Multiple sequence alignment - TraesCS2D01G220200

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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 TraesCS2D01G220200 chr2D 100.000 3713 0 0 1 3713 187532497 187528785 0.000000e+00 6857
1 TraesCS2D01G220200 chr2B 96.770 3467 93 12 1 3455 243572099 243568640 0.000000e+00 5764
2 TraesCS2D01G220200 chr2B 95.376 173 7 1 3542 3713 363772885 363772713 1.310000e-69 274
3 TraesCS2D01G220200 chr2A 97.744 3236 72 1 1 3236 200181959 200178725 0.000000e+00 5570
4 TraesCS2D01G220200 chr2A 89.083 229 15 7 3316 3542 200178730 200178510 3.650000e-70 276
5 TraesCS2D01G220200 chr5B 97.110 173 4 1 3542 3713 590180412 590180584 1.300000e-74 291
6 TraesCS2D01G220200 chr3D 97.059 170 5 0 3544 3713 134007731 134007562 1.690000e-73 287
7 TraesCS2D01G220200 chr3D 95.376 173 7 1 3542 3713 463681507 463681679 1.310000e-69 274
8 TraesCS2D01G220200 chr7B 95.376 173 7 1 3542 3713 747358625 747358797 1.310000e-69 274
9 TraesCS2D01G220200 chr6D 95.349 172 8 0 3542 3713 143958445 143958616 1.310000e-69 274
10 TraesCS2D01G220200 chr6D 94.798 173 8 1 3542 3713 377864192 377864020 6.110000e-68 268
11 TraesCS2D01G220200 chr6A 95.376 173 7 1 3542 3713 617751685 617751857 1.310000e-69 274
12 TraesCS2D01G220200 chr7A 92.391 184 14 0 3530 3713 6342251 6342068 2.840000e-66 263


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 TraesCS2D01G220200 chr2D 187528785 187532497 3712 True 6857 6857 100.0000 1 3713 1 chr2D.!!$R1 3712
1 TraesCS2D01G220200 chr2B 243568640 243572099 3459 True 5764 5764 96.7700 1 3455 1 chr2B.!!$R1 3454
2 TraesCS2D01G220200 chr2A 200178510 200181959 3449 True 2923 5570 93.4135 1 3542 2 chr2A.!!$R1 3541

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
276 277 1.167851 TGCGGAATTTTGGAGAGCTG 58.832 50.000 0.00 0.0 0.0 4.24 F
848 852 1.339535 CCTGTTGCCTCTTCCTCCTTC 60.340 57.143 0.00 0.0 0.0 3.46 F
1507 1511 1.002134 CCTGGAGTTGTTCGGCCAT 60.002 57.895 2.24 0.0 0.0 4.40 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1278 1282 2.890945 TCTCACTTGGATGTTCTCACGA 59.109 45.455 0.00 0.0 0.00 4.35 R
2472 2476 1.006086 CGCAGGCGATTATGTTCACA 58.994 50.000 8.15 0.0 42.83 3.58 R
3302 3314 0.108138 ATCCTGTTGCTACTGACGCC 60.108 55.000 6.74 0.0 0.00 5.68 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
186 187 3.630312 TGTGGTTGTCCTTTAAGCTTGAC 59.370 43.478 9.86 8.46 34.23 3.18
276 277 1.167851 TGCGGAATTTTGGAGAGCTG 58.832 50.000 0.00 0.00 0.00 4.24
319 320 2.295885 CATAGAGGAAAGGCAAGCAGG 58.704 52.381 0.00 0.00 0.00 4.85
345 346 9.030301 GCAAATTAAAGAAAACTTGCTCTTGTA 57.970 29.630 0.00 0.00 37.17 2.41
428 429 9.693739 TTTTATTCTTGTATTAATGGGCTCTCA 57.306 29.630 0.00 0.00 0.00 3.27
525 526 7.114811 CCGTTTCAGAAAATACCACTCAAATTG 59.885 37.037 0.00 0.00 0.00 2.32
838 842 1.576421 CTTTGTCGCCTGTTGCCTC 59.424 57.895 0.00 0.00 36.24 4.70
848 852 1.339535 CCTGTTGCCTCTTCCTCCTTC 60.340 57.143 0.00 0.00 0.00 3.46
865 869 6.792473 TCCTCCTTCCCTCTAAATTATATGCA 59.208 38.462 0.00 0.00 0.00 3.96
1194 1198 2.342179 GCTCTTAGCAACACTCCAGAC 58.658 52.381 0.00 0.00 41.89 3.51
1507 1511 1.002134 CCTGGAGTTGTTCGGCCAT 60.002 57.895 2.24 0.00 0.00 4.40
1581 1585 2.910977 ACGACAAAGGGAGTTAAGGGAT 59.089 45.455 0.00 0.00 0.00 3.85
1593 1597 4.759782 AGTTAAGGGATGATCGACAACAG 58.240 43.478 0.00 0.00 0.00 3.16
2481 2485 3.088532 GGCCAAGGACATTGTGAACATA 58.911 45.455 0.00 0.00 37.17 2.29
2737 2741 2.571212 TGCTCAGCGGAAGAAGAAAAA 58.429 42.857 0.00 0.00 0.00 1.94
2962 2966 0.963962 CAGGCATGCTCTTGTTGGTT 59.036 50.000 18.92 0.00 0.00 3.67
3019 3023 3.768633 CAGAGTATGCCCTGGTCAC 57.231 57.895 0.00 0.00 0.00 3.67
3036 3040 0.179073 CACGGGGCCTGTGAAGATAG 60.179 60.000 37.00 11.02 39.73 2.08
3040 3044 1.134068 GGGGCCTGTGAAGATAGGTTC 60.134 57.143 0.84 0.00 36.44 3.62
3100 3104 0.252696 AGTGGTGTAGGATCAGGGCA 60.253 55.000 0.00 0.00 0.00 5.36
3143 3147 1.468914 GCTTTGGGTCGAGATTTGGAC 59.531 52.381 0.00 0.00 0.00 4.02
3184 3188 2.857592 ACGTTCGTTCTACACTGTGT 57.142 45.000 18.51 18.51 0.00 3.72
3193 3197 4.618227 CGTTCTACACTGTGTGGATGATGA 60.618 45.833 24.57 9.29 37.70 2.92
3290 3302 0.539438 TGGGCAATGATATTCCGGGC 60.539 55.000 0.00 0.00 0.00 6.13
3314 3326 4.735132 GGCACGGCGTCAGTAGCA 62.735 66.667 10.85 0.00 36.08 3.49
3354 3366 7.526608 CGAACAAAATGGAGTTTAGCTGATTA 58.473 34.615 0.00 0.00 0.00 1.75
3370 3383 1.344763 GATTACCTCCGAGTCCCATGG 59.655 57.143 4.14 4.14 0.00 3.66
3386 3399 2.669781 CATGGCATACAACCCTCCAAT 58.330 47.619 0.00 0.00 0.00 3.16
3404 3418 3.891366 CCAATGTCCAAACTCCAAGTCTT 59.109 43.478 0.00 0.00 0.00 3.01
3474 3488 0.249322 ACGTTCTCTGTGGTGAACCG 60.249 55.000 0.00 0.00 40.65 4.44
3484 3498 3.580794 GTGGTGAACCGCGTATTATTC 57.419 47.619 4.92 1.40 39.43 1.75
3489 3503 4.260091 GGTGAACCGCGTATTATTCTGAAC 60.260 45.833 4.92 0.00 0.00 3.18
3493 3507 6.474427 TGAACCGCGTATTATTCTGAACTTAG 59.526 38.462 4.92 0.00 0.00 2.18
3499 3513 7.997104 CGCGTATTATTCTGAACTTAGTTTAGC 59.003 37.037 11.40 0.00 30.72 3.09
3516 3530 3.136123 CCTTCCGGCGGTACTCGA 61.136 66.667 27.32 1.27 42.43 4.04
3517 3531 2.408022 CTTCCGGCGGTACTCGAG 59.592 66.667 27.32 11.84 42.43 4.04
3525 3539 0.456312 GCGGTACTCGAGTTCAGTGG 60.456 60.000 25.44 9.96 42.43 4.00
3526 3540 1.162698 CGGTACTCGAGTTCAGTGGA 58.837 55.000 25.44 0.00 42.43 4.02
3529 3543 2.818432 GGTACTCGAGTTCAGTGGAAGA 59.182 50.000 25.44 0.00 32.62 2.87
3538 3552 5.050702 CGAGTTCAGTGGAAGAAGAAGTTTC 60.051 44.000 0.00 0.00 32.62 2.78
3542 3556 3.877508 CAGTGGAAGAAGAAGTTTCCGTT 59.122 43.478 0.00 0.00 44.66 4.44
3543 3557 4.335594 CAGTGGAAGAAGAAGTTTCCGTTT 59.664 41.667 0.00 0.00 44.66 3.60
3544 3558 4.948004 AGTGGAAGAAGAAGTTTCCGTTTT 59.052 37.500 0.00 0.00 44.66 2.43
3545 3559 5.417894 AGTGGAAGAAGAAGTTTCCGTTTTT 59.582 36.000 0.00 0.00 44.66 1.94
3562 3576 3.872560 TTTTTCGAGAAAGCTTCCGAC 57.127 42.857 15.13 2.42 34.01 4.79
3563 3577 1.792006 TTTCGAGAAAGCTTCCGACC 58.208 50.000 15.13 0.00 34.01 4.79
3564 3578 0.966920 TTCGAGAAAGCTTCCGACCT 59.033 50.000 15.13 2.50 34.01 3.85
3565 3579 1.830279 TCGAGAAAGCTTCCGACCTA 58.170 50.000 12.52 0.00 30.97 3.08
3566 3580 2.376109 TCGAGAAAGCTTCCGACCTAT 58.624 47.619 12.52 0.00 30.97 2.57
3567 3581 2.758979 TCGAGAAAGCTTCCGACCTATT 59.241 45.455 12.52 0.00 30.97 1.73
3568 3582 3.117046 CGAGAAAGCTTCCGACCTATTC 58.883 50.000 0.00 0.00 0.00 1.75
3569 3583 3.428999 CGAGAAAGCTTCCGACCTATTCA 60.429 47.826 0.00 0.00 0.00 2.57
3570 3584 4.698575 GAGAAAGCTTCCGACCTATTCAT 58.301 43.478 0.00 0.00 0.00 2.57
3571 3585 4.698575 AGAAAGCTTCCGACCTATTCATC 58.301 43.478 0.00 0.00 0.00 2.92
3572 3586 4.407296 AGAAAGCTTCCGACCTATTCATCT 59.593 41.667 0.00 0.00 0.00 2.90
3573 3587 4.762289 AAGCTTCCGACCTATTCATCTT 57.238 40.909 0.00 0.00 0.00 2.40
3574 3588 4.329462 AGCTTCCGACCTATTCATCTTC 57.671 45.455 0.00 0.00 0.00 2.87
3575 3589 3.706594 AGCTTCCGACCTATTCATCTTCA 59.293 43.478 0.00 0.00 0.00 3.02
3576 3590 4.162320 AGCTTCCGACCTATTCATCTTCAA 59.838 41.667 0.00 0.00 0.00 2.69
3577 3591 5.059833 GCTTCCGACCTATTCATCTTCAAT 58.940 41.667 0.00 0.00 0.00 2.57
3578 3592 5.529060 GCTTCCGACCTATTCATCTTCAATT 59.471 40.000 0.00 0.00 0.00 2.32
3579 3593 6.706270 GCTTCCGACCTATTCATCTTCAATTA 59.294 38.462 0.00 0.00 0.00 1.40
3580 3594 7.389053 GCTTCCGACCTATTCATCTTCAATTAT 59.611 37.037 0.00 0.00 0.00 1.28
3581 3595 8.607441 TTCCGACCTATTCATCTTCAATTATG 57.393 34.615 0.00 0.00 0.00 1.90
3582 3596 7.161404 TCCGACCTATTCATCTTCAATTATGG 58.839 38.462 0.00 0.00 0.00 2.74
3583 3597 6.128172 CCGACCTATTCATCTTCAATTATGGC 60.128 42.308 0.00 0.00 0.00 4.40
3584 3598 6.427853 CGACCTATTCATCTTCAATTATGGCA 59.572 38.462 0.00 0.00 0.00 4.92
3585 3599 7.360691 CGACCTATTCATCTTCAATTATGGCAG 60.361 40.741 0.00 0.00 0.00 4.85
3586 3600 7.293073 ACCTATTCATCTTCAATTATGGCAGT 58.707 34.615 0.00 0.00 0.00 4.40
3587 3601 8.439971 ACCTATTCATCTTCAATTATGGCAGTA 58.560 33.333 0.00 0.00 0.00 2.74
3588 3602 8.725148 CCTATTCATCTTCAATTATGGCAGTAC 58.275 37.037 0.00 0.00 0.00 2.73
3589 3603 9.276590 CTATTCATCTTCAATTATGGCAGTACA 57.723 33.333 0.00 0.00 0.00 2.90
3590 3604 7.936496 TTCATCTTCAATTATGGCAGTACAA 57.064 32.000 0.00 0.00 0.00 2.41
3591 3605 7.320443 TCATCTTCAATTATGGCAGTACAAC 57.680 36.000 0.00 0.00 0.00 3.32
3592 3606 5.794687 TCTTCAATTATGGCAGTACAACG 57.205 39.130 0.00 0.00 0.00 4.10
3593 3607 5.483811 TCTTCAATTATGGCAGTACAACGA 58.516 37.500 0.00 0.00 0.00 3.85
3594 3608 5.935206 TCTTCAATTATGGCAGTACAACGAA 59.065 36.000 0.00 0.00 0.00 3.85
3595 3609 5.539582 TCAATTATGGCAGTACAACGAAC 57.460 39.130 0.00 0.00 0.00 3.95
3596 3610 4.998033 TCAATTATGGCAGTACAACGAACA 59.002 37.500 0.00 0.00 0.00 3.18
3597 3611 4.939509 ATTATGGCAGTACAACGAACAC 57.060 40.909 0.00 0.00 0.00 3.32
3598 3612 1.519408 ATGGCAGTACAACGAACACC 58.481 50.000 0.00 0.00 0.00 4.16
3599 3613 0.178301 TGGCAGTACAACGAACACCA 59.822 50.000 0.00 0.00 0.00 4.17
3600 3614 0.865769 GGCAGTACAACGAACACCAG 59.134 55.000 0.00 0.00 0.00 4.00
3601 3615 1.539496 GGCAGTACAACGAACACCAGA 60.539 52.381 0.00 0.00 0.00 3.86
3602 3616 2.206750 GCAGTACAACGAACACCAGAA 58.793 47.619 0.00 0.00 0.00 3.02
3603 3617 2.610374 GCAGTACAACGAACACCAGAAA 59.390 45.455 0.00 0.00 0.00 2.52
3604 3618 3.250040 GCAGTACAACGAACACCAGAAAT 59.750 43.478 0.00 0.00 0.00 2.17
3605 3619 4.449743 GCAGTACAACGAACACCAGAAATA 59.550 41.667 0.00 0.00 0.00 1.40
3606 3620 5.049954 GCAGTACAACGAACACCAGAAATAA 60.050 40.000 0.00 0.00 0.00 1.40
3607 3621 6.348213 GCAGTACAACGAACACCAGAAATAAT 60.348 38.462 0.00 0.00 0.00 1.28
3608 3622 7.148540 GCAGTACAACGAACACCAGAAATAATA 60.149 37.037 0.00 0.00 0.00 0.98
3609 3623 8.714179 CAGTACAACGAACACCAGAAATAATAA 58.286 33.333 0.00 0.00 0.00 1.40
3610 3624 9.275398 AGTACAACGAACACCAGAAATAATAAA 57.725 29.630 0.00 0.00 0.00 1.40
3611 3625 9.881529 GTACAACGAACACCAGAAATAATAAAA 57.118 29.630 0.00 0.00 0.00 1.52
3613 3627 9.974980 ACAACGAACACCAGAAATAATAAAAAT 57.025 25.926 0.00 0.00 0.00 1.82
3632 3646 7.787725 AAAAATTACATCCAGATCCGTAGAC 57.212 36.000 0.00 0.00 0.00 2.59
3633 3647 5.470047 AATTACATCCAGATCCGTAGACC 57.530 43.478 0.00 0.00 0.00 3.85
3634 3648 2.454336 ACATCCAGATCCGTAGACCA 57.546 50.000 0.00 0.00 0.00 4.02
3635 3649 2.032620 ACATCCAGATCCGTAGACCAC 58.967 52.381 0.00 0.00 0.00 4.16
3636 3650 1.341531 CATCCAGATCCGTAGACCACC 59.658 57.143 0.00 0.00 0.00 4.61
3637 3651 0.333652 TCCAGATCCGTAGACCACCA 59.666 55.000 0.00 0.00 0.00 4.17
3638 3652 1.191535 CCAGATCCGTAGACCACCAA 58.808 55.000 0.00 0.00 0.00 3.67
3639 3653 1.137086 CCAGATCCGTAGACCACCAAG 59.863 57.143 0.00 0.00 0.00 3.61
3640 3654 0.824759 AGATCCGTAGACCACCAAGC 59.175 55.000 0.00 0.00 0.00 4.01
3641 3655 0.527817 GATCCGTAGACCACCAAGCG 60.528 60.000 0.00 0.00 0.00 4.68
3642 3656 0.968901 ATCCGTAGACCACCAAGCGA 60.969 55.000 0.00 0.00 0.00 4.93
3643 3657 1.445582 CCGTAGACCACCAAGCGAC 60.446 63.158 0.00 0.00 0.00 5.19
3644 3658 1.800315 CGTAGACCACCAAGCGACG 60.800 63.158 0.00 0.00 0.00 5.12
3645 3659 1.582968 GTAGACCACCAAGCGACGA 59.417 57.895 0.00 0.00 0.00 4.20
3646 3660 0.731855 GTAGACCACCAAGCGACGAC 60.732 60.000 0.00 0.00 0.00 4.34
3647 3661 0.892358 TAGACCACCAAGCGACGACT 60.892 55.000 0.00 0.00 0.00 4.18
3648 3662 0.892358 AGACCACCAAGCGACGACTA 60.892 55.000 0.00 0.00 0.00 2.59
3649 3663 0.731855 GACCACCAAGCGACGACTAC 60.732 60.000 0.00 0.00 0.00 2.73
3650 3664 1.287815 CCACCAAGCGACGACTACA 59.712 57.895 0.00 0.00 0.00 2.74
3651 3665 0.319211 CCACCAAGCGACGACTACAA 60.319 55.000 0.00 0.00 0.00 2.41
3652 3666 1.060713 CACCAAGCGACGACTACAAG 58.939 55.000 0.00 0.00 0.00 3.16
3653 3667 0.666577 ACCAAGCGACGACTACAAGC 60.667 55.000 0.00 0.00 0.00 4.01
3654 3668 0.666274 CCAAGCGACGACTACAAGCA 60.666 55.000 0.00 0.00 0.00 3.91
3655 3669 0.435008 CAAGCGACGACTACAAGCAC 59.565 55.000 0.00 0.00 0.00 4.40
3656 3670 0.314302 AAGCGACGACTACAAGCACT 59.686 50.000 0.00 0.00 0.00 4.40
3657 3671 0.387367 AGCGACGACTACAAGCACTG 60.387 55.000 0.00 0.00 0.00 3.66
3658 3672 0.386858 GCGACGACTACAAGCACTGA 60.387 55.000 0.00 0.00 0.00 3.41
3659 3673 1.929038 GCGACGACTACAAGCACTGAA 60.929 52.381 0.00 0.00 0.00 3.02
3660 3674 1.979469 CGACGACTACAAGCACTGAAG 59.021 52.381 0.00 0.00 0.00 3.02
3661 3675 1.721926 GACGACTACAAGCACTGAAGC 59.278 52.381 0.00 0.00 0.00 3.86
3662 3676 0.710567 CGACTACAAGCACTGAAGCG 59.289 55.000 0.00 0.00 40.15 4.68
3663 3677 1.666023 CGACTACAAGCACTGAAGCGA 60.666 52.381 0.00 0.00 40.15 4.93
3664 3678 1.989165 GACTACAAGCACTGAAGCGAG 59.011 52.381 0.00 0.00 40.15 5.03
3665 3679 0.718343 CTACAAGCACTGAAGCGAGC 59.282 55.000 0.00 0.00 40.15 5.03
3666 3680 0.670546 TACAAGCACTGAAGCGAGCC 60.671 55.000 0.00 0.00 40.15 4.70
3667 3681 2.740055 AAGCACTGAAGCGAGCCG 60.740 61.111 0.00 0.00 40.15 5.52
3668 3682 3.226429 AAGCACTGAAGCGAGCCGA 62.226 57.895 0.00 0.00 40.15 5.54
3669 3683 2.715532 AAGCACTGAAGCGAGCCGAA 62.716 55.000 0.00 0.00 40.15 4.30
3670 3684 2.734673 GCACTGAAGCGAGCCGAAG 61.735 63.158 0.00 0.00 0.00 3.79
3697 3711 3.917760 CGTCATCGCCCCTCCCTC 61.918 72.222 0.00 0.00 0.00 4.30
3698 3712 3.917760 GTCATCGCCCCTCCCTCG 61.918 72.222 0.00 0.00 0.00 4.63
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
319 320 7.909267 ACAAGAGCAAGTTTTCTTTAATTTGC 58.091 30.769 8.07 8.07 45.55 3.68
345 346 6.045072 TCTCACGGACCAAACACTAAATAT 57.955 37.500 0.00 0.00 0.00 1.28
497 498 4.753107 TGAGTGGTATTTTCTGAAACGGAC 59.247 41.667 1.58 1.55 0.00 4.79
500 501 7.358352 GCAATTTGAGTGGTATTTTCTGAAACG 60.358 37.037 1.58 0.00 0.00 3.60
525 526 7.483307 TCTAGTAAATTTTGCATCAAGATGGC 58.517 34.615 11.66 5.17 39.16 4.40
565 566 7.124448 CAGTGATAGTACTCTACCTTTCCCTTT 59.876 40.741 0.00 0.00 0.00 3.11
606 607 6.135290 ACGTGACATTCCAATTCATTATGG 57.865 37.500 0.00 0.00 38.09 2.74
707 711 9.775539 ACAGTATCTGGTGATATGTAGGATAAT 57.224 33.333 1.90 0.00 37.48 1.28
838 842 7.826744 GCATATAATTTAGAGGGAAGGAGGAAG 59.173 40.741 0.00 0.00 0.00 3.46
848 852 8.887717 GCAACTCTATGCATATAATTTAGAGGG 58.112 37.037 19.53 13.83 45.70 4.30
1194 1198 3.244215 TGGTTTCAGTAGAGCTCTGGTTG 60.244 47.826 26.78 19.44 34.15 3.77
1278 1282 2.890945 TCTCACTTGGATGTTCTCACGA 59.109 45.455 0.00 0.00 0.00 4.35
1507 1511 4.150897 GGTATCCACCAGATGCAAAGTA 57.849 45.455 0.00 0.00 45.04 2.24
1581 1585 3.996363 CCTTCACAATCTGTTGTCGATCA 59.004 43.478 0.00 0.00 45.14 2.92
1593 1597 6.884836 ACTTGGTTAATAGACCCTTCACAATC 59.115 38.462 0.00 0.00 39.01 2.67
2103 2107 9.444600 GTAAACTCCAAAGGTATATTGAACTCA 57.555 33.333 0.00 0.00 0.00 3.41
2472 2476 1.006086 CGCAGGCGATTATGTTCACA 58.994 50.000 8.15 0.00 42.83 3.58
2737 2741 6.013293 ACTTGGCTCTATAACCTCTGTTTTCT 60.013 38.462 0.00 0.00 35.87 2.52
2962 2966 1.403679 CGTGAGTGGAAAACTTTGCCA 59.596 47.619 0.00 0.00 40.07 4.92
3019 3023 1.338136 ACCTATCTTCACAGGCCCCG 61.338 60.000 0.00 0.00 35.14 5.73
3036 3040 2.587522 AGAGAAAACCCTTGCAGAACC 58.412 47.619 0.00 0.00 0.00 3.62
3040 3044 4.761739 TGACATAAGAGAAAACCCTTGCAG 59.238 41.667 0.00 0.00 0.00 4.41
3184 3188 3.129813 GCAACAGAATTGCTCATCATCCA 59.870 43.478 4.40 0.00 41.87 3.41
3193 3197 1.174712 ACAGCGGCAACAGAATTGCT 61.175 50.000 11.12 0.00 44.36 3.91
3270 3281 1.538047 CCCGGAATATCATTGCCCAG 58.462 55.000 0.73 0.00 0.00 4.45
3301 3313 2.094659 CCTGTTGCTACTGACGCCG 61.095 63.158 6.74 0.00 0.00 6.46
3302 3314 0.108138 ATCCTGTTGCTACTGACGCC 60.108 55.000 6.74 0.00 0.00 5.68
3311 3323 0.745845 CGCTTGCCTATCCTGTTGCT 60.746 55.000 0.00 0.00 0.00 3.91
3314 3326 1.003118 TGTTCGCTTGCCTATCCTGTT 59.997 47.619 0.00 0.00 0.00 3.16
3354 3366 3.083997 GCCATGGGACTCGGAGGT 61.084 66.667 15.13 0.00 0.00 3.85
3370 3383 2.024414 GGACATTGGAGGGTTGTATGC 58.976 52.381 0.00 0.00 0.00 3.14
3386 3399 3.391296 AGCTAAGACTTGGAGTTTGGACA 59.609 43.478 2.22 0.00 0.00 4.02
3404 3418 3.733988 CGACCTGAAAATGTCGCTAGCTA 60.734 47.826 13.93 0.00 46.41 3.32
3474 3488 8.274248 GGCTAAACTAAGTTCAGAATAATACGC 58.726 37.037 0.00 0.00 0.00 4.42
3481 3495 5.875359 CGGAAGGCTAAACTAAGTTCAGAAT 59.125 40.000 0.00 0.00 0.00 2.40
3509 3523 4.215827 TCTTCTTCCACTGAACTCGAGTAC 59.784 45.833 20.39 0.00 0.00 2.73
3515 3529 5.237561 GGAAACTTCTTCTTCCACTGAACTC 59.762 44.000 0.00 0.00 40.79 3.01
3516 3530 5.126779 GGAAACTTCTTCTTCCACTGAACT 58.873 41.667 0.00 0.00 40.79 3.01
3517 3531 4.024809 CGGAAACTTCTTCTTCCACTGAAC 60.025 45.833 2.07 0.00 41.10 3.18
3542 3556 2.546789 GGTCGGAAGCTTTCTCGAAAAA 59.453 45.455 17.59 0.00 35.34 1.94
3543 3557 2.140717 GGTCGGAAGCTTTCTCGAAAA 58.859 47.619 17.59 0.00 35.34 2.29
3544 3558 1.343465 AGGTCGGAAGCTTTCTCGAAA 59.657 47.619 17.59 0.00 35.34 3.46
3545 3559 0.966920 AGGTCGGAAGCTTTCTCGAA 59.033 50.000 17.59 4.77 35.34 3.71
3546 3560 1.830279 TAGGTCGGAAGCTTTCTCGA 58.170 50.000 13.75 13.75 34.40 4.04
3547 3561 2.873133 ATAGGTCGGAAGCTTTCTCG 57.127 50.000 0.00 5.94 34.40 4.04
3548 3562 4.124851 TGAATAGGTCGGAAGCTTTCTC 57.875 45.455 0.00 0.00 34.40 2.87
3549 3563 4.407296 AGATGAATAGGTCGGAAGCTTTCT 59.593 41.667 0.00 0.00 34.40 2.52
3550 3564 4.698575 AGATGAATAGGTCGGAAGCTTTC 58.301 43.478 0.00 0.00 34.40 2.62
3551 3565 4.762289 AGATGAATAGGTCGGAAGCTTT 57.238 40.909 0.00 0.00 34.40 3.51
3552 3566 4.162320 TGAAGATGAATAGGTCGGAAGCTT 59.838 41.667 0.00 0.00 34.40 3.74
3553 3567 3.706594 TGAAGATGAATAGGTCGGAAGCT 59.293 43.478 0.00 0.00 37.01 3.74
3554 3568 4.060038 TGAAGATGAATAGGTCGGAAGC 57.940 45.455 0.00 0.00 0.00 3.86
3555 3569 8.715998 CATAATTGAAGATGAATAGGTCGGAAG 58.284 37.037 0.00 0.00 0.00 3.46
3556 3570 7.661437 CCATAATTGAAGATGAATAGGTCGGAA 59.339 37.037 0.00 0.00 0.00 4.30
3557 3571 7.161404 CCATAATTGAAGATGAATAGGTCGGA 58.839 38.462 0.00 0.00 0.00 4.55
3558 3572 6.128172 GCCATAATTGAAGATGAATAGGTCGG 60.128 42.308 0.00 0.00 0.00 4.79
3559 3573 6.427853 TGCCATAATTGAAGATGAATAGGTCG 59.572 38.462 0.00 0.00 0.00 4.79
3560 3574 7.446625 ACTGCCATAATTGAAGATGAATAGGTC 59.553 37.037 0.00 0.00 0.00 3.85
3561 3575 7.293073 ACTGCCATAATTGAAGATGAATAGGT 58.707 34.615 0.00 0.00 0.00 3.08
3562 3576 7.756395 ACTGCCATAATTGAAGATGAATAGG 57.244 36.000 0.00 0.00 0.00 2.57
3563 3577 9.276590 TGTACTGCCATAATTGAAGATGAATAG 57.723 33.333 0.00 0.00 0.00 1.73
3564 3578 9.625747 TTGTACTGCCATAATTGAAGATGAATA 57.374 29.630 0.00 0.00 0.00 1.75
3565 3579 8.408601 GTTGTACTGCCATAATTGAAGATGAAT 58.591 33.333 0.00 0.00 0.00 2.57
3566 3580 7.413988 CGTTGTACTGCCATAATTGAAGATGAA 60.414 37.037 0.00 0.00 0.00 2.57
3567 3581 6.037062 CGTTGTACTGCCATAATTGAAGATGA 59.963 38.462 0.00 0.00 0.00 2.92
3568 3582 6.037062 TCGTTGTACTGCCATAATTGAAGATG 59.963 38.462 0.00 0.00 0.00 2.90
3569 3583 6.112734 TCGTTGTACTGCCATAATTGAAGAT 58.887 36.000 0.00 0.00 0.00 2.40
3570 3584 5.483811 TCGTTGTACTGCCATAATTGAAGA 58.516 37.500 0.00 0.00 0.00 2.87
3571 3585 5.794687 TCGTTGTACTGCCATAATTGAAG 57.205 39.130 0.00 0.00 0.00 3.02
3572 3586 5.470437 TGTTCGTTGTACTGCCATAATTGAA 59.530 36.000 0.00 0.00 0.00 2.69
3573 3587 4.998033 TGTTCGTTGTACTGCCATAATTGA 59.002 37.500 0.00 0.00 0.00 2.57
3574 3588 5.086058 GTGTTCGTTGTACTGCCATAATTG 58.914 41.667 0.00 0.00 0.00 2.32
3575 3589 4.155280 GGTGTTCGTTGTACTGCCATAATT 59.845 41.667 0.00 0.00 0.00 1.40
3576 3590 3.687698 GGTGTTCGTTGTACTGCCATAAT 59.312 43.478 0.00 0.00 0.00 1.28
3577 3591 3.068560 GGTGTTCGTTGTACTGCCATAA 58.931 45.455 0.00 0.00 0.00 1.90
3578 3592 2.037381 TGGTGTTCGTTGTACTGCCATA 59.963 45.455 0.00 0.00 0.00 2.74
3579 3593 1.202710 TGGTGTTCGTTGTACTGCCAT 60.203 47.619 0.00 0.00 0.00 4.40
3580 3594 0.178301 TGGTGTTCGTTGTACTGCCA 59.822 50.000 0.00 0.00 0.00 4.92
3581 3595 0.865769 CTGGTGTTCGTTGTACTGCC 59.134 55.000 0.00 0.00 0.00 4.85
3582 3596 1.860676 TCTGGTGTTCGTTGTACTGC 58.139 50.000 0.00 0.00 0.00 4.40
3583 3597 6.533819 TTATTTCTGGTGTTCGTTGTACTG 57.466 37.500 0.00 0.00 0.00 2.74
3584 3598 8.836268 TTATTATTTCTGGTGTTCGTTGTACT 57.164 30.769 0.00 0.00 0.00 2.73
3585 3599 9.881529 TTTTATTATTTCTGGTGTTCGTTGTAC 57.118 29.630 0.00 0.00 0.00 2.90
3587 3601 9.974980 ATTTTTATTATTTCTGGTGTTCGTTGT 57.025 25.926 0.00 0.00 0.00 3.32
3606 3620 9.490379 GTCTACGGATCTGGATGTAATTTTTAT 57.510 33.333 6.47 0.00 0.00 1.40
3607 3621 7.929785 GGTCTACGGATCTGGATGTAATTTTTA 59.070 37.037 6.47 0.00 0.00 1.52
3608 3622 6.766467 GGTCTACGGATCTGGATGTAATTTTT 59.234 38.462 6.47 0.00 0.00 1.94
3609 3623 6.126883 TGGTCTACGGATCTGGATGTAATTTT 60.127 38.462 6.47 0.00 0.00 1.82
3610 3624 5.365605 TGGTCTACGGATCTGGATGTAATTT 59.634 40.000 6.47 0.00 0.00 1.82
3611 3625 4.899457 TGGTCTACGGATCTGGATGTAATT 59.101 41.667 6.47 0.00 0.00 1.40
3612 3626 4.281182 GTGGTCTACGGATCTGGATGTAAT 59.719 45.833 6.47 0.00 0.00 1.89
3613 3627 3.635373 GTGGTCTACGGATCTGGATGTAA 59.365 47.826 6.47 0.00 0.00 2.41
3614 3628 3.220110 GTGGTCTACGGATCTGGATGTA 58.780 50.000 6.47 0.00 0.00 2.29
3615 3629 2.032620 GTGGTCTACGGATCTGGATGT 58.967 52.381 6.47 0.00 0.00 3.06
3616 3630 1.341531 GGTGGTCTACGGATCTGGATG 59.658 57.143 6.47 0.00 0.00 3.51
3617 3631 1.063190 TGGTGGTCTACGGATCTGGAT 60.063 52.381 6.47 0.00 0.00 3.41
3618 3632 0.333652 TGGTGGTCTACGGATCTGGA 59.666 55.000 6.47 0.00 0.00 3.86
3619 3633 1.137086 CTTGGTGGTCTACGGATCTGG 59.863 57.143 6.47 0.00 0.00 3.86
3620 3634 1.471676 GCTTGGTGGTCTACGGATCTG 60.472 57.143 0.00 0.00 0.00 2.90
3621 3635 0.824759 GCTTGGTGGTCTACGGATCT 59.175 55.000 0.00 0.00 0.00 2.75
3622 3636 0.527817 CGCTTGGTGGTCTACGGATC 60.528 60.000 0.00 0.00 0.00 3.36
3623 3637 0.968901 TCGCTTGGTGGTCTACGGAT 60.969 55.000 0.00 0.00 0.00 4.18
3624 3638 1.604308 TCGCTTGGTGGTCTACGGA 60.604 57.895 0.00 0.00 0.00 4.69
3625 3639 1.445582 GTCGCTTGGTGGTCTACGG 60.446 63.158 0.00 0.00 0.00 4.02
3626 3640 1.800315 CGTCGCTTGGTGGTCTACG 60.800 63.158 0.00 0.00 0.00 3.51
3627 3641 0.731855 GTCGTCGCTTGGTGGTCTAC 60.732 60.000 0.00 0.00 0.00 2.59
3628 3642 0.892358 AGTCGTCGCTTGGTGGTCTA 60.892 55.000 0.00 0.00 0.00 2.59
3629 3643 0.892358 TAGTCGTCGCTTGGTGGTCT 60.892 55.000 0.00 0.00 0.00 3.85
3630 3644 0.731855 GTAGTCGTCGCTTGGTGGTC 60.732 60.000 0.00 0.00 0.00 4.02
3631 3645 1.288127 GTAGTCGTCGCTTGGTGGT 59.712 57.895 0.00 0.00 0.00 4.16
3632 3646 0.319211 TTGTAGTCGTCGCTTGGTGG 60.319 55.000 0.00 0.00 0.00 4.61
3633 3647 1.060713 CTTGTAGTCGTCGCTTGGTG 58.939 55.000 0.00 0.00 0.00 4.17
3634 3648 0.666577 GCTTGTAGTCGTCGCTTGGT 60.667 55.000 0.00 0.00 0.00 3.67
3635 3649 0.666274 TGCTTGTAGTCGTCGCTTGG 60.666 55.000 0.00 0.00 0.00 3.61
3636 3650 0.435008 GTGCTTGTAGTCGTCGCTTG 59.565 55.000 0.00 0.00 0.00 4.01
3637 3651 0.314302 AGTGCTTGTAGTCGTCGCTT 59.686 50.000 0.00 0.00 0.00 4.68
3638 3652 0.387367 CAGTGCTTGTAGTCGTCGCT 60.387 55.000 0.00 0.00 0.00 4.93
3639 3653 0.386858 TCAGTGCTTGTAGTCGTCGC 60.387 55.000 0.00 0.00 0.00 5.19
3640 3654 1.979469 CTTCAGTGCTTGTAGTCGTCG 59.021 52.381 0.00 0.00 0.00 5.12
3641 3655 1.721926 GCTTCAGTGCTTGTAGTCGTC 59.278 52.381 0.00 0.00 0.00 4.20
3642 3656 1.784525 GCTTCAGTGCTTGTAGTCGT 58.215 50.000 0.00 0.00 0.00 4.34
3643 3657 0.710567 CGCTTCAGTGCTTGTAGTCG 59.289 55.000 0.00 0.00 0.00 4.18
3644 3658 1.989165 CTCGCTTCAGTGCTTGTAGTC 59.011 52.381 0.00 0.00 0.00 2.59
3645 3659 1.937108 GCTCGCTTCAGTGCTTGTAGT 60.937 52.381 0.00 0.00 0.00 2.73
3646 3660 0.718343 GCTCGCTTCAGTGCTTGTAG 59.282 55.000 0.00 0.00 0.00 2.74
3647 3661 0.670546 GGCTCGCTTCAGTGCTTGTA 60.671 55.000 0.00 0.00 0.00 2.41
3648 3662 1.963338 GGCTCGCTTCAGTGCTTGT 60.963 57.895 0.00 0.00 0.00 3.16
3649 3663 2.866028 GGCTCGCTTCAGTGCTTG 59.134 61.111 0.00 0.00 0.00 4.01
3650 3664 2.715532 TTCGGCTCGCTTCAGTGCTT 62.716 55.000 0.00 0.00 0.00 3.91
3651 3665 3.226429 TTCGGCTCGCTTCAGTGCT 62.226 57.895 0.00 0.00 0.00 4.40
3652 3666 2.734673 CTTCGGCTCGCTTCAGTGC 61.735 63.158 0.00 0.00 0.00 4.40
3653 3667 2.097038 CCTTCGGCTCGCTTCAGTG 61.097 63.158 0.00 0.00 0.00 3.66
3654 3668 2.262915 CCTTCGGCTCGCTTCAGT 59.737 61.111 0.00 0.00 0.00 3.41
3655 3669 3.191539 GCCTTCGGCTCGCTTCAG 61.192 66.667 0.00 0.00 46.69 3.02
3680 3694 3.917760 GAGGGAGGGGCGATGACG 61.918 72.222 0.00 0.00 42.93 4.35
3681 3695 3.917760 CGAGGGAGGGGCGATGAC 61.918 72.222 0.00 0.00 0.00 3.06


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

AutoCloner maintained by Alex Coulton.