Multiple sequence alignment - TraesCS4D01G129900

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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 TraesCS4D01G129900 chr4D 100.000 7454 0 0 1 7454 115940752 115933299 0.000000e+00 13766.0
1 TraesCS4D01G129900 chr4A 95.443 7570 169 76 1 7454 460896361 460903870 0.000000e+00 11906.0
2 TraesCS4D01G129900 chr4A 88.539 1335 126 12 4031 5361 359894177 359895488 0.000000e+00 1592.0
3 TraesCS4D01G129900 chr4A 85.020 247 18 9 3929 4175 666478191 666478418 4.500000e-57 233.0
4 TraesCS4D01G129900 chr4B 94.164 7180 217 100 1 7063 176259315 176266409 0.000000e+00 10752.0
5 TraesCS4D01G129900 chr4B 95.477 398 12 3 7062 7454 176266570 176266966 1.360000e-176 630.0
6 TraesCS4D01G129900 chr2B 93.823 1117 57 6 4113 5226 637454265 637453158 0.000000e+00 1670.0
7 TraesCS4D01G129900 chr2B 90.014 721 43 12 3936 4654 615568603 615567910 0.000000e+00 905.0
8 TraesCS4D01G129900 chr2B 92.561 578 41 2 4650 5226 615558840 615558264 0.000000e+00 828.0
9 TraesCS4D01G129900 chr6D 92.868 645 38 5 4622 5265 429405238 429404601 0.000000e+00 929.0
10 TraesCS4D01G129900 chr6D 96.078 102 4 0 5260 5361 429398506 429398405 4.630000e-37 167.0
11 TraesCS4D01G129900 chr6D 96.610 59 2 0 5260 5318 429402576 429402518 1.710000e-16 99.0
12 TraesCS4D01G129900 chr2D 88.418 354 16 6 4791 5143 582155554 582155225 3.240000e-108 403.0
13 TraesCS4D01G129900 chr2D 85.714 70 3 1 5299 5361 582155235 582155166 4.830000e-07 67.6
14 TraesCS4D01G129900 chr7B 92.683 82 6 0 4598 4679 156919399 156919318 1.310000e-22 119.0
15 TraesCS4D01G129900 chr5B 96.970 66 2 0 4265 4330 533442050 533441985 2.200000e-20 111.0
16 TraesCS4D01G129900 chr1D 95.455 66 3 0 4265 4330 4550591 4550526 1.020000e-18 106.0
17 TraesCS4D01G129900 chr1D 97.619 42 1 0 4542 4583 484187322 484187363 1.040000e-08 73.1
18 TraesCS4D01G129900 chr3B 93.939 66 4 0 4265 4330 751098193 751098128 4.760000e-17 100.0
19 TraesCS4D01G129900 chr3B 97.222 36 1 0 1540 1575 640067431 640067396 2.250000e-05 62.1
20 TraesCS4D01G129900 chr3B 96.875 32 1 0 2535 2566 637618470 637618439 4.000000e-03 54.7
21 TraesCS4D01G129900 chr3A 95.238 63 3 0 4600 4662 157997652 157997590 4.760000e-17 100.0
22 TraesCS4D01G129900 chr3A 97.222 36 1 0 1540 1575 623053203 623053168 2.250000e-05 62.1
23 TraesCS4D01G129900 chr3D 97.619 42 1 0 4542 4583 33322996 33323037 1.040000e-08 73.1
24 TraesCS4D01G129900 chr3D 97.222 36 1 0 1540 1575 479619461 479619426 2.250000e-05 62.1


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 TraesCS4D01G129900 chr4D 115933299 115940752 7453 True 13766 13766 100.0000 1 7454 1 chr4D.!!$R1 7453
1 TraesCS4D01G129900 chr4A 460896361 460903870 7509 False 11906 11906 95.4430 1 7454 1 chr4A.!!$F2 7453
2 TraesCS4D01G129900 chr4A 359894177 359895488 1311 False 1592 1592 88.5390 4031 5361 1 chr4A.!!$F1 1330
3 TraesCS4D01G129900 chr4B 176259315 176266966 7651 False 5691 10752 94.8205 1 7454 2 chr4B.!!$F1 7453
4 TraesCS4D01G129900 chr2B 637453158 637454265 1107 True 1670 1670 93.8230 4113 5226 1 chr2B.!!$R3 1113
5 TraesCS4D01G129900 chr2B 615567910 615568603 693 True 905 905 90.0140 3936 4654 1 chr2B.!!$R2 718
6 TraesCS4D01G129900 chr2B 615558264 615558840 576 True 828 828 92.5610 4650 5226 1 chr2B.!!$R1 576
7 TraesCS4D01G129900 chr6D 429402518 429405238 2720 True 514 929 94.7390 4622 5318 2 chr6D.!!$R2 696

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
477 511 0.106719 CTTCCTCCTCCTCGCTCTCT 60.107 60.000 0.00 0.0 0.00 3.10 F
478 512 0.106918 TTCCTCCTCCTCGCTCTCTC 60.107 60.000 0.00 0.0 0.00 3.20 F
480 514 0.535102 CCTCCTCCTCGCTCTCTCTC 60.535 65.000 0.00 0.0 0.00 3.20 F
2012 2127 1.202604 AGCAAGCAAGCAAAAGCACAT 60.203 42.857 3.19 0.0 36.85 3.21 F
2649 2797 0.107703 GCACCAGCAGCAGGTACATA 60.108 55.000 9.56 0.0 41.58 2.29 F
2829 2977 0.251354 CTGGTGCCATGTCAGTAGCT 59.749 55.000 0.00 0.0 0.00 3.32 F
3933 4104 1.251251 GTTCCTGGAGCAATGCAACT 58.749 50.000 8.35 0.0 0.00 3.16 F
5743 7973 0.250467 GGCAGCAGACTCTTCACCAA 60.250 55.000 0.00 0.0 0.00 3.67 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1985 2096 0.528901 TTGCTTGCTTGCTTGCACAG 60.529 50.000 11.07 6.54 43.20 3.66 R
2231 2351 0.534873 TGCCGCTGTAGCAGTATCAA 59.465 50.000 4.59 0.00 42.21 2.57 R
2426 2574 6.210385 TGCCCAGAAAACAAACACATGTATAT 59.790 34.615 0.00 0.00 32.02 0.86 R
2830 2978 0.771127 TTGGAAGTTGTGGCCTAGCT 59.229 50.000 3.32 0.00 0.00 3.32 R
4243 4415 2.493278 GGTGCACATGGTGAATTAGCTT 59.507 45.455 20.43 0.00 35.23 3.74 R
4537 4724 2.716217 AGCAGCACCTGGAAAATAGAC 58.284 47.619 0.00 0.00 31.21 2.59 R
5767 7997 0.322975 AGAAACATCGAGCTGCCTGT 59.677 50.000 0.00 0.00 0.00 4.00 R
6601 8842 2.544480 TCTGATGACAGTTCTACGCG 57.456 50.000 3.53 3.53 43.81 6.01 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
174 181 4.757594 AGCACAAATTTTCTTCAACAGCA 58.242 34.783 0.00 0.00 0.00 4.41
276 304 3.629087 AGCATGGATGGAAAAGAGAAGG 58.371 45.455 0.00 0.00 0.00 3.46
471 505 0.820871 CACCTTCTTCCTCCTCCTCG 59.179 60.000 0.00 0.00 0.00 4.63
472 506 0.973496 ACCTTCTTCCTCCTCCTCGC 60.973 60.000 0.00 0.00 0.00 5.03
473 507 0.686112 CCTTCTTCCTCCTCCTCGCT 60.686 60.000 0.00 0.00 0.00 4.93
474 508 0.744281 CTTCTTCCTCCTCCTCGCTC 59.256 60.000 0.00 0.00 0.00 5.03
475 509 0.333312 TTCTTCCTCCTCCTCGCTCT 59.667 55.000 0.00 0.00 0.00 4.09
476 510 0.106918 TCTTCCTCCTCCTCGCTCTC 60.107 60.000 0.00 0.00 0.00 3.20
477 511 0.106719 CTTCCTCCTCCTCGCTCTCT 60.107 60.000 0.00 0.00 0.00 3.10
478 512 0.106918 TTCCTCCTCCTCGCTCTCTC 60.107 60.000 0.00 0.00 0.00 3.20
479 513 0.986019 TCCTCCTCCTCGCTCTCTCT 60.986 60.000 0.00 0.00 0.00 3.10
480 514 0.535102 CCTCCTCCTCGCTCTCTCTC 60.535 65.000 0.00 0.00 0.00 3.20
487 527 1.414181 CCTCGCTCTCTCTCTCTCTCT 59.586 57.143 0.00 0.00 0.00 3.10
490 530 2.362397 TCGCTCTCTCTCTCTCTCTCTC 59.638 54.545 0.00 0.00 0.00 3.20
491 531 2.546795 CGCTCTCTCTCTCTCTCTCTCC 60.547 59.091 0.00 0.00 0.00 3.71
494 534 3.713764 CTCTCTCTCTCTCTCTCTCCCTT 59.286 52.174 0.00 0.00 0.00 3.95
516 556 6.540189 CCTTTCTTTCTCTCTTCACAGTTCAA 59.460 38.462 0.00 0.00 0.00 2.69
517 557 7.254727 CCTTTCTTTCTCTCTTCACAGTTCAAG 60.255 40.741 0.00 0.00 0.00 3.02
637 677 2.448705 GGCGAAAGAGAGCGTCTGC 61.449 63.158 0.00 0.00 43.24 4.26
864 905 8.838649 TTGCTGAGGTAGATATATAGGCATAA 57.161 34.615 0.00 0.00 0.00 1.90
870 911 7.306781 AGGTAGATATATAGGCATAAGGGGTC 58.693 42.308 0.00 0.00 0.00 4.46
904 945 3.819368 TGCTCATGTGAGGTTTTCTTGA 58.181 40.909 11.66 0.00 42.29 3.02
1074 1115 2.092267 TCATCATGTGCTTGGCTATGGT 60.092 45.455 0.00 0.00 0.00 3.55
1122 1163 4.473520 AACTCCATGCCTCCCGCG 62.474 66.667 0.00 0.00 42.08 6.46
1186 1229 2.861935 TCTTTCTCGTCGTGGTTTTGTC 59.138 45.455 0.00 0.00 0.00 3.18
1187 1230 2.589798 TTCTCGTCGTGGTTTTGTCT 57.410 45.000 0.00 0.00 0.00 3.41
1188 1231 2.589798 TCTCGTCGTGGTTTTGTCTT 57.410 45.000 0.00 0.00 0.00 3.01
1189 1232 2.198406 TCTCGTCGTGGTTTTGTCTTG 58.802 47.619 0.00 0.00 0.00 3.02
1190 1233 1.931172 CTCGTCGTGGTTTTGTCTTGT 59.069 47.619 0.00 0.00 0.00 3.16
1191 1234 2.348660 TCGTCGTGGTTTTGTCTTGTT 58.651 42.857 0.00 0.00 0.00 2.83
1192 1235 2.743126 TCGTCGTGGTTTTGTCTTGTTT 59.257 40.909 0.00 0.00 0.00 2.83
1193 1236 3.188873 TCGTCGTGGTTTTGTCTTGTTTT 59.811 39.130 0.00 0.00 0.00 2.43
1194 1237 3.299542 CGTCGTGGTTTTGTCTTGTTTTG 59.700 43.478 0.00 0.00 0.00 2.44
1195 1238 4.231439 GTCGTGGTTTTGTCTTGTTTTGT 58.769 39.130 0.00 0.00 0.00 2.83
1207 1250 6.744112 TGTCTTGTTTTGTTTTGTCTTGTCT 58.256 32.000 0.00 0.00 0.00 3.41
1208 1251 7.206687 TGTCTTGTTTTGTTTTGTCTTGTCTT 58.793 30.769 0.00 0.00 0.00 3.01
1210 1253 8.003784 GTCTTGTTTTGTTTTGTCTTGTCTTTG 58.996 33.333 0.00 0.00 0.00 2.77
1351 1395 1.264288 GCGTATTGCCTTGTATGGAGC 59.736 52.381 0.00 0.00 37.76 4.70
1434 1491 5.905480 ACACACATACATGCATACATACG 57.095 39.130 0.00 0.00 33.67 3.06
1446 1503 7.171508 ACATGCATACATACGTAGGAATCTTTG 59.828 37.037 15.09 7.21 33.67 2.77
1985 2096 2.438075 CTCTGGCTTGGCTGGCTC 60.438 66.667 2.00 0.00 0.00 4.70
2012 2127 1.202604 AGCAAGCAAGCAAAAGCACAT 60.203 42.857 3.19 0.00 36.85 3.21
2231 2351 1.489560 GCCTTCCCCAGTACTGTGGT 61.490 60.000 21.91 0.00 35.60 4.16
2374 2494 5.104941 ACTCCGTATCATCATTCAAGGACAA 60.105 40.000 0.00 0.00 0.00 3.18
2375 2495 5.739959 TCCGTATCATCATTCAAGGACAAA 58.260 37.500 0.00 0.00 0.00 2.83
2376 2496 6.176896 TCCGTATCATCATTCAAGGACAAAA 58.823 36.000 0.00 0.00 0.00 2.44
2377 2497 6.828273 TCCGTATCATCATTCAAGGACAAAAT 59.172 34.615 0.00 0.00 0.00 1.82
2378 2498 7.990314 TCCGTATCATCATTCAAGGACAAAATA 59.010 33.333 0.00 0.00 0.00 1.40
2379 2499 8.620416 CCGTATCATCATTCAAGGACAAAATAA 58.380 33.333 0.00 0.00 0.00 1.40
2419 2567 5.652994 TGCACCTAAAACTGTTTTCACTT 57.347 34.783 20.72 0.89 34.19 3.16
2426 2574 9.398538 ACCTAAAACTGTTTTCACTTATGTGTA 57.601 29.630 20.72 0.00 44.14 2.90
2540 2688 3.581770 ACATGGACTCATCGGATCATCAT 59.418 43.478 0.00 0.00 0.00 2.45
2543 2691 3.836562 TGGACTCATCGGATCATCATCAT 59.163 43.478 0.00 0.00 0.00 2.45
2558 2706 0.679960 ATCATCAGCAGCAGCAGCAA 60.680 50.000 12.92 0.00 45.49 3.91
2643 2791 4.655647 ACCAGCACCAGCAGCAGG 62.656 66.667 1.37 1.37 45.49 4.85
2644 2792 4.655647 CCAGCACCAGCAGCAGGT 62.656 66.667 2.99 2.99 45.49 4.00
2645 2793 2.348620 CAGCACCAGCAGCAGGTA 59.651 61.111 9.56 0.00 45.49 3.08
2646 2794 2.037136 CAGCACCAGCAGCAGGTAC 61.037 63.158 9.56 3.84 45.49 3.34
2647 2795 2.032528 GCACCAGCAGCAGGTACA 59.967 61.111 9.56 0.00 41.58 2.90
2648 2796 1.377725 GCACCAGCAGCAGGTACAT 60.378 57.895 9.56 0.00 41.58 2.29
2649 2797 0.107703 GCACCAGCAGCAGGTACATA 60.108 55.000 9.56 0.00 41.58 2.29
2650 2798 1.656652 CACCAGCAGCAGGTACATAC 58.343 55.000 9.56 0.00 37.23 2.39
2651 2799 1.208052 CACCAGCAGCAGGTACATACT 59.792 52.381 9.56 0.00 37.23 2.12
2652 2800 2.430694 CACCAGCAGCAGGTACATACTA 59.569 50.000 9.56 0.00 37.23 1.82
2653 2801 2.431057 ACCAGCAGCAGGTACATACTAC 59.569 50.000 7.93 0.00 37.67 2.73
2654 2802 2.695666 CCAGCAGCAGGTACATACTACT 59.304 50.000 0.00 0.00 0.00 2.57
2656 2804 3.634448 CAGCAGCAGGTACATACTACTCT 59.366 47.826 0.00 0.00 0.00 3.24
2670 2818 7.866729 ACATACTACTCTACTGTGAATGATCG 58.133 38.462 0.00 0.00 0.00 3.69
2828 2976 0.745845 CCTGGTGCCATGTCAGTAGC 60.746 60.000 0.00 0.00 0.00 3.58
2829 2977 0.251354 CTGGTGCCATGTCAGTAGCT 59.749 55.000 0.00 0.00 0.00 3.32
2830 2978 1.482182 CTGGTGCCATGTCAGTAGCTA 59.518 52.381 0.00 0.00 0.00 3.32
2831 2979 1.482182 TGGTGCCATGTCAGTAGCTAG 59.518 52.381 0.00 0.00 0.00 3.42
2897 3049 2.681848 CCATAGGCAGCACAAGAAAGAG 59.318 50.000 0.00 0.00 0.00 2.85
3243 3409 7.922278 TCAATTAGTTGGATGCTTGAATAATGC 59.078 33.333 0.00 0.00 35.99 3.56
3307 3473 1.270550 GTCAATTGGTGAACTGCCAGG 59.729 52.381 5.42 0.00 38.23 4.45
3401 3568 4.756084 AATCCACGCTTCTTTCTCAAAG 57.244 40.909 0.00 0.00 39.88 2.77
3617 3786 8.132362 GCATGCAGTAGAGACCATACTATATAC 58.868 40.741 14.21 0.00 32.24 1.47
3777 3948 6.153067 GTCGTGACCCATATATTTGAGAGAG 58.847 44.000 0.00 0.00 0.00 3.20
3885 4056 4.335647 ACAGGACTGGCAAGGCGG 62.336 66.667 4.14 0.35 28.70 6.13
3933 4104 1.251251 GTTCCTGGAGCAATGCAACT 58.749 50.000 8.35 0.00 0.00 3.16
4127 4298 4.989797 TGCCAAGTTATTGACTTTTGCATG 59.010 37.500 9.79 0.00 46.34 4.06
4243 4415 3.580022 TCTCAGGTGCTTCTCATTTCTGA 59.420 43.478 0.00 0.00 32.46 3.27
4499 4686 6.725834 ACTGATTAGAATGTGGTGGGAATTTT 59.274 34.615 0.00 0.00 0.00 1.82
4537 4724 4.494484 TGGACTGAATACGAACTGTGATG 58.506 43.478 0.00 0.00 0.00 3.07
4893 5087 8.488979 AAAAATAGAAACGAAATCAACTGTCG 57.511 30.769 0.00 0.00 40.56 4.35
4910 5104 9.047371 TCAACTGTCGTTTTCATTTCATAGTTA 57.953 29.630 0.00 0.00 0.00 2.24
5397 7627 3.828451 AGGCAAATGTAGCAACAATCTGT 59.172 39.130 0.00 0.00 39.58 3.41
5522 7752 8.324163 AGTACTTCCACTAATAGTGCAAAAAG 57.676 34.615 14.60 14.97 44.63 2.27
5743 7973 0.250467 GGCAGCAGACTCTTCACCAA 60.250 55.000 0.00 0.00 0.00 3.67
5767 7997 3.578282 TGCACAGGATTCTGACAGTTAGA 59.422 43.478 8.39 0.00 43.49 2.10
5998 8237 2.348411 GCAAGGGCTTAATAGAGGCA 57.652 50.000 0.91 0.00 43.48 4.75
6188 8427 7.659652 AAAGAACTAGAGATGGTTTCTTTCG 57.340 36.000 0.00 0.00 33.74 3.46
6198 8437 4.301637 TGGTTTCTTTCGCTTTTTCCTC 57.698 40.909 0.00 0.00 0.00 3.71
6199 8438 3.697045 TGGTTTCTTTCGCTTTTTCCTCA 59.303 39.130 0.00 0.00 0.00 3.86
6204 8443 3.753272 TCTTTCGCTTTTTCCTCAGATGG 59.247 43.478 0.00 0.00 0.00 3.51
6319 8560 3.933332 GGTTCAGCAGTTGTAGTACCATC 59.067 47.826 0.00 0.00 0.00 3.51
6512 8753 3.740832 GCATAAGCAAAACAACTGGGAAC 59.259 43.478 0.00 0.00 41.58 3.62
6577 8818 2.586425 CTGGGAAACAAAGGAAGCTCA 58.414 47.619 0.00 0.00 0.00 4.26
6601 8842 5.066593 AGAAATGGGAGAACTTGTCAGAAC 58.933 41.667 0.00 0.00 0.00 3.01
6696 8937 7.161773 ACACCCAGAGTTCATTATTGAAATG 57.838 36.000 5.15 4.07 43.29 2.32
7011 9256 6.017934 CACACACTGCTGTTGAGTTATAACTT 60.018 38.462 18.96 3.63 39.88 2.66
7076 9483 7.072202 AGGCTAGTACCTAGATAGTACTCACAA 59.928 40.741 12.01 0.00 45.70 3.33
7170 9583 8.115490 AGGATAAGTTCAAGTTTCTTCCATTG 57.885 34.615 4.84 0.00 0.00 2.82
7189 9602 7.281098 TCCATTGTAAACCAAAGTGTACACTA 58.719 34.615 28.13 8.61 44.68 2.74
7263 9676 6.573357 CACACATACATTGAACAAACACGTAG 59.427 38.462 0.00 0.00 0.00 3.51
7266 9679 7.853437 CACATACATTGAACAAACACGTAGAAA 59.147 33.333 0.00 0.00 0.00 2.52
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
174 181 6.475727 CGTGAGAACGTATCCATTCTTTATGT 59.524 38.462 0.00 0.00 35.29 2.29
276 304 1.077429 GTCCATGTCCAGCCCTTCC 60.077 63.158 0.00 0.00 0.00 3.46
471 505 2.224402 GGGAGAGAGAGAGAGAGAGAGC 60.224 59.091 0.00 0.00 0.00 4.09
472 506 3.312890 AGGGAGAGAGAGAGAGAGAGAG 58.687 54.545 0.00 0.00 0.00 3.20
473 507 3.421394 AGGGAGAGAGAGAGAGAGAGA 57.579 52.381 0.00 0.00 0.00 3.10
474 508 4.164988 AGAAAGGGAGAGAGAGAGAGAGAG 59.835 50.000 0.00 0.00 0.00 3.20
475 509 4.111577 AGAAAGGGAGAGAGAGAGAGAGA 58.888 47.826 0.00 0.00 0.00 3.10
476 510 4.510167 AGAAAGGGAGAGAGAGAGAGAG 57.490 50.000 0.00 0.00 0.00 3.20
477 511 4.946160 AAGAAAGGGAGAGAGAGAGAGA 57.054 45.455 0.00 0.00 0.00 3.10
478 512 5.264395 AGAAAGAAAGGGAGAGAGAGAGAG 58.736 45.833 0.00 0.00 0.00 3.20
479 513 5.015178 AGAGAAAGAAAGGGAGAGAGAGAGA 59.985 44.000 0.00 0.00 0.00 3.10
480 514 5.264395 AGAGAAAGAAAGGGAGAGAGAGAG 58.736 45.833 0.00 0.00 0.00 3.20
487 527 4.901849 TGTGAAGAGAGAAAGAAAGGGAGA 59.098 41.667 0.00 0.00 0.00 3.71
490 530 4.967036 ACTGTGAAGAGAGAAAGAAAGGG 58.033 43.478 0.00 0.00 0.00 3.95
491 531 6.051717 TGAACTGTGAAGAGAGAAAGAAAGG 58.948 40.000 0.00 0.00 0.00 3.11
494 534 6.878317 TCTTGAACTGTGAAGAGAGAAAGAA 58.122 36.000 0.00 0.00 0.00 2.52
516 556 8.980481 TTTAATTTGTTTTGGTCTCTCTCTCT 57.020 30.769 0.00 0.00 0.00 3.10
517 557 7.805542 GCTTTAATTTGTTTTGGTCTCTCTCTC 59.194 37.037 0.00 0.00 0.00 3.20
569 609 2.420687 GCTAATCCCACAGTTGAGAGGG 60.421 54.545 0.00 0.00 42.86 4.30
637 677 2.981898 TGTCTTGATGCATCTGACAGG 58.018 47.619 32.26 16.42 36.69 4.00
870 911 1.509644 ATGAGCAACACACACAGGCG 61.510 55.000 0.00 0.00 0.00 5.52
1122 1163 1.813178 GGTTGCTCTTACAAGAAGGCC 59.187 52.381 0.00 0.00 34.03 5.19
1186 1229 8.071122 TCAAAGACAAGACAAAACAAAACAAG 57.929 30.769 0.00 0.00 0.00 3.16
1187 1230 8.600449 ATCAAAGACAAGACAAAACAAAACAA 57.400 26.923 0.00 0.00 0.00 2.83
1188 1231 8.087750 AGATCAAAGACAAGACAAAACAAAACA 58.912 29.630 0.00 0.00 0.00 2.83
1189 1232 8.466086 AGATCAAAGACAAGACAAAACAAAAC 57.534 30.769 0.00 0.00 0.00 2.43
1190 1233 8.522830 AGAGATCAAAGACAAGACAAAACAAAA 58.477 29.630 0.00 0.00 0.00 2.44
1191 1234 8.055279 AGAGATCAAAGACAAGACAAAACAAA 57.945 30.769 0.00 0.00 0.00 2.83
1192 1235 7.554118 AGAGAGATCAAAGACAAGACAAAACAA 59.446 33.333 0.00 0.00 0.00 2.83
1193 1236 7.050377 AGAGAGATCAAAGACAAGACAAAACA 58.950 34.615 0.00 0.00 0.00 2.83
1194 1237 7.489574 AGAGAGATCAAAGACAAGACAAAAC 57.510 36.000 0.00 0.00 0.00 2.43
1195 1238 7.989741 AGAAGAGAGATCAAAGACAAGACAAAA 59.010 33.333 0.00 0.00 0.00 2.44
1207 1250 5.936956 GGAAAGAAGCAGAAGAGAGATCAAA 59.063 40.000 0.00 0.00 0.00 2.69
1208 1251 5.486526 GGAAAGAAGCAGAAGAGAGATCAA 58.513 41.667 0.00 0.00 0.00 2.57
1210 1253 4.441792 GGGAAAGAAGCAGAAGAGAGATC 58.558 47.826 0.00 0.00 0.00 2.75
1365 1410 3.759418 CATGAAGCATGAAGAACAGCAG 58.241 45.455 0.00 0.00 43.81 4.24
1446 1503 7.745972 TCACCGAATACGTGATATATCTACAC 58.254 38.462 13.79 3.93 37.88 2.90
1466 1530 2.023673 ACCATTACATTGCCATCACCG 58.976 47.619 0.00 0.00 0.00 4.94
1985 2096 0.528901 TTGCTTGCTTGCTTGCACAG 60.529 50.000 11.07 6.54 43.20 3.66
2083 2198 1.004277 TGTGATCACAAAGGGGTAGGC 59.996 52.381 26.02 0.00 38.56 3.93
2231 2351 0.534873 TGCCGCTGTAGCAGTATCAA 59.465 50.000 4.59 0.00 42.21 2.57
2376 2496 9.150348 GGTGCAAAATGCTTGTAGTAATTTTAT 57.850 29.630 3.78 0.00 45.31 1.40
2377 2497 8.364142 AGGTGCAAAATGCTTGTAGTAATTTTA 58.636 29.630 3.78 0.00 45.31 1.52
2378 2498 7.216494 AGGTGCAAAATGCTTGTAGTAATTTT 58.784 30.769 3.78 0.00 45.31 1.82
2379 2499 6.758254 AGGTGCAAAATGCTTGTAGTAATTT 58.242 32.000 3.78 0.00 45.31 1.82
2426 2574 6.210385 TGCCCAGAAAACAAACACATGTATAT 59.790 34.615 0.00 0.00 32.02 0.86
2486 2634 1.153588 GCTGCTGCTCTCTGAGTCC 60.154 63.158 8.53 0.00 36.03 3.85
2540 2688 1.302993 TTGCTGCTGCTGCTGATGA 60.303 52.632 27.67 8.50 40.01 2.92
2543 2691 2.203238 TGTTGCTGCTGCTGCTGA 60.203 55.556 27.67 16.03 40.01 4.26
2558 2706 1.898863 ATCCTACCATCCCTTGCTGT 58.101 50.000 0.00 0.00 0.00 4.40
2644 2792 8.989980 CGATCATTCACAGTAGAGTAGTATGTA 58.010 37.037 0.00 0.00 0.00 2.29
2645 2793 7.499563 ACGATCATTCACAGTAGAGTAGTATGT 59.500 37.037 0.00 0.00 0.00 2.29
2646 2794 7.866729 ACGATCATTCACAGTAGAGTAGTATG 58.133 38.462 0.00 0.00 0.00 2.39
2647 2795 8.991026 GTACGATCATTCACAGTAGAGTAGTAT 58.009 37.037 0.00 0.00 0.00 2.12
2648 2796 7.983484 TGTACGATCATTCACAGTAGAGTAGTA 59.017 37.037 0.00 0.00 0.00 1.82
2649 2797 6.822170 TGTACGATCATTCACAGTAGAGTAGT 59.178 38.462 0.00 0.00 0.00 2.73
2650 2798 7.247929 TGTACGATCATTCACAGTAGAGTAG 57.752 40.000 0.00 0.00 0.00 2.57
2651 2799 7.247929 CTGTACGATCATTCACAGTAGAGTA 57.752 40.000 0.00 0.00 34.91 2.59
2652 2800 6.125327 CTGTACGATCATTCACAGTAGAGT 57.875 41.667 0.00 0.00 34.91 3.24
2670 2818 9.740239 ATGCATTGAATGAATTTGATACTGTAC 57.260 29.630 9.76 0.00 0.00 2.90
2828 2976 1.555075 TGGAAGTTGTGGCCTAGCTAG 59.445 52.381 14.20 14.20 0.00 3.42
2829 2977 1.651737 TGGAAGTTGTGGCCTAGCTA 58.348 50.000 3.32 0.00 0.00 3.32
2830 2978 0.771127 TTGGAAGTTGTGGCCTAGCT 59.229 50.000 3.32 0.00 0.00 3.32
2831 2979 1.168714 CTTGGAAGTTGTGGCCTAGC 58.831 55.000 3.32 0.00 0.00 3.42
2897 3049 4.065789 ACCGTGTGGATTCTTTCTTTCTC 58.934 43.478 0.00 0.00 39.21 2.87
3202 3368 5.140454 ACTAATTGAGGCCACAGTTTCTTT 58.860 37.500 15.65 2.04 0.00 2.52
3405 3572 7.443879 TCAGCTGAGTGTGAATTGTTTGTTATA 59.556 33.333 13.74 0.00 0.00 0.98
3406 3573 6.262944 TCAGCTGAGTGTGAATTGTTTGTTAT 59.737 34.615 13.74 0.00 0.00 1.89
3407 3574 5.588246 TCAGCTGAGTGTGAATTGTTTGTTA 59.412 36.000 13.74 0.00 0.00 2.41
3408 3575 4.398988 TCAGCTGAGTGTGAATTGTTTGTT 59.601 37.500 13.74 0.00 0.00 2.83
3409 3576 3.947196 TCAGCTGAGTGTGAATTGTTTGT 59.053 39.130 13.74 0.00 0.00 2.83
3410 3577 4.556942 TCAGCTGAGTGTGAATTGTTTG 57.443 40.909 13.74 0.00 0.00 2.93
3411 3578 5.357878 TCTTTCAGCTGAGTGTGAATTGTTT 59.642 36.000 17.43 0.00 32.79 2.83
3426 3593 1.299321 GCAGGGCTCTCTTTCAGCT 59.701 57.895 0.00 0.00 37.05 4.24
3617 3786 8.492673 TGGTAGAATCAAGCAAATACTTAGTG 57.507 34.615 0.00 0.00 0.00 2.74
3637 3806 4.396166 GGAAGAACAATGTGTCCATGGTAG 59.604 45.833 12.58 0.00 33.94 3.18
3638 3807 4.202514 TGGAAGAACAATGTGTCCATGGTA 60.203 41.667 12.58 0.00 33.94 3.25
3885 4056 3.869065 TCGATGGTACCTTTGGATCAAC 58.131 45.455 14.36 0.00 0.00 3.18
4127 4298 4.083110 GCCTACACATGATGGATAATGCAC 60.083 45.833 0.00 0.00 0.00 4.57
4243 4415 2.493278 GGTGCACATGGTGAATTAGCTT 59.507 45.455 20.43 0.00 35.23 3.74
4499 4686 5.076182 TCAGTCCAATGCCAAATCTTAACA 58.924 37.500 0.00 0.00 0.00 2.41
4537 4724 2.716217 AGCAGCACCTGGAAAATAGAC 58.284 47.619 0.00 0.00 31.21 2.59
4870 5064 7.186021 ACGACAGTTGATTTCGTTTCTATTT 57.814 32.000 0.00 0.00 43.23 1.40
5354 7579 5.240844 GCCTACAAGTTTTACCAGTCATTGT 59.759 40.000 0.00 0.00 34.15 2.71
5397 7627 6.550854 CCAGAGCAATAAATTTCCCCTGAATA 59.449 38.462 0.00 0.00 0.00 1.75
5743 7973 3.430042 ACTGTCAGAATCCTGTGCATT 57.570 42.857 6.91 0.00 41.16 3.56
5767 7997 0.322975 AGAAACATCGAGCTGCCTGT 59.677 50.000 0.00 0.00 0.00 4.00
6188 8427 4.802999 CTGAAACCATCTGAGGAAAAAGC 58.197 43.478 0.00 0.00 0.00 3.51
6198 8437 3.474600 CAGGGATAGCTGAAACCATCTG 58.525 50.000 0.00 0.00 0.00 2.90
6199 8438 2.158696 GCAGGGATAGCTGAAACCATCT 60.159 50.000 0.00 0.00 0.00 2.90
6204 8443 1.065126 ACAGGCAGGGATAGCTGAAAC 60.065 52.381 0.00 0.00 0.00 2.78
6577 8818 5.310409 TCTGACAAGTTCTCCCATTTCTT 57.690 39.130 0.00 0.00 0.00 2.52
6601 8842 2.544480 TCTGATGACAGTTCTACGCG 57.456 50.000 3.53 3.53 43.81 6.01
6892 9133 5.456763 CCCCTTTGTTCCCTCCTAATGATAG 60.457 48.000 0.00 0.00 0.00 2.08
7189 9602 3.947196 TCACAGCAAAATCAGTCTTGTGT 59.053 39.130 0.00 0.00 0.00 3.72
7195 9608 5.825507 ACTCTTTTCACAGCAAAATCAGTC 58.174 37.500 0.00 0.00 0.00 3.51
7263 9676 5.010012 TGAAGATGCAGGAAAGTCCTTTTTC 59.990 40.000 0.00 0.00 46.91 2.29
7266 9679 4.077822 CTGAAGATGCAGGAAAGTCCTTT 58.922 43.478 0.00 0.00 46.91 3.11


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

AutoCloner maintained by Alex Coulton.