Multiple sequence alignment - TraesCS6A01G072200

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 TraesCS6A01G072200 chr6A 100.000 3550 0 0 1 3550 39437415 39440964 0.000000e+00 6556.0
1 TraesCS6A01G072200 chr6D 94.212 3473 171 14 1 3466 35486770 35490219 0.000000e+00 5273.0
2 TraesCS6A01G072200 chr6B 89.054 2092 185 23 918 2975 73159440 73161521 0.000000e+00 2555.0
3 TraesCS6A01G072200 chr6B 93.347 481 27 5 1 481 73158106 73158581 0.000000e+00 706.0
4 TraesCS6A01G072200 chr6B 89.677 310 19 5 512 819 73158584 73158882 2.000000e-102 383.0
5 TraesCS6A01G072200 chr5B 85.398 226 32 1 31 255 51057599 51057374 2.130000e-57 233.0
6 TraesCS6A01G072200 chr1A 83.628 226 36 1 31 256 479826937 479826713 9.980000e-51 211.0
7 TraesCS6A01G072200 chr3D 80.859 256 47 2 1 255 175504712 175504966 2.160000e-47 200.0
8 TraesCS6A01G072200 chr3D 90.698 86 5 1 3462 3547 68079919 68080001 1.040000e-20 111.0
9 TraesCS6A01G072200 chr3D 90.476 84 5 1 3461 3544 68079999 68079919 1.350000e-19 108.0
10 TraesCS6A01G072200 chr7D 82.192 219 39 0 27 245 184995609 184995827 4.680000e-44 189.0
11 TraesCS6A01G072200 chr2D 80.870 230 41 3 27 255 368556070 368556297 1.010000e-40 178.0
12 TraesCS6A01G072200 chr2D 90.625 64 6 0 262 325 627125911 627125974 6.310000e-13 86.1
13 TraesCS6A01G072200 chr7B 81.308 214 40 0 30 243 154816841 154817054 1.310000e-39 174.0
14 TraesCS6A01G072200 chr7B 90.244 82 8 0 263 344 493366038 493365957 1.350000e-19 108.0
15 TraesCS6A01G072200 chr7B 92.188 64 4 1 346 409 32551522 32551584 4.880000e-14 89.8
16 TraesCS6A01G072200 chr2B 78.346 254 48 6 1 249 485872636 485872887 1.320000e-34 158.0
17 TraesCS6A01G072200 chr3A 91.860 86 4 1 3462 3547 80090218 80090136 2.240000e-22 117.0
18 TraesCS6A01G072200 chr3A 92.593 81 3 1 3461 3541 80090138 80090215 2.900000e-21 113.0
19 TraesCS6A01G072200 chr3A 90.000 80 5 1 3465 3541 507310402 507310481 2.260000e-17 100.0
20 TraesCS6A01G072200 chr4D 89.130 92 5 2 3458 3545 79705975 79706065 3.750000e-20 110.0
21 TraesCS6A01G072200 chr4D 91.026 78 4 3 3468 3542 287544088 287544165 6.270000e-18 102.0
22 TraesCS6A01G072200 chr4A 91.026 78 4 3 3468 3542 207361735 207361812 6.270000e-18 102.0
23 TraesCS6A01G072200 chr4A 90.909 77 4 2 3465 3538 207361811 207361735 2.260000e-17 100.0


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 TraesCS6A01G072200 chr6A 39437415 39440964 3549 False 6556.000000 6556 100.000000 1 3550 1 chr6A.!!$F1 3549
1 TraesCS6A01G072200 chr6D 35486770 35490219 3449 False 5273.000000 5273 94.212000 1 3466 1 chr6D.!!$F1 3465
2 TraesCS6A01G072200 chr6B 73158106 73161521 3415 False 1214.666667 2555 90.692667 1 2975 3 chr6B.!!$F1 2974

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
464 466 0.035056 GGTTGGATGCACTGGCTAGT 60.035 55.0 0.0 0.0 41.91 2.57 F
1766 2233 0.034574 TGGTGGCGAAATGCTATGGT 60.035 50.0 0.0 0.0 45.43 3.55 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1900 2367 0.321346 TCGCATCTTCTTCAGCCACA 59.679 50.0 0.0 0.0 0.0 4.17 R
2811 3302 0.112995 AAGGCACATCAAAGCAGGGA 59.887 50.0 0.0 0.0 0.0 4.20 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
56 57 3.689649 AGGATTTTGTGGTTGCGACTATC 59.310 43.478 3.59 0.00 0.00 2.08
108 109 2.370189 CCGAGATTTAGGGGCTTGATCT 59.630 50.000 0.00 0.00 0.00 2.75
189 190 2.605837 TTACTTTCAGTGCACGTCCA 57.394 45.000 12.01 0.00 0.00 4.02
200 201 0.582005 GCACGTCCACACTCTTCAAC 59.418 55.000 0.00 0.00 0.00 3.18
202 203 1.120530 ACGTCCACACTCTTCAACCT 58.879 50.000 0.00 0.00 0.00 3.50
212 213 6.030228 CACACTCTTCAACCTCAAACTTTTC 58.970 40.000 0.00 0.00 0.00 2.29
215 216 4.519213 TCTTCAACCTCAAACTTTTCCGA 58.481 39.130 0.00 0.00 0.00 4.55
250 252 4.157849 TGGTGAGACATGTGTTTAACCA 57.842 40.909 17.06 17.06 34.00 3.67
378 380 8.424731 GTGATTTAAACTTTCGGCAATGTTTAG 58.575 33.333 14.29 0.00 40.49 1.85
464 466 0.035056 GGTTGGATGCACTGGCTAGT 60.035 55.000 0.00 0.00 41.91 2.57
481 483 0.696501 AGTAAAATGTGGACGGGGCT 59.303 50.000 0.00 0.00 0.00 5.19
482 484 1.910671 AGTAAAATGTGGACGGGGCTA 59.089 47.619 0.00 0.00 0.00 3.93
484 486 2.296073 AAAATGTGGACGGGGCTAAA 57.704 45.000 0.00 0.00 0.00 1.85
485 487 1.541379 AAATGTGGACGGGGCTAAAC 58.459 50.000 0.00 0.00 0.00 2.01
486 488 0.675522 AATGTGGACGGGGCTAAACG 60.676 55.000 0.00 0.00 0.00 3.60
487 489 2.435410 GTGGACGGGGCTAAACGG 60.435 66.667 0.00 0.00 0.00 4.44
488 490 2.924101 TGGACGGGGCTAAACGGT 60.924 61.111 0.00 0.00 0.00 4.83
501 503 1.412453 AAACGGTGCCCCTACTGTCA 61.412 55.000 0.00 0.00 39.17 3.58
520 522 7.601856 ACTGTCAATTCAAACAGACAAAAAGA 58.398 30.769 15.53 0.00 44.54 2.52
522 524 7.825681 TGTCAATTCAAACAGACAAAAAGAGA 58.174 30.769 0.00 0.00 37.99 3.10
531 533 9.525409 CAAACAGACAAAAAGAGAATCAAATCT 57.475 29.630 0.00 0.00 37.82 2.40
577 579 3.617263 CGAGTTGCCCATACTTTAGTGTC 59.383 47.826 0.00 0.00 0.00 3.67
578 580 4.620803 CGAGTTGCCCATACTTTAGTGTCT 60.621 45.833 0.00 0.00 0.00 3.41
806 809 7.494952 GGAACCATTAAGTCTACATCTACAACC 59.505 40.741 0.00 0.00 0.00 3.77
810 813 7.222224 CCATTAAGTCTACATCTACAACCGAAC 59.778 40.741 0.00 0.00 0.00 3.95
929 1219 2.439507 TCTCCTTTTGAGCACTCTGGTT 59.560 45.455 0.00 0.00 41.18 3.67
962 1426 9.991388 GATAGATAAGGTACGTTCATCTGATAC 57.009 37.037 19.42 10.81 0.00 2.24
997 1462 4.684134 GCTCCTGCCCCCAAGCAA 62.684 66.667 0.00 0.00 43.52 3.91
1350 1817 1.226018 CGCCGGCGAAATTCTGAAC 60.226 57.895 44.86 0.00 42.83 3.18
1511 1978 2.487428 CTCGAGTCCACCGCTGAG 59.513 66.667 3.62 0.00 0.00 3.35
1587 2054 0.474184 CCGGGCCATGGATTTCTACT 59.526 55.000 18.40 0.00 0.00 2.57
1658 2125 5.337956 ACATGGCCATGATTAAATCCCTA 57.662 39.130 44.72 1.04 41.20 3.53
1766 2233 0.034574 TGGTGGCGAAATGCTATGGT 60.035 50.000 0.00 0.00 45.43 3.55
1817 2284 2.283298 GTGATTGCGTCCATGTCTGAT 58.717 47.619 0.00 0.00 0.00 2.90
1862 2329 1.608025 GCGGTGAACATTGTCCTCTCA 60.608 52.381 0.00 0.00 0.00 3.27
1883 2350 2.730672 CTACAGCGCTTGCCGTGAC 61.731 63.158 7.50 0.00 40.41 3.67
1886 2353 4.704833 AGCGCTTGCCGTGACCAT 62.705 61.111 2.64 0.00 40.41 3.55
1889 2356 2.672996 GCTTGCCGTGACCATGGT 60.673 61.111 19.89 19.89 39.68 3.55
1899 2366 3.431626 CCGTGACCATGGTAAGATGCTAA 60.432 47.826 19.80 0.00 32.81 3.09
1900 2367 4.380531 CGTGACCATGGTAAGATGCTAAT 58.619 43.478 19.80 0.00 0.00 1.73
1958 2425 3.058501 CGACCACGAAAGCCTACAATTTT 60.059 43.478 0.00 0.00 42.66 1.82
1970 2437 4.466828 CCTACAATTTTGTGCTCAACTCG 58.533 43.478 6.21 0.00 42.31 4.18
1979 2446 2.338620 CTCAACTCGTGCCCGACA 59.661 61.111 0.00 0.00 38.40 4.35
1994 2461 1.741770 GACAGTGGTGTCGATGGCC 60.742 63.158 0.00 0.00 43.75 5.36
1997 2464 4.388499 GTGGTGTCGATGGCCCGT 62.388 66.667 0.00 0.00 0.00 5.28
2015 2482 0.393808 GTGAATTGGGCCCTTCGCTA 60.394 55.000 25.70 0.00 37.74 4.26
2051 2518 3.416156 GAAGTTGGTGAGGAAGCTCAAT 58.584 45.455 0.00 0.00 34.88 2.57
2055 2522 4.287067 AGTTGGTGAGGAAGCTCAATTCTA 59.713 41.667 0.00 0.00 34.88 2.10
2264 2731 3.649986 GTGTCTGTGGTGTGCGGC 61.650 66.667 0.00 0.00 0.00 6.53
2460 2927 0.179124 GGAGAGCACGGATCAGTCAC 60.179 60.000 0.00 0.00 0.00 3.67
2767 3243 3.632333 GGCAGCTCCCTTAAGGTAATTT 58.368 45.455 20.22 0.00 36.75 1.82
2768 3244 4.023980 GGCAGCTCCCTTAAGGTAATTTT 58.976 43.478 20.22 0.00 36.75 1.82
2905 3396 4.691216 CCTAGTAACCTCAGCTGTGTTTTC 59.309 45.833 22.80 17.35 0.00 2.29
2906 3397 4.423625 AGTAACCTCAGCTGTGTTTTCT 57.576 40.909 22.80 18.67 0.00 2.52
2938 3429 5.819379 GCACAAGAACATCTATTGGATCTCA 59.181 40.000 0.00 0.00 31.27 3.27
2980 3475 3.181462 TGACATAGCTGCATCTTACCCAG 60.181 47.826 1.02 0.00 0.00 4.45
2982 3477 3.649981 ACATAGCTGCATCTTACCCAGAT 59.350 43.478 1.02 0.00 43.80 2.90
3021 3516 7.186021 ACTATTGTTTCTTGAACCGTAACAG 57.814 36.000 0.00 0.00 37.45 3.16
3036 3531 5.694910 ACCGTAACAGATCTTTGTTAGTGTG 59.305 40.000 7.59 1.66 42.44 3.82
3068 3563 7.717436 GCTTATTATCTTCTTGGAGTAAAGCCT 59.283 37.037 0.00 0.00 0.00 4.58
3084 3579 1.127343 GCCTGTGCCTCTATTCCTCT 58.873 55.000 0.00 0.00 0.00 3.69
3156 3651 6.403878 GTGCTAGGTTTACTGTTGGAGATAA 58.596 40.000 0.00 0.00 0.00 1.75
3168 3663 8.718102 ACTGTTGGAGATAATGTTACATGTAC 57.282 34.615 4.68 1.95 0.00 2.90
3169 3664 8.540388 ACTGTTGGAGATAATGTTACATGTACT 58.460 33.333 4.68 0.00 0.00 2.73
3194 3689 6.959671 TCAAGTGCTTTTGTTTACTTTTGG 57.040 33.333 0.00 0.00 31.47 3.28
3202 3697 9.606631 TGCTTTTGTTTACTTTTGGATATTTGT 57.393 25.926 0.00 0.00 0.00 2.83
3219 3714 9.274206 GGATATTTGTTGAGGTAGGTCTAATTC 57.726 37.037 0.00 0.00 0.00 2.17
3220 3715 9.832445 GATATTTGTTGAGGTAGGTCTAATTCA 57.168 33.333 0.00 0.00 0.00 2.57
3270 3765 4.672413 CAGCAGCGAACTGTTTCTTTTAAG 59.328 41.667 0.00 0.00 46.30 1.85
3284 3779 4.466827 TCTTTTAAGGTTGAAGGTGTCCC 58.533 43.478 0.00 0.00 0.00 4.46
3297 3792 4.416738 GTCCCTGGCTCCCTGCAC 62.417 72.222 0.00 0.00 45.15 4.57
3338 3833 3.069586 GTGTCCTGGGATGATACGATCAA 59.930 47.826 0.00 0.00 43.50 2.57
3376 3871 2.289694 CCAGGTAACACTTAGCAGCTGT 60.290 50.000 16.64 4.79 35.31 4.40
3381 3876 6.149474 CAGGTAACACTTAGCAGCTGTATTTT 59.851 38.462 16.64 2.77 41.41 1.82
3445 3940 6.567687 TTCTGTTGAAACTTGAAACTGTCA 57.432 33.333 0.00 0.00 0.00 3.58
3448 3943 5.938322 TGTTGAAACTTGAAACTGTCAGTC 58.062 37.500 5.82 0.00 37.61 3.51
3466 3961 6.127703 TGTCAGTCTCTGCATACTTAAGGTAC 60.128 42.308 7.53 0.00 32.72 3.34
3468 3963 6.319152 TCAGTCTCTGCATACTTAAGGTACTC 59.681 42.308 7.53 0.00 38.49 2.59
3469 3964 5.595133 AGTCTCTGCATACTTAAGGTACTCC 59.405 44.000 7.53 0.00 38.49 3.85
3470 3965 4.894114 TCTCTGCATACTTAAGGTACTCCC 59.106 45.833 7.53 0.00 38.49 4.30
3472 3967 4.894114 TCTGCATACTTAAGGTACTCCCTC 59.106 45.833 7.53 0.00 45.47 4.30
3473 3968 3.965347 TGCATACTTAAGGTACTCCCTCC 59.035 47.826 7.53 0.00 45.47 4.30
3474 3969 3.005578 GCATACTTAAGGTACTCCCTCCG 59.994 52.174 7.53 0.00 45.47 4.63
3475 3970 2.915657 ACTTAAGGTACTCCCTCCGT 57.084 50.000 7.53 0.00 45.47 4.69
3476 3971 2.732763 ACTTAAGGTACTCCCTCCGTC 58.267 52.381 7.53 0.00 45.47 4.79
3477 3972 2.030371 CTTAAGGTACTCCCTCCGTCC 58.970 57.143 0.00 0.00 45.47 4.79
3478 3973 0.259938 TAAGGTACTCCCTCCGTCCC 59.740 60.000 0.00 0.00 45.47 4.46
3479 3974 1.807771 AAGGTACTCCCTCCGTCCCA 61.808 60.000 0.00 0.00 45.47 4.37
3480 3975 1.305549 GGTACTCCCTCCGTCCCAA 60.306 63.158 0.00 0.00 0.00 4.12
3481 3976 0.906282 GGTACTCCCTCCGTCCCAAA 60.906 60.000 0.00 0.00 0.00 3.28
3482 3977 0.978907 GTACTCCCTCCGTCCCAAAA 59.021 55.000 0.00 0.00 0.00 2.44
3483 3978 1.558294 GTACTCCCTCCGTCCCAAAAT 59.442 52.381 0.00 0.00 0.00 1.82
3484 3979 0.328258 ACTCCCTCCGTCCCAAAATG 59.672 55.000 0.00 0.00 0.00 2.32
3485 3980 0.328258 CTCCCTCCGTCCCAAAATGT 59.672 55.000 0.00 0.00 0.00 2.71
3486 3981 1.557832 CTCCCTCCGTCCCAAAATGTA 59.442 52.381 0.00 0.00 0.00 2.29
3487 3982 1.986631 TCCCTCCGTCCCAAAATGTAA 59.013 47.619 0.00 0.00 0.00 2.41
3488 3983 2.026636 TCCCTCCGTCCCAAAATGTAAG 60.027 50.000 0.00 0.00 0.00 2.34
3489 3984 2.026636 CCCTCCGTCCCAAAATGTAAGA 60.027 50.000 0.00 0.00 0.00 2.10
3490 3985 3.007635 CCTCCGTCCCAAAATGTAAGAC 58.992 50.000 0.00 0.00 0.00 3.01
3491 3986 3.007635 CTCCGTCCCAAAATGTAAGACC 58.992 50.000 0.00 0.00 0.00 3.85
3492 3987 2.372504 TCCGTCCCAAAATGTAAGACCA 59.627 45.455 0.00 0.00 0.00 4.02
3493 3988 3.009695 TCCGTCCCAAAATGTAAGACCAT 59.990 43.478 0.00 0.00 0.00 3.55
3494 3989 3.761752 CCGTCCCAAAATGTAAGACCATT 59.238 43.478 0.00 0.00 36.62 3.16
3495 3990 4.219725 CCGTCCCAAAATGTAAGACCATTT 59.780 41.667 0.00 0.00 44.71 2.32
3532 4027 9.248291 CAAAAATGATCTTATATTTTGGGACGG 57.752 33.333 3.10 0.00 36.80 4.79
3533 4028 8.760980 AAAATGATCTTATATTTTGGGACGGA 57.239 30.769 0.00 0.00 35.73 4.69
3534 4029 7.986085 AATGATCTTATATTTTGGGACGGAG 57.014 36.000 0.00 0.00 0.00 4.63
3535 4030 5.865085 TGATCTTATATTTTGGGACGGAGG 58.135 41.667 0.00 0.00 0.00 4.30
3536 4031 4.699925 TCTTATATTTTGGGACGGAGGG 57.300 45.455 0.00 0.00 0.00 4.30
3537 4032 4.300345 TCTTATATTTTGGGACGGAGGGA 58.700 43.478 0.00 0.00 0.00 4.20
3538 4033 4.347000 TCTTATATTTTGGGACGGAGGGAG 59.653 45.833 0.00 0.00 0.00 4.30
3539 4034 1.961133 TATTTTGGGACGGAGGGAGT 58.039 50.000 0.00 0.00 0.00 3.85
3540 4035 1.961133 ATTTTGGGACGGAGGGAGTA 58.039 50.000 0.00 0.00 0.00 2.59
3541 4036 1.961133 TTTTGGGACGGAGGGAGTAT 58.039 50.000 0.00 0.00 0.00 2.12
3542 4037 1.492764 TTTGGGACGGAGGGAGTATC 58.507 55.000 0.00 0.00 0.00 2.24
3543 4038 0.635009 TTGGGACGGAGGGAGTATCT 59.365 55.000 0.00 0.00 33.73 1.98
3544 4039 0.635009 TGGGACGGAGGGAGTATCTT 59.365 55.000 0.00 0.00 33.73 2.40
3545 4040 1.007963 TGGGACGGAGGGAGTATCTTT 59.992 52.381 0.00 0.00 33.73 2.52
3546 4041 2.117051 GGGACGGAGGGAGTATCTTTT 58.883 52.381 0.00 0.00 33.73 2.27
3547 4042 2.504585 GGGACGGAGGGAGTATCTTTTT 59.495 50.000 0.00 0.00 33.73 1.94
3548 4043 3.532542 GGACGGAGGGAGTATCTTTTTG 58.467 50.000 0.00 0.00 33.73 2.44
3549 4044 3.055312 GGACGGAGGGAGTATCTTTTTGT 60.055 47.826 0.00 0.00 33.73 2.83
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
56 57 0.784178 CAATGTGGTCACTGACGACG 59.216 55.000 16.71 0.00 42.66 5.12
85 86 4.401657 AGCCCCTAAATCTCGGCT 57.598 55.556 0.00 0.00 46.96 5.52
86 87 0.180406 TCAAGCCCCTAAATCTCGGC 59.820 55.000 0.00 0.00 41.96 5.54
92 93 2.224402 GCTCGAGATCAAGCCCCTAAAT 60.224 50.000 18.75 0.00 32.22 1.40
189 190 5.125578 GGAAAAGTTTGAGGTTGAAGAGTGT 59.874 40.000 0.00 0.00 0.00 3.55
200 201 0.237498 GGCGTCGGAAAAGTTTGAGG 59.763 55.000 0.00 0.00 0.00 3.86
202 203 1.935925 CGGCGTCGGAAAAGTTTGA 59.064 52.632 0.00 0.00 0.00 2.69
404 406 1.002134 GGCCGGTATGCAGCCATAT 60.002 57.895 8.94 0.00 46.34 1.78
438 440 2.359850 TGCATCCAACCGGCTGAC 60.360 61.111 6.38 0.00 29.21 3.51
464 466 3.083293 GTTTAGCCCCGTCCACATTTTA 58.917 45.455 0.00 0.00 0.00 1.52
487 489 2.489938 TGAATTGACAGTAGGGGCAC 57.510 50.000 0.00 0.00 0.00 5.01
488 490 3.153919 GTTTGAATTGACAGTAGGGGCA 58.846 45.455 0.00 0.00 0.00 5.36
493 495 8.909708 TTTTTGTCTGTTTGAATTGACAGTAG 57.090 30.769 11.03 0.00 42.90 2.57
501 503 9.874205 TTGATTCTCTTTTTGTCTGTTTGAATT 57.126 25.926 0.00 0.00 0.00 2.17
520 522 4.024048 ACAAACGAACGCAGATTTGATTCT 60.024 37.500 12.39 0.00 35.93 2.40
522 524 3.974401 CACAAACGAACGCAGATTTGATT 59.026 39.130 12.39 0.00 35.93 2.57
531 533 3.007516 CCGACACAAACGAACGCA 58.992 55.556 0.00 0.00 0.00 5.24
746 748 6.772716 GGAGCAATGTAGGATTTTATTGGAGA 59.227 38.462 0.00 0.00 32.59 3.71
762 764 5.248020 TGGTTCCATTTTATTGGAGCAATGT 59.752 36.000 9.14 0.00 45.80 2.71
929 1219 8.229253 TGAACGTACCTTATCTATCTGCTTAA 57.771 34.615 0.00 0.00 0.00 1.85
962 1426 3.503363 GCGCTAGGCTGTGCAAGG 61.503 66.667 14.66 1.92 42.40 3.61
1350 1817 2.778075 TTCGTAGAACTGCGGCAAACG 61.778 52.381 3.44 9.27 45.90 3.60
1511 1978 1.222113 GCAGTAGAAGAGGGCCACC 59.778 63.158 6.18 0.00 0.00 4.61
1512 1979 1.153549 CGCAGTAGAAGAGGGCCAC 60.154 63.158 6.18 0.00 0.00 5.01
1627 2094 1.212688 TCATGGCCATGTAGGTCTTGG 59.787 52.381 38.18 14.89 44.86 3.61
1658 2125 2.596631 GCGAGGCCCATCATGCAT 60.597 61.111 0.00 0.00 0.00 3.96
1727 2194 2.093306 ATCCGAACTGAAACGCATCA 57.907 45.000 0.00 0.00 0.00 3.07
1846 2313 3.708403 AGCATGAGAGGACAATGTTCA 57.292 42.857 0.00 0.00 0.00 3.18
1862 2329 3.197790 CGGCAAGCGCTGTAGCAT 61.198 61.111 24.86 1.68 42.21 3.79
1883 2350 3.254166 GCCACATTAGCATCTTACCATGG 59.746 47.826 11.19 11.19 0.00 3.66
1886 2353 3.199727 TCAGCCACATTAGCATCTTACCA 59.800 43.478 0.00 0.00 0.00 3.25
1889 2356 5.357742 TCTTCAGCCACATTAGCATCTTA 57.642 39.130 0.00 0.00 0.00 2.10
1899 2366 1.065926 TCGCATCTTCTTCAGCCACAT 60.066 47.619 0.00 0.00 0.00 3.21
1900 2367 0.321346 TCGCATCTTCTTCAGCCACA 59.679 50.000 0.00 0.00 0.00 4.17
1934 2401 1.291272 GTAGGCTTTCGTGGTCGGT 59.709 57.895 0.00 0.00 37.69 4.69
1958 2425 2.280797 GGGCACGAGTTGAGCACA 60.281 61.111 2.03 0.00 37.54 4.57
1970 2437 2.665185 GACACCACTGTCGGGCAC 60.665 66.667 0.00 0.00 37.67 5.01
1979 2446 4.082523 CGGGCCATCGACACCACT 62.083 66.667 4.39 0.00 0.00 4.00
1994 2461 2.406616 CGAAGGGCCCAATTCACGG 61.407 63.158 27.56 3.64 0.00 4.94
1997 2464 0.393808 GTAGCGAAGGGCCCAATTCA 60.394 55.000 27.56 1.02 45.17 2.57
2005 2472 2.047560 ACAACGGTAGCGAAGGGC 60.048 61.111 22.88 0.00 44.05 5.19
2019 2486 3.342627 CAACTTCGCCGCCGACAA 61.343 61.111 0.00 0.00 44.30 3.18
2051 2518 0.758734 CCGGCCATGGAGATGTAGAA 59.241 55.000 18.40 0.00 0.00 2.10
2055 2522 3.410628 TGCCGGCCATGGAGATGT 61.411 61.111 26.77 0.00 0.00 3.06
2216 2683 2.671963 GTGCGGTCCCCTTTCACC 60.672 66.667 0.00 0.00 0.00 4.02
2264 2731 2.034879 ATTGCTGTGCTTCCCGACG 61.035 57.895 0.00 0.00 0.00 5.12
2359 2826 2.282180 GCCGGCCTTTGTTCCTCA 60.282 61.111 18.11 0.00 0.00 3.86
2360 2827 2.034221 AGCCGGCCTTTGTTCCTC 59.966 61.111 26.15 0.00 0.00 3.71
2460 2927 3.256383 TGTTGCTGATCACTTGAATTGGG 59.744 43.478 0.00 0.00 0.00 4.12
2656 3132 7.913674 AGTTCACCATTAGAAAAGAGATGAC 57.086 36.000 0.00 0.00 0.00 3.06
2767 3243 2.584835 AAATGTCAGCAGGGCAGTAA 57.415 45.000 0.00 0.00 0.00 2.24
2768 3244 2.584835 AAAATGTCAGCAGGGCAGTA 57.415 45.000 0.00 0.00 0.00 2.74
2790 3266 6.948309 AGGGATTAAACATCAGCTACAAGTTT 59.052 34.615 9.64 9.64 36.49 2.66
2811 3302 0.112995 AAGGCACATCAAAGCAGGGA 59.887 50.000 0.00 0.00 0.00 4.20
2879 3370 4.097418 ACACAGCTGAGGTTACTAGGAAT 58.903 43.478 23.35 0.00 0.00 3.01
2905 3396 4.573900 AGATGTTCTTGTGCAGGACTTAG 58.426 43.478 0.00 0.00 31.03 2.18
2906 3397 4.623932 AGATGTTCTTGTGCAGGACTTA 57.376 40.909 0.00 0.00 31.03 2.24
2938 3429 4.585162 GTCAGTACTAGGATGCACATACCT 59.415 45.833 0.00 0.00 37.76 3.08
2982 3477 9.817809 AGAAACAATAGTATCAGCTTCGATTAA 57.182 29.630 0.00 0.00 0.00 1.40
3021 3516 6.787085 AGCAGTTACACACTAACAAAGATC 57.213 37.500 0.00 0.00 32.76 2.75
3036 3531 8.950208 ACTCCAAGAAGATAATAAGCAGTTAC 57.050 34.615 0.00 0.00 0.00 2.50
3062 3557 1.918957 AGGAATAGAGGCACAGGCTTT 59.081 47.619 0.00 0.00 38.98 3.51
3068 3563 5.188434 CAAATTCAGAGGAATAGAGGCACA 58.812 41.667 0.00 0.00 42.87 4.57
3084 3579 7.672983 TGGCTAAACAAACAAAACAAATTCA 57.327 28.000 0.00 0.00 0.00 2.57
3156 3651 8.792830 AAAGCACTTGATAGTACATGTAACAT 57.207 30.769 7.25 3.65 31.96 2.71
3167 3662 9.301153 CAAAAGTAAACAAAAGCACTTGATAGT 57.699 29.630 4.93 0.00 31.80 2.12
3168 3663 8.755018 CCAAAAGTAAACAAAAGCACTTGATAG 58.245 33.333 4.93 0.00 31.80 2.08
3169 3664 8.470805 TCCAAAAGTAAACAAAAGCACTTGATA 58.529 29.630 4.93 0.00 31.80 2.15
3170 3665 7.327214 TCCAAAAGTAAACAAAAGCACTTGAT 58.673 30.769 4.93 0.00 31.80 2.57
3171 3666 6.692486 TCCAAAAGTAAACAAAAGCACTTGA 58.308 32.000 4.93 0.00 31.80 3.02
3172 3667 6.959671 TCCAAAAGTAAACAAAAGCACTTG 57.040 33.333 0.00 0.00 31.80 3.16
3173 3668 9.830975 AATATCCAAAAGTAAACAAAAGCACTT 57.169 25.926 0.00 0.00 32.73 3.16
3174 3669 9.830975 AAATATCCAAAAGTAAACAAAAGCACT 57.169 25.926 0.00 0.00 0.00 4.40
3175 3670 9.862585 CAAATATCCAAAAGTAAACAAAAGCAC 57.137 29.630 0.00 0.00 0.00 4.40
3176 3671 9.606631 ACAAATATCCAAAAGTAAACAAAAGCA 57.393 25.926 0.00 0.00 0.00 3.91
3194 3689 9.832445 TGAATTAGACCTACCTCAACAAATATC 57.168 33.333 0.00 0.00 0.00 1.63
3202 3697 6.212589 TGACACATGAATTAGACCTACCTCAA 59.787 38.462 0.00 0.00 0.00 3.02
3219 3714 8.080417 ACTTCAAGAAAAATCATCTGACACATG 58.920 33.333 0.00 0.00 0.00 3.21
3220 3715 8.174733 ACTTCAAGAAAAATCATCTGACACAT 57.825 30.769 0.00 0.00 0.00 3.21
3284 3779 1.624479 ATCTCAGTGCAGGGAGCCAG 61.624 60.000 9.22 0.00 44.83 4.85
3308 3803 0.475632 ATCCCAGGACACTTCCCACA 60.476 55.000 0.00 0.00 44.10 4.17
3338 3833 5.048846 ACCTGGCCGATTTTGTAAGATAT 57.951 39.130 0.00 0.00 0.00 1.63
3353 3848 1.739067 CTGCTAAGTGTTACCTGGCC 58.261 55.000 0.00 0.00 0.00 5.36
3354 3849 1.087501 GCTGCTAAGTGTTACCTGGC 58.912 55.000 0.00 0.00 0.00 4.85
3445 3940 5.595133 GGAGTACCTTAAGTATGCAGAGACT 59.405 44.000 0.97 0.00 32.28 3.24
3448 3943 5.203060 GGGAGTACCTTAAGTATGCAGAG 57.797 47.826 0.97 0.00 35.85 3.35
3466 3961 0.328258 ACATTTTGGGACGGAGGGAG 59.672 55.000 0.00 0.00 0.00 4.30
3467 3962 1.659022 TACATTTTGGGACGGAGGGA 58.341 50.000 0.00 0.00 0.00 4.20
3468 3963 2.026636 TCTTACATTTTGGGACGGAGGG 60.027 50.000 0.00 0.00 0.00 4.30
3469 3964 3.007635 GTCTTACATTTTGGGACGGAGG 58.992 50.000 0.00 0.00 0.00 4.30
3470 3965 3.007635 GGTCTTACATTTTGGGACGGAG 58.992 50.000 0.00 0.00 0.00 4.63
3471 3966 2.372504 TGGTCTTACATTTTGGGACGGA 59.627 45.455 0.00 0.00 0.00 4.69
3472 3967 2.785562 TGGTCTTACATTTTGGGACGG 58.214 47.619 0.00 0.00 0.00 4.79
3473 3968 5.385509 AAATGGTCTTACATTTTGGGACG 57.614 39.130 0.00 0.00 45.94 4.79
3506 4001 9.248291 CCGTCCCAAAATATAAGATCATTTTTG 57.752 33.333 0.00 3.98 37.14 2.44
3507 4002 9.196139 TCCGTCCCAAAATATAAGATCATTTTT 57.804 29.630 0.00 0.00 33.23 1.94
3508 4003 8.760980 TCCGTCCCAAAATATAAGATCATTTT 57.239 30.769 0.00 0.00 35.30 1.82
3509 4004 7.448469 CCTCCGTCCCAAAATATAAGATCATTT 59.552 37.037 0.00 0.00 0.00 2.32
3510 4005 6.942576 CCTCCGTCCCAAAATATAAGATCATT 59.057 38.462 0.00 0.00 0.00 2.57
3511 4006 6.476378 CCTCCGTCCCAAAATATAAGATCAT 58.524 40.000 0.00 0.00 0.00 2.45
3512 4007 5.221843 CCCTCCGTCCCAAAATATAAGATCA 60.222 44.000 0.00 0.00 0.00 2.92
3513 4008 5.012768 TCCCTCCGTCCCAAAATATAAGATC 59.987 44.000 0.00 0.00 0.00 2.75
3514 4009 4.911522 TCCCTCCGTCCCAAAATATAAGAT 59.088 41.667 0.00 0.00 0.00 2.40
3515 4010 4.300345 TCCCTCCGTCCCAAAATATAAGA 58.700 43.478 0.00 0.00 0.00 2.10
3516 4011 4.102681 ACTCCCTCCGTCCCAAAATATAAG 59.897 45.833 0.00 0.00 0.00 1.73
3517 4012 4.042174 ACTCCCTCCGTCCCAAAATATAA 58.958 43.478 0.00 0.00 0.00 0.98
3518 4013 3.660959 ACTCCCTCCGTCCCAAAATATA 58.339 45.455 0.00 0.00 0.00 0.86
3519 4014 2.488836 ACTCCCTCCGTCCCAAAATAT 58.511 47.619 0.00 0.00 0.00 1.28
3520 4015 1.961133 ACTCCCTCCGTCCCAAAATA 58.039 50.000 0.00 0.00 0.00 1.40
3521 4016 1.961133 TACTCCCTCCGTCCCAAAAT 58.039 50.000 0.00 0.00 0.00 1.82
3522 4017 1.835531 GATACTCCCTCCGTCCCAAAA 59.164 52.381 0.00 0.00 0.00 2.44
3523 4018 1.007963 AGATACTCCCTCCGTCCCAAA 59.992 52.381 0.00 0.00 0.00 3.28
3524 4019 0.635009 AGATACTCCCTCCGTCCCAA 59.365 55.000 0.00 0.00 0.00 4.12
3525 4020 0.635009 AAGATACTCCCTCCGTCCCA 59.365 55.000 0.00 0.00 0.00 4.37
3526 4021 1.790818 AAAGATACTCCCTCCGTCCC 58.209 55.000 0.00 0.00 0.00 4.46
3527 4022 3.055312 ACAAAAAGATACTCCCTCCGTCC 60.055 47.826 0.00 0.00 0.00 4.79
3528 4023 4.203654 ACAAAAAGATACTCCCTCCGTC 57.796 45.455 0.00 0.00 0.00 4.79


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

AutoCloner maintained by Alex Coulton.