Multiple sequence alignment - TraesCS1D01G058600

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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 TraesCS1D01G058600 chr1D 100.000 3171 0 0 1 3171 38654263 38657433 0.000000e+00 5856.0
1 TraesCS1D01G058600 chr1D 81.560 1231 196 23 1038 2254 39651486 39652699 0.000000e+00 987.0
2 TraesCS1D01G058600 chr1D 79.094 1325 243 24 948 2252 38294076 38295386 0.000000e+00 881.0
3 TraesCS1D01G058600 chr1D 81.362 778 130 13 948 1718 38250316 38251085 1.250000e-173 619.0
4 TraesCS1D01G058600 chr1B 94.029 2579 115 14 553 3105 58539704 58542269 0.000000e+00 3873.0
5 TraesCS1D01G058600 chr1B 82.155 1216 188 17 966 2173 58752942 58754136 0.000000e+00 1016.0
6 TraesCS1D01G058600 chr1B 80.146 1234 216 22 948 2164 57782649 57783870 0.000000e+00 894.0
7 TraesCS1D01G058600 chr1B 79.385 1334 223 35 944 2251 58031466 58032773 0.000000e+00 893.0
8 TraesCS1D01G058600 chr1B 90.022 451 14 10 1 426 58539216 58539660 3.570000e-154 555.0
9 TraesCS1D01G058600 chr1B 96.154 78 3 0 3094 3171 58544615 58544692 9.230000e-26 128.0
10 TraesCS1D01G058600 chr1B 79.082 196 18 20 98 273 58022764 58022956 2.590000e-21 113.0
11 TraesCS1D01G058600 chr1B 78.756 193 18 20 100 273 58079010 58079198 1.200000e-19 108.0
12 TraesCS1D01G058600 chr1B 77.228 202 25 13 2064 2251 58082255 58082449 7.240000e-17 99.0
13 TraesCS1D01G058600 chr1B 77.835 194 18 21 100 273 58080957 58081145 2.600000e-16 97.1
14 TraesCS1D01G058600 chr1B 76.733 202 26 13 2064 2251 58108343 58108537 3.370000e-15 93.5
15 TraesCS1D01G058600 chr1A 93.835 1249 50 12 548 1779 38358800 38360038 0.000000e+00 1855.0
16 TraesCS1D01G058600 chr1A 97.180 922 26 0 1806 2727 38360033 38360954 0.000000e+00 1559.0
17 TraesCS1D01G058600 chr1A 79.970 1313 222 31 948 2235 37466614 37467910 0.000000e+00 929.0
18 TraesCS1D01G058600 chr1A 92.584 445 13 4 1 426 38358315 38358758 3.470000e-174 621.0
19 TraesCS1D01G058600 chr1A 93.289 298 12 6 2879 3171 38366612 38366906 1.750000e-117 433.0


These results show the homologous regions that are presented in the multiple sequence alignment. HSPs from the BLAST search that are within 2000 bases of each other have been grouped together. Homologous regions that are purely upstream or downstream may be removed if they don't overlap both primers.

query scaffold start end length rev.comp avg.bitscore max.bitscore avg.percent.identical query.start query.end num_hsp groupid homo_length
0 TraesCS1D01G058600 chr1D 38654263 38657433 3170 False 5856.000000 5856 100.000000 1 3171 1 chr1D.!!$F3 3170
1 TraesCS1D01G058600 chr1D 39651486 39652699 1213 False 987.000000 987 81.560000 1038 2254 1 chr1D.!!$F4 1216
2 TraesCS1D01G058600 chr1D 38294076 38295386 1310 False 881.000000 881 79.094000 948 2252 1 chr1D.!!$F2 1304
3 TraesCS1D01G058600 chr1D 38250316 38251085 769 False 619.000000 619 81.362000 948 1718 1 chr1D.!!$F1 770
4 TraesCS1D01G058600 chr1B 58539216 58544692 5476 False 1518.666667 3873 93.401667 1 3171 3 chr1B.!!$F7 3170
5 TraesCS1D01G058600 chr1B 58752942 58754136 1194 False 1016.000000 1016 82.155000 966 2173 1 chr1B.!!$F5 1207
6 TraesCS1D01G058600 chr1B 57782649 57783870 1221 False 894.000000 894 80.146000 948 2164 1 chr1B.!!$F1 1216
7 TraesCS1D01G058600 chr1B 58031466 58032773 1307 False 893.000000 893 79.385000 944 2251 1 chr1B.!!$F3 1307
8 TraesCS1D01G058600 chr1A 38358315 38360954 2639 False 1345.000000 1855 94.533000 1 2727 3 chr1A.!!$F3 2726
9 TraesCS1D01G058600 chr1A 37466614 37467910 1296 False 929.000000 929 79.970000 948 2235 1 chr1A.!!$F1 1287

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
441 467 0.038744 AGGGAGGGTGTGCTTGATTG 59.961 55.0 0.00 0.00 0.0 2.67 F
443 469 0.251341 GGAGGGTGTGCTTGATTGGT 60.251 55.0 0.00 0.00 0.0 3.67 F
1532 1589 0.318955 CTTCAGTTTGGCGGGCAAAG 60.319 55.0 27.32 17.66 0.0 2.77 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1595 1652 0.250234 GGCTTCCCCCATGAAAAAGC 59.750 55.000 11.34 11.34 41.18 3.51 R
1743 1801 1.145803 GAAACTACTCACGGGTGCAC 58.854 55.000 8.80 8.80 0.00 4.57 R
2945 3017 1.153901 CCTTCGTTTCCTAGCGCGA 60.154 57.895 12.10 0.00 0.00 5.87 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
69 71 3.650942 TCCCTGAAGAAACCTTCAAGCTA 59.349 43.478 8.89 0.00 46.48 3.32
426 452 0.991920 CCCTTTGCTGGAAGTAGGGA 59.008 55.000 12.02 0.00 45.93 4.20
428 454 1.065126 CCTTTGCTGGAAGTAGGGAGG 60.065 57.143 0.00 0.00 35.30 4.30
430 456 0.178873 TTGCTGGAAGTAGGGAGGGT 60.179 55.000 0.00 0.00 35.30 4.34
431 457 0.909610 TGCTGGAAGTAGGGAGGGTG 60.910 60.000 0.00 0.00 35.30 4.61
432 458 0.910088 GCTGGAAGTAGGGAGGGTGT 60.910 60.000 0.00 0.00 35.30 4.16
433 459 0.905357 CTGGAAGTAGGGAGGGTGTG 59.095 60.000 0.00 0.00 0.00 3.82
434 460 1.198759 TGGAAGTAGGGAGGGTGTGC 61.199 60.000 0.00 0.00 0.00 4.57
435 461 0.910088 GGAAGTAGGGAGGGTGTGCT 60.910 60.000 0.00 0.00 0.00 4.40
436 462 0.984995 GAAGTAGGGAGGGTGTGCTT 59.015 55.000 0.00 0.00 0.00 3.91
437 463 0.693049 AAGTAGGGAGGGTGTGCTTG 59.307 55.000 0.00 0.00 0.00 4.01
438 464 0.178903 AGTAGGGAGGGTGTGCTTGA 60.179 55.000 0.00 0.00 0.00 3.02
439 465 0.912486 GTAGGGAGGGTGTGCTTGAT 59.088 55.000 0.00 0.00 0.00 2.57
440 466 1.282157 GTAGGGAGGGTGTGCTTGATT 59.718 52.381 0.00 0.00 0.00 2.57
441 467 0.038744 AGGGAGGGTGTGCTTGATTG 59.961 55.000 0.00 0.00 0.00 2.67
442 468 0.967380 GGGAGGGTGTGCTTGATTGG 60.967 60.000 0.00 0.00 0.00 3.16
443 469 0.251341 GGAGGGTGTGCTTGATTGGT 60.251 55.000 0.00 0.00 0.00 3.67
444 470 1.620822 GAGGGTGTGCTTGATTGGTT 58.379 50.000 0.00 0.00 0.00 3.67
445 471 1.541588 GAGGGTGTGCTTGATTGGTTC 59.458 52.381 0.00 0.00 0.00 3.62
446 472 1.133513 AGGGTGTGCTTGATTGGTTCA 60.134 47.619 0.00 0.00 0.00 3.18
447 473 1.000274 GGGTGTGCTTGATTGGTTCAC 60.000 52.381 0.00 0.00 32.84 3.18
448 474 1.956477 GGTGTGCTTGATTGGTTCACT 59.044 47.619 0.00 0.00 32.84 3.41
449 475 3.146066 GGTGTGCTTGATTGGTTCACTA 58.854 45.455 0.00 0.00 32.84 2.74
450 476 3.758554 GGTGTGCTTGATTGGTTCACTAT 59.241 43.478 0.00 0.00 32.84 2.12
451 477 4.379813 GGTGTGCTTGATTGGTTCACTATG 60.380 45.833 0.00 0.00 32.84 2.23
470 496 2.532843 TGGGTTAGGAGTACCACTGTC 58.467 52.381 0.00 0.00 37.40 3.51
471 497 2.111255 TGGGTTAGGAGTACCACTGTCT 59.889 50.000 0.00 0.00 37.40 3.41
472 498 3.334581 TGGGTTAGGAGTACCACTGTCTA 59.665 47.826 0.00 0.00 37.40 2.59
474 500 4.583907 GGGTTAGGAGTACCACTGTCTATC 59.416 50.000 0.00 0.00 37.40 2.08
476 502 7.637011 GGGTTAGGAGTACCACTGTCTATCAG 61.637 50.000 0.00 0.00 39.82 2.90
489 515 6.083098 CTGTCTATCAGTCTATGGTTCTGG 57.917 45.833 0.00 0.00 39.17 3.86
490 516 5.519808 TGTCTATCAGTCTATGGTTCTGGT 58.480 41.667 0.00 0.00 0.00 4.00
491 517 6.669631 TGTCTATCAGTCTATGGTTCTGGTA 58.330 40.000 0.00 0.00 0.00 3.25
492 518 7.298374 TGTCTATCAGTCTATGGTTCTGGTAT 58.702 38.462 0.00 0.00 0.00 2.73
493 519 7.231519 TGTCTATCAGTCTATGGTTCTGGTATG 59.768 40.741 0.00 0.00 0.00 2.39
494 520 4.672587 TCAGTCTATGGTTCTGGTATGC 57.327 45.455 0.00 0.00 0.00 3.14
495 521 4.030216 TCAGTCTATGGTTCTGGTATGCA 58.970 43.478 0.00 0.00 0.00 3.96
496 522 4.122776 CAGTCTATGGTTCTGGTATGCAC 58.877 47.826 0.00 0.00 0.00 4.57
497 523 3.134804 AGTCTATGGTTCTGGTATGCACC 59.865 47.826 0.00 0.00 46.00 5.01
505 531 3.799753 GGTATGCACCACTGCTCG 58.200 61.111 0.00 0.00 45.04 5.03
506 532 1.218047 GGTATGCACCACTGCTCGA 59.782 57.895 0.00 0.00 45.04 4.04
507 533 0.807667 GGTATGCACCACTGCTCGAG 60.808 60.000 8.45 8.45 45.04 4.04
508 534 0.807667 GTATGCACCACTGCTCGAGG 60.808 60.000 15.58 0.00 44.57 4.63
509 535 1.257750 TATGCACCACTGCTCGAGGT 61.258 55.000 15.58 0.12 44.57 3.85
510 536 1.257750 ATGCACCACTGCTCGAGGTA 61.258 55.000 15.58 0.00 44.57 3.08
511 537 1.292223 GCACCACTGCTCGAGGTAA 59.708 57.895 15.58 0.00 40.63 2.85
512 538 0.320421 GCACCACTGCTCGAGGTAAA 60.320 55.000 15.58 0.00 40.63 2.01
513 539 1.676014 GCACCACTGCTCGAGGTAAAT 60.676 52.381 15.58 0.00 40.63 1.40
514 540 2.699954 CACCACTGCTCGAGGTAAATT 58.300 47.619 15.58 0.00 34.60 1.82
515 541 2.416547 CACCACTGCTCGAGGTAAATTG 59.583 50.000 15.58 0.00 34.60 2.32
516 542 2.301870 ACCACTGCTCGAGGTAAATTGA 59.698 45.455 15.58 0.00 34.60 2.57
517 543 2.673368 CCACTGCTCGAGGTAAATTGAC 59.327 50.000 15.58 0.00 0.00 3.18
518 544 2.345641 CACTGCTCGAGGTAAATTGACG 59.654 50.000 15.58 0.00 0.00 4.35
519 545 2.230508 ACTGCTCGAGGTAAATTGACGA 59.769 45.455 15.58 0.00 0.00 4.20
522 548 2.876091 CTCGAGGTAAATTGACGAGCA 58.124 47.619 3.91 0.00 42.39 4.26
523 549 2.599082 CTCGAGGTAAATTGACGAGCAC 59.401 50.000 3.91 0.00 42.39 4.40
524 550 2.029739 TCGAGGTAAATTGACGAGCACA 60.030 45.455 0.00 0.00 0.00 4.57
525 551 2.734606 CGAGGTAAATTGACGAGCACAA 59.265 45.455 0.00 0.00 0.00 3.33
526 552 3.181530 CGAGGTAAATTGACGAGCACAAG 60.182 47.826 0.00 0.00 0.00 3.16
527 553 3.994392 GAGGTAAATTGACGAGCACAAGA 59.006 43.478 0.00 0.00 0.00 3.02
528 554 4.385825 AGGTAAATTGACGAGCACAAGAA 58.614 39.130 0.00 0.00 0.00 2.52
529 555 4.819630 AGGTAAATTGACGAGCACAAGAAA 59.180 37.500 0.00 0.00 0.00 2.52
530 556 5.473504 AGGTAAATTGACGAGCACAAGAAAT 59.526 36.000 0.00 0.00 0.00 2.17
531 557 6.016276 AGGTAAATTGACGAGCACAAGAAATT 60.016 34.615 0.00 0.00 0.00 1.82
532 558 6.640907 GGTAAATTGACGAGCACAAGAAATTT 59.359 34.615 0.00 0.00 32.32 1.82
533 559 6.753897 AAATTGACGAGCACAAGAAATTTC 57.246 33.333 10.33 10.33 0.00 2.17
534 560 4.891627 TTGACGAGCACAAGAAATTTCA 57.108 36.364 19.99 0.00 0.00 2.69
535 561 4.891627 TGACGAGCACAAGAAATTTCAA 57.108 36.364 19.99 0.00 0.00 2.69
536 562 4.847633 TGACGAGCACAAGAAATTTCAAG 58.152 39.130 19.99 13.45 0.00 3.02
537 563 3.632189 ACGAGCACAAGAAATTTCAAGC 58.368 40.909 19.99 15.98 0.00 4.01
538 564 3.316308 ACGAGCACAAGAAATTTCAAGCT 59.684 39.130 19.99 19.76 0.00 3.74
539 565 3.667261 CGAGCACAAGAAATTTCAAGCTG 59.333 43.478 22.58 15.34 0.00 4.24
540 566 4.555313 CGAGCACAAGAAATTTCAAGCTGA 60.555 41.667 22.58 0.00 0.00 4.26
541 567 5.266733 AGCACAAGAAATTTCAAGCTGAA 57.733 34.783 19.99 0.00 34.03 3.02
577 606 4.454847 CCAGATAGAATGCAATGCTACCAG 59.545 45.833 6.82 0.00 37.26 4.00
586 615 2.954318 GCAATGCTACCAGTGGATTGAT 59.046 45.455 18.40 0.00 43.00 2.57
587 616 3.004106 GCAATGCTACCAGTGGATTGATC 59.996 47.826 18.40 0.11 43.00 2.92
589 618 1.490490 TGCTACCAGTGGATTGATCCC 59.510 52.381 18.40 0.00 46.59 3.85
599 628 2.107031 TGGATTGATCCCTGCAGTATGG 59.893 50.000 13.81 7.08 46.59 2.74
621 650 8.593945 ATGGCATCCTATTTCTTTGTAAAAGA 57.406 30.769 0.00 0.00 0.00 2.52
636 665 6.055231 TGTAAAAGATAATTTCCGCATCCG 57.945 37.500 0.00 0.00 0.00 4.18
671 717 5.102967 TCCCAGTAACCCATTAGTAAACCT 58.897 41.667 0.00 0.00 0.00 3.50
822 868 6.569780 TGAGATGCATGAAATTCAAGGAATG 58.430 36.000 2.46 0.00 32.14 2.67
826 872 4.142116 TGCATGAAATTCAAGGAATGCGAT 60.142 37.500 12.12 0.00 42.53 4.58
856 902 5.959618 AAGTGCTGGGTTAATAAGTTGAC 57.040 39.130 0.00 0.00 0.00 3.18
863 909 7.668052 TGCTGGGTTAATAAGTTGACTTGTTAT 59.332 33.333 12.01 0.00 38.64 1.89
904 951 0.657840 CGGTTCGAATGGGATGAAGC 59.342 55.000 0.00 0.00 36.91 3.86
1007 1058 1.800586 CTGACACAAGAACATGGACCG 59.199 52.381 0.00 0.00 0.00 4.79
1199 1250 1.014352 CTGTACCAAGCCCGCAATAC 58.986 55.000 0.00 0.00 0.00 1.89
1490 1542 4.926238 GTCACCACACTTCTATGTCTTCAG 59.074 45.833 0.00 0.00 0.00 3.02
1503 1555 4.604843 TGTCTTCAGCTTTAATCGCATG 57.395 40.909 0.00 0.00 0.00 4.06
1532 1589 0.318955 CTTCAGTTTGGCGGGCAAAG 60.319 55.000 27.32 17.66 0.00 2.77
1559 1616 1.957186 TTTTCGTCTGCCGGTTCCG 60.957 57.895 1.90 4.08 37.11 4.30
1595 1652 8.491958 TGGATGATGAATGGGATTCTGATATAG 58.508 37.037 0.00 0.00 39.96 1.31
1743 1801 3.006110 ACCATTGACTTGCCATTTGACTG 59.994 43.478 0.00 0.00 0.00 3.51
2505 2573 4.151689 TGAGTTTGCATTACAACTCTACGC 59.848 41.667 22.92 4.74 38.23 4.42
2516 2584 0.683504 ACTCTACGCTACACCTGGGG 60.684 60.000 0.00 0.00 0.00 4.96
2540 2608 6.460676 GGCTATATGATGCTTTGCTTTTGACT 60.461 38.462 0.00 0.00 0.00 3.41
2592 2661 2.472695 TTCTCTGCATGTGTGGTACC 57.527 50.000 4.43 4.43 0.00 3.34
2741 2810 2.037251 GCAGGTAGAGTGTTCCAACAGA 59.963 50.000 0.00 0.00 40.05 3.41
2793 2862 2.849318 AGATCCAGCTAGGCTTCCTTTT 59.151 45.455 0.00 0.00 36.40 2.27
2945 3017 6.888088 TCAAGATCAAATGATGGAGATTGTGT 59.112 34.615 0.00 0.00 34.37 3.72
2948 3020 3.374988 TCAAATGATGGAGATTGTGTCGC 59.625 43.478 0.00 0.00 0.00 5.19
2951 3023 0.807667 GATGGAGATTGTGTCGCGCT 60.808 55.000 5.56 0.00 0.00 5.92
2971 3043 2.365408 AGGAAACGAAGGTTAGCTCG 57.635 50.000 0.00 0.00 40.87 5.03
2979 3051 5.774878 ACGAAGGTTAGCTCGTTAAAATC 57.225 39.130 0.00 0.00 45.58 2.17
3022 3094 8.157476 ACACAGGATACACTTTTTATGAACTCT 58.843 33.333 0.00 0.00 41.41 3.24
3051 3123 3.314693 TCCAGGGGCTACTTGGTTATAG 58.685 50.000 9.25 0.00 0.00 1.31
3058 3130 5.356190 GGGGCTACTTGGTTATAGTTGTTTC 59.644 44.000 0.00 0.00 0.00 2.78
3059 3131 5.941647 GGGCTACTTGGTTATAGTTGTTTCA 59.058 40.000 0.00 0.00 0.00 2.69
3074 3146 5.934625 AGTTGTTTCATCACACTATGAGTCC 59.065 40.000 0.00 0.00 41.91 3.85
3104 5533 1.355210 CACCACGTGGAGTTTGCAC 59.645 57.895 40.21 0.00 38.94 4.57
3112 5541 0.033601 TGGAGTTTGCACTGGTTGGT 60.034 50.000 0.00 0.00 31.22 3.67
3166 5595 5.639506 ACAAGTATACACAGTAAAGCAGCAG 59.360 40.000 5.50 0.00 0.00 4.24
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
78 80 1.042559 CCAGAGAGAGGTCAGAGGGC 61.043 65.000 0.00 0.00 0.00 5.19
321 347 0.392193 AGAAATCAGACCTGCAGGCG 60.392 55.000 33.06 20.83 39.32 5.52
426 452 1.133513 TGAACCAATCAAGCACACCCT 60.134 47.619 0.00 0.00 34.30 4.34
428 454 1.956477 AGTGAACCAATCAAGCACACC 59.044 47.619 0.00 0.00 40.50 4.16
430 456 3.758023 CCATAGTGAACCAATCAAGCACA 59.242 43.478 0.00 0.00 40.50 4.57
431 457 3.129287 CCCATAGTGAACCAATCAAGCAC 59.871 47.826 0.00 0.00 40.50 4.40
432 458 3.245229 ACCCATAGTGAACCAATCAAGCA 60.245 43.478 0.00 0.00 40.50 3.91
433 459 3.356290 ACCCATAGTGAACCAATCAAGC 58.644 45.455 0.00 0.00 40.50 4.01
434 460 5.590259 CCTAACCCATAGTGAACCAATCAAG 59.410 44.000 0.00 0.00 40.50 3.02
435 461 5.251932 TCCTAACCCATAGTGAACCAATCAA 59.748 40.000 0.00 0.00 40.50 2.57
436 462 4.785914 TCCTAACCCATAGTGAACCAATCA 59.214 41.667 0.00 0.00 35.05 2.57
437 463 5.104485 ACTCCTAACCCATAGTGAACCAATC 60.104 44.000 0.00 0.00 0.00 2.67
438 464 4.788617 ACTCCTAACCCATAGTGAACCAAT 59.211 41.667 0.00 0.00 0.00 3.16
439 465 4.172807 ACTCCTAACCCATAGTGAACCAA 58.827 43.478 0.00 0.00 0.00 3.67
440 466 3.798515 ACTCCTAACCCATAGTGAACCA 58.201 45.455 0.00 0.00 0.00 3.67
441 467 4.100653 GGTACTCCTAACCCATAGTGAACC 59.899 50.000 0.00 0.00 0.00 3.62
442 468 4.713321 TGGTACTCCTAACCCATAGTGAAC 59.287 45.833 0.00 0.00 36.06 3.18
443 469 4.713321 GTGGTACTCCTAACCCATAGTGAA 59.287 45.833 0.00 0.00 36.06 3.18
444 470 4.016851 AGTGGTACTCCTAACCCATAGTGA 60.017 45.833 0.00 0.00 36.06 3.41
445 471 4.099573 CAGTGGTACTCCTAACCCATAGTG 59.900 50.000 0.00 0.00 36.06 2.74
446 472 4.264713 ACAGTGGTACTCCTAACCCATAGT 60.265 45.833 0.00 0.00 36.06 2.12
447 473 4.287552 ACAGTGGTACTCCTAACCCATAG 58.712 47.826 0.00 0.00 36.06 2.23
448 474 4.016851 AGACAGTGGTACTCCTAACCCATA 60.017 45.833 0.00 0.00 36.06 2.74
449 475 3.105283 GACAGTGGTACTCCTAACCCAT 58.895 50.000 0.00 0.00 36.06 4.00
450 476 2.111255 AGACAGTGGTACTCCTAACCCA 59.889 50.000 0.00 0.00 36.06 4.51
451 477 2.817665 AGACAGTGGTACTCCTAACCC 58.182 52.381 0.00 0.00 36.06 4.11
470 496 6.015095 TGCATACCAGAACCATAGACTGATAG 60.015 42.308 0.00 0.00 34.07 2.08
471 497 5.838521 TGCATACCAGAACCATAGACTGATA 59.161 40.000 0.00 0.00 34.07 2.15
472 498 4.655649 TGCATACCAGAACCATAGACTGAT 59.344 41.667 0.00 0.00 34.07 2.90
474 500 4.122776 GTGCATACCAGAACCATAGACTG 58.877 47.826 0.00 0.00 0.00 3.51
476 502 3.467803 GGTGCATACCAGAACCATAGAC 58.532 50.000 0.00 0.00 46.71 2.59
494 520 2.386661 ATTTACCTCGAGCAGTGGTG 57.613 50.000 6.99 0.00 45.47 4.17
496 522 2.673368 GTCAATTTACCTCGAGCAGTGG 59.327 50.000 6.99 0.00 39.33 4.00
497 523 2.345641 CGTCAATTTACCTCGAGCAGTG 59.654 50.000 6.99 0.17 0.00 3.66
498 524 2.230508 TCGTCAATTTACCTCGAGCAGT 59.769 45.455 6.99 2.95 0.00 4.40
499 525 2.854777 CTCGTCAATTTACCTCGAGCAG 59.145 50.000 6.99 0.00 40.65 4.24
500 526 2.876091 CTCGTCAATTTACCTCGAGCA 58.124 47.619 6.99 0.00 40.65 4.26
502 528 2.599082 GTGCTCGTCAATTTACCTCGAG 59.401 50.000 5.13 5.13 46.76 4.04
503 529 2.029739 TGTGCTCGTCAATTTACCTCGA 60.030 45.455 0.00 0.00 0.00 4.04
504 530 2.333926 TGTGCTCGTCAATTTACCTCG 58.666 47.619 0.00 0.00 0.00 4.63
505 531 3.994392 TCTTGTGCTCGTCAATTTACCTC 59.006 43.478 0.00 0.00 0.00 3.85
506 532 4.002906 TCTTGTGCTCGTCAATTTACCT 57.997 40.909 0.00 0.00 0.00 3.08
507 533 4.742438 TTCTTGTGCTCGTCAATTTACC 57.258 40.909 0.00 0.00 0.00 2.85
508 534 7.378461 TGAAATTTCTTGTGCTCGTCAATTTAC 59.622 33.333 18.64 0.00 0.00 2.01
509 535 7.421599 TGAAATTTCTTGTGCTCGTCAATTTA 58.578 30.769 18.64 0.00 0.00 1.40
510 536 6.272318 TGAAATTTCTTGTGCTCGTCAATTT 58.728 32.000 18.64 0.00 0.00 1.82
511 537 5.830912 TGAAATTTCTTGTGCTCGTCAATT 58.169 33.333 18.64 0.00 0.00 2.32
512 538 5.437289 TGAAATTTCTTGTGCTCGTCAAT 57.563 34.783 18.64 0.00 0.00 2.57
513 539 4.891627 TGAAATTTCTTGTGCTCGTCAA 57.108 36.364 18.64 0.00 0.00 3.18
514 540 4.789481 GCTTGAAATTTCTTGTGCTCGTCA 60.789 41.667 18.64 0.00 0.00 4.35
515 541 3.665871 GCTTGAAATTTCTTGTGCTCGTC 59.334 43.478 18.64 0.00 0.00 4.20
516 542 3.316308 AGCTTGAAATTTCTTGTGCTCGT 59.684 39.130 18.64 1.22 0.00 4.18
517 543 3.667261 CAGCTTGAAATTTCTTGTGCTCG 59.333 43.478 18.64 12.10 0.00 5.03
518 544 4.863491 TCAGCTTGAAATTTCTTGTGCTC 58.137 39.130 18.64 2.36 0.00 4.26
519 545 4.924305 TCAGCTTGAAATTTCTTGTGCT 57.076 36.364 18.64 17.14 0.00 4.40
520 546 5.971895 TTTCAGCTTGAAATTTCTTGTGC 57.028 34.783 18.64 15.50 41.02 4.57
521 547 7.741198 TGTTTTTCAGCTTGAAATTTCTTGTG 58.259 30.769 18.64 10.79 44.75 3.33
522 548 7.903995 TGTTTTTCAGCTTGAAATTTCTTGT 57.096 28.000 18.64 0.00 44.75 3.16
530 556 9.290988 TGGTAGTATATGTTTTTCAGCTTGAAA 57.709 29.630 7.09 7.09 43.84 2.69
531 557 8.856153 TGGTAGTATATGTTTTTCAGCTTGAA 57.144 30.769 0.00 0.00 34.03 2.69
532 558 8.318412 TCTGGTAGTATATGTTTTTCAGCTTGA 58.682 33.333 0.00 0.00 0.00 3.02
533 559 8.492673 TCTGGTAGTATATGTTTTTCAGCTTG 57.507 34.615 0.00 0.00 0.00 4.01
535 561 9.988815 CTATCTGGTAGTATATGTTTTTCAGCT 57.011 33.333 0.00 0.00 0.00 4.24
536 562 9.982651 TCTATCTGGTAGTATATGTTTTTCAGC 57.017 33.333 0.00 0.00 0.00 4.26
544 570 9.881649 CATTGCATTCTATCTGGTAGTATATGT 57.118 33.333 0.00 0.00 0.00 2.29
545 571 8.824781 GCATTGCATTCTATCTGGTAGTATATG 58.175 37.037 3.15 0.29 0.00 1.78
546 572 8.766476 AGCATTGCATTCTATCTGGTAGTATAT 58.234 33.333 11.91 0.00 0.00 0.86
547 573 8.138928 AGCATTGCATTCTATCTGGTAGTATA 57.861 34.615 11.91 0.00 0.00 1.47
548 574 7.013823 AGCATTGCATTCTATCTGGTAGTAT 57.986 36.000 11.91 0.00 0.00 2.12
549 575 6.425210 AGCATTGCATTCTATCTGGTAGTA 57.575 37.500 11.91 0.00 0.00 1.82
550 576 5.301835 AGCATTGCATTCTATCTGGTAGT 57.698 39.130 11.91 0.00 0.00 2.73
551 577 5.641209 GGTAGCATTGCATTCTATCTGGTAG 59.359 44.000 11.91 0.00 0.00 3.18
555 581 5.049612 CACTGGTAGCATTGCATTCTATCTG 60.050 44.000 11.91 1.84 0.00 2.90
586 615 0.695462 AGGATGCCATACTGCAGGGA 60.695 55.000 19.93 5.78 45.93 4.20
587 616 1.059098 TAGGATGCCATACTGCAGGG 58.941 55.000 19.93 11.00 45.93 4.45
589 618 4.649692 AGAAATAGGATGCCATACTGCAG 58.350 43.478 13.48 13.48 45.93 4.41
621 650 2.519377 TCGACGGATGCGGAAATTAT 57.481 45.000 12.44 0.00 0.00 1.28
629 658 3.306166 GGGATATTTAATCGACGGATGCG 59.694 47.826 4.58 4.58 31.83 4.73
636 665 6.527423 TGGGTTACTGGGATATTTAATCGAC 58.473 40.000 0.00 0.00 0.00 4.20
699 745 6.819146 GGGAACAAATTGTTTCTGGTGTTTAA 59.181 34.615 15.91 0.00 41.28 1.52
700 746 6.342111 GGGAACAAATTGTTTCTGGTGTTTA 58.658 36.000 15.91 0.00 41.28 2.01
701 747 5.182487 GGGAACAAATTGTTTCTGGTGTTT 58.818 37.500 15.91 0.00 41.28 2.83
822 868 2.289002 CCCAGCACTTTCTATCAATCGC 59.711 50.000 0.00 0.00 0.00 4.58
826 872 8.107095 ACTTATTAACCCAGCACTTTCTATCAA 58.893 33.333 0.00 0.00 0.00 2.57
904 951 7.175641 AGACAAAAGGAAATAGTTGACATGGAG 59.824 37.037 0.00 0.00 0.00 3.86
996 1047 1.635663 CCTTGCGACGGTCCATGTTC 61.636 60.000 1.91 0.00 0.00 3.18
997 1048 1.671054 CCTTGCGACGGTCCATGTT 60.671 57.895 1.91 0.00 0.00 2.71
1007 1058 0.669625 AGCGGTAACTTCCTTGCGAC 60.670 55.000 0.00 0.00 0.00 5.19
1199 1250 0.460284 AACAAGCGGGATAGCAGACG 60.460 55.000 0.00 0.00 40.15 4.18
1490 1542 5.461078 AGAAATGAATGCATGCGATTAAAGC 59.539 36.000 14.09 0.00 34.26 3.51
1503 1555 3.365820 CGCCAAACTGAAGAAATGAATGC 59.634 43.478 0.00 0.00 0.00 3.56
1532 1589 3.188895 GGCAGACGAAAACATCTCAAC 57.811 47.619 0.00 0.00 0.00 3.18
1559 1616 1.026182 TCATCATCCACAAGCCACGC 61.026 55.000 0.00 0.00 0.00 5.34
1595 1652 0.250234 GGCTTCCCCCATGAAAAAGC 59.750 55.000 11.34 11.34 41.18 3.51
1743 1801 1.145803 GAAACTACTCACGGGTGCAC 58.854 55.000 8.80 8.80 0.00 4.57
2366 2434 6.349300 TGAGCCTAAGAAAGACATGTAATCC 58.651 40.000 0.00 0.00 0.00 3.01
2419 2487 7.552687 TCTTATCCACAAACAGATATGACCAAC 59.447 37.037 0.00 0.00 29.20 3.77
2423 2491 9.202273 GAGATCTTATCCACAAACAGATATGAC 57.798 37.037 0.00 0.00 34.11 3.06
2425 2493 8.986847 GTGAGATCTTATCCACAAACAGATATG 58.013 37.037 0.00 0.00 33.49 1.78
2505 2573 3.369892 GCATCATATAGCCCCAGGTGTAG 60.370 52.174 0.00 0.00 0.00 2.74
2516 2584 6.501781 AGTCAAAAGCAAAGCATCATATAGC 58.498 36.000 0.00 0.00 0.00 2.97
2592 2661 4.864916 ACATTCATTCGATCCAGTTTCG 57.135 40.909 0.00 0.00 37.94 3.46
2741 2810 7.588497 AATCTTTAGTTGGAAGCAGAGTTTT 57.412 32.000 0.00 0.00 0.00 2.43
2817 2886 6.664428 TTCATTAGCAAAACTAGGCCTTTT 57.336 33.333 12.58 2.84 30.79 2.27
2914 2986 7.823665 TCTCCATCATTTGATCTTGAAACTTG 58.176 34.615 0.00 0.00 31.21 3.16
2945 3017 1.153901 CCTTCGTTTCCTAGCGCGA 60.154 57.895 12.10 0.00 0.00 5.87
2948 3020 1.925185 GCTAACCTTCGTTTCCTAGCG 59.075 52.381 0.00 0.00 33.17 4.26
2951 3023 2.821969 ACGAGCTAACCTTCGTTTCCTA 59.178 45.455 0.00 0.00 35.08 2.94
2979 3051 8.613060 ATCCTGTGTGCAAATTAGATATACAG 57.387 34.615 0.00 0.00 34.40 2.74
3051 3123 5.934625 AGGACTCATAGTGTGATGAAACAAC 59.065 40.000 0.00 0.00 35.44 3.32
3058 3130 3.378427 TCGACAGGACTCATAGTGTGATG 59.622 47.826 0.00 0.00 35.97 3.07
3059 3131 3.621558 TCGACAGGACTCATAGTGTGAT 58.378 45.455 0.00 0.00 35.97 3.06
3074 3146 1.194547 CACGTGGTGGAATTTCGACAG 59.805 52.381 7.95 6.62 0.00 3.51
3104 5533 2.884012 TGAAGTACATTGCACCAACCAG 59.116 45.455 0.00 0.00 0.00 4.00
3112 5541 4.257731 TCGCCTAAATGAAGTACATTGCA 58.742 39.130 0.00 0.00 46.90 4.08


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

AutoCloner maintained by Alex Coulton.