Multiple sequence alignment - TraesCS6B01G158000

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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 TraesCS6B01G158000 chr6B 100.000 3285 0 0 1 3285 160684108 160680824 0.000000e+00 6067
1 TraesCS6B01G158000 chr6B 87.461 2536 269 29 769 3285 159990022 159987517 0.000000e+00 2876
2 TraesCS6B01G158000 chr6B 89.323 2229 233 3 920 3147 160717021 160714797 0.000000e+00 2793
3 TraesCS6B01G158000 chr6B 92.708 96 7 0 216 311 160710007 160709912 4.420000e-29 139
4 TraesCS6B01G158000 chr6D 87.825 2538 271 25 769 3285 84232044 84229524 0.000000e+00 2940
5 TraesCS6B01G158000 chr6D 89.412 2229 231 3 920 3147 84631063 84628839 0.000000e+00 2804
6 TraesCS6B01G158000 chr6D 87.364 2390 269 21 770 3147 84620238 84617870 0.000000e+00 2710
7 TraesCS6B01G158000 chr6D 85.774 2383 291 28 808 3175 84224569 84222220 0.000000e+00 2479
8 TraesCS6B01G158000 chr6D 84.537 2244 290 32 953 3176 84653918 84651712 0.000000e+00 2169
9 TraesCS6B01G158000 chr6D 83.848 2297 343 18 891 3177 84474125 84471847 0.000000e+00 2161
10 TraesCS6B01G158000 chr6D 92.391 736 26 6 1 732 84621103 84620394 0.000000e+00 1022
11 TraesCS6B01G158000 chr6A 87.461 2536 277 27 769 3285 101562860 101560347 0.000000e+00 2883
12 TraesCS6B01G158000 chr6A 86.194 2383 294 23 808 3175 101554927 101552565 0.000000e+00 2545
13 TraesCS6B01G158000 chr6A 77.622 286 39 17 216 494 101852087 101851820 2.040000e-32 150


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 TraesCS6B01G158000 chr6B 160680824 160684108 3284 True 6067 6067 100.0000 1 3285 1 chr6B.!!$R2 3284
1 TraesCS6B01G158000 chr6B 159987517 159990022 2505 True 2876 2876 87.4610 769 3285 1 chr6B.!!$R1 2516
2 TraesCS6B01G158000 chr6B 160714797 160717021 2224 True 2793 2793 89.3230 920 3147 1 chr6B.!!$R4 2227
3 TraesCS6B01G158000 chr6D 84229524 84232044 2520 True 2940 2940 87.8250 769 3285 1 chr6D.!!$R2 2516
4 TraesCS6B01G158000 chr6D 84628839 84631063 2224 True 2804 2804 89.4120 920 3147 1 chr6D.!!$R4 2227
5 TraesCS6B01G158000 chr6D 84222220 84224569 2349 True 2479 2479 85.7740 808 3175 1 chr6D.!!$R1 2367
6 TraesCS6B01G158000 chr6D 84651712 84653918 2206 True 2169 2169 84.5370 953 3176 1 chr6D.!!$R5 2223
7 TraesCS6B01G158000 chr6D 84471847 84474125 2278 True 2161 2161 83.8480 891 3177 1 chr6D.!!$R3 2286
8 TraesCS6B01G158000 chr6D 84617870 84621103 3233 True 1866 2710 89.8775 1 3147 2 chr6D.!!$R6 3146
9 TraesCS6B01G158000 chr6A 101560347 101562860 2513 True 2883 2883 87.4610 769 3285 1 chr6A.!!$R2 2516
10 TraesCS6B01G158000 chr6A 101552565 101554927 2362 True 2545 2545 86.1940 808 3175 1 chr6A.!!$R1 2367

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
463 464 0.400213 TTCCCAGTAACCCACAGCTG 59.600 55.0 13.48 13.48 0.00 4.24 F
1884 2035 0.396417 TAGGTCAGCTCAGGAGGCTC 60.396 60.0 5.78 5.78 38.03 4.70 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2241 2394 0.175760 GGACGCTGATGCTCCTACAA 59.824 55.000 0.00 0.0 35.26 2.41 R
2913 3066 1.345415 AGCTGGCCTTTTGTTGGAATG 59.655 47.619 3.32 0.0 0.00 2.67 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
72 73 3.395054 ACCCCCAGTACTCTACTAACC 57.605 52.381 0.00 0.00 37.23 2.85
130 131 5.470047 TGAACTGAGAAGAGGAAACCTAC 57.530 43.478 0.00 0.00 31.76 3.18
147 148 2.101582 CCTACCTGAACTCTTCCCATCG 59.898 54.545 0.00 0.00 0.00 3.84
161 162 1.336440 CCCATCGTGCAAGAAACAACA 59.664 47.619 6.39 0.00 0.00 3.33
268 269 4.338879 ACCATTTGACTCTCATTTCCAGG 58.661 43.478 0.00 0.00 0.00 4.45
308 309 6.128607 TGCATTAAAGCATGGAAAACAAATCG 60.129 34.615 0.28 0.00 40.11 3.34
322 323 2.289547 ACAAATCGTGTGGTGTAACTGC 59.710 45.455 0.00 0.00 39.72 4.40
323 324 1.519408 AATCGTGTGGTGTAACTGCC 58.481 50.000 0.00 0.00 36.74 4.85
324 325 0.685097 ATCGTGTGGTGTAACTGCCT 59.315 50.000 0.00 0.00 36.74 4.75
325 326 1.330234 TCGTGTGGTGTAACTGCCTA 58.670 50.000 0.00 0.00 36.74 3.93
326 327 1.687660 TCGTGTGGTGTAACTGCCTAA 59.312 47.619 0.00 0.00 36.74 2.69
327 328 1.796459 CGTGTGGTGTAACTGCCTAAC 59.204 52.381 0.00 0.00 36.74 2.34
328 329 2.547218 CGTGTGGTGTAACTGCCTAACT 60.547 50.000 0.00 0.00 36.74 2.24
329 330 2.806244 GTGTGGTGTAACTGCCTAACTG 59.194 50.000 0.00 0.00 36.74 3.16
330 331 2.224426 TGTGGTGTAACTGCCTAACTGG 60.224 50.000 0.00 0.00 36.74 4.00
331 332 2.038033 GTGGTGTAACTGCCTAACTGGA 59.962 50.000 0.00 0.00 35.50 3.86
439 440 5.781306 TCAAGTATACCAACTGTAGGGTGAA 59.219 40.000 12.75 0.62 38.06 3.18
452 453 4.351407 TGTAGGGTGAACAAATTCCCAGTA 59.649 41.667 0.00 0.00 42.12 2.74
453 454 4.463050 AGGGTGAACAAATTCCCAGTAA 57.537 40.909 0.00 0.00 42.12 2.24
454 455 4.149598 AGGGTGAACAAATTCCCAGTAAC 58.850 43.478 0.00 0.00 42.12 2.50
455 456 3.257375 GGGTGAACAAATTCCCAGTAACC 59.743 47.826 0.00 0.00 39.68 2.85
456 457 3.257375 GGTGAACAAATTCCCAGTAACCC 59.743 47.826 0.00 0.00 33.49 4.11
457 458 3.892588 GTGAACAAATTCCCAGTAACCCA 59.107 43.478 0.00 0.00 33.49 4.51
458 459 3.892588 TGAACAAATTCCCAGTAACCCAC 59.107 43.478 0.00 0.00 33.49 4.61
459 460 3.603965 ACAAATTCCCAGTAACCCACA 57.396 42.857 0.00 0.00 0.00 4.17
460 461 3.496331 ACAAATTCCCAGTAACCCACAG 58.504 45.455 0.00 0.00 0.00 3.66
461 462 2.215942 AATTCCCAGTAACCCACAGC 57.784 50.000 0.00 0.00 0.00 4.40
462 463 1.372501 ATTCCCAGTAACCCACAGCT 58.627 50.000 0.00 0.00 0.00 4.24
463 464 0.400213 TTCCCAGTAACCCACAGCTG 59.600 55.000 13.48 13.48 0.00 4.24
464 465 1.002134 CCCAGTAACCCACAGCTGG 60.002 63.158 19.93 6.95 45.86 4.85
465 466 1.675641 CCAGTAACCCACAGCTGGC 60.676 63.158 19.93 0.00 41.46 4.85
466 467 1.675641 CAGTAACCCACAGCTGGCC 60.676 63.158 19.93 0.00 36.00 5.36
467 468 2.361230 GTAACCCACAGCTGGCCC 60.361 66.667 19.93 0.00 36.00 5.80
468 469 2.856494 TAACCCACAGCTGGCCCA 60.856 61.111 19.93 0.00 36.00 5.36
534 535 5.178797 CCACTAGCATATGTACTATTGGGC 58.821 45.833 14.14 0.00 36.21 5.36
535 536 5.046304 CCACTAGCATATGTACTATTGGGCT 60.046 44.000 14.14 0.00 36.21 5.19
537 538 3.679389 AGCATATGTACTATTGGGCTGC 58.321 45.455 4.29 0.00 0.00 5.25
552 553 2.543653 GGGCTGCAACGCAATAAATAGG 60.544 50.000 0.50 0.00 38.41 2.57
556 557 4.591202 CTGCAACGCAATAAATAGGTCAG 58.409 43.478 0.00 0.00 38.41 3.51
564 565 8.142994 ACGCAATAAATAGGTCAGTTAAGATG 57.857 34.615 0.00 0.00 0.00 2.90
623 627 5.973899 TTTCAGCCATGTAAACATAAGCA 57.026 34.783 15.61 0.00 37.31 3.91
659 663 6.054295 GCTGGTAGATGACAGATTGATTTCT 58.946 40.000 0.00 0.00 36.86 2.52
660 664 6.202570 GCTGGTAGATGACAGATTGATTTCTC 59.797 42.308 0.00 0.00 36.86 2.87
661 665 7.429374 TGGTAGATGACAGATTGATTTCTCT 57.571 36.000 0.00 0.00 0.00 3.10
702 706 8.621532 GGATACAATGCCTAACATCAATCTAA 57.378 34.615 0.00 0.00 38.34 2.10
705 709 7.516198 ACAATGCCTAACATCAATCTAATCC 57.484 36.000 0.00 0.00 38.34 3.01
762 864 6.346096 AGCTTTATAAACTAGTTGATGGCGA 58.654 36.000 14.89 0.00 0.00 5.54
763 865 6.480320 AGCTTTATAAACTAGTTGATGGCGAG 59.520 38.462 14.89 8.42 0.00 5.03
765 867 7.437267 GCTTTATAAACTAGTTGATGGCGAGTA 59.563 37.037 14.89 0.00 0.00 2.59
767 869 6.710597 ATAAACTAGTTGATGGCGAGTAGA 57.289 37.500 9.34 0.00 35.71 2.59
792 914 0.810031 CGGATGTAGCTTTCCCACGG 60.810 60.000 0.00 0.00 0.00 4.94
800 922 1.549170 AGCTTTCCCACGGTAGTACTG 59.451 52.381 5.39 7.62 0.00 2.74
804 926 1.153628 CCCACGGTAGTACTGCAGC 60.154 63.158 15.27 0.00 0.00 5.25
821 944 0.975040 AGCCTTTTGTGCACCAACCA 60.975 50.000 15.69 0.00 31.20 3.67
858 986 3.544684 CTTAAGCTGCACCCATGACATA 58.455 45.455 1.02 0.00 0.00 2.29
862 990 1.133025 GCTGCACCCATGACATAACAC 59.867 52.381 0.00 0.00 0.00 3.32
865 993 1.677518 GCACCCATGACATAACACGGA 60.678 52.381 0.00 0.00 0.00 4.69
869 997 3.008594 ACCCATGACATAACACGGAGAAA 59.991 43.478 0.00 0.00 0.00 2.52
870 998 4.006989 CCCATGACATAACACGGAGAAAA 58.993 43.478 0.00 0.00 0.00 2.29
872 1000 5.449041 CCCATGACATAACACGGAGAAAATG 60.449 44.000 0.00 0.00 0.00 2.32
873 1001 5.123820 CCATGACATAACACGGAGAAAATGT 59.876 40.000 0.00 0.00 0.00 2.71
874 1002 6.349280 CCATGACATAACACGGAGAAAATGTT 60.349 38.462 0.00 0.00 39.75 2.71
875 1003 7.148323 CCATGACATAACACGGAGAAAATGTTA 60.148 37.037 0.00 0.00 41.64 2.41
876 1004 7.915293 TGACATAACACGGAGAAAATGTTAT 57.085 32.000 3.59 3.59 45.81 1.89
881 1009 5.862924 ACACGGAGAAAATGTTATGAGTG 57.137 39.130 0.00 0.00 0.00 3.51
882 1010 4.695455 ACACGGAGAAAATGTTATGAGTGG 59.305 41.667 0.00 0.00 0.00 4.00
885 1013 4.695455 CGGAGAAAATGTTATGAGTGGTGT 59.305 41.667 0.00 0.00 0.00 4.16
887 1015 6.183360 CGGAGAAAATGTTATGAGTGGTGTAC 60.183 42.308 0.00 0.00 0.00 2.90
888 1016 6.653320 GGAGAAAATGTTATGAGTGGTGTACA 59.347 38.462 0.00 0.00 0.00 2.90
912 1040 3.499537 TGTTCATTGACTCTGATGCACAC 59.500 43.478 0.00 0.00 27.28 3.82
928 1057 2.610232 GCACACAATAAAGCCCCTGTTG 60.610 50.000 0.00 0.00 0.00 3.33
936 1065 3.979501 AAAGCCCCTGTTGGATGATAT 57.020 42.857 0.00 0.00 35.39 1.63
938 1067 4.647564 AAGCCCCTGTTGGATGATATAG 57.352 45.455 0.00 0.00 35.39 1.31
970 1100 1.828595 TGCATGCATCCTTCAAGCAAT 59.171 42.857 18.46 0.00 42.15 3.56
1005 1153 0.673437 AGAAACACCAACCAATGCGG 59.327 50.000 0.00 0.00 42.50 5.69
1023 1172 1.295746 GTTCCTCACCGTTCCTCCC 59.704 63.158 0.00 0.00 0.00 4.30
1035 1184 4.457496 CCTCCCGTCGTGCTGCAT 62.457 66.667 5.27 0.00 0.00 3.96
1104 1253 1.003233 GGAGAAGCGCAACCTCCTT 60.003 57.895 25.65 5.61 42.36 3.36
1119 1268 1.125093 TCCTTCAGTTCCTTGCCGGA 61.125 55.000 5.05 0.00 41.06 5.14
1125 1274 1.207089 CAGTTCCTTGCCGGACTATCA 59.793 52.381 5.05 0.00 42.97 2.15
1131 1280 2.271800 CTTGCCGGACTATCACAAGAC 58.728 52.381 5.05 0.00 40.06 3.01
1284 1435 3.314331 CTGGCCGACCTCACCAGT 61.314 66.667 0.00 0.00 44.91 4.00
1320 1471 3.082548 CCTCTCGTACAACTCCTTCTCA 58.917 50.000 0.00 0.00 0.00 3.27
1443 1594 3.241530 ACTGACCGGCCTCTGCAA 61.242 61.111 0.00 0.00 40.13 4.08
1458 1609 3.838120 TCTGCAAGTACTCAACATCTCG 58.162 45.455 0.00 0.00 33.76 4.04
1573 1724 3.325870 CACATACCGTCTTCTCTTTGCA 58.674 45.455 0.00 0.00 0.00 4.08
1580 1731 2.227388 CGTCTTCTCTTTGCATTGGCTT 59.773 45.455 0.00 0.00 41.91 4.35
1623 1774 2.421424 CCTCTGCTACAACCAATTGAGC 59.579 50.000 7.12 8.07 39.30 4.26
1884 2035 0.396417 TAGGTCAGCTCAGGAGGCTC 60.396 60.000 5.78 5.78 38.03 4.70
1932 2085 3.473647 TCTGGGGAGCTGCCATCG 61.474 66.667 26.95 13.08 38.95 3.84
1993 2146 5.436175 TGAAGATCAACAACTTCAGTGGAA 58.564 37.500 0.00 0.00 44.59 3.53
2024 2177 1.676916 GGTAAACTTCGCCACCCTACC 60.677 57.143 0.00 0.00 0.00 3.18
2036 2189 3.376234 GCCACCCTACCGAATCTAAAAAC 59.624 47.826 0.00 0.00 0.00 2.43
2071 2224 8.212995 TCATGAAGAATAATCTCAGTGGCATAA 58.787 33.333 0.00 0.00 33.77 1.90
2122 2275 2.974148 CTGCACTGCGGCTGTCAA 60.974 61.111 9.71 0.70 34.04 3.18
2123 2276 2.281692 TGCACTGCGGCTGTCAAT 60.282 55.556 9.71 0.00 34.04 2.57
2136 2289 3.578688 GCTGTCAATCAACCATTTCCAC 58.421 45.455 0.00 0.00 0.00 4.02
2145 2298 2.819608 CAACCATTTCCACGGTGAGATT 59.180 45.455 10.28 0.00 35.08 2.40
2149 2302 3.505680 CCATTTCCACGGTGAGATTTCAA 59.494 43.478 10.28 0.00 34.49 2.69
2192 2345 4.870991 GCACTTGTCCTTCCTATCACTTAC 59.129 45.833 0.00 0.00 0.00 2.34
2194 2347 6.102663 CACTTGTCCTTCCTATCACTTACTG 58.897 44.000 0.00 0.00 0.00 2.74
2222 2375 5.418840 ACTCCTTCACAAACATCACAAAAGT 59.581 36.000 0.00 0.00 0.00 2.66
2236 2389 3.002553 CACAAAAGTTTTGCATGCCCTTC 59.997 43.478 24.86 3.59 0.00 3.46
2241 2394 1.615392 GTTTTGCATGCCCTTCAGAGT 59.385 47.619 16.68 0.00 0.00 3.24
2249 2402 1.902508 TGCCCTTCAGAGTTGTAGGAG 59.097 52.381 2.24 0.00 42.72 3.69
2343 2496 5.535753 TCCAGAATCTTCAATATCTCGCA 57.464 39.130 0.00 0.00 0.00 5.10
2344 2497 5.536260 TCCAGAATCTTCAATATCTCGCAG 58.464 41.667 0.00 0.00 0.00 5.18
2445 2598 0.902531 ATCGACTCACCGGACCAATT 59.097 50.000 9.46 0.00 0.00 2.32
2539 2692 3.284617 CCAATCACCTTGATGCAGATGA 58.715 45.455 0.00 0.00 37.15 2.92
2653 2806 3.621268 TCAATACCGCATAAACAGTGCTC 59.379 43.478 0.00 0.00 40.37 4.26
2778 2931 4.222336 ACTTCTATGGAGAGATCCCACAG 58.778 47.826 0.00 0.00 36.36 3.66
2797 2950 1.743958 AGTCGATCGGTAACCTCACTG 59.256 52.381 16.41 0.00 0.00 3.66
2913 3066 3.503800 AACAACAACCTAGAAGGACCC 57.496 47.619 0.00 0.00 37.67 4.46
2982 3135 0.815095 GGAACCCAAAACTATGCGGG 59.185 55.000 0.00 0.00 44.88 6.13
3065 3218 3.855689 ACAATGCAGCAATAAGGTCAC 57.144 42.857 0.00 0.00 0.00 3.67
3072 3225 2.557924 CAGCAATAAGGTCACCTTTGCA 59.442 45.455 27.75 7.90 44.94 4.08
3177 3337 7.966812 TCAACTGTAATATGATCCAGTATGCT 58.033 34.615 1.20 0.00 37.18 3.79
3184 3344 7.746243 AATATGATCCAGTATGCTATGGTCT 57.254 36.000 0.00 0.00 37.84 3.85
3187 3347 4.464244 TGATCCAGTATGCTATGGTCTAGC 59.536 45.833 0.00 0.00 40.76 3.42
3194 3354 2.962859 TGCTATGGTCTAGCATCCAGA 58.037 47.619 2.92 2.73 44.65 3.86
3211 3371 6.707608 GCATCCAGATATGTTGTTCACATCTA 59.292 38.462 0.00 0.00 43.17 1.98
3212 3372 7.095313 GCATCCAGATATGTTGTTCACATCTAG 60.095 40.741 0.00 0.00 43.17 2.43
3215 3375 6.481313 CCAGATATGTTGTTCACATCTAGGTG 59.519 42.308 0.04 0.04 43.17 4.00
3219 3379 4.631131 TGTTGTTCACATCTAGGTGTCTG 58.369 43.478 5.41 0.00 39.76 3.51
3220 3380 3.319137 TGTTCACATCTAGGTGTCTGC 57.681 47.619 5.41 0.00 39.76 4.26
3221 3381 2.632512 TGTTCACATCTAGGTGTCTGCA 59.367 45.455 5.41 2.38 39.76 4.41
3223 3383 4.256920 GTTCACATCTAGGTGTCTGCATT 58.743 43.478 5.41 0.00 39.76 3.56
3228 3388 5.007430 CACATCTAGGTGTCTGCATTCAATC 59.993 44.000 5.41 0.00 34.09 2.67
3229 3389 5.104610 ACATCTAGGTGTCTGCATTCAATCT 60.105 40.000 1.73 0.00 0.00 2.40
3279 3439 9.851686 ATCATTAGAAGTAGAATATTGTTGGCA 57.148 29.630 0.00 0.00 0.00 4.92
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
30 31 9.403583 GGGGTATTTGTGTTTCAATAGAATCTA 57.596 33.333 0.00 0.00 35.84 1.98
55 56 3.705051 TGGTGGTTAGTAGAGTACTGGG 58.295 50.000 0.00 0.00 39.81 4.45
72 73 0.169672 CTCCATGCTCGCTTTTGGTG 59.830 55.000 0.00 1.90 0.00 4.17
130 131 2.009042 GCACGATGGGAAGAGTTCAGG 61.009 57.143 0.00 0.00 0.00 3.86
147 148 6.972328 TCTTACTTCATTGTTGTTTCTTGCAC 59.028 34.615 0.00 0.00 0.00 4.57
308 309 2.806244 CAGTTAGGCAGTTACACCACAC 59.194 50.000 0.00 0.00 0.00 3.82
322 323 3.071874 TGCAGAATGGTTCCAGTTAGG 57.928 47.619 0.00 0.00 35.86 2.69
323 324 6.949352 ATAATGCAGAATGGTTCCAGTTAG 57.051 37.500 0.00 0.00 35.86 2.34
324 325 7.716799 AAATAATGCAGAATGGTTCCAGTTA 57.283 32.000 0.00 0.00 35.86 2.24
325 326 6.610075 AAATAATGCAGAATGGTTCCAGTT 57.390 33.333 0.00 0.00 35.86 3.16
326 327 7.560991 TGATAAATAATGCAGAATGGTTCCAGT 59.439 33.333 0.00 0.00 35.86 4.00
327 328 7.944061 TGATAAATAATGCAGAATGGTTCCAG 58.056 34.615 0.00 0.00 35.86 3.86
328 329 7.894753 TGATAAATAATGCAGAATGGTTCCA 57.105 32.000 0.00 0.00 35.86 3.53
329 330 9.768662 ATTTGATAAATAATGCAGAATGGTTCC 57.231 29.630 0.00 0.00 35.86 3.62
379 380 2.498885 GACCGTACCCAAAGATACCAGT 59.501 50.000 0.00 0.00 0.00 4.00
429 430 3.139397 ACTGGGAATTTGTTCACCCTACA 59.861 43.478 0.00 0.00 42.49 2.74
439 440 3.496331 CTGTGGGTTACTGGGAATTTGT 58.504 45.455 0.00 0.00 0.00 2.83
452 453 2.887738 TTTTGGGCCAGCTGTGGGTT 62.888 55.000 13.81 0.00 45.17 4.11
453 454 3.387609 TTTTGGGCCAGCTGTGGGT 62.388 57.895 13.81 0.00 45.17 4.51
454 455 2.523902 TTTTGGGCCAGCTGTGGG 60.524 61.111 13.81 0.00 45.17 4.61
456 457 0.883833 CTAGTTTTGGGCCAGCTGTG 59.116 55.000 13.81 5.37 0.00 3.66
457 458 0.251341 CCTAGTTTTGGGCCAGCTGT 60.251 55.000 13.81 0.00 0.00 4.40
458 459 0.967380 CCCTAGTTTTGGGCCAGCTG 60.967 60.000 6.23 6.78 37.99 4.24
459 460 1.384191 CCCTAGTTTTGGGCCAGCT 59.616 57.895 6.23 9.38 37.99 4.24
460 461 4.018409 CCCTAGTTTTGGGCCAGC 57.982 61.111 6.23 1.09 37.99 4.85
489 490 1.670406 GCTGCCATCGATAGCCTGG 60.670 63.158 13.35 5.48 40.35 4.45
534 535 4.094887 ACTGACCTATTTATTGCGTTGCAG 59.905 41.667 0.00 0.00 40.61 4.41
535 536 4.006989 ACTGACCTATTTATTGCGTTGCA 58.993 39.130 0.00 0.00 36.47 4.08
537 538 7.970384 TCTTAACTGACCTATTTATTGCGTTG 58.030 34.615 0.00 0.00 0.00 4.10
623 627 0.625849 CTACCAGCCCCAAGGTTCAT 59.374 55.000 0.00 0.00 39.31 2.57
762 864 1.409427 GCTACATCCGTGCCTTCTACT 59.591 52.381 0.00 0.00 0.00 2.57
763 865 1.409427 AGCTACATCCGTGCCTTCTAC 59.591 52.381 0.00 0.00 0.00 2.59
765 867 0.905357 AAGCTACATCCGTGCCTTCT 59.095 50.000 0.00 0.00 0.00 2.85
767 869 1.679032 GGAAAGCTACATCCGTGCCTT 60.679 52.381 0.00 0.00 0.00 4.35
792 914 2.095718 GCACAAAAGGCTGCAGTACTAC 60.096 50.000 16.64 0.00 33.31 2.73
800 922 1.143620 TTGGTGCACAAAAGGCTGC 59.856 52.632 20.43 0.00 35.79 5.25
804 926 1.650825 GTTGGTTGGTGCACAAAAGG 58.349 50.000 20.43 0.00 41.58 3.11
838 961 2.512692 ATGTCATGGGTGCAGCTTAA 57.487 45.000 16.65 2.31 0.00 1.85
858 986 5.181245 CCACTCATAACATTTTCTCCGTGTT 59.819 40.000 0.00 0.00 39.26 3.32
862 990 4.695455 ACACCACTCATAACATTTTCTCCG 59.305 41.667 0.00 0.00 0.00 4.63
865 993 7.435068 GTGTACACCACTCATAACATTTTCT 57.565 36.000 15.42 0.00 41.11 2.52
879 1007 4.127171 AGTCAATGAACAGTGTACACCAC 58.873 43.478 22.28 11.49 44.89 4.16
880 1008 4.100963 AGAGTCAATGAACAGTGTACACCA 59.899 41.667 22.28 13.22 0.00 4.17
881 1009 4.449068 CAGAGTCAATGAACAGTGTACACC 59.551 45.833 22.28 7.67 0.00 4.16
882 1010 5.289595 TCAGAGTCAATGAACAGTGTACAC 58.710 41.667 18.56 18.56 0.00 2.90
885 1013 4.931601 GCATCAGAGTCAATGAACAGTGTA 59.068 41.667 0.00 0.00 0.00 2.90
887 1015 3.749609 TGCATCAGAGTCAATGAACAGTG 59.250 43.478 9.12 0.00 0.00 3.66
888 1016 3.750130 GTGCATCAGAGTCAATGAACAGT 59.250 43.478 10.38 0.00 32.53 3.55
889 1017 3.749609 TGTGCATCAGAGTCAATGAACAG 59.250 43.478 12.92 0.00 36.67 3.16
896 1024 5.335113 GCTTTATTGTGTGCATCAGAGTCAA 60.335 40.000 0.00 0.00 0.00 3.18
898 1026 4.437930 GGCTTTATTGTGTGCATCAGAGTC 60.438 45.833 0.00 0.00 0.00 3.36
899 1027 3.441572 GGCTTTATTGTGTGCATCAGAGT 59.558 43.478 0.00 0.00 0.00 3.24
912 1040 3.364549 TCATCCAACAGGGGCTTTATTG 58.635 45.455 0.00 0.00 37.22 1.90
928 1057 5.623368 GCACTGCTGGTACTCTATATCATCC 60.623 48.000 0.00 0.00 0.00 3.51
936 1065 2.967599 CATGCACTGCTGGTACTCTA 57.032 50.000 1.98 0.00 0.00 2.43
959 1088 4.687483 CCTTGTTTTGCTATTGCTTGAAGG 59.313 41.667 0.00 2.02 40.48 3.46
970 1100 4.098807 GTGTTTCTTCCCCTTGTTTTGCTA 59.901 41.667 0.00 0.00 0.00 3.49
1005 1153 1.295746 GGGAGGAACGGTGAGGAAC 59.704 63.158 0.00 0.00 0.00 3.62
1009 1158 2.572284 GACGGGAGGAACGGTGAG 59.428 66.667 0.00 0.00 35.23 3.51
1023 1172 1.417592 GAACAGATGCAGCACGACG 59.582 57.895 4.07 0.00 0.00 5.12
1035 1184 3.259374 CCAAGAAGAGTAGCAGGAACAGA 59.741 47.826 0.00 0.00 0.00 3.41
1119 1268 1.153628 GCCGCCGTCTTGTGATAGT 60.154 57.895 0.00 0.00 0.00 2.12
1284 1435 0.689055 AGAGGTTGACATGCAGCAGA 59.311 50.000 0.00 0.00 0.00 4.26
1443 1594 3.367498 GGTTGCTCGAGATGTTGAGTACT 60.367 47.826 18.75 0.00 36.63 2.73
1623 1774 0.385473 GTGTGTTTGGAATGTCGCCG 60.385 55.000 0.00 0.00 0.00 6.46
1690 1841 4.035112 TCAACCGGTAGAATCCCACTTAT 58.965 43.478 8.00 0.00 0.00 1.73
1704 1855 1.818674 GCATGGAAGATTTCAACCGGT 59.181 47.619 0.00 0.00 0.00 5.28
1707 1858 4.273318 AGGTAGCATGGAAGATTTCAACC 58.727 43.478 0.00 0.00 0.00 3.77
1884 2035 0.830648 TACCCAAATGGAGCTCCTCG 59.169 55.000 32.28 17.39 37.39 4.63
1932 2085 4.394300 AGATTTGTGCAGTTGCTCATAGTC 59.606 41.667 9.37 8.17 42.97 2.59
1993 2146 3.939592 GCGAAGTTTACCTTGCCTAGATT 59.060 43.478 0.00 0.00 32.03 2.40
2122 2275 2.039746 TCTCACCGTGGAAATGGTTGAT 59.960 45.455 0.00 0.00 35.96 2.57
2123 2276 1.418264 TCTCACCGTGGAAATGGTTGA 59.582 47.619 0.00 0.00 35.96 3.18
2136 2289 5.447818 GCCTATTCTTGTTGAAATCTCACCG 60.448 44.000 0.00 0.00 38.29 4.94
2145 2298 6.349611 GCTTCAGATTGCCTATTCTTGTTGAA 60.350 38.462 0.00 0.00 39.24 2.69
2149 2302 4.397417 GTGCTTCAGATTGCCTATTCTTGT 59.603 41.667 0.00 0.00 0.00 3.16
2192 2345 5.973565 GTGATGTTTGTGAAGGAGTTTTCAG 59.026 40.000 0.00 0.00 37.72 3.02
2194 2347 5.890334 TGTGATGTTTGTGAAGGAGTTTTC 58.110 37.500 0.00 0.00 0.00 2.29
2222 2375 1.999648 ACTCTGAAGGGCATGCAAAA 58.000 45.000 21.36 0.00 0.00 2.44
2236 2389 2.548875 GCTGATGCTCCTACAACTCTG 58.451 52.381 0.00 0.00 36.03 3.35
2241 2394 0.175760 GGACGCTGATGCTCCTACAA 59.824 55.000 0.00 0.00 35.26 2.41
2343 2496 1.333619 GTCAACGAACAATGGTGCACT 59.666 47.619 17.98 0.00 0.00 4.40
2344 2497 1.333619 AGTCAACGAACAATGGTGCAC 59.666 47.619 8.80 8.80 0.00 4.57
2391 2544 6.667414 AGTCTAGGATCTTCAGATTTGTGAGT 59.333 38.462 0.00 0.00 34.37 3.41
2539 2692 6.183360 CCGGCCTTATCTGATTTAAACATTGT 60.183 38.462 0.00 0.00 0.00 2.71
2653 2806 0.393537 AGATTCAGCTCTTTGGCCCG 60.394 55.000 0.00 0.00 0.00 6.13
2778 2931 1.741706 TCAGTGAGGTTACCGATCGAC 59.258 52.381 18.66 6.80 0.00 4.20
2797 2950 5.729510 AGACAAATCTAGCTTCTGAAGGTC 58.270 41.667 23.83 15.68 40.27 3.85
2913 3066 1.345415 AGCTGGCCTTTTGTTGGAATG 59.655 47.619 3.32 0.00 0.00 2.67
2973 3126 1.776662 TAAGCAGAGACCCGCATAGT 58.223 50.000 0.00 0.00 0.00 2.12
2976 3129 3.467803 GTTAATAAGCAGAGACCCGCAT 58.532 45.455 0.00 0.00 0.00 4.73
2982 3135 6.985188 TCACAATGGTTAATAAGCAGAGAC 57.015 37.500 10.71 0.00 42.84 3.36
3065 3218 1.874872 CACCAAAGGCAATTGCAAAGG 59.125 47.619 30.32 25.21 44.36 3.11
3072 3225 4.190772 CAAAGAACACACCAAAGGCAATT 58.809 39.130 0.00 0.00 0.00 2.32
3177 3337 6.498303 ACAACATATCTGGATGCTAGACCATA 59.502 38.462 0.00 0.00 35.54 2.74
3184 3344 5.988287 TGTGAACAACATATCTGGATGCTA 58.012 37.500 0.00 0.00 32.36 3.49
3211 3371 3.755378 GACAAGATTGAATGCAGACACCT 59.245 43.478 0.00 0.00 0.00 4.00
3212 3372 3.755378 AGACAAGATTGAATGCAGACACC 59.245 43.478 0.00 0.00 0.00 4.16
3258 3418 7.885922 TGGTTTGCCAACAATATTCTACTTCTA 59.114 33.333 2.78 0.00 42.83 2.10


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

AutoCloner maintained by Alex Coulton.