Multiple sequence alignment - TraesCS3B01G427400

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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 TraesCS3B01G427400 chr3B 100.000 3588 0 0 1 3588 666448975 666452562 0.000000e+00 6626
1 TraesCS3B01G427400 chr3B 90.640 203 16 1 2754 2956 666451614 666451813 2.350000e-67 267
2 TraesCS3B01G427400 chr3B 90.640 203 16 1 2640 2839 666451728 666451930 2.350000e-67 267
3 TraesCS3B01G427400 chr3B 100.000 70 0 0 3897 3966 666452871 666452940 3.220000e-26 130
4 TraesCS3B01G427400 chr3D 93.319 3293 158 33 308 3588 504738897 504742139 0.000000e+00 4806
5 TraesCS3B01G427400 chr3D 87.943 282 23 2 1 271 504738436 504738717 4.940000e-84 322
6 TraesCS3B01G427400 chr3D 91.626 203 14 1 2754 2956 504741219 504741418 1.090000e-70 278
7 TraesCS3B01G427400 chr3D 90.640 203 16 1 2640 2839 504741333 504741535 2.350000e-67 267
8 TraesCS3B01G427400 chr3A 93.513 2158 101 18 485 2636 642924937 642927061 0.000000e+00 3173
9 TraesCS3B01G427400 chr3A 85.839 572 50 15 2754 3300 642927179 642927744 2.660000e-161 579
10 TraesCS3B01G427400 chr3A 92.213 244 19 0 2592 2835 642927131 642927374 2.930000e-91 346
11 TraesCS3B01G427400 chr3A 86.986 292 29 7 3300 3586 642927859 642928146 1.780000e-83 320
12 TraesCS3B01G427400 chr3A 93.023 215 15 0 13 227 642924125 642924339 8.270000e-82 315
13 TraesCS3B01G427400 chr3A 94.545 165 9 0 2631 2795 642927008 642927172 5.090000e-64 255
14 TraesCS3B01G427400 chr3A 86.979 192 20 4 296 486 642924645 642924832 1.120000e-50 211
15 TraesCS3B01G427400 chr3A 85.185 189 20 4 2725 2912 642926991 642927172 1.880000e-43 187


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 TraesCS3B01G427400 chr3B 666448975 666452940 3965 False 1822.50 6626 95.320000 1 3966 4 chr3B.!!$F1 3965
1 TraesCS3B01G427400 chr3D 504738436 504742139 3703 False 1418.25 4806 90.882000 1 3588 4 chr3D.!!$F1 3587
2 TraesCS3B01G427400 chr3A 642924125 642928146 4021 False 673.25 3173 89.785375 13 3586 8 chr3A.!!$F1 3573

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
139 151 0.106619 ACCAAACCTTGTTACCGCCA 60.107 50.0 0.00 0.00 0.00 5.69 F
1066 1427 0.036765 CTTAGCCGTGCTGGTTACCA 60.037 55.0 3.29 3.29 40.10 3.25 F
2182 2548 0.027979 CATTACCGCACCAGCATTCG 59.972 55.0 0.00 0.00 42.27 3.34 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1089 1450 0.538287 AAGGTGGTGGCAAGCTTCTC 60.538 55.000 0.0 0.0 29.63 2.87 R
2806 3220 1.003928 GGTGGGGATTGGTACGAGTTT 59.996 52.381 0.0 0.0 0.00 2.66 R
3936 4495 0.250901 ACTGCATTCCAAGCTCGGTT 60.251 50.000 0.0 0.0 0.00 4.44 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
103 104 2.554344 GGAGTGGAAACTTATGTGCCCA 60.554 50.000 0.00 0.00 0.00 5.36
139 151 0.106619 ACCAAACCTTGTTACCGCCA 60.107 50.000 0.00 0.00 0.00 5.69
152 164 2.710698 CGCCACGGTTTTGTCGTT 59.289 55.556 0.00 0.00 38.94 3.85
167 179 3.501950 TGTCGTTGAAGTCGATGATGAG 58.498 45.455 0.00 0.00 39.45 2.90
174 186 0.397675 AGTCGATGATGAGGGCCAGA 60.398 55.000 6.18 0.00 0.00 3.86
188 200 2.695147 GGGCCAGACCTATTTCATTTGG 59.305 50.000 4.39 0.00 39.10 3.28
250 262 1.283613 TGGACACACCTGGAACTTTGT 59.716 47.619 0.00 0.00 39.86 2.83
271 283 6.969993 TGTCAGTTTTGGTAAATAAGGCTT 57.030 33.333 4.58 4.58 0.00 4.35
272 284 7.354751 TGTCAGTTTTGGTAAATAAGGCTTT 57.645 32.000 4.45 0.00 0.00 3.51
273 285 8.466617 TGTCAGTTTTGGTAAATAAGGCTTTA 57.533 30.769 4.45 0.00 0.00 1.85
274 286 8.915036 TGTCAGTTTTGGTAAATAAGGCTTTAA 58.085 29.630 4.45 0.00 0.00 1.52
275 287 9.188588 GTCAGTTTTGGTAAATAAGGCTTTAAC 57.811 33.333 4.45 0.00 0.00 2.01
276 288 8.361889 TCAGTTTTGGTAAATAAGGCTTTAACC 58.638 33.333 4.45 8.87 29.01 2.85
277 289 8.364894 CAGTTTTGGTAAATAAGGCTTTAACCT 58.635 33.333 4.45 0.00 43.91 3.50
285 297 2.287977 AGGCTTTAACCTTCACCACC 57.712 50.000 0.00 0.00 36.28 4.61
286 298 1.780919 AGGCTTTAACCTTCACCACCT 59.219 47.619 0.00 0.00 36.28 4.00
287 299 2.160205 GGCTTTAACCTTCACCACCTC 58.840 52.381 0.00 0.00 0.00 3.85
288 300 2.160205 GCTTTAACCTTCACCACCTCC 58.840 52.381 0.00 0.00 0.00 4.30
289 301 2.791655 CTTTAACCTTCACCACCTCCC 58.208 52.381 0.00 0.00 0.00 4.30
290 302 1.069775 TTAACCTTCACCACCTCCCC 58.930 55.000 0.00 0.00 0.00 4.81
291 303 0.843343 TAACCTTCACCACCTCCCCC 60.843 60.000 0.00 0.00 0.00 5.40
370 622 4.102524 TGATACACCTTCAAAGACACTGGT 59.897 41.667 0.00 0.00 0.00 4.00
373 625 4.850680 ACACCTTCAAAGACACTGGTTTA 58.149 39.130 0.00 0.00 0.00 2.01
374 626 5.445964 ACACCTTCAAAGACACTGGTTTAT 58.554 37.500 0.00 0.00 0.00 1.40
375 627 5.299279 ACACCTTCAAAGACACTGGTTTATG 59.701 40.000 0.00 0.00 0.00 1.90
376 628 4.278419 ACCTTCAAAGACACTGGTTTATGC 59.722 41.667 0.00 0.00 0.00 3.14
377 629 4.520492 CCTTCAAAGACACTGGTTTATGCT 59.480 41.667 0.00 0.00 0.00 3.79
380 632 7.255451 CCTTCAAAGACACTGGTTTATGCTAAA 60.255 37.037 0.00 0.00 0.00 1.85
381 633 7.575414 TCAAAGACACTGGTTTATGCTAAAA 57.425 32.000 0.00 0.00 0.00 1.52
382 634 7.648142 TCAAAGACACTGGTTTATGCTAAAAG 58.352 34.615 0.00 0.00 0.00 2.27
384 636 7.817418 AAGACACTGGTTTATGCTAAAAGAA 57.183 32.000 0.00 0.00 0.00 2.52
385 637 7.817418 AGACACTGGTTTATGCTAAAAGAAA 57.183 32.000 0.00 0.00 0.00 2.52
386 638 7.649057 AGACACTGGTTTATGCTAAAAGAAAC 58.351 34.615 0.00 0.00 0.00 2.78
387 639 6.435428 ACACTGGTTTATGCTAAAAGAAACG 58.565 36.000 0.00 0.00 33.51 3.60
388 640 6.038936 ACACTGGTTTATGCTAAAAGAAACGT 59.961 34.615 0.00 0.00 33.51 3.99
389 641 7.227116 ACACTGGTTTATGCTAAAAGAAACGTA 59.773 33.333 0.00 0.00 33.51 3.57
390 642 8.071368 CACTGGTTTATGCTAAAAGAAACGTAA 58.929 33.333 0.00 0.00 33.51 3.18
394 646 9.667989 GGTTTATGCTAAAAGAAACGTAAGAAA 57.332 29.630 0.00 0.00 43.62 2.52
532 890 4.997395 TGCTCTTTTACATTCAGGTGAGAC 59.003 41.667 0.00 0.00 0.00 3.36
660 1018 6.426633 TGGATAACATAATTGTGTATCTGCGG 59.573 38.462 8.37 0.00 35.83 5.69
725 1083 5.707298 ACAGGCAGATTTATATACACCATGC 59.293 40.000 0.00 0.00 0.00 4.06
726 1084 5.706833 CAGGCAGATTTATATACACCATGCA 59.293 40.000 0.00 0.00 32.92 3.96
727 1085 5.942236 AGGCAGATTTATATACACCATGCAG 59.058 40.000 0.00 0.00 32.92 4.41
731 1089 7.604164 GCAGATTTATATACACCATGCAGTACT 59.396 37.037 0.00 0.00 0.00 2.73
854 1215 5.426689 ACAGGCTCTAATCACTCAAATGA 57.573 39.130 0.00 0.00 0.00 2.57
855 1216 5.999044 ACAGGCTCTAATCACTCAAATGAT 58.001 37.500 0.00 0.00 41.20 2.45
859 1220 7.228906 CAGGCTCTAATCACTCAAATGATCATT 59.771 37.037 15.36 15.36 38.40 2.57
910 1271 4.290622 CCCTGCCAAGTGCCACCT 62.291 66.667 0.00 0.00 40.16 4.00
927 1288 7.834181 AGTGCCACCTTGAACATTATAAATACT 59.166 33.333 0.00 0.00 0.00 2.12
960 1321 5.122711 CCAAAGCCAAAATCATTCACATTCC 59.877 40.000 0.00 0.00 0.00 3.01
980 1341 1.703411 CCCATCTCCTCCTCTCACTC 58.297 60.000 0.00 0.00 0.00 3.51
1041 1402 0.394899 AGCCAAAGGGTCAGCTATGC 60.395 55.000 0.00 0.00 36.17 3.14
1063 1424 0.248289 GGTCTTAGCCGTGCTGGTTA 59.752 55.000 8.44 0.00 40.10 2.85
1066 1427 0.036765 CTTAGCCGTGCTGGTTACCA 60.037 55.000 3.29 3.29 40.10 3.25
1068 1429 0.107897 TAGCCGTGCTGGTTACCATG 60.108 55.000 3.88 0.28 40.10 3.66
1258 1619 7.667043 TCAGTTATTTGCAGTTCTCGTTATT 57.333 32.000 0.00 0.00 0.00 1.40
1400 1761 4.397417 CCAAGAACATGGCTAGAGGAAAAG 59.603 45.833 0.00 0.00 32.78 2.27
1527 1890 8.470040 TTTAGTGTTTTAGAAGCCTATACGTG 57.530 34.615 0.00 0.00 0.00 4.49
1629 1992 5.779922 TGGATATGCGACTAATACCAAGAC 58.220 41.667 0.00 0.00 0.00 3.01
1752 2117 8.397906 TCAGCATTTCATACTGCAACTTAATAC 58.602 33.333 0.00 0.00 40.88 1.89
1823 2189 2.026641 CCAATGACCAGGCAATAGTGG 58.973 52.381 0.00 0.00 39.98 4.00
1870 2236 3.443681 GCAAATACAGTGTGGCCATTACT 59.556 43.478 9.72 14.56 0.00 2.24
1873 2239 0.771127 ACAGTGTGGCCATTACTGGT 59.229 50.000 36.14 25.86 44.56 4.00
1906 2272 1.455849 CACCTTTGGGGCTGACTCA 59.544 57.895 0.00 0.00 39.10 3.41
2132 2498 0.536006 GCCACTCCCATACCAGCATC 60.536 60.000 0.00 0.00 0.00 3.91
2182 2548 0.027979 CATTACCGCACCAGCATTCG 59.972 55.000 0.00 0.00 42.27 3.34
2416 2782 2.505982 CCATACCTGCAGTCCCCG 59.494 66.667 13.81 0.00 0.00 5.73
2437 2803 2.026636 GCCCCCATACAACTACAAGTCA 60.027 50.000 0.00 0.00 0.00 3.41
2441 2807 4.468510 CCCCATACAACTACAAGTCACCTA 59.531 45.833 0.00 0.00 0.00 3.08
2535 2901 4.166144 CCCACCTTACCAATATTCTCCACT 59.834 45.833 0.00 0.00 0.00 4.00
2539 2905 4.818546 CCTTACCAATATTCTCCACTGCTG 59.181 45.833 0.00 0.00 0.00 4.41
2604 2970 3.117491 ACCAGCATCAATATCTCCACG 57.883 47.619 0.00 0.00 0.00 4.94
2606 2972 2.224378 CCAGCATCAATATCTCCACGGT 60.224 50.000 0.00 0.00 0.00 4.83
2611 2977 4.218635 GCATCAATATCTCCACGGTCTCTA 59.781 45.833 0.00 0.00 0.00 2.43
2647 3013 2.158623 TCCACCACCAGCATCAATATCC 60.159 50.000 0.00 0.00 0.00 2.59
2681 3047 0.692419 CCCCTACAGCTCTCCACCAT 60.692 60.000 0.00 0.00 0.00 3.55
2805 3219 1.450312 CTCCACCACCATCGCTTCC 60.450 63.158 0.00 0.00 0.00 3.46
2806 3220 2.184020 CTCCACCACCATCGCTTCCA 62.184 60.000 0.00 0.00 0.00 3.53
2969 3383 2.353704 CCGAGTCACCTGTCATAAGCAA 60.354 50.000 0.00 0.00 0.00 3.91
2979 3394 3.674997 TGTCATAAGCAACAGGAAGGAC 58.325 45.455 0.00 0.00 0.00 3.85
3093 3508 8.500753 AATTTGAATAGCCGTAATGTGAAGTA 57.499 30.769 0.00 0.00 0.00 2.24
3163 3579 4.832248 TGGTTAGATGACTGCCAAGTAAG 58.168 43.478 0.00 0.00 36.52 2.34
3171 3587 5.738619 TGACTGCCAAGTAAGTAGATTCA 57.261 39.130 0.00 0.00 36.52 2.57
3329 3881 2.990066 ACCCAAGTATCTACTGCTGC 57.010 50.000 0.00 0.00 36.50 5.25
3381 3933 6.699575 ATTCCAGCAATGTAACCATAAGTC 57.300 37.500 0.00 0.00 0.00 3.01
3391 3946 6.947644 TGTAACCATAAGTCGTATGAGCTA 57.052 37.500 7.29 0.00 42.07 3.32
3394 3949 7.865889 TGTAACCATAAGTCGTATGAGCTATTG 59.134 37.037 7.29 0.00 42.07 1.90
3400 3958 8.906693 CATAAGTCGTATGAGCTATTGTTAGTG 58.093 37.037 0.00 0.00 42.07 2.74
3403 3961 7.416022 AGTCGTATGAGCTATTGTTAGTGTAC 58.584 38.462 0.00 0.00 0.00 2.90
3413 3971 6.090898 GCTATTGTTAGTGTACCACTGTTCTG 59.909 42.308 7.13 0.00 45.01 3.02
3415 3973 6.468333 TTGTTAGTGTACCACTGTTCTGTA 57.532 37.500 7.13 0.00 45.01 2.74
3416 3974 5.835257 TGTTAGTGTACCACTGTTCTGTAC 58.165 41.667 7.13 0.00 45.01 2.90
3430 3988 9.770097 CACTGTTCTGTACTCAATCCAATATAT 57.230 33.333 0.00 0.00 0.00 0.86
3462 4020 4.885907 GGGTTCCTTACAGCCCTAAAATAC 59.114 45.833 0.00 0.00 38.12 1.89
3485 4043 7.573968 ACTTTCTACTGTGCATTTCTTTCTT 57.426 32.000 0.00 0.00 0.00 2.52
3513 4072 6.749923 AACTGGAACAAAATAGAGAGATGC 57.250 37.500 0.00 0.00 38.70 3.91
3529 4088 2.595463 GCTGTGGCTTGACTGGCA 60.595 61.111 0.00 0.00 40.25 4.92
3530 4089 2.623915 GCTGTGGCTTGACTGGCAG 61.624 63.158 14.16 14.16 43.14 4.85
3531 4090 1.071987 CTGTGGCTTGACTGGCAGA 59.928 57.895 23.66 0.00 43.14 4.26
3555 4114 4.941263 TCCACTTATTCCAGATTTGTTCCG 59.059 41.667 0.00 0.00 0.00 4.30
3568 4127 0.604243 TGTTCCGCCGTTTATGCTGT 60.604 50.000 0.00 0.00 0.00 4.40
3920 4479 7.707624 TTCTATGGCTCAAATTCAATTCAGT 57.292 32.000 0.00 0.00 0.00 3.41
3921 4480 8.806429 TTCTATGGCTCAAATTCAATTCAGTA 57.194 30.769 0.00 0.00 0.00 2.74
3922 4481 8.806429 TCTATGGCTCAAATTCAATTCAGTAA 57.194 30.769 0.00 0.00 0.00 2.24
3923 4482 9.412460 TCTATGGCTCAAATTCAATTCAGTAAT 57.588 29.630 0.00 0.00 0.00 1.89
3924 4483 9.674824 CTATGGCTCAAATTCAATTCAGTAATC 57.325 33.333 0.00 0.00 0.00 1.75
3925 4484 7.465353 TGGCTCAAATTCAATTCAGTAATCA 57.535 32.000 0.00 0.00 0.00 2.57
3926 4485 7.894708 TGGCTCAAATTCAATTCAGTAATCAA 58.105 30.769 0.00 0.00 0.00 2.57
3927 4486 8.366401 TGGCTCAAATTCAATTCAGTAATCAAA 58.634 29.630 0.00 0.00 0.00 2.69
3928 4487 9.206870 GGCTCAAATTCAATTCAGTAATCAAAA 57.793 29.630 0.00 0.00 0.00 2.44
3939 4498 8.887036 ATTCAGTAATCAAAAGTTGGAAAACC 57.113 30.769 0.00 0.00 0.00 3.27
3940 4499 6.500041 TCAGTAATCAAAAGTTGGAAAACCG 58.500 36.000 0.00 0.00 0.00 4.44
3941 4500 6.319152 TCAGTAATCAAAAGTTGGAAAACCGA 59.681 34.615 0.00 0.00 0.00 4.69
3942 4501 6.636850 CAGTAATCAAAAGTTGGAAAACCGAG 59.363 38.462 0.00 0.00 0.00 4.63
3943 4502 3.430333 TCAAAAGTTGGAAAACCGAGC 57.570 42.857 0.00 0.00 0.00 5.03
3944 4503 3.020984 TCAAAAGTTGGAAAACCGAGCT 58.979 40.909 0.00 0.00 0.00 4.09
3945 4504 3.445805 TCAAAAGTTGGAAAACCGAGCTT 59.554 39.130 0.00 0.00 0.00 3.74
3946 4505 3.436700 AAAGTTGGAAAACCGAGCTTG 57.563 42.857 0.00 0.00 0.00 4.01
3947 4506 1.318576 AGTTGGAAAACCGAGCTTGG 58.681 50.000 19.26 19.26 0.00 3.61
3948 4507 1.133915 AGTTGGAAAACCGAGCTTGGA 60.134 47.619 27.65 0.00 0.00 3.53
3949 4508 1.679153 GTTGGAAAACCGAGCTTGGAA 59.321 47.619 27.65 6.21 0.00 3.53
3950 4509 2.286365 TGGAAAACCGAGCTTGGAAT 57.714 45.000 27.65 11.96 0.00 3.01
3951 4510 1.885887 TGGAAAACCGAGCTTGGAATG 59.114 47.619 27.65 0.00 0.00 2.67
3952 4511 1.402852 GGAAAACCGAGCTTGGAATGC 60.403 52.381 27.65 12.62 37.24 3.56
3953 4512 1.269448 GAAAACCGAGCTTGGAATGCA 59.731 47.619 27.65 0.00 39.85 3.96
3954 4513 0.883833 AAACCGAGCTTGGAATGCAG 59.116 50.000 27.65 0.00 39.85 4.41
3955 4514 0.250901 AACCGAGCTTGGAATGCAGT 60.251 50.000 27.65 0.00 39.85 4.40
3956 4515 0.957395 ACCGAGCTTGGAATGCAGTG 60.957 55.000 27.65 0.00 39.85 3.66
3957 4516 1.136147 CGAGCTTGGAATGCAGTGC 59.864 57.895 8.58 8.58 39.85 4.40
3958 4517 1.136147 GAGCTTGGAATGCAGTGCG 59.864 57.895 11.20 0.00 39.85 5.34
3959 4518 2.505557 GCTTGGAATGCAGTGCGC 60.506 61.111 11.20 0.00 42.89 6.09
3960 4519 2.986306 GCTTGGAATGCAGTGCGCT 61.986 57.895 9.73 0.00 43.06 5.92
3961 4520 1.136147 CTTGGAATGCAGTGCGCTC 59.864 57.895 9.73 4.74 43.06 5.03
3962 4521 1.579964 CTTGGAATGCAGTGCGCTCA 61.580 55.000 9.73 3.45 43.06 4.26
3963 4522 1.855213 TTGGAATGCAGTGCGCTCAC 61.855 55.000 9.73 0.00 43.06 3.51
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
60 61 1.977854 TGGAGTATTCACAGTGGTGCT 59.022 47.619 0.00 0.00 44.87 4.40
103 104 1.612950 TGGTTTGATGTCAATTGCGCT 59.387 42.857 9.73 0.00 35.55 5.92
139 151 1.325338 CGACTTCAACGACAAAACCGT 59.675 47.619 0.00 0.00 42.61 4.83
152 164 0.465705 GGCCCTCATCATCGACTTCA 59.534 55.000 0.00 0.00 0.00 3.02
167 179 2.695147 CCAAATGAAATAGGTCTGGCCC 59.305 50.000 0.00 0.00 38.26 5.80
174 186 5.121105 GCTACGGTACCAAATGAAATAGGT 58.879 41.667 13.54 0.00 38.29 3.08
188 200 3.241067 TGATTTGTCAGGCTACGGTAC 57.759 47.619 0.00 0.00 0.00 3.34
245 257 7.433680 AGCCTTATTTACCAAAACTGACAAAG 58.566 34.615 0.00 0.00 0.00 2.77
250 262 8.361889 GGTTAAAGCCTTATTTACCAAAACTGA 58.638 33.333 0.00 0.00 0.00 3.41
271 283 1.069775 GGGGAGGTGGTGAAGGTTAA 58.930 55.000 0.00 0.00 0.00 2.01
272 284 0.843343 GGGGGAGGTGGTGAAGGTTA 60.843 60.000 0.00 0.00 0.00 2.85
273 285 2.160853 GGGGGAGGTGGTGAAGGTT 61.161 63.158 0.00 0.00 0.00 3.50
274 286 2.531942 GGGGGAGGTGGTGAAGGT 60.532 66.667 0.00 0.00 0.00 3.50
302 551 8.429641 GGTAGATCAAGGTGGTGAATTTCTATA 58.570 37.037 0.00 0.00 0.00 1.31
304 553 6.352737 GGGTAGATCAAGGTGGTGAATTTCTA 60.353 42.308 0.00 0.00 0.00 2.10
306 555 4.640647 GGGTAGATCAAGGTGGTGAATTTC 59.359 45.833 0.00 0.00 0.00 2.17
320 569 1.289231 AGCTCTGACCAGGGTAGATCA 59.711 52.381 0.00 0.00 0.00 2.92
385 637 9.992910 ACGTTTCTTTTAGAAATTTTCTTACGT 57.007 25.926 16.39 15.40 44.94 3.57
494 852 3.258971 AGAGCAGAGCAGTTTGGTATC 57.741 47.619 0.00 0.00 0.00 2.24
532 890 6.653183 CAGTTTATCCTGCATACTGAATTCG 58.347 40.000 0.04 0.00 38.74 3.34
638 996 7.801716 AACCGCAGATACACAATTATGTTAT 57.198 32.000 0.00 0.00 37.82 1.89
704 1062 5.707298 ACTGCATGGTGTATATAAATCTGCC 59.293 40.000 0.00 0.00 0.00 4.85
725 1083 3.551846 ACCTTTTGTGGTTGGAGTACTG 58.448 45.455 0.00 0.00 36.89 2.74
726 1084 3.945640 ACCTTTTGTGGTTGGAGTACT 57.054 42.857 0.00 0.00 36.89 2.73
778 1137 2.558359 GTCAACCACTTGATTTCAGGGG 59.442 50.000 0.00 0.00 38.69 4.79
854 1215 4.101741 GTGGAGCTGGTAAGGTAGAATGAT 59.898 45.833 0.00 0.00 33.19 2.45
855 1216 3.451178 GTGGAGCTGGTAAGGTAGAATGA 59.549 47.826 0.00 0.00 33.19 2.57
859 1220 1.361543 AGGTGGAGCTGGTAAGGTAGA 59.638 52.381 0.00 0.00 33.19 2.59
927 1288 5.022122 TGATTTTGGCTTTGGTATGGATGA 58.978 37.500 0.00 0.00 0.00 2.92
960 1321 0.264359 AGTGAGAGGAGGAGATGGGG 59.736 60.000 0.00 0.00 0.00 4.96
980 1341 1.294659 GGCTGGACAGTGCTTTCTCG 61.295 60.000 0.82 0.00 0.00 4.04
1041 1402 1.448540 CAGCACGGCTAAGACCAGG 60.449 63.158 0.00 0.00 36.40 4.45
1063 1424 2.048023 CACCGAGCATTGCCATGGT 61.048 57.895 14.67 8.07 44.10 3.55
1066 1427 1.452651 CCTCACCGAGCATTGCCAT 60.453 57.895 4.70 0.00 0.00 4.40
1068 1429 3.512516 GCCTCACCGAGCATTGCC 61.513 66.667 4.70 0.00 0.00 4.52
1089 1450 0.538287 AAGGTGGTGGCAAGCTTCTC 60.538 55.000 0.00 0.00 29.63 2.87
1629 1992 2.014128 ACACTTTGGGTTCACAGTTCG 58.986 47.619 0.00 0.00 32.12 3.95
1752 2117 6.547141 TCCTGCACCAGATAATGATAAAAAGG 59.453 38.462 0.00 0.00 32.44 3.11
1823 2189 1.132453 GCTTTCGGTGTAGCCAAATCC 59.868 52.381 0.00 0.00 36.97 3.01
1870 2236 4.073052 CCGCTAAGTGGCAAACCA 57.927 55.556 0.00 0.00 46.51 3.67
1906 2272 1.471119 CATGGAGCTCAACCTTGCAT 58.529 50.000 17.19 4.79 0.00 3.96
2132 2498 1.486726 GTAGTTGGATGGAGGTGAGGG 59.513 57.143 0.00 0.00 0.00 4.30
2182 2548 2.861147 ACTTGTTAGAAGGAGGTGGC 57.139 50.000 0.00 0.00 0.00 5.01
2416 2782 2.026636 TGACTTGTAGTTGTATGGGGGC 60.027 50.000 0.00 0.00 0.00 5.80
2419 2785 4.553330 AGGTGACTTGTAGTTGTATGGG 57.447 45.455 0.00 0.00 37.44 4.00
2422 2788 8.693625 GGTAGAATAGGTGACTTGTAGTTGTAT 58.306 37.037 0.00 0.00 43.67 2.29
2535 2901 2.224744 TGTAGATGTTTTGGAGGCAGCA 60.225 45.455 0.00 0.00 0.00 4.41
2539 2905 3.153919 TGGTTGTAGATGTTTTGGAGGC 58.846 45.455 0.00 0.00 0.00 4.70
2604 2970 3.476485 AGCCATAGGGGTATAGAGACC 57.524 52.381 0.00 0.00 44.90 3.85
2647 3013 1.208165 AGGGGTAAAGAGGCTGTGGG 61.208 60.000 0.00 0.00 0.00 4.61
2681 3047 5.010719 GGGATTGGTACGAGTTCAGATATGA 59.989 44.000 0.00 0.00 0.00 2.15
2805 3219 2.081462 GTGGGGATTGGTACGAGTTTG 58.919 52.381 0.00 0.00 0.00 2.93
2806 3220 1.003928 GGTGGGGATTGGTACGAGTTT 59.996 52.381 0.00 0.00 0.00 2.66
2969 3383 5.053978 ACATTTCAAGAAGTCCTTCCTGT 57.946 39.130 3.47 0.00 40.33 4.00
2979 3394 8.507249 CCACTAGGAAACTTACATTTCAAGAAG 58.493 37.037 0.00 0.00 43.67 2.85
3059 3474 6.183309 ACGGCTATTCAAATTCAAAGAGAC 57.817 37.500 0.00 0.00 0.00 3.36
3077 3492 7.916914 AAGTTTAATACTTCACATTACGGCT 57.083 32.000 0.00 0.00 43.67 5.52
3119 3534 7.989826 ACCAATGCTATCTTTTATGTTGAGTC 58.010 34.615 0.00 0.00 0.00 3.36
3171 3587 8.932610 AGAGATGGATTGAGTCATATACTTTGT 58.067 33.333 0.00 0.00 39.07 2.83
3326 3878 1.959282 ACAAAGGGAAAGCTGAAGCAG 59.041 47.619 4.90 0.00 45.16 4.24
3329 3881 3.638627 AGGAAACAAAGGGAAAGCTGAAG 59.361 43.478 0.00 0.00 0.00 3.02
3381 3933 6.500910 TGGTACACTAACAATAGCTCATACG 58.499 40.000 0.00 0.00 31.96 3.06
3400 3958 5.169295 GGATTGAGTACAGAACAGTGGTAC 58.831 45.833 0.00 0.00 38.08 3.34
3403 3961 4.271696 TGGATTGAGTACAGAACAGTGG 57.728 45.455 0.00 0.00 0.00 4.00
3437 3995 0.622446 TAGGGCTGTAAGGAACCCCC 60.622 60.000 0.00 0.00 43.96 5.40
3440 3998 5.752650 AGTATTTTAGGGCTGTAAGGAACC 58.247 41.667 0.00 0.00 0.00 3.62
3441 3999 7.610692 AGAAAGTATTTTAGGGCTGTAAGGAAC 59.389 37.037 0.00 0.00 39.27 3.62
3443 4001 7.266905 AGAAAGTATTTTAGGGCTGTAAGGA 57.733 36.000 0.00 0.00 39.27 3.36
3445 4003 9.099454 CAGTAGAAAGTATTTTAGGGCTGTAAG 57.901 37.037 0.00 0.00 39.27 2.34
3451 4009 5.646360 TGCACAGTAGAAAGTATTTTAGGGC 59.354 40.000 0.00 0.00 39.27 5.19
3462 4020 7.642669 TCAAGAAAGAAATGCACAGTAGAAAG 58.357 34.615 0.00 0.00 0.00 2.62
3485 4043 7.735917 TCTCTCTATTTTGTTCCAGTTTCTCA 58.264 34.615 0.00 0.00 0.00 3.27
3513 4072 0.322277 ATCTGCCAGTCAAGCCACAG 60.322 55.000 0.00 0.00 0.00 3.66
3529 4088 6.830838 GGAACAAATCTGGAATAAGTGGATCT 59.169 38.462 0.00 0.00 0.00 2.75
3530 4089 6.238484 CGGAACAAATCTGGAATAAGTGGATC 60.238 42.308 0.00 0.00 0.00 3.36
3531 4090 5.590259 CGGAACAAATCTGGAATAAGTGGAT 59.410 40.000 0.00 0.00 0.00 3.41
3555 4114 3.273048 TGCCACAGCATAAACGGC 58.727 55.556 0.00 0.00 46.52 5.68
3896 4455 7.707624 ACTGAATTGAATTTGAGCCATAGAA 57.292 32.000 0.00 0.00 0.00 2.10
3897 4456 8.806429 TTACTGAATTGAATTTGAGCCATAGA 57.194 30.769 0.00 0.00 0.00 1.98
3898 4457 9.674824 GATTACTGAATTGAATTTGAGCCATAG 57.325 33.333 0.00 0.00 0.00 2.23
3899 4458 9.187996 TGATTACTGAATTGAATTTGAGCCATA 57.812 29.630 0.00 0.00 0.00 2.74
3900 4459 8.070034 TGATTACTGAATTGAATTTGAGCCAT 57.930 30.769 0.00 0.00 0.00 4.40
3901 4460 7.465353 TGATTACTGAATTGAATTTGAGCCA 57.535 32.000 0.00 0.00 0.00 4.75
3902 4461 8.761575 TTTGATTACTGAATTGAATTTGAGCC 57.238 30.769 0.00 0.00 0.00 4.70
3913 4472 9.325198 GGTTTTCCAACTTTTGATTACTGAATT 57.675 29.630 0.00 0.00 40.31 2.17
3914 4473 7.651704 CGGTTTTCCAACTTTTGATTACTGAAT 59.348 33.333 0.00 0.00 40.70 2.57
3915 4474 6.975772 CGGTTTTCCAACTTTTGATTACTGAA 59.024 34.615 0.00 0.00 40.70 3.02
3916 4475 6.319152 TCGGTTTTCCAACTTTTGATTACTGA 59.681 34.615 0.00 0.00 40.70 3.41
3917 4476 6.500041 TCGGTTTTCCAACTTTTGATTACTG 58.500 36.000 0.00 0.00 40.70 2.74
3918 4477 6.702716 TCGGTTTTCCAACTTTTGATTACT 57.297 33.333 0.00 0.00 40.70 2.24
3919 4478 5.401376 GCTCGGTTTTCCAACTTTTGATTAC 59.599 40.000 0.00 0.00 40.70 1.89
3920 4479 5.300792 AGCTCGGTTTTCCAACTTTTGATTA 59.699 36.000 0.00 0.00 40.70 1.75
3921 4480 4.099419 AGCTCGGTTTTCCAACTTTTGATT 59.901 37.500 0.00 0.00 40.70 2.57
3922 4481 3.636764 AGCTCGGTTTTCCAACTTTTGAT 59.363 39.130 0.00 0.00 40.70 2.57
3923 4482 3.020984 AGCTCGGTTTTCCAACTTTTGA 58.979 40.909 0.00 0.00 40.70 2.69
3924 4483 3.436700 AGCTCGGTTTTCCAACTTTTG 57.563 42.857 0.00 0.00 40.70 2.44
3925 4484 3.430236 CCAAGCTCGGTTTTCCAACTTTT 60.430 43.478 0.00 0.00 40.70 2.27
3926 4485 2.100749 CCAAGCTCGGTTTTCCAACTTT 59.899 45.455 0.00 0.00 40.70 2.66
3927 4486 1.681264 CCAAGCTCGGTTTTCCAACTT 59.319 47.619 0.00 0.00 40.70 2.66
3928 4487 1.133915 TCCAAGCTCGGTTTTCCAACT 60.134 47.619 0.00 0.00 40.70 3.16
3929 4488 1.314730 TCCAAGCTCGGTTTTCCAAC 58.685 50.000 0.00 0.00 40.70 3.77
3930 4489 2.060050 TTCCAAGCTCGGTTTTCCAA 57.940 45.000 0.00 0.00 40.70 3.53
3931 4490 1.885887 CATTCCAAGCTCGGTTTTCCA 59.114 47.619 0.00 0.00 40.70 3.53
3932 4491 1.402852 GCATTCCAAGCTCGGTTTTCC 60.403 52.381 0.00 0.00 0.00 3.13
3933 4492 1.269448 TGCATTCCAAGCTCGGTTTTC 59.731 47.619 0.00 0.00 0.00 2.29
3934 4493 1.270550 CTGCATTCCAAGCTCGGTTTT 59.729 47.619 0.00 0.00 0.00 2.43
3935 4494 0.883833 CTGCATTCCAAGCTCGGTTT 59.116 50.000 0.00 0.00 0.00 3.27
3936 4495 0.250901 ACTGCATTCCAAGCTCGGTT 60.251 50.000 0.00 0.00 0.00 4.44
3937 4496 0.957395 CACTGCATTCCAAGCTCGGT 60.957 55.000 0.00 0.00 0.00 4.69
3938 4497 1.798735 CACTGCATTCCAAGCTCGG 59.201 57.895 0.00 0.00 0.00 4.63
3939 4498 1.136147 GCACTGCATTCCAAGCTCG 59.864 57.895 0.00 0.00 0.00 5.03
3940 4499 1.136147 CGCACTGCATTCCAAGCTC 59.864 57.895 1.11 0.00 0.00 4.09
3941 4500 2.986306 GCGCACTGCATTCCAAGCT 61.986 57.895 0.30 0.00 45.45 3.74
3942 4501 2.505557 GCGCACTGCATTCCAAGC 60.506 61.111 0.30 0.00 45.45 4.01


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

AutoCloner maintained by Alex Coulton.