Multiple sequence alignment - TraesCS2D01G136200

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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 TraesCS2D01G136200 chr2D 100.000 7103 0 0 1 7103 79981048 79988150 0.000000e+00 13117
1 TraesCS2D01G136200 chr2A 96.491 4503 125 14 2623 7103 80589209 80593700 0.000000e+00 7409
2 TraesCS2D01G136200 chr2A 93.882 2321 78 27 309 2599 80586847 80589133 0.000000e+00 3441
3 TraesCS2D01G136200 chr2A 87.313 134 6 2 1 124 80586608 80586740 7.430000e-30 143
4 TraesCS2D01G136200 chr2A 90.541 74 7 0 193 266 80586762 80586835 1.630000e-16 99
5 TraesCS2D01G136200 chr2B 96.566 4281 121 11 2834 7103 131570621 131574886 0.000000e+00 7068
6 TraesCS2D01G136200 chr2B 91.175 2697 105 57 1 2623 131567749 131570386 0.000000e+00 3539
7 TraesCS2D01G136200 chr4B 91.845 466 24 7 2093 2554 653276407 653276862 7.770000e-179 638
8 TraesCS2D01G136200 chr4B 100.000 157 0 0 1506 1662 653276255 653276411 2.510000e-74 291


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 TraesCS2D01G136200 chr2D 79981048 79988150 7102 False 13117.0 13117 100.00000 1 7103 1 chr2D.!!$F1 7102
1 TraesCS2D01G136200 chr2A 80586608 80593700 7092 False 2773.0 7409 92.05675 1 7103 4 chr2A.!!$F1 7102
2 TraesCS2D01G136200 chr2B 131567749 131574886 7137 False 5303.5 7068 93.87050 1 7103 2 chr2B.!!$F1 7102
3 TraesCS2D01G136200 chr4B 653276255 653276862 607 False 464.5 638 95.92250 1506 2554 2 chr4B.!!$F1 1048

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
842 911 0.036388 ACACGACGGCAGAATCCAAT 60.036 50.000 0.00 0.00 0.00 3.16 F
913 987 0.320858 TCGCCGCTCCATTGTTGTTA 60.321 50.000 0.00 0.00 0.00 2.41 F
1164 1251 1.525077 GTTCACGCAGACCAACCCA 60.525 57.895 0.00 0.00 0.00 4.51 F
1986 2073 2.034066 AGCCACATTGTCACCGGG 59.966 61.111 6.32 0.00 0.00 5.73 F
3398 3570 0.883833 CACCAGACAAGGGCAATGTC 59.116 55.000 12.41 12.41 45.94 3.06 F
4010 4182 1.201921 CGTCGAAGCTATGCAAACACC 60.202 52.381 0.00 0.00 0.00 4.16 F
4430 4602 1.747355 GGCAGGACCATTGAAGATGTG 59.253 52.381 0.00 0.00 38.86 3.21 F
5958 6131 0.107459 GGAAGAGGCTGATGGACACC 60.107 60.000 0.00 0.00 0.00 4.16 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2488 2579 0.035152 AATGCATGCGACTTCCCTGA 60.035 50.0 14.09 0.00 0.0 3.86 R
2692 2852 0.588252 CAGTTTTCAGCGTGACAGGG 59.412 55.0 0.00 0.00 0.0 4.45 R
2693 2853 1.581934 TCAGTTTTCAGCGTGACAGG 58.418 50.0 0.00 0.00 0.0 4.00 R
3743 3915 0.036732 AGAACAGAAGCCGCATTGGA 59.963 50.0 0.00 0.00 42.0 3.53 R
4430 4602 0.175073 CCTTGTCGCTACCCCTGTAC 59.825 60.0 0.00 0.00 0.0 2.90 R
5595 5768 0.378962 CCGTCAGTGAGATCTCCGAC 59.621 60.0 20.03 19.78 0.0 4.79 R
6012 6185 0.755686 CTGATGTCTCCCAGTAGCCC 59.244 60.0 0.00 0.00 0.0 5.19 R
6893 7076 0.108756 GTACACCGCTGACTTCTCCC 60.109 60.0 0.00 0.00 0.0 4.30 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
49 50 4.098044 CAGCATCAAATTCTTGGCAGAGAT 59.902 41.667 0.00 0.00 33.01 2.75
51 52 4.788840 GCATCAAATTCTTGGCAGAGATCG 60.789 45.833 0.00 0.00 33.01 3.69
52 53 2.679837 TCAAATTCTTGGCAGAGATCGC 59.320 45.455 0.00 0.00 33.01 4.58
62 74 2.802256 GCAGAGATCGCCAAAAATTCC 58.198 47.619 0.00 0.00 0.00 3.01
66 78 3.445096 AGAGATCGCCAAAAATTCCAAGG 59.555 43.478 0.00 0.00 0.00 3.61
135 147 2.281276 ACGAGACCCGCCAAAACC 60.281 61.111 0.00 0.00 43.32 3.27
148 160 1.835267 AAAACCGAAACCCCTGGCC 60.835 57.895 0.00 0.00 0.00 5.36
160 172 3.138798 CTGGCCACCATGCAGCTC 61.139 66.667 0.00 0.00 30.82 4.09
165 177 3.138798 CACCATGCAGCTCCAGCC 61.139 66.667 0.00 0.00 43.38 4.85
166 178 3.336568 ACCATGCAGCTCCAGCCT 61.337 61.111 0.00 0.00 43.38 4.58
168 180 2.516460 CATGCAGCTCCAGCCTCC 60.516 66.667 0.00 0.00 43.38 4.30
169 181 3.013327 ATGCAGCTCCAGCCTCCA 61.013 61.111 0.00 0.00 43.38 3.86
180 192 4.039092 GCCTCCAGCTGCAGGGAA 62.039 66.667 25.30 0.00 38.99 3.97
181 193 2.271497 CCTCCAGCTGCAGGGAAG 59.729 66.667 16.71 4.50 31.58 3.46
182 194 2.271497 CTCCAGCTGCAGGGAAGG 59.729 66.667 17.12 0.00 31.58 3.46
183 195 3.991725 CTCCAGCTGCAGGGAAGGC 62.992 68.421 17.12 0.00 31.58 4.35
184 196 4.355720 CCAGCTGCAGGGAAGGCA 62.356 66.667 17.12 0.00 39.32 4.75
185 197 2.282674 CAGCTGCAGGGAAGGCAA 60.283 61.111 17.12 0.00 41.39 4.52
186 198 2.282745 AGCTGCAGGGAAGGCAAC 60.283 61.111 17.12 0.00 41.39 4.17
187 199 2.598394 GCTGCAGGGAAGGCAACA 60.598 61.111 17.12 0.00 41.39 3.33
188 200 2.202395 GCTGCAGGGAAGGCAACAA 61.202 57.895 17.12 0.00 41.39 2.83
189 201 1.538687 GCTGCAGGGAAGGCAACAAT 61.539 55.000 17.12 0.00 41.39 2.71
190 202 0.529378 CTGCAGGGAAGGCAACAATC 59.471 55.000 5.57 0.00 41.39 2.67
191 203 0.899717 TGCAGGGAAGGCAACAATCC 60.900 55.000 0.00 0.00 42.43 3.01
224 236 0.392193 ACGGCAGAAAGGCAGAGATG 60.392 55.000 0.00 0.00 44.47 2.90
241 253 0.831711 ATGGCAACCTTTGTCCCCAC 60.832 55.000 0.00 0.00 33.37 4.61
267 279 4.838486 GACGCGTCGCCCAGAGAG 62.838 72.222 25.19 0.00 0.00 3.20
270 282 4.443266 GCGTCGCCCAGAGAGCTT 62.443 66.667 5.75 0.00 32.88 3.74
271 283 2.202676 CGTCGCCCAGAGAGCTTC 60.203 66.667 0.00 0.00 0.00 3.86
272 284 2.202676 GTCGCCCAGAGAGCTTCG 60.203 66.667 0.00 0.00 0.00 3.79
284 296 0.806492 GAGCTTCGTTCGGACCATCC 60.806 60.000 0.00 0.00 0.00 3.51
285 297 1.079405 GCTTCGTTCGGACCATCCA 60.079 57.895 0.00 0.00 35.91 3.41
286 298 0.462047 GCTTCGTTCGGACCATCCAT 60.462 55.000 0.00 0.00 35.91 3.41
287 299 1.571919 CTTCGTTCGGACCATCCATC 58.428 55.000 0.00 0.00 35.91 3.51
288 300 0.179121 TTCGTTCGGACCATCCATCG 60.179 55.000 0.00 0.00 35.91 3.84
289 301 2.237751 CGTTCGGACCATCCATCGC 61.238 63.158 0.00 0.00 35.91 4.58
293 305 4.271016 GGACCATCCATCGCCCCC 62.271 72.222 0.00 0.00 36.28 5.40
371 388 1.227823 GCAAAAGGCCCCACAAACC 60.228 57.895 0.00 0.00 36.11 3.27
372 389 1.977293 GCAAAAGGCCCCACAAACCA 61.977 55.000 0.00 0.00 36.11 3.67
374 391 1.681486 AAAAGGCCCCACAAACCACG 61.681 55.000 0.00 0.00 0.00 4.94
378 395 3.959975 CCCCACAAACCACGCACG 61.960 66.667 0.00 0.00 0.00 5.34
432 455 0.388520 GAAAATGCACGGCCCAAGAC 60.389 55.000 0.00 0.00 0.00 3.01
444 469 2.198406 GCCCAAGACGGAAAAACAAAC 58.802 47.619 0.00 0.00 36.56 2.93
497 526 0.249398 CACGGGAAGGTAGGAGGTTG 59.751 60.000 0.00 0.00 0.00 3.77
498 527 0.908180 ACGGGAAGGTAGGAGGTTGG 60.908 60.000 0.00 0.00 0.00 3.77
665 694 1.090052 CGATCCGCTTTTCTCACCCC 61.090 60.000 0.00 0.00 0.00 4.95
815 884 3.535962 CTCGCTCCTCCCCTGCTC 61.536 72.222 0.00 0.00 0.00 4.26
830 899 2.878429 CTCCAGAGGGACACGACG 59.122 66.667 0.00 0.00 38.64 5.12
831 900 2.675423 TCCAGAGGGACACGACGG 60.675 66.667 0.00 0.00 38.64 4.79
842 911 0.036388 ACACGACGGCAGAATCCAAT 60.036 50.000 0.00 0.00 0.00 3.16
854 923 4.637534 GCAGAATCCAATAACAGAGCAAGA 59.362 41.667 0.00 0.00 0.00 3.02
856 925 6.549952 CAGAATCCAATAACAGAGCAAGAAC 58.450 40.000 0.00 0.00 0.00 3.01
888 962 1.397692 CTCCGAAGAGACGAGGTGTAC 59.602 57.143 0.00 0.00 43.39 2.90
895 969 3.018149 AGAGACGAGGTGTACTTGGATC 58.982 50.000 0.00 0.00 34.66 3.36
913 987 0.320858 TCGCCGCTCCATTGTTGTTA 60.321 50.000 0.00 0.00 0.00 2.41
1164 1251 1.525077 GTTCACGCAGACCAACCCA 60.525 57.895 0.00 0.00 0.00 4.51
1314 1401 2.202453 GCCGAGTTCGAGGTCGTC 60.202 66.667 14.97 1.51 43.02 4.20
1782 1869 4.509737 GTCTCCTACGTGCCGGCC 62.510 72.222 26.77 14.70 0.00 6.13
1802 1889 3.499737 CAAGGGCGCCGACATCAC 61.500 66.667 22.54 4.09 0.00 3.06
1986 2073 2.034066 AGCCACATTGTCACCGGG 59.966 61.111 6.32 0.00 0.00 5.73
2076 2163 4.516195 GGCGGGCTCGACTTCTCC 62.516 72.222 12.03 0.00 42.13 3.71
2484 2575 3.569701 TGGGAATGCTCTTTCTTGTGTTC 59.430 43.478 0.00 0.00 0.00 3.18
2488 2579 5.335191 GGAATGCTCTTTCTTGTGTTCGATT 60.335 40.000 0.00 0.00 0.00 3.34
2590 2681 7.067494 GGAAAACTAAGGTATGCATCTCACATT 59.933 37.037 0.19 2.48 0.00 2.71
2605 2696 2.492881 TCACATTGATCCACATGGTTGC 59.507 45.455 0.00 0.00 36.34 4.17
2607 2698 3.695556 CACATTGATCCACATGGTTGCTA 59.304 43.478 0.00 0.00 36.34 3.49
2614 2705 7.926674 TGATCCACATGGTTGCTATATATTG 57.073 36.000 0.00 0.00 36.34 1.90
2616 2707 6.199557 TCCACATGGTTGCTATATATTGGT 57.800 37.500 0.00 0.00 36.34 3.67
2617 2708 7.323052 TCCACATGGTTGCTATATATTGGTA 57.677 36.000 0.00 0.00 36.34 3.25
2618 2709 7.394016 TCCACATGGTTGCTATATATTGGTAG 58.606 38.462 0.00 0.00 36.34 3.18
2619 2710 7.017155 TCCACATGGTTGCTATATATTGGTAGT 59.983 37.037 0.00 0.00 36.34 2.73
2620 2711 8.318412 CCACATGGTTGCTATATATTGGTAGTA 58.682 37.037 0.00 0.00 0.00 1.82
2621 2712 9.890629 CACATGGTTGCTATATATTGGTAGTAT 57.109 33.333 0.00 0.00 0.00 2.12
2667 2827 9.698309 AATAGACAAACTCATCGACATATTAGG 57.302 33.333 0.00 0.00 0.00 2.69
2668 2828 5.986135 AGACAAACTCATCGACATATTAGGC 59.014 40.000 0.00 0.00 0.00 3.93
2669 2829 5.918608 ACAAACTCATCGACATATTAGGCT 58.081 37.500 0.00 0.00 0.00 4.58
2671 2831 7.671302 ACAAACTCATCGACATATTAGGCTAT 58.329 34.615 0.00 0.00 0.00 2.97
2672 2832 8.150945 ACAAACTCATCGACATATTAGGCTATT 58.849 33.333 0.00 0.00 0.00 1.73
2673 2833 9.639601 CAAACTCATCGACATATTAGGCTATTA 57.360 33.333 0.00 0.00 0.00 0.98
2700 2860 5.010820 AGTTCAACTACTAGTTCCCTGTCAC 59.989 44.000 0.00 0.00 36.03 3.67
2712 2872 1.581934 CCTGTCACGCTGAAAACTGA 58.418 50.000 0.00 0.00 0.00 3.41
2725 2885 5.340667 GCTGAAAACTGAAACTGCTTATTCG 59.659 40.000 0.00 0.00 0.00 3.34
2734 2894 3.389687 ACTGCTTATTCGATTTGTGCG 57.610 42.857 0.00 0.00 0.00 5.34
2762 2922 9.108284 CAAACCTTCAACCATGTTTAAGAAAAT 57.892 29.630 3.18 0.00 30.29 1.82
2763 2923 9.679661 AAACCTTCAACCATGTTTAAGAAAATT 57.320 25.926 3.18 0.00 0.00 1.82
2764 2924 9.679661 AACCTTCAACCATGTTTAAGAAAATTT 57.320 25.926 3.18 0.00 0.00 1.82
2891 3058 5.066117 ACTCGCTCAGTTGATCGATTAACTA 59.934 40.000 28.70 18.17 41.06 2.24
2929 3096 4.223556 TCACCCACTGAACAGTTTGTTA 57.776 40.909 4.63 0.00 41.28 2.41
3054 3222 6.902948 CGTCGAAGTTCAATGAAAAGTAACAA 59.097 34.615 0.00 0.00 0.00 2.83
3109 3277 5.181622 ACTGACTGAACTTCTACTTACTCCG 59.818 44.000 0.00 0.00 0.00 4.63
3302 3471 7.721402 TCTTGTATACACAGGTTTGCAAAAAT 58.279 30.769 14.67 2.18 35.67 1.82
3339 3511 9.203421 AGTAATTACCTTTTAATTGTTTGCTGC 57.797 29.630 12.05 0.00 0.00 5.25
3398 3570 0.883833 CACCAGACAAGGGCAATGTC 59.116 55.000 12.41 12.41 45.94 3.06
3743 3915 4.019174 CCACTTTTGGCTATGAAGGTGAT 58.981 43.478 0.00 0.00 35.58 3.06
3794 3966 2.342650 CCCTCACCATGGGTTTGCG 61.343 63.158 18.09 0.00 39.82 4.85
4010 4182 1.201921 CGTCGAAGCTATGCAAACACC 60.202 52.381 0.00 0.00 0.00 4.16
4097 4269 1.751351 CTCATCGCCTCTTACCAGTCA 59.249 52.381 0.00 0.00 0.00 3.41
4430 4602 1.747355 GGCAGGACCATTGAAGATGTG 59.253 52.381 0.00 0.00 38.86 3.21
4529 4701 2.173569 AGGTGCCTTTGTTGAGAAGACT 59.826 45.455 0.00 0.00 0.00 3.24
4561 4733 5.355596 CAAAGGGCAAGTTGTTGATGTTAA 58.644 37.500 4.48 0.00 35.46 2.01
4564 4736 5.600696 AGGGCAAGTTGTTGATGTTAAAAG 58.399 37.500 4.48 0.00 35.46 2.27
4590 4762 2.490903 CTCAGTTCCATCCTTGGCTTTG 59.509 50.000 0.00 0.00 43.29 2.77
4625 4797 2.287829 GGTGGAGTACCTGTCCCAG 58.712 63.158 0.00 0.00 46.51 4.45
5167 5340 2.596904 TGAACTAATACCGCTCTGCC 57.403 50.000 0.00 0.00 0.00 4.85
5289 5462 4.614535 GCAGTAAAGATGGTTGCTGAACTG 60.615 45.833 7.13 0.00 42.02 3.16
5613 5786 3.907927 GTCGGAGATCTCACTGACG 57.092 57.895 23.85 16.83 40.67 4.35
5712 5885 1.795768 ACATAGCAGACACAACCACG 58.204 50.000 0.00 0.00 0.00 4.94
5922 6095 5.163622 CGAGGAAGCAAATACCACATTCATT 60.164 40.000 0.00 0.00 0.00 2.57
5958 6131 0.107459 GGAAGAGGCTGATGGACACC 60.107 60.000 0.00 0.00 0.00 4.16
5961 6134 0.326264 AGAGGCTGATGGACACCAAC 59.674 55.000 0.00 0.00 36.95 3.77
5979 6152 2.625790 CAACCCCAATTCGTTCAGGAAA 59.374 45.455 0.00 0.00 0.00 3.13
6150 6323 6.009589 TCCAGCATTTGACCAAGAAGAAATA 58.990 36.000 0.00 0.00 0.00 1.40
6151 6324 6.664816 TCCAGCATTTGACCAAGAAGAAATAT 59.335 34.615 0.00 0.00 0.00 1.28
6170 6343 2.175878 TTCTTCTGCCTTGCTGAGTC 57.824 50.000 0.00 0.00 37.75 3.36
6212 6385 9.632807 TGTGATTTATAAAAGTTGTAACATGCC 57.367 29.630 1.21 0.00 0.00 4.40
6386 6569 7.858052 AACATTTGAAGTTTAGCATTCTTCG 57.142 32.000 0.00 0.00 39.97 3.79
6413 6596 7.075121 TGTTATCTTTACATTGAACTGCAACG 58.925 34.615 0.00 0.00 39.78 4.10
6420 6603 1.464734 TTGAACTGCAACGGTCCAAA 58.535 45.000 0.00 0.00 0.00 3.28
6437 6620 6.447162 GGTCCAAAAGGTAAAGATTTCACAG 58.553 40.000 0.00 0.00 0.00 3.66
6442 6625 7.309194 CCAAAAGGTAAAGATTTCACAGTAGGG 60.309 40.741 0.00 0.00 0.00 3.53
6479 6662 5.316327 TGTGATCATGTGAGACTACTGAC 57.684 43.478 0.00 0.00 0.00 3.51
6487 6670 5.707242 TGTGAGACTACTGACAAGGTAAG 57.293 43.478 0.00 0.00 37.32 2.34
6489 6672 5.831525 TGTGAGACTACTGACAAGGTAAGAA 59.168 40.000 0.00 0.00 37.32 2.52
6542 6725 4.293368 AGGGAGGATGAAGAGGAACAAAAT 59.707 41.667 0.00 0.00 0.00 1.82
6588 6771 0.189822 TTCCCCTTCCCAACCCAAAG 59.810 55.000 0.00 0.00 0.00 2.77
6603 6786 9.245481 CCCAACCCAAAGTATACAATTTTAGTA 57.755 33.333 5.50 0.00 0.00 1.82
6672 6855 4.378774 CTGAAGCCATGACTCTGATTAGG 58.621 47.826 0.00 0.00 0.00 2.69
6714 6897 4.684724 TCTCAACCTTCATAGGGTACACT 58.315 43.478 1.68 1.68 40.45 3.55
6750 6933 5.711036 AGGAGTATATATCGCCGAGAAAGTT 59.289 40.000 0.00 0.00 0.00 2.66
6755 6938 8.521176 AGTATATATCGCCGAGAAAGTTGTATT 58.479 33.333 0.00 0.00 0.00 1.89
6798 6981 5.351948 AAGCAAGTTTTCCCAAAGCTTTA 57.648 34.783 12.25 0.00 39.48 1.85
6836 7019 3.119495 GGTACATCCATTGCAAGGAACAC 60.119 47.826 13.66 13.16 38.93 3.32
6876 7059 3.843619 TGTGATGGATGTCTAGGTTTCCA 59.156 43.478 9.82 9.82 42.18 3.53
6893 7076 6.206048 AGGTTTCCAATAACTTTAACGAGGTG 59.794 38.462 0.00 0.00 0.00 4.00
6904 7087 0.969894 AACGAGGTGGGAGAAGTCAG 59.030 55.000 0.00 0.00 0.00 3.51
6954 7137 6.710597 ATCTCACTGCTGCAATGAATTATT 57.289 33.333 15.07 0.00 0.00 1.40
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
49 50 3.244044 CCTTTCCTTGGAATTTTTGGCGA 60.244 43.478 2.65 0.00 0.00 5.54
51 52 2.813754 GCCTTTCCTTGGAATTTTTGGC 59.186 45.455 2.65 8.46 0.00 4.52
52 53 3.814842 GTGCCTTTCCTTGGAATTTTTGG 59.185 43.478 2.65 3.13 0.00 3.28
53 54 4.450053 TGTGCCTTTCCTTGGAATTTTTG 58.550 39.130 2.65 0.00 0.00 2.44
59 71 1.408969 GGTTGTGCCTTTCCTTGGAA 58.591 50.000 0.00 0.00 0.00 3.53
135 147 3.583882 ATGGTGGCCAGGGGTTTCG 62.584 63.158 5.11 0.00 36.75 3.46
148 160 3.138798 GGCTGGAGCTGCATGGTG 61.139 66.667 8.91 0.00 41.70 4.17
165 177 2.271497 CCTTCCCTGCAGCTGGAG 59.729 66.667 26.95 26.95 30.91 3.86
166 178 4.039092 GCCTTCCCTGCAGCTGGA 62.039 66.667 19.69 12.70 0.00 3.86
168 180 2.282674 TTGCCTTCCCTGCAGCTG 60.283 61.111 10.11 10.11 40.35 4.24
169 181 2.282745 GTTGCCTTCCCTGCAGCT 60.283 61.111 8.66 0.00 40.35 4.24
171 183 0.529378 GATTGTTGCCTTCCCTGCAG 59.471 55.000 6.78 6.78 40.35 4.41
172 184 0.899717 GGATTGTTGCCTTCCCTGCA 60.900 55.000 0.00 0.00 36.84 4.41
173 185 1.607801 GGGATTGTTGCCTTCCCTGC 61.608 60.000 0.00 0.00 44.86 4.85
174 186 2.583472 GGGATTGTTGCCTTCCCTG 58.417 57.895 0.00 0.00 44.86 4.45
177 189 1.482182 GGAATGGGATTGTTGCCTTCC 59.518 52.381 0.00 0.00 35.31 3.46
178 190 1.482182 GGGAATGGGATTGTTGCCTTC 59.518 52.381 0.00 0.00 33.54 3.46
179 191 1.203288 TGGGAATGGGATTGTTGCCTT 60.203 47.619 0.00 0.00 36.83 4.35
180 192 0.413037 TGGGAATGGGATTGTTGCCT 59.587 50.000 0.00 0.00 36.83 4.75
181 193 1.499368 ATGGGAATGGGATTGTTGCC 58.501 50.000 0.00 0.00 36.48 4.52
182 194 2.158914 GGAATGGGAATGGGATTGTTGC 60.159 50.000 0.00 0.00 0.00 4.17
183 195 2.435437 GGGAATGGGAATGGGATTGTTG 59.565 50.000 0.00 0.00 0.00 3.33
184 196 2.045605 TGGGAATGGGAATGGGATTGTT 59.954 45.455 0.00 0.00 0.00 2.83
185 197 1.650700 TGGGAATGGGAATGGGATTGT 59.349 47.619 0.00 0.00 0.00 2.71
186 198 2.041701 GTGGGAATGGGAATGGGATTG 58.958 52.381 0.00 0.00 0.00 2.67
187 199 1.411501 CGTGGGAATGGGAATGGGATT 60.412 52.381 0.00 0.00 0.00 3.01
188 200 0.185901 CGTGGGAATGGGAATGGGAT 59.814 55.000 0.00 0.00 0.00 3.85
189 201 1.612513 CGTGGGAATGGGAATGGGA 59.387 57.895 0.00 0.00 0.00 4.37
190 202 1.455587 CCGTGGGAATGGGAATGGG 60.456 63.158 0.00 0.00 0.00 4.00
191 203 2.127232 GCCGTGGGAATGGGAATGG 61.127 63.158 0.00 0.00 0.00 3.16
192 204 1.379710 TGCCGTGGGAATGGGAATG 60.380 57.895 0.00 0.00 0.00 2.67
193 205 1.076777 CTGCCGTGGGAATGGGAAT 60.077 57.895 0.00 0.00 0.00 3.01
194 206 1.784301 TTCTGCCGTGGGAATGGGAA 61.784 55.000 0.00 0.00 0.00 3.97
224 236 2.561037 CGTGGGGACAAAGGTTGCC 61.561 63.158 0.00 0.00 46.06 4.52
259 271 1.153745 CCGAACGAAGCTCTCTGGG 60.154 63.158 0.00 0.00 0.00 4.45
266 278 1.218316 GGATGGTCCGAACGAAGCT 59.782 57.895 0.00 0.00 0.00 3.74
267 279 0.462047 ATGGATGGTCCGAACGAAGC 60.462 55.000 0.00 0.00 40.17 3.86
268 280 1.571919 GATGGATGGTCCGAACGAAG 58.428 55.000 0.00 0.00 40.17 3.79
269 281 0.179121 CGATGGATGGTCCGAACGAA 60.179 55.000 0.00 0.00 40.17 3.85
270 282 1.435925 CGATGGATGGTCCGAACGA 59.564 57.895 0.00 0.00 40.17 3.85
271 283 2.237751 GCGATGGATGGTCCGAACG 61.238 63.158 0.00 0.00 40.17 3.95
272 284 1.887707 GGCGATGGATGGTCCGAAC 60.888 63.158 0.00 0.00 40.17 3.95
304 316 4.086547 GTTTGCTGGGCATGGGGC 62.087 66.667 0.00 0.00 38.76 5.80
310 322 1.687146 TTTGGTGGTTTGCTGGGCA 60.687 52.632 0.00 0.00 36.47 5.36
388 405 3.488090 GCTACAGTTCCGCGGTGC 61.488 66.667 27.15 18.74 0.00 5.01
390 407 1.153628 GATGCTACAGTTCCGCGGT 60.154 57.895 27.15 7.91 0.00 5.68
391 408 0.739462 TTGATGCTACAGTTCCGCGG 60.739 55.000 22.12 22.12 0.00 6.46
392 409 1.075542 TTTGATGCTACAGTTCCGCG 58.924 50.000 0.00 0.00 0.00 6.46
393 410 1.201921 CGTTTGATGCTACAGTTCCGC 60.202 52.381 0.00 0.00 0.00 5.54
394 411 2.333926 TCGTTTGATGCTACAGTTCCG 58.666 47.619 0.00 0.00 0.00 4.30
395 412 4.742438 TTTCGTTTGATGCTACAGTTCC 57.258 40.909 0.00 0.00 0.00 3.62
396 413 5.059710 GCATTTTCGTTTGATGCTACAGTTC 59.940 40.000 0.00 0.00 42.12 3.01
398 415 4.023279 TGCATTTTCGTTTGATGCTACAGT 60.023 37.500 8.73 0.00 44.84 3.55
400 417 4.225984 GTGCATTTTCGTTTGATGCTACA 58.774 39.130 8.73 0.00 44.84 2.74
401 418 3.297979 CGTGCATTTTCGTTTGATGCTAC 59.702 43.478 8.73 5.11 44.84 3.58
402 419 3.487536 CGTGCATTTTCGTTTGATGCTA 58.512 40.909 8.73 0.00 44.84 3.49
432 455 3.955771 TCTCCTTCGTTTGTTTTTCCG 57.044 42.857 0.00 0.00 0.00 4.30
444 469 1.278238 CGGATTCCGTTTCTCCTTCG 58.722 55.000 17.08 0.00 42.73 3.79
815 884 4.436998 GCCGTCGTGTCCCTCTGG 62.437 72.222 0.00 0.00 0.00 3.86
830 899 3.282021 TGCTCTGTTATTGGATTCTGCC 58.718 45.455 0.00 0.00 0.00 4.85
831 900 4.637534 TCTTGCTCTGTTATTGGATTCTGC 59.362 41.667 0.00 0.00 0.00 4.26
842 911 2.352814 GCTCTCGGTTCTTGCTCTGTTA 60.353 50.000 0.00 0.00 0.00 2.41
854 923 3.003763 GGAGGGTGGCTCTCGGTT 61.004 66.667 0.00 0.00 32.34 4.44
895 969 0.519519 TTAACAACAATGGAGCGGCG 59.480 50.000 0.51 0.51 0.00 6.46
913 987 5.045140 ACCACTGGCACCTAGTATATTGTTT 60.045 40.000 0.00 0.00 0.00 2.83
919 993 4.531357 ACTACCACTGGCACCTAGTATA 57.469 45.455 0.00 0.00 0.00 1.47
1263 1350 2.097160 GCGTTGAGCTGCATCACG 59.903 61.111 1.02 7.75 44.04 4.35
1311 1398 3.109612 CTCGACCAGGTAGCCGACG 62.110 68.421 0.00 0.00 0.00 5.12
1314 1401 2.439701 TCCTCGACCAGGTAGCCG 60.440 66.667 0.00 0.00 43.95 5.52
1731 1818 1.344763 AGGAAGTTCTGGAGGTTGTCG 59.655 52.381 2.25 0.00 0.00 4.35
1782 1869 4.473520 ATGTCGGCGCCCTTGAGG 62.474 66.667 23.46 5.48 39.47 3.86
1986 2073 3.741476 ACGTAGTGGCCGTCGTCC 61.741 66.667 0.00 0.00 42.51 4.79
2418 2505 2.283145 AGCAAATCAGAGCAACAGGT 57.717 45.000 0.00 0.00 0.00 4.00
2484 2575 0.933097 CATGCGACTTCCCTGAATCG 59.067 55.000 0.00 0.00 37.63 3.34
2488 2579 0.035152 AATGCATGCGACTTCCCTGA 60.035 50.000 14.09 0.00 0.00 3.86
2541 2632 2.996249 TGAGTTCTGCCCATCTGATC 57.004 50.000 0.00 0.00 0.00 2.92
2590 2681 6.885918 CCAATATATAGCAACCATGTGGATCA 59.114 38.462 5.96 0.00 38.94 2.92
2632 2789 9.132923 TCGATGAGTTTGTCTATTTATACCTCT 57.867 33.333 0.00 0.00 0.00 3.69
2647 2807 8.539770 AATAGCCTAATATGTCGATGAGTTTG 57.460 34.615 0.00 0.00 0.00 2.93
2671 2831 9.317827 ACAGGGAACTAGTAGTTGAACTAATAA 57.682 33.333 20.21 0.00 38.80 1.40
2672 2832 8.890410 ACAGGGAACTAGTAGTTGAACTAATA 57.110 34.615 20.21 9.38 38.80 0.98
2673 2833 7.453752 TGACAGGGAACTAGTAGTTGAACTAAT 59.546 37.037 20.21 10.31 38.80 1.73
2674 2834 6.779049 TGACAGGGAACTAGTAGTTGAACTAA 59.221 38.462 20.21 0.00 38.80 2.24
2675 2835 6.208204 GTGACAGGGAACTAGTAGTTGAACTA 59.792 42.308 20.21 0.00 38.80 2.24
2676 2836 5.010820 GTGACAGGGAACTAGTAGTTGAACT 59.989 44.000 20.21 11.61 38.80 3.01
2677 2837 5.228665 GTGACAGGGAACTAGTAGTTGAAC 58.771 45.833 20.21 9.79 38.80 3.18
2678 2838 4.022589 CGTGACAGGGAACTAGTAGTTGAA 60.023 45.833 20.21 0.00 38.80 2.69
2679 2839 3.504906 CGTGACAGGGAACTAGTAGTTGA 59.495 47.826 20.21 0.00 38.80 3.18
2680 2840 3.834610 CGTGACAGGGAACTAGTAGTTG 58.165 50.000 20.21 9.04 38.80 3.16
2681 2841 2.230750 GCGTGACAGGGAACTAGTAGTT 59.769 50.000 15.48 15.48 41.95 2.24
2692 2852 0.588252 CAGTTTTCAGCGTGACAGGG 59.412 55.000 0.00 0.00 0.00 4.45
2693 2853 1.581934 TCAGTTTTCAGCGTGACAGG 58.418 50.000 0.00 0.00 0.00 4.00
2700 2860 2.763249 AGCAGTTTCAGTTTTCAGCG 57.237 45.000 0.00 0.00 0.00 5.18
2712 2872 4.158384 CGCACAAATCGAATAAGCAGTTT 58.842 39.130 0.00 0.00 0.00 2.66
2734 2894 6.801575 TCTTAAACATGGTTGAAGGTTTGAC 58.198 36.000 6.16 0.00 35.33 3.18
2780 2942 6.382087 AGGGGACTCAAATTTTCTTAAACCT 58.618 36.000 0.00 0.00 32.90 3.50
2840 3007 8.345565 AGTTTCAGTTTTTAGCATGACAGTTAG 58.654 33.333 0.00 0.00 0.00 2.34
2891 3058 3.701040 GGGTGAATGGTGCAAGATACAAT 59.299 43.478 0.00 0.00 0.00 2.71
2929 3096 3.006537 AGGCTTACGGCGTTGATATACAT 59.993 43.478 21.24 0.00 42.94 2.29
3054 3222 5.373222 TGTTAGCTTAACCTTGTGATGTGT 58.627 37.500 0.00 0.00 37.88 3.72
3146 3315 8.485976 AGTTTAAGATTCTGCAGTGAAGTATC 57.514 34.615 14.67 9.26 0.00 2.24
3240 3409 6.889177 TGTATAATGTTTTCAGCCATGAGGAA 59.111 34.615 0.00 0.00 36.61 3.36
3273 3442 4.517453 GCAAACCTGTGTATACAAGAACCA 59.483 41.667 7.25 0.00 36.14 3.67
3285 3454 5.940470 TGGTTTTATTTTTGCAAACCTGTGT 59.060 32.000 12.39 0.00 46.62 3.72
3328 3500 2.241160 TGTCCATCTGCAGCAAACAAT 58.759 42.857 9.47 0.00 0.00 2.71
3336 3508 3.373439 GCTAGTTTCTTGTCCATCTGCAG 59.627 47.826 7.63 7.63 0.00 4.41
3339 3511 3.942829 TGGCTAGTTTCTTGTCCATCTG 58.057 45.455 0.00 0.00 0.00 2.90
3398 3570 2.124983 AGGTATGCTGCAGTGCCG 60.125 61.111 16.64 7.53 0.00 5.69
3743 3915 0.036732 AGAACAGAAGCCGCATTGGA 59.963 50.000 0.00 0.00 42.00 3.53
3794 3966 6.426937 TCTTCTCAACAAAAGTGTAGTATGCC 59.573 38.462 0.00 0.00 36.80 4.40
4010 4182 2.236146 TGGTGGTGTCAGGTAGCTTATG 59.764 50.000 0.00 0.00 0.00 1.90
4097 4269 4.003788 CGGCCCGTGTCCTTGAGT 62.004 66.667 0.00 0.00 0.00 3.41
4316 4488 2.280797 GTGGCCACAGCTTCGACA 60.281 61.111 31.23 0.00 39.73 4.35
4430 4602 0.175073 CCTTGTCGCTACCCCTGTAC 59.825 60.000 0.00 0.00 0.00 2.90
4529 4701 2.383855 ACTTGCCCTTTGCTGTTTGTA 58.616 42.857 0.00 0.00 42.00 2.41
4561 4733 3.837355 AGGATGGAACTGAGTTTGCTTT 58.163 40.909 0.00 0.00 0.00 3.51
4564 4736 3.565905 CAAGGATGGAACTGAGTTTGC 57.434 47.619 0.00 0.00 0.00 3.68
4590 4762 0.980231 ACCCATGGCTCTGAGAGACC 60.980 60.000 13.73 13.71 36.76 3.85
4625 4797 1.026718 CCGCCCTGATGAACTTGGTC 61.027 60.000 0.00 0.00 0.00 4.02
5289 5462 4.205587 AGTTCATCTCAATTGGCTCATCC 58.794 43.478 5.42 0.00 0.00 3.51
5496 5669 1.354040 CTGGAGCATCACTGTCGAAC 58.646 55.000 0.00 0.00 36.25 3.95
5595 5768 0.378962 CCGTCAGTGAGATCTCCGAC 59.621 60.000 20.03 19.78 0.00 4.79
5613 5786 1.476891 TCGAAGTAGTGGCTGACATCC 59.523 52.381 0.00 0.00 0.00 3.51
5922 6095 5.363292 CCTCTTCCTCATCTCTTCATCTTCA 59.637 44.000 0.00 0.00 0.00 3.02
5958 6131 1.904287 TCCTGAACGAATTGGGGTTG 58.096 50.000 0.00 0.00 0.00 3.77
5961 6134 2.228822 CAGTTTCCTGAACGAATTGGGG 59.771 50.000 0.00 0.00 43.20 4.96
5979 6152 4.646572 CTTCTAGGAAGGTTTGAAGCAGT 58.353 43.478 0.00 0.00 0.00 4.40
6012 6185 0.755686 CTGATGTCTCCCAGTAGCCC 59.244 60.000 0.00 0.00 0.00 5.19
6150 6323 2.709213 GACTCAGCAAGGCAGAAGAAT 58.291 47.619 0.00 0.00 30.88 2.40
6151 6324 1.606480 CGACTCAGCAAGGCAGAAGAA 60.606 52.381 0.00 0.00 29.11 2.52
6212 6385 6.149474 CACCCTCTTTGTTAAAGGTCTGTATG 59.851 42.308 1.88 0.00 39.01 2.39
6360 6543 8.840867 CGAAGAATGCTAAACTTCAAATGTTAC 58.159 33.333 0.00 0.00 39.64 2.50
6386 6569 8.690840 GTTGCAGTTCAATGTAAAGATAACAAC 58.309 33.333 0.00 0.00 36.99 3.32
6413 6596 6.040504 ACTGTGAAATCTTTACCTTTTGGACC 59.959 38.462 0.00 0.00 44.07 4.46
6420 6603 6.697641 TCCCTACTGTGAAATCTTTACCTT 57.302 37.500 0.00 0.00 0.00 3.50
6437 6620 5.708230 TCACATTAACACCATTGTTCCCTAC 59.292 40.000 0.00 0.00 42.67 3.18
6442 6625 7.274033 CACATGATCACATTAACACCATTGTTC 59.726 37.037 0.00 0.00 39.55 3.18
6548 6731 7.300320 GGGAAACAAAACTACGATCGTTAAAT 58.700 34.615 27.88 8.25 0.00 1.40
6714 6897 4.694760 ATATACTCCTGAAGCACATGCA 57.305 40.909 6.64 0.00 45.16 3.96
6750 6933 4.320861 CGGACAAACTTGCCATCAAATACA 60.321 41.667 0.00 0.00 0.00 2.29
6755 6938 1.974265 TCGGACAAACTTGCCATCAA 58.026 45.000 0.00 0.00 0.00 2.57
6798 6981 3.482436 TGTACCGAGCAATTTTGAACCT 58.518 40.909 0.00 0.00 0.00 3.50
6836 7019 0.396139 CACCATTGGAGTCCCCATGG 60.396 60.000 26.11 26.11 46.10 3.66
6876 7059 5.750352 TCTCCCACCTCGTTAAAGTTATT 57.250 39.130 0.00 0.00 0.00 1.40
6893 7076 0.108756 GTACACCGCTGACTTCTCCC 60.109 60.000 0.00 0.00 0.00 4.30
6954 7137 8.635765 ACAAAAGAAGCATAGGTGAAGATAAA 57.364 30.769 0.00 0.00 0.00 1.40


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

AutoCloner maintained by Alex Coulton.