Multiple sequence alignment - TraesCS7D01G512700

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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 TraesCS7D01G512700 chr7D 100.000 2258 0 0 1 2258 614216331 614214074 0.000000e+00 4170
1 TraesCS7D01G512700 chr7D 95.161 186 8 1 2073 2258 98488554 98488370 2.190000e-75 292
2 TraesCS7D01G512700 chr7D 96.045 177 7 0 2082 2258 580881596 580881420 2.840000e-74 289
3 TraesCS7D01G512700 chr7D 94.149 188 9 2 2072 2258 353906859 353906673 3.670000e-73 285
4 TraesCS7D01G512700 chr7D 94.444 144 8 0 1 144 23644916 23645059 2.920000e-54 222
5 TraesCS7D01G512700 chr7D 76.190 210 37 12 662 864 614705654 614705451 5.130000e-17 99
6 TraesCS7D01G512700 chr7A 90.125 1357 93 21 395 1748 706279467 706278149 0.000000e+00 1725
7 TraesCS7D01G512700 chr7A 91.118 304 21 5 1791 2094 706278151 706277854 7.510000e-110 407
8 TraesCS7D01G512700 chr7A 97.345 226 6 0 141 366 706279852 706279627 3.520000e-103 385
9 TraesCS7D01G512700 chr7A 95.105 143 7 0 1 143 91928226 91928084 2.260000e-55 226
10 TraesCS7D01G512700 chr7A 93.750 144 9 0 1 144 136447542 136447685 1.360000e-52 217
11 TraesCS7D01G512700 chr7A 76.953 256 50 8 1500 1752 706712666 706712417 1.090000e-28 137
12 TraesCS7D01G512700 chr7B 90.425 1295 81 15 804 2096 706046679 706045426 0.000000e+00 1664
13 TraesCS7D01G512700 chr7B 92.951 610 40 3 141 749 706047284 706046677 0.000000e+00 885
14 TraesCS7D01G512700 chr6D 97.633 169 4 0 2090 2258 296171639 296171471 7.890000e-75 291
15 TraesCS7D01G512700 chr6D 94.086 186 9 2 2075 2258 20941294 20941109 4.750000e-72 281
16 TraesCS7D01G512700 chr5D 97.633 169 3 1 2090 2258 72485755 72485588 2.840000e-74 289
17 TraesCS7D01G512700 chr5D 94.406 143 8 0 1 143 279293013 279292871 1.050000e-53 220
18 TraesCS7D01G512700 chr3D 97.076 171 5 0 2088 2258 61056360 61056190 2.840000e-74 289
19 TraesCS7D01G512700 chr4D 97.076 171 4 1 2088 2258 496634827 496634996 1.020000e-73 287
20 TraesCS7D01G512700 chr4D 82.114 123 20 1 1883 2003 428260550 428260428 1.100000e-18 104
21 TraesCS7D01G512700 chr3A 93.548 186 10 2 2074 2258 269442365 269442181 2.210000e-70 276
22 TraesCS7D01G512700 chr3A 93.793 145 9 0 1 145 711681281 711681425 3.780000e-53 219
23 TraesCS7D01G512700 chr6A 74.916 598 118 20 1446 2027 603028948 603029529 6.230000e-61 244
24 TraesCS7D01G512700 chr6A 79.618 157 28 4 1910 2065 177039477 177039324 2.370000e-20 110
25 TraesCS7D01G512700 chr1B 74.219 640 138 19 1406 2027 432607798 432608428 2.240000e-60 243
26 TraesCS7D01G512700 chr1B 93.706 143 9 0 1 143 295093778 295093636 4.880000e-52 215
27 TraesCS7D01G512700 chr5B 74.441 626 127 26 1415 2026 67466408 67467014 2.900000e-59 239
28 TraesCS7D01G512700 chr4A 94.406 143 8 0 1 143 589590742 589590884 1.050000e-53 220
29 TraesCS7D01G512700 chrUn 93.706 143 9 0 1 143 105424083 105423941 4.880000e-52 215
30 TraesCS7D01G512700 chrUn 72.533 608 126 33 1415 2000 69366638 69366050 2.320000e-35 159
31 TraesCS7D01G512700 chr2D 93.706 143 9 0 1 143 315859106 315859248 4.880000e-52 215
32 TraesCS7D01G512700 chr1A 81.600 125 20 3 1908 2032 97961992 97962113 1.430000e-17 100


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 TraesCS7D01G512700 chr7D 614214074 614216331 2257 True 4170.0 4170 100.000000 1 2258 1 chr7D.!!$R4 2257
1 TraesCS7D01G512700 chr7A 706277854 706279852 1998 True 839.0 1725 92.862667 141 2094 3 chr7A.!!$R3 1953
2 TraesCS7D01G512700 chr7B 706045426 706047284 1858 True 1274.5 1664 91.688000 141 2096 2 chr7B.!!$R1 1955
3 TraesCS7D01G512700 chr6A 603028948 603029529 581 False 244.0 244 74.916000 1446 2027 1 chr6A.!!$F1 581
4 TraesCS7D01G512700 chr1B 432607798 432608428 630 False 243.0 243 74.219000 1406 2027 1 chr1B.!!$F1 621
5 TraesCS7D01G512700 chr5B 67466408 67467014 606 False 239.0 239 74.441000 1415 2026 1 chr5B.!!$F1 611

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
519 652 0.756294 TCTCGTTCAGCTTCCAACCA 59.244 50.0 0.0 0.0 0.0 3.67 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1706 1854 0.606604 GGTGCTCCTTTCCGTGTCTA 59.393 55.0 0.0 0.0 0.0 2.59 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
97 98 7.575332 TTTGTCAAAGTTTACAAAGCTTGAC 57.425 32.000 0.00 15.49 39.88 3.18
98 99 6.509418 TGTCAAAGTTTACAAAGCTTGACT 57.491 33.333 19.48 0.00 39.29 3.41
99 100 6.919721 TGTCAAAGTTTACAAAGCTTGACTT 58.080 32.000 19.48 3.36 39.29 3.01
116 117 7.174082 GCTTGACTTTGACTAAAGCTAATACG 58.826 38.462 0.00 0.00 45.72 3.06
117 118 6.642683 TGACTTTGACTAAAGCTAATACGC 57.357 37.500 0.00 0.00 45.72 4.42
118 119 5.287752 TGACTTTGACTAAAGCTAATACGCG 59.712 40.000 3.53 3.53 45.72 6.01
119 120 4.565564 ACTTTGACTAAAGCTAATACGCGG 59.434 41.667 12.47 0.00 45.72 6.46
120 121 4.374843 TTGACTAAAGCTAATACGCGGA 57.625 40.909 12.47 0.00 34.40 5.54
121 122 3.699067 TGACTAAAGCTAATACGCGGAC 58.301 45.455 12.47 0.00 34.40 4.79
122 123 3.379372 TGACTAAAGCTAATACGCGGACT 59.621 43.478 12.47 0.00 34.40 3.85
123 124 4.576053 TGACTAAAGCTAATACGCGGACTA 59.424 41.667 12.47 0.00 34.40 2.59
124 125 5.066375 TGACTAAAGCTAATACGCGGACTAA 59.934 40.000 12.47 0.00 34.40 2.24
125 126 5.894807 ACTAAAGCTAATACGCGGACTAAA 58.105 37.500 12.47 0.00 34.40 1.85
126 127 6.510536 ACTAAAGCTAATACGCGGACTAAAT 58.489 36.000 12.47 0.00 34.40 1.40
127 128 7.651808 ACTAAAGCTAATACGCGGACTAAATA 58.348 34.615 12.47 0.00 34.40 1.40
128 129 8.137437 ACTAAAGCTAATACGCGGACTAAATAA 58.863 33.333 12.47 0.00 34.40 1.40
129 130 7.775397 AAAGCTAATACGCGGACTAAATAAA 57.225 32.000 12.47 0.00 34.40 1.40
130 131 7.775397 AAGCTAATACGCGGACTAAATAAAA 57.225 32.000 12.47 0.00 34.40 1.52
131 132 7.775397 AGCTAATACGCGGACTAAATAAAAA 57.225 32.000 12.47 0.00 34.40 1.94
132 133 7.624661 AGCTAATACGCGGACTAAATAAAAAC 58.375 34.615 12.47 0.00 34.40 2.43
133 134 6.567512 GCTAATACGCGGACTAAATAAAAACG 59.432 38.462 12.47 0.00 0.00 3.60
134 135 3.727780 ACGCGGACTAAATAAAAACGG 57.272 42.857 12.47 0.00 0.00 4.44
135 136 3.324993 ACGCGGACTAAATAAAAACGGA 58.675 40.909 12.47 0.00 0.00 4.69
136 137 3.368843 ACGCGGACTAAATAAAAACGGAG 59.631 43.478 12.47 0.00 0.00 4.63
137 138 3.242188 CGCGGACTAAATAAAAACGGAGG 60.242 47.826 0.00 0.00 0.00 4.30
138 139 3.064408 GCGGACTAAATAAAAACGGAGGG 59.936 47.826 0.00 0.00 0.00 4.30
139 140 4.506758 CGGACTAAATAAAAACGGAGGGA 58.493 43.478 0.00 0.00 0.00 4.20
217 218 2.034879 CCGTTCAACTCGCCATGCT 61.035 57.895 0.00 0.00 0.00 3.79
312 313 3.451141 TTTGTGTTCAATTGTCCTGCC 57.549 42.857 5.13 0.00 33.32 4.85
366 367 6.816640 CCTTCTTAACGTTAGTTGATGGATGA 59.183 38.462 21.57 4.64 41.35 2.92
405 537 3.989595 GCTAGCATCGAACGCGCC 61.990 66.667 10.63 0.00 37.46 6.53
444 576 2.173382 CTACGCAACAACGCTGCC 59.827 61.111 0.00 0.00 36.40 4.85
519 652 0.756294 TCTCGTTCAGCTTCCAACCA 59.244 50.000 0.00 0.00 0.00 3.67
523 656 4.404394 TCTCGTTCAGCTTCCAACCATATA 59.596 41.667 0.00 0.00 0.00 0.86
591 724 3.449377 TCTTATCAGCGGTGGATTGTACA 59.551 43.478 15.67 0.00 0.00 2.90
603 736 5.395546 GGTGGATTGTACATTGATGCCAATT 60.396 40.000 0.00 0.00 40.81 2.32
697 831 3.066380 TCCACATGTGATGACTTGTTCG 58.934 45.455 27.46 5.73 38.16 3.95
796 930 2.092321 AGAGTGCTCTATAGACGGTGGT 60.092 50.000 0.00 0.00 38.35 4.16
882 1017 0.823460 TCACGATGCACATCTAGGCA 59.177 50.000 8.87 0.00 45.23 4.75
887 1022 3.055591 CGATGCACATCTAGGCAAGTAG 58.944 50.000 8.87 0.00 44.20 2.57
889 1024 3.526931 TGCACATCTAGGCAAGTAGAC 57.473 47.619 0.00 0.00 37.03 2.59
890 1025 2.831526 TGCACATCTAGGCAAGTAGACA 59.168 45.455 0.00 0.00 37.03 3.41
891 1026 3.452264 TGCACATCTAGGCAAGTAGACAT 59.548 43.478 0.00 0.00 37.03 3.06
892 1027 3.806521 GCACATCTAGGCAAGTAGACATG 59.193 47.826 0.00 0.00 31.75 3.21
918 1053 7.758528 GCATACGGGACTATAAATTAGTACAGG 59.241 40.741 0.00 0.00 29.53 4.00
945 1080 2.111384 TGAGCCCATACCAGAAGAGAC 58.889 52.381 0.00 0.00 0.00 3.36
1041 1184 3.489738 GCATTACCACCATGATTGTGCTC 60.490 47.826 0.00 0.00 32.30 4.26
1045 1188 0.179181 CACCATGATTGTGCTCGTGC 60.179 55.000 1.71 1.71 40.20 5.34
1057 1200 1.944035 CTCGTGCTGCTGCTTCAAA 59.056 52.632 17.00 0.00 40.48 2.69
1110 1253 2.159310 TGGTTTTTGTCAAAGCGACCAG 60.159 45.455 18.67 0.00 44.71 4.00
1155 1298 4.628074 TGTCAACTAGCACAAGGAAGTAC 58.372 43.478 0.00 0.00 0.00 2.73
1225 1368 1.604604 CCCAGAAGGAAAACGCTTCA 58.395 50.000 0.00 0.00 38.24 3.02
1286 1431 7.704899 TGCGTGTACAATCCATATACATATAGC 59.295 37.037 0.00 0.00 31.79 2.97
1371 1516 5.020132 AGTACTGATGCTACTCAGGTCTTT 58.980 41.667 13.57 0.00 45.67 2.52
1464 1609 5.257345 TGAAAAGCAACAACGAAACAAAC 57.743 34.783 0.00 0.00 0.00 2.93
1498 1644 7.225734 CCGATCGATACATAGTGATGAGATAGT 59.774 40.741 18.66 0.00 36.48 2.12
1580 1726 6.535508 GCTACCGAAAGATAACACAGAAAGAT 59.464 38.462 0.00 0.00 0.00 2.40
1582 1728 5.122396 ACCGAAAGATAACACAGAAAGATGC 59.878 40.000 0.00 0.00 0.00 3.91
1601 1748 2.624316 CGAGTACAACGCCACTCTAA 57.376 50.000 0.00 0.00 39.23 2.10
1706 1854 2.237542 AGGTTTTCACCCGGAACCT 58.762 52.632 16.72 16.72 45.63 3.50
2057 2228 2.099592 CGCCAACCATTTGCATCATAGT 59.900 45.455 0.00 0.00 0.00 2.12
2097 2268 4.136978 GAGGAAGGCACCTCCTGA 57.863 61.111 16.44 0.00 46.94 3.86
2098 2269 2.377136 GAGGAAGGCACCTCCTGAA 58.623 57.895 16.44 0.00 46.94 3.02
2099 2270 0.251634 GAGGAAGGCACCTCCTGAAG 59.748 60.000 16.44 0.00 46.94 3.02
2111 2282 3.872459 CTCCTGAAGGAAATATGCCCT 57.128 47.619 0.00 0.00 44.91 5.19
2112 2283 4.982241 CTCCTGAAGGAAATATGCCCTA 57.018 45.455 0.00 0.00 44.91 3.53
2113 2284 4.904241 CTCCTGAAGGAAATATGCCCTAG 58.096 47.826 0.00 0.00 44.91 3.02
2114 2285 4.566837 TCCTGAAGGAAATATGCCCTAGA 58.433 43.478 0.00 0.00 42.18 2.43
2115 2286 4.594920 TCCTGAAGGAAATATGCCCTAGAG 59.405 45.833 0.00 0.00 42.18 2.43
2116 2287 4.263243 CCTGAAGGAAATATGCCCTAGAGG 60.263 50.000 0.00 0.00 37.39 3.69
2132 2303 7.881775 CCCTAGAGGCAATAATAAAGTTGTT 57.118 36.000 0.00 0.00 0.00 2.83
2133 2304 8.974060 CCCTAGAGGCAATAATAAAGTTGTTA 57.026 34.615 0.00 0.00 0.00 2.41
2134 2305 9.574516 CCCTAGAGGCAATAATAAAGTTGTTAT 57.425 33.333 0.00 0.00 0.00 1.89
2192 2363 8.773645 TCATTCATGCTAGAATTGTATTAACCG 58.226 33.333 0.00 0.00 36.13 4.44
2193 2364 7.490962 TTCATGCTAGAATTGTATTAACCGG 57.509 36.000 0.00 0.00 0.00 5.28
2194 2365 6.822442 TCATGCTAGAATTGTATTAACCGGA 58.178 36.000 9.46 0.00 0.00 5.14
2195 2366 7.276658 TCATGCTAGAATTGTATTAACCGGAA 58.723 34.615 9.46 0.00 0.00 4.30
2196 2367 7.771361 TCATGCTAGAATTGTATTAACCGGAAA 59.229 33.333 9.46 1.61 0.00 3.13
2197 2368 7.311364 TGCTAGAATTGTATTAACCGGAAAC 57.689 36.000 9.46 0.00 0.00 2.78
2198 2369 7.107542 TGCTAGAATTGTATTAACCGGAAACT 58.892 34.615 9.46 0.00 0.00 2.66
2199 2370 7.608761 TGCTAGAATTGTATTAACCGGAAACTT 59.391 33.333 9.46 0.00 0.00 2.66
2200 2371 9.101655 GCTAGAATTGTATTAACCGGAAACTTA 57.898 33.333 9.46 0.00 0.00 2.24
2205 2376 9.723601 AATTGTATTAACCGGAAACTTAGTACA 57.276 29.630 9.46 10.88 28.23 2.90
2206 2377 9.895138 ATTGTATTAACCGGAAACTTAGTACAT 57.105 29.630 9.46 2.28 29.53 2.29
2207 2378 8.706492 TGTATTAACCGGAAACTTAGTACATG 57.294 34.615 9.46 0.00 0.00 3.21
2208 2379 8.313292 TGTATTAACCGGAAACTTAGTACATGT 58.687 33.333 9.46 2.69 0.00 3.21
2209 2380 7.605410 ATTAACCGGAAACTTAGTACATGTG 57.395 36.000 9.46 0.00 0.00 3.21
2210 2381 4.612264 ACCGGAAACTTAGTACATGTGT 57.388 40.909 9.46 0.00 0.00 3.72
2211 2382 4.312443 ACCGGAAACTTAGTACATGTGTG 58.688 43.478 9.46 0.00 0.00 3.82
2212 2383 4.039488 ACCGGAAACTTAGTACATGTGTGA 59.961 41.667 9.46 0.00 0.00 3.58
2213 2384 4.992319 CCGGAAACTTAGTACATGTGTGAA 59.008 41.667 9.11 0.00 0.00 3.18
2214 2385 5.642063 CCGGAAACTTAGTACATGTGTGAAT 59.358 40.000 9.11 0.00 0.00 2.57
2215 2386 6.814644 CCGGAAACTTAGTACATGTGTGAATA 59.185 38.462 9.11 0.00 0.00 1.75
2216 2387 7.201496 CCGGAAACTTAGTACATGTGTGAATAC 60.201 40.741 9.11 0.00 0.00 1.89
2217 2388 7.329962 CGGAAACTTAGTACATGTGTGAATACA 59.670 37.037 9.11 0.00 34.63 2.29
2218 2389 9.162764 GGAAACTTAGTACATGTGTGAATACAT 57.837 33.333 9.11 0.00 41.77 2.29
2226 2397 9.890629 AGTACATGTGTGAATACATAGACAAAT 57.109 29.630 9.11 0.00 39.17 2.32
2229 2400 9.890629 ACATGTGTGAATACATAGACAAATAGT 57.109 29.630 0.00 0.00 39.17 2.12
2231 2402 9.890629 ATGTGTGAATACATAGACAAATAGTGT 57.109 29.630 0.00 0.00 40.42 3.55
2232 2403 9.150348 TGTGTGAATACATAGACAAATAGTGTG 57.850 33.333 0.00 0.00 38.89 3.82
2233 2404 9.151471 GTGTGAATACATAGACAAATAGTGTGT 57.849 33.333 0.00 0.00 38.89 3.72
2234 2405 9.366216 TGTGAATACATAGACAAATAGTGTGTC 57.634 33.333 0.00 0.00 41.96 3.67
2235 2406 9.366216 GTGAATACATAGACAAATAGTGTGTCA 57.634 33.333 7.26 0.00 46.44 3.58
2236 2407 9.366216 TGAATACATAGACAAATAGTGTGTCAC 57.634 33.333 7.26 0.00 46.44 3.67
2237 2408 9.587772 GAATACATAGACAAATAGTGTGTCACT 57.412 33.333 4.27 7.54 46.44 3.41
2248 2419 3.702792 AGTGTGTCACTAGTATGCCTCT 58.297 45.455 4.27 0.00 43.46 3.69
2249 2420 4.856509 AGTGTGTCACTAGTATGCCTCTA 58.143 43.478 4.27 0.00 43.46 2.43
2250 2421 4.641094 AGTGTGTCACTAGTATGCCTCTAC 59.359 45.833 4.27 0.00 43.46 2.59
2251 2422 4.641094 GTGTGTCACTAGTATGCCTCTACT 59.359 45.833 4.27 0.00 36.04 2.57
2252 2423 5.125739 GTGTGTCACTAGTATGCCTCTACTT 59.874 44.000 4.27 0.00 33.96 2.24
2253 2424 6.318144 GTGTGTCACTAGTATGCCTCTACTTA 59.682 42.308 4.27 0.00 33.96 2.24
2254 2425 6.888088 TGTGTCACTAGTATGCCTCTACTTAA 59.112 38.462 4.27 0.00 33.96 1.85
2255 2426 7.148120 TGTGTCACTAGTATGCCTCTACTTAAC 60.148 40.741 4.27 0.00 33.96 2.01
2256 2427 7.067251 GTGTCACTAGTATGCCTCTACTTAACT 59.933 40.741 0.00 0.00 33.96 2.24
2257 2428 8.270030 TGTCACTAGTATGCCTCTACTTAACTA 58.730 37.037 0.00 0.00 33.96 2.24
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
73 74 7.375053 AGTCAAGCTTTGTAAACTTTGACAAA 58.625 30.769 20.02 0.00 41.90 2.83
74 75 6.919721 AGTCAAGCTTTGTAAACTTTGACAA 58.080 32.000 20.02 0.88 33.81 3.18
75 76 6.509418 AGTCAAGCTTTGTAAACTTTGACA 57.491 33.333 20.02 0.00 30.59 3.58
76 77 7.812309 AAAGTCAAGCTTTGTAAACTTTGAC 57.188 32.000 14.76 14.88 45.00 3.18
88 89 7.568199 TTAGCTTTAGTCAAAGTCAAGCTTT 57.432 32.000 9.81 0.00 46.35 3.51
89 90 7.751768 ATTAGCTTTAGTCAAAGTCAAGCTT 57.248 32.000 9.81 0.00 46.35 3.74
91 92 7.174082 CGTATTAGCTTTAGTCAAAGTCAAGC 58.826 38.462 0.00 0.00 42.71 4.01
92 93 7.174082 GCGTATTAGCTTTAGTCAAAGTCAAG 58.826 38.462 0.00 0.00 42.71 3.02
93 94 6.183360 CGCGTATTAGCTTTAGTCAAAGTCAA 60.183 38.462 0.00 0.00 42.71 3.18
94 95 5.287752 CGCGTATTAGCTTTAGTCAAAGTCA 59.712 40.000 0.00 0.00 42.71 3.41
95 96 5.276254 CCGCGTATTAGCTTTAGTCAAAGTC 60.276 44.000 4.92 0.00 42.71 3.01
96 97 4.565564 CCGCGTATTAGCTTTAGTCAAAGT 59.434 41.667 4.92 0.00 42.71 2.66
97 98 4.802039 TCCGCGTATTAGCTTTAGTCAAAG 59.198 41.667 4.92 0.00 43.46 2.77
98 99 4.563976 GTCCGCGTATTAGCTTTAGTCAAA 59.436 41.667 4.92 0.00 34.40 2.69
99 100 4.107622 GTCCGCGTATTAGCTTTAGTCAA 58.892 43.478 4.92 0.00 34.40 3.18
100 101 3.379372 AGTCCGCGTATTAGCTTTAGTCA 59.621 43.478 4.92 0.00 34.40 3.41
101 102 3.962423 AGTCCGCGTATTAGCTTTAGTC 58.038 45.455 4.92 0.00 34.40 2.59
102 103 5.505173 TTAGTCCGCGTATTAGCTTTAGT 57.495 39.130 4.92 0.00 34.40 2.24
103 104 8.511465 TTATTTAGTCCGCGTATTAGCTTTAG 57.489 34.615 4.92 0.00 34.40 1.85
104 105 8.870160 TTTATTTAGTCCGCGTATTAGCTTTA 57.130 30.769 4.92 0.00 34.40 1.85
105 106 7.775397 TTTATTTAGTCCGCGTATTAGCTTT 57.225 32.000 4.92 0.00 34.40 3.51
106 107 7.775397 TTTTATTTAGTCCGCGTATTAGCTT 57.225 32.000 4.92 0.00 34.40 3.74
107 108 7.515684 CGTTTTTATTTAGTCCGCGTATTAGCT 60.516 37.037 4.92 0.00 34.40 3.32
108 109 6.567512 CGTTTTTATTTAGTCCGCGTATTAGC 59.432 38.462 4.92 0.00 0.00 3.09
109 110 7.043458 TCCGTTTTTATTTAGTCCGCGTATTAG 60.043 37.037 4.92 0.00 0.00 1.73
110 111 6.754209 TCCGTTTTTATTTAGTCCGCGTATTA 59.246 34.615 4.92 0.00 0.00 0.98
111 112 5.580297 TCCGTTTTTATTTAGTCCGCGTATT 59.420 36.000 4.92 0.00 0.00 1.89
112 113 5.108517 TCCGTTTTTATTTAGTCCGCGTAT 58.891 37.500 4.92 0.00 0.00 3.06
113 114 4.489810 TCCGTTTTTATTTAGTCCGCGTA 58.510 39.130 4.92 0.00 0.00 4.42
114 115 3.324993 TCCGTTTTTATTTAGTCCGCGT 58.675 40.909 4.92 0.00 0.00 6.01
115 116 3.242188 CCTCCGTTTTTATTTAGTCCGCG 60.242 47.826 0.00 0.00 0.00 6.46
116 117 3.064408 CCCTCCGTTTTTATTTAGTCCGC 59.936 47.826 0.00 0.00 0.00 5.54
117 118 4.506758 TCCCTCCGTTTTTATTTAGTCCG 58.493 43.478 0.00 0.00 0.00 4.79
118 119 5.494724 ACTCCCTCCGTTTTTATTTAGTCC 58.505 41.667 0.00 0.00 0.00 3.85
119 120 7.767659 ACATACTCCCTCCGTTTTTATTTAGTC 59.232 37.037 0.00 0.00 0.00 2.59
120 121 7.627311 ACATACTCCCTCCGTTTTTATTTAGT 58.373 34.615 0.00 0.00 0.00 2.24
121 122 7.042925 CGACATACTCCCTCCGTTTTTATTTAG 60.043 40.741 0.00 0.00 0.00 1.85
122 123 6.757947 CGACATACTCCCTCCGTTTTTATTTA 59.242 38.462 0.00 0.00 0.00 1.40
123 124 5.583457 CGACATACTCCCTCCGTTTTTATTT 59.417 40.000 0.00 0.00 0.00 1.40
124 125 5.114081 CGACATACTCCCTCCGTTTTTATT 58.886 41.667 0.00 0.00 0.00 1.40
125 126 4.690122 CGACATACTCCCTCCGTTTTTAT 58.310 43.478 0.00 0.00 0.00 1.40
126 127 3.676873 GCGACATACTCCCTCCGTTTTTA 60.677 47.826 0.00 0.00 0.00 1.52
127 128 2.933928 GCGACATACTCCCTCCGTTTTT 60.934 50.000 0.00 0.00 0.00 1.94
128 129 1.405121 GCGACATACTCCCTCCGTTTT 60.405 52.381 0.00 0.00 0.00 2.43
129 130 0.175073 GCGACATACTCCCTCCGTTT 59.825 55.000 0.00 0.00 0.00 3.60
130 131 0.683504 AGCGACATACTCCCTCCGTT 60.684 55.000 0.00 0.00 0.00 4.44
131 132 1.076923 AGCGACATACTCCCTCCGT 60.077 57.895 0.00 0.00 0.00 4.69
132 133 1.360551 CAGCGACATACTCCCTCCG 59.639 63.158 0.00 0.00 0.00 4.63
133 134 1.043673 ACCAGCGACATACTCCCTCC 61.044 60.000 0.00 0.00 0.00 4.30
134 135 0.103208 CACCAGCGACATACTCCCTC 59.897 60.000 0.00 0.00 0.00 4.30
135 136 0.324368 TCACCAGCGACATACTCCCT 60.324 55.000 0.00 0.00 0.00 4.20
136 137 0.535335 TTCACCAGCGACATACTCCC 59.465 55.000 0.00 0.00 0.00 4.30
137 138 1.471676 CCTTCACCAGCGACATACTCC 60.472 57.143 0.00 0.00 0.00 3.85
138 139 1.476891 TCCTTCACCAGCGACATACTC 59.523 52.381 0.00 0.00 0.00 2.59
139 140 1.478510 CTCCTTCACCAGCGACATACT 59.521 52.381 0.00 0.00 0.00 2.12
217 218 0.174845 CGGCTATCTCCACGGAAACA 59.825 55.000 0.00 0.00 0.00 2.83
366 367 1.901085 GTCTGAAGTGAGGGCCGAT 59.099 57.895 0.00 0.00 0.00 4.18
405 537 2.565645 CCCCCATACCTCGCTCGAG 61.566 68.421 8.45 8.45 41.63 4.04
428 560 3.350612 GGGCAGCGTTGTTGCGTA 61.351 61.111 0.00 0.00 40.59 4.42
459 591 4.210331 ACATTAGAATGATGAACCAGCCC 58.790 43.478 9.21 0.00 39.67 5.19
523 656 7.629027 GTACTAGCGTACAAGTTAACAAGTT 57.371 36.000 8.61 0.00 44.29 2.66
591 724 5.133221 GGTAGGTAGACAATTGGCATCAAT 58.867 41.667 15.18 0.00 44.77 2.57
603 736 6.182507 AGAAACACATTTGGTAGGTAGACA 57.817 37.500 0.00 0.00 0.00 3.41
697 831 3.182972 GCATGCATTCGATTGGCATTAAC 59.817 43.478 14.21 5.95 45.34 2.01
763 897 8.821817 TCTATAGAGCACTCTAGATCTGTGTAT 58.178 37.037 12.61 2.71 44.47 2.29
796 930 9.425577 TGTATCTGATGAACATTAACGTGTAAA 57.574 29.630 0.00 0.00 0.00 2.01
882 1017 3.031736 AGTCCCGTATGCATGTCTACTT 58.968 45.455 10.16 0.00 0.00 2.24
887 1022 7.817962 ACTAATTTATAGTCCCGTATGCATGTC 59.182 37.037 10.16 1.37 0.00 3.06
889 1024 9.084164 GTACTAATTTATAGTCCCGTATGCATG 57.916 37.037 10.16 0.00 0.00 4.06
890 1025 8.809066 TGTACTAATTTATAGTCCCGTATGCAT 58.191 33.333 3.79 3.79 0.00 3.96
891 1026 8.180706 TGTACTAATTTATAGTCCCGTATGCA 57.819 34.615 0.00 0.00 0.00 3.96
892 1027 7.758528 CCTGTACTAATTTATAGTCCCGTATGC 59.241 40.741 0.00 0.00 0.00 3.14
918 1053 4.623932 TCTGGTATGGGCTCACATTATC 57.376 45.455 0.00 0.00 32.39 1.75
1041 1184 1.370900 GGTTTGAAGCAGCAGCACG 60.371 57.895 3.17 0.00 45.49 5.34
1110 1253 1.912763 TTGGCAATCCACCAAGCCC 60.913 57.895 0.00 0.00 46.45 5.19
1155 1298 1.559149 GCCATGTTTGCTTGTTGCCG 61.559 55.000 0.00 0.00 42.00 5.69
1225 1368 3.408229 CCATCTCTGGGTGCACCT 58.592 61.111 33.91 11.78 39.04 4.00
1371 1516 7.360113 TGATACATGATCTAGCCTTACAACA 57.640 36.000 0.00 0.00 35.37 3.33
1443 1588 5.509605 AGTTTGTTTCGTTGTTGCTTTTC 57.490 34.783 0.00 0.00 0.00 2.29
1498 1644 3.858135 AGGGATCGGCTTTATAAGAGGA 58.142 45.455 0.00 0.00 0.00 3.71
1506 1652 5.962433 CGATTATTCTAGGGATCGGCTTTA 58.038 41.667 8.88 0.00 38.11 1.85
1582 1728 2.516923 CTTAGAGTGGCGTTGTACTCG 58.483 52.381 0.00 0.40 46.05 4.18
1601 1748 3.515502 TGGAGCTTAGATGTGTTAGTGCT 59.484 43.478 0.00 0.00 0.00 4.40
1706 1854 0.606604 GGTGCTCCTTTCCGTGTCTA 59.393 55.000 0.00 0.00 0.00 2.59
1885 2044 4.057428 GTGGCTCGGACGCACTCT 62.057 66.667 0.00 0.00 0.00 3.24
2057 2228 0.840617 TCCTTACTGTGGTTGGTGCA 59.159 50.000 0.00 0.00 0.00 4.57
2108 2279 7.881775 AACAACTTTATTATTGCCTCTAGGG 57.118 36.000 0.00 0.00 35.18 3.53
2166 2337 8.773645 CGGTTAATACAATTCTAGCATGAATGA 58.226 33.333 0.00 0.00 36.84 2.57
2167 2338 8.017373 CCGGTTAATACAATTCTAGCATGAATG 58.983 37.037 0.00 3.53 36.84 2.67
2168 2339 7.936847 TCCGGTTAATACAATTCTAGCATGAAT 59.063 33.333 0.00 0.00 38.19 2.57
2169 2340 7.276658 TCCGGTTAATACAATTCTAGCATGAA 58.723 34.615 0.00 0.00 0.00 2.57
2170 2341 6.822442 TCCGGTTAATACAATTCTAGCATGA 58.178 36.000 0.00 0.00 0.00 3.07
2171 2342 7.490962 TTCCGGTTAATACAATTCTAGCATG 57.509 36.000 0.00 0.00 0.00 4.06
2172 2343 7.773690 AGTTTCCGGTTAATACAATTCTAGCAT 59.226 33.333 0.00 0.00 0.00 3.79
2173 2344 7.107542 AGTTTCCGGTTAATACAATTCTAGCA 58.892 34.615 0.00 0.00 0.00 3.49
2174 2345 7.549615 AGTTTCCGGTTAATACAATTCTAGC 57.450 36.000 0.00 0.00 0.00 3.42
2179 2350 9.723601 TGTACTAAGTTTCCGGTTAATACAATT 57.276 29.630 0.00 0.00 0.00 2.32
2180 2351 9.895138 ATGTACTAAGTTTCCGGTTAATACAAT 57.105 29.630 0.00 0.00 28.05 2.71
2181 2352 9.153721 CATGTACTAAGTTTCCGGTTAATACAA 57.846 33.333 0.00 0.00 28.05 2.41
2182 2353 8.313292 ACATGTACTAAGTTTCCGGTTAATACA 58.687 33.333 0.00 3.81 28.60 2.29
2183 2354 8.598075 CACATGTACTAAGTTTCCGGTTAATAC 58.402 37.037 0.00 0.00 0.00 1.89
2184 2355 8.313292 ACACATGTACTAAGTTTCCGGTTAATA 58.687 33.333 0.00 0.00 0.00 0.98
2185 2356 7.118680 CACACATGTACTAAGTTTCCGGTTAAT 59.881 37.037 0.00 0.00 0.00 1.40
2186 2357 6.424509 CACACATGTACTAAGTTTCCGGTTAA 59.575 38.462 0.00 0.00 0.00 2.01
2187 2358 5.927689 CACACATGTACTAAGTTTCCGGTTA 59.072 40.000 0.00 0.00 0.00 2.85
2188 2359 4.753107 CACACATGTACTAAGTTTCCGGTT 59.247 41.667 0.00 0.00 0.00 4.44
2189 2360 4.039488 TCACACATGTACTAAGTTTCCGGT 59.961 41.667 0.00 0.00 0.00 5.28
2190 2361 4.562082 TCACACATGTACTAAGTTTCCGG 58.438 43.478 0.00 0.00 0.00 5.14
2191 2362 6.721571 ATTCACACATGTACTAAGTTTCCG 57.278 37.500 0.00 0.00 0.00 4.30
2192 2363 8.542497 TGTATTCACACATGTACTAAGTTTCC 57.458 34.615 0.00 0.00 0.00 3.13
2200 2371 9.890629 ATTTGTCTATGTATTCACACATGTACT 57.109 29.630 0.00 0.00 39.46 2.73
2203 2374 9.890629 ACTATTTGTCTATGTATTCACACATGT 57.109 29.630 0.00 0.00 39.46 3.21
2205 2376 9.890629 ACACTATTTGTCTATGTATTCACACAT 57.109 29.630 0.00 0.00 37.06 3.21
2206 2377 9.150348 CACACTATTTGTCTATGTATTCACACA 57.850 33.333 0.00 0.00 34.83 3.72
2207 2378 9.151471 ACACACTATTTGTCTATGTATTCACAC 57.849 33.333 0.00 0.00 34.83 3.82
2208 2379 9.366216 GACACACTATTTGTCTATGTATTCACA 57.634 33.333 0.00 0.00 40.30 3.58
2209 2380 9.366216 TGACACACTATTTGTCTATGTATTCAC 57.634 33.333 4.27 0.00 43.30 3.18
2210 2381 9.366216 GTGACACACTATTTGTCTATGTATTCA 57.634 33.333 0.00 0.00 43.30 2.57
2211 2382 9.587772 AGTGACACACTATTTGTCTATGTATTC 57.412 33.333 8.59 0.00 43.46 1.75
2214 2385 9.239551 ACTAGTGACACACTATTTGTCTATGTA 57.760 33.333 8.59 0.00 44.49 2.29
2215 2386 8.123639 ACTAGTGACACACTATTTGTCTATGT 57.876 34.615 8.59 1.84 44.49 2.29
2218 2389 8.188799 GCATACTAGTGACACACTATTTGTCTA 58.811 37.037 5.39 0.00 44.49 2.59
2219 2390 7.036220 GCATACTAGTGACACACTATTTGTCT 58.964 38.462 5.39 0.00 44.49 3.41
2220 2391 6.255887 GGCATACTAGTGACACACTATTTGTC 59.744 42.308 5.39 7.88 44.49 3.18
2221 2392 6.070767 AGGCATACTAGTGACACACTATTTGT 60.071 38.462 5.39 8.96 44.49 2.83
2222 2393 6.341316 AGGCATACTAGTGACACACTATTTG 58.659 40.000 5.39 10.15 44.49 2.32
2223 2394 6.381420 AGAGGCATACTAGTGACACACTATTT 59.619 38.462 5.39 5.59 44.49 1.40
2224 2395 5.894393 AGAGGCATACTAGTGACACACTATT 59.106 40.000 5.39 8.91 44.49 1.73
2225 2396 5.450453 AGAGGCATACTAGTGACACACTAT 58.550 41.667 5.39 5.87 44.49 2.12
2226 2397 4.856509 AGAGGCATACTAGTGACACACTA 58.143 43.478 5.39 10.49 43.46 2.74
2228 2399 4.641094 AGTAGAGGCATACTAGTGACACAC 59.359 45.833 5.39 0.00 34.21 3.82
2229 2400 4.856509 AGTAGAGGCATACTAGTGACACA 58.143 43.478 5.39 0.00 34.21 3.72
2230 2401 5.838531 AAGTAGAGGCATACTAGTGACAC 57.161 43.478 5.39 0.00 34.90 3.67
2231 2402 7.117397 AGTTAAGTAGAGGCATACTAGTGACA 58.883 38.462 5.39 0.00 34.90 3.58
2232 2403 7.571080 AGTTAAGTAGAGGCATACTAGTGAC 57.429 40.000 5.39 0.00 34.90 3.67


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

AutoCloner maintained by Alex Coulton.