Multiple sequence alignment - TraesCS5A01G281300

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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 TraesCS5A01G281300 chr5A 100.000 3536 0 0 1 3536 490326698 490323163 0.000000e+00 6530.0
1 TraesCS5A01G281300 chr5A 91.399 1465 75 19 6 1431 490416728 490415276 0.000000e+00 1960.0
2 TraesCS5A01G281300 chr5A 92.840 838 60 0 1464 2301 490415280 490414443 0.000000e+00 1216.0
3 TraesCS5A01G281300 chr5A 75.783 1181 243 30 1140 2296 490652339 490651178 1.110000e-154 556.0
4 TraesCS5A01G281300 chr5A 89.922 129 7 2 271 399 573836684 573836806 1.020000e-35 161.0
5 TraesCS5A01G281300 chr5D 95.953 3064 71 13 1 3021 387684199 387681146 0.000000e+00 4922.0
6 TraesCS5A01G281300 chr5D 75.588 1233 264 27 1140 2350 387706516 387705299 3.060000e-160 575.0
7 TraesCS5A01G281300 chr5D 92.766 235 3 6 3089 3310 387663894 387663661 9.460000e-86 327.0
8 TraesCS5A01G281300 chr5D 80.952 399 61 11 1907 2296 387712287 387711895 5.740000e-78 302.0
9 TraesCS5A01G281300 chr5D 99.091 110 1 0 3126 3235 387663968 387663859 7.740000e-47 198.0
10 TraesCS5A01G281300 chr5D 98.131 107 2 0 3019 3125 387664175 387664069 1.680000e-43 187.0
11 TraesCS5A01G281300 chr5D 90.152 132 7 2 271 402 484999679 484999554 2.180000e-37 167.0
12 TraesCS5A01G281300 chr5B 92.000 1950 109 18 615 2528 466007222 466005284 0.000000e+00 2693.0
13 TraesCS5A01G281300 chr5B 89.474 570 35 9 1 551 466007785 466007222 0.000000e+00 697.0
14 TraesCS5A01G281300 chr5B 75.770 1234 262 27 1140 2350 466173137 466171918 3.930000e-164 588.0
15 TraesCS5A01G281300 chr5B 74.203 973 204 31 1140 2088 466027260 466026311 2.590000e-96 363.0
16 TraesCS5A01G281300 chr6B 91.393 639 40 7 271 901 529173079 529172448 0.000000e+00 861.0
17 TraesCS5A01G281300 chr4D 89.922 129 7 2 271 399 64562503 64562625 1.020000e-35 161.0
18 TraesCS5A01G281300 chr4D 91.667 96 6 1 2618 2713 499682470 499682377 7.960000e-27 132.0
19 TraesCS5A01G281300 chr2A 84.043 188 9 6 2617 2785 333796070 333795885 1.020000e-35 161.0
20 TraesCS5A01G281300 chr1A 84.043 188 9 6 2617 2785 415791301 415791116 1.020000e-35 161.0
21 TraesCS5A01G281300 chr1A 91.262 103 5 3 2611 2713 27878837 27878935 1.710000e-28 137.0
22 TraesCS5A01G281300 chr2D 93.750 96 4 1 2618 2713 22868469 22868376 3.680000e-30 143.0
23 TraesCS5A01G281300 chr3A 92.708 96 5 1 2618 2713 570474520 570474613 1.710000e-28 137.0
24 TraesCS5A01G281300 chr1D 92.708 96 5 1 2618 2713 47030352 47030259 1.710000e-28 137.0
25 TraesCS5A01G281300 chr1D 95.833 48 2 0 543 590 60405152 60405105 1.050000e-10 78.7
26 TraesCS5A01G281300 chr3B 91.667 96 6 1 2618 2713 160982538 160982445 7.960000e-27 132.0
27 TraesCS5A01G281300 chr4A 93.151 73 1 4 547 618 12209475 12209406 1.740000e-18 104.0
28 TraesCS5A01G281300 chr2B 86.047 86 9 1 543 625 58295617 58295532 4.860000e-14 89.8
29 TraesCS5A01G281300 chr2B 86.486 74 7 1 548 618 58295539 58295612 1.050000e-10 78.7
30 TraesCS5A01G281300 chr7A 85.897 78 8 2 548 625 634386524 634386450 2.930000e-11 80.5
31 TraesCS5A01G281300 chr6A 89.655 58 5 1 530 586 480647870 480647927 4.900000e-09 73.1


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 TraesCS5A01G281300 chr5A 490323163 490326698 3535 True 6530.000000 6530 100.000000 1 3536 1 chr5A.!!$R1 3535
1 TraesCS5A01G281300 chr5A 490414443 490416728 2285 True 1588.000000 1960 92.119500 6 2301 2 chr5A.!!$R3 2295
2 TraesCS5A01G281300 chr5A 490651178 490652339 1161 True 556.000000 556 75.783000 1140 2296 1 chr5A.!!$R2 1156
3 TraesCS5A01G281300 chr5D 387681146 387684199 3053 True 4922.000000 4922 95.953000 1 3021 1 chr5D.!!$R1 3020
4 TraesCS5A01G281300 chr5D 387705299 387706516 1217 True 575.000000 575 75.588000 1140 2350 1 chr5D.!!$R2 1210
5 TraesCS5A01G281300 chr5D 387663661 387664175 514 True 237.333333 327 96.662667 3019 3310 3 chr5D.!!$R5 291
6 TraesCS5A01G281300 chr5B 466005284 466007785 2501 True 1695.000000 2693 90.737000 1 2528 2 chr5B.!!$R3 2527
7 TraesCS5A01G281300 chr5B 466171918 466173137 1219 True 588.000000 588 75.770000 1140 2350 1 chr5B.!!$R2 1210
8 TraesCS5A01G281300 chr5B 466026311 466027260 949 True 363.000000 363 74.203000 1140 2088 1 chr5B.!!$R1 948
9 TraesCS5A01G281300 chr6B 529172448 529173079 631 True 861.000000 861 91.393000 271 901 1 chr6B.!!$R1 630

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
282 298 0.034896 GTACCAGTCCACCACCACAG 59.965 60.000 0.00 0.00 0.00 3.66 F
903 947 0.747255 ATCCACTCGCTGCGATTACT 59.253 50.000 26.15 6.82 34.61 2.24 F
1772 1868 1.079336 GGTACACTCGGACCAAGCC 60.079 63.158 0.00 0.00 35.65 4.35 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1985 2088 2.727916 GCCGGTGAAATAGCTTCGTTTG 60.728 50.0 1.90 0.0 36.78 2.93 R
2416 2519 1.127343 AGTGCTCTATGGGCTTCCTC 58.873 55.0 0.00 0.0 0.00 3.71 R
3482 3835 0.109412 CTCGACTACTTTCGCGGGTT 60.109 55.0 6.13 0.0 38.95 4.11 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
25 26 5.769484 ATTGACAGATGGATTGATTGCTC 57.231 39.130 0.00 0.00 0.00 4.26
72 73 2.291465 GCGCCAGCAAGATGATTATTCA 59.709 45.455 0.00 0.00 44.35 2.57
96 97 2.137528 TGGTGCTCGTCCAAGACCA 61.138 57.895 0.00 0.00 34.26 4.02
183 190 9.752961 AATACCATTGTGTGTTTTACTTTTACC 57.247 29.630 0.00 0.00 0.00 2.85
184 191 7.412853 ACCATTGTGTGTTTTACTTTTACCT 57.587 32.000 0.00 0.00 0.00 3.08
185 192 7.262048 ACCATTGTGTGTTTTACTTTTACCTG 58.738 34.615 0.00 0.00 0.00 4.00
210 226 8.377034 TGGTACTGGTGAAAATTTTACTAGCTA 58.623 33.333 12.55 0.00 0.00 3.32
282 298 0.034896 GTACCAGTCCACCACCACAG 59.965 60.000 0.00 0.00 0.00 3.66
308 324 9.884465 GTACTTTCTTCATTGGCATATGATTAC 57.116 33.333 6.97 0.00 34.67 1.89
309 325 7.945134 ACTTTCTTCATTGGCATATGATTACC 58.055 34.615 6.97 0.00 34.67 2.85
310 326 6.558771 TTCTTCATTGGCATATGATTACCG 57.441 37.500 6.97 0.00 34.67 4.02
311 327 4.455533 TCTTCATTGGCATATGATTACCGC 59.544 41.667 6.97 0.00 34.67 5.68
344 360 5.882557 ACCAAACTTAGAATCATGCTAGGTG 59.117 40.000 0.00 0.00 29.90 4.00
348 364 2.338577 AGAATCATGCTAGGTGTGCC 57.661 50.000 0.00 0.00 0.00 5.01
390 406 4.971939 TGATGACAAGTTCTGACAATCCA 58.028 39.130 0.00 0.00 33.38 3.41
673 703 8.856153 TTTTGTTTAGATGCCATACTGACTTA 57.144 30.769 0.00 0.00 0.00 2.24
897 941 2.169789 CCTCAATCCACTCGCTGCG 61.170 63.158 17.25 17.25 0.00 5.18
903 947 0.747255 ATCCACTCGCTGCGATTACT 59.253 50.000 26.15 6.82 34.61 2.24
983 1034 6.923199 TCTGCATTCTCAGGACATATATCA 57.077 37.500 0.00 0.00 34.91 2.15
1294 1370 1.485895 GAGCAGGGATTGAAGAGCTCT 59.514 52.381 11.45 11.45 43.68 4.09
1326 1415 3.698539 TGTCTCTTATCAGTGAGGCAGAG 59.301 47.826 15.39 15.39 39.61 3.35
1772 1868 1.079336 GGTACACTCGGACCAAGCC 60.079 63.158 0.00 0.00 35.65 4.35
1935 2038 3.261643 TGCAGATGATCAGTACACCAACT 59.738 43.478 0.09 0.00 0.00 3.16
1985 2088 9.013490 CAAATACTTGCACATTACTCTAAATGC 57.987 33.333 0.00 0.00 39.93 3.56
2139 2242 4.813296 AAACAACTGAAACGGTCATCTC 57.187 40.909 0.00 0.00 35.07 2.75
2151 2254 3.118738 ACGGTCATCTCGGCTTTCTATTT 60.119 43.478 0.00 0.00 0.00 1.40
2360 2463 3.724374 TGGACACTAGTTTCGGTTCTTG 58.276 45.455 3.02 0.00 0.00 3.02
2700 2830 9.651913 ATCATAAAAACAAAACACTTGTTCTGT 57.348 25.926 3.52 0.00 40.58 3.41
3042 3172 7.606858 AGATCATCGCAGTAATTAATCCATG 57.393 36.000 0.00 0.00 0.00 3.66
3054 3184 8.632679 AGTAATTAATCCATGTGGTAAGCATTG 58.367 33.333 0.00 0.00 36.34 2.82
3155 3385 5.699458 TGCTATGACATTGCATAGAGATGTG 59.301 40.000 18.72 0.00 46.81 3.21
3256 3609 3.376234 ACATGCTATGACATTGCACAGAC 59.624 43.478 23.70 0.00 43.29 3.51
3310 3663 2.602878 GTTGGCGTCGAAGAATCAGTA 58.397 47.619 1.37 0.00 39.69 2.74
3311 3664 2.273370 TGGCGTCGAAGAATCAGTAC 57.727 50.000 1.37 0.00 39.69 2.73
3312 3665 1.542472 TGGCGTCGAAGAATCAGTACA 59.458 47.619 1.37 0.00 39.69 2.90
3313 3666 1.918609 GGCGTCGAAGAATCAGTACAC 59.081 52.381 1.37 0.00 39.69 2.90
3314 3667 1.578023 GCGTCGAAGAATCAGTACACG 59.422 52.381 1.37 0.00 39.69 4.49
3315 3668 2.726989 GCGTCGAAGAATCAGTACACGA 60.727 50.000 1.37 0.00 39.69 4.35
3316 3669 3.681855 CGTCGAAGAATCAGTACACGAT 58.318 45.455 0.00 0.00 39.69 3.73
3317 3670 4.096311 CGTCGAAGAATCAGTACACGATT 58.904 43.478 9.57 9.57 39.69 3.34
3318 3671 4.028429 CGTCGAAGAATCAGTACACGATTG 60.028 45.833 13.49 2.40 39.69 2.67
3319 3672 4.265556 GTCGAAGAATCAGTACACGATTGG 59.734 45.833 13.49 3.37 39.69 3.16
3320 3673 3.551890 CGAAGAATCAGTACACGATTGGG 59.448 47.826 13.49 0.00 33.26 4.12
3321 3674 3.543680 AGAATCAGTACACGATTGGGG 57.456 47.619 13.49 0.00 33.26 4.96
3322 3675 2.838202 AGAATCAGTACACGATTGGGGT 59.162 45.455 13.49 0.00 33.26 4.95
3323 3676 2.981859 ATCAGTACACGATTGGGGTC 57.018 50.000 0.00 0.00 0.00 4.46
3324 3677 0.528924 TCAGTACACGATTGGGGTCG 59.471 55.000 0.00 0.00 46.56 4.79
3325 3678 0.528924 CAGTACACGATTGGGGTCGA 59.471 55.000 3.09 0.00 44.06 4.20
3326 3679 1.067425 CAGTACACGATTGGGGTCGAA 60.067 52.381 3.09 0.00 44.06 3.71
3327 3680 1.203994 AGTACACGATTGGGGTCGAAG 59.796 52.381 3.09 0.00 44.06 3.79
3328 3681 1.203052 GTACACGATTGGGGTCGAAGA 59.797 52.381 3.09 0.00 44.06 2.87
3329 3682 0.682852 ACACGATTGGGGTCGAAGAA 59.317 50.000 3.09 0.00 44.06 2.52
3330 3683 1.278127 ACACGATTGGGGTCGAAGAAT 59.722 47.619 3.09 0.00 44.06 2.40
3331 3684 1.933853 CACGATTGGGGTCGAAGAATC 59.066 52.381 3.09 0.00 44.06 2.52
3332 3685 1.553248 ACGATTGGGGTCGAAGAATCA 59.447 47.619 3.09 0.00 44.06 2.57
3333 3686 2.205074 CGATTGGGGTCGAAGAATCAG 58.795 52.381 0.00 0.00 44.06 2.90
3334 3687 2.418746 CGATTGGGGTCGAAGAATCAGT 60.419 50.000 0.00 0.00 44.06 3.41
3335 3688 3.610911 GATTGGGGTCGAAGAATCAGTT 58.389 45.455 0.00 0.00 39.69 3.16
3336 3689 2.472695 TGGGGTCGAAGAATCAGTTG 57.527 50.000 0.00 0.00 39.69 3.16
3337 3690 1.003118 TGGGGTCGAAGAATCAGTTGG 59.997 52.381 0.00 0.00 39.69 3.77
3338 3691 1.087501 GGGTCGAAGAATCAGTTGGC 58.912 55.000 0.00 0.00 39.69 4.52
3339 3692 0.721718 GGTCGAAGAATCAGTTGGCG 59.278 55.000 0.00 0.00 39.69 5.69
3340 3693 1.429463 GTCGAAGAATCAGTTGGCGT 58.571 50.000 0.00 0.00 39.69 5.68
3341 3694 1.390463 GTCGAAGAATCAGTTGGCGTC 59.610 52.381 0.00 0.00 39.69 5.19
3342 3695 0.366871 CGAAGAATCAGTTGGCGTCG 59.633 55.000 0.00 0.00 0.00 5.12
3343 3696 0.721718 GAAGAATCAGTTGGCGTCGG 59.278 55.000 0.00 0.00 0.00 4.79
3344 3697 1.298859 AAGAATCAGTTGGCGTCGGC 61.299 55.000 12.58 12.58 38.90 5.54
3345 3698 3.083600 GAATCAGTTGGCGTCGGCG 62.084 63.158 14.58 4.29 41.24 6.46
3389 3742 4.957164 GGGATCAACCGGGAAGTC 57.043 61.111 6.32 0.00 40.11 3.01
3390 3743 2.297937 GGGATCAACCGGGAAGTCT 58.702 57.895 6.32 0.00 40.11 3.24
3391 3744 0.618981 GGGATCAACCGGGAAGTCTT 59.381 55.000 6.32 0.00 40.11 3.01
3392 3745 1.407025 GGGATCAACCGGGAAGTCTTC 60.407 57.143 6.32 3.80 40.11 2.87
3393 3746 4.643386 GGGATCAACCGGGAAGTCTTCC 62.643 59.091 21.73 21.73 41.37 3.46
3404 3757 3.526534 GGAAGTCTTCCTCGAATTCAGG 58.473 50.000 22.42 14.40 46.57 3.86
3405 3758 3.526534 GAAGTCTTCCTCGAATTCAGGG 58.473 50.000 18.22 13.26 37.78 4.45
3406 3759 2.821437 AGTCTTCCTCGAATTCAGGGA 58.179 47.619 18.22 14.94 0.00 4.20
3407 3760 3.173965 AGTCTTCCTCGAATTCAGGGAA 58.826 45.455 20.75 20.75 36.56 3.97
3409 3762 3.618690 CTTCCTCGAATTCAGGGAAGT 57.381 47.619 29.47 0.00 45.59 3.01
3410 3763 3.526534 CTTCCTCGAATTCAGGGAAGTC 58.473 50.000 29.47 0.00 45.59 3.01
3415 3768 2.365408 GAATTCAGGGAAGTCGTCGT 57.635 50.000 0.00 0.00 27.52 4.34
3416 3769 3.498927 GAATTCAGGGAAGTCGTCGTA 57.501 47.619 0.00 0.00 27.52 3.43
3417 3770 3.436496 GAATTCAGGGAAGTCGTCGTAG 58.564 50.000 0.00 0.00 27.52 3.51
3418 3771 0.524862 TTCAGGGAAGTCGTCGTAGC 59.475 55.000 0.00 0.00 0.00 3.58
3419 3772 1.226323 CAGGGAAGTCGTCGTAGCG 60.226 63.158 0.00 0.00 0.00 4.26
3420 3773 2.578981 GGGAAGTCGTCGTAGCGC 60.579 66.667 0.00 0.00 0.00 5.92
3421 3774 2.943034 GGAAGTCGTCGTAGCGCG 60.943 66.667 0.00 0.00 43.01 6.86
3422 3775 3.595759 GAAGTCGTCGTAGCGCGC 61.596 66.667 26.66 26.66 41.07 6.86
3442 3795 4.699522 GCGTCCCGGGCAACTTCT 62.700 66.667 18.49 0.00 0.00 2.85
3443 3796 2.742372 CGTCCCGGGCAACTTCTG 60.742 66.667 18.49 0.00 0.00 3.02
3451 3804 4.233408 GCAACTTCTGCCAAAGCG 57.767 55.556 0.00 0.00 46.13 4.68
3452 3805 1.372128 GCAACTTCTGCCAAAGCGG 60.372 57.895 0.00 0.00 46.13 5.52
3476 3829 2.049433 CGACGCGGACCAGAAACT 60.049 61.111 12.47 0.00 0.00 2.66
3477 3830 2.372690 CGACGCGGACCAGAAACTG 61.373 63.158 12.47 0.00 0.00 3.16
3497 3850 4.565531 CGAACCCGCGAAAGTAGT 57.434 55.556 8.23 0.00 0.00 2.73
3498 3851 2.356794 CGAACCCGCGAAAGTAGTC 58.643 57.895 8.23 0.00 0.00 2.59
3499 3852 1.400990 CGAACCCGCGAAAGTAGTCG 61.401 60.000 8.23 5.67 43.98 4.18
3500 3853 0.109597 GAACCCGCGAAAGTAGTCGA 60.110 55.000 8.23 0.00 43.86 4.20
3501 3854 0.109412 AACCCGCGAAAGTAGTCGAG 60.109 55.000 8.23 0.00 43.86 4.04
3503 3856 4.379221 CGCGAAAGTAGTCGAGGG 57.621 61.111 0.00 0.00 43.86 4.30
3504 3857 1.505353 CGCGAAAGTAGTCGAGGGT 59.495 57.895 0.00 0.00 43.86 4.34
3505 3858 0.729116 CGCGAAAGTAGTCGAGGGTA 59.271 55.000 0.00 0.00 43.86 3.69
3506 3859 1.267932 CGCGAAAGTAGTCGAGGGTAG 60.268 57.143 0.00 0.00 43.86 3.18
3507 3860 1.065251 GCGAAAGTAGTCGAGGGTAGG 59.935 57.143 0.00 0.00 43.86 3.18
3508 3861 1.674962 CGAAAGTAGTCGAGGGTAGGG 59.325 57.143 0.00 0.00 43.86 3.53
3509 3862 2.732763 GAAAGTAGTCGAGGGTAGGGT 58.267 52.381 0.00 0.00 0.00 4.34
3510 3863 2.433662 AAGTAGTCGAGGGTAGGGTC 57.566 55.000 0.00 0.00 0.00 4.46
3511 3864 0.179936 AGTAGTCGAGGGTAGGGTCG 59.820 60.000 0.00 0.00 37.54 4.79
3512 3865 1.153086 TAGTCGAGGGTAGGGTCGC 60.153 63.158 0.00 0.00 36.11 5.19
3513 3866 2.615227 TAGTCGAGGGTAGGGTCGCC 62.615 65.000 0.00 0.00 36.11 5.54
3514 3867 4.828296 TCGAGGGTAGGGTCGCCC 62.828 72.222 6.80 6.80 45.90 6.13
3525 3878 2.811317 GTCGCCCTTGACGAGCTG 60.811 66.667 0.00 0.00 40.80 4.24
3526 3879 4.742201 TCGCCCTTGACGAGCTGC 62.742 66.667 0.00 0.00 33.96 5.25
3528 3881 3.123620 GCCCTTGACGAGCTGCAG 61.124 66.667 10.11 10.11 0.00 4.41
3529 3882 2.435586 CCCTTGACGAGCTGCAGG 60.436 66.667 17.12 0.73 0.00 4.85
3530 3883 2.659016 CCTTGACGAGCTGCAGGA 59.341 61.111 17.12 0.00 0.00 3.86
3531 3884 1.447489 CCTTGACGAGCTGCAGGAG 60.447 63.158 17.12 0.00 0.00 3.69
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
72 73 0.107410 TTGGACGAGCACCACTTTGT 60.107 50.000 0.00 0.00 37.13 2.83
179 186 8.000127 AGTAAAATTTTCACCAGTACCAGGTAA 59.000 33.333 6.72 0.28 37.23 2.85
180 187 7.519927 AGTAAAATTTTCACCAGTACCAGGTA 58.480 34.615 6.72 0.00 37.23 3.08
182 189 6.894339 AGTAAAATTTTCACCAGTACCAGG 57.106 37.500 6.72 0.58 0.00 4.45
183 190 7.390718 AGCTAGTAAAATTTTCACCAGTACCAG 59.609 37.037 6.72 0.00 0.00 4.00
184 191 7.228590 AGCTAGTAAAATTTTCACCAGTACCA 58.771 34.615 6.72 0.00 0.00 3.25
185 192 7.683437 AGCTAGTAAAATTTTCACCAGTACC 57.317 36.000 6.72 0.00 0.00 3.34
282 298 9.884465 GTAATCATATGCCAATGAAGAAAGTAC 57.116 33.333 0.00 0.00 39.25 2.73
308 324 0.889186 AGTTTGGTTGTAGCAGGCGG 60.889 55.000 0.00 0.00 0.00 6.13
309 325 0.951558 AAGTTTGGTTGTAGCAGGCG 59.048 50.000 0.00 0.00 0.00 5.52
310 326 3.408634 TCTAAGTTTGGTTGTAGCAGGC 58.591 45.455 0.00 0.00 0.00 4.85
311 327 5.705441 TGATTCTAAGTTTGGTTGTAGCAGG 59.295 40.000 0.00 0.00 0.00 4.85
344 360 8.467598 TCATAATCTTATACTCCGAATAGGCAC 58.532 37.037 0.00 0.00 40.77 5.01
420 440 1.001378 GCGCAAGGTCTCAACATTGTT 60.001 47.619 0.30 0.00 46.28 2.83
521 551 3.325870 TGAACATTTAGAGCCACAGACG 58.674 45.455 0.00 0.00 0.00 4.18
942 991 3.505293 GCAGAAGCACAGAAAGGAGAAAT 59.495 43.478 0.00 0.00 41.58 2.17
1294 1370 4.223700 ACTGATAAGAGACAGCAACATGGA 59.776 41.667 0.00 0.00 37.61 3.41
1326 1415 3.618690 AGAGAGCATGGGAAGTTGTAC 57.381 47.619 0.00 0.00 0.00 2.90
1640 1730 6.594159 ACCGATGTCAAAACTCGAGATATTTT 59.406 34.615 21.68 12.69 34.41 1.82
1706 1796 6.812160 ACACGTTATCCTCATGTTCTTTACTC 59.188 38.462 0.00 0.00 0.00 2.59
1772 1868 6.051074 TCAACATTCAGTACAGATGGCATAG 58.949 40.000 0.00 0.00 0.00 2.23
1832 1929 6.591935 ACCCTATGATCATCACAACGTTTAT 58.408 36.000 12.53 0.00 0.00 1.40
1935 2038 3.370527 GGTGCAGGAATTTGCTAGGTAGA 60.371 47.826 3.90 0.00 44.38 2.59
1985 2088 2.727916 GCCGGTGAAATAGCTTCGTTTG 60.728 50.000 1.90 0.00 36.78 2.93
2139 2242 4.873827 TGCTGTACCTAAAATAGAAAGCCG 59.126 41.667 0.00 0.00 0.00 5.52
2151 2254 5.222079 TCATGTCAGTTTGCTGTACCTAA 57.778 39.130 0.00 0.00 43.05 2.69
2360 2463 1.392510 GTTTATCGACCGAACAGCCAC 59.607 52.381 0.00 0.00 0.00 5.01
2416 2519 1.127343 AGTGCTCTATGGGCTTCCTC 58.873 55.000 0.00 0.00 0.00 3.71
2615 2718 2.229543 TGCAGTTCCTGAAATGACATGC 59.770 45.455 11.16 2.61 38.53 4.06
2700 2830 5.745312 TTAGCTTCTCTCAGATTTGTGGA 57.255 39.130 0.00 0.00 0.00 4.02
3042 3172 1.535462 ACTCAACGCAATGCTTACCAC 59.465 47.619 2.94 0.00 0.00 4.16
3054 3184 6.782150 AGGCATAACTTTATTAACTCAACGC 58.218 36.000 0.00 0.00 0.00 4.84
3256 3609 9.469807 GTGTATGGAGTGAGAACTTTATATCTG 57.530 37.037 0.00 0.00 0.00 2.90
3310 3663 0.682852 TTCTTCGACCCCAATCGTGT 59.317 50.000 0.00 0.00 42.80 4.49
3311 3664 1.933853 GATTCTTCGACCCCAATCGTG 59.066 52.381 0.00 0.00 42.80 4.35
3312 3665 1.553248 TGATTCTTCGACCCCAATCGT 59.447 47.619 0.00 0.00 42.80 3.73
3313 3666 2.205074 CTGATTCTTCGACCCCAATCG 58.795 52.381 0.00 0.00 43.63 3.34
3314 3667 3.268023 ACTGATTCTTCGACCCCAATC 57.732 47.619 0.00 0.00 0.00 2.67
3315 3668 3.347216 CAACTGATTCTTCGACCCCAAT 58.653 45.455 0.00 0.00 0.00 3.16
3316 3669 2.552155 CCAACTGATTCTTCGACCCCAA 60.552 50.000 0.00 0.00 0.00 4.12
3317 3670 1.003118 CCAACTGATTCTTCGACCCCA 59.997 52.381 0.00 0.00 0.00 4.96
3318 3671 1.739067 CCAACTGATTCTTCGACCCC 58.261 55.000 0.00 0.00 0.00 4.95
3319 3672 1.087501 GCCAACTGATTCTTCGACCC 58.912 55.000 0.00 0.00 0.00 4.46
3320 3673 0.721718 CGCCAACTGATTCTTCGACC 59.278 55.000 0.00 0.00 0.00 4.79
3321 3674 1.390463 GACGCCAACTGATTCTTCGAC 59.610 52.381 0.00 0.00 0.00 4.20
3322 3675 1.710013 GACGCCAACTGATTCTTCGA 58.290 50.000 0.00 0.00 0.00 3.71
3323 3676 0.366871 CGACGCCAACTGATTCTTCG 59.633 55.000 0.00 0.00 0.00 3.79
3324 3677 0.721718 CCGACGCCAACTGATTCTTC 59.278 55.000 0.00 0.00 0.00 2.87
3325 3678 1.298859 GCCGACGCCAACTGATTCTT 61.299 55.000 0.00 0.00 0.00 2.52
3326 3679 1.741770 GCCGACGCCAACTGATTCT 60.742 57.895 0.00 0.00 0.00 2.40
3327 3680 2.785258 GCCGACGCCAACTGATTC 59.215 61.111 0.00 0.00 0.00 2.52
3328 3681 3.118454 CGCCGACGCCAACTGATT 61.118 61.111 0.00 0.00 0.00 2.57
3360 3713 4.222847 GATCCCGAGCCGGTGTCC 62.223 72.222 1.90 0.00 46.80 4.02
3361 3714 3.014085 TTGATCCCGAGCCGGTGTC 62.014 63.158 1.90 0.00 46.80 3.67
3362 3715 3.000819 TTGATCCCGAGCCGGTGT 61.001 61.111 1.90 0.00 46.80 4.16
3363 3716 2.511600 GTTGATCCCGAGCCGGTG 60.512 66.667 1.90 4.81 46.80 4.94
3364 3717 3.782443 GGTTGATCCCGAGCCGGT 61.782 66.667 1.90 0.00 46.80 5.28
3372 3725 0.618981 AAGACTTCCCGGTTGATCCC 59.381 55.000 0.00 0.00 0.00 3.85
3373 3726 1.407025 GGAAGACTTCCCGGTTGATCC 60.407 57.143 21.88 0.00 44.30 3.36
3374 3727 2.025589 GGAAGACTTCCCGGTTGATC 57.974 55.000 21.88 0.00 44.30 2.92
3384 3737 3.195825 TCCCTGAATTCGAGGAAGACTTC 59.804 47.826 19.56 6.66 31.48 3.01
3385 3738 3.173965 TCCCTGAATTCGAGGAAGACTT 58.826 45.455 19.56 0.00 31.48 3.01
3386 3739 2.821437 TCCCTGAATTCGAGGAAGACT 58.179 47.619 19.56 0.00 31.48 3.24
3387 3740 3.611766 TTCCCTGAATTCGAGGAAGAC 57.388 47.619 19.79 0.00 33.48 3.01
3390 3743 2.094182 CGACTTCCCTGAATTCGAGGAA 60.094 50.000 21.44 21.44 43.82 3.36
3391 3744 1.476891 CGACTTCCCTGAATTCGAGGA 59.523 52.381 19.56 15.83 43.82 3.71
3392 3745 1.204941 ACGACTTCCCTGAATTCGAGG 59.795 52.381 19.09 13.87 43.82 4.63
3393 3746 2.531206 GACGACTTCCCTGAATTCGAG 58.469 52.381 19.09 0.00 43.82 4.04
3394 3747 1.135489 CGACGACTTCCCTGAATTCGA 60.135 52.381 19.09 0.00 43.82 3.71
3395 3748 1.269166 CGACGACTTCCCTGAATTCG 58.731 55.000 12.96 12.96 45.55 3.34
3396 3749 2.365408 ACGACGACTTCCCTGAATTC 57.635 50.000 0.00 0.00 0.00 2.17
3397 3750 2.416972 GCTACGACGACTTCCCTGAATT 60.417 50.000 0.00 0.00 0.00 2.17
3398 3751 1.134560 GCTACGACGACTTCCCTGAAT 59.865 52.381 0.00 0.00 0.00 2.57
3399 3752 0.524862 GCTACGACGACTTCCCTGAA 59.475 55.000 0.00 0.00 0.00 3.02
3400 3753 1.642037 CGCTACGACGACTTCCCTGA 61.642 60.000 0.00 0.00 34.06 3.86
3401 3754 1.226323 CGCTACGACGACTTCCCTG 60.226 63.158 0.00 0.00 34.06 4.45
3402 3755 3.048941 GCGCTACGACGACTTCCCT 62.049 63.158 0.00 0.00 34.06 4.20
3403 3756 2.578981 GCGCTACGACGACTTCCC 60.579 66.667 0.00 0.00 34.06 3.97
3435 3788 4.950744 CCGCTTTGGCAGAAGTTG 57.049 55.556 9.90 4.93 38.60 3.16
3459 3812 2.049433 AGTTTCTGGTCCGCGTCG 60.049 61.111 4.92 0.00 0.00 5.12
3460 3813 2.027625 CCAGTTTCTGGTCCGCGTC 61.028 63.158 4.92 0.00 45.82 5.19
3461 3814 2.030562 CCAGTTTCTGGTCCGCGT 59.969 61.111 4.92 0.00 45.82 6.01
3480 3833 1.400990 CGACTACTTTCGCGGGTTCG 61.401 60.000 6.13 6.85 39.81 3.95
3481 3834 0.109597 TCGACTACTTTCGCGGGTTC 60.110 55.000 6.13 0.00 38.95 3.62
3482 3835 0.109412 CTCGACTACTTTCGCGGGTT 60.109 55.000 6.13 0.00 38.95 4.11
3483 3836 1.505353 CTCGACTACTTTCGCGGGT 59.495 57.895 6.13 5.88 38.95 5.28
3484 3837 1.226603 CCTCGACTACTTTCGCGGG 60.227 63.158 6.13 0.00 39.69 6.13
3485 3838 1.226603 CCCTCGACTACTTTCGCGG 60.227 63.158 6.13 0.00 42.42 6.46
3486 3839 0.729116 TACCCTCGACTACTTTCGCG 59.271 55.000 0.00 0.00 38.95 5.87
3487 3840 1.065251 CCTACCCTCGACTACTTTCGC 59.935 57.143 0.00 0.00 38.95 4.70
3488 3841 1.674962 CCCTACCCTCGACTACTTTCG 59.325 57.143 0.00 0.00 40.53 3.46
3489 3842 2.687425 GACCCTACCCTCGACTACTTTC 59.313 54.545 0.00 0.00 0.00 2.62
3490 3843 2.732763 GACCCTACCCTCGACTACTTT 58.267 52.381 0.00 0.00 0.00 2.66
3491 3844 1.407989 CGACCCTACCCTCGACTACTT 60.408 57.143 0.00 0.00 31.24 2.24
3492 3845 0.179936 CGACCCTACCCTCGACTACT 59.820 60.000 0.00 0.00 31.24 2.57
3493 3846 1.443322 GCGACCCTACCCTCGACTAC 61.443 65.000 0.00 0.00 31.24 2.73
3494 3847 1.153086 GCGACCCTACCCTCGACTA 60.153 63.158 0.00 0.00 31.24 2.59
3495 3848 2.439883 GCGACCCTACCCTCGACT 60.440 66.667 0.00 0.00 31.24 4.18
3496 3849 3.525545 GGCGACCCTACCCTCGAC 61.526 72.222 0.00 0.00 31.24 4.20
3512 3865 2.435586 CCTGCAGCTCGTCAAGGG 60.436 66.667 8.66 0.00 0.00 3.95
3513 3866 1.447489 CTCCTGCAGCTCGTCAAGG 60.447 63.158 8.66 0.00 0.00 3.61
3514 3867 2.099431 GCTCCTGCAGCTCGTCAAG 61.099 63.158 8.66 0.00 45.83 3.02
3515 3868 2.047844 GCTCCTGCAGCTCGTCAA 60.048 61.111 8.66 0.00 45.83 3.18


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

AutoCloner maintained by Alex Coulton.