Multiple sequence alignment - TraesCS1B01G440900

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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 TraesCS1B01G440900 chr1B 100.000 2519 0 0 1 2519 662036958 662039476 0.000000e+00 4652
1 TraesCS1B01G440900 chr1B 79.265 1741 279 30 289 1997 662152952 662154642 0.000000e+00 1140
2 TraesCS1B01G440900 chr1B 97.318 522 13 1 1998 2519 662045572 662046092 0.000000e+00 885
3 TraesCS1B01G440900 chr1B 97.318 522 13 1 1998 2519 662052188 662052708 0.000000e+00 885
4 TraesCS1B01G440900 chr1B 84.653 202 26 5 53 250 376055268 376055468 1.980000e-46 196
5 TraesCS1B01G440900 chr5B 93.713 1702 73 13 250 1937 556795855 556794174 0.000000e+00 2519
6 TraesCS1B01G440900 chr5B 85.345 1665 201 20 354 1997 621238288 621236646 0.000000e+00 1683
7 TraesCS1B01G440900 chr5B 86.700 203 23 4 52 250 647953834 647953632 3.260000e-54 222
8 TraesCS1B01G440900 chr6B 91.799 1634 109 7 376 1997 15381521 15379901 0.000000e+00 2252
9 TraesCS1B01G440900 chr6B 86.786 1453 163 16 499 1937 15397815 15396378 0.000000e+00 1592
10 TraesCS1B01G440900 chr6B 91.196 886 74 3 1112 1997 16321334 16322215 0.000000e+00 1201
11 TraesCS1B01G440900 chr6B 77.523 654 128 10 882 1532 15298992 15298355 2.370000e-100 375
12 TraesCS1B01G440900 chr6A 86.018 1695 190 27 323 1997 9461418 9463085 0.000000e+00 1773
13 TraesCS1B01G440900 chr6A 87.276 1454 155 16 499 1937 9355318 9356756 0.000000e+00 1633
14 TraesCS1B01G440900 chr6A 75.715 1223 225 42 353 1533 9473109 9474301 4.740000e-152 547
15 TraesCS1B01G440900 chr6A 73.884 1210 255 35 354 1535 10511157 10509981 6.440000e-116 427
16 TraesCS1B01G440900 chr5D 84.496 1606 193 24 354 1939 499865081 499863512 0.000000e+00 1535
17 TraesCS1B01G440900 chr5D 92.913 254 13 3 1 250 332370408 332370660 5.120000e-97 364
18 TraesCS1B01G440900 chr6D 84.068 1519 203 22 499 1997 8987369 8988868 0.000000e+00 1428
19 TraesCS1B01G440900 chr6D 82.165 1469 215 24 499 1945 8552663 8551220 0.000000e+00 1218
20 TraesCS1B01G440900 chr6D 77.180 1227 216 40 340 1533 8967557 8968752 0.000000e+00 656
21 TraesCS1B01G440900 chr6D 75.381 1247 231 43 305 1517 8899465 8900669 1.330000e-147 532
22 TraesCS1B01G440900 chr6D 89.723 253 21 4 1 250 341198848 341198598 4.040000e-83 318
23 TraesCS1B01G440900 chr6D 87.629 194 19 4 53 244 82470201 82470391 1.170000e-53 220
24 TraesCS1B01G440900 chr2B 95.825 527 22 0 1993 2519 791591996 791591470 0.000000e+00 852
25 TraesCS1B01G440900 chr2B 95.019 522 24 2 1998 2519 690441214 690440695 0.000000e+00 819
26 TraesCS1B01G440900 chr2B 77.589 1062 193 25 499 1536 709426037 709424997 3.590000e-168 601
27 TraesCS1B01G440900 chr2B 86.070 201 22 4 53 250 117876477 117876280 7.060000e-51 211
28 TraesCS1B01G440900 chr3B 95.977 522 21 0 1998 2519 679823300 679822779 0.000000e+00 848
29 TraesCS1B01G440900 chr3B 95.019 522 26 0 1998 2519 454829298 454829819 0.000000e+00 821
30 TraesCS1B01G440900 chr3B 94.646 523 28 0 1997 2519 641260251 641259729 0.000000e+00 811
31 TraesCS1B01G440900 chr4B 94.837 523 27 0 1997 2519 46090259 46089737 0.000000e+00 817
32 TraesCS1B01G440900 chr7B 94.667 525 26 1 1997 2519 494936912 494936388 0.000000e+00 813
33 TraesCS1B01G440900 chr7B 82.542 842 104 19 360 1186 32348068 32347255 0.000000e+00 701
34 TraesCS1B01G440900 chr7B 94.690 226 10 1 1 224 634169412 634169187 1.430000e-92 350
35 TraesCS1B01G440900 chr2D 74.617 1044 214 31 499 1512 582489154 582490176 1.800000e-111 412
36 TraesCS1B01G440900 chr4A 94.071 253 12 2 1 250 627604747 627604999 5.080000e-102 381
37 TraesCS1B01G440900 chr5A 85.015 327 31 8 354 676 624205263 624204951 1.450000e-82 316
38 TraesCS1B01G440900 chr5A 85.052 194 27 2 59 250 521313547 521313354 1.980000e-46 196


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 TraesCS1B01G440900 chr1B 662036958 662039476 2518 False 4652 4652 100.000 1 2519 1 chr1B.!!$F2 2518
1 TraesCS1B01G440900 chr1B 662152952 662154642 1690 False 1140 1140 79.265 289 1997 1 chr1B.!!$F5 1708
2 TraesCS1B01G440900 chr1B 662045572 662046092 520 False 885 885 97.318 1998 2519 1 chr1B.!!$F3 521
3 TraesCS1B01G440900 chr1B 662052188 662052708 520 False 885 885 97.318 1998 2519 1 chr1B.!!$F4 521
4 TraesCS1B01G440900 chr5B 556794174 556795855 1681 True 2519 2519 93.713 250 1937 1 chr5B.!!$R1 1687
5 TraesCS1B01G440900 chr5B 621236646 621238288 1642 True 1683 1683 85.345 354 1997 1 chr5B.!!$R2 1643
6 TraesCS1B01G440900 chr6B 15379901 15381521 1620 True 2252 2252 91.799 376 1997 1 chr6B.!!$R2 1621
7 TraesCS1B01G440900 chr6B 15396378 15397815 1437 True 1592 1592 86.786 499 1937 1 chr6B.!!$R3 1438
8 TraesCS1B01G440900 chr6B 16321334 16322215 881 False 1201 1201 91.196 1112 1997 1 chr6B.!!$F1 885
9 TraesCS1B01G440900 chr6B 15298355 15298992 637 True 375 375 77.523 882 1532 1 chr6B.!!$R1 650
10 TraesCS1B01G440900 chr6A 9461418 9463085 1667 False 1773 1773 86.018 323 1997 1 chr6A.!!$F2 1674
11 TraesCS1B01G440900 chr6A 9355318 9356756 1438 False 1633 1633 87.276 499 1937 1 chr6A.!!$F1 1438
12 TraesCS1B01G440900 chr6A 9473109 9474301 1192 False 547 547 75.715 353 1533 1 chr6A.!!$F3 1180
13 TraesCS1B01G440900 chr6A 10509981 10511157 1176 True 427 427 73.884 354 1535 1 chr6A.!!$R1 1181
14 TraesCS1B01G440900 chr5D 499863512 499865081 1569 True 1535 1535 84.496 354 1939 1 chr5D.!!$R1 1585
15 TraesCS1B01G440900 chr6D 8987369 8988868 1499 False 1428 1428 84.068 499 1997 1 chr6D.!!$F3 1498
16 TraesCS1B01G440900 chr6D 8551220 8552663 1443 True 1218 1218 82.165 499 1945 1 chr6D.!!$R1 1446
17 TraesCS1B01G440900 chr6D 8967557 8968752 1195 False 656 656 77.180 340 1533 1 chr6D.!!$F2 1193
18 TraesCS1B01G440900 chr6D 8899465 8900669 1204 False 532 532 75.381 305 1517 1 chr6D.!!$F1 1212
19 TraesCS1B01G440900 chr2B 791591470 791591996 526 True 852 852 95.825 1993 2519 1 chr2B.!!$R4 526
20 TraesCS1B01G440900 chr2B 690440695 690441214 519 True 819 819 95.019 1998 2519 1 chr2B.!!$R2 521
21 TraesCS1B01G440900 chr2B 709424997 709426037 1040 True 601 601 77.589 499 1536 1 chr2B.!!$R3 1037
22 TraesCS1B01G440900 chr3B 679822779 679823300 521 True 848 848 95.977 1998 2519 1 chr3B.!!$R2 521
23 TraesCS1B01G440900 chr3B 454829298 454829819 521 False 821 821 95.019 1998 2519 1 chr3B.!!$F1 521
24 TraesCS1B01G440900 chr3B 641259729 641260251 522 True 811 811 94.646 1997 2519 1 chr3B.!!$R1 522
25 TraesCS1B01G440900 chr4B 46089737 46090259 522 True 817 817 94.837 1997 2519 1 chr4B.!!$R1 522
26 TraesCS1B01G440900 chr7B 494936388 494936912 524 True 813 813 94.667 1997 2519 1 chr7B.!!$R2 522
27 TraesCS1B01G440900 chr7B 32347255 32348068 813 True 701 701 82.542 360 1186 1 chr7B.!!$R1 826
28 TraesCS1B01G440900 chr2D 582489154 582490176 1022 False 412 412 74.617 499 1512 1 chr2D.!!$F1 1013

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
174 175 0.109412 GCAACCAGACAGCTCATTGC 60.109 55.0 0.0 0.0 43.29 3.56 F
933 1007 0.830444 AGTGCGGGTTAGGTGACTGA 60.830 55.0 0.0 0.0 43.88 3.41 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1014 1088 1.182667 GGGGCACACCTATGTTTTCC 58.817 55.000 0.0 0.0 36.72 3.13 R
1821 1912 3.256704 ACCCACAAATGAAGGAGACCTA 58.743 45.455 0.0 0.0 31.13 3.08 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
20 21 3.687572 CCATGCAGTCAAGCTCAATAC 57.312 47.619 0.00 0.00 34.99 1.89
21 22 3.011818 CCATGCAGTCAAGCTCAATACA 58.988 45.455 0.00 0.00 34.99 2.29
22 23 3.064958 CCATGCAGTCAAGCTCAATACAG 59.935 47.826 0.00 0.00 34.99 2.74
23 24 2.079158 TGCAGTCAAGCTCAATACAGC 58.921 47.619 0.00 0.00 39.99 4.40
24 25 2.079158 GCAGTCAAGCTCAATACAGCA 58.921 47.619 0.00 0.00 42.40 4.41
25 26 2.159599 GCAGTCAAGCTCAATACAGCAC 60.160 50.000 0.00 0.00 42.40 4.40
26 27 3.069289 CAGTCAAGCTCAATACAGCACA 58.931 45.455 0.00 0.00 42.40 4.57
27 28 3.070018 AGTCAAGCTCAATACAGCACAC 58.930 45.455 0.00 0.00 42.40 3.82
28 29 3.070018 GTCAAGCTCAATACAGCACACT 58.930 45.455 0.00 0.00 42.40 3.55
37 38 3.272574 ATACAGCACACTGGATCCTTG 57.727 47.619 14.23 12.51 44.80 3.61
38 39 2.177950 CAGCACACTGGATCCTTGC 58.822 57.895 14.23 15.37 40.48 4.01
39 40 1.376424 AGCACACTGGATCCTTGCG 60.376 57.895 14.23 5.50 38.26 4.85
40 41 1.375908 GCACACTGGATCCTTGCGA 60.376 57.895 14.23 0.00 0.00 5.10
41 42 0.745845 GCACACTGGATCCTTGCGAT 60.746 55.000 14.23 0.00 0.00 4.58
42 43 1.012086 CACACTGGATCCTTGCGATG 58.988 55.000 14.23 4.80 0.00 3.84
43 44 0.615331 ACACTGGATCCTTGCGATGT 59.385 50.000 14.23 5.41 0.00 3.06
44 45 1.293924 CACTGGATCCTTGCGATGTC 58.706 55.000 14.23 0.00 0.00 3.06
45 46 0.179100 ACTGGATCCTTGCGATGTCG 60.179 55.000 14.23 0.00 43.27 4.35
46 47 0.179100 CTGGATCCTTGCGATGTCGT 60.179 55.000 14.23 0.00 42.22 4.34
47 48 0.249120 TGGATCCTTGCGATGTCGTT 59.751 50.000 14.23 0.00 42.22 3.85
48 49 0.931005 GGATCCTTGCGATGTCGTTC 59.069 55.000 3.84 0.00 42.22 3.95
49 50 1.471676 GGATCCTTGCGATGTCGTTCT 60.472 52.381 3.84 0.00 42.22 3.01
50 51 2.271800 GATCCTTGCGATGTCGTTCTT 58.728 47.619 4.20 0.00 42.22 2.52
51 52 2.163818 TCCTTGCGATGTCGTTCTTT 57.836 45.000 4.20 0.00 42.22 2.52
52 53 2.489971 TCCTTGCGATGTCGTTCTTTT 58.510 42.857 4.20 0.00 42.22 2.27
53 54 2.478894 TCCTTGCGATGTCGTTCTTTTC 59.521 45.455 4.20 0.00 42.22 2.29
54 55 2.223144 CCTTGCGATGTCGTTCTTTTCA 59.777 45.455 4.20 0.00 42.22 2.69
55 56 3.473367 CTTGCGATGTCGTTCTTTTCAG 58.527 45.455 4.20 0.00 42.22 3.02
56 57 1.194547 TGCGATGTCGTTCTTTTCAGC 59.805 47.619 4.20 0.00 42.22 4.26
57 58 1.461127 GCGATGTCGTTCTTTTCAGCT 59.539 47.619 4.20 0.00 42.22 4.24
58 59 2.723010 GCGATGTCGTTCTTTTCAGCTG 60.723 50.000 7.63 7.63 42.22 4.24
59 60 2.723010 CGATGTCGTTCTTTTCAGCTGC 60.723 50.000 9.47 0.00 34.11 5.25
60 61 1.953559 TGTCGTTCTTTTCAGCTGCT 58.046 45.000 9.47 0.00 0.00 4.24
61 62 1.867233 TGTCGTTCTTTTCAGCTGCTC 59.133 47.619 9.47 0.00 0.00 4.26
62 63 1.867233 GTCGTTCTTTTCAGCTGCTCA 59.133 47.619 9.47 0.00 0.00 4.26
63 64 2.096516 GTCGTTCTTTTCAGCTGCTCAG 60.097 50.000 9.47 4.15 0.00 3.35
64 65 1.869767 CGTTCTTTTCAGCTGCTCAGT 59.130 47.619 9.47 0.00 0.00 3.41
65 66 2.289002 CGTTCTTTTCAGCTGCTCAGTT 59.711 45.455 9.47 0.00 0.00 3.16
66 67 3.242870 CGTTCTTTTCAGCTGCTCAGTTT 60.243 43.478 9.47 0.00 0.00 2.66
67 68 4.676546 GTTCTTTTCAGCTGCTCAGTTTT 58.323 39.130 9.47 0.00 0.00 2.43
68 69 4.989279 TCTTTTCAGCTGCTCAGTTTTT 57.011 36.364 9.47 0.00 0.00 1.94
137 138 9.849166 GCAGTTTTGCCAATACTAAAGTATTAA 57.151 29.630 13.58 4.36 44.44 1.40
156 157 8.528643 AGTATTAAAATCACTGTTTTTAGGGGC 58.471 33.333 5.56 0.00 33.62 5.80
157 158 6.732896 TTAAAATCACTGTTTTTAGGGGCA 57.267 33.333 5.56 0.00 33.62 5.36
158 159 5.622346 AAAATCACTGTTTTTAGGGGCAA 57.378 34.783 0.00 0.00 0.00 4.52
159 160 4.600692 AATCACTGTTTTTAGGGGCAAC 57.399 40.909 0.00 0.00 0.00 4.17
160 161 6.463190 TAAAATCACTGTTTTTAGGGGCAACC 60.463 38.462 2.22 0.00 43.04 3.77
161 162 8.781414 TAAAATCACTGTTTTTAGGGGCAACCA 61.781 37.037 0.00 0.00 44.31 3.67
171 172 4.730487 GGCAACCAGACAGCTCAT 57.270 55.556 0.00 0.00 0.00 2.90
172 173 2.952714 GGCAACCAGACAGCTCATT 58.047 52.632 0.00 0.00 0.00 2.57
173 174 0.524862 GGCAACCAGACAGCTCATTG 59.475 55.000 0.00 0.00 0.00 2.82
174 175 0.109412 GCAACCAGACAGCTCATTGC 60.109 55.000 0.00 0.00 43.29 3.56
175 176 1.241165 CAACCAGACAGCTCATTGCA 58.759 50.000 0.00 0.00 45.94 4.08
176 177 1.610038 CAACCAGACAGCTCATTGCAA 59.390 47.619 0.00 0.00 45.94 4.08
177 178 1.985473 ACCAGACAGCTCATTGCAAA 58.015 45.000 1.71 0.00 45.94 3.68
178 179 1.610522 ACCAGACAGCTCATTGCAAAC 59.389 47.619 1.71 0.00 45.94 2.93
179 180 1.610038 CCAGACAGCTCATTGCAAACA 59.390 47.619 1.71 0.00 45.94 2.83
180 181 2.034939 CCAGACAGCTCATTGCAAACAA 59.965 45.455 1.71 0.00 45.94 2.83
181 182 3.491276 CCAGACAGCTCATTGCAAACAAA 60.491 43.478 1.71 0.00 45.94 2.83
182 183 4.114073 CAGACAGCTCATTGCAAACAAAA 58.886 39.130 1.71 0.00 45.94 2.44
183 184 4.026310 CAGACAGCTCATTGCAAACAAAAC 60.026 41.667 1.71 0.00 45.94 2.43
184 185 4.114794 GACAGCTCATTGCAAACAAAACT 58.885 39.130 1.71 0.00 45.94 2.66
185 186 5.067674 AGACAGCTCATTGCAAACAAAACTA 59.932 36.000 1.71 0.00 45.94 2.24
186 187 5.846203 ACAGCTCATTGCAAACAAAACTAT 58.154 33.333 1.71 0.00 45.94 2.12
187 188 5.693104 ACAGCTCATTGCAAACAAAACTATG 59.307 36.000 1.71 0.00 45.94 2.23
188 189 5.921976 CAGCTCATTGCAAACAAAACTATGA 59.078 36.000 1.71 0.00 45.94 2.15
189 190 6.588756 CAGCTCATTGCAAACAAAACTATGAT 59.411 34.615 1.71 0.00 45.94 2.45
190 191 7.756272 CAGCTCATTGCAAACAAAACTATGATA 59.244 33.333 1.71 0.00 45.94 2.15
191 192 8.306038 AGCTCATTGCAAACAAAACTATGATAA 58.694 29.630 1.71 0.00 45.94 1.75
192 193 9.090692 GCTCATTGCAAACAAAACTATGATAAT 57.909 29.630 1.71 0.00 39.77 1.28
245 246 9.744468 ACTTAAAAATACTTTGCTACCAAACAG 57.256 29.630 0.00 0.00 36.09 3.16
246 247 9.191995 CTTAAAAATACTTTGCTACCAAACAGG 57.808 33.333 0.00 0.00 45.67 4.00
247 248 5.722021 AAATACTTTGCTACCAAACAGGG 57.278 39.130 0.00 0.00 43.89 4.45
248 249 1.328279 ACTTTGCTACCAAACAGGGC 58.672 50.000 0.00 0.00 43.89 5.19
269 270 3.705604 CCGCAATCTCTTCTCTTCTCTC 58.294 50.000 0.00 0.00 0.00 3.20
270 271 3.381272 CCGCAATCTCTTCTCTTCTCTCT 59.619 47.826 0.00 0.00 0.00 3.10
282 283 2.900546 TCTTCTCTCTTCCCCACAGAAC 59.099 50.000 0.00 0.00 0.00 3.01
283 284 2.398754 TCTCTCTTCCCCACAGAACA 57.601 50.000 0.00 0.00 0.00 3.18
413 425 1.675552 GTCTCCTCTCCTCTTCTCCG 58.324 60.000 0.00 0.00 0.00 4.63
494 530 2.897350 GGATTTGCCGCGGAGGAG 60.897 66.667 33.48 0.95 45.00 3.69
495 531 2.125106 GATTTGCCGCGGAGGAGT 60.125 61.111 33.48 10.19 45.00 3.85
496 532 1.143183 GATTTGCCGCGGAGGAGTA 59.857 57.895 33.48 7.35 45.00 2.59
497 533 1.152383 GATTTGCCGCGGAGGAGTAC 61.152 60.000 33.48 9.92 45.00 2.73
611 647 4.421479 CGTGCTCGCCTTCCTCGT 62.421 66.667 0.00 0.00 0.00 4.18
680 729 1.205064 CGTTGTTCCTCTGCGCAAG 59.795 57.895 13.05 11.91 43.44 4.01
781 849 3.556843 CCACAAATTCCGCCAAAAAGGAT 60.557 43.478 0.00 0.00 41.22 3.24
933 1007 0.830444 AGTGCGGGTTAGGTGACTGA 60.830 55.000 0.00 0.00 43.88 3.41
972 1046 2.099921 CGTCTCAAGACCGAGGATGATT 59.900 50.000 4.63 0.00 41.86 2.57
1148 1222 3.104512 TGAGGAATACGTTCAGGTGGAT 58.895 45.455 0.00 0.00 36.01 3.41
1200 1274 8.271458 TCTAAGTATCCATTGGTGCTGAATAAA 58.729 33.333 1.86 0.00 0.00 1.40
1285 1359 1.209128 CATTGCTCATCGACCCGTAC 58.791 55.000 0.00 0.00 0.00 3.67
1376 1455 3.127533 GCTCAAGCGCGACCCAAT 61.128 61.111 12.10 0.00 0.00 3.16
1385 1467 2.488545 AGCGCGACCCAATCTACTATAG 59.511 50.000 12.10 0.00 0.00 1.31
1584 1672 4.160252 TGCTGTATGTCTGTTAGATGCTGA 59.840 41.667 0.00 0.00 0.00 4.26
1588 1676 7.404671 TGTATGTCTGTTAGATGCTGAGTTA 57.595 36.000 0.00 0.00 0.00 2.24
1706 1796 4.024387 TGGAAACTTTTTCGTCCTCATTCG 60.024 41.667 0.00 0.00 0.00 3.34
1821 1912 4.340381 GCATTGAGATAATGAGCCAAGGTT 59.660 41.667 3.97 0.00 0.00 3.50
1843 1946 3.256704 AGGTCTCCTTCATTTGTGGGTA 58.743 45.455 0.00 0.00 0.00 3.69
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
2 3 2.681848 GCTGTATTGAGCTTGACTGCAT 59.318 45.455 12.16 0.00 36.92 3.96
4 5 2.079158 TGCTGTATTGAGCTTGACTGC 58.921 47.619 10.89 10.89 39.90 4.40
5 6 3.069289 TGTGCTGTATTGAGCTTGACTG 58.931 45.455 0.00 0.00 39.90 3.51
6 7 3.070018 GTGTGCTGTATTGAGCTTGACT 58.930 45.455 0.00 0.00 39.90 3.41
7 8 3.070018 AGTGTGCTGTATTGAGCTTGAC 58.930 45.455 0.00 0.00 39.90 3.18
8 9 3.069289 CAGTGTGCTGTATTGAGCTTGA 58.931 45.455 0.00 0.00 39.90 3.02
9 10 2.161012 CCAGTGTGCTGTATTGAGCTTG 59.839 50.000 0.00 0.00 41.02 4.01
10 11 2.038952 TCCAGTGTGCTGTATTGAGCTT 59.961 45.455 0.00 0.00 41.02 3.74
11 12 1.625315 TCCAGTGTGCTGTATTGAGCT 59.375 47.619 0.00 0.00 41.02 4.09
12 13 2.099141 TCCAGTGTGCTGTATTGAGC 57.901 50.000 0.00 0.00 41.02 4.26
13 14 3.118482 AGGATCCAGTGTGCTGTATTGAG 60.118 47.826 15.82 0.00 41.02 3.02
14 15 2.840038 AGGATCCAGTGTGCTGTATTGA 59.160 45.455 15.82 0.00 41.02 2.57
15 16 3.272574 AGGATCCAGTGTGCTGTATTG 57.727 47.619 15.82 0.00 41.02 1.90
16 17 3.614092 CAAGGATCCAGTGTGCTGTATT 58.386 45.455 15.82 0.00 41.02 1.89
17 18 2.681976 GCAAGGATCCAGTGTGCTGTAT 60.682 50.000 15.82 0.00 41.02 2.29
18 19 1.339055 GCAAGGATCCAGTGTGCTGTA 60.339 52.381 15.82 0.00 41.02 2.74
19 20 0.607489 GCAAGGATCCAGTGTGCTGT 60.607 55.000 15.82 0.00 41.02 4.40
20 21 1.642037 CGCAAGGATCCAGTGTGCTG 61.642 60.000 15.82 9.98 42.22 4.41
21 22 1.376424 CGCAAGGATCCAGTGTGCT 60.376 57.895 15.82 0.00 32.99 4.40
22 23 0.745845 ATCGCAAGGATCCAGTGTGC 60.746 55.000 15.82 15.84 38.47 4.57
23 24 1.012086 CATCGCAAGGATCCAGTGTG 58.988 55.000 15.82 17.40 31.28 3.82
24 25 0.615331 ACATCGCAAGGATCCAGTGT 59.385 50.000 15.82 6.23 31.28 3.55
25 26 1.293924 GACATCGCAAGGATCCAGTG 58.706 55.000 15.82 12.68 31.28 3.66
26 27 0.179100 CGACATCGCAAGGATCCAGT 60.179 55.000 15.82 0.00 31.28 4.00
27 28 0.179100 ACGACATCGCAAGGATCCAG 60.179 55.000 15.82 7.22 44.43 3.86
28 29 0.249120 AACGACATCGCAAGGATCCA 59.751 50.000 15.82 0.00 44.43 3.41
29 30 0.931005 GAACGACATCGCAAGGATCC 59.069 55.000 2.48 2.48 44.43 3.36
30 31 1.927895 AGAACGACATCGCAAGGATC 58.072 50.000 0.14 0.00 44.43 3.36
31 32 2.386661 AAGAACGACATCGCAAGGAT 57.613 45.000 0.14 0.00 44.43 3.24
32 33 2.163818 AAAGAACGACATCGCAAGGA 57.836 45.000 0.14 0.00 44.43 3.36
33 34 2.223144 TGAAAAGAACGACATCGCAAGG 59.777 45.455 0.14 0.00 44.43 3.61
34 35 3.473367 CTGAAAAGAACGACATCGCAAG 58.527 45.455 0.14 0.00 44.43 4.01
35 36 2.349438 GCTGAAAAGAACGACATCGCAA 60.349 45.455 0.14 0.00 44.43 4.85
36 37 1.194547 GCTGAAAAGAACGACATCGCA 59.805 47.619 0.14 0.00 44.43 5.10
37 38 1.461127 AGCTGAAAAGAACGACATCGC 59.539 47.619 0.14 0.00 44.43 4.58
38 39 2.723010 GCAGCTGAAAAGAACGACATCG 60.723 50.000 20.43 0.00 46.33 3.84
39 40 2.481952 AGCAGCTGAAAAGAACGACATC 59.518 45.455 20.43 0.00 0.00 3.06
40 41 2.481952 GAGCAGCTGAAAAGAACGACAT 59.518 45.455 20.43 0.00 0.00 3.06
41 42 1.867233 GAGCAGCTGAAAAGAACGACA 59.133 47.619 20.43 0.00 0.00 4.35
42 43 1.867233 TGAGCAGCTGAAAAGAACGAC 59.133 47.619 20.43 0.00 0.00 4.34
43 44 2.138320 CTGAGCAGCTGAAAAGAACGA 58.862 47.619 20.43 0.00 0.00 3.85
44 45 1.869767 ACTGAGCAGCTGAAAAGAACG 59.130 47.619 20.43 0.00 0.00 3.95
45 46 3.978718 AACTGAGCAGCTGAAAAGAAC 57.021 42.857 20.43 0.00 0.00 3.01
46 47 4.989279 AAAACTGAGCAGCTGAAAAGAA 57.011 36.364 20.43 0.00 0.00 2.52
47 48 4.989279 AAAAACTGAGCAGCTGAAAAGA 57.011 36.364 20.43 0.00 0.00 2.52
107 108 5.782893 TTAGTATTGGCAAAACTGCAGTT 57.217 34.783 26.36 26.36 40.50 3.16
108 109 5.301805 ACTTTAGTATTGGCAAAACTGCAGT 59.698 36.000 15.25 15.25 36.33 4.40
109 110 5.772521 ACTTTAGTATTGGCAAAACTGCAG 58.227 37.500 13.48 13.48 36.33 4.41
110 111 5.782893 ACTTTAGTATTGGCAAAACTGCA 57.217 34.783 3.01 0.00 36.33 4.41
130 131 8.528643 GCCCCTAAAAACAGTGATTTTAATACT 58.471 33.333 16.28 0.00 33.26 2.12
131 132 8.308207 TGCCCCTAAAAACAGTGATTTTAATAC 58.692 33.333 16.28 9.00 33.26 1.89
132 133 8.423906 TGCCCCTAAAAACAGTGATTTTAATA 57.576 30.769 16.28 0.99 33.26 0.98
133 134 7.309770 TGCCCCTAAAAACAGTGATTTTAAT 57.690 32.000 16.28 0.00 33.26 1.40
134 135 6.732896 TGCCCCTAAAAACAGTGATTTTAA 57.267 33.333 16.28 2.51 33.26 1.52
135 136 6.463190 GGTTGCCCCTAAAAACAGTGATTTTA 60.463 38.462 15.15 15.15 31.50 1.52
136 137 5.364778 GTTGCCCCTAAAAACAGTGATTTT 58.635 37.500 14.56 14.56 33.13 1.82
137 138 4.202315 GGTTGCCCCTAAAAACAGTGATTT 60.202 41.667 0.00 0.00 0.00 2.17
138 139 3.323691 GGTTGCCCCTAAAAACAGTGATT 59.676 43.478 0.00 0.00 0.00 2.57
139 140 2.897326 GGTTGCCCCTAAAAACAGTGAT 59.103 45.455 0.00 0.00 0.00 3.06
140 141 2.312390 GGTTGCCCCTAAAAACAGTGA 58.688 47.619 0.00 0.00 0.00 3.41
141 142 2.035632 TGGTTGCCCCTAAAAACAGTG 58.964 47.619 0.00 0.00 0.00 3.66
142 143 2.091555 TCTGGTTGCCCCTAAAAACAGT 60.092 45.455 0.82 0.00 41.07 3.55
143 144 2.296190 GTCTGGTTGCCCCTAAAAACAG 59.704 50.000 0.00 0.00 41.54 3.16
144 145 2.312390 GTCTGGTTGCCCCTAAAAACA 58.688 47.619 0.00 0.00 0.00 2.83
145 146 2.296190 CTGTCTGGTTGCCCCTAAAAAC 59.704 50.000 0.00 0.00 0.00 2.43
146 147 2.593026 CTGTCTGGTTGCCCCTAAAAA 58.407 47.619 0.00 0.00 0.00 1.94
147 148 1.821666 GCTGTCTGGTTGCCCCTAAAA 60.822 52.381 0.00 0.00 0.00 1.52
148 149 0.251165 GCTGTCTGGTTGCCCCTAAA 60.251 55.000 0.00 0.00 0.00 1.85
149 150 1.133809 AGCTGTCTGGTTGCCCCTAA 61.134 55.000 0.00 0.00 0.00 2.69
150 151 1.538876 AGCTGTCTGGTTGCCCCTA 60.539 57.895 0.00 0.00 0.00 3.53
151 152 2.856000 AGCTGTCTGGTTGCCCCT 60.856 61.111 0.00 0.00 0.00 4.79
152 153 2.360475 GAGCTGTCTGGTTGCCCC 60.360 66.667 0.00 0.00 0.00 5.80
153 154 0.610232 AATGAGCTGTCTGGTTGCCC 60.610 55.000 0.00 0.00 0.00 5.36
154 155 0.524862 CAATGAGCTGTCTGGTTGCC 59.475 55.000 0.00 0.00 0.00 4.52
155 156 0.109412 GCAATGAGCTGTCTGGTTGC 60.109 55.000 0.00 0.00 41.15 4.17
156 157 1.241165 TGCAATGAGCTGTCTGGTTG 58.759 50.000 0.00 0.00 45.94 3.77
157 158 1.985473 TTGCAATGAGCTGTCTGGTT 58.015 45.000 0.00 0.00 45.94 3.67
158 159 1.610522 GTTTGCAATGAGCTGTCTGGT 59.389 47.619 0.00 0.00 45.94 4.00
159 160 1.610038 TGTTTGCAATGAGCTGTCTGG 59.390 47.619 0.00 0.00 45.94 3.86
160 161 3.358707 TTGTTTGCAATGAGCTGTCTG 57.641 42.857 0.00 0.00 45.94 3.51
161 162 4.114794 GTTTTGTTTGCAATGAGCTGTCT 58.885 39.130 0.00 0.00 45.94 3.41
162 163 4.114794 AGTTTTGTTTGCAATGAGCTGTC 58.885 39.130 0.00 0.00 45.94 3.51
163 164 4.127566 AGTTTTGTTTGCAATGAGCTGT 57.872 36.364 0.00 0.00 45.94 4.40
164 165 5.921976 TCATAGTTTTGTTTGCAATGAGCTG 59.078 36.000 0.00 0.00 45.94 4.24
165 166 6.088016 TCATAGTTTTGTTTGCAATGAGCT 57.912 33.333 0.00 0.00 45.94 4.09
166 167 6.956299 ATCATAGTTTTGTTTGCAATGAGC 57.044 33.333 0.00 0.00 45.96 4.26
219 220 9.744468 CTGTTTGGTAGCAAAGTATTTTTAAGT 57.256 29.630 19.87 0.00 35.03 2.24
220 221 9.191995 CCTGTTTGGTAGCAAAGTATTTTTAAG 57.808 33.333 19.87 7.03 35.03 1.85
221 222 8.145122 CCCTGTTTGGTAGCAAAGTATTTTTAA 58.855 33.333 19.87 0.00 35.03 1.52
222 223 7.662897 CCCTGTTTGGTAGCAAAGTATTTTTA 58.337 34.615 19.87 0.00 35.03 1.52
223 224 6.521162 CCCTGTTTGGTAGCAAAGTATTTTT 58.479 36.000 19.87 0.00 35.03 1.94
224 225 5.510690 GCCCTGTTTGGTAGCAAAGTATTTT 60.511 40.000 19.87 0.00 35.03 1.82
225 226 4.021456 GCCCTGTTTGGTAGCAAAGTATTT 60.021 41.667 19.87 0.00 40.26 1.40
226 227 3.509967 GCCCTGTTTGGTAGCAAAGTATT 59.490 43.478 19.87 0.00 0.00 1.89
227 228 3.089284 GCCCTGTTTGGTAGCAAAGTAT 58.911 45.455 19.87 0.00 0.00 2.12
228 229 2.510613 GCCCTGTTTGGTAGCAAAGTA 58.489 47.619 19.87 11.34 0.00 2.24
229 230 1.328279 GCCCTGTTTGGTAGCAAAGT 58.672 50.000 19.87 0.00 0.00 2.66
230 231 0.603065 GGCCCTGTTTGGTAGCAAAG 59.397 55.000 19.87 9.59 0.00 2.77
231 232 1.175983 CGGCCCTGTTTGGTAGCAAA 61.176 55.000 15.83 15.83 0.00 3.68
232 233 1.602323 CGGCCCTGTTTGGTAGCAA 60.602 57.895 2.54 2.54 0.00 3.91
233 234 2.033448 CGGCCCTGTTTGGTAGCA 59.967 61.111 0.00 0.00 0.00 3.49
234 235 3.440415 GCGGCCCTGTTTGGTAGC 61.440 66.667 0.00 0.00 0.00 3.58
235 236 0.965363 ATTGCGGCCCTGTTTGGTAG 60.965 55.000 0.00 0.00 0.00 3.18
236 237 0.963355 GATTGCGGCCCTGTTTGGTA 60.963 55.000 0.00 0.00 0.00 3.25
237 238 2.203625 ATTGCGGCCCTGTTTGGT 60.204 55.556 0.00 0.00 0.00 3.67
238 239 1.937546 GAGATTGCGGCCCTGTTTGG 61.938 60.000 0.00 0.00 0.00 3.28
239 240 0.962356 AGAGATTGCGGCCCTGTTTG 60.962 55.000 0.00 0.00 0.00 2.93
240 241 0.251341 AAGAGATTGCGGCCCTGTTT 60.251 50.000 0.00 0.00 0.00 2.83
241 242 0.678048 GAAGAGATTGCGGCCCTGTT 60.678 55.000 0.00 0.00 0.00 3.16
242 243 1.078143 GAAGAGATTGCGGCCCTGT 60.078 57.895 0.00 0.00 0.00 4.00
243 244 0.813210 GAGAAGAGATTGCGGCCCTG 60.813 60.000 0.00 0.00 0.00 4.45
244 245 0.980231 AGAGAAGAGATTGCGGCCCT 60.980 55.000 0.00 0.00 0.00 5.19
245 246 0.107459 AAGAGAAGAGATTGCGGCCC 60.107 55.000 0.00 0.00 0.00 5.80
246 247 1.134551 AGAAGAGAAGAGATTGCGGCC 60.135 52.381 0.00 0.00 0.00 6.13
247 248 2.159114 AGAGAAGAGAAGAGATTGCGGC 60.159 50.000 0.00 0.00 0.00 6.53
248 249 3.381272 AGAGAGAAGAGAAGAGATTGCGG 59.619 47.826 0.00 0.00 0.00 5.69
294 297 2.357034 GGAAAGTGCGACGGCTGA 60.357 61.111 0.00 0.00 40.82 4.26
389 401 2.835895 GAGGAGAGGAGACGGGCC 60.836 72.222 0.00 0.00 0.00 5.80
413 425 4.554036 GATGCGGGAGAGGTGGCC 62.554 72.222 0.00 0.00 0.00 5.36
664 700 2.260869 GGCTTGCGCAGAGGAACAA 61.261 57.895 11.31 0.00 38.10 2.83
933 1007 1.019673 CGCACAGCTTGGCAATATCT 58.980 50.000 0.00 0.00 0.00 1.98
1014 1088 1.182667 GGGGCACACCTATGTTTTCC 58.817 55.000 0.00 0.00 36.72 3.13
1148 1222 2.311070 ATGCCCACCTCAGCATCCA 61.311 57.895 0.00 0.00 46.58 3.41
1200 1274 1.760192 GCTGCAGTGATTCCTTGGAT 58.240 50.000 16.64 0.00 0.00 3.41
1376 1455 7.148120 CGGACTCCTTGAAAACACTATAGTAGA 60.148 40.741 4.74 0.00 0.00 2.59
1385 1467 2.557317 TGTCGGACTCCTTGAAAACAC 58.443 47.619 9.88 0.00 0.00 3.32
1508 1590 3.433031 CCCGTCCTTGGCTTATGTGAATA 60.433 47.826 0.00 0.00 0.00 1.75
1584 1672 7.450074 TCATCACTCATTAACAACCACTAACT 58.550 34.615 0.00 0.00 0.00 2.24
1588 1676 5.182001 GCTTCATCACTCATTAACAACCACT 59.818 40.000 0.00 0.00 0.00 4.00
1821 1912 3.256704 ACCCACAAATGAAGGAGACCTA 58.743 45.455 0.00 0.00 31.13 3.08
1869 1972 9.632638 AAATTATCCACTATGAATTGCACTAGT 57.367 29.630 0.00 0.00 0.00 2.57
1870 1973 9.888878 CAAATTATCCACTATGAATTGCACTAG 57.111 33.333 0.00 0.00 0.00 2.57
1872 1975 8.523915 TCAAATTATCCACTATGAATTGCACT 57.476 30.769 0.00 0.00 0.00 4.40
1873 1976 7.864379 CCTCAAATTATCCACTATGAATTGCAC 59.136 37.037 0.00 0.00 0.00 4.57
2086 2191 8.084684 GGAAAATAGAAAACAGAACATGCTCTT 58.915 33.333 0.00 0.00 0.00 2.85


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

AutoCloner maintained by Alex Coulton.