Multiple sequence alignment - TraesCS2B01G490700

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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 TraesCS2B01G490700 chr2B 100.000 5165 0 0 1 5165 688429739 688434903 0.000000e+00 9539.0
1 TraesCS2B01G490700 chr2B 86.504 452 49 7 4474 4915 182354599 182355048 2.160000e-133 486.0
2 TraesCS2B01G490700 chr2B 80.428 654 74 28 1050 1684 688374523 688375141 2.840000e-122 449.0
3 TraesCS2B01G490700 chr2B 87.783 221 14 5 1835 2046 311739309 311739525 3.990000e-61 246.0
4 TraesCS2B01G490700 chr2B 81.955 266 30 12 478 728 688373120 688373382 5.240000e-50 209.0
5 TraesCS2B01G490700 chr2B 87.943 141 12 3 718 855 688373414 688373552 1.490000e-35 161.0
6 TraesCS2B01G490700 chr2B 79.487 195 16 11 850 1031 688373934 688374117 3.270000e-22 117.0
7 TraesCS2B01G490700 chr2D 93.035 2771 147 31 1688 4438 572732891 572735635 0.000000e+00 4006.0
8 TraesCS2B01G490700 chr2D 90.331 724 55 10 966 1687 572732147 572732857 0.000000e+00 935.0
9 TraesCS2B01G490700 chr2D 80.123 649 69 23 1050 1687 572693760 572694359 3.700000e-116 429.0
10 TraesCS2B01G490700 chr2D 81.930 487 64 10 4451 4915 348079251 348078767 1.740000e-104 390.0
11 TraesCS2B01G490700 chr2D 91.760 267 10 4 1788 2045 622712941 622713204 1.370000e-95 361.0
12 TraesCS2B01G490700 chr2D 91.469 211 7 8 736 942 572731953 572732156 3.940000e-71 279.0
13 TraesCS2B01G490700 chr2D 92.754 69 4 1 849 916 572693333 572693401 1.180000e-16 99.0
14 TraesCS2B01G490700 chr2A 89.612 2782 173 53 1688 4396 711968965 711971703 0.000000e+00 3430.0
15 TraesCS2B01G490700 chr2A 86.498 1422 118 34 307 1687 711967543 711968931 0.000000e+00 1495.0
16 TraesCS2B01G490700 chr2A 93.548 527 19 3 4653 5165 71077170 71077695 0.000000e+00 771.0
17 TraesCS2B01G490700 chr2A 81.481 648 79 22 1050 1687 711939813 711940429 1.290000e-135 494.0
18 TraesCS2B01G490700 chr2A 90.826 218 8 4 1838 2046 387015212 387015426 1.090000e-71 281.0
19 TraesCS2B01G490700 chr2A 94.413 179 8 2 1788 1965 736665476 736665653 1.830000e-69 274.0
20 TraesCS2B01G490700 chr2A 93.296 179 10 2 1788 1965 121689159 121689336 3.970000e-66 263.0
21 TraesCS2B01G490700 chr2A 95.541 157 6 1 4477 4632 71074707 71074863 3.090000e-62 250.0
22 TraesCS2B01G490700 chr2A 82.331 266 26 13 480 728 711933194 711933455 1.460000e-50 211.0
23 TraesCS2B01G490700 chr2A 85.816 141 16 2 718 855 711933488 711933627 4.170000e-31 147.0
24 TraesCS2B01G490700 chr3B 82.449 735 78 18 4477 5165 39439924 39439195 3.440000e-166 595.0
25 TraesCS2B01G490700 chr5D 81.114 736 81 25 4477 5165 339304453 339303729 2.120000e-148 536.0
26 TraesCS2B01G490700 chr5D 88.022 359 30 5 1698 2046 12872532 12872177 3.720000e-111 412.0
27 TraesCS2B01G490700 chr5D 81.285 529 66 23 1168 1687 12873075 12872571 1.040000e-106 398.0
28 TraesCS2B01G490700 chr5D 89.869 306 31 0 1 306 520111401 520111706 1.350000e-105 394.0
29 TraesCS2B01G490700 chr5D 83.178 107 18 0 3554 3660 488863877 488863983 1.180000e-16 99.0
30 TraesCS2B01G490700 chr5B 83.789 512 51 16 4476 4963 60970995 60971498 1.700000e-124 457.0
31 TraesCS2B01G490700 chr5B 90.099 303 28 2 1 303 464315938 464316238 4.850000e-105 392.0
32 TraesCS2B01G490700 chr5B 89.869 306 29 2 1 306 464318630 464318933 4.850000e-105 392.0
33 TraesCS2B01G490700 chr5B 89.869 306 29 2 1 306 464319977 464320280 4.850000e-105 392.0
34 TraesCS2B01G490700 chr5B 79.921 508 65 23 1168 1664 670366093 670365612 6.410000e-89 339.0
35 TraesCS2B01G490700 chr5B 93.182 44 3 0 4435 4478 150905460 150905503 1.200000e-06 65.8
36 TraesCS2B01G490700 chr7A 82.879 514 59 12 4474 4976 34968952 34969447 7.940000e-118 435.0
37 TraesCS2B01G490700 chr7A 88.056 360 27 8 1698 2046 594163190 594162836 3.720000e-111 412.0
38 TraesCS2B01G490700 chr7A 80.414 531 67 26 1168 1687 594163734 594163230 2.270000e-98 370.0
39 TraesCS2B01G490700 chr3A 84.116 447 60 6 4477 4913 323382878 323383323 6.180000e-114 422.0
40 TraesCS2B01G490700 chr6D 90.132 304 30 0 1 304 27033859 27034162 3.750000e-106 396.0
41 TraesCS2B01G490700 chr6D 89.577 307 31 1 1 307 121158689 121158384 6.270000e-104 388.0
42 TraesCS2B01G490700 chr6B 89.902 307 31 0 1 307 213228966 213228660 3.750000e-106 396.0
43 TraesCS2B01G490700 chr6B 89.836 305 31 0 1 305 627545432 627545736 4.850000e-105 392.0
44 TraesCS2B01G490700 chr6B 89.850 266 15 4 1788 2044 310605055 310604793 1.070000e-86 331.0
45 TraesCS2B01G490700 chr3D 89.610 308 31 1 1 308 481928990 481929296 1.740000e-104 390.0
46 TraesCS2B01G490700 chr3D 84.524 336 40 8 4590 4915 75769922 75769589 6.450000e-84 322.0
47 TraesCS2B01G490700 chr4A 80.038 521 52 23 4477 4976 527579383 527578894 6.410000e-89 339.0
48 TraesCS2B01G490700 chr4A 89.041 219 11 5 1838 2046 416574381 416574166 5.130000e-65 259.0
49 TraesCS2B01G490700 chr4B 86.909 275 24 6 4652 4915 376427528 376427255 1.090000e-76 298.0
50 TraesCS2B01G490700 chr4B 92.593 135 5 4 1838 1971 655488911 655488781 6.830000e-44 189.0
51 TraesCS2B01G490700 chr5A 90.826 218 8 4 1838 2046 568231037 568230823 1.090000e-71 281.0
52 TraesCS2B01G490700 chr1A 94.972 179 7 2 1788 1965 564807216 564807039 3.940000e-71 279.0
53 TraesCS2B01G490700 chr4D 92.442 172 11 1 4990 5161 301955641 301955472 1.440000e-60 244.0
54 TraesCS2B01G490700 chr4D 88.172 186 12 5 4652 4828 301956036 301955852 4.050000e-51 213.0


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 TraesCS2B01G490700 chr2B 688429739 688434903 5164 False 9539.0 9539 100.000000 1 5165 1 chr2B.!!$F3 5164
1 TraesCS2B01G490700 chr2B 688373120 688375141 2021 False 234.0 449 82.453250 478 1684 4 chr2B.!!$F4 1206
2 TraesCS2B01G490700 chr2D 572731953 572735635 3682 False 1740.0 4006 91.611667 736 4438 3 chr2D.!!$F3 3702
3 TraesCS2B01G490700 chr2D 572693333 572694359 1026 False 264.0 429 86.438500 849 1687 2 chr2D.!!$F2 838
4 TraesCS2B01G490700 chr2A 711967543 711971703 4160 False 2462.5 3430 88.055000 307 4396 2 chr2A.!!$F7 4089
5 TraesCS2B01G490700 chr2A 71074707 71077695 2988 False 510.5 771 94.544500 4477 5165 2 chr2A.!!$F5 688
6 TraesCS2B01G490700 chr2A 711939813 711940429 616 False 494.0 494 81.481000 1050 1687 1 chr2A.!!$F3 637
7 TraesCS2B01G490700 chr3B 39439195 39439924 729 True 595.0 595 82.449000 4477 5165 1 chr3B.!!$R1 688
8 TraesCS2B01G490700 chr5D 339303729 339304453 724 True 536.0 536 81.114000 4477 5165 1 chr5D.!!$R1 688
9 TraesCS2B01G490700 chr5D 12872177 12873075 898 True 405.0 412 84.653500 1168 2046 2 chr5D.!!$R2 878
10 TraesCS2B01G490700 chr5B 60970995 60971498 503 False 457.0 457 83.789000 4476 4963 1 chr5B.!!$F1 487
11 TraesCS2B01G490700 chr5B 464315938 464320280 4342 False 392.0 392 89.945667 1 306 3 chr5B.!!$F3 305
12 TraesCS2B01G490700 chr7A 594162836 594163734 898 True 391.0 412 84.235000 1168 2046 2 chr7A.!!$R1 878
13 TraesCS2B01G490700 chr4D 301955472 301956036 564 True 228.5 244 90.307000 4652 5161 2 chr4D.!!$R1 509

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
191 192 0.457337 CCTTCGGCTTGCTTCAATGC 60.457 55.0 0.00 0.0 0.00 3.56 F
1011 4189 0.320683 TTGGCGACATGTGAGTCCTG 60.321 55.0 1.15 0.0 42.32 3.86 F
1367 5612 1.023513 ATCGGCTTGACTGCTTGCTC 61.024 55.0 0.00 0.0 0.00 4.26 F
3062 7389 1.168714 GGTTCATCTTGCCTCCACAC 58.831 55.0 0.00 0.0 0.00 3.82 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1037 4215 0.529992 GAACGAGGCAGGGTAATCCG 60.530 60.0 0.00 0.00 41.52 4.18 R
2758 7085 0.606401 CGCCTTGGTCAGTTGGTCAT 60.606 55.0 0.00 0.00 0.00 3.06 R
3360 7713 0.385974 GACGTCCTGCATTTGTGCAC 60.386 55.0 10.75 10.75 40.23 4.57 R
4472 8848 0.039527 CAACCAAACACGCCCTTAGC 60.040 55.0 0.00 0.00 38.52 3.09 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
23 24 2.687425 TGTTCATGTGTGTTCAGGTTGG 59.313 45.455 0.00 0.00 0.00 3.77
27 28 3.148412 CATGTGTGTTCAGGTTGGATCA 58.852 45.455 0.00 0.00 0.00 2.92
52 53 5.102020 TCGATCTAAGCTTCTCTTCATCG 57.898 43.478 0.00 8.52 42.86 3.84
55 56 2.123342 CTAAGCTTCTCTTCATCGGCG 58.877 52.381 0.00 0.00 36.25 6.46
63 64 4.690719 TTCATCGGCGGCGGTTGT 62.691 61.111 31.73 12.34 0.00 3.32
65 66 4.459331 CATCGGCGGCGGTTGTTG 62.459 66.667 31.73 16.47 0.00 3.33
68 69 4.258932 CGGCGGCGGTTGTTGTTT 62.259 61.111 25.36 0.00 0.00 2.83
89 90 1.600107 GTGCGTTGGTCCTATGGGA 59.400 57.895 0.00 0.00 39.70 4.37
107 108 1.615502 GACCTTAGCACGACGACTTC 58.384 55.000 0.00 0.00 0.00 3.01
108 109 1.199558 GACCTTAGCACGACGACTTCT 59.800 52.381 0.00 0.00 0.00 2.85
109 110 1.612463 ACCTTAGCACGACGACTTCTT 59.388 47.619 0.00 0.00 0.00 2.52
188 189 3.354678 GCCTTCGGCTTGCTTCAA 58.645 55.556 0.00 0.00 46.69 2.69
191 192 0.457337 CCTTCGGCTTGCTTCAATGC 60.457 55.000 0.00 0.00 0.00 3.56
222 223 1.001597 CGCTAGGTGGTCTACGAATCC 60.002 57.143 0.00 0.00 0.00 3.01
223 224 2.029623 GCTAGGTGGTCTACGAATCCA 58.970 52.381 0.00 0.00 0.00 3.41
230 2923 4.261656 GGTGGTCTACGAATCCAGATGTAG 60.262 50.000 0.00 0.00 36.49 2.74
286 2979 8.237949 GCCATGATTGAAGATGAATAGATTGAG 58.762 37.037 0.00 0.00 0.00 3.02
296 2989 6.922957 AGATGAATAGATTGAGAGTTTCTCGC 59.077 38.462 2.01 0.00 46.25 5.03
335 3028 7.273381 GTCAAATTGGATTTATGAAACTCCACG 59.727 37.037 0.00 0.00 37.51 4.94
344 3037 8.786826 ATTTATGAAACTCCACGACTTATGAA 57.213 30.769 0.00 0.00 0.00 2.57
347 3040 4.994852 TGAAACTCCACGACTTATGAAAGG 59.005 41.667 0.00 0.00 37.01 3.11
350 3043 3.055094 ACTCCACGACTTATGAAAGGCAT 60.055 43.478 0.00 0.00 41.24 4.40
351 3044 3.270027 TCCACGACTTATGAAAGGCATG 58.730 45.455 0.00 0.00 41.24 4.06
353 3046 3.063997 CCACGACTTATGAAAGGCATGAC 59.936 47.826 0.00 0.00 35.93 3.06
354 3047 3.063997 CACGACTTATGAAAGGCATGACC 59.936 47.826 0.00 0.00 35.93 4.02
355 3048 3.270027 CGACTTATGAAAGGCATGACCA 58.730 45.455 0.00 0.00 41.24 4.02
376 3069 4.660771 CCAGAAGTCATAAACCCTATCCCT 59.339 45.833 0.00 0.00 0.00 4.20
380 3073 6.437793 AGAAGTCATAAACCCTATCCCTATCG 59.562 42.308 0.00 0.00 0.00 2.92
383 3076 4.775780 TCATAAACCCTATCCCTATCGGTG 59.224 45.833 0.00 0.00 0.00 4.94
389 3082 3.499926 CCCTATCCCTATCGGTGTAGTGT 60.500 52.174 0.00 0.00 0.00 3.55
396 3089 4.063689 CCTATCGGTGTAGTGTATCTCGT 58.936 47.826 0.00 0.00 0.00 4.18
397 3090 3.965292 ATCGGTGTAGTGTATCTCGTG 57.035 47.619 0.00 0.00 0.00 4.35
418 3111 3.575256 TGTAGTTTCGTCCACCATAGTGT 59.425 43.478 0.00 0.00 42.88 3.55
419 3112 3.764237 AGTTTCGTCCACCATAGTGTT 57.236 42.857 0.00 0.00 42.88 3.32
423 3116 1.346395 TCGTCCACCATAGTGTTGCTT 59.654 47.619 0.00 0.00 42.88 3.91
452 3145 7.013823 ACTCATGAGATCCCCATATTTGTAG 57.986 40.000 29.27 0.00 0.00 2.74
456 3149 4.665009 TGAGATCCCCATATTTGTAGCCTT 59.335 41.667 0.00 0.00 0.00 4.35
458 3151 3.485463 TCCCCATATTTGTAGCCTTCG 57.515 47.619 0.00 0.00 0.00 3.79
468 3161 1.736126 TGTAGCCTTCGTCGTACTCTG 59.264 52.381 0.00 0.00 0.00 3.35
469 3162 1.736681 GTAGCCTTCGTCGTACTCTGT 59.263 52.381 0.00 0.00 0.00 3.41
472 3165 1.199558 GCCTTCGTCGTACTCTGTCTT 59.800 52.381 0.00 0.00 0.00 3.01
473 3166 2.852748 CCTTCGTCGTACTCTGTCTTG 58.147 52.381 0.00 0.00 0.00 3.02
494 3187 9.554724 GTCTTGATATAAAAATTGTCGCTTTGA 57.445 29.630 0.00 0.00 0.00 2.69
580 3275 2.111384 TCTCAAGGGACTGATACCAGC 58.889 52.381 0.00 0.00 44.16 4.85
602 3297 7.336396 CAGCATCCTATTCCATCATCTCAATA 58.664 38.462 0.00 0.00 0.00 1.90
642 3356 4.752604 TGCTAACAAAAGCTGATCACGTTA 59.247 37.500 0.00 0.00 43.19 3.18
714 3428 9.887862 AATACCATCATTATCTTCCTTCCATTT 57.112 29.630 0.00 0.00 0.00 2.32
715 3429 7.592885 ACCATCATTATCTTCCTTCCATTTG 57.407 36.000 0.00 0.00 0.00 2.32
716 3430 7.356680 ACCATCATTATCTTCCTTCCATTTGA 58.643 34.615 0.00 0.00 0.00 2.69
755 3517 3.065655 CAACATGCCTCTGAGCTATAGC 58.934 50.000 17.33 17.33 42.49 2.97
756 3518 2.323599 ACATGCCTCTGAGCTATAGCA 58.676 47.619 26.07 6.04 45.16 3.49
757 3519 2.299582 ACATGCCTCTGAGCTATAGCAG 59.700 50.000 26.07 15.61 45.16 4.24
910 4078 4.394712 CCCTGTTCCGCTTCCGCT 62.395 66.667 0.00 0.00 0.00 5.52
911 4079 2.815647 CCTGTTCCGCTTCCGCTC 60.816 66.667 0.00 0.00 0.00 5.03
912 4080 2.815647 CTGTTCCGCTTCCGCTCC 60.816 66.667 0.00 0.00 0.00 4.70
913 4081 3.589654 CTGTTCCGCTTCCGCTCCA 62.590 63.158 0.00 0.00 0.00 3.86
914 4082 2.815647 GTTCCGCTTCCGCTCCAG 60.816 66.667 0.00 0.00 0.00 3.86
915 4083 4.760047 TTCCGCTTCCGCTCCAGC 62.760 66.667 0.00 0.00 37.78 4.85
1011 4189 0.320683 TTGGCGACATGTGAGTCCTG 60.321 55.000 1.15 0.00 42.32 3.86
1037 4215 4.702612 GGTTCCTTTCCTCTCATTTCCTTC 59.297 45.833 0.00 0.00 0.00 3.46
1166 5404 5.319139 TCGAAAGTAACATCTCGAACTACG 58.681 41.667 0.00 0.00 37.38 3.51
1172 5410 5.819379 AGTAACATCTCGAACTACGGATACA 59.181 40.000 0.00 0.00 42.82 2.29
1192 5430 7.120873 GGATACAGAATCAGGAATTCATGGATG 59.879 40.741 19.21 14.26 45.34 3.51
1209 5448 2.740981 GGATGGATTCTGCAGCTAATCG 59.259 50.000 17.35 0.00 33.72 3.34
1335 5580 2.872732 AGGGTGTACTGTCTTCGAGAA 58.127 47.619 0.00 0.00 0.00 2.87
1367 5612 1.023513 ATCGGCTTGACTGCTTGCTC 61.024 55.000 0.00 0.00 0.00 4.26
1373 5618 2.492012 CTTGACTGCTTGCTCTGTTCT 58.508 47.619 0.00 0.00 0.00 3.01
1382 5627 3.677596 GCTTGCTCTGTTCTTAGAGACAC 59.322 47.826 6.95 0.00 45.61 3.67
1393 5638 9.868277 CTGTTCTTAGAGACACAGATAGATTTT 57.132 33.333 6.69 0.00 36.43 1.82
1408 5653 4.559862 AGATTTTACTGGGGACTGACAG 57.440 45.455 0.00 0.00 40.48 3.51
1695 5984 5.676552 TGAACTGTGCTTGTTAAGTAAGGA 58.323 37.500 2.59 0.00 0.00 3.36
1718 6007 6.879458 GGAGGTAGAAAGAGCTTCAACATTAA 59.121 38.462 0.00 0.00 36.40 1.40
1719 6008 7.148390 GGAGGTAGAAAGAGCTTCAACATTAAC 60.148 40.741 0.00 0.00 36.40 2.01
2065 6376 2.160417 GGCAATTTCGTCAGGAACTCTG 59.840 50.000 0.00 0.00 44.68 3.35
2081 6392 9.246670 CAGGAACTCTGAGAGAAGATATATGAT 57.753 37.037 17.71 0.00 46.18 2.45
2105 6420 4.591929 TCATCATACATACATGCATGGGG 58.408 43.478 29.41 19.68 33.39 4.96
2128 6443 6.243148 GGAGAAGTACCCCTGTTGAAAATAA 58.757 40.000 0.00 0.00 0.00 1.40
2131 6446 7.295340 AGAAGTACCCCTGTTGAAAATAACTT 58.705 34.615 0.00 0.00 0.00 2.66
2133 6448 7.991084 AGTACCCCTGTTGAAAATAACTTAC 57.009 36.000 0.00 0.00 0.00 2.34
2134 6449 7.752638 AGTACCCCTGTTGAAAATAACTTACT 58.247 34.615 0.00 0.00 0.00 2.24
2135 6450 8.883302 AGTACCCCTGTTGAAAATAACTTACTA 58.117 33.333 0.00 0.00 0.00 1.82
2136 6451 7.991084 ACCCCTGTTGAAAATAACTTACTAC 57.009 36.000 0.00 0.00 0.00 2.73
2281 6601 2.258755 CACGCGTACTGATTGATGTGA 58.741 47.619 13.44 0.00 0.00 3.58
2298 6618 1.603802 GTGACCCATATCAACATGGCG 59.396 52.381 0.00 0.00 43.63 5.69
2349 6669 3.995526 GATCATGATCGCTCCCACA 57.004 52.632 19.55 0.00 0.00 4.17
2531 6851 6.364701 CCATAATGGTTTGGAAGATCACCTA 58.635 40.000 9.71 0.84 34.81 3.08
2536 6856 4.262617 GGTTTGGAAGATCACCTAACTCC 58.737 47.826 23.27 12.61 40.78 3.85
2657 6981 3.585732 TGGAAAGGGTTAACTCAGTAGGG 59.414 47.826 8.50 0.00 0.00 3.53
2688 7012 5.857822 ACGTTTCTTCCAGCTTTATGTAC 57.142 39.130 0.00 0.00 0.00 2.90
2693 7017 5.648178 TCTTCCAGCTTTATGTACGTGTA 57.352 39.130 0.00 0.00 0.00 2.90
2694 7018 5.647589 TCTTCCAGCTTTATGTACGTGTAG 58.352 41.667 0.00 0.00 0.00 2.74
2718 7042 5.121454 GTCTTCAGCTTCACAAACTATGAGG 59.879 44.000 0.00 0.00 0.00 3.86
2732 7059 7.829211 ACAAACTATGAGGCTAATAACATGTGT 59.171 33.333 0.00 0.00 0.00 3.72
2869 7196 2.125106 GGGTTCAAGGCGATCGCT 60.125 61.111 36.25 21.17 41.60 4.93
2956 7283 4.204799 ACAGATGTGCACATTATCATGCT 58.795 39.130 31.82 19.49 42.55 3.79
2959 7286 6.017357 ACAGATGTGCACATTATCATGCTAAG 60.017 38.462 31.82 14.03 42.55 2.18
2962 7289 5.882553 TGTGCACATTATCATGCTAAGTTG 58.117 37.500 17.42 0.00 42.55 3.16
2967 7294 6.427974 CACATTATCATGCTAAGTTGCTGAG 58.572 40.000 0.00 0.00 33.05 3.35
2974 7301 6.172630 TCATGCTAAGTTGCTGAGTAAATGA 58.827 36.000 0.00 0.00 0.00 2.57
2976 7303 7.337689 TCATGCTAAGTTGCTGAGTAAATGATT 59.662 33.333 0.00 0.00 0.00 2.57
3002 7329 5.499004 TCCATTTTACTAGGAACTGCACT 57.501 39.130 0.00 0.00 41.52 4.40
3003 7330 5.245531 TCCATTTTACTAGGAACTGCACTG 58.754 41.667 0.00 0.00 41.52 3.66
3049 7376 6.114187 TCTGATAACTTGTGACAGGTTCAT 57.886 37.500 16.52 8.84 35.40 2.57
3062 7389 1.168714 GGTTCATCTTGCCTCCACAC 58.831 55.000 0.00 0.00 0.00 3.82
3118 7445 4.638421 CGGCAAGATGGACAAGGTTAATTA 59.362 41.667 0.00 0.00 0.00 1.40
3134 7461 5.106830 GGTTAATTACCTGACAACCAAGTCG 60.107 44.000 0.00 0.00 44.10 4.18
3142 7469 4.201980 CCTGACAACCAAGTCGATCGTATA 60.202 45.833 15.94 0.00 41.41 1.47
3171 7524 9.046296 AGAAATCGCCTAAGTAGAATGTTATTG 57.954 33.333 0.00 0.00 0.00 1.90
3172 7525 6.787085 ATCGCCTAAGTAGAATGTTATTGC 57.213 37.500 0.00 0.00 0.00 3.56
3218 7571 1.674962 GCTTGCCAGACAGATGATTCC 59.325 52.381 0.00 0.00 0.00 3.01
3233 7586 1.984288 ATTCCGGGCTGGCTTCCTAC 61.984 60.000 7.74 0.00 37.80 3.18
3333 7686 4.161565 TGGGAGTTATCATTAGCACTTCGT 59.838 41.667 0.00 0.00 0.00 3.85
3360 7713 8.355169 CCTGAATGGAATAATTAACACTGATGG 58.645 37.037 0.00 0.00 38.35 3.51
3386 7739 0.108585 AATGCAGGACGTCAAGTGGT 59.891 50.000 18.91 0.00 0.00 4.16
3505 7858 0.182061 TCCCAGAATGCTGCATCTCC 59.818 55.000 16.55 8.39 40.91 3.71
3699 8052 1.041447 AGCCGCACCCGTAGTTCTAT 61.041 55.000 0.00 0.00 0.00 1.98
3732 8096 4.201763 GCAGATAAAGTTCAGGAAGCTTCG 60.202 45.833 19.91 7.66 0.00 3.79
3735 8100 1.884235 AAGTTCAGGAAGCTTCGGTG 58.116 50.000 19.91 18.49 0.00 4.94
3777 8142 5.649557 TGCATATATTGACCAAAAGTGTGC 58.350 37.500 0.00 0.00 0.00 4.57
3778 8143 5.184671 TGCATATATTGACCAAAAGTGTGCA 59.815 36.000 10.31 10.31 35.60 4.57
3794 8159 3.932089 GTGTGCACAAACAAATTCAGGTT 59.068 39.130 23.59 0.00 0.00 3.50
3814 8179 3.393970 CAGAGAGGCGAAGGGGCA 61.394 66.667 0.00 0.00 45.36 5.36
3875 8240 4.389576 GTGTTCAAGGCGCTGGCG 62.390 66.667 7.64 10.80 41.24 5.69
3903 8268 0.665369 CGCGGGAGTGTTCGTAAGTT 60.665 55.000 0.00 0.00 35.18 2.66
3906 8271 2.746269 CGGGAGTGTTCGTAAGTTCAA 58.254 47.619 0.00 0.00 39.48 2.69
3937 8302 1.946768 TCTGCGTGTTTCTTTCTTGGG 59.053 47.619 0.00 0.00 0.00 4.12
3950 8315 4.488136 TTGGGCGGCGATGCTGAT 62.488 61.111 12.98 0.00 37.02 2.90
3953 8318 4.916293 GGCGGCGATGCTGATGGA 62.916 66.667 12.98 0.00 37.02 3.41
3970 8335 1.805945 GACGCTCGATGTGTGGGTC 60.806 63.158 5.92 4.76 43.63 4.46
4202 8571 1.038681 TCCGGCCTCAGCAATACGTA 61.039 55.000 0.00 0.00 42.56 3.57
4213 8584 0.583083 CAATACGTACTTGTGCGCGC 60.583 55.000 27.26 27.26 0.00 6.86
4268 8639 2.488204 TGTGCCTCCATTTGATCGAA 57.512 45.000 0.00 0.00 0.00 3.71
4276 8647 4.209288 CCTCCATTTGATCGAACGATGTAC 59.791 45.833 14.33 1.43 34.60 2.90
4287 8658 2.922740 ACGATGTACCGGGCAATAAT 57.077 45.000 6.32 0.00 0.00 1.28
4291 8662 3.562141 CGATGTACCGGGCAATAATTTCA 59.438 43.478 6.32 0.00 0.00 2.69
4324 8695 2.401766 GGAGAAGGGTGCATGCGTG 61.402 63.158 14.09 0.09 0.00 5.34
4340 8714 2.986979 TGGTCGCGTAGTCTGCCA 60.987 61.111 5.77 1.83 0.00 4.92
4374 8748 3.145286 TGATCACGTTCTGATTTTGGCA 58.855 40.909 0.00 0.00 39.96 4.92
4405 8781 4.487948 CTCTGTCGGGTTTCGTATTGTTA 58.512 43.478 0.00 0.00 40.32 2.41
4411 8787 6.372103 TGTCGGGTTTCGTATTGTTATCATTT 59.628 34.615 0.00 0.00 40.32 2.32
4413 8789 7.427318 GTCGGGTTTCGTATTGTTATCATTTTC 59.573 37.037 0.00 0.00 40.32 2.29
4419 8795 7.946918 TCGTATTGTTATCATTTTCAAAGCG 57.053 32.000 0.00 0.00 0.00 4.68
4422 8798 5.820926 TTGTTATCATTTTCAAAGCGTGC 57.179 34.783 0.00 0.00 0.00 5.34
4424 8800 4.233789 GTTATCATTTTCAAAGCGTGCCA 58.766 39.130 0.00 0.00 0.00 4.92
4438 8814 1.247567 GTGCCAAGCAGAAGCCTTAA 58.752 50.000 0.00 0.00 40.08 1.85
4439 8815 1.613437 GTGCCAAGCAGAAGCCTTAAA 59.387 47.619 0.00 0.00 40.08 1.52
4440 8816 1.613437 TGCCAAGCAGAAGCCTTAAAC 59.387 47.619 0.00 0.00 43.56 2.01
4441 8817 1.067565 GCCAAGCAGAAGCCTTAAACC 60.068 52.381 0.00 0.00 43.56 3.27
4442 8818 2.519013 CCAAGCAGAAGCCTTAAACCT 58.481 47.619 0.00 0.00 43.56 3.50
4443 8819 2.489722 CCAAGCAGAAGCCTTAAACCTC 59.510 50.000 0.00 0.00 43.56 3.85
4444 8820 3.416156 CAAGCAGAAGCCTTAAACCTCT 58.584 45.455 0.00 0.00 43.56 3.69
4445 8821 3.797559 AGCAGAAGCCTTAAACCTCTT 57.202 42.857 0.00 0.00 43.56 2.85
4446 8822 3.680490 AGCAGAAGCCTTAAACCTCTTC 58.320 45.455 0.00 0.00 43.56 2.87
4447 8823 2.750166 GCAGAAGCCTTAAACCTCTTCC 59.250 50.000 0.00 0.00 36.50 3.46
4448 8824 3.810743 GCAGAAGCCTTAAACCTCTTCCA 60.811 47.826 0.00 0.00 36.50 3.53
4449 8825 4.398319 CAGAAGCCTTAAACCTCTTCCAA 58.602 43.478 0.00 0.00 36.50 3.53
4450 8826 5.012893 CAGAAGCCTTAAACCTCTTCCAAT 58.987 41.667 0.00 0.00 36.50 3.16
4451 8827 5.012893 AGAAGCCTTAAACCTCTTCCAATG 58.987 41.667 0.00 0.00 36.50 2.82
4452 8828 3.092301 AGCCTTAAACCTCTTCCAATGC 58.908 45.455 0.00 0.00 0.00 3.56
4453 8829 2.825532 GCCTTAAACCTCTTCCAATGCA 59.174 45.455 0.00 0.00 0.00 3.96
4454 8830 3.258123 GCCTTAAACCTCTTCCAATGCAA 59.742 43.478 0.00 0.00 0.00 4.08
4455 8831 4.262420 GCCTTAAACCTCTTCCAATGCAAA 60.262 41.667 0.00 0.00 0.00 3.68
4456 8832 5.473039 CCTTAAACCTCTTCCAATGCAAAG 58.527 41.667 0.00 0.00 0.00 2.77
4457 8833 5.467035 TTAAACCTCTTCCAATGCAAAGG 57.533 39.130 0.00 0.00 0.00 3.11
4458 8834 2.683211 ACCTCTTCCAATGCAAAGGT 57.317 45.000 7.57 2.08 32.35 3.50
4459 8835 2.242043 ACCTCTTCCAATGCAAAGGTG 58.758 47.619 7.57 3.35 35.84 4.00
4491 8867 0.039527 GCTAAGGGCGTGTTTGGTTG 60.040 55.000 0.00 0.00 0.00 3.77
4584 8960 2.125952 GCCCGGCTGATGCAAAAC 60.126 61.111 0.71 0.00 41.91 2.43
4588 8965 1.213537 CGGCTGATGCAAAACAGGG 59.786 57.895 16.54 0.00 41.91 4.45
4707 11372 2.388232 GGTCGATTCACACCCGCAC 61.388 63.158 0.00 0.00 0.00 5.34
4737 11402 3.902218 CTCTCCTCACTCCTCTCATCTT 58.098 50.000 0.00 0.00 0.00 2.40
4744 11409 2.235650 CACTCCTCTCATCTTTCCTGCA 59.764 50.000 0.00 0.00 0.00 4.41
4845 11518 1.582624 TCTTCCATCTCTCCCCATCCT 59.417 52.381 0.00 0.00 0.00 3.24
5091 11849 5.936686 ATGTGTGATTAGCATGCATCTAC 57.063 39.130 21.98 16.63 0.00 2.59
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
23 24 7.651304 TGAAGAGAAGCTTAGATCGAAATGATC 59.349 37.037 0.00 0.00 44.50 2.92
27 28 6.640499 CGATGAAGAGAAGCTTAGATCGAAAT 59.360 38.462 0.00 0.00 44.25 2.17
39 40 2.529619 GCCGCCGATGAAGAGAAGC 61.530 63.158 0.00 0.00 0.00 3.86
52 53 2.105328 AAAACAACAACCGCCGCC 59.895 55.556 0.00 0.00 0.00 6.13
55 56 1.425267 GCACCAAAACAACAACCGCC 61.425 55.000 0.00 0.00 0.00 6.13
63 64 0.173708 GGACCAACGCACCAAAACAA 59.826 50.000 0.00 0.00 0.00 2.83
65 66 1.310904 TAGGACCAACGCACCAAAAC 58.689 50.000 0.00 0.00 0.00 2.43
68 69 0.322098 CCATAGGACCAACGCACCAA 60.322 55.000 0.00 0.00 0.00 3.67
89 90 1.245732 AGAAGTCGTCGTGCTAAGGT 58.754 50.000 0.00 0.00 0.00 3.50
90 91 1.986378 CAAGAAGTCGTCGTGCTAAGG 59.014 52.381 0.00 0.00 0.00 2.69
91 92 2.657372 GTCAAGAAGTCGTCGTGCTAAG 59.343 50.000 0.00 0.00 35.86 2.18
107 108 6.757010 ACAACTTGTTGTAGTAGACAGTCAAG 59.243 38.462 16.35 16.04 46.09 3.02
108 109 6.636705 ACAACTTGTTGTAGTAGACAGTCAA 58.363 36.000 16.35 0.00 39.88 3.18
109 110 6.216801 ACAACTTGTTGTAGTAGACAGTCA 57.783 37.500 16.35 0.00 39.88 3.41
144 145 2.764128 TCATCGCCCCTCCCTCAC 60.764 66.667 0.00 0.00 0.00 3.51
188 189 2.233922 ACCTAGCGACAACTACAAGCAT 59.766 45.455 0.00 0.00 0.00 3.79
191 192 2.029290 ACCACCTAGCGACAACTACAAG 60.029 50.000 0.00 0.00 0.00 3.16
238 2931 5.505985 GGCAGTACAACGAACACCAAAAATA 60.506 40.000 0.00 0.00 0.00 1.40
243 2936 1.301423 GGCAGTACAACGAACACCAA 58.699 50.000 0.00 0.00 0.00 3.67
304 2997 9.525826 AGTTTCATAAATCCAATTTGACTCTCT 57.474 29.630 0.00 0.00 33.82 3.10
305 2998 9.780413 GAGTTTCATAAATCCAATTTGACTCTC 57.220 33.333 0.00 0.00 33.82 3.20
323 3016 5.643777 CCTTTCATAAGTCGTGGAGTTTCAT 59.356 40.000 0.00 0.00 0.00 2.57
328 3021 2.301870 TGCCTTTCATAAGTCGTGGAGT 59.698 45.455 0.00 0.00 0.00 3.85
335 3028 4.517285 TCTGGTCATGCCTTTCATAAGTC 58.483 43.478 7.54 0.00 38.35 3.01
351 3044 5.454897 GGGATAGGGTTTATGACTTCTGGTC 60.455 48.000 0.00 0.00 44.70 4.02
353 3046 4.660771 AGGGATAGGGTTTATGACTTCTGG 59.339 45.833 0.00 0.00 0.00 3.86
354 3047 5.896073 AGGGATAGGGTTTATGACTTCTG 57.104 43.478 0.00 0.00 0.00 3.02
355 3048 6.437793 CGATAGGGATAGGGTTTATGACTTCT 59.562 42.308 0.00 0.00 0.00 2.85
376 3069 4.445453 ACACGAGATACACTACACCGATA 58.555 43.478 0.00 0.00 0.00 2.92
380 3073 5.557891 AACTACACGAGATACACTACACC 57.442 43.478 0.00 0.00 0.00 4.16
383 3076 5.862811 ACGAAACTACACGAGATACACTAC 58.137 41.667 0.00 0.00 0.00 2.73
389 3082 3.127548 GGTGGACGAAACTACACGAGATA 59.872 47.826 0.00 0.00 34.78 1.98
396 3089 3.575256 ACACTATGGTGGACGAAACTACA 59.425 43.478 14.25 0.00 46.85 2.74
397 3090 4.184079 ACACTATGGTGGACGAAACTAC 57.816 45.455 14.25 0.00 46.85 2.73
418 3111 4.012374 GGATCTCATGAGTTGGAAAGCAA 58.988 43.478 21.92 0.00 0.00 3.91
419 3112 3.614092 GGATCTCATGAGTTGGAAAGCA 58.386 45.455 21.92 0.00 0.00 3.91
423 3116 2.561187 TGGGGATCTCATGAGTTGGAA 58.439 47.619 21.92 2.94 0.00 3.53
439 3132 3.139077 GACGAAGGCTACAAATATGGGG 58.861 50.000 0.00 0.00 0.00 4.96
452 3145 0.803740 AGACAGAGTACGACGAAGGC 59.196 55.000 0.00 0.00 0.00 4.35
456 3149 7.543947 TTTATATCAAGACAGAGTACGACGA 57.456 36.000 0.00 0.00 0.00 4.20
468 3161 9.554724 TCAAAGCGACAATTTTTATATCAAGAC 57.445 29.630 0.00 0.00 0.00 3.01
469 3162 9.554724 GTCAAAGCGACAATTTTTATATCAAGA 57.445 29.630 0.00 0.00 44.69 3.02
580 3275 7.773690 TGCATATTGAGATGATGGAATAGGATG 59.226 37.037 0.00 0.00 0.00 3.51
618 3313 3.058914 ACGTGATCAGCTTTTGTTAGCAC 60.059 43.478 0.00 0.00 43.68 4.40
642 3356 7.824289 TGTACTTAAAGCAGATTCTAGCATGTT 59.176 33.333 9.67 0.00 0.00 2.71
714 3428 8.834465 CATGTTGGAAATGGTGTTTAAAAATCA 58.166 29.630 0.00 0.00 0.00 2.57
715 3429 7.802720 GCATGTTGGAAATGGTGTTTAAAAATC 59.197 33.333 0.00 0.00 0.00 2.17
716 3430 7.255416 GGCATGTTGGAAATGGTGTTTAAAAAT 60.255 33.333 0.00 0.00 0.00 1.82
725 3483 2.094390 CAGAGGCATGTTGGAAATGGTG 60.094 50.000 0.00 0.00 0.00 4.17
909 4077 2.985456 GTGTCCTGGAGGCTGGAG 59.015 66.667 0.00 0.00 32.36 3.86
910 4078 2.997315 CGTGTCCTGGAGGCTGGA 60.997 66.667 0.00 0.00 34.44 3.86
911 4079 4.087892 CCGTGTCCTGGAGGCTGG 62.088 72.222 0.00 0.00 34.44 4.85
912 4080 2.997315 TCCGTGTCCTGGAGGCTG 60.997 66.667 0.00 0.00 34.44 4.85
913 4081 2.997897 GTCCGTGTCCTGGAGGCT 60.998 66.667 0.00 0.00 35.82 4.58
914 4082 4.436998 CGTCCGTGTCCTGGAGGC 62.437 72.222 0.00 0.00 35.82 4.70
915 4083 2.675423 TCGTCCGTGTCCTGGAGG 60.675 66.667 0.00 0.00 41.59 4.30
970 4138 3.827898 GAGAGGAGCGGTGGACGG 61.828 72.222 0.00 0.00 44.51 4.79
972 4140 3.462678 GGGAGAGGAGCGGTGGAC 61.463 72.222 0.00 0.00 0.00 4.02
976 4144 4.012721 AAGGGGGAGAGGAGCGGT 62.013 66.667 0.00 0.00 0.00 5.68
977 4145 3.474570 CAAGGGGGAGAGGAGCGG 61.475 72.222 0.00 0.00 0.00 5.52
979 4147 3.803162 GCCAAGGGGGAGAGGAGC 61.803 72.222 0.00 0.00 40.01 4.70
980 4148 3.474570 CGCCAAGGGGGAGAGGAG 61.475 72.222 0.00 0.00 39.08 3.69
983 4151 2.370445 ATGTCGCCAAGGGGGAGAG 61.370 63.158 1.88 0.00 46.91 3.20
1011 4189 2.797177 ATGAGAGGAAAGGAACCAGC 57.203 50.000 0.00 0.00 0.00 4.85
1037 4215 0.529992 GAACGAGGCAGGGTAATCCG 60.530 60.000 0.00 0.00 41.52 4.18
1166 5404 6.537355 TCCATGAATTCCTGATTCTGTATCC 58.463 40.000 11.84 0.00 43.74 2.59
1172 5410 5.658198 TCCATCCATGAATTCCTGATTCT 57.342 39.130 11.84 0.00 43.74 2.40
1192 5430 3.056304 GAGTCGATTAGCTGCAGAATCC 58.944 50.000 20.43 7.04 0.00 3.01
1351 5596 0.888285 ACAGAGCAAGCAGTCAAGCC 60.888 55.000 0.00 0.00 34.23 4.35
1367 5612 9.868277 AAAATCTATCTGTGTCTCTAAGAACAG 57.132 33.333 10.45 10.45 36.06 3.16
1373 5618 8.696374 CCCAGTAAAATCTATCTGTGTCTCTAA 58.304 37.037 0.00 0.00 0.00 2.10
1382 5627 6.127054 TGTCAGTCCCCAGTAAAATCTATCTG 60.127 42.308 0.00 0.00 0.00 2.90
1393 5638 2.391926 TTCACTGTCAGTCCCCAGTA 57.608 50.000 1.37 0.00 39.83 2.74
1408 5653 0.804989 CCCCTGCTCGAACAATTCAC 59.195 55.000 0.00 0.00 0.00 3.18
1574 5820 4.896482 ACCTGCTACTTTGGAGGATAGTAG 59.104 45.833 8.97 0.00 46.72 2.57
1575 5821 4.880164 ACCTGCTACTTTGGAGGATAGTA 58.120 43.478 8.97 0.00 46.72 1.82
1576 5822 3.707102 GACCTGCTACTTTGGAGGATAGT 59.293 47.826 8.97 0.00 46.72 2.12
1638 5890 2.386661 ACCAAATAGACACAGCTCGG 57.613 50.000 0.00 0.00 0.00 4.63
1695 5984 7.454225 AGTTAATGTTGAAGCTCTTTCTACCT 58.546 34.615 0.00 0.00 39.73 3.08
1718 6007 7.725251 TCTTTTATGTCATCCTTGCAAAAAGT 58.275 30.769 0.00 0.00 35.34 2.66
1719 6008 8.592105 TTCTTTTATGTCATCCTTGCAAAAAG 57.408 30.769 0.00 3.71 35.20 2.27
2105 6420 6.940867 AGTTATTTTCAACAGGGGTACTTCTC 59.059 38.462 0.00 0.00 0.00 2.87
2131 6446 9.856162 AAGGTAGAAGTTTGAATTTTGGTAGTA 57.144 29.630 0.00 0.00 0.00 1.82
2134 6449 9.810545 CAAAAGGTAGAAGTTTGAATTTTGGTA 57.189 29.630 0.00 0.00 34.80 3.25
2135 6450 7.768582 CCAAAAGGTAGAAGTTTGAATTTTGGT 59.231 33.333 14.80 0.00 45.16 3.67
2136 6451 8.141835 CCAAAAGGTAGAAGTTTGAATTTTGG 57.858 34.615 10.62 10.62 45.03 3.28
2224 6543 7.801547 AAACAAAATGAAATCATAGTCTGCG 57.198 32.000 0.00 0.00 35.10 5.18
2281 6601 1.211703 TGTCGCCATGTTGATATGGGT 59.788 47.619 8.57 0.00 46.23 4.51
2298 6618 2.095718 GTCGAAGCCCAAGATGTTTGTC 60.096 50.000 0.00 0.00 0.00 3.18
2401 6721 5.073437 TGGAAAAGAAAAAGGAGATGGGA 57.927 39.130 0.00 0.00 0.00 4.37
2455 6775 5.022122 AGCAAGCTCTCCTGCATATATAGA 58.978 41.667 10.57 0.00 34.99 1.98
2457 6777 5.954752 AGTAGCAAGCTCTCCTGCATATATA 59.045 40.000 10.57 0.00 34.99 0.86
2531 6851 5.690464 AGATCAAAGATGCTACAGGAGTT 57.310 39.130 0.00 0.00 0.00 3.01
2536 6856 5.188434 TGGGAAAGATCAAAGATGCTACAG 58.812 41.667 0.00 0.00 0.00 2.74
2657 6981 0.812811 GGAAGAAACGTATCCCGGGC 60.813 60.000 18.49 0.00 42.24 6.13
2688 7012 3.013276 TGTGAAGCTGAAGACTACACG 57.987 47.619 0.00 0.00 0.00 4.49
2693 7017 5.858381 TCATAGTTTGTGAAGCTGAAGACT 58.142 37.500 0.00 0.00 0.00 3.24
2694 7018 5.121454 CCTCATAGTTTGTGAAGCTGAAGAC 59.879 44.000 0.00 0.00 0.00 3.01
2745 7072 7.390718 GGTCAGTTGGTCATGTTAAAGAATACT 59.609 37.037 0.00 0.00 0.00 2.12
2746 7073 7.174253 TGGTCAGTTGGTCATGTTAAAGAATAC 59.826 37.037 0.00 0.00 0.00 1.89
2747 7074 7.227873 TGGTCAGTTGGTCATGTTAAAGAATA 58.772 34.615 0.00 0.00 0.00 1.75
2748 7075 6.068010 TGGTCAGTTGGTCATGTTAAAGAAT 58.932 36.000 0.00 0.00 0.00 2.40
2758 7085 0.606401 CGCCTTGGTCAGTTGGTCAT 60.606 55.000 0.00 0.00 0.00 3.06
2869 7196 0.820482 TTGGAGTGTCGACGGTGAGA 60.820 55.000 11.62 0.00 0.00 3.27
2908 7235 5.237344 GGATTTGGACCTGTTCTTGATATCG 59.763 44.000 0.00 0.00 0.00 2.92
2959 7286 9.807649 AATGGAATAAATCATTTACTCAGCAAC 57.192 29.630 1.26 0.00 30.27 4.17
2974 7301 9.474313 TGCAGTTCCTAGTAAAATGGAATAAAT 57.526 29.630 0.00 0.00 41.23 1.40
2976 7303 8.107095 AGTGCAGTTCCTAGTAAAATGGAATAA 58.893 33.333 0.00 0.00 41.23 1.40
3002 7329 4.341366 TTCAGATTTCAGAGTGCAGACA 57.659 40.909 0.00 0.00 0.00 3.41
3003 7330 5.876612 AATTCAGATTTCAGAGTGCAGAC 57.123 39.130 0.00 0.00 0.00 3.51
3027 7354 6.169094 AGATGAACCTGTCACAAGTTATCAG 58.831 40.000 0.00 0.00 39.72 2.90
3037 7364 2.079925 GAGGCAAGATGAACCTGTCAC 58.920 52.381 0.00 0.00 39.72 3.67
3062 7389 1.242076 CAAAGTTCTCCAGCACCAGG 58.758 55.000 0.00 0.00 0.00 4.45
3118 7445 1.336887 CGATCGACTTGGTTGTCAGGT 60.337 52.381 10.26 0.00 38.47 4.00
3132 7459 3.489444 GCGATTTCTGCTATACGATCGA 58.511 45.455 24.34 5.87 38.81 3.59
3134 7461 3.839293 AGGCGATTTCTGCTATACGATC 58.161 45.455 0.00 0.00 0.00 3.69
3142 7469 4.737855 TTCTACTTAGGCGATTTCTGCT 57.262 40.909 0.00 0.00 0.00 4.24
3218 7571 3.310860 AACGTAGGAAGCCAGCCCG 62.311 63.158 0.00 0.00 0.00 6.13
3233 7586 1.805945 GTCGACCTGGCTAGCAACG 60.806 63.158 18.24 13.39 0.00 4.10
3360 7713 0.385974 GACGTCCTGCATTTGTGCAC 60.386 55.000 10.75 10.75 40.23 4.57
3386 7739 2.225491 GCAACGAGGTAATTGTCTGCAA 59.775 45.455 0.00 0.00 39.16 4.08
3467 7820 2.107750 CGGAGGCGTGCATCTCAT 59.892 61.111 6.46 0.00 0.00 2.90
3491 7844 2.165845 AGCAAAAGGAGATGCAGCATTC 59.834 45.455 9.90 8.92 44.95 2.67
3505 7858 1.315257 ACAGGCCGCCATAGCAAAAG 61.315 55.000 13.15 0.00 39.83 2.27
3532 7885 5.074430 GCATTTTGCACAAGTTTCTTCAG 57.926 39.130 0.00 0.00 44.26 3.02
3689 8042 7.525688 TCTGCAATTTCTCAATAGAACTACG 57.474 36.000 0.00 0.00 41.48 3.51
3699 8052 7.448161 TCCTGAACTTTATCTGCAATTTCTCAA 59.552 33.333 0.00 0.00 0.00 3.02
3743 8108 6.941436 TGGTCAATATATGCATGCATGTAGAA 59.059 34.615 37.43 21.28 37.82 2.10
3747 8112 6.408107 TTTGGTCAATATATGCATGCATGT 57.592 33.333 37.43 33.30 37.82 3.21
3757 8122 6.832520 TGTGCACACTTTTGGTCAATATAT 57.167 33.333 17.42 0.00 0.00 0.86
3758 8123 6.641169 TTGTGCACACTTTTGGTCAATATA 57.359 33.333 21.56 0.00 0.00 0.86
3777 8142 5.649557 TCTGACAACCTGAATTTGTTTGTG 58.350 37.500 1.36 0.00 37.31 3.33
3778 8143 5.652014 TCTCTGACAACCTGAATTTGTTTGT 59.348 36.000 0.00 0.00 37.31 2.83
3794 8159 1.984570 CCCCTTCGCCTCTCTGACA 60.985 63.158 0.00 0.00 0.00 3.58
3814 8179 4.379243 CGAGGAACACCGGCAGCT 62.379 66.667 0.00 0.00 0.00 4.24
3903 8268 2.157474 CACGCAGATCGATTGTGTTTGA 59.843 45.455 18.05 0.00 41.67 2.69
3906 8271 1.795768 ACACGCAGATCGATTGTGTT 58.204 45.000 18.05 10.79 40.63 3.32
3912 8277 3.589988 AGAAAGAAACACGCAGATCGAT 58.410 40.909 0.00 0.00 41.67 3.59
3937 8302 3.643978 GTCCATCAGCATCGCCGC 61.644 66.667 0.00 0.00 0.00 6.53
3950 8315 2.261361 CCACACATCGAGCGTCCA 59.739 61.111 0.00 0.00 0.00 4.02
3952 8317 1.805945 GACCCACACATCGAGCGTC 60.806 63.158 0.00 0.00 0.00 5.19
3953 8318 2.261671 GACCCACACATCGAGCGT 59.738 61.111 0.00 0.00 0.00 5.07
3970 8335 2.124983 CCCGATCTGCCACACCAG 60.125 66.667 0.00 0.00 0.00 4.00
4032 8401 1.376424 CATCTGCAGCACCTTCCGT 60.376 57.895 9.47 0.00 0.00 4.69
4196 8565 2.502123 CGCGCGCACAAGTACGTAT 61.502 57.895 32.61 0.00 0.00 3.06
4213 8584 3.629491 AAATCGACAACAGCGCGCG 62.629 57.895 28.44 28.44 0.00 6.86
4220 8591 1.731709 CGGCATCTCAAATCGACAACA 59.268 47.619 0.00 0.00 0.00 3.33
4221 8592 1.529826 GCGGCATCTCAAATCGACAAC 60.530 52.381 0.00 0.00 0.00 3.32
4223 8594 0.108186 AGCGGCATCTCAAATCGACA 60.108 50.000 1.45 0.00 0.00 4.35
4268 8639 2.922740 ATTATTGCCCGGTACATCGT 57.077 45.000 0.00 0.00 0.00 3.73
4276 8647 9.410556 CTTTATTTCTATGAAATTATTGCCCGG 57.589 33.333 10.25 0.00 0.00 5.73
4287 8658 9.672673 CCTTCTCCAGTCTTTATTTCTATGAAA 57.327 33.333 0.00 0.00 0.00 2.69
4291 8662 7.569240 CACCCTTCTCCAGTCTTTATTTCTAT 58.431 38.462 0.00 0.00 0.00 1.98
4304 8675 2.110967 CGCATGCACCCTTCTCCAG 61.111 63.158 19.57 0.00 0.00 3.86
4324 8695 2.202623 CTGGCAGACTACGCGACC 60.203 66.667 15.93 2.59 0.00 4.79
4329 8703 0.647410 CATTTCGCTGGCAGACTACG 59.353 55.000 20.86 12.40 0.00 3.51
4374 8748 2.348888 CCCGACAGAGGGCGTAGTT 61.349 63.158 0.00 0.00 45.72 2.24
4405 8781 3.319755 CTTGGCACGCTTTGAAAATGAT 58.680 40.909 0.00 0.00 0.00 2.45
4411 8787 1.100463 TCTGCTTGGCACGCTTTGAA 61.100 50.000 17.27 0.00 33.79 2.69
4413 8789 0.662374 CTTCTGCTTGGCACGCTTTG 60.662 55.000 17.27 7.55 33.79 2.77
4419 8795 1.247567 TTAAGGCTTCTGCTTGGCAC 58.752 50.000 1.30 0.00 39.59 5.01
4422 8798 2.489722 GAGGTTTAAGGCTTCTGCTTGG 59.510 50.000 1.30 0.00 39.59 3.61
4424 8800 3.797559 AGAGGTTTAAGGCTTCTGCTT 57.202 42.857 1.30 0.00 39.59 3.91
4438 8814 2.629617 CACCTTTGCATTGGAAGAGGTT 59.370 45.455 16.37 5.76 35.43 3.50
4439 8815 2.242043 CACCTTTGCATTGGAAGAGGT 58.758 47.619 14.47 14.47 37.98 3.85
4452 8828 2.159653 GCATCTCGTGTAAGCACCTTTG 60.160 50.000 0.00 0.00 42.39 2.77
4453 8829 2.076863 GCATCTCGTGTAAGCACCTTT 58.923 47.619 0.00 0.00 42.39 3.11
4454 8830 1.276421 AGCATCTCGTGTAAGCACCTT 59.724 47.619 0.00 0.00 42.39 3.50
4455 8831 0.898320 AGCATCTCGTGTAAGCACCT 59.102 50.000 0.00 0.00 42.39 4.00
4456 8832 2.579207 TAGCATCTCGTGTAAGCACC 57.421 50.000 0.00 0.00 42.39 5.01
4457 8833 2.860735 CCTTAGCATCTCGTGTAAGCAC 59.139 50.000 0.00 0.00 41.97 4.40
4458 8834 2.159099 CCCTTAGCATCTCGTGTAAGCA 60.159 50.000 0.00 0.00 0.00 3.91
4459 8835 2.474816 CCCTTAGCATCTCGTGTAAGC 58.525 52.381 0.00 0.00 0.00 3.09
4460 8836 2.474816 GCCCTTAGCATCTCGTGTAAG 58.525 52.381 0.00 0.00 42.97 2.34
4461 8837 1.202371 CGCCCTTAGCATCTCGTGTAA 60.202 52.381 0.00 0.00 44.04 2.41
4462 8838 0.384309 CGCCCTTAGCATCTCGTGTA 59.616 55.000 0.00 0.00 44.04 2.90
4463 8839 1.141881 CGCCCTTAGCATCTCGTGT 59.858 57.895 0.00 0.00 44.04 4.49
4464 8840 1.141881 ACGCCCTTAGCATCTCGTG 59.858 57.895 0.00 0.00 44.04 4.35
4465 8841 1.141881 CACGCCCTTAGCATCTCGT 59.858 57.895 0.00 0.00 44.04 4.18
4466 8842 0.460284 AACACGCCCTTAGCATCTCG 60.460 55.000 0.00 0.00 44.04 4.04
4467 8843 1.398390 CAAACACGCCCTTAGCATCTC 59.602 52.381 0.00 0.00 44.04 2.75
4468 8844 1.453155 CAAACACGCCCTTAGCATCT 58.547 50.000 0.00 0.00 44.04 2.90
4469 8845 0.451783 CCAAACACGCCCTTAGCATC 59.548 55.000 0.00 0.00 44.04 3.91
4470 8846 0.251165 ACCAAACACGCCCTTAGCAT 60.251 50.000 0.00 0.00 44.04 3.79
4471 8847 0.466555 AACCAAACACGCCCTTAGCA 60.467 50.000 0.00 0.00 44.04 3.49
4472 8848 0.039527 CAACCAAACACGCCCTTAGC 60.040 55.000 0.00 0.00 38.52 3.09
4473 8849 0.596082 CCAACCAAACACGCCCTTAG 59.404 55.000 0.00 0.00 0.00 2.18
4474 8850 0.106619 ACCAACCAAACACGCCCTTA 60.107 50.000 0.00 0.00 0.00 2.69
4491 8867 2.056481 GATGCAGATGCGAGGCAACC 62.056 60.000 0.00 0.00 43.62 3.77
4520 8896 4.175516 ACCAAACATTGCGAATATTGCAG 58.824 39.130 10.89 5.60 44.28 4.41
4737 11402 1.442769 GCGAGATCTGTTTGCAGGAA 58.557 50.000 0.00 0.00 42.78 3.36
4744 11409 1.153549 GAGGCGGCGAGATCTGTTT 60.154 57.895 12.98 0.00 0.00 2.83
4845 11518 1.230497 GATGAGAGGGGTCCGAGGA 59.770 63.158 0.00 0.00 0.00 3.71
4895 11569 3.573491 GCCGGCTTACATCCGCAC 61.573 66.667 22.15 0.00 45.19 5.34
5091 11849 3.728076 TTACTAGCCCAATAGCTCACG 57.272 47.619 0.00 0.00 43.67 4.35


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

AutoCloner maintained by Alex Coulton.