Multiple sequence alignment - TraesCS3D01G432000

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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 TraesCS3D01G432000 chr3D 100.000 6432 0 0 1 6432 545919941 545913510 0.000000e+00 11878.0
1 TraesCS3D01G432000 chr3A 92.708 2962 171 17 2693 5622 682329109 682326161 0.000000e+00 4231.0
2 TraesCS3D01G432000 chr3A 91.681 1719 80 33 750 2430 682330798 682329105 0.000000e+00 2324.0
3 TraesCS3D01G432000 chr3A 93.228 694 40 5 5691 6380 682326146 682325456 0.000000e+00 1014.0
4 TraesCS3D01G432000 chr3A 86.200 529 40 15 3 500 682331909 682331383 5.670000e-150 542.0
5 TraesCS3D01G432000 chr3A 94.585 277 10 5 2421 2693 663295655 663295380 2.140000e-114 424.0
6 TraesCS3D01G432000 chr3B 91.884 2797 180 29 2847 5611 722361908 722359127 0.000000e+00 3864.0
7 TraesCS3D01G432000 chr3B 93.836 1087 43 15 761 1831 722363712 722362634 0.000000e+00 1615.0
8 TraesCS3D01G432000 chr3B 91.768 741 35 10 5696 6432 722359122 722358404 0.000000e+00 1007.0
9 TraesCS3D01G432000 chr3B 85.600 750 73 10 1 729 722364776 722364041 0.000000e+00 754.0
10 TraesCS3D01G432000 chr3B 93.814 388 18 3 1841 2226 722362564 722362181 4.320000e-161 579.0
11 TraesCS3D01G432000 chr2A 96.947 262 7 1 2432 2692 706216076 706216337 7.660000e-119 438.0
12 TraesCS3D01G432000 chr6D 96.591 264 8 1 2430 2692 446719260 446719523 2.750000e-118 436.0
13 TraesCS3D01G432000 chr4D 96.591 264 8 1 2431 2693 349005055 349005318 2.750000e-118 436.0
14 TraesCS3D01G432000 chr4D 96.212 264 9 1 2430 2692 349006848 349007111 1.280000e-116 431.0
15 TraesCS3D01G432000 chr7A 96.226 265 9 1 2430 2693 726480039 726479775 3.560000e-117 433.0
16 TraesCS3D01G432000 chr7A 90.698 43 3 1 2128 2170 230592679 230592720 1.000000e-03 56.5
17 TraesCS3D01G432000 chr5A 96.212 264 9 1 2430 2692 643338040 643338303 1.280000e-116 431.0
18 TraesCS3D01G432000 chr2D 96.212 264 8 2 2431 2693 88291341 88291603 1.280000e-116 431.0
19 TraesCS3D01G432000 chr2D 96.212 264 9 1 2430 2692 559299613 559299350 1.280000e-116 431.0
20 TraesCS3D01G432000 chr5B 84.066 182 17 3 3814 3995 493088471 493088302 1.430000e-36 165.0
21 TraesCS3D01G432000 chr7D 87.629 97 11 1 3277 3373 126612822 126612917 1.900000e-20 111.0
22 TraesCS3D01G432000 chr7B 90.698 43 3 1 2128 2170 182149257 182149216 1.000000e-03 56.5


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

query scaffold start end length rev.comp avg.bitscore max.bitscore avg.percent.identical query.start query.end num_hsp groupid homo_length
0 TraesCS3D01G432000 chr3D 545913510 545919941 6431 True 11878.00 11878 100.00000 1 6432 1 chr3D.!!$R1 6431
1 TraesCS3D01G432000 chr3A 682325456 682331909 6453 True 2027.75 4231 90.95425 3 6380 4 chr3A.!!$R2 6377
2 TraesCS3D01G432000 chr3B 722358404 722364776 6372 True 1563.80 3864 91.38040 1 6432 5 chr3B.!!$R1 6431
3 TraesCS3D01G432000 chr4D 349005055 349007111 2056 False 433.50 436 96.40150 2430 2693 2 chr4D.!!$F1 263

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
336 356 0.179051 TAAAACTGAACCGCCACCGT 60.179 50.000 0.00 0.0 0.00 4.83 F
1473 2196 0.600255 CTGTCCCGCGTTCTTGAACT 60.600 55.000 4.92 0.0 0.00 3.01 F
1674 2400 0.391528 GAGCCGGGCCGTTAAACTAA 60.392 55.000 26.32 0.0 0.00 2.24 F
2401 3201 0.165295 GCTTGTTAACTCGGGTTCGC 59.835 55.000 2.54 0.0 36.92 4.70 F
3054 4694 1.144708 TCTTGGACCACTGCAAATGGA 59.855 47.619 20.84 0.0 39.87 3.41 F
4011 5664 1.370064 CCCGGACGAACAGAGGTTT 59.630 57.895 0.73 0.0 37.36 3.27 F
4765 6426 1.478105 AGAAAATTGAGGGCGAATGGC 59.522 47.619 0.00 0.0 42.51 4.40 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1675 2401 0.165944 GGGATTTGTTCGTGTCTGCG 59.834 55.0 0.00 0.0 0.00 5.18 R
2382 3182 0.165295 GCGAACCCGAGTTAACAAGC 59.835 55.0 8.61 0.0 35.94 4.01 R
2500 3300 2.367567 CCCTAAGCAAGCGACCCTTATA 59.632 50.0 0.00 0.0 31.00 0.98 R
3912 5565 0.033504 CCAACGCTGTAGTGAGTGGT 59.966 55.0 0.00 0.0 33.10 4.16 R
4851 6512 0.321346 CTTTGGGTTTCCATGTGGCC 59.679 55.0 0.00 0.0 43.63 5.36 R
5254 6915 0.321671 CCTTCTTCGGGCTGTTCAGA 59.678 55.0 3.84 0.0 0.00 3.27 R
6398 8091 0.248377 GTCTCATTCAGGCGCATTGC 60.248 55.0 10.83 0.0 45.38 3.56 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
48 49 1.338674 ACCGATGAATTTGCCTCGACA 60.339 47.619 0.00 0.00 33.07 4.35
114 116 2.802719 TCTTTGGTCCCCATTAGTTGC 58.197 47.619 0.00 0.00 31.53 4.17
130 132 1.810151 GTTGCCACATTATGTCACCGT 59.190 47.619 0.00 0.00 0.00 4.83
154 158 7.519809 CGTGGTTGTCATTTTAAGAGTGAATGA 60.520 37.037 0.00 0.00 37.43 2.57
161 165 8.394121 GTCATTTTAAGAGTGAATGATCTCCAC 58.606 37.037 3.50 0.00 40.63 4.02
175 179 8.768957 AATGATCTCCACGAAGATTATGTATG 57.231 34.615 0.00 0.00 36.13 2.39
247 251 7.523873 GCAAAGTTAGAAGGGCTGTTTAGATTT 60.524 37.037 0.00 0.00 0.00 2.17
258 262 2.100197 GTTTAGATTTGGCCTCCACCC 58.900 52.381 3.32 0.00 30.78 4.61
322 342 2.413634 CGCCGAGGAATTGGTGTAAAAC 60.414 50.000 0.00 0.00 0.00 2.43
336 356 0.179051 TAAAACTGAACCGCCACCGT 60.179 50.000 0.00 0.00 0.00 4.83
342 362 4.752879 AACCGCCACCGTGGATCG 62.753 66.667 22.37 15.32 42.83 3.69
351 371 2.565645 CCGTGGATCGAGCCTAGGG 61.566 68.421 22.18 17.12 42.86 3.53
359 379 0.691078 TCGAGCCTAGGGAAGCCAAT 60.691 55.000 11.72 0.00 0.00 3.16
361 381 1.408822 CGAGCCTAGGGAAGCCAATTT 60.409 52.381 11.72 0.00 0.00 1.82
362 382 2.739943 GAGCCTAGGGAAGCCAATTTT 58.260 47.619 11.72 0.00 0.00 1.82
408 428 0.657077 CACACCACACAATCAACGCG 60.657 55.000 3.53 3.53 0.00 6.01
411 431 1.018148 ACCACACAATCAACGCGAAA 58.982 45.000 15.93 0.00 0.00 3.46
465 495 9.880157 ATCCAAATATATCCAAAATGCATAAGC 57.120 29.630 0.00 0.00 42.57 3.09
485 515 6.713792 AAGCGTTAACAACAACAAAATTGT 57.286 29.167 6.39 0.00 44.72 2.71
486 516 7.813852 AAGCGTTAACAACAACAAAATTGTA 57.186 28.000 6.39 0.00 41.31 2.41
487 517 7.212032 AGCGTTAACAACAACAAAATTGTAC 57.788 32.000 6.39 0.00 41.31 2.90
488 518 6.807230 AGCGTTAACAACAACAAAATTGTACA 59.193 30.769 6.39 0.00 41.31 2.90
490 520 8.111224 GCGTTAACAACAACAAAATTGTACAAT 58.889 29.630 15.47 15.47 41.31 2.71
534 902 4.826274 ATAGGAGAGTTACAAGCAGCAA 57.174 40.909 0.00 0.00 0.00 3.91
574 942 0.780637 TTTGGGGGCATCCTGTAACA 59.219 50.000 0.00 0.00 35.33 2.41
612 980 1.135170 GTACCCAACTAGGCACGAGTC 60.135 57.143 0.00 0.00 45.31 3.36
619 987 4.330074 CCAACTAGGCACGAGTCATTTTAG 59.670 45.833 0.00 0.00 45.31 1.85
625 993 4.578928 AGGCACGAGTCATTTTAGTTTTGT 59.421 37.500 0.00 0.00 0.00 2.83
646 1028 5.723295 TGTATTTGTACTCCCTCCGTAAAC 58.277 41.667 0.00 0.00 0.00 2.01
648 1030 3.947910 TTGTACTCCCTCCGTAAACAG 57.052 47.619 0.00 0.00 0.00 3.16
650 1032 3.087031 TGTACTCCCTCCGTAAACAGAG 58.913 50.000 0.00 0.00 0.00 3.35
655 1037 1.558233 CCTCCGTAAACAGAGGGAGT 58.442 55.000 4.69 0.00 45.95 3.85
657 1039 2.426381 CCTCCGTAAACAGAGGGAGTAC 59.574 54.545 4.69 0.00 45.95 2.73
658 1040 3.354467 CTCCGTAAACAGAGGGAGTACT 58.646 50.000 0.00 0.00 43.54 2.73
659 1041 3.762823 CTCCGTAAACAGAGGGAGTACTT 59.237 47.826 0.00 0.00 43.54 2.24
660 1042 3.508793 TCCGTAAACAGAGGGAGTACTTG 59.491 47.826 0.00 0.00 0.00 3.16
661 1043 3.251571 CGTAAACAGAGGGAGTACTTGC 58.748 50.000 0.00 0.00 0.00 4.01
662 1044 2.861147 AAACAGAGGGAGTACTTGCC 57.139 50.000 0.00 0.00 37.61 4.52
675 1061 6.324254 GGGAGTACTTGCCTTCTAGAATCTTA 59.676 42.308 5.44 0.00 33.76 2.10
696 1082 7.546358 TCTTAAATACAACCCAGAATGCATTG 58.454 34.615 18.59 3.70 36.05 2.82
697 1083 5.743636 AAATACAACCCAGAATGCATTGT 57.256 34.783 18.59 10.58 42.70 2.71
740 1129 9.838339 CTTCATGGTAAATAATACTCCAACTCT 57.162 33.333 0.00 0.00 0.00 3.24
755 1144 8.930846 ACTCCAACTCTAGTAGTACTACAAAA 57.069 34.615 29.87 16.28 37.50 2.44
756 1145 9.531158 ACTCCAACTCTAGTAGTACTACAAAAT 57.469 33.333 29.87 14.97 37.50 1.82
797 1493 2.429250 CAAAACGGGGTCAAAAAGTCCT 59.571 45.455 0.00 0.00 0.00 3.85
871 1569 3.615509 GACCGGTCGCCCATTTCCA 62.616 63.158 20.85 0.00 0.00 3.53
944 1642 2.260088 CTCCCGTCGTCTCCTCCTCT 62.260 65.000 0.00 0.00 0.00 3.69
945 1643 2.115911 CCCGTCGTCTCCTCCTCTG 61.116 68.421 0.00 0.00 0.00 3.35
1330 2049 3.353836 CGGCCGTCTTTGGTGGTG 61.354 66.667 19.50 0.00 0.00 4.17
1362 2081 1.082690 GCTTGGCCTTTTCTCTCTCG 58.917 55.000 3.32 0.00 0.00 4.04
1393 2112 2.962827 CTGCAGCAGCGAGTGGTTG 61.963 63.158 10.14 0.00 46.23 3.77
1431 2151 2.220824 GTGGTTTTGCTTCGATTTTGGC 59.779 45.455 0.00 0.00 0.00 4.52
1447 2167 1.076533 TGGCTCGCGATTTCGTTCTC 61.077 55.000 10.36 0.00 42.22 2.87
1471 2194 1.959226 GCTGTCCCGCGTTCTTGAA 60.959 57.895 4.92 0.00 0.00 2.69
1473 2196 0.600255 CTGTCCCGCGTTCTTGAACT 60.600 55.000 4.92 0.00 0.00 3.01
1497 2221 4.811557 AGTAAAATCAGATAGCTTGCCGTC 59.188 41.667 0.00 0.00 0.00 4.79
1498 2222 3.550437 AAATCAGATAGCTTGCCGTCT 57.450 42.857 0.00 0.00 0.00 4.18
1576 2302 4.800914 GCTGCAGAGAAGTAAGGAACAAGA 60.801 45.833 20.43 0.00 0.00 3.02
1672 2398 2.046604 GAGCCGGGCCGTTAAACT 60.047 61.111 26.32 13.47 0.00 2.66
1674 2400 0.391528 GAGCCGGGCCGTTAAACTAA 60.392 55.000 26.32 0.00 0.00 2.24
1675 2401 0.674581 AGCCGGGCCGTTAAACTAAC 60.675 55.000 26.32 2.29 35.37 2.34
1706 2432 1.625818 ACAAATCCCGAGCTCTGTTCT 59.374 47.619 12.85 0.00 0.00 3.01
1952 2740 1.164041 ACAGCAACGTGTACAAGGCC 61.164 55.000 13.47 0.00 0.00 5.19
2096 2884 0.895530 ACAATGTCGTCCGACTCCAT 59.104 50.000 19.30 3.76 44.80 3.41
2283 3072 4.386049 GTGTCACTCACCTTCTTGAATACG 59.614 45.833 0.00 0.00 40.84 3.06
2288 3077 4.755123 ACTCACCTTCTTGAATACGTTTGG 59.245 41.667 0.00 0.00 0.00 3.28
2307 3096 0.932399 GCCATGAATTGAAATGCGCC 59.068 50.000 4.18 0.00 0.00 6.53
2319 3114 1.737838 AATGCGCCTTCGAGAATTCA 58.262 45.000 4.18 0.00 38.10 2.57
2320 3115 1.737838 ATGCGCCTTCGAGAATTCAA 58.262 45.000 4.18 0.00 38.10 2.69
2322 3117 2.899976 TGCGCCTTCGAGAATTCAATA 58.100 42.857 4.18 0.00 38.10 1.90
2326 3121 4.260784 GCGCCTTCGAGAATTCAATATGTT 60.261 41.667 8.44 0.00 38.10 2.71
2336 3131 9.793252 CGAGAATTCAATATGTTCCTGAAAAAT 57.207 29.630 8.44 0.00 33.08 1.82
2401 3201 0.165295 GCTTGTTAACTCGGGTTCGC 59.835 55.000 2.54 0.00 36.92 4.70
2425 3225 6.580791 GCGAAAAACTGCTTGTTCATAATGTA 59.419 34.615 0.00 0.00 38.03 2.29
2426 3226 7.409343 GCGAAAAACTGCTTGTTCATAATGTAC 60.409 37.037 0.00 0.00 38.03 2.90
2427 3227 7.201149 CGAAAAACTGCTTGTTCATAATGTACG 60.201 37.037 0.00 0.00 38.03 3.67
2428 3228 6.554334 AAACTGCTTGTTCATAATGTACGT 57.446 33.333 0.00 0.00 38.03 3.57
2429 3229 5.530519 ACTGCTTGTTCATAATGTACGTG 57.469 39.130 0.00 0.00 0.00 4.49
2430 3230 4.994852 ACTGCTTGTTCATAATGTACGTGT 59.005 37.500 0.00 0.00 0.00 4.49
2431 3231 5.107104 ACTGCTTGTTCATAATGTACGTGTG 60.107 40.000 0.00 0.00 0.00 3.82
2432 3232 4.752604 TGCTTGTTCATAATGTACGTGTGT 59.247 37.500 0.00 0.00 0.00 3.72
2433 3233 5.237561 TGCTTGTTCATAATGTACGTGTGTT 59.762 36.000 0.00 0.00 0.00 3.32
2434 3234 6.424207 TGCTTGTTCATAATGTACGTGTGTTA 59.576 34.615 0.00 0.00 0.00 2.41
2435 3235 6.953743 GCTTGTTCATAATGTACGTGTGTTAG 59.046 38.462 0.00 0.00 0.00 2.34
2436 3236 7.148705 GCTTGTTCATAATGTACGTGTGTTAGA 60.149 37.037 0.00 0.00 0.00 2.10
2437 3237 7.806149 TGTTCATAATGTACGTGTGTTAGAG 57.194 36.000 0.00 0.00 0.00 2.43
2438 3238 7.372714 TGTTCATAATGTACGTGTGTTAGAGT 58.627 34.615 0.00 0.00 0.00 3.24
2439 3239 8.513774 TGTTCATAATGTACGTGTGTTAGAGTA 58.486 33.333 0.00 0.00 0.00 2.59
2440 3240 9.512435 GTTCATAATGTACGTGTGTTAGAGTAT 57.488 33.333 0.00 0.00 0.00 2.12
2500 3300 7.472522 GCCCGTTAGTCTTAGGGTTAATTAGAT 60.473 40.741 1.07 0.00 45.48 1.98
2769 3693 8.462016 AGCTTAATGGACTATTGCACTTTTAAG 58.538 33.333 0.00 0.00 0.00 1.85
2776 3700 9.738832 TGGACTATTGCACTTTTAAGTAAAAAC 57.261 29.630 0.00 0.00 37.08 2.43
2794 3718 6.751514 AAAAACGATCTGGTACATATGCAA 57.248 33.333 1.58 0.00 38.20 4.08
2819 3774 2.025155 TGAACTAAACCTTTTGGCGCA 58.975 42.857 10.83 0.00 45.59 6.09
3054 4694 1.144708 TCTTGGACCACTGCAAATGGA 59.855 47.619 20.84 0.00 39.87 3.41
3218 4864 7.909121 ACAGTAATTTCGAAGTATACTCAGTCG 59.091 37.037 16.03 16.03 0.00 4.18
3264 4911 6.317857 CGAATGGAACCAAATTTCTCTTCTC 58.682 40.000 0.00 0.00 0.00 2.87
3399 5046 3.594603 ATCTGTTGGACTACCGAAGTG 57.405 47.619 0.00 0.00 39.07 3.16
3411 5061 7.093201 TGGACTACCGAAGTGGAGTATTTTTAT 60.093 37.037 0.00 0.00 42.00 1.40
3434 5084 2.425668 AGGTTTGAACTTTGAACACGGG 59.574 45.455 0.00 0.00 0.00 5.28
3435 5085 2.190161 GTTTGAACTTTGAACACGGGC 58.810 47.619 0.00 0.00 0.00 6.13
3477 5127 3.316308 ACAGACACTCCAATGTTTTCTGC 59.684 43.478 0.00 0.00 33.80 4.26
3600 5253 1.416030 TCTTTTCCCAAAAGCAAGGCC 59.584 47.619 0.00 0.00 45.79 5.19
3605 5258 1.491274 CCCAAAAGCAAGGCCCCAAT 61.491 55.000 0.00 0.00 0.00 3.16
3714 5367 5.352569 GTGAAGTGCTACATGAAACAGCTAT 59.647 40.000 0.00 0.00 36.26 2.97
3719 5372 4.329801 TGCTACATGAAACAGCTATTGTCG 59.670 41.667 0.00 0.00 39.73 4.35
3800 5453 1.541310 TTGTCAGCGAGGACGGGATT 61.541 55.000 0.00 0.00 40.72 3.01
3812 5465 3.579151 AGGACGGGATTCTTAAGATAGCC 59.421 47.826 5.89 9.32 0.00 3.93
3911 5564 1.940613 CCGCCTGAACTAATGTTAGGC 59.059 52.381 0.00 0.00 42.59 3.93
3912 5565 2.627945 CGCCTGAACTAATGTTAGGCA 58.372 47.619 13.29 2.23 44.15 4.75
4011 5664 1.370064 CCCGGACGAACAGAGGTTT 59.630 57.895 0.73 0.00 37.36 3.27
4028 5685 3.949754 AGGTTTGTCCATACGATACGAGA 59.050 43.478 0.00 0.00 39.02 4.04
4037 5694 4.964555 CCATACGATACGAGATTCGCATAG 59.035 45.833 0.00 0.00 45.12 2.23
4059 5716 5.237048 AGTTATTTGCGGAAAATTGCACAT 58.763 33.333 6.08 0.00 41.57 3.21
4318 5975 6.720288 ACAGTGAGGTTAATACTACTGTCACT 59.280 38.462 0.00 0.00 43.57 3.41
4356 6014 6.981559 ACTTTGAACAGTAGAAAGTCAGTCTC 59.018 38.462 4.63 0.00 35.48 3.36
4360 6018 5.203060 ACAGTAGAAAGTCAGTCTCAACC 57.797 43.478 0.00 0.00 0.00 3.77
4393 6053 5.703592 TGCTAAATTCAACCGAAAGCTAGAA 59.296 36.000 0.00 0.00 34.80 2.10
4427 6087 7.758980 CAGAGTAGCCACTATGCAATAAGATAG 59.241 40.741 0.00 0.00 37.20 2.08
4432 6092 8.608844 AGCCACTATGCAATAAGATAGTTTAC 57.391 34.615 0.00 0.00 33.90 2.01
4453 6113 4.299155 ACGATTGATCACGATACATGGAC 58.701 43.478 12.18 0.00 0.00 4.02
4462 6123 5.647589 TCACGATACATGGACTAAACTGAC 58.352 41.667 0.00 0.00 0.00 3.51
4544 6205 3.641436 TCTTCTCCTCACAAGTGCTTACA 59.359 43.478 0.00 0.00 0.00 2.41
4681 6342 2.050144 AGGTCCTGCTCAACTCTTTCA 58.950 47.619 0.00 0.00 0.00 2.69
4728 6389 3.565482 GTCACAAGAAGCTTCAACATCCA 59.435 43.478 27.57 3.09 0.00 3.41
4765 6426 1.478105 AGAAAATTGAGGGCGAATGGC 59.522 47.619 0.00 0.00 42.51 4.40
4777 6438 1.736032 GCGAATGGCTCAGTAGAACGT 60.736 52.381 0.00 0.00 39.11 3.99
4785 6446 2.981140 GCTCAGTAGAACGTCAGACAAC 59.019 50.000 0.41 0.00 0.00 3.32
4786 6447 3.550233 GCTCAGTAGAACGTCAGACAACA 60.550 47.826 0.41 0.00 0.00 3.33
4917 6578 5.342433 TGCAAGAATTTTGTCTCAACTGTG 58.658 37.500 0.00 0.00 0.00 3.66
4918 6579 5.125257 TGCAAGAATTTTGTCTCAACTGTGA 59.875 36.000 0.00 0.00 0.00 3.58
4919 6580 6.035843 GCAAGAATTTTGTCTCAACTGTGAA 58.964 36.000 0.00 0.00 31.88 3.18
4925 6586 6.507958 TTTTGTCTCAACTGTGAAATGTGA 57.492 33.333 0.00 0.00 31.88 3.58
4927 6588 5.484173 TGTCTCAACTGTGAAATGTGAAC 57.516 39.130 0.00 0.00 31.88 3.18
4928 6589 5.185454 TGTCTCAACTGTGAAATGTGAACT 58.815 37.500 0.00 0.00 31.88 3.01
4929 6590 5.065090 TGTCTCAACTGTGAAATGTGAACTG 59.935 40.000 0.00 0.00 31.88 3.16
4932 6593 6.992123 TCTCAACTGTGAAATGTGAACTGTAT 59.008 34.615 0.00 0.00 31.88 2.29
4933 6594 6.958255 TCAACTGTGAAATGTGAACTGTATG 58.042 36.000 0.00 0.00 0.00 2.39
4935 6596 7.445096 TCAACTGTGAAATGTGAACTGTATGAT 59.555 33.333 0.00 0.00 0.00 2.45
4936 6597 8.720562 CAACTGTGAAATGTGAACTGTATGATA 58.279 33.333 0.00 0.00 0.00 2.15
4937 6598 8.256611 ACTGTGAAATGTGAACTGTATGATAC 57.743 34.615 0.00 0.00 0.00 2.24
4938 6599 7.334421 ACTGTGAAATGTGAACTGTATGATACC 59.666 37.037 0.00 0.00 0.00 2.73
4940 6601 6.533723 GTGAAATGTGAACTGTATGATACCGA 59.466 38.462 0.00 0.00 0.00 4.69
4941 6602 7.064134 GTGAAATGTGAACTGTATGATACCGAA 59.936 37.037 0.00 0.00 0.00 4.30
4942 6603 7.604545 TGAAATGTGAACTGTATGATACCGAAA 59.395 33.333 0.00 0.00 0.00 3.46
4943 6604 8.506168 AAATGTGAACTGTATGATACCGAAAT 57.494 30.769 0.00 0.00 0.00 2.17
4948 6609 6.982141 TGAACTGTATGATACCGAAATACCAC 59.018 38.462 0.00 0.00 0.00 4.16
4949 6610 6.726490 ACTGTATGATACCGAAATACCACT 57.274 37.500 0.00 0.00 0.00 4.00
4982 6643 7.493320 TCACGTTTAATTGTACTTCTTGTGTCT 59.507 33.333 0.00 0.00 0.00 3.41
5209 6870 3.260632 TCTTCTCATCATCGGTTGTGGAA 59.739 43.478 0.00 0.00 0.00 3.53
5254 6915 9.314321 CTACTATTTGGTCACGTGAAATCTTAT 57.686 33.333 21.95 11.38 0.00 1.73
5408 7069 2.624838 CAGCTCAGAGCCAAAGGAAAAA 59.375 45.455 19.40 0.00 43.77 1.94
5410 7071 3.899980 AGCTCAGAGCCAAAGGAAAAATT 59.100 39.130 19.40 0.00 43.77 1.82
5524 7212 8.847196 AGTAGCTGTTCATCTTAATACACGATA 58.153 33.333 0.00 0.00 0.00 2.92
5611 7299 7.619965 TGTACATATGAGATTTCACCAGTGAA 58.380 34.615 10.38 9.12 46.72 3.18
5630 7318 5.241403 TGAAACGGATTCAGGCCATATAT 57.759 39.130 5.01 0.00 43.08 0.86
5631 7319 5.003160 TGAAACGGATTCAGGCCATATATG 58.997 41.667 5.01 5.68 43.08 1.78
5632 7320 2.991250 ACGGATTCAGGCCATATATGC 58.009 47.619 5.01 3.21 0.00 3.14
5633 7321 2.305635 ACGGATTCAGGCCATATATGCA 59.694 45.455 5.01 0.00 0.00 3.96
5634 7322 3.244875 ACGGATTCAGGCCATATATGCAA 60.245 43.478 5.01 0.00 0.00 4.08
5636 7324 4.400251 CGGATTCAGGCCATATATGCAAAT 59.600 41.667 5.01 2.42 0.00 2.32
5637 7325 5.105635 CGGATTCAGGCCATATATGCAAATT 60.106 40.000 5.01 0.00 0.00 1.82
5638 7326 6.103997 GGATTCAGGCCATATATGCAAATTG 58.896 40.000 5.01 1.79 0.00 2.32
5639 7327 6.295462 GGATTCAGGCCATATATGCAAATTGT 60.295 38.462 5.01 0.00 0.00 2.71
5640 7328 5.456548 TCAGGCCATATATGCAAATTGTG 57.543 39.130 5.01 0.00 0.00 3.33
5641 7329 4.894705 TCAGGCCATATATGCAAATTGTGT 59.105 37.500 5.01 0.00 0.00 3.72
5642 7330 6.067350 TCAGGCCATATATGCAAATTGTGTA 58.933 36.000 5.01 0.00 0.00 2.90
5643 7331 6.207221 TCAGGCCATATATGCAAATTGTGTAG 59.793 38.462 5.01 0.00 0.00 2.74
5644 7332 5.477984 AGGCCATATATGCAAATTGTGTAGG 59.522 40.000 5.01 0.00 0.00 3.18
5645 7333 5.243730 GGCCATATATGCAAATTGTGTAGGT 59.756 40.000 7.24 0.00 0.00 3.08
5646 7334 6.151691 GCCATATATGCAAATTGTGTAGGTG 58.848 40.000 7.24 0.00 0.00 4.00
5647 7335 6.016360 GCCATATATGCAAATTGTGTAGGTGA 60.016 38.462 7.24 0.00 0.00 4.02
5648 7336 7.362662 CCATATATGCAAATTGTGTAGGTGAC 58.637 38.462 7.24 0.00 0.00 3.67
5650 7338 8.623903 CATATATGCAAATTGTGTAGGTGACTT 58.376 33.333 0.00 0.00 43.67 3.01
5651 7339 4.829064 TGCAAATTGTGTAGGTGACTTC 57.171 40.909 0.00 0.00 43.67 3.01
5652 7340 4.460263 TGCAAATTGTGTAGGTGACTTCT 58.540 39.130 0.00 0.00 43.67 2.85
5653 7341 4.515191 TGCAAATTGTGTAGGTGACTTCTC 59.485 41.667 0.00 0.00 43.67 2.87
5654 7342 4.515191 GCAAATTGTGTAGGTGACTTCTCA 59.485 41.667 0.00 0.00 43.67 3.27
5655 7343 5.560953 GCAAATTGTGTAGGTGACTTCTCAC 60.561 44.000 0.00 0.00 45.54 3.51
5683 7371 9.866655 ATATATGCAAATTAGAGGAAAAGGTGA 57.133 29.630 0.00 0.00 0.00 4.02
5684 7372 6.916360 ATGCAAATTAGAGGAAAAGGTGAA 57.084 33.333 0.00 0.00 0.00 3.18
5685 7373 6.723298 TGCAAATTAGAGGAAAAGGTGAAA 57.277 33.333 0.00 0.00 0.00 2.69
5686 7374 7.118496 TGCAAATTAGAGGAAAAGGTGAAAA 57.882 32.000 0.00 0.00 0.00 2.29
5687 7375 7.560368 TGCAAATTAGAGGAAAAGGTGAAAAA 58.440 30.769 0.00 0.00 0.00 1.94
5688 7376 8.210265 TGCAAATTAGAGGAAAAGGTGAAAAAT 58.790 29.630 0.00 0.00 0.00 1.82
5689 7377 8.498358 GCAAATTAGAGGAAAAGGTGAAAAATG 58.502 33.333 0.00 0.00 0.00 2.32
5694 7382 5.660864 AGAGGAAAAGGTGAAAAATGGACAA 59.339 36.000 0.00 0.00 0.00 3.18
5769 7458 7.226325 CCCTCTAGCATTCAAGAACAGATAAAG 59.774 40.741 0.00 0.00 0.00 1.85
5809 7499 3.451141 TGCATGAACAGTTTCCAAACC 57.549 42.857 0.00 0.00 39.71 3.27
5877 7567 3.904136 AATGAACAAAAGGAGCACTCG 57.096 42.857 0.00 0.00 0.00 4.18
6008 7698 6.567050 ACTGAATCATCCACATTTTACATGC 58.433 36.000 0.00 0.00 0.00 4.06
6109 7799 2.281970 GGACGGCGGGGAGTTTTT 60.282 61.111 13.24 0.00 0.00 1.94
6140 7833 2.328319 GATGAGGAGGAGGAGCTGAAT 58.672 52.381 0.00 0.00 0.00 2.57
6158 7851 3.817084 TGAATTTCTCTTGCTGTGACAGG 59.183 43.478 15.24 0.00 31.21 4.00
6171 7864 2.232696 TGTGACAGGCGATAAAGCTGTA 59.767 45.455 0.00 0.00 37.29 2.74
6214 7907 2.190488 CTCTGACCTTCAGCCACCCC 62.190 65.000 0.00 0.00 43.95 4.95
6346 8039 3.599343 CATTGTGGAGGATCGTTCTTCA 58.401 45.455 7.77 0.00 34.37 3.02
6374 8067 1.040646 AGAGTCGTGTCTGCAAGGAA 58.959 50.000 0.00 0.00 0.00 3.36
6377 8070 3.449018 AGAGTCGTGTCTGCAAGGAATAT 59.551 43.478 0.00 0.00 0.00 1.28
6380 8073 2.499693 TCGTGTCTGCAAGGAATATGGA 59.500 45.455 0.00 0.00 0.00 3.41
6381 8074 2.609459 CGTGTCTGCAAGGAATATGGAC 59.391 50.000 0.00 0.00 0.00 4.02
6382 8075 2.609459 GTGTCTGCAAGGAATATGGACG 59.391 50.000 0.00 0.00 0.00 4.79
6383 8076 2.499693 TGTCTGCAAGGAATATGGACGA 59.500 45.455 0.00 0.00 0.00 4.20
6398 8091 1.126846 GGACGATTCAAAGTGTCAGCG 59.873 52.381 0.00 0.00 33.04 5.18
6399 8092 0.512952 ACGATTCAAAGTGTCAGCGC 59.487 50.000 0.00 0.00 0.00 5.92
6415 8108 4.704007 GCAATGCGCCTGAATGAG 57.296 55.556 4.18 0.00 32.94 2.90
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
16 17 1.470051 TCATCGGTGAAGACGGATCA 58.530 50.000 0.00 0.00 39.46 2.92
130 132 7.815840 TCATTCACTCTTAAAATGACAACCA 57.184 32.000 0.00 0.00 35.17 3.67
154 158 6.672266 ACCATACATAATCTTCGTGGAGAT 57.328 37.500 0.00 0.00 37.99 2.75
161 165 4.214119 CCTGGCAACCATACATAATCTTCG 59.786 45.833 0.00 0.00 30.82 3.79
322 342 3.605749 ATCCACGGTGGCGGTTCAG 62.606 63.158 22.42 0.00 37.47 3.02
336 356 1.115930 GCTTCCCTAGGCTCGATCCA 61.116 60.000 8.23 0.00 0.00 3.41
408 428 3.260632 ACACCTGCCCAACCAAATATTTC 59.739 43.478 0.00 0.00 0.00 2.17
411 431 2.566724 CAACACCTGCCCAACCAAATAT 59.433 45.455 0.00 0.00 0.00 1.28
439 469 9.880157 GCTTATGCATTTTGGATATATTTGGAT 57.120 29.630 3.54 0.00 39.41 3.41
517 885 2.494059 TGGTTGCTGCTTGTAACTCTC 58.506 47.619 0.00 0.00 40.41 3.20
528 896 1.271656 AGCAGATCTTTTGGTTGCTGC 59.728 47.619 0.00 0.00 46.58 5.25
534 902 3.370840 TGCCATAGCAGATCTTTTGGT 57.629 42.857 0.00 0.00 46.52 3.67
574 942 4.020485 GGGTACATGTCACTCCTACTTGTT 60.020 45.833 0.00 0.00 36.79 2.83
619 987 4.999311 ACGGAGGGAGTACAAATACAAAAC 59.001 41.667 0.00 0.00 33.30 2.43
625 993 5.716228 TCTGTTTACGGAGGGAGTACAAATA 59.284 40.000 0.00 0.00 0.00 1.40
646 1028 2.183679 AGAAGGCAAGTACTCCCTCTG 58.816 52.381 13.68 1.81 0.00 3.35
648 1030 3.633418 TCTAGAAGGCAAGTACTCCCTC 58.367 50.000 13.68 3.81 0.00 4.30
650 1032 4.651962 AGATTCTAGAAGGCAAGTACTCCC 59.348 45.833 11.53 0.00 0.00 4.30
651 1033 5.862678 AGATTCTAGAAGGCAAGTACTCC 57.137 43.478 11.53 0.00 0.00 3.85
652 1034 9.825109 ATTTAAGATTCTAGAAGGCAAGTACTC 57.175 33.333 11.53 0.32 0.00 2.59
658 1040 9.174166 GGTTGTATTTAAGATTCTAGAAGGCAA 57.826 33.333 11.53 0.00 0.00 4.52
659 1041 7.773690 GGGTTGTATTTAAGATTCTAGAAGGCA 59.226 37.037 11.53 0.00 0.00 4.75
660 1042 7.773690 TGGGTTGTATTTAAGATTCTAGAAGGC 59.226 37.037 11.53 5.73 0.00 4.35
661 1043 9.331282 CTGGGTTGTATTTAAGATTCTAGAAGG 57.669 37.037 11.53 0.00 0.00 3.46
675 1061 5.481473 AGACAATGCATTCTGGGTTGTATTT 59.519 36.000 9.53 0.00 33.55 1.40
730 1119 8.930846 TTTTGTAGTACTACTAGAGTTGGAGT 57.069 34.615 28.56 0.00 39.81 3.85
765 1154 4.283978 TGACCCCGTTTTGTTCATACTCTA 59.716 41.667 0.00 0.00 0.00 2.43
797 1493 0.320073 CGTTCGGCAGTTTGGACCTA 60.320 55.000 0.00 0.00 0.00 3.08
871 1569 1.384643 CGGGAGGGAAGGGAAGGAT 60.385 63.158 0.00 0.00 0.00 3.24
945 1643 4.742201 TTGGTCGCGAGCAGAGGC 62.742 66.667 35.64 11.49 40.18 4.70
1330 2049 1.006220 CCAAGCTTTTCCGGCAACC 60.006 57.895 0.00 0.00 0.00 3.77
1378 2097 3.052082 CCCAACCACTCGCTGCTG 61.052 66.667 0.00 0.00 0.00 4.41
1431 2151 2.288969 GGGAGAACGAAATCGCGAG 58.711 57.895 16.66 2.71 44.43 5.03
1471 2194 5.986135 CGGCAAGCTATCTGATTTTACTAGT 59.014 40.000 0.00 0.00 0.00 2.57
1473 2196 5.914033 ACGGCAAGCTATCTGATTTTACTA 58.086 37.500 0.00 0.00 0.00 1.82
1559 2285 6.334102 TCTCACTCTTGTTCCTTACTTCTC 57.666 41.667 0.00 0.00 0.00 2.87
1596 2322 3.394940 AGAGGGCATCATCAATGATCACT 59.605 43.478 0.00 5.07 45.23 3.41
1672 2398 2.477375 GGATTTGTTCGTGTCTGCGTTA 59.523 45.455 0.00 0.00 0.00 3.18
1674 2400 0.865769 GGATTTGTTCGTGTCTGCGT 59.134 50.000 0.00 0.00 0.00 5.24
1675 2401 0.165944 GGGATTTGTTCGTGTCTGCG 59.834 55.000 0.00 0.00 0.00 5.18
1706 2432 3.758554 GAGGCTGCTGGTTTCTTAAATCA 59.241 43.478 0.00 0.00 0.00 2.57
1952 2740 2.786495 CCCGGTCTCCACCTCGATG 61.786 68.421 0.00 0.00 41.17 3.84
2066 2854 2.912986 GACATTGTCGTGCTCACCA 58.087 52.632 0.13 0.00 0.00 4.17
2096 2884 2.635338 CGTGACGTGACGAGTCCA 59.365 61.111 23.39 0.80 42.10 4.02
2202 2990 2.203294 GGGCAAGGTGAACCGTGT 60.203 61.111 15.41 0.00 45.45 4.49
2263 3052 4.866508 ACGTATTCAAGAAGGTGAGTGA 57.133 40.909 0.00 0.00 0.00 3.41
2266 3055 4.378459 GCCAAACGTATTCAAGAAGGTGAG 60.378 45.833 0.00 0.00 0.00 3.51
2267 3056 3.500680 GCCAAACGTATTCAAGAAGGTGA 59.499 43.478 0.00 0.00 0.00 4.02
2280 3069 4.855715 TTTCAATTCATGGCCAAACGTA 57.144 36.364 10.96 0.00 0.00 3.57
2283 3072 3.181518 CGCATTTCAATTCATGGCCAAAC 60.182 43.478 10.96 0.00 0.00 2.93
2288 3077 0.932399 GGCGCATTTCAATTCATGGC 59.068 50.000 10.83 0.00 0.00 4.40
2307 3096 7.776933 TCAGGAACATATTGAATTCTCGAAG 57.223 36.000 7.05 0.00 0.00 3.79
2322 3117 8.814038 AAGCTACATCTATTTTTCAGGAACAT 57.186 30.769 0.00 0.00 0.00 2.71
2382 3182 0.165295 GCGAACCCGAGTTAACAAGC 59.835 55.000 8.61 0.00 35.94 4.01
2401 3201 6.991485 ACATTATGAACAAGCAGTTTTTCG 57.009 33.333 0.00 0.00 41.51 3.46
2425 3225 5.657474 CCCATTACATACTCTAACACACGT 58.343 41.667 0.00 0.00 0.00 4.49
2426 3226 4.506654 GCCCATTACATACTCTAACACACG 59.493 45.833 0.00 0.00 0.00 4.49
2427 3227 4.814771 GGCCCATTACATACTCTAACACAC 59.185 45.833 0.00 0.00 0.00 3.82
2428 3228 4.719773 AGGCCCATTACATACTCTAACACA 59.280 41.667 0.00 0.00 0.00 3.72
2429 3229 5.291905 AGGCCCATTACATACTCTAACAC 57.708 43.478 0.00 0.00 0.00 3.32
2430 3230 7.450074 CATTAGGCCCATTACATACTCTAACA 58.550 38.462 0.00 0.00 0.00 2.41
2431 3231 6.879458 CCATTAGGCCCATTACATACTCTAAC 59.121 42.308 0.00 0.00 0.00 2.34
2432 3232 7.016153 CCATTAGGCCCATTACATACTCTAA 57.984 40.000 0.00 0.00 0.00 2.10
2433 3233 6.620877 CCATTAGGCCCATTACATACTCTA 57.379 41.667 0.00 0.00 0.00 2.43
2434 3234 5.505181 CCATTAGGCCCATTACATACTCT 57.495 43.478 0.00 0.00 0.00 3.24
2500 3300 2.367567 CCCTAAGCAAGCGACCCTTATA 59.632 50.000 0.00 0.00 31.00 0.98
2717 3518 6.591001 ACAAAAGAACAGGTTTTATGCCAAT 58.409 32.000 0.00 0.00 0.00 3.16
2759 3683 7.136772 ACCAGATCGTTTTTACTTAAAAGTGC 58.863 34.615 5.62 0.00 40.07 4.40
2769 3693 7.241663 TGCATATGTACCAGATCGTTTTTAC 57.758 36.000 4.29 0.00 0.00 2.01
2776 3700 6.369615 TCAATCATTGCATATGTACCAGATCG 59.630 38.462 4.29 0.00 0.00 3.69
2781 3705 8.744568 TTAGTTCAATCATTGCATATGTACCA 57.255 30.769 4.29 0.00 0.00 3.25
2794 3718 5.469479 CGCCAAAAGGTTTAGTTCAATCAT 58.531 37.500 0.00 0.00 0.00 2.45
2819 3774 9.362539 CCATGAAAAATCAATCTCTTCGAAATT 57.637 29.630 0.00 0.00 0.00 1.82
3168 4812 9.582648 TGTATCCTACTTAATCAGCTATGTGTA 57.417 33.333 0.00 0.00 0.00 2.90
3218 4864 4.985409 CGGAGAGTATCACATTTTAGCTCC 59.015 45.833 0.00 0.00 37.82 4.70
3221 4867 6.073548 CCATTCGGAGAGTATCACATTTTAGC 60.074 42.308 0.00 0.00 38.43 3.09
3229 4875 3.132289 TGGTTCCATTCGGAGAGTATCAC 59.868 47.826 0.00 0.00 44.10 3.06
3264 4911 6.367149 TCTGTCAATGATTCTTCTTCTGTTCG 59.633 38.462 0.00 0.00 0.00 3.95
3411 5061 4.096682 CCCGTGTTCAAAGTTCAAACCTAA 59.903 41.667 0.00 0.00 0.00 2.69
3477 5127 3.358707 TTCTTGCAAGCAATGTGTGAG 57.641 42.857 21.99 0.00 35.20 3.51
3566 5219 3.740832 GGGAAAAGAAAGGCATTTTCACG 59.259 43.478 13.37 0.00 46.20 4.35
3621 5274 8.431222 TCAATGATATCATAAGTGTGTCCATGA 58.569 33.333 18.47 10.66 35.10 3.07
3714 5367 0.389817 CAGTGCTCGATTCCCGACAA 60.390 55.000 0.00 0.00 43.23 3.18
3719 5372 2.109126 GTGGCAGTGCTCGATTCCC 61.109 63.158 16.11 0.00 0.00 3.97
3746 5399 1.006825 TGATGTCGCGGTGAAGAACG 61.007 55.000 6.13 0.00 0.00 3.95
3749 5402 0.601057 TCTTGATGTCGCGGTGAAGA 59.399 50.000 6.13 5.58 0.00 2.87
3812 5465 2.432628 GTGGCCAGTCCGAAGTCG 60.433 66.667 5.11 0.00 37.80 4.18
3911 5564 1.139989 CAACGCTGTAGTGAGTGGTG 58.860 55.000 0.00 0.00 34.95 4.17
3912 5565 0.033504 CCAACGCTGTAGTGAGTGGT 59.966 55.000 0.00 0.00 33.10 4.16
4011 5664 3.364664 GCGAATCTCGTATCGTATGGACA 60.365 47.826 0.00 0.00 42.81 4.02
4037 5694 4.981389 TGTGCAATTTTCCGCAAATAAC 57.019 36.364 0.00 0.00 40.44 1.89
4046 5703 4.886579 AGTCTCCAAATGTGCAATTTTCC 58.113 39.130 0.00 0.00 0.00 3.13
4059 5716 4.415881 TGAGCACAAGTTAGTCTCCAAA 57.584 40.909 0.00 0.00 0.00 3.28
4318 5975 5.827797 ACTGTTCAAAGTAGATGCCTTGAAA 59.172 36.000 0.00 0.00 0.00 2.69
4356 6014 3.915437 ATTTAGCAGTGTTTCCGGTTG 57.085 42.857 0.00 0.00 0.00 3.77
4360 6018 4.226761 GGTTGAATTTAGCAGTGTTTCCG 58.773 43.478 0.00 0.00 0.00 4.30
4393 6053 6.884295 TGCATAGTGGCTACTCTGTTTTTATT 59.116 34.615 5.78 0.00 38.36 1.40
4427 6087 6.419710 TCCATGTATCGTGATCAATCGTAAAC 59.580 38.462 0.00 0.00 0.00 2.01
4432 6092 4.550422 AGTCCATGTATCGTGATCAATCG 58.450 43.478 0.00 0.00 0.00 3.34
4513 6174 7.148052 GCACTTGTGAGGAGAAGACTACTATTA 60.148 40.741 4.79 0.00 37.45 0.98
4518 6179 3.257127 AGCACTTGTGAGGAGAAGACTAC 59.743 47.826 4.79 0.00 0.00 2.73
4544 6205 5.357878 TGAAGAACTGAATTCACAGCAAACT 59.642 36.000 3.38 0.00 40.09 2.66
4580 6241 1.135199 GCTTGATGGTTCACAGGCATG 60.135 52.381 0.00 0.00 38.61 4.06
4648 6309 1.532868 CAGGACCTTTTGTGCTTCTCG 59.467 52.381 0.00 0.00 44.14 4.04
4701 6362 4.398988 TGTTGAAGCTTCTTGTGACACAAT 59.601 37.500 26.09 5.53 37.48 2.71
4765 6426 4.224715 TGTTGTCTGACGTTCTACTGAG 57.775 45.455 2.98 0.00 0.00 3.35
4768 6429 3.131577 TGGTTGTTGTCTGACGTTCTACT 59.868 43.478 2.98 0.00 0.00 2.57
4777 6438 2.297701 GGCTTTCTGGTTGTTGTCTGA 58.702 47.619 0.00 0.00 0.00 3.27
4785 6446 1.815003 GTGAGATGGGCTTTCTGGTTG 59.185 52.381 0.00 0.00 0.00 3.77
4786 6447 1.425066 TGTGAGATGGGCTTTCTGGTT 59.575 47.619 0.00 0.00 0.00 3.67
4840 6501 3.738982 TCCATGTGGCCTATTATTGACG 58.261 45.455 3.32 0.00 34.44 4.35
4851 6512 0.321346 CTTTGGGTTTCCATGTGGCC 59.679 55.000 0.00 0.00 43.63 5.36
4917 6578 7.534085 TTCGGTATCATACAGTTCACATTTC 57.466 36.000 0.00 0.00 0.00 2.17
4918 6579 7.915293 TTTCGGTATCATACAGTTCACATTT 57.085 32.000 0.00 0.00 0.00 2.32
4919 6580 9.042008 GTATTTCGGTATCATACAGTTCACATT 57.958 33.333 0.00 0.00 0.00 2.71
4925 6586 7.120923 AGTGGTATTTCGGTATCATACAGTT 57.879 36.000 0.00 0.00 0.00 3.16
4927 6588 9.537192 TTTTAGTGGTATTTCGGTATCATACAG 57.463 33.333 0.00 0.00 0.00 2.74
4928 6589 9.887629 TTTTTAGTGGTATTTCGGTATCATACA 57.112 29.630 0.00 0.00 0.00 2.29
4955 6616 8.149973 ACACAAGAAGTACAATTAAACGTGAT 57.850 30.769 0.00 0.00 0.00 3.06
4957 6618 7.627340 AGACACAAGAAGTACAATTAAACGTG 58.373 34.615 0.00 0.00 0.00 4.49
4958 6619 7.781548 AGACACAAGAAGTACAATTAAACGT 57.218 32.000 0.00 0.00 0.00 3.99
4959 6620 8.548721 AGAAGACACAAGAAGTACAATTAAACG 58.451 33.333 0.00 0.00 0.00 3.60
4962 6623 9.607988 TGAAGAAGACACAAGAAGTACAATTAA 57.392 29.630 0.00 0.00 0.00 1.40
4963 6624 9.607988 TTGAAGAAGACACAAGAAGTACAATTA 57.392 29.630 0.00 0.00 0.00 1.40
4964 6625 8.506168 TTGAAGAAGACACAAGAAGTACAATT 57.494 30.769 0.00 0.00 0.00 2.32
4965 6626 8.682936 ATTGAAGAAGACACAAGAAGTACAAT 57.317 30.769 0.00 0.00 0.00 2.71
4968 6629 8.064814 GTCAATTGAAGAAGACACAAGAAGTAC 58.935 37.037 10.35 0.00 0.00 2.73
4982 6643 8.864069 TTTGATAAAAAGCGTCAATTGAAGAA 57.136 26.923 23.23 4.29 0.00 2.52
5209 6870 3.073274 AGGCTCGGCATTTTCTTTAGT 57.927 42.857 0.00 0.00 0.00 2.24
5254 6915 0.321671 CCTTCTTCGGGCTGTTCAGA 59.678 55.000 3.84 0.00 0.00 3.27
5302 6963 3.860930 AACCGTGGAAGGCGCCATT 62.861 57.895 31.54 19.82 40.68 3.16
5408 7069 7.458397 TGTCATTTGACTAAACCTACTGGAAT 58.542 34.615 11.67 0.00 44.99 3.01
5410 7071 6.428083 TGTCATTTGACTAAACCTACTGGA 57.572 37.500 11.67 0.00 44.99 3.86
5474 7140 3.010138 TGACCAGGGGATGTAAGAAAAGG 59.990 47.826 0.00 0.00 0.00 3.11
5611 7299 3.244875 TGCATATATGGCCTGAATCCGTT 60.245 43.478 14.51 0.00 0.00 4.44
5613 7301 2.989909 TGCATATATGGCCTGAATCCG 58.010 47.619 14.51 0.00 0.00 4.18
5622 7310 6.016360 TCACCTACACAATTTGCATATATGGC 60.016 38.462 14.51 7.40 0.00 4.40
5623 7311 7.229306 AGTCACCTACACAATTTGCATATATGG 59.771 37.037 14.51 0.00 0.00 2.74
5624 7312 8.158169 AGTCACCTACACAATTTGCATATATG 57.842 34.615 8.45 8.45 0.00 1.78
5630 7318 4.460263 AGAAGTCACCTACACAATTTGCA 58.540 39.130 0.00 0.00 0.00 4.08
5631 7319 4.515191 TGAGAAGTCACCTACACAATTTGC 59.485 41.667 0.00 0.00 0.00 3.68
5632 7320 5.990408 GTGAGAAGTCACCTACACAATTTG 58.010 41.667 0.00 0.00 46.58 2.32
5657 7345 9.866655 TCACCTTTTCCTCTAATTTGCATATAT 57.133 29.630 0.00 0.00 0.00 0.86
5658 7346 9.693739 TTCACCTTTTCCTCTAATTTGCATATA 57.306 29.630 0.00 0.00 0.00 0.86
5659 7347 8.593945 TTCACCTTTTCCTCTAATTTGCATAT 57.406 30.769 0.00 0.00 0.00 1.78
5660 7348 8.415950 TTTCACCTTTTCCTCTAATTTGCATA 57.584 30.769 0.00 0.00 0.00 3.14
5661 7349 6.916360 TTCACCTTTTCCTCTAATTTGCAT 57.084 33.333 0.00 0.00 0.00 3.96
5662 7350 6.723298 TTTCACCTTTTCCTCTAATTTGCA 57.277 33.333 0.00 0.00 0.00 4.08
5663 7351 8.498358 CATTTTTCACCTTTTCCTCTAATTTGC 58.502 33.333 0.00 0.00 0.00 3.68
5664 7352 8.992073 CCATTTTTCACCTTTTCCTCTAATTTG 58.008 33.333 0.00 0.00 0.00 2.32
5665 7353 8.933653 TCCATTTTTCACCTTTTCCTCTAATTT 58.066 29.630 0.00 0.00 0.00 1.82
5666 7354 8.367911 GTCCATTTTTCACCTTTTCCTCTAATT 58.632 33.333 0.00 0.00 0.00 1.40
5667 7355 7.508977 TGTCCATTTTTCACCTTTTCCTCTAAT 59.491 33.333 0.00 0.00 0.00 1.73
5668 7356 6.836527 TGTCCATTTTTCACCTTTTCCTCTAA 59.163 34.615 0.00 0.00 0.00 2.10
5669 7357 6.369629 TGTCCATTTTTCACCTTTTCCTCTA 58.630 36.000 0.00 0.00 0.00 2.43
5670 7358 5.208121 TGTCCATTTTTCACCTTTTCCTCT 58.792 37.500 0.00 0.00 0.00 3.69
5671 7359 5.529581 TGTCCATTTTTCACCTTTTCCTC 57.470 39.130 0.00 0.00 0.00 3.71
5672 7360 5.948742 TTGTCCATTTTTCACCTTTTCCT 57.051 34.783 0.00 0.00 0.00 3.36
5673 7361 5.049474 GCATTGTCCATTTTTCACCTTTTCC 60.049 40.000 0.00 0.00 0.00 3.13
5674 7362 5.526846 TGCATTGTCCATTTTTCACCTTTTC 59.473 36.000 0.00 0.00 0.00 2.29
5675 7363 5.435291 TGCATTGTCCATTTTTCACCTTTT 58.565 33.333 0.00 0.00 0.00 2.27
5676 7364 5.033589 TGCATTGTCCATTTTTCACCTTT 57.966 34.783 0.00 0.00 0.00 3.11
5677 7365 4.344679 TCTGCATTGTCCATTTTTCACCTT 59.655 37.500 0.00 0.00 0.00 3.50
5678 7366 3.896888 TCTGCATTGTCCATTTTTCACCT 59.103 39.130 0.00 0.00 0.00 4.00
5679 7367 4.255833 TCTGCATTGTCCATTTTTCACC 57.744 40.909 0.00 0.00 0.00 4.02
5680 7368 7.062605 CAGTTATCTGCATTGTCCATTTTTCAC 59.937 37.037 0.00 0.00 34.79 3.18
5681 7369 7.092079 CAGTTATCTGCATTGTCCATTTTTCA 58.908 34.615 0.00 0.00 34.79 2.69
5682 7370 6.532657 CCAGTTATCTGCATTGTCCATTTTTC 59.467 38.462 0.00 0.00 40.09 2.29
5683 7371 6.211184 TCCAGTTATCTGCATTGTCCATTTTT 59.789 34.615 0.00 0.00 40.09 1.94
5684 7372 5.716228 TCCAGTTATCTGCATTGTCCATTTT 59.284 36.000 0.00 0.00 40.09 1.82
5685 7373 5.263599 TCCAGTTATCTGCATTGTCCATTT 58.736 37.500 0.00 0.00 40.09 2.32
5686 7374 4.858850 TCCAGTTATCTGCATTGTCCATT 58.141 39.130 0.00 0.00 40.09 3.16
5687 7375 4.508551 TCCAGTTATCTGCATTGTCCAT 57.491 40.909 0.00 0.00 40.09 3.41
5688 7376 3.998913 TCCAGTTATCTGCATTGTCCA 57.001 42.857 0.00 0.00 40.09 4.02
5689 7377 5.450965 CCATTTCCAGTTATCTGCATTGTCC 60.451 44.000 0.00 0.00 40.09 4.02
5694 7382 5.121380 AGACCATTTCCAGTTATCTGCAT 57.879 39.130 0.00 0.00 40.09 3.96
5769 7458 4.217118 TGCAAGCCTTCTCTTCTGAAAATC 59.783 41.667 0.00 0.00 0.00 2.17
5773 7462 2.936919 TGCAAGCCTTCTCTTCTGAA 57.063 45.000 0.00 0.00 0.00 3.02
5774 7463 2.303890 TCATGCAAGCCTTCTCTTCTGA 59.696 45.455 0.00 0.00 0.00 3.27
5809 7499 6.798482 TGCAGAAAAATGGATAAGCATACTG 58.202 36.000 0.00 0.00 0.00 2.74
5892 7582 1.863454 CATATGAGCAACTGGTCTCGC 59.137 52.381 10.05 0.00 42.60 5.03
5896 7586 1.945394 CCTGCATATGAGCAACTGGTC 59.055 52.381 6.97 1.92 45.13 4.02
5971 7661 2.166459 TGATTCAGTCACCTCCGATGAC 59.834 50.000 0.00 0.00 45.70 3.06
6109 7799 1.306397 TCCTCATCCTCCTGCTGCA 60.306 57.895 0.88 0.88 0.00 4.41
6140 7833 1.597742 GCCTGTCACAGCAAGAGAAA 58.402 50.000 0.00 0.00 0.00 2.52
6214 7907 2.094545 GCAGTTGCCCAAATGTAAGGAG 60.095 50.000 9.75 0.00 38.50 3.69
6346 8039 2.214181 GACACGACTCTGGCGGTCAT 62.214 60.000 0.00 0.00 33.73 3.06
6374 8067 4.572389 GCTGACACTTTGAATCGTCCATAT 59.428 41.667 0.00 0.00 0.00 1.78
6377 8070 2.143122 GCTGACACTTTGAATCGTCCA 58.857 47.619 0.00 0.00 0.00 4.02
6380 8073 0.512952 GCGCTGACACTTTGAATCGT 59.487 50.000 0.00 0.00 0.00 3.73
6381 8074 0.512518 TGCGCTGACACTTTGAATCG 59.487 50.000 9.73 0.00 0.00 3.34
6382 8075 2.686558 TTGCGCTGACACTTTGAATC 57.313 45.000 9.73 0.00 0.00 2.52
6383 8076 2.923605 GCATTGCGCTGACACTTTGAAT 60.924 45.455 9.73 0.00 37.77 2.57
6398 8091 0.248377 GTCTCATTCAGGCGCATTGC 60.248 55.000 10.83 0.00 45.38 3.56
6399 8092 1.376543 AGTCTCATTCAGGCGCATTG 58.623 50.000 10.83 7.35 0.00 2.82
6405 8098 2.771089 TCACACAAGTCTCATTCAGGC 58.229 47.619 0.00 0.00 0.00 4.85


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

AutoCloner maintained by Alex Coulton.