Multiple sequence alignment - TraesCS5D01G480900

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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 TraesCS5D01G480900 chr5D 100.000 3311 0 0 1 3311 519058085 519054775 0.000000e+00 6115
1 TraesCS5D01G480900 chr5D 93.125 640 43 1 2673 3311 168014288 168013649 0.000000e+00 937
2 TraesCS5D01G480900 chr5D 92.724 646 44 3 2668 3311 272356448 272355804 0.000000e+00 929
3 TraesCS5D01G480900 chr5D 83.929 224 32 3 27 247 411786800 411787022 9.310000e-51 211
4 TraesCS5D01G480900 chr5B 91.312 1082 74 9 1310 2376 652730582 652731658 0.000000e+00 1459
5 TraesCS5D01G480900 chr5B 93.268 817 40 5 1 817 652728949 652729750 0.000000e+00 1190
6 TraesCS5D01G480900 chr5B 91.753 291 21 2 2386 2674 652731761 652732050 5.150000e-108 401
7 TraesCS5D01G480900 chr5B 85.792 366 30 17 818 1174 652729793 652730145 5.220000e-98 368
8 TraesCS5D01G480900 chr5B 74.895 474 107 8 1744 2211 578815550 578816017 4.330000e-49 206
9 TraesCS5D01G480900 chr5B 82.648 219 35 3 27 243 422036605 422036822 1.210000e-44 191
10 TraesCS5D01G480900 chr5B 72.857 560 116 26 1744 2281 579003542 579004087 3.420000e-35 159
11 TraesCS5D01G480900 chr5B 87.069 116 12 1 1173 1288 652730305 652730417 9.640000e-26 128
12 TraesCS5D01G480900 chr5B 72.107 484 104 23 1744 2213 579079416 579079882 2.090000e-22 117
13 TraesCS5D01G480900 chr6D 93.750 640 37 3 2673 3311 17972244 17972881 0.000000e+00 957
14 TraesCS5D01G480900 chr6D 73.029 482 109 17 1748 2217 448810352 448810824 2.060000e-32 150
15 TraesCS5D01G480900 chr7D 93.302 642 39 4 2671 3311 32649165 32648527 0.000000e+00 944
16 TraesCS5D01G480900 chr7D 93.260 638 42 1 2675 3311 75958724 75958087 0.000000e+00 939
17 TraesCS5D01G480900 chr7D 83.065 248 37 5 1 245 136404750 136404995 1.550000e-53 220
18 TraesCS5D01G480900 chr3D 93.260 638 40 3 2675 3311 115643808 115643173 0.000000e+00 937
19 TraesCS5D01G480900 chr3D 92.724 646 42 4 2668 3311 66145429 66146071 0.000000e+00 928
20 TraesCS5D01G480900 chr1D 92.747 648 41 5 2666 3311 452692101 452692744 0.000000e+00 931
21 TraesCS5D01G480900 chr1A 93.114 639 39 5 2675 3311 19309353 19308718 0.000000e+00 931
22 TraesCS5D01G480900 chr2B 77.437 554 110 11 1673 2217 248690768 248691315 1.920000e-82 316
23 TraesCS5D01G480900 chr2A 85.153 229 31 3 12 239 732957319 732957545 7.150000e-57 231
24 TraesCS5D01G480900 chr7B 83.562 219 27 5 31 240 505479236 505479018 2.610000e-46 196
25 TraesCS5D01G480900 chr3A 81.405 242 39 5 1 239 104555217 104554979 3.370000e-45 193
26 TraesCS5D01G480900 chr4D 81.356 236 41 3 10 242 378447947 378448182 4.360000e-44 189
27 TraesCS5D01G480900 chr3B 79.757 247 44 5 1 245 56134340 56134582 1.220000e-39 174
28 TraesCS5D01G480900 chr5A 75.893 336 70 8 1744 2072 591673683 591674014 9.510000e-36 161
29 TraesCS5D01G480900 chr5A 76.208 269 53 8 1949 2213 591977218 591977479 7.460000e-27 132


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 TraesCS5D01G480900 chr5D 519054775 519058085 3310 True 6115.0 6115 100.0000 1 3311 1 chr5D.!!$R3 3310
1 TraesCS5D01G480900 chr5D 168013649 168014288 639 True 937.0 937 93.1250 2673 3311 1 chr5D.!!$R1 638
2 TraesCS5D01G480900 chr5D 272355804 272356448 644 True 929.0 929 92.7240 2668 3311 1 chr5D.!!$R2 643
3 TraesCS5D01G480900 chr5B 652728949 652732050 3101 False 709.2 1459 89.8388 1 2674 5 chr5B.!!$F5 2673
4 TraesCS5D01G480900 chr6D 17972244 17972881 637 False 957.0 957 93.7500 2673 3311 1 chr6D.!!$F1 638
5 TraesCS5D01G480900 chr7D 32648527 32649165 638 True 944.0 944 93.3020 2671 3311 1 chr7D.!!$R1 640
6 TraesCS5D01G480900 chr7D 75958087 75958724 637 True 939.0 939 93.2600 2675 3311 1 chr7D.!!$R2 636
7 TraesCS5D01G480900 chr3D 115643173 115643808 635 True 937.0 937 93.2600 2675 3311 1 chr3D.!!$R1 636
8 TraesCS5D01G480900 chr3D 66145429 66146071 642 False 928.0 928 92.7240 2668 3311 1 chr3D.!!$F1 643
9 TraesCS5D01G480900 chr1D 452692101 452692744 643 False 931.0 931 92.7470 2666 3311 1 chr1D.!!$F1 645
10 TraesCS5D01G480900 chr1A 19308718 19309353 635 True 931.0 931 93.1140 2675 3311 1 chr1A.!!$R1 636
11 TraesCS5D01G480900 chr2B 248690768 248691315 547 False 316.0 316 77.4370 1673 2217 1 chr2B.!!$F1 544

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
299 300 0.250901 AATTCGTGAGGCAGTGGCTT 60.251 50.0 21.55 4.42 38.98 4.35 F
898 941 0.534203 AGTAACACCTGGCACAACCG 60.534 55.0 0.00 0.00 43.94 4.44 F
1650 2031 0.238289 ACATGCAGCTTAACGCACAC 59.762 50.0 0.00 0.00 41.79 3.82 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1470 1839 0.249911 AGTGAAAGCTCGTCCACCAC 60.250 55.000 0.0 0.0 0.0 4.16 R
1904 2291 0.389948 GCTCAAGGTGTACAGGTCCG 60.390 60.000 0.0 0.0 0.0 4.79 R
2508 2988 1.623311 CCAGCATATATCCGGTCCACA 59.377 52.381 0.0 0.0 0.0 4.17 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
53 54 3.371380 GCATGGTCTCCCTCTCATTTCTT 60.371 47.826 0.00 0.00 0.00 2.52
56 57 4.171234 TGGTCTCCCTCTCATTTCTTTCT 58.829 43.478 0.00 0.00 0.00 2.52
65 66 4.072131 TCTCATTTCTTTCTTCCCAACCG 58.928 43.478 0.00 0.00 0.00 4.44
69 70 1.133363 TCTTTCTTCCCAACCGGACA 58.867 50.000 9.46 0.00 41.83 4.02
83 84 1.209504 CCGGACACCACACCATAATCT 59.790 52.381 0.00 0.00 0.00 2.40
89 90 5.371526 GACACCACACCATAATCTCATCAT 58.628 41.667 0.00 0.00 0.00 2.45
102 103 4.541973 TCTCATCATATGGATTGTCCCG 57.458 45.455 2.13 0.00 35.03 5.14
119 120 2.830321 TCCCGACCTACTTTTTCTCCTC 59.170 50.000 0.00 0.00 0.00 3.71
123 124 3.007614 CGACCTACTTTTTCTCCTCCCAA 59.992 47.826 0.00 0.00 0.00 4.12
126 127 2.271944 ACTTTTTCTCCTCCCAACCG 57.728 50.000 0.00 0.00 0.00 4.44
127 128 1.202891 ACTTTTTCTCCTCCCAACCGG 60.203 52.381 0.00 0.00 0.00 5.28
134 135 3.120108 TCTCCTCCCAACCGGATATTTT 58.880 45.455 9.46 0.00 41.00 1.82
147 148 8.806634 CAACCGGATATTTTGTGATTAACATTG 58.193 33.333 9.46 0.00 38.99 2.82
158 159 4.641989 GTGATTAACATTGGATGGCTCACT 59.358 41.667 0.00 0.00 31.57 3.41
199 200 1.661617 CACGTCCAGACACAAAAACGA 59.338 47.619 0.00 0.00 34.46 3.85
208 209 6.932400 TCCAGACACAAAAACGAACATATACT 59.068 34.615 0.00 0.00 0.00 2.12
209 210 8.089597 TCCAGACACAAAAACGAACATATACTA 58.910 33.333 0.00 0.00 0.00 1.82
239 240 3.195698 GGTCGGCGTTGGAGATGC 61.196 66.667 6.85 0.00 39.65 3.91
250 251 2.755103 GTTGGAGATGCCCTTAGTTTGG 59.245 50.000 0.00 0.00 34.97 3.28
293 294 4.438744 GGTCCAATTAAATTCGTGAGGCAG 60.439 45.833 0.00 0.00 0.00 4.85
299 300 0.250901 AATTCGTGAGGCAGTGGCTT 60.251 50.000 21.55 4.42 38.98 4.35
300 301 0.957395 ATTCGTGAGGCAGTGGCTTG 60.957 55.000 21.55 13.63 38.98 4.01
356 357 4.939255 AGTTGGATGGATGGTTGAAATCT 58.061 39.130 0.00 0.00 0.00 2.40
368 369 4.082125 GGTTGAAATCTGTTGGACTCCAT 58.918 43.478 0.00 0.00 31.53 3.41
423 424 3.142217 ACATAGGAGTAGGAGTGGCCATA 59.858 47.826 9.72 0.00 40.02 2.74
474 475 4.627467 GCTAAGTTATGGACGGCATATCAG 59.373 45.833 0.00 0.00 0.00 2.90
487 488 2.224378 GCATATCAGGCTGCCTTGACTA 60.224 50.000 20.79 8.49 32.15 2.59
560 561 5.893255 TCATTGATGGGATAGGAAGTTTTGG 59.107 40.000 0.00 0.00 0.00 3.28
596 597 3.682292 AAGATTCGACCAGGCGGGC 62.682 63.158 2.69 0.00 42.05 6.13
601 602 3.814268 CGACCAGGCGGGCATTTG 61.814 66.667 2.69 0.00 42.68 2.32
773 774 7.924103 AAATAAAGGAAAACAAACGTGCTAG 57.076 32.000 0.00 0.00 0.00 3.42
779 780 1.512926 AACAAACGTGCTAGCCTCTG 58.487 50.000 13.29 5.13 0.00 3.35
791 792 1.192146 AGCCTCTGCGGGTTGACTAA 61.192 55.000 0.00 0.00 41.88 2.24
835 878 6.089954 GGAAACCGTGTACTTGTACATTCTAC 59.910 42.308 15.41 3.38 32.03 2.59
837 880 5.947443 ACCGTGTACTTGTACATTCTACTC 58.053 41.667 15.41 2.17 32.03 2.59
854 897 2.599677 ACTCAGTATGTAGCTAGCCCC 58.400 52.381 12.13 2.30 37.40 5.80
874 917 4.836736 CCCCACCTATATATATGTACCCCG 59.163 50.000 5.44 0.00 0.00 5.73
890 933 1.295423 CCGTGGGAGTAACACCTGG 59.705 63.158 0.00 0.00 35.46 4.45
893 936 0.605589 GTGGGAGTAACACCTGGCAC 60.606 60.000 0.00 0.00 32.80 5.01
896 939 1.235724 GGAGTAACACCTGGCACAAC 58.764 55.000 0.00 0.00 38.70 3.32
898 941 0.534203 AGTAACACCTGGCACAACCG 60.534 55.000 0.00 0.00 43.94 4.44
948 991 4.278678 ACTGCTTCAACAAAAGAGAACG 57.721 40.909 0.00 0.00 0.00 3.95
989 1036 8.826765 TCTGGATCTTTAGTTGGAGAAATAGTT 58.173 33.333 0.00 0.00 0.00 2.24
998 1045 7.761038 AGTTGGAGAAATAGTTAAAGTTGGG 57.239 36.000 0.00 0.00 0.00 4.12
1054 1101 1.530441 CGACGCATTTGATGGCAAGAG 60.530 52.381 0.00 0.00 35.04 2.85
1073 1120 4.320971 CGGCTCCGGTTCTATTCG 57.679 61.111 0.00 0.00 35.56 3.34
1074 1121 1.299926 CGGCTCCGGTTCTATTCGG 60.300 63.158 0.00 0.00 46.89 4.30
1120 1167 1.145759 ACGCGTTGCTCGATGGTATG 61.146 55.000 5.58 0.00 42.86 2.39
1121 1168 1.276844 GCGTTGCTCGATGGTATGC 59.723 57.895 6.11 0.00 42.86 3.14
1123 1170 1.145759 CGTTGCTCGATGGTATGCGT 61.146 55.000 0.00 0.00 42.86 5.24
1124 1171 1.847818 GTTGCTCGATGGTATGCGTA 58.152 50.000 0.00 0.00 0.00 4.42
1229 1455 2.357154 GGCATGGGTTCATAGGAAGTGT 60.357 50.000 0.00 0.00 32.62 3.55
1230 1456 3.118038 GGCATGGGTTCATAGGAAGTGTA 60.118 47.826 0.00 0.00 32.62 2.90
1231 1457 4.446311 GGCATGGGTTCATAGGAAGTGTAT 60.446 45.833 0.00 0.00 32.62 2.29
1233 1459 5.701290 GCATGGGTTCATAGGAAGTGTATAC 59.299 44.000 0.00 0.00 32.62 1.47
1236 1462 6.128486 TGGGTTCATAGGAAGTGTATACGTA 58.872 40.000 0.00 0.00 32.62 3.57
1237 1463 6.039717 TGGGTTCATAGGAAGTGTATACGTAC 59.960 42.308 0.00 0.00 32.62 3.67
1238 1464 6.138761 GGTTCATAGGAAGTGTATACGTACG 58.861 44.000 15.01 15.01 32.62 3.67
1240 1466 6.530913 TCATAGGAAGTGTATACGTACGTC 57.469 41.667 26.53 11.59 33.36 4.34
1241 1467 3.933155 AGGAAGTGTATACGTACGTCG 57.067 47.619 26.53 0.00 46.00 5.12
1262 1488 2.537401 GTACGTGGCATAAGGAGACAC 58.463 52.381 0.00 0.00 0.00 3.67
1263 1489 1.267121 ACGTGGCATAAGGAGACACT 58.733 50.000 0.00 0.00 0.00 3.55
1264 1490 1.066858 ACGTGGCATAAGGAGACACTG 60.067 52.381 0.00 0.00 0.00 3.66
1300 1526 3.211245 TGCCAGGCGTGCATATGC 61.211 61.111 21.09 21.09 42.50 3.14
1334 1703 6.820470 TTTCTTTTCAGCCAAATTAACGTG 57.180 33.333 0.00 0.00 0.00 4.49
1335 1704 5.508200 TCTTTTCAGCCAAATTAACGTGT 57.492 34.783 0.00 0.00 0.00 4.49
1336 1705 5.277825 TCTTTTCAGCCAAATTAACGTGTG 58.722 37.500 0.00 0.00 0.00 3.82
1351 1720 9.517609 AATTAACGTGTGAACTGATCTATCTAC 57.482 33.333 0.00 0.00 0.00 2.59
1437 1806 1.519455 CGTCATGGAGAAGGACCGC 60.519 63.158 0.00 0.00 0.00 5.68
1438 1807 1.519455 GTCATGGAGAAGGACCGCG 60.519 63.158 0.00 0.00 0.00 6.46
1502 1871 2.603173 GCTTTCACTTTCACTTGGAGCG 60.603 50.000 0.00 0.00 0.00 5.03
1539 1908 0.872388 ACGAACGTTCCATCTTTGGC 59.128 50.000 22.07 0.00 43.29 4.52
1545 1914 1.261619 CGTTCCATCTTTGGCGCTATC 59.738 52.381 7.64 0.00 43.29 2.08
1646 2027 1.667724 AGATGACATGCAGCTTAACGC 59.332 47.619 0.00 0.00 41.24 4.84
1650 2031 0.238289 ACATGCAGCTTAACGCACAC 59.762 50.000 0.00 0.00 41.79 3.82
1654 2035 0.519175 GCAGCTTAACGCACACATCG 60.519 55.000 0.00 0.00 42.61 3.84
1691 2072 4.749310 CTCCAACCGCTCGCAGCT 62.749 66.667 6.58 0.00 39.60 4.24
1725 2106 4.680237 CGCAACCTCCTCGCCACA 62.680 66.667 0.00 0.00 0.00 4.17
1729 2110 2.584391 AACCTCCTCGCCACAGTCC 61.584 63.158 0.00 0.00 0.00 3.85
1739 2120 1.742880 CCACAGTCCACAGCCGATG 60.743 63.158 0.00 0.00 0.00 3.84
1891 2275 1.128507 TCATCAACTTGACGCATTCGC 59.871 47.619 0.00 0.00 39.84 4.70
1915 2302 0.594602 CGACAAGACGGACCTGTACA 59.405 55.000 0.00 0.00 0.00 2.90
1926 2313 2.417719 GACCTGTACACCTTGAGCAAG 58.582 52.381 3.27 3.27 38.14 4.01
2041 2428 1.009389 CGTGCACGAGAAGGACTTCC 61.009 60.000 34.93 0.00 43.02 3.46
2080 2467 1.282447 ACTACTTCGAGCAGAGGGAGA 59.718 52.381 9.90 0.00 39.10 3.71
2165 2552 1.241315 TTTTACCTGCTCGGCAAGGC 61.241 55.000 11.40 0.00 38.41 4.35
2211 2598 0.950836 CATCAGCAACGGTGTGGAAA 59.049 50.000 0.66 0.00 32.43 3.13
2221 2608 0.949397 GGTGTGGAAAAACTCGACCC 59.051 55.000 0.00 0.00 32.03 4.46
2222 2609 1.670791 GTGTGGAAAAACTCGACCCA 58.329 50.000 0.00 0.00 32.03 4.51
2224 2611 2.031157 GTGTGGAAAAACTCGACCCATG 60.031 50.000 0.00 0.00 32.03 3.66
2225 2612 2.227194 GTGGAAAAACTCGACCCATGT 58.773 47.619 0.00 0.00 0.00 3.21
2226 2613 2.225727 GTGGAAAAACTCGACCCATGTC 59.774 50.000 0.00 0.00 38.18 3.06
2238 2625 3.869272 CATGTCTGCCGCCTTCGC 61.869 66.667 0.00 0.00 0.00 4.70
2241 2628 4.742201 GTCTGCCGCCTTCGCTCA 62.742 66.667 0.00 0.00 0.00 4.26
2244 2631 4.393155 TGCCGCCTTCGCTCACAT 62.393 61.111 0.00 0.00 0.00 3.21
2245 2632 3.869272 GCCGCCTTCGCTCACATG 61.869 66.667 0.00 0.00 0.00 3.21
2255 2642 0.671472 CGCTCACATGGTCTCAAGCA 60.671 55.000 0.00 0.00 37.29 3.91
2272 2659 1.873165 CAATGGTGGAAACCGGACG 59.127 57.895 9.46 0.00 0.00 4.79
2291 2678 2.027469 ACGGTGAACTTATCTTGACCCC 60.027 50.000 0.00 0.00 0.00 4.95
2344 2731 4.894114 AGTGAGTATTACCGCCTTATCTGT 59.106 41.667 0.00 0.00 0.00 3.41
2406 2886 9.649167 CTCCGAGGAAGTAGTAAAATAAGAAAA 57.351 33.333 0.00 0.00 0.00 2.29
2440 2920 1.271656 ACACTACAAGTACCGTGGAGC 59.728 52.381 6.34 0.00 29.08 4.70
2445 2925 1.007336 CAAGTACCGTGGAGCGTGAC 61.007 60.000 0.00 0.00 39.32 3.67
2524 3004 6.750501 CGTACTAATTGTGGACCGGATATATG 59.249 42.308 9.46 0.00 0.00 1.78
2533 3013 4.161565 TGGACCGGATATATGCTGGAATAC 59.838 45.833 9.46 8.17 0.00 1.89
2536 3016 4.098044 ACCGGATATATGCTGGAATACTCG 59.902 45.833 9.46 0.00 0.00 4.18
2591 3073 5.046910 CCCGCTGGCTATAAAATTATGTG 57.953 43.478 0.00 0.00 0.00 3.21
2599 3081 8.165239 TGGCTATAAAATTATGTGATGTCACC 57.835 34.615 10.40 0.00 45.88 4.02
2600 3082 7.998383 TGGCTATAAAATTATGTGATGTCACCT 59.002 33.333 10.40 3.69 45.88 4.00
2601 3083 9.502091 GGCTATAAAATTATGTGATGTCACCTA 57.498 33.333 10.40 2.75 45.88 3.08
2751 3233 3.805422 TCACCACTCATTTTGTCACGTAC 59.195 43.478 0.00 0.00 0.00 3.67
2858 3341 9.058174 TCTGTTTTAACCATTAAATTCGTCTCA 57.942 29.630 0.00 0.00 35.26 3.27
2907 3390 7.201232 CCATGTTGATATGTTTCGACGAAAAAC 60.201 37.037 23.59 20.96 37.18 2.43
2954 3437 6.937465 TGATGTTTACACTGTAGTTGCCATAA 59.063 34.615 0.00 0.00 0.00 1.90
2964 3447 6.432783 ACTGTAGTTGCCATAATGCTTAAACA 59.567 34.615 0.00 0.00 0.00 2.83
3205 3688 9.468532 GAAGAAAATAGCTGAAACAAATCAAGT 57.531 29.630 0.00 0.00 0.00 3.16
3227 3710 7.426929 AGTCAACTTCAGTGTAAACATCATC 57.573 36.000 0.00 0.00 0.00 2.92
3255 3738 4.112716 CATGTGCAATAGACATGGCAAA 57.887 40.909 0.00 0.00 42.87 3.68
3262 3745 7.823310 TGTGCAATAGACATGGCAAATTTTAAT 59.177 29.630 0.00 0.00 42.87 1.40
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
12 13 5.182570 CCATGCATGTGAAGAGAGAGAAAAA 59.817 40.000 24.58 0.00 0.00 1.94
65 66 3.627395 TGAGATTATGGTGTGGTGTCC 57.373 47.619 0.00 0.00 0.00 4.02
69 70 6.273026 TCCATATGATGAGATTATGGTGTGGT 59.727 38.462 3.65 0.00 41.96 4.16
83 84 3.007940 GGTCGGGACAATCCATATGATGA 59.992 47.826 3.65 0.00 38.64 2.92
89 90 3.323774 AGTAGGTCGGGACAATCCATA 57.676 47.619 0.75 0.00 38.64 2.74
93 94 4.576879 AGAAAAAGTAGGTCGGGACAATC 58.423 43.478 0.75 0.00 0.00 2.67
102 103 4.325119 GTTGGGAGGAGAAAAAGTAGGTC 58.675 47.826 0.00 0.00 0.00 3.85
119 120 6.127591 TGTTAATCACAAAATATCCGGTTGGG 60.128 38.462 0.00 0.00 30.81 4.12
123 124 7.340743 TCCAATGTTAATCACAAAATATCCGGT 59.659 33.333 0.00 0.00 39.50 5.28
126 127 9.480053 CCATCCAATGTTAATCACAAAATATCC 57.520 33.333 0.00 0.00 39.50 2.59
127 128 8.981647 GCCATCCAATGTTAATCACAAAATATC 58.018 33.333 0.00 0.00 39.50 1.63
134 135 4.398988 GTGAGCCATCCAATGTTAATCACA 59.601 41.667 0.00 0.00 40.71 3.58
147 148 3.112205 ATGCCGGAGTGAGCCATCC 62.112 63.158 5.05 0.00 0.00 3.51
199 200 9.174166 GACCCACAAATGTCTTTAGTATATGTT 57.826 33.333 0.00 0.00 0.00 2.71
208 209 2.156098 GCCGACCCACAAATGTCTTTA 58.844 47.619 0.00 0.00 0.00 1.85
209 210 0.958822 GCCGACCCACAAATGTCTTT 59.041 50.000 0.00 0.00 0.00 2.52
220 221 3.000819 ATCTCCAACGCCGACCCA 61.001 61.111 0.00 0.00 0.00 4.51
250 251 4.336280 ACCTATTCAAGTTCAGCCTTTCC 58.664 43.478 0.00 0.00 0.00 3.13
307 308 1.681666 TGGCTCCTGGCAGAGAAAG 59.318 57.895 17.94 8.77 44.10 2.62
322 323 3.152341 CCATCCAACTCTATCCAATGGC 58.848 50.000 0.00 0.00 0.00 4.40
356 357 1.691976 ACGAGTTCATGGAGTCCAACA 59.308 47.619 17.71 2.17 36.95 3.33
368 369 7.931578 AACCAATATAAATGGAACGAGTTCA 57.068 32.000 16.56 4.82 40.56 3.18
423 424 6.186957 TGCTCACATTTTAGGGTGTTGATAT 58.813 36.000 0.00 0.00 36.43 1.63
474 475 2.781681 TAAGGTTAGTCAAGGCAGCC 57.218 50.000 1.84 1.84 0.00 4.85
487 488 5.880901 TCAGAAGGAGCAAATCTTAAGGTT 58.119 37.500 1.85 0.00 0.00 3.50
560 561 3.149196 TCTTTCTCACAATTGGGTCAGC 58.851 45.455 7.75 0.00 0.00 4.26
596 597 1.304713 AGGCAGGCCCAGTCAAATG 60.305 57.895 6.70 0.00 36.58 2.32
601 602 1.763546 GATAGGAGGCAGGCCCAGTC 61.764 65.000 6.70 0.00 36.58 3.51
708 709 1.270465 ACGTTAGGTACCCAAGCACAC 60.270 52.381 8.74 0.00 0.00 3.82
747 748 7.603963 AGCACGTTTGTTTTCCTTTATTTTT 57.396 28.000 0.00 0.00 0.00 1.94
748 749 7.042992 GCTAGCACGTTTGTTTTCCTTTATTTT 60.043 33.333 10.63 0.00 0.00 1.82
749 750 6.419710 GCTAGCACGTTTGTTTTCCTTTATTT 59.580 34.615 10.63 0.00 0.00 1.40
750 751 5.918576 GCTAGCACGTTTGTTTTCCTTTATT 59.081 36.000 10.63 0.00 0.00 1.40
751 752 5.458015 GCTAGCACGTTTGTTTTCCTTTAT 58.542 37.500 10.63 0.00 0.00 1.40
752 753 4.261280 GGCTAGCACGTTTGTTTTCCTTTA 60.261 41.667 18.24 0.00 0.00 1.85
753 754 3.490249 GGCTAGCACGTTTGTTTTCCTTT 60.490 43.478 18.24 0.00 0.00 3.11
754 755 2.034179 GGCTAGCACGTTTGTTTTCCTT 59.966 45.455 18.24 0.00 0.00 3.36
773 774 0.107654 ATTAGTCAACCCGCAGAGGC 60.108 55.000 0.00 0.00 39.21 4.70
835 878 2.297597 GTGGGGCTAGCTACATACTGAG 59.702 54.545 15.72 0.00 0.00 3.35
837 880 1.344763 GGTGGGGCTAGCTACATACTG 59.655 57.143 15.72 0.00 0.00 2.74
854 897 5.303589 CCCACGGGGTACATATATATAGGTG 59.696 48.000 18.03 6.13 38.25 4.00
874 917 0.605589 GTGCCAGGTGTTACTCCCAC 60.606 60.000 0.00 0.00 0.00 4.61
893 936 4.697756 TGCTCCTTCCGGCGGTTG 62.698 66.667 27.32 18.76 0.00 3.77
898 941 1.153549 CTAGTGTGCTCCTTCCGGC 60.154 63.158 0.00 0.00 0.00 6.13
989 1036 2.042433 CCCAAGTCCATCCCCAACTTTA 59.958 50.000 0.00 0.00 31.04 1.85
998 1045 0.322546 GTGGTCACCCAAGTCCATCC 60.323 60.000 0.00 0.00 44.15 3.51
1056 1103 4.320971 CGAATAGAACCGGAGCCG 57.679 61.111 9.46 1.06 39.44 5.52
1061 1108 3.660501 TCATCATCCGAATAGAACCGG 57.339 47.619 0.00 0.00 46.57 5.28
1062 1109 5.119279 GTCAATCATCATCCGAATAGAACCG 59.881 44.000 0.00 0.00 0.00 4.44
1063 1110 6.146837 CAGTCAATCATCATCCGAATAGAACC 59.853 42.308 0.00 0.00 0.00 3.62
1064 1111 6.146837 CCAGTCAATCATCATCCGAATAGAAC 59.853 42.308 0.00 0.00 0.00 3.01
1065 1112 6.183361 ACCAGTCAATCATCATCCGAATAGAA 60.183 38.462 0.00 0.00 0.00 2.10
1066 1113 5.305386 ACCAGTCAATCATCATCCGAATAGA 59.695 40.000 0.00 0.00 0.00 1.98
1067 1114 5.545588 ACCAGTCAATCATCATCCGAATAG 58.454 41.667 0.00 0.00 0.00 1.73
1068 1115 5.551305 ACCAGTCAATCATCATCCGAATA 57.449 39.130 0.00 0.00 0.00 1.75
1069 1116 4.428294 ACCAGTCAATCATCATCCGAAT 57.572 40.909 0.00 0.00 0.00 3.34
1070 1117 3.912496 ACCAGTCAATCATCATCCGAA 57.088 42.857 0.00 0.00 0.00 4.30
1071 1118 4.344968 ACATACCAGTCAATCATCATCCGA 59.655 41.667 0.00 0.00 0.00 4.55
1072 1119 4.635223 ACATACCAGTCAATCATCATCCG 58.365 43.478 0.00 0.00 0.00 4.18
1073 1120 6.425114 GTGTACATACCAGTCAATCATCATCC 59.575 42.308 0.00 0.00 0.00 3.51
1074 1121 6.144563 CGTGTACATACCAGTCAATCATCATC 59.855 42.308 0.00 0.00 0.00 2.92
1075 1122 5.985530 CGTGTACATACCAGTCAATCATCAT 59.014 40.000 0.00 0.00 0.00 2.45
1076 1123 5.105513 ACGTGTACATACCAGTCAATCATCA 60.106 40.000 0.00 0.00 0.00 3.07
1077 1124 5.348986 ACGTGTACATACCAGTCAATCATC 58.651 41.667 0.00 0.00 0.00 2.92
1078 1125 5.339008 ACGTGTACATACCAGTCAATCAT 57.661 39.130 0.00 0.00 0.00 2.45
1079 1126 4.794278 ACGTGTACATACCAGTCAATCA 57.206 40.909 0.00 0.00 0.00 2.57
1107 1154 2.817844 AGTATACGCATACCATCGAGCA 59.182 45.455 2.05 0.00 38.24 4.26
1120 1167 1.434555 TGCACACCACAAGTATACGC 58.565 50.000 0.00 0.00 0.00 4.42
1121 1168 4.678509 AAATGCACACCACAAGTATACG 57.321 40.909 0.00 0.00 0.00 3.06
1123 1170 4.155099 CGGAAAATGCACACCACAAGTATA 59.845 41.667 0.00 0.00 0.00 1.47
1124 1171 3.057596 CGGAAAATGCACACCACAAGTAT 60.058 43.478 0.00 0.00 0.00 2.12
1208 1434 2.301346 CACTTCCTATGAACCCATGCC 58.699 52.381 0.00 0.00 34.31 4.40
1238 1464 0.457035 TCCTTATGCCACGTACCGAC 59.543 55.000 0.00 0.00 0.00 4.79
1240 1466 0.742505 TCTCCTTATGCCACGTACCG 59.257 55.000 0.00 0.00 0.00 4.02
1241 1467 1.479323 TGTCTCCTTATGCCACGTACC 59.521 52.381 0.00 0.00 0.00 3.34
1248 1474 1.834263 ACTCCAGTGTCTCCTTATGCC 59.166 52.381 0.00 0.00 0.00 4.40
1283 1509 3.211245 GCATATGCACGCCTGGCA 61.211 61.111 22.84 0.00 46.66 4.92
1294 1520 4.380841 AGAAAACTGTGGCATGCATATG 57.619 40.909 21.36 9.12 37.36 1.78
1295 1521 5.410355 AAAGAAAACTGTGGCATGCATAT 57.590 34.783 21.36 0.00 0.00 1.78
1296 1522 4.870123 AAAGAAAACTGTGGCATGCATA 57.130 36.364 21.36 4.71 0.00 3.14
1297 1523 3.756933 AAAGAAAACTGTGGCATGCAT 57.243 38.095 21.36 0.00 0.00 3.96
1298 1524 3.118847 TGAAAAGAAAACTGTGGCATGCA 60.119 39.130 21.36 2.54 0.00 3.96
1300 1526 3.492011 GCTGAAAAGAAAACTGTGGCATG 59.508 43.478 0.00 0.00 0.00 4.06
1302 1528 2.159114 GGCTGAAAAGAAAACTGTGGCA 60.159 45.455 0.00 0.00 0.00 4.92
1303 1529 2.159114 TGGCTGAAAAGAAAACTGTGGC 60.159 45.455 0.00 0.00 0.00 5.01
1304 1530 3.799281 TGGCTGAAAAGAAAACTGTGG 57.201 42.857 0.00 0.00 0.00 4.17
1307 1533 7.010091 ACGTTAATTTGGCTGAAAAGAAAACTG 59.990 33.333 0.00 0.00 0.00 3.16
1308 1534 7.010091 CACGTTAATTTGGCTGAAAAGAAAACT 59.990 33.333 0.00 0.00 0.00 2.66
1334 1703 8.542497 AGATAGTCGTAGATAGATCAGTTCAC 57.458 38.462 0.00 0.00 40.67 3.18
1351 1720 6.715718 TCCTCTTTGTCCCTATAAGATAGTCG 59.284 42.308 0.00 0.00 0.00 4.18
1441 1810 3.720601 TTGCGCCCTGCTCCATCT 61.721 61.111 4.18 0.00 46.63 2.90
1470 1839 0.249911 AGTGAAAGCTCGTCCACCAC 60.250 55.000 0.00 0.00 0.00 4.16
1502 1871 3.188786 CCTCAAGTAGGCGCGTGC 61.189 66.667 13.78 13.78 38.97 5.34
1539 1908 1.209275 GCACGTGCCTGTAGATAGCG 61.209 60.000 30.12 0.00 34.31 4.26
1569 1941 2.281345 GCGGAGGGATGATGCTGG 60.281 66.667 0.00 0.00 0.00 4.85
1621 1993 3.623906 AAGCTGCATGTCATCTACTGT 57.376 42.857 1.02 0.00 0.00 3.55
1622 1994 4.026228 CGTTAAGCTGCATGTCATCTACTG 60.026 45.833 1.02 0.00 0.00 2.74
1623 1995 4.115516 CGTTAAGCTGCATGTCATCTACT 58.884 43.478 1.02 0.00 0.00 2.57
1626 2007 1.667724 GCGTTAAGCTGCATGTCATCT 59.332 47.619 1.02 0.00 44.04 2.90
1638 2019 3.274196 CACGATGTGTGCGTTAAGC 57.726 52.632 0.00 0.00 42.70 3.09
1654 2035 1.163420 TCATGCACGGTGTTGGTCAC 61.163 55.000 10.24 0.00 45.47 3.67
1722 2103 2.393768 GCATCGGCTGTGGACTGTG 61.394 63.158 0.00 0.00 36.96 3.66
1725 2106 1.153289 GATGCATCGGCTGTGGACT 60.153 57.895 11.68 0.00 41.91 3.85
1739 2120 1.812922 CCTGTGAGCCAGACGATGC 60.813 63.158 0.00 0.00 44.49 3.91
1798 2182 1.202533 CCGGTGGTCTAGCATTAGGTG 60.203 57.143 0.00 0.00 0.00 4.00
1808 2192 4.382320 GGTTGCGCCGGTGGTCTA 62.382 66.667 18.41 0.00 0.00 2.59
1891 2275 2.126580 GTCCGTCTTGTCGTCCGG 60.127 66.667 0.00 0.00 41.75 5.14
1904 2291 0.389948 GCTCAAGGTGTACAGGTCCG 60.390 60.000 0.00 0.00 0.00 4.79
1926 2313 4.400961 AGGCCAGCCTTGACGAGC 62.401 66.667 5.04 0.00 45.70 5.03
2016 2403 0.732880 CCTTCTCGTGCACGTACAGG 60.733 60.000 35.74 30.61 40.80 4.00
2043 2430 2.109126 GTCGATGAAGCCCTGGCAC 61.109 63.158 11.38 4.77 44.88 5.01
2203 2590 1.670791 TGGGTCGAGTTTTTCCACAC 58.329 50.000 0.00 0.00 0.00 3.82
2221 2608 3.869272 GCGAAGGCGGCAGACATG 61.869 66.667 13.08 0.00 38.16 3.21
2222 2609 4.087892 AGCGAAGGCGGCAGACAT 62.088 61.111 13.08 0.00 46.35 3.06
2224 2611 4.742201 TGAGCGAAGGCGGCAGAC 62.742 66.667 13.08 0.47 46.35 3.51
2225 2612 4.742201 GTGAGCGAAGGCGGCAGA 62.742 66.667 13.08 0.00 46.35 4.26
2238 2625 2.422479 CCATTGCTTGAGACCATGTGAG 59.578 50.000 0.00 0.00 0.00 3.51
2241 2628 2.165167 CACCATTGCTTGAGACCATGT 58.835 47.619 0.00 0.00 0.00 3.21
2244 2631 0.770499 TCCACCATTGCTTGAGACCA 59.230 50.000 0.00 0.00 0.00 4.02
2245 2632 1.909700 TTCCACCATTGCTTGAGACC 58.090 50.000 0.00 0.00 0.00 3.85
2255 2642 1.302993 CCGTCCGGTTTCCACCATT 60.303 57.895 0.00 0.00 44.53 3.16
2272 2659 3.713826 TGGGGTCAAGATAAGTTCACC 57.286 47.619 0.00 0.00 0.00 4.02
2283 2670 6.902088 TATGTGTAACGCCTTGGGGTCAAG 62.902 50.000 9.79 0.00 44.63 3.02
2291 2678 5.583061 TCCACTTAATATGTGTAACGCCTTG 59.417 40.000 5.72 0.00 42.39 3.61
2299 2686 7.563556 TCACTCCAGATCCACTTAATATGTGTA 59.436 37.037 5.72 0.00 33.92 2.90
2377 2764 9.857656 TCTTATTTTACTACTTCCTCGGAGATA 57.142 33.333 6.58 0.00 33.89 1.98
2380 2767 9.649167 TTTTCTTATTTTACTACTTCCTCGGAG 57.351 33.333 0.00 0.00 0.00 4.63
2406 2886 2.633967 TGTAGTGTACGTGGGTCCAAAT 59.366 45.455 0.00 0.00 0.00 2.32
2407 2887 2.037901 TGTAGTGTACGTGGGTCCAAA 58.962 47.619 0.00 0.00 0.00 3.28
2408 2888 1.702182 TGTAGTGTACGTGGGTCCAA 58.298 50.000 0.00 0.00 0.00 3.53
2440 2920 5.498069 GCACACATAACAATACTACGTCACG 60.498 44.000 0.00 0.00 0.00 4.35
2490 2970 7.689400 CGGTCCACAATTAGTACGAAAATAAAC 59.311 37.037 0.00 0.00 0.00 2.01
2503 2983 5.582269 CAGCATATATCCGGTCCACAATTAG 59.418 44.000 0.00 0.00 0.00 1.73
2508 2988 1.623311 CCAGCATATATCCGGTCCACA 59.377 52.381 0.00 0.00 0.00 4.17
2513 2993 4.098044 CGAGTATTCCAGCATATATCCGGT 59.902 45.833 0.00 0.00 0.00 5.28
2524 3004 5.637006 ATCTATCACTCGAGTATTCCAGC 57.363 43.478 19.57 0.00 0.00 4.85
2533 3013 5.471797 TCCTTGCTCTAATCTATCACTCGAG 59.528 44.000 11.84 11.84 0.00 4.04
2591 3073 7.547370 GGCTTTATGATGACTATAGGTGACATC 59.453 40.741 16.85 16.85 38.13 3.06
2599 3081 6.233434 TGGCTTGGCTTTATGATGACTATAG 58.767 40.000 0.00 0.00 0.00 1.31
2600 3082 6.186420 TGGCTTGGCTTTATGATGACTATA 57.814 37.500 0.00 0.00 0.00 1.31
2601 3083 5.052693 TGGCTTGGCTTTATGATGACTAT 57.947 39.130 0.00 0.00 0.00 2.12
2606 3088 7.218228 TGTTATATGGCTTGGCTTTATGATG 57.782 36.000 0.00 0.00 0.00 3.07
2654 3136 6.445357 TCCGAATCTTTAATAAAGGCAACC 57.555 37.500 12.29 0.00 39.01 3.77
2751 3233 5.366829 TTTCTGCTGATGTCATCTGTTTG 57.633 39.130 17.91 10.30 0.00 2.93
2858 3341 5.880887 GGGGTCTAATTTTGAAGATCTCGTT 59.119 40.000 0.00 0.00 0.00 3.85
2874 3357 5.820423 CGAAACATATCAACATGGGGTCTAA 59.180 40.000 0.00 0.00 0.00 2.10
2907 3390 2.686915 TGGCAACTTTTGGGCAAAATTG 59.313 40.909 0.00 2.11 39.29 2.32
2954 3437 5.236911 CACATGGCAACTTTTGTTTAAGCAT 59.763 36.000 0.00 0.00 41.35 3.79
3198 3681 7.624360 TGTTTACACTGAAGTTGACTTGATT 57.376 32.000 0.30 0.00 36.11 2.57
3203 3686 6.146184 CGATGATGTTTACACTGAAGTTGACT 59.854 38.462 0.00 0.00 0.00 3.41
3205 3688 5.107104 GCGATGATGTTTACACTGAAGTTGA 60.107 40.000 0.00 0.00 0.00 3.18
3227 3710 4.018649 TGTCTATTGCACATGAATTGCG 57.981 40.909 0.00 0.00 43.34 4.85


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

AutoCloner maintained by Alex Coulton.