Multiple sequence alignment - TraesCS2A01G299500

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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 TraesCS2A01G299500 chr2A 100.000 4412 0 0 1 4412 515297568 515301979 0.000000e+00 8148.0
1 TraesCS2A01G299500 chr2A 95.588 272 11 1 4103 4374 585819143 585818873 6.780000e-118 435.0
2 TraesCS2A01G299500 chr2A 71.694 915 218 31 2501 3383 611297959 611298864 2.670000e-52 217.0
3 TraesCS2A01G299500 chr2D 93.812 3814 177 28 1 3774 380073165 380076959 0.000000e+00 5681.0
4 TraesCS2A01G299500 chr2D 95.166 331 13 2 3776 4103 380077275 380077605 1.820000e-143 520.0
5 TraesCS2A01G299500 chr2D 72.475 901 210 25 2498 3367 599928019 599928912 5.660000e-64 255.0
6 TraesCS2A01G299500 chr2B 93.393 3799 209 26 1 3774 451449091 451452872 0.000000e+00 5587.0
7 TraesCS2A01G299500 chr2B 90.476 336 23 6 3776 4103 451453190 451453524 6.780000e-118 435.0
8 TraesCS2A01G299500 chr2B 72.693 1073 229 44 1064 2091 117994132 117993079 2.580000e-77 300.0
9 TraesCS2A01G299500 chr2B 79.295 227 39 5 1812 2031 451416768 451416543 7.640000e-33 152.0
10 TraesCS2A01G299500 chr7D 73.336 2359 532 73 1070 3375 543640313 543637999 0.000000e+00 782.0
11 TraesCS2A01G299500 chr7D 77.480 857 174 11 2533 3376 543562099 543561249 3.070000e-136 496.0
12 TraesCS2A01G299500 chr7D 96.457 254 9 0 4103 4356 426171938 426172191 1.900000e-113 420.0
13 TraesCS2A01G299500 chr7D 87.500 56 7 0 4357 4412 117755365 117755310 1.020000e-06 65.8
14 TraesCS2A01G299500 chr7D 86.792 53 7 0 4357 4409 542950022 542950074 4.770000e-05 60.2
15 TraesCS2A01G299500 chr7A 77.480 897 188 11 2487 3376 625533739 625532850 3.910000e-145 525.0
16 TraesCS2A01G299500 chr7A 97.244 254 7 0 4103 4356 535468315 535468568 8.770000e-117 431.0
17 TraesCS2A01G299500 chr4D 97.638 254 6 0 4103 4356 48708660 48708913 1.880000e-118 436.0
18 TraesCS2A01G299500 chr4D 97.244 254 7 0 4103 4356 47750710 47750963 8.770000e-117 431.0
19 TraesCS2A01G299500 chr5D 97.244 254 7 0 4103 4356 87803356 87803609 8.770000e-117 431.0
20 TraesCS2A01G299500 chr5D 96.850 254 7 1 4103 4356 447307393 447307645 1.470000e-114 424.0
21 TraesCS2A01G299500 chr3D 96.457 254 9 0 4103 4356 416217333 416217586 1.900000e-113 420.0
22 TraesCS2A01G299500 chr3D 96.800 250 8 0 4107 4356 164545444 164545693 6.830000e-113 418.0
23 TraesCS2A01G299500 chr3D 93.617 47 3 0 4365 4411 103637965 103638011 2.200000e-08 71.3
24 TraesCS2A01G299500 chr1D 73.021 619 142 17 2504 3102 407670949 407670336 1.250000e-45 195.0
25 TraesCS2A01G299500 chr1D 71.205 830 199 31 2504 3307 5522536 5521721 5.870000e-39 172.0
26 TraesCS2A01G299500 chr1A 71.429 826 204 27 2504 3307 7189875 7189060 5.830000e-44 189.0
27 TraesCS2A01G299500 chr1B 70.673 832 212 27 2498 3307 8259957 8259136 5.910000e-34 156.0
28 TraesCS2A01G299500 chr1B 85.714 56 8 0 4357 4412 568569397 568569342 4.770000e-05 60.2
29 TraesCS2A01G299500 chr3A 79.141 163 32 2 2855 3016 131424220 131424059 1.300000e-20 111.0
30 TraesCS2A01G299500 chr7B 91.071 56 5 0 4357 4412 734265476 734265531 4.730000e-10 76.8
31 TraesCS2A01G299500 chr7B 85.714 56 7 1 4357 4412 78546964 78546910 1.710000e-04 58.4
32 TraesCS2A01G299500 chr3B 93.478 46 3 0 4366 4411 763118955 763118910 7.920000e-08 69.4
33 TraesCS2A01G299500 chr5B 85.714 56 8 0 4357 4412 354989008 354988953 4.770000e-05 60.2


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 TraesCS2A01G299500 chr2A 515297568 515301979 4411 False 8148.0 8148 100.0000 1 4412 1 chr2A.!!$F1 4411
1 TraesCS2A01G299500 chr2A 611297959 611298864 905 False 217.0 217 71.6940 2501 3383 1 chr2A.!!$F2 882
2 TraesCS2A01G299500 chr2D 380073165 380077605 4440 False 3100.5 5681 94.4890 1 4103 2 chr2D.!!$F2 4102
3 TraesCS2A01G299500 chr2D 599928019 599928912 893 False 255.0 255 72.4750 2498 3367 1 chr2D.!!$F1 869
4 TraesCS2A01G299500 chr2B 451449091 451453524 4433 False 3011.0 5587 91.9345 1 4103 2 chr2B.!!$F1 4102
5 TraesCS2A01G299500 chr2B 117993079 117994132 1053 True 300.0 300 72.6930 1064 2091 1 chr2B.!!$R1 1027
6 TraesCS2A01G299500 chr7D 543637999 543640313 2314 True 782.0 782 73.3360 1070 3375 1 chr7D.!!$R3 2305
7 TraesCS2A01G299500 chr7D 543561249 543562099 850 True 496.0 496 77.4800 2533 3376 1 chr7D.!!$R2 843
8 TraesCS2A01G299500 chr7A 625532850 625533739 889 True 525.0 525 77.4800 2487 3376 1 chr7A.!!$R1 889

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
944 988 0.711184 AGAGCACCCACCCTACTACT 59.289 55.0 0.00 0.0 0.00 2.57 F
1644 1708 0.817634 TGCCATATTGGTACAGCGGC 60.818 55.0 0.00 0.0 42.39 6.53 F
2812 2906 0.251916 CAGGTACCAAATCGCCCTCA 59.748 55.0 15.94 0.0 0.00 3.86 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1905 1975 0.096976 GTAGCGCGTTGTCATTGCAT 59.903 50.0 8.43 0.0 0.0 3.96 R
3319 3429 0.105760 ATCTCAGACAGCCCCTCGAT 60.106 55.0 0.00 0.0 0.0 3.59 R
4345 4787 0.323957 GAGGCAGTACCCTCCGTTTT 59.676 55.0 6.87 0.0 44.6 2.43 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
60 62 6.312399 TGAACACTTCATTTCCACATACAC 57.688 37.500 0.00 0.00 34.08 2.90
61 63 5.825151 TGAACACTTCATTTCCACATACACA 59.175 36.000 0.00 0.00 34.08 3.72
74 76 8.879342 TTCCACATACACAAACATTTTAAAGG 57.121 30.769 0.00 0.00 0.00 3.11
120 126 6.166982 TCACATTAACATGTTGTATGTCCGA 58.833 36.000 25.82 20.78 41.16 4.55
125 131 4.487714 ACATGTTGTATGTCCGAGGATT 57.512 40.909 0.00 0.00 0.00 3.01
265 296 5.683859 CAGGCTATATCAAGCGTCAAAATC 58.316 41.667 0.00 0.00 43.74 2.17
285 316 6.428385 AATCAAATGATGACTTCGAGGAAC 57.572 37.500 0.00 0.00 41.93 3.62
305 336 2.880890 ACAGTTGGTAAGCTTTGCTCAG 59.119 45.455 3.20 0.00 38.25 3.35
376 407 4.726416 CTGACAAATGTATCTGCACCAAC 58.274 43.478 0.00 0.00 0.00 3.77
453 488 5.687285 GGCAAAGTATTGTTGTTTGTCTGAG 59.313 40.000 0.00 0.00 38.85 3.35
496 531 5.666969 TTTTGGTTGTCGATGTAGAGTTG 57.333 39.130 0.00 0.00 0.00 3.16
497 532 4.330944 TTGGTTGTCGATGTAGAGTTGT 57.669 40.909 0.00 0.00 0.00 3.32
498 533 5.456548 TTGGTTGTCGATGTAGAGTTGTA 57.543 39.130 0.00 0.00 0.00 2.41
499 534 5.055642 TGGTTGTCGATGTAGAGTTGTAG 57.944 43.478 0.00 0.00 0.00 2.74
504 539 7.414873 GGTTGTCGATGTAGAGTTGTAGACATA 60.415 40.741 0.00 0.00 37.25 2.29
505 540 7.247929 TGTCGATGTAGAGTTGTAGACATAG 57.752 40.000 0.00 0.00 32.75 2.23
506 541 6.260271 TGTCGATGTAGAGTTGTAGACATAGG 59.740 42.308 0.00 0.00 32.75 2.57
507 542 6.482641 GTCGATGTAGAGTTGTAGACATAGGA 59.517 42.308 0.00 0.00 32.75 2.94
508 543 6.706716 TCGATGTAGAGTTGTAGACATAGGAG 59.293 42.308 0.00 0.00 32.75 3.69
509 544 6.483974 CGATGTAGAGTTGTAGACATAGGAGT 59.516 42.308 0.00 0.00 32.75 3.85
510 545 7.656542 CGATGTAGAGTTGTAGACATAGGAGTA 59.343 40.741 0.00 0.00 32.75 2.59
511 546 8.680039 ATGTAGAGTTGTAGACATAGGAGTAC 57.320 38.462 0.00 0.00 30.83 2.73
512 547 7.859540 TGTAGAGTTGTAGACATAGGAGTACT 58.140 38.462 0.00 0.00 0.00 2.73
513 548 8.985922 TGTAGAGTTGTAGACATAGGAGTACTA 58.014 37.037 0.00 0.00 35.80 1.82
564 599 6.582672 GGCTAAATTAACAAGACTGTTTCAGC 59.417 38.462 0.00 0.00 43.45 4.26
568 603 6.942532 ATTAACAAGACTGTTTCAGCTTGA 57.057 33.333 24.90 13.25 43.45 3.02
569 604 4.622701 AACAAGACTGTTTCAGCTTGAC 57.377 40.909 24.90 0.00 43.45 3.18
614 651 1.269448 GTTGCCGTGATGTGGATGTTT 59.731 47.619 0.00 0.00 0.00 2.83
622 659 3.737266 GTGATGTGGATGTTTTGCACTTG 59.263 43.478 0.00 0.00 46.12 3.16
625 662 4.669206 TGTGGATGTTTTGCACTTGATT 57.331 36.364 0.00 0.00 46.12 2.57
635 672 8.654230 TGTTTTGCACTTGATTGCTAAATTAA 57.346 26.923 7.73 0.00 44.92 1.40
644 681 7.814587 ACTTGATTGCTAAATTAAACCTGAAGC 59.185 33.333 0.00 0.00 0.00 3.86
698 736 5.615925 ACTCCGCTATCAAGGAAAATAGT 57.384 39.130 0.00 0.00 35.90 2.12
743 781 5.115480 GCCTTAGATCTGGTGAAGAAAGAG 58.885 45.833 5.18 0.00 38.79 2.85
767 809 1.284982 CGTGAGGCGGAGTGTCAAAG 61.285 60.000 0.00 0.00 36.85 2.77
787 829 2.106418 GTTTTCGACGAAACTGCCAAC 58.894 47.619 21.96 12.76 36.75 3.77
795 837 1.135402 CGAAACTGCCAACCCAATAGC 60.135 52.381 0.00 0.00 0.00 2.97
808 852 2.286872 CCAATAGCTGCAGTTCCTCAG 58.713 52.381 16.64 0.00 0.00 3.35
840 884 3.622163 CCTGAATCTCACATCTTCACAGC 59.378 47.826 0.00 0.00 0.00 4.40
844 888 1.613437 TCTCACATCTTCACAGCGACA 59.387 47.619 0.00 0.00 0.00 4.35
853 897 3.876914 TCTTCACAGCGACATTTTTCACT 59.123 39.130 0.00 0.00 0.00 3.41
881 925 1.723608 TTGGCGGTTGTGCTTGACTG 61.724 55.000 0.00 0.00 34.52 3.51
884 928 1.280746 CGGTTGTGCTTGACTGCTG 59.719 57.895 0.00 0.00 0.00 4.41
897 941 1.005037 CTGCTGGTTCACCACGCTA 60.005 57.895 16.48 6.96 42.01 4.26
944 988 0.711184 AGAGCACCCACCCTACTACT 59.289 55.000 0.00 0.00 0.00 2.57
980 1026 3.513750 AACTGCAAGCCACCCCTCC 62.514 63.158 0.00 0.00 37.60 4.30
1084 1130 1.304217 ACGACGGACACCATCTCCT 60.304 57.895 0.00 0.00 0.00 3.69
1105 1151 4.003788 CCCAACCACTCGTCGGCT 62.004 66.667 0.00 0.00 0.00 5.52
1123 1169 2.507324 GCGACAAGCTCGTCTCCC 60.507 66.667 2.81 0.00 44.92 4.30
1167 1213 4.116328 TTCGAGACCGGCAGCGAG 62.116 66.667 0.00 0.00 34.01 5.03
1287 1351 3.121019 CTCACGATCTCCGGGGAC 58.879 66.667 5.91 0.00 43.16 4.46
1417 1481 1.001746 TCCTGCAGAACAGCTCTTCAG 59.998 52.381 17.39 0.00 45.78 3.02
1644 1708 0.817634 TGCCATATTGGTACAGCGGC 60.818 55.000 0.00 0.00 42.39 6.53
1879 1949 2.497138 CCAAAGCTCAGTGTGATGTCA 58.503 47.619 0.00 0.00 0.00 3.58
1923 1993 1.646189 TATGCAATGACAACGCGCTA 58.354 45.000 5.73 0.00 0.00 4.26
1962 2032 4.827481 GGCTTCGCCGTAAGATCA 57.173 55.556 0.00 0.00 39.62 2.92
2080 2156 1.340991 ACCCCATGCCATGTGTTAGAC 60.341 52.381 3.63 0.00 0.00 2.59
2085 2161 0.673333 TGCCATGTGTTAGACTGCCG 60.673 55.000 0.00 0.00 0.00 5.69
2292 2368 4.404654 CTTCGCCTTGCCGCCAAC 62.405 66.667 0.00 0.00 0.00 3.77
2316 2392 0.545309 TTCCCAGTCAGCAGGCTAGT 60.545 55.000 0.00 0.00 0.00 2.57
2652 2731 2.107953 GAGGTGAGCTCCATCGGC 59.892 66.667 12.15 0.00 0.00 5.54
2710 2789 1.956629 TTGCTGCGAGGGTAGTAGGC 61.957 60.000 0.00 0.00 0.00 3.93
2812 2906 0.251916 CAGGTACCAAATCGCCCTCA 59.748 55.000 15.94 0.00 0.00 3.86
2871 2965 2.353889 CCAAGACTGCATCATACACTGC 59.646 50.000 0.00 0.00 38.87 4.40
3072 3166 1.221840 CAGCTACGGGATGGTGCTT 59.778 57.895 0.00 0.00 0.00 3.91
3178 3281 1.134848 CCCAGAAGCTTCTCGAAGGAG 60.135 57.143 26.18 12.80 41.89 3.69
3317 3427 5.153950 ACAATGGGAGAAGTAGTTCAGAC 57.846 43.478 12.77 3.85 34.82 3.51
3319 3429 6.017192 ACAATGGGAGAAGTAGTTCAGACTA 58.983 40.000 12.77 1.02 37.33 2.59
3389 3499 1.526887 CTATGAGCGGCAGGGGAAA 59.473 57.895 1.45 0.00 0.00 3.13
3407 3517 2.463553 AATTCGCATTCGACATGCTG 57.536 45.000 21.77 17.07 45.43 4.41
3597 3711 4.865905 ACAACTATATGTGGCATTGGGAA 58.134 39.130 0.00 0.00 30.82 3.97
3606 3720 3.509575 TGTGGCATTGGGAAAGAATACAC 59.490 43.478 0.00 0.00 0.00 2.90
3616 3730 4.394729 GGAAAGAATACACAGTGTTCCCA 58.605 43.478 12.53 0.00 34.88 4.37
3761 3875 0.625849 CCCCAAAGCCCTAGTGATGT 59.374 55.000 0.00 0.00 0.00 3.06
3774 3888 5.338708 CCCTAGTGATGTCAATCTTCAGGTT 60.339 44.000 0.00 0.00 33.61 3.50
3783 4215 4.453819 GTCAATCTTCAGGTTCCTTGAGTG 59.546 45.833 0.00 0.00 0.00 3.51
3976 4411 7.119699 TGAGCGTTCACTTCAGAATATTTTCAT 59.880 33.333 0.00 0.00 34.08 2.57
4000 4436 9.712359 CATCACATAAACAGACAACTGATATTG 57.288 33.333 0.00 0.00 46.03 1.90
4011 4447 7.641411 CAGACAACTGATATTGCCTTAATTTCG 59.359 37.037 0.00 0.00 46.03 3.46
4021 4461 1.133025 CCTTAATTTCGCTGCAGTGGG 59.867 52.381 26.23 13.96 0.00 4.61
4041 4481 2.084546 GCGTCACCTAGGCAAGAATTT 58.915 47.619 9.30 0.00 38.86 1.82
4065 4505 2.007608 GACCAAACTAATCGACCCAGC 58.992 52.381 0.00 0.00 0.00 4.85
4086 4528 5.355350 CAGCCTTTAGTTTCAAGATACTGGG 59.645 44.000 3.83 4.83 0.00 4.45
4103 4545 3.515901 ACTGGGACACTCCTTGATAAGTC 59.484 47.826 0.00 0.00 36.57 3.01
4104 4546 2.838202 TGGGACACTCCTTGATAAGTCC 59.162 50.000 0.00 0.00 43.60 3.85
4105 4547 3.545366 GGACACTCCTTGATAAGTCCC 57.455 52.381 0.00 0.00 39.61 4.46
4106 4548 3.108376 GGACACTCCTTGATAAGTCCCT 58.892 50.000 0.00 0.00 39.61 4.20
4107 4549 3.133183 GGACACTCCTTGATAAGTCCCTC 59.867 52.174 0.00 0.00 39.61 4.30
4108 4550 3.108376 ACACTCCTTGATAAGTCCCTCC 58.892 50.000 0.00 0.00 0.00 4.30
4109 4551 2.101582 CACTCCTTGATAAGTCCCTCCG 59.898 54.545 0.00 0.00 0.00 4.63
4110 4552 2.292323 ACTCCTTGATAAGTCCCTCCGT 60.292 50.000 0.00 0.00 0.00 4.69
4111 4553 2.766828 CTCCTTGATAAGTCCCTCCGTT 59.233 50.000 0.00 0.00 0.00 4.44
4112 4554 3.178865 TCCTTGATAAGTCCCTCCGTTT 58.821 45.455 0.00 0.00 0.00 3.60
4113 4555 3.585732 TCCTTGATAAGTCCCTCCGTTTT 59.414 43.478 0.00 0.00 0.00 2.43
4114 4556 4.042435 TCCTTGATAAGTCCCTCCGTTTTT 59.958 41.667 0.00 0.00 0.00 1.94
4115 4557 5.248934 TCCTTGATAAGTCCCTCCGTTTTTA 59.751 40.000 0.00 0.00 0.00 1.52
4116 4558 6.069847 TCCTTGATAAGTCCCTCCGTTTTTAT 60.070 38.462 0.00 0.00 0.00 1.40
4117 4559 6.602009 CCTTGATAAGTCCCTCCGTTTTTATT 59.398 38.462 0.00 0.00 0.00 1.40
4118 4560 7.122204 CCTTGATAAGTCCCTCCGTTTTTATTT 59.878 37.037 0.00 0.00 0.00 1.40
4119 4561 9.169592 CTTGATAAGTCCCTCCGTTTTTATTTA 57.830 33.333 0.00 0.00 0.00 1.40
4120 4562 8.496707 TGATAAGTCCCTCCGTTTTTATTTAC 57.503 34.615 0.00 0.00 0.00 2.01
4121 4563 8.323567 TGATAAGTCCCTCCGTTTTTATTTACT 58.676 33.333 0.00 0.00 0.00 2.24
4122 4564 8.728337 ATAAGTCCCTCCGTTTTTATTTACTC 57.272 34.615 0.00 0.00 0.00 2.59
4123 4565 5.494724 AGTCCCTCCGTTTTTATTTACTCC 58.505 41.667 0.00 0.00 0.00 3.85
4124 4566 4.330894 GTCCCTCCGTTTTTATTTACTCCG 59.669 45.833 0.00 0.00 0.00 4.63
4125 4567 3.064408 CCCTCCGTTTTTATTTACTCCGC 59.936 47.826 0.00 0.00 0.00 5.54
4126 4568 3.685756 CCTCCGTTTTTATTTACTCCGCA 59.314 43.478 0.00 0.00 0.00 5.69
4127 4569 4.334481 CCTCCGTTTTTATTTACTCCGCAT 59.666 41.667 0.00 0.00 0.00 4.73
4128 4570 5.524646 CCTCCGTTTTTATTTACTCCGCATA 59.475 40.000 0.00 0.00 0.00 3.14
4129 4571 6.204108 CCTCCGTTTTTATTTACTCCGCATAT 59.796 38.462 0.00 0.00 0.00 1.78
4130 4572 7.255001 CCTCCGTTTTTATTTACTCCGCATATT 60.255 37.037 0.00 0.00 0.00 1.28
4131 4573 8.659925 TCCGTTTTTATTTACTCCGCATATTA 57.340 30.769 0.00 0.00 0.00 0.98
4132 4574 8.767085 TCCGTTTTTATTTACTCCGCATATTAG 58.233 33.333 0.00 0.00 0.00 1.73
4133 4575 8.553696 CCGTTTTTATTTACTCCGCATATTAGT 58.446 33.333 0.00 0.00 0.00 2.24
4134 4576 9.925268 CGTTTTTATTTACTCCGCATATTAGTT 57.075 29.630 0.00 0.00 0.00 2.24
4139 4581 7.875327 ATTTACTCCGCATATTAGTTTTGGT 57.125 32.000 0.00 0.00 0.00 3.67
4140 4582 6.913873 TTACTCCGCATATTAGTTTTGGTC 57.086 37.500 0.00 0.00 0.00 4.02
4141 4583 4.839121 ACTCCGCATATTAGTTTTGGTCA 58.161 39.130 0.00 0.00 0.00 4.02
4142 4584 5.250200 ACTCCGCATATTAGTTTTGGTCAA 58.750 37.500 0.00 0.00 0.00 3.18
4143 4585 5.708230 ACTCCGCATATTAGTTTTGGTCAAA 59.292 36.000 0.00 0.00 0.00 2.69
4144 4586 6.128007 ACTCCGCATATTAGTTTTGGTCAAAG 60.128 38.462 0.00 0.00 0.00 2.77
4145 4587 5.708230 TCCGCATATTAGTTTTGGTCAAAGT 59.292 36.000 0.00 0.00 32.41 2.66
4146 4588 6.027749 CCGCATATTAGTTTTGGTCAAAGTC 58.972 40.000 0.00 0.00 30.16 3.01
4147 4589 6.348950 CCGCATATTAGTTTTGGTCAAAGTCA 60.349 38.462 0.00 0.00 30.16 3.41
4148 4590 7.081349 CGCATATTAGTTTTGGTCAAAGTCAA 58.919 34.615 0.00 0.00 30.16 3.18
4149 4591 7.271223 CGCATATTAGTTTTGGTCAAAGTCAAG 59.729 37.037 0.00 0.00 30.16 3.02
4150 4592 7.062255 GCATATTAGTTTTGGTCAAAGTCAAGC 59.938 37.037 0.00 0.00 30.16 4.01
4151 4593 6.715347 ATTAGTTTTGGTCAAAGTCAAGCT 57.285 33.333 0.00 0.00 30.16 3.74
4152 4594 6.524101 TTAGTTTTGGTCAAAGTCAAGCTT 57.476 33.333 0.00 0.00 39.52 3.74
4154 4596 6.524101 AGTTTTGGTCAAAGTCAAGCTTTA 57.476 33.333 0.00 0.00 44.95 1.85
4155 4597 6.330278 AGTTTTGGTCAAAGTCAAGCTTTAC 58.670 36.000 2.40 2.40 44.95 2.01
4156 4598 5.906113 TTTGGTCAAAGTCAAGCTTTACA 57.094 34.783 13.07 0.00 44.95 2.41
4157 4599 5.906113 TTGGTCAAAGTCAAGCTTTACAA 57.094 34.783 13.07 0.00 44.95 2.41
4158 4600 5.906113 TGGTCAAAGTCAAGCTTTACAAA 57.094 34.783 13.07 0.00 44.95 2.83
4159 4601 5.646606 TGGTCAAAGTCAAGCTTTACAAAC 58.353 37.500 13.07 5.27 44.95 2.93
4160 4602 5.417580 TGGTCAAAGTCAAGCTTTACAAACT 59.582 36.000 13.07 2.11 44.95 2.66
4161 4603 6.071616 TGGTCAAAGTCAAGCTTTACAAACTT 60.072 34.615 13.07 7.60 44.95 2.66
4162 4604 6.811665 GGTCAAAGTCAAGCTTTACAAACTTT 59.188 34.615 13.07 12.29 44.95 2.66
4165 4607 7.812309 AAAGTCAAGCTTTACAAACTTTGAC 57.188 32.000 13.07 6.64 44.90 3.18
4166 4608 6.509418 AGTCAAGCTTTACAAACTTTGACA 57.491 33.333 13.07 0.00 30.59 3.58
4167 4609 6.919721 AGTCAAGCTTTACAAACTTTGACAA 58.080 32.000 13.07 0.00 30.59 3.18
4168 4610 7.375053 AGTCAAGCTTTACAAACTTTGACAAA 58.625 30.769 13.07 0.00 30.59 2.83
4169 4611 7.542130 AGTCAAGCTTTACAAACTTTGACAAAG 59.458 33.333 23.41 23.41 44.10 2.77
4226 4668 9.787532 AACAAATCAATACCATTAGATTCGTTG 57.212 29.630 0.00 0.00 29.38 4.10
4227 4669 8.956426 ACAAATCAATACCATTAGATTCGTTGT 58.044 29.630 0.00 0.00 30.87 3.32
4228 4670 9.787532 CAAATCAATACCATTAGATTCGTTGTT 57.212 29.630 0.00 0.00 30.87 2.83
4229 4671 9.787532 AAATCAATACCATTAGATTCGTTGTTG 57.212 29.630 0.00 0.00 30.87 3.33
4230 4672 8.731275 ATCAATACCATTAGATTCGTTGTTGA 57.269 30.769 0.00 0.00 0.00 3.18
4231 4673 8.554835 TCAATACCATTAGATTCGTTGTTGAA 57.445 30.769 0.00 0.00 0.00 2.69
4232 4674 9.173021 TCAATACCATTAGATTCGTTGTTGAAT 57.827 29.630 0.00 0.00 41.16 2.57
4233 4675 9.225201 CAATACCATTAGATTCGTTGTTGAATG 57.775 33.333 0.00 0.00 38.65 2.67
4234 4676 6.817765 ACCATTAGATTCGTTGTTGAATGT 57.182 33.333 0.00 0.00 38.65 2.71
4235 4677 7.915293 ACCATTAGATTCGTTGTTGAATGTA 57.085 32.000 0.00 0.00 38.65 2.29
4236 4678 7.748847 ACCATTAGATTCGTTGTTGAATGTAC 58.251 34.615 0.00 0.00 38.65 2.90
4237 4679 7.606456 ACCATTAGATTCGTTGTTGAATGTACT 59.394 33.333 0.00 0.00 38.65 2.73
4238 4680 8.450964 CCATTAGATTCGTTGTTGAATGTACTT 58.549 33.333 0.00 0.00 38.65 2.24
4239 4681 9.478019 CATTAGATTCGTTGTTGAATGTACTTC 57.522 33.333 0.00 0.00 38.65 3.01
4240 4682 6.481954 AGATTCGTTGTTGAATGTACTTCC 57.518 37.500 0.00 0.00 38.65 3.46
4241 4683 5.995282 AGATTCGTTGTTGAATGTACTTCCA 59.005 36.000 0.00 0.00 38.65 3.53
4242 4684 5.412526 TTCGTTGTTGAATGTACTTCCAC 57.587 39.130 0.00 0.00 32.49 4.02
4243 4685 4.443621 TCGTTGTTGAATGTACTTCCACA 58.556 39.130 0.00 1.71 37.64 4.17
4244 4686 5.060506 TCGTTGTTGAATGTACTTCCACAT 58.939 37.500 10.54 0.00 38.77 3.21
4245 4687 5.178623 TCGTTGTTGAATGTACTTCCACATC 59.821 40.000 10.54 9.49 38.77 3.06
4246 4688 5.049749 CGTTGTTGAATGTACTTCCACATCA 60.050 40.000 10.54 0.00 38.77 3.07
4247 4689 6.348458 CGTTGTTGAATGTACTTCCACATCAT 60.348 38.462 10.54 0.00 38.77 2.45
4248 4690 7.148490 CGTTGTTGAATGTACTTCCACATCATA 60.148 37.037 10.54 0.00 38.77 2.15
4249 4691 8.677300 GTTGTTGAATGTACTTCCACATCATAT 58.323 33.333 10.54 0.00 38.77 1.78
4250 4692 9.898152 TTGTTGAATGTACTTCCACATCATATA 57.102 29.630 10.54 0.00 38.77 0.86
4310 4752 9.744468 ATAAATTTGGTCAAACTGTACAAAGTC 57.256 29.630 0.00 0.00 34.91 3.01
4311 4753 7.404671 AATTTGGTCAAACTGTACAAAGTCT 57.595 32.000 0.00 0.00 34.91 3.24
4312 4754 5.811399 TTGGTCAAACTGTACAAAGTCTG 57.189 39.130 0.00 0.00 0.00 3.51
4313 4755 5.092554 TGGTCAAACTGTACAAAGTCTGA 57.907 39.130 0.00 0.00 0.00 3.27
4314 4756 4.873827 TGGTCAAACTGTACAAAGTCTGAC 59.126 41.667 11.43 11.43 44.14 3.51
4315 4757 5.116882 GGTCAAACTGTACAAAGTCTGACT 58.883 41.667 16.73 4.06 44.25 3.41
4316 4758 5.585047 GGTCAAACTGTACAAAGTCTGACTT 59.415 40.000 17.00 17.00 44.25 3.01
4317 4759 6.238130 GGTCAAACTGTACAAAGTCTGACTTC 60.238 42.308 22.24 11.07 44.25 3.01
4318 4760 6.312918 GTCAAACTGTACAAAGTCTGACTTCA 59.687 38.462 22.24 14.70 42.42 3.02
4319 4761 6.535150 TCAAACTGTACAAAGTCTGACTTCAG 59.465 38.462 24.17 24.17 37.47 3.02
4320 4762 5.599999 ACTGTACAAAGTCTGACTTCAGT 57.400 39.130 25.09 25.09 44.12 3.41
4321 4763 5.593010 ACTGTACAAAGTCTGACTTCAGTC 58.407 41.667 25.09 18.39 44.12 3.51
4335 4777 6.503616 GACTTCAGTCAACTCTAATATGCG 57.496 41.667 1.86 0.00 44.18 4.73
4336 4778 5.352284 ACTTCAGTCAACTCTAATATGCGG 58.648 41.667 0.00 0.00 0.00 5.69
4337 4779 5.127194 ACTTCAGTCAACTCTAATATGCGGA 59.873 40.000 0.00 0.00 0.00 5.54
4338 4780 5.188327 TCAGTCAACTCTAATATGCGGAG 57.812 43.478 0.00 0.00 0.00 4.63
4339 4781 4.645136 TCAGTCAACTCTAATATGCGGAGT 59.355 41.667 0.00 0.00 41.37 3.85
4340 4782 5.826208 TCAGTCAACTCTAATATGCGGAGTA 59.174 40.000 6.10 0.00 39.09 2.59
4341 4783 6.320418 TCAGTCAACTCTAATATGCGGAGTAA 59.680 38.462 6.10 0.00 39.09 2.24
4342 4784 6.638873 CAGTCAACTCTAATATGCGGAGTAAG 59.361 42.308 6.10 3.88 39.09 2.34
4343 4785 6.321690 AGTCAACTCTAATATGCGGAGTAAGT 59.678 38.462 6.10 0.00 39.09 2.24
4344 4786 7.501559 AGTCAACTCTAATATGCGGAGTAAGTA 59.498 37.037 6.10 0.00 39.09 2.24
4345 4787 8.133627 GTCAACTCTAATATGCGGAGTAAGTAA 58.866 37.037 6.10 0.00 39.09 2.24
4346 4788 8.689061 TCAACTCTAATATGCGGAGTAAGTAAA 58.311 33.333 6.10 0.00 39.09 2.01
4347 4789 9.309516 CAACTCTAATATGCGGAGTAAGTAAAA 57.690 33.333 6.10 0.00 39.09 1.52
4348 4790 9.880157 AACTCTAATATGCGGAGTAAGTAAAAA 57.120 29.630 6.10 0.00 39.09 1.94
4349 4791 9.310716 ACTCTAATATGCGGAGTAAGTAAAAAC 57.689 33.333 0.00 0.00 38.37 2.43
4350 4792 8.343974 TCTAATATGCGGAGTAAGTAAAAACG 57.656 34.615 0.00 0.00 0.00 3.60
4351 4793 5.978934 ATATGCGGAGTAAGTAAAAACGG 57.021 39.130 0.00 0.00 0.00 4.44
4352 4794 3.383620 TGCGGAGTAAGTAAAAACGGA 57.616 42.857 0.00 0.00 0.00 4.69
4353 4795 3.319755 TGCGGAGTAAGTAAAAACGGAG 58.680 45.455 0.00 0.00 0.00 4.63
4354 4796 2.669924 GCGGAGTAAGTAAAAACGGAGG 59.330 50.000 0.00 0.00 0.00 4.30
4355 4797 3.256558 CGGAGTAAGTAAAAACGGAGGG 58.743 50.000 0.00 0.00 0.00 4.30
4356 4798 3.306294 CGGAGTAAGTAAAAACGGAGGGT 60.306 47.826 0.00 0.00 0.00 4.34
4357 4799 4.082245 CGGAGTAAGTAAAAACGGAGGGTA 60.082 45.833 0.00 0.00 0.00 3.69
4358 4800 5.171476 GGAGTAAGTAAAAACGGAGGGTAC 58.829 45.833 0.00 0.00 0.00 3.34
4359 4801 5.047021 GGAGTAAGTAAAAACGGAGGGTACT 60.047 44.000 0.00 0.00 0.00 2.73
4360 4802 5.787380 AGTAAGTAAAAACGGAGGGTACTG 58.213 41.667 0.00 0.00 0.00 2.74
4361 4803 3.049708 AGTAAAAACGGAGGGTACTGC 57.950 47.619 0.00 0.00 0.00 4.40
4362 4804 2.079158 GTAAAAACGGAGGGTACTGCC 58.921 52.381 0.00 0.00 0.00 4.85
4363 4805 0.769247 AAAAACGGAGGGTACTGCCT 59.231 50.000 0.00 0.00 37.43 4.75
4364 4806 0.323957 AAAACGGAGGGTACTGCCTC 59.676 55.000 9.14 9.14 37.43 4.70
4365 4807 1.551019 AAACGGAGGGTACTGCCTCC 61.551 60.000 21.51 21.51 46.51 4.30
4367 4809 2.363925 GGAGGGTACTGCCTCCGT 60.364 66.667 18.24 0.00 42.35 4.69
4368 4810 1.988406 GGAGGGTACTGCCTCCGTT 60.988 63.158 18.24 0.00 42.35 4.44
4369 4811 1.516423 GAGGGTACTGCCTCCGTTC 59.484 63.158 6.87 0.00 37.43 3.95
4370 4812 1.229082 AGGGTACTGCCTCCGTTCA 60.229 57.895 0.00 0.00 37.43 3.18
4371 4813 0.617820 AGGGTACTGCCTCCGTTCAT 60.618 55.000 0.00 0.00 37.43 2.57
4372 4814 0.462047 GGGTACTGCCTCCGTTCATG 60.462 60.000 0.00 0.00 37.43 3.07
4373 4815 0.535335 GGTACTGCCTCCGTTCATGA 59.465 55.000 0.00 0.00 0.00 3.07
4374 4816 1.066430 GGTACTGCCTCCGTTCATGAA 60.066 52.381 3.38 3.38 0.00 2.57
4375 4817 2.420129 GGTACTGCCTCCGTTCATGAAT 60.420 50.000 12.12 0.00 0.00 2.57
4376 4818 3.181469 GGTACTGCCTCCGTTCATGAATA 60.181 47.826 12.12 0.00 0.00 1.75
4377 4819 3.845781 ACTGCCTCCGTTCATGAATAT 57.154 42.857 12.12 0.00 0.00 1.28
4378 4820 4.955811 ACTGCCTCCGTTCATGAATATA 57.044 40.909 12.12 0.00 0.00 0.86
4379 4821 5.290493 ACTGCCTCCGTTCATGAATATAA 57.710 39.130 12.12 0.00 0.00 0.98
4380 4822 5.300752 ACTGCCTCCGTTCATGAATATAAG 58.699 41.667 12.12 7.18 0.00 1.73
4381 4823 5.070446 ACTGCCTCCGTTCATGAATATAAGA 59.930 40.000 12.12 3.89 0.00 2.10
4382 4824 6.114187 TGCCTCCGTTCATGAATATAAGAT 57.886 37.500 12.12 0.00 0.00 2.40
4383 4825 5.934043 TGCCTCCGTTCATGAATATAAGATG 59.066 40.000 12.12 3.41 0.00 2.90
4384 4826 5.934625 GCCTCCGTTCATGAATATAAGATGT 59.065 40.000 12.12 0.00 0.00 3.06
4385 4827 6.428159 GCCTCCGTTCATGAATATAAGATGTT 59.572 38.462 12.12 0.00 0.00 2.71
4386 4828 7.041098 GCCTCCGTTCATGAATATAAGATGTTT 60.041 37.037 12.12 0.00 0.00 2.83
4387 4829 8.840321 CCTCCGTTCATGAATATAAGATGTTTT 58.160 33.333 12.12 0.00 0.00 2.43
4388 4830 9.655769 CTCCGTTCATGAATATAAGATGTTTTG 57.344 33.333 12.12 0.00 0.00 2.44
4389 4831 8.620416 TCCGTTCATGAATATAAGATGTTTTGG 58.380 33.333 12.12 0.00 0.00 3.28
4390 4832 8.620416 CCGTTCATGAATATAAGATGTTTTGGA 58.380 33.333 12.12 0.00 0.00 3.53
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
265 296 4.692625 ACTGTTCCTCGAAGTCATCATTTG 59.307 41.667 0.00 0.00 0.00 2.32
285 316 2.351157 GCTGAGCAAAGCTTACCAACTG 60.351 50.000 0.00 0.00 39.88 3.16
305 336 1.897560 AGGTTTGACTGGCTTGTAGC 58.102 50.000 0.00 0.00 41.46 3.58
307 338 3.395639 CGTTAGGTTTGACTGGCTTGTA 58.604 45.455 0.00 0.00 0.00 2.41
308 339 2.218603 CGTTAGGTTTGACTGGCTTGT 58.781 47.619 0.00 0.00 0.00 3.16
376 407 8.931385 AATTAAGCAATTTTGGCTGTATACTG 57.069 30.769 4.17 4.85 41.66 2.74
432 463 8.956426 TCTTTCTCAGACAAACAACAATACTTT 58.044 29.630 0.00 0.00 0.00 2.66
484 519 6.483974 ACTCCTATGTCTACAACTCTACATCG 59.516 42.308 0.00 0.00 34.54 3.84
487 522 7.859540 AGTACTCCTATGTCTACAACTCTACA 58.140 38.462 0.00 0.00 0.00 2.74
499 534 8.402472 GCATGTGAGATATAGTACTCCTATGTC 58.598 40.741 0.00 7.07 41.92 3.06
504 539 7.673504 AGAATGCATGTGAGATATAGTACTCCT 59.326 37.037 0.00 0.00 32.84 3.69
505 540 7.835822 AGAATGCATGTGAGATATAGTACTCC 58.164 38.462 0.00 0.00 32.84 3.85
506 541 9.781834 GTAGAATGCATGTGAGATATAGTACTC 57.218 37.037 0.00 0.00 0.00 2.59
507 542 9.301897 TGTAGAATGCATGTGAGATATAGTACT 57.698 33.333 0.00 0.00 0.00 2.73
508 543 9.914131 TTGTAGAATGCATGTGAGATATAGTAC 57.086 33.333 0.00 0.00 0.00 2.73
510 545 9.265901 GTTTGTAGAATGCATGTGAGATATAGT 57.734 33.333 0.00 0.00 0.00 2.12
511 546 9.264719 TGTTTGTAGAATGCATGTGAGATATAG 57.735 33.333 0.00 0.00 0.00 1.31
512 547 9.783081 ATGTTTGTAGAATGCATGTGAGATATA 57.217 29.630 0.00 0.00 0.00 0.86
513 548 8.565416 CATGTTTGTAGAATGCATGTGAGATAT 58.435 33.333 0.00 0.00 34.10 1.63
514 549 7.012610 CCATGTTTGTAGAATGCATGTGAGATA 59.987 37.037 0.00 0.00 36.23 1.98
515 550 6.183360 CCATGTTTGTAGAATGCATGTGAGAT 60.183 38.462 0.00 0.00 36.23 2.75
516 551 5.124297 CCATGTTTGTAGAATGCATGTGAGA 59.876 40.000 0.00 0.00 36.23 3.27
517 552 5.337554 CCATGTTTGTAGAATGCATGTGAG 58.662 41.667 0.00 0.68 36.23 3.51
518 553 4.380761 GCCATGTTTGTAGAATGCATGTGA 60.381 41.667 0.00 0.00 36.23 3.58
519 554 3.861113 GCCATGTTTGTAGAATGCATGTG 59.139 43.478 0.00 8.23 36.23 3.21
520 555 3.765511 AGCCATGTTTGTAGAATGCATGT 59.234 39.130 0.00 0.00 36.23 3.21
521 556 4.380841 AGCCATGTTTGTAGAATGCATG 57.619 40.909 0.00 9.35 37.32 4.06
522 557 6.528537 TTTAGCCATGTTTGTAGAATGCAT 57.471 33.333 0.00 0.00 0.00 3.96
523 558 5.973899 TTTAGCCATGTTTGTAGAATGCA 57.026 34.783 0.00 0.00 0.00 3.96
552 587 3.118261 TCTTGGTCAAGCTGAAACAGTCT 60.118 43.478 5.88 0.00 38.28 3.24
564 599 5.046591 TCTGGGTGTTATACTCTTGGTCAAG 60.047 44.000 4.44 4.44 39.71 3.02
568 603 3.518303 GGTCTGGGTGTTATACTCTTGGT 59.482 47.826 0.00 0.00 0.00 3.67
569 604 3.517901 TGGTCTGGGTGTTATACTCTTGG 59.482 47.826 0.00 0.00 0.00 3.61
622 659 7.538575 TCTGCTTCAGGTTTAATTTAGCAATC 58.461 34.615 0.00 0.00 36.80 2.67
625 662 6.886459 AGATCTGCTTCAGGTTTAATTTAGCA 59.114 34.615 0.00 0.00 35.97 3.49
644 681 3.308053 CAGTATGCGGTGTTGAAGATCTG 59.692 47.826 0.00 0.00 0.00 2.90
676 714 5.615925 ACTATTTTCCTTGATAGCGGAGT 57.384 39.130 0.00 0.00 30.65 3.85
743 781 1.136984 CACTCCGCCTCACGTCTAC 59.863 63.158 0.00 0.00 41.42 2.59
767 809 2.106418 GTTGGCAGTTTCGTCGAAAAC 58.894 47.619 21.29 14.97 39.03 2.43
787 829 1.065199 TGAGGAACTGCAGCTATTGGG 60.065 52.381 15.27 0.00 41.55 4.12
795 837 5.163713 GGCTTAATTTACTGAGGAACTGCAG 60.164 44.000 13.48 13.48 41.55 4.41
808 852 8.443953 AGATGTGAGATTCAGGCTTAATTTAC 57.556 34.615 0.00 0.00 0.00 2.01
840 884 4.503741 ACCAATGGAGTGAAAAATGTCG 57.496 40.909 6.16 0.00 0.00 4.35
844 888 4.388485 GCCAAACCAATGGAGTGAAAAAT 58.612 39.130 6.16 0.00 43.54 1.82
853 897 0.757188 ACAACCGCCAAACCAATGGA 60.757 50.000 6.16 0.00 43.54 3.41
884 928 6.190954 AGAAATAATTTAGCGTGGTGAACC 57.809 37.500 0.00 0.00 0.00 3.62
897 941 3.795877 CCGCCATGGCAAGAAATAATTT 58.204 40.909 34.93 0.00 42.06 1.82
944 988 0.391228 TTGCAGAGACCGCAACTGTA 59.609 50.000 0.00 0.00 44.13 2.74
972 1018 4.825679 GGGAGAGGGGGAGGGGTG 62.826 77.778 0.00 0.00 0.00 4.61
980 1026 1.685820 GTGAACCAAGGGAGAGGGG 59.314 63.158 0.00 0.00 0.00 4.79
1084 1130 3.998672 GACGAGTGGTTGGGCGGA 61.999 66.667 0.00 0.00 0.00 5.54
1123 1169 1.453155 AGAGCGTACCTGCCATTTTG 58.547 50.000 0.00 0.00 34.65 2.44
1167 1213 0.037590 TGCCCATGTACCAGTTGGAC 59.962 55.000 4.92 0.00 38.94 4.02
1287 1351 0.321564 TCAGGATGACAAGGTTGCCG 60.322 55.000 0.00 0.00 42.56 5.69
1879 1949 1.271597 GGAAGGTCCACAGACTGCATT 60.272 52.381 1.25 0.00 43.05 3.56
1905 1975 0.096976 GTAGCGCGTTGTCATTGCAT 59.903 50.000 8.43 0.00 0.00 3.96
1923 1993 4.164221 CCCTTCATACAGTTACAGGATGGT 59.836 45.833 0.13 0.00 43.62 3.55
1962 2032 1.076677 TCTAGTTCCCAGTCCTTCGGT 59.923 52.381 0.00 0.00 0.00 4.69
2080 2156 2.855660 TGATCATCATTTTGCGGCAG 57.144 45.000 1.67 0.00 0.00 4.85
2085 2161 4.684703 GGCTTGCTATGATCATCATTTTGC 59.315 41.667 12.53 8.92 38.26 3.68
2120 2196 1.417517 TCTGTGCACACTCACCAGAAT 59.582 47.619 17.42 0.00 36.17 2.40
2292 2368 1.089920 CCTGCTGACTGGGAAATTCG 58.910 55.000 0.00 0.00 0.00 3.34
2710 2789 1.725641 TGCTCATAGACAAGCAACCG 58.274 50.000 0.00 0.00 45.09 4.44
2792 2886 0.252197 GAGGGCGATTTGGTACCTGT 59.748 55.000 14.36 0.00 0.00 4.00
2812 2906 1.488393 GGCCAATCCTCTAGCAACTCT 59.512 52.381 0.00 0.00 0.00 3.24
2871 2965 4.216257 AGGATGTTTTCTGGTTTGATGTCG 59.784 41.667 0.00 0.00 0.00 4.35
3072 3166 3.664624 TCCTCCCAGATATGATCTCCAGA 59.335 47.826 0.00 0.00 37.58 3.86
3317 3427 0.958091 CTCAGACAGCCCCTCGATAG 59.042 60.000 0.00 0.00 0.00 2.08
3319 3429 0.105760 ATCTCAGACAGCCCCTCGAT 60.106 55.000 0.00 0.00 0.00 3.59
3438 3548 8.910944 ACAATTTCATGGATTCCAGAATAGAAG 58.089 33.333 11.78 0.85 36.75 2.85
3469 3583 4.678287 GCAACTTCATTTCTGACACATGTG 59.322 41.667 24.25 24.25 0.00 3.21
3521 3635 4.417506 TCACACAAACGGTCTATCATACG 58.582 43.478 0.00 0.00 0.00 3.06
3633 3747 6.134535 TGGATTAAAGTTTCCCTAAGCTCA 57.865 37.500 0.00 0.00 0.00 4.26
3761 3875 4.103153 ACACTCAAGGAACCTGAAGATTGA 59.897 41.667 8.93 1.54 0.00 2.57
3774 3888 5.055265 TGTGGGAAAAATACACTCAAGGA 57.945 39.130 0.00 0.00 36.16 3.36
3783 4215 8.288913 CACCAAATTTGAATGTGGGAAAAATAC 58.711 33.333 19.86 0.00 46.25 1.89
3976 4411 7.148255 GGCAATATCAGTTGTCTGTTTATGTGA 60.148 37.037 0.00 0.00 41.91 3.58
4000 4436 1.468054 CCACTGCAGCGAAATTAAGGC 60.468 52.381 15.27 0.00 0.00 4.35
4021 4461 1.739067 AATTCTTGCCTAGGTGACGC 58.261 50.000 11.31 0.00 0.00 5.19
4041 4481 4.462133 TGGGTCGATTAGTTTGGTCAAAA 58.538 39.130 0.00 0.00 31.33 2.44
4065 4505 6.371825 GTGTCCCAGTATCTTGAAACTAAAGG 59.628 42.308 0.00 0.00 0.00 3.11
4086 4528 3.133183 GGAGGGACTTATCAAGGAGTGTC 59.867 52.174 0.00 0.00 41.55 3.67
4103 4545 3.064408 GCGGAGTAAATAAAAACGGAGGG 59.936 47.826 0.00 0.00 0.00 4.30
4104 4546 3.685756 TGCGGAGTAAATAAAAACGGAGG 59.314 43.478 0.00 0.00 0.00 4.30
4105 4547 4.932268 TGCGGAGTAAATAAAAACGGAG 57.068 40.909 0.00 0.00 0.00 4.63
4106 4548 7.556733 AATATGCGGAGTAAATAAAAACGGA 57.443 32.000 0.00 0.00 0.00 4.69
4107 4549 8.553696 ACTAATATGCGGAGTAAATAAAAACGG 58.446 33.333 0.00 0.00 0.00 4.44
4108 4550 9.925268 AACTAATATGCGGAGTAAATAAAAACG 57.075 29.630 0.00 0.00 0.00 3.60
4113 4555 9.398538 ACCAAAACTAATATGCGGAGTAAATAA 57.601 29.630 0.00 0.00 0.00 1.40
4114 4556 8.967664 ACCAAAACTAATATGCGGAGTAAATA 57.032 30.769 0.00 0.00 0.00 1.40
4115 4557 7.554835 TGACCAAAACTAATATGCGGAGTAAAT 59.445 33.333 0.00 0.00 0.00 1.40
4116 4558 6.879993 TGACCAAAACTAATATGCGGAGTAAA 59.120 34.615 0.00 0.00 0.00 2.01
4117 4559 6.408035 TGACCAAAACTAATATGCGGAGTAA 58.592 36.000 0.00 0.00 0.00 2.24
4118 4560 5.979993 TGACCAAAACTAATATGCGGAGTA 58.020 37.500 0.00 0.00 0.00 2.59
4119 4561 4.839121 TGACCAAAACTAATATGCGGAGT 58.161 39.130 0.00 0.00 0.00 3.85
4120 4562 5.811399 TTGACCAAAACTAATATGCGGAG 57.189 39.130 0.00 0.00 0.00 4.63
4121 4563 5.708230 ACTTTGACCAAAACTAATATGCGGA 59.292 36.000 0.00 0.00 0.00 5.54
4122 4564 5.949735 ACTTTGACCAAAACTAATATGCGG 58.050 37.500 0.00 0.00 0.00 5.69
4123 4565 6.607689 TGACTTTGACCAAAACTAATATGCG 58.392 36.000 0.00 0.00 0.00 4.73
4124 4566 7.062255 GCTTGACTTTGACCAAAACTAATATGC 59.938 37.037 0.00 0.00 0.00 3.14
4125 4567 8.299570 AGCTTGACTTTGACCAAAACTAATATG 58.700 33.333 0.00 0.00 0.00 1.78
4126 4568 8.409358 AGCTTGACTTTGACCAAAACTAATAT 57.591 30.769 0.00 0.00 0.00 1.28
4127 4569 7.817418 AGCTTGACTTTGACCAAAACTAATA 57.183 32.000 0.00 0.00 0.00 0.98
4128 4570 6.715347 AGCTTGACTTTGACCAAAACTAAT 57.285 33.333 0.00 0.00 0.00 1.73
4129 4571 6.524101 AAGCTTGACTTTGACCAAAACTAA 57.476 33.333 0.00 0.00 33.71 2.24
4130 4572 6.524101 AAAGCTTGACTTTGACCAAAACTA 57.476 33.333 0.00 0.00 47.00 2.24
4131 4573 5.405935 AAAGCTTGACTTTGACCAAAACT 57.594 34.783 0.00 0.00 47.00 2.66
4135 4577 7.524698 AAGTTTGTAAAGCTTGACTTTGACCAA 60.525 33.333 15.19 0.00 45.94 3.67
4136 4578 6.071616 AAGTTTGTAAAGCTTGACTTTGACCA 60.072 34.615 15.19 0.00 45.94 4.02
4137 4579 6.330278 AAGTTTGTAAAGCTTGACTTTGACC 58.670 36.000 15.19 0.00 45.94 4.02
4200 4642 9.787532 CAACGAATCTAATGGTATTGATTTGTT 57.212 29.630 11.95 11.95 46.17 2.83
4201 4643 8.956426 ACAACGAATCTAATGGTATTGATTTGT 58.044 29.630 0.00 0.00 42.17 2.83
4202 4644 9.787532 AACAACGAATCTAATGGTATTGATTTG 57.212 29.630 0.00 0.00 36.74 2.32
4203 4645 9.787532 CAACAACGAATCTAATGGTATTGATTT 57.212 29.630 0.00 0.00 30.41 2.17
4204 4646 9.173021 TCAACAACGAATCTAATGGTATTGATT 57.827 29.630 0.00 0.00 32.59 2.57
4205 4647 8.731275 TCAACAACGAATCTAATGGTATTGAT 57.269 30.769 0.00 0.00 0.00 2.57
4206 4648 8.554835 TTCAACAACGAATCTAATGGTATTGA 57.445 30.769 0.00 0.00 0.00 2.57
4207 4649 9.225201 CATTCAACAACGAATCTAATGGTATTG 57.775 33.333 0.00 0.00 33.27 1.90
4208 4650 8.956426 ACATTCAACAACGAATCTAATGGTATT 58.044 29.630 0.00 0.00 33.27 1.89
4209 4651 8.506168 ACATTCAACAACGAATCTAATGGTAT 57.494 30.769 0.00 0.00 33.27 2.73
4210 4652 7.915293 ACATTCAACAACGAATCTAATGGTA 57.085 32.000 0.00 0.00 33.27 3.25
4211 4653 6.817765 ACATTCAACAACGAATCTAATGGT 57.182 33.333 0.00 0.00 33.27 3.55
4212 4654 7.974675 AGTACATTCAACAACGAATCTAATGG 58.025 34.615 0.00 0.00 33.27 3.16
4213 4655 9.478019 GAAGTACATTCAACAACGAATCTAATG 57.522 33.333 0.00 0.00 37.88 1.90
4214 4656 8.665685 GGAAGTACATTCAACAACGAATCTAAT 58.334 33.333 0.00 0.00 39.91 1.73
4215 4657 7.658167 TGGAAGTACATTCAACAACGAATCTAA 59.342 33.333 0.00 0.00 39.91 2.10
4216 4658 7.117236 GTGGAAGTACATTCAACAACGAATCTA 59.883 37.037 0.00 0.00 41.01 1.98
4217 4659 5.995282 TGGAAGTACATTCAACAACGAATCT 59.005 36.000 0.00 0.00 39.91 2.40
4218 4660 6.077838 GTGGAAGTACATTCAACAACGAATC 58.922 40.000 0.00 0.00 41.01 2.52
4219 4661 5.529430 TGTGGAAGTACATTCAACAACGAAT 59.471 36.000 10.88 0.00 46.75 3.34
4220 4662 4.876679 TGTGGAAGTACATTCAACAACGAA 59.123 37.500 10.88 0.00 46.75 3.85
4221 4663 4.443621 TGTGGAAGTACATTCAACAACGA 58.556 39.130 10.88 0.00 46.75 3.85
4222 4664 4.804608 TGTGGAAGTACATTCAACAACG 57.195 40.909 10.88 0.00 46.75 4.10
4284 4726 9.744468 GACTTTGTACAGTTTGACCAAATTTAT 57.256 29.630 0.00 0.00 32.36 1.40
4285 4727 8.962679 AGACTTTGTACAGTTTGACCAAATTTA 58.037 29.630 0.00 0.00 32.36 1.40
4286 4728 7.759433 CAGACTTTGTACAGTTTGACCAAATTT 59.241 33.333 0.00 0.00 31.83 1.82
4287 4729 7.122055 TCAGACTTTGTACAGTTTGACCAAATT 59.878 33.333 4.85 0.00 33.97 1.82
4288 4730 6.601613 TCAGACTTTGTACAGTTTGACCAAAT 59.398 34.615 4.85 0.00 33.97 2.32
4289 4731 5.941058 TCAGACTTTGTACAGTTTGACCAAA 59.059 36.000 4.85 0.00 33.97 3.28
4290 4732 5.353123 GTCAGACTTTGTACAGTTTGACCAA 59.647 40.000 19.94 1.22 46.23 3.67
4291 4733 4.873827 GTCAGACTTTGTACAGTTTGACCA 59.126 41.667 19.94 0.00 46.23 4.02
4292 4734 5.405331 GTCAGACTTTGTACAGTTTGACC 57.595 43.478 19.94 8.81 46.23 4.02
4294 4736 6.403049 TGAAGTCAGACTTTGTACAGTTTGA 58.597 36.000 17.19 4.85 38.80 2.69
4295 4737 6.313905 ACTGAAGTCAGACTTTGTACAGTTTG 59.686 38.462 21.55 7.12 46.59 2.93
4296 4738 6.407202 ACTGAAGTCAGACTTTGTACAGTTT 58.593 36.000 21.55 7.77 46.59 2.66
4297 4739 5.978814 ACTGAAGTCAGACTTTGTACAGTT 58.021 37.500 21.55 11.43 46.59 3.16
4298 4740 5.593010 GACTGAAGTCAGACTTTGTACAGT 58.407 41.667 24.99 24.99 46.59 3.55
4312 4754 5.460419 CCGCATATTAGAGTTGACTGAAGTC 59.540 44.000 3.41 3.41 44.97 3.01
4313 4755 5.127194 TCCGCATATTAGAGTTGACTGAAGT 59.873 40.000 0.00 0.00 0.00 3.01
4314 4756 5.592054 TCCGCATATTAGAGTTGACTGAAG 58.408 41.667 0.00 0.00 0.00 3.02
4315 4757 5.127194 ACTCCGCATATTAGAGTTGACTGAA 59.873 40.000 0.00 0.00 37.60 3.02
4316 4758 4.645136 ACTCCGCATATTAGAGTTGACTGA 59.355 41.667 0.00 0.00 37.60 3.41
4317 4759 4.938080 ACTCCGCATATTAGAGTTGACTG 58.062 43.478 0.00 0.00 37.60 3.51
4318 4760 6.321690 ACTTACTCCGCATATTAGAGTTGACT 59.678 38.462 4.78 0.00 41.09 3.41
4319 4761 6.505272 ACTTACTCCGCATATTAGAGTTGAC 58.495 40.000 4.78 0.00 41.09 3.18
4320 4762 6.710597 ACTTACTCCGCATATTAGAGTTGA 57.289 37.500 4.78 0.00 41.09 3.18
4321 4763 8.867112 TTTACTTACTCCGCATATTAGAGTTG 57.133 34.615 4.78 2.76 41.09 3.16
4322 4764 9.880157 TTTTTACTTACTCCGCATATTAGAGTT 57.120 29.630 4.78 0.00 41.09 3.01
4323 4765 9.310716 GTTTTTACTTACTCCGCATATTAGAGT 57.689 33.333 0.00 0.00 43.17 3.24
4324 4766 8.477709 CGTTTTTACTTACTCCGCATATTAGAG 58.522 37.037 0.00 0.00 0.00 2.43
4325 4767 7.436080 CCGTTTTTACTTACTCCGCATATTAGA 59.564 37.037 0.00 0.00 0.00 2.10
4326 4768 7.436080 TCCGTTTTTACTTACTCCGCATATTAG 59.564 37.037 0.00 0.00 0.00 1.73
4327 4769 7.264221 TCCGTTTTTACTTACTCCGCATATTA 58.736 34.615 0.00 0.00 0.00 0.98
4328 4770 6.108015 TCCGTTTTTACTTACTCCGCATATT 58.892 36.000 0.00 0.00 0.00 1.28
4329 4771 5.663456 TCCGTTTTTACTTACTCCGCATAT 58.337 37.500 0.00 0.00 0.00 1.78
4330 4772 5.070770 TCCGTTTTTACTTACTCCGCATA 57.929 39.130 0.00 0.00 0.00 3.14
4331 4773 3.929094 TCCGTTTTTACTTACTCCGCAT 58.071 40.909 0.00 0.00 0.00 4.73
4332 4774 3.319755 CTCCGTTTTTACTTACTCCGCA 58.680 45.455 0.00 0.00 0.00 5.69
4333 4775 2.669924 CCTCCGTTTTTACTTACTCCGC 59.330 50.000 0.00 0.00 0.00 5.54
4334 4776 3.256558 CCCTCCGTTTTTACTTACTCCG 58.743 50.000 0.00 0.00 0.00 4.63
4335 4777 4.277515 ACCCTCCGTTTTTACTTACTCC 57.722 45.455 0.00 0.00 0.00 3.85
4336 4778 5.866092 CAGTACCCTCCGTTTTTACTTACTC 59.134 44.000 0.00 0.00 0.00 2.59
4337 4779 5.787380 CAGTACCCTCCGTTTTTACTTACT 58.213 41.667 0.00 0.00 0.00 2.24
4338 4780 4.389992 GCAGTACCCTCCGTTTTTACTTAC 59.610 45.833 0.00 0.00 0.00 2.34
4339 4781 4.563374 GGCAGTACCCTCCGTTTTTACTTA 60.563 45.833 0.00 0.00 0.00 2.24
4340 4782 3.405831 GCAGTACCCTCCGTTTTTACTT 58.594 45.455 0.00 0.00 0.00 2.24
4341 4783 2.289882 GGCAGTACCCTCCGTTTTTACT 60.290 50.000 0.00 0.00 0.00 2.24
4342 4784 2.079158 GGCAGTACCCTCCGTTTTTAC 58.921 52.381 0.00 0.00 0.00 2.01
4343 4785 1.980036 AGGCAGTACCCTCCGTTTTTA 59.020 47.619 0.00 0.00 40.58 1.52
4344 4786 0.769247 AGGCAGTACCCTCCGTTTTT 59.231 50.000 0.00 0.00 40.58 1.94
4345 4787 0.323957 GAGGCAGTACCCTCCGTTTT 59.676 55.000 6.87 0.00 44.60 2.43
4346 4788 1.980844 GAGGCAGTACCCTCCGTTT 59.019 57.895 6.87 0.00 44.60 3.60
4347 4789 3.709567 GAGGCAGTACCCTCCGTT 58.290 61.111 6.87 0.00 44.60 4.44
4352 4794 0.617820 ATGAACGGAGGCAGTACCCT 60.618 55.000 0.00 0.00 40.58 4.34
4353 4795 0.462047 CATGAACGGAGGCAGTACCC 60.462 60.000 0.00 0.00 40.58 3.69
4354 4796 0.535335 TCATGAACGGAGGCAGTACC 59.465 55.000 0.00 0.00 39.61 3.34
4355 4797 2.380084 TTCATGAACGGAGGCAGTAC 57.620 50.000 3.38 0.00 0.00 2.73
4356 4798 4.955811 ATATTCATGAACGGAGGCAGTA 57.044 40.909 11.07 0.00 0.00 2.74
4357 4799 3.845781 ATATTCATGAACGGAGGCAGT 57.154 42.857 11.07 0.00 0.00 4.40
4358 4800 5.541845 TCTTATATTCATGAACGGAGGCAG 58.458 41.667 11.07 1.31 0.00 4.85
4359 4801 5.545063 TCTTATATTCATGAACGGAGGCA 57.455 39.130 11.07 0.00 0.00 4.75
4360 4802 5.934625 ACATCTTATATTCATGAACGGAGGC 59.065 40.000 11.07 0.00 0.00 4.70
4361 4803 7.969536 AACATCTTATATTCATGAACGGAGG 57.030 36.000 11.07 8.74 0.00 4.30
4362 4804 9.655769 CAAAACATCTTATATTCATGAACGGAG 57.344 33.333 11.07 6.92 0.00 4.63
4363 4805 8.620416 CCAAAACATCTTATATTCATGAACGGA 58.380 33.333 11.07 5.34 0.00 4.69
4364 4806 8.620416 TCCAAAACATCTTATATTCATGAACGG 58.380 33.333 11.07 0.00 0.00 4.44


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

AutoCloner maintained by Alex Coulton.