Multiple sequence alignment - TraesCS5A01G120800

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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 TraesCS5A01G120800 chr5A 100.000 2405 0 0 1 2405 258777172 258774768 0.000000e+00 4442.0
1 TraesCS5A01G120800 chr5A 93.705 826 50 2 1580 2404 250573752 250572928 0.000000e+00 1236.0
2 TraesCS5A01G120800 chr5A 93.470 827 51 3 1581 2405 285522897 285522072 0.000000e+00 1225.0
3 TraesCS5A01G120800 chr5A 87.692 130 12 2 1 130 98385681 98385806 5.360000e-32 148.0
4 TraesCS5A01G120800 chr5D 93.876 1584 90 5 1 1580 317669462 317667882 0.000000e+00 2381.0
5 TraesCS5A01G120800 chr5D 93.885 278 16 1 431 708 152540584 152540860 3.700000e-113 418.0
6 TraesCS5A01G120800 chr4A 93.947 826 48 2 1581 2405 278049921 278050745 0.000000e+00 1247.0
7 TraesCS5A01G120800 chr4A 93.576 825 51 2 1581 2404 278169797 278170620 0.000000e+00 1229.0
8 TraesCS5A01G120800 chr4A 86.154 130 14 2 1 130 565475824 565475949 1.160000e-28 137.0
9 TraesCS5A01G120800 chr6D 93.841 828 49 2 1580 2405 221250236 221249409 0.000000e+00 1245.0
10 TraesCS5A01G120800 chr1D 93.445 839 52 3 1568 2404 280627035 280626198 0.000000e+00 1242.0
11 TraesCS5A01G120800 chr1D 93.042 618 39 2 704 1317 189345188 189344571 0.000000e+00 900.0
12 TraesCS5A01G120800 chr1D 91.667 528 39 3 704 1228 263519109 263519634 0.000000e+00 726.0
13 TraesCS5A01G120800 chr1D 92.218 257 19 1 1324 1580 189344594 189344339 1.760000e-96 363.0
14 TraesCS5A01G120800 chr1D 91.732 254 20 1 1324 1577 263527988 263528240 3.800000e-93 351.0
15 TraesCS5A01G120800 chr3A 93.591 827 51 2 1581 2405 303447481 303446655 0.000000e+00 1232.0
16 TraesCS5A01G120800 chr6A 93.455 825 54 0 1581 2405 259734639 259735463 0.000000e+00 1225.0
17 TraesCS5A01G120800 chr6A 93.439 823 54 0 1583 2405 265324900 265324078 0.000000e+00 1221.0
18 TraesCS5A01G120800 chr6A 89.535 86 5 2 1 86 279829181 279829262 3.270000e-19 106.0
19 TraesCS5A01G120800 chrUn 90.249 882 79 5 704 1580 67177127 67176248 0.000000e+00 1146.0
20 TraesCS5A01G120800 chrUn 87.324 142 17 1 138 279 117169050 117169190 6.880000e-36 161.0
21 TraesCS5A01G120800 chr2B 91.956 547 38 4 166 708 355948152 355948696 0.000000e+00 761.0
22 TraesCS5A01G120800 chr2B 90.450 555 47 3 704 1255 612851930 612851379 0.000000e+00 726.0
23 TraesCS5A01G120800 chr5B 91.743 545 39 4 169 708 51556079 51555536 0.000000e+00 752.0
24 TraesCS5A01G120800 chr5B 90.631 555 49 2 704 1255 496644379 496644933 0.000000e+00 734.0
25 TraesCS5A01G120800 chr2A 90.119 587 39 4 704 1287 377610193 377610763 0.000000e+00 745.0
26 TraesCS5A01G120800 chr1B 90.991 555 47 2 704 1255 82615073 82615627 0.000000e+00 745.0
27 TraesCS5A01G120800 chr1B 85.870 92 5 6 1412 1497 330729518 330729429 9.160000e-15 91.6
28 TraesCS5A01G120800 chr3B 91.058 548 43 4 166 708 446516110 446516656 0.000000e+00 736.0
29 TraesCS5A01G120800 chr3B 87.943 141 16 1 138 278 327793723 327793862 5.320000e-37 165.0
30 TraesCS5A01G120800 chr3B 82.051 78 10 3 1377 1453 80771570 80771496 2.000000e-06 63.9
31 TraesCS5A01G120800 chr1A 89.560 546 44 9 169 708 477502031 477501493 0.000000e+00 680.0
32 TraesCS5A01G120800 chr1A 89.385 537 45 8 177 708 531810379 531810908 0.000000e+00 665.0
33 TraesCS5A01G120800 chr1A 89.231 130 13 1 1 130 531810244 531810372 6.880000e-36 161.0
34 TraesCS5A01G120800 chr4B 95.105 286 14 0 704 989 340783180 340783465 3.650000e-123 451.0
35 TraesCS5A01G120800 chr6B 87.702 309 31 7 401 706 223038401 223038097 1.060000e-93 353.0
36 TraesCS5A01G120800 chr6B 85.915 142 19 1 138 279 311475499 311475639 1.490000e-32 150.0
37 TraesCS5A01G120800 chr6B 85.870 92 5 6 1412 1497 531100242 531100331 9.160000e-15 91.6
38 TraesCS5A01G120800 chr6B 83.117 77 11 1 1377 1453 44466608 44466534 4.290000e-08 69.4
39 TraesCS5A01G120800 chr7A 87.500 312 30 8 400 706 408610094 408609787 3.800000e-93 351.0
40 TraesCS5A01G120800 chr7B 84.615 78 8 3 1377 1453 478082379 478082305 9.220000e-10 75.0


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 TraesCS5A01G120800 chr5A 258774768 258777172 2404 True 4442.0 4442 100.000 1 2405 1 chr5A.!!$R2 2404
1 TraesCS5A01G120800 chr5A 250572928 250573752 824 True 1236.0 1236 93.705 1580 2404 1 chr5A.!!$R1 824
2 TraesCS5A01G120800 chr5A 285522072 285522897 825 True 1225.0 1225 93.470 1581 2405 1 chr5A.!!$R3 824
3 TraesCS5A01G120800 chr5D 317667882 317669462 1580 True 2381.0 2381 93.876 1 1580 1 chr5D.!!$R1 1579
4 TraesCS5A01G120800 chr4A 278049921 278050745 824 False 1247.0 1247 93.947 1581 2405 1 chr4A.!!$F1 824
5 TraesCS5A01G120800 chr4A 278169797 278170620 823 False 1229.0 1229 93.576 1581 2404 1 chr4A.!!$F2 823
6 TraesCS5A01G120800 chr6D 221249409 221250236 827 True 1245.0 1245 93.841 1580 2405 1 chr6D.!!$R1 825
7 TraesCS5A01G120800 chr1D 280626198 280627035 837 True 1242.0 1242 93.445 1568 2404 1 chr1D.!!$R1 836
8 TraesCS5A01G120800 chr1D 263519109 263519634 525 False 726.0 726 91.667 704 1228 1 chr1D.!!$F1 524
9 TraesCS5A01G120800 chr1D 189344339 189345188 849 True 631.5 900 92.630 704 1580 2 chr1D.!!$R2 876
10 TraesCS5A01G120800 chr3A 303446655 303447481 826 True 1232.0 1232 93.591 1581 2405 1 chr3A.!!$R1 824
11 TraesCS5A01G120800 chr6A 259734639 259735463 824 False 1225.0 1225 93.455 1581 2405 1 chr6A.!!$F1 824
12 TraesCS5A01G120800 chr6A 265324078 265324900 822 True 1221.0 1221 93.439 1583 2405 1 chr6A.!!$R1 822
13 TraesCS5A01G120800 chrUn 67176248 67177127 879 True 1146.0 1146 90.249 704 1580 1 chrUn.!!$R1 876
14 TraesCS5A01G120800 chr2B 355948152 355948696 544 False 761.0 761 91.956 166 708 1 chr2B.!!$F1 542
15 TraesCS5A01G120800 chr2B 612851379 612851930 551 True 726.0 726 90.450 704 1255 1 chr2B.!!$R1 551
16 TraesCS5A01G120800 chr5B 51555536 51556079 543 True 752.0 752 91.743 169 708 1 chr5B.!!$R1 539
17 TraesCS5A01G120800 chr5B 496644379 496644933 554 False 734.0 734 90.631 704 1255 1 chr5B.!!$F1 551
18 TraesCS5A01G120800 chr2A 377610193 377610763 570 False 745.0 745 90.119 704 1287 1 chr2A.!!$F1 583
19 TraesCS5A01G120800 chr1B 82615073 82615627 554 False 745.0 745 90.991 704 1255 1 chr1B.!!$F1 551
20 TraesCS5A01G120800 chr3B 446516110 446516656 546 False 736.0 736 91.058 166 708 1 chr3B.!!$F2 542
21 TraesCS5A01G120800 chr1A 477501493 477502031 538 True 680.0 680 89.560 169 708 1 chr1A.!!$R1 539
22 TraesCS5A01G120800 chr1A 531810244 531810908 664 False 413.0 665 89.308 1 708 2 chr1A.!!$F1 707

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
32 33 0.539438 TTTCAATTGCAGGCGGAGGT 60.539 50.000 0.0 0.0 0.0 3.85 F
734 788 1.131126 GTGGATTTGTGGTGCTCATCG 59.869 52.381 0.0 0.0 0.0 3.84 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1065 1136 0.104855 ACGCTGACTCTTCACAAGCA 59.895 50.0 0.0 0.0 0.0 3.91 R
1653 1730 0.587768 TCTTCGCACGTTCGTAGTCA 59.412 50.0 13.1 0.0 0.0 3.41 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
32 33 0.539438 TTTCAATTGCAGGCGGAGGT 60.539 50.000 0.00 0.00 0.00 3.85
33 34 1.243342 TTCAATTGCAGGCGGAGGTG 61.243 55.000 0.00 0.00 0.00 4.00
41 42 2.044946 GGCGGAGGTGGCAAAGAT 60.045 61.111 0.00 0.00 0.00 2.40
51 52 3.135530 AGGTGGCAAAGATAGAGCTAAGG 59.864 47.826 0.00 0.00 0.00 2.69
78 79 9.823647 GATCCAGTAGAGTTTATTGATTGAAGA 57.176 33.333 0.00 0.00 0.00 2.87
116 117 9.076781 TCTATGATTTTCAGTTCACATTTTCCA 57.923 29.630 0.00 0.00 0.00 3.53
124 125 8.961294 TTCAGTTCACATTTTCCATGATTTTT 57.039 26.923 0.00 0.00 0.00 1.94
133 134 9.829507 ACATTTTCCATGATTTTTAGTTCAACA 57.170 25.926 0.00 0.00 0.00 3.33
135 136 8.885494 TTTTCCATGATTTTTAGTTCAACAGG 57.115 30.769 0.00 0.00 0.00 4.00
136 137 6.024552 TCCATGATTTTTAGTTCAACAGGC 57.975 37.500 0.00 0.00 0.00 4.85
137 138 5.774690 TCCATGATTTTTAGTTCAACAGGCT 59.225 36.000 0.00 0.00 0.00 4.58
138 139 6.267471 TCCATGATTTTTAGTTCAACAGGCTT 59.733 34.615 0.00 0.00 0.00 4.35
139 140 6.587608 CCATGATTTTTAGTTCAACAGGCTTC 59.412 38.462 0.00 0.00 0.00 3.86
140 141 6.084326 TGATTTTTAGTTCAACAGGCTTCC 57.916 37.500 0.00 0.00 0.00 3.46
141 142 5.833131 TGATTTTTAGTTCAACAGGCTTCCT 59.167 36.000 0.00 0.00 0.00 3.36
142 143 7.001674 TGATTTTTAGTTCAACAGGCTTCCTA 58.998 34.615 0.00 0.00 29.64 2.94
143 144 7.669722 TGATTTTTAGTTCAACAGGCTTCCTAT 59.330 33.333 0.00 0.00 29.64 2.57
144 145 7.833285 TTTTTAGTTCAACAGGCTTCCTATT 57.167 32.000 0.00 0.00 29.64 1.73
145 146 7.833285 TTTTAGTTCAACAGGCTTCCTATTT 57.167 32.000 0.00 0.00 29.64 1.40
146 147 7.448748 TTTAGTTCAACAGGCTTCCTATTTC 57.551 36.000 0.00 0.00 29.64 2.17
147 148 4.985538 AGTTCAACAGGCTTCCTATTTCA 58.014 39.130 0.00 0.00 29.64 2.69
148 149 5.574188 AGTTCAACAGGCTTCCTATTTCAT 58.426 37.500 0.00 0.00 29.64 2.57
149 150 5.649831 AGTTCAACAGGCTTCCTATTTCATC 59.350 40.000 0.00 0.00 29.64 2.92
150 151 5.178096 TCAACAGGCTTCCTATTTCATCA 57.822 39.130 0.00 0.00 29.64 3.07
151 152 4.943705 TCAACAGGCTTCCTATTTCATCAC 59.056 41.667 0.00 0.00 29.64 3.06
152 153 3.891049 ACAGGCTTCCTATTTCATCACC 58.109 45.455 0.00 0.00 29.64 4.02
153 154 3.266772 ACAGGCTTCCTATTTCATCACCA 59.733 43.478 0.00 0.00 29.64 4.17
154 155 3.881688 CAGGCTTCCTATTTCATCACCAG 59.118 47.826 0.00 0.00 29.64 4.00
155 156 3.117738 AGGCTTCCTATTTCATCACCAGG 60.118 47.826 0.00 0.00 28.47 4.45
156 157 3.217626 GCTTCCTATTTCATCACCAGGG 58.782 50.000 0.00 0.00 0.00 4.45
157 158 3.372025 GCTTCCTATTTCATCACCAGGGT 60.372 47.826 0.00 0.00 0.00 4.34
158 159 4.141482 GCTTCCTATTTCATCACCAGGGTA 60.141 45.833 0.00 0.00 0.00 3.69
159 160 5.631481 GCTTCCTATTTCATCACCAGGGTAA 60.631 44.000 0.00 0.00 0.00 2.85
160 161 5.367945 TCCTATTTCATCACCAGGGTAAC 57.632 43.478 0.00 0.00 0.00 2.50
161 162 5.036916 TCCTATTTCATCACCAGGGTAACT 58.963 41.667 0.00 0.00 0.00 2.24
162 163 6.206787 TCCTATTTCATCACCAGGGTAACTA 58.793 40.000 0.00 0.00 0.00 2.24
163 164 6.674861 TCCTATTTCATCACCAGGGTAACTAA 59.325 38.462 0.00 0.00 0.00 2.24
164 165 7.183112 TCCTATTTCATCACCAGGGTAACTAAA 59.817 37.037 0.00 0.00 0.00 1.85
165 166 7.832187 CCTATTTCATCACCAGGGTAACTAAAA 59.168 37.037 0.00 0.00 0.00 1.52
166 167 7.703058 ATTTCATCACCAGGGTAACTAAAAG 57.297 36.000 0.00 0.00 0.00 2.27
167 168 4.585879 TCATCACCAGGGTAACTAAAAGC 58.414 43.478 0.00 0.00 0.00 3.51
173 214 1.626825 AGGGTAACTAAAAGCTCCGCA 59.373 47.619 0.00 0.00 0.00 5.69
236 277 5.549742 AGATGCAAGGAACAAAATTTCCA 57.450 34.783 4.76 0.00 46.76 3.53
247 288 6.540551 GGAACAAAATTTCCAGCCAACTTTTA 59.459 34.615 0.00 0.00 44.14 1.52
321 363 5.932883 TGTACACAGTAACAAGAAACACACA 59.067 36.000 0.00 0.00 0.00 3.72
330 375 8.250332 AGTAACAAGAAACACACAAACATGATT 58.750 29.630 0.00 0.00 0.00 2.57
516 563 4.914983 TGAAGAGATGAAGCTCAAACCAT 58.085 39.130 0.00 0.00 37.37 3.55
526 573 5.811613 TGAAGCTCAAACCATGTTCAAAAAG 59.188 36.000 0.00 0.00 0.00 2.27
542 589 9.528018 TGTTCAAAAAGTGTTTCCTTCATAATC 57.472 29.630 0.00 0.00 0.00 1.75
632 686 9.337091 GTGTGTATTGTAATTGTAATTGTGGTC 57.663 33.333 0.27 0.00 0.00 4.02
702 756 8.299570 CAAAACATTCAGTAATTCTGTAAGCCT 58.700 33.333 5.26 0.00 43.97 4.58
721 775 5.025453 AGCCTAAAATCACATGGTGGATTT 58.975 37.500 13.32 13.32 33.87 2.17
730 784 1.203052 CATGGTGGATTTGTGGTGCTC 59.797 52.381 0.00 0.00 0.00 4.26
734 788 1.131126 GTGGATTTGTGGTGCTCATCG 59.869 52.381 0.00 0.00 0.00 3.84
860 916 4.399303 ACTGTGCCAAGACCAAATATTAGC 59.601 41.667 0.00 0.00 0.00 3.09
884 940 2.921221 TCCTTCTTCCACTTCCTCCAT 58.079 47.619 0.00 0.00 0.00 3.41
925 981 3.953612 AGATTCTGTGTTTCCACTTGCAA 59.046 39.130 0.00 0.00 42.34 4.08
936 992 5.843673 TTCCACTTGCAAAACAACTCATA 57.156 34.783 0.00 0.00 33.68 2.15
1001 1057 7.944729 ACAAAGCATAGTACATCAGGAAAAT 57.055 32.000 0.00 0.00 0.00 1.82
1010 1066 1.679680 CATCAGGAAAATGCCATCGCT 59.320 47.619 0.00 0.00 35.36 4.93
1042 1113 4.007644 CCGCCTCCTGTCAGCACA 62.008 66.667 0.00 0.00 0.00 4.57
1065 1136 4.047125 CCCGCCTCCCCACACATT 62.047 66.667 0.00 0.00 0.00 2.71
1084 1155 0.104855 TGCTTGTGAAGAGTCAGCGT 59.895 50.000 0.00 0.00 33.27 5.07
1147 1218 1.674441 CCAGGACGACGTTGCTATCTA 59.326 52.381 0.13 0.00 0.00 1.98
1190 1261 3.520569 GCTCATCTTTCTCTCACACTCC 58.479 50.000 0.00 0.00 0.00 3.85
1262 1336 6.049149 AGATAGCGTTGCAGCTTAAAGATAA 58.951 36.000 5.70 0.00 46.80 1.75
1268 1343 6.912591 GCGTTGCAGCTTAAAGATAATGTATT 59.087 34.615 0.00 0.00 0.00 1.89
1322 1398 1.072489 TGGCCATGAACCGTTGAACTA 59.928 47.619 0.00 0.00 0.00 2.24
1336 1412 4.485163 GTTGAACTATTGCGAATTTGGCT 58.515 39.130 4.99 0.00 0.00 4.75
1349 1425 5.669357 GCGAATTTGGCTGTGAATCATTTTG 60.669 40.000 0.00 0.00 0.00 2.44
1394 1470 0.615331 GGGTCAGCTGTCATTCCTCA 59.385 55.000 14.67 0.00 0.00 3.86
1408 1484 7.223584 TGTCATTCCTCAGTTTGAATAGTTGA 58.776 34.615 0.00 0.00 30.31 3.18
1453 1529 4.564769 TGAACTGAACCGTTGAAAAATTGC 59.435 37.500 0.00 0.00 0.00 3.56
1464 1540 5.546526 GTTGAAAAATTGCCCATGAACCTA 58.453 37.500 0.00 0.00 0.00 3.08
1503 1579 5.437946 ACTGATGAACTGATGAATCATGCT 58.562 37.500 0.00 0.00 36.02 3.79
1521 1597 5.817296 TCATGCTATTTAGTCGCACTGAAAT 59.183 36.000 0.00 0.00 36.37 2.17
1526 1602 8.673711 TGCTATTTAGTCGCACTGAAATTAATT 58.326 29.630 0.00 0.00 27.31 1.40
1594 1670 0.456221 CCGTGTGATAGAGGCGAAGT 59.544 55.000 0.00 0.00 0.00 3.01
1645 1722 2.526304 TTTCTGTGGGAGTCGACTTG 57.474 50.000 21.08 6.43 0.00 3.16
1646 1723 0.033504 TTCTGTGGGAGTCGACTTGC 59.966 55.000 21.08 7.69 0.00 4.01
1653 1730 0.171455 GGAGTCGACTTGCACGATCT 59.829 55.000 21.08 0.00 41.62 2.75
1707 1784 3.821841 CAATCGCTAAACCAACTTCCAC 58.178 45.455 0.00 0.00 0.00 4.02
1752 1830 0.544357 ATCAACCTGACCACGAGGGA 60.544 55.000 3.29 0.00 41.15 4.20
1781 1859 3.366679 CCTGCGAGCAAATGAAGAACAAT 60.367 43.478 0.00 0.00 0.00 2.71
1788 1866 6.805271 CGAGCAAATGAAGAACAATCAAGAAT 59.195 34.615 0.00 0.00 0.00 2.40
1802 1880 9.582431 AACAATCAAGAATCTAAGATTGCAATG 57.418 29.630 25.25 1.99 46.90 2.82
1884 1962 2.218603 GTCTGGTCGTTGGACACAAAT 58.781 47.619 0.00 0.00 45.28 2.32
1891 1969 4.454504 GGTCGTTGGACACAAATGAAGTAT 59.545 41.667 0.00 0.00 45.28 2.12
1894 1972 4.320129 CGTTGGACACAAATGAAGTATGCA 60.320 41.667 0.00 0.00 38.54 3.96
1990 2070 0.919710 AGGAAGAGGGGGAATTTCGG 59.080 55.000 0.00 0.00 0.00 4.30
2048 2128 0.037017 TGTTTCCCCACACATACGGG 59.963 55.000 0.00 0.00 42.67 5.28
2173 2253 6.363577 AGTGGCATCTTGTATATTTTGTCG 57.636 37.500 0.00 0.00 0.00 4.35
2198 2278 3.433598 GGCTTCATGCACTCCTTATGGTA 60.434 47.826 0.00 0.00 45.15 3.25
2209 2289 5.352569 CACTCCTTATGGTAGCTTCAAAGTG 59.647 44.000 0.00 0.00 34.23 3.16
2210 2290 5.013183 ACTCCTTATGGTAGCTTCAAAGTGT 59.987 40.000 0.00 0.00 34.23 3.55
2239 2319 4.282449 TCATCACTTGGAACTCCGTTCTTA 59.718 41.667 6.68 0.00 41.70 2.10
2297 2377 0.107459 GCTCCAGTGTTCATCCCTCC 60.107 60.000 0.00 0.00 0.00 4.30
2311 2391 0.833834 CCCTCCTATCCATGCGAGGT 60.834 60.000 0.00 0.00 40.34 3.85
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
32 33 3.384168 TCCCTTAGCTCTATCTTTGCCA 58.616 45.455 0.00 0.00 0.00 4.92
33 34 4.564613 GGATCCCTTAGCTCTATCTTTGCC 60.565 50.000 0.00 0.00 0.00 4.52
41 42 4.665957 ACTCTACTGGATCCCTTAGCTCTA 59.334 45.833 9.90 0.00 0.00 2.43
51 52 8.964476 TTCAATCAATAAACTCTACTGGATCC 57.036 34.615 4.20 4.20 0.00 3.36
92 93 9.642327 CATGGAAAATGTGAACTGAAAATCATA 57.358 29.630 0.00 0.00 0.00 2.15
116 117 6.494835 AGGAAGCCTGTTGAACTAAAAATCAT 59.505 34.615 0.00 0.00 29.57 2.45
124 125 6.121776 TGAAATAGGAAGCCTGTTGAACTA 57.878 37.500 0.00 0.00 35.20 2.24
128 129 4.943705 GTGATGAAATAGGAAGCCTGTTGA 59.056 41.667 0.00 0.00 35.20 3.18
129 130 4.096984 GGTGATGAAATAGGAAGCCTGTTG 59.903 45.833 0.00 0.00 35.20 3.33
130 131 4.263905 TGGTGATGAAATAGGAAGCCTGTT 60.264 41.667 0.00 0.00 36.53 3.16
131 132 3.266772 TGGTGATGAAATAGGAAGCCTGT 59.733 43.478 0.00 0.00 34.61 4.00
132 133 3.881688 CTGGTGATGAAATAGGAAGCCTG 59.118 47.826 0.00 0.00 34.61 4.85
133 134 3.117738 CCTGGTGATGAAATAGGAAGCCT 60.118 47.826 0.00 0.00 37.71 4.58
134 135 3.217626 CCTGGTGATGAAATAGGAAGCC 58.782 50.000 0.00 0.00 0.00 4.35
135 136 3.217626 CCCTGGTGATGAAATAGGAAGC 58.782 50.000 0.00 0.00 0.00 3.86
136 137 4.510167 ACCCTGGTGATGAAATAGGAAG 57.490 45.455 0.00 0.00 0.00 3.46
137 138 5.491078 AGTTACCCTGGTGATGAAATAGGAA 59.509 40.000 0.00 0.00 0.00 3.36
138 139 5.036916 AGTTACCCTGGTGATGAAATAGGA 58.963 41.667 0.00 0.00 0.00 2.94
139 140 5.373812 AGTTACCCTGGTGATGAAATAGG 57.626 43.478 0.00 0.00 0.00 2.57
140 141 8.801882 TTTTAGTTACCCTGGTGATGAAATAG 57.198 34.615 0.00 0.00 0.00 1.73
141 142 7.338449 GCTTTTAGTTACCCTGGTGATGAAATA 59.662 37.037 0.00 0.00 0.00 1.40
142 143 6.152831 GCTTTTAGTTACCCTGGTGATGAAAT 59.847 38.462 0.00 0.00 0.00 2.17
143 144 5.475564 GCTTTTAGTTACCCTGGTGATGAAA 59.524 40.000 0.00 0.00 0.00 2.69
144 145 5.007682 GCTTTTAGTTACCCTGGTGATGAA 58.992 41.667 0.00 0.00 0.00 2.57
145 146 4.288626 AGCTTTTAGTTACCCTGGTGATGA 59.711 41.667 0.00 0.00 0.00 2.92
146 147 4.589908 AGCTTTTAGTTACCCTGGTGATG 58.410 43.478 0.00 0.00 0.00 3.07
147 148 4.324331 GGAGCTTTTAGTTACCCTGGTGAT 60.324 45.833 0.00 0.00 0.00 3.06
148 149 3.008704 GGAGCTTTTAGTTACCCTGGTGA 59.991 47.826 0.00 0.00 0.00 4.02
149 150 3.344515 GGAGCTTTTAGTTACCCTGGTG 58.655 50.000 0.00 0.00 0.00 4.17
150 151 2.027469 CGGAGCTTTTAGTTACCCTGGT 60.027 50.000 0.00 0.00 0.00 4.00
151 152 2.629051 CGGAGCTTTTAGTTACCCTGG 58.371 52.381 0.00 0.00 0.00 4.45
167 168 6.448207 TGAGATATTCTATCAGATGCGGAG 57.552 41.667 0.00 0.00 0.00 4.63
210 251 7.015098 TGGAAATTTTGTTCCTTGCATCTAGAA 59.985 33.333 0.00 0.00 46.29 2.10
236 277 6.840780 ATATCAGCAAAGTAAAAGTTGGCT 57.159 33.333 0.00 0.00 0.00 4.75
247 288 8.796475 ACACAACTTGATTTATATCAGCAAAGT 58.204 29.630 0.00 0.00 41.60 2.66
321 363 6.599638 GGCCAACTTCTCTACTAATCATGTTT 59.400 38.462 0.00 0.00 0.00 2.83
330 375 2.570302 GGGTTGGCCAACTTCTCTACTA 59.430 50.000 39.80 4.79 40.94 1.82
516 563 9.528018 GATTATGAAGGAAACACTTTTTGAACA 57.472 29.630 0.00 0.00 0.00 3.18
686 740 9.686683 ATGTGATTTTAGGCTTACAGAATTACT 57.313 29.630 0.00 0.00 0.00 2.24
702 756 5.541868 ACCACAAATCCACCATGTGATTTTA 59.458 36.000 6.70 0.00 45.61 1.52
721 775 1.184970 TGAGACCGATGAGCACCACA 61.185 55.000 0.00 0.00 0.00 4.17
730 784 4.442375 ACTAGTTGAACTGAGACCGATG 57.558 45.455 8.33 0.00 0.00 3.84
860 916 4.471386 TGGAGGAAGTGGAAGAAGGATTAG 59.529 45.833 0.00 0.00 0.00 1.73
925 981 8.958119 TGTAGAAGTTGTTCTATGAGTTGTTT 57.042 30.769 0.00 0.00 45.16 2.83
936 992 5.081032 AGCTAGGTCTGTAGAAGTTGTTCT 58.919 41.667 0.00 0.00 45.48 3.01
1065 1136 0.104855 ACGCTGACTCTTCACAAGCA 59.895 50.000 0.00 0.00 0.00 3.91
1084 1155 1.664649 CCGTCGTCTTCAGCAGCAA 60.665 57.895 0.00 0.00 0.00 3.91
1147 1218 1.146930 CACACCTATGGCCGAGCAT 59.853 57.895 0.00 0.00 0.00 3.79
1190 1261 3.499050 GCAGCAGCTCCTCACATG 58.501 61.111 0.00 0.00 37.91 3.21
1268 1343 5.472137 GCACCATACTTCCTGTAGAAAACAA 59.528 40.000 0.00 0.00 37.74 2.83
1322 1398 3.056678 TGATTCACAGCCAAATTCGCAAT 60.057 39.130 0.83 0.00 0.00 3.56
1362 1438 4.655649 ACAGCTGACCCATCATACTTCATA 59.344 41.667 23.35 0.00 33.22 2.15
1453 1529 4.599041 TCAAAAGGTCATAGGTTCATGGG 58.401 43.478 0.00 0.00 0.00 4.00
1464 1540 7.232127 AGTTCATCAGTTCAATCAAAAGGTCAT 59.768 33.333 0.00 0.00 0.00 3.06
1549 1625 4.894896 CCGGCCTAACCCCATGCC 62.895 72.222 0.00 0.00 40.54 4.40
1594 1670 2.289133 TGTCATCGAAACATCGGGACAA 60.289 45.455 17.61 7.51 41.18 3.18
1614 1690 6.516718 ACTCCCACAGAAAACGATATCTATG 58.483 40.000 0.34 0.00 0.00 2.23
1645 1722 1.181001 CGTTCGTAGTCAGATCGTGC 58.819 55.000 0.00 0.00 0.00 5.34
1646 1723 2.522372 ACGTTCGTAGTCAGATCGTG 57.478 50.000 0.00 0.00 40.91 4.35
1653 1730 0.587768 TCTTCGCACGTTCGTAGTCA 59.412 50.000 13.10 0.00 0.00 3.41
1752 1830 3.609853 TCATTTGCTCGCAGGAAATAGT 58.390 40.909 12.65 0.00 43.05 2.12
1781 1859 6.885918 TCCACATTGCAATCTTAGATTCTTGA 59.114 34.615 9.53 0.00 0.00 3.02
1802 1880 4.394920 TCCTCTTTTGTTCGCAATATCCAC 59.605 41.667 0.00 0.00 36.91 4.02
1894 1972 1.200020 GTTCGCCATAGCTGCAACTTT 59.800 47.619 1.02 0.00 36.60 2.66
2025 2105 2.482721 CGTATGTGTGGGGAAACAAGAC 59.517 50.000 0.00 0.00 0.00 3.01
2173 2253 1.831580 AAGGAGTGCATGAAGCCTTC 58.168 50.000 0.00 0.00 44.83 3.46
2209 2289 5.617751 CGGAGTTCCAAGTGATGATTTCAAC 60.618 44.000 0.00 0.00 33.66 3.18
2210 2290 4.455533 CGGAGTTCCAAGTGATGATTTCAA 59.544 41.667 0.00 0.00 33.66 2.69
2239 2319 3.149648 GGCATGCGCAAGGGGATT 61.150 61.111 17.11 0.00 41.24 3.01
2297 2377 1.688735 TGAAGGACCTCGCATGGATAG 59.311 52.381 0.00 0.00 0.00 2.08


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

AutoCloner maintained by Alex Coulton.