Multiple sequence alignment - TraesCS3B01G149400

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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 TraesCS3B01G149400 chr3B 100.000 3970 0 0 1 3970 140858793 140854824 0.000000e+00 7332.0
1 TraesCS3B01G149400 chr3B 93.000 100 6 1 3322 3421 797463965 797463867 1.150000e-30 145.0
2 TraesCS3B01G149400 chr3B 98.462 65 1 0 3179 3243 52418179 52418115 9.020000e-22 115.0
3 TraesCS3B01G149400 chr3B 100.000 61 0 0 3183 3243 209723662 209723722 3.240000e-21 113.0
4 TraesCS3B01G149400 chr3D 89.097 2614 138 56 668 3185 91226412 91223850 0.000000e+00 3112.0
5 TraesCS3B01G149400 chr3D 89.465 636 33 18 1 615 91227116 91226494 0.000000e+00 773.0
6 TraesCS3B01G149400 chr3D 93.089 246 14 2 3726 3970 91223569 91223326 1.360000e-94 357.0
7 TraesCS3B01G149400 chr3A 89.181 2588 152 58 668 3183 107405444 107402913 0.000000e+00 3110.0
8 TraesCS3B01G149400 chr3A 87.742 465 38 7 3506 3970 107402775 107402330 3.510000e-145 525.0
9 TraesCS3B01G149400 chr3A 82.589 448 30 25 4 434 107407557 107407141 6.310000e-93 351.0
10 TraesCS3B01G149400 chr3A 88.623 167 15 2 3242 3407 26040198 26040035 2.420000e-47 200.0
11 TraesCS3B01G149400 chr6A 90.845 142 9 1 3184 3325 73067719 73067856 1.880000e-43 187.0
12 TraesCS3B01G149400 chr7A 90.141 142 8 3 3184 3325 420780776 420780911 3.150000e-41 180.0
13 TraesCS3B01G149400 chr7A 100.000 84 0 0 3242 3325 663538214 663538297 5.310000e-34 156.0
14 TraesCS3B01G149400 chr7A 92.308 104 7 1 3322 3425 663538229 663538331 3.200000e-31 147.0
15 TraesCS3B01G149400 chrUn 98.810 84 1 0 3242 3325 191163416 191163333 2.470000e-32 150.0
16 TraesCS3B01G149400 chr2D 98.810 84 1 0 3242 3325 507464193 507464110 2.470000e-32 150.0
17 TraesCS3B01G149400 chr2B 98.810 84 1 0 3242 3325 436038174 436038091 2.470000e-32 150.0
18 TraesCS3B01G149400 chr1B 98.810 84 1 0 3242 3325 518809566 518809649 2.470000e-32 150.0
19 TraesCS3B01G149400 chr1B 98.810 84 1 0 3242 3325 577672077 577672160 2.470000e-32 150.0
20 TraesCS3B01G149400 chr1B 90.426 94 7 2 1261 1353 172001786 172001878 5.390000e-24 122.0
21 TraesCS3B01G149400 chr7B 92.233 103 8 0 3322 3424 697933583 697933481 3.200000e-31 147.0
22 TraesCS3B01G149400 chr7B 96.970 66 1 1 3181 3246 123804647 123804583 4.190000e-20 110.0
23 TraesCS3B01G149400 chr5B 93.814 97 6 0 3322 3418 94384964 94384868 3.200000e-31 147.0
24 TraesCS3B01G149400 chr5B 88.034 117 12 2 3322 3438 358816947 358817061 1.920000e-28 137.0
25 TraesCS3B01G149400 chr5B 85.366 82 9 3 1286 1366 321559466 321559387 9.140000e-12 82.4
26 TraesCS3B01G149400 chr4A 90.179 112 8 3 3322 3433 642395385 642395277 4.140000e-30 143.0
27 TraesCS3B01G149400 chr4A 92.958 71 3 2 3174 3243 37367737 37367668 7.020000e-18 102.0
28 TraesCS3B01G149400 chr6B 91.429 105 6 2 3322 3425 644577258 644577156 1.490000e-29 141.0
29 TraesCS3B01G149400 chr6B 90.000 80 6 2 3168 3246 645949251 645949173 7.020000e-18 102.0
30 TraesCS3B01G149400 chr6B 86.022 93 7 3 3185 3271 672096786 672096878 1.170000e-15 95.3
31 TraesCS3B01G149400 chr5A 90.654 107 8 2 3322 3427 658989108 658989003 1.490000e-29 141.0
32 TraesCS3B01G149400 chr5A 95.652 69 3 0 3175 3243 399297077 399297145 1.170000e-20 111.0
33 TraesCS3B01G149400 chr5A 85.366 82 9 3 1286 1366 375573070 375572991 9.140000e-12 82.4
34 TraesCS3B01G149400 chr1D 91.489 94 6 2 1261 1353 112462198 112462290 1.160000e-25 128.0
35 TraesCS3B01G149400 chr1A 90.000 100 7 3 1256 1353 119704058 119704156 4.160000e-25 126.0
36 TraesCS3B01G149400 chr5D 85.227 88 10 3 1280 1366 283356029 283355944 1.970000e-13 87.9


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 TraesCS3B01G149400 chr3B 140854824 140858793 3969 True 7332.000000 7332 100.000000 1 3970 1 chr3B.!!$R2 3969
1 TraesCS3B01G149400 chr3D 91223326 91227116 3790 True 1414.000000 3112 90.550333 1 3970 3 chr3D.!!$R1 3969
2 TraesCS3B01G149400 chr3A 107402330 107407557 5227 True 1328.666667 3110 86.504000 4 3970 3 chr3A.!!$R2 3966

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
625 2095 0.318441 GCCTTCCTTCCTTTTGGCAC 59.682 55.0 0.00 0.0 40.04 5.01 F
1952 3540 0.324943 CACCGGAGAACATTGTCCCT 59.675 55.0 9.46 0.0 37.33 4.20 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2528 4142 0.179034 GGTAGCCATGGAAGCAGAGG 60.179 60.0 18.4 0.0 0.0 3.69 R
3750 5443 0.034756 GGGAATGTTTGGTTGGTGCC 59.965 55.0 0.0 0.0 0.0 5.01 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
127 134 1.067142 CACACCAGTAGCCATGTACGT 60.067 52.381 0.00 0.00 0.00 3.57
219 237 3.755628 GGCGCCGTGGACTACTCA 61.756 66.667 12.58 0.00 0.00 3.41
288 306 0.679505 TTCCCGATCATGATCCGGTC 59.320 55.000 30.29 11.85 37.44 4.79
344 363 2.674747 GCCACCACCGTCGTTATTCTTA 60.675 50.000 0.00 0.00 0.00 2.10
347 366 4.269363 CCACCACCGTCGTTATTCTTATTC 59.731 45.833 0.00 0.00 0.00 1.75
350 369 6.753279 CACCACCGTCGTTATTCTTATTCTTA 59.247 38.462 0.00 0.00 0.00 2.10
371 390 2.462125 TATCACACGGCTTGGCTGCA 62.462 55.000 0.50 0.00 38.71 4.41
427 446 1.758440 TATGCATCCTCAGGCGGGTC 61.758 60.000 0.19 0.00 29.29 4.46
434 453 1.447643 CTCAGGCGGGTCCTATTGG 59.552 63.158 0.00 0.00 45.52 3.16
435 454 2.203209 CAGGCGGGTCCTATTGGC 60.203 66.667 0.00 0.00 45.52 4.52
436 455 2.690881 AGGCGGGTCCTATTGGCA 60.691 61.111 0.00 0.00 45.41 4.92
437 456 2.078665 AGGCGGGTCCTATTGGCAT 61.079 57.895 0.00 0.00 45.41 4.40
438 457 1.898574 GGCGGGTCCTATTGGCATG 60.899 63.158 0.00 0.00 0.00 4.06
445 494 0.466739 TCCTATTGGCATGGCAGCAG 60.467 55.000 22.17 20.53 35.83 4.24
471 520 1.590238 GAGATGATGGCACGAGTTTCG 59.410 52.381 0.00 0.00 46.93 3.46
488 1945 6.573725 CGAGTTTCGTCAGAAAATAAAACCAG 59.426 38.462 0.00 0.00 46.63 4.00
498 1955 7.015098 TCAGAAAATAAAACCAGGCATCAGAAA 59.985 33.333 0.00 0.00 0.00 2.52
508 1966 3.037549 AGGCATCAGAAAACCAAAACCA 58.962 40.909 0.00 0.00 0.00 3.67
519 1977 3.751479 ACCAAAACCATGAGCTTTTCC 57.249 42.857 0.00 0.00 0.00 3.13
521 1979 3.454082 ACCAAAACCATGAGCTTTTCCAA 59.546 39.130 0.00 0.00 0.00 3.53
522 1980 3.809279 CCAAAACCATGAGCTTTTCCAAC 59.191 43.478 0.00 0.00 0.00 3.77
524 1982 1.247567 ACCATGAGCTTTTCCAACGG 58.752 50.000 0.00 0.00 0.00 4.44
525 1983 1.202879 ACCATGAGCTTTTCCAACGGA 60.203 47.619 0.00 0.00 0.00 4.69
526 1984 1.470098 CCATGAGCTTTTCCAACGGAG 59.530 52.381 0.00 0.00 31.21 4.63
527 1985 2.426522 CATGAGCTTTTCCAACGGAGA 58.573 47.619 0.00 0.00 31.21 3.71
528 1986 2.169832 TGAGCTTTTCCAACGGAGAG 57.830 50.000 0.00 0.00 31.21 3.20
529 1987 1.416401 TGAGCTTTTCCAACGGAGAGT 59.584 47.619 0.00 0.00 31.21 3.24
530 1988 2.158813 TGAGCTTTTCCAACGGAGAGTT 60.159 45.455 0.00 0.00 45.45 3.01
531 1989 2.879026 GAGCTTTTCCAACGGAGAGTTT 59.121 45.455 0.00 0.00 42.02 2.66
532 1990 2.879026 AGCTTTTCCAACGGAGAGTTTC 59.121 45.455 0.00 0.00 42.02 2.78
534 1992 3.253432 GCTTTTCCAACGGAGAGTTTCAT 59.747 43.478 0.00 0.00 42.02 2.57
535 1993 4.613850 GCTTTTCCAACGGAGAGTTTCATC 60.614 45.833 0.00 0.00 42.02 2.92
536 1994 3.762407 TTCCAACGGAGAGTTTCATCA 57.238 42.857 0.00 0.00 42.02 3.07
604 2074 1.298713 CTCGCCATCGTCTTCCTCG 60.299 63.158 0.00 0.00 36.96 4.63
614 2084 2.266055 CTTCCTCGCGCCTTCCTT 59.734 61.111 0.00 0.00 0.00 3.36
615 2085 1.811679 CTTCCTCGCGCCTTCCTTC 60.812 63.158 0.00 0.00 0.00 3.46
616 2086 3.310860 TTCCTCGCGCCTTCCTTCC 62.311 63.158 0.00 0.00 0.00 3.46
617 2087 3.775654 CCTCGCGCCTTCCTTCCT 61.776 66.667 0.00 0.00 0.00 3.36
618 2088 2.266055 CTCGCGCCTTCCTTCCTT 59.734 61.111 0.00 0.00 0.00 3.36
619 2089 1.376037 CTCGCGCCTTCCTTCCTTT 60.376 57.895 0.00 0.00 0.00 3.11
620 2090 0.955919 CTCGCGCCTTCCTTCCTTTT 60.956 55.000 0.00 0.00 0.00 2.27
621 2091 1.210155 CGCGCCTTCCTTCCTTTTG 59.790 57.895 0.00 0.00 0.00 2.44
622 2092 1.586541 GCGCCTTCCTTCCTTTTGG 59.413 57.895 0.00 0.00 42.21 3.28
623 2093 1.586541 CGCCTTCCTTCCTTTTGGC 59.413 57.895 0.00 0.00 40.12 4.52
624 2094 1.178534 CGCCTTCCTTCCTTTTGGCA 61.179 55.000 0.00 0.00 40.27 4.92
625 2095 0.318441 GCCTTCCTTCCTTTTGGCAC 59.682 55.000 0.00 0.00 40.04 5.01
626 2096 0.598065 CCTTCCTTCCTTTTGGCACG 59.402 55.000 0.00 0.00 40.12 5.34
627 2097 0.598065 CTTCCTTCCTTTTGGCACGG 59.402 55.000 0.00 0.00 40.12 4.94
628 2098 0.825840 TTCCTTCCTTTTGGCACGGG 60.826 55.000 0.00 0.00 40.12 5.28
629 2099 2.275380 CCTTCCTTTTGGCACGGGG 61.275 63.158 0.00 0.00 40.12 5.73
654 2124 4.702081 GCCACTCGTGACGCTCGT 62.702 66.667 0.00 0.00 0.00 4.18
675 2176 2.484889 AGTTGACGGCTGTTCTTTCTC 58.515 47.619 0.00 0.00 0.00 2.87
682 2204 1.349357 GGCTGTTCTTTCTCTCCCTGT 59.651 52.381 0.00 0.00 0.00 4.00
767 2295 6.515531 GCCACACATTACATATTCCATTCCAG 60.516 42.308 0.00 0.00 0.00 3.86
788 2316 4.373116 ACGTACCGCCCACTGCAG 62.373 66.667 13.48 13.48 41.33 4.41
955 2512 1.587054 CTATAAGGGAGGCGGCTCG 59.413 63.158 29.95 12.61 0.00 5.03
997 2554 4.657824 AACCACGAGGACACGGCG 62.658 66.667 4.80 4.80 38.69 6.46
1137 2694 4.286320 CCTCTCCGGATTCGCGGG 62.286 72.222 3.57 0.00 38.28 6.13
1153 2710 2.361737 GGCAGCAGAAGGTTCCCC 60.362 66.667 0.00 0.00 0.00 4.81
1154 2711 2.759795 GCAGCAGAAGGTTCCCCT 59.240 61.111 0.00 0.00 45.63 4.79
1157 2717 1.151810 AGCAGAAGGTTCCCCTCCA 60.152 57.895 0.00 0.00 41.56 3.86
1159 2719 1.492993 GCAGAAGGTTCCCCTCCACT 61.493 60.000 0.00 0.00 41.56 4.00
1182 2742 3.443925 TCCCTGTCGCTGCTCTCG 61.444 66.667 0.00 0.00 0.00 4.04
1357 2917 1.616865 TCTACAACAAGCAGGTACGCT 59.383 47.619 0.00 0.00 46.67 5.07
1358 2918 2.821378 TCTACAACAAGCAGGTACGCTA 59.179 45.455 0.00 0.00 42.89 4.26
1359 2919 1.792006 ACAACAAGCAGGTACGCTAC 58.208 50.000 0.00 0.00 42.89 3.58
1360 2920 0.713883 CAACAAGCAGGTACGCTACG 59.286 55.000 0.00 0.00 42.89 3.51
1361 2921 1.012486 AACAAGCAGGTACGCTACGC 61.012 55.000 0.00 0.00 42.89 4.42
1362 2922 1.445410 CAAGCAGGTACGCTACGCA 60.445 57.895 0.00 0.00 42.89 5.24
1363 2923 1.445582 AAGCAGGTACGCTACGCAC 60.446 57.895 0.00 0.00 42.89 5.34
1364 2924 3.245315 GCAGGTACGCTACGCACG 61.245 66.667 0.00 0.00 0.00 5.34
1365 2925 3.245315 CAGGTACGCTACGCACGC 61.245 66.667 0.00 0.00 0.00 5.34
1545 3129 1.634973 TCATCTTCTTCATGTGGGCCA 59.365 47.619 0.00 0.00 0.00 5.36
1593 3177 3.680786 CCGCACAGGTCCGTCAGA 61.681 66.667 0.00 0.00 34.51 3.27
1611 3195 6.074888 CCGTCAGACATTTGAACAACAATTTC 60.075 38.462 0.41 0.00 38.36 2.17
1634 3222 5.936956 TCTTCCTCTGCTTTTCTCTGAATTC 59.063 40.000 0.00 0.00 0.00 2.17
1643 3231 1.884926 CTCTGAATTCGCTCCCCGC 60.885 63.158 0.04 0.00 36.73 6.13
1777 3365 3.041940 CACACCGTCAAGGCGTCC 61.042 66.667 0.00 0.00 46.52 4.79
1819 3407 2.283676 TCCGCCTTCTTCCTCGGT 60.284 61.111 0.00 0.00 42.28 4.69
1935 3523 2.433318 GTCTGCTCCGCTGACCAC 60.433 66.667 12.91 0.00 46.67 4.16
1951 3539 0.676782 CCACCGGAGAACATTGTCCC 60.677 60.000 9.46 0.00 37.33 4.46
1952 3540 0.324943 CACCGGAGAACATTGTCCCT 59.675 55.000 9.46 0.00 37.33 4.20
1953 3541 1.553248 CACCGGAGAACATTGTCCCTA 59.447 52.381 9.46 0.00 37.33 3.53
2045 3635 4.565564 GTCGCTTTCTCACGGTACATAAAT 59.434 41.667 0.00 0.00 0.00 1.40
2054 3644 5.045215 TCACGGTACATAAATGATTCCGTC 58.955 41.667 19.05 0.00 43.36 4.79
2057 3647 4.381863 CGGTACATAAATGATTCCGTCGAG 59.618 45.833 0.00 0.00 35.78 4.04
2193 3786 4.275936 AGTTCACCAGTAACAATTCAGCAC 59.724 41.667 0.00 0.00 0.00 4.40
2194 3787 4.085357 TCACCAGTAACAATTCAGCACT 57.915 40.909 0.00 0.00 0.00 4.40
2195 3788 3.814842 TCACCAGTAACAATTCAGCACTG 59.185 43.478 0.00 0.00 37.06 3.66
2196 3789 3.565482 CACCAGTAACAATTCAGCACTGT 59.435 43.478 0.00 0.00 35.85 3.55
2197 3790 4.754618 CACCAGTAACAATTCAGCACTGTA 59.245 41.667 0.00 0.00 35.85 2.74
2198 3791 4.755123 ACCAGTAACAATTCAGCACTGTAC 59.245 41.667 0.00 0.00 35.85 2.90
2204 3797 8.314751 AGTAACAATTCAGCACTGTACTATCTT 58.685 33.333 0.00 0.00 0.00 2.40
2206 3799 8.480643 AACAATTCAGCACTGTACTATCTTAC 57.519 34.615 0.00 0.00 0.00 2.34
2256 3849 5.780984 TGAATTTGTTCATGTAATGCTGCA 58.219 33.333 4.13 4.13 46.21 4.41
2397 3990 2.022129 GCACCGTGAGTCAACCTCG 61.022 63.158 1.65 0.00 43.64 4.63
2442 4035 7.400599 AGTTGAACTGTTGCATCATCATAAT 57.599 32.000 0.00 0.00 0.00 1.28
2447 4040 7.774625 TGAACTGTTGCATCATCATAATTCCTA 59.225 33.333 0.00 0.00 0.00 2.94
2448 4041 7.741027 ACTGTTGCATCATCATAATTCCTAG 57.259 36.000 0.00 0.00 0.00 3.02
2450 4043 8.432013 ACTGTTGCATCATCATAATTCCTAGTA 58.568 33.333 0.00 0.00 0.00 1.82
2451 4044 8.837788 TGTTGCATCATCATAATTCCTAGTAG 57.162 34.615 0.00 0.00 0.00 2.57
2452 4045 8.650490 TGTTGCATCATCATAATTCCTAGTAGA 58.350 33.333 0.00 0.00 0.00 2.59
2453 4046 8.930760 GTTGCATCATCATAATTCCTAGTAGAC 58.069 37.037 0.00 0.00 0.00 2.59
2454 4047 8.427902 TGCATCATCATAATTCCTAGTAGACT 57.572 34.615 0.00 0.00 0.00 3.24
2478 4092 8.322091 ACTAATAAACTATTGTGAACTCTGGCT 58.678 33.333 0.00 0.00 0.00 4.75
2576 4191 4.683781 GTGAGAGAGAGACACATGACAAAC 59.316 45.833 0.00 0.00 35.06 2.93
2578 4193 2.989840 GAGAGAGACACATGACAAACCG 59.010 50.000 0.00 0.00 0.00 4.44
2669 4284 1.341976 GGTCCTGGCAATGGTAATGGT 60.342 52.381 0.00 0.00 0.00 3.55
2794 4409 2.109126 GCCCATCTCGCCTGTCAAC 61.109 63.158 0.00 0.00 0.00 3.18
2816 4431 3.492756 CGCACTGGGTAAAAACAAATTGG 59.507 43.478 0.00 0.00 0.00 3.16
2817 4432 3.249799 GCACTGGGTAAAAACAAATTGGC 59.750 43.478 0.00 0.00 0.00 4.52
2828 4443 1.417145 ACAAATTGGCCACACTGCAAT 59.583 42.857 3.88 0.00 0.00 3.56
2890 4513 4.130118 TCTTCTGACTTGTTTCTCCTTGC 58.870 43.478 0.00 0.00 0.00 4.01
2915 4538 4.643387 GGGACTGGTGCGGCACTT 62.643 66.667 29.92 16.17 34.40 3.16
2949 4572 4.008074 CTGTACTCCAGGCTCAAGAAAA 57.992 45.455 0.00 0.00 37.54 2.29
2973 4596 2.709213 AGCCAAAGAGCTCATGAAGAC 58.291 47.619 17.77 5.36 39.48 3.01
2974 4597 2.039480 AGCCAAAGAGCTCATGAAGACA 59.961 45.455 17.77 0.00 39.48 3.41
2977 4600 4.438472 GCCAAAGAGCTCATGAAGACATTC 60.438 45.833 17.77 0.00 34.15 2.67
2993 4634 7.502226 TGAAGACATTCTGATACAGGTTTTTGT 59.498 33.333 0.00 0.00 36.33 2.83
2995 4636 6.207417 AGACATTCTGATACAGGTTTTTGTGG 59.793 38.462 0.00 0.00 32.56 4.17
2998 4639 6.870971 TTCTGATACAGGTTTTTGTGGTAC 57.129 37.500 0.00 0.00 32.56 3.34
3000 4641 6.358178 TCTGATACAGGTTTTTGTGGTACAA 58.642 36.000 0.00 0.00 33.45 2.41
3007 4648 7.057894 ACAGGTTTTTGTGGTACAAGATTAGA 58.942 34.615 0.00 0.00 44.16 2.10
3109 4753 0.240411 GCCACAGCAGCTTCTTTCAG 59.760 55.000 0.00 0.00 39.53 3.02
3115 4759 4.991056 CACAGCAGCTTCTTTCAGTAGTAA 59.009 41.667 0.00 0.00 0.00 2.24
3128 4772 5.209818 TCAGTAGTAACAGGACCAAACTG 57.790 43.478 0.00 0.00 41.64 3.16
3142 4786 2.291741 CCAAACTGCTGGTCTTGAAGAC 59.708 50.000 16.70 16.70 44.32 3.01
3166 4810 7.056635 ACTTGTAACATCCTCCCTGAATAATG 58.943 38.462 0.00 0.00 0.00 1.90
3167 4811 6.575244 TGTAACATCCTCCCTGAATAATGT 57.425 37.500 0.00 0.00 0.00 2.71
3189 4834 6.670077 GTCAAATCTCCTGACAAATACTCC 57.330 41.667 0.00 0.00 42.32 3.85
3190 4835 5.586643 GTCAAATCTCCTGACAAATACTCCC 59.413 44.000 0.00 0.00 42.32 4.30
3191 4836 5.488919 TCAAATCTCCTGACAAATACTCCCT 59.511 40.000 0.00 0.00 0.00 4.20
3192 4837 5.622346 AATCTCCTGACAAATACTCCCTC 57.378 43.478 0.00 0.00 0.00 4.30
3193 4838 3.375699 TCTCCTGACAAATACTCCCTCC 58.624 50.000 0.00 0.00 0.00 4.30
3194 4839 2.101582 CTCCTGACAAATACTCCCTCCG 59.898 54.545 0.00 0.00 0.00 4.63
3195 4840 1.831736 CCTGACAAATACTCCCTCCGT 59.168 52.381 0.00 0.00 0.00 4.69
3196 4841 2.159085 CCTGACAAATACTCCCTCCGTC 60.159 54.545 0.00 0.00 0.00 4.79
3197 4842 1.829222 TGACAAATACTCCCTCCGTCC 59.171 52.381 0.00 0.00 0.00 4.79
3198 4843 1.829222 GACAAATACTCCCTCCGTCCA 59.171 52.381 0.00 0.00 0.00 4.02
3199 4844 1.831736 ACAAATACTCCCTCCGTCCAG 59.168 52.381 0.00 0.00 0.00 3.86
3200 4845 2.108168 CAAATACTCCCTCCGTCCAGA 58.892 52.381 0.00 0.00 0.00 3.86
3201 4846 2.500098 CAAATACTCCCTCCGTCCAGAA 59.500 50.000 0.00 0.00 0.00 3.02
3202 4847 2.544844 ATACTCCCTCCGTCCAGAAA 57.455 50.000 0.00 0.00 0.00 2.52
3203 4848 2.544844 TACTCCCTCCGTCCAGAAAT 57.455 50.000 0.00 0.00 0.00 2.17
3204 4849 2.544844 ACTCCCTCCGTCCAGAAATA 57.455 50.000 0.00 0.00 0.00 1.40
3205 4850 2.108970 ACTCCCTCCGTCCAGAAATAC 58.891 52.381 0.00 0.00 0.00 1.89
3206 4851 2.292323 ACTCCCTCCGTCCAGAAATACT 60.292 50.000 0.00 0.00 0.00 2.12
3207 4852 2.766828 CTCCCTCCGTCCAGAAATACTT 59.233 50.000 0.00 0.00 0.00 2.24
3208 4853 2.500098 TCCCTCCGTCCAGAAATACTTG 59.500 50.000 0.00 0.00 0.00 3.16
3209 4854 2.236395 CCCTCCGTCCAGAAATACTTGT 59.764 50.000 0.00 0.00 0.00 3.16
3210 4855 3.522553 CCTCCGTCCAGAAATACTTGTC 58.477 50.000 0.00 0.00 0.00 3.18
3211 4856 3.056107 CCTCCGTCCAGAAATACTTGTCA 60.056 47.826 0.00 0.00 0.00 3.58
3212 4857 4.383118 CCTCCGTCCAGAAATACTTGTCAT 60.383 45.833 0.00 0.00 0.00 3.06
3213 4858 4.755411 TCCGTCCAGAAATACTTGTCATC 58.245 43.478 0.00 0.00 0.00 2.92
3214 4859 4.221924 TCCGTCCAGAAATACTTGTCATCA 59.778 41.667 0.00 0.00 0.00 3.07
3215 4860 4.935205 CCGTCCAGAAATACTTGTCATCAA 59.065 41.667 0.00 0.00 0.00 2.57
3216 4861 5.411361 CCGTCCAGAAATACTTGTCATCAAA 59.589 40.000 0.00 0.00 32.87 2.69
3217 4862 6.072728 CCGTCCAGAAATACTTGTCATCAAAA 60.073 38.462 0.00 0.00 32.87 2.44
3218 4863 7.362056 CCGTCCAGAAATACTTGTCATCAAAAT 60.362 37.037 0.00 0.00 32.87 1.82
3219 4864 7.482743 CGTCCAGAAATACTTGTCATCAAAATG 59.517 37.037 0.00 0.00 32.87 2.32
3220 4865 8.514594 GTCCAGAAATACTTGTCATCAAAATGA 58.485 33.333 0.00 0.00 39.63 2.57
3221 4866 9.076781 TCCAGAAATACTTGTCATCAAAATGAA 57.923 29.630 0.00 0.00 43.42 2.57
3222 4867 9.865321 CCAGAAATACTTGTCATCAAAATGAAT 57.135 29.630 0.00 0.00 43.42 2.57
3230 4875 9.492973 ACTTGTCATCAAAATGAATAAAAAGGG 57.507 29.630 0.00 0.00 43.42 3.95
3231 4876 9.709495 CTTGTCATCAAAATGAATAAAAAGGGA 57.291 29.630 0.00 0.00 43.42 4.20
3233 4878 9.656040 TGTCATCAAAATGAATAAAAAGGGATG 57.344 29.630 0.00 0.00 43.42 3.51
3234 4879 9.657419 GTCATCAAAATGAATAAAAAGGGATGT 57.343 29.630 0.00 0.00 43.42 3.06
3250 4895 8.783660 AAAGGGATGTATCTAGATACTTGTCA 57.216 34.615 32.67 19.06 43.04 3.58
3251 4896 8.964533 AAGGGATGTATCTAGATACTTGTCAT 57.035 34.615 32.67 22.04 43.04 3.06
3252 4897 8.588290 AGGGATGTATCTAGATACTTGTCATC 57.412 38.462 32.67 26.51 43.04 2.92
3253 4898 8.173412 AGGGATGTATCTAGATACTTGTCATCA 58.827 37.037 32.67 17.31 43.04 3.07
3254 4899 8.807118 GGGATGTATCTAGATACTTGTCATCAA 58.193 37.037 32.67 16.69 43.04 2.57
3269 4914 9.492973 ACTTGTCATCAAAATGAATAAAAAGGG 57.507 29.630 0.00 0.00 43.42 3.95
3270 4915 9.709495 CTTGTCATCAAAATGAATAAAAAGGGA 57.291 29.630 0.00 0.00 43.42 4.20
3272 4917 9.656040 TGTCATCAAAATGAATAAAAAGGGATG 57.344 29.630 0.00 0.00 43.42 3.51
3273 4918 9.657419 GTCATCAAAATGAATAAAAAGGGATGT 57.343 29.630 0.00 0.00 43.42 3.06
3394 5039 5.930837 TTTTGTCCCTTTTGATGACAAGT 57.069 34.783 0.00 0.00 46.27 3.16
3395 5040 7.411486 TTTTTGTCCCTTTTGATGACAAGTA 57.589 32.000 0.00 0.00 46.27 2.24
3396 5041 7.595819 TTTTGTCCCTTTTGATGACAAGTAT 57.404 32.000 0.00 0.00 46.27 2.12
3397 5042 7.595819 TTTGTCCCTTTTGATGACAAGTATT 57.404 32.000 0.00 0.00 46.27 1.89
3398 5043 7.595819 TTGTCCCTTTTGATGACAAGTATTT 57.404 32.000 0.00 0.00 42.36 1.40
3399 5044 7.214467 TGTCCCTTTTGATGACAAGTATTTC 57.786 36.000 0.00 0.00 36.16 2.17
3400 5045 6.208599 TGTCCCTTTTGATGACAAGTATTTCC 59.791 38.462 0.00 0.00 36.16 3.13
3401 5046 6.208599 GTCCCTTTTGATGACAAGTATTTCCA 59.791 38.462 0.00 0.00 37.32 3.53
3402 5047 6.434028 TCCCTTTTGATGACAAGTATTTCCAG 59.566 38.462 0.00 0.00 37.32 3.86
3403 5048 6.434028 CCCTTTTGATGACAAGTATTTCCAGA 59.566 38.462 0.00 0.00 37.32 3.86
3404 5049 7.308435 CCTTTTGATGACAAGTATTTCCAGAC 58.692 38.462 0.00 0.00 37.32 3.51
3405 5050 6.480524 TTTGATGACAAGTATTTCCAGACG 57.519 37.500 0.00 0.00 37.32 4.18
3406 5051 4.503910 TGATGACAAGTATTTCCAGACGG 58.496 43.478 0.00 0.00 0.00 4.79
3407 5052 4.221924 TGATGACAAGTATTTCCAGACGGA 59.778 41.667 0.00 0.00 40.60 4.69
3408 5053 4.188247 TGACAAGTATTTCCAGACGGAG 57.812 45.455 0.00 0.00 44.10 4.63
3409 5054 3.056107 TGACAAGTATTTCCAGACGGAGG 60.056 47.826 0.00 0.00 44.10 4.30
3410 5055 2.904434 ACAAGTATTTCCAGACGGAGGT 59.096 45.455 0.00 0.00 44.10 3.85
3411 5056 4.091549 ACAAGTATTTCCAGACGGAGGTA 58.908 43.478 0.00 0.00 44.10 3.08
3412 5057 4.159879 ACAAGTATTTCCAGACGGAGGTAG 59.840 45.833 0.00 0.00 44.10 3.18
3413 5058 3.978610 AGTATTTCCAGACGGAGGTAGT 58.021 45.455 0.00 0.00 44.10 2.73
3414 5059 5.121380 AGTATTTCCAGACGGAGGTAGTA 57.879 43.478 0.00 0.00 44.10 1.82
3415 5060 5.131784 AGTATTTCCAGACGGAGGTAGTAG 58.868 45.833 0.00 0.00 44.10 2.57
3416 5061 3.446442 TTTCCAGACGGAGGTAGTAGT 57.554 47.619 0.00 0.00 44.10 2.73
3417 5062 4.574674 TTTCCAGACGGAGGTAGTAGTA 57.425 45.455 0.00 0.00 44.10 1.82
3420 5065 3.118482 TCCAGACGGAGGTAGTAGTACAG 60.118 52.174 9.89 1.13 35.91 2.74
3431 5076 6.056884 AGGTAGTAGTACAGTATGCTCAGAC 58.943 44.000 9.89 0.00 42.53 3.51
3435 5080 0.744874 TACAGTATGCTCAGACGCCC 59.255 55.000 0.00 0.00 42.53 6.13
3449 5094 1.139058 GACGCCCTGAGAATACCACAT 59.861 52.381 0.00 0.00 0.00 3.21
3450 5095 2.364324 GACGCCCTGAGAATACCACATA 59.636 50.000 0.00 0.00 0.00 2.29
3451 5096 2.769663 ACGCCCTGAGAATACCACATAA 59.230 45.455 0.00 0.00 0.00 1.90
3453 5098 3.431626 CGCCCTGAGAATACCACATAACA 60.432 47.826 0.00 0.00 0.00 2.41
3454 5099 4.523083 GCCCTGAGAATACCACATAACAA 58.477 43.478 0.00 0.00 0.00 2.83
3456 5101 5.594317 GCCCTGAGAATACCACATAACAAAT 59.406 40.000 0.00 0.00 0.00 2.32
3539 5232 2.232208 CCCTCTGTTGGCCAAAATCTTC 59.768 50.000 22.47 7.21 0.00 2.87
3541 5234 1.885887 TCTGTTGGCCAAAATCTTCGG 59.114 47.619 22.47 11.91 0.00 4.30
3555 5248 7.420002 CAAAATCTTCGGAATATGCAAGATCA 58.580 34.615 0.00 0.00 35.05 2.92
3597 5290 0.318120 AACCAGCCAAATGAAAGCCG 59.682 50.000 0.00 0.00 0.00 5.52
3600 5293 1.669795 CCAGCCAAATGAAAGCCGAAC 60.670 52.381 0.00 0.00 0.00 3.95
3611 5304 0.820871 AAGCCGAACTTTTGCCAACA 59.179 45.000 0.00 0.00 33.71 3.33
3612 5305 0.820871 AGCCGAACTTTTGCCAACAA 59.179 45.000 0.00 0.00 0.00 2.83
3613 5306 1.412343 AGCCGAACTTTTGCCAACAAT 59.588 42.857 0.00 0.00 35.21 2.71
3614 5307 1.792367 GCCGAACTTTTGCCAACAATC 59.208 47.619 0.00 0.00 35.21 2.67
3615 5308 2.050691 CCGAACTTTTGCCAACAATCG 58.949 47.619 0.00 0.00 35.40 3.34
3616 5309 2.050691 CGAACTTTTGCCAACAATCGG 58.949 47.619 0.00 0.00 35.21 4.18
3622 5315 3.111038 GCCAACAATCGGCTAGCC 58.889 61.111 24.75 24.75 46.56 3.93
3623 5316 1.748879 GCCAACAATCGGCTAGCCA 60.749 57.895 32.47 19.90 46.56 4.75
3624 5317 1.312371 GCCAACAATCGGCTAGCCAA 61.312 55.000 32.47 17.13 46.56 4.52
3625 5318 1.173043 CCAACAATCGGCTAGCCAAA 58.827 50.000 32.47 20.47 35.37 3.28
3626 5319 1.543802 CCAACAATCGGCTAGCCAAAA 59.456 47.619 32.47 17.87 35.37 2.44
3650 5343 1.581447 GCTGGAGGTCGCCAAAAAG 59.419 57.895 0.00 0.00 37.52 2.27
3681 5374 3.251729 TCTGAGTTGAGTTTGCAAGATGC 59.748 43.478 0.00 0.00 45.29 3.91
3697 5390 5.782047 CAAGATGCCACAGATAACCAAAAA 58.218 37.500 0.00 0.00 0.00 1.94
3732 5425 3.414269 CAAATGAAGGGCTGCCAAAATT 58.586 40.909 22.05 11.16 0.00 1.82
3773 5466 2.046292 ACCAACCAAACATTCCCCTTG 58.954 47.619 0.00 0.00 0.00 3.61
3778 5471 1.001181 CCAAACATTCCCCTTGTGCTG 59.999 52.381 0.00 0.00 0.00 4.41
3788 5482 2.301346 CCCTTGTGCTGTGAGAAAACT 58.699 47.619 0.00 0.00 0.00 2.66
3792 5486 2.368439 TGTGCTGTGAGAAAACTTGCT 58.632 42.857 0.00 0.00 0.00 3.91
3793 5487 3.540617 TGTGCTGTGAGAAAACTTGCTA 58.459 40.909 0.00 0.00 0.00 3.49
3814 5508 1.170919 AGAGCACAAGCAAGGCACAG 61.171 55.000 0.00 0.00 45.49 3.66
3839 5533 1.595489 GCACAACAGTTCAGCAGTTCG 60.595 52.381 2.31 0.00 0.00 3.95
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
21 22 3.225940 CAAGGAGGCTCTTCCAAACTTT 58.774 45.455 15.23 0.00 39.84 2.66
127 134 4.386951 TCCGTCCGTCCGTCCGTA 62.387 66.667 0.00 0.00 0.00 4.02
140 147 3.257933 GACGTACAGTCCGTCCGT 58.742 61.111 7.42 0.00 46.73 4.69
179 194 1.667724 CTCAACTGACCGATTGGATGC 59.332 52.381 5.81 0.00 39.21 3.91
219 237 3.371063 ACGTGTGCTCGGTCGGAT 61.371 61.111 0.00 0.00 34.94 4.18
344 363 4.275936 GCCAAGCCGTGTGATAATAAGAAT 59.724 41.667 0.00 0.00 0.00 2.40
347 366 3.002656 CAGCCAAGCCGTGTGATAATAAG 59.997 47.826 0.00 0.00 0.00 1.73
350 369 1.382522 CAGCCAAGCCGTGTGATAAT 58.617 50.000 0.00 0.00 0.00 1.28
427 446 2.038690 CTGCTGCCATGCCAATAGG 58.961 57.895 0.00 0.00 38.23 2.57
434 453 2.126071 CTGTTGCTGCTGCCATGC 60.126 61.111 13.47 0.00 38.71 4.06
435 454 0.958876 TCTCTGTTGCTGCTGCCATG 60.959 55.000 13.47 1.30 38.71 3.66
436 455 0.034380 ATCTCTGTTGCTGCTGCCAT 60.034 50.000 13.47 0.00 38.71 4.40
437 456 0.958876 CATCTCTGTTGCTGCTGCCA 60.959 55.000 13.47 3.81 38.71 4.92
438 457 0.675837 TCATCTCTGTTGCTGCTGCC 60.676 55.000 13.47 0.00 38.71 4.85
445 494 0.376152 CGTGCCATCATCTCTGTTGC 59.624 55.000 0.00 0.00 0.00 4.17
471 520 6.024552 TGATGCCTGGTTTTATTTTCTGAC 57.975 37.500 0.00 0.00 0.00 3.51
488 1945 3.467374 TGGTTTTGGTTTTCTGATGCC 57.533 42.857 0.00 0.00 0.00 4.40
508 1966 2.039084 ACTCTCCGTTGGAAAAGCTCAT 59.961 45.455 0.00 0.00 0.00 2.90
519 1977 3.919216 AGACTGATGAAACTCTCCGTTG 58.081 45.455 0.00 0.00 35.61 4.10
521 1979 2.494073 GGAGACTGATGAAACTCTCCGT 59.506 50.000 0.00 0.00 39.55 4.69
522 1980 2.159170 GGGAGACTGATGAAACTCTCCG 60.159 54.545 6.49 0.00 46.91 4.63
524 1982 2.494073 ACGGGAGACTGATGAAACTCTC 59.506 50.000 0.00 0.00 41.09 3.20
525 1983 2.232452 CACGGGAGACTGATGAAACTCT 59.768 50.000 0.00 0.00 41.09 3.24
526 1984 2.611518 CACGGGAGACTGATGAAACTC 58.388 52.381 0.00 0.00 41.09 3.01
527 1985 1.276421 CCACGGGAGACTGATGAAACT 59.724 52.381 0.00 0.00 41.09 2.66
528 1986 1.726853 CCACGGGAGACTGATGAAAC 58.273 55.000 0.00 0.00 41.09 2.78
529 1987 0.036388 GCCACGGGAGACTGATGAAA 60.036 55.000 0.00 0.00 41.09 2.69
530 1988 1.596934 GCCACGGGAGACTGATGAA 59.403 57.895 0.00 0.00 41.09 2.57
531 1989 2.710902 CGCCACGGGAGACTGATGA 61.711 63.158 0.00 0.00 41.09 2.92
532 1990 2.202797 CGCCACGGGAGACTGATG 60.203 66.667 0.00 0.00 41.09 3.07
534 1992 2.599281 TTCGCCACGGGAGACTGA 60.599 61.111 0.00 0.00 41.09 3.41
535 1993 2.125912 CTTCGCCACGGGAGACTG 60.126 66.667 0.00 0.00 44.60 3.51
536 1994 4.070552 GCTTCGCCACGGGAGACT 62.071 66.667 0.00 0.00 29.75 3.24
567 2033 4.623814 CAGGAATTGCCGCTCTGA 57.376 55.556 0.00 0.00 43.43 3.27
604 2074 1.586541 CCAAAAGGAAGGAAGGCGC 59.413 57.895 0.00 0.00 0.00 6.53
614 2084 1.075896 AAACCCCGTGCCAAAAGGA 60.076 52.632 0.00 0.00 0.00 3.36
615 2085 1.365999 GAAACCCCGTGCCAAAAGG 59.634 57.895 0.00 0.00 0.00 3.11
616 2086 1.365999 GGAAACCCCGTGCCAAAAG 59.634 57.895 0.00 0.00 0.00 2.27
617 2087 1.381327 TGGAAACCCCGTGCCAAAA 60.381 52.632 0.00 0.00 37.93 2.44
618 2088 2.128507 GTGGAAACCCCGTGCCAAA 61.129 57.895 0.00 0.00 37.93 3.28
619 2089 2.519780 GTGGAAACCCCGTGCCAA 60.520 61.111 0.00 0.00 37.93 4.52
620 2090 4.939368 CGTGGAAACCCCGTGCCA 62.939 66.667 0.00 0.00 37.93 4.92
623 2093 4.939368 TGGCGTGGAAACCCCGTG 62.939 66.667 0.00 0.00 37.93 4.94
624 2094 4.941309 GTGGCGTGGAAACCCCGT 62.941 66.667 0.00 0.00 37.93 5.28
625 2095 4.636435 AGTGGCGTGGAAACCCCG 62.636 66.667 0.00 0.00 37.93 5.73
626 2096 2.671963 GAGTGGCGTGGAAACCCC 60.672 66.667 0.00 0.00 0.00 4.95
627 2097 3.047877 CGAGTGGCGTGGAAACCC 61.048 66.667 0.00 0.00 34.64 4.11
654 2124 3.321111 AGAGAAAGAACAGCCGTCAACTA 59.679 43.478 0.00 0.00 0.00 2.24
667 2168 3.214328 GCAACAACAGGGAGAGAAAGAA 58.786 45.455 0.00 0.00 0.00 2.52
675 2176 1.294659 GAGAGCGCAACAACAGGGAG 61.295 60.000 11.47 0.00 0.00 4.30
682 2204 1.438651 GTATGTGGAGAGCGCAACAA 58.561 50.000 11.47 0.00 0.00 2.83
891 2434 1.176527 TAACGACGTTACAGGGAGGG 58.823 55.000 16.19 0.00 0.00 4.30
1128 2685 2.817423 CTTCTGCTGCCCGCGAATC 61.817 63.158 8.23 0.00 43.27 2.52
1147 2704 0.253327 GACATGGAGTGGAGGGGAAC 59.747 60.000 0.00 0.00 0.00 3.62
1148 2705 0.914417 GGACATGGAGTGGAGGGGAA 60.914 60.000 0.00 0.00 0.00 3.97
1149 2706 1.306997 GGACATGGAGTGGAGGGGA 60.307 63.158 0.00 0.00 0.00 4.81
1153 2710 0.539051 GACAGGGACATGGAGTGGAG 59.461 60.000 0.00 0.00 0.00 3.86
1154 2711 1.257750 CGACAGGGACATGGAGTGGA 61.258 60.000 0.00 0.00 0.00 4.02
1157 2717 1.610673 AGCGACAGGGACATGGAGT 60.611 57.895 0.00 0.00 0.00 3.85
1159 2719 2.981302 CAGCGACAGGGACATGGA 59.019 61.111 0.00 0.00 0.00 3.41
1425 3002 0.597377 GGCAAAGCGGGTTTGTTGAG 60.597 55.000 27.37 8.22 46.44 3.02
1457 3041 0.750546 GCAATGGCAGCATCTGGAGA 60.751 55.000 0.00 0.00 40.72 3.71
1545 3129 2.113139 CACGGGGTGGAGCTTTGT 59.887 61.111 0.00 0.00 0.00 2.83
1547 3131 4.660938 GGCACGGGGTGGAGCTTT 62.661 66.667 0.00 0.00 33.64 3.51
1593 3177 7.707893 CAGAGGAAGAAATTGTTGTTCAAATGT 59.292 33.333 0.00 0.00 38.47 2.71
1596 3180 6.042143 GCAGAGGAAGAAATTGTTGTTCAAA 58.958 36.000 0.00 0.00 38.47 2.69
1597 3181 5.360714 AGCAGAGGAAGAAATTGTTGTTCAA 59.639 36.000 0.00 0.00 38.47 2.69
1611 3195 5.163874 CGAATTCAGAGAAAAGCAGAGGAAG 60.164 44.000 6.22 0.00 0.00 3.46
1744 3332 3.303135 TGCGTGAAGGAGACGGCT 61.303 61.111 0.00 0.00 37.30 5.52
1774 3362 1.079057 GGTGAAGAAGGGCTCGGAC 60.079 63.158 0.00 0.00 0.00 4.79
1777 3365 1.738099 CACGGTGAAGAAGGGCTCG 60.738 63.158 0.74 0.00 0.00 5.03
1935 3523 3.343941 TTTAGGGACAATGTTCTCCGG 57.656 47.619 0.00 0.00 0.00 5.14
1951 3539 8.455903 AATATAATCATCGGGCCATGATTTAG 57.544 34.615 30.97 10.40 46.87 1.85
1952 3540 7.502226 GGAATATAATCATCGGGCCATGATTTA 59.498 37.037 30.97 24.72 46.87 1.40
1953 3541 6.322201 GGAATATAATCATCGGGCCATGATTT 59.678 38.462 30.97 23.96 46.87 2.17
2045 3635 2.721167 CCCTGCCTCGACGGAATCA 61.721 63.158 5.24 0.00 33.16 2.57
2054 3644 2.107141 GAATCCGACCCTGCCTCG 59.893 66.667 0.00 0.00 0.00 4.63
2057 3647 2.190578 CCAGAATCCGACCCTGCC 59.809 66.667 0.00 0.00 0.00 4.85
2204 3797 5.770663 TGTTTGGGATTTGGAAAGAATCGTA 59.229 36.000 0.00 0.00 34.97 3.43
2206 3799 4.923281 GTGTTTGGGATTTGGAAAGAATCG 59.077 41.667 0.00 0.00 34.97 3.34
2221 3814 5.599732 TGAACAAATTCATCAGTGTTTGGG 58.400 37.500 7.74 0.00 40.01 4.12
2256 3849 0.908198 GTCCATGAACTCCTCCTGCT 59.092 55.000 0.00 0.00 0.00 4.24
2450 4043 9.877178 CCAGAGTTCACAATAGTTTATTAGTCT 57.123 33.333 0.00 0.00 0.00 3.24
2451 4044 8.604890 GCCAGAGTTCACAATAGTTTATTAGTC 58.395 37.037 0.00 0.00 0.00 2.59
2452 4045 8.322091 AGCCAGAGTTCACAATAGTTTATTAGT 58.678 33.333 0.00 0.00 0.00 2.24
2453 4046 8.723942 AGCCAGAGTTCACAATAGTTTATTAG 57.276 34.615 0.00 0.00 0.00 1.73
2454 4047 8.946085 CAAGCCAGAGTTCACAATAGTTTATTA 58.054 33.333 0.00 0.00 0.00 0.98
2466 4080 1.946283 GCCCTACAAGCCAGAGTTCAC 60.946 57.143 0.00 0.00 0.00 3.18
2478 4092 1.378762 GCAGGTTCAGGCCCTACAA 59.621 57.895 0.00 0.00 0.00 2.41
2528 4142 0.179034 GGTAGCCATGGAAGCAGAGG 60.179 60.000 18.40 0.00 0.00 3.69
2578 4193 0.531974 TGAAGCCAGAACCGTGTGAC 60.532 55.000 0.00 0.00 0.00 3.67
2669 4284 2.623416 CCAGGATCATGTACGACAGCTA 59.377 50.000 6.62 0.00 0.00 3.32
2794 4409 3.492756 CCAATTTGTTTTTACCCAGTGCG 59.507 43.478 0.00 0.00 0.00 5.34
2816 4431 3.375782 AAAAAGAGATTGCAGTGTGGC 57.624 42.857 0.00 0.00 0.00 5.01
2838 4453 3.570550 AGTAGAAAAGACACTGCTCGAGT 59.429 43.478 15.13 0.00 34.02 4.18
2849 4464 7.386299 TCAGAAGAGAATTGCAGTAGAAAAGAC 59.614 37.037 0.00 0.00 0.00 3.01
2866 4481 5.605534 CAAGGAGAAACAAGTCAGAAGAGA 58.394 41.667 0.00 0.00 0.00 3.10
2890 4513 2.263741 GCACCAGTCCCTGCAGTTG 61.264 63.158 13.81 3.36 33.31 3.16
2915 4538 1.547372 GAGTACAGGTAAACTCCCGCA 59.453 52.381 0.00 0.00 36.86 5.69
2949 4572 2.867624 TCATGAGCTCTTTGGCTTTGT 58.132 42.857 16.19 0.00 43.20 2.83
2973 4596 6.331369 ACCACAAAAACCTGTATCAGAATG 57.669 37.500 0.00 0.00 32.44 2.67
2974 4597 7.001674 TGTACCACAAAAACCTGTATCAGAAT 58.998 34.615 0.00 0.00 32.44 2.40
2977 4600 6.485313 TCTTGTACCACAAAAACCTGTATCAG 59.515 38.462 0.00 0.00 37.69 2.90
3021 4662 9.206690 ACCTATCTCAATACATTTTCTCTCTGA 57.793 33.333 0.00 0.00 0.00 3.27
3022 4663 9.829507 AACCTATCTCAATACATTTTCTCTCTG 57.170 33.333 0.00 0.00 0.00 3.35
3023 4664 9.829507 CAACCTATCTCAATACATTTTCTCTCT 57.170 33.333 0.00 0.00 0.00 3.10
3024 4665 9.606631 ACAACCTATCTCAATACATTTTCTCTC 57.393 33.333 0.00 0.00 0.00 3.20
3092 4736 3.397482 ACTACTGAAAGAAGCTGCTGTG 58.603 45.455 1.35 0.00 37.43 3.66
3109 4753 3.746492 CAGCAGTTTGGTCCTGTTACTAC 59.254 47.826 0.00 0.00 32.41 2.73
3115 4759 4.907457 CCAGCAGTTTGGTCCTGT 57.093 55.556 0.00 0.00 33.38 4.00
3128 4772 4.127171 TGTTACAAGTCTTCAAGACCAGC 58.873 43.478 14.27 0.61 46.18 4.85
3142 4786 7.056635 ACATTATTCAGGGAGGATGTTACAAG 58.943 38.462 0.00 0.00 0.00 3.16
3166 4810 5.586643 GGGAGTATTTGTCAGGAGATTTGAC 59.413 44.000 0.00 0.00 44.03 3.18
3167 4811 5.488919 AGGGAGTATTTGTCAGGAGATTTGA 59.511 40.000 0.00 0.00 0.00 2.69
3185 4830 2.108970 GTATTTCTGGACGGAGGGAGT 58.891 52.381 0.00 0.00 0.00 3.85
3186 4831 2.389715 AGTATTTCTGGACGGAGGGAG 58.610 52.381 0.00 0.00 0.00 4.30
3187 4832 2.500098 CAAGTATTTCTGGACGGAGGGA 59.500 50.000 0.00 0.00 0.00 4.20
3188 4833 2.236395 ACAAGTATTTCTGGACGGAGGG 59.764 50.000 0.00 0.00 0.00 4.30
3189 4834 3.056107 TGACAAGTATTTCTGGACGGAGG 60.056 47.826 0.00 0.00 0.00 4.30
3190 4835 4.188247 TGACAAGTATTTCTGGACGGAG 57.812 45.455 0.00 0.00 0.00 4.63
3191 4836 4.221924 TGATGACAAGTATTTCTGGACGGA 59.778 41.667 0.00 0.00 0.00 4.69
3192 4837 4.503910 TGATGACAAGTATTTCTGGACGG 58.496 43.478 0.00 0.00 0.00 4.79
3193 4838 6.480524 TTTGATGACAAGTATTTCTGGACG 57.519 37.500 0.00 0.00 37.32 4.79
3194 4839 8.514594 TCATTTTGATGACAAGTATTTCTGGAC 58.485 33.333 0.00 0.00 37.32 4.02
3195 4840 8.634335 TCATTTTGATGACAAGTATTTCTGGA 57.366 30.769 0.00 0.00 37.32 3.86
3196 4841 9.865321 ATTCATTTTGATGACAAGTATTTCTGG 57.135 29.630 0.00 0.00 37.32 3.86
3204 4849 9.492973 CCCTTTTTATTCATTTTGATGACAAGT 57.507 29.630 0.00 0.00 37.32 3.16
3205 4850 9.709495 TCCCTTTTTATTCATTTTGATGACAAG 57.291 29.630 0.00 0.00 37.32 3.16
3207 4852 9.656040 CATCCCTTTTTATTCATTTTGATGACA 57.344 29.630 0.00 0.00 0.00 3.58
3208 4853 9.657419 ACATCCCTTTTTATTCATTTTGATGAC 57.343 29.630 0.00 0.00 32.39 3.06
3224 4869 9.213777 TGACAAGTATCTAGATACATCCCTTTT 57.786 33.333 33.87 20.04 44.58 2.27
3225 4870 8.783660 TGACAAGTATCTAGATACATCCCTTT 57.216 34.615 33.87 20.60 44.58 3.11
3226 4871 8.964533 ATGACAAGTATCTAGATACATCCCTT 57.035 34.615 33.87 21.17 44.58 3.95
3227 4872 8.173412 TGATGACAAGTATCTAGATACATCCCT 58.827 37.037 33.87 20.79 44.58 4.20
3228 4873 8.354711 TGATGACAAGTATCTAGATACATCCC 57.645 38.462 33.87 23.01 44.58 3.85
3243 4888 9.492973 CCCTTTTTATTCATTTTGATGACAAGT 57.507 29.630 0.00 0.00 37.32 3.16
3244 4889 9.709495 TCCCTTTTTATTCATTTTGATGACAAG 57.291 29.630 0.00 0.00 37.32 3.16
3246 4891 9.656040 CATCCCTTTTTATTCATTTTGATGACA 57.344 29.630 0.00 0.00 0.00 3.58
3247 4892 9.657419 ACATCCCTTTTTATTCATTTTGATGAC 57.343 29.630 0.00 0.00 32.39 3.06
3374 5019 7.255801 GGAAATACTTGTCATCAAAAGGGACAA 60.256 37.037 0.00 0.00 46.09 3.18
3375 5020 6.208599 GGAAATACTTGTCATCAAAAGGGACA 59.791 38.462 0.00 0.00 39.60 4.02
3376 5021 6.208599 TGGAAATACTTGTCATCAAAAGGGAC 59.791 38.462 0.00 0.00 32.87 4.46
3377 5022 6.310941 TGGAAATACTTGTCATCAAAAGGGA 58.689 36.000 0.00 0.00 32.87 4.20
3378 5023 6.434028 TCTGGAAATACTTGTCATCAAAAGGG 59.566 38.462 0.00 0.00 32.87 3.95
3379 5024 7.308435 GTCTGGAAATACTTGTCATCAAAAGG 58.692 38.462 0.00 0.00 32.87 3.11
3380 5025 7.017645 CGTCTGGAAATACTTGTCATCAAAAG 58.982 38.462 0.00 0.00 32.87 2.27
3381 5026 6.072728 CCGTCTGGAAATACTTGTCATCAAAA 60.073 38.462 0.00 0.00 37.49 2.44
3382 5027 5.411361 CCGTCTGGAAATACTTGTCATCAAA 59.589 40.000 0.00 0.00 37.49 2.69
3383 5028 4.935205 CCGTCTGGAAATACTTGTCATCAA 59.065 41.667 0.00 0.00 37.49 2.57
3384 5029 4.221924 TCCGTCTGGAAATACTTGTCATCA 59.778 41.667 0.00 0.00 42.85 3.07
3385 5030 4.755411 TCCGTCTGGAAATACTTGTCATC 58.245 43.478 0.00 0.00 42.85 2.92
3386 5031 4.383118 CCTCCGTCTGGAAATACTTGTCAT 60.383 45.833 0.00 0.00 45.87 3.06
3387 5032 3.056107 CCTCCGTCTGGAAATACTTGTCA 60.056 47.826 0.00 0.00 45.87 3.58
3388 5033 3.056035 ACCTCCGTCTGGAAATACTTGTC 60.056 47.826 0.00 0.00 45.87 3.18
3389 5034 2.904434 ACCTCCGTCTGGAAATACTTGT 59.096 45.455 0.00 0.00 45.87 3.16
3390 5035 3.611766 ACCTCCGTCTGGAAATACTTG 57.388 47.619 0.00 0.00 45.87 3.16
3391 5036 4.351127 ACTACCTCCGTCTGGAAATACTT 58.649 43.478 0.00 0.00 45.87 2.24
3392 5037 3.978610 ACTACCTCCGTCTGGAAATACT 58.021 45.455 0.00 0.00 45.87 2.12
3393 5038 4.886489 ACTACTACCTCCGTCTGGAAATAC 59.114 45.833 0.00 0.00 45.87 1.89
3394 5039 5.121380 ACTACTACCTCCGTCTGGAAATA 57.879 43.478 0.00 0.00 45.87 1.40
3395 5040 3.978610 ACTACTACCTCCGTCTGGAAAT 58.021 45.455 0.00 0.00 45.87 2.17
3396 5041 3.446442 ACTACTACCTCCGTCTGGAAA 57.554 47.619 0.00 0.00 45.87 3.13
3397 5042 3.264193 TGTACTACTACCTCCGTCTGGAA 59.736 47.826 0.00 0.00 45.87 3.53
3398 5043 2.840038 TGTACTACTACCTCCGTCTGGA 59.160 50.000 0.00 0.00 43.88 3.86
3399 5044 3.204526 CTGTACTACTACCTCCGTCTGG 58.795 54.545 0.00 0.00 0.00 3.86
3400 5045 3.871485 ACTGTACTACTACCTCCGTCTG 58.129 50.000 0.00 0.00 0.00 3.51
3401 5046 5.609423 CATACTGTACTACTACCTCCGTCT 58.391 45.833 0.00 0.00 0.00 4.18
3402 5047 4.213059 GCATACTGTACTACTACCTCCGTC 59.787 50.000 0.00 0.00 0.00 4.79
3403 5048 4.133078 GCATACTGTACTACTACCTCCGT 58.867 47.826 0.00 0.00 0.00 4.69
3404 5049 4.387598 AGCATACTGTACTACTACCTCCG 58.612 47.826 0.00 0.00 0.00 4.63
3405 5050 5.374921 TGAGCATACTGTACTACTACCTCC 58.625 45.833 0.00 0.00 0.00 4.30
3406 5051 6.203338 GTCTGAGCATACTGTACTACTACCTC 59.797 46.154 0.00 0.00 0.00 3.85
3407 5052 6.056884 GTCTGAGCATACTGTACTACTACCT 58.943 44.000 0.00 0.00 0.00 3.08
3408 5053 5.050227 CGTCTGAGCATACTGTACTACTACC 60.050 48.000 0.00 0.00 0.00 3.18
3409 5054 5.558653 GCGTCTGAGCATACTGTACTACTAC 60.559 48.000 0.00 0.00 37.05 2.73
3410 5055 4.510711 GCGTCTGAGCATACTGTACTACTA 59.489 45.833 0.00 0.00 37.05 1.82
3411 5056 3.312973 GCGTCTGAGCATACTGTACTACT 59.687 47.826 0.00 0.00 37.05 2.57
3412 5057 3.548415 GGCGTCTGAGCATACTGTACTAC 60.548 52.174 0.00 0.00 39.27 2.73
3413 5058 2.617308 GGCGTCTGAGCATACTGTACTA 59.383 50.000 0.00 0.00 39.27 1.82
3414 5059 1.405821 GGCGTCTGAGCATACTGTACT 59.594 52.381 0.00 0.00 39.27 2.73
3415 5060 1.536284 GGGCGTCTGAGCATACTGTAC 60.536 57.143 0.00 0.00 39.27 2.90
3416 5061 0.744874 GGGCGTCTGAGCATACTGTA 59.255 55.000 0.00 0.00 39.27 2.74
3417 5062 0.972983 AGGGCGTCTGAGCATACTGT 60.973 55.000 0.00 0.00 39.27 3.55
3420 5065 1.816537 TCAGGGCGTCTGAGCATAC 59.183 57.895 6.53 0.00 46.71 2.39
3431 5076 3.131396 GTTATGTGGTATTCTCAGGGCG 58.869 50.000 0.00 0.00 0.00 6.13
3449 5094 4.747605 GCCCGCTTTTCTCAAAATTTGTTA 59.252 37.500 5.56 0.00 0.00 2.41
3450 5095 3.559655 GCCCGCTTTTCTCAAAATTTGTT 59.440 39.130 5.56 0.00 0.00 2.83
3451 5096 3.130633 GCCCGCTTTTCTCAAAATTTGT 58.869 40.909 5.56 0.00 0.00 2.83
3453 5098 3.467374 TGCCCGCTTTTCTCAAAATTT 57.533 38.095 0.00 0.00 0.00 1.82
3454 5099 3.244181 ACATGCCCGCTTTTCTCAAAATT 60.244 39.130 0.00 0.00 0.00 1.82
3456 5101 1.686052 ACATGCCCGCTTTTCTCAAAA 59.314 42.857 0.00 0.00 0.00 2.44
3465 5138 2.209315 AAGCCAAACATGCCCGCTT 61.209 52.632 0.00 0.00 35.02 4.68
3504 5197 2.107204 ACAGAGGGTCAAGCAATGTCTT 59.893 45.455 0.00 0.00 0.00 3.01
3520 5213 2.095059 CCGAAGATTTTGGCCAACAGAG 60.095 50.000 20.35 6.09 0.00 3.35
3539 5232 4.093998 GCCTATGTGATCTTGCATATTCCG 59.906 45.833 0.00 0.00 0.00 4.30
3541 5234 6.376978 GTTGCCTATGTGATCTTGCATATTC 58.623 40.000 0.00 0.00 0.00 1.75
3577 5270 1.543802 CGGCTTTCATTTGGCTGGTTA 59.456 47.619 0.00 0.00 0.00 2.85
3579 5272 0.539438 TCGGCTTTCATTTGGCTGGT 60.539 50.000 0.00 0.00 33.63 4.00
3583 5276 2.438868 AAGTTCGGCTTTCATTTGGC 57.561 45.000 0.00 0.00 32.57 4.52
3624 5317 0.603065 GCGACCTCCAGCCAATTTTT 59.397 50.000 0.00 0.00 0.00 1.94
3625 5318 2.267045 GCGACCTCCAGCCAATTTT 58.733 52.632 0.00 0.00 0.00 1.82
3626 5319 4.002797 GCGACCTCCAGCCAATTT 57.997 55.556 0.00 0.00 0.00 1.82
3646 5339 3.953612 TCAACTCAGATGTTGCCACTTTT 59.046 39.130 0.00 0.00 44.83 2.27
3650 5343 2.498167 ACTCAACTCAGATGTTGCCAC 58.502 47.619 0.00 0.00 44.83 5.01
3732 5425 2.650322 TGCCCAGATTTACCCTACCAAA 59.350 45.455 0.00 0.00 0.00 3.28
3738 5431 1.080638 TTGGTGCCCAGATTTACCCT 58.919 50.000 0.00 0.00 33.81 4.34
3750 5443 0.034756 GGGAATGTTTGGTTGGTGCC 59.965 55.000 0.00 0.00 0.00 5.01
3766 5459 0.843309 TTTCTCACAGCACAAGGGGA 59.157 50.000 0.00 0.00 0.00 4.81
3773 5466 4.756084 ATAGCAAGTTTTCTCACAGCAC 57.244 40.909 0.00 0.00 0.00 4.40
3792 5486 2.027285 TGTGCCTTGCTTGTGCTCTATA 60.027 45.455 0.00 0.00 40.48 1.31
3793 5487 1.271543 TGTGCCTTGCTTGTGCTCTAT 60.272 47.619 0.00 0.00 40.48 1.98
3814 5508 1.334556 TGCTGAACTGTTGTGCACATC 59.665 47.619 22.39 20.44 33.76 3.06
3822 5516 0.383491 CGCGAACTGCTGAACTGTTG 60.383 55.000 0.00 0.00 40.19 3.33
3823 5517 0.810031 ACGCGAACTGCTGAACTGTT 60.810 50.000 15.93 0.00 42.51 3.16
3825 5519 1.202568 CACGCGAACTGCTGAACTG 59.797 57.895 15.93 0.00 43.27 3.16
3839 5533 1.212751 GAACTGAAATGCCCCACGC 59.787 57.895 0.00 0.00 38.31 5.34
3843 5537 2.562298 TGATGTTGAACTGAAATGCCCC 59.438 45.455 0.00 0.00 0.00 5.80


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

AutoCloner maintained by Alex Coulton.