Multiple sequence alignment - TraesCS2D01G189100

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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 TraesCS2D01G189100 chr2D 100.000 3413 0 0 1 3413 132705640 132702228 0.000000e+00 6303.0
1 TraesCS2D01G189100 chr2A 90.824 3422 126 64 1 3314 140367051 140363710 0.000000e+00 4407.0
2 TraesCS2D01G189100 chr2A 97.368 38 1 0 3376 3413 140363676 140363639 7.910000e-07 65.8
3 TraesCS2D01G189100 chr2B 94.308 2723 77 35 619 3313 188471089 188468417 0.000000e+00 4098.0
4 TraesCS2D01G189100 chr2B 89.571 326 30 3 1 323 188471612 188471288 8.810000e-111 411.0
5 TraesCS2D01G189100 chr2B 79.564 367 43 18 2868 3209 53460955 53461314 2.050000e-57 233.0
6 TraesCS2D01G189100 chr2B 77.861 402 45 27 2954 3323 519434563 519434174 3.450000e-50 209.0
7 TraesCS2D01G189100 chr3D 88.496 226 25 1 1545 1769 120747871 120748096 4.340000e-69 272.0
8 TraesCS2D01G189100 chr1A 82.517 286 34 10 2868 3140 565150100 565150382 1.580000e-58 237.0
9 TraesCS2D01G189100 chr7D 81.231 325 24 22 854 1176 28069200 28069489 9.530000e-56 228.0
10 TraesCS2D01G189100 chr5B 93.793 145 9 0 2868 3012 262567867 262567723 5.730000e-53 219.0
11 TraesCS2D01G189100 chr5B 75.888 394 52 22 2961 3323 71162337 71161956 9.800000e-36 161.0
12 TraesCS2D01G189100 chr5B 89.655 116 4 1 2946 3061 708404475 708404368 1.280000e-29 141.0
13 TraesCS2D01G189100 chr5B 87.879 66 6 2 3076 3140 262567640 262567576 3.650000e-10 76.8
14 TraesCS2D01G189100 chr3B 94.366 142 8 0 2868 3009 735974086 735974227 5.730000e-53 219.0
15 TraesCS2D01G189100 chr3B 89.286 112 4 1 2950 3061 413565306 413565409 2.140000e-27 134.0
16 TraesCS2D01G189100 chr3B 87.069 116 7 1 2946 3061 461803126 461803019 1.290000e-24 124.0
17 TraesCS2D01G189100 chr3B 87.879 66 6 2 3076 3140 735974313 735974377 3.650000e-10 76.8
18 TraesCS2D01G189100 chr3A 83.913 230 32 4 1545 1769 560137759 560137988 7.420000e-52 215.0
19 TraesCS2D01G189100 chr7B 90.625 64 4 2 1651 1712 312434120 312434057 2.180000e-12 84.2
20 TraesCS2D01G189100 chr6B 94.444 54 3 0 1715 1768 130501510 130501563 2.180000e-12 84.2
21 TraesCS2D01G189100 chr6B 89.655 58 6 0 1655 1712 126525658 126525715 1.310000e-09 75.0
22 TraesCS2D01G189100 chr4D 96.970 33 1 0 2225 2257 52215648 52215680 4.760000e-04 56.5
23 TraesCS2D01G189100 chr4B 96.970 33 1 0 2225 2257 76565482 76565450 4.760000e-04 56.5
24 TraesCS2D01G189100 chr4A 96.970 33 1 0 2225 2257 544397633 544397665 4.760000e-04 56.5


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 TraesCS2D01G189100 chr2D 132702228 132705640 3412 True 6303.0 6303 100.0000 1 3413 1 chr2D.!!$R1 3412
1 TraesCS2D01G189100 chr2A 140363639 140367051 3412 True 2236.4 4407 94.0960 1 3413 2 chr2A.!!$R1 3412
2 TraesCS2D01G189100 chr2B 188468417 188471612 3195 True 2254.5 4098 91.9395 1 3313 2 chr2B.!!$R2 3312

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
607 641 0.179084 CGGCGACTCTCTCTCTCTCT 60.179 60.0 0.0 0.0 0.0 3.1 F
2094 2153 0.594602 TCGACACCTACACCTCGTTG 59.405 55.0 0.0 0.0 0.0 4.1 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2322 2381 1.153939 CTCCTGCTCCTCGTTGACG 60.154 63.158 0.0 0.0 41.45 4.35 R
3316 3434 0.114364 TCTCTGTGGCAGTACTCCCA 59.886 55.000 0.0 0.0 32.61 4.37 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
96 97 2.156343 AAAGAAACTCGCTCGAGCTT 57.844 45.000 32.88 21.26 45.54 3.74
97 98 2.156343 AAGAAACTCGCTCGAGCTTT 57.844 45.000 32.88 25.77 45.54 3.51
121 122 4.818534 ATCATTATGTGACGATGGTTGC 57.181 40.909 0.00 0.00 40.28 4.17
188 214 9.964354 ATATGCACAGCTATAATTTCATCCTTA 57.036 29.630 0.00 0.00 0.00 2.69
217 243 2.558359 ACTTTATGTGCAAGCAAGACCC 59.442 45.455 0.00 0.00 0.00 4.46
223 249 1.055849 TGCAAGCAAGACCCTCTACA 58.944 50.000 0.00 0.00 0.00 2.74
320 349 5.298276 GTGTGGGCTATCCGAATAAAATGAA 59.702 40.000 0.00 0.00 38.76 2.57
321 350 5.888724 TGTGGGCTATCCGAATAAAATGAAA 59.111 36.000 0.00 0.00 38.76 2.69
322 351 6.183360 TGTGGGCTATCCGAATAAAATGAAAC 60.183 38.462 0.00 0.00 38.76 2.78
323 352 5.300792 TGGGCTATCCGAATAAAATGAAACC 59.699 40.000 0.00 0.00 38.76 3.27
380 409 6.169094 AGATTCATAGGATTACAATCGGCAG 58.831 40.000 0.00 0.00 36.27 4.85
381 410 4.955811 TCATAGGATTACAATCGGCAGT 57.044 40.909 0.00 0.00 36.27 4.40
392 421 3.244078 ACAATCGGCAGTGACTAGTTCAA 60.244 43.478 0.00 0.00 35.39 2.69
400 429 7.174253 TCGGCAGTGACTAGTTCAAAATAAAAT 59.826 33.333 0.00 0.00 35.39 1.82
424 453 3.899052 ACCTATTAAACGCTGGTGCTA 57.101 42.857 0.00 0.00 36.97 3.49
550 584 2.779755 ATGTTTGACCGGCACATCTA 57.220 45.000 0.00 0.00 0.00 1.98
555 589 2.430248 TGACCGGCACATCTAGACTA 57.570 50.000 0.00 0.00 0.00 2.59
567 601 5.049749 CACATCTAGACTAGACAGGTCATCG 60.050 48.000 14.47 0.00 37.69 3.84
603 637 1.747367 CCACGGCGACTCTCTCTCT 60.747 63.158 16.62 0.00 0.00 3.10
604 638 1.711060 CCACGGCGACTCTCTCTCTC 61.711 65.000 16.62 0.00 0.00 3.20
605 639 0.742990 CACGGCGACTCTCTCTCTCT 60.743 60.000 16.62 0.00 0.00 3.10
606 640 0.461339 ACGGCGACTCTCTCTCTCTC 60.461 60.000 16.62 0.00 0.00 3.20
607 641 0.179084 CGGCGACTCTCTCTCTCTCT 60.179 60.000 0.00 0.00 0.00 3.10
608 642 1.583054 GGCGACTCTCTCTCTCTCTC 58.417 60.000 0.00 0.00 0.00 3.20
609 643 1.139058 GGCGACTCTCTCTCTCTCTCT 59.861 57.143 0.00 0.00 0.00 3.10
610 644 2.474816 GCGACTCTCTCTCTCTCTCTC 58.525 57.143 0.00 0.00 0.00 3.20
611 645 2.101582 GCGACTCTCTCTCTCTCTCTCT 59.898 54.545 0.00 0.00 0.00 3.10
612 646 3.797184 GCGACTCTCTCTCTCTCTCTCTC 60.797 56.522 0.00 0.00 0.00 3.20
613 647 3.634448 CGACTCTCTCTCTCTCTCTCTCT 59.366 52.174 0.00 0.00 0.00 3.10
614 648 4.261405 CGACTCTCTCTCTCTCTCTCTCTC 60.261 54.167 0.00 0.00 0.00 3.20
615 649 4.877773 ACTCTCTCTCTCTCTCTCTCTCT 58.122 47.826 0.00 0.00 0.00 3.10
616 650 4.892934 ACTCTCTCTCTCTCTCTCTCTCTC 59.107 50.000 0.00 0.00 0.00 3.20
617 651 5.136068 TCTCTCTCTCTCTCTCTCTCTCT 57.864 47.826 0.00 0.00 0.00 3.10
618 652 5.136828 TCTCTCTCTCTCTCTCTCTCTCTC 58.863 50.000 0.00 0.00 0.00 3.20
619 653 5.103728 TCTCTCTCTCTCTCTCTCTCTCTCT 60.104 48.000 0.00 0.00 0.00 3.10
620 654 5.136828 TCTCTCTCTCTCTCTCTCTCTCTC 58.863 50.000 0.00 0.00 0.00 3.20
621 655 5.103728 TCTCTCTCTCTCTCTCTCTCTCTCT 60.104 48.000 0.00 0.00 0.00 3.10
622 656 5.136828 TCTCTCTCTCTCTCTCTCTCTCTC 58.863 50.000 0.00 0.00 0.00 3.20
623 657 5.103728 TCTCTCTCTCTCTCTCTCTCTCTCT 60.104 48.000 0.00 0.00 0.00 3.10
624 658 5.136828 TCTCTCTCTCTCTCTCTCTCTCTC 58.863 50.000 0.00 0.00 0.00 3.20
625 659 5.103728 TCTCTCTCTCTCTCTCTCTCTCTCT 60.104 48.000 0.00 0.00 0.00 3.10
626 660 4.892345 TCTCTCTCTCTCTCTCTCTCTCTG 59.108 50.000 0.00 0.00 0.00 3.35
627 661 3.963374 TCTCTCTCTCTCTCTCTCTCTGG 59.037 52.174 0.00 0.00 0.00 3.86
628 662 3.041211 TCTCTCTCTCTCTCTCTCTGGG 58.959 54.545 0.00 0.00 0.00 4.45
679 714 6.238511 GGGTGTCAGTTTGTTTGTTTTGTTTT 60.239 34.615 0.00 0.00 0.00 2.43
680 715 6.630840 GGTGTCAGTTTGTTTGTTTTGTTTTG 59.369 34.615 0.00 0.00 0.00 2.44
681 716 7.183433 GTGTCAGTTTGTTTGTTTTGTTTTGT 58.817 30.769 0.00 0.00 0.00 2.83
682 717 7.694367 GTGTCAGTTTGTTTGTTTTGTTTTGTT 59.306 29.630 0.00 0.00 0.00 2.83
683 718 8.237267 TGTCAGTTTGTTTGTTTTGTTTTGTTT 58.763 25.926 0.00 0.00 0.00 2.83
977 1015 2.393768 CCGCATCGCTGCTTCTTGT 61.394 57.895 9.85 0.00 46.65 3.16
981 1019 1.016130 CATCGCTGCTTCTTGTCCGT 61.016 55.000 0.00 0.00 0.00 4.69
982 1020 0.737715 ATCGCTGCTTCTTGTCCGTC 60.738 55.000 0.00 0.00 0.00 4.79
1095 1136 3.591254 GAAGGGCTTCTCGTGCGGT 62.591 63.158 0.00 0.00 36.69 5.68
1427 1468 2.576317 GTACGACGAGGCTGACGC 60.576 66.667 0.00 0.00 0.00 5.19
1428 1469 2.745100 TACGACGAGGCTGACGCT 60.745 61.111 0.00 0.00 36.09 5.07
1429 1470 3.035576 TACGACGAGGCTGACGCTG 62.036 63.158 0.00 0.00 36.09 5.18
1430 1471 4.103103 CGACGAGGCTGACGCTGA 62.103 66.667 0.00 0.00 36.09 4.26
1431 1472 2.505118 GACGAGGCTGACGCTGAC 60.505 66.667 0.00 0.00 36.09 3.51
1498 1551 4.521062 CGGAAGCGGAGGCAGAGG 62.521 72.222 0.00 0.00 43.41 3.69
1501 1554 2.038007 AAGCGGAGGCAGAGGAGA 59.962 61.111 0.00 0.00 43.41 3.71
1521 1580 3.274690 AGAAGGAGGAGGAAGAGGAGATT 59.725 47.826 0.00 0.00 0.00 2.40
1830 1889 2.383527 CGCCAAGACCAAGAGCGTC 61.384 63.158 0.00 0.00 41.78 5.19
2094 2153 0.594602 TCGACACCTACACCTCGTTG 59.405 55.000 0.00 0.00 0.00 4.10
2415 2474 1.002274 ATCGGAGGAGGCCTGAACT 59.998 57.895 12.00 5.20 31.76 3.01
2554 2626 1.511305 CGCTCCAAGCTCGAAGGTA 59.489 57.895 0.00 0.00 39.60 3.08
2555 2627 0.526524 CGCTCCAAGCTCGAAGGTAG 60.527 60.000 0.00 0.00 39.60 3.18
2595 2670 6.096846 CCAAGAAAGAAACCCAAGAAGAAGAA 59.903 38.462 0.00 0.00 0.00 2.52
2596 2671 6.951062 AGAAAGAAACCCAAGAAGAAGAAG 57.049 37.500 0.00 0.00 0.00 2.85
2597 2672 6.663734 AGAAAGAAACCCAAGAAGAAGAAGA 58.336 36.000 0.00 0.00 0.00 2.87
2781 2873 8.810041 AGATGAACTCAAATGCTATTCCTTTTT 58.190 29.630 0.00 0.00 0.00 1.94
3014 3111 0.675837 CTGACCTGACCGACCGACTA 60.676 60.000 0.00 0.00 0.00 2.59
3046 3147 0.746659 AGCAACCAAGCAACCAACTC 59.253 50.000 0.00 0.00 36.85 3.01
3061 3162 2.483876 CAACTCCTTTGCTTCAGTCGA 58.516 47.619 0.00 0.00 0.00 4.20
3062 3163 2.156343 ACTCCTTTGCTTCAGTCGAC 57.844 50.000 7.70 7.70 0.00 4.20
3063 3164 1.412710 ACTCCTTTGCTTCAGTCGACA 59.587 47.619 19.50 0.00 0.00 4.35
3064 3165 2.064762 CTCCTTTGCTTCAGTCGACAG 58.935 52.381 19.50 10.43 0.00 3.51
3065 3166 1.151668 CCTTTGCTTCAGTCGACAGG 58.848 55.000 19.50 9.11 0.00 4.00
3066 3167 1.151668 CTTTGCTTCAGTCGACAGGG 58.848 55.000 19.50 6.95 0.00 4.45
3067 3168 0.468226 TTTGCTTCAGTCGACAGGGT 59.532 50.000 19.50 0.00 0.00 4.34
3068 3169 0.249868 TTGCTTCAGTCGACAGGGTG 60.250 55.000 19.50 7.29 0.00 4.61
3069 3170 1.112916 TGCTTCAGTCGACAGGGTGA 61.113 55.000 19.50 9.79 0.00 4.02
3070 3171 0.667792 GCTTCAGTCGACAGGGTGAC 60.668 60.000 19.50 0.00 35.33 3.67
3072 3173 1.068588 CTTCAGTCGACAGGGTGACAA 59.931 52.381 19.50 0.00 37.58 3.18
3074 3175 1.272490 TCAGTCGACAGGGTGACAATC 59.728 52.381 19.50 0.00 37.58 2.67
3076 3177 0.608640 GTCGACAGGGTGACAATCCT 59.391 55.000 11.55 0.00 35.20 3.24
3077 3178 0.895530 TCGACAGGGTGACAATCCTC 59.104 55.000 0.00 0.00 0.00 3.71
3078 3179 0.608130 CGACAGGGTGACAATCCTCA 59.392 55.000 0.00 0.00 0.00 3.86
3079 3180 1.404717 CGACAGGGTGACAATCCTCAG 60.405 57.143 0.00 0.00 0.00 3.35
3080 3181 0.326264 ACAGGGTGACAATCCTCAGC 59.674 55.000 0.00 0.00 37.85 4.26
3083 3184 3.890527 GGTGACAATCCTCAGCCAT 57.109 52.632 0.00 0.00 33.34 4.40
3084 3185 2.134789 GGTGACAATCCTCAGCCATT 57.865 50.000 0.00 0.00 33.34 3.16
3085 3186 2.019984 GGTGACAATCCTCAGCCATTC 58.980 52.381 0.00 0.00 33.34 2.67
3087 3188 1.634973 TGACAATCCTCAGCCATTCCA 59.365 47.619 0.00 0.00 0.00 3.53
3089 3190 1.637553 ACAATCCTCAGCCATTCCACT 59.362 47.619 0.00 0.00 0.00 4.00
3091 3192 0.549950 ATCCTCAGCCATTCCACTGG 59.450 55.000 0.00 0.00 39.45 4.00
3223 3341 8.306680 CATGAAAGAATGCAAATTTTCAGACT 57.693 30.769 20.24 8.14 41.28 3.24
3282 3400 4.586421 TGGTGAAATGATTGGTTAGCACAA 59.414 37.500 0.00 0.00 0.00 3.33
3296 3414 3.308438 AGCACAATGGAGCAACAAATC 57.692 42.857 3.03 0.00 32.55 2.17
3302 3420 6.369615 GCACAATGGAGCAACAAATCTTTATT 59.630 34.615 0.00 0.00 0.00 1.40
3314 3432 6.546395 ACAAATCTTTATTACGAGCAAGCAG 58.454 36.000 0.00 0.00 0.00 4.24
3316 3434 4.202245 TCTTTATTACGAGCAAGCAGGT 57.798 40.909 0.00 0.00 0.00 4.00
3317 3435 3.932710 TCTTTATTACGAGCAAGCAGGTG 59.067 43.478 0.00 0.00 0.00 4.00
3318 3436 2.309528 TATTACGAGCAAGCAGGTGG 57.690 50.000 0.00 0.00 0.00 4.61
3320 3438 1.476845 TTACGAGCAAGCAGGTGGGA 61.477 55.000 0.00 0.00 0.00 4.37
3323 3441 1.888436 CGAGCAAGCAGGTGGGAGTA 61.888 60.000 0.00 0.00 0.00 2.59
3325 3443 0.838122 AGCAAGCAGGTGGGAGTACT 60.838 55.000 0.00 0.00 0.00 2.73
3326 3444 0.674895 GCAAGCAGGTGGGAGTACTG 60.675 60.000 0.00 0.00 35.40 2.74
3334 3452 2.671145 TGGGAGTACTGCCACAGAG 58.329 57.895 30.31 0.00 46.48 3.35
3335 3453 0.114364 TGGGAGTACTGCCACAGAGA 59.886 55.000 30.31 8.41 46.48 3.10
3336 3454 1.267121 GGGAGTACTGCCACAGAGAA 58.733 55.000 27.06 0.00 41.16 2.87
3337 3455 1.623811 GGGAGTACTGCCACAGAGAAA 59.376 52.381 27.06 0.00 41.16 2.52
3338 3456 2.038557 GGGAGTACTGCCACAGAGAAAA 59.961 50.000 27.06 0.00 41.16 2.29
3339 3457 3.496160 GGGAGTACTGCCACAGAGAAAAA 60.496 47.826 27.06 0.00 41.16 1.94
3359 3477 6.909550 AAAAAGGATGTGTATACCAAGCAA 57.090 33.333 0.00 0.00 0.00 3.91
3360 3478 6.515272 AAAAGGATGTGTATACCAAGCAAG 57.485 37.500 0.00 0.00 0.00 4.01
3361 3479 3.545703 AGGATGTGTATACCAAGCAAGC 58.454 45.455 0.00 0.00 0.00 4.01
3362 3480 3.054434 AGGATGTGTATACCAAGCAAGCA 60.054 43.478 0.00 0.00 0.00 3.91
3363 3481 3.885297 GGATGTGTATACCAAGCAAGCAT 59.115 43.478 0.00 0.00 0.00 3.79
3364 3482 4.261322 GGATGTGTATACCAAGCAAGCATG 60.261 45.833 0.00 0.00 0.00 4.06
3404 3522 1.206849 CCTTGCTTCTCACTCTCCCTC 59.793 57.143 0.00 0.00 0.00 4.30
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
96 97 7.148171 TGCAACCATCGTCACATAATGATTTAA 60.148 33.333 0.00 0.00 40.28 1.52
97 98 6.317391 TGCAACCATCGTCACATAATGATTTA 59.683 34.615 0.00 0.00 40.28 1.40
121 122 9.786105 TTGTTGTGTAATGCATTGTTATATCTG 57.214 29.630 22.27 0.00 0.00 2.90
166 190 7.496529 TGTAAGGATGAAATTATAGCTGTGC 57.503 36.000 0.00 0.00 0.00 4.57
354 383 7.323420 TGCCGATTGTAATCCTATGAATCTAG 58.677 38.462 0.00 0.00 31.68 2.43
355 384 7.039011 ACTGCCGATTGTAATCCTATGAATCTA 60.039 37.037 0.00 0.00 31.68 1.98
363 392 3.704566 AGTCACTGCCGATTGTAATCCTA 59.295 43.478 0.00 0.00 31.68 2.94
400 429 3.189702 GCACCAGCGTTTAATAGGTTTCA 59.810 43.478 0.00 0.00 0.00 2.69
424 453 9.516314 GTTTCAAAGATTTTGTTGCTTAGTAGT 57.484 29.630 1.92 0.00 0.00 2.73
491 525 5.494390 TGATATAGCTCACCATTCATGCT 57.506 39.130 0.00 0.00 37.72 3.79
523 557 3.489416 GTGCCGGTCAAACATTTCTTTTC 59.511 43.478 1.90 0.00 0.00 2.29
550 584 3.537580 GACTCGATGACCTGTCTAGTCT 58.462 50.000 0.00 0.00 35.21 3.24
555 589 1.178276 GTGGACTCGATGACCTGTCT 58.822 55.000 0.00 0.00 0.00 3.41
603 637 4.892345 CAGAGAGAGAGAGAGAGAGAGAGA 59.108 50.000 0.00 0.00 0.00 3.10
604 638 4.039004 CCAGAGAGAGAGAGAGAGAGAGAG 59.961 54.167 0.00 0.00 0.00 3.20
605 639 3.963374 CCAGAGAGAGAGAGAGAGAGAGA 59.037 52.174 0.00 0.00 0.00 3.10
606 640 3.070734 CCCAGAGAGAGAGAGAGAGAGAG 59.929 56.522 0.00 0.00 0.00 3.20
607 641 3.041211 CCCAGAGAGAGAGAGAGAGAGA 58.959 54.545 0.00 0.00 0.00 3.10
608 642 2.774234 ACCCAGAGAGAGAGAGAGAGAG 59.226 54.545 0.00 0.00 0.00 3.20
609 643 2.505407 CACCCAGAGAGAGAGAGAGAGA 59.495 54.545 0.00 0.00 0.00 3.10
610 644 2.421952 CCACCCAGAGAGAGAGAGAGAG 60.422 59.091 0.00 0.00 0.00 3.20
611 645 1.563879 CCACCCAGAGAGAGAGAGAGA 59.436 57.143 0.00 0.00 0.00 3.10
612 646 1.410083 CCCACCCAGAGAGAGAGAGAG 60.410 61.905 0.00 0.00 0.00 3.20
613 647 0.628522 CCCACCCAGAGAGAGAGAGA 59.371 60.000 0.00 0.00 0.00 3.10
614 648 0.334676 ACCCACCCAGAGAGAGAGAG 59.665 60.000 0.00 0.00 0.00 3.20
615 649 0.040351 CACCCACCCAGAGAGAGAGA 59.960 60.000 0.00 0.00 0.00 3.10
616 650 0.975040 CCACCCACCCAGAGAGAGAG 60.975 65.000 0.00 0.00 0.00 3.20
617 651 1.079256 CCACCCACCCAGAGAGAGA 59.921 63.158 0.00 0.00 0.00 3.10
618 652 1.992277 CCCACCCACCCAGAGAGAG 60.992 68.421 0.00 0.00 0.00 3.20
619 653 2.122729 CCCACCCACCCAGAGAGA 59.877 66.667 0.00 0.00 0.00 3.10
620 654 2.203998 ACCCACCCACCCAGAGAG 60.204 66.667 0.00 0.00 0.00 3.20
621 655 2.529136 CACCCACCCACCCAGAGA 60.529 66.667 0.00 0.00 0.00 3.10
622 656 2.854032 ACACCCACCCACCCAGAG 60.854 66.667 0.00 0.00 0.00 3.35
623 657 3.174987 CACACCCACCCACCCAGA 61.175 66.667 0.00 0.00 0.00 3.86
624 658 4.284550 CCACACCCACCCACCCAG 62.285 72.222 0.00 0.00 0.00 4.45
627 661 4.596585 CACCCACACCCACCCACC 62.597 72.222 0.00 0.00 0.00 4.61
628 662 3.816090 ACACCCACACCCACCCAC 61.816 66.667 0.00 0.00 0.00 4.61
1431 1472 4.039357 AGCAGGTCCACGTCGTCG 62.039 66.667 0.00 0.00 43.34 5.12
1432 1473 2.430921 CAGCAGGTCCACGTCGTC 60.431 66.667 0.00 0.00 0.00 4.20
1485 1538 2.038007 TTCTCCTCTGCCTCCGCT 59.962 61.111 0.00 0.00 35.36 5.52
1494 1547 2.244769 CTCTTCCTCCTCCTTCTCCTCT 59.755 54.545 0.00 0.00 0.00 3.69
1498 1551 2.243736 TCTCCTCTTCCTCCTCCTTCTC 59.756 54.545 0.00 0.00 0.00 2.87
1501 1554 3.013417 TCAATCTCCTCTTCCTCCTCCTT 59.987 47.826 0.00 0.00 0.00 3.36
1830 1889 1.568612 TTCGCTTCTTGCTCTTGGCG 61.569 55.000 0.00 0.00 45.43 5.69
1956 2015 1.596934 CGCCTGGTAGGAGCTGAAA 59.403 57.895 0.00 0.00 37.67 2.69
2153 2212 2.670934 CGGCTGGCTTCTTGCTGT 60.671 61.111 0.00 0.00 42.39 4.40
2321 2380 2.811317 CCTGCTCCTCGTTGACGC 60.811 66.667 0.00 0.00 39.60 5.19
2322 2381 1.153939 CTCCTGCTCCTCGTTGACG 60.154 63.158 0.00 0.00 41.45 4.35
2323 2382 1.446966 GCTCCTGCTCCTCGTTGAC 60.447 63.158 0.00 0.00 36.03 3.18
2324 2383 1.881903 CTGCTCCTGCTCCTCGTTGA 61.882 60.000 0.00 0.00 40.48 3.18
2325 2384 1.447489 CTGCTCCTGCTCCTCGTTG 60.447 63.158 0.00 0.00 40.48 4.10
2326 2385 2.654079 CCTGCTCCTGCTCCTCGTT 61.654 63.158 0.00 0.00 40.48 3.85
2373 2432 2.434359 GGCGGGAAGTTGAGGTCG 60.434 66.667 0.00 0.00 0.00 4.79
2554 2626 6.953520 TCTTTCTTGGAAGATTCTCTCTCTCT 59.046 38.462 0.00 0.00 34.49 3.10
2555 2627 7.169158 TCTTTCTTGGAAGATTCTCTCTCTC 57.831 40.000 0.00 0.00 34.49 3.20
2595 2670 3.258123 GGCTTCTCTGAACTCTGAACTCT 59.742 47.826 0.00 0.00 0.00 3.24
2596 2671 3.006323 TGGCTTCTCTGAACTCTGAACTC 59.994 47.826 0.00 0.00 0.00 3.01
2597 2672 2.968574 TGGCTTCTCTGAACTCTGAACT 59.031 45.455 0.00 0.00 0.00 3.01
2781 2873 9.985730 AAACTATGACGACCCGATAATAATAAA 57.014 29.630 0.00 0.00 0.00 1.40
2892 2989 7.225427 CATGGACATGGGTAGCAATTAGCAC 62.225 48.000 4.39 0.61 39.39 4.40
3014 3111 1.980765 TGGTTGCTGGAGATCTCAGTT 59.019 47.619 23.85 0.00 34.89 3.16
3046 3147 1.151668 CCTGTCGACTGAAGCAAAGG 58.848 55.000 22.46 11.49 0.00 3.11
3061 3162 0.326264 GCTGAGGATTGTCACCCTGT 59.674 55.000 0.00 0.00 31.84 4.00
3062 3163 0.393537 GGCTGAGGATTGTCACCCTG 60.394 60.000 0.00 0.00 31.84 4.45
3063 3164 0.842030 TGGCTGAGGATTGTCACCCT 60.842 55.000 0.00 0.00 35.02 4.34
3064 3165 0.257039 ATGGCTGAGGATTGTCACCC 59.743 55.000 0.00 0.00 0.00 4.61
3065 3166 2.019984 GAATGGCTGAGGATTGTCACC 58.980 52.381 0.00 0.00 0.00 4.02
3066 3167 2.019984 GGAATGGCTGAGGATTGTCAC 58.980 52.381 0.00 0.00 0.00 3.67
3067 3168 1.634973 TGGAATGGCTGAGGATTGTCA 59.365 47.619 0.00 0.00 0.00 3.58
3068 3169 2.019984 GTGGAATGGCTGAGGATTGTC 58.980 52.381 0.00 0.00 0.00 3.18
3069 3170 1.637553 AGTGGAATGGCTGAGGATTGT 59.362 47.619 0.00 0.00 0.00 2.71
3070 3171 2.022195 CAGTGGAATGGCTGAGGATTG 58.978 52.381 0.00 0.00 34.87 2.67
3072 3173 0.549950 CCAGTGGAATGGCTGAGGAT 59.450 55.000 1.68 0.00 34.87 3.24
3074 3175 4.651867 CCAGTGGAATGGCTGAGG 57.348 61.111 1.68 0.00 34.87 3.86
3091 3192 1.375268 GTCAGTCAGAGGCACCAGC 60.375 63.158 0.00 0.00 41.10 4.85
3213 3331 4.914983 TGAGCTTCCATCAGTCTGAAAAT 58.085 39.130 6.64 0.00 0.00 1.82
3246 3364 1.873698 TTCACCAGTACGTTTCAGGC 58.126 50.000 0.00 0.00 0.00 4.85
3247 3365 4.062293 TCATTTCACCAGTACGTTTCAGG 58.938 43.478 0.00 0.00 0.00 3.86
3249 3367 5.049060 CCAATCATTTCACCAGTACGTTTCA 60.049 40.000 0.00 0.00 0.00 2.69
3250 3368 5.048991 ACCAATCATTTCACCAGTACGTTTC 60.049 40.000 0.00 0.00 0.00 2.78
3251 3369 4.825085 ACCAATCATTTCACCAGTACGTTT 59.175 37.500 0.00 0.00 0.00 3.60
3252 3370 4.394729 ACCAATCATTTCACCAGTACGTT 58.605 39.130 0.00 0.00 0.00 3.99
3253 3371 4.015872 ACCAATCATTTCACCAGTACGT 57.984 40.909 0.00 0.00 0.00 3.57
3254 3372 5.447279 GCTAACCAATCATTTCACCAGTACG 60.447 44.000 0.00 0.00 0.00 3.67
3282 3400 7.624360 TCGTAATAAAGATTTGTTGCTCCAT 57.376 32.000 0.00 0.00 0.00 3.41
3296 3414 3.063997 CCACCTGCTTGCTCGTAATAAAG 59.936 47.826 0.00 0.00 0.00 1.85
3302 3420 1.888436 CTCCCACCTGCTTGCTCGTA 61.888 60.000 0.00 0.00 0.00 3.43
3316 3434 0.114364 TCTCTGTGGCAGTACTCCCA 59.886 55.000 0.00 0.00 32.61 4.37
3317 3435 1.267121 TTCTCTGTGGCAGTACTCCC 58.733 55.000 0.00 0.00 32.61 4.30
3318 3436 3.402628 TTTTCTCTGTGGCAGTACTCC 57.597 47.619 0.00 0.00 32.61 3.85
3336 3454 6.572314 GCTTGCTTGGTATACACATCCTTTTT 60.572 38.462 5.01 0.00 0.00 1.94
3337 3455 5.105756 GCTTGCTTGGTATACACATCCTTTT 60.106 40.000 5.01 0.00 0.00 2.27
3338 3456 4.399303 GCTTGCTTGGTATACACATCCTTT 59.601 41.667 5.01 0.00 0.00 3.11
3339 3457 3.947834 GCTTGCTTGGTATACACATCCTT 59.052 43.478 5.01 0.00 0.00 3.36
3341 3459 3.278574 TGCTTGCTTGGTATACACATCC 58.721 45.455 5.01 0.00 0.00 3.51
3342 3460 4.790766 GCATGCTTGCTTGGTATACACATC 60.791 45.833 16.80 0.00 45.77 3.06
3343 3461 3.067180 GCATGCTTGCTTGGTATACACAT 59.933 43.478 16.80 0.00 45.77 3.21
3344 3462 2.423185 GCATGCTTGCTTGGTATACACA 59.577 45.455 16.80 0.00 45.77 3.72
3345 3463 3.070429 GCATGCTTGCTTGGTATACAC 57.930 47.619 16.80 0.00 45.77 2.90
3357 3475 0.958876 TGTGCTCTCCTGCATGCTTG 60.959 55.000 20.33 11.54 45.23 4.01
3358 3476 0.677098 CTGTGCTCTCCTGCATGCTT 60.677 55.000 20.33 0.00 45.23 3.91
3359 3477 1.078356 CTGTGCTCTCCTGCATGCT 60.078 57.895 20.33 0.00 45.23 3.79
3360 3478 2.113433 CCTGTGCTCTCCTGCATGC 61.113 63.158 11.82 11.82 45.23 4.06
3361 3479 0.743701 GTCCTGTGCTCTCCTGCATG 60.744 60.000 0.00 0.00 45.23 4.06
3362 3480 1.601171 GTCCTGTGCTCTCCTGCAT 59.399 57.895 0.00 0.00 45.23 3.96
3363 3481 2.935740 CGTCCTGTGCTCTCCTGCA 61.936 63.158 0.00 0.00 41.05 4.41
3364 3482 2.125753 CGTCCTGTGCTCTCCTGC 60.126 66.667 0.00 0.00 0.00 4.85
3365 3483 1.510383 CTCGTCCTGTGCTCTCCTG 59.490 63.158 0.00 0.00 0.00 3.86
3366 3484 2.347322 GCTCGTCCTGTGCTCTCCT 61.347 63.158 0.00 0.00 34.28 3.69
3367 3485 2.183046 GCTCGTCCTGTGCTCTCC 59.817 66.667 0.00 0.00 34.28 3.71
3368 3486 1.882989 AAGGCTCGTCCTGTGCTCTC 61.883 60.000 0.00 0.00 46.94 3.20
3369 3487 1.910772 AAGGCTCGTCCTGTGCTCT 60.911 57.895 0.00 0.00 46.94 4.09
3370 3488 1.739562 CAAGGCTCGTCCTGTGCTC 60.740 63.158 0.00 0.00 46.94 4.26
3371 3489 2.345244 CAAGGCTCGTCCTGTGCT 59.655 61.111 0.00 0.00 46.94 4.40
3372 3490 3.426568 GCAAGGCTCGTCCTGTGC 61.427 66.667 13.01 13.01 46.94 4.57
3373 3491 1.294659 GAAGCAAGGCTCGTCCTGTG 61.295 60.000 0.00 3.22 46.94 3.66
3374 3492 1.004440 GAAGCAAGGCTCGTCCTGT 60.004 57.895 0.00 0.00 46.94 4.00


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

AutoCloner maintained by Alex Coulton.