Multiple sequence alignment - TraesCS2D01G425700

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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 TraesCS2D01G425700 chr2D 100.000 2654 0 0 1 2654 538056337 538053684 0.000000e+00 4902
1 TraesCS2D01G425700 chr2D 87.200 125 12 3 441 564 531675847 531675968 3.560000e-29 139
2 TraesCS2D01G425700 chr2B 91.710 1713 66 35 582 2239 640765816 640764125 0.000000e+00 2307
3 TraesCS2D01G425700 chr2B 86.449 428 21 12 2245 2654 640764090 640763682 4.060000e-118 435
4 TraesCS2D01G425700 chr2B 83.596 445 32 22 18 453 640766238 640765826 1.930000e-101 379
5 TraesCS2D01G425700 chr2A 91.333 1696 71 37 575 2244 680358201 680356556 0.000000e+00 2248
6 TraesCS2D01G425700 chr2A 87.356 435 17 16 2246 2654 680356526 680356104 5.170000e-127 464
7 TraesCS2D01G425700 chr2A 81.667 420 21 21 70 453 680358600 680358201 5.550000e-77 298
8 TraesCS2D01G425700 chr2A 82.946 129 18 3 456 581 569370350 569370223 2.160000e-21 113
9 TraesCS2D01G425700 chr6D 90.110 182 15 3 1057 1237 139916316 139916495 1.590000e-57 233
10 TraesCS2D01G425700 chr6B 90.805 174 14 2 1065 1237 239729260 239729432 5.710000e-57 231
11 TraesCS2D01G425700 chr6A 90.805 174 14 2 1065 1237 183188186 183188358 5.710000e-57 231
12 TraesCS2D01G425700 chr1B 81.955 266 32 13 1069 1327 552474257 552474001 7.440000e-51 211
13 TraesCS2D01G425700 chr1B 86.726 113 13 2 456 566 502961244 502961356 9.970000e-25 124
14 TraesCS2D01G425700 chr1D 86.559 186 25 0 1069 1254 410072045 410071860 3.460000e-49 206
15 TraesCS2D01G425700 chr1A 81.203 266 37 10 1069 1327 505925841 505925582 4.480000e-48 202
16 TraesCS2D01G425700 chr7B 90.000 100 9 1 466 564 452511731 452511632 7.710000e-26 128
17 TraesCS2D01G425700 chr7B 85.593 118 13 4 448 564 413595613 413595499 1.290000e-23 121
18 TraesCS2D01G425700 chr4A 80.347 173 30 2 1068 1238 3370736 3370906 7.710000e-26 128
19 TraesCS2D01G425700 chr7D 85.246 122 14 3 444 564 443163350 443163232 3.590000e-24 122
20 TraesCS2D01G425700 chr7A 83.721 129 17 3 456 581 48516564 48516691 4.640000e-23 119
21 TraesCS2D01G425700 chr3D 83.721 129 17 3 456 581 384143971 384144098 4.640000e-23 119
22 TraesCS2D01G425700 chr3B 83.721 129 17 3 456 581 104392893 104393020 4.640000e-23 119


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 TraesCS2D01G425700 chr2D 538053684 538056337 2653 True 4902.000000 4902 100.000000 1 2654 1 chr2D.!!$R1 2653
1 TraesCS2D01G425700 chr2B 640763682 640766238 2556 True 1040.333333 2307 87.251667 18 2654 3 chr2B.!!$R1 2636
2 TraesCS2D01G425700 chr2A 680356104 680358600 2496 True 1003.333333 2248 86.785333 70 2654 3 chr2A.!!$R2 2584

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
303 335 0.031994 GCCACGTGCATTTTTGGTCT 59.968 50.0 10.91 0.0 40.77 3.85 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2059 2159 0.108585 ACAGCCACACACCGAAGAAT 59.891 50.0 0.0 0.0 0.0 2.4 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
165 170 0.521291 GCGCATGTGTGGAAAGCTAA 59.479 50.000 0.30 0.00 0.00 3.09
166 171 1.133025 GCGCATGTGTGGAAAGCTAAT 59.867 47.619 0.30 0.00 0.00 1.73
197 202 2.793933 TCGGTAGAAGAAGCGATTTCG 58.206 47.619 0.00 0.00 43.75 3.46
206 212 2.858344 AGAAGCGATTTCGTTCGTATGG 59.142 45.455 1.55 0.00 40.86 2.74
226 232 2.419159 GGTCCGGTAATTACCTTTCGCT 60.419 50.000 27.89 0.00 44.25 4.93
251 278 3.192422 TGCAAAGTGATTAAATCCGTGGG 59.808 43.478 0.00 0.00 0.00 4.61
255 282 3.214328 AGTGATTAAATCCGTGGGCATC 58.786 45.455 0.00 0.00 0.00 3.91
298 330 2.338257 CGGGCCACGTGCATTTTT 59.662 55.556 10.91 0.00 43.89 1.94
299 331 2.021039 CGGGCCACGTGCATTTTTG 61.021 57.895 10.91 0.00 43.89 2.44
300 332 1.667510 GGGCCACGTGCATTTTTGG 60.668 57.895 10.91 0.00 43.89 3.28
302 334 0.943835 GGCCACGTGCATTTTTGGTC 60.944 55.000 10.91 0.00 43.89 4.02
303 335 0.031994 GCCACGTGCATTTTTGGTCT 59.968 50.000 10.91 0.00 40.77 3.85
352 387 4.255833 ACGAATACCGAACCAACTAACA 57.744 40.909 0.00 0.00 41.76 2.41
355 390 4.687483 CGAATACCGAACCAACTAACACTT 59.313 41.667 0.00 0.00 41.76 3.16
362 397 2.129607 ACCAACTAACACTTGCGTACG 58.870 47.619 11.84 11.84 0.00 3.67
386 421 0.509929 CGACGAGGGGAAAACGAAAC 59.490 55.000 0.00 0.00 0.00 2.78
391 426 2.738314 CGAGGGGAAAACGAAACGTAAT 59.262 45.455 0.00 0.00 39.99 1.89
392 427 3.181527 CGAGGGGAAAACGAAACGTAATC 60.182 47.826 0.00 0.00 39.99 1.75
393 428 3.742385 AGGGGAAAACGAAACGTAATCA 58.258 40.909 0.00 0.00 39.99 2.57
394 429 4.136051 AGGGGAAAACGAAACGTAATCAA 58.864 39.130 0.00 0.00 39.99 2.57
395 430 4.214758 AGGGGAAAACGAAACGTAATCAAG 59.785 41.667 0.00 0.00 39.99 3.02
405 440 3.418684 ACGTAATCAAGGCCTGAAACT 57.581 42.857 5.69 0.00 37.67 2.66
412 447 4.404654 GGCCTGAAACTTGCGCGG 62.405 66.667 8.83 0.00 0.00 6.46
429 464 1.531149 GCGGTTACCATTCCATCGATG 59.469 52.381 18.76 18.76 0.00 3.84
453 488 5.366829 ACGGCCAGAATAAAAAGTTGTAC 57.633 39.130 2.24 0.00 0.00 2.90
454 489 4.083696 ACGGCCAGAATAAAAAGTTGTACG 60.084 41.667 2.24 0.00 0.00 3.67
455 490 4.083696 CGGCCAGAATAAAAAGTTGTACGT 60.084 41.667 2.24 0.00 0.00 3.57
456 491 5.120519 CGGCCAGAATAAAAAGTTGTACGTA 59.879 40.000 2.24 0.00 0.00 3.57
457 492 6.309436 GGCCAGAATAAAAAGTTGTACGTAC 58.691 40.000 18.90 18.90 0.00 3.67
458 493 6.309436 GCCAGAATAAAAAGTTGTACGTACC 58.691 40.000 22.43 8.47 0.00 3.34
459 494 6.621380 GCCAGAATAAAAAGTTGTACGTACCC 60.621 42.308 22.43 13.03 0.00 3.69
460 495 6.128200 CCAGAATAAAAAGTTGTACGTACCCC 60.128 42.308 22.43 12.69 0.00 4.95
461 496 6.652062 CAGAATAAAAAGTTGTACGTACCCCT 59.348 38.462 22.43 14.68 0.00 4.79
462 497 6.875726 AGAATAAAAAGTTGTACGTACCCCTC 59.124 38.462 22.43 10.14 0.00 4.30
463 498 4.694760 AAAAAGTTGTACGTACCCCTCT 57.305 40.909 22.43 12.05 0.00 3.69
464 499 3.672767 AAAGTTGTACGTACCCCTCTG 57.327 47.619 22.43 0.00 0.00 3.35
465 500 2.299326 AGTTGTACGTACCCCTCTGT 57.701 50.000 22.43 0.00 0.00 3.41
466 501 2.165998 AGTTGTACGTACCCCTCTGTC 58.834 52.381 22.43 4.76 0.00 3.51
467 502 1.203287 GTTGTACGTACCCCTCTGTCC 59.797 57.143 22.43 0.00 0.00 4.02
468 503 0.405198 TGTACGTACCCCTCTGTCCA 59.595 55.000 22.43 0.00 0.00 4.02
469 504 1.203038 TGTACGTACCCCTCTGTCCAA 60.203 52.381 22.43 0.00 0.00 3.53
470 505 1.895131 GTACGTACCCCTCTGTCCAAA 59.105 52.381 15.00 0.00 0.00 3.28
471 506 1.426751 ACGTACCCCTCTGTCCAAAA 58.573 50.000 0.00 0.00 0.00 2.44
472 507 1.770061 ACGTACCCCTCTGTCCAAAAA 59.230 47.619 0.00 0.00 0.00 1.94
473 508 2.374170 ACGTACCCCTCTGTCCAAAAAT 59.626 45.455 0.00 0.00 0.00 1.82
474 509 3.583966 ACGTACCCCTCTGTCCAAAAATA 59.416 43.478 0.00 0.00 0.00 1.40
475 510 4.226620 ACGTACCCCTCTGTCCAAAAATAT 59.773 41.667 0.00 0.00 0.00 1.28
476 511 5.190677 CGTACCCCTCTGTCCAAAAATATT 58.809 41.667 0.00 0.00 0.00 1.28
477 512 5.650703 CGTACCCCTCTGTCCAAAAATATTT 59.349 40.000 0.00 0.00 0.00 1.40
478 513 6.824704 CGTACCCCTCTGTCCAAAAATATTTA 59.175 38.462 0.01 0.00 0.00 1.40
479 514 7.501225 CGTACCCCTCTGTCCAAAAATATTTAT 59.499 37.037 0.01 0.00 0.00 1.40
480 515 9.197306 GTACCCCTCTGTCCAAAAATATTTATT 57.803 33.333 0.01 0.00 0.00 1.40
482 517 9.777008 ACCCCTCTGTCCAAAAATATTTATTAA 57.223 29.630 0.01 0.00 0.00 1.40
543 578 7.969536 ACATTTAGATACATCCATTTCTCCG 57.030 36.000 0.00 0.00 0.00 4.63
544 579 7.735917 ACATTTAGATACATCCATTTCTCCGA 58.264 34.615 0.00 0.00 0.00 4.55
545 580 7.657761 ACATTTAGATACATCCATTTCTCCGAC 59.342 37.037 0.00 0.00 0.00 4.79
546 581 6.724893 TTAGATACATCCATTTCTCCGACA 57.275 37.500 0.00 0.00 0.00 4.35
547 582 5.614324 AGATACATCCATTTCTCCGACAA 57.386 39.130 0.00 0.00 0.00 3.18
548 583 5.605534 AGATACATCCATTTCTCCGACAAG 58.394 41.667 0.00 0.00 0.00 3.16
549 584 3.703001 ACATCCATTTCTCCGACAAGT 57.297 42.857 0.00 0.00 0.00 3.16
550 585 4.819105 ACATCCATTTCTCCGACAAGTA 57.181 40.909 0.00 0.00 0.00 2.24
551 586 5.359194 ACATCCATTTCTCCGACAAGTAT 57.641 39.130 0.00 0.00 0.00 2.12
552 587 5.745227 ACATCCATTTCTCCGACAAGTATT 58.255 37.500 0.00 0.00 0.00 1.89
553 588 6.180472 ACATCCATTTCTCCGACAAGTATTT 58.820 36.000 0.00 0.00 0.00 1.40
554 589 6.659242 ACATCCATTTCTCCGACAAGTATTTT 59.341 34.615 0.00 0.00 0.00 1.82
555 590 7.176690 ACATCCATTTCTCCGACAAGTATTTTT 59.823 33.333 0.00 0.00 0.00 1.94
556 591 6.908825 TCCATTTCTCCGACAAGTATTTTTG 58.091 36.000 0.00 0.00 0.00 2.44
557 592 6.072175 TCCATTTCTCCGACAAGTATTTTTGG 60.072 38.462 0.00 0.00 32.32 3.28
558 593 6.072175 CCATTTCTCCGACAAGTATTTTTGGA 60.072 38.462 0.00 0.00 32.32 3.53
559 594 5.934935 TTCTCCGACAAGTATTTTTGGAC 57.065 39.130 0.00 0.00 32.32 4.02
560 595 3.991773 TCTCCGACAAGTATTTTTGGACG 59.008 43.478 0.00 0.00 34.41 4.79
561 596 3.068560 TCCGACAAGTATTTTTGGACGG 58.931 45.455 15.12 15.12 44.84 4.79
562 597 3.068560 CCGACAAGTATTTTTGGACGGA 58.931 45.455 15.77 0.00 45.53 4.69
563 598 3.124636 CCGACAAGTATTTTTGGACGGAG 59.875 47.826 15.77 0.00 45.53 4.63
564 599 3.991773 CGACAAGTATTTTTGGACGGAGA 59.008 43.478 0.00 0.00 32.62 3.71
565 600 4.091509 CGACAAGTATTTTTGGACGGAGAG 59.908 45.833 0.00 0.00 32.62 3.20
566 601 3.751698 ACAAGTATTTTTGGACGGAGAGC 59.248 43.478 0.00 0.00 32.32 4.09
567 602 3.983044 AGTATTTTTGGACGGAGAGCT 57.017 42.857 0.00 0.00 0.00 4.09
568 603 5.175859 CAAGTATTTTTGGACGGAGAGCTA 58.824 41.667 0.00 0.00 0.00 3.32
569 604 4.756502 AGTATTTTTGGACGGAGAGCTAC 58.243 43.478 0.00 0.00 0.00 3.58
570 605 3.695830 ATTTTTGGACGGAGAGCTACA 57.304 42.857 0.00 0.00 0.00 2.74
571 606 3.478857 TTTTTGGACGGAGAGCTACAA 57.521 42.857 0.00 0.00 0.00 2.41
572 607 3.478857 TTTTGGACGGAGAGCTACAAA 57.521 42.857 0.00 0.00 0.00 2.83
573 608 2.743636 TTGGACGGAGAGCTACAAAG 57.256 50.000 0.00 0.00 0.00 2.77
574 609 1.919240 TGGACGGAGAGCTACAAAGA 58.081 50.000 0.00 0.00 0.00 2.52
580 615 3.827302 ACGGAGAGCTACAAAGAAAGAGA 59.173 43.478 0.00 0.00 0.00 3.10
586 624 7.233389 AGAGCTACAAAGAAAGAGATACACA 57.767 36.000 0.00 0.00 0.00 3.72
650 695 1.532868 CAAACCAGCACTGCTCAGTAC 59.467 52.381 0.00 0.00 40.20 2.73
656 701 2.029918 CAGCACTGCTCAGTACAGTACA 60.030 50.000 13.37 0.00 46.44 2.90
657 702 2.230025 AGCACTGCTCAGTACAGTACAG 59.770 50.000 13.37 5.12 46.44 2.74
658 703 2.029828 GCACTGCTCAGTACAGTACAGT 60.030 50.000 13.37 4.41 46.44 3.55
659 704 3.190744 GCACTGCTCAGTACAGTACAGTA 59.809 47.826 13.37 1.57 46.44 2.74
660 705 4.724303 CACTGCTCAGTACAGTACAGTAC 58.276 47.826 18.11 18.11 46.44 2.73
935 989 1.687612 CTCCAACCAGCCAGACCAT 59.312 57.895 0.00 0.00 0.00 3.55
1323 1402 2.986413 AGCAGCACCGTCGAGTCT 60.986 61.111 0.00 0.00 0.00 3.24
1705 1790 2.046700 CGGCCCGGAAGTAAAGCA 60.047 61.111 0.73 0.00 0.00 3.91
1710 1795 0.168128 CCCGGAAGTAAAGCAAAGCG 59.832 55.000 0.73 0.00 0.00 4.68
1751 1837 5.857822 AAGTTTAGAAGAATGGCGTGTAC 57.142 39.130 0.00 0.00 0.00 2.90
1752 1838 5.148651 AGTTTAGAAGAATGGCGTGTACT 57.851 39.130 0.00 0.00 0.00 2.73
1753 1839 5.548406 AGTTTAGAAGAATGGCGTGTACTT 58.452 37.500 0.00 0.00 0.00 2.24
1754 1840 6.694447 AGTTTAGAAGAATGGCGTGTACTTA 58.306 36.000 0.00 0.00 0.00 2.24
1868 1962 3.125376 GCATGGGGAGGCAGGTAGG 62.125 68.421 0.00 0.00 0.00 3.18
1873 1967 0.694444 GGGGAGGCAGGTAGGATGAA 60.694 60.000 0.00 0.00 0.00 2.57
1875 1969 1.134068 GGGAGGCAGGTAGGATGAAAC 60.134 57.143 0.00 0.00 0.00 2.78
2004 2104 8.131731 TGTACAATATTTGATCTCTGTCTCTCG 58.868 37.037 0.00 0.00 0.00 4.04
2059 2159 2.388310 TGACCGTGTGTTGTTCTTCA 57.612 45.000 0.00 0.00 0.00 3.02
2071 2171 4.035091 TGTTGTTCTTCATTCTTCGGTGTG 59.965 41.667 0.00 0.00 0.00 3.82
2093 2221 5.181245 GTGTGGCTGTTGTGTATGATTAGTT 59.819 40.000 0.00 0.00 0.00 2.24
2096 2224 6.000840 TGGCTGTTGTGTATGATTAGTTGAA 58.999 36.000 0.00 0.00 0.00 2.69
2106 2234 9.155975 GTGTATGATTAGTTGAACTGTCTTGAT 57.844 33.333 8.33 0.00 0.00 2.57
2124 2252 7.227314 TGTCTTGATTAATTACTGGCATGCTAG 59.773 37.037 27.56 27.56 0.00 3.42
2125 2253 7.227512 GTCTTGATTAATTACTGGCATGCTAGT 59.772 37.037 34.77 34.77 40.78 2.57
2126 2254 8.428852 TCTTGATTAATTACTGGCATGCTAGTA 58.571 33.333 32.73 32.73 38.66 1.82
2140 2271 9.653287 TGGCATGCTAGTAATAGTAATCATAAC 57.347 33.333 18.92 0.00 0.00 1.89
2163 2294 4.837093 TGGTTCTTTGGGGTATCTACTG 57.163 45.455 0.00 0.00 0.00 2.74
2177 2308 6.310711 GGGTATCTACTGACTTGTTTTTCGAG 59.689 42.308 0.00 0.00 0.00 4.04
2208 2339 3.254827 TCGATCATCGAAGAAGTAGCG 57.745 47.619 7.45 0.00 46.90 4.26
2241 2372 4.015872 TCGGACCAGCAAAAGAAACTAT 57.984 40.909 0.00 0.00 0.00 2.12
2242 2373 4.000988 TCGGACCAGCAAAAGAAACTATC 58.999 43.478 0.00 0.00 0.00 2.08
2260 2420 1.194781 TCCAGTTCAGTCCCTCTGGC 61.195 60.000 5.33 0.00 44.76 4.85
2264 2424 0.393537 GTTCAGTCCCTCTGGCATGG 60.394 60.000 0.00 0.00 43.76 3.66
2320 2491 1.961277 CGTCCCGACTGCAAAAGCT 60.961 57.895 0.00 0.00 0.00 3.74
2321 2492 0.669318 CGTCCCGACTGCAAAAGCTA 60.669 55.000 0.00 0.00 0.00 3.32
2326 2497 2.095718 CCCGACTGCAAAAGCTAAGAAC 60.096 50.000 0.00 0.00 0.00 3.01
2356 2542 1.868498 GTCGTTGAATTGAACGGTCCA 59.132 47.619 26.10 7.65 46.93 4.02
2443 2633 2.506061 CGGGGCATCCTGAGAGAGG 61.506 68.421 0.00 0.00 42.08 3.69
2444 2634 2.817056 GGGGCATCCTGAGAGAGGC 61.817 68.421 0.08 0.08 42.47 4.70
2486 2678 4.717629 CTTGGAGCCGACGACGCA 62.718 66.667 0.64 0.00 38.29 5.24
2495 2687 4.134187 GACGACGCACGGTGCATG 62.134 66.667 30.23 20.96 45.36 4.06
2562 2760 4.747529 GGGTCCGCCCGTACACAC 62.748 72.222 0.00 0.00 46.51 3.82
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 2.742372 GTGCGATTCGGTGGCAGT 60.742 61.111 8.34 0.00 42.49 4.40
1 2 3.853330 CGTGCGATTCGGTGGCAG 61.853 66.667 8.34 0.00 42.49 4.85
4 5 4.147322 GTGCGTGCGATTCGGTGG 62.147 66.667 8.34 0.00 0.00 4.61
5 6 4.483683 CGTGCGTGCGATTCGGTG 62.484 66.667 8.34 0.00 0.00 4.94
15 16 4.121227 CTAGTGCGTGCGTGCGTG 62.121 66.667 3.11 0.00 37.81 5.34
191 196 1.856597 CCGGACCATACGAACGAAATC 59.143 52.381 0.00 0.00 0.00 2.17
192 197 1.205417 ACCGGACCATACGAACGAAAT 59.795 47.619 9.46 0.00 0.00 2.17
193 198 0.602562 ACCGGACCATACGAACGAAA 59.397 50.000 9.46 0.00 0.00 3.46
194 199 1.458398 TACCGGACCATACGAACGAA 58.542 50.000 9.46 0.00 0.00 3.85
195 200 1.458398 TTACCGGACCATACGAACGA 58.542 50.000 9.46 0.00 0.00 3.85
196 201 2.497107 ATTACCGGACCATACGAACG 57.503 50.000 9.46 0.00 0.00 3.95
197 202 4.051237 GGTAATTACCGGACCATACGAAC 58.949 47.826 18.70 0.00 36.50 3.95
226 232 3.505680 ACGGATTTAATCACTTTGCAGCA 59.494 39.130 7.29 0.00 0.00 4.41
251 278 1.661112 GAGAGCAACAGTTACCGATGC 59.339 52.381 0.00 0.00 37.28 3.91
255 282 0.038526 ACCGAGAGCAACAGTTACCG 60.039 55.000 0.00 0.00 0.00 4.02
327 362 3.192466 AGTTGGTTCGGTATTCGTATGC 58.808 45.455 0.00 0.00 40.32 3.14
362 397 1.422388 GTTTTCCCCTCGTCGTACAC 58.578 55.000 0.00 0.00 0.00 2.90
386 421 3.670627 GCAAGTTTCAGGCCTTGATTACG 60.671 47.826 0.00 0.00 40.36 3.18
391 426 1.795170 GCGCAAGTTTCAGGCCTTGA 61.795 55.000 0.00 0.71 40.36 3.02
392 427 1.372128 GCGCAAGTTTCAGGCCTTG 60.372 57.895 0.00 0.00 40.77 3.61
393 428 2.908073 CGCGCAAGTTTCAGGCCTT 61.908 57.895 0.00 0.00 41.68 4.35
394 429 3.357079 CGCGCAAGTTTCAGGCCT 61.357 61.111 8.75 0.00 41.68 5.19
395 430 4.404654 CCGCGCAAGTTTCAGGCC 62.405 66.667 8.75 0.00 41.68 5.19
405 440 0.678366 ATGGAATGGTAACCGCGCAA 60.678 50.000 8.75 0.00 0.00 4.85
429 464 3.254903 ACAACTTTTTATTCTGGCCGTCC 59.745 43.478 0.00 0.00 0.00 4.79
430 465 4.499037 ACAACTTTTTATTCTGGCCGTC 57.501 40.909 0.00 0.00 0.00 4.79
453 488 2.554370 TTTTTGGACAGAGGGGTACG 57.446 50.000 0.00 0.00 0.00 3.67
454 489 8.762481 ATAAATATTTTTGGACAGAGGGGTAC 57.238 34.615 5.91 0.00 0.00 3.34
456 491 9.777008 TTAATAAATATTTTTGGACAGAGGGGT 57.223 29.630 5.91 0.00 0.00 4.95
517 552 9.658799 CGGAGAAATGGATGTATCTAAATGTAT 57.341 33.333 0.00 0.00 0.00 2.29
518 553 8.866093 TCGGAGAAATGGATGTATCTAAATGTA 58.134 33.333 0.00 0.00 0.00 2.29
519 554 7.657761 GTCGGAGAAATGGATGTATCTAAATGT 59.342 37.037 0.00 0.00 39.69 2.71
520 555 7.657354 TGTCGGAGAAATGGATGTATCTAAATG 59.343 37.037 0.00 0.00 39.69 2.32
521 556 7.735917 TGTCGGAGAAATGGATGTATCTAAAT 58.264 34.615 0.00 0.00 39.69 1.40
522 557 7.119709 TGTCGGAGAAATGGATGTATCTAAA 57.880 36.000 0.00 0.00 39.69 1.85
523 558 6.724893 TGTCGGAGAAATGGATGTATCTAA 57.275 37.500 0.00 0.00 39.69 2.10
524 559 6.323996 ACTTGTCGGAGAAATGGATGTATCTA 59.676 38.462 0.00 0.00 39.69 1.98
525 560 5.129485 ACTTGTCGGAGAAATGGATGTATCT 59.871 40.000 0.00 0.00 39.69 1.98
526 561 5.360591 ACTTGTCGGAGAAATGGATGTATC 58.639 41.667 0.00 0.00 39.69 2.24
527 562 5.359194 ACTTGTCGGAGAAATGGATGTAT 57.641 39.130 0.00 0.00 39.69 2.29
528 563 4.819105 ACTTGTCGGAGAAATGGATGTA 57.181 40.909 0.00 0.00 39.69 2.29
529 564 3.703001 ACTTGTCGGAGAAATGGATGT 57.297 42.857 0.00 0.00 39.69 3.06
530 565 6.683974 AAATACTTGTCGGAGAAATGGATG 57.316 37.500 0.00 0.00 39.69 3.51
531 566 7.362920 CCAAAAATACTTGTCGGAGAAATGGAT 60.363 37.037 0.00 0.00 39.69 3.41
532 567 6.072175 CCAAAAATACTTGTCGGAGAAATGGA 60.072 38.462 0.00 0.00 39.69 3.41
533 568 6.072175 TCCAAAAATACTTGTCGGAGAAATGG 60.072 38.462 0.00 0.00 39.69 3.16
534 569 6.801862 GTCCAAAAATACTTGTCGGAGAAATG 59.198 38.462 0.00 0.00 39.69 2.32
535 570 6.348213 CGTCCAAAAATACTTGTCGGAGAAAT 60.348 38.462 0.00 0.00 39.69 2.17
536 571 5.049954 CGTCCAAAAATACTTGTCGGAGAAA 60.050 40.000 0.00 0.00 39.69 2.52
537 572 4.449743 CGTCCAAAAATACTTGTCGGAGAA 59.550 41.667 0.00 0.00 39.69 2.87
538 573 3.991773 CGTCCAAAAATACTTGTCGGAGA 59.008 43.478 0.00 0.00 0.00 3.71
539 574 3.124636 CCGTCCAAAAATACTTGTCGGAG 59.875 47.826 9.84 0.00 40.80 4.63
540 575 3.068560 CCGTCCAAAAATACTTGTCGGA 58.931 45.455 9.84 0.00 40.80 4.55
541 576 3.068560 TCCGTCCAAAAATACTTGTCGG 58.931 45.455 0.00 0.00 40.25 4.79
542 577 3.991773 TCTCCGTCCAAAAATACTTGTCG 59.008 43.478 0.00 0.00 0.00 4.35
543 578 4.142881 GCTCTCCGTCCAAAAATACTTGTC 60.143 45.833 0.00 0.00 0.00 3.18
544 579 3.751698 GCTCTCCGTCCAAAAATACTTGT 59.248 43.478 0.00 0.00 0.00 3.16
545 580 4.003648 AGCTCTCCGTCCAAAAATACTTG 58.996 43.478 0.00 0.00 0.00 3.16
546 581 4.287766 AGCTCTCCGTCCAAAAATACTT 57.712 40.909 0.00 0.00 0.00 2.24
547 582 3.983044 AGCTCTCCGTCCAAAAATACT 57.017 42.857 0.00 0.00 0.00 2.12
548 583 4.501071 TGTAGCTCTCCGTCCAAAAATAC 58.499 43.478 0.00 0.00 0.00 1.89
549 584 4.811969 TGTAGCTCTCCGTCCAAAAATA 57.188 40.909 0.00 0.00 0.00 1.40
550 585 3.695830 TGTAGCTCTCCGTCCAAAAAT 57.304 42.857 0.00 0.00 0.00 1.82
551 586 3.478857 TTGTAGCTCTCCGTCCAAAAA 57.521 42.857 0.00 0.00 0.00 1.94
552 587 3.070446 TCTTTGTAGCTCTCCGTCCAAAA 59.930 43.478 0.00 0.00 0.00 2.44
553 588 2.631062 TCTTTGTAGCTCTCCGTCCAAA 59.369 45.455 0.00 0.00 0.00 3.28
554 589 2.244695 TCTTTGTAGCTCTCCGTCCAA 58.755 47.619 0.00 0.00 0.00 3.53
555 590 1.919240 TCTTTGTAGCTCTCCGTCCA 58.081 50.000 0.00 0.00 0.00 4.02
556 591 3.056749 TCTTTCTTTGTAGCTCTCCGTCC 60.057 47.826 0.00 0.00 0.00 4.79
557 592 4.082679 TCTCTTTCTTTGTAGCTCTCCGTC 60.083 45.833 0.00 0.00 0.00 4.79
558 593 3.827302 TCTCTTTCTTTGTAGCTCTCCGT 59.173 43.478 0.00 0.00 0.00 4.69
559 594 4.442375 TCTCTTTCTTTGTAGCTCTCCG 57.558 45.455 0.00 0.00 0.00 4.63
560 595 6.754675 GTGTATCTCTTTCTTTGTAGCTCTCC 59.245 42.308 0.00 0.00 0.00 3.71
561 596 7.274686 GTGTGTATCTCTTTCTTTGTAGCTCTC 59.725 40.741 0.00 0.00 0.00 3.20
562 597 7.093992 GTGTGTATCTCTTTCTTTGTAGCTCT 58.906 38.462 0.00 0.00 0.00 4.09
563 598 6.311690 GGTGTGTATCTCTTTCTTTGTAGCTC 59.688 42.308 0.00 0.00 0.00 4.09
564 599 6.166982 GGTGTGTATCTCTTTCTTTGTAGCT 58.833 40.000 0.00 0.00 0.00 3.32
565 600 5.062308 CGGTGTGTATCTCTTTCTTTGTAGC 59.938 44.000 0.00 0.00 0.00 3.58
566 601 6.089551 CACGGTGTGTATCTCTTTCTTTGTAG 59.910 42.308 0.00 0.00 0.00 2.74
567 602 5.924254 CACGGTGTGTATCTCTTTCTTTGTA 59.076 40.000 0.00 0.00 0.00 2.41
568 603 4.750098 CACGGTGTGTATCTCTTTCTTTGT 59.250 41.667 0.00 0.00 0.00 2.83
569 604 4.988540 TCACGGTGTGTATCTCTTTCTTTG 59.011 41.667 8.17 0.00 34.79 2.77
570 605 5.209818 TCACGGTGTGTATCTCTTTCTTT 57.790 39.130 8.17 0.00 34.79 2.52
571 606 4.866508 TCACGGTGTGTATCTCTTTCTT 57.133 40.909 8.17 0.00 34.79 2.52
572 607 4.281182 AGTTCACGGTGTGTATCTCTTTCT 59.719 41.667 8.17 0.00 34.79 2.52
573 608 4.557205 AGTTCACGGTGTGTATCTCTTTC 58.443 43.478 8.17 0.00 34.79 2.62
574 609 4.602340 AGTTCACGGTGTGTATCTCTTT 57.398 40.909 8.17 0.00 34.79 2.52
601 646 2.242965 TGAGGTACCCCGATTCTCTACA 59.757 50.000 8.74 0.00 35.12 2.74
650 695 4.799678 CTTGGTCACTCTGTACTGTACTG 58.200 47.826 17.98 16.98 0.00 2.74
656 701 1.269998 GTCGCTTGGTCACTCTGTACT 59.730 52.381 0.00 0.00 0.00 2.73
657 702 1.669211 GGTCGCTTGGTCACTCTGTAC 60.669 57.143 0.00 0.00 0.00 2.90
658 703 0.601558 GGTCGCTTGGTCACTCTGTA 59.398 55.000 0.00 0.00 0.00 2.74
659 704 1.367840 GGTCGCTTGGTCACTCTGT 59.632 57.895 0.00 0.00 0.00 3.41
660 705 0.249868 TTGGTCGCTTGGTCACTCTG 60.250 55.000 0.00 0.00 0.00 3.35
978 1045 1.660575 AAGTGTTCGACCGTGCTCG 60.661 57.895 0.14 0.14 34.83 5.03
979 1046 1.853319 CAAGTGTTCGACCGTGCTC 59.147 57.895 0.00 0.00 0.00 4.26
980 1047 2.244651 GCAAGTGTTCGACCGTGCT 61.245 57.895 8.79 0.00 34.59 4.40
981 1048 2.248431 GCAAGTGTTCGACCGTGC 59.752 61.111 0.00 0.00 0.00 5.34
982 1049 1.227999 ATGGCAAGTGTTCGACCGTG 61.228 55.000 0.00 0.00 0.00 4.94
983 1050 1.070786 ATGGCAAGTGTTCGACCGT 59.929 52.632 0.00 0.00 0.00 4.83
984 1051 1.497278 CATGGCAAGTGTTCGACCG 59.503 57.895 0.00 0.00 0.00 4.79
985 1052 1.875963 CCATGGCAAGTGTTCGACC 59.124 57.895 0.00 0.00 0.00 4.79
1705 1790 0.601558 TTCTACCACGAGAGCGCTTT 59.398 50.000 13.26 5.40 42.48 3.51
1710 1795 6.723131 AACTTTAAATTCTACCACGAGAGC 57.277 37.500 0.00 0.00 0.00 4.09
1751 1837 6.445475 GGCCGATTAACCTCTTACTAGTAAG 58.555 44.000 29.36 29.36 42.86 2.34
1752 1838 5.009010 CGGCCGATTAACCTCTTACTAGTAA 59.991 44.000 24.07 14.52 0.00 2.24
1753 1839 4.516698 CGGCCGATTAACCTCTTACTAGTA 59.483 45.833 24.07 0.00 0.00 1.82
1754 1840 3.317430 CGGCCGATTAACCTCTTACTAGT 59.683 47.826 24.07 0.00 0.00 2.57
1873 1967 3.072184 GGGAGCAGATAGATGGATGTGTT 59.928 47.826 0.00 0.00 0.00 3.32
1875 1969 2.636403 TGGGAGCAGATAGATGGATGTG 59.364 50.000 0.00 0.00 0.00 3.21
1933 2030 4.281657 ACTGGCTTCTTCCTTTTTGTCTT 58.718 39.130 0.00 0.00 0.00 3.01
1934 2034 3.903467 ACTGGCTTCTTCCTTTTTGTCT 58.097 40.909 0.00 0.00 0.00 3.41
1935 2035 4.822350 ACTACTGGCTTCTTCCTTTTTGTC 59.178 41.667 0.00 0.00 0.00 3.18
1936 2036 4.793201 ACTACTGGCTTCTTCCTTTTTGT 58.207 39.130 0.00 0.00 0.00 2.83
1937 2037 6.231211 TCTACTACTGGCTTCTTCCTTTTTG 58.769 40.000 0.00 0.00 0.00 2.44
1996 2096 7.921786 AAATTTCACATTAATCCGAGAGACA 57.078 32.000 0.00 0.00 0.00 3.41
2041 2141 3.560068 AGAATGAAGAACAACACACGGTC 59.440 43.478 0.00 0.00 0.00 4.79
2059 2159 0.108585 ACAGCCACACACCGAAGAAT 59.891 50.000 0.00 0.00 0.00 2.40
2071 2171 5.411361 TCAACTAATCATACACAACAGCCAC 59.589 40.000 0.00 0.00 0.00 5.01
2093 2221 6.939730 TGCCAGTAATTAATCAAGACAGTTCA 59.060 34.615 0.00 0.00 0.00 3.18
2096 2224 6.183360 GCATGCCAGTAATTAATCAAGACAGT 60.183 38.462 6.36 0.00 0.00 3.55
2109 2237 9.877178 GATTACTATTACTAGCATGCCAGTAAT 57.123 33.333 36.67 36.67 45.43 1.89
2127 2255 9.354673 CCCAAAGAACCATGTTATGATTACTAT 57.645 33.333 0.00 0.00 0.00 2.12
2128 2256 7.777910 CCCCAAAGAACCATGTTATGATTACTA 59.222 37.037 0.00 0.00 0.00 1.82
2140 2271 5.104527 TCAGTAGATACCCCAAAGAACCATG 60.105 44.000 0.00 0.00 0.00 3.66
2151 2282 5.350640 CGAAAAACAAGTCAGTAGATACCCC 59.649 44.000 0.00 0.00 0.00 4.95
2163 2294 4.497507 CCAGTTTCCCTCGAAAAACAAGTC 60.498 45.833 15.81 0.00 39.66 3.01
2177 2308 1.933853 CGATGATCGAACCAGTTTCCC 59.066 52.381 9.62 0.00 43.74 3.97
2200 2331 4.499758 CCGAACATAAGAACTCGCTACTTC 59.500 45.833 0.00 0.00 0.00 3.01
2202 2333 3.693085 TCCGAACATAAGAACTCGCTACT 59.307 43.478 0.00 0.00 0.00 2.57
2208 2339 2.930682 GCTGGTCCGAACATAAGAACTC 59.069 50.000 0.00 0.00 0.00 3.01
2242 2373 1.298014 GCCAGAGGGACTGAACTGG 59.702 63.158 0.00 0.00 46.83 4.00
2260 2420 1.952296 GGGTAATCTTCAGCAGCCATG 59.048 52.381 0.00 0.00 0.00 3.66
2264 2424 3.206964 GGTAAGGGTAATCTTCAGCAGC 58.793 50.000 0.00 0.00 0.00 5.25
2320 2491 1.443194 GACGCGTCCGCAGTTCTTA 60.443 57.895 28.61 0.00 42.06 2.10
2321 2492 2.733593 GACGCGTCCGCAGTTCTT 60.734 61.111 28.61 0.00 42.06 2.52
2356 2542 1.300697 GCAGTTTCGTCGACCCACT 60.301 57.895 10.58 6.55 0.00 4.00
2624 2822 4.074526 TCACTCGCTCAGCTGCCC 62.075 66.667 9.47 0.67 0.00 5.36


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

AutoCloner maintained by Alex Coulton.