Multiple sequence alignment - TraesCS7A01G308000

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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 TraesCS7A01G308000 chr7A 100.000 2671 0 0 1 2671 435866337 435863667 0.000000e+00 4933
1 TraesCS7A01G308000 chr7A 96.019 854 26 3 776 1627 435827734 435826887 0.000000e+00 1382
2 TraesCS7A01G308000 chr7A 90.833 120 11 0 543 662 543069363 543069482 7.650000e-36 161
3 TraesCS7A01G308000 chr7B 90.083 1684 102 32 679 2328 380864324 380862672 0.000000e+00 2124
4 TraesCS7A01G308000 chr7B 93.672 885 38 8 776 1644 380856634 380855752 0.000000e+00 1308
5 TraesCS7A01G308000 chr7B 85.630 682 54 15 5 662 380864972 380864311 0.000000e+00 676
6 TraesCS7A01G308000 chr7B 87.279 283 30 3 191 471 380837035 380836757 4.290000e-83 318
7 TraesCS7A01G308000 chr7B 93.464 153 10 0 2519 2671 380861932 380861780 7.440000e-56 228
8 TraesCS7A01G308000 chr7B 86.792 106 10 4 662 764 682235566 682235670 6.040000e-22 115
9 TraesCS7A01G308000 chr7B 89.011 91 9 1 680 770 91133482 91133393 7.820000e-21 111
10 TraesCS7A01G308000 chr7D 92.806 973 47 10 678 1644 386563761 386562806 0.000000e+00 1387
11 TraesCS7A01G308000 chr7D 89.717 671 52 11 5 662 386564413 386563747 0.000000e+00 841
12 TraesCS7A01G308000 chr7D 84.274 248 23 10 422 662 401849879 401850117 7.440000e-56 228
13 TraesCS7A01G308000 chr6B 89.157 249 19 3 422 662 410237717 410237965 1.200000e-78 303
14 TraesCS7A01G308000 chr6B 88.800 250 19 6 422 662 410684934 410685183 5.590000e-77 298
15 TraesCS7A01G308000 chr2D 82.258 248 31 6 425 662 578640940 578640696 4.510000e-48 202
16 TraesCS7A01G308000 chr2D 88.525 122 13 1 541 662 649388449 649388329 2.140000e-31 147
17 TraesCS7A01G308000 chr3D 81.746 252 35 3 422 662 295662647 295662396 1.620000e-47 200
18 TraesCS7A01G308000 chr3D 89.362 94 9 1 677 770 463113917 463113825 1.680000e-22 117
19 TraesCS7A01G308000 chr1B 80.080 251 37 9 422 662 620125701 620125454 9.830000e-40 174
20 TraesCS7A01G308000 chr4B 82.439 205 29 6 425 625 32257008 32256807 3.540000e-39 172
21 TraesCS7A01G308000 chr3A 90.000 120 12 0 543 662 195192449 195192330 3.560000e-34 156
22 TraesCS7A01G308000 chr2A 78.571 252 41 4 422 662 81166010 81165761 1.280000e-33 154
23 TraesCS7A01G308000 chr2A 90.217 92 8 1 679 770 660264396 660264306 4.670000e-23 119
24 TraesCS7A01G308000 chr1D 90.217 92 8 1 679 770 466940805 466940715 4.670000e-23 119
25 TraesCS7A01G308000 chr1D 84.821 112 14 3 661 770 43121028 43120918 2.810000e-20 110
26 TraesCS7A01G308000 chr5D 87.500 96 10 2 678 773 128663608 128663701 2.810000e-20 110


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 TraesCS7A01G308000 chr7A 435863667 435866337 2670 True 4933.000000 4933 100.000000 1 2671 1 chr7A.!!$R2 2670
1 TraesCS7A01G308000 chr7A 435826887 435827734 847 True 1382.000000 1382 96.019000 776 1627 1 chr7A.!!$R1 851
2 TraesCS7A01G308000 chr7B 380855752 380856634 882 True 1308.000000 1308 93.672000 776 1644 1 chr7B.!!$R3 868
3 TraesCS7A01G308000 chr7B 380861780 380864972 3192 True 1009.333333 2124 89.725667 5 2671 3 chr7B.!!$R4 2666
4 TraesCS7A01G308000 chr7D 386562806 386564413 1607 True 1114.000000 1387 91.261500 5 1644 2 chr7D.!!$R1 1639

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
276 279 0.105039 GATCAAGCAGTAGGGACCCG 59.895 60.0 4.4 0.0 0.0 5.28 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1966 2025 0.101219 GCACAATTTCGGGATGGCTC 59.899 55.0 0.0 0.0 0.0 4.7 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
41 42 3.604494 CTCGCGGCACACGTAGACA 62.604 63.158 6.13 0.00 46.52 3.41
101 102 3.795688 TTCACAGAGAAGATGCCCTTT 57.204 42.857 0.00 0.00 34.68 3.11
103 104 2.639347 TCACAGAGAAGATGCCCTTTGA 59.361 45.455 0.00 0.00 34.68 2.69
106 107 3.840666 ACAGAGAAGATGCCCTTTGAGTA 59.159 43.478 0.00 0.00 34.68 2.59
114 115 1.077787 CCCTTTGAGTATGGCGCCA 60.078 57.895 34.80 34.80 0.00 5.69
115 116 1.376609 CCCTTTGAGTATGGCGCCAC 61.377 60.000 35.50 21.24 0.00 5.01
135 138 0.391130 GCAAGTACGTCATCCAGCCA 60.391 55.000 0.00 0.00 0.00 4.75
208 211 1.668151 GTGAAGCTGGACGTCCCAC 60.668 63.158 31.19 25.08 40.82 4.61
214 217 4.567597 TGGACGTCCCACCCACCT 62.568 66.667 31.19 0.00 40.82 4.00
216 219 1.914764 GGACGTCCCACCCACCTTA 60.915 63.158 24.75 0.00 34.14 2.69
249 252 1.069765 CAGCTACCCGGCAGTATGG 59.930 63.158 0.00 0.00 35.86 2.74
253 256 1.831736 GCTACCCGGCAGTATGGATAT 59.168 52.381 0.00 0.00 35.86 1.63
276 279 0.105039 GATCAAGCAGTAGGGACCCG 59.895 60.000 4.40 0.00 0.00 5.28
288 291 5.480772 CAGTAGGGACCCGATATGTCTAAAT 59.519 44.000 4.40 0.00 33.22 1.40
319 322 8.252417 TCCCATGACTAATGAAAATGACAAATG 58.748 33.333 0.00 0.00 38.72 2.32
376 381 2.031769 GTGCAACCGTTGGTAAACCTAC 60.032 50.000 13.12 3.93 38.19 3.18
377 382 2.220313 GCAACCGTTGGTAAACCTACA 58.780 47.619 13.12 0.00 40.94 2.74
410 423 9.347240 CCAGATGACCTTTCATAGAACATAAAT 57.653 33.333 0.00 0.00 42.95 1.40
427 442 9.727627 GAACATAAATTTAGGATCTTGCTTCAG 57.272 33.333 16.26 0.00 0.00 3.02
453 468 1.699083 TCATGAAGCCAAGTCTCACCA 59.301 47.619 0.00 0.00 0.00 4.17
492 507 7.479352 TTTTCAGCCATTCATTAAAGATCCA 57.521 32.000 0.00 0.00 0.00 3.41
494 509 7.664552 TTCAGCCATTCATTAAAGATCCAAT 57.335 32.000 0.00 0.00 0.00 3.16
495 510 7.046292 TCAGCCATTCATTAAAGATCCAATG 57.954 36.000 6.12 6.12 34.17 2.82
612 637 5.888161 AGTTTCACTCCATTTGGATGTATCC 59.112 40.000 3.91 3.91 44.46 2.59
627 652 7.681939 GGATGTATCCTTTGTGAGTAAACAA 57.318 36.000 3.63 0.00 43.73 2.83
740 765 7.411486 TGAAACTTTCCCAGAATACAAAACA 57.589 32.000 0.00 0.00 0.00 2.83
785 813 9.241317 GGATTTTATTCTGACAATTATGCAGTG 57.759 33.333 0.00 0.00 34.42 3.66
801 829 2.480419 GCAGTGCGTATGTATGGAATCC 59.520 50.000 0.00 0.00 0.00 3.01
863 891 5.945155 TCAACGAGCCCACATTTTAATTAC 58.055 37.500 0.00 0.00 0.00 1.89
895 923 0.524816 CCAGATCGACCCGTACAACG 60.525 60.000 0.00 0.00 42.11 4.10
961 996 1.402259 CAACGAGCTACCGTCTCATCT 59.598 52.381 0.47 0.00 42.54 2.90
962 997 1.301423 ACGAGCTACCGTCTCATCTC 58.699 55.000 0.00 0.00 38.56 2.75
963 998 1.300481 CGAGCTACCGTCTCATCTCA 58.700 55.000 0.00 0.00 0.00 3.27
964 999 1.876799 CGAGCTACCGTCTCATCTCAT 59.123 52.381 0.00 0.00 0.00 2.90
1004 1043 8.962884 AGTATCATCATATGCTACAACACAAA 57.037 30.769 0.00 0.00 35.05 2.83
1044 1083 3.944650 CTCGATCATACATCCCTCGATCT 59.055 47.826 0.00 0.00 37.68 2.75
1086 1134 2.758979 TCGGGTCATCTTCTCAACTACC 59.241 50.000 0.00 0.00 0.00 3.18
1653 1712 3.865745 GTCATCAACGACAACCTCCATAG 59.134 47.826 0.00 0.00 35.88 2.23
1655 1714 7.356396 GTCATCAACGACAACCTCCATAGGA 62.356 48.000 0.00 0.00 39.35 2.94
1722 1781 3.951775 TGACTTTCTCCTCTCTCAAGC 57.048 47.619 0.00 0.00 0.00 4.01
1735 1794 2.262211 TCTCAAGCGTGATTGATCGTG 58.738 47.619 1.88 0.00 38.47 4.35
1736 1795 0.721154 TCAAGCGTGATTGATCGTGC 59.279 50.000 0.00 0.59 34.31 5.34
1749 1808 2.839629 TCGTGCGCACATGATTCTT 58.160 47.368 37.03 0.00 36.89 2.52
1751 1810 1.136000 TCGTGCGCACATGATTCTTTG 60.136 47.619 37.03 18.36 36.89 2.77
1753 1812 2.159720 CGTGCGCACATGATTCTTTGTA 60.160 45.455 37.03 0.00 34.49 2.41
1768 1827 8.655970 TGATTCTTTGTATAGTCAAATGTGTCG 58.344 33.333 0.00 0.00 36.83 4.35
1826 1885 1.735018 CATGGCATTTCGTTGACCGTA 59.265 47.619 0.00 0.00 37.94 4.02
1866 1925 3.194116 ACAGTGGATCAATTTCATGGCAC 59.806 43.478 0.00 0.00 0.00 5.01
1867 1926 3.446161 CAGTGGATCAATTTCATGGCACT 59.554 43.478 0.00 0.00 0.00 4.40
1873 1932 7.005902 TGGATCAATTTCATGGCACTATATGT 58.994 34.615 0.00 0.00 0.00 2.29
1874 1933 7.175467 TGGATCAATTTCATGGCACTATATGTC 59.825 37.037 0.00 0.00 0.00 3.06
1941 2000 5.530171 CCCATGAGATACAACCAAGATCAAG 59.470 44.000 0.00 0.00 0.00 3.02
1945 2004 6.173339 TGAGATACAACCAAGATCAAGGAAC 58.827 40.000 10.11 0.00 0.00 3.62
1952 2011 2.504367 CAAGATCAAGGAACCAACGGT 58.496 47.619 0.00 0.00 37.65 4.83
1983 2042 0.035439 ACGAGCCATCCCGAAATTGT 60.035 50.000 0.00 0.00 0.00 2.71
2011 2081 2.847327 ATCACCAATGGCTAGATCCG 57.153 50.000 0.00 0.00 0.00 4.18
2022 2092 1.202533 GCTAGATCCGGCTGCTTGTTA 60.203 52.381 0.00 0.00 0.00 2.41
2024 2094 1.739067 AGATCCGGCTGCTTGTTAAC 58.261 50.000 0.00 0.00 0.00 2.01
2025 2095 0.733150 GATCCGGCTGCTTGTTAACC 59.267 55.000 2.48 0.00 0.00 2.85
2027 2097 0.037590 TCCGGCTGCTTGTTAACCAT 59.962 50.000 2.48 0.00 0.00 3.55
2033 2109 4.380444 CGGCTGCTTGTTAACCATTACAAT 60.380 41.667 2.48 0.00 34.10 2.71
2040 2116 9.685828 TGCTTGTTAACCATTACAATAAGAAAC 57.314 29.630 2.48 0.00 34.10 2.78
2068 2144 7.763985 ACAAAGTTTATAAATGGCACCAATAGC 59.236 33.333 0.31 0.00 0.00 2.97
2072 2148 4.836125 ATAAATGGCACCAATAGCTTCG 57.164 40.909 0.00 0.00 0.00 3.79
2105 2181 8.790718 AGCATTCTCAATAATAGGCTTATTGTG 58.209 33.333 11.12 13.48 41.03 3.33
2122 2198 7.413438 GCTTATTGTGAATTGTCAGTGTCTAGG 60.413 40.741 0.00 0.00 33.27 3.02
2138 2214 4.041567 TGTCTAGGCAAGGACATCAAAAGA 59.958 41.667 0.00 0.00 37.52 2.52
2142 2218 4.154942 AGGCAAGGACATCAAAAGACAAT 58.845 39.130 0.00 0.00 0.00 2.71
2148 2224 6.729690 AGGACATCAAAAGACAATCCAAAA 57.270 33.333 0.00 0.00 0.00 2.44
2153 2229 8.237811 ACATCAAAAGACAATCCAAAAGTAGT 57.762 30.769 0.00 0.00 0.00 2.73
2166 2242 2.150397 AAGTAGTGACGAGTGTTGCC 57.850 50.000 0.00 0.00 0.00 4.52
2169 2245 0.319555 TAGTGACGAGTGTTGCCTGC 60.320 55.000 0.00 0.00 0.00 4.85
2180 2256 0.108329 GTTGCCTGCGCTAGTCCTAA 60.108 55.000 9.73 0.00 35.36 2.69
2183 2259 0.389391 GCCTGCGCTAGTCCTAATGA 59.611 55.000 9.73 0.00 0.00 2.57
2185 2261 2.928731 GCCTGCGCTAGTCCTAATGATC 60.929 54.545 9.73 0.00 0.00 2.92
2191 2267 5.182190 TGCGCTAGTCCTAATGATCTTCTAG 59.818 44.000 9.73 0.00 0.00 2.43
2195 2271 6.127730 GCTAGTCCTAATGATCTTCTAGGAGC 60.128 46.154 14.62 12.03 41.45 4.70
2205 2283 7.816300 TGATCTTCTAGGAGCTAGTAGGATA 57.184 40.000 0.00 0.00 33.97 2.59
2223 2301 4.886496 GATACCCCTTGTATCCTACCAC 57.114 50.000 1.71 0.00 46.84 4.16
2226 2304 3.538387 ACCCCTTGTATCCTACCACTTT 58.462 45.455 0.00 0.00 0.00 2.66
2285 2364 6.473455 GCAAGTGAAGAATATGTGGTTATTGC 59.527 38.462 0.00 0.00 0.00 3.56
2312 2391 1.202758 TGACCTCACAAAGCGGACAAT 60.203 47.619 0.00 0.00 0.00 2.71
2322 2401 1.959042 AGCGGACAATGGTCATCATC 58.041 50.000 1.86 0.00 46.17 2.92
2333 2435 0.390860 GTCATCATCGGGACCAGAGG 59.609 60.000 0.00 0.00 0.00 3.69
2341 2443 0.978146 CGGGACCAGAGGAAGACCAT 60.978 60.000 0.00 0.00 38.94 3.55
2349 2451 5.688807 ACCAGAGGAAGACCATTATGAATG 58.311 41.667 0.00 0.00 38.94 2.67
2358 2460 8.636213 GGAAGACCATTATGAATGAATTGTCAT 58.364 33.333 0.70 0.00 41.46 3.06
2372 2501 6.215121 TGAATTGTCATTGAATCAACCACAC 58.785 36.000 0.00 0.00 0.00 3.82
2381 2510 8.253810 TCATTGAATCAACCACACTTTTGTTAA 58.746 29.630 0.00 0.00 31.66 2.01
2387 2516 3.120041 ACCACACTTTTGTTAATTGCGC 58.880 40.909 0.00 0.00 31.66 6.09
2437 2566 6.882768 AATAGAGAGACCTTGTGGAGAAAT 57.117 37.500 0.00 0.00 37.04 2.17
2453 2582 4.195416 GAGAAATAACCAGAGGGCTCAAG 58.805 47.826 0.00 0.00 37.90 3.02
2471 2600 7.137426 GGCTCAAGATGCTAGTAATCAAATTG 58.863 38.462 9.39 6.20 0.00 2.32
2472 2601 7.201767 GGCTCAAGATGCTAGTAATCAAATTGT 60.202 37.037 9.39 0.00 0.00 2.71
2481 2610 7.962373 TGCTAGTAATCAAATTGTGTTTCATCG 59.038 33.333 0.00 0.00 0.00 3.84
2483 2612 9.478019 CTAGTAATCAAATTGTGTTTCATCGAC 57.522 33.333 0.00 0.00 0.00 4.20
2486 2615 3.810386 TCAAATTGTGTTTCATCGACGGA 59.190 39.130 0.00 0.00 0.00 4.69
2497 2626 2.036733 TCATCGACGGAATAACCCCATC 59.963 50.000 0.00 0.00 34.64 3.51
2517 2646 3.349927 TCCAGGTCAAAGATCAAGCATG 58.650 45.455 0.00 0.00 0.00 4.06
2532 3159 1.601419 GCATGCCCACATTGCTGACT 61.601 55.000 6.36 0.00 32.87 3.41
2549 3176 3.565307 TGACTCCATTGTCCAAAAAGCT 58.435 40.909 0.00 0.00 36.21 3.74
2553 3180 2.627699 TCCATTGTCCAAAAAGCTCACC 59.372 45.455 0.00 0.00 0.00 4.02
2564 3191 4.647424 AAAAGCTCACCGAAATGAAACA 57.353 36.364 0.00 0.00 0.00 2.83
2567 3194 1.068541 GCTCACCGAAATGAAACACCC 60.069 52.381 0.00 0.00 0.00 4.61
2619 3246 2.509052 ATCACACACGATATGGACGG 57.491 50.000 0.00 0.00 34.93 4.79
2621 3248 2.028876 TCACACACGATATGGACGGAT 58.971 47.619 0.00 0.00 34.93 4.18
2648 3275 1.136529 CGATGACGACAAAGCACACAG 60.137 52.381 0.00 0.00 42.66 3.66
2664 3291 7.582667 AGCACACAGTAGGAAAATAAAAACT 57.417 32.000 0.00 0.00 0.00 2.66
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 2.368875 AGGGCTCCAGACGGTAATATTG 59.631 50.000 0.00 0.00 0.00 1.90
1 2 2.690840 AGGGCTCCAGACGGTAATATT 58.309 47.619 0.00 0.00 0.00 1.28
2 3 2.400467 AGGGCTCCAGACGGTAATAT 57.600 50.000 0.00 0.00 0.00 1.28
3 4 2.176364 AGTAGGGCTCCAGACGGTAATA 59.824 50.000 0.00 0.00 0.00 0.98
41 42 4.274459 GCTCATGAGGAAAAATATCGCACT 59.726 41.667 23.89 0.00 0.00 4.40
80 81 4.015084 CAAAGGGCATCTTCTCTGTGAAT 58.985 43.478 0.00 0.00 33.94 2.57
115 116 1.421410 GGCTGGATGACGTACTTGCG 61.421 60.000 0.00 0.00 37.94 4.85
208 211 3.359950 ACTACTAACCGAGTAAGGTGGG 58.640 50.000 0.00 0.00 45.21 4.61
214 217 6.428385 GTAGCTGAACTACTAACCGAGTAA 57.572 41.667 0.00 0.00 46.65 2.24
216 219 4.961435 GTAGCTGAACTACTAACCGAGT 57.039 45.455 0.00 0.00 46.65 4.18
249 252 6.460399 GGTCCCTACTGCTTGATCGATATATC 60.460 46.154 0.00 2.34 0.00 1.63
253 256 2.891580 GGTCCCTACTGCTTGATCGATA 59.108 50.000 0.00 0.00 0.00 2.92
276 279 8.592809 AGTCATGGGAGAAGATTTAGACATATC 58.407 37.037 0.00 0.00 0.00 1.63
288 291 7.554118 GTCATTTTCATTAGTCATGGGAGAAGA 59.446 37.037 0.00 0.00 33.07 2.87
319 322 8.867248 TTTTTCATTTCTAAACAACGCAAAAC 57.133 26.923 0.00 0.00 0.00 2.43
351 356 2.783828 TTACCAACGGTTGCACAATG 57.216 45.000 15.31 3.41 37.09 2.82
376 381 4.520179 TGAAAGGTCATCTGGATCACATG 58.480 43.478 0.00 0.00 0.00 3.21
377 382 4.849813 TGAAAGGTCATCTGGATCACAT 57.150 40.909 0.00 0.00 0.00 3.21
410 423 5.489792 AGTCACTGAAGCAAGATCCTAAA 57.510 39.130 0.00 0.00 0.00 1.85
411 424 5.012046 TGAAGTCACTGAAGCAAGATCCTAA 59.988 40.000 0.00 0.00 0.00 2.69
492 507 6.881065 CGGAATATGGGTCAATCTGATACATT 59.119 38.462 0.00 0.00 31.36 2.71
494 509 5.542251 TCGGAATATGGGTCAATCTGATACA 59.458 40.000 0.00 0.00 0.00 2.29
495 510 6.037786 TCGGAATATGGGTCAATCTGATAC 57.962 41.667 0.00 0.00 0.00 2.24
676 701 6.325286 TGGGTTTGTGATTAACTAGCCTTTTT 59.675 34.615 0.00 0.00 35.67 1.94
677 702 5.836358 TGGGTTTGTGATTAACTAGCCTTTT 59.164 36.000 0.00 0.00 35.67 2.27
678 703 5.390387 TGGGTTTGTGATTAACTAGCCTTT 58.610 37.500 0.00 0.00 35.67 3.11
679 704 4.993028 TGGGTTTGTGATTAACTAGCCTT 58.007 39.130 0.00 0.00 35.67 4.35
680 705 4.650972 TGGGTTTGTGATTAACTAGCCT 57.349 40.909 0.00 0.00 35.67 4.58
681 706 4.521256 TGTTGGGTTTGTGATTAACTAGCC 59.479 41.667 0.00 0.00 34.81 3.93
773 801 5.179182 TCCATACATACGCACTGCATAATTG 59.821 40.000 1.11 0.00 0.00 2.32
774 802 5.304778 TCCATACATACGCACTGCATAATT 58.695 37.500 1.11 0.00 0.00 1.40
785 813 3.935203 CCTGATGGATTCCATACATACGC 59.065 47.826 18.20 4.91 45.26 4.42
801 829 0.755079 TGCTAGCCTACTGCCTGATG 59.245 55.000 13.29 0.00 42.71 3.07
863 891 3.059570 GTCGATCTGGAAATTATAGCGCG 59.940 47.826 0.00 0.00 0.00 6.86
895 923 1.346365 TAGCATTTGACTCACGCGTC 58.654 50.000 9.86 0.00 34.52 5.19
962 997 9.956720 TGATGATACTCTGCGATATATACAATG 57.043 33.333 0.00 0.00 0.00 2.82
990 1029 5.853936 TCTAGTCTGTTTGTGTTGTAGCAT 58.146 37.500 0.00 0.00 0.00 3.79
991 1030 5.270893 TCTAGTCTGTTTGTGTTGTAGCA 57.729 39.130 0.00 0.00 0.00 3.49
1004 1043 0.322997 AGGTCGCAGCTCTAGTCTGT 60.323 55.000 13.47 0.00 34.21 3.41
1044 1083 4.398319 GAGAAGGGTTGGAATGTTGAGAA 58.602 43.478 0.00 0.00 0.00 2.87
1086 1134 1.303309 GAATGCCAATCGAGGGACTG 58.697 55.000 9.93 0.00 41.55 3.51
1693 1752 3.578716 AGAGGAGAAAGTCATCACGGAAA 59.421 43.478 0.00 0.00 38.52 3.13
1694 1753 3.165875 AGAGGAGAAAGTCATCACGGAA 58.834 45.455 0.00 0.00 38.52 4.30
1722 1781 1.296145 GTGCGCACGATCAATCACG 60.296 57.895 26.77 0.00 0.00 4.35
1735 1794 5.006649 TGACTATACAAAGAATCATGTGCGC 59.993 40.000 0.00 0.00 0.00 6.09
1736 1795 6.588348 TGACTATACAAAGAATCATGTGCG 57.412 37.500 0.00 0.00 0.00 5.34
1745 1804 7.956420 ACGACACATTTGACTATACAAAGAA 57.044 32.000 0.00 0.00 41.87 2.52
1746 1805 7.956420 AACGACACATTTGACTATACAAAGA 57.044 32.000 0.00 0.00 41.87 2.52
1747 1806 9.445786 AAAAACGACACATTTGACTATACAAAG 57.554 29.630 0.00 0.00 41.87 2.77
1801 1860 2.030363 GTCAACGAAATGCCATGAACCA 60.030 45.455 0.00 0.00 0.00 3.67
1802 1861 2.595386 GTCAACGAAATGCCATGAACC 58.405 47.619 0.00 0.00 0.00 3.62
1914 1973 3.202818 TCTTGGTTGTATCTCATGGGCAT 59.797 43.478 0.00 0.00 0.00 4.40
1915 1974 2.575735 TCTTGGTTGTATCTCATGGGCA 59.424 45.455 0.00 0.00 0.00 5.36
1916 1975 3.281727 TCTTGGTTGTATCTCATGGGC 57.718 47.619 0.00 0.00 0.00 5.36
1941 2000 0.666577 CTCACTCGACCGTTGGTTCC 60.667 60.000 0.00 0.00 35.25 3.62
1945 2004 2.432628 GCCTCACTCGACCGTTGG 60.433 66.667 0.00 0.00 0.00 3.77
1952 2011 3.749064 GCTCGTGGCCTCACTCGA 61.749 66.667 3.32 5.89 41.53 4.04
1966 2025 0.101219 GCACAATTTCGGGATGGCTC 59.899 55.000 0.00 0.00 0.00 4.70
1983 2042 1.273048 GCCATTGGTGATTTCACTGCA 59.727 47.619 10.32 0.00 45.73 4.41
2002 2072 0.462759 AACAAGCAGCCGGATCTAGC 60.463 55.000 5.05 0.00 0.00 3.42
2006 2076 0.733150 GGTTAACAAGCAGCCGGATC 59.267 55.000 5.05 0.00 0.00 3.36
2011 2081 4.513198 TTGTAATGGTTAACAAGCAGCC 57.487 40.909 8.10 0.00 42.84 4.85
2022 2092 8.700973 ACTTTGTGGTTTCTTATTGTAATGGTT 58.299 29.630 0.00 0.00 0.00 3.67
2024 2094 9.541143 AAACTTTGTGGTTTCTTATTGTAATGG 57.459 29.630 0.00 0.00 34.79 3.16
2033 2109 9.699703 GCCATTTATAAACTTTGTGGTTTCTTA 57.300 29.630 13.68 0.00 39.66 2.10
2040 2116 5.788450 TGGTGCCATTTATAAACTTTGTGG 58.212 37.500 9.52 9.52 0.00 4.17
2068 2144 0.857935 GAGAATGCTCATCGGCGAAG 59.142 55.000 15.93 10.47 40.96 3.79
2091 2167 7.394359 ACACTGACAATTCACAATAAGCCTATT 59.606 33.333 0.00 0.00 0.00 1.73
2093 2169 6.237901 ACACTGACAATTCACAATAAGCCTA 58.762 36.000 0.00 0.00 0.00 3.93
2094 2170 5.072741 ACACTGACAATTCACAATAAGCCT 58.927 37.500 0.00 0.00 0.00 4.58
2095 2171 5.182001 AGACACTGACAATTCACAATAAGCC 59.818 40.000 0.00 0.00 0.00 4.35
2096 2172 6.246420 AGACACTGACAATTCACAATAAGC 57.754 37.500 0.00 0.00 0.00 3.09
2105 2181 3.686726 CCTTGCCTAGACACTGACAATTC 59.313 47.826 0.00 0.00 0.00 2.17
2122 2198 4.022068 TGGATTGTCTTTTGATGTCCTTGC 60.022 41.667 0.00 0.00 31.62 4.01
2138 2214 4.750098 CACTCGTCACTACTTTTGGATTGT 59.250 41.667 0.00 0.00 0.00 2.71
2142 2218 4.116961 CAACACTCGTCACTACTTTTGGA 58.883 43.478 0.00 0.00 0.00 3.53
2148 2224 1.000163 CAGGCAACACTCGTCACTACT 60.000 52.381 0.00 0.00 41.41 2.57
2153 2229 2.661537 CGCAGGCAACACTCGTCA 60.662 61.111 0.00 0.00 41.41 4.35
2166 2242 3.932545 AGATCATTAGGACTAGCGCAG 57.067 47.619 11.47 7.81 0.00 5.18
2169 2245 5.941058 TCCTAGAAGATCATTAGGACTAGCG 59.059 44.000 13.05 0.00 38.37 4.26
2180 2256 6.712114 TCCTACTAGCTCCTAGAAGATCAT 57.288 41.667 6.29 0.00 37.49 2.45
2183 2259 6.069264 GGGTATCCTACTAGCTCCTAGAAGAT 60.069 46.154 6.29 7.23 37.49 2.40
2185 2261 5.503002 GGGTATCCTACTAGCTCCTAGAAG 58.497 50.000 6.29 0.00 37.49 2.85
2205 2283 2.963654 AGTGGTAGGATACAAGGGGT 57.036 50.000 0.00 0.00 45.43 4.95
2221 2299 3.004629 TGTGGTGCTGCTTTCATAAAGTG 59.995 43.478 0.00 0.00 40.64 3.16
2223 2301 3.921119 TGTGGTGCTGCTTTCATAAAG 57.079 42.857 0.00 0.00 41.46 1.85
2226 2304 4.662468 TTTTTGTGGTGCTGCTTTCATA 57.338 36.364 0.00 0.00 0.00 2.15
2269 2348 4.385825 TCGAGGGCAATAACCACATATTC 58.614 43.478 0.00 0.00 0.00 1.75
2285 2364 2.009042 GCTTTGTGAGGTCATCGAGGG 61.009 57.143 0.00 0.00 0.00 4.30
2322 2401 0.978146 ATGGTCTTCCTCTGGTCCCG 60.978 60.000 0.00 0.00 34.23 5.14
2349 2451 6.449698 AGTGTGGTTGATTCAATGACAATTC 58.550 36.000 12.47 4.46 0.00 2.17
2358 2460 8.877779 CAATTAACAAAAGTGTGGTTGATTCAA 58.122 29.630 0.00 0.00 38.27 2.69
2363 2465 4.800993 CGCAATTAACAAAAGTGTGGTTGA 59.199 37.500 0.00 0.00 38.27 3.18
2364 2466 4.549871 GCGCAATTAACAAAAGTGTGGTTG 60.550 41.667 0.30 0.00 38.27 3.77
2372 2501 1.345410 CCCGGCGCAATTAACAAAAG 58.655 50.000 10.83 0.00 0.00 2.27
2408 2537 5.783360 TCCACAAGGTCTCTCTATTAAACCA 59.217 40.000 0.00 0.00 35.89 3.67
2412 2541 7.792364 TTTCTCCACAAGGTCTCTCTATTAA 57.208 36.000 0.00 0.00 35.89 1.40
2414 2543 6.882768 ATTTCTCCACAAGGTCTCTCTATT 57.117 37.500 0.00 0.00 35.89 1.73
2437 2566 1.210478 GCATCTTGAGCCCTCTGGTTA 59.790 52.381 0.00 0.00 0.00 2.85
2453 2582 9.793252 ATGAAACACAATTTGATTACTAGCATC 57.207 29.630 2.79 0.00 0.00 3.91
2471 2600 3.063045 GGGTTATTCCGTCGATGAAACAC 59.937 47.826 6.11 2.73 37.00 3.32
2472 2601 3.264104 GGGTTATTCCGTCGATGAAACA 58.736 45.455 6.11 0.00 37.00 2.83
2481 2610 1.202770 CCTGGATGGGGTTATTCCGTC 60.203 57.143 0.00 0.00 39.08 4.79
2483 2612 0.843984 ACCTGGATGGGGTTATTCCG 59.156 55.000 0.00 0.00 41.11 4.30
2486 2615 3.596046 TCTTTGACCTGGATGGGGTTATT 59.404 43.478 0.00 0.00 41.11 1.40
2497 2626 2.159282 GCATGCTTGATCTTTGACCTGG 60.159 50.000 11.37 0.00 0.00 4.45
2517 2646 0.682209 ATGGAGTCAGCAATGTGGGC 60.682 55.000 0.00 0.00 0.00 5.36
2532 3159 2.627699 GGTGAGCTTTTTGGACAATGGA 59.372 45.455 0.00 0.00 0.00 3.41
2549 3176 2.649531 AGGGTGTTTCATTTCGGTGA 57.350 45.000 0.00 0.00 0.00 4.02
2553 3180 6.548441 TTAGTGTAAGGGTGTTTCATTTCG 57.452 37.500 0.00 0.00 0.00 3.46
2564 3191 5.339695 CCCCATTGTGTATTAGTGTAAGGGT 60.340 44.000 0.00 0.00 0.00 4.34
2567 3194 5.437060 AGCCCCATTGTGTATTAGTGTAAG 58.563 41.667 0.00 0.00 0.00 2.34
2619 3246 1.067693 TGTCGTCATCGCACACAATC 58.932 50.000 0.00 0.00 36.96 2.67
2621 3248 1.260297 CTTTGTCGTCATCGCACACAA 59.740 47.619 0.00 0.00 36.96 3.33


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

AutoCloner maintained by Alex Coulton.