Multiple sequence alignment - TraesCS2D01G333300

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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 TraesCS2D01G333300 chr2D 100.000 4469 0 0 1 4469 426941498 426945966 0.000000e+00 8253.0
1 TraesCS2D01G333300 chr2D 96.154 78 3 0 3528 3605 426944956 426945033 1.300000e-25 128.0
2 TraesCS2D01G333300 chr2D 96.154 78 3 0 3459 3536 426945025 426945102 1.300000e-25 128.0
3 TraesCS2D01G333300 chr2D 89.333 75 7 1 2555 2629 76629924 76629997 4.760000e-15 93.5
4 TraesCS2D01G333300 chr2D 97.222 36 1 0 3413 3448 424678722 424678687 1.340000e-05 62.1
5 TraesCS2D01G333300 chr2A 95.695 3554 112 16 2 3536 561557503 561553972 0.000000e+00 5677.0
6 TraesCS2D01G333300 chr2A 91.027 925 50 10 3558 4458 561554019 561553104 0.000000e+00 1218.0
7 TraesCS2D01G333300 chr2A 72.588 456 104 19 1202 1645 761305507 761305953 3.630000e-26 130.0
8 TraesCS2D01G333300 chr2A 85.417 96 9 3 4316 4408 561553615 561553522 1.320000e-15 95.3
9 TraesCS2D01G333300 chr2A 97.059 34 1 0 3415 3448 563919128 563919161 1.740000e-04 58.4
10 TraesCS2D01G333300 chr2B 95.403 3546 141 9 2 3536 503769774 503773308 0.000000e+00 5626.0
11 TraesCS2D01G333300 chr2B 95.052 384 16 3 4087 4469 503773883 503774264 6.400000e-168 601.0
12 TraesCS2D01G333300 chr2B 81.261 587 34 23 3528 4066 503773230 503773788 5.380000e-109 405.0
13 TraesCS2D01G333300 chr2B 76.812 483 72 22 2575 3032 499561478 499561011 7.470000e-58 235.0
14 TraesCS2D01G333300 chr2B 82.857 140 7 9 4234 4371 503773589 503773713 4.730000e-20 110.0
15 TraesCS2D01G333300 chr2B 88.372 86 10 0 3949 4034 503774111 503774196 2.200000e-18 104.0
16 TraesCS2D01G333300 chr2B 97.222 36 1 0 3413 3448 499560880 499560845 1.340000e-05 62.1
17 TraesCS2D01G333300 chr7B 91.166 883 39 20 2610 3483 738144216 738145068 0.000000e+00 1162.0
18 TraesCS2D01G333300 chr7B 87.614 985 56 21 1542 2509 738143249 738144184 0.000000e+00 1083.0
19 TraesCS2D01G333300 chr7B 75.110 1137 204 58 1348 2452 540248443 540249532 4.070000e-125 459.0
20 TraesCS2D01G333300 chr7B 79.375 320 53 11 2131 2442 663488293 663488607 3.500000e-51 213.0
21 TraesCS2D01G333300 chr7D 77.892 977 194 18 2498 3463 511326202 511327167 4.980000e-164 588.0
22 TraesCS2D01G333300 chr7D 74.978 1143 198 66 1348 2452 511325037 511326129 3.170000e-121 446.0
23 TraesCS2D01G333300 chr7A 75.263 1140 200 62 1348 2452 583871780 583872872 6.770000e-128 468.0


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 TraesCS2D01G333300 chr2D 426941498 426945966 4468 False 2836.333333 8253 97.436 1 4469 3 chr2D.!!$F2 4468
1 TraesCS2D01G333300 chr2A 561553104 561557503 4399 True 2330.100000 5677 90.713 2 4458 3 chr2A.!!$R1 4456
2 TraesCS2D01G333300 chr2B 503769774 503774264 4490 False 1369.200000 5626 88.589 2 4469 5 chr2B.!!$F1 4467
3 TraesCS2D01G333300 chr7B 738143249 738145068 1819 False 1122.500000 1162 89.390 1542 3483 2 chr7B.!!$F3 1941
4 TraesCS2D01G333300 chr7B 540248443 540249532 1089 False 459.000000 459 75.110 1348 2452 1 chr7B.!!$F1 1104
5 TraesCS2D01G333300 chr7D 511325037 511327167 2130 False 517.000000 588 76.435 1348 3463 2 chr7D.!!$F1 2115
6 TraesCS2D01G333300 chr7A 583871780 583872872 1092 False 468.000000 468 75.263 1348 2452 1 chr7A.!!$F1 1104

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
797 801 1.463444 GCGGTCACACAATCTTACCAC 59.537 52.381 0.00 0.0 0.0 4.16 F
2562 2652 2.031314 TACACCAACGCGCACCAT 59.969 55.556 5.73 0.0 0.0 3.55 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2650 2740 0.676782 GGCTTCCCGTACAAGCACAT 60.677 55.0 15.81 0.0 46.94 3.21 R
3637 3763 0.253044 GAGTGGCTTGCCAGGATGTA 59.747 55.0 15.31 0.0 0.00 2.29 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
40 41 5.261216 ACAAATGGATCGATAAACCAAGGT 58.739 37.500 8.26 4.87 37.24 3.50
41 42 5.357032 ACAAATGGATCGATAAACCAAGGTC 59.643 40.000 8.26 0.00 37.24 3.85
42 43 3.173668 TGGATCGATAAACCAAGGTCG 57.826 47.619 0.00 0.00 35.55 4.79
108 109 6.670695 AGAAACCAAGGAATAATTTGCAGT 57.329 33.333 0.00 0.00 0.00 4.40
115 116 7.029563 CCAAGGAATAATTTGCAGTAAGACAC 58.970 38.462 0.00 0.00 0.00 3.67
127 128 5.761234 TGCAGTAAGACACGGAGTAAATTTT 59.239 36.000 0.00 0.00 41.61 1.82
457 460 7.387122 TCTGCTGAGAAATCATCTACAATATGC 59.613 37.037 0.00 0.00 38.96 3.14
522 526 5.557891 AGAGAAGAAGAATCATTTTGCGG 57.442 39.130 0.00 0.00 0.00 5.69
587 591 3.782046 ACGCATTACAGTACAGATGTCC 58.218 45.455 0.00 0.00 32.02 4.02
630 634 5.888724 TGGAAACTTCACAATACAGTTGGAA 59.111 36.000 0.00 0.00 31.00 3.53
631 635 6.378564 TGGAAACTTCACAATACAGTTGGAAA 59.621 34.615 0.00 0.00 31.00 3.13
771 775 2.202932 CCTCCGCGTCCATGGAAG 60.203 66.667 21.96 21.96 32.89 3.46
792 796 2.325082 GGCGCGGTCACACAATCTT 61.325 57.895 8.83 0.00 0.00 2.40
797 801 1.463444 GCGGTCACACAATCTTACCAC 59.537 52.381 0.00 0.00 0.00 4.16
875 887 2.100584 AGCAGTACTAGCTGACTGATGC 59.899 50.000 22.40 13.93 44.88 3.91
897 909 2.221906 CTGCCACCTTTGCATGCCTC 62.222 60.000 16.68 0.00 38.22 4.70
2561 2651 2.968156 GTACACCAACGCGCACCA 60.968 61.111 5.73 0.00 0.00 4.17
2562 2652 2.031314 TACACCAACGCGCACCAT 59.969 55.556 5.73 0.00 0.00 3.55
2649 2739 2.569134 GTCTCTCTCGCCAGCGTT 59.431 61.111 12.32 0.00 40.74 4.84
2650 2740 1.801332 GTCTCTCTCGCCAGCGTTA 59.199 57.895 12.32 0.57 40.74 3.18
2700 2790 0.972983 AGATGCACTACGTCCAGCCT 60.973 55.000 0.00 0.00 34.56 4.58
3007 3133 2.685017 AGCTCATCCTGCCGACCA 60.685 61.111 0.00 0.00 0.00 4.02
3025 3151 3.903208 ATGTTCCTGTACATGGCCC 57.097 52.632 0.00 0.00 37.36 5.80
3463 3589 4.033776 CCAGGGCCGACACCATGT 62.034 66.667 0.00 0.00 39.89 3.21
3476 3602 3.000041 ACACCATGTTGTAGCATGTACG 59.000 45.455 0.00 0.00 43.33 3.67
3478 3604 3.000041 ACCATGTTGTAGCATGTACGTG 59.000 45.455 10.89 10.89 43.33 4.49
3483 3609 1.985334 TGTAGCATGTACGTGGTTCG 58.015 50.000 23.69 0.00 46.00 3.95
3493 3619 2.695087 CGTGGTTCGTTGCGATTTG 58.305 52.632 0.00 0.00 35.23 2.32
3494 3620 0.041663 CGTGGTTCGTTGCGATTTGT 60.042 50.000 0.00 0.00 35.23 2.83
3495 3621 1.595976 CGTGGTTCGTTGCGATTTGTT 60.596 47.619 0.00 0.00 35.23 2.83
3496 3622 2.041244 GTGGTTCGTTGCGATTTGTTC 58.959 47.619 0.00 0.00 35.23 3.18
3497 3623 1.671328 TGGTTCGTTGCGATTTGTTCA 59.329 42.857 0.00 0.00 35.23 3.18
3498 3624 2.292016 TGGTTCGTTGCGATTTGTTCAT 59.708 40.909 0.00 0.00 35.23 2.57
3499 3625 2.656422 GGTTCGTTGCGATTTGTTCATG 59.344 45.455 0.00 0.00 35.23 3.07
3500 3626 3.296628 GTTCGTTGCGATTTGTTCATGT 58.703 40.909 0.00 0.00 35.23 3.21
3501 3627 2.914861 TCGTTGCGATTTGTTCATGTG 58.085 42.857 0.00 0.00 0.00 3.21
3502 3628 2.289274 TCGTTGCGATTTGTTCATGTGT 59.711 40.909 0.00 0.00 0.00 3.72
3503 3629 3.042189 CGTTGCGATTTGTTCATGTGTT 58.958 40.909 0.00 0.00 0.00 3.32
3504 3630 3.485378 CGTTGCGATTTGTTCATGTGTTT 59.515 39.130 0.00 0.00 0.00 2.83
3505 3631 4.026968 CGTTGCGATTTGTTCATGTGTTTT 60.027 37.500 0.00 0.00 0.00 2.43
3506 3632 5.189625 GTTGCGATTTGTTCATGTGTTTTG 58.810 37.500 0.00 0.00 0.00 2.44
3507 3633 4.428209 TGCGATTTGTTCATGTGTTTTGT 58.572 34.783 0.00 0.00 0.00 2.83
3508 3634 4.867047 TGCGATTTGTTCATGTGTTTTGTT 59.133 33.333 0.00 0.00 0.00 2.83
3509 3635 5.005203 TGCGATTTGTTCATGTGTTTTGTTC 59.995 36.000 0.00 0.00 0.00 3.18
3510 3636 5.646021 CGATTTGTTCATGTGTTTTGTTCG 58.354 37.500 0.00 0.00 0.00 3.95
3511 3637 5.453909 CGATTTGTTCATGTGTTTTGTTCGA 59.546 36.000 0.00 0.00 0.00 3.71
3512 3638 6.142161 CGATTTGTTCATGTGTTTTGTTCGAT 59.858 34.615 0.00 0.00 0.00 3.59
3513 3639 7.305935 CGATTTGTTCATGTGTTTTGTTCGATT 60.306 33.333 0.00 0.00 0.00 3.34
3514 3640 6.804534 TTGTTCATGTGTTTTGTTCGATTC 57.195 33.333 0.00 0.00 0.00 2.52
3515 3641 6.130298 TGTTCATGTGTTTTGTTCGATTCT 57.870 33.333 0.00 0.00 0.00 2.40
3516 3642 6.559810 TGTTCATGTGTTTTGTTCGATTCTT 58.440 32.000 0.00 0.00 0.00 2.52
3517 3643 6.690957 TGTTCATGTGTTTTGTTCGATTCTTC 59.309 34.615 0.00 0.00 0.00 2.87
3518 3644 6.370433 TCATGTGTTTTGTTCGATTCTTCA 57.630 33.333 0.00 0.00 0.00 3.02
3519 3645 6.429624 TCATGTGTTTTGTTCGATTCTTCAG 58.570 36.000 0.00 0.00 0.00 3.02
3520 3646 5.811399 TGTGTTTTGTTCGATTCTTCAGT 57.189 34.783 0.00 0.00 0.00 3.41
3521 3647 6.189677 TGTGTTTTGTTCGATTCTTCAGTT 57.810 33.333 0.00 0.00 0.00 3.16
3522 3648 6.255215 TGTGTTTTGTTCGATTCTTCAGTTC 58.745 36.000 0.00 0.00 0.00 3.01
3523 3649 6.128145 TGTGTTTTGTTCGATTCTTCAGTTCA 60.128 34.615 0.00 0.00 0.00 3.18
3524 3650 6.194692 GTGTTTTGTTCGATTCTTCAGTTCAC 59.805 38.462 0.00 0.00 0.00 3.18
3525 3651 6.093495 TGTTTTGTTCGATTCTTCAGTTCACT 59.907 34.615 0.00 0.00 0.00 3.41
3526 3652 5.657470 TTGTTCGATTCTTCAGTTCACTG 57.343 39.130 0.02 0.02 45.08 3.66
3527 3653 3.494626 TGTTCGATTCTTCAGTTCACTGC 59.505 43.478 1.74 0.00 43.46 4.40
3528 3654 2.688507 TCGATTCTTCAGTTCACTGCC 58.311 47.619 1.74 0.00 43.46 4.85
3529 3655 2.037121 TCGATTCTTCAGTTCACTGCCA 59.963 45.455 1.74 0.00 43.46 4.92
3530 3656 3.005554 CGATTCTTCAGTTCACTGCCAT 58.994 45.455 1.74 0.00 43.46 4.40
3531 3657 3.181513 CGATTCTTCAGTTCACTGCCATG 60.182 47.826 1.74 0.00 43.46 3.66
3532 3658 2.936919 TCTTCAGTTCACTGCCATGT 57.063 45.000 1.74 0.00 43.46 3.21
3533 3659 3.213206 TCTTCAGTTCACTGCCATGTT 57.787 42.857 1.74 0.00 43.46 2.71
3534 3660 2.880268 TCTTCAGTTCACTGCCATGTTG 59.120 45.455 1.74 0.00 43.46 3.33
3535 3661 2.346766 TCAGTTCACTGCCATGTTGT 57.653 45.000 1.74 0.00 43.46 3.32
3536 3662 3.483808 TCAGTTCACTGCCATGTTGTA 57.516 42.857 1.74 0.00 43.46 2.41
3537 3663 3.402110 TCAGTTCACTGCCATGTTGTAG 58.598 45.455 1.74 0.00 43.46 2.74
3538 3664 2.095567 CAGTTCACTGCCATGTTGTAGC 60.096 50.000 0.00 0.00 37.15 3.58
3539 3665 1.879380 GTTCACTGCCATGTTGTAGCA 59.121 47.619 0.00 0.00 34.79 3.49
3540 3666 2.489329 GTTCACTGCCATGTTGTAGCAT 59.511 45.455 0.00 0.00 35.64 3.79
3541 3667 2.086094 TCACTGCCATGTTGTAGCATG 58.914 47.619 2.18 2.18 44.18 4.06
3542 3668 1.814394 CACTGCCATGTTGTAGCATGT 59.186 47.619 7.72 0.00 43.33 3.21
3543 3669 3.009026 CACTGCCATGTTGTAGCATGTA 58.991 45.455 7.72 0.00 43.33 2.29
3544 3670 3.009723 ACTGCCATGTTGTAGCATGTAC 58.990 45.455 7.72 0.00 43.33 2.90
3545 3671 2.006169 TGCCATGTTGTAGCATGTACG 58.994 47.619 7.72 0.00 43.33 3.67
3548 3674 2.351418 CCATGTTGTAGCATGTACGTGG 59.649 50.000 16.68 0.00 43.33 4.94
3551 3677 3.061322 TGTTGTAGCATGTACGTGGTTC 58.939 45.455 23.69 18.89 0.00 3.62
3570 3696 2.914861 TCGTTGCGATTTGTTCATGTG 58.085 42.857 0.00 0.00 0.00 3.21
3576 3702 4.428209 TGCGATTTGTTCATGTGTTTTGT 58.572 34.783 0.00 0.00 0.00 2.83
3608 3734 1.011968 TTCGCTGCCGTGATGTGTAC 61.012 55.000 0.00 0.00 35.54 2.90
3609 3735 1.446099 CGCTGCCGTGATGTGTACT 60.446 57.895 0.00 0.00 0.00 2.73
3610 3736 0.179148 CGCTGCCGTGATGTGTACTA 60.179 55.000 0.00 0.00 0.00 1.82
3620 3746 5.330295 CGTGATGTGTACTAGTAAGTGTCC 58.670 45.833 3.61 0.00 36.36 4.02
3677 3803 5.821470 ACTCTCACCAGCATGATCAAAATAG 59.179 40.000 0.00 0.00 39.69 1.73
3678 3804 5.993055 TCTCACCAGCATGATCAAAATAGA 58.007 37.500 0.00 0.00 39.69 1.98
3681 3807 4.337274 CACCAGCATGATCAAAATAGAGCA 59.663 41.667 0.00 0.00 39.69 4.26
3689 3815 7.683704 GCATGATCAAAATAGAGCAAATCCACT 60.684 37.037 0.00 0.00 37.48 4.00
3710 3836 3.734463 TGCTAAATGTCGGTGAACTTCA 58.266 40.909 0.00 0.00 0.00 3.02
3725 3851 4.889409 TGAACTTCAAAGTGAAATGCCTCT 59.111 37.500 0.00 0.00 39.66 3.69
3749 3875 5.943416 TGAACGGGACTGATATTTTTCACAT 59.057 36.000 0.00 0.00 0.00 3.21
3754 3880 5.123227 GGACTGATATTTTTCACATCGGGA 58.877 41.667 0.00 0.00 30.71 5.14
3756 3882 6.263168 GGACTGATATTTTTCACATCGGGATT 59.737 38.462 0.00 0.00 30.71 3.01
3757 3883 7.201821 GGACTGATATTTTTCACATCGGGATTT 60.202 37.037 0.00 0.00 30.71 2.17
3770 3896 2.092968 TCGGGATTTGTGCTGCTATTCT 60.093 45.455 0.00 0.00 0.00 2.40
3775 3901 5.125417 GGGATTTGTGCTGCTATTCTTGTAA 59.875 40.000 0.00 0.00 0.00 2.41
3776 3902 6.261118 GGATTTGTGCTGCTATTCTTGTAAG 58.739 40.000 0.00 0.00 0.00 2.34
3777 3903 6.127897 GGATTTGTGCTGCTATTCTTGTAAGT 60.128 38.462 0.00 0.00 0.00 2.24
3778 3904 5.611796 TTGTGCTGCTATTCTTGTAAGTG 57.388 39.130 0.00 0.00 0.00 3.16
3779 3905 3.436704 TGTGCTGCTATTCTTGTAAGTGC 59.563 43.478 0.00 0.00 0.00 4.40
3804 3956 6.795144 TTTGTTTGCCATATCTGAATCCAT 57.205 33.333 0.00 0.00 0.00 3.41
3870 4022 3.321111 GGCATGCATTTCAGAGGAATGAT 59.679 43.478 21.36 0.00 31.93 2.45
3923 4075 6.801539 TTCATGTGTTACAGTTTGATCCTC 57.198 37.500 0.00 0.00 0.00 3.71
3965 4125 2.611225 ATACTTCTGCAGGCTGTAGC 57.389 50.000 25.50 8.06 41.14 3.58
3967 4127 0.617413 ACTTCTGCAGGCTGTAGCAT 59.383 50.000 25.50 11.66 44.36 3.79
4049 4222 6.413892 TCCAGCAACATAAATGTATCTCACA 58.586 36.000 0.00 0.00 40.80 3.58
4080 4335 4.556699 GCGAGTACTTCTTTTGTTTGCCAT 60.557 41.667 0.00 0.00 0.00 4.40
4096 4351 8.070034 TGTTTGCCATATCTGAATCATTTTCT 57.930 30.769 0.00 0.00 0.00 2.52
4099 4354 7.425577 TGCCATATCTGAATCATTTTCTACG 57.574 36.000 0.00 0.00 0.00 3.51
4156 4411 3.011032 AGGGAATGCACTTCAGAGGAATT 59.989 43.478 0.00 0.00 35.41 2.17
4157 4412 3.766051 GGGAATGCACTTCAGAGGAATTT 59.234 43.478 0.00 0.00 35.41 1.82
4240 4495 0.548989 TGTACCAACCCTTGCAGTGT 59.451 50.000 0.00 0.00 0.00 3.55
4272 4527 5.875224 TCATGTGTTCCAGTTTGATCCTTA 58.125 37.500 0.00 0.00 0.00 2.69
4302 4557 6.591750 TTCCAGAACCTAGAACAGAGTTAG 57.408 41.667 0.00 0.00 0.00 2.34
4358 4613 3.585289 TCTGATAAACCTTGGTACCAGCA 59.415 43.478 15.65 0.00 0.00 4.41
4374 4629 2.624838 CCAGCAAGACAACCACTTCAAT 59.375 45.455 0.00 0.00 0.00 2.57
4379 4634 4.441356 GCAAGACAACCACTTCAATTTCCA 60.441 41.667 0.00 0.00 0.00 3.53
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
16 17 6.419791 ACCTTGGTTTATCGATCCATTTGTA 58.580 36.000 0.00 0.00 0.00 2.41
40 41 0.739462 CCTTTGCACTATGTCGGCGA 60.739 55.000 4.99 4.99 0.00 5.54
41 42 0.739462 TCCTTTGCACTATGTCGGCG 60.739 55.000 0.00 0.00 0.00 6.46
42 43 1.599542 GATCCTTTGCACTATGTCGGC 59.400 52.381 0.00 0.00 0.00 5.54
108 109 9.415544 GAGAACTAAAATTTACTCCGTGTCTTA 57.584 33.333 0.00 0.00 0.00 2.10
115 116 7.445836 CACTTCGAGAACTAAAATTTACTCCG 58.554 38.462 0.00 0.00 0.00 4.63
127 128 3.439476 GTCCAGTAGCACTTCGAGAACTA 59.561 47.826 0.00 0.00 0.00 2.24
482 485 5.032100 TCTCTAACATCGCGTATAGAAGC 57.968 43.478 5.77 0.00 0.00 3.86
587 591 3.070446 TCCACAGTAGTGTAAACCAGGTG 59.930 47.826 2.08 0.00 44.39 4.00
630 634 1.605712 GCCTGCGTCTGTTACTCTGTT 60.606 52.381 0.00 0.00 0.00 3.16
631 635 0.038159 GCCTGCGTCTGTTACTCTGT 60.038 55.000 0.00 0.00 0.00 3.41
632 636 0.038251 TGCCTGCGTCTGTTACTCTG 60.038 55.000 0.00 0.00 0.00 3.35
633 637 0.244994 CTGCCTGCGTCTGTTACTCT 59.755 55.000 0.00 0.00 0.00 3.24
634 638 0.038159 ACTGCCTGCGTCTGTTACTC 60.038 55.000 0.00 0.00 0.00 2.59
635 639 0.393077 AACTGCCTGCGTCTGTTACT 59.607 50.000 0.00 0.00 0.00 2.24
636 640 1.194772 GAAACTGCCTGCGTCTGTTAC 59.805 52.381 0.00 0.00 0.00 2.50
637 641 1.508632 GAAACTGCCTGCGTCTGTTA 58.491 50.000 0.00 0.00 0.00 2.41
773 777 3.799755 GATTGTGTGACCGCGCCC 61.800 66.667 0.00 0.00 0.00 6.13
792 796 0.480690 AGCATTTGTGGTGGGTGGTA 59.519 50.000 0.00 0.00 0.00 3.25
797 801 1.001181 CCTTGAAGCATTTGTGGTGGG 59.999 52.381 0.00 0.00 0.00 4.61
875 887 1.080093 CATGCAAAGGTGGCAGCAG 60.080 57.895 20.04 9.30 45.68 4.24
1054 1066 1.526575 ATTGCGCCCTTGGACTTGTG 61.527 55.000 4.18 0.00 0.00 3.33
1178 1196 0.387202 ATCATAAGCACTCGCGAGCT 59.613 50.000 34.83 25.41 45.49 4.09
1280 1298 3.066814 GCACCTCGACGTAGGGGT 61.067 66.667 15.28 15.28 42.56 4.95
1335 1353 3.068691 TCCGGGCTCGACTTCCTG 61.069 66.667 8.08 0.00 39.00 3.86
1346 1364 4.410400 CCTGGTTCCACTCCGGGC 62.410 72.222 0.00 0.00 43.45 6.13
2256 2319 0.898320 CGGTCTTCATGGGAGTGAGT 59.102 55.000 0.00 0.00 0.00 3.41
2419 2482 4.210304 GTCGAACATGGCGAGCGC 62.210 66.667 12.34 6.27 38.59 5.92
2561 2651 2.125912 GGTGCAGCACGACGAGAT 60.126 61.111 19.42 0.00 34.83 2.75
2562 2652 4.357947 GGGTGCAGCACGACGAGA 62.358 66.667 19.42 0.00 34.83 4.04
2649 2739 1.406341 GGCTTCCCGTACAAGCACATA 60.406 52.381 15.81 0.00 46.94 2.29
2650 2740 0.676782 GGCTTCCCGTACAAGCACAT 60.677 55.000 15.81 0.00 46.94 3.21
2700 2790 4.408821 AGCTGCGGGATGGCGAAA 62.409 61.111 0.00 0.00 35.06 3.46
3007 3133 1.064463 CAGGGCCATGTACAGGAACAT 60.064 52.381 9.85 0.00 40.75 2.71
3463 3589 2.330286 CGAACCACGTACATGCTACAA 58.670 47.619 0.00 0.00 37.22 2.41
3476 3602 2.041244 GAACAAATCGCAACGAACCAC 58.959 47.619 0.00 0.00 39.99 4.16
3478 3604 2.392933 TGAACAAATCGCAACGAACC 57.607 45.000 0.00 0.00 39.99 3.62
3483 3609 5.189625 CAAAACACATGAACAAATCGCAAC 58.810 37.500 0.00 0.00 0.00 4.17
3484 3610 4.867047 ACAAAACACATGAACAAATCGCAA 59.133 33.333 0.00 0.00 0.00 4.85
3485 3611 4.428209 ACAAAACACATGAACAAATCGCA 58.572 34.783 0.00 0.00 0.00 5.10
3486 3612 5.388225 AACAAAACACATGAACAAATCGC 57.612 34.783 0.00 0.00 0.00 4.58
3487 3613 5.453909 TCGAACAAAACACATGAACAAATCG 59.546 36.000 0.00 0.14 0.00 3.34
3488 3614 6.804534 TCGAACAAAACACATGAACAAATC 57.195 33.333 0.00 0.00 0.00 2.17
3489 3615 7.706179 AGAATCGAACAAAACACATGAACAAAT 59.294 29.630 0.00 0.00 0.00 2.32
3490 3616 7.032580 AGAATCGAACAAAACACATGAACAAA 58.967 30.769 0.00 0.00 0.00 2.83
3491 3617 6.559810 AGAATCGAACAAAACACATGAACAA 58.440 32.000 0.00 0.00 0.00 2.83
3492 3618 6.130298 AGAATCGAACAAAACACATGAACA 57.870 33.333 0.00 0.00 0.00 3.18
3493 3619 6.690957 TGAAGAATCGAACAAAACACATGAAC 59.309 34.615 0.00 0.00 0.00 3.18
3494 3620 6.790282 TGAAGAATCGAACAAAACACATGAA 58.210 32.000 0.00 0.00 0.00 2.57
3495 3621 6.038161 ACTGAAGAATCGAACAAAACACATGA 59.962 34.615 0.00 0.00 0.00 3.07
3496 3622 6.201517 ACTGAAGAATCGAACAAAACACATG 58.798 36.000 0.00 0.00 0.00 3.21
3497 3623 6.377327 ACTGAAGAATCGAACAAAACACAT 57.623 33.333 0.00 0.00 0.00 3.21
3498 3624 5.811399 ACTGAAGAATCGAACAAAACACA 57.189 34.783 0.00 0.00 0.00 3.72
3499 3625 6.194692 GTGAACTGAAGAATCGAACAAAACAC 59.805 38.462 0.00 0.00 0.00 3.32
3500 3626 6.093495 AGTGAACTGAAGAATCGAACAAAACA 59.907 34.615 0.00 0.00 0.00 2.83
3501 3627 6.412072 CAGTGAACTGAAGAATCGAACAAAAC 59.588 38.462 4.36 0.00 46.59 2.43
3502 3628 6.486248 CAGTGAACTGAAGAATCGAACAAAA 58.514 36.000 4.36 0.00 46.59 2.44
3503 3629 5.504010 GCAGTGAACTGAAGAATCGAACAAA 60.504 40.000 14.58 0.00 46.59 2.83
3504 3630 4.024893 GCAGTGAACTGAAGAATCGAACAA 60.025 41.667 14.58 0.00 46.59 2.83
3505 3631 3.494626 GCAGTGAACTGAAGAATCGAACA 59.505 43.478 14.58 0.00 46.59 3.18
3506 3632 3.120511 GGCAGTGAACTGAAGAATCGAAC 60.121 47.826 14.58 0.00 46.59 3.95
3507 3633 3.067106 GGCAGTGAACTGAAGAATCGAA 58.933 45.455 14.58 0.00 46.59 3.71
3508 3634 2.037121 TGGCAGTGAACTGAAGAATCGA 59.963 45.455 14.58 0.00 46.59 3.59
3509 3635 2.416747 TGGCAGTGAACTGAAGAATCG 58.583 47.619 14.58 0.00 46.59 3.34
3510 3636 3.755378 ACATGGCAGTGAACTGAAGAATC 59.245 43.478 14.58 0.00 46.59 2.52
3511 3637 3.759581 ACATGGCAGTGAACTGAAGAAT 58.240 40.909 14.58 0.00 46.59 2.40
3512 3638 3.213206 ACATGGCAGTGAACTGAAGAA 57.787 42.857 14.58 0.00 46.59 2.52
3513 3639 2.880268 CAACATGGCAGTGAACTGAAGA 59.120 45.455 14.58 0.00 46.59 2.87
3514 3640 2.620115 ACAACATGGCAGTGAACTGAAG 59.380 45.455 14.58 3.07 46.59 3.02
3515 3641 2.653726 ACAACATGGCAGTGAACTGAA 58.346 42.857 14.58 1.95 46.59 3.02
3516 3642 2.346766 ACAACATGGCAGTGAACTGA 57.653 45.000 14.58 0.00 46.59 3.41
3517 3643 2.095567 GCTACAACATGGCAGTGAACTG 60.096 50.000 6.08 6.08 46.40 3.16
3518 3644 2.154462 GCTACAACATGGCAGTGAACT 58.846 47.619 0.00 0.00 34.21 3.01
3519 3645 1.879380 TGCTACAACATGGCAGTGAAC 59.121 47.619 0.00 0.00 40.40 3.18
3520 3646 2.268762 TGCTACAACATGGCAGTGAA 57.731 45.000 0.00 0.00 40.40 3.18
3528 3654 7.616698 CGAACCACGTACATGCTACAACATG 62.617 48.000 3.07 3.07 43.62 3.21
3529 3655 3.328382 ACCACGTACATGCTACAACAT 57.672 42.857 0.00 0.00 0.00 2.71
3530 3656 2.823924 ACCACGTACATGCTACAACA 57.176 45.000 0.00 0.00 0.00 3.33
3531 3657 2.091588 CGAACCACGTACATGCTACAAC 59.908 50.000 0.00 0.00 37.22 3.32
3532 3658 2.330286 CGAACCACGTACATGCTACAA 58.670 47.619 0.00 0.00 37.22 2.41
3533 3659 1.985334 CGAACCACGTACATGCTACA 58.015 50.000 0.00 0.00 37.22 2.74
3545 3671 2.041244 GAACAAATCGCAACGAACCAC 58.959 47.619 0.00 0.00 39.99 4.16
3548 3674 3.117832 CACATGAACAAATCGCAACGAAC 59.882 43.478 0.00 0.00 39.99 3.95
3551 3677 2.649516 ACACATGAACAAATCGCAACG 58.350 42.857 0.00 0.00 0.00 4.10
3556 3682 5.453909 TCGAACAAAACACATGAACAAATCG 59.546 36.000 0.00 0.14 0.00 3.34
3570 3696 4.375988 GCGAACTGAAGAATCGAACAAAAC 59.624 41.667 12.21 0.00 38.82 2.43
3620 3746 2.683859 TAGCCGTCACTCCGTCACG 61.684 63.158 0.00 0.00 0.00 4.35
3637 3763 0.253044 GAGTGGCTTGCCAGGATGTA 59.747 55.000 15.31 0.00 0.00 2.29
3681 3807 3.440173 CACCGACATTTAGCAGTGGATTT 59.560 43.478 0.00 0.00 0.00 2.17
3689 3815 3.734463 TGAAGTTCACCGACATTTAGCA 58.266 40.909 0.08 0.00 0.00 3.49
3710 3836 2.554032 CCGTTCAGAGGCATTTCACTTT 59.446 45.455 0.00 0.00 0.00 2.66
3725 3851 5.309638 TGTGAAAAATATCAGTCCCGTTCA 58.690 37.500 0.00 0.00 0.00 3.18
3749 3875 2.092968 AGAATAGCAGCACAAATCCCGA 60.093 45.455 0.00 0.00 0.00 5.14
3754 3880 6.615088 CACTTACAAGAATAGCAGCACAAAT 58.385 36.000 0.00 0.00 0.00 2.32
3756 3882 4.083324 GCACTTACAAGAATAGCAGCACAA 60.083 41.667 0.00 0.00 0.00 3.33
3757 3883 3.436704 GCACTTACAAGAATAGCAGCACA 59.563 43.478 0.00 0.00 0.00 4.57
3770 3896 4.193826 TGGCAAACAAAAGCACTTACAA 57.806 36.364 0.00 0.00 0.00 2.41
3775 3901 4.523943 TCAGATATGGCAAACAAAAGCACT 59.476 37.500 0.00 0.00 0.00 4.40
3776 3902 4.808558 TCAGATATGGCAAACAAAAGCAC 58.191 39.130 0.00 0.00 0.00 4.40
3777 3903 5.465532 TTCAGATATGGCAAACAAAAGCA 57.534 34.783 0.00 0.00 0.00 3.91
3778 3904 5.521372 GGATTCAGATATGGCAAACAAAAGC 59.479 40.000 0.00 0.00 0.00 3.51
3779 3905 6.632909 TGGATTCAGATATGGCAAACAAAAG 58.367 36.000 0.00 0.00 0.00 2.27
3870 4022 3.885724 TGCATTTGTCCTGTCGATCTA 57.114 42.857 0.00 0.00 0.00 1.98
3923 4075 2.156917 TGCAACTCTGGAAAGATGCTG 58.843 47.619 7.50 0.00 43.31 4.41
3965 4125 5.185454 TGGTAGCAAGGTTTGTCAGATATG 58.815 41.667 0.00 0.00 0.00 1.78
3967 4127 4.832248 CTGGTAGCAAGGTTTGTCAGATA 58.168 43.478 0.00 0.00 0.00 1.98
4049 4222 5.531287 ACAAAAGAAGTACTCGCCTGATTTT 59.469 36.000 0.00 0.00 0.00 1.82
4096 4351 7.864108 ATGTTGAATGGATTCAGATTTCGTA 57.136 32.000 2.46 0.00 46.34 3.43
4099 4354 8.896744 TCAGTATGTTGAATGGATTCAGATTTC 58.103 33.333 2.46 0.00 40.72 2.17
4156 4411 4.416516 TCTACAGGACCTGTCAATCTGAA 58.583 43.478 30.43 9.76 41.21 3.02
4157 4412 4.047627 TCTACAGGACCTGTCAATCTGA 57.952 45.455 30.43 15.93 41.21 3.27
4203 4458 5.356751 TGGTACAAATGCGCTGATAAGAATT 59.643 36.000 9.73 0.00 31.92 2.17
4240 4495 7.284261 TCAAACTGGAACACATGAATCTGTTTA 59.716 33.333 0.00 0.00 30.59 2.01
4272 4527 4.287067 TGTTCTAGGTTCTGGAAAGATGCT 59.713 41.667 0.00 0.00 33.06 3.79
4358 4613 5.200483 TCTGGAAATTGAAGTGGTTGTCTT 58.800 37.500 0.00 0.00 0.00 3.01
4374 4629 5.938125 GCTGGAACTACATTTACTCTGGAAA 59.062 40.000 0.00 0.00 0.00 3.13
4379 4634 5.865085 TGTTGCTGGAACTACATTTACTCT 58.135 37.500 13.23 0.00 35.37 3.24


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

AutoCloner maintained by Alex Coulton.