Multiple sequence alignment - TraesCS6A01G137200

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 TraesCS6A01G137200 chr6A 100.000 2721 0 0 1 2721 108200368 108203088 0.000000e+00 5025.0
1 TraesCS6A01G137200 chr6A 89.091 220 23 1 1268 1486 108179913 108180132 3.450000e-69 272.0
2 TraesCS6A01G137200 chr6B 91.571 1127 47 22 814 1909 172323685 172324794 0.000000e+00 1511.0
3 TraesCS6A01G137200 chr6B 92.000 425 24 6 2287 2711 172325318 172325732 3.020000e-164 588.0
4 TraesCS6A01G137200 chr6B 91.981 424 23 6 381 800 172316378 172316794 3.900000e-163 584.0
5 TraesCS6A01G137200 chr6B 91.123 383 25 8 1 378 172315076 172315454 6.720000e-141 510.0
6 TraesCS6A01G137200 chr6B 87.603 363 35 5 1934 2289 172324930 172325289 1.950000e-111 412.0
7 TraesCS6A01G137200 chr6B 89.427 227 22 2 1268 1493 172265141 172265366 4.430000e-73 285.0
8 TraesCS6A01G137200 chr6D 92.088 1087 30 26 809 1867 89822345 89823403 0.000000e+00 1480.0
9 TraesCS6A01G137200 chr6D 92.148 433 28 3 2287 2719 89823815 89824241 8.330000e-170 606.0
10 TraesCS6A01G137200 chr6D 91.903 247 12 3 554 800 89822000 89822238 3.360000e-89 339.0
11 TraesCS6A01G137200 chr6D 89.868 227 21 2 1268 1493 89734113 89734338 9.530000e-75 291.0
12 TraesCS6A01G137200 chr6D 90.055 181 13 3 18 194 89810711 89810890 2.110000e-56 230.0
13 TraesCS6A01G137200 chr6D 100.000 30 0 0 183 212 89810934 89810963 3.780000e-04 56.5
14 TraesCS6A01G137200 chr7D 89.286 140 15 0 2339 2478 563825504 563825365 2.780000e-40 176.0
15 TraesCS6A01G137200 chr7B 89.286 140 15 0 2339 2478 614220473 614220612 2.780000e-40 176.0
16 TraesCS6A01G137200 chr7A 89.286 140 15 0 2339 2478 649425147 649425286 2.780000e-40 176.0
17 TraesCS6A01G137200 chr7A 89.691 97 10 0 2547 2643 649425433 649425529 1.020000e-24 124.0
18 TraesCS6A01G137200 chr1D 88.571 140 16 0 2339 2478 421494138 421493999 1.300000e-38 171.0
19 TraesCS6A01G137200 chr2D 87.857 140 17 0 2339 2478 558943578 558943717 6.030000e-37 165.0
20 TraesCS6A01G137200 chr3D 86.429 140 19 0 2339 2478 577441834 577441695 1.300000e-33 154.0


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 TraesCS6A01G137200 chr6A 108200368 108203088 2720 False 5025.000000 5025 100.000000 1 2721 1 chr6A.!!$F2 2720
1 TraesCS6A01G137200 chr6B 172323685 172325732 2047 False 837.000000 1511 90.391333 814 2711 3 chr6B.!!$F3 1897
2 TraesCS6A01G137200 chr6B 172315076 172316794 1718 False 547.000000 584 91.552000 1 800 2 chr6B.!!$F2 799
3 TraesCS6A01G137200 chr6D 89822000 89824241 2241 False 808.333333 1480 92.046333 554 2719 3 chr6D.!!$F3 2165

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
805 1741 0.105778 GTGCATGCCTCCTCCTCTAC 59.894 60.0 16.68 0.0 0.0 2.59 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2611 3852 0.247736 AGGTCAAGGCTGATCGTGAC 59.752 55.0 7.58 7.58 42.55 3.67 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
44 45 1.148310 CATCACCTTCACCGTCACAC 58.852 55.000 0.00 0.00 0.00 3.82
54 55 1.961277 CCGTCACACAGCAACCCTC 60.961 63.158 0.00 0.00 0.00 4.30
96 97 1.671742 CCCGATCAATACCTCCCCG 59.328 63.158 0.00 0.00 0.00 5.73
98 99 1.004918 CGATCAATACCTCCCCGCC 60.005 63.158 0.00 0.00 0.00 6.13
216 217 4.207165 ACAGTAACATGCAACTGGAGTTT 58.793 39.130 24.21 7.35 45.94 2.66
235 237 6.075046 GGAGTTTCACAAACGTTTGCTATTTC 60.075 38.462 34.70 24.45 45.88 2.17
238 240 5.158101 TCACAAACGTTTGCTATTTCGAA 57.842 34.783 34.70 11.48 41.79 3.71
246 248 9.537848 AAACGTTTGCTATTTCGAATTTAGTAG 57.462 29.630 13.81 0.00 0.00 2.57
255 257 6.854496 TTTCGAATTTAGTAGTGTGCAACT 57.146 33.333 0.00 0.00 43.40 3.16
326 328 2.664698 GCAAAAGCTAGTCGAAAACCGG 60.665 50.000 0.00 0.00 39.14 5.28
330 332 3.116079 AGCTAGTCGAAAACCGGAAAA 57.884 42.857 9.46 0.00 39.14 2.29
331 333 3.671716 AGCTAGTCGAAAACCGGAAAAT 58.328 40.909 9.46 0.00 39.14 1.82
341 344 8.791605 GTCGAAAACCGGAAAATATATGAAAAC 58.208 33.333 9.46 0.00 39.14 2.43
345 348 8.980143 AAACCGGAAAATATATGAAAACACAG 57.020 30.769 9.46 0.00 0.00 3.66
363 367 4.516698 ACACAGTGACCTATGAAAAAGCTG 59.483 41.667 7.81 0.00 0.00 4.24
366 370 4.761739 CAGTGACCTATGAAAAAGCTGGAA 59.238 41.667 0.00 0.00 0.00 3.53
392 1317 7.725251 AGACATTCCTTGCTGTTTAAAAATGA 58.275 30.769 10.44 0.00 0.00 2.57
393 1318 8.203485 AGACATTCCTTGCTGTTTAAAAATGAA 58.797 29.630 10.44 2.67 0.00 2.57
395 1320 7.442062 ACATTCCTTGCTGTTTAAAAATGAAGG 59.558 33.333 10.44 9.42 0.00 3.46
396 1321 5.852827 TCCTTGCTGTTTAAAAATGAAGGG 58.147 37.500 12.53 2.53 31.43 3.95
404 1329 7.661437 GCTGTTTAAAAATGAAGGGAAAAGGAT 59.339 33.333 0.00 0.00 0.00 3.24
417 1342 8.986929 AAGGGAAAAGGATTAGAGTCATTATG 57.013 34.615 0.00 0.00 0.00 1.90
419 1344 6.207614 GGGAAAAGGATTAGAGTCATTATGCC 59.792 42.308 0.00 0.00 0.00 4.40
475 1401 9.515020 TCAAATTAAAGAGTGTAAACAGCTTTG 57.485 29.630 15.69 0.00 35.06 2.77
493 1419 4.505922 GCTTTGGTAGATCGATCTGTCTTG 59.494 45.833 33.22 20.05 37.76 3.02
522 1449 4.014406 TGTGCGTTGATCTTCTCCTACTA 58.986 43.478 0.00 0.00 0.00 1.82
523 1450 4.645136 TGTGCGTTGATCTTCTCCTACTAT 59.355 41.667 0.00 0.00 0.00 2.12
544 1471 2.426522 ACATCAATCACCAAGTCACCG 58.573 47.619 0.00 0.00 0.00 4.94
545 1472 1.131126 CATCAATCACCAAGTCACCGC 59.869 52.381 0.00 0.00 0.00 5.68
548 1475 2.002586 CAATCACCAAGTCACCGCTAG 58.997 52.381 0.00 0.00 0.00 3.42
563 1492 1.598701 GCTAGCCCAGGGTGCAAAAG 61.599 60.000 7.55 0.00 0.00 2.27
568 1497 1.247567 CCCAGGGTGCAAAAGTACAG 58.752 55.000 0.00 0.00 0.00 2.74
575 1504 2.286772 GGTGCAAAAGTACAGACCGTTG 60.287 50.000 0.00 0.00 0.00 4.10
800 1736 2.821366 CACGTGCATGCCTCCTCC 60.821 66.667 16.68 0.00 0.00 4.30
801 1737 3.005539 ACGTGCATGCCTCCTCCT 61.006 61.111 16.68 0.00 0.00 3.69
803 1739 2.729479 CGTGCATGCCTCCTCCTCT 61.729 63.158 16.68 0.00 0.00 3.69
804 1740 1.395045 CGTGCATGCCTCCTCCTCTA 61.395 60.000 16.68 0.00 0.00 2.43
805 1741 0.105778 GTGCATGCCTCCTCCTCTAC 59.894 60.000 16.68 0.00 0.00 2.59
806 1742 1.365633 GCATGCCTCCTCCTCTACG 59.634 63.158 6.36 0.00 0.00 3.51
924 1959 3.962481 GCCTACGACTACAAATACGTACG 59.038 47.826 15.01 15.01 39.59 3.67
925 1960 4.494199 GCCTACGACTACAAATACGTACGT 60.494 45.833 25.98 25.98 39.59 3.57
927 1962 6.120812 CCTACGACTACAAATACGTACGTAC 58.879 44.000 28.99 15.90 39.59 3.67
928 1963 4.893795 ACGACTACAAATACGTACGTACC 58.106 43.478 28.99 10.43 37.22 3.34
931 1966 2.559998 ACAAATACGTACGTACCCCG 57.440 50.000 28.99 19.16 44.03 5.73
949 1997 2.280552 GGCCGCCTATACCCATCGA 61.281 63.158 0.71 0.00 0.00 3.59
990 2042 5.117287 CGAGAGTGCAGTTTCTACTTTGTAC 59.883 44.000 10.11 0.00 30.26 2.90
991 2043 6.163135 AGAGTGCAGTTTCTACTTTGTACT 57.837 37.500 0.00 0.00 29.83 2.73
992 2044 7.286215 AGAGTGCAGTTTCTACTTTGTACTA 57.714 36.000 0.00 0.00 28.18 1.82
999 2051 7.313646 CAGTTTCTACTTTGTACTAGCTAGCA 58.686 38.462 20.91 4.89 30.26 3.49
1010 2062 0.030773 TAGCTAGCAATGTCGAGCCG 59.969 55.000 18.83 0.00 35.67 5.52
1196 2254 1.081509 GTACGTAACCGCACGACCA 60.082 57.895 0.00 0.00 44.69 4.02
1197 2255 1.081509 TACGTAACCGCACGACCAC 60.082 57.895 9.04 0.00 44.69 4.16
1199 2257 2.341176 GTAACCGCACGACCACCT 59.659 61.111 0.00 0.00 0.00 4.00
1201 2259 0.881600 GTAACCGCACGACCACCTTT 60.882 55.000 0.00 0.00 0.00 3.11
1202 2260 0.600782 TAACCGCACGACCACCTTTC 60.601 55.000 0.00 0.00 0.00 2.62
1204 2262 1.671054 CCGCACGACCACCTTTCAT 60.671 57.895 0.00 0.00 0.00 2.57
1243 2324 4.671377 GTGATTTTGATGTGTGTGTGTGT 58.329 39.130 0.00 0.00 0.00 3.72
1245 2326 4.157472 TGATTTTGATGTGTGTGTGTGTGT 59.843 37.500 0.00 0.00 0.00 3.72
1246 2327 3.484334 TTTGATGTGTGTGTGTGTGTG 57.516 42.857 0.00 0.00 0.00 3.82
1248 2329 1.736681 TGATGTGTGTGTGTGTGTGTG 59.263 47.619 0.00 0.00 0.00 3.82
1249 2330 2.006169 GATGTGTGTGTGTGTGTGTGA 58.994 47.619 0.00 0.00 0.00 3.58
1250 2331 2.106477 TGTGTGTGTGTGTGTGTGAT 57.894 45.000 0.00 0.00 0.00 3.06
1251 2332 2.431454 TGTGTGTGTGTGTGTGTGATT 58.569 42.857 0.00 0.00 0.00 2.57
1252 2333 2.418280 TGTGTGTGTGTGTGTGTGATTC 59.582 45.455 0.00 0.00 0.00 2.52
1253 2334 2.418280 GTGTGTGTGTGTGTGTGATTCA 59.582 45.455 0.00 0.00 0.00 2.57
1254 2335 3.065233 GTGTGTGTGTGTGTGTGATTCAT 59.935 43.478 0.00 0.00 0.00 2.57
1255 2336 3.065095 TGTGTGTGTGTGTGTGATTCATG 59.935 43.478 0.00 0.00 0.00 3.07
1339 2422 4.430765 CCGGCCGACTACAACGCT 62.431 66.667 30.73 0.00 0.00 5.07
1354 2437 1.938814 CGCTTGCAACACCAACACG 60.939 57.895 0.00 0.00 0.00 4.49
1735 2827 5.238650 TGCTTTCTAGTACTGCTTTCCAAAC 59.761 40.000 5.39 0.00 0.00 2.93
1768 2860 1.616159 CTCCTTTTCAAAGCCGGGAA 58.384 50.000 2.18 0.00 34.69 3.97
1797 2889 2.800250 CTCCTTTTCAGAGGGCAATGT 58.200 47.619 0.00 0.00 37.41 2.71
1828 2920 4.635765 TGCTCAGATTCTTTTCCGTTATGG 59.364 41.667 0.00 0.00 40.09 2.74
1872 2964 3.776969 TGGTTCCTGAATGAGATAGCACT 59.223 43.478 0.00 0.00 0.00 4.40
1873 2965 4.141846 TGGTTCCTGAATGAGATAGCACTC 60.142 45.833 0.00 0.00 37.42 3.51
1892 2984 0.459585 CAGCATTGGCATTCCAGCAC 60.460 55.000 0.00 0.00 44.53 4.40
1893 2985 0.901114 AGCATTGGCATTCCAGCACA 60.901 50.000 0.00 0.00 44.53 4.57
1894 2986 0.037139 GCATTGGCATTCCAGCACAA 60.037 50.000 0.00 0.00 44.53 3.33
1909 3001 9.970553 ATTCCAGCACAACATATTATCAGATAT 57.029 29.630 0.00 0.00 0.00 1.63
1959 3163 7.902920 ATCAGAAACCATAATAAGGCATGTT 57.097 32.000 0.00 0.00 0.00 2.71
1967 3171 5.639506 CCATAATAAGGCATGTTCGGACTAG 59.360 44.000 0.00 0.00 0.00 2.57
1968 3172 6.455647 CATAATAAGGCATGTTCGGACTAGA 58.544 40.000 0.00 0.00 0.00 2.43
1970 3174 3.914426 AAGGCATGTTCGGACTAGAAT 57.086 42.857 0.00 0.00 32.25 2.40
1971 3175 6.665992 ATAAGGCATGTTCGGACTAGAATA 57.334 37.500 0.00 0.00 32.25 1.75
1972 3176 5.552870 AAGGCATGTTCGGACTAGAATAT 57.447 39.130 0.00 0.00 33.21 1.28
1973 3177 5.552870 AGGCATGTTCGGACTAGAATATT 57.447 39.130 0.00 0.00 31.08 1.28
2001 3205 5.928264 TGCATAAATACACGATCAGAGATGG 59.072 40.000 0.00 0.00 0.00 3.51
2028 3232 1.506493 CGAAGCACAGCTCTGAAACT 58.494 50.000 3.60 0.00 38.25 2.66
2029 3233 1.194098 CGAAGCACAGCTCTGAAACTG 59.806 52.381 3.60 5.96 38.25 3.16
2030 3234 2.487934 GAAGCACAGCTCTGAAACTGA 58.512 47.619 12.75 0.00 38.25 3.41
2032 3236 1.139654 AGCACAGCTCTGAAACTGACA 59.860 47.619 12.75 0.00 37.35 3.58
2033 3237 1.530293 GCACAGCTCTGAAACTGACAG 59.470 52.381 12.75 0.00 37.35 3.51
2034 3238 2.831333 CACAGCTCTGAAACTGACAGT 58.169 47.619 1.07 1.07 37.35 3.55
2036 3240 4.371786 CACAGCTCTGAAACTGACAGTAA 58.628 43.478 8.91 0.00 37.35 2.24
2037 3241 4.811024 CACAGCTCTGAAACTGACAGTAAA 59.189 41.667 8.91 0.00 37.35 2.01
2043 3247 6.853362 GCTCTGAAACTGACAGTAAACAAATC 59.147 38.462 8.91 0.49 36.81 2.17
2044 3248 7.259290 TCTGAAACTGACAGTAAACAAATCC 57.741 36.000 8.91 0.00 36.81 3.01
2050 3257 5.820947 ACTGACAGTAAACAAATCCGAACTT 59.179 36.000 6.24 0.00 0.00 2.66
2063 3270 4.884668 TCCGAACTTGGAGTAAACTGAT 57.115 40.909 0.00 0.00 33.05 2.90
2064 3271 4.817517 TCCGAACTTGGAGTAAACTGATC 58.182 43.478 0.00 0.00 33.05 2.92
2068 3275 2.301870 ACTTGGAGTAAACTGATCGGCA 59.698 45.455 0.00 0.00 0.00 5.69
2095 3305 9.344772 ACTACATAGGATCTATAAGGCTATTCG 57.655 37.037 0.00 0.00 0.00 3.34
2099 3309 8.687242 CATAGGATCTATAAGGCTATTCGAACA 58.313 37.037 0.00 0.00 0.00 3.18
2100 3310 6.926313 AGGATCTATAAGGCTATTCGAACAC 58.074 40.000 0.00 0.00 0.00 3.32
2102 3312 5.117355 TCTATAAGGCTATTCGAACACCG 57.883 43.478 0.00 0.00 40.25 4.94
2167 3377 1.011595 ACAGCCTCCTTCCTCTCCTA 58.988 55.000 0.00 0.00 0.00 2.94
2170 3380 0.032017 GCCTCCTTCCTCTCCTACCA 60.032 60.000 0.00 0.00 0.00 3.25
2182 3392 1.078426 CCTACCACCCTTTCTGCGG 60.078 63.158 0.00 0.00 0.00 5.69
2200 3410 1.961277 GGTGCTGTCAGTGGGAACG 60.961 63.158 0.93 0.00 0.00 3.95
2227 3437 2.670414 CACGTCCTCTGCAAAGAGAATC 59.330 50.000 4.59 0.00 38.13 2.52
2236 3446 6.041423 TCTGCAAAGAGAATCAGACATACA 57.959 37.500 0.00 0.00 37.82 2.29
2239 3449 7.609146 TCTGCAAAGAGAATCAGACATACAATT 59.391 33.333 0.00 0.00 37.82 2.32
2263 3473 9.740710 ATTATTAGTTCTATGCCCAATAAGGAC 57.259 33.333 0.00 0.00 41.22 3.85
2266 3476 4.058817 GTTCTATGCCCAATAAGGACGAG 58.941 47.826 0.00 0.00 41.22 4.18
2300 3541 8.075574 TGAAACAGCAAAGTAACAAGATATGTG 58.924 33.333 0.00 0.00 42.99 3.21
2328 3569 4.294523 GCATATATGCGGCGGGAA 57.705 55.556 21.33 0.00 44.67 3.97
2329 3570 2.089854 GCATATATGCGGCGGGAAG 58.910 57.895 21.33 0.00 44.67 3.46
2330 3571 0.673644 GCATATATGCGGCGGGAAGT 60.674 55.000 21.33 0.00 44.67 3.01
2465 3706 1.443194 GTGCAAAGCAGTGATGCCG 60.443 57.895 11.82 0.00 40.08 5.69
2468 3709 1.136147 CAAAGCAGTGATGCCGAGC 59.864 57.895 0.00 0.00 34.90 5.03
2484 3725 4.443266 GCTCCTGGAAGCGCGAGT 62.443 66.667 12.10 0.00 31.56 4.18
2485 3726 2.507992 CTCCTGGAAGCGCGAGTG 60.508 66.667 12.10 0.00 0.00 3.51
2486 3727 3.997064 CTCCTGGAAGCGCGAGTGG 62.997 68.421 12.10 2.17 0.00 4.00
2491 3732 1.206831 GGAAGCGCGAGTGGAAAAC 59.793 57.895 12.10 0.00 0.00 2.43
2496 3737 3.173668 AGCGCGAGTGGAAAACATATA 57.826 42.857 12.10 0.00 0.00 0.86
2506 3747 7.041780 CGAGTGGAAAACATATAAGAATCCTGG 60.042 40.741 0.00 0.00 0.00 4.45
2508 3749 8.506083 AGTGGAAAACATATAAGAATCCTGGAT 58.494 33.333 2.57 2.57 0.00 3.41
2510 3751 8.281531 TGGAAAACATATAAGAATCCTGGATGT 58.718 33.333 10.54 0.00 0.00 3.06
2513 3754 9.799106 AAAACATATAAGAATCCTGGATGTAGG 57.201 33.333 10.54 3.73 39.29 3.18
2516 3757 3.567478 AAGAATCCTGGATGTAGGCAC 57.433 47.619 10.54 0.00 37.76 5.01
2517 3758 1.771255 AGAATCCTGGATGTAGGCACC 59.229 52.381 10.54 0.00 37.76 5.01
2518 3759 1.771255 GAATCCTGGATGTAGGCACCT 59.229 52.381 10.54 0.00 37.76 4.00
2519 3760 1.135094 ATCCTGGATGTAGGCACCTG 58.865 55.000 8.75 0.00 37.76 4.00
2563 3804 1.611491 CCCATACAAACCTTGCAACGT 59.389 47.619 0.00 0.00 0.00 3.99
2569 3810 2.331019 AAACCTTGCAACGTGTCGCC 62.331 55.000 0.00 0.00 0.00 5.54
2584 3825 0.321346 TCGCCACATCTTGAGAAGCA 59.679 50.000 0.00 0.00 0.00 3.91
2611 3852 1.797046 GCTGCATATGGTGATGACTCG 59.203 52.381 4.56 0.00 0.00 4.18
2652 3893 5.303589 CCTTCATTCCACCTGCATTGATTAT 59.696 40.000 0.00 0.00 0.00 1.28
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
3 4 2.125912 CTCGAGTGGTGGCCTTCG 60.126 66.667 3.32 6.09 34.47 3.79
44 45 0.890996 GAGGTGTTGGAGGGTTGCTG 60.891 60.000 0.00 0.00 0.00 4.41
54 55 0.401738 ACCTGTGATGGAGGTGTTGG 59.598 55.000 0.00 0.00 42.56 3.77
114 115 2.687566 ACCTACCCCTCTTGGCGG 60.688 66.667 0.00 0.00 0.00 6.13
116 117 0.470341 GATCACCTACCCCTCTTGGC 59.530 60.000 0.00 0.00 0.00 4.52
118 119 2.571653 TGTTGATCACCTACCCCTCTTG 59.428 50.000 0.00 0.00 0.00 3.02
120 121 2.188817 GTGTTGATCACCTACCCCTCT 58.811 52.381 0.00 0.00 40.84 3.69
121 122 2.693267 GTGTTGATCACCTACCCCTC 57.307 55.000 0.00 0.00 40.84 4.30
193 194 4.617253 ACTCCAGTTGCATGTTACTGTA 57.383 40.909 20.57 10.03 40.06 2.74
216 217 4.797693 TCGAAATAGCAAACGTTTGTGA 57.202 36.364 34.39 25.02 40.24 3.58
235 237 5.591643 ACAGTTGCACACTACTAAATTCG 57.408 39.130 0.00 0.00 32.76 3.34
238 240 6.365247 CGACTTACAGTTGCACACTACTAAAT 59.635 38.462 0.00 0.00 32.76 1.40
331 333 9.952030 TTTCATAGGTCACTGTGTTTTCATATA 57.048 29.630 7.79 0.00 37.16 0.86
341 344 4.083110 CCAGCTTTTTCATAGGTCACTGTG 60.083 45.833 0.17 0.17 37.19 3.66
345 348 5.473504 TCTTTCCAGCTTTTTCATAGGTCAC 59.526 40.000 0.00 0.00 0.00 3.67
366 370 8.203485 TCATTTTTAAACAGCAAGGAATGTCTT 58.797 29.630 0.00 0.00 0.00 3.01
378 382 6.989759 TCCTTTTCCCTTCATTTTTAAACAGC 59.010 34.615 0.00 0.00 0.00 4.40
379 383 9.559732 AATCCTTTTCCCTTCATTTTTAAACAG 57.440 29.630 0.00 0.00 0.00 3.16
392 1317 7.503902 GCATAATGACTCTAATCCTTTTCCCTT 59.496 37.037 0.00 0.00 0.00 3.95
393 1318 7.001073 GCATAATGACTCTAATCCTTTTCCCT 58.999 38.462 0.00 0.00 0.00 4.20
395 1320 7.001073 AGGCATAATGACTCTAATCCTTTTCC 58.999 38.462 0.00 0.00 18.29 3.13
417 1342 5.500645 AACACTTTTGACTTACAAGAGGC 57.499 39.130 0.00 0.00 42.59 4.70
474 1400 4.017126 ACACAAGACAGATCGATCTACCA 58.983 43.478 26.87 0.00 34.85 3.25
475 1401 4.640789 ACACAAGACAGATCGATCTACC 57.359 45.455 26.87 19.95 34.85 3.18
493 1419 4.177026 AGAAGATCAACGCACATCTACAC 58.823 43.478 0.00 0.00 0.00 2.90
522 1449 4.191544 CGGTGACTTGGTGATTGATGTAT 58.808 43.478 0.00 0.00 0.00 2.29
523 1450 3.595173 CGGTGACTTGGTGATTGATGTA 58.405 45.455 0.00 0.00 0.00 2.29
544 1471 1.598701 CTTTTGCACCCTGGGCTAGC 61.599 60.000 14.08 15.25 0.00 3.42
545 1472 0.251341 ACTTTTGCACCCTGGGCTAG 60.251 55.000 14.08 4.18 0.00 3.42
548 1475 0.825840 TGTACTTTTGCACCCTGGGC 60.826 55.000 14.08 0.00 0.00 5.36
563 1492 0.032952 TCAGGTGCAACGGTCTGTAC 59.967 55.000 0.72 0.00 38.12 2.90
568 1497 2.668550 GGGTCAGGTGCAACGGTC 60.669 66.667 0.72 0.00 38.12 4.79
575 1504 2.040544 CATTGGTCGGGTCAGGTGC 61.041 63.158 0.00 0.00 0.00 5.01
674 1603 1.705337 CGAATCGATGCTTTGCCGGT 61.705 55.000 1.90 0.00 0.00 5.28
725 1661 3.443045 CCACCCCATTGCGACTGC 61.443 66.667 0.00 0.00 43.20 4.40
726 1662 3.443045 GCCACCCCATTGCGACTG 61.443 66.667 0.00 0.00 0.00 3.51
727 1663 3.965258 TGCCACCCCATTGCGACT 61.965 61.111 0.00 0.00 0.00 4.18
805 1741 3.303001 GCCTCAAGCTACGTACTACTACG 60.303 52.174 0.00 1.02 44.23 3.51
806 1742 3.303001 CGCCTCAAGCTACGTACTACTAC 60.303 52.174 0.00 0.00 40.39 2.73
812 1846 0.525029 GGTCGCCTCAAGCTACGTAC 60.525 60.000 0.00 0.00 38.04 3.67
924 1959 2.601367 TATAGGCGGCCGGGGTAC 60.601 66.667 29.38 9.53 0.00 3.34
925 1960 2.601367 GTATAGGCGGCCGGGGTA 60.601 66.667 29.38 0.10 0.00 3.69
931 1966 2.264794 CGATGGGTATAGGCGGCC 59.735 66.667 12.11 12.11 0.00 6.13
935 1970 3.259876 TGTATTGGTCGATGGGTATAGGC 59.740 47.826 0.00 0.00 0.00 3.93
938 1973 4.345547 TGCTTGTATTGGTCGATGGGTATA 59.654 41.667 0.00 0.00 0.00 1.47
939 1974 3.135712 TGCTTGTATTGGTCGATGGGTAT 59.864 43.478 0.00 0.00 0.00 2.73
949 1997 4.141846 ACTCTCGATGATGCTTGTATTGGT 60.142 41.667 0.00 0.00 0.00 3.67
990 2042 1.777101 GGCTCGACATTGCTAGCTAG 58.223 55.000 16.84 16.84 35.30 3.42
991 2043 0.030773 CGGCTCGACATTGCTAGCTA 59.969 55.000 17.23 9.14 35.30 3.32
992 2044 1.227089 CGGCTCGACATTGCTAGCT 60.227 57.895 17.23 0.00 35.30 3.32
999 2051 2.427453 ACAAGATCTACGGCTCGACATT 59.573 45.455 0.00 0.00 0.00 2.71
1010 2062 2.014068 GCACCAGGCCACAAGATCTAC 61.014 57.143 5.01 0.00 36.11 2.59
1187 2245 0.591170 AAATGAAAGGTGGTCGTGCG 59.409 50.000 0.00 0.00 0.00 5.34
1196 2254 2.094545 GCCGAGATGCAAAATGAAAGGT 60.095 45.455 0.00 0.00 0.00 3.50
1197 2255 2.533266 GCCGAGATGCAAAATGAAAGG 58.467 47.619 0.00 0.00 0.00 3.11
1199 2257 1.809547 TCGCCGAGATGCAAAATGAAA 59.190 42.857 0.00 0.00 0.00 2.69
1201 2259 0.726827 GTCGCCGAGATGCAAAATGA 59.273 50.000 0.00 0.00 0.00 2.57
1202 2260 0.587242 CGTCGCCGAGATGCAAAATG 60.587 55.000 0.00 0.00 35.63 2.32
1204 2262 1.666553 ACGTCGCCGAGATGCAAAA 60.667 52.632 0.00 0.00 39.47 2.44
1270 2351 0.580104 GGTACACGAACACTGCACAC 59.420 55.000 0.00 0.00 0.00 3.82
1339 2422 0.374063 CGTACGTGTTGGTGTTGCAA 59.626 50.000 7.22 0.00 0.00 4.08
1354 2437 0.782384 CGGTGAACTGCTTGTCGTAC 59.218 55.000 0.00 0.00 0.00 3.67
1516 2599 3.595758 GTTGCTGTTGCTGCGGGT 61.596 61.111 0.00 0.00 40.48 5.28
1519 2602 2.425773 GTCGTTGCTGTTGCTGCG 60.426 61.111 0.00 0.00 40.48 5.18
1686 2778 0.248458 GGCGTATCCAAACAATGCCG 60.248 55.000 0.00 0.00 35.70 5.69
1735 2827 5.248640 TGAAAAGGAGCAGTGAAAGATAGG 58.751 41.667 0.00 0.00 0.00 2.57
1768 2860 5.012893 CCCTCTGAAAAGGAGCAAATAGTT 58.987 41.667 0.00 0.00 38.87 2.24
1797 2889 5.477510 GAAAAGAATCTGAGCAGAGAGACA 58.522 41.667 6.34 0.00 41.33 3.41
1828 2920 6.982141 ACCATCATATTGCATTTGTCATTGAC 59.018 34.615 9.93 9.93 0.00 3.18
1872 2964 0.612453 TGCTGGAATGCCAATGCTGA 60.612 50.000 5.59 0.00 45.41 4.26
1873 2965 0.459585 GTGCTGGAATGCCAATGCTG 60.460 55.000 5.59 0.00 45.41 4.41
1913 3005 9.950496 CTGATAATATGGTTGGCTCTTATTAGT 57.050 33.333 0.00 0.00 0.00 2.24
1916 3008 9.866655 TTTCTGATAATATGGTTGGCTCTTATT 57.133 29.630 0.00 0.00 0.00 1.40
1917 3009 9.289782 GTTTCTGATAATATGGTTGGCTCTTAT 57.710 33.333 0.00 0.00 0.00 1.73
1918 3010 7.719633 GGTTTCTGATAATATGGTTGGCTCTTA 59.280 37.037 0.00 0.00 0.00 2.10
1920 3012 6.064717 GGTTTCTGATAATATGGTTGGCTCT 58.935 40.000 0.00 0.00 0.00 4.09
1921 3013 5.827797 TGGTTTCTGATAATATGGTTGGCTC 59.172 40.000 0.00 0.00 0.00 4.70
1932 3024 9.592196 ACATGCCTTATTATGGTTTCTGATAAT 57.408 29.630 0.00 0.00 0.00 1.28
1973 3177 8.262715 TCTCTGATCGTGTATTTATGCAAAAA 57.737 30.769 0.00 0.00 0.00 1.94
1977 3181 5.928264 CCATCTCTGATCGTGTATTTATGCA 59.072 40.000 0.00 0.00 0.00 3.96
2001 3205 0.948141 AGCTGTGCTTCGCTTCAGAC 60.948 55.000 12.74 6.77 33.89 3.51
2026 3230 5.365619 AGTTCGGATTTGTTTACTGTCAGT 58.634 37.500 10.99 10.99 0.00 3.41
2027 3231 5.924475 AGTTCGGATTTGTTTACTGTCAG 57.076 39.130 0.00 0.00 0.00 3.51
2028 3232 5.008217 CCAAGTTCGGATTTGTTTACTGTCA 59.992 40.000 0.00 0.00 0.00 3.58
2029 3233 5.237779 TCCAAGTTCGGATTTGTTTACTGTC 59.762 40.000 0.00 0.00 0.00 3.51
2030 3234 5.127491 TCCAAGTTCGGATTTGTTTACTGT 58.873 37.500 0.00 0.00 0.00 3.55
2032 3236 5.374071 ACTCCAAGTTCGGATTTGTTTACT 58.626 37.500 0.00 0.00 33.56 2.24
2033 3237 5.684550 ACTCCAAGTTCGGATTTGTTTAC 57.315 39.130 0.00 0.00 33.56 2.01
2034 3238 7.499895 AGTTTACTCCAAGTTCGGATTTGTTTA 59.500 33.333 0.00 0.00 33.56 2.01
2036 3240 5.826208 AGTTTACTCCAAGTTCGGATTTGTT 59.174 36.000 0.00 0.00 33.56 2.83
2037 3241 5.238650 CAGTTTACTCCAAGTTCGGATTTGT 59.761 40.000 0.00 0.00 33.56 2.83
2043 3247 3.612860 CGATCAGTTTACTCCAAGTTCGG 59.387 47.826 0.00 0.00 0.00 4.30
2044 3248 3.612860 CCGATCAGTTTACTCCAAGTTCG 59.387 47.826 0.00 0.00 0.00 3.95
2050 3257 2.301870 AGTTGCCGATCAGTTTACTCCA 59.698 45.455 0.00 0.00 0.00 3.86
2063 3270 6.377429 CCTTATAGATCCTATGTAGTTGCCGA 59.623 42.308 0.00 0.00 0.00 5.54
2064 3271 6.565234 CCTTATAGATCCTATGTAGTTGCCG 58.435 44.000 0.00 0.00 0.00 5.69
2095 3305 2.279136 CGTGATCGAGAATTCGGTGTTC 59.721 50.000 0.00 0.20 46.67 3.18
2099 3309 0.527817 GCCGTGATCGAGAATTCGGT 60.528 55.000 14.92 0.00 46.67 4.69
2100 3310 1.215655 GGCCGTGATCGAGAATTCGG 61.216 60.000 0.00 11.13 46.67 4.30
2102 3312 1.528586 CATGGCCGTGATCGAGAATTC 59.471 52.381 21.08 0.00 39.71 2.17
2109 3319 0.596083 GTCTCTCATGGCCGTGATCG 60.596 60.000 27.70 20.11 0.00 3.69
2113 3323 0.873312 CATCGTCTCTCATGGCCGTG 60.873 60.000 19.62 19.62 0.00 4.94
2117 3327 3.935203 TCTTTTTCATCGTCTCTCATGGC 59.065 43.478 0.00 0.00 0.00 4.40
2182 3392 1.961277 CGTTCCCACTGACAGCACC 60.961 63.158 1.25 0.00 0.00 5.01
2200 3410 4.083862 GCAGAGGACGTGACCCCC 62.084 72.222 0.00 0.00 0.00 5.40
2239 3449 7.233962 TCGTCCTTATTGGGCATAGAACTAATA 59.766 37.037 0.00 0.00 41.50 0.98
2262 3472 1.873591 GCTGTTTCATTGTGGTCTCGT 59.126 47.619 0.00 0.00 0.00 4.18
2263 3473 1.872952 TGCTGTTTCATTGTGGTCTCG 59.127 47.619 0.00 0.00 0.00 4.04
2266 3476 4.045636 ACTTTGCTGTTTCATTGTGGTC 57.954 40.909 0.00 0.00 0.00 4.02
2321 3562 2.014857 GGTAAATTCTGACTTCCCGCC 58.985 52.381 0.00 0.00 0.00 6.13
2326 3567 5.296813 ACGCATTGGTAAATTCTGACTTC 57.703 39.130 0.00 0.00 0.00 3.01
2327 3568 4.156008 GGACGCATTGGTAAATTCTGACTT 59.844 41.667 0.00 0.00 0.00 3.01
2328 3569 3.689649 GGACGCATTGGTAAATTCTGACT 59.310 43.478 0.00 0.00 0.00 3.41
2329 3570 3.438781 TGGACGCATTGGTAAATTCTGAC 59.561 43.478 0.00 0.00 0.00 3.51
2330 3571 3.680490 TGGACGCATTGGTAAATTCTGA 58.320 40.909 0.00 0.00 0.00 3.27
2465 3706 4.135153 TCGCGCTTCCAGGAGCTC 62.135 66.667 4.71 4.71 40.52 4.09
2468 3709 2.507992 CACTCGCGCTTCCAGGAG 60.508 66.667 5.56 5.97 0.00 3.69
2481 3722 7.993183 TCCAGGATTCTTATATGTTTTCCACTC 59.007 37.037 0.00 0.00 0.00 3.51
2484 3725 8.281531 ACATCCAGGATTCTTATATGTTTTCCA 58.718 33.333 0.00 0.00 0.00 3.53
2485 3726 8.697507 ACATCCAGGATTCTTATATGTTTTCC 57.302 34.615 0.00 0.00 0.00 3.13
2491 3732 6.820656 GTGCCTACATCCAGGATTCTTATATG 59.179 42.308 0.00 0.00 38.00 1.78
2496 3737 2.173569 GGTGCCTACATCCAGGATTCTT 59.826 50.000 0.00 0.00 38.00 2.52
2506 3747 3.334583 TTCTGTTCAGGTGCCTACATC 57.665 47.619 0.00 0.00 0.00 3.06
2508 3749 3.569194 TTTTCTGTTCAGGTGCCTACA 57.431 42.857 0.00 0.00 0.00 2.74
2510 3751 5.488341 GACTATTTTCTGTTCAGGTGCCTA 58.512 41.667 0.00 0.00 0.00 3.93
2512 3753 3.440522 GGACTATTTTCTGTTCAGGTGCC 59.559 47.826 0.00 0.00 0.00 5.01
2513 3754 4.072131 TGGACTATTTTCTGTTCAGGTGC 58.928 43.478 0.00 0.00 0.00 5.01
2516 3757 7.452880 TTCATTGGACTATTTTCTGTTCAGG 57.547 36.000 0.00 0.00 0.00 3.86
2517 3758 7.540055 GCTTTCATTGGACTATTTTCTGTTCAG 59.460 37.037 0.00 0.00 0.00 3.02
2518 3759 7.370383 GCTTTCATTGGACTATTTTCTGTTCA 58.630 34.615 0.00 0.00 0.00 3.18
2519 3760 6.808704 GGCTTTCATTGGACTATTTTCTGTTC 59.191 38.462 0.00 0.00 0.00 3.18
2563 3804 1.941209 GCTTCTCAAGATGTGGCGACA 60.941 52.381 3.31 3.31 36.22 4.35
2611 3852 0.247736 AGGTCAAGGCTGATCGTGAC 59.752 55.000 7.58 7.58 42.55 3.67
2652 3893 9.549078 GGTTTAAAAGTAAATTTGATTGTCCCA 57.451 29.630 0.00 0.00 31.94 4.37


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

AutoCloner maintained by Alex Coulton.