Multiple sequence alignment - TraesCS1D01G096600

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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 TraesCS1D01G096600 chr1D 100.000 3575 0 0 1 3575 81742145 81745719 0.000000e+00 6602
1 TraesCS1D01G096600 chr1D 91.575 2896 181 25 341 3225 83690462 83693305 0.000000e+00 3938
2 TraesCS1D01G096600 chr1D 78.089 1319 259 24 940 2246 70595947 70594647 0.000000e+00 808
3 TraesCS1D01G096600 chr1D 90.541 148 12 2 49 196 7349710 7349855 1.010000e-45 195
4 TraesCS1D01G096600 chr1A 91.816 3458 182 33 1 3431 100269927 100273310 0.000000e+00 4724
5 TraesCS1D01G096600 chr1A 77.828 1317 266 22 940 2246 71089135 71087835 0.000000e+00 791
6 TraesCS1D01G096600 chr1A 76.793 1297 274 21 946 2230 15193513 15194794 0.000000e+00 702
7 TraesCS1D01G096600 chr1A 84.615 104 16 0 2492 2595 100272336 100272439 1.760000e-18 104
8 TraesCS1D01G096600 chr1B 93.503 2509 112 12 1 2493 136627322 136629795 0.000000e+00 3683
9 TraesCS1D01G096600 chr1B 78.588 1317 256 22 940 2246 112204490 112203190 0.000000e+00 846
10 TraesCS1D01G096600 chr1B 86.370 719 63 19 2492 3184 136629704 136630413 0.000000e+00 752
11 TraesCS1D01G096600 chr1B 76.988 1295 276 20 946 2229 20175215 20176498 0.000000e+00 721
12 TraesCS1D01G096600 chr7B 90.667 150 12 2 52 201 505937457 505937310 7.830000e-47 198
13 TraesCS1D01G096600 chr4D 90.345 145 14 0 52 196 74079495 74079351 1.310000e-44 191
14 TraesCS1D01G096600 chr7D 90.345 145 12 2 52 196 33102712 33102854 4.710000e-44 189
15 TraesCS1D01G096600 chr3B 89.726 146 14 1 52 196 328715589 328715444 6.090000e-43 185
16 TraesCS1D01G096600 chr2A 91.241 137 11 1 49 185 141506324 141506459 6.090000e-43 185
17 TraesCS1D01G096600 chr5A 88.742 151 16 1 46 196 660831101 660831250 2.190000e-42 183


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 TraesCS1D01G096600 chr1D 81742145 81745719 3574 False 6602.0 6602 100.0000 1 3575 1 chr1D.!!$F2 3574
1 TraesCS1D01G096600 chr1D 83690462 83693305 2843 False 3938.0 3938 91.5750 341 3225 1 chr1D.!!$F3 2884
2 TraesCS1D01G096600 chr1D 70594647 70595947 1300 True 808.0 808 78.0890 940 2246 1 chr1D.!!$R1 1306
3 TraesCS1D01G096600 chr1A 100269927 100273310 3383 False 2414.0 4724 88.2155 1 3431 2 chr1A.!!$F2 3430
4 TraesCS1D01G096600 chr1A 71087835 71089135 1300 True 791.0 791 77.8280 940 2246 1 chr1A.!!$R1 1306
5 TraesCS1D01G096600 chr1A 15193513 15194794 1281 False 702.0 702 76.7930 946 2230 1 chr1A.!!$F1 1284
6 TraesCS1D01G096600 chr1B 136627322 136630413 3091 False 2217.5 3683 89.9365 1 3184 2 chr1B.!!$F2 3183
7 TraesCS1D01G096600 chr1B 112203190 112204490 1300 True 846.0 846 78.5880 940 2246 1 chr1B.!!$R1 1306
8 TraesCS1D01G096600 chr1B 20175215 20176498 1283 False 721.0 721 76.9880 946 2229 1 chr1B.!!$F1 1283

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
490 511 2.648059 AGTTATCAGGTCAATGCTGCC 58.352 47.619 0.0 0.0 0.00 4.85 F
1163 1185 1.007734 GTTCCAGTGACGACAGCGA 60.008 57.895 0.0 0.0 41.64 4.93 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2453 2479 1.229496 TCTCTAGCCCAGTGCCCAA 60.229 57.895 0.00 0.0 42.71 4.12 R
3072 3132 0.906282 TGGGCTGAGATCTGCACTGA 60.906 55.000 14.02 0.0 43.49 3.41 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
21 22 3.425659 GGATCCCTTATTGGCAATCTCC 58.574 50.000 17.41 10.31 31.24 3.71
26 27 4.476846 TCCCTTATTGGCAATCTCCACTTA 59.523 41.667 17.41 0.00 35.50 2.24
38 39 6.239036 GCAATCTCCACTTACCCAAATTATCC 60.239 42.308 0.00 0.00 0.00 2.59
60 68 7.129109 TCCTTCTTTTTGCTACGTTCATAAG 57.871 36.000 0.00 0.55 0.00 1.73
210 225 9.185680 ACAATGGGAGTATTAAACATTTCCTAC 57.814 33.333 0.00 0.00 30.00 3.18
309 330 4.385310 GCCCATAACAGTAAATGGAGTCCT 60.385 45.833 11.33 0.00 44.62 3.85
351 372 8.879427 TTCTGGTAGAGCTACTTATATATGCA 57.121 34.615 7.51 0.00 36.36 3.96
415 436 4.379499 GGTTTTCGTTTCAGGGTCATCATC 60.379 45.833 0.00 0.00 0.00 2.92
431 452 6.093495 GGTCATCATCGTTATCCAACTTGAAA 59.907 38.462 0.00 0.00 31.98 2.69
445 466 4.045636 ACTTGAAATGGTGCAAACTGAC 57.954 40.909 0.00 0.00 0.00 3.51
490 511 2.648059 AGTTATCAGGTCAATGCTGCC 58.352 47.619 0.00 0.00 0.00 4.85
583 604 3.952323 ACATGGCATTTTCTCCTGATCAG 59.048 43.478 16.24 16.24 0.00 2.90
584 605 4.204799 CATGGCATTTTCTCCTGATCAGA 58.795 43.478 24.62 9.26 0.00 3.27
585 606 3.614092 TGGCATTTTCTCCTGATCAGAC 58.386 45.455 24.62 0.00 0.00 3.51
926 948 3.186001 GTCACTGCAAAGACTGATCACTG 59.814 47.826 10.14 0.00 0.00 3.66
964 986 4.515028 TCCTTTGATCTCCTTGATGCAT 57.485 40.909 0.00 0.00 35.14 3.96
1066 1088 7.720957 TGTATTTCATATCTGGAGGATTGTTGG 59.279 37.037 0.00 0.00 35.98 3.77
1163 1185 1.007734 GTTCCAGTGACGACAGCGA 60.008 57.895 0.00 0.00 41.64 4.93
1194 1216 6.482898 TGGCAGCAATATAATTTCCAACAT 57.517 33.333 0.00 0.00 0.00 2.71
1341 1364 2.439507 ACTGAAGGACATGTCTGGTTGT 59.560 45.455 24.50 15.04 0.00 3.32
1365 1388 5.208121 AGTGTGGAAATAACATTATGGGGG 58.792 41.667 0.00 0.00 0.00 5.40
1713 1736 7.036996 TGAAGCTACAATTTCACACATCAAA 57.963 32.000 0.00 0.00 0.00 2.69
1845 1868 5.390356 GCAGAGCTCTCAAAATTGTGAGTAC 60.390 44.000 22.35 16.06 45.61 2.73
1849 1872 4.143094 GCTCTCAAAATTGTGAGTACCGAC 60.143 45.833 22.35 6.17 45.61 4.79
2007 2030 7.195646 CACGATTTGCAGAAATAATACATGGT 58.804 34.615 0.00 0.00 31.58 3.55
2077 2100 4.147322 GTGATGAACCGCGCGTGG 62.147 66.667 35.76 35.76 0.00 4.94
2131 2154 4.055360 CCACACATCAAACAAGAGTCGTA 58.945 43.478 0.00 0.00 0.00 3.43
2151 2174 6.688813 GTCGTATTTTTGATCTTGGAGCATTC 59.311 38.462 0.00 0.00 0.00 2.67
2422 2448 2.074576 CATATGGCTCTTCTGCATCCG 58.925 52.381 0.00 0.00 34.04 4.18
2479 2505 1.110442 CTGGGCTAGAGACTGTCCAG 58.890 60.000 3.76 0.00 36.28 3.86
2572 2598 0.966370 GGCTAGAGACTGTCCGGTGT 60.966 60.000 0.00 0.00 0.00 4.16
2606 2638 0.320771 GGCTCTTCAGCTGGAAACGA 60.321 55.000 15.13 0.00 46.03 3.85
2673 2705 1.079256 TCCTAGTGACTGCCCAGCT 59.921 57.895 0.00 0.00 0.00 4.24
2693 2725 1.168714 CCCTACTCTTTTGCAGGTGC 58.831 55.000 0.00 0.00 42.50 5.01
2741 2774 5.465532 TTCAAAAATAATCAGCCTGTGCA 57.534 34.783 0.00 0.00 41.13 4.57
2745 2778 2.814805 ATAATCAGCCTGTGCACCTT 57.185 45.000 15.69 0.00 41.13 3.50
2848 2881 6.258068 GCCTATGTTGGTAATGTCTGAAGTAC 59.742 42.308 0.00 0.00 0.00 2.73
2855 2888 3.618690 AATGTCTGAAGTACTCTGCCC 57.381 47.619 0.00 0.00 0.00 5.36
2875 2908 4.280174 GCCCATCATGTAGCATCTTGATTT 59.720 41.667 0.00 0.00 32.46 2.17
2887 2921 3.829886 TCTTGATTTGGCTTAGTTGCG 57.170 42.857 0.00 0.00 0.00 4.85
2888 2922 3.146066 TCTTGATTTGGCTTAGTTGCGT 58.854 40.909 0.00 0.00 0.00 5.24
2950 2987 3.241678 GCTATCGTTGTTCACTTGCTACG 60.242 47.826 0.00 0.00 35.77 3.51
2954 2991 2.790448 CGTTGTTCACTTGCTACGTACA 59.210 45.455 0.00 0.00 0.00 2.90
2977 3020 7.097192 ACATATGTATGGACCTTGTATTAGCG 58.903 38.462 6.56 0.00 38.00 4.26
3072 3132 7.573843 GCGATTTGCTTGTTATATGCCTCTATT 60.574 37.037 0.00 0.00 41.73 1.73
3110 3171 3.306919 CCCACCGTTTACAAGTAGGCTAA 60.307 47.826 0.00 0.00 0.00 3.09
3162 3223 7.123247 ACCTCTTTGTAGCATTGCATATTTTCT 59.877 33.333 11.91 0.00 0.00 2.52
3184 3245 1.912417 TGGACCGGTTGTTATTTGGG 58.088 50.000 9.42 0.00 0.00 4.12
3235 3298 2.666190 CCGTGCCACTGGAGTGTG 60.666 66.667 0.00 0.00 44.21 3.82
3266 3329 1.077787 GATCCATGGTCCAACGGCA 60.078 57.895 12.58 0.00 0.00 5.69
3279 3342 1.604604 AACGGCATTGCAGTTGTAGT 58.395 45.000 23.35 2.06 44.27 2.73
3281 3344 0.168788 CGGCATTGCAGTTGTAGTGG 59.831 55.000 11.39 0.00 0.00 4.00
3306 3369 1.846439 TCAATCCTCCAATCCTCCCAC 59.154 52.381 0.00 0.00 0.00 4.61
3307 3370 0.839946 AATCCTCCAATCCTCCCACG 59.160 55.000 0.00 0.00 0.00 4.94
3308 3371 1.056700 ATCCTCCAATCCTCCCACGG 61.057 60.000 0.00 0.00 0.00 4.94
3309 3372 1.689233 CCTCCAATCCTCCCACGGA 60.689 63.158 0.00 0.00 37.50 4.69
3310 3373 1.522569 CTCCAATCCTCCCACGGAC 59.477 63.158 0.00 0.00 35.52 4.79
3311 3374 1.972660 CTCCAATCCTCCCACGGACC 61.973 65.000 0.00 0.00 35.52 4.46
3312 3375 2.590092 CAATCCTCCCACGGACCC 59.410 66.667 0.00 0.00 35.52 4.46
3313 3376 2.124085 AATCCTCCCACGGACCCA 59.876 61.111 0.00 0.00 35.52 4.51
3314 3377 2.298661 AATCCTCCCACGGACCCAC 61.299 63.158 0.00 0.00 35.52 4.61
3354 3417 2.226330 CGAAGACGAGATCCTGATCCT 58.774 52.381 3.55 0.00 42.66 3.24
3386 3449 1.467734 GGAACTCACAGCATGCTGAAG 59.532 52.381 45.50 38.48 46.30 3.02
3395 3458 1.970917 GCATGCTGAAGACGAACCCG 61.971 60.000 11.37 0.00 42.50 5.28
3458 3521 4.719616 GCAACGGTGCGTCGAAGC 62.720 66.667 10.98 16.84 41.93 3.86
3459 3522 3.334751 CAACGGTGCGTCGAAGCA 61.335 61.111 22.28 22.28 45.96 3.91
3465 3528 3.422303 TGCGTCGAAGCATGGCAC 61.422 61.111 22.28 0.00 42.92 5.01
3466 3529 4.505217 GCGTCGAAGCATGGCACG 62.505 66.667 18.72 0.44 37.05 5.34
3467 3530 4.505217 CGTCGAAGCATGGCACGC 62.505 66.667 0.00 0.00 32.90 5.34
3468 3531 3.422303 GTCGAAGCATGGCACGCA 61.422 61.111 8.75 0.00 32.90 5.24
3469 3532 3.120385 TCGAAGCATGGCACGCAG 61.120 61.111 8.75 0.00 32.90 5.18
3470 3533 4.824166 CGAAGCATGGCACGCAGC 62.824 66.667 8.75 1.29 44.65 5.25
3490 3553 4.704103 TCCTGCCAGGACGGAGCT 62.704 66.667 10.05 0.00 40.06 4.09
3491 3554 4.154347 CCTGCCAGGACGGAGCTC 62.154 72.222 4.15 4.71 37.67 4.09
3492 3555 4.504916 CTGCCAGGACGGAGCTCG 62.505 72.222 7.83 5.83 45.88 5.03
3501 3564 2.325166 CGGAGCTCGTCTACTCGC 59.675 66.667 7.83 0.00 33.55 5.03
3502 3565 2.174969 CGGAGCTCGTCTACTCGCT 61.175 63.158 7.83 0.00 33.55 4.93
3503 3566 1.644913 GGAGCTCGTCTACTCGCTC 59.355 63.158 7.83 10.31 46.06 5.03
3504 3567 1.274476 GAGCTCGTCTACTCGCTCG 59.726 63.158 0.00 0.00 39.39 5.03
3505 3568 2.351435 GCTCGTCTACTCGCTCGC 60.351 66.667 0.00 0.00 0.00 5.03
3506 3569 2.325166 CTCGTCTACTCGCTCGCC 59.675 66.667 0.00 0.00 0.00 5.54
3507 3570 3.494454 CTCGTCTACTCGCTCGCCG 62.494 68.421 0.00 0.00 38.61 6.46
3509 3572 4.908877 GTCTACTCGCTCGCCGCC 62.909 72.222 0.00 0.00 36.73 6.13
3511 3574 4.914420 CTACTCGCTCGCCGCCTG 62.914 72.222 0.00 0.00 36.73 4.85
3517 3580 3.900892 GCTCGCCGCCTGCTACTA 61.901 66.667 0.00 0.00 38.05 1.82
3518 3581 2.026301 CTCGCCGCCTGCTACTAC 59.974 66.667 0.00 0.00 38.05 2.73
3519 3582 2.439701 TCGCCGCCTGCTACTACT 60.440 61.111 0.00 0.00 38.05 2.57
3520 3583 2.278857 CGCCGCCTGCTACTACTG 60.279 66.667 0.00 0.00 38.05 2.74
3521 3584 2.586357 GCCGCCTGCTACTACTGC 60.586 66.667 0.00 0.00 36.87 4.40
3522 3585 3.082579 GCCGCCTGCTACTACTGCT 62.083 63.158 0.00 0.00 36.87 4.24
3523 3586 1.066587 CCGCCTGCTACTACTGCTC 59.933 63.158 0.00 0.00 0.00 4.26
3524 3587 1.066587 CGCCTGCTACTACTGCTCC 59.933 63.158 0.00 0.00 0.00 4.70
3525 3588 1.066587 GCCTGCTACTACTGCTCCG 59.933 63.158 0.00 0.00 0.00 4.63
3526 3589 1.384989 GCCTGCTACTACTGCTCCGA 61.385 60.000 0.00 0.00 0.00 4.55
3527 3590 0.665835 CCTGCTACTACTGCTCCGAG 59.334 60.000 0.00 0.00 0.00 4.63
3528 3591 0.665835 CTGCTACTACTGCTCCGAGG 59.334 60.000 0.00 0.00 0.00 4.63
3529 3592 0.255033 TGCTACTACTGCTCCGAGGA 59.745 55.000 0.00 0.00 0.00 3.71
3530 3593 0.948678 GCTACTACTGCTCCGAGGAG 59.051 60.000 14.91 14.91 44.56 3.69
3531 3594 1.600023 CTACTACTGCTCCGAGGAGG 58.400 60.000 19.87 6.73 42.19 4.30
3533 3596 0.394625 ACTACTGCTCCGAGGAGGAC 60.395 60.000 19.87 5.66 45.98 3.85
3534 3597 0.394488 CTACTGCTCCGAGGAGGACA 60.394 60.000 19.87 9.70 45.98 4.02
3535 3598 0.259065 TACTGCTCCGAGGAGGACAT 59.741 55.000 19.87 9.10 45.98 3.06
3536 3599 1.040339 ACTGCTCCGAGGAGGACATC 61.040 60.000 19.87 4.31 45.98 3.06
3546 3609 3.165606 GAGGACATCCAACTGCAGG 57.834 57.895 19.93 0.43 38.89 4.85
3547 3610 0.326264 GAGGACATCCAACTGCAGGT 59.674 55.000 19.93 9.19 38.89 4.00
3548 3611 0.037303 AGGACATCCAACTGCAGGTG 59.963 55.000 25.38 25.38 38.89 4.00
3549 3612 0.036732 GGACATCCAACTGCAGGTGA 59.963 55.000 33.30 18.80 35.64 4.02
3550 3613 1.340405 GGACATCCAACTGCAGGTGAT 60.340 52.381 33.30 20.17 35.64 3.06
3551 3614 1.741706 GACATCCAACTGCAGGTGATG 59.258 52.381 33.30 29.97 35.64 3.07
3552 3615 1.100510 CATCCAACTGCAGGTGATGG 58.899 55.000 33.30 24.64 29.79 3.51
3553 3616 0.994247 ATCCAACTGCAGGTGATGGA 59.006 50.000 33.30 28.41 43.79 3.41
3557 3620 2.593978 CTGCAGGTGATGGAGGGG 59.406 66.667 5.57 0.00 43.30 4.79
3558 3621 1.997311 CTGCAGGTGATGGAGGGGA 60.997 63.158 5.57 0.00 43.30 4.81
3559 3622 1.541118 TGCAGGTGATGGAGGGGAA 60.541 57.895 0.00 0.00 0.00 3.97
3560 3623 1.077429 GCAGGTGATGGAGGGGAAC 60.077 63.158 0.00 0.00 0.00 3.62
3561 3624 1.852157 GCAGGTGATGGAGGGGAACA 61.852 60.000 0.00 0.00 0.00 3.18
3562 3625 0.698238 CAGGTGATGGAGGGGAACAA 59.302 55.000 0.00 0.00 0.00 2.83
3563 3626 0.995024 AGGTGATGGAGGGGAACAAG 59.005 55.000 0.00 0.00 0.00 3.16
3564 3627 0.034089 GGTGATGGAGGGGAACAAGG 60.034 60.000 0.00 0.00 0.00 3.61
3565 3628 0.991920 GTGATGGAGGGGAACAAGGA 59.008 55.000 0.00 0.00 0.00 3.36
3566 3629 1.065126 GTGATGGAGGGGAACAAGGAG 60.065 57.143 0.00 0.00 0.00 3.69
3567 3630 0.106967 GATGGAGGGGAACAAGGAGC 60.107 60.000 0.00 0.00 0.00 4.70
3568 3631 0.551131 ATGGAGGGGAACAAGGAGCT 60.551 55.000 0.00 0.00 0.00 4.09
3569 3632 1.201429 TGGAGGGGAACAAGGAGCTC 61.201 60.000 4.71 4.71 0.00 4.09
3570 3633 1.219393 GAGGGGAACAAGGAGCTCG 59.781 63.158 7.83 0.00 0.00 5.03
3571 3634 1.229209 AGGGGAACAAGGAGCTCGA 60.229 57.895 7.83 0.00 0.00 4.04
3572 3635 0.618968 AGGGGAACAAGGAGCTCGAT 60.619 55.000 7.83 0.00 0.00 3.59
3573 3636 0.462759 GGGGAACAAGGAGCTCGATG 60.463 60.000 7.83 11.50 0.00 3.84
3574 3637 0.462759 GGGAACAAGGAGCTCGATGG 60.463 60.000 18.26 6.40 0.00 3.51
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
2 3 3.464833 AGTGGAGATTGCCAATAAGGGAT 59.535 43.478 0.00 0.00 40.20 3.85
11 12 1.367346 TGGGTAAGTGGAGATTGCCA 58.633 50.000 0.00 0.00 34.41 4.92
21 22 9.423061 CAAAAAGAAGGATAATTTGGGTAAGTG 57.577 33.333 0.00 0.00 0.00 3.16
26 27 6.686484 AGCAAAAAGAAGGATAATTTGGGT 57.314 33.333 0.00 0.00 32.91 4.51
98 106 6.599244 TCTGTTTGTTCACTCATTTCAGTCTT 59.401 34.615 0.00 0.00 0.00 3.01
309 330 5.755849 ACCAGAAGAGAAGTTTCAAGGAAA 58.244 37.500 0.00 0.00 0.00 3.13
415 436 4.165779 GCACCATTTCAAGTTGGATAACG 58.834 43.478 2.34 0.00 41.71 3.18
431 452 3.114527 TGCAGTCAGTTTGCACCAT 57.885 47.368 0.00 0.00 45.89 3.55
445 466 0.459237 GACTCCCGATCAGTGTGCAG 60.459 60.000 0.00 0.00 0.00 4.41
490 511 6.125029 AGAACAGGATCTGATATTTGGTTGG 58.875 40.000 1.59 0.00 35.18 3.77
583 604 2.638556 TAGAAGAGCGCAACAGAGTC 57.361 50.000 11.47 0.00 0.00 3.36
584 605 3.257393 CAATAGAAGAGCGCAACAGAGT 58.743 45.455 11.47 0.00 0.00 3.24
585 606 2.030213 GCAATAGAAGAGCGCAACAGAG 59.970 50.000 11.47 0.00 0.00 3.35
616 637 3.362831 GCAGATTGTTCACAGCATTTTCG 59.637 43.478 0.00 0.00 0.00 3.46
884 906 2.926329 ACCCTACCCTTGATTGTCCATT 59.074 45.455 0.00 0.00 0.00 3.16
926 948 1.069935 GATAAGGCTCTCCCGTGGC 59.930 63.158 0.00 0.00 39.21 5.01
964 986 1.626321 TGCACGAATTTCTCCACCCTA 59.374 47.619 0.00 0.00 0.00 3.53
1066 1088 3.782889 AAACAACTTCTGTGCTGGTTC 57.217 42.857 0.00 0.00 38.67 3.62
1163 1185 2.761786 ATATTGCTGCCAAGGGATGT 57.238 45.000 0.00 0.00 33.80 3.06
1211 1233 5.652014 TCAACCATGAATCCACTTTCCATAC 59.348 40.000 0.00 0.00 30.99 2.39
1218 1240 4.529377 AGCAAATCAACCATGAATCCACTT 59.471 37.500 0.00 0.00 39.49 3.16
1341 1364 6.160636 TCCCCCATAATGTTATTTCCACACTA 59.839 38.462 0.00 0.00 0.00 2.74
1365 1388 3.929610 GACCTTCAGCATTACAGACACTC 59.070 47.826 0.00 0.00 0.00 3.51
1713 1736 8.302438 CAAGCTGGATAAGAAAATTTCTCAGTT 58.698 33.333 17.66 12.17 39.61 3.16
1933 1956 2.027745 TGAAAAGCTCTTCCGCTGAGAT 60.028 45.455 0.00 0.00 40.79 2.75
2007 2030 4.081406 ACAGAAATTGCTGATAACAGGCA 58.919 39.130 20.85 0.00 43.62 4.75
2077 2100 2.641305 AGCCTTCATGATGCTGACTTC 58.359 47.619 16.88 0.00 33.23 3.01
2131 2154 5.902613 TCGAATGCTCCAAGATCAAAAAT 57.097 34.783 0.00 0.00 0.00 1.82
2174 2197 2.433446 CACCAGGTGCTGAGCCTT 59.567 61.111 6.67 0.00 33.31 4.35
2371 2397 3.994853 GCCCCAACCTGTTGCTGC 61.995 66.667 4.48 5.56 39.16 5.25
2453 2479 1.229496 TCTCTAGCCCAGTGCCCAA 60.229 57.895 0.00 0.00 42.71 4.12
2479 2505 4.468689 GTACGAGGTGGCCTGCCC 62.469 72.222 3.32 0.69 31.76 5.36
2606 2638 1.734388 GAAACCAAGGCTGCCGTTGT 61.734 55.000 21.28 15.18 35.60 3.32
2673 2705 1.271379 GCACCTGCAAAAGAGTAGGGA 60.271 52.381 3.25 0.00 44.63 4.20
2713 2746 4.183865 GGCTGATTATTTTTGAAGCCCAC 58.816 43.478 0.00 0.00 43.56 4.61
2741 2774 3.986054 TGGACAGTCCAGCAAGGT 58.014 55.556 19.21 0.00 42.67 3.50
2785 2818 2.983592 CACCGTTCCCACAAGCCC 60.984 66.667 0.00 0.00 0.00 5.19
2848 2881 2.038689 AGATGCTACATGATGGGCAGAG 59.961 50.000 17.17 0.48 34.82 3.35
2855 2888 5.009710 AGCCAAATCAAGATGCTACATGATG 59.990 40.000 0.00 0.00 33.06 3.07
2875 2908 1.746220 ACAAAACACGCAACTAAGCCA 59.254 42.857 0.00 0.00 0.00 4.75
2950 2987 9.367444 GCTAATACAAGGTCCATACATATGTAC 57.633 37.037 17.69 7.77 32.72 2.90
2954 2991 6.070767 AGCGCTAATACAAGGTCCATACATAT 60.071 38.462 8.99 0.00 0.00 1.78
3001 3049 4.990257 ACGACATGCTACTTAACATACGT 58.010 39.130 0.00 0.00 35.37 3.57
3016 3064 2.995466 ACCAGAAATGCAACGACATG 57.005 45.000 0.00 0.00 0.00 3.21
3072 3132 0.906282 TGGGCTGAGATCTGCACTGA 60.906 55.000 14.02 0.00 43.49 3.41
3162 3223 2.623889 CCAAATAACAACCGGTCCAACA 59.376 45.455 8.04 0.00 0.00 3.33
3184 3245 0.949397 ATGTGCCGATGATGCATCAC 59.051 50.000 30.92 21.72 40.54 3.06
3213 3274 2.842462 TCCAGTGGCACGGTGACT 60.842 61.111 16.16 6.09 0.00 3.41
3235 3298 1.027357 ATGGATCCGACTTGCAATGC 58.973 50.000 7.39 0.00 0.00 3.56
3266 3329 1.586154 GCGGCCACTACAACTGCAAT 61.586 55.000 2.24 0.00 35.72 3.56
3276 3339 1.686325 GGAGGATTGAGCGGCCACTA 61.686 60.000 2.24 0.00 0.00 2.74
3279 3342 1.925285 ATTGGAGGATTGAGCGGCCA 61.925 55.000 2.24 0.00 0.00 5.36
3281 3344 1.169034 GGATTGGAGGATTGAGCGGC 61.169 60.000 0.00 0.00 0.00 6.53
3306 3369 1.252904 TAGGTTCTTCCGTGGGTCCG 61.253 60.000 0.00 0.00 41.99 4.79
3307 3370 0.248565 GTAGGTTCTTCCGTGGGTCC 59.751 60.000 0.00 0.00 41.99 4.46
3308 3371 0.971386 TGTAGGTTCTTCCGTGGGTC 59.029 55.000 0.00 0.00 41.99 4.46
3309 3372 0.974383 CTGTAGGTTCTTCCGTGGGT 59.026 55.000 0.00 0.00 41.99 4.51
3310 3373 0.391263 GCTGTAGGTTCTTCCGTGGG 60.391 60.000 0.00 0.00 41.99 4.61
3311 3374 0.320374 TGCTGTAGGTTCTTCCGTGG 59.680 55.000 0.00 0.00 41.99 4.94
3312 3375 2.002586 CATGCTGTAGGTTCTTCCGTG 58.997 52.381 0.00 0.00 41.99 4.94
3313 3376 1.676014 GCATGCTGTAGGTTCTTCCGT 60.676 52.381 11.37 0.00 41.99 4.69
3314 3377 1.009829 GCATGCTGTAGGTTCTTCCG 58.990 55.000 11.37 0.00 41.99 4.30
3354 3417 0.539669 TGAGTTCCACGAGAGGCAGA 60.540 55.000 0.00 0.00 0.00 4.26
3395 3458 1.003233 GCTGGTCTGGTTCCTCCAC 60.003 63.158 0.00 0.00 41.93 4.02
3396 3459 1.152030 AGCTGGTCTGGTTCCTCCA 60.152 57.895 0.00 0.00 45.01 3.86
3431 3494 3.112075 ACCGTTGCGATGCTCGTG 61.112 61.111 7.27 0.00 42.81 4.35
3432 3495 3.112075 CACCGTTGCGATGCTCGT 61.112 61.111 7.27 0.00 42.81 4.18
3433 3496 4.505217 GCACCGTTGCGATGCTCG 62.505 66.667 0.04 1.80 43.89 5.03
3441 3504 4.719616 GCTTCGACGCACCGTTGC 62.720 66.667 9.30 0.00 46.21 4.17
3442 3505 2.667318 ATGCTTCGACGCACCGTTG 61.667 57.895 19.66 0.00 43.61 4.10
3443 3506 2.357034 ATGCTTCGACGCACCGTT 60.357 55.556 19.66 0.00 43.61 4.44
3444 3507 3.112075 CATGCTTCGACGCACCGT 61.112 61.111 19.66 0.04 43.61 4.83
3445 3508 3.853330 CCATGCTTCGACGCACCG 61.853 66.667 19.66 12.90 43.61 4.94
3446 3509 4.166011 GCCATGCTTCGACGCACC 62.166 66.667 19.66 6.98 43.61 5.01
3447 3510 3.422303 TGCCATGCTTCGACGCAC 61.422 61.111 19.66 7.37 43.61 5.34
3448 3511 3.422303 GTGCCATGCTTCGACGCA 61.422 61.111 19.55 19.55 45.10 5.24
3449 3512 4.505217 CGTGCCATGCTTCGACGC 62.505 66.667 6.99 6.99 0.00 5.19
3450 3513 4.505217 GCGTGCCATGCTTCGACG 62.505 66.667 0.54 0.00 0.00 5.12
3451 3514 3.372676 CTGCGTGCCATGCTTCGAC 62.373 63.158 10.72 0.00 0.00 4.20
3452 3515 3.120385 CTGCGTGCCATGCTTCGA 61.120 61.111 10.72 0.00 0.00 3.71
3453 3516 4.824166 GCTGCGTGCCATGCTTCG 62.824 66.667 10.72 0.07 35.15 3.79
3454 3517 3.678717 CTGCTGCGTGCCATGCTTC 62.679 63.158 10.72 2.45 42.00 3.86
3455 3518 3.744719 CTGCTGCGTGCCATGCTT 61.745 61.111 10.72 0.00 42.00 3.91
3457 3520 4.471726 GACTGCTGCGTGCCATGC 62.472 66.667 0.83 0.83 42.00 4.06
3458 3521 3.807538 GGACTGCTGCGTGCCATG 61.808 66.667 2.10 0.00 42.00 3.66
3459 3522 4.025858 AGGACTGCTGCGTGCCAT 62.026 61.111 11.07 0.00 42.00 4.40
3460 3523 4.994471 CAGGACTGCTGCGTGCCA 62.994 66.667 11.07 0.00 42.00 4.92
3473 3536 4.704103 AGCTCCGTCCTGGCAGGA 62.704 66.667 32.01 32.01 43.43 3.86
3474 3537 4.154347 GAGCTCCGTCCTGGCAGG 62.154 72.222 28.01 28.01 37.80 4.85
3475 3538 4.504916 CGAGCTCCGTCCTGGCAG 62.505 72.222 7.75 7.75 37.80 4.85
3484 3547 2.174969 AGCGAGTAGACGAGCTCCG 61.175 63.158 8.47 4.99 45.44 4.63
3485 3548 3.816388 AGCGAGTAGACGAGCTCC 58.184 61.111 8.47 0.00 34.48 4.70
3487 3550 2.815298 GCGAGCGAGTAGACGAGCT 61.815 63.158 4.93 4.93 43.33 4.09
3488 3551 2.351435 GCGAGCGAGTAGACGAGC 60.351 66.667 0.00 0.00 35.09 5.03
3489 3552 2.325166 GGCGAGCGAGTAGACGAG 59.675 66.667 0.00 0.00 35.09 4.18
3490 3553 3.561213 CGGCGAGCGAGTAGACGA 61.561 66.667 0.00 0.00 35.09 4.20
3504 3567 2.586357 GCAGTAGTAGCAGGCGGC 60.586 66.667 0.00 0.00 45.30 6.53
3505 3568 1.066587 GAGCAGTAGTAGCAGGCGG 59.933 63.158 0.00 0.00 0.00 6.13
3506 3569 1.066587 GGAGCAGTAGTAGCAGGCG 59.933 63.158 0.00 0.00 0.00 5.52
3507 3570 1.066587 CGGAGCAGTAGTAGCAGGC 59.933 63.158 0.00 0.00 0.00 4.85
3508 3571 0.665835 CTCGGAGCAGTAGTAGCAGG 59.334 60.000 0.00 0.00 0.00 4.85
3509 3572 0.665835 CCTCGGAGCAGTAGTAGCAG 59.334 60.000 0.00 0.00 0.00 4.24
3510 3573 0.255033 TCCTCGGAGCAGTAGTAGCA 59.745 55.000 0.00 0.00 0.00 3.49
3511 3574 0.948678 CTCCTCGGAGCAGTAGTAGC 59.051 60.000 0.00 0.00 35.31 3.58
3512 3575 1.141254 TCCTCCTCGGAGCAGTAGTAG 59.859 57.143 7.46 0.00 40.69 2.57
3513 3576 1.134159 GTCCTCCTCGGAGCAGTAGTA 60.134 57.143 7.46 0.00 44.20 1.82
3514 3577 0.394625 GTCCTCCTCGGAGCAGTAGT 60.395 60.000 7.46 0.00 44.20 2.73
3515 3578 0.394488 TGTCCTCCTCGGAGCAGTAG 60.394 60.000 7.46 0.00 44.20 2.57
3516 3579 0.259065 ATGTCCTCCTCGGAGCAGTA 59.741 55.000 7.46 0.00 44.20 2.74
3517 3580 1.000993 ATGTCCTCCTCGGAGCAGT 59.999 57.895 7.46 0.00 44.20 4.40
3518 3581 1.739049 GATGTCCTCCTCGGAGCAG 59.261 63.158 7.46 0.00 44.20 4.24
3519 3582 1.758514 GGATGTCCTCCTCGGAGCA 60.759 63.158 7.46 1.92 44.20 4.26
3520 3583 1.330655 TTGGATGTCCTCCTCGGAGC 61.331 60.000 7.46 0.00 44.20 4.70
3521 3584 0.461961 GTTGGATGTCCTCCTCGGAG 59.538 60.000 5.97 5.97 44.20 4.63
3522 3585 0.041238 AGTTGGATGTCCTCCTCGGA 59.959 55.000 0.09 0.00 45.21 4.55
3523 3586 0.176680 CAGTTGGATGTCCTCCTCGG 59.823 60.000 0.09 0.00 45.21 4.63
3524 3587 0.460987 GCAGTTGGATGTCCTCCTCG 60.461 60.000 0.09 0.00 45.21 4.63
3525 3588 0.615331 TGCAGTTGGATGTCCTCCTC 59.385 55.000 0.09 0.00 45.21 3.71
3526 3589 0.617413 CTGCAGTTGGATGTCCTCCT 59.383 55.000 5.25 0.00 45.21 3.69
3527 3590 0.393537 CCTGCAGTTGGATGTCCTCC 60.394 60.000 13.81 0.00 45.19 4.30
3528 3591 0.326264 ACCTGCAGTTGGATGTCCTC 59.674 55.000 13.81 0.00 36.82 3.71
3529 3592 0.037303 CACCTGCAGTTGGATGTCCT 59.963 55.000 13.81 0.00 36.82 3.85
3530 3593 0.036732 TCACCTGCAGTTGGATGTCC 59.963 55.000 11.72 0.00 0.00 4.02
3531 3594 1.741706 CATCACCTGCAGTTGGATGTC 59.258 52.381 21.90 0.00 32.68 3.06
3532 3595 1.615116 CCATCACCTGCAGTTGGATGT 60.615 52.381 25.25 10.70 34.89 3.06
3533 3596 1.100510 CCATCACCTGCAGTTGGATG 58.899 55.000 22.68 22.68 36.10 3.51
3534 3597 0.994247 TCCATCACCTGCAGTTGGAT 59.006 50.000 11.72 8.61 31.65 3.41
3535 3598 0.325933 CTCCATCACCTGCAGTTGGA 59.674 55.000 11.72 15.85 34.58 3.53
3536 3599 0.679002 CCTCCATCACCTGCAGTTGG 60.679 60.000 11.72 12.66 0.00 3.77
3537 3600 0.679002 CCCTCCATCACCTGCAGTTG 60.679 60.000 13.81 9.31 0.00 3.16
3538 3601 1.687612 CCCTCCATCACCTGCAGTT 59.312 57.895 13.81 0.00 0.00 3.16
3539 3602 2.304056 CCCCTCCATCACCTGCAGT 61.304 63.158 13.81 0.00 0.00 4.40
3540 3603 1.565390 TTCCCCTCCATCACCTGCAG 61.565 60.000 6.78 6.78 0.00 4.41
3541 3604 1.541118 TTCCCCTCCATCACCTGCA 60.541 57.895 0.00 0.00 0.00 4.41
3542 3605 1.077429 GTTCCCCTCCATCACCTGC 60.077 63.158 0.00 0.00 0.00 4.85
3543 3606 0.698238 TTGTTCCCCTCCATCACCTG 59.302 55.000 0.00 0.00 0.00 4.00
3544 3607 0.995024 CTTGTTCCCCTCCATCACCT 59.005 55.000 0.00 0.00 0.00 4.00
3545 3608 0.034089 CCTTGTTCCCCTCCATCACC 60.034 60.000 0.00 0.00 0.00 4.02
3546 3609 0.991920 TCCTTGTTCCCCTCCATCAC 59.008 55.000 0.00 0.00 0.00 3.06
3547 3610 1.289160 CTCCTTGTTCCCCTCCATCA 58.711 55.000 0.00 0.00 0.00 3.07
3548 3611 0.106967 GCTCCTTGTTCCCCTCCATC 60.107 60.000 0.00 0.00 0.00 3.51
3549 3612 0.551131 AGCTCCTTGTTCCCCTCCAT 60.551 55.000 0.00 0.00 0.00 3.41
3550 3613 1.151810 AGCTCCTTGTTCCCCTCCA 60.152 57.895 0.00 0.00 0.00 3.86
3551 3614 1.604915 GAGCTCCTTGTTCCCCTCC 59.395 63.158 0.87 0.00 0.00 4.30
3552 3615 1.219393 CGAGCTCCTTGTTCCCCTC 59.781 63.158 8.47 0.00 0.00 4.30
3553 3616 0.618968 ATCGAGCTCCTTGTTCCCCT 60.619 55.000 8.47 0.00 0.00 4.79
3554 3617 0.462759 CATCGAGCTCCTTGTTCCCC 60.463 60.000 8.47 0.00 0.00 4.81
3555 3618 0.462759 CCATCGAGCTCCTTGTTCCC 60.463 60.000 8.47 0.00 0.00 3.97
3556 3619 3.071580 CCATCGAGCTCCTTGTTCC 57.928 57.895 8.47 0.00 0.00 3.62


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

AutoCloner maintained by Alex Coulton.