Multiple sequence alignment - TraesCS2D01G325300

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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 TraesCS2D01G325300 chr2D 100.000 2715 0 0 1 2715 419023868 419026582 0.000000e+00 5014
1 TraesCS2D01G325300 chr2D 99.387 163 1 0 271 433 168159697 168159535 2.040000e-76 296
2 TraesCS2D01G325300 chr2B 93.371 2278 118 18 445 2715 491022115 491024366 0.000000e+00 3339
3 TraesCS2D01G325300 chr2B 90.643 171 16 0 268 438 683308696 683308526 7.560000e-56 228
4 TraesCS2D01G325300 chr2B 89.714 175 16 2 261 434 775415875 775416048 3.520000e-54 222
5 TraesCS2D01G325300 chr2B 93.478 92 5 1 1 91 491021924 491022015 4.720000e-28 135
6 TraesCS2D01G325300 chr2A 91.259 1533 96 18 439 1962 571150984 571149481 0.000000e+00 2054
7 TraesCS2D01G325300 chr2A 93.872 767 45 2 1950 2715 571149466 571148701 0.000000e+00 1155
8 TraesCS2D01G325300 chr2A 94.186 258 12 3 1 257 571151240 571150985 9.110000e-105 390
9 TraesCS2D01G325300 chr5B 92.857 168 12 0 266 433 640759356 640759189 7.510000e-61 244
10 TraesCS2D01G325300 chr3A 91.813 171 13 1 267 436 648037003 648037173 1.260000e-58 237
11 TraesCS2D01G325300 chr1A 91.716 169 13 1 266 434 492657475 492657308 1.630000e-57 233
12 TraesCS2D01G325300 chr5D 91.617 167 14 0 268 434 321383972 321384138 5.850000e-57 231
13 TraesCS2D01G325300 chr5D 90.964 166 15 0 269 434 488868765 488868600 9.780000e-55 224
14 TraesCS2D01G325300 chr4B 92.025 163 13 0 271 433 83135495 83135657 2.100000e-56 230
15 TraesCS2D01G325300 chr4A 92.241 116 8 1 91 205 627748380 627748495 2.160000e-36 163
16 TraesCS2D01G325300 chr6B 92.035 113 8 1 92 204 612851096 612850985 1.010000e-34 158
17 TraesCS2D01G325300 chr6A 92.661 109 6 2 98 205 17704951 17705058 3.620000e-34 156
18 TraesCS2D01G325300 chrUn 91.228 114 9 1 92 204 51454433 51454320 1.300000e-33 154
19 TraesCS2D01G325300 chr7D 91.150 113 10 0 92 204 365079940 365079828 1.300000e-33 154
20 TraesCS2D01G325300 chr1D 91.071 112 10 0 92 203 258301916 258302027 4.680000e-33 152
21 TraesCS2D01G325300 chr1D 90.435 115 11 0 91 205 318585739 318585625 4.680000e-33 152
22 TraesCS2D01G325300 chr3D 90.435 115 9 2 92 204 590751869 590751755 1.680000e-32 150


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 TraesCS2D01G325300 chr2D 419023868 419026582 2714 False 5014.000000 5014 100.000000 1 2715 1 chr2D.!!$F1 2714
1 TraesCS2D01G325300 chr2B 491021924 491024366 2442 False 1737.000000 3339 93.424500 1 2715 2 chr2B.!!$F2 2714
2 TraesCS2D01G325300 chr2A 571148701 571151240 2539 True 1199.666667 2054 93.105667 1 2715 3 chr2A.!!$R1 2714

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
181 183 0.159554 CGCGTATGTATGAGCGCTTG 59.840 55.0 13.26 0.0 46.56 4.01 F
529 565 0.318107 CTTTGCTCCTTGGTTGCACG 60.318 55.0 8.85 0.0 36.37 5.34 F
593 629 0.818445 CTTGCTGCAGGCCATCTAGG 60.818 60.0 17.12 0.0 40.92 3.02 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1275 1315 0.104304 GGGACATATTCACGGCGACT 59.896 55.000 16.62 0.00 0.0 4.18 R
1354 1394 1.136305 GCGCTGAGTTATGGTACCTGA 59.864 52.381 14.36 0.00 0.0 3.86 R
2522 2591 2.229784 GACCCAAAATGAACCAGCTGAG 59.770 50.000 17.39 8.04 0.0 3.35 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
99 101 2.403252 ATTAAAGTCCACCGGCTCAG 57.597 50.000 0.00 0.00 0.00 3.35
100 102 1.053424 TTAAAGTCCACCGGCTCAGT 58.947 50.000 0.00 0.00 0.00 3.41
106 108 1.979155 CCACCGGCTCAGTCTCTCA 60.979 63.158 0.00 0.00 0.00 3.27
119 121 4.528206 TCAGTCTCTCAAAGGTGCTCATAA 59.472 41.667 0.00 0.00 0.00 1.90
127 129 0.343372 AGGTGCTCATAAGGGGAGGA 59.657 55.000 0.00 0.00 32.96 3.71
154 156 3.068560 GTGTGTGCGTTTATAGGGTTGA 58.931 45.455 0.00 0.00 0.00 3.18
156 158 2.095372 GTGTGCGTTTATAGGGTTGAGC 59.905 50.000 0.00 0.00 0.00 4.26
181 183 0.159554 CGCGTATGTATGAGCGCTTG 59.840 55.000 13.26 0.00 46.56 4.01
185 187 1.593006 GTATGTATGAGCGCTTGCGTT 59.407 47.619 13.26 10.61 45.69 4.84
196 198 1.267832 CGCTTGCGTTTGTACTGTGTT 60.268 47.619 6.86 0.00 0.00 3.32
228 231 6.037830 ACCGTATTAAAGTCCAAATTCGGATG 59.962 38.462 16.54 0.00 44.20 3.51
261 293 6.539649 TGCTGCTAATTATTCCGTAATGAC 57.460 37.500 0.00 0.00 33.32 3.06
267 299 9.549078 TGCTAATTATTCCGTAATGACATGTTA 57.451 29.630 0.00 0.00 33.32 2.41
275 307 9.871238 ATTCCGTAATGACATGTTATATACTCC 57.129 33.333 3.20 0.00 0.00 3.85
276 308 7.833786 TCCGTAATGACATGTTATATACTCCC 58.166 38.462 3.20 0.00 0.00 4.30
278 310 7.974501 CCGTAATGACATGTTATATACTCCCTC 59.025 40.741 3.20 0.00 0.00 4.30
279 311 7.974501 CGTAATGACATGTTATATACTCCCTCC 59.025 40.741 3.20 0.00 0.00 4.30
280 312 5.977489 TGACATGTTATATACTCCCTCCG 57.023 43.478 0.00 0.00 0.00 4.63
281 313 5.391256 TGACATGTTATATACTCCCTCCGT 58.609 41.667 0.00 0.00 0.00 4.69
282 314 5.836898 TGACATGTTATATACTCCCTCCGTT 59.163 40.000 0.00 0.00 0.00 4.44
283 315 6.015688 TGACATGTTATATACTCCCTCCGTTC 60.016 42.308 0.00 0.00 0.00 3.95
286 318 5.210430 TGTTATATACTCCCTCCGTTCCAA 58.790 41.667 0.00 0.00 0.00 3.53
288 320 6.156602 TGTTATATACTCCCTCCGTTCCAAAA 59.843 38.462 0.00 0.00 0.00 2.44
289 321 5.906772 ATATACTCCCTCCGTTCCAAAAT 57.093 39.130 0.00 0.00 0.00 1.82
290 322 8.370182 GTTATATACTCCCTCCGTTCCAAAATA 58.630 37.037 0.00 0.00 0.00 1.40
291 323 5.906772 ATACTCCCTCCGTTCCAAAATAT 57.093 39.130 0.00 0.00 0.00 1.28
292 324 8.674925 ATATACTCCCTCCGTTCCAAAATATA 57.325 34.615 0.00 0.00 0.00 0.86
293 325 5.703730 ACTCCCTCCGTTCCAAAATATAA 57.296 39.130 0.00 0.00 0.00 0.98
294 326 5.681639 ACTCCCTCCGTTCCAAAATATAAG 58.318 41.667 0.00 0.00 0.00 1.73
295 327 5.191124 ACTCCCTCCGTTCCAAAATATAAGT 59.809 40.000 0.00 0.00 0.00 2.24
296 328 5.677567 TCCCTCCGTTCCAAAATATAAGTC 58.322 41.667 0.00 0.00 0.00 3.01
297 329 5.427481 TCCCTCCGTTCCAAAATATAAGTCT 59.573 40.000 0.00 0.00 0.00 3.24
298 330 6.069847 TCCCTCCGTTCCAAAATATAAGTCTT 60.070 38.462 0.00 0.00 0.00 3.01
299 331 6.602009 CCCTCCGTTCCAAAATATAAGTCTTT 59.398 38.462 0.00 0.00 0.00 2.52
300 332 7.415206 CCCTCCGTTCCAAAATATAAGTCTTTG 60.415 40.741 0.00 0.00 0.00 2.77
301 333 7.335924 CCTCCGTTCCAAAATATAAGTCTTTGA 59.664 37.037 0.00 0.00 32.87 2.69
302 334 8.624367 TCCGTTCCAAAATATAAGTCTTTGAA 57.376 30.769 0.00 0.00 32.87 2.69
303 335 9.069082 TCCGTTCCAAAATATAAGTCTTTGAAA 57.931 29.630 0.00 0.00 32.87 2.69
304 336 9.685828 CCGTTCCAAAATATAAGTCTTTGAAAA 57.314 29.630 0.00 0.00 32.87 2.29
350 382 8.948631 ACGGATGTATATAGATGCATTTTAGG 57.051 34.615 11.19 0.00 38.38 2.69
351 383 8.540388 ACGGATGTATATAGATGCATTTTAGGT 58.460 33.333 11.19 0.00 38.38 3.08
352 384 8.820933 CGGATGTATATAGATGCATTTTAGGTG 58.179 37.037 11.19 0.00 38.38 4.00
353 385 9.672673 GGATGTATATAGATGCATTTTAGGTGT 57.327 33.333 0.00 0.00 38.38 4.16
355 387 8.846943 TGTATATAGATGCATTTTAGGTGTGG 57.153 34.615 0.00 0.00 0.00 4.17
356 388 8.655901 TGTATATAGATGCATTTTAGGTGTGGA 58.344 33.333 0.00 0.00 0.00 4.02
357 389 9.672673 GTATATAGATGCATTTTAGGTGTGGAT 57.327 33.333 0.00 0.00 0.00 3.41
359 391 7.902920 ATAGATGCATTTTAGGTGTGGATTT 57.097 32.000 0.00 0.00 0.00 2.17
360 392 8.995027 ATAGATGCATTTTAGGTGTGGATTTA 57.005 30.769 0.00 0.00 0.00 1.40
361 393 7.902920 AGATGCATTTTAGGTGTGGATTTAT 57.097 32.000 0.00 0.00 0.00 1.40
362 394 8.310122 AGATGCATTTTAGGTGTGGATTTATT 57.690 30.769 0.00 0.00 0.00 1.40
363 395 8.416329 AGATGCATTTTAGGTGTGGATTTATTC 58.584 33.333 0.00 0.00 0.00 1.75
364 396 7.473735 TGCATTTTAGGTGTGGATTTATTCA 57.526 32.000 0.00 0.00 0.00 2.57
365 397 8.076910 TGCATTTTAGGTGTGGATTTATTCAT 57.923 30.769 0.00 0.00 0.00 2.57
366 398 8.538701 TGCATTTTAGGTGTGGATTTATTCATT 58.461 29.630 0.00 0.00 0.00 2.57
367 399 9.382275 GCATTTTAGGTGTGGATTTATTCATTT 57.618 29.630 0.00 0.00 0.00 2.32
374 406 8.458843 AGGTGTGGATTTATTCATTTTACTTCG 58.541 33.333 0.00 0.00 0.00 3.79
375 407 8.241367 GGTGTGGATTTATTCATTTTACTTCGT 58.759 33.333 0.00 0.00 0.00 3.85
427 459 9.853177 ATAAAGACTTACATTTAGGAATGGAGG 57.147 33.333 4.39 0.00 45.56 4.30
428 460 6.253946 AGACTTACATTTAGGAATGGAGGG 57.746 41.667 4.39 0.00 45.56 4.30
429 461 5.970640 AGACTTACATTTAGGAATGGAGGGA 59.029 40.000 4.39 0.00 45.56 4.20
430 462 6.100424 AGACTTACATTTAGGAATGGAGGGAG 59.900 42.308 4.39 0.00 45.56 4.30
431 463 5.731678 ACTTACATTTAGGAATGGAGGGAGT 59.268 40.000 4.39 0.00 45.56 3.85
432 464 6.906901 ACTTACATTTAGGAATGGAGGGAGTA 59.093 38.462 4.39 0.00 45.56 2.59
433 465 7.572861 ACTTACATTTAGGAATGGAGGGAGTAT 59.427 37.037 4.39 0.00 45.56 2.12
434 466 6.848562 ACATTTAGGAATGGAGGGAGTATT 57.151 37.500 4.39 0.00 45.56 1.89
435 467 7.226059 ACATTTAGGAATGGAGGGAGTATTT 57.774 36.000 4.39 0.00 45.56 1.40
436 468 8.344939 ACATTTAGGAATGGAGGGAGTATTTA 57.655 34.615 4.39 0.00 45.56 1.40
437 469 8.960064 ACATTTAGGAATGGAGGGAGTATTTAT 58.040 33.333 4.39 0.00 45.56 1.40
442 474 6.014156 AGGAATGGAGGGAGTATTTATCTTCG 60.014 42.308 0.00 0.00 0.00 3.79
505 541 6.795144 TGCCAAAATTGTGATGAGGATATT 57.205 33.333 0.00 0.00 0.00 1.28
529 565 0.318107 CTTTGCTCCTTGGTTGCACG 60.318 55.000 8.85 0.00 36.37 5.34
571 607 3.420893 TGCAGTGTTCCATCTAAAAGGG 58.579 45.455 0.00 0.00 0.00 3.95
593 629 0.818445 CTTGCTGCAGGCCATCTAGG 60.818 60.000 17.12 0.00 40.92 3.02
614 650 3.368013 GGCACCTTATTTTAGCAACACCC 60.368 47.826 0.00 0.00 0.00 4.61
647 683 7.872993 GGCTGTAATTTCTCATGTGCTATAGTA 59.127 37.037 0.84 0.00 0.00 1.82
648 684 9.429359 GCTGTAATTTCTCATGTGCTATAGTAT 57.571 33.333 0.84 0.00 0.00 2.12
662 698 6.862090 GTGCTATAGTATTCGGTTAGGACTTG 59.138 42.308 0.84 0.00 31.10 3.16
726 762 1.480312 CCCACTTCACATGAAACCCCA 60.480 52.381 0.00 0.00 33.07 4.96
798 834 1.819632 GCAATCCCAACGCTCCGAT 60.820 57.895 0.00 0.00 0.00 4.18
842 878 3.272766 CGGCTCTTCACGCATATCA 57.727 52.632 0.00 0.00 0.00 2.15
871 911 1.260561 CAACGTTCAACTTCACGGAGG 59.739 52.381 0.00 0.00 40.84 4.30
903 943 4.118995 ACGCCGTTGCCATGCATG 62.119 61.111 20.19 20.19 38.76 4.06
904 944 3.813143 CGCCGTTGCCATGCATGA 61.813 61.111 28.31 6.08 38.76 3.07
905 945 2.809706 GCCGTTGCCATGCATGAT 59.190 55.556 28.31 0.00 38.76 2.45
906 946 1.590525 GCCGTTGCCATGCATGATG 60.591 57.895 28.31 13.23 38.76 3.07
907 947 1.590525 CCGTTGCCATGCATGATGC 60.591 57.895 28.31 22.48 45.29 3.91
923 963 1.071385 GATGCATCCCGTTCCTCAGAT 59.929 52.381 16.23 0.00 0.00 2.90
935 975 4.932200 CGTTCCTCAGATGCTATAAATCCC 59.068 45.833 0.00 0.00 0.00 3.85
980 1020 3.055891 TCGATCAGATTCTTCACAGGCAA 60.056 43.478 0.00 0.00 0.00 4.52
1059 1099 2.633509 GCTGCTGCTGGTTTCCCTG 61.634 63.158 8.53 0.00 36.03 4.45
1065 1105 3.966543 CTGGTTTCCCTGCCCCGT 61.967 66.667 0.00 0.00 0.00 5.28
1099 1139 2.841044 AACCACAGACGACGGGGT 60.841 61.111 0.00 0.00 0.00 4.95
1287 1327 3.000819 TCCCCAGTCGCCGTGAAT 61.001 61.111 0.00 0.00 0.00 2.57
1430 1470 1.074727 TGATTTTCTTCGGCCAGGGAA 59.925 47.619 2.24 0.00 0.00 3.97
1433 1473 0.991920 TTTCTTCGGCCAGGGAATCT 59.008 50.000 2.24 0.00 0.00 2.40
1434 1474 1.874129 TTCTTCGGCCAGGGAATCTA 58.126 50.000 2.24 0.00 0.00 1.98
1435 1475 1.120530 TCTTCGGCCAGGGAATCTAC 58.879 55.000 2.24 0.00 0.00 2.59
1440 1480 1.691976 CGGCCAGGGAATCTACACATA 59.308 52.381 2.24 0.00 0.00 2.29
1441 1481 2.548067 CGGCCAGGGAATCTACACATAC 60.548 54.545 2.24 0.00 0.00 2.39
1442 1482 2.706190 GGCCAGGGAATCTACACATACT 59.294 50.000 0.00 0.00 0.00 2.12
1443 1483 3.495100 GGCCAGGGAATCTACACATACTG 60.495 52.174 0.00 0.00 0.00 2.74
1444 1484 3.388024 GCCAGGGAATCTACACATACTGA 59.612 47.826 0.00 0.00 0.00 3.41
1458 1498 5.635280 ACACATACTGAACTGAAATGTCTCG 59.365 40.000 0.00 0.00 0.00 4.04
1462 1502 3.809832 ACTGAACTGAAATGTCTCGTTGG 59.190 43.478 0.00 0.00 0.00 3.77
1465 1505 5.063204 TGAACTGAAATGTCTCGTTGGATT 58.937 37.500 0.00 0.00 0.00 3.01
1507 1547 1.701031 TTCCAGCGGGACAAGAACCA 61.701 55.000 4.56 0.00 44.89 3.67
1730 1770 4.033472 GCTTCTAGCGTTCTGAAAAGATCC 59.967 45.833 0.00 0.00 0.00 3.36
1752 1792 4.867608 CCTCTAGACTTTCTGCAAACTAGC 59.132 45.833 0.00 0.00 0.00 3.42
1753 1793 5.468540 TCTAGACTTTCTGCAAACTAGCA 57.531 39.130 0.00 0.00 43.35 3.49
1780 1820 7.672122 TTCCTAGAGAACTTAGTTATTCCCC 57.328 40.000 0.00 0.00 0.00 4.81
1924 1964 1.688197 CCATTTGTGCACTGGGTTCTT 59.312 47.619 19.41 0.00 0.00 2.52
1953 1994 6.261603 TCAGCCAAGCACTATCTTGATAAATG 59.738 38.462 5.19 0.00 44.61 2.32
2155 2224 4.757149 ACCTTGCTACATTCACAAACTCTC 59.243 41.667 0.00 0.00 0.00 3.20
2522 2591 8.894768 AATAGATGTAAGATAACCTGAACTGC 57.105 34.615 0.00 0.00 0.00 4.40
2605 2674 0.671251 AAGATGTCGAGCGATCCCTC 59.329 55.000 0.00 0.00 0.00 4.30
2627 2696 1.152440 CCGGTCCCTCCTAGCATCT 60.152 63.158 0.00 0.00 0.00 2.90
2642 2711 0.534412 CATCTGTGAAGAGGAGCGGT 59.466 55.000 0.00 0.00 0.00 5.68
2666 2735 0.607489 ACAGCAGTGTCCAGGCAATC 60.607 55.000 0.00 0.00 26.76 2.67
2689 2758 7.345422 TCACAAAATTGAACAATCCTTCTGA 57.655 32.000 0.00 0.27 0.00 3.27
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
99 101 4.187694 CCTTATGAGCACCTTTGAGAGAC 58.812 47.826 0.00 0.00 0.00 3.36
100 102 3.198635 CCCTTATGAGCACCTTTGAGAGA 59.801 47.826 0.00 0.00 0.00 3.10
106 108 1.566231 CCTCCCCTTATGAGCACCTTT 59.434 52.381 0.00 0.00 0.00 3.11
119 121 2.607750 ACACGCACATCCTCCCCT 60.608 61.111 0.00 0.00 0.00 4.79
127 129 0.871722 ATAAACGCACACACGCACAT 59.128 45.000 0.00 0.00 36.19 3.21
156 158 1.317611 GCTCATACATACGCGCATACG 59.682 52.381 5.73 0.00 44.07 3.06
228 231 7.515684 CGGAATAATTAGCAGCAAATCAAAAGC 60.516 37.037 0.00 0.00 0.00 3.51
261 293 5.245301 TGGAACGGAGGGAGTATATAACATG 59.755 44.000 0.00 0.00 0.00 3.21
267 299 5.906772 ATTTTGGAACGGAGGGAGTATAT 57.093 39.130 0.00 0.00 0.00 0.86
270 302 6.384886 ACTTATATTTTGGAACGGAGGGAGTA 59.615 38.462 0.00 0.00 0.00 2.59
271 303 5.191124 ACTTATATTTTGGAACGGAGGGAGT 59.809 40.000 0.00 0.00 0.00 3.85
272 304 5.681639 ACTTATATTTTGGAACGGAGGGAG 58.318 41.667 0.00 0.00 0.00 4.30
274 306 5.681639 AGACTTATATTTTGGAACGGAGGG 58.318 41.667 0.00 0.00 0.00 4.30
275 307 7.335924 TCAAAGACTTATATTTTGGAACGGAGG 59.664 37.037 0.00 0.00 33.70 4.30
276 308 8.263940 TCAAAGACTTATATTTTGGAACGGAG 57.736 34.615 0.00 0.00 33.70 4.63
278 310 9.685828 TTTTCAAAGACTTATATTTTGGAACGG 57.314 29.630 0.00 0.00 31.03 4.44
325 357 8.540388 ACCTAAAATGCATCTATATACATCCGT 58.460 33.333 0.00 0.00 0.00 4.69
326 358 8.820933 CACCTAAAATGCATCTATATACATCCG 58.179 37.037 0.00 0.00 0.00 4.18
327 359 9.672673 ACACCTAAAATGCATCTATATACATCC 57.327 33.333 0.00 0.00 0.00 3.51
329 361 9.453572 CCACACCTAAAATGCATCTATATACAT 57.546 33.333 0.00 0.00 0.00 2.29
330 362 8.655901 TCCACACCTAAAATGCATCTATATACA 58.344 33.333 0.00 0.00 0.00 2.29
331 363 9.672673 ATCCACACCTAAAATGCATCTATATAC 57.327 33.333 0.00 0.00 0.00 1.47
333 365 9.592196 AAATCCACACCTAAAATGCATCTATAT 57.408 29.630 0.00 0.00 0.00 0.86
334 366 8.995027 AAATCCACACCTAAAATGCATCTATA 57.005 30.769 0.00 0.00 0.00 1.31
335 367 7.902920 AAATCCACACCTAAAATGCATCTAT 57.097 32.000 0.00 0.00 0.00 1.98
336 368 8.995027 ATAAATCCACACCTAAAATGCATCTA 57.005 30.769 0.00 0.00 0.00 1.98
337 369 7.902920 ATAAATCCACACCTAAAATGCATCT 57.097 32.000 0.00 0.00 0.00 2.90
338 370 8.196771 TGAATAAATCCACACCTAAAATGCATC 58.803 33.333 0.00 0.00 0.00 3.91
339 371 8.076910 TGAATAAATCCACACCTAAAATGCAT 57.923 30.769 0.00 0.00 0.00 3.96
340 372 7.473735 TGAATAAATCCACACCTAAAATGCA 57.526 32.000 0.00 0.00 0.00 3.96
341 373 8.947055 AATGAATAAATCCACACCTAAAATGC 57.053 30.769 0.00 0.00 0.00 3.56
348 380 8.458843 CGAAGTAAAATGAATAAATCCACACCT 58.541 33.333 0.00 0.00 0.00 4.00
349 381 8.241367 ACGAAGTAAAATGAATAAATCCACACC 58.759 33.333 0.00 0.00 41.94 4.16
401 433 9.853177 CCTCCATTCCTAAATGTAAGTCTTTAT 57.147 33.333 0.00 0.00 40.63 1.40
402 434 8.272173 CCCTCCATTCCTAAATGTAAGTCTTTA 58.728 37.037 0.00 0.00 40.63 1.85
403 435 7.036863 TCCCTCCATTCCTAAATGTAAGTCTTT 60.037 37.037 0.00 0.00 40.63 2.52
404 436 6.447084 TCCCTCCATTCCTAAATGTAAGTCTT 59.553 38.462 0.00 0.00 40.63 3.01
405 437 5.970640 TCCCTCCATTCCTAAATGTAAGTCT 59.029 40.000 0.00 0.00 40.63 3.24
406 438 6.126739 ACTCCCTCCATTCCTAAATGTAAGTC 60.127 42.308 0.00 0.00 40.63 3.01
407 439 5.731678 ACTCCCTCCATTCCTAAATGTAAGT 59.268 40.000 0.00 0.00 40.63 2.24
408 440 6.253946 ACTCCCTCCATTCCTAAATGTAAG 57.746 41.667 0.00 0.00 40.63 2.34
409 441 7.947782 ATACTCCCTCCATTCCTAAATGTAA 57.052 36.000 0.00 0.00 40.63 2.41
410 442 7.947782 AATACTCCCTCCATTCCTAAATGTA 57.052 36.000 0.00 0.00 40.63 2.29
411 443 6.848562 AATACTCCCTCCATTCCTAAATGT 57.151 37.500 0.00 0.00 40.63 2.71
412 444 9.454859 GATAAATACTCCCTCCATTCCTAAATG 57.545 37.037 0.00 0.00 41.69 2.32
413 445 9.411848 AGATAAATACTCCCTCCATTCCTAAAT 57.588 33.333 0.00 0.00 0.00 1.40
414 446 8.814448 AGATAAATACTCCCTCCATTCCTAAA 57.186 34.615 0.00 0.00 0.00 1.85
415 447 8.814448 AAGATAAATACTCCCTCCATTCCTAA 57.186 34.615 0.00 0.00 0.00 2.69
416 448 7.178628 CGAAGATAAATACTCCCTCCATTCCTA 59.821 40.741 0.00 0.00 0.00 2.94
417 449 6.014156 CGAAGATAAATACTCCCTCCATTCCT 60.014 42.308 0.00 0.00 0.00 3.36
418 450 6.014499 TCGAAGATAAATACTCCCTCCATTCC 60.014 42.308 0.00 0.00 0.00 3.01
419 451 6.994221 TCGAAGATAAATACTCCCTCCATTC 58.006 40.000 0.00 0.00 0.00 2.67
420 452 6.996180 TCGAAGATAAATACTCCCTCCATT 57.004 37.500 0.00 0.00 0.00 3.16
421 453 6.996180 TTCGAAGATAAATACTCCCTCCAT 57.004 37.500 0.00 0.00 35.04 3.41
422 454 6.801718 TTTCGAAGATAAATACTCCCTCCA 57.198 37.500 0.00 0.00 35.04 3.86
423 455 8.678593 AAATTTCGAAGATAAATACTCCCTCC 57.321 34.615 0.00 0.00 35.04 4.30
424 456 9.326413 TGAAATTTCGAAGATAAATACTCCCTC 57.674 33.333 13.34 0.00 35.04 4.30
425 457 9.681062 TTGAAATTTCGAAGATAAATACTCCCT 57.319 29.630 13.34 0.00 35.04 4.20
426 458 9.717892 GTTGAAATTTCGAAGATAAATACTCCC 57.282 33.333 9.77 0.00 35.04 4.30
427 459 9.717892 GGTTGAAATTTCGAAGATAAATACTCC 57.282 33.333 9.77 0.00 35.04 3.85
436 468 8.925700 GCTAAATTTGGTTGAAATTTCGAAGAT 58.074 29.630 9.77 0.13 46.83 2.40
437 469 7.383843 GGCTAAATTTGGTTGAAATTTCGAAGA 59.616 33.333 9.77 0.00 46.83 2.87
442 474 7.226523 ACAGTGGCTAAATTTGGTTGAAATTTC 59.773 33.333 11.41 11.41 46.83 2.17
463 495 3.555956 GGCATCAGTAAATACCGACAGTG 59.444 47.826 0.00 0.00 0.00 3.66
466 498 3.897141 TGGCATCAGTAAATACCGACA 57.103 42.857 0.00 0.00 0.00 4.35
505 541 2.031120 CAACCAAGGAGCAAAGGAACA 58.969 47.619 0.00 0.00 0.00 3.18
571 607 0.964358 AGATGGCCTGCAGCAAGTTC 60.964 55.000 8.66 1.02 46.50 3.01
593 629 3.257127 TGGGTGTTGCTAAAATAAGGTGC 59.743 43.478 0.00 0.00 0.00 5.01
614 650 7.622672 GCACATGAGAAATTACAGCCAAATTTG 60.623 37.037 11.40 11.40 36.82 2.32
647 683 2.262637 TGTCCCAAGTCCTAACCGAAT 58.737 47.619 0.00 0.00 0.00 3.34
648 684 1.719529 TGTCCCAAGTCCTAACCGAA 58.280 50.000 0.00 0.00 0.00 4.30
649 685 1.946984 ATGTCCCAAGTCCTAACCGA 58.053 50.000 0.00 0.00 0.00 4.69
650 686 2.236395 AGAATGTCCCAAGTCCTAACCG 59.764 50.000 0.00 0.00 0.00 4.44
662 698 1.450312 CCGCTGACCAGAATGTCCC 60.450 63.158 0.47 0.00 34.25 4.46
726 762 3.849563 TGTACTGCCTTGTTGTAGGTT 57.150 42.857 0.00 0.00 37.63 3.50
798 834 2.593026 GGATGGGGAGTTTTGTGTGAA 58.407 47.619 0.00 0.00 0.00 3.18
841 877 5.633601 TGAAGTTGAACGTTGCTACTAGATG 59.366 40.000 5.00 0.00 0.00 2.90
842 878 5.634020 GTGAAGTTGAACGTTGCTACTAGAT 59.366 40.000 5.00 0.00 0.00 1.98
903 943 0.465705 TCTGAGGAACGGGATGCATC 59.534 55.000 18.81 18.81 0.00 3.91
904 944 1.135094 ATCTGAGGAACGGGATGCAT 58.865 50.000 0.00 0.00 0.00 3.96
905 945 0.178767 CATCTGAGGAACGGGATGCA 59.821 55.000 0.00 0.00 31.03 3.96
906 946 2.997899 CATCTGAGGAACGGGATGC 58.002 57.895 0.00 0.00 31.03 3.91
907 947 0.467384 AGCATCTGAGGAACGGGATG 59.533 55.000 0.00 0.00 38.69 3.51
908 948 2.088104 TAGCATCTGAGGAACGGGAT 57.912 50.000 0.00 0.00 0.00 3.85
909 949 2.088104 ATAGCATCTGAGGAACGGGA 57.912 50.000 0.00 0.00 0.00 5.14
923 963 2.441750 GTGGAGGTGGGGATTTATAGCA 59.558 50.000 0.00 0.00 0.00 3.49
996 1036 3.576356 GCCATCGGTGCCATCGTG 61.576 66.667 0.00 0.00 0.00 4.35
1099 1139 4.400109 GCAGCTGGACGACGACGA 62.400 66.667 17.12 0.00 42.66 4.20
1275 1315 0.104304 GGGACATATTCACGGCGACT 59.896 55.000 16.62 0.00 0.00 4.18
1315 1355 2.026879 GAGATCGAGCCGGCAGAC 59.973 66.667 31.54 18.19 0.00 3.51
1354 1394 1.136305 GCGCTGAGTTATGGTACCTGA 59.864 52.381 14.36 0.00 0.00 3.86
1430 1470 8.535335 AGACATTTCAGTTCAGTATGTGTAGAT 58.465 33.333 0.00 0.00 37.40 1.98
1433 1473 6.806739 CGAGACATTTCAGTTCAGTATGTGTA 59.193 38.462 0.00 0.00 37.40 2.90
1434 1474 5.635280 CGAGACATTTCAGTTCAGTATGTGT 59.365 40.000 0.00 0.00 37.40 3.72
1435 1475 5.635280 ACGAGACATTTCAGTTCAGTATGTG 59.365 40.000 0.00 0.00 37.40 3.21
1440 1480 3.809832 CCAACGAGACATTTCAGTTCAGT 59.190 43.478 0.00 0.00 0.00 3.41
1441 1481 4.058124 TCCAACGAGACATTTCAGTTCAG 58.942 43.478 0.00 0.00 0.00 3.02
1442 1482 4.066646 TCCAACGAGACATTTCAGTTCA 57.933 40.909 0.00 0.00 0.00 3.18
1443 1483 5.613358 AATCCAACGAGACATTTCAGTTC 57.387 39.130 0.00 0.00 0.00 3.01
1444 1484 7.687941 ATTAATCCAACGAGACATTTCAGTT 57.312 32.000 0.00 0.00 0.00 3.16
1458 1498 7.628580 GCCCTTCAAGACAGTTATTAATCCAAC 60.629 40.741 0.00 0.00 0.00 3.77
1462 1502 6.261158 GGAGCCCTTCAAGACAGTTATTAATC 59.739 42.308 0.00 0.00 0.00 1.75
1465 1505 4.783227 AGGAGCCCTTCAAGACAGTTATTA 59.217 41.667 0.00 0.00 0.00 0.98
1730 1770 5.473931 TGCTAGTTTGCAGAAAGTCTAGAG 58.526 41.667 0.00 0.00 38.12 2.43
1780 1820 7.592938 TGTTACAGATGCTAAGAAAAACATGG 58.407 34.615 0.00 0.00 0.00 3.66
1924 1964 3.423539 AGATAGTGCTTGGCTGAAACA 57.576 42.857 0.00 0.00 0.00 2.83
2120 2189 4.331968 TGTAGCAAGGTTTATCCCAGTTG 58.668 43.478 0.00 0.00 36.75 3.16
2155 2224 4.272504 TCAGAACGTGAAACCAAAAGCTAG 59.727 41.667 0.00 0.00 29.64 3.42
2522 2591 2.229784 GACCCAAAATGAACCAGCTGAG 59.770 50.000 17.39 8.04 0.00 3.35
2627 2696 2.038814 TTGCACCGCTCCTCTTCACA 62.039 55.000 0.00 0.00 0.00 3.58
2666 2735 6.979817 TGTCAGAAGGATTGTTCAATTTTGTG 59.020 34.615 0.00 6.89 0.00 3.33
2689 2758 1.602165 CGTCAGTCGTTGCTTAGGTGT 60.602 52.381 0.00 0.00 34.52 4.16


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

AutoCloner maintained by Alex Coulton.