Multiple sequence alignment - TraesCS3D01G496900

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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 TraesCS3D01G496900 chr3D 100.000 3899 0 0 1 3899 588320707 588316809 0.000000e+00 7201
1 TraesCS3D01G496900 chr3B 91.752 2061 108 22 777 2807 786726065 786724037 0.000000e+00 2808
2 TraesCS3D01G496900 chr3B 90.926 529 26 6 2841 3365 786724037 786723527 0.000000e+00 691
3 TraesCS3D01G496900 chr3B 92.617 447 20 5 3363 3808 786723588 786723154 7.110000e-177 630
4 TraesCS3D01G496900 chr3B 92.734 289 16 1 3069 3357 168990074 168989791 2.800000e-111 412
5 TraesCS3D01G496900 chr3A 93.054 1454 72 15 1912 3365 718353347 718351923 0.000000e+00 2098
6 TraesCS3D01G496900 chr3A 90.346 694 53 7 1390 2082 718353893 718353213 0.000000e+00 898
7 TraesCS3D01G496900 chr3A 91.429 525 38 6 3363 3886 718351984 718351466 0.000000e+00 713
8 TraesCS3D01G496900 chr3A 88.809 554 40 5 777 1318 718354687 718354144 0.000000e+00 660
9 TraesCS3D01G496900 chr3A 87.764 474 48 7 1 470 718355616 718355149 2.650000e-151 545
10 TraesCS3D01G496900 chr2D 85.569 1476 127 45 1912 3365 644722145 644720734 0.000000e+00 1467
11 TraesCS3D01G496900 chr2D 89.493 552 35 10 3363 3899 644720795 644720252 0.000000e+00 676
12 TraesCS3D01G496900 chr2D 84.766 512 57 17 1585 2082 644722551 644722047 9.730000e-136 494
13 TraesCS3D01G496900 chr2D 83.511 376 59 2 2062 2437 565982384 565982012 8.020000e-92 348
14 TraesCS3D01G496900 chr2A 88.730 1189 98 17 1918 3084 770013336 770012162 0.000000e+00 1421
15 TraesCS3D01G496900 chr2A 90.792 543 40 4 3358 3899 770011983 770011450 0.000000e+00 717
16 TraesCS3D01G496900 chr2A 81.877 618 78 21 1489 2082 770013815 770013208 1.260000e-134 490
17 TraesCS3D01G496900 chr2B 84.647 1472 120 48 1912 3362 790751914 790753300 0.000000e+00 1369
18 TraesCS3D01G496900 chr2B 90.538 539 40 5 3363 3899 790860635 790861164 0.000000e+00 702
19 TraesCS3D01G496900 chr2B 90.149 538 44 3 3363 3899 790753242 790753771 0.000000e+00 691
20 TraesCS3D01G496900 chr2B 86.301 365 49 1 1718 2082 790751685 790752048 2.820000e-106 396
21 TraesCS3D01G496900 chr2B 92.593 216 13 3 3363 3576 17482161 17482375 1.360000e-79 307
22 TraesCS3D01G496900 chr4A 92.734 289 16 1 3069 3357 655273149 655273432 2.800000e-111 412
23 TraesCS3D01G496900 chr7B 92.388 289 17 1 3069 3357 571235321 571235038 1.300000e-109 407
24 TraesCS3D01G496900 chr4B 92.388 289 17 1 3069 3357 76501901 76501618 1.300000e-109 407
25 TraesCS3D01G496900 chr4B 92.593 216 13 3 3363 3576 76501671 76501457 1.360000e-79 307
26 TraesCS3D01G496900 chr1B 92.388 289 17 1 3069 3357 10526202 10526485 1.300000e-109 407
27 TraesCS3D01G496900 chr1B 92.042 289 18 1 3069 3357 687189434 687189151 6.070000e-108 401
28 TraesCS3D01G496900 chr1A 92.042 289 18 1 3069 3357 575302061 575301778 6.070000e-108 401
29 TraesCS3D01G496900 chr1A 92.130 216 14 3 3363 3576 575301831 575301617 6.330000e-78 302
30 TraesCS3D01G496900 chrUn 92.130 216 14 3 3363 3576 34685131 34685345 6.330000e-78 302


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 TraesCS3D01G496900 chr3D 588316809 588320707 3898 True 7201.000000 7201 100.000000 1 3899 1 chr3D.!!$R1 3898
1 TraesCS3D01G496900 chr3B 786723154 786726065 2911 True 1376.333333 2808 91.765000 777 3808 3 chr3B.!!$R2 3031
2 TraesCS3D01G496900 chr3A 718351466 718355616 4150 True 982.800000 2098 90.280400 1 3886 5 chr3A.!!$R1 3885
3 TraesCS3D01G496900 chr2D 644720252 644722551 2299 True 879.000000 1467 86.609333 1585 3899 3 chr2D.!!$R2 2314
4 TraesCS3D01G496900 chr2A 770011450 770013815 2365 True 876.000000 1421 87.133000 1489 3899 3 chr2A.!!$R1 2410
5 TraesCS3D01G496900 chr2B 790751685 790753771 2086 False 818.666667 1369 87.032333 1718 3899 3 chr2B.!!$F3 2181
6 TraesCS3D01G496900 chr2B 790860635 790861164 529 False 702.000000 702 90.538000 3363 3899 1 chr2B.!!$F2 536

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
334 338 0.036010 ACATGTAGGTCTGGCAGTGC 60.036 55.0 15.27 6.55 0.00 4.40 F
629 823 0.458669 GTGAAGATAACGAGGGGCGA 59.541 55.0 0.00 0.00 44.57 5.54 F
1345 1555 0.032017 AGCTCCCCGGTCTAACTGAT 60.032 55.0 0.00 0.00 0.00 2.90 F
1982 2501 0.033796 CTGATGGCAGGATGGGTGTT 60.034 55.0 0.00 0.00 38.51 3.32 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1329 1539 0.256752 TCGATCAGTTAGACCGGGGA 59.743 55.0 6.32 0.0 0.0 4.81 R
2034 2589 0.332632 CCACCCATCCTGTCACCAAT 59.667 55.0 0.00 0.0 0.0 3.16 R
2642 3201 0.101399 AGCCGCGATCTAAGACTGTG 59.899 55.0 8.23 0.0 0.0 3.66 R
3102 3686 0.617413 CTGCACAGGAGATTCACCCT 59.383 55.0 0.00 0.0 0.0 4.34 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
50 51 0.804989 CGAGTTGAGATTGGTTGCCC 59.195 55.000 0.00 0.00 0.00 5.36
60 61 0.185416 TTGGTTGCCCGGTTAGGAAA 59.815 50.000 0.00 0.00 45.00 3.13
61 62 0.537828 TGGTTGCCCGGTTAGGAAAC 60.538 55.000 0.00 0.00 45.00 2.78
62 63 0.251033 GGTTGCCCGGTTAGGAAACT 60.251 55.000 0.00 0.00 45.00 2.66
64 65 1.268625 GTTGCCCGGTTAGGAAACTTG 59.731 52.381 0.00 0.00 45.00 3.16
65 66 0.891904 TGCCCGGTTAGGAAACTTGC 60.892 55.000 0.00 0.00 45.00 4.01
71 75 3.552068 CCGGTTAGGAAACTTGCCAAAAG 60.552 47.826 0.00 0.00 45.00 2.27
81 85 2.501316 ACTTGCCAAAAGAACTTTGCCT 59.499 40.909 0.45 0.00 42.74 4.75
127 131 1.856629 ATGCTTTGGATCCCAACAGG 58.143 50.000 9.90 0.00 43.82 4.00
141 145 4.509756 CAGGATCACTGCCTCACG 57.490 61.111 0.00 0.00 40.97 4.35
166 170 6.773685 GGACTCTCTAGCTTGGAGATTTAGTA 59.226 42.308 16.07 0.00 38.85 1.82
167 171 7.450323 GGACTCTCTAGCTTGGAGATTTAGTAT 59.550 40.741 16.07 1.77 38.85 2.12
169 173 8.224720 ACTCTCTAGCTTGGAGATTTAGTATCT 58.775 37.037 16.07 0.00 38.85 1.98
171 175 7.389330 TCTCTAGCTTGGAGATTTAGTATCTCG 59.611 40.741 12.99 0.00 44.04 4.04
181 185 7.646130 GGAGATTTAGTATCTCGAAGAACAGTG 59.354 40.741 8.27 0.00 44.04 3.66
184 188 2.159366 AGTATCTCGAAGAACAGTGGCG 60.159 50.000 0.00 0.00 34.09 5.69
202 206 2.316119 CGAAGCTACACAACCAAAGC 57.684 50.000 0.00 0.00 35.16 3.51
233 237 4.589908 CAGGTACAAAGGAATGCCTACTT 58.410 43.478 0.00 0.00 46.28 2.24
234 238 5.010282 CAGGTACAAAGGAATGCCTACTTT 58.990 41.667 0.00 0.00 46.28 2.66
235 239 5.476945 CAGGTACAAAGGAATGCCTACTTTT 59.523 40.000 0.00 0.00 46.28 2.27
262 266 5.332743 TCTTTCTGATGGCCCAATTTACTT 58.667 37.500 0.00 0.00 0.00 2.24
263 267 5.779771 TCTTTCTGATGGCCCAATTTACTTT 59.220 36.000 0.00 0.00 0.00 2.66
276 280 7.544217 GCCCAATTTACTTTTAATACCACACTG 59.456 37.037 0.00 0.00 0.00 3.66
290 294 3.117663 ACCACACTGTGTTTTCTATGGGT 60.118 43.478 11.40 9.90 0.00 4.51
294 298 2.890945 ACTGTGTTTTCTATGGGTTGGC 59.109 45.455 0.00 0.00 0.00 4.52
297 301 2.231235 GTGTTTTCTATGGGTTGGCTGG 59.769 50.000 0.00 0.00 0.00 4.85
323 327 4.097892 GTGGCCCATTTTCTAACATGTAGG 59.902 45.833 0.00 0.00 0.00 3.18
325 329 4.338400 GGCCCATTTTCTAACATGTAGGTC 59.662 45.833 0.00 0.00 0.00 3.85
326 330 5.193679 GCCCATTTTCTAACATGTAGGTCT 58.806 41.667 0.00 0.00 0.00 3.85
328 332 5.590259 CCCATTTTCTAACATGTAGGTCTGG 59.410 44.000 0.00 0.98 0.00 3.86
330 334 4.901197 TTTCTAACATGTAGGTCTGGCA 57.099 40.909 0.00 0.00 0.00 4.92
334 338 0.036010 ACATGTAGGTCTGGCAGTGC 60.036 55.000 15.27 6.55 0.00 4.40
379 383 7.445945 ACTCCATATAAGTGCTTCTTACATCC 58.554 38.462 4.58 0.00 40.80 3.51
387 391 5.869579 AGTGCTTCTTACATCCAAGAGAAA 58.130 37.500 0.00 0.00 35.99 2.52
388 392 5.703130 AGTGCTTCTTACATCCAAGAGAAAC 59.297 40.000 0.00 0.00 35.99 2.78
404 408 4.953579 AGAGAAACTTTTGTTGGCAAGGTA 59.046 37.500 0.00 0.00 42.67 3.08
414 418 2.735134 GTTGGCAAGGTAGTTCTACACG 59.265 50.000 0.00 1.62 0.00 4.49
416 420 1.547372 GGCAAGGTAGTTCTACACGGA 59.453 52.381 11.34 0.00 0.00 4.69
454 458 1.662876 CGAAGGGTTCGCAAACACATG 60.663 52.381 0.00 0.00 46.97 3.21
458 462 0.584396 GGTTCGCAAACACATGACGA 59.416 50.000 0.00 0.00 37.10 4.20
459 463 1.398451 GGTTCGCAAACACATGACGAG 60.398 52.381 0.00 0.00 37.10 4.18
470 474 4.810790 ACACATGACGAGTTAAGAGGAAG 58.189 43.478 0.00 0.00 0.00 3.46
471 475 4.281182 ACACATGACGAGTTAAGAGGAAGT 59.719 41.667 0.00 0.00 0.00 3.01
472 476 4.859798 CACATGACGAGTTAAGAGGAAGTC 59.140 45.833 0.00 0.00 0.00 3.01
473 477 4.767928 ACATGACGAGTTAAGAGGAAGTCT 59.232 41.667 0.00 0.00 36.94 3.24
474 478 5.944599 ACATGACGAGTTAAGAGGAAGTCTA 59.055 40.000 0.00 0.00 32.65 2.59
475 479 6.433404 ACATGACGAGTTAAGAGGAAGTCTAA 59.567 38.462 0.00 0.00 32.65 2.10
476 480 6.251655 TGACGAGTTAAGAGGAAGTCTAAC 57.748 41.667 0.00 0.00 32.65 2.34
477 481 5.182760 TGACGAGTTAAGAGGAAGTCTAACC 59.817 44.000 0.00 0.00 32.65 2.85
478 482 4.462132 ACGAGTTAAGAGGAAGTCTAACCC 59.538 45.833 0.00 0.00 32.65 4.11
479 483 4.705991 CGAGTTAAGAGGAAGTCTAACCCT 59.294 45.833 0.00 0.00 32.65 4.34
480 484 5.185442 CGAGTTAAGAGGAAGTCTAACCCTT 59.815 44.000 0.00 0.00 32.65 3.95
481 485 6.295180 CGAGTTAAGAGGAAGTCTAACCCTTT 60.295 42.308 0.00 0.00 32.65 3.11
482 486 7.006865 AGTTAAGAGGAAGTCTAACCCTTTC 57.993 40.000 0.00 0.00 32.65 2.62
483 487 4.912317 AAGAGGAAGTCTAACCCTTTCC 57.088 45.455 0.00 0.00 39.47 3.13
484 488 3.182976 AGAGGAAGTCTAACCCTTTCCC 58.817 50.000 0.00 0.00 39.91 3.97
485 489 2.910977 GAGGAAGTCTAACCCTTTCCCA 59.089 50.000 0.00 0.00 39.91 4.37
486 490 3.329814 GAGGAAGTCTAACCCTTTCCCAA 59.670 47.826 0.00 0.00 39.91 4.12
487 491 3.725267 AGGAAGTCTAACCCTTTCCCAAA 59.275 43.478 0.00 0.00 39.91 3.28
488 492 4.169264 AGGAAGTCTAACCCTTTCCCAAAA 59.831 41.667 0.00 0.00 39.91 2.44
489 493 4.897076 GGAAGTCTAACCCTTTCCCAAAAA 59.103 41.667 0.00 0.00 34.38 1.94
490 494 5.010719 GGAAGTCTAACCCTTTCCCAAAAAG 59.989 44.000 0.00 0.00 34.38 2.27
491 495 5.138758 AGTCTAACCCTTTCCCAAAAAGT 57.861 39.130 0.00 0.00 0.00 2.66
492 496 5.525484 AGTCTAACCCTTTCCCAAAAAGTT 58.475 37.500 0.00 0.00 0.00 2.66
493 497 5.962031 AGTCTAACCCTTTCCCAAAAAGTTT 59.038 36.000 0.00 0.00 0.00 2.66
494 498 6.097839 AGTCTAACCCTTTCCCAAAAAGTTTC 59.902 38.462 0.00 0.00 0.00 2.78
495 499 5.958987 TCTAACCCTTTCCCAAAAAGTTTCA 59.041 36.000 0.00 0.00 0.00 2.69
496 500 5.506730 AACCCTTTCCCAAAAAGTTTCAA 57.493 34.783 0.00 0.00 0.00 2.69
497 501 4.839121 ACCCTTTCCCAAAAAGTTTCAAC 58.161 39.130 0.00 0.00 0.00 3.18
498 502 4.196193 CCCTTTCCCAAAAAGTTTCAACC 58.804 43.478 0.00 0.00 0.00 3.77
518 702 5.188988 ACCCACCCTCTTTAATCCTTTAC 57.811 43.478 0.00 0.00 0.00 2.01
525 709 9.304335 CACCCTCTTTAATCCTTTACCTAAAAA 57.696 33.333 0.00 0.00 0.00 1.94
566 753 9.927668 ATTGAAAATAAGTTACCCTCATTGTTG 57.072 29.630 0.00 0.00 0.00 3.33
573 767 0.773644 ACCCTCATTGTTGAGCACCT 59.226 50.000 0.00 0.00 46.76 4.00
581 775 5.129634 TCATTGTTGAGCACCTGAAGTAAA 58.870 37.500 0.00 0.00 0.00 2.01
600 794 6.365520 AGTAAATTTTCCCATATCTTCCGCT 58.634 36.000 0.00 0.00 0.00 5.52
615 809 3.184683 GCTCGCTCGCCAGTGAAG 61.185 66.667 0.00 0.00 38.73 3.02
629 823 0.458669 GTGAAGATAACGAGGGGCGA 59.541 55.000 0.00 0.00 44.57 5.54
645 839 4.779733 GAGGGAGAGGCCGGTGGA 62.780 72.222 1.90 0.00 37.63 4.02
665 859 1.027357 TCGGTATAGGGACTCAACGC 58.973 55.000 0.00 0.00 41.75 4.84
667 861 1.117150 GGTATAGGGACTCAACGCCA 58.883 55.000 0.00 0.00 41.75 5.69
698 892 1.551883 GCGGAGTAGGTCAAACCCTAA 59.448 52.381 0.00 0.00 39.75 2.69
699 893 2.169978 GCGGAGTAGGTCAAACCCTAAT 59.830 50.000 0.00 0.00 39.75 1.73
700 894 3.740452 GCGGAGTAGGTCAAACCCTAATC 60.740 52.174 6.22 6.22 46.52 1.75
702 896 3.455327 GAGTAGGTCAAACCCTAATCGC 58.545 50.000 0.00 0.00 40.96 4.58
717 911 4.755123 CCTAATCGCGAGGGTAAATTTCAT 59.245 41.667 16.66 0.00 0.00 2.57
741 935 3.059884 CACACTGCATATCCGATGGTAC 58.940 50.000 0.00 0.00 0.00 3.34
742 936 2.288213 ACACTGCATATCCGATGGTACG 60.288 50.000 0.00 0.00 0.00 3.67
743 937 2.030274 CACTGCATATCCGATGGTACGA 60.030 50.000 0.00 0.00 35.09 3.43
744 938 2.626266 ACTGCATATCCGATGGTACGAA 59.374 45.455 0.00 0.00 35.09 3.85
745 939 3.245797 CTGCATATCCGATGGTACGAAG 58.754 50.000 0.00 0.00 35.09 3.79
746 940 1.993370 GCATATCCGATGGTACGAAGC 59.007 52.381 0.00 0.00 35.09 3.86
747 941 2.352814 GCATATCCGATGGTACGAAGCT 60.353 50.000 0.00 0.00 35.09 3.74
748 942 3.245797 CATATCCGATGGTACGAAGCTG 58.754 50.000 0.00 0.00 35.09 4.24
749 943 1.399714 ATCCGATGGTACGAAGCTGA 58.600 50.000 0.00 0.00 35.09 4.26
750 944 1.399714 TCCGATGGTACGAAGCTGAT 58.600 50.000 0.00 0.00 35.09 2.90
751 945 1.754803 TCCGATGGTACGAAGCTGATT 59.245 47.619 0.00 0.00 35.09 2.57
752 946 2.167693 TCCGATGGTACGAAGCTGATTT 59.832 45.455 0.00 0.00 35.09 2.17
753 947 2.936498 CCGATGGTACGAAGCTGATTTT 59.064 45.455 0.00 0.00 35.09 1.82
754 948 3.242413 CCGATGGTACGAAGCTGATTTTG 60.242 47.826 0.00 0.00 35.09 2.44
755 949 3.616821 CGATGGTACGAAGCTGATTTTGA 59.383 43.478 0.00 0.00 35.09 2.69
756 950 4.092821 CGATGGTACGAAGCTGATTTTGAA 59.907 41.667 0.00 0.00 35.09 2.69
757 951 5.390461 CGATGGTACGAAGCTGATTTTGAAA 60.390 40.000 0.00 0.00 35.09 2.69
758 952 5.759506 TGGTACGAAGCTGATTTTGAAAA 57.240 34.783 0.00 0.00 0.00 2.29
759 953 6.137794 TGGTACGAAGCTGATTTTGAAAAA 57.862 33.333 0.00 0.00 0.00 1.94
799 993 3.285484 AGCTGATTTTGATGAAGCGGAT 58.715 40.909 0.00 0.00 38.90 4.18
807 1001 1.203928 GATGAAGCGGATCAGTCACG 58.796 55.000 0.00 0.00 31.76 4.35
815 1009 0.716108 GGATCAGTCACGAACAAGCG 59.284 55.000 0.00 0.00 37.29 4.68
881 1075 1.447643 CGGCCTAGAGATGGGTTGG 59.552 63.158 0.00 0.00 0.00 3.77
892 1086 4.735358 GGGTTGGGTCGGGCCTTC 62.735 72.222 0.84 0.00 37.43 3.46
895 1089 3.562232 TTGGGTCGGGCCTTCGTT 61.562 61.111 0.84 0.00 37.43 3.85
945 1139 6.098838 TGAAGATATTGGATCAGCTACACAGT 59.901 38.462 0.00 0.00 0.00 3.55
946 1140 6.491714 AGATATTGGATCAGCTACACAGTT 57.508 37.500 0.00 0.00 0.00 3.16
947 1141 6.520272 AGATATTGGATCAGCTACACAGTTC 58.480 40.000 0.00 0.00 0.00 3.01
984 1181 1.468520 CGTCTCGTTAGGTTTCCCGTA 59.531 52.381 0.00 0.00 35.12 4.02
985 1182 2.476854 CGTCTCGTTAGGTTTCCCGTAG 60.477 54.545 0.00 0.00 35.12 3.51
996 1193 1.344065 TTCCCGTAGCTTCAACTCCA 58.656 50.000 0.00 0.00 0.00 3.86
998 1195 1.906574 TCCCGTAGCTTCAACTCCAAT 59.093 47.619 0.00 0.00 0.00 3.16
1002 1199 2.644676 GTAGCTTCAACTCCAATCCCC 58.355 52.381 0.00 0.00 0.00 4.81
1003 1200 1.075601 AGCTTCAACTCCAATCCCCA 58.924 50.000 0.00 0.00 0.00 4.96
1004 1201 1.642762 AGCTTCAACTCCAATCCCCAT 59.357 47.619 0.00 0.00 0.00 4.00
1118 1321 3.636231 CCCCGCACAACTCCTCCA 61.636 66.667 0.00 0.00 0.00 3.86
1329 1539 1.817447 GACAAGGTACGTCTACCAGCT 59.183 52.381 10.09 0.00 44.75 4.24
1345 1555 0.032017 AGCTCCCCGGTCTAACTGAT 60.032 55.000 0.00 0.00 0.00 2.90
1372 1582 0.171231 GCTCCCTTCCGTTGCATTTC 59.829 55.000 0.00 0.00 0.00 2.17
1373 1583 0.811281 CTCCCTTCCGTTGCATTTCC 59.189 55.000 0.00 0.00 0.00 3.13
1465 1854 0.336392 TCAGGAGCTAGGCCTCTCAA 59.664 55.000 20.07 5.39 32.12 3.02
1483 1890 1.157870 AACTCGAGTGGCACAAACCG 61.158 55.000 20.85 16.37 44.16 4.44
1487 1894 2.518349 AGTGGCACAAACCGGTGG 60.518 61.111 21.41 6.38 44.16 4.61
1521 1928 7.722728 TCATTTCATGGGGATTAGAAGAAGATG 59.277 37.037 0.00 0.00 0.00 2.90
1525 1932 5.878406 TGGGGATTAGAAGAAGATGAGAC 57.122 43.478 0.00 0.00 0.00 3.36
1546 1954 3.871594 ACGAAAACAGAGGAGTTCTTGTG 59.128 43.478 0.00 0.00 32.41 3.33
1548 1956 4.570772 CGAAAACAGAGGAGTTCTTGTGAA 59.429 41.667 0.00 0.00 32.41 3.18
1549 1957 5.064707 CGAAAACAGAGGAGTTCTTGTGAAA 59.935 40.000 0.00 0.00 32.41 2.69
1641 2064 2.111043 CGGTGCCTGTTGGTGACT 59.889 61.111 0.00 0.00 35.27 3.41
1714 2159 3.625764 ACGTACACACACTTTTTCTGCAT 59.374 39.130 0.00 0.00 0.00 3.96
1982 2501 0.033796 CTGATGGCAGGATGGGTGTT 60.034 55.000 0.00 0.00 38.51 3.32
1985 2504 2.244510 TGATGGCAGGATGGGTGTTAAT 59.755 45.455 0.00 0.00 35.86 1.40
1997 2516 3.245229 TGGGTGTTAATGGATTCACAGCT 60.245 43.478 12.97 0.00 40.37 4.24
2034 2589 0.109532 TGGAAACGGATTCACAGCCA 59.890 50.000 0.36 0.00 39.98 4.75
2041 2596 1.838112 GGATTCACAGCCATTGGTGA 58.162 50.000 4.26 0.00 42.66 4.02
2333 2888 0.693049 AGATTGGCCTCAAGTCGGTT 59.307 50.000 3.32 0.00 36.19 4.44
2731 3290 6.692681 GGTGATGGATTTGTTTTGATATGACG 59.307 38.462 0.00 0.00 0.00 4.35
2742 3306 3.258971 TGATATGACGTGGTTGCATGA 57.741 42.857 0.00 0.00 0.00 3.07
2743 3307 3.807553 TGATATGACGTGGTTGCATGAT 58.192 40.909 0.00 0.00 0.00 2.45
2788 3352 8.654230 ATTTCCTATATAATGATAGCACTGCG 57.346 34.615 0.00 0.00 0.00 5.18
2888 3463 5.859648 CGGGTTTCGCACTAAAATAATGTTT 59.140 36.000 0.00 0.00 0.00 2.83
2925 3500 3.615155 CTCTGTCCCCTCATTTTTCCTC 58.385 50.000 0.00 0.00 0.00 3.71
2957 3532 7.130917 CCAGCGAGAAAATATTCTGAGATTTG 58.869 38.462 0.00 0.00 45.91 2.32
3064 3648 1.918957 CATGTTCCCTCTTCCCCTCTT 59.081 52.381 0.00 0.00 0.00 2.85
3102 3686 3.826524 TGAAGCATTGGAGTGGTTACAA 58.173 40.909 0.00 0.00 39.68 2.41
3146 3730 8.832735 AGTTAATTAGAAGGGTGGAATTAGTGA 58.167 33.333 0.00 0.00 0.00 3.41
3306 3904 3.054878 GCAGCAAGGAAAACACTGAATG 58.945 45.455 0.00 0.00 0.00 2.67
3319 3917 3.251729 ACACTGAATGTTGACAGCATCAC 59.748 43.478 5.16 4.27 38.98 3.06
3357 3955 6.894339 TGGAATGAGATGAATGATTCCATG 57.106 37.500 7.98 0.00 45.74 3.66
3358 3956 6.607019 TGGAATGAGATGAATGATTCCATGA 58.393 36.000 7.98 0.00 45.74 3.07
3359 3957 7.238710 TGGAATGAGATGAATGATTCCATGAT 58.761 34.615 7.98 0.00 45.74 2.45
3360 3958 7.728532 TGGAATGAGATGAATGATTCCATGATT 59.271 33.333 7.98 0.00 45.74 2.57
3361 3959 8.585881 GGAATGAGATGAATGATTCCATGATTT 58.414 33.333 2.26 0.00 42.36 2.17
3377 3975 6.017687 TCCATGATTTAATCTTGACAGCATCG 60.018 38.462 18.50 3.78 36.78 3.84
3378 3976 5.160699 TGATTTAATCTTGACAGCATCGC 57.839 39.130 6.50 0.00 0.00 4.58
3383 3981 1.131218 CTTGACAGCATCGCACACG 59.869 57.895 0.00 0.00 42.01 4.49
3391 3989 2.819595 ATCGCACACGGACCATGC 60.820 61.111 2.87 2.87 40.63 4.06
3530 4143 9.747898 AAATCATAGTTAACCCAGATTACAACA 57.252 29.630 13.89 0.00 0.00 3.33
3531 4144 9.747898 AATCATAGTTAACCCAGATTACAACAA 57.252 29.630 12.58 0.00 0.00 2.83
3575 4188 1.238439 GGTGCACACACTACTGCATT 58.762 50.000 20.43 0.00 44.93 3.56
3677 4291 1.238439 CCACGCCCATATCCATCAAC 58.762 55.000 0.00 0.00 0.00 3.18
3700 4314 5.983720 ACCGTCGGCATATATAAATAGCATC 59.016 40.000 12.28 0.00 0.00 3.91
3701 4315 6.183360 ACCGTCGGCATATATAAATAGCATCT 60.183 38.462 12.28 0.00 0.00 2.90
3702 4316 6.363626 CCGTCGGCATATATAAATAGCATCTC 59.636 42.308 0.00 0.00 0.00 2.75
3703 4317 6.363626 CGTCGGCATATATAAATAGCATCTCC 59.636 42.308 0.00 0.00 0.00 3.71
3704 4318 7.210174 GTCGGCATATATAAATAGCATCTCCA 58.790 38.462 0.00 0.00 0.00 3.86
3705 4319 7.383572 GTCGGCATATATAAATAGCATCTCCAG 59.616 40.741 0.00 0.00 0.00 3.86
3706 4320 6.648310 CGGCATATATAAATAGCATCTCCAGG 59.352 42.308 0.00 0.00 0.00 4.45
3826 4444 3.170717 GGTAATGATCCCCCTCGATACA 58.829 50.000 0.00 0.00 0.00 2.29
3858 4476 7.978414 CCTTGCTGACTGAATATATATCATCGT 59.022 37.037 0.00 0.00 0.00 3.73
3875 4493 0.532862 CGTTGTGAAGAGTGTGGGCT 60.533 55.000 0.00 0.00 0.00 5.19
3894 4512 2.885894 GCTTACGCCACTAGATCTACCT 59.114 50.000 0.00 0.00 0.00 3.08
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
10 11 0.865769 ATCGGTTTCACAAGTGACGC 59.134 50.000 1.73 0.00 39.66 5.19
50 51 3.316868 TCTTTTGGCAAGTTTCCTAACCG 59.683 43.478 0.00 0.00 34.71 4.44
65 66 7.552458 AAACATTTAGGCAAAGTTCTTTTGG 57.448 32.000 2.28 0.00 45.09 3.28
93 97 1.754234 GCATTCGGGCATCCCTGTT 60.754 57.895 0.00 0.00 42.67 3.16
95 99 1.039233 AAAGCATTCGGGCATCCCTG 61.039 55.000 0.00 0.00 42.67 4.45
96 100 1.039233 CAAAGCATTCGGGCATCCCT 61.039 55.000 0.00 0.00 42.67 4.20
97 101 1.438814 CAAAGCATTCGGGCATCCC 59.561 57.895 0.00 0.00 41.09 3.85
104 108 1.134946 GTTGGGATCCAAAGCATTCGG 59.865 52.381 15.23 0.00 45.73 4.30
141 145 5.596772 ACTAAATCTCCAAGCTAGAGAGTCC 59.403 44.000 18.31 0.00 43.36 3.85
166 170 0.888619 TCGCCACTGTTCTTCGAGAT 59.111 50.000 0.00 0.00 0.00 2.75
167 171 0.671796 TTCGCCACTGTTCTTCGAGA 59.328 50.000 0.00 0.00 0.00 4.04
169 173 0.944311 GCTTCGCCACTGTTCTTCGA 60.944 55.000 0.00 0.00 0.00 3.71
171 175 1.727335 GTAGCTTCGCCACTGTTCTTC 59.273 52.381 0.00 0.00 0.00 2.87
177 181 0.512952 GTTGTGTAGCTTCGCCACTG 59.487 55.000 0.00 0.00 0.00 3.66
181 185 0.948678 TTTGGTTGTGTAGCTTCGCC 59.051 50.000 0.00 0.00 0.00 5.54
184 188 2.030805 CCAGCTTTGGTTGTGTAGCTTC 60.031 50.000 0.00 0.00 41.76 3.86
202 206 1.247567 CTTTGTACCTGCCAACCCAG 58.752 55.000 0.00 0.00 0.00 4.45
235 239 5.565455 AATTGGGCCATCAGAAAGAAAAA 57.435 34.783 7.26 0.00 0.00 1.94
237 241 5.779771 AGTAAATTGGGCCATCAGAAAGAAA 59.220 36.000 7.26 0.00 0.00 2.52
238 242 5.332743 AGTAAATTGGGCCATCAGAAAGAA 58.667 37.500 7.26 0.00 0.00 2.52
239 243 4.934356 AGTAAATTGGGCCATCAGAAAGA 58.066 39.130 7.26 0.00 0.00 2.52
240 244 5.665916 AAGTAAATTGGGCCATCAGAAAG 57.334 39.130 7.26 0.00 0.00 2.62
245 249 7.400339 TGGTATTAAAAGTAAATTGGGCCATCA 59.600 33.333 7.26 0.00 0.00 3.07
252 256 9.405587 CACAGTGTGGTATTAAAAGTAAATTGG 57.594 33.333 15.86 0.00 0.00 3.16
253 257 9.959749 ACACAGTGTGGTATTAAAAGTAAATTG 57.040 29.630 26.40 0.00 37.94 2.32
262 266 8.788806 CCATAGAAAACACAGTGTGGTATTAAA 58.211 33.333 26.40 6.95 37.94 1.52
263 267 7.392113 CCCATAGAAAACACAGTGTGGTATTAA 59.608 37.037 26.40 8.34 37.94 1.40
276 280 2.231235 CCAGCCAACCCATAGAAAACAC 59.769 50.000 0.00 0.00 0.00 3.32
297 301 0.172578 GTTAGAAAATGGGCCACGGC 59.827 55.000 9.28 0.00 41.06 5.68
328 332 1.404391 CCATGAATTCTCTGGCACTGC 59.596 52.381 7.05 0.00 0.00 4.40
334 338 5.009410 GGAGTATTTGCCATGAATTCTCTGG 59.991 44.000 18.15 18.15 33.79 3.86
377 381 3.766591 TGCCAACAAAAGTTTCTCTTGGA 59.233 39.130 17.22 5.61 36.40 3.53
379 383 4.567959 CCTTGCCAACAAAAGTTTCTCTTG 59.432 41.667 0.00 0.00 36.40 3.02
387 391 4.278310 AGAACTACCTTGCCAACAAAAGT 58.722 39.130 0.00 0.00 34.74 2.66
388 392 4.918810 AGAACTACCTTGCCAACAAAAG 57.081 40.909 0.00 0.00 34.74 2.27
404 408 3.143211 AGTCAGTCTCCGTGTAGAACT 57.857 47.619 0.00 0.00 0.00 3.01
414 418 2.221981 CGTGCTTTGAAAGTCAGTCTCC 59.778 50.000 6.81 0.00 0.00 3.71
416 420 3.179443 TCGTGCTTTGAAAGTCAGTCT 57.821 42.857 6.81 0.00 0.00 3.24
449 453 4.810790 ACTTCCTCTTAACTCGTCATGTG 58.189 43.478 0.00 0.00 0.00 3.21
454 458 5.392919 GGGTTAGACTTCCTCTTAACTCGTC 60.393 48.000 0.00 0.00 0.00 4.20
458 462 6.013553 GGAAAGGGTTAGACTTCCTCTTAACT 60.014 42.308 0.00 0.00 0.00 2.24
459 463 6.171921 GGAAAGGGTTAGACTTCCTCTTAAC 58.828 44.000 0.00 0.00 0.00 2.01
470 474 5.864418 AACTTTTTGGGAAAGGGTTAGAC 57.136 39.130 3.85 0.00 0.00 2.59
471 475 5.958987 TGAAACTTTTTGGGAAAGGGTTAGA 59.041 36.000 3.85 0.00 32.59 2.10
472 476 6.228616 TGAAACTTTTTGGGAAAGGGTTAG 57.771 37.500 3.85 0.00 32.59 2.34
473 477 6.408035 GTTGAAACTTTTTGGGAAAGGGTTA 58.592 36.000 3.85 0.00 32.59 2.85
474 478 5.250200 GTTGAAACTTTTTGGGAAAGGGTT 58.750 37.500 3.85 0.00 34.82 4.11
475 479 4.323945 GGTTGAAACTTTTTGGGAAAGGGT 60.324 41.667 3.85 0.00 0.00 4.34
476 480 4.196193 GGTTGAAACTTTTTGGGAAAGGG 58.804 43.478 3.85 0.00 0.00 3.95
477 481 4.196193 GGGTTGAAACTTTTTGGGAAAGG 58.804 43.478 3.85 0.00 0.00 3.11
478 482 4.634004 GTGGGTTGAAACTTTTTGGGAAAG 59.366 41.667 0.00 0.00 0.00 2.62
479 483 4.565861 GGTGGGTTGAAACTTTTTGGGAAA 60.566 41.667 0.00 0.00 0.00 3.13
480 484 3.055021 GGTGGGTTGAAACTTTTTGGGAA 60.055 43.478 0.00 0.00 0.00 3.97
481 485 2.502130 GGTGGGTTGAAACTTTTTGGGA 59.498 45.455 0.00 0.00 0.00 4.37
482 486 2.420827 GGGTGGGTTGAAACTTTTTGGG 60.421 50.000 0.00 0.00 0.00 4.12
483 487 2.503765 AGGGTGGGTTGAAACTTTTTGG 59.496 45.455 0.00 0.00 0.00 3.28
484 488 3.450817 AGAGGGTGGGTTGAAACTTTTTG 59.549 43.478 0.00 0.00 0.00 2.44
485 489 3.719871 AGAGGGTGGGTTGAAACTTTTT 58.280 40.909 0.00 0.00 0.00 1.94
486 490 3.398318 AGAGGGTGGGTTGAAACTTTT 57.602 42.857 0.00 0.00 0.00 2.27
487 491 3.398318 AAGAGGGTGGGTTGAAACTTT 57.602 42.857 0.00 0.00 0.00 2.66
488 492 3.398318 AAAGAGGGTGGGTTGAAACTT 57.602 42.857 0.00 0.00 0.00 2.66
489 493 4.529716 TTAAAGAGGGTGGGTTGAAACT 57.470 40.909 0.00 0.00 0.00 2.66
490 494 4.219944 GGATTAAAGAGGGTGGGTTGAAAC 59.780 45.833 0.00 0.00 0.00 2.78
491 495 4.107311 AGGATTAAAGAGGGTGGGTTGAAA 59.893 41.667 0.00 0.00 0.00 2.69
492 496 3.660669 AGGATTAAAGAGGGTGGGTTGAA 59.339 43.478 0.00 0.00 0.00 2.69
493 497 3.265489 AGGATTAAAGAGGGTGGGTTGA 58.735 45.455 0.00 0.00 0.00 3.18
494 498 3.739401 AGGATTAAAGAGGGTGGGTTG 57.261 47.619 0.00 0.00 0.00 3.77
495 499 4.759793 AAAGGATTAAAGAGGGTGGGTT 57.240 40.909 0.00 0.00 0.00 4.11
496 500 4.017775 GGTAAAGGATTAAAGAGGGTGGGT 60.018 45.833 0.00 0.00 0.00 4.51
497 501 4.229812 AGGTAAAGGATTAAAGAGGGTGGG 59.770 45.833 0.00 0.00 0.00 4.61
498 502 5.452341 AGGTAAAGGATTAAAGAGGGTGG 57.548 43.478 0.00 0.00 0.00 4.61
532 716 9.374711 AGGGTAACTTATTTTCAATTTGAGGAA 57.625 29.630 0.00 0.20 0.00 3.36
566 753 4.522789 TGGGAAAATTTACTTCAGGTGCTC 59.477 41.667 0.00 0.00 0.00 4.26
573 767 7.201785 GCGGAAGATATGGGAAAATTTACTTCA 60.202 37.037 0.00 0.00 34.76 3.02
581 775 3.403038 CGAGCGGAAGATATGGGAAAAT 58.597 45.455 0.00 0.00 0.00 1.82
600 794 0.815095 TTATCTTCACTGGCGAGCGA 59.185 50.000 0.00 0.00 0.00 4.93
611 805 0.744874 CTCGCCCCTCGTTATCTTCA 59.255 55.000 0.00 0.00 39.67 3.02
612 806 0.032267 CCTCGCCCCTCGTTATCTTC 59.968 60.000 0.00 0.00 39.67 2.87
615 809 1.807495 CTCCCTCGCCCCTCGTTATC 61.807 65.000 0.00 0.00 39.67 1.75
629 823 4.095400 ATCCACCGGCCTCTCCCT 62.095 66.667 0.00 0.00 0.00 4.20
645 839 1.612463 GCGTTGAGTCCCTATACCGAT 59.388 52.381 0.00 0.00 0.00 4.18
674 868 1.019805 GTTTGACCTACTCCGCCAGC 61.020 60.000 0.00 0.00 0.00 4.85
675 869 0.391263 GGTTTGACCTACTCCGCCAG 60.391 60.000 0.00 0.00 34.73 4.85
681 875 3.455327 GCGATTAGGGTTTGACCTACTC 58.545 50.000 0.00 0.00 42.63 2.59
698 892 2.290641 GCATGAAATTTACCCTCGCGAT 59.709 45.455 10.36 0.00 0.00 4.58
699 893 1.668751 GCATGAAATTTACCCTCGCGA 59.331 47.619 9.26 9.26 0.00 5.87
700 894 1.268539 GGCATGAAATTTACCCTCGCG 60.269 52.381 0.00 0.00 0.00 5.87
701 895 1.748493 TGGCATGAAATTTACCCTCGC 59.252 47.619 0.00 0.00 0.00 5.03
702 896 2.752354 TGTGGCATGAAATTTACCCTCG 59.248 45.455 0.00 0.00 0.00 4.63
759 953 6.329496 TCAGCTTCGTTTGTCTCAAATTTTT 58.671 32.000 0.00 0.00 0.00 1.94
760 954 5.890334 TCAGCTTCGTTTGTCTCAAATTTT 58.110 33.333 0.00 0.00 0.00 1.82
761 955 5.499139 TCAGCTTCGTTTGTCTCAAATTT 57.501 34.783 0.00 0.00 0.00 1.82
762 956 5.695851 ATCAGCTTCGTTTGTCTCAAATT 57.304 34.783 0.00 0.00 0.00 1.82
763 957 5.695851 AATCAGCTTCGTTTGTCTCAAAT 57.304 34.783 0.00 0.00 0.00 2.32
764 958 5.499139 AAATCAGCTTCGTTTGTCTCAAA 57.501 34.783 0.00 0.00 0.00 2.69
765 959 5.065859 TCAAAATCAGCTTCGTTTGTCTCAA 59.934 36.000 10.83 0.00 33.62 3.02
766 960 4.574421 TCAAAATCAGCTTCGTTTGTCTCA 59.426 37.500 10.83 0.00 33.62 3.27
767 961 5.095691 TCAAAATCAGCTTCGTTTGTCTC 57.904 39.130 10.83 0.00 33.62 3.36
768 962 5.239306 TCATCAAAATCAGCTTCGTTTGTCT 59.761 36.000 10.83 1.22 33.62 3.41
769 963 5.451908 TCATCAAAATCAGCTTCGTTTGTC 58.548 37.500 10.83 0.00 33.62 3.18
770 964 5.437289 TCATCAAAATCAGCTTCGTTTGT 57.563 34.783 10.83 0.21 33.62 2.83
771 965 5.164119 GCTTCATCAAAATCAGCTTCGTTTG 60.164 40.000 6.46 6.46 33.26 2.93
772 966 4.919754 GCTTCATCAAAATCAGCTTCGTTT 59.080 37.500 0.00 0.00 0.00 3.60
773 967 4.479619 GCTTCATCAAAATCAGCTTCGTT 58.520 39.130 0.00 0.00 0.00 3.85
774 968 3.425359 CGCTTCATCAAAATCAGCTTCGT 60.425 43.478 0.00 0.00 0.00 3.85
775 969 3.096461 CGCTTCATCAAAATCAGCTTCG 58.904 45.455 0.00 0.00 0.00 3.79
799 993 0.312729 TAGCGCTTGTTCGTGACTGA 59.687 50.000 18.68 0.00 0.00 3.41
807 1001 3.384702 GCTGGTTTAGCGCTTGTTC 57.615 52.632 18.68 4.24 43.63 3.18
869 1063 1.995626 CCCGACCCAACCCATCTCT 60.996 63.158 0.00 0.00 0.00 3.10
881 1075 2.281276 AACAACGAAGGCCCGACC 60.281 61.111 8.49 0.00 39.61 4.79
892 1086 2.800096 GCAAGTGGATGCAACAACG 58.200 52.632 0.00 0.00 45.70 4.10
984 1181 1.075601 TGGGGATTGGAGTTGAAGCT 58.924 50.000 0.00 0.00 0.00 3.74
985 1182 2.149973 ATGGGGATTGGAGTTGAAGC 57.850 50.000 0.00 0.00 0.00 3.86
1012 1209 4.588951 GTGGGGATTGGAGTTCTTCTTTTT 59.411 41.667 0.00 0.00 0.00 1.94
1013 1210 4.152647 GTGGGGATTGGAGTTCTTCTTTT 58.847 43.478 0.00 0.00 0.00 2.27
1014 1211 3.500471 GGTGGGGATTGGAGTTCTTCTTT 60.500 47.826 0.00 0.00 0.00 2.52
1017 1214 1.679032 CGGTGGGGATTGGAGTTCTTC 60.679 57.143 0.00 0.00 0.00 2.87
1020 1217 1.749258 GCGGTGGGGATTGGAGTTC 60.749 63.158 0.00 0.00 0.00 3.01
1321 1531 0.396695 TTAGACCGGGGAGCTGGTAG 60.397 60.000 6.32 0.00 38.99 3.18
1329 1539 0.256752 TCGATCAGTTAGACCGGGGA 59.743 55.000 6.32 0.00 0.00 4.81
1345 1555 2.771639 CGGAAGGGAGCGATGTCGA 61.772 63.158 6.60 0.00 43.02 4.20
1352 1562 1.586154 AAATGCAACGGAAGGGAGCG 61.586 55.000 0.00 0.00 0.00 5.03
1372 1582 4.323104 GGCTAGATGGGTCTAATTAGCTGG 60.323 50.000 7.67 1.72 36.54 4.85
1373 1583 4.619394 CGGCTAGATGGGTCTAATTAGCTG 60.619 50.000 7.67 0.00 36.54 4.24
1465 1854 1.594293 CGGTTTGTGCCACTCGAGT 60.594 57.895 13.58 13.58 0.00 4.18
1521 1928 4.245845 AGAACTCCTCTGTTTTCGTCTC 57.754 45.455 0.00 0.00 31.12 3.36
1525 1932 4.119862 TCACAAGAACTCCTCTGTTTTCG 58.880 43.478 0.00 0.00 33.37 3.46
1546 1954 9.906111 CAGTAGCAAAGAAACAAAGAAATTTTC 57.094 29.630 0.66 0.66 0.00 2.29
1549 1957 9.516314 GTACAGTAGCAAAGAAACAAAGAAATT 57.484 29.630 0.00 0.00 0.00 1.82
1689 2134 5.137403 GCAGAAAAAGTGTGTGTACGTATG 58.863 41.667 0.00 0.00 0.00 2.39
1997 2516 1.930133 ACCCATCCTGCCATCACCA 60.930 57.895 0.00 0.00 0.00 4.17
2034 2589 0.332632 CCACCCATCCTGTCACCAAT 59.667 55.000 0.00 0.00 0.00 3.16
2041 2596 2.602676 CCGGTTCCACCCATCCTGT 61.603 63.158 0.00 0.00 33.75 4.00
2198 2753 2.234296 CCCAGCCTTCCTGTTCCCT 61.234 63.158 0.00 0.00 40.06 4.20
2333 2888 5.304686 AGTATCCTTTCACCTTCACAACA 57.695 39.130 0.00 0.00 0.00 3.33
2642 3201 0.101399 AGCCGCGATCTAAGACTGTG 59.899 55.000 8.23 0.00 0.00 3.66
2655 3214 2.392933 TTTGACTTACAAAAGCCGCG 57.607 45.000 0.00 0.00 44.16 6.46
2731 3290 1.474077 GAGGGAACATCATGCAACCAC 59.526 52.381 0.00 0.00 0.00 4.16
2742 3306 2.716424 TCCACAAAAGGAGAGGGAACAT 59.284 45.455 0.00 0.00 32.77 2.71
2743 3307 2.131854 TCCACAAAAGGAGAGGGAACA 58.868 47.619 0.00 0.00 32.77 3.18
2788 3352 1.135257 AGCATCTCAGCACGTACACTC 60.135 52.381 0.00 0.00 36.85 3.51
2888 3463 4.038642 GGACAGAGCCAACCATTAAAACAA 59.961 41.667 0.00 0.00 0.00 2.83
2925 3500 8.450964 TCAGAATATTTTCTCGCTGGTTAAAAG 58.549 33.333 0.00 0.00 40.28 2.27
3009 3587 5.105392 TGCATATTTTGGCCTAAAGAGTTGG 60.105 40.000 17.29 6.20 0.00 3.77
3064 3648 5.670485 TGCTTCAACAGAGAAGTTTGAGTA 58.330 37.500 5.70 0.00 45.28 2.59
3102 3686 0.617413 CTGCACAGGAGATTCACCCT 59.383 55.000 0.00 0.00 0.00 4.34
3170 3754 5.477637 ACTCCTTCTAACTACACTGGAGAAC 59.522 44.000 12.33 0.00 41.31 3.01
3279 3867 3.316308 AGTGTTTTCCTTGCTGCAACTAG 59.684 43.478 11.69 1.52 0.00 2.57
3306 3904 2.032549 GTCTGTGTGTGATGCTGTCAAC 60.033 50.000 0.00 0.00 38.90 3.18
3347 3945 8.358148 GCTGTCAAGATTAAATCATGGAATCAT 58.642 33.333 0.00 0.00 32.96 2.45
3348 3946 7.339976 TGCTGTCAAGATTAAATCATGGAATCA 59.660 33.333 0.00 0.00 32.96 2.57
3349 3947 7.709947 TGCTGTCAAGATTAAATCATGGAATC 58.290 34.615 0.00 0.00 0.00 2.52
3350 3948 7.649533 TGCTGTCAAGATTAAATCATGGAAT 57.350 32.000 0.00 0.00 0.00 3.01
3351 3949 7.467675 CGATGCTGTCAAGATTAAATCATGGAA 60.468 37.037 0.00 0.00 0.00 3.53
3352 3950 6.017687 CGATGCTGTCAAGATTAAATCATGGA 60.018 38.462 0.00 0.00 0.00 3.41
3353 3951 6.140786 CGATGCTGTCAAGATTAAATCATGG 58.859 40.000 0.00 0.00 0.00 3.66
3354 3952 5.624081 GCGATGCTGTCAAGATTAAATCATG 59.376 40.000 0.00 0.00 0.00 3.07
3355 3953 5.297527 TGCGATGCTGTCAAGATTAAATCAT 59.702 36.000 0.00 0.00 0.00 2.45
3356 3954 4.635324 TGCGATGCTGTCAAGATTAAATCA 59.365 37.500 0.00 0.00 0.00 2.57
3357 3955 4.966366 GTGCGATGCTGTCAAGATTAAATC 59.034 41.667 0.00 0.00 0.00 2.17
3358 3956 4.395854 TGTGCGATGCTGTCAAGATTAAAT 59.604 37.500 0.00 0.00 0.00 1.40
3359 3957 3.750652 TGTGCGATGCTGTCAAGATTAAA 59.249 39.130 0.00 0.00 0.00 1.52
3360 3958 3.125146 GTGTGCGATGCTGTCAAGATTAA 59.875 43.478 0.00 0.00 0.00 1.40
3361 3959 2.672874 GTGTGCGATGCTGTCAAGATTA 59.327 45.455 0.00 0.00 0.00 1.75
3377 3975 2.486504 CATGCATGGTCCGTGTGC 59.513 61.111 19.40 9.48 39.26 4.57
3378 3976 3.189921 CCATGCATGGTCCGTGTG 58.810 61.111 33.68 9.10 43.05 3.82
3391 3989 6.894339 TGGAATCATTCATCTCATTCCATG 57.106 37.500 7.93 0.00 46.13 3.66
3396 3994 9.143155 TGAAATCATGGAATCATTCATCTCATT 57.857 29.630 0.00 0.00 0.00 2.57
3502 4105 9.967451 TTGTAATCTGGGTTAACTATGATTTCA 57.033 29.630 18.07 16.68 0.00 2.69
3531 4144 7.414319 CCAAAATTCAGTGTTGTCTGCATTTTT 60.414 33.333 11.82 5.43 43.18 1.94
3575 4188 6.513230 GCATTCATGTACAAGCCGAATGATTA 60.513 38.462 27.45 6.21 43.55 1.75
3637 4251 3.007635 GTGGAAAAAGGATCGATCGGTT 58.992 45.455 18.81 11.94 0.00 4.44
3638 4252 2.629051 GTGGAAAAAGGATCGATCGGT 58.371 47.619 18.81 8.34 0.00 4.69
3677 4291 6.216569 AGATGCTATTTATATATGCCGACGG 58.783 40.000 10.29 10.29 0.00 4.79
3706 4320 2.556840 TACAATGCTGGGGCTGGAGC 62.557 60.000 0.00 0.00 39.59 4.70
3848 4466 6.273071 CCACACTCTTCACAACGATGATATA 58.727 40.000 0.00 0.00 0.00 0.86
3858 4476 2.805295 CGTAAGCCCACACTCTTCACAA 60.805 50.000 0.00 0.00 0.00 3.33
3875 4493 3.117776 TGGAGGTAGATCTAGTGGCGTAA 60.118 47.826 1.64 0.00 0.00 3.18


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

AutoCloner maintained by Alex Coulton.