Multiple sequence alignment - TraesCS4A01G346100

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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 TraesCS4A01G346100 chr4A 100.000 3293 0 0 1 3293 625167242 625163950 0.000000e+00 6082.0
1 TraesCS4A01G346100 chr4A 84.874 1937 228 44 592 2494 625078031 625076126 0.000000e+00 1893.0
2 TraesCS4A01G346100 chr4A 79.223 1261 247 13 999 2250 624369657 624370911 0.000000e+00 863.0
3 TraesCS4A01G346100 chr4A 98.611 144 2 0 3150 3293 30770597 30770454 4.220000e-64 255.0
4 TraesCS4A01G346100 chr4A 91.667 108 8 1 2904 3010 142465985 142465878 7.360000e-32 148.0
5 TraesCS4A01G346100 chr4A 80.380 158 12 8 1 149 625078407 625078260 5.810000e-18 102.0
6 TraesCS4A01G346100 chr4A 89.855 69 7 0 2497 2565 37059006 37059074 4.530000e-14 89.8
7 TraesCS4A01G346100 chr4A 97.222 36 1 0 592 627 625091846 625091811 9.870000e-06 62.1
8 TraesCS4A01G346100 chr5D 93.401 2349 94 16 582 2906 544148573 544150884 0.000000e+00 3422.0
9 TraesCS4A01G346100 chr5D 84.248 1949 247 38 583 2495 544231047 544232971 0.000000e+00 1844.0
10 TraesCS4A01G346100 chr5D 79.055 1270 250 13 999 2260 544481609 544482870 0.000000e+00 857.0
11 TraesCS4A01G346100 chr5D 86.819 349 25 6 5 339 544148231 544148572 1.440000e-98 370.0
12 TraesCS4A01G346100 chr5D 83.750 160 11 10 183 342 544213960 544214104 1.590000e-28 137.0
13 TraesCS4A01G346100 chr5D 89.583 96 10 0 3018 3113 544150886 544150981 4.460000e-24 122.0
14 TraesCS4A01G346100 chr5D 80.380 158 14 9 1 149 544230668 544230817 1.620000e-18 104.0
15 TraesCS4A01G346100 chr5D 100.000 28 0 0 668 695 544481226 544481253 6.000000e-03 52.8
16 TraesCS4A01G346100 chr5B 92.086 2464 138 22 473 2902 686200577 686203017 0.000000e+00 3417.0
17 TraesCS4A01G346100 chr5B 89.601 1327 103 14 1599 2906 686342922 686344232 0.000000e+00 1653.0
18 TraesCS4A01G346100 chr5B 85.667 1514 193 12 998 2495 686432236 686433741 0.000000e+00 1572.0
19 TraesCS4A01G346100 chr5B 78.228 1332 255 22 999 2320 686769939 686771245 0.000000e+00 821.0
20 TraesCS4A01G346100 chr5B 78.116 1316 257 20 1010 2320 686761973 686763262 0.000000e+00 806.0
21 TraesCS4A01G346100 chr5B 88.167 431 28 9 26 448 686199946 686200361 2.950000e-135 492.0
22 TraesCS4A01G346100 chr5B 95.833 144 6 0 3150 3293 88332765 88332908 1.980000e-57 233.0
23 TraesCS4A01G346100 chr5B 92.647 68 5 0 2497 2564 341534135 341534202 7.520000e-17 99.0
24 TraesCS4A01G346100 chr3A 98.621 145 2 0 3149 3293 13451054 13451198 1.170000e-64 257.0
25 TraesCS4A01G346100 chr3A 91.262 103 8 1 2904 3005 661650805 661650703 4.430000e-29 139.0
26 TraesCS4A01G346100 chr3B 95.833 144 6 0 3150 3293 180481585 180481442 1.980000e-57 233.0
27 TraesCS4A01G346100 chr3B 94.444 144 8 0 3150 3293 182350191 182350048 4.280000e-54 222.0
28 TraesCS4A01G346100 chr7B 95.139 144 7 0 3150 3293 685902617 685902474 9.190000e-56 228.0
29 TraesCS4A01G346100 chr7B 88.679 53 6 0 359 411 108269948 108269896 7.630000e-07 65.8
30 TraesCS4A01G346100 chr6B 95.139 144 7 0 3150 3293 149456641 149456498 9.190000e-56 228.0
31 TraesCS4A01G346100 chr6B 90.991 111 9 1 2901 3010 451336996 451336886 7.360000e-32 148.0
32 TraesCS4A01G346100 chr2B 94.444 144 8 0 3150 3293 661443090 661442947 4.280000e-54 222.0
33 TraesCS4A01G346100 chr2B 93.750 144 9 0 3150 3293 655609998 655610141 1.990000e-52 217.0
34 TraesCS4A01G346100 chr2A 81.865 193 29 6 1744 1934 409437638 409437826 1.220000e-34 158.0
35 TraesCS4A01G346100 chr2A 93.939 66 4 0 2497 2562 652565023 652565088 2.090000e-17 100.0
36 TraesCS4A01G346100 chr6A 92.381 105 7 1 2903 3006 352670713 352670817 7.360000e-32 148.0
37 TraesCS4A01G346100 chr6A 90.741 108 9 1 2904 3010 50117727 50117620 3.430000e-30 143.0
38 TraesCS4A01G346100 chr5A 91.589 107 8 1 2904 3009 26132648 26132542 2.650000e-31 147.0
39 TraesCS4A01G346100 chr5A 91.429 105 8 1 2907 3010 327585910 327585806 3.430000e-30 143.0
40 TraesCS4A01G346100 chr5A 91.429 105 8 1 2903 3006 386247722 386247826 3.430000e-30 143.0
41 TraesCS4A01G346100 chr1A 88.496 113 11 2 2900 3010 149631226 149631114 5.730000e-28 135.0
42 TraesCS4A01G346100 chr4D 94.118 68 4 0 2497 2564 21147799 21147732 1.620000e-18 104.0
43 TraesCS4A01G346100 chr3D 91.429 70 6 0 2497 2566 149764717 149764786 2.700000e-16 97.1
44 TraesCS4A01G346100 chr3D 90.141 71 7 0 2497 2567 607380480 607380410 3.500000e-15 93.5


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 TraesCS4A01G346100 chr4A 625163950 625167242 3292 True 6082.000000 6082 100.000000 1 3293 1 chr4A.!!$R4 3292
1 TraesCS4A01G346100 chr4A 625076126 625078407 2281 True 997.500000 1893 82.627000 1 2494 2 chr4A.!!$R5 2493
2 TraesCS4A01G346100 chr4A 624369657 624370911 1254 False 863.000000 863 79.223000 999 2250 1 chr4A.!!$F2 1251
3 TraesCS4A01G346100 chr5D 544148231 544150981 2750 False 1304.666667 3422 89.934333 5 3113 3 chr5D.!!$F2 3108
4 TraesCS4A01G346100 chr5D 544230668 544232971 2303 False 974.000000 1844 82.314000 1 2495 2 chr5D.!!$F3 2494
5 TraesCS4A01G346100 chr5D 544481226 544482870 1644 False 454.900000 857 89.527500 668 2260 2 chr5D.!!$F4 1592
6 TraesCS4A01G346100 chr5B 686199946 686203017 3071 False 1954.500000 3417 90.126500 26 2902 2 chr5B.!!$F7 2876
7 TraesCS4A01G346100 chr5B 686342922 686344232 1310 False 1653.000000 1653 89.601000 1599 2906 1 chr5B.!!$F3 1307
8 TraesCS4A01G346100 chr5B 686432236 686433741 1505 False 1572.000000 1572 85.667000 998 2495 1 chr5B.!!$F4 1497
9 TraesCS4A01G346100 chr5B 686769939 686771245 1306 False 821.000000 821 78.228000 999 2320 1 chr5B.!!$F6 1321
10 TraesCS4A01G346100 chr5B 686761973 686763262 1289 False 806.000000 806 78.116000 1010 2320 1 chr5B.!!$F5 1310

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
227 285 1.421410 GCATACGTGACAAGAGCCGG 61.421 60.000 0.0 0.0 0.0 6.13 F
1312 1765 1.691976 TCCTCGGCTCAAACTCTTTCA 59.308 47.619 0.0 0.0 0.0 2.69 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1341 1794 0.598942 GCTTCCTTAGCCTAGCGAGC 60.599 60.0 0.0 0.0 44.48 5.03 R
3151 3652 0.032130 CAAGGCGCGCTCCTTATCTA 59.968 55.0 29.9 0.0 44.24 1.98 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
149 161 4.363990 AGACGAGCGCCACAGTGG 62.364 66.667 16.16 16.16 41.55 4.00
150 162 4.357947 GACGAGCGCCACAGTGGA 62.358 66.667 24.96 0.00 40.96 4.02
151 163 4.664677 ACGAGCGCCACAGTGGAC 62.665 66.667 24.96 14.13 40.96 4.02
152 164 4.662961 CGAGCGCCACAGTGGACA 62.663 66.667 24.96 0.00 40.96 4.02
153 165 2.740055 GAGCGCCACAGTGGACAG 60.740 66.667 24.96 14.09 40.96 3.51
154 166 3.521529 GAGCGCCACAGTGGACAGT 62.522 63.158 24.96 3.72 40.96 3.55
155 167 3.349006 GCGCCACAGTGGACAGTG 61.349 66.667 24.96 7.72 40.96 3.66
176 188 3.006430 TGCATCCTGACTTTTGACGACTA 59.994 43.478 0.00 0.00 0.00 2.59
199 257 2.821366 GTGGCCGCACAGGATCAG 60.821 66.667 12.58 0.00 45.00 2.90
213 271 4.100189 ACAGGATCAGTGAACTAGGCATAC 59.900 45.833 0.00 0.00 0.00 2.39
227 285 1.421410 GCATACGTGACAAGAGCCGG 61.421 60.000 0.00 0.00 0.00 6.13
347 412 4.444536 CTCGTCTAGTTGCTACTACCTCT 58.555 47.826 3.76 0.00 35.78 3.69
352 417 5.648960 GTCTAGTTGCTACTACCTCTGTTCT 59.351 44.000 3.76 0.00 35.78 3.01
368 433 7.769044 ACCTCTGTTCTATAATGTGCGTATTTT 59.231 33.333 0.00 0.00 0.00 1.82
369 434 8.612619 CCTCTGTTCTATAATGTGCGTATTTTT 58.387 33.333 0.00 0.00 0.00 1.94
370 435 9.638300 CTCTGTTCTATAATGTGCGTATTTTTC 57.362 33.333 0.00 0.00 0.00 2.29
423 488 7.039882 TGACCGACTTTATGGAGAAAACTATC 58.960 38.462 0.00 0.00 0.00 2.08
500 755 7.977818 TGATATAGGTTTGGCATTCTAGATGT 58.022 34.615 0.00 0.00 0.00 3.06
504 759 6.670695 AGGTTTGGCATTCTAGATGTTTTT 57.329 33.333 0.00 0.00 0.00 1.94
505 760 6.691508 AGGTTTGGCATTCTAGATGTTTTTC 58.308 36.000 0.00 0.00 0.00 2.29
596 854 4.469657 AGAGGGAGTACTAGATGAGCTTG 58.530 47.826 0.00 0.00 0.00 4.01
807 1237 5.465724 GGCCACGGTCTAAACATTCTTATAG 59.534 44.000 0.00 0.00 0.00 1.31
1189 1642 2.360350 AAGGTGTGGGCTGCGATG 60.360 61.111 0.00 0.00 0.00 3.84
1266 1719 1.836604 CCCAGGAGCCTCTCTAGCC 60.837 68.421 0.00 0.00 0.00 3.93
1302 1755 2.277858 GGAACTCTTCCTCGGCTCA 58.722 57.895 0.00 0.00 46.57 4.26
1312 1765 1.691976 TCCTCGGCTCAAACTCTTTCA 59.308 47.619 0.00 0.00 0.00 2.69
1537 1990 1.077429 AATGGCTTCTCCGGCTTCC 60.077 57.895 0.00 0.00 37.80 3.46
1569 2022 6.017192 CGTCTCTGTCATCACTATCATCTCTT 60.017 42.308 0.00 0.00 0.00 2.85
1574 2027 5.218885 GTCATCACTATCATCTCTTCGTGG 58.781 45.833 0.00 0.00 0.00 4.94
1979 2436 1.340502 TGGGAGCAACAACACTGTCAA 60.341 47.619 0.00 0.00 33.45 3.18
2097 2554 3.506067 GGGACAACAATGTTCTAACTGGG 59.494 47.826 0.00 0.00 40.74 4.45
2344 2806 1.219124 GCGAGATCCCAGAGCACAA 59.781 57.895 0.00 0.00 0.00 3.33
2394 2865 5.118990 TCTTCACTCAGAACTGAAAACCTG 58.881 41.667 6.01 0.00 39.39 4.00
2511 2988 7.764695 TTCCGCAATTATATACATCCGTATG 57.235 36.000 0.00 0.00 38.79 2.39
2588 3065 8.361592 AGTATGTATTTCCGTACTTGCAATAC 57.638 34.615 0.00 4.41 34.28 1.89
2591 3068 8.951787 ATGTATTTCCGTACTTGCAATACTAA 57.048 30.769 0.00 0.75 33.34 2.24
2627 3104 7.932491 CCAGCCTATCATGAGAATTATATCCAG 59.068 40.741 0.09 0.00 0.00 3.86
2638 3115 4.541973 ATTATATCCAGCGATGCACTCA 57.458 40.909 0.00 0.00 0.00 3.41
2690 3167 9.899661 ACAGCTTGTGGTTATTGTTATTAGATA 57.100 29.630 0.00 0.00 0.00 1.98
2777 3254 6.238621 CCATTAGTGCTAACTGTCAACAACAA 60.239 38.462 0.00 0.00 37.45 2.83
2825 3302 0.120377 TGAGGTGGGGAAGTGGGTAT 59.880 55.000 0.00 0.00 0.00 2.73
2906 3401 1.425412 GTTGGACGTTCGCATGTACT 58.575 50.000 0.00 0.00 0.00 2.73
2907 3402 1.389106 GTTGGACGTTCGCATGTACTC 59.611 52.381 0.00 0.00 0.00 2.59
2908 3403 0.108992 TGGACGTTCGCATGTACTCC 60.109 55.000 0.00 1.60 0.00 3.85
2909 3404 0.804933 GGACGTTCGCATGTACTCCC 60.805 60.000 0.00 0.00 0.00 4.30
2910 3405 0.172803 GACGTTCGCATGTACTCCCT 59.827 55.000 0.00 0.00 0.00 4.20
2911 3406 0.172803 ACGTTCGCATGTACTCCCTC 59.827 55.000 0.00 0.00 0.00 4.30
2912 3407 0.456221 CGTTCGCATGTACTCCCTCT 59.544 55.000 0.00 0.00 0.00 3.69
2913 3408 1.799181 CGTTCGCATGTACTCCCTCTG 60.799 57.143 0.00 0.00 0.00 3.35
2914 3409 1.204941 GTTCGCATGTACTCCCTCTGT 59.795 52.381 0.00 0.00 0.00 3.41
2915 3410 1.557099 TCGCATGTACTCCCTCTGTT 58.443 50.000 0.00 0.00 0.00 3.16
2916 3411 1.476891 TCGCATGTACTCCCTCTGTTC 59.523 52.381 0.00 0.00 0.00 3.18
2917 3412 1.471676 CGCATGTACTCCCTCTGTTCC 60.472 57.143 0.00 0.00 0.00 3.62
2918 3413 1.555075 GCATGTACTCCCTCTGTTCCA 59.445 52.381 0.00 0.00 0.00 3.53
2919 3414 2.419297 GCATGTACTCCCTCTGTTCCAG 60.419 54.545 0.00 0.00 0.00 3.86
2920 3415 2.992847 TGTACTCCCTCTGTTCCAGA 57.007 50.000 0.00 0.00 38.25 3.86
2921 3416 3.474798 TGTACTCCCTCTGTTCCAGAT 57.525 47.619 0.00 0.00 39.92 2.90
2922 3417 3.791320 TGTACTCCCTCTGTTCCAGATT 58.209 45.455 0.00 0.00 39.92 2.40
2923 3418 4.942944 TGTACTCCCTCTGTTCCAGATTA 58.057 43.478 0.00 0.00 39.92 1.75
2924 3419 4.710375 TGTACTCCCTCTGTTCCAGATTAC 59.290 45.833 0.00 0.00 39.92 1.89
2925 3420 4.067944 ACTCCCTCTGTTCCAGATTACT 57.932 45.455 0.00 0.00 39.92 2.24
2926 3421 4.027437 ACTCCCTCTGTTCCAGATTACTC 58.973 47.826 0.00 0.00 39.92 2.59
2927 3422 4.026744 CTCCCTCTGTTCCAGATTACTCA 58.973 47.826 0.00 0.00 39.92 3.41
2928 3423 4.624913 TCCCTCTGTTCCAGATTACTCAT 58.375 43.478 0.00 0.00 39.92 2.90
2929 3424 4.651503 TCCCTCTGTTCCAGATTACTCATC 59.348 45.833 0.00 0.00 39.92 2.92
2930 3425 4.406972 CCCTCTGTTCCAGATTACTCATCA 59.593 45.833 0.00 0.00 39.92 3.07
2931 3426 5.355596 CCTCTGTTCCAGATTACTCATCAC 58.644 45.833 0.00 0.00 39.92 3.06
2932 3427 5.105187 CCTCTGTTCCAGATTACTCATCACA 60.105 44.000 0.00 0.00 39.92 3.58
2933 3428 5.970592 TCTGTTCCAGATTACTCATCACAG 58.029 41.667 0.00 0.00 35.39 3.66
2934 3429 5.716703 TCTGTTCCAGATTACTCATCACAGA 59.283 40.000 0.00 0.00 38.21 3.41
2935 3430 6.211384 TCTGTTCCAGATTACTCATCACAGAA 59.789 38.462 0.00 0.00 37.86 3.02
2936 3431 6.768483 TGTTCCAGATTACTCATCACAGAAA 58.232 36.000 0.00 0.00 33.75 2.52
2937 3432 7.397221 TGTTCCAGATTACTCATCACAGAAAT 58.603 34.615 0.00 0.00 33.75 2.17
2938 3433 7.335171 TGTTCCAGATTACTCATCACAGAAATG 59.665 37.037 0.00 0.00 33.75 2.32
2939 3434 6.351711 TCCAGATTACTCATCACAGAAATGG 58.648 40.000 0.00 0.00 33.75 3.16
2940 3435 6.156775 TCCAGATTACTCATCACAGAAATGGA 59.843 38.462 0.00 0.00 33.75 3.41
2941 3436 6.996879 CCAGATTACTCATCACAGAAATGGAT 59.003 38.462 0.00 0.00 33.75 3.41
2942 3437 8.152898 CCAGATTACTCATCACAGAAATGGATA 58.847 37.037 0.00 0.00 33.75 2.59
2943 3438 9.722184 CAGATTACTCATCACAGAAATGGATAT 57.278 33.333 0.00 0.00 33.75 1.63
2985 3480 8.793592 ACATTAGATACATCTATACTTGCGACA 58.206 33.333 0.00 0.00 39.02 4.35
2986 3481 9.626045 CATTAGATACATCTATACTTGCGACAA 57.374 33.333 0.00 0.00 39.02 3.18
2987 3482 9.847706 ATTAGATACATCTATACTTGCGACAAG 57.152 33.333 15.16 15.16 39.02 3.16
2988 3483 7.278461 AGATACATCTATACTTGCGACAAGT 57.722 36.000 22.53 22.53 34.85 3.16
2989 3484 8.392372 AGATACATCTATACTTGCGACAAGTA 57.608 34.615 24.52 24.52 37.18 2.24
2990 3485 8.847196 AGATACATCTATACTTGCGACAAGTAA 58.153 33.333 25.44 15.64 36.45 2.24
2991 3486 9.627395 GATACATCTATACTTGCGACAAGTAAT 57.373 33.333 25.44 16.91 36.45 1.89
2992 3487 9.982651 ATACATCTATACTTGCGACAAGTAATT 57.017 29.630 25.44 17.22 36.45 1.40
2993 3488 8.354011 ACATCTATACTTGCGACAAGTAATTC 57.646 34.615 25.44 0.00 36.45 2.17
2994 3489 7.979537 ACATCTATACTTGCGACAAGTAATTCA 59.020 33.333 25.44 15.42 36.45 2.57
2995 3490 7.987268 TCTATACTTGCGACAAGTAATTCAG 57.013 36.000 25.44 20.42 36.45 3.02
2996 3491 7.768240 TCTATACTTGCGACAAGTAATTCAGA 58.232 34.615 25.44 21.58 36.45 3.27
2997 3492 8.248253 TCTATACTTGCGACAAGTAATTCAGAA 58.752 33.333 25.44 11.09 36.45 3.02
2998 3493 5.344207 ACTTGCGACAAGTAATTCAGAAC 57.656 39.130 19.21 0.00 0.00 3.01
2999 3494 4.084537 ACTTGCGACAAGTAATTCAGAACG 60.085 41.667 19.21 0.00 0.00 3.95
3000 3495 2.734606 TGCGACAAGTAATTCAGAACGG 59.265 45.455 0.00 0.00 0.00 4.44
3001 3496 2.991190 GCGACAAGTAATTCAGAACGGA 59.009 45.455 0.00 0.00 0.00 4.69
3002 3497 3.060895 GCGACAAGTAATTCAGAACGGAG 59.939 47.826 0.00 0.00 0.00 4.63
3003 3498 3.612860 CGACAAGTAATTCAGAACGGAGG 59.387 47.826 0.00 0.00 0.00 4.30
3004 3499 3.933332 GACAAGTAATTCAGAACGGAGGG 59.067 47.826 0.00 0.00 0.00 4.30
3005 3500 3.581332 ACAAGTAATTCAGAACGGAGGGA 59.419 43.478 0.00 0.00 0.00 4.20
3006 3501 4.041198 ACAAGTAATTCAGAACGGAGGGAA 59.959 41.667 0.00 0.00 0.00 3.97
3007 3502 5.186198 CAAGTAATTCAGAACGGAGGGAAT 58.814 41.667 0.00 0.00 0.00 3.01
3008 3503 6.070424 ACAAGTAATTCAGAACGGAGGGAATA 60.070 38.462 0.00 0.00 30.29 1.75
3009 3504 5.915175 AGTAATTCAGAACGGAGGGAATAC 58.085 41.667 0.00 0.00 30.29 1.89
3010 3505 3.840124 ATTCAGAACGGAGGGAATACC 57.160 47.619 0.00 0.00 40.67 2.73
3051 3546 1.784525 CACTCGACCTGACTTTGACC 58.215 55.000 0.00 0.00 0.00 4.02
3056 3551 0.250338 GACCTGACTTTGACCGGCTT 60.250 55.000 0.00 0.00 0.00 4.35
3057 3552 0.182775 ACCTGACTTTGACCGGCTTT 59.817 50.000 0.00 0.00 0.00 3.51
3058 3553 0.593128 CCTGACTTTGACCGGCTTTG 59.407 55.000 0.00 0.00 0.00 2.77
3059 3554 0.593128 CTGACTTTGACCGGCTTTGG 59.407 55.000 0.00 0.00 0.00 3.28
3060 3555 0.181587 TGACTTTGACCGGCTTTGGA 59.818 50.000 0.00 0.00 0.00 3.53
3061 3556 0.875059 GACTTTGACCGGCTTTGGAG 59.125 55.000 0.00 0.00 0.00 3.86
3062 3557 0.537371 ACTTTGACCGGCTTTGGAGG 60.537 55.000 0.00 0.00 0.00 4.30
3100 3601 2.092429 TGACTTTGACTGGCTTTGGAGT 60.092 45.455 0.00 0.00 0.00 3.85
3113 3614 3.763897 GCTTTGGAGTTCTCTCTCTCTCT 59.236 47.826 0.00 0.00 40.29 3.10
3114 3615 4.142381 GCTTTGGAGTTCTCTCTCTCTCTC 60.142 50.000 0.00 0.00 40.29 3.20
3115 3616 4.927267 TTGGAGTTCTCTCTCTCTCTCT 57.073 45.455 0.00 0.00 40.29 3.10
3116 3617 4.487714 TGGAGTTCTCTCTCTCTCTCTC 57.512 50.000 0.00 0.00 40.29 3.20
3117 3618 4.104086 TGGAGTTCTCTCTCTCTCTCTCT 58.896 47.826 0.00 0.00 40.29 3.10
3118 3619 4.162320 TGGAGTTCTCTCTCTCTCTCTCTC 59.838 50.000 0.00 0.00 40.29 3.20
3119 3620 4.407296 GGAGTTCTCTCTCTCTCTCTCTCT 59.593 50.000 0.00 0.00 40.29 3.10
3120 3621 5.452636 GGAGTTCTCTCTCTCTCTCTCTCTC 60.453 52.000 0.00 0.00 40.29 3.20
3121 3622 5.276440 AGTTCTCTCTCTCTCTCTCTCTCT 58.724 45.833 0.00 0.00 0.00 3.10
3122 3623 5.362430 AGTTCTCTCTCTCTCTCTCTCTCTC 59.638 48.000 0.00 0.00 0.00 3.20
3123 3624 5.136068 TCTCTCTCTCTCTCTCTCTCTCT 57.864 47.826 0.00 0.00 0.00 3.10
3124 3625 5.136828 TCTCTCTCTCTCTCTCTCTCTCTC 58.863 50.000 0.00 0.00 0.00 3.20
3125 3626 5.103728 TCTCTCTCTCTCTCTCTCTCTCTCT 60.104 48.000 0.00 0.00 0.00 3.10
3126 3627 5.136828 TCTCTCTCTCTCTCTCTCTCTCTC 58.863 50.000 0.00 0.00 0.00 3.20
3127 3628 5.103728 TCTCTCTCTCTCTCTCTCTCTCTCT 60.104 48.000 0.00 0.00 0.00 3.10
3128 3629 5.136828 TCTCTCTCTCTCTCTCTCTCTCTC 58.863 50.000 0.00 0.00 0.00 3.20
3129 3630 5.103728 TCTCTCTCTCTCTCTCTCTCTCTCT 60.104 48.000 0.00 0.00 0.00 3.10
3130 3631 5.136828 TCTCTCTCTCTCTCTCTCTCTCTC 58.863 50.000 0.00 0.00 0.00 3.20
3131 3632 5.103728 TCTCTCTCTCTCTCTCTCTCTCTCT 60.104 48.000 0.00 0.00 0.00 3.10
3132 3633 5.136828 TCTCTCTCTCTCTCTCTCTCTCTC 58.863 50.000 0.00 0.00 0.00 3.20
3133 3634 5.103728 TCTCTCTCTCTCTCTCTCTCTCTCT 60.104 48.000 0.00 0.00 0.00 3.10
3134 3635 5.136828 TCTCTCTCTCTCTCTCTCTCTCTC 58.863 50.000 0.00 0.00 0.00 3.20
3135 3636 5.103728 TCTCTCTCTCTCTCTCTCTCTCTCT 60.104 48.000 0.00 0.00 0.00 3.10
3136 3637 5.136828 TCTCTCTCTCTCTCTCTCTCTCTC 58.863 50.000 0.00 0.00 0.00 3.20
3137 3638 5.103728 TCTCTCTCTCTCTCTCTCTCTCTCT 60.104 48.000 0.00 0.00 0.00 3.10
3138 3639 5.136828 TCTCTCTCTCTCTCTCTCTCTCTC 58.863 50.000 0.00 0.00 0.00 3.20
3139 3640 5.103728 TCTCTCTCTCTCTCTCTCTCTCTCT 60.104 48.000 0.00 0.00 0.00 3.10
3140 3641 5.136828 TCTCTCTCTCTCTCTCTCTCTCTC 58.863 50.000 0.00 0.00 0.00 3.20
3141 3642 4.871822 TCTCTCTCTCTCTCTCTCTCTCA 58.128 47.826 0.00 0.00 0.00 3.27
3142 3643 5.462240 TCTCTCTCTCTCTCTCTCTCTCAT 58.538 45.833 0.00 0.00 0.00 2.90
3143 3644 5.303845 TCTCTCTCTCTCTCTCTCTCTCATG 59.696 48.000 0.00 0.00 0.00 3.07
3144 3645 4.964897 TCTCTCTCTCTCTCTCTCTCATGT 59.035 45.833 0.00 0.00 0.00 3.21
3145 3646 6.136155 TCTCTCTCTCTCTCTCTCTCATGTA 58.864 44.000 0.00 0.00 0.00 2.29
3146 3647 6.266330 TCTCTCTCTCTCTCTCTCTCATGTAG 59.734 46.154 0.00 0.00 0.00 2.74
3147 3648 5.899547 TCTCTCTCTCTCTCTCTCATGTAGT 59.100 44.000 0.00 0.00 0.00 2.73
3148 3649 6.040955 TCTCTCTCTCTCTCTCTCATGTAGTC 59.959 46.154 0.00 0.00 0.00 2.59
3149 3650 5.660864 TCTCTCTCTCTCTCTCATGTAGTCA 59.339 44.000 0.00 0.00 0.00 3.41
3150 3651 5.670485 TCTCTCTCTCTCTCATGTAGTCAC 58.330 45.833 0.00 0.00 0.00 3.67
3151 3652 5.425217 TCTCTCTCTCTCTCATGTAGTCACT 59.575 44.000 0.00 0.00 0.00 3.41
3152 3653 6.609616 TCTCTCTCTCTCTCATGTAGTCACTA 59.390 42.308 0.00 0.00 0.00 2.74
3153 3654 6.816136 TCTCTCTCTCTCATGTAGTCACTAG 58.184 44.000 0.00 0.00 0.00 2.57
3154 3655 6.609616 TCTCTCTCTCTCATGTAGTCACTAGA 59.390 42.308 0.00 0.00 0.00 2.43
3155 3656 7.290014 TCTCTCTCTCTCATGTAGTCACTAGAT 59.710 40.741 0.00 0.00 0.00 1.98
3156 3657 8.485578 TCTCTCTCTCATGTAGTCACTAGATA 57.514 38.462 0.00 0.00 0.00 1.98
3157 3658 8.929487 TCTCTCTCTCATGTAGTCACTAGATAA 58.071 37.037 0.00 0.00 0.00 1.75
3158 3659 9.208022 CTCTCTCTCATGTAGTCACTAGATAAG 57.792 40.741 0.00 0.00 0.00 1.73
3159 3660 8.154203 TCTCTCTCATGTAGTCACTAGATAAGG 58.846 40.741 0.00 0.00 0.00 2.69
3160 3661 8.035448 TCTCTCATGTAGTCACTAGATAAGGA 57.965 38.462 0.00 0.00 0.00 3.36
3161 3662 8.154203 TCTCTCATGTAGTCACTAGATAAGGAG 58.846 40.741 0.00 3.62 0.00 3.69
3162 3663 6.712998 TCTCATGTAGTCACTAGATAAGGAGC 59.287 42.308 0.00 0.00 0.00 4.70
3163 3664 5.470437 TCATGTAGTCACTAGATAAGGAGCG 59.530 44.000 0.00 0.00 0.00 5.03
3164 3665 3.564644 TGTAGTCACTAGATAAGGAGCGC 59.435 47.826 0.00 0.00 0.00 5.92
3165 3666 1.604755 AGTCACTAGATAAGGAGCGCG 59.395 52.381 0.00 0.00 0.00 6.86
3166 3667 0.311165 TCACTAGATAAGGAGCGCGC 59.689 55.000 26.66 26.66 0.00 6.86
3167 3668 0.664767 CACTAGATAAGGAGCGCGCC 60.665 60.000 30.33 23.92 0.00 6.53
3168 3669 0.824182 ACTAGATAAGGAGCGCGCCT 60.824 55.000 28.32 28.32 40.93 5.52
3192 3693 4.717313 GAGGGTGCCGGTCCCAAC 62.717 72.222 29.22 21.14 46.82 3.77
3194 3695 4.360405 GGGTGCCGGTCCCAACAT 62.360 66.667 25.06 0.00 44.05 2.71
3195 3696 2.282887 GGTGCCGGTCCCAACATT 60.283 61.111 1.90 0.00 0.00 2.71
3196 3697 1.906333 GGTGCCGGTCCCAACATTT 60.906 57.895 1.90 0.00 0.00 2.32
3197 3698 1.468506 GGTGCCGGTCCCAACATTTT 61.469 55.000 1.90 0.00 0.00 1.82
3198 3699 0.319469 GTGCCGGTCCCAACATTTTG 60.319 55.000 1.90 0.00 0.00 2.44
3208 3709 3.457610 CCAACATTTTGGTCAAGCAGT 57.542 42.857 2.21 0.00 46.63 4.40
3209 3710 3.795877 CCAACATTTTGGTCAAGCAGTT 58.204 40.909 2.21 0.00 46.63 3.16
3210 3711 3.556775 CCAACATTTTGGTCAAGCAGTTG 59.443 43.478 2.21 12.72 46.63 3.16
3211 3712 3.457610 ACATTTTGGTCAAGCAGTTGG 57.542 42.857 0.00 0.00 34.09 3.77
3212 3713 3.030291 ACATTTTGGTCAAGCAGTTGGA 58.970 40.909 0.00 0.00 34.09 3.53
3213 3714 3.450457 ACATTTTGGTCAAGCAGTTGGAA 59.550 39.130 0.00 0.00 34.09 3.53
3214 3715 3.799281 TTTTGGTCAAGCAGTTGGAAG 57.201 42.857 0.00 0.00 34.09 3.46
3215 3716 1.032014 TTGGTCAAGCAGTTGGAAGC 58.968 50.000 0.00 0.00 34.09 3.86
3216 3717 1.165907 TGGTCAAGCAGTTGGAAGCG 61.166 55.000 0.00 0.00 34.09 4.68
3217 3718 0.884704 GGTCAAGCAGTTGGAAGCGA 60.885 55.000 0.00 0.00 34.09 4.93
3218 3719 1.160137 GTCAAGCAGTTGGAAGCGAT 58.840 50.000 0.00 0.00 34.09 4.58
3219 3720 1.135859 GTCAAGCAGTTGGAAGCGATG 60.136 52.381 0.00 0.00 34.09 3.84
3220 3721 0.455633 CAAGCAGTTGGAAGCGATGC 60.456 55.000 0.00 0.00 37.15 3.91
3221 3722 1.589716 AAGCAGTTGGAAGCGATGCC 61.590 55.000 0.00 0.00 37.61 4.40
3222 3723 2.334946 GCAGTTGGAAGCGATGCCA 61.335 57.895 0.00 0.00 0.00 4.92
3223 3724 1.660560 GCAGTTGGAAGCGATGCCAT 61.661 55.000 0.00 0.00 33.46 4.40
3224 3725 0.379669 CAGTTGGAAGCGATGCCATC 59.620 55.000 0.00 0.00 33.46 3.51
3225 3726 0.749454 AGTTGGAAGCGATGCCATCC 60.749 55.000 0.00 0.00 36.15 3.51
3226 3727 1.031571 GTTGGAAGCGATGCCATCCA 61.032 55.000 0.00 9.17 41.25 3.41
3227 3728 0.323269 TTGGAAGCGATGCCATCCAA 60.323 50.000 17.62 17.62 45.88 3.53
3228 3729 0.323269 TGGAAGCGATGCCATCCAAA 60.323 50.000 0.00 0.00 40.45 3.28
3229 3730 0.101219 GGAAGCGATGCCATCCAAAC 59.899 55.000 0.00 0.00 35.82 2.93
3230 3731 0.810648 GAAGCGATGCCATCCAAACA 59.189 50.000 0.00 0.00 0.00 2.83
3231 3732 1.406539 GAAGCGATGCCATCCAAACAT 59.593 47.619 0.00 0.00 0.00 2.71
3232 3733 2.346766 AGCGATGCCATCCAAACATA 57.653 45.000 0.00 0.00 0.00 2.29
3233 3734 2.224606 AGCGATGCCATCCAAACATAG 58.775 47.619 0.00 0.00 0.00 2.23
3234 3735 2.158769 AGCGATGCCATCCAAACATAGA 60.159 45.455 0.00 0.00 0.00 1.98
3235 3736 2.816087 GCGATGCCATCCAAACATAGAT 59.184 45.455 0.00 0.00 0.00 1.98
3236 3737 4.002982 GCGATGCCATCCAAACATAGATA 58.997 43.478 0.00 0.00 0.00 1.98
3237 3738 4.093998 GCGATGCCATCCAAACATAGATAG 59.906 45.833 0.00 0.00 0.00 2.08
3238 3739 5.240891 CGATGCCATCCAAACATAGATAGT 58.759 41.667 0.00 0.00 0.00 2.12
3239 3740 5.121298 CGATGCCATCCAAACATAGATAGTG 59.879 44.000 0.00 0.00 0.00 2.74
3240 3741 4.717877 TGCCATCCAAACATAGATAGTGG 58.282 43.478 0.00 0.00 0.00 4.00
3241 3742 4.165950 TGCCATCCAAACATAGATAGTGGT 59.834 41.667 0.00 0.00 0.00 4.16
3242 3743 5.368230 TGCCATCCAAACATAGATAGTGGTA 59.632 40.000 0.00 0.00 0.00 3.25
3243 3744 5.934625 GCCATCCAAACATAGATAGTGGTAG 59.065 44.000 0.00 0.00 0.00 3.18
3244 3745 6.464465 GCCATCCAAACATAGATAGTGGTAGT 60.464 42.308 0.00 0.00 0.00 2.73
3245 3746 6.931281 CCATCCAAACATAGATAGTGGTAGTG 59.069 42.308 0.00 0.00 0.00 2.74
3246 3747 5.914033 TCCAAACATAGATAGTGGTAGTGC 58.086 41.667 0.00 0.00 0.00 4.40
3247 3748 5.057149 CCAAACATAGATAGTGGTAGTGCC 58.943 45.833 0.00 0.00 37.90 5.01
3248 3749 5.163301 CCAAACATAGATAGTGGTAGTGCCT 60.163 44.000 0.00 0.00 38.35 4.75
3249 3750 6.349300 CAAACATAGATAGTGGTAGTGCCTT 58.651 40.000 0.00 0.00 38.35 4.35
3250 3751 6.561519 AACATAGATAGTGGTAGTGCCTTT 57.438 37.500 0.00 0.00 38.35 3.11
3251 3752 5.918608 ACATAGATAGTGGTAGTGCCTTTG 58.081 41.667 0.00 0.00 38.35 2.77
3252 3753 5.425539 ACATAGATAGTGGTAGTGCCTTTGT 59.574 40.000 0.00 0.00 38.35 2.83
3253 3754 4.473477 AGATAGTGGTAGTGCCTTTGTC 57.527 45.455 0.00 0.00 38.35 3.18
3254 3755 4.097418 AGATAGTGGTAGTGCCTTTGTCT 58.903 43.478 0.00 0.00 38.35 3.41
3255 3756 4.532521 AGATAGTGGTAGTGCCTTTGTCTT 59.467 41.667 0.00 0.00 38.35 3.01
3256 3757 3.127425 AGTGGTAGTGCCTTTGTCTTC 57.873 47.619 0.00 0.00 38.35 2.87
3257 3758 1.798813 GTGGTAGTGCCTTTGTCTTCG 59.201 52.381 0.00 0.00 38.35 3.79
3258 3759 1.414919 TGGTAGTGCCTTTGTCTTCGT 59.585 47.619 0.00 0.00 38.35 3.85
3259 3760 2.158871 TGGTAGTGCCTTTGTCTTCGTT 60.159 45.455 0.00 0.00 38.35 3.85
3260 3761 3.069872 TGGTAGTGCCTTTGTCTTCGTTA 59.930 43.478 0.00 0.00 38.35 3.18
3261 3762 4.251268 GGTAGTGCCTTTGTCTTCGTTAT 58.749 43.478 0.00 0.00 0.00 1.89
3262 3763 4.694037 GGTAGTGCCTTTGTCTTCGTTATT 59.306 41.667 0.00 0.00 0.00 1.40
3263 3764 5.870978 GGTAGTGCCTTTGTCTTCGTTATTA 59.129 40.000 0.00 0.00 0.00 0.98
3264 3765 6.369615 GGTAGTGCCTTTGTCTTCGTTATTAA 59.630 38.462 0.00 0.00 0.00 1.40
3265 3766 7.065443 GGTAGTGCCTTTGTCTTCGTTATTAAT 59.935 37.037 0.00 0.00 0.00 1.40
3266 3767 7.073342 AGTGCCTTTGTCTTCGTTATTAATC 57.927 36.000 0.00 0.00 0.00 1.75
3267 3768 6.653320 AGTGCCTTTGTCTTCGTTATTAATCA 59.347 34.615 0.00 0.00 0.00 2.57
3268 3769 7.174253 AGTGCCTTTGTCTTCGTTATTAATCAA 59.826 33.333 0.00 0.00 0.00 2.57
3269 3770 7.806014 GTGCCTTTGTCTTCGTTATTAATCAAA 59.194 33.333 0.00 0.00 0.00 2.69
3270 3771 8.020819 TGCCTTTGTCTTCGTTATTAATCAAAG 58.979 33.333 11.96 11.96 39.67 2.77
3271 3772 8.234546 GCCTTTGTCTTCGTTATTAATCAAAGA 58.765 33.333 17.17 9.26 41.28 2.52
3285 3786 7.744087 TTAATCAAAGAACATGTACTGTGCT 57.256 32.000 0.00 0.00 46.56 4.40
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
77 80 3.599285 GACGGCCGGATTGTGACCA 62.599 63.158 31.76 0.00 0.00 4.02
149 161 3.058639 GTCAAAAGTCAGGATGCACTGTC 60.059 47.826 4.42 0.00 39.48 3.51
150 162 2.880890 GTCAAAAGTCAGGATGCACTGT 59.119 45.455 4.42 0.00 39.48 3.55
151 163 2.096069 CGTCAAAAGTCAGGATGCACTG 60.096 50.000 0.00 0.00 39.84 3.66
152 164 2.146342 CGTCAAAAGTCAGGATGCACT 58.854 47.619 0.00 0.00 34.76 4.40
153 165 2.096218 GTCGTCAAAAGTCAGGATGCAC 60.096 50.000 0.00 0.00 34.76 4.57
154 166 2.143122 GTCGTCAAAAGTCAGGATGCA 58.857 47.619 0.00 0.00 34.76 3.96
155 167 2.417719 AGTCGTCAAAAGTCAGGATGC 58.582 47.619 0.00 0.00 34.76 3.91
199 257 3.226346 TGTCACGTATGCCTAGTTCAC 57.774 47.619 0.00 0.00 0.00 3.18
213 271 2.432628 GGTCCGGCTCTTGTCACG 60.433 66.667 0.00 0.00 0.00 4.35
227 285 2.113860 TCCTTATGCAAGCACAGGTC 57.886 50.000 17.34 0.00 33.58 3.85
398 463 5.223449 AGTTTTCTCCATAAAGTCGGTCA 57.777 39.130 0.00 0.00 0.00 4.02
400 465 7.184067 AGATAGTTTTCTCCATAAAGTCGGT 57.816 36.000 0.00 0.00 0.00 4.69
472 620 8.206126 TCTAGAATGCCAAACCTATATCATCA 57.794 34.615 0.00 0.00 0.00 3.07
473 621 9.107177 CATCTAGAATGCCAAACCTATATCATC 57.893 37.037 0.00 0.00 0.00 2.92
474 622 8.609483 ACATCTAGAATGCCAAACCTATATCAT 58.391 33.333 0.00 0.00 0.00 2.45
476 624 8.854614 AACATCTAGAATGCCAAACCTATATC 57.145 34.615 0.00 0.00 0.00 1.63
482 737 6.691508 AGAAAAACATCTAGAATGCCAAACC 58.308 36.000 0.00 0.00 0.00 3.27
569 827 7.302184 AGCTCATCTAGTACTCCCTCTATTTT 58.698 38.462 0.00 0.00 0.00 1.82
570 828 6.858941 AGCTCATCTAGTACTCCCTCTATTT 58.141 40.000 0.00 0.00 0.00 1.40
871 1301 4.099120 CGGTGCATCTATCTTATAGCGTC 58.901 47.826 0.00 0.00 0.00 5.19
1098 1548 2.970639 CTGAGGTCTCCGGCGAAA 59.029 61.111 9.30 0.00 0.00 3.46
1302 1755 1.073923 AGGACGCCCATGAAAGAGTTT 59.926 47.619 0.00 0.00 33.88 2.66
1341 1794 0.598942 GCTTCCTTAGCCTAGCGAGC 60.599 60.000 0.00 0.00 44.48 5.03
1405 1858 2.741092 GTGTGTGAGCTCCCCGAA 59.259 61.111 12.15 0.00 0.00 4.30
1410 1863 1.004440 GGTGAGGTGTGTGAGCTCC 60.004 63.158 12.15 3.09 46.98 4.70
1537 1990 3.362399 ATGACAGAGACGGCGGCAG 62.362 63.158 18.30 6.96 0.00 4.85
1569 2022 3.691342 CGGAGGTTGAGCCCACGA 61.691 66.667 0.00 0.00 38.61 4.35
1979 2436 1.959085 CTGTTGTTGCGCCCAGATT 59.041 52.632 4.18 0.00 0.00 2.40
2097 2554 1.202533 CCAGATACGACATGGTGGTCC 60.203 57.143 0.00 0.00 34.24 4.46
2223 2680 3.199071 TCCCAGATACCGTATTGTTGCTT 59.801 43.478 0.00 0.00 0.00 3.91
2326 2788 1.086634 GTTGTGCTCTGGGATCTCGC 61.087 60.000 0.00 0.00 0.00 5.03
2344 2806 4.098044 TCTTCTGTTCACGACTCTCTTTGT 59.902 41.667 0.00 0.00 0.00 2.83
2516 2993 7.462571 AGCCCTTTTAGAAAATTCAATACGT 57.537 32.000 0.00 0.00 0.00 3.57
2588 3065 7.933577 TCATGATAGGCTGGAAGTTAACATTAG 59.066 37.037 8.61 1.98 35.30 1.73
2591 3068 6.100279 TCTCATGATAGGCTGGAAGTTAACAT 59.900 38.462 8.61 0.00 35.30 2.71
2638 3115 5.824624 ACAAAGACATTCATCAATAGGCGAT 59.175 36.000 0.00 0.00 0.00 4.58
2642 3119 7.912250 GCTGTAACAAAGACATTCATCAATAGG 59.088 37.037 0.00 0.00 0.00 2.57
2690 3167 4.891756 GGGATCATTCAACAGGATTCACAT 59.108 41.667 0.00 0.00 0.00 3.21
2765 3242 6.075415 CGCAAAGAATAAGTTGTTGTTGACAG 60.075 38.462 8.65 0.00 39.94 3.51
2777 3254 8.958119 TTTGTATCTATCCGCAAAGAATAAGT 57.042 30.769 0.00 0.00 0.00 2.24
2825 3302 4.286297 ACCTAGCAACAACAGCTTATCA 57.714 40.909 0.00 0.00 43.25 2.15
2912 3407 6.358974 TTCTGTGATGAGTAATCTGGAACA 57.641 37.500 0.00 0.00 36.15 3.18
2913 3408 7.201679 CCATTTCTGTGATGAGTAATCTGGAAC 60.202 40.741 0.00 0.00 36.15 3.62
2914 3409 6.825213 CCATTTCTGTGATGAGTAATCTGGAA 59.175 38.462 0.00 0.00 36.15 3.53
2915 3410 6.156775 TCCATTTCTGTGATGAGTAATCTGGA 59.843 38.462 0.00 0.00 36.15 3.86
2916 3411 6.351711 TCCATTTCTGTGATGAGTAATCTGG 58.648 40.000 0.00 0.00 36.15 3.86
2917 3412 9.722184 ATATCCATTTCTGTGATGAGTAATCTG 57.278 33.333 0.00 0.00 36.15 2.90
2959 3454 8.793592 TGTCGCAAGTATAGATGTATCTAATGT 58.206 33.333 5.75 0.00 39.79 2.71
2960 3455 9.626045 TTGTCGCAAGTATAGATGTATCTAATG 57.374 33.333 5.75 4.94 39.79 1.90
2961 3456 9.847706 CTTGTCGCAAGTATAGATGTATCTAAT 57.152 33.333 5.75 0.00 39.79 1.73
2962 3457 8.847196 ACTTGTCGCAAGTATAGATGTATCTAA 58.153 33.333 19.21 0.00 39.79 2.10
2963 3458 8.392372 ACTTGTCGCAAGTATAGATGTATCTA 57.608 34.615 19.21 4.22 40.29 1.98
2964 3459 7.278461 ACTTGTCGCAAGTATAGATGTATCT 57.722 36.000 19.21 0.00 38.75 1.98
2965 3460 9.627395 ATTACTTGTCGCAAGTATAGATGTATC 57.373 33.333 23.59 0.00 33.27 2.24
2966 3461 9.982651 AATTACTTGTCGCAAGTATAGATGTAT 57.017 29.630 23.59 14.31 33.27 2.29
2967 3462 9.459640 GAATTACTTGTCGCAAGTATAGATGTA 57.540 33.333 23.59 13.16 33.27 2.29
2968 3463 7.979537 TGAATTACTTGTCGCAAGTATAGATGT 59.020 33.333 23.59 11.70 33.27 3.06
2969 3464 8.352752 TGAATTACTTGTCGCAAGTATAGATG 57.647 34.615 23.59 2.90 33.27 2.90
2970 3465 8.414003 TCTGAATTACTTGTCGCAAGTATAGAT 58.586 33.333 23.59 15.77 33.27 1.98
2971 3466 7.768240 TCTGAATTACTTGTCGCAAGTATAGA 58.232 34.615 23.59 20.62 33.27 1.98
2972 3467 7.987268 TCTGAATTACTTGTCGCAAGTATAG 57.013 36.000 23.59 19.45 33.27 1.31
2973 3468 7.008901 CGTTCTGAATTACTTGTCGCAAGTATA 59.991 37.037 23.59 17.37 33.27 1.47
2974 3469 6.183360 CGTTCTGAATTACTTGTCGCAAGTAT 60.183 38.462 23.59 14.96 33.27 2.12
2975 3470 5.118050 CGTTCTGAATTACTTGTCGCAAGTA 59.882 40.000 20.95 20.95 39.48 2.24
2976 3471 4.084537 CGTTCTGAATTACTTGTCGCAAGT 60.085 41.667 22.53 22.53 39.48 3.16
2977 3472 4.386230 CGTTCTGAATTACTTGTCGCAAG 58.614 43.478 15.16 15.16 0.00 4.01
2978 3473 3.185594 CCGTTCTGAATTACTTGTCGCAA 59.814 43.478 0.00 0.00 0.00 4.85
2979 3474 2.734606 CCGTTCTGAATTACTTGTCGCA 59.265 45.455 0.00 0.00 0.00 5.10
2980 3475 2.991190 TCCGTTCTGAATTACTTGTCGC 59.009 45.455 0.00 0.00 0.00 5.19
2981 3476 3.612860 CCTCCGTTCTGAATTACTTGTCG 59.387 47.826 0.00 0.00 0.00 4.35
2982 3477 3.933332 CCCTCCGTTCTGAATTACTTGTC 59.067 47.826 0.00 0.00 0.00 3.18
2983 3478 3.581332 TCCCTCCGTTCTGAATTACTTGT 59.419 43.478 0.00 0.00 0.00 3.16
2984 3479 4.202245 TCCCTCCGTTCTGAATTACTTG 57.798 45.455 0.00 0.00 0.00 3.16
2985 3480 4.903045 TTCCCTCCGTTCTGAATTACTT 57.097 40.909 0.00 0.00 0.00 2.24
2986 3481 5.163332 GGTATTCCCTCCGTTCTGAATTACT 60.163 44.000 0.00 0.00 0.00 2.24
2987 3482 5.055144 GGTATTCCCTCCGTTCTGAATTAC 58.945 45.833 0.00 0.00 0.00 1.89
2988 3483 5.286267 GGTATTCCCTCCGTTCTGAATTA 57.714 43.478 0.00 0.00 0.00 1.40
2989 3484 4.152284 GGTATTCCCTCCGTTCTGAATT 57.848 45.455 0.00 0.00 0.00 2.17
2990 3485 3.840124 GGTATTCCCTCCGTTCTGAAT 57.160 47.619 0.00 0.00 0.00 2.57
3002 3497 4.037506 GCAAGTGCAAGTGGGTATTCCC 62.038 54.545 0.00 0.00 46.63 3.97
3003 3498 1.202348 GCAAGTGCAAGTGGGTATTCC 59.798 52.381 0.00 0.00 41.59 3.01
3004 3499 2.636768 GCAAGTGCAAGTGGGTATTC 57.363 50.000 0.00 0.00 41.59 1.75
3051 3546 0.174617 GAGAGAGACCTCCAAAGCCG 59.825 60.000 0.00 0.00 40.30 5.52
3056 3551 1.909986 TCGAGAGAGAGAGACCTCCAA 59.090 52.381 0.00 0.00 40.30 3.53
3057 3552 1.208535 GTCGAGAGAGAGAGACCTCCA 59.791 57.143 0.00 0.00 43.49 3.86
3058 3553 1.474498 GGTCGAGAGAGAGAGACCTCC 60.474 61.905 6.26 0.00 46.99 4.30
3059 3554 1.949465 GGTCGAGAGAGAGAGACCTC 58.051 60.000 6.26 0.00 46.99 3.85
3062 3557 2.093658 AGTCAGGTCGAGAGAGAGAGAC 60.094 54.545 0.00 0.00 43.49 3.36
3100 3601 5.523588 AGAGAGAGAGAGAGAGAGAGAGAA 58.476 45.833 0.00 0.00 0.00 2.87
3113 3614 5.103728 AGAGAGAGAGAGAGAGAGAGAGAGA 60.104 48.000 0.00 0.00 0.00 3.10
3114 3615 5.139727 AGAGAGAGAGAGAGAGAGAGAGAG 58.860 50.000 0.00 0.00 0.00 3.20
3115 3616 5.103728 AGAGAGAGAGAGAGAGAGAGAGAGA 60.104 48.000 0.00 0.00 0.00 3.10
3116 3617 5.139727 AGAGAGAGAGAGAGAGAGAGAGAG 58.860 50.000 0.00 0.00 0.00 3.20
3117 3618 5.136068 AGAGAGAGAGAGAGAGAGAGAGA 57.864 47.826 0.00 0.00 0.00 3.10
3118 3619 4.892345 TGAGAGAGAGAGAGAGAGAGAGAG 59.108 50.000 0.00 0.00 0.00 3.20
3119 3620 4.871822 TGAGAGAGAGAGAGAGAGAGAGA 58.128 47.826 0.00 0.00 0.00 3.10
3120 3621 5.070180 ACATGAGAGAGAGAGAGAGAGAGAG 59.930 48.000 0.00 0.00 0.00 3.20
3121 3622 4.964897 ACATGAGAGAGAGAGAGAGAGAGA 59.035 45.833 0.00 0.00 0.00 3.10
3122 3623 5.287674 ACATGAGAGAGAGAGAGAGAGAG 57.712 47.826 0.00 0.00 0.00 3.20
3123 3624 5.899547 ACTACATGAGAGAGAGAGAGAGAGA 59.100 44.000 0.00 0.00 0.00 3.10
3124 3625 6.166984 ACTACATGAGAGAGAGAGAGAGAG 57.833 45.833 0.00 0.00 0.00 3.20
3125 3626 5.660864 TGACTACATGAGAGAGAGAGAGAGA 59.339 44.000 0.00 0.00 0.00 3.10
3126 3627 5.755375 GTGACTACATGAGAGAGAGAGAGAG 59.245 48.000 0.00 0.00 0.00 3.20
3127 3628 5.425217 AGTGACTACATGAGAGAGAGAGAGA 59.575 44.000 0.00 0.00 0.00 3.10
3128 3629 5.674525 AGTGACTACATGAGAGAGAGAGAG 58.325 45.833 0.00 0.00 0.00 3.20
3129 3630 5.692115 AGTGACTACATGAGAGAGAGAGA 57.308 43.478 0.00 0.00 0.00 3.10
3130 3631 6.816136 TCTAGTGACTACATGAGAGAGAGAG 58.184 44.000 0.00 0.00 0.00 3.20
3131 3632 6.800072 TCTAGTGACTACATGAGAGAGAGA 57.200 41.667 0.00 0.00 0.00 3.10
3132 3633 9.208022 CTTATCTAGTGACTACATGAGAGAGAG 57.792 40.741 0.00 0.00 0.00 3.20
3133 3634 8.154203 CCTTATCTAGTGACTACATGAGAGAGA 58.846 40.741 0.00 0.00 0.00 3.10
3134 3635 8.154203 TCCTTATCTAGTGACTACATGAGAGAG 58.846 40.741 0.00 0.00 0.00 3.20
3135 3636 8.035448 TCCTTATCTAGTGACTACATGAGAGA 57.965 38.462 0.00 0.00 0.00 3.10
3136 3637 7.094805 GCTCCTTATCTAGTGACTACATGAGAG 60.095 44.444 0.00 0.00 0.00 3.20
3137 3638 6.712998 GCTCCTTATCTAGTGACTACATGAGA 59.287 42.308 0.00 0.00 0.00 3.27
3138 3639 6.348132 CGCTCCTTATCTAGTGACTACATGAG 60.348 46.154 0.00 0.00 0.00 2.90
3139 3640 5.470437 CGCTCCTTATCTAGTGACTACATGA 59.530 44.000 0.00 0.00 0.00 3.07
3140 3641 5.694816 CGCTCCTTATCTAGTGACTACATG 58.305 45.833 0.00 0.00 0.00 3.21
3141 3642 4.216687 GCGCTCCTTATCTAGTGACTACAT 59.783 45.833 0.00 0.00 0.00 2.29
3142 3643 3.564644 GCGCTCCTTATCTAGTGACTACA 59.435 47.826 0.00 0.00 0.00 2.74
3143 3644 3.364167 CGCGCTCCTTATCTAGTGACTAC 60.364 52.174 5.56 0.00 0.00 2.73
3144 3645 2.806818 CGCGCTCCTTATCTAGTGACTA 59.193 50.000 5.56 0.00 0.00 2.59
3145 3646 1.604755 CGCGCTCCTTATCTAGTGACT 59.395 52.381 5.56 0.00 0.00 3.41
3146 3647 1.926827 GCGCGCTCCTTATCTAGTGAC 60.927 57.143 26.67 0.00 0.00 3.67
3147 3648 0.311165 GCGCGCTCCTTATCTAGTGA 59.689 55.000 26.67 0.00 0.00 3.41
3148 3649 0.664767 GGCGCGCTCCTTATCTAGTG 60.665 60.000 32.29 0.00 0.00 2.74
3149 3650 0.824182 AGGCGCGCTCCTTATCTAGT 60.824 55.000 32.29 0.00 30.82 2.57
3150 3651 0.315568 AAGGCGCGCTCCTTATCTAG 59.684 55.000 29.45 0.00 44.23 2.43
3151 3652 0.032130 CAAGGCGCGCTCCTTATCTA 59.968 55.000 29.90 0.00 44.24 1.98
3152 3653 1.227380 CAAGGCGCGCTCCTTATCT 60.227 57.895 29.90 14.85 44.24 1.98
3153 3654 2.247437 CCAAGGCGCGCTCCTTATC 61.247 63.158 29.90 12.47 44.24 1.75
3154 3655 2.203070 CCAAGGCGCGCTCCTTAT 60.203 61.111 29.90 8.20 44.24 1.73
3175 3676 4.717313 GTTGGGACCGGCACCCTC 62.717 72.222 29.42 20.89 46.82 4.30
3177 3678 3.879180 AATGTTGGGACCGGCACCC 62.879 63.158 25.07 25.07 46.87 4.61
3178 3679 1.468506 AAAATGTTGGGACCGGCACC 61.469 55.000 0.00 4.30 0.00 5.01
3179 3680 0.319469 CAAAATGTTGGGACCGGCAC 60.319 55.000 0.00 0.00 0.00 5.01
3180 3681 2.045280 CAAAATGTTGGGACCGGCA 58.955 52.632 0.00 0.00 0.00 5.69
3181 3682 4.985845 CAAAATGTTGGGACCGGC 57.014 55.556 0.00 0.00 0.00 6.13
3189 3690 3.556775 CCAACTGCTTGACCAAAATGTTG 59.443 43.478 0.00 0.00 34.96 3.33
3190 3691 3.450457 TCCAACTGCTTGACCAAAATGTT 59.550 39.130 0.00 0.00 0.00 2.71
3191 3692 3.030291 TCCAACTGCTTGACCAAAATGT 58.970 40.909 0.00 0.00 0.00 2.71
3192 3693 3.731652 TCCAACTGCTTGACCAAAATG 57.268 42.857 0.00 0.00 0.00 2.32
3193 3694 3.493176 GCTTCCAACTGCTTGACCAAAAT 60.493 43.478 0.00 0.00 0.00 1.82
3194 3695 2.159114 GCTTCCAACTGCTTGACCAAAA 60.159 45.455 0.00 0.00 0.00 2.44
3195 3696 1.408702 GCTTCCAACTGCTTGACCAAA 59.591 47.619 0.00 0.00 0.00 3.28
3196 3697 1.032014 GCTTCCAACTGCTTGACCAA 58.968 50.000 0.00 0.00 0.00 3.67
3197 3698 1.165907 CGCTTCCAACTGCTTGACCA 61.166 55.000 0.00 0.00 0.00 4.02
3198 3699 0.884704 TCGCTTCCAACTGCTTGACC 60.885 55.000 0.00 0.00 0.00 4.02
3199 3700 1.135859 CATCGCTTCCAACTGCTTGAC 60.136 52.381 0.00 0.00 0.00 3.18
3200 3701 1.159285 CATCGCTTCCAACTGCTTGA 58.841 50.000 0.00 0.00 0.00 3.02
3201 3702 0.455633 GCATCGCTTCCAACTGCTTG 60.456 55.000 0.00 0.00 0.00 4.01
3202 3703 1.589716 GGCATCGCTTCCAACTGCTT 61.590 55.000 0.00 0.00 33.43 3.91
3203 3704 2.042831 GGCATCGCTTCCAACTGCT 61.043 57.895 0.00 0.00 33.43 4.24
3204 3705 1.660560 ATGGCATCGCTTCCAACTGC 61.661 55.000 0.00 0.00 35.75 4.40
3205 3706 0.379669 GATGGCATCGCTTCCAACTG 59.620 55.000 12.40 0.00 35.75 3.16
3206 3707 0.749454 GGATGGCATCGCTTCCAACT 60.749 55.000 20.50 0.00 35.75 3.16
3207 3708 1.031571 TGGATGGCATCGCTTCCAAC 61.032 55.000 20.50 5.39 37.66 3.77
3208 3709 0.323269 TTGGATGGCATCGCTTCCAA 60.323 50.000 20.50 17.06 43.07 3.53
3209 3710 0.323269 TTTGGATGGCATCGCTTCCA 60.323 50.000 20.50 11.87 38.37 3.53
3210 3711 0.101219 GTTTGGATGGCATCGCTTCC 59.899 55.000 20.50 9.21 33.65 3.46
3211 3712 0.810648 TGTTTGGATGGCATCGCTTC 59.189 50.000 20.50 11.72 0.00 3.86
3212 3713 1.477553 ATGTTTGGATGGCATCGCTT 58.522 45.000 20.50 6.90 0.00 4.68
3213 3714 2.158769 TCTATGTTTGGATGGCATCGCT 60.159 45.455 20.50 4.70 0.00 4.93
3214 3715 2.221169 TCTATGTTTGGATGGCATCGC 58.779 47.619 20.50 13.93 0.00 4.58
3215 3716 5.121298 CACTATCTATGTTTGGATGGCATCG 59.879 44.000 20.50 5.02 0.00 3.84
3216 3717 5.413833 CCACTATCTATGTTTGGATGGCATC 59.586 44.000 19.23 19.23 0.00 3.91
3217 3718 5.163055 ACCACTATCTATGTTTGGATGGCAT 60.163 40.000 0.00 0.00 0.00 4.40
3218 3719 4.165950 ACCACTATCTATGTTTGGATGGCA 59.834 41.667 0.00 0.00 0.00 4.92
3219 3720 4.718961 ACCACTATCTATGTTTGGATGGC 58.281 43.478 0.00 0.00 0.00 4.40
3220 3721 6.931281 CACTACCACTATCTATGTTTGGATGG 59.069 42.308 0.00 0.00 0.00 3.51
3221 3722 6.425114 GCACTACCACTATCTATGTTTGGATG 59.575 42.308 0.00 0.00 0.00 3.51
3222 3723 6.464465 GGCACTACCACTATCTATGTTTGGAT 60.464 42.308 0.00 0.00 38.86 3.41
3223 3724 5.163343 GGCACTACCACTATCTATGTTTGGA 60.163 44.000 0.00 0.00 38.86 3.53
3224 3725 5.057149 GGCACTACCACTATCTATGTTTGG 58.943 45.833 0.00 0.00 38.86 3.28
3225 3726 5.918608 AGGCACTACCACTATCTATGTTTG 58.081 41.667 0.00 0.00 43.14 2.93
3226 3727 6.561519 AAGGCACTACCACTATCTATGTTT 57.438 37.500 0.00 0.00 43.14 2.83
3227 3728 6.070194 ACAAAGGCACTACCACTATCTATGTT 60.070 38.462 0.00 0.00 43.14 2.71
3228 3729 5.425539 ACAAAGGCACTACCACTATCTATGT 59.574 40.000 0.00 0.00 43.14 2.29
3229 3730 5.918608 ACAAAGGCACTACCACTATCTATG 58.081 41.667 0.00 0.00 43.14 2.23
3230 3731 5.900123 AGACAAAGGCACTACCACTATCTAT 59.100 40.000 0.00 0.00 43.14 1.98
3231 3732 5.269991 AGACAAAGGCACTACCACTATCTA 58.730 41.667 0.00 0.00 43.14 1.98
3232 3733 4.097418 AGACAAAGGCACTACCACTATCT 58.903 43.478 0.00 0.00 43.14 1.98
3233 3734 4.473477 AGACAAAGGCACTACCACTATC 57.527 45.455 0.00 0.00 43.14 2.08
3234 3735 4.620803 CGAAGACAAAGGCACTACCACTAT 60.621 45.833 0.00 0.00 43.14 2.12
3235 3736 3.305813 CGAAGACAAAGGCACTACCACTA 60.306 47.826 0.00 0.00 43.14 2.74
3236 3737 2.548067 CGAAGACAAAGGCACTACCACT 60.548 50.000 0.00 0.00 43.14 4.00
3237 3738 1.798813 CGAAGACAAAGGCACTACCAC 59.201 52.381 0.00 0.00 43.14 4.16
3238 3739 1.414919 ACGAAGACAAAGGCACTACCA 59.585 47.619 0.00 0.00 43.14 3.25
3239 3740 2.165319 ACGAAGACAAAGGCACTACC 57.835 50.000 0.00 0.00 38.49 3.18
3240 3741 5.857822 AATAACGAAGACAAAGGCACTAC 57.142 39.130 0.00 0.00 38.49 2.73
3241 3742 7.820386 TGATTAATAACGAAGACAAAGGCACTA 59.180 33.333 0.00 0.00 38.49 2.74
3243 3744 6.837992 TGATTAATAACGAAGACAAAGGCAC 58.162 36.000 0.00 0.00 0.00 5.01
3244 3745 7.441890 TTGATTAATAACGAAGACAAAGGCA 57.558 32.000 0.00 0.00 0.00 4.75
3245 3746 8.234546 TCTTTGATTAATAACGAAGACAAAGGC 58.765 33.333 16.02 0.00 41.40 4.35
3259 3760 9.448438 AGCACAGTACATGTTCTTTGATTAATA 57.552 29.630 19.26 0.00 41.41 0.98
3260 3761 8.340618 AGCACAGTACATGTTCTTTGATTAAT 57.659 30.769 19.26 0.00 41.41 1.40
3261 3762 7.744087 AGCACAGTACATGTTCTTTGATTAA 57.256 32.000 19.26 0.00 41.41 1.40
3262 3763 7.744087 AAGCACAGTACATGTTCTTTGATTA 57.256 32.000 17.13 0.00 41.83 1.75
3263 3764 6.639632 AAGCACAGTACATGTTCTTTGATT 57.360 33.333 19.26 16.65 41.83 2.57
3268 3769 7.986085 ATCTAAAAGCACAGTACATGTTCTT 57.014 32.000 2.30 0.44 45.71 2.52


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

AutoCloner maintained by Alex Coulton.