Multiple sequence alignment - TraesCS7D01G489800

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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 TraesCS7D01G489800 chr7D 100.000 2950 0 0 1 2950 599393385 599396334 0.000000e+00 5448
1 TraesCS7D01G489800 chr7D 96.604 2238 54 9 611 2831 390864243 390862011 0.000000e+00 3692
2 TraesCS7D01G489800 chr7D 94.866 2240 87 12 609 2831 579360012 579357784 0.000000e+00 3474
3 TraesCS7D01G489800 chr7D 100.000 564 0 0 3162 3725 599396546 599397109 0.000000e+00 1042
4 TraesCS7D01G489800 chr7D 97.122 139 4 0 3162 3300 390861507 390861369 6.220000e-58 235
5 TraesCS7D01G489800 chr7D 94.595 148 7 1 3550 3696 599465548 599465695 1.040000e-55 228
6 TraesCS7D01G489800 chr7D 93.662 142 9 0 3162 3303 579340813 579340672 2.910000e-51 213
7 TraesCS7D01G489800 chr7D 92.568 148 10 1 3550 3696 599469851 599469998 1.050000e-50 211
8 TraesCS7D01G489800 chr7D 90.647 139 13 0 3162 3300 78629530 78629392 6.350000e-43 185
9 TraesCS7D01G489800 chr7D 94.382 89 4 1 2841 2929 78629725 78629638 6.490000e-28 135
10 TraesCS7D01G489800 chr7D 98.529 68 1 0 2862 2929 390861661 390861594 1.820000e-23 121
11 TraesCS7D01G489800 chr7D 89.888 89 1 4 2841 2929 579340994 579340914 1.410000e-19 108
12 TraesCS7D01G489800 chr2D 96.131 2223 80 5 613 2831 481683677 481681457 0.000000e+00 3624
13 TraesCS7D01G489800 chr2D 97.445 1096 27 1 613 1707 6437065 6435970 0.000000e+00 1868
14 TraesCS7D01G489800 chr2D 97.122 139 4 0 3162 3300 6435923 6435785 6.220000e-58 235
15 TraesCS7D01G489800 chr2D 94.964 139 7 0 3162 3300 481671959 481671821 6.260000e-53 219
16 TraesCS7D01G489800 chr2D 91.892 74 6 0 15 88 192319414 192319341 1.830000e-18 104
17 TraesCS7D01G489800 chr1D 95.553 2226 92 6 610 2831 413791909 413794131 0.000000e+00 3555
18 TraesCS7D01G489800 chr1D 92.466 146 10 1 3162 3307 413810780 413810924 1.360000e-49 207
19 TraesCS7D01G489800 chr1D 95.506 89 3 1 2841 2929 413810591 413810678 1.390000e-29 141
20 TraesCS7D01G489800 chr3D 93.514 2220 102 15 613 2829 45628932 45626752 0.000000e+00 3264
21 TraesCS7D01G489800 chr3D 93.750 144 8 1 3162 3304 45625257 45625114 8.100000e-52 215
22 TraesCS7D01G489800 chr3D 97.753 89 1 1 2841 2929 45625452 45625365 6.440000e-33 152
23 TraesCS7D01G489800 chr7B 92.935 1104 73 5 611 1710 614610569 614611671 0.000000e+00 1602
24 TraesCS7D01G489800 chr7B 93.922 510 29 2 2315 2823 614612018 614612526 0.000000e+00 769
25 TraesCS7D01G489800 chr7B 93.197 147 10 0 3550 3696 678749172 678749318 2.250000e-52 217
26 TraesCS7D01G489800 chr7B 92.806 139 10 0 3162 3300 614613789 614613927 6.310000e-48 202
27 TraesCS7D01G489800 chr6A 93.980 598 21 4 1 589 447798337 447798928 0.000000e+00 891
28 TraesCS7D01G489800 chr6A 93.478 598 23 9 1 589 447805714 447806304 0.000000e+00 874
29 TraesCS7D01G489800 chr6A 92.617 596 29 4 3 589 447803248 447803837 0.000000e+00 843
30 TraesCS7D01G489800 chr6A 92.486 519 29 3 80 589 447800860 447801377 0.000000e+00 734
31 TraesCS7D01G489800 chr6A 92.982 399 18 3 200 589 572762159 572761762 1.160000e-159 573
32 TraesCS7D01G489800 chr6A 92.500 400 19 4 200 589 572776133 572775735 2.510000e-156 562
33 TraesCS7D01G489800 chr6A 92.250 400 20 4 200 589 572769403 572769005 1.170000e-154 556
34 TraesCS7D01G489800 chr6A 96.047 253 9 1 3300 3551 447798926 447799178 9.630000e-111 411
35 TraesCS7D01G489800 chr6A 96.032 252 10 0 3300 3551 447803835 447804086 9.630000e-111 411
36 TraesCS7D01G489800 chr6A 96.032 252 9 1 3300 3551 447806302 447806552 3.460000e-110 409
37 TraesCS7D01G489800 chr6A 95.238 252 12 0 3300 3551 447801375 447801626 2.080000e-107 399
38 TraesCS7D01G489800 chr6A 95.238 252 12 0 3300 3551 572761764 572761513 2.080000e-107 399
39 TraesCS7D01G489800 chr6A 95.238 252 12 0 3300 3551 572769007 572768756 2.080000e-107 399
40 TraesCS7D01G489800 chr6A 95.238 252 12 0 3300 3551 572775737 572775486 2.080000e-107 399
41 TraesCS7D01G489800 chr6A 98.039 204 4 0 1 204 572765027 572764824 4.580000e-94 355
42 TraesCS7D01G489800 chr6A 97.549 204 5 0 1 204 572772272 572772069 2.130000e-92 350
43 TraesCS7D01G489800 chr6A 97.549 204 5 0 1 204 572778991 572778788 2.130000e-92 350
44 TraesCS7D01G489800 chr6A 91.908 173 14 0 3550 3722 447804140 447804312 3.720000e-60 243
45 TraesCS7D01G489800 chr6A 91.329 173 15 0 3550 3722 572775432 572775260 1.730000e-58 237
46 TraesCS7D01G489800 chr6A 90.751 173 16 0 3550 3722 572761459 572761287 8.050000e-57 231
47 TraesCS7D01G489800 chr6A 89.595 173 18 0 3550 3722 447801680 447801852 1.740000e-53 220
48 TraesCS7D01G489800 chr7A 94.061 522 17 6 1 510 691514753 691515272 0.000000e+00 780
49 TraesCS7D01G489800 chr7A 84.109 516 70 8 70 582 238543747 238543241 4.320000e-134 488
50 TraesCS7D01G489800 chr7A 95.652 253 10 1 3300 3551 691515327 691515579 4.480000e-109 405
51 TraesCS7D01G489800 chr7A 91.379 174 14 1 3550 3722 691515633 691515806 1.730000e-58 237
52 TraesCS7D01G489800 chr3B 83.531 844 116 12 609 1432 764107888 764107048 0.000000e+00 767
53 TraesCS7D01G489800 chr3B 84.375 448 64 6 2258 2702 764106145 764105701 5.710000e-118 435
54 TraesCS7D01G489800 chr1A 83.274 837 119 8 613 1429 561388516 561389351 0.000000e+00 750
55 TraesCS7D01G489800 chr1A 84.598 448 63 6 2258 2702 561390264 561390708 1.230000e-119 440
56 TraesCS7D01G489800 chr1A 96.047 253 9 1 3300 3551 50522411 50522159 9.630000e-111 411
57 TraesCS7D01G489800 chr1A 95.378 238 8 2 354 589 50522645 50522409 3.510000e-100 375
58 TraesCS7D01G489800 chr1A 91.716 169 14 0 3550 3718 50522105 50521937 6.220000e-58 235
59 TraesCS7D01G489800 chr1A 87.857 140 15 2 3162 3300 561391120 561391258 2.980000e-36 163
60 TraesCS7D01G489800 chr1B 84.116 447 67 4 2258 2702 121581888 121582332 2.660000e-116 429
61 TraesCS7D01G489800 chr1B 84.211 133 20 1 1252 1383 563745956 563745824 1.090000e-25 128


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 TraesCS7D01G489800 chr7D 599393385 599397109 3724 False 3245.000000 5448 100.000000 1 3725 2 chr7D.!!$F3 3724
1 TraesCS7D01G489800 chr7D 579357784 579360012 2228 True 3474.000000 3474 94.866000 609 2831 1 chr7D.!!$R1 2222
2 TraesCS7D01G489800 chr7D 390861369 390864243 2874 True 1349.333333 3692 97.418333 611 3300 3 chr7D.!!$R3 2689
3 TraesCS7D01G489800 chr2D 481681457 481683677 2220 True 3624.000000 3624 96.131000 613 2831 1 chr2D.!!$R3 2218
4 TraesCS7D01G489800 chr2D 6435785 6437065 1280 True 1051.500000 1868 97.283500 613 3300 2 chr2D.!!$R4 2687
5 TraesCS7D01G489800 chr1D 413791909 413794131 2222 False 3555.000000 3555 95.553000 610 2831 1 chr1D.!!$F1 2221
6 TraesCS7D01G489800 chr3D 45625114 45628932 3818 True 1210.333333 3264 95.005667 613 3304 3 chr3D.!!$R1 2691
7 TraesCS7D01G489800 chr7B 614610569 614613927 3358 False 857.666667 1602 93.221000 611 3300 3 chr7B.!!$F2 2689
8 TraesCS7D01G489800 chr6A 447798337 447806552 8215 False 543.500000 891 93.741300 1 3722 10 chr6A.!!$F1 3721
9 TraesCS7D01G489800 chr6A 572761287 572778991 17704 True 401.000000 573 94.423909 1 3722 11 chr6A.!!$R1 3721
10 TraesCS7D01G489800 chr7A 238543241 238543747 506 True 488.000000 488 84.109000 70 582 1 chr7A.!!$R1 512
11 TraesCS7D01G489800 chr7A 691514753 691515806 1053 False 474.000000 780 93.697333 1 3722 3 chr7A.!!$F1 3721
12 TraesCS7D01G489800 chr3B 764105701 764107888 2187 True 601.000000 767 83.953000 609 2702 2 chr3B.!!$R1 2093
13 TraesCS7D01G489800 chr1A 561388516 561391258 2742 False 451.000000 750 85.243000 613 3300 3 chr1A.!!$F1 2687
14 TraesCS7D01G489800 chr1A 50521937 50522645 708 True 340.333333 411 94.380333 354 3718 3 chr1A.!!$R1 3364

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
317 2982 1.027357 GCCAGCGGATGATTGTCAAT 58.973 50.0 0.0 0.0 0.0 2.57 F
1200 3905 0.392863 CGATGTGGAGATGGTGGCAA 60.393 55.0 0.0 0.0 0.0 4.52 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1291 3996 2.037527 ACACGTCCCTCCTCTCCC 59.962 66.667 0.0 0.0 0.00 4.30 R
2835 20551 0.107165 ACCCCGCAAGCTTATCTTCC 60.107 55.000 0.0 0.0 31.27 3.46 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
74 75 2.637382 TGGCATTCTAGAGTTGTGTCCA 59.363 45.455 0.00 1.72 0.00 4.02
75 76 3.072330 TGGCATTCTAGAGTTGTGTCCAA 59.928 43.478 0.00 0.00 0.00 3.53
76 77 3.686726 GGCATTCTAGAGTTGTGTCCAAG 59.313 47.826 0.00 0.00 0.00 3.61
77 78 3.126000 GCATTCTAGAGTTGTGTCCAAGC 59.874 47.826 0.00 0.00 0.00 4.01
78 79 4.318332 CATTCTAGAGTTGTGTCCAAGCA 58.682 43.478 0.00 0.00 0.00 3.91
112 118 3.118149 AGCATGACTGTGGAAGATATGCA 60.118 43.478 0.00 0.00 44.15 3.96
121 127 8.353423 ACTGTGGAAGATATGCAACTAAATTT 57.647 30.769 0.00 0.00 0.00 1.82
236 2901 9.142014 TGGGGATTCGAATTATGTTAAATCAAT 57.858 29.630 12.81 0.00 0.00 2.57
317 2982 1.027357 GCCAGCGGATGATTGTCAAT 58.973 50.000 0.00 0.00 0.00 2.57
455 3127 6.428159 ACTTTGGATAGTGACTTGTTGCTTAG 59.572 38.462 0.00 0.00 0.00 2.18
456 3128 4.253685 TGGATAGTGACTTGTTGCTTAGC 58.746 43.478 0.00 0.00 0.00 3.09
457 3129 3.623510 GGATAGTGACTTGTTGCTTAGCC 59.376 47.826 0.29 0.00 0.00 3.93
458 3130 2.938956 AGTGACTTGTTGCTTAGCCT 57.061 45.000 0.29 0.00 0.00 4.58
535 3208 9.784531 AAGAAGATTTTCTGAATAAGTCACTGA 57.215 29.630 0.00 0.00 42.80 3.41
536 3209 9.956640 AGAAGATTTTCTGAATAAGTCACTGAT 57.043 29.630 0.00 0.00 42.04 2.90
543 3216 9.950680 TTTCTGAATAAGTCACTGATTTTGTTC 57.049 29.630 0.00 1.77 31.13 3.18
544 3217 8.675705 TCTGAATAAGTCACTGATTTTGTTCA 57.324 30.769 13.13 13.13 31.13 3.18
545 3218 9.119418 TCTGAATAAGTCACTGATTTTGTTCAA 57.881 29.630 14.01 7.45 31.13 2.69
546 3219 9.173939 CTGAATAAGTCACTGATTTTGTTCAAC 57.826 33.333 14.01 0.00 31.13 3.18
547 3220 8.681806 TGAATAAGTCACTGATTTTGTTCAACA 58.318 29.630 12.16 0.00 0.00 3.33
548 3221 8.856490 AATAAGTCACTGATTTTGTTCAACAC 57.144 30.769 0.00 0.00 0.00 3.32
549 3222 5.895636 AGTCACTGATTTTGTTCAACACA 57.104 34.783 0.00 0.00 0.00 3.72
550 3223 6.455360 AGTCACTGATTTTGTTCAACACAT 57.545 33.333 0.00 0.00 34.43 3.21
551 3224 7.566760 AGTCACTGATTTTGTTCAACACATA 57.433 32.000 0.00 0.00 34.43 2.29
552 3225 7.417612 AGTCACTGATTTTGTTCAACACATAC 58.582 34.615 0.00 0.00 34.43 2.39
553 3226 6.356977 GTCACTGATTTTGTTCAACACATACG 59.643 38.462 0.00 0.00 34.43 3.06
554 3227 6.037720 TCACTGATTTTGTTCAACACATACGT 59.962 34.615 0.00 0.00 34.43 3.57
556 3229 6.037720 ACTGATTTTGTTCAACACATACGTGA 59.962 34.615 0.00 0.00 46.80 4.35
557 3230 6.426327 TGATTTTGTTCAACACATACGTGAG 58.574 36.000 0.00 0.00 46.80 3.51
558 3231 3.870723 TTGTTCAACACATACGTGAGC 57.129 42.857 0.00 0.00 46.80 4.26
559 3232 3.106242 TGTTCAACACATACGTGAGCT 57.894 42.857 0.00 0.00 46.80 4.09
560 3233 4.245845 TGTTCAACACATACGTGAGCTA 57.754 40.909 0.00 0.00 46.80 3.32
561 3234 4.234574 TGTTCAACACATACGTGAGCTAG 58.765 43.478 0.00 0.00 46.80 3.42
562 3235 4.235360 GTTCAACACATACGTGAGCTAGT 58.765 43.478 0.00 0.00 46.80 2.57
563 3236 4.092771 TCAACACATACGTGAGCTAGTC 57.907 45.455 0.00 0.00 46.80 2.59
564 3237 3.504520 TCAACACATACGTGAGCTAGTCA 59.495 43.478 0.00 0.00 46.80 3.41
577 3250 6.156748 TGAGCTAGTCACTAAACTTTGTGA 57.843 37.500 3.11 3.11 39.84 3.58
578 3251 6.578944 TGAGCTAGTCACTAAACTTTGTGAA 58.421 36.000 8.05 0.00 42.71 3.18
579 3252 7.217200 TGAGCTAGTCACTAAACTTTGTGAAT 58.783 34.615 10.76 10.76 42.71 2.57
580 3253 7.171508 TGAGCTAGTCACTAAACTTTGTGAATG 59.828 37.037 14.30 7.78 42.71 2.67
581 3254 6.992715 AGCTAGTCACTAAACTTTGTGAATGT 59.007 34.615 14.30 4.54 42.71 2.71
582 3255 7.499232 AGCTAGTCACTAAACTTTGTGAATGTT 59.501 33.333 14.30 3.74 42.71 2.71
583 3256 7.798982 GCTAGTCACTAAACTTTGTGAATGTTC 59.201 37.037 14.30 1.98 42.71 3.18
584 3257 7.624360 AGTCACTAAACTTTGTGAATGTTCA 57.376 32.000 8.05 0.00 42.71 3.18
585 3258 8.225603 AGTCACTAAACTTTGTGAATGTTCAT 57.774 30.769 8.05 0.00 42.71 2.57
586 3259 8.131100 AGTCACTAAACTTTGTGAATGTTCATG 58.869 33.333 8.05 0.00 42.71 3.07
587 3260 8.128582 GTCACTAAACTTTGTGAATGTTCATGA 58.871 33.333 8.05 0.00 42.71 3.07
588 3261 8.681806 TCACTAAACTTTGTGAATGTTCATGAA 58.318 29.630 3.38 3.38 39.34 2.57
589 3262 8.961092 CACTAAACTTTGTGAATGTTCATGAAG 58.039 33.333 8.80 14.28 39.73 3.02
590 3263 6.833342 AAACTTTGTGAATGTTCATGAAGC 57.167 33.333 8.80 4.81 39.73 3.86
591 3264 5.518848 ACTTTGTGAATGTTCATGAAGCA 57.481 34.783 8.80 10.45 39.73 3.91
592 3265 5.904941 ACTTTGTGAATGTTCATGAAGCAA 58.095 33.333 8.80 5.13 39.73 3.91
593 3266 6.339730 ACTTTGTGAATGTTCATGAAGCAAA 58.660 32.000 8.80 11.64 39.73 3.68
594 3267 6.817641 ACTTTGTGAATGTTCATGAAGCAAAA 59.182 30.769 8.80 3.99 39.73 2.44
595 3268 7.333921 ACTTTGTGAATGTTCATGAAGCAAAAA 59.666 29.630 8.80 10.94 39.73 1.94
1155 3845 1.222567 AGTTGGGGAGAGTTTGGTGT 58.777 50.000 0.00 0.00 0.00 4.16
1159 3849 1.752833 GGGAGAGTTTGGTGTCGGT 59.247 57.895 0.00 0.00 0.00 4.69
1200 3905 0.392863 CGATGTGGAGATGGTGGCAA 60.393 55.000 0.00 0.00 0.00 4.52
1707 18995 4.486090 GTCTCTGCATTGTTCGAAGTAGA 58.514 43.478 0.00 0.15 0.00 2.59
1827 19137 6.033966 GCGGTTGATAAAAACATTCCCTAAG 58.966 40.000 0.00 0.00 0.00 2.18
1975 19286 2.354902 GCAAAGGGCATGTGTTCCT 58.645 52.632 0.00 0.00 43.97 3.36
2312 20023 5.963176 ATACATGATGTGACTTGTTGCAA 57.037 34.783 8.61 0.00 32.12 4.08
2488 20202 5.757320 CGAAACTATGCTGAGAATCCAAGAT 59.243 40.000 0.00 0.00 0.00 2.40
2528 20242 4.079253 ACTATTGGCACGACCTTTGATTT 58.921 39.130 0.00 0.00 40.22 2.17
2541 20255 3.696548 CCTTTGATTTTGTAGGAGAGGCC 59.303 47.826 0.00 0.00 0.00 5.19
2577 20292 5.955961 ATTTGTATTCATGGGAAAAGGGG 57.044 39.130 0.00 0.00 36.43 4.79
2749 20464 8.419076 AATTTTGTGTTCTTGTGGTACATTTC 57.581 30.769 0.00 0.00 44.52 2.17
2814 20530 3.445450 TGCGAATGCCCAGCTTTAATAAA 59.555 39.130 0.00 0.00 41.78 1.40
2823 20539 5.635120 CCCAGCTTTAATAAAGGCTCCTAT 58.365 41.667 13.89 0.00 44.04 2.57
2835 20551 2.757313 CTCCTATGAGCAGAGGGGG 58.243 63.158 10.94 1.88 40.14 5.40
2936 21972 0.669318 TCCGTTTGTGAGATCCGTGC 60.669 55.000 0.00 0.00 0.00 5.34
3301 22337 3.262420 GGCTCAGAATAGCACTTTCGAA 58.738 45.455 0.00 0.00 44.64 3.71
3303 22339 4.333926 GGCTCAGAATAGCACTTTCGAAAT 59.666 41.667 11.70 0.00 44.64 2.17
3305 22341 6.317857 GCTCAGAATAGCACTTTCGAAATTT 58.682 36.000 11.70 0.00 42.30 1.82
3306 22342 6.803807 GCTCAGAATAGCACTTTCGAAATTTT 59.196 34.615 11.70 0.00 42.30 1.82
3307 22343 7.201299 GCTCAGAATAGCACTTTCGAAATTTTG 60.201 37.037 11.70 10.05 42.30 2.44
3308 22344 7.083858 TCAGAATAGCACTTTCGAAATTTTGG 58.916 34.615 11.70 1.62 0.00 3.28
3309 22345 7.040755 TCAGAATAGCACTTTCGAAATTTTGGA 60.041 33.333 11.70 0.00 0.00 3.53
3310 22346 7.756722 CAGAATAGCACTTTCGAAATTTTGGAT 59.243 33.333 11.70 1.22 0.00 3.41
3311 22347 8.956426 AGAATAGCACTTTCGAAATTTTGGATA 58.044 29.630 11.70 3.37 0.00 2.59
3312 22348 9.226345 GAATAGCACTTTCGAAATTTTGGATAG 57.774 33.333 11.70 9.08 0.00 2.08
3313 22349 6.575162 AGCACTTTCGAAATTTTGGATAGT 57.425 33.333 11.70 10.08 31.93 2.12
3314 22350 6.381801 AGCACTTTCGAAATTTTGGATAGTG 58.618 36.000 25.76 25.76 44.21 2.74
3315 22351 6.206634 AGCACTTTCGAAATTTTGGATAGTGA 59.793 34.615 30.17 4.40 44.17 3.41
3316 22352 6.305638 GCACTTTCGAAATTTTGGATAGTGAC 59.694 38.462 30.17 22.32 44.17 3.67
3317 22353 7.584987 CACTTTCGAAATTTTGGATAGTGACT 58.415 34.615 25.86 0.00 44.17 3.41
3318 22354 8.076178 CACTTTCGAAATTTTGGATAGTGACTT 58.924 33.333 25.86 3.69 44.17 3.01
3319 22355 8.076178 ACTTTCGAAATTTTGGATAGTGACTTG 58.924 33.333 11.70 0.00 30.98 3.16
3320 22356 5.938322 TCGAAATTTTGGATAGTGACTTGC 58.062 37.500 5.58 0.00 0.00 4.01
3321 22357 5.705441 TCGAAATTTTGGATAGTGACTTGCT 59.295 36.000 5.58 0.00 0.00 3.91
3322 22358 5.796935 CGAAATTTTGGATAGTGACTTGCTG 59.203 40.000 0.00 0.00 0.00 4.41
3323 22359 4.708726 ATTTTGGATAGTGACTTGCTGC 57.291 40.909 0.00 0.00 0.00 5.25
3324 22360 3.423539 TTTGGATAGTGACTTGCTGCT 57.576 42.857 0.00 0.00 0.00 4.24
3325 22361 3.423539 TTGGATAGTGACTTGCTGCTT 57.576 42.857 0.00 0.00 0.00 3.91
3326 22362 4.551702 TTGGATAGTGACTTGCTGCTTA 57.448 40.909 0.00 0.00 0.00 3.09
3327 22363 3.861840 TGGATAGTGACTTGCTGCTTAC 58.138 45.455 0.00 0.00 0.00 2.34
3328 22364 3.260632 TGGATAGTGACTTGCTGCTTACA 59.739 43.478 0.00 0.00 0.00 2.41
3342 22378 5.611796 CTGCTTACAGCTTACACATCAAA 57.388 39.130 0.00 0.00 42.97 2.69
3343 22379 6.000891 CTGCTTACAGCTTACACATCAAAA 57.999 37.500 0.00 0.00 42.97 2.44
3344 22380 6.000891 TGCTTACAGCTTACACATCAAAAG 57.999 37.500 0.00 0.00 42.97 2.27
3345 22381 5.530915 TGCTTACAGCTTACACATCAAAAGT 59.469 36.000 0.00 0.00 42.97 2.66
3346 22382 5.853282 GCTTACAGCTTACACATCAAAAGTG 59.147 40.000 0.00 0.00 39.43 3.16
3347 22383 4.836125 ACAGCTTACACATCAAAAGTGG 57.164 40.909 0.00 0.00 41.21 4.00
3348 22384 4.460263 ACAGCTTACACATCAAAAGTGGA 58.540 39.130 0.00 0.00 41.21 4.02
3349 22385 4.516698 ACAGCTTACACATCAAAAGTGGAG 59.483 41.667 0.00 0.00 41.21 3.86
3350 22386 4.756642 CAGCTTACACATCAAAAGTGGAGA 59.243 41.667 0.00 0.00 41.21 3.71
3351 22387 5.239306 CAGCTTACACATCAAAAGTGGAGAA 59.761 40.000 0.00 0.00 41.21 2.87
3352 22388 5.827797 AGCTTACACATCAAAAGTGGAGAAA 59.172 36.000 0.00 0.00 41.21 2.52
3353 22389 6.016777 AGCTTACACATCAAAAGTGGAGAAAG 60.017 38.462 0.00 0.00 41.21 2.62
3354 22390 4.574599 ACACATCAAAAGTGGAGAAAGC 57.425 40.909 0.00 0.00 41.21 3.51
3355 22391 3.003689 ACACATCAAAAGTGGAGAAAGCG 59.996 43.478 0.00 0.00 41.21 4.68
3356 22392 3.250762 CACATCAAAAGTGGAGAAAGCGA 59.749 43.478 0.00 0.00 33.43 4.93
3357 22393 3.251004 ACATCAAAAGTGGAGAAAGCGAC 59.749 43.478 0.00 0.00 0.00 5.19
3358 22394 2.218603 TCAAAAGTGGAGAAAGCGACC 58.781 47.619 0.00 0.00 0.00 4.79
3359 22395 1.266989 CAAAAGTGGAGAAAGCGACCC 59.733 52.381 0.00 0.00 0.00 4.46
3360 22396 0.250770 AAAGTGGAGAAAGCGACCCC 60.251 55.000 0.00 0.00 0.00 4.95
3361 22397 1.415672 AAGTGGAGAAAGCGACCCCA 61.416 55.000 0.00 0.00 0.00 4.96
3362 22398 1.376037 GTGGAGAAAGCGACCCCAG 60.376 63.158 0.00 0.00 0.00 4.45
3363 22399 2.436824 GGAGAAAGCGACCCCAGC 60.437 66.667 0.00 0.00 0.00 4.85
3364 22400 2.436824 GAGAAAGCGACCCCAGCC 60.437 66.667 0.00 0.00 34.64 4.85
3365 22401 3.978571 GAGAAAGCGACCCCAGCCC 62.979 68.421 0.00 0.00 34.64 5.19
3366 22402 4.344865 GAAAGCGACCCCAGCCCA 62.345 66.667 0.00 0.00 34.64 5.36
3367 22403 4.660938 AAAGCGACCCCAGCCCAC 62.661 66.667 0.00 0.00 34.64 4.61
3371 22407 3.322466 CGACCCCAGCCCACTTCT 61.322 66.667 0.00 0.00 0.00 2.85
3372 22408 2.352805 GACCCCAGCCCACTTCTG 59.647 66.667 0.00 0.00 0.00 3.02
3373 22409 3.927481 GACCCCAGCCCACTTCTGC 62.927 68.421 0.00 0.00 0.00 4.26
3374 22410 3.970410 CCCCAGCCCACTTCTGCA 61.970 66.667 0.00 0.00 0.00 4.41
3375 22411 2.115910 CCCAGCCCACTTCTGCAA 59.884 61.111 0.00 0.00 0.00 4.08
3376 22412 2.270986 CCCAGCCCACTTCTGCAAC 61.271 63.158 0.00 0.00 0.00 4.17
3377 22413 1.228367 CCAGCCCACTTCTGCAACT 60.228 57.895 0.00 0.00 0.00 3.16
3378 22414 1.239968 CCAGCCCACTTCTGCAACTC 61.240 60.000 0.00 0.00 0.00 3.01
3379 22415 0.535780 CAGCCCACTTCTGCAACTCA 60.536 55.000 0.00 0.00 0.00 3.41
3380 22416 0.183492 AGCCCACTTCTGCAACTCAA 59.817 50.000 0.00 0.00 0.00 3.02
3381 22417 1.032014 GCCCACTTCTGCAACTCAAA 58.968 50.000 0.00 0.00 0.00 2.69
3382 22418 1.408702 GCCCACTTCTGCAACTCAAAA 59.591 47.619 0.00 0.00 0.00 2.44
3383 22419 2.544486 GCCCACTTCTGCAACTCAAAAG 60.544 50.000 0.00 0.00 0.00 2.27
3384 22420 2.544486 CCCACTTCTGCAACTCAAAAGC 60.544 50.000 0.00 0.00 0.00 3.51
3385 22421 2.360165 CCACTTCTGCAACTCAAAAGCT 59.640 45.455 0.00 0.00 0.00 3.74
3386 22422 3.181483 CCACTTCTGCAACTCAAAAGCTT 60.181 43.478 0.00 0.00 0.00 3.74
3387 22423 4.427312 CACTTCTGCAACTCAAAAGCTTT 58.573 39.130 5.69 5.69 0.00 3.51
3388 22424 5.450412 CCACTTCTGCAACTCAAAAGCTTTA 60.450 40.000 13.10 0.00 0.00 1.85
3389 22425 6.211515 CACTTCTGCAACTCAAAAGCTTTAT 58.788 36.000 13.10 0.00 0.00 1.40
3390 22426 7.362662 CACTTCTGCAACTCAAAAGCTTTATA 58.637 34.615 13.10 2.61 0.00 0.98
3391 22427 7.324616 CACTTCTGCAACTCAAAAGCTTTATAC 59.675 37.037 13.10 0.00 0.00 1.47
3392 22428 6.254281 TCTGCAACTCAAAAGCTTTATACC 57.746 37.500 13.10 0.00 0.00 2.73
3393 22429 5.767665 TCTGCAACTCAAAAGCTTTATACCA 59.232 36.000 13.10 3.30 0.00 3.25
3394 22430 6.264292 TCTGCAACTCAAAAGCTTTATACCAA 59.736 34.615 13.10 0.00 0.00 3.67
3395 22431 6.810911 TGCAACTCAAAAGCTTTATACCAAA 58.189 32.000 13.10 0.00 0.00 3.28
3396 22432 6.922957 TGCAACTCAAAAGCTTTATACCAAAG 59.077 34.615 13.10 5.20 0.00 2.77
3397 22433 7.145323 GCAACTCAAAAGCTTTATACCAAAGA 58.855 34.615 13.10 0.61 0.00 2.52
3398 22434 7.651704 GCAACTCAAAAGCTTTATACCAAAGAA 59.348 33.333 13.10 0.00 0.00 2.52
3399 22435 9.696917 CAACTCAAAAGCTTTATACCAAAGAAT 57.303 29.630 13.10 0.00 0.00 2.40
3417 22453 5.991328 AGAATATATGCTTTGACCACACG 57.009 39.130 0.00 0.00 0.00 4.49
3418 22454 5.670485 AGAATATATGCTTTGACCACACGA 58.330 37.500 0.00 0.00 0.00 4.35
3419 22455 5.523916 AGAATATATGCTTTGACCACACGAC 59.476 40.000 0.00 0.00 0.00 4.34
3420 22456 2.831685 TATGCTTTGACCACACGACT 57.168 45.000 0.00 0.00 0.00 4.18
3421 22457 1.229428 ATGCTTTGACCACACGACTG 58.771 50.000 0.00 0.00 0.00 3.51
3422 22458 0.176910 TGCTTTGACCACACGACTGA 59.823 50.000 0.00 0.00 0.00 3.41
3423 22459 0.861837 GCTTTGACCACACGACTGAG 59.138 55.000 0.00 0.00 0.00 3.35
3424 22460 1.538204 GCTTTGACCACACGACTGAGA 60.538 52.381 0.00 0.00 0.00 3.27
3425 22461 2.821546 CTTTGACCACACGACTGAGAA 58.178 47.619 0.00 0.00 0.00 2.87
3426 22462 2.971660 TTGACCACACGACTGAGAAA 57.028 45.000 0.00 0.00 0.00 2.52
3427 22463 2.971660 TGACCACACGACTGAGAAAA 57.028 45.000 0.00 0.00 0.00 2.29
3428 22464 3.469008 TGACCACACGACTGAGAAAAT 57.531 42.857 0.00 0.00 0.00 1.82
3429 22465 3.390135 TGACCACACGACTGAGAAAATC 58.610 45.455 0.00 0.00 0.00 2.17
3430 22466 3.181470 TGACCACACGACTGAGAAAATCA 60.181 43.478 0.00 0.00 36.21 2.57
3431 22467 3.131396 ACCACACGACTGAGAAAATCAC 58.869 45.455 0.00 0.00 33.22 3.06
3432 22468 3.181465 ACCACACGACTGAGAAAATCACT 60.181 43.478 0.00 0.00 33.22 3.41
3433 22469 3.185188 CCACACGACTGAGAAAATCACTG 59.815 47.826 0.00 0.00 33.22 3.66
3434 22470 4.051237 CACACGACTGAGAAAATCACTGA 58.949 43.478 0.00 0.00 33.22 3.41
3435 22471 4.687948 CACACGACTGAGAAAATCACTGAT 59.312 41.667 0.00 0.00 33.22 2.90
3436 22472 5.178252 CACACGACTGAGAAAATCACTGATT 59.822 40.000 0.00 0.00 33.25 2.57
3437 22473 5.760253 ACACGACTGAGAAAATCACTGATTT 59.240 36.000 10.71 10.71 43.07 2.17
3467 22503 9.772973 TTCAACACATAAGTACATAACTGAACT 57.227 29.630 0.00 0.00 38.88 3.01
3476 22512 7.997773 AGTACATAACTGAACTAGTCACTGA 57.002 36.000 0.00 0.00 39.18 3.41
3477 22513 8.405418 AGTACATAACTGAACTAGTCACTGAA 57.595 34.615 0.00 0.00 39.18 3.02
3478 22514 9.026121 AGTACATAACTGAACTAGTCACTGAAT 57.974 33.333 0.00 0.00 39.18 2.57
3479 22515 9.640963 GTACATAACTGAACTAGTCACTGAATT 57.359 33.333 0.00 0.00 39.18 2.17
3481 22517 9.561069 ACATAACTGAACTAGTCACTGAATTTT 57.439 29.630 0.00 0.00 39.18 1.82
3482 22518 9.817365 CATAACTGAACTAGTCACTGAATTTTG 57.183 33.333 0.00 0.00 39.18 2.44
3483 22519 7.865706 AACTGAACTAGTCACTGAATTTTGT 57.134 32.000 0.00 0.00 39.18 2.83
3484 22520 7.251704 ACTGAACTAGTCACTGAATTTTGTG 57.748 36.000 0.00 5.69 33.17 3.33
3485 22521 6.260936 ACTGAACTAGTCACTGAATTTTGTGG 59.739 38.462 0.00 0.49 33.17 4.17
3486 22522 5.008613 TGAACTAGTCACTGAATTTTGTGGC 59.991 40.000 0.00 7.89 38.89 5.01
3487 22523 4.460263 ACTAGTCACTGAATTTTGTGGCA 58.540 39.130 15.37 0.00 40.81 4.92
3488 22524 4.887071 ACTAGTCACTGAATTTTGTGGCAA 59.113 37.500 15.37 0.00 40.81 4.52
3489 22525 4.045636 AGTCACTGAATTTTGTGGCAAC 57.954 40.909 15.37 6.57 40.81 4.17
3504 22540 4.804868 TGGCAACAGCAAACATGATATT 57.195 36.364 0.00 0.00 46.17 1.28
3505 22541 5.149973 TGGCAACAGCAAACATGATATTT 57.850 34.783 0.00 0.00 46.17 1.40
3506 22542 5.549347 TGGCAACAGCAAACATGATATTTT 58.451 33.333 0.00 0.00 46.17 1.82
3507 22543 6.695429 TGGCAACAGCAAACATGATATTTTA 58.305 32.000 0.00 0.00 46.17 1.52
3508 22544 7.157347 TGGCAACAGCAAACATGATATTTTAA 58.843 30.769 0.00 0.00 46.17 1.52
3509 22545 7.117523 TGGCAACAGCAAACATGATATTTTAAC 59.882 33.333 0.00 0.00 46.17 2.01
3533 22569 0.675633 GAAAAGCTGAGCCAAAGCCA 59.324 50.000 0.00 0.00 41.82 4.75
3551 22587 1.808945 CCACTGATCTGAACAAGGCAC 59.191 52.381 6.60 0.00 0.00 5.01
3553 22589 2.225019 CACTGATCTGAACAAGGCACAC 59.775 50.000 6.60 0.00 0.00 3.82
3554 22590 2.105477 ACTGATCTGAACAAGGCACACT 59.895 45.455 6.60 0.00 0.00 3.55
3556 22592 4.019860 ACTGATCTGAACAAGGCACACTAT 60.020 41.667 6.60 0.00 0.00 2.12
3614 22706 3.634448 CAGGCTACAGACTACAGCACTAT 59.366 47.826 9.11 0.00 37.02 2.12
3623 22715 4.582656 AGACTACAGCACTATAGCTTCCTG 59.417 45.833 0.00 4.12 43.70 3.86
3695 22787 2.046314 CCATCCAGGGCGTCGTTT 60.046 61.111 0.00 0.00 0.00 3.60
3722 22814 3.149981 TCATCAGACTCGTCTTCACAGT 58.850 45.455 0.00 0.00 37.98 3.55
3723 22815 3.570125 TCATCAGACTCGTCTTCACAGTT 59.430 43.478 0.00 0.00 37.98 3.16
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
74 75 2.086610 TGCTCCTTTTCCCTTTGCTT 57.913 45.000 0.00 0.00 0.00 3.91
75 76 1.897802 CATGCTCCTTTTCCCTTTGCT 59.102 47.619 0.00 0.00 0.00 3.91
76 77 1.895131 TCATGCTCCTTTTCCCTTTGC 59.105 47.619 0.00 0.00 0.00 3.68
77 78 3.057033 CAGTCATGCTCCTTTTCCCTTTG 60.057 47.826 0.00 0.00 0.00 2.77
78 79 3.160269 CAGTCATGCTCCTTTTCCCTTT 58.840 45.455 0.00 0.00 0.00 3.11
112 118 6.252995 TGGTATCAGGGAGCAAAATTTAGTT 58.747 36.000 0.00 0.00 0.00 2.24
121 127 6.495181 TGTTAAAATTTGGTATCAGGGAGCAA 59.505 34.615 0.00 0.00 32.71 3.91
301 2966 3.056678 TGCAAAATTGACAATCATCCGCT 60.057 39.130 0.05 0.00 0.00 5.52
317 2982 8.522003 TCTGAGCAAAGAATACATAATGCAAAA 58.478 29.630 0.00 0.00 36.30 2.44
406 3078 7.283807 AGTTTCCTGAACATTTACGGTAGTTTT 59.716 33.333 0.00 0.00 40.84 2.43
414 3086 6.067263 TCCAAAGTTTCCTGAACATTTACG 57.933 37.500 0.00 0.00 40.84 3.18
474 3147 0.334676 CCTGGGATGGCCTTAACCAA 59.665 55.000 3.32 0.00 44.65 3.67
520 3193 9.173939 GTTGAACAAAATCAGTGACTTATTCAG 57.826 33.333 11.50 0.00 33.71 3.02
522 3195 8.958043 GTGTTGAACAAAATCAGTGACTTATTC 58.042 33.333 0.00 0.00 0.00 1.75
523 3196 8.465999 TGTGTTGAACAAAATCAGTGACTTATT 58.534 29.630 0.00 0.00 35.24 1.40
524 3197 7.995289 TGTGTTGAACAAAATCAGTGACTTAT 58.005 30.769 0.00 0.00 35.24 1.73
525 3198 7.384439 TGTGTTGAACAAAATCAGTGACTTA 57.616 32.000 0.00 0.00 35.24 2.24
526 3199 6.266168 TGTGTTGAACAAAATCAGTGACTT 57.734 33.333 0.00 0.00 35.24 3.01
527 3200 5.895636 TGTGTTGAACAAAATCAGTGACT 57.104 34.783 0.00 0.00 35.24 3.41
528 3201 6.356977 CGTATGTGTTGAACAAAATCAGTGAC 59.643 38.462 0.00 0.00 43.61 3.67
529 3202 6.037720 ACGTATGTGTTGAACAAAATCAGTGA 59.962 34.615 0.00 0.00 43.61 3.41
530 3203 6.140580 CACGTATGTGTTGAACAAAATCAGTG 59.859 38.462 6.93 7.41 43.61 3.66
531 3204 6.037720 TCACGTATGTGTTGAACAAAATCAGT 59.962 34.615 14.63 0.00 46.49 3.41
532 3205 6.426327 TCACGTATGTGTTGAACAAAATCAG 58.574 36.000 14.63 0.00 46.49 2.90
533 3206 6.364945 TCACGTATGTGTTGAACAAAATCA 57.635 33.333 14.63 0.00 46.49 2.57
534 3207 5.339611 GCTCACGTATGTGTTGAACAAAATC 59.660 40.000 14.63 0.00 46.49 2.17
535 3208 5.008613 AGCTCACGTATGTGTTGAACAAAAT 59.991 36.000 14.63 0.00 46.49 1.82
536 3209 4.334203 AGCTCACGTATGTGTTGAACAAAA 59.666 37.500 14.63 0.00 46.49 2.44
537 3210 3.874543 AGCTCACGTATGTGTTGAACAAA 59.125 39.130 14.63 0.00 46.49 2.83
538 3211 3.462982 AGCTCACGTATGTGTTGAACAA 58.537 40.909 14.63 0.00 46.49 2.83
539 3212 3.106242 AGCTCACGTATGTGTTGAACA 57.894 42.857 14.63 0.00 46.49 3.18
540 3213 4.235360 ACTAGCTCACGTATGTGTTGAAC 58.765 43.478 14.63 0.00 46.49 3.18
541 3214 4.022676 TGACTAGCTCACGTATGTGTTGAA 60.023 41.667 14.63 0.00 46.49 2.69
542 3215 3.504520 TGACTAGCTCACGTATGTGTTGA 59.495 43.478 14.63 0.00 46.49 3.18
543 3216 3.608506 GTGACTAGCTCACGTATGTGTTG 59.391 47.826 14.63 10.00 46.49 3.33
544 3217 3.834610 GTGACTAGCTCACGTATGTGTT 58.165 45.455 14.63 5.12 46.49 3.32
545 3218 3.489180 GTGACTAGCTCACGTATGTGT 57.511 47.619 14.63 0.00 46.49 3.72
554 3227 6.156748 TCACAAAGTTTAGTGACTAGCTCA 57.843 37.500 13.46 0.00 39.65 4.26
555 3228 7.171678 ACATTCACAAAGTTTAGTGACTAGCTC 59.828 37.037 15.80 0.00 43.80 4.09
556 3229 6.992715 ACATTCACAAAGTTTAGTGACTAGCT 59.007 34.615 15.80 0.00 43.80 3.32
557 3230 7.190920 ACATTCACAAAGTTTAGTGACTAGC 57.809 36.000 15.80 0.00 43.80 3.42
558 3231 8.826710 TGAACATTCACAAAGTTTAGTGACTAG 58.173 33.333 15.80 12.27 43.80 2.57
559 3232 8.725405 TGAACATTCACAAAGTTTAGTGACTA 57.275 30.769 15.80 0.00 43.80 2.59
560 3233 7.624360 TGAACATTCACAAAGTTTAGTGACT 57.376 32.000 15.80 10.68 43.80 3.41
561 3234 8.128582 TCATGAACATTCACAAAGTTTAGTGAC 58.871 33.333 15.80 8.47 43.80 3.67
562 3235 8.219546 TCATGAACATTCACAAAGTTTAGTGA 57.780 30.769 13.46 13.46 42.55 3.41
563 3236 8.854979 TTCATGAACATTCACAAAGTTTAGTG 57.145 30.769 3.38 10.24 40.49 2.74
564 3237 7.649306 GCTTCATGAACATTCACAAAGTTTAGT 59.351 33.333 3.38 0.00 40.49 2.24
565 3238 7.648908 TGCTTCATGAACATTCACAAAGTTTAG 59.351 33.333 3.38 0.00 40.49 1.85
566 3239 7.487484 TGCTTCATGAACATTCACAAAGTTTA 58.513 30.769 3.38 0.00 40.49 2.01
567 3240 6.339730 TGCTTCATGAACATTCACAAAGTTT 58.660 32.000 3.38 0.00 40.49 2.66
568 3241 5.904941 TGCTTCATGAACATTCACAAAGTT 58.095 33.333 3.38 0.00 40.49 2.66
569 3242 5.518848 TGCTTCATGAACATTCACAAAGT 57.481 34.783 3.38 0.00 40.49 2.66
570 3243 6.831727 TTTGCTTCATGAACATTCACAAAG 57.168 33.333 3.38 11.06 40.49 2.77
571 3244 7.606858 TTTTTGCTTCATGAACATTCACAAA 57.393 28.000 3.38 6.08 40.49 2.83
594 3267 3.558006 CGCGTTCCCAAAATTTCCTTTTT 59.442 39.130 0.00 0.00 34.80 1.94
595 3268 3.127589 CGCGTTCCCAAAATTTCCTTTT 58.872 40.909 0.00 0.00 37.54 2.27
596 3269 2.547007 CCGCGTTCCCAAAATTTCCTTT 60.547 45.455 4.92 0.00 0.00 3.11
597 3270 1.000394 CCGCGTTCCCAAAATTTCCTT 60.000 47.619 4.92 0.00 0.00 3.36
598 3271 0.601057 CCGCGTTCCCAAAATTTCCT 59.399 50.000 4.92 0.00 0.00 3.36
599 3272 0.599060 TCCGCGTTCCCAAAATTTCC 59.401 50.000 4.92 0.00 0.00 3.13
600 3273 1.268625 ACTCCGCGTTCCCAAAATTTC 59.731 47.619 4.92 0.00 0.00 2.17
601 3274 1.324383 ACTCCGCGTTCCCAAAATTT 58.676 45.000 4.92 0.00 0.00 1.82
602 3275 2.188062 TACTCCGCGTTCCCAAAATT 57.812 45.000 4.92 0.00 0.00 1.82
603 3276 2.093128 AGATACTCCGCGTTCCCAAAAT 60.093 45.455 4.92 0.00 0.00 1.82
604 3277 1.276989 AGATACTCCGCGTTCCCAAAA 59.723 47.619 4.92 0.00 0.00 2.44
605 3278 0.899720 AGATACTCCGCGTTCCCAAA 59.100 50.000 4.92 0.00 0.00 3.28
606 3279 1.766494 TAGATACTCCGCGTTCCCAA 58.234 50.000 4.92 0.00 0.00 4.12
607 3280 1.611977 CATAGATACTCCGCGTTCCCA 59.388 52.381 4.92 0.00 0.00 4.37
608 3281 1.669211 GCATAGATACTCCGCGTTCCC 60.669 57.143 4.92 0.00 0.00 3.97
609 3282 1.699343 GCATAGATACTCCGCGTTCC 58.301 55.000 4.92 0.00 0.00 3.62
1200 3905 2.915659 TCCTTCCGTCACCTGCGT 60.916 61.111 0.00 0.00 0.00 5.24
1291 3996 2.037527 ACACGTCCCTCCTCTCCC 59.962 66.667 0.00 0.00 0.00 4.30
1827 19137 3.933861 ATCACAATTGGACCTACCCTC 57.066 47.619 10.83 0.00 38.00 4.30
1975 19286 6.625362 TCTCAAGCACAAAAACATACAACAA 58.375 32.000 0.00 0.00 0.00 2.83
2189 19512 4.858850 AGATGTGCCTGACCAAAATATCA 58.141 39.130 0.00 0.00 0.00 2.15
2488 20202 3.953712 AGTCGGTGTGATCACATTGTA 57.046 42.857 30.10 14.15 45.45 2.41
2528 20242 1.203187 AGTCACAGGCCTCTCCTACAA 60.203 52.381 0.00 0.00 45.52 2.41
2577 20292 6.058183 ACTCTTGCCATATCTGATACCAAAC 58.942 40.000 0.00 0.00 0.00 2.93
2749 20464 2.037847 CCAGCTTTTCCCTGGGGG 59.962 66.667 14.00 0.00 44.87 5.40
2833 20549 0.819666 CCCGCAAGCTTATCTTCCCC 60.820 60.000 0.00 0.00 31.27 4.81
2834 20550 0.819666 CCCCGCAAGCTTATCTTCCC 60.820 60.000 0.00 0.00 31.27 3.97
2835 20551 0.107165 ACCCCGCAAGCTTATCTTCC 60.107 55.000 0.00 0.00 31.27 3.46
3167 22203 5.467738 TGGATGCTTTTCTAGAGGATAGGA 58.532 41.667 0.00 0.00 0.00 2.94
3301 22337 4.768968 AGCAGCAAGTCACTATCCAAAATT 59.231 37.500 0.00 0.00 0.00 1.82
3303 22339 3.754965 AGCAGCAAGTCACTATCCAAAA 58.245 40.909 0.00 0.00 0.00 2.44
3305 22341 3.423539 AAGCAGCAAGTCACTATCCAA 57.576 42.857 0.00 0.00 0.00 3.53
3306 22342 3.260632 TGTAAGCAGCAAGTCACTATCCA 59.739 43.478 0.00 0.00 0.00 3.41
3307 22343 3.861840 TGTAAGCAGCAAGTCACTATCC 58.138 45.455 0.00 0.00 0.00 2.59
3322 22358 7.057104 CCACTTTTGATGTGTAAGCTGTAAGC 61.057 42.308 0.00 0.00 46.50 3.09
3323 22359 6.204688 TCCACTTTTGATGTGTAAGCTGTAAG 59.795 38.462 0.00 0.00 33.92 2.34
3324 22360 6.058833 TCCACTTTTGATGTGTAAGCTGTAA 58.941 36.000 0.00 0.00 33.92 2.41
3325 22361 5.616270 TCCACTTTTGATGTGTAAGCTGTA 58.384 37.500 0.00 0.00 33.92 2.74
3326 22362 4.460263 TCCACTTTTGATGTGTAAGCTGT 58.540 39.130 0.00 0.00 33.92 4.40
3327 22363 4.756642 TCTCCACTTTTGATGTGTAAGCTG 59.243 41.667 0.00 0.00 33.92 4.24
3328 22364 4.973168 TCTCCACTTTTGATGTGTAAGCT 58.027 39.130 0.00 0.00 33.92 3.74
3329 22365 5.689383 TTCTCCACTTTTGATGTGTAAGC 57.311 39.130 0.00 0.00 33.92 3.09
3330 22366 6.145535 GCTTTCTCCACTTTTGATGTGTAAG 58.854 40.000 0.00 0.00 33.92 2.34
3331 22367 5.277779 CGCTTTCTCCACTTTTGATGTGTAA 60.278 40.000 0.00 0.00 33.92 2.41
3332 22368 4.213270 CGCTTTCTCCACTTTTGATGTGTA 59.787 41.667 0.00 0.00 33.92 2.90
3333 22369 3.003689 CGCTTTCTCCACTTTTGATGTGT 59.996 43.478 0.00 0.00 33.92 3.72
3334 22370 3.250762 TCGCTTTCTCCACTTTTGATGTG 59.749 43.478 0.00 0.00 35.39 3.21
3335 22371 3.251004 GTCGCTTTCTCCACTTTTGATGT 59.749 43.478 0.00 0.00 0.00 3.06
3336 22372 3.365364 GGTCGCTTTCTCCACTTTTGATG 60.365 47.826 0.00 0.00 0.00 3.07
3337 22373 2.814336 GGTCGCTTTCTCCACTTTTGAT 59.186 45.455 0.00 0.00 0.00 2.57
3338 22374 2.218603 GGTCGCTTTCTCCACTTTTGA 58.781 47.619 0.00 0.00 0.00 2.69
3339 22375 1.266989 GGGTCGCTTTCTCCACTTTTG 59.733 52.381 0.00 0.00 0.00 2.44
3340 22376 1.605753 GGGTCGCTTTCTCCACTTTT 58.394 50.000 0.00 0.00 0.00 2.27
3341 22377 0.250770 GGGGTCGCTTTCTCCACTTT 60.251 55.000 0.00 0.00 0.00 2.66
3342 22378 1.375326 GGGGTCGCTTTCTCCACTT 59.625 57.895 0.00 0.00 0.00 3.16
3343 22379 1.831652 CTGGGGTCGCTTTCTCCACT 61.832 60.000 0.00 0.00 0.00 4.00
3344 22380 1.376037 CTGGGGTCGCTTTCTCCAC 60.376 63.158 0.00 0.00 0.00 4.02
3345 22381 3.068881 CTGGGGTCGCTTTCTCCA 58.931 61.111 0.00 0.00 0.00 3.86
3346 22382 2.436824 GCTGGGGTCGCTTTCTCC 60.437 66.667 0.00 0.00 0.00 3.71
3347 22383 2.436824 GGCTGGGGTCGCTTTCTC 60.437 66.667 0.00 0.00 0.00 2.87
3348 22384 4.035102 GGGCTGGGGTCGCTTTCT 62.035 66.667 0.00 0.00 0.00 2.52
3349 22385 4.344865 TGGGCTGGGGTCGCTTTC 62.345 66.667 0.00 0.00 0.00 2.62
3350 22386 4.660938 GTGGGCTGGGGTCGCTTT 62.661 66.667 0.00 0.00 0.00 3.51
3354 22390 3.322466 AGAAGTGGGCTGGGGTCG 61.322 66.667 0.00 0.00 0.00 4.79
3355 22391 2.352805 CAGAAGTGGGCTGGGGTC 59.647 66.667 0.00 0.00 0.00 4.46
3356 22392 3.971702 GCAGAAGTGGGCTGGGGT 61.972 66.667 0.00 0.00 34.00 4.95
3357 22393 3.512154 TTGCAGAAGTGGGCTGGGG 62.512 63.158 0.00 0.00 34.00 4.96
3358 22394 2.115910 TTGCAGAAGTGGGCTGGG 59.884 61.111 0.00 0.00 34.00 4.45
3359 22395 1.228367 AGTTGCAGAAGTGGGCTGG 60.228 57.895 0.00 0.00 34.00 4.85
3360 22396 0.535780 TGAGTTGCAGAAGTGGGCTG 60.536 55.000 0.00 0.00 36.47 4.85
3361 22397 0.183492 TTGAGTTGCAGAAGTGGGCT 59.817 50.000 0.00 0.00 0.00 5.19
3362 22398 1.032014 TTTGAGTTGCAGAAGTGGGC 58.968 50.000 0.00 0.00 0.00 5.36
3363 22399 2.544486 GCTTTTGAGTTGCAGAAGTGGG 60.544 50.000 0.00 0.00 40.02 4.61
3364 22400 2.360165 AGCTTTTGAGTTGCAGAAGTGG 59.640 45.455 0.00 0.00 40.02 4.00
3365 22401 3.705043 AGCTTTTGAGTTGCAGAAGTG 57.295 42.857 0.00 0.00 40.02 3.16
3366 22402 4.725790 AAAGCTTTTGAGTTGCAGAAGT 57.274 36.364 5.69 0.00 40.02 3.01
3367 22403 6.803807 GGTATAAAGCTTTTGAGTTGCAGAAG 59.196 38.462 18.47 0.00 40.63 2.85
3368 22404 6.264292 TGGTATAAAGCTTTTGAGTTGCAGAA 59.736 34.615 18.47 0.00 0.00 3.02
3369 22405 5.767665 TGGTATAAAGCTTTTGAGTTGCAGA 59.232 36.000 18.47 0.00 0.00 4.26
3370 22406 6.012658 TGGTATAAAGCTTTTGAGTTGCAG 57.987 37.500 18.47 0.00 0.00 4.41
3371 22407 6.398234 TTGGTATAAAGCTTTTGAGTTGCA 57.602 33.333 18.47 0.00 0.00 4.08
3372 22408 7.145323 TCTTTGGTATAAAGCTTTTGAGTTGC 58.855 34.615 18.47 1.74 0.00 4.17
3373 22409 9.696917 ATTCTTTGGTATAAAGCTTTTGAGTTG 57.303 29.630 18.47 2.19 0.00 3.16
3388 22424 8.850156 GTGGTCAAAGCATATATTCTTTGGTAT 58.150 33.333 26.98 0.51 45.45 2.73
3389 22425 7.831690 TGTGGTCAAAGCATATATTCTTTGGTA 59.168 33.333 26.98 16.12 45.45 3.25
3390 22426 6.663093 TGTGGTCAAAGCATATATTCTTTGGT 59.337 34.615 26.98 4.01 45.45 3.67
3391 22427 6.974622 GTGTGGTCAAAGCATATATTCTTTGG 59.025 38.462 26.98 14.92 45.45 3.28
3392 22428 6.688385 CGTGTGGTCAAAGCATATATTCTTTG 59.312 38.462 23.82 23.82 46.27 2.77
3393 22429 6.597672 TCGTGTGGTCAAAGCATATATTCTTT 59.402 34.615 4.72 4.72 33.20 2.52
3394 22430 6.037172 GTCGTGTGGTCAAAGCATATATTCTT 59.963 38.462 0.00 0.00 0.00 2.52
3395 22431 5.523916 GTCGTGTGGTCAAAGCATATATTCT 59.476 40.000 0.00 0.00 0.00 2.40
3396 22432 5.523916 AGTCGTGTGGTCAAAGCATATATTC 59.476 40.000 0.00 0.00 0.00 1.75
3397 22433 5.294306 CAGTCGTGTGGTCAAAGCATATATT 59.706 40.000 0.00 0.00 0.00 1.28
3398 22434 4.811024 CAGTCGTGTGGTCAAAGCATATAT 59.189 41.667 0.00 0.00 0.00 0.86
3399 22435 4.081917 TCAGTCGTGTGGTCAAAGCATATA 60.082 41.667 0.00 0.00 0.00 0.86
3400 22436 3.002791 CAGTCGTGTGGTCAAAGCATAT 58.997 45.455 0.00 0.00 0.00 1.78
3401 22437 2.036604 TCAGTCGTGTGGTCAAAGCATA 59.963 45.455 0.00 0.00 0.00 3.14
3402 22438 1.202639 TCAGTCGTGTGGTCAAAGCAT 60.203 47.619 0.00 0.00 0.00 3.79
3403 22439 0.176910 TCAGTCGTGTGGTCAAAGCA 59.823 50.000 0.00 0.00 0.00 3.91
3404 22440 0.861837 CTCAGTCGTGTGGTCAAAGC 59.138 55.000 0.00 0.00 0.00 3.51
3405 22441 2.509052 TCTCAGTCGTGTGGTCAAAG 57.491 50.000 0.00 0.00 0.00 2.77
3406 22442 2.971660 TTCTCAGTCGTGTGGTCAAA 57.028 45.000 0.00 0.00 0.00 2.69
3407 22443 2.971660 TTTCTCAGTCGTGTGGTCAA 57.028 45.000 0.00 0.00 0.00 3.18
3408 22444 2.971660 TTTTCTCAGTCGTGTGGTCA 57.028 45.000 0.00 0.00 0.00 4.02
3409 22445 3.184581 GTGATTTTCTCAGTCGTGTGGTC 59.815 47.826 0.00 0.00 33.51 4.02
3410 22446 3.131396 GTGATTTTCTCAGTCGTGTGGT 58.869 45.455 0.00 0.00 33.51 4.16
3411 22447 3.185188 CAGTGATTTTCTCAGTCGTGTGG 59.815 47.826 0.00 0.00 35.23 4.17
3412 22448 4.051237 TCAGTGATTTTCTCAGTCGTGTG 58.949 43.478 0.00 0.00 35.23 3.82
3413 22449 4.322080 TCAGTGATTTTCTCAGTCGTGT 57.678 40.909 0.00 0.00 35.23 4.49
3414 22450 5.852738 AATCAGTGATTTTCTCAGTCGTG 57.147 39.130 12.75 0.00 35.23 4.35
3415 22451 6.867662 AAAATCAGTGATTTTCTCAGTCGT 57.132 33.333 29.81 11.62 45.45 4.34
3441 22477 9.772973 AGTTCAGTTATGTACTTATGTGTTGAA 57.227 29.630 0.00 0.00 33.69 2.69
3450 22486 9.511272 TCAGTGACTAGTTCAGTTATGTACTTA 57.489 33.333 0.00 0.00 38.02 2.24
3451 22487 8.405418 TCAGTGACTAGTTCAGTTATGTACTT 57.595 34.615 0.00 0.00 38.02 2.24
3452 22488 7.997773 TCAGTGACTAGTTCAGTTATGTACT 57.002 36.000 0.00 0.00 39.94 2.73
3453 22489 9.640963 AATTCAGTGACTAGTTCAGTTATGTAC 57.359 33.333 0.00 0.00 37.72 2.90
3455 22491 9.561069 AAAATTCAGTGACTAGTTCAGTTATGT 57.439 29.630 0.00 0.00 37.72 2.29
3456 22492 9.817365 CAAAATTCAGTGACTAGTTCAGTTATG 57.183 33.333 0.00 0.00 37.72 1.90
3457 22493 9.561069 ACAAAATTCAGTGACTAGTTCAGTTAT 57.439 29.630 0.00 0.00 37.72 1.89
3458 22494 8.826710 CACAAAATTCAGTGACTAGTTCAGTTA 58.173 33.333 0.00 0.00 37.72 2.24
3459 22495 7.201732 CCACAAAATTCAGTGACTAGTTCAGTT 60.202 37.037 10.77 0.00 37.72 3.16
3460 22496 6.260936 CCACAAAATTCAGTGACTAGTTCAGT 59.739 38.462 10.77 0.00 41.47 3.41
3461 22497 6.662616 CCACAAAATTCAGTGACTAGTTCAG 58.337 40.000 10.77 0.00 37.97 3.02
3462 22498 5.008613 GCCACAAAATTCAGTGACTAGTTCA 59.991 40.000 10.77 0.00 37.97 3.18
3463 22499 5.008613 TGCCACAAAATTCAGTGACTAGTTC 59.991 40.000 10.77 0.00 37.97 3.01
3464 22500 4.887071 TGCCACAAAATTCAGTGACTAGTT 59.113 37.500 10.77 0.00 37.97 2.24
3465 22501 4.460263 TGCCACAAAATTCAGTGACTAGT 58.540 39.130 10.77 0.00 37.97 2.57
3466 22502 5.215160 GTTGCCACAAAATTCAGTGACTAG 58.785 41.667 10.77 0.00 37.97 2.57
3467 22503 4.642437 TGTTGCCACAAAATTCAGTGACTA 59.358 37.500 10.77 0.00 37.97 2.59
3468 22504 3.446873 TGTTGCCACAAAATTCAGTGACT 59.553 39.130 10.77 0.00 37.97 3.41
3469 22505 3.779759 TGTTGCCACAAAATTCAGTGAC 58.220 40.909 10.77 1.65 37.97 3.67
3470 22506 3.737663 GCTGTTGCCACAAAATTCAGTGA 60.738 43.478 10.77 0.00 37.97 3.41
3471 22507 2.540931 GCTGTTGCCACAAAATTCAGTG 59.459 45.455 0.00 3.84 35.56 3.66
3472 22508 2.168106 TGCTGTTGCCACAAAATTCAGT 59.832 40.909 0.00 0.00 38.71 3.41
3473 22509 2.823984 TGCTGTTGCCACAAAATTCAG 58.176 42.857 0.00 0.00 38.71 3.02
3474 22510 2.975732 TGCTGTTGCCACAAAATTCA 57.024 40.000 0.00 0.00 38.71 2.57
3475 22511 3.373439 TGTTTGCTGTTGCCACAAAATTC 59.627 39.130 0.00 0.00 35.25 2.17
3476 22512 3.341823 TGTTTGCTGTTGCCACAAAATT 58.658 36.364 0.00 0.00 35.25 1.82
3477 22513 2.983229 TGTTTGCTGTTGCCACAAAAT 58.017 38.095 0.00 0.00 35.25 1.82
3478 22514 2.462456 TGTTTGCTGTTGCCACAAAA 57.538 40.000 0.00 0.00 35.25 2.44
3479 22515 2.093816 TCATGTTTGCTGTTGCCACAAA 60.094 40.909 0.00 0.00 35.76 2.83
3480 22516 1.479730 TCATGTTTGCTGTTGCCACAA 59.520 42.857 0.00 0.00 35.76 3.33
3481 22517 1.109609 TCATGTTTGCTGTTGCCACA 58.890 45.000 0.00 0.00 38.71 4.17
3482 22518 2.443887 ATCATGTTTGCTGTTGCCAC 57.556 45.000 0.00 0.00 38.71 5.01
3483 22519 4.804868 AATATCATGTTTGCTGTTGCCA 57.195 36.364 0.00 0.00 38.71 4.92
3484 22520 7.117523 TGTTAAAATATCATGTTTGCTGTTGCC 59.882 33.333 0.00 0.00 38.71 4.52
3485 22521 8.016497 TGTTAAAATATCATGTTTGCTGTTGC 57.984 30.769 0.00 0.00 40.20 4.17
3487 22523 9.206870 CCTTGTTAAAATATCATGTTTGCTGTT 57.793 29.630 0.00 0.00 0.00 3.16
3488 22524 7.818930 CCCTTGTTAAAATATCATGTTTGCTGT 59.181 33.333 0.00 0.00 0.00 4.40
3489 22525 8.034215 TCCCTTGTTAAAATATCATGTTTGCTG 58.966 33.333 0.00 0.00 0.00 4.41
3490 22526 8.133024 TCCCTTGTTAAAATATCATGTTTGCT 57.867 30.769 0.00 0.00 0.00 3.91
3491 22527 8.770438 TTCCCTTGTTAAAATATCATGTTTGC 57.230 30.769 0.00 0.00 0.00 3.68
3494 22530 9.435688 GCTTTTCCCTTGTTAAAATATCATGTT 57.564 29.630 0.00 0.00 0.00 2.71
3495 22531 8.815912 AGCTTTTCCCTTGTTAAAATATCATGT 58.184 29.630 0.00 0.00 0.00 3.21
3496 22532 9.090692 CAGCTTTTCCCTTGTTAAAATATCATG 57.909 33.333 0.00 0.00 0.00 3.07
3497 22533 9.034800 TCAGCTTTTCCCTTGTTAAAATATCAT 57.965 29.630 0.00 0.00 0.00 2.45
3498 22534 8.415950 TCAGCTTTTCCCTTGTTAAAATATCA 57.584 30.769 0.00 0.00 0.00 2.15
3499 22535 7.489435 GCTCAGCTTTTCCCTTGTTAAAATATC 59.511 37.037 0.00 0.00 0.00 1.63
3500 22536 7.323420 GCTCAGCTTTTCCCTTGTTAAAATAT 58.677 34.615 0.00 0.00 0.00 1.28
3501 22537 6.295067 GGCTCAGCTTTTCCCTTGTTAAAATA 60.295 38.462 0.00 0.00 0.00 1.40
3502 22538 5.511373 GGCTCAGCTTTTCCCTTGTTAAAAT 60.511 40.000 0.00 0.00 0.00 1.82
3503 22539 4.202212 GGCTCAGCTTTTCCCTTGTTAAAA 60.202 41.667 0.00 0.00 0.00 1.52
3504 22540 3.320826 GGCTCAGCTTTTCCCTTGTTAAA 59.679 43.478 0.00 0.00 0.00 1.52
3505 22541 2.890945 GGCTCAGCTTTTCCCTTGTTAA 59.109 45.455 0.00 0.00 0.00 2.01
3506 22542 2.158534 TGGCTCAGCTTTTCCCTTGTTA 60.159 45.455 0.00 0.00 0.00 2.41
3507 22543 1.332195 GGCTCAGCTTTTCCCTTGTT 58.668 50.000 0.00 0.00 0.00 2.83
3508 22544 0.185901 TGGCTCAGCTTTTCCCTTGT 59.814 50.000 0.00 0.00 0.00 3.16
3509 22545 1.331214 TTGGCTCAGCTTTTCCCTTG 58.669 50.000 0.00 0.00 0.00 3.61
3533 22569 2.105477 AGTGTGCCTTGTTCAGATCAGT 59.895 45.455 0.00 0.00 0.00 3.41
3551 22587 1.024271 CCCCAATGAACGGCATAGTG 58.976 55.000 0.00 0.00 35.78 2.74
3553 22589 1.455383 GCCCCCAATGAACGGCATAG 61.455 60.000 0.00 0.00 41.25 2.23
3554 22590 1.454847 GCCCCCAATGAACGGCATA 60.455 57.895 0.00 0.00 41.25 3.14
3559 22595 2.099405 AGTATTTGCCCCCAATGAACG 58.901 47.619 0.00 0.00 0.00 3.95
3560 22596 5.869649 AATAGTATTTGCCCCCAATGAAC 57.130 39.130 0.00 0.00 0.00 3.18
3567 22658 4.072839 GCAGAGTAATAGTATTTGCCCCC 58.927 47.826 0.00 0.00 0.00 5.40
3623 22715 1.587613 GCAGTCTCTCGTGATCCGC 60.588 63.158 0.00 0.00 36.19 5.54
3668 22760 2.693864 CTGGATGGCCTCCCCTGT 60.694 66.667 15.98 0.00 44.23 4.00
3695 22787 2.271607 GACGAGTCTGATGAGGCGCA 62.272 60.000 10.83 0.00 0.00 6.09


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

AutoCloner maintained by Alex Coulton.