Multiple sequence alignment - TraesCS1B01G404100

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 TraesCS1B01G404100 chr1B 100.000 2797 0 0 1 2797 633322055 633319259 0.000000e+00 5166.0
1 TraesCS1B01G404100 chr1D 92.808 2030 95 16 1 2026 461118668 461116686 0.000000e+00 2892.0
2 TraesCS1B01G404100 chr1D 79.581 382 61 14 197 572 482216737 482216367 9.940000e-65 257.0
3 TraesCS1B01G404100 chr1D 81.395 258 40 8 117 369 371219977 371220231 1.310000e-48 204.0
4 TraesCS1B01G404100 chr1D 86.585 82 9 2 414 494 461118701 461118621 3.840000e-14 89.8
5 TraesCS1B01G404100 chr1D 92.453 53 3 1 117 168 461118871 461118819 1.070000e-09 75.0
6 TraesCS1B01G404100 chr1A 93.639 1682 76 18 1120 2797 552182002 552180348 0.000000e+00 2484.0
7 TraesCS1B01G404100 chr1A 93.414 1078 68 2 1 1078 552203504 552202430 0.000000e+00 1594.0
8 TraesCS1B01G404100 chr1A 92.177 997 61 9 82 1076 552182989 552182008 0.000000e+00 1393.0
9 TraesCS1B01G404100 chr1A 94.708 718 27 4 1118 1834 552202430 552201723 0.000000e+00 1105.0
10 TraesCS1B01G404100 chr1A 76.724 232 36 14 313 542 552203630 552203415 2.280000e-21 113.0
11 TraesCS1B01G404100 chr1A 89.583 48 4 1 126 172 552203709 552203662 3.010000e-05 60.2
12 TraesCS1B01G404100 chr5B 82.927 246 33 7 138 381 692280627 692280865 2.180000e-51 213.0
13 TraesCS1B01G404100 chr3D 76.733 404 78 16 138 534 554389961 554390355 7.850000e-51 211.0
14 TraesCS1B01G404100 chr4D 79.375 320 43 19 249 560 69125746 69125442 1.310000e-48 204.0
15 TraesCS1B01G404100 chr2A 80.377 265 42 9 123 381 680101605 680101865 2.840000e-45 193.0
16 TraesCS1B01G404100 chr4A 75.106 470 84 23 121 578 615224343 615224791 3.680000e-44 189.0


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 TraesCS1B01G404100 chr1B 633319259 633322055 2796 True 5166.000000 5166 100.000000 1 2797 1 chr1B.!!$R1 2796
1 TraesCS1B01G404100 chr1D 461116686 461118871 2185 True 1018.933333 2892 90.615333 1 2026 3 chr1D.!!$R2 2025
2 TraesCS1B01G404100 chr1A 552180348 552182989 2641 True 1938.500000 2484 92.908000 82 2797 2 chr1A.!!$R1 2715
3 TraesCS1B01G404100 chr1A 552201723 552203709 1986 True 718.050000 1594 88.607250 1 1834 4 chr1A.!!$R2 1833

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
113 329 0.824759 CGGACCTACTAGGCAAGCTT 59.175 55.0 1.55 0.0 39.63 3.74 F
1086 1304 0.478507 CTCTCTCTCTCCCTCCCTCC 59.521 65.0 0.00 0.0 0.00 4.30 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1720 1941 0.179004 TTCCTTGTTGCCCATCGTGT 60.179 50.0 0.0 0.0 0.00 4.49 R
2297 2518 0.592247 CGCCGCAGCAATTAATCCAC 60.592 55.0 0.0 0.0 39.83 4.02 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
57 273 6.894339 AAAGTCAATAGAAATTTCGGTGGT 57.106 33.333 12.42 0.00 0.00 4.16
58 274 7.989416 AAAGTCAATAGAAATTTCGGTGGTA 57.011 32.000 12.42 0.00 0.00 3.25
59 275 8.575649 AAAGTCAATAGAAATTTCGGTGGTAT 57.424 30.769 12.42 2.27 0.00 2.73
60 276 7.553881 AGTCAATAGAAATTTCGGTGGTATG 57.446 36.000 12.42 6.66 0.00 2.39
61 277 6.542370 AGTCAATAGAAATTTCGGTGGTATGG 59.458 38.462 12.42 3.06 0.00 2.74
113 329 0.824759 CGGACCTACTAGGCAAGCTT 59.175 55.000 1.55 0.00 39.63 3.74
115 331 2.223758 CGGACCTACTAGGCAAGCTTAC 60.224 54.545 0.00 0.00 39.63 2.34
235 451 7.452880 AAGAATTGATTTGATCCGAGTTTGA 57.547 32.000 0.00 0.00 0.00 2.69
238 454 7.972277 AGAATTGATTTGATCCGAGTTTGAATG 59.028 33.333 0.00 0.00 0.00 2.67
244 460 3.118629 TGATCCGAGTTTGAATGGGAGAG 60.119 47.826 0.00 0.00 0.00 3.20
248 464 2.028112 CGAGTTTGAATGGGAGAGGACA 60.028 50.000 0.00 0.00 0.00 4.02
311 527 5.878484 TCTGATATGGGTATGGGTAGAGA 57.122 43.478 0.00 0.00 0.00 3.10
327 543 5.247084 GGTAGAGAAAGGGAAGGAAAGTTC 58.753 45.833 0.00 0.00 0.00 3.01
351 567 9.801873 TTCTGTTTTAGTTGAGATTTTGGAAAG 57.198 29.630 0.00 0.00 0.00 2.62
395 611 7.809331 TGAGTTAATGCAATGTCTGAATTTGAC 59.191 33.333 0.00 5.82 34.79 3.18
404 620 8.223100 GCAATGTCTGAATTTGACAAAAATACC 58.777 33.333 15.75 0.00 45.82 2.73
505 723 8.722480 AAAAATCAAAGAAAACCAAGAAGAGG 57.278 30.769 0.00 0.00 0.00 3.69
515 733 0.891373 CAAGAAGAGGAGGAGCGTGA 59.109 55.000 0.00 0.00 0.00 4.35
550 768 4.450053 CAGGAAGGATGTGAAGAGAATCC 58.550 47.826 0.00 0.00 40.24 3.01
634 852 7.961326 AACTGGCTTGTTAATCTTTGGATAT 57.039 32.000 0.00 0.00 0.00 1.63
709 927 9.394767 TGTCACTAGTTGCATGTCAAATATATT 57.605 29.630 9.38 0.00 35.09 1.28
949 1167 9.632638 AATATTATATATACCAAGGCCAGCAAG 57.367 33.333 5.01 0.00 0.00 4.01
959 1177 1.075659 GCCAGCAAGAGGTTTCCCT 59.924 57.895 0.00 0.00 46.66 4.20
984 1202 5.409712 AGATCAGATCCTCATTCCATACCA 58.590 41.667 6.80 0.00 0.00 3.25
1024 1242 1.487452 TTGTGTCGCACGCACTCTTC 61.487 55.000 15.06 0.00 38.47 2.87
1060 1278 4.332543 TGCTTGCATTATTCTTCGTGGTAG 59.667 41.667 0.00 0.00 0.00 3.18
1078 1296 3.244249 GGTAGCTCTCTCTCTCTCTCTCC 60.244 56.522 0.00 0.00 0.00 3.71
1082 1300 2.370189 CTCTCTCTCTCTCTCTCCCTCC 59.630 59.091 0.00 0.00 0.00 4.30
1086 1304 0.478507 CTCTCTCTCTCCCTCCCTCC 59.521 65.000 0.00 0.00 0.00 4.30
1088 1306 0.998945 CTCTCTCTCCCTCCCTCCCT 60.999 65.000 0.00 0.00 0.00 4.20
1089 1307 0.996762 TCTCTCTCCCTCCCTCCCTC 60.997 65.000 0.00 0.00 0.00 4.30
1090 1308 0.998945 CTCTCTCCCTCCCTCCCTCT 60.999 65.000 0.00 0.00 0.00 3.69
1091 1309 0.996762 TCTCTCCCTCCCTCCCTCTC 60.997 65.000 0.00 0.00 0.00 3.20
1092 1310 0.998945 CTCTCCCTCCCTCCCTCTCT 60.999 65.000 0.00 0.00 0.00 3.10
1093 1311 0.996762 TCTCCCTCCCTCCCTCTCTC 60.997 65.000 0.00 0.00 0.00 3.20
1094 1312 0.998945 CTCCCTCCCTCCCTCTCTCT 60.999 65.000 0.00 0.00 0.00 3.10
1095 1313 0.996762 TCCCTCCCTCCCTCTCTCTC 60.997 65.000 0.00 0.00 0.00 3.20
1096 1314 0.998945 CCCTCCCTCCCTCTCTCTCT 60.999 65.000 0.00 0.00 0.00 3.10
1097 1315 0.478507 CCTCCCTCCCTCTCTCTCTC 59.521 65.000 0.00 0.00 0.00 3.20
1098 1316 1.522900 CTCCCTCCCTCTCTCTCTCT 58.477 60.000 0.00 0.00 0.00 3.10
1099 1317 1.421646 CTCCCTCCCTCTCTCTCTCTC 59.578 61.905 0.00 0.00 0.00 3.20
1100 1318 1.010793 TCCCTCCCTCTCTCTCTCTCT 59.989 57.143 0.00 0.00 0.00 3.10
1101 1319 1.421646 CCCTCCCTCTCTCTCTCTCTC 59.578 61.905 0.00 0.00 0.00 3.20
1102 1320 2.412591 CCTCCCTCTCTCTCTCTCTCT 58.587 57.143 0.00 0.00 0.00 3.10
1103 1321 2.370189 CCTCCCTCTCTCTCTCTCTCTC 59.630 59.091 0.00 0.00 0.00 3.20
1104 1322 3.041211 CTCCCTCTCTCTCTCTCTCTCA 58.959 54.545 0.00 0.00 0.00 3.27
1105 1323 2.771943 TCCCTCTCTCTCTCTCTCTCAC 59.228 54.545 0.00 0.00 0.00 3.51
1106 1324 2.505407 CCCTCTCTCTCTCTCTCTCACA 59.495 54.545 0.00 0.00 0.00 3.58
1107 1325 3.535561 CCTCTCTCTCTCTCTCTCACAC 58.464 54.545 0.00 0.00 0.00 3.82
1108 1326 3.055167 CCTCTCTCTCTCTCTCTCACACA 60.055 52.174 0.00 0.00 0.00 3.72
1109 1327 3.935203 CTCTCTCTCTCTCTCTCACACAC 59.065 52.174 0.00 0.00 0.00 3.82
1110 1328 3.326297 TCTCTCTCTCTCTCTCACACACA 59.674 47.826 0.00 0.00 0.00 3.72
1111 1329 3.407698 TCTCTCTCTCTCTCACACACAC 58.592 50.000 0.00 0.00 0.00 3.82
1112 1330 3.145286 CTCTCTCTCTCTCACACACACA 58.855 50.000 0.00 0.00 0.00 3.72
1113 1331 2.881513 TCTCTCTCTCTCACACACACAC 59.118 50.000 0.00 0.00 0.00 3.82
1114 1332 2.620585 CTCTCTCTCTCACACACACACA 59.379 50.000 0.00 0.00 0.00 3.72
1115 1333 2.359214 TCTCTCTCTCACACACACACAC 59.641 50.000 0.00 0.00 0.00 3.82
1116 1334 2.099405 TCTCTCTCACACACACACACA 58.901 47.619 0.00 0.00 0.00 3.72
1168 1386 6.343716 TGTTTAACCATGAGTTGCAATCAT 57.656 33.333 0.59 10.17 39.67 2.45
1429 1649 4.122046 TCTAAGTCCATGCATGTCAATCG 58.878 43.478 24.58 8.85 0.00 3.34
1502 1722 5.441718 ACATGAGCATTCTAGGAGGAAAA 57.558 39.130 0.00 0.00 0.00 2.29
1651 1872 2.621338 CAAGATCCGTTGCTCAGCTAA 58.379 47.619 0.00 0.00 0.00 3.09
1720 1941 2.732016 CCTGTGTGTTCCGTCCGA 59.268 61.111 0.00 0.00 0.00 4.55
1742 1963 1.089920 CGATGGGCAACAAGGAAGAG 58.910 55.000 0.00 0.00 39.74 2.85
1761 1982 1.153147 TGCCCGTGCTACAACAACA 60.153 52.632 0.00 0.00 38.71 3.33
1805 2026 0.921896 AGTGCCCCTGATATGCTTGT 59.078 50.000 0.00 0.00 0.00 3.16
1826 2047 2.203280 CCGTGTGTGGCCTCCAAA 60.203 61.111 3.32 0.00 34.18 3.28
2006 2227 1.818060 GCCATACTTTGCCACACATCA 59.182 47.619 0.00 0.00 0.00 3.07
2038 2259 2.438021 TCTGGCAAGTTAGGTCACTGTT 59.562 45.455 0.00 0.00 0.00 3.16
2068 2289 2.675348 GCCACAGCATAGTCAAGTTCTC 59.325 50.000 0.00 0.00 39.53 2.87
2069 2290 3.618507 GCCACAGCATAGTCAAGTTCTCT 60.619 47.826 0.00 0.00 39.53 3.10
2070 2291 4.573900 CCACAGCATAGTCAAGTTCTCTT 58.426 43.478 0.00 0.00 0.00 2.85
2071 2292 4.999950 CCACAGCATAGTCAAGTTCTCTTT 59.000 41.667 0.00 0.00 0.00 2.52
2072 2293 5.121454 CCACAGCATAGTCAAGTTCTCTTTC 59.879 44.000 0.00 0.00 0.00 2.62
2073 2294 5.931146 CACAGCATAGTCAAGTTCTCTTTCT 59.069 40.000 0.00 0.00 0.00 2.52
2074 2295 6.426328 CACAGCATAGTCAAGTTCTCTTTCTT 59.574 38.462 0.00 0.00 0.00 2.52
2075 2296 6.995091 ACAGCATAGTCAAGTTCTCTTTCTTT 59.005 34.615 0.00 0.00 0.00 2.52
2076 2297 7.172361 ACAGCATAGTCAAGTTCTCTTTCTTTC 59.828 37.037 0.00 0.00 0.00 2.62
2106 2327 3.569250 TTCTTTGGACAAATAAGCGCC 57.431 42.857 2.29 0.00 0.00 6.53
2113 2334 3.951037 TGGACAAATAAGCGCCATATGTT 59.049 39.130 2.29 0.00 0.00 2.71
2114 2335 4.400884 TGGACAAATAAGCGCCATATGTTT 59.599 37.500 2.29 0.00 0.00 2.83
2115 2336 5.590663 TGGACAAATAAGCGCCATATGTTTA 59.409 36.000 2.29 0.00 0.00 2.01
2116 2337 6.264292 TGGACAAATAAGCGCCATATGTTTAT 59.736 34.615 2.29 0.00 0.00 1.40
2117 2338 7.445707 TGGACAAATAAGCGCCATATGTTTATA 59.554 33.333 2.29 0.00 0.00 0.98
2118 2339 7.749126 GGACAAATAAGCGCCATATGTTTATAC 59.251 37.037 2.29 0.00 0.00 1.47
2119 2340 8.391075 ACAAATAAGCGCCATATGTTTATACT 57.609 30.769 2.29 0.00 0.00 2.12
2162 2383 8.564574 CATATGGCCATATGTACTTAAAACGTT 58.435 33.333 40.41 15.80 43.40 3.99
2177 2398 9.027129 ACTTAAAACGTTTAAGAGGCAAATTTC 57.973 29.630 24.33 0.00 36.23 2.17
2178 2399 8.928270 TTAAAACGTTTAAGAGGCAAATTTCA 57.072 26.923 15.03 0.00 0.00 2.69
2251 2472 1.522302 TAGCGCCTTTGCATTGCACA 61.522 50.000 11.66 3.74 38.71 4.57
2252 2473 1.955157 GCGCCTTTGCATTGCACAA 60.955 52.632 11.66 8.24 38.71 3.33
2297 2518 3.274288 GAAGGCATACTGAAACAGAGGG 58.726 50.000 5.76 0.00 35.18 4.30
2309 2532 4.462483 TGAAACAGAGGGTGGATTAATTGC 59.538 41.667 0.00 0.00 0.00 3.56
2313 2536 1.334869 GAGGGTGGATTAATTGCTGCG 59.665 52.381 0.00 0.00 0.00 5.18
2333 2556 2.407210 GCGGGTGTGTGTGTGTTG 59.593 61.111 0.00 0.00 0.00 3.33
2334 2557 2.403378 GCGGGTGTGTGTGTGTTGT 61.403 57.895 0.00 0.00 0.00 3.32
2335 2558 1.719117 CGGGTGTGTGTGTGTTGTC 59.281 57.895 0.00 0.00 0.00 3.18
2336 2559 1.719117 GGGTGTGTGTGTGTTGTCG 59.281 57.895 0.00 0.00 0.00 4.35
2337 2560 1.061887 GGTGTGTGTGTGTTGTCGC 59.938 57.895 0.00 0.00 0.00 5.19
2374 2597 2.028112 GGTGCACCAAGTAGAGACATCA 60.028 50.000 31.23 0.00 35.64 3.07
2411 2634 2.026915 AGTTGACATGCTATGTGCCTCA 60.027 45.455 6.52 0.00 45.03 3.86
2455 2678 1.064654 GGGAAGCATCTGAAATGACGC 59.935 52.381 0.00 0.00 0.00 5.19
2456 2679 2.012673 GGAAGCATCTGAAATGACGCT 58.987 47.619 0.00 0.00 37.06 5.07
2459 2682 4.260538 GGAAGCATCTGAAATGACGCTAAG 60.261 45.833 0.00 0.00 34.21 2.18
2465 2688 6.848296 GCATCTGAAATGACGCTAAGATTTAC 59.152 38.462 0.00 0.00 0.00 2.01
2472 2695 4.539726 TGACGCTAAGATTTACTAGGGGA 58.460 43.478 0.00 0.00 0.00 4.81
2477 2700 6.552350 ACGCTAAGATTTACTAGGGGAATACA 59.448 38.462 0.00 0.00 0.00 2.29
2478 2701 7.234988 ACGCTAAGATTTACTAGGGGAATACAT 59.765 37.037 0.00 0.00 0.00 2.29
2564 2787 7.328737 TCTAGACTTGTATTTAACTTCCTGGC 58.671 38.462 0.00 0.00 0.00 4.85
2567 2790 6.375455 AGACTTGTATTTAACTTCCTGGCATG 59.625 38.462 0.00 0.00 0.00 4.06
2630 2853 3.357823 GTCGTGCACAAAAATTCATCGTC 59.642 43.478 18.64 0.00 0.00 4.20
2638 2861 4.156008 ACAAAAATTCATCGTCTAGGGCAC 59.844 41.667 0.00 0.00 0.00 5.01
2652 2875 4.047834 GCACTTTGGGCCAAAAGC 57.952 55.556 29.40 29.38 40.20 3.51
2653 2876 1.145819 GCACTTTGGGCCAAAAGCA 59.854 52.632 33.62 16.85 46.50 3.91
2654 2877 0.463474 GCACTTTGGGCCAAAAGCAA 60.463 50.000 33.62 16.53 46.50 3.91
2655 2878 1.815021 GCACTTTGGGCCAAAAGCAAT 60.815 47.619 33.62 10.27 46.50 3.56
2656 2879 1.874872 CACTTTGGGCCAAAAGCAATG 59.125 47.619 29.40 17.90 46.50 2.82
2657 2880 0.876399 CTTTGGGCCAAAAGCAATGC 59.124 50.000 30.00 0.00 46.50 3.56
2658 2881 0.182061 TTTGGGCCAAAAGCAATGCA 59.818 45.000 28.69 3.04 46.50 3.96
2669 2892 3.354948 AAGCAATGCACCAGTAGATGA 57.645 42.857 8.35 0.00 0.00 2.92
2708 2932 4.160252 CAGCCCCAAGTGCTACAAATTTAT 59.840 41.667 0.00 0.00 36.81 1.40
2766 2990 2.203437 AGAAACCCAACCGCCACC 60.203 61.111 0.00 0.00 0.00 4.61
2769 2993 4.596585 AACCCAACCGCCACCCTG 62.597 66.667 0.00 0.00 0.00 4.45
2781 3005 1.754201 GCCACCCTGAAACTTCCTTGT 60.754 52.381 0.00 0.00 0.00 3.16
2786 3010 2.437413 CCTGAAACTTCCTTGTAGCCC 58.563 52.381 0.00 0.00 0.00 5.19
2790 3014 0.323957 AACTTCCTTGTAGCCCGACC 59.676 55.000 0.00 0.00 0.00 4.79
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
3 4 3.149981 TCAACCGATGCCACACAAAATA 58.850 40.909 0.00 0.00 0.00 1.40
4 5 1.959985 TCAACCGATGCCACACAAAAT 59.040 42.857 0.00 0.00 0.00 1.82
12 228 3.342377 TTACAATCTCAACCGATGCCA 57.658 42.857 0.00 0.00 0.00 4.92
77 293 2.284995 GCCTCACCTCCTCCCTGT 60.285 66.667 0.00 0.00 0.00 4.00
113 329 0.536233 ATTGCAACACACGGGCAGTA 60.536 50.000 0.00 0.00 38.97 2.74
115 331 1.372004 CATTGCAACACACGGGCAG 60.372 57.895 0.00 0.00 38.97 4.85
235 451 7.508977 TCAAAATTTTACTTGTCCTCTCCCATT 59.491 33.333 2.44 0.00 0.00 3.16
238 454 6.894339 TCAAAATTTTACTTGTCCTCTCCC 57.106 37.500 2.44 0.00 0.00 4.30
311 527 6.895756 ACTAAAACAGAACTTTCCTTCCCTTT 59.104 34.615 0.00 0.00 0.00 3.11
327 543 9.971922 ATCTTTCCAAAATCTCAACTAAAACAG 57.028 29.630 0.00 0.00 0.00 3.16
383 599 8.742554 AATCGGTATTTTTGTCAAATTCAGAC 57.257 30.769 0.00 4.50 36.55 3.51
385 601 8.434661 CCAAATCGGTATTTTTGTCAAATTCAG 58.565 33.333 0.00 0.00 32.87 3.02
439 655 4.462307 CCGCACAAAATAAAAACCAATGC 58.538 39.130 0.00 0.00 0.00 3.56
500 718 0.682855 CTCCTCACGCTCCTCCTCTT 60.683 60.000 0.00 0.00 0.00 2.85
505 723 0.608640 TTTTCCTCCTCACGCTCCTC 59.391 55.000 0.00 0.00 0.00 3.71
537 755 3.244561 GGAGTTGGTGGATTCTCTTCACA 60.245 47.826 0.00 0.00 33.45 3.58
550 768 7.343357 TCTGTATTATTAAAGGGGAGTTGGTG 58.657 38.462 0.00 0.00 0.00 4.17
610 828 7.961326 ATATCCAAAGATTAACAAGCCAGTT 57.039 32.000 0.00 0.00 33.67 3.16
634 852 3.907221 ACTAGCTAGGGAATACGGTCAA 58.093 45.455 24.35 0.00 0.00 3.18
683 901 8.962884 ATATATTTGACATGCAACTAGTGACA 57.037 30.769 0.00 0.00 35.91 3.58
709 927 4.589798 CCATCCAAAAGGATCCATAATGCA 59.410 41.667 15.82 0.00 0.00 3.96
731 949 7.178628 TGGTATGGAGTAGAAGATAACTATGCC 59.821 40.741 0.00 0.00 0.00 4.40
737 955 7.826918 AGTCTGGTATGGAGTAGAAGATAAC 57.173 40.000 0.00 0.00 0.00 1.89
959 1177 7.018769 TGGTATGGAATGAGGATCTGATCTTA 58.981 38.462 16.61 4.86 34.92 2.10
984 1202 1.815003 GCCATGCTTCTTAGTTGCACT 59.185 47.619 4.46 0.00 39.63 4.40
1024 1242 1.619827 TGCAAGCAAGAAAGGAATGGG 59.380 47.619 0.00 0.00 0.00 4.00
1060 1278 1.771255 AGGGAGAGAGAGAGAGAGAGC 59.229 57.143 0.00 0.00 0.00 4.09
1078 1296 0.478507 GAGAGAGAGAGGGAGGGAGG 59.521 65.000 0.00 0.00 0.00 4.30
1082 1300 2.370189 GAGAGAGAGAGAGAGAGGGAGG 59.630 59.091 0.00 0.00 0.00 4.30
1086 1304 3.055167 TGTGTGAGAGAGAGAGAGAGAGG 60.055 52.174 0.00 0.00 0.00 3.69
1088 1306 3.326297 TGTGTGTGAGAGAGAGAGAGAGA 59.674 47.826 0.00 0.00 0.00 3.10
1089 1307 3.436704 GTGTGTGTGAGAGAGAGAGAGAG 59.563 52.174 0.00 0.00 0.00 3.20
1090 1308 3.181450 TGTGTGTGTGAGAGAGAGAGAGA 60.181 47.826 0.00 0.00 0.00 3.10
1091 1309 3.058293 GTGTGTGTGTGAGAGAGAGAGAG 60.058 52.174 0.00 0.00 0.00 3.20
1092 1310 2.881513 GTGTGTGTGTGAGAGAGAGAGA 59.118 50.000 0.00 0.00 0.00 3.10
1093 1311 2.620585 TGTGTGTGTGTGAGAGAGAGAG 59.379 50.000 0.00 0.00 0.00 3.20
1094 1312 2.359214 GTGTGTGTGTGTGAGAGAGAGA 59.641 50.000 0.00 0.00 0.00 3.10
1095 1313 2.099756 TGTGTGTGTGTGTGAGAGAGAG 59.900 50.000 0.00 0.00 0.00 3.20
1096 1314 2.099405 TGTGTGTGTGTGTGAGAGAGA 58.901 47.619 0.00 0.00 0.00 3.10
1097 1315 2.196749 GTGTGTGTGTGTGTGAGAGAG 58.803 52.381 0.00 0.00 0.00 3.20
1098 1316 1.548269 TGTGTGTGTGTGTGTGAGAGA 59.452 47.619 0.00 0.00 0.00 3.10
1099 1317 2.008752 TGTGTGTGTGTGTGTGAGAG 57.991 50.000 0.00 0.00 0.00 3.20
1100 1318 2.464157 TTGTGTGTGTGTGTGTGAGA 57.536 45.000 0.00 0.00 0.00 3.27
1101 1319 6.368516 TGATATATTGTGTGTGTGTGTGTGAG 59.631 38.462 0.00 0.00 0.00 3.51
1102 1320 6.226787 TGATATATTGTGTGTGTGTGTGTGA 58.773 36.000 0.00 0.00 0.00 3.58
1103 1321 6.479095 TGATATATTGTGTGTGTGTGTGTG 57.521 37.500 0.00 0.00 0.00 3.82
1104 1322 6.710295 AGTTGATATATTGTGTGTGTGTGTGT 59.290 34.615 0.00 0.00 0.00 3.72
1105 1323 7.017055 CAGTTGATATATTGTGTGTGTGTGTG 58.983 38.462 0.00 0.00 0.00 3.82
1106 1324 6.710295 ACAGTTGATATATTGTGTGTGTGTGT 59.290 34.615 0.00 0.00 0.00 3.72
1107 1325 7.132694 ACAGTTGATATATTGTGTGTGTGTG 57.867 36.000 0.00 0.00 0.00 3.82
1108 1326 7.443879 TCAACAGTTGATATATTGTGTGTGTGT 59.556 33.333 12.24 0.00 34.08 3.72
1109 1327 7.805700 TCAACAGTTGATATATTGTGTGTGTG 58.194 34.615 12.24 0.00 34.08 3.82
1110 1328 7.977789 TCAACAGTTGATATATTGTGTGTGT 57.022 32.000 12.24 0.00 34.08 3.72
1227 1446 4.438200 CCAACGCCATGGAAATAGTACAAC 60.438 45.833 18.40 0.00 43.54 3.32
1228 1447 3.692101 CCAACGCCATGGAAATAGTACAA 59.308 43.478 18.40 0.00 43.54 2.41
1651 1872 2.653726 TGCATGGTTTCTTGTGTGACT 58.346 42.857 0.00 0.00 0.00 3.41
1720 1941 0.179004 TTCCTTGTTGCCCATCGTGT 60.179 50.000 0.00 0.00 0.00 4.49
1725 1946 1.915141 CACTCTTCCTTGTTGCCCAT 58.085 50.000 0.00 0.00 0.00 4.00
1742 1963 1.281656 GTTGTTGTAGCACGGGCAC 59.718 57.895 14.57 9.03 44.61 5.01
1761 1982 1.002069 TTGCCATCCTGGGTCTTCAT 58.998 50.000 0.00 0.00 38.19 2.57
1809 2030 1.178534 AATTTGGAGGCCACACACGG 61.179 55.000 5.01 0.00 30.78 4.94
1826 2047 8.373048 TGTTCGATACAACAAGACTGTAAAAT 57.627 30.769 0.00 0.00 33.45 1.82
1900 2121 7.130681 ACCTATCTCCTATTTTGTCTCCAAG 57.869 40.000 0.00 0.00 0.00 3.61
2006 2227 6.384305 ACCTAACTTGCCAGACTTGTCTATAT 59.616 38.462 2.72 0.00 0.00 0.86
2038 2259 2.571653 ACTATGCTGTGGCTAGAACCAA 59.428 45.455 0.00 0.00 42.70 3.67
2068 2289 9.860898 TCCAAAGAAAGAAAGAAAGAAAGAAAG 57.139 29.630 0.00 0.00 0.00 2.62
2069 2290 9.639601 GTCCAAAGAAAGAAAGAAAGAAAGAAA 57.360 29.630 0.00 0.00 0.00 2.52
2070 2291 8.802267 TGTCCAAAGAAAGAAAGAAAGAAAGAA 58.198 29.630 0.00 0.00 0.00 2.52
2071 2292 8.348285 TGTCCAAAGAAAGAAAGAAAGAAAGA 57.652 30.769 0.00 0.00 0.00 2.52
2072 2293 8.986477 TTGTCCAAAGAAAGAAAGAAAGAAAG 57.014 30.769 0.00 0.00 0.00 2.62
2073 2294 9.942850 ATTTGTCCAAAGAAAGAAAGAAAGAAA 57.057 25.926 0.00 0.00 33.32 2.52
2088 2309 3.508744 ATGGCGCTTATTTGTCCAAAG 57.491 42.857 7.64 0.00 33.32 2.77
2142 2363 9.698617 CTCTTAAACGTTTTAAGTACATATGGC 57.301 33.333 20.19 0.00 34.51 4.40
2202 2423 5.172205 TGTTTGGTTGGAACTTTGCTTTAC 58.828 37.500 0.00 0.00 0.00 2.01
2240 2461 1.265635 GTAGTCCGTTGTGCAATGCAA 59.734 47.619 10.44 0.00 41.47 4.08
2251 2472 8.262227 TCATAGATGGTAAAAATGTAGTCCGTT 58.738 33.333 0.00 0.00 0.00 4.44
2252 2473 7.788026 TCATAGATGGTAAAAATGTAGTCCGT 58.212 34.615 0.00 0.00 0.00 4.69
2297 2518 0.592247 CGCCGCAGCAATTAATCCAC 60.592 55.000 0.00 0.00 39.83 4.02
2374 2597 3.251004 GTCAACTTGTTGCTCGGATCTTT 59.749 43.478 8.48 0.00 0.00 2.52
2411 2634 3.066291 TGTGGGTGTGCTTTATCGAAT 57.934 42.857 0.00 0.00 0.00 3.34
2446 2669 6.424207 CCCCTAGTAAATCTTAGCGTCATTTC 59.576 42.308 0.00 0.00 0.00 2.17
2465 2688 8.850156 CCAACTAAAATGAATGTATTCCCCTAG 58.150 37.037 2.41 0.00 35.97 3.02
2506 2729 4.678309 CGCACCAAGTTTTCTAAACCCAAA 60.678 41.667 0.00 0.00 0.00 3.28
2516 2739 3.907894 TTATCACCGCACCAAGTTTTC 57.092 42.857 0.00 0.00 0.00 2.29
2567 2790 3.895232 TGGAGATGTCTAAGGCAAGAC 57.105 47.619 11.78 11.78 45.10 3.01
2604 2827 5.579384 ATGAATTTTTGTGCACGACAATG 57.421 34.783 17.24 0.00 44.23 2.82
2605 2828 4.382457 CGATGAATTTTTGTGCACGACAAT 59.618 37.500 13.13 12.44 44.23 2.71
2638 2861 0.876399 GCATTGCTTTTGGCCCAAAG 59.124 50.000 22.08 22.08 40.92 2.77
2650 2873 3.211865 CATCATCTACTGGTGCATTGCT 58.788 45.455 10.49 0.00 0.00 3.91
2749 2973 2.203437 GGTGGCGGTTGGGTTTCT 60.203 61.111 0.00 0.00 0.00 2.52
2766 2990 2.437413 GGGCTACAAGGAAGTTTCAGG 58.563 52.381 0.00 0.00 0.00 3.86
2769 2993 2.074576 GTCGGGCTACAAGGAAGTTTC 58.925 52.381 0.00 0.00 0.00 2.78


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

AutoCloner maintained by Alex Coulton.