATATCATC 57.460 34.615 0.00 0.00 0.00 2.92
64 65 7.604164 ACCGTCATCATTTCAGTAATATCATCC 59.396 37.037 0.00 0.00 0.00 3.51
65 66 7.821359 CCGTCATCATTTCAGTAATATCATCCT 59.179 37.037 0.00 0.00 0.00 3.24
66 67 9.212641 CGTCATCATTTCAGTAATATCATCCTT 57.787 33.333 0.00 0.00 0.00 3.36
68 69 9.730705 TCATCATTTCAGTAATATCATCCTTCC 57.269 33.333 0.00 0.00 0.00 3.46
69 70 9.736414 CATCATTTCAGTAATATCATCCTTCCT 57.264 33.333 0.00 0.00 0.00 3.36
71 72 9.565090 TCATTTCAGTAATATCATCCTTCCTTG 57.435 33.333 0.00 0.00 0.00 3.61
72 73 9.347240 CATTTCAGTAATATCATCCTTCCTTGT 57.653 33.333 0.00 0.00 0.00 3.16
74 75 9.832445 TTTCAGTAATATCATCCTTCCTTGTAC 57.168 33.333 0.00 0.00 0.00 2.90
75 76 8.547481 TCAGTAATATCATCCTTCCTTGTACA 57.453 34.615 0.00 0.00 0.00 2.90
76 77 8.988060 TCAGTAATATCATCCTTCCTTGTACAA 58.012 33.333 8.28 8.28 0.00 2.41
77 78 9.784531 CAGTAATATCATCCTTCCTTGTACAAT 57.215 33.333 9.13 0.00 0.00 2.71
83 84 7.496346 TCATCCTTCCTTGTACAATCTTAGT 57.504 36.000 9.13 0.00 0.00 2.24
84 85 7.918076 TCATCCTTCCTTGTACAATCTTAGTT 58.082 34.615 9.13 0.00 0.00 2.24
85 86 7.824289 TCATCCTTCCTTGTACAATCTTAGTTG 59.176 37.037 9.13 3.67 35.25 3.16
86 87 7.074653 TCCTTCCTTGTACAATCTTAGTTGT 57.925 36.000 9.13 5.75 44.09 3.32
87 88 7.159372 TCCTTCCTTGTACAATCTTAGTTGTC 58.841 38.462 9.13 0.00 41.18 3.18
88 89 7.016268 TCCTTCCTTGTACAATCTTAGTTGTCT 59.984 37.037 9.13 0.00 41.18 3.41
89 90 7.118390 CCTTCCTTGTACAATCTTAGTTGTCTG 59.882 40.741 9.13 0.00 41.18 3.51
90 91 5.932303 TCCTTGTACAATCTTAGTTGTCTGC 59.068 40.000 9.13 0.00 41.18 4.26
91 92 5.122396 CCTTGTACAATCTTAGTTGTCTGCC 59.878 44.000 9.13 0.00 41.18 4.85
92 93 5.483685 TGTACAATCTTAGTTGTCTGCCT 57.516 39.130 0.00 0.00 41.18 4.75
93 94 5.865085 TGTACAATCTTAGTTGTCTGCCTT 58.135 37.500 0.00 0.00 41.18 4.35
94 95 5.700832 TGTACAATCTTAGTTGTCTGCCTTG 59.299 40.000 0.00 0.00 41.18 3.61
95 96 3.503748 ACAATCTTAGTTGTCTGCCTTGC 59.496 43.478 0.00 0.00 37.80 4.01
96 97 2.185004 TCTTAGTTGTCTGCCTTGCC 57.815 50.000 0.00 0.00 0.00 4.52
97 98 1.168714 CTTAGTTGTCTGCCTTGCCC 58.831 55.000 0.00 0.00 0.00 5.36
98 99 0.251165 TTAGTTGTCTGCCTTGCCCC 60.251 55.000 0.00 0.00 0.00 5.80
99 100 1.133809 TAGTTGTCTGCCTTGCCCCT 61.134 55.000 0.00 0.00 0.00 4.79
100 101 1.531602 GTTGTCTGCCTTGCCCCTT 60.532 57.895 0.00 0.00 0.00 3.95
101 102 1.115326 GTTGTCTGCCTTGCCCCTTT 61.115 55.000 0.00 0.00 0.00 3.11
102 103 0.398381 TTGTCTGCCTTGCCCCTTTT 60.398 50.000 0.00 0.00 0.00 2.27
103 104 0.398381 TGTCTGCCTTGCCCCTTTTT 60.398 50.000 0.00 0.00 0.00 1.94
141 142 9.865321 ATCAACATTTCACTAATTTCATCCTTG 57.135 29.630 0.00 0.00 0.00 3.61
142 143 8.859090 TCAACATTTCACTAATTTCATCCTTGT 58.141 29.630 0.00 0.00 0.00 3.16
195 196 3.056891 AGTTGACCACACACAACCAAAAG 60.057 43.478 0.00 0.00 44.79 2.27
215 216 5.619625 AAGCAGCAAATCTAGTTGTCTTC 57.380 39.130 0.00 0.00 0.00 2.87
260 261 4.603989 TGGCTCAAAATGAAGCATCAAA 57.396 36.364 0.00 0.00 39.49 2.69
343 344 5.773176 GGAGTTTTTCCCACCTGAATCTTTA 59.227 40.000 0.00 0.00 40.37 1.85
472 473 0.800631 CGCAGCATTCAGAGCTTTCA 59.199 50.000 0.00 0.00 41.14 2.69
816 817 5.083533 TGAAAAGAAAACATGTGGCTGTT 57.916 34.783 0.00 0.00 41.01 3.16
1841 1934 1.296392 CTTGTCACAGGGCGGATGA 59.704 57.895 0.00 0.00 0.00 2.92
1853 1946 1.475034 GGCGGATGACCAATGAAGCTA 60.475 52.381 0.00 0.00 35.59 3.32
1854 1947 1.599542 GCGGATGACCAATGAAGCTAC 59.400 52.381 0.00 0.00 35.59 3.58
1856 1949 3.270027 CGGATGACCAATGAAGCTACAA 58.730 45.455 0.00 0.00 35.59 2.41
1895 1988 1.398692 TTGGGCACAGAACAACTTCC 58.601 50.000 0.00 0.00 0.00 3.46
1899 1992 1.529865 GGCACAGAACAACTTCCGTAC 59.470 52.381 0.00 0.00 0.00 3.67
1922 2015 4.473643 TGGCGAACCAACAGGAAG 57.526 55.556 0.00 0.00 45.37 3.46
1923 2016 1.896660 TGGCGAACCAACAGGAAGC 60.897 57.895 0.00 0.00 45.37 3.86
1924 2017 1.896660 GGCGAACCAACAGGAAGCA 60.897 57.895 0.00 0.00 35.26 3.91
1946 2039 2.054021 TCCAGAATGTTGTGGACAGGA 58.946 47.619 7.47 0.00 44.68 3.86
1971 2064 1.066858 ACCAGATCAAGCACGGTACAG 60.067 52.381 0.00 0.00 0.00 2.74
2072 2165 3.916392 CTCAAACGACTCCGCCGCT 62.916 63.158 0.00 0.00 39.95 5.52
2123 2216 0.798776 CACCGGCTTTCTGATGTGAC 59.201 55.000 0.00 0.00 0.00 3.67
2133 2226 1.139989 CTGATGTGACGCTCGTTGTT 58.860 50.000 0.00 0.00 0.00 2.83
2162 2255 5.886715 TTTTGAAAGAACATTCACGCATG 57.113 34.783 0.00 0.00 38.95 4.06
2163 2256 2.932498 TGAAAGAACATTCACGCATGC 58.068 42.857 7.91 7.91 34.50 4.06
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 6.391227 AGGTAAGACAAACAACAAAGATGG 57.609 37.500 0.00 0.00 0.00 3.51
1 2 8.702163 AAAAGGTAAGACAAACAACAAAGATG 57.298 30.769 0.00 0.00 0.00 2.90
25 26 8.934507 AAATGATGACGGTACAAAAAGAAAAA 57.065 26.923 0.00 0.00 0.00 1.94
26 27 8.191446 TGAAATGATGACGGTACAAAAAGAAAA 58.809 29.630 0.00 0.00 0.00 2.29
27 28 7.708051 TGAAATGATGACGGTACAAAAAGAAA 58.292 30.769 0.00 0.00 0.00 2.52
28 29 7.012894 ACTGAAATGATGACGGTACAAAAAGAA 59.987 33.333 0.00 0.00 0.00 2.52
29 30 6.485313 ACTGAAATGATGACGGTACAAAAAGA 59.515 34.615 0.00 0.00 0.00 2.52
30 31 6.668323 ACTGAAATGATGACGGTACAAAAAG 58.332 36.000 0.00 0.00 0.00 2.27
31 32 6.627395 ACTGAAATGATGACGGTACAAAAA 57.373 33.333 0.00 0.00 0.00 1.94
32 33 7.731882 TTACTGAAATGATGACGGTACAAAA 57.268 32.000 0.00 0.00 0.00 2.44
33 34 7.915293 ATTACTGAAATGATGACGGTACAAA 57.085 32.000 0.00 0.00 0.00 2.83
34 35 9.256477 GATATTACTGAAATGATGACGGTACAA 57.744 33.333 0.00 0.00 0.00 2.41
35 36 8.417884 TGATATTACTGAAATGATGACGGTACA 58.582 33.333 0.00 0.00 0.00 2.90
36 37 8.812147 TGATATTACTGAAATGATGACGGTAC 57.188 34.615 0.00 0.00 0.00 3.34
37 38 9.639601 GATGATATTACTGAAATGATGACGGTA 57.360 33.333 0.00 0.00 0.00 4.02
38 39 7.604164 GGATGATATTACTGAAATGATGACGGT 59.396 37.037 0.00 0.00 0.00 4.83
39 40 7.821359 AGGATGATATTACTGAAATGATGACGG 59.179 37.037 0.00 0.00 0.00 4.79
40 41 8.768957 AGGATGATATTACTGAAATGATGACG 57.231 34.615 0.00 0.00 0.00 4.35
42 43 9.730705 GGAAGGATGATATTACTGAAATGATGA 57.269 33.333 0.00 0.00 0.00 2.92
43 44 9.736414 AGGAAGGATGATATTACTGAAATGATG 57.264 33.333 0.00 0.00 0.00 3.07
45 46 9.565090 CAAGGAAGGATGATATTACTGAAATGA 57.435 33.333 0.00 0.00 0.00 2.57
46 47 9.347240 ACAAGGAAGGATGATATTACTGAAATG 57.653 33.333 0.00 0.00 0.00 2.32
48 49 9.832445 GTACAAGGAAGGATGATATTACTGAAA 57.168 33.333 0.00 0.00 0.00 2.69
49 50 8.988060 TGTACAAGGAAGGATGATATTACTGAA 58.012 33.333 0.00 0.00 0.00 3.02
50 51 8.547481 TGTACAAGGAAGGATGATATTACTGA 57.453 34.615 0.00 0.00 0.00 3.41
51 52 9.784531 ATTGTACAAGGAAGGATGATATTACTG 57.215 33.333 14.65 0.00 0.00 2.74
57 58 9.213777 ACTAAGATTGTACAAGGAAGGATGATA 57.786 33.333 14.65 0.00 0.00 2.15
58 59 8.095452 ACTAAGATTGTACAAGGAAGGATGAT 57.905 34.615 14.65 0.00 0.00 2.45
59 60 7.496346 ACTAAGATTGTACAAGGAAGGATGA 57.504 36.000 14.65 0.00 0.00 2.92
60 61 7.607991 ACAACTAAGATTGTACAAGGAAGGATG 59.392 37.037 14.65 10.42 41.04 3.51
61 62 7.690256 ACAACTAAGATTGTACAAGGAAGGAT 58.310 34.615 14.65 0.00 41.04 3.24
62 63 7.016268 AGACAACTAAGATTGTACAAGGAAGGA 59.984 37.037 14.65 0.00 42.89 3.36
63 64 7.118390 CAGACAACTAAGATTGTACAAGGAAGG 59.882 40.741 14.65 6.76 42.89 3.46
64 65 7.360438 GCAGACAACTAAGATTGTACAAGGAAG 60.360 40.741 14.65 10.65 42.89 3.46
65 66 6.426937 GCAGACAACTAAGATTGTACAAGGAA 59.573 38.462 14.65 0.00 42.89 3.36
66 67 5.932303 GCAGACAACTAAGATTGTACAAGGA 59.068 40.000 14.65 0.00 42.89 3.36
67 68 5.122396 GGCAGACAACTAAGATTGTACAAGG 59.878 44.000 14.65 4.47 42.89 3.61
68 69 5.934625 AGGCAGACAACTAAGATTGTACAAG 59.065 40.000 14.65 2.08 42.89 3.16
69 70 5.865085 AGGCAGACAACTAAGATTGTACAA 58.135 37.500 11.41 11.41 42.89 2.41
70 71 5.483685 AGGCAGACAACTAAGATTGTACA 57.516 39.130 0.00 0.00 42.89 2.90
71 72 5.390991 GCAAGGCAGACAACTAAGATTGTAC 60.391 44.000 0.00 0.00 42.89 2.90
72 73 4.695455 GCAAGGCAGACAACTAAGATTGTA 59.305 41.667 0.00 0.00 42.89 2.41
73 74 3.503748 GCAAGGCAGACAACTAAGATTGT 59.496 43.478 0.00 0.00 45.52 2.71
74 75 3.119708 GGCAAGGCAGACAACTAAGATTG 60.120 47.826 0.00 0.00 35.59 2.67
75 76 3.084786 GGCAAGGCAGACAACTAAGATT 58.915 45.455 0.00 0.00 0.00 2.40
76 77 2.619074 GGGCAAGGCAGACAACTAAGAT 60.619 50.000 0.00 0.00 0.00 2.40
77 78 1.271379 GGGCAAGGCAGACAACTAAGA 60.271 52.381 0.00 0.00 0.00 2.10
78 79 1.168714 GGGCAAGGCAGACAACTAAG 58.831 55.000 0.00 0.00 0.00 2.18
79 80 0.251165 GGGGCAAGGCAGACAACTAA 60.251 55.000 0.00 0.00 0.00 2.24
80 81 1.133809 AGGGGCAAGGCAGACAACTA 61.134 55.000 0.00 0.00 0.00 2.24
81 82 2.011617 AAGGGGCAAGGCAGACAACT 62.012 55.000 0.00 0.00 0.00 3.16
82 83 1.115326 AAAGGGGCAAGGCAGACAAC 61.115 55.000 0.00 0.00 0.00 3.32
83 84 0.398381 AAAAGGGGCAAGGCAGACAA 60.398 50.000 0.00 0.00 0.00 3.18
84 85 0.398381 AAAAAGGGGCAAGGCAGACA 60.398 50.000 0.00 0.00 0.00 3.41
85 86 2.440946 AAAAAGGGGCAAGGCAGAC 58.559 52.632 0.00 0.00 0.00 3.51
115 116 9.865321 CAAGGATGAAATTAGTGAAATGTTGAT 57.135 29.630 0.00 0.00 0.00 2.57
116 117 8.859090 ACAAGGATGAAATTAGTGAAATGTTGA 58.141 29.630 0.00 0.00 0.00 3.18
119 120 9.295825 TGTACAAGGATGAAATTAGTGAAATGT 57.704 29.630 0.00 0.00 0.00 2.71
131 132 9.904198 TCTGATGATAATTGTACAAGGATGAAA 57.096 29.630 14.65 0.00 0.00 2.69
132 133 9.904198 TTCTGATGATAATTGTACAAGGATGAA 57.096 29.630 14.65 6.36 0.00 2.57
133 134 9.904198 TTTCTGATGATAATTGTACAAGGATGA 57.096 29.630 14.65 4.45 0.00 2.92
161 162 5.221283 TGTGTGGTCAACTATTCGTAGTTCA 60.221 40.000 0.00 0.00 38.14 3.18
195 196 5.619625 AAGAAGACAACTAGATTTGCTGC 57.380 39.130 0.00 0.00 0.00 5.25
215 216 8.338259 CCAATAAAATCCACACTCTATCGAAAG 58.662 37.037 0.00 0.00 0.00 2.62
260 261 7.067494 ACAGACAACTAGATTTGCTGTTTTCTT 59.933 33.333 12.88 0.00 39.07 2.52
343 344 1.974957 GTTTTGGCCCCTGTTAATGGT 59.025 47.619 0.00 0.00 0.00 3.55
472 473 1.689233 TATGGAGGGTGCGGCTTCT 60.689 57.895 0.00 0.00 0.00 2.85
629 630 8.641499 TTTTGTGCCTTTTGAAATAGTAACAG 57.359 30.769 0.00 0.00 0.00 3.16
816 817 8.338072 TGAGCCAATAAAAAGTAATCCGTTTA 57.662 30.769 0.00 0.00 0.00 2.01
1841 1934 4.012374 CCATCTGTTGTAGCTTCATTGGT 58.988 43.478 0.00 0.00 0.00 3.67
1853 1946 1.541147 CGCCAAATGACCATCTGTTGT 59.459 47.619 0.00 0.00 0.00 3.32
1854 1947 1.811965 TCGCCAAATGACCATCTGTTG 59.188 47.619 0.00 0.00 0.00 3.33
1856 1949 2.198827 TTCGCCAAATGACCATCTGT 57.801 45.000 0.00 0.00 0.00 3.41
1895 1988 0.389296 TGGTTCGCCATCAGTGTACG 60.389 55.000 0.00 0.00 43.56 3.67
1924 2017 3.074390 TCCTGTCCACAACATTCTGGAAT 59.926 43.478 0.00 0.00 38.33 3.01
1932 2025 2.356125 GGTATGCTCCTGTCCACAACAT 60.356 50.000 0.00 0.00 37.23 2.71
1946 2039 1.473965 CCGTGCTTGATCTGGTATGCT 60.474 52.381 0.00 0.00 0.00 3.79
1971 2064 0.393537 CACAGTTGCCATCTCCTCCC 60.394 60.000 0.00 0.00 0.00 4.30
2108 2201 0.723981 GAGCGTCACATCAGAAAGCC 59.276 55.000 0.00 0.00 0.00 4.35
2112 2205 1.269569 ACAACGAGCGTCACATCAGAA 60.270 47.619 0.00 0.00 0.00 3.02
2140 2233 4.208873 GCATGCGTGAATGTTCTTTCAAAA 59.791 37.500 10.93 0.00 37.36 2.44
2141 2234 3.735240 GCATGCGTGAATGTTCTTTCAAA 59.265 39.130 10.93 0.00 37.36 2.69
2142 2235 3.243334 TGCATGCGTGAATGTTCTTTCAA 60.243 39.130 14.09 0.00 37.36 2.69
2143 2236 2.292845 TGCATGCGTGAATGTTCTTTCA 59.707 40.909 14.09 0.00 33.32 2.69
2144 2237 2.932498 TGCATGCGTGAATGTTCTTTC 58.068 42.857 14.09 0.00 0.00 2.62
2145 2238 3.247442 CATGCATGCGTGAATGTTCTTT 58.753 40.909 31.95 0.00 36.73 2.52
2147 2240 2.554806 CATGCATGCGTGAATGTTCT 57.445 45.000 31.95 0.00 36.73 3.01
2151 2244 2.291190 TCCATACATGCATGCGTGAATG 59.709 45.455 39.42 26.06 45.47 2.67
2152 2245 2.291465 GTCCATACATGCATGCGTGAAT 59.709 45.455 39.42 23.97 36.80 2.57
2153 2246 1.670295 GTCCATACATGCATGCGTGAA 59.330 47.619 39.42 19.27 36.80 3.18
2154 2247 1.298602 GTCCATACATGCATGCGTGA 58.701 50.000 39.42 25.24 36.80 4.35
2155 2248 0.308684 GGTCCATACATGCATGCGTG 59.691 55.000 33.18 33.18 38.78 5.34
2156 2249 0.107263 TGGTCCATACATGCATGCGT 60.107 50.000 26.53 10.53 0.00 5.24
2157 2250 1.241165 ATGGTCCATACATGCATGCG 58.759 50.000 26.53 14.69 0.00 4.73
2158 2251 4.011698 TCATATGGTCCATACATGCATGC 58.988 43.478 26.53 11.82 0.00 4.06
2159 2252 5.883673 TCATCATATGGTCCATACATGCATG 59.116 40.000 25.09 25.09 0.00 4.06
2160 2253 5.884232 GTCATCATATGGTCCATACATGCAT 59.116 40.000 14.01 0.00 0.00 3.96
2161 2254 5.013391 AGTCATCATATGGTCCATACATGCA 59.987 40.000 14.01 7.05 0.00 3.96
2162 2255 5.494724 AGTCATCATATGGTCCATACATGC 58.505 41.667 14.01 13.38 0.00 4.06
2163 2256 5.809051 CGAGTCATCATATGGTCCATACATG 59.191 44.000 14.01 17.07 0.00 3.21


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

AutoCloner maintained by Alex Coulton.