Multiple sequence alignment - TraesCS6D01G189200

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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 TraesCS6D01G189200 chr6D 100.000 7676 0 0 734 8409 262186464 262178789 0.000000e+00 14176.0
1 TraesCS6D01G189200 chr6D 89.309 1375 82 29 5807 7160 248507439 248506109 0.000000e+00 1664.0
2 TraesCS6D01G189200 chr6D 88.576 1173 95 14 1049 2211 248509120 248507977 0.000000e+00 1387.0
3 TraesCS6D01G189200 chr6D 83.186 1243 180 22 3158 4385 80508800 80507572 0.000000e+00 1110.0
4 TraesCS6D01G189200 chr6D 100.000 524 0 0 1 524 262187197 262186674 0.000000e+00 968.0
5 TraesCS6D01G189200 chr6D 87.329 513 53 9 5254 5760 248507943 248507437 2.040000e-160 577.0
6 TraesCS6D01G189200 chr6D 77.778 612 99 27 3151 3732 121548259 121548863 8.080000e-90 342.0
7 TraesCS6D01G189200 chr6D 78.442 385 58 20 5 378 248510198 248509828 2.360000e-55 228.0
8 TraesCS6D01G189200 chr6D 83.824 136 20 2 3156 3289 349734323 349734188 2.460000e-25 128.0
9 TraesCS6D01G189200 chr6D 79.630 108 20 2 2826 2931 308887200 308887307 9.050000e-10 76.8
10 TraesCS6D01G189200 chr6A 92.006 7756 491 55 734 8409 324286550 324294256 0.000000e+00 10768.0
11 TraesCS6D01G189200 chr6A 89.351 1371 93 21 5807 7160 326392750 326394084 0.000000e+00 1674.0
12 TraesCS6D01G189200 chr6A 88.917 1173 97 20 1049 2211 326391064 326392213 0.000000e+00 1415.0
13 TraesCS6D01G189200 chr6A 90.824 534 37 8 1 524 324285936 324286467 0.000000e+00 704.0
14 TraesCS6D01G189200 chr6B 96.503 2545 75 4 5395 7933 348854212 348856748 0.000000e+00 4194.0
15 TraesCS6D01G189200 chr6B 93.567 2394 105 18 734 3098 348851830 348854203 0.000000e+00 3522.0
16 TraesCS6D01G189200 chr6B 88.983 1180 95 12 1049 2221 349467020 349468171 0.000000e+00 1426.0
17 TraesCS6D01G189200 chr6B 82.768 1120 151 29 3158 4266 153638055 153636967 0.000000e+00 961.0
18 TraesCS6D01G189200 chr6B 93.659 615 36 3 5807 6419 349468658 349469271 0.000000e+00 917.0
19 TraesCS6D01G189200 chr6B 89.353 695 47 14 6483 7160 349470590 349471274 0.000000e+00 848.0
20 TraesCS6D01G189200 chr6B 93.446 534 25 9 1 524 348851226 348851759 0.000000e+00 784.0
21 TraesCS6D01G189200 chr6B 93.029 416 19 4 7994 8407 348856764 348857171 4.340000e-167 599.0
22 TraesCS6D01G189200 chr6B 86.544 327 31 8 5254 5574 349468190 349468509 1.740000e-91 348.0
23 TraesCS6D01G189200 chr6B 79.124 388 57 19 1 377 349465974 349466348 6.520000e-61 246.0
24 TraesCS6D01G189200 chr6B 87.838 148 15 2 5616 5760 349468513 349468660 4.040000e-38 171.0
25 TraesCS6D01G189200 chr6B 87.719 114 12 1 7155 7266 349471356 349471469 1.900000e-26 132.0
26 TraesCS6D01G189200 chr5D 86.133 1298 153 21 3160 4437 118006041 118007331 0.000000e+00 1375.0
27 TraesCS6D01G189200 chr5D 78.402 463 75 20 3151 3600 66580980 66580530 2.310000e-70 278.0
28 TraesCS6D01G189200 chr3B 83.514 1292 168 32 3155 4414 524956095 524957373 0.000000e+00 1164.0
29 TraesCS6D01G189200 chr4B 81.516 1293 196 26 3158 4441 187014035 187012777 0.000000e+00 1024.0
30 TraesCS6D01G189200 chr4B 77.174 276 53 9 8062 8331 470113528 470113257 1.460000e-32 152.0
31 TraesCS6D01G189200 chr4B 78.862 123 21 4 118 236 106795253 106795132 2.520000e-10 78.7
32 TraesCS6D01G189200 chr2B 83.153 1015 145 12 3427 4436 257531248 257530255 0.000000e+00 904.0
33 TraesCS6D01G189200 chr2B 86.747 83 10 1 3153 3234 43048110 43048028 3.230000e-14 91.6
34 TraesCS6D01G189200 chr1D 84.690 823 119 6 3321 4140 230676282 230677100 0.000000e+00 815.0
35 TraesCS6D01G189200 chr7D 82.383 965 134 30 3158 4103 535739546 535738599 0.000000e+00 808.0
36 TraesCS6D01G189200 chr7D 84.196 367 49 6 8044 8407 239045714 239046074 1.740000e-91 348.0
37 TraesCS6D01G189200 chr7D 78.616 159 28 5 135 288 53487005 53486848 5.370000e-17 100.0
38 TraesCS6D01G189200 chr5B 82.310 961 143 19 3158 4103 520174517 520175465 0.000000e+00 808.0
39 TraesCS6D01G189200 chr2D 84.891 642 88 9 3146 3782 136610533 136611170 2.560000e-179 640.0
40 TraesCS6D01G189200 chr2D 78.084 616 90 33 3151 3732 328736231 328736835 1.740000e-91 348.0
41 TraesCS6D01G189200 chr2D 78.182 385 71 10 3318 3699 80227800 80227426 5.080000e-57 233.0
42 TraesCS6D01G189200 chr2D 75.882 170 28 11 115 274 461372352 461372186 3.260000e-09 75.0
43 TraesCS6D01G189200 chrUn 92.526 388 21 5 6490 6871 480163773 480164158 4.440000e-152 549.0
44 TraesCS6D01G189200 chr3A 80.000 240 37 10 111 343 67436695 67436930 5.220000e-37 167.0
45 TraesCS6D01G189200 chr3A 85.075 134 18 2 3158 3289 610341097 610341230 1.470000e-27 135.0
46 TraesCS6D01G189200 chr7B 78.212 179 30 9 133 306 496886115 496886289 1.150000e-18 106.0
47 TraesCS6D01G189200 chr1B 78.986 138 25 4 3155 3289 671620024 671619888 3.230000e-14 91.6
48 TraesCS6D01G189200 chr3D 77.536 138 29 2 3152 3287 84928499 84928636 1.950000e-11 82.4


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 TraesCS6D01G189200 chr6D 262178789 262187197 8408 True 7572.00 14176 100.000000 1 8409 2 chr6D.!!$R4 8408
1 TraesCS6D01G189200 chr6D 80507572 80508800 1228 True 1110.00 1110 83.186000 3158 4385 1 chr6D.!!$R1 1227
2 TraesCS6D01G189200 chr6D 248506109 248510198 4089 True 964.00 1664 85.914000 5 7160 4 chr6D.!!$R3 7155
3 TraesCS6D01G189200 chr6D 121548259 121548863 604 False 342.00 342 77.778000 3151 3732 1 chr6D.!!$F1 581
4 TraesCS6D01G189200 chr6A 324285936 324294256 8320 False 5736.00 10768 91.415000 1 8409 2 chr6A.!!$F1 8408
5 TraesCS6D01G189200 chr6A 326391064 326394084 3020 False 1544.50 1674 89.134000 1049 7160 2 chr6A.!!$F2 6111
6 TraesCS6D01G189200 chr6B 348851226 348857171 5945 False 2274.75 4194 94.136250 1 8407 4 chr6B.!!$F1 8406
7 TraesCS6D01G189200 chr6B 153636967 153638055 1088 True 961.00 961 82.768000 3158 4266 1 chr6B.!!$R1 1108
8 TraesCS6D01G189200 chr6B 349465974 349471469 5495 False 584.00 1426 87.602857 1 7266 7 chr6B.!!$F2 7265
9 TraesCS6D01G189200 chr5D 118006041 118007331 1290 False 1375.00 1375 86.133000 3160 4437 1 chr5D.!!$F1 1277
10 TraesCS6D01G189200 chr3B 524956095 524957373 1278 False 1164.00 1164 83.514000 3155 4414 1 chr3B.!!$F1 1259
11 TraesCS6D01G189200 chr4B 187012777 187014035 1258 True 1024.00 1024 81.516000 3158 4441 1 chr4B.!!$R2 1283
12 TraesCS6D01G189200 chr2B 257530255 257531248 993 True 904.00 904 83.153000 3427 4436 1 chr2B.!!$R2 1009
13 TraesCS6D01G189200 chr1D 230676282 230677100 818 False 815.00 815 84.690000 3321 4140 1 chr1D.!!$F1 819
14 TraesCS6D01G189200 chr7D 535738599 535739546 947 True 808.00 808 82.383000 3158 4103 1 chr7D.!!$R2 945
15 TraesCS6D01G189200 chr5B 520174517 520175465 948 False 808.00 808 82.310000 3158 4103 1 chr5B.!!$F1 945
16 TraesCS6D01G189200 chr2D 136610533 136611170 637 False 640.00 640 84.891000 3146 3782 1 chr2D.!!$F1 636
17 TraesCS6D01G189200 chr2D 328736231 328736835 604 False 348.00 348 78.084000 3151 3732 1 chr2D.!!$F2 581

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
832 975 1.224592 CTAGGCATTTGCGGGAGGT 59.775 57.895 0.00 0.00 43.26 3.85 F
1394 1700 0.343372 TGATGGAGGAGCTTAGGGGT 59.657 55.000 0.00 0.00 0.00 4.95 F
2555 2882 0.109086 CTCACTAGTGCCACCACGAG 60.109 60.000 18.45 3.84 46.62 4.18 F
2737 3064 0.034477 CCCAAAATAGGCGGACCACT 60.034 55.000 0.00 0.00 39.06 4.00 F
4600 5046 0.105039 CCGAGCCAATCCTCACCTAC 59.895 60.000 0.00 0.00 0.00 3.18 F
5218 5679 0.102663 TGCGTCACTCGTTGTGGTTA 59.897 50.000 10.35 0.00 46.20 2.85 F
5238 5699 0.250081 GGTGGGCGAATTTTTGGCAA 60.250 50.000 0.00 0.00 38.79 4.52 F
5239 5700 0.865111 GTGGGCGAATTTTTGGCAAC 59.135 50.000 0.00 1.63 38.79 4.17 F
5876 6351 1.138036 TCGTACCATCGCCAACTCG 59.862 57.895 0.00 0.00 0.00 4.18 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2504 2831 0.035152 AGATCCATGCTTTGGCGTCA 60.035 50.000 0.00 0.00 46.01 4.35 R
2649 2976 0.321919 TAGGTGACGAGCGGTGTAGT 60.322 55.000 0.00 0.00 0.00 2.73 R
4244 4662 0.466739 ACACACCCGTCCCTTTTTCC 60.467 55.000 0.00 0.00 0.00 3.13 R
4702 5148 0.678048 GCAGAAGGTGATGGTGTCCC 60.678 60.000 0.00 0.00 0.00 4.46 R
5789 6263 0.391597 AACGAGGAACCGCTCTTTCA 59.608 50.000 0.00 0.00 0.00 2.69 R
6757 8524 1.275471 GCTTTTCGGCGGTTTCAAGC 61.275 55.000 7.21 10.06 0.00 4.01 R
7222 9088 3.880047 ACCGATCTGGAAATGAACGTA 57.120 42.857 10.05 0.00 42.00 3.57 R
7248 9114 0.453793 TGTTTTGTCAAGCACCACCG 59.546 50.000 0.00 0.00 0.00 4.94 R
7589 9455 0.810031 GTAGGGTGCCATGCTACACG 60.810 60.000 5.88 0.00 37.68 4.49 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
90 92 4.307032 ACACATATTCAAGAACCCTGCT 57.693 40.909 0.00 0.00 0.00 4.24
204 212 7.095355 ACGTCTTAGACACATACAAAATGGAAC 60.095 37.037 13.14 0.00 32.09 3.62
205 213 7.527457 GTCTTAGACACATACAAAATGGAACC 58.473 38.462 7.59 0.00 32.09 3.62
468 525 2.759973 CTGGCCGAGTAGCTCCCA 60.760 66.667 0.00 0.00 0.00 4.37
469 526 2.041922 TGGCCGAGTAGCTCCCAT 60.042 61.111 0.00 0.00 0.00 4.00
832 975 1.224592 CTAGGCATTTGCGGGAGGT 59.775 57.895 0.00 0.00 43.26 3.85
839 982 1.472480 CATTTGCGGGAGGTCGAAAAT 59.528 47.619 0.00 0.00 45.98 1.82
874 1017 9.411801 CATTTTAGCTTCTTCCTTTTTCTTACC 57.588 33.333 0.00 0.00 0.00 2.85
1074 1380 0.535102 AGGTCCAAACAACAGCCGAG 60.535 55.000 0.00 0.00 0.00 4.63
1311 1617 3.093814 TGCTACCTCTTATGTTCCACGA 58.906 45.455 0.00 0.00 0.00 4.35
1394 1700 0.343372 TGATGGAGGAGCTTAGGGGT 59.657 55.000 0.00 0.00 0.00 4.95
1461 1767 4.537965 CGAGTCTTACCCTGATATGAACG 58.462 47.826 0.00 0.00 0.00 3.95
1464 1770 4.038162 AGTCTTACCCTGATATGAACGAGC 59.962 45.833 0.00 0.00 0.00 5.03
1469 1775 3.117888 ACCCTGATATGAACGAGCCAATT 60.118 43.478 0.00 0.00 0.00 2.32
1528 1834 5.774690 TCTTGGCATACCTTTTGTTGATTCT 59.225 36.000 0.00 0.00 36.63 2.40
1529 1835 5.389859 TGGCATACCTTTTGTTGATTCTG 57.610 39.130 0.00 0.00 36.63 3.02
1968 2292 6.970191 AGGCAGTTATTTCCTTACCTTGTAT 58.030 36.000 0.00 0.00 0.00 2.29
2013 2337 1.747206 GCTGTTCCCGGCACAATAGAT 60.747 52.381 0.00 0.00 42.86 1.98
2325 2652 0.879090 GGGAGCCCTTTTACACAACG 59.121 55.000 0.00 0.00 0.00 4.10
2355 2682 3.570125 GGATATCCAGGCAACCTAAAAGC 59.430 47.826 17.34 0.00 35.64 3.51
2516 2843 2.892334 GCTCGTTGACGCCAAAGCA 61.892 57.895 3.59 0.00 36.58 3.91
2546 2873 2.750166 TCACTCAGTAGCTCACTAGTGC 59.250 50.000 18.45 7.57 45.72 4.40
2552 2879 0.895530 TAGCTCACTAGTGCCACCAC 59.104 55.000 18.45 3.61 42.39 4.16
2555 2882 0.109086 CTCACTAGTGCCACCACGAG 60.109 60.000 18.45 3.84 46.62 4.18
2623 2950 3.660111 GACGCCACTGCCCACAAC 61.660 66.667 0.00 0.00 0.00 3.32
2662 2989 2.256591 ACACGACTACACCGCTCGT 61.257 57.895 0.00 0.00 41.23 4.18
2664 2991 1.962822 ACGACTACACCGCTCGTCA 60.963 57.895 0.00 0.00 35.82 4.35
2667 2994 1.584380 GACTACACCGCTCGTCACCT 61.584 60.000 0.00 0.00 0.00 4.00
2694 3021 1.139853 CCAAGAGACATAGCCACCTCC 59.860 57.143 0.00 0.00 0.00 4.30
2725 3052 4.344679 TGATGCTTGTCAAAGACCCAAAAT 59.655 37.500 0.00 0.00 35.19 1.82
2737 3064 0.034477 CCCAAAATAGGCGGACCACT 60.034 55.000 0.00 0.00 39.06 4.00
2787 3114 2.766263 CTCCTAGACACTGCCAACCATA 59.234 50.000 0.00 0.00 0.00 2.74
2865 3192 0.108377 CGACATCAATCACCGGGTCA 60.108 55.000 6.32 0.00 0.00 4.02
2870 3197 1.348064 TCAATCACCGGGTCAGAGTT 58.652 50.000 6.32 0.00 0.00 3.01
2889 3216 2.577593 GTGCCTCCACGGTAGGAC 59.422 66.667 1.04 0.00 36.08 3.85
2899 3226 4.814294 GGTAGGACGCGCCCACAG 62.814 72.222 15.72 0.00 37.37 3.66
2925 3253 3.075005 CAGTCGGTCCCGGTGGAT 61.075 66.667 5.80 0.00 44.28 3.41
2965 3293 4.662961 CTGCTGACGGCCGACACA 62.663 66.667 35.90 27.35 40.92 3.72
2979 3307 3.005554 CCGACACAGAGCAAGATCAAAT 58.994 45.455 0.00 0.00 0.00 2.32
2989 3317 2.198406 CAAGATCAAATGCCGCCATTG 58.802 47.619 0.00 0.00 40.69 2.82
3014 3342 1.507630 CACCGGTGTCGATCCGTTA 59.492 57.895 26.95 0.00 45.63 3.18
3015 3343 0.109179 CACCGGTGTCGATCCGTTAA 60.109 55.000 26.95 0.00 45.63 2.01
3016 3344 0.819582 ACCGGTGTCGATCCGTTAAT 59.180 50.000 23.29 9.19 45.63 1.40
3078 3428 1.367102 CAACGCAAGGCAACCCAAT 59.633 52.632 0.00 0.00 46.39 3.16
3106 3456 1.989966 ATCACTCCGTCGTACCTGCG 61.990 60.000 0.00 0.00 0.00 5.18
3107 3457 2.670934 ACTCCGTCGTACCTGCGT 60.671 61.111 0.00 0.00 0.00 5.24
3109 3459 2.974489 CTCCGTCGTACCTGCGTGT 61.974 63.158 0.00 0.00 0.00 4.49
3144 3494 0.898320 ACCACCTCGAACCAGATCAG 59.102 55.000 0.00 0.00 0.00 2.90
3153 3503 4.100084 CCAGATCAGCACCGCCCA 62.100 66.667 0.00 0.00 0.00 5.36
3211 3562 1.883926 CGGTTTTGTCCGGATTTCCTT 59.116 47.619 7.81 0.00 45.88 3.36
3454 3831 5.519206 CCAACTTCTATAACTGCTCCGTAAC 59.481 44.000 0.00 0.00 0.00 2.50
3517 3895 4.394300 CGGAGTCTTGATCTTGAATGCTTT 59.606 41.667 0.00 0.00 0.00 3.51
3565 3960 6.842437 AGAGTTGCTTCTTCACATCTAGTA 57.158 37.500 0.00 0.00 0.00 1.82
3573 3968 9.136323 TGCTTCTTCACATCTAGTATCATCTAA 57.864 33.333 0.00 0.00 0.00 2.10
3771 4179 1.487482 TCGTTTGAGCACTTGACGAG 58.513 50.000 0.00 0.00 37.76 4.18
3805 4214 3.066291 TGTTCCGGCATTGTAGAACAT 57.934 42.857 0.00 0.00 42.61 2.71
3972 4381 1.673033 GCGAAGTCAGTACCTGCATGT 60.673 52.381 0.00 0.00 0.00 3.21
3975 4384 1.352083 AGTCAGTACCTGCATGTGGT 58.648 50.000 15.02 15.02 41.28 4.16
3984 4393 1.913951 CTGCATGTGGTCTAGGGGCA 61.914 60.000 0.00 0.00 0.00 5.36
4169 4582 1.961277 GTGCTTGGCTGCTACACGT 60.961 57.895 0.00 0.00 0.00 4.49
4175 4588 4.771356 GCTGCTACACGTCCGCGA 62.771 66.667 8.23 0.00 42.00 5.87
4204 4619 1.479757 GCTAGGGACGAGAAGGGAGAT 60.480 57.143 0.00 0.00 30.78 2.75
4229 4644 3.177883 GGTGTGCGACCAATGTTTG 57.822 52.632 0.00 0.00 45.34 2.93
4244 4662 0.617535 GTTTGGGGGAAGGGGGAATG 60.618 60.000 0.00 0.00 0.00 2.67
4274 4692 2.642254 GGGTGTGTCATCGACGGGA 61.642 63.158 0.00 0.00 34.95 5.14
4349 4769 6.282167 TGACCACAAACACGATCTAAACTTA 58.718 36.000 0.00 0.00 0.00 2.24
4361 4781 6.127310 ACGATCTAAACTTAGGCTGAGAATGT 60.127 38.462 13.85 0.00 0.00 2.71
4438 4867 0.879090 GTTTCTGCCTGTTTACCCCG 59.121 55.000 0.00 0.00 0.00 5.73
4447 4876 2.099098 CCTGTTTACCCCGAATGAATGC 59.901 50.000 0.00 0.00 0.00 3.56
4455 4884 1.927210 CGAATGAATGCGGACGAGG 59.073 57.895 0.00 0.00 0.00 4.63
4456 4885 0.806102 CGAATGAATGCGGACGAGGT 60.806 55.000 0.00 0.00 0.00 3.85
4457 4886 0.931005 GAATGAATGCGGACGAGGTC 59.069 55.000 0.00 0.00 0.00 3.85
4458 4887 0.249120 AATGAATGCGGACGAGGTCA 59.751 50.000 0.00 0.00 33.68 4.02
4460 4889 0.460109 TGAATGCGGACGAGGTCATG 60.460 55.000 0.00 0.00 33.68 3.07
4461 4890 1.766143 GAATGCGGACGAGGTCATGC 61.766 60.000 0.00 2.21 36.49 4.06
4470 4899 3.665675 GAGGTCATGCGCCGGAGTT 62.666 63.158 5.05 0.00 0.00 3.01
4471 4900 3.499737 GGTCATGCGCCGGAGTTG 61.500 66.667 5.05 4.58 0.00 3.16
4513 4952 2.332514 CACCAAACCACAGCAGCG 59.667 61.111 0.00 0.00 0.00 5.18
4600 5046 0.105039 CCGAGCCAATCCTCACCTAC 59.895 60.000 0.00 0.00 0.00 3.18
4601 5047 0.105039 CGAGCCAATCCTCACCTACC 59.895 60.000 0.00 0.00 0.00 3.18
4607 5053 1.049289 AATCCTCACCTACCCGGAGC 61.049 60.000 0.73 0.00 36.31 4.70
4660 5106 0.179040 GGTCAAAACCACCTCCGTCA 60.179 55.000 0.00 0.00 45.68 4.35
4662 5108 0.531090 TCAAAACCACCTCCGTCACG 60.531 55.000 0.00 0.00 0.00 4.35
4664 5110 4.657824 AACCACCTCCGTCACGCG 62.658 66.667 3.53 3.53 40.95 6.01
4666 5112 4.351938 CCACCTCCGTCACGCGAA 62.352 66.667 15.93 0.00 44.77 4.70
4667 5113 3.103911 CACCTCCGTCACGCGAAC 61.104 66.667 15.93 9.94 44.77 3.95
4677 5123 4.210093 ACGCGAACGGTCCACACA 62.210 61.111 15.93 0.00 46.04 3.72
4699 5145 3.003173 TGGCCCGGACAGGAGAAG 61.003 66.667 0.73 0.00 45.00 2.85
4702 5148 3.083997 CCCGGACAGGAGAAGGGG 61.084 72.222 0.73 0.00 45.00 4.79
4736 5182 4.652131 TGCACCCCGCCGTCAAAT 62.652 61.111 0.00 0.00 41.33 2.32
4784 5230 3.419759 GCCGTCGACCAACGCAAT 61.420 61.111 10.58 0.00 41.26 3.56
4797 5243 0.537143 ACGCAATCACCAAGAGCCAA 60.537 50.000 0.00 0.00 0.00 4.52
4798 5244 0.109597 CGCAATCACCAAGAGCCAAC 60.110 55.000 0.00 0.00 0.00 3.77
4800 5246 1.547372 GCAATCACCAAGAGCCAACAT 59.453 47.619 0.00 0.00 0.00 2.71
4857 5306 1.477685 CCACGACCCAACCTACCACT 61.478 60.000 0.00 0.00 0.00 4.00
4861 5310 2.292061 ACGACCCAACCTACCACTAGAT 60.292 50.000 0.00 0.00 0.00 1.98
4929 5378 1.946267 CACGCTAACCACCCAACAC 59.054 57.895 0.00 0.00 0.00 3.32
4965 5425 4.722700 GCCCACACGCATCCACCT 62.723 66.667 0.00 0.00 0.00 4.00
4966 5426 2.986290 CCCACACGCATCCACCTA 59.014 61.111 0.00 0.00 0.00 3.08
4977 5437 2.752030 CATCCACCTAGAGGAAGACCA 58.248 52.381 1.60 0.00 38.93 4.02
5021 5482 2.740714 GCCAAGGACATCGACGCAC 61.741 63.158 0.00 0.00 0.00 5.34
5041 5502 0.759436 AGACACTTGACGACCACCCT 60.759 55.000 0.00 0.00 0.00 4.34
5044 5505 0.321671 CACTTGACGACCACCCTGAT 59.678 55.000 0.00 0.00 0.00 2.90
5141 5602 4.858680 TGCCGCACCAACCGACAA 62.859 61.111 0.00 0.00 0.00 3.18
5142 5603 3.587933 GCCGCACCAACCGACAAA 61.588 61.111 0.00 0.00 0.00 2.83
5163 5624 0.469518 GCGGTGGAGGATAGGTAGGT 60.470 60.000 0.00 0.00 0.00 3.08
5164 5625 2.033208 GCGGTGGAGGATAGGTAGGTT 61.033 57.143 0.00 0.00 0.00 3.50
5176 5637 1.227383 GTAGGTTGGATGGGGGCTG 59.773 63.158 0.00 0.00 0.00 4.85
5205 5666 1.469251 GCTAGATTTCCGTCTGCGTCA 60.469 52.381 0.00 0.00 36.15 4.35
5206 5667 2.186076 CTAGATTTCCGTCTGCGTCAC 58.814 52.381 0.00 0.00 36.15 3.67
5207 5668 0.603569 AGATTTCCGTCTGCGTCACT 59.396 50.000 0.00 0.00 36.15 3.41
5209 5670 0.732880 ATTTCCGTCTGCGTCACTCG 60.733 55.000 0.00 0.00 43.12 4.18
5210 5671 2.067091 TTTCCGTCTGCGTCACTCGT 62.067 55.000 0.00 0.00 42.13 4.18
5211 5672 2.050351 CCGTCTGCGTCACTCGTT 60.050 61.111 0.00 0.00 42.13 3.85
5212 5673 2.365068 CCGTCTGCGTCACTCGTTG 61.365 63.158 0.00 0.00 42.13 4.10
5213 5674 1.657487 CGTCTGCGTCACTCGTTGT 60.657 57.895 0.00 0.00 42.13 3.32
5215 5676 1.299850 TCTGCGTCACTCGTTGTGG 60.300 57.895 10.35 0.00 46.20 4.17
5216 5677 1.591594 CTGCGTCACTCGTTGTGGT 60.592 57.895 10.35 0.00 46.20 4.16
5217 5678 1.151777 CTGCGTCACTCGTTGTGGTT 61.152 55.000 10.35 0.00 46.20 3.67
5218 5679 0.102663 TGCGTCACTCGTTGTGGTTA 59.897 50.000 10.35 0.00 46.20 2.85
5225 5686 0.953960 CTCGTTGTGGTTAGGTGGGC 60.954 60.000 0.00 0.00 0.00 5.36
5228 5689 0.535553 GTTGTGGTTAGGTGGGCGAA 60.536 55.000 0.00 0.00 0.00 4.70
5235 5696 2.353307 GGTTAGGTGGGCGAATTTTTGG 60.353 50.000 0.00 0.00 0.00 3.28
5236 5697 0.892063 TAGGTGGGCGAATTTTTGGC 59.108 50.000 0.00 0.00 36.46 4.52
5238 5699 0.250081 GGTGGGCGAATTTTTGGCAA 60.250 50.000 0.00 0.00 38.79 4.52
5239 5700 0.865111 GTGGGCGAATTTTTGGCAAC 59.135 50.000 0.00 1.63 38.79 4.17
5252 5713 1.733526 GGCAACAACCAGTCACCAC 59.266 57.895 0.00 0.00 0.00 4.16
5256 5717 1.401552 CAACAACCAGTCACCACACAG 59.598 52.381 0.00 0.00 0.00 3.66
5296 5757 7.351166 TGGTTTTCAGGGAAGGGTAAATATAG 58.649 38.462 0.00 0.00 0.00 1.31
5328 5789 3.498397 ACATTTCTGGACTAGTTTGTGCG 59.502 43.478 0.00 0.00 0.00 5.34
5329 5790 2.163818 TTCTGGACTAGTTTGTGCGG 57.836 50.000 0.00 0.00 36.23 5.69
5358 5819 3.417069 AGTGCACAATGTAGGCAGTTA 57.583 42.857 21.04 0.00 37.94 2.24
5439 5902 5.309638 TGGTATCGACAAATTCTTGGACAA 58.690 37.500 0.00 0.00 36.82 3.18
5548 6015 4.761739 TGGTCCAGTTCACAGAATGATTTC 59.238 41.667 0.00 0.00 39.69 2.17
5578 6045 2.615912 GTCTCTGCAAGCACAAGTTCTT 59.384 45.455 0.00 0.00 0.00 2.52
5630 6097 7.612633 TCAGGGAGGTGGTTAAATTGTTTATAC 59.387 37.037 0.00 0.00 0.00 1.47
5762 6236 6.638468 GCTTCCTTGTGTCTCAATTAGTTTTG 59.362 38.462 0.00 0.00 35.35 2.44
5789 6263 8.888716 GTTGTCATAAATTTTCCAAAAAGGTGT 58.111 29.630 0.00 0.00 39.02 4.16
5876 6351 1.138036 TCGTACCATCGCCAACTCG 59.862 57.895 0.00 0.00 0.00 4.18
5888 6363 2.543848 CGCCAACTCGCATGTTATGTAT 59.456 45.455 0.00 0.00 0.00 2.29
6330 6809 4.201891 GCACCAGATAAGATGTTGCTCAAG 60.202 45.833 0.00 0.00 0.00 3.02
6514 8275 7.599630 TTTTTCATAGCGACGGTAAATACTT 57.400 32.000 11.22 0.00 0.00 2.24
6605 8370 9.896645 ATTCTATGATATTGACGGCTATTTCAT 57.103 29.630 18.90 18.90 34.43 2.57
6757 8524 5.301805 TCCTAAAGAAAGGGCAAAGAAAGTG 59.698 40.000 0.00 0.00 37.24 3.16
6920 8687 3.542969 AATCTGTTTTGGCCCCTTAGT 57.457 42.857 0.00 0.00 0.00 2.24
6971 8742 6.317789 TCATCAGTTTGTGAGGATTTGTTC 57.682 37.500 0.00 0.00 41.05 3.18
6972 8743 5.241506 TCATCAGTTTGTGAGGATTTGTTCC 59.758 40.000 0.00 0.00 41.05 3.62
6992 8763 5.772393 TCCACTTCCACCTGTTATATGTT 57.228 39.130 0.00 0.00 0.00 2.71
7279 9145 5.275741 GCTTGACAAAACAAAAAGCTACGTC 60.276 40.000 0.00 0.00 40.04 4.34
7283 9149 4.201980 ACAAAACAAAAAGCTACGTCTCCC 60.202 41.667 0.00 0.00 0.00 4.30
7298 9164 3.447586 CGTCTCCCTGATTCTTTCCACTA 59.552 47.826 0.00 0.00 0.00 2.74
7476 9342 5.770162 TGCTCTCTGGTATATTTGATCTCGA 59.230 40.000 0.00 0.00 0.00 4.04
7482 9348 3.921021 GGTATATTTGATCTCGAGTGCGG 59.079 47.826 13.13 0.00 38.28 5.69
7589 9455 0.681564 TCCAGAGAGAAGGACTCCGC 60.682 60.000 0.00 0.00 45.96 5.54
7682 9548 3.058501 CACAACAATTCGTCCTGTTACCC 60.059 47.826 0.00 0.00 0.00 3.69
7791 9662 2.030946 GGCAAATTACTCTACTGCAGCG 59.969 50.000 15.27 5.33 34.66 5.18
7914 9785 0.904649 ATCATGTGCGTTCTCTGGGA 59.095 50.000 0.00 0.00 0.00 4.37
7915 9786 0.247460 TCATGTGCGTTCTCTGGGAG 59.753 55.000 0.00 0.00 0.00 4.30
7977 9849 1.944024 ACGACGGTGCATTTTCTCAAA 59.056 42.857 0.00 0.00 0.00 2.69
7978 9850 2.552315 ACGACGGTGCATTTTCTCAAAT 59.448 40.909 0.00 0.00 32.36 2.32
8052 9924 2.943033 GCTTGGATACTAACGGTGCAAT 59.057 45.455 0.00 0.00 37.61 3.56
8060 9932 6.877322 GGATACTAACGGTGCAATATACCAAT 59.123 38.462 0.00 0.00 38.11 3.16
8085 9958 4.341199 TTGGTAGGGGTCCAAGCA 57.659 55.556 0.00 0.00 39.62 3.91
8115 9988 2.518587 TCGGATCGGAGGTCGCAT 60.519 61.111 0.00 0.00 39.05 4.73
8123 9996 2.101783 TCGGAGGTCGCATAAAGGTTA 58.898 47.619 0.00 0.00 39.05 2.85
8124 9997 2.159198 TCGGAGGTCGCATAAAGGTTAC 60.159 50.000 0.00 0.00 39.05 2.50
8125 9998 2.159142 CGGAGGTCGCATAAAGGTTACT 60.159 50.000 0.00 0.00 0.00 2.24
8172 10047 1.812571 CCCTACGTCATGCTTGCTTTT 59.187 47.619 0.00 0.00 0.00 2.27
8217 10092 2.482316 CGTGCGAGGGATTACAATGGTA 60.482 50.000 0.00 0.00 0.00 3.25
8231 10106 9.155975 GATTACAATGGTATATGAGGTTGCTAG 57.844 37.037 0.00 0.00 0.00 3.42
8277 10152 0.398664 CCCTAGATGGTTCCCCGACT 60.399 60.000 0.00 0.00 0.00 4.18
8326 10201 2.538449 GGTTTACACGATGGTAGATGCG 59.462 50.000 0.00 0.00 0.00 4.73
8340 10215 0.315706 GATGCGATCTTCAGCGTTGC 60.316 55.000 0.00 0.00 35.87 4.17
8357 10233 2.750350 CGCCCTTGTCTTGGAGGT 59.250 61.111 0.00 0.00 0.00 3.85
8382 10258 1.186267 AGGTCTTCGACGCTCCCTTT 61.186 55.000 0.00 0.00 32.65 3.11
8399 10275 0.188342 TTTGGGCTTCTCCTTTGCCT 59.812 50.000 0.00 0.00 45.45 4.75
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
81 83 6.239036 GGGATATATGTTTTTCAGCAGGGTTC 60.239 42.308 0.00 0.00 0.00 3.62
378 413 3.916761 TCTTTCACTGATTTGCATTGGC 58.083 40.909 0.00 0.00 41.68 4.52
441 498 1.224592 CTCGGCCAGCCCAATACTT 59.775 57.895 2.24 0.00 0.00 2.24
468 525 3.578716 TCCTCTCGACTTTTGTTCCTCAT 59.421 43.478 0.00 0.00 0.00 2.90
469 526 2.963101 TCCTCTCGACTTTTGTTCCTCA 59.037 45.455 0.00 0.00 0.00 3.86
874 1017 4.070716 GGATTGCTGAGAACCATAGGATG 58.929 47.826 0.00 0.00 0.00 3.51
884 1029 2.229792 GTGTGGTTGGATTGCTGAGAA 58.770 47.619 0.00 0.00 0.00 2.87
1037 1184 4.160814 GGACCTACAAAAACCAACCTTTGT 59.839 41.667 5.60 5.60 45.33 2.83
1074 1380 6.237542 CGTGCTAAATTAATTCATGCACCAAC 60.238 38.462 27.82 15.58 44.13 3.77
1226 1532 2.226962 AATGCATCAAGAGTGGCCTT 57.773 45.000 3.32 0.00 0.00 4.35
1311 1617 6.222038 TCTCTTTGCGGAAGTGAACTATAT 57.778 37.500 0.00 0.00 35.54 0.86
1461 1767 4.184079 ACTGCTCAAATTCAATTGGCTC 57.816 40.909 5.42 0.00 31.75 4.70
1464 1770 5.143376 AGGAACTGCTCAAATTCAATTGG 57.857 39.130 5.42 0.00 37.18 3.16
1469 1775 4.202567 ACCCTAAGGAACTGCTCAAATTCA 60.203 41.667 0.00 0.00 40.86 2.57
1547 1855 7.764331 TCATACATGAGTGAAAATGTGGAATG 58.236 34.615 0.00 0.00 37.57 2.67
1646 1960 2.528564 TCTTTTGGCCTCCTGATTTGG 58.471 47.619 3.32 0.00 0.00 3.28
1842 2156 0.609131 AAAGCAGAACACCATCCCCG 60.609 55.000 0.00 0.00 0.00 5.73
1968 2292 6.335471 ACATTGATCAACTTGCTGATTCAA 57.665 33.333 11.07 0.00 36.15 2.69
2013 2337 6.596888 CCTTCTTTGTATTGATTGCTCTCTCA 59.403 38.462 0.00 0.00 0.00 3.27
2097 2421 9.010029 CCAATGTTAACTAGAGTACAACCAATT 57.990 33.333 7.22 0.00 0.00 2.32
2315 2642 1.898472 TCCCGGGATACGTTGTGTAAA 59.102 47.619 22.63 0.00 42.24 2.01
2343 2670 1.602377 AGTCGTGTGCTTTTAGGTTGC 59.398 47.619 0.00 0.00 0.00 4.17
2355 2682 4.478699 TCTTTCGGTAATGTAGTCGTGTG 58.521 43.478 0.00 0.00 0.00 3.82
2499 2826 0.453282 CATGCTTTGGCGTCAACGAG 60.453 55.000 10.78 3.60 43.02 4.18
2504 2831 0.035152 AGATCCATGCTTTGGCGTCA 60.035 50.000 0.00 0.00 46.01 4.35
2516 2843 4.713814 TGAGCTACTGAGTGAAAGATCCAT 59.286 41.667 0.00 0.00 0.00 3.41
2546 2873 2.124983 CTGGATGCCTCGTGGTGG 60.125 66.667 5.26 0.00 35.27 4.61
2552 2879 1.450312 GGTGGTTCTGGATGCCTCG 60.450 63.158 0.00 0.00 0.00 4.63
2555 2882 3.134127 GCGGTGGTTCTGGATGCC 61.134 66.667 0.00 0.00 0.00 4.40
2559 2886 2.225791 CTCATCGCGGTGGTTCTGGA 62.226 60.000 21.08 0.00 0.00 3.86
2644 2971 2.180131 GACGAGCGGTGTAGTCGTGT 62.180 60.000 2.91 0.00 46.49 4.49
2649 2976 0.321919 TAGGTGACGAGCGGTGTAGT 60.322 55.000 0.00 0.00 0.00 2.73
2662 2989 2.224695 TGTCTCTTGGTCGACTAGGTGA 60.225 50.000 16.46 13.31 0.00 4.02
2664 2991 2.581216 TGTCTCTTGGTCGACTAGGT 57.419 50.000 16.46 0.00 0.00 3.08
2667 2994 2.950309 GGCTATGTCTCTTGGTCGACTA 59.050 50.000 16.46 6.50 0.00 2.59
2694 3021 0.745486 TGACAAGCATCATGGAGGCG 60.745 55.000 0.00 0.00 44.44 5.52
2725 3052 1.481802 CCCCTTATAGTGGTCCGCCTA 60.482 57.143 0.00 0.00 35.27 3.93
2787 3114 2.106338 TGGTTGTGTGGTCATGAGATGT 59.894 45.455 0.00 0.00 0.00 3.06
2899 3226 2.424733 GGACCGACTGGGAGGTAGC 61.425 68.421 0.00 0.00 41.51 3.58
2925 3253 1.200519 CTGGGTTGTATTCTCCCCGA 58.799 55.000 0.00 0.00 40.20 5.14
2965 3293 0.737219 GCGGCATTTGATCTTGCTCT 59.263 50.000 13.15 0.00 38.88 4.09
2994 3322 3.755628 CGGATCGACACCGGTGGT 61.756 66.667 36.47 22.65 45.65 4.16
3014 3342 1.595357 GTCGGTCCGAGTTGGGATT 59.405 57.895 15.95 0.00 38.61 3.01
3015 3343 2.707849 CGTCGGTCCGAGTTGGGAT 61.708 63.158 15.95 0.00 38.61 3.85
3016 3344 3.367743 CGTCGGTCCGAGTTGGGA 61.368 66.667 15.95 0.00 36.23 4.37
3106 3456 4.645921 GGCAACGCCCAGCAACAC 62.646 66.667 0.00 0.00 44.06 3.32
3153 3503 0.605589 GCGTTGGAGTTGGCCTAAGT 60.606 55.000 3.32 0.00 0.00 2.24
3209 3560 1.463674 CCATTCCGACCCCAAAGAAG 58.536 55.000 0.00 0.00 0.00 2.85
3211 3562 1.688811 CCCATTCCGACCCCAAAGA 59.311 57.895 0.00 0.00 0.00 2.52
3454 3831 3.526931 TCGAGAAGGCACTAATCCAAG 57.473 47.619 0.00 0.00 38.49 3.61
3565 3960 6.835174 TGCTTGAATAGAGGCTTTAGATGAT 58.165 36.000 0.00 0.00 0.00 2.45
3573 3968 4.217118 CACTTGTTGCTTGAATAGAGGCTT 59.783 41.667 0.00 0.00 0.00 4.35
3771 4179 0.815615 GGAACATCTCGGATGGGTGC 60.816 60.000 15.41 7.03 0.00 5.01
3805 4214 1.600636 CAAGGAAGGTCTTGCGCCA 60.601 57.895 4.18 0.00 37.84 5.69
3932 4341 2.722094 CCTCTAGCCGCTCAGATCTAT 58.278 52.381 0.00 0.00 0.00 1.98
3972 4381 3.006677 GGCAATGCCCCTAGACCA 58.993 61.111 14.47 0.00 44.06 4.02
3984 4393 2.749044 CTGCACAGCTCCGGCAAT 60.749 61.111 0.00 0.00 41.70 3.56
3992 4402 2.657237 GTACCGGTCTGCACAGCT 59.343 61.111 12.40 0.00 0.00 4.24
4053 4463 2.743183 GCGGATCTAGCTGGATTTGTGT 60.743 50.000 14.40 0.00 0.00 3.72
4224 4639 1.083363 ATTCCCCCTTCCCCCAAACA 61.083 55.000 0.00 0.00 0.00 2.83
4229 4644 1.523818 TTTCCATTCCCCCTTCCCCC 61.524 60.000 0.00 0.00 0.00 5.40
4234 4652 1.798941 TCCCTTTTTCCATTCCCCCTT 59.201 47.619 0.00 0.00 0.00 3.95
4244 4662 0.466739 ACACACCCGTCCCTTTTTCC 60.467 55.000 0.00 0.00 0.00 3.13
4274 4692 1.766461 CCTTATCCGTCCTGGCCCT 60.766 63.158 0.00 0.00 37.80 5.19
4309 4729 1.300620 TCAAACAGACACGCTCGGG 60.301 57.895 0.00 0.00 0.00 5.14
4340 4760 6.014584 TGACACATTCTCAGCCTAAGTTTAGA 60.015 38.462 0.51 0.00 32.47 2.10
4349 4769 2.555757 GCTTTTGACACATTCTCAGCCT 59.444 45.455 0.00 0.00 0.00 4.58
4361 4781 2.210116 GTTCTCGGTCTGCTTTTGACA 58.790 47.619 0.00 0.00 36.26 3.58
4438 4867 0.931005 GACCTCGTCCGCATTCATTC 59.069 55.000 0.00 0.00 0.00 2.67
4454 4883 3.499737 CAACTCCGGCGCATGACC 61.500 66.667 10.83 0.00 0.00 4.02
4455 4884 4.166011 GCAACTCCGGCGCATGAC 62.166 66.667 10.83 0.00 0.00 3.06
4489 4928 4.279043 GTGGTTTGGTGGCGGTGC 62.279 66.667 0.00 0.00 0.00 5.01
4632 5078 4.862371 AGGTGGTTTTGACCAAGAGTTTA 58.138 39.130 0.00 0.00 42.10 2.01
4660 5106 4.210093 TGTGTGGACCGTTCGCGT 62.210 61.111 5.77 0.00 39.32 6.01
4662 5108 2.279918 AGTGTGTGGACCGTTCGC 60.280 61.111 0.00 0.00 0.00 4.70
4664 5110 1.227556 AGCAGTGTGTGGACCGTTC 60.228 57.895 0.00 0.00 0.00 3.95
4666 5112 2.108976 CAGCAGTGTGTGGACCGT 59.891 61.111 0.00 0.00 0.00 4.83
4667 5113 2.666190 CCAGCAGTGTGTGGACCG 60.666 66.667 7.69 0.00 35.67 4.79
4702 5148 0.678048 GCAGAAGGTGATGGTGTCCC 60.678 60.000 0.00 0.00 0.00 4.46
4778 5224 0.537143 TTGGCTCTTGGTGATTGCGT 60.537 50.000 0.00 0.00 0.00 5.24
4779 5225 0.109597 GTTGGCTCTTGGTGATTGCG 60.110 55.000 0.00 0.00 0.00 4.85
4784 5230 3.073798 TCCTTTATGTTGGCTCTTGGTGA 59.926 43.478 0.00 0.00 0.00 4.02
4797 5243 2.173569 GGTCTGCCCTGATCCTTTATGT 59.826 50.000 0.00 0.00 0.00 2.29
4798 5244 2.808202 CGGTCTGCCCTGATCCTTTATG 60.808 54.545 0.00 0.00 0.00 1.90
4800 5246 0.830648 CGGTCTGCCCTGATCCTTTA 59.169 55.000 0.00 0.00 0.00 1.85
4823 5269 1.754745 GTGGTGGAGCTCTTGACCA 59.245 57.895 21.62 21.62 36.10 4.02
4824 5270 1.374758 CGTGGTGGAGCTCTTGACC 60.375 63.158 14.64 16.75 0.00 4.02
4857 5306 2.780714 GCCTCGGCACTAGACTATCTA 58.219 52.381 2.41 0.00 41.49 1.98
4873 5322 1.147153 GGCCTGGTATGACTGCCTC 59.853 63.158 0.00 0.00 39.05 4.70
4875 5324 2.203070 CGGCCTGGTATGACTGCC 60.203 66.667 0.00 0.00 38.74 4.85
4916 5365 2.039746 CCAGATCAGTGTTGGGTGGTTA 59.960 50.000 0.00 0.00 0.00 2.85
4929 5378 2.818132 GACCTCCGGCCAGATCAG 59.182 66.667 2.24 0.00 0.00 2.90
4951 5411 0.179100 CCTCTAGGTGGATGCGTGTG 60.179 60.000 0.00 0.00 0.00 3.82
4964 5424 0.970937 TGCGGGTGGTCTTCCTCTAG 60.971 60.000 0.00 0.00 34.23 2.43
4965 5425 0.543410 TTGCGGGTGGTCTTCCTCTA 60.543 55.000 0.00 0.00 34.23 2.43
4966 5426 1.841556 TTGCGGGTGGTCTTCCTCT 60.842 57.895 0.00 0.00 34.23 3.69
4996 5456 3.329542 GATGTCCTTGGCCCGCTCA 62.330 63.158 0.00 0.00 0.00 4.26
5002 5462 3.195698 GCGTCGATGTCCTTGGCC 61.196 66.667 6.48 0.00 0.00 5.36
5003 5463 2.434185 TGCGTCGATGTCCTTGGC 60.434 61.111 6.48 0.00 0.00 4.52
5006 5467 0.388649 GTCTGTGCGTCGATGTCCTT 60.389 55.000 6.48 0.00 0.00 3.36
5021 5482 0.600255 GGGTGGTCGTCAAGTGTCTG 60.600 60.000 0.00 0.00 0.00 3.51
5138 5599 0.541863 CTATCCTCCACCGCCTTTGT 59.458 55.000 0.00 0.00 0.00 2.83
5140 5601 0.620700 ACCTATCCTCCACCGCCTTT 60.621 55.000 0.00 0.00 0.00 3.11
5141 5602 0.263765 TACCTATCCTCCACCGCCTT 59.736 55.000 0.00 0.00 0.00 4.35
5142 5603 0.178958 CTACCTATCCTCCACCGCCT 60.179 60.000 0.00 0.00 0.00 5.52
5176 5637 0.535328 GGAAATCTAGCTTCCGGGGC 60.535 60.000 0.00 6.95 33.40 5.80
5181 5642 2.205911 GCAGACGGAAATCTAGCTTCC 58.794 52.381 11.56 11.56 39.25 3.46
5205 5666 0.395312 CCCACCTAACCACAACGAGT 59.605 55.000 0.00 0.00 0.00 4.18
5206 5667 0.953960 GCCCACCTAACCACAACGAG 60.954 60.000 0.00 0.00 0.00 4.18
5207 5668 1.071814 GCCCACCTAACCACAACGA 59.928 57.895 0.00 0.00 0.00 3.85
5209 5670 0.535553 TTCGCCCACCTAACCACAAC 60.536 55.000 0.00 0.00 0.00 3.32
5210 5671 0.402504 ATTCGCCCACCTAACCACAA 59.597 50.000 0.00 0.00 0.00 3.33
5211 5672 0.402504 AATTCGCCCACCTAACCACA 59.597 50.000 0.00 0.00 0.00 4.17
5212 5673 1.541379 AAATTCGCCCACCTAACCAC 58.459 50.000 0.00 0.00 0.00 4.16
5213 5674 2.296073 AAAATTCGCCCACCTAACCA 57.704 45.000 0.00 0.00 0.00 3.67
5214 5675 2.353307 CCAAAAATTCGCCCACCTAACC 60.353 50.000 0.00 0.00 0.00 2.85
5215 5676 2.929161 GCCAAAAATTCGCCCACCTAAC 60.929 50.000 0.00 0.00 0.00 2.34
5216 5677 1.273886 GCCAAAAATTCGCCCACCTAA 59.726 47.619 0.00 0.00 0.00 2.69
5217 5678 0.892063 GCCAAAAATTCGCCCACCTA 59.108 50.000 0.00 0.00 0.00 3.08
5218 5679 1.118356 TGCCAAAAATTCGCCCACCT 61.118 50.000 0.00 0.00 0.00 4.00
5225 5686 3.194062 ACTGGTTGTTGCCAAAAATTCG 58.806 40.909 0.00 0.00 38.18 3.34
5228 5689 3.530535 GTGACTGGTTGTTGCCAAAAAT 58.469 40.909 0.00 0.00 38.18 1.82
5235 5696 0.100503 GTGTGGTGACTGGTTGTTGC 59.899 55.000 0.00 0.00 0.00 4.17
5236 5697 1.401552 CTGTGTGGTGACTGGTTGTTG 59.598 52.381 0.00 0.00 0.00 3.33
5238 5699 0.908910 TCTGTGTGGTGACTGGTTGT 59.091 50.000 0.00 0.00 0.00 3.32
5239 5700 2.036958 TTCTGTGTGGTGACTGGTTG 57.963 50.000 0.00 0.00 0.00 3.77
5241 5702 3.239449 TCTATTCTGTGTGGTGACTGGT 58.761 45.455 0.00 0.00 0.00 4.00
5244 5705 5.070446 TCAACTTCTATTCTGTGTGGTGACT 59.930 40.000 0.00 0.00 0.00 3.41
5252 5713 6.867662 AACCAACTCAACTTCTATTCTGTG 57.132 37.500 0.00 0.00 0.00 3.66
5256 5717 7.363431 CCTGAAAACCAACTCAACTTCTATTC 58.637 38.462 0.00 0.00 0.00 1.75
5321 5782 2.287547 GCACTTCAAAGATCCGCACAAA 60.288 45.455 0.00 0.00 0.00 2.83
5328 5789 4.510038 ACATTGTGCACTTCAAAGATCC 57.490 40.909 19.41 0.00 0.00 3.36
5329 5790 5.634896 CCTACATTGTGCACTTCAAAGATC 58.365 41.667 19.41 0.00 0.00 2.75
5453 5920 6.813152 GCAAAGCACATTTATGTTTCTGGTAT 59.187 34.615 0.00 0.00 39.39 2.73
5468 5935 3.932545 TTTATCCGTTGCAAAGCACAT 57.067 38.095 0.00 0.00 38.71 3.21
5548 6015 4.872124 TGTGCTTGCAGAGACATTGTATAG 59.128 41.667 0.00 0.00 0.00 1.31
5762 6236 8.341903 CACCTTTTTGGAAAATTTATGACAACC 58.658 33.333 0.00 0.00 39.71 3.77
5789 6263 0.391597 AACGAGGAACCGCTCTTTCA 59.608 50.000 0.00 0.00 0.00 2.69
6448 6927 6.019559 GCATTTTTCAGGTCTGTTTTGTCTTC 60.020 38.462 0.00 0.00 0.00 2.87
6499 8260 4.916099 AAGTCAAAGTATTTACCGTCGC 57.084 40.909 0.00 0.00 35.03 5.19
6541 8306 8.137437 GCTACATAAACATGCCATAAAAGTCAT 58.863 33.333 0.00 0.00 0.00 3.06
6757 8524 1.275471 GCTTTTCGGCGGTTTCAAGC 61.275 55.000 7.21 10.06 0.00 4.01
6969 8740 5.772393 ACATATAACAGGTGGAAGTGGAA 57.228 39.130 0.00 0.00 0.00 3.53
6970 8741 5.772393 AACATATAACAGGTGGAAGTGGA 57.228 39.130 0.00 0.00 0.00 4.02
6971 8742 6.180472 AGAAACATATAACAGGTGGAAGTGG 58.820 40.000 0.00 0.00 0.00 4.00
6972 8743 7.687941 AAGAAACATATAACAGGTGGAAGTG 57.312 36.000 0.00 0.00 0.00 3.16
6973 8744 9.802039 TTTAAGAAACATATAACAGGTGGAAGT 57.198 29.630 0.00 0.00 0.00 3.01
7089 8866 6.700960 TGATAAACCATTTCTGCACAAGTTTG 59.299 34.615 0.00 0.00 0.00 2.93
7222 9088 3.880047 ACCGATCTGGAAATGAACGTA 57.120 42.857 10.05 0.00 42.00 3.57
7248 9114 0.453793 TGTTTTGTCAAGCACCACCG 59.546 50.000 0.00 0.00 0.00 4.94
7279 9145 3.195825 ACGTAGTGGAAAGAATCAGGGAG 59.804 47.826 0.00 0.00 42.51 4.30
7283 9149 5.661458 ACCATACGTAGTGGAAAGAATCAG 58.339 41.667 22.74 2.15 45.73 2.90
7476 9342 1.302033 CTGCTTTGAGGTCCGCACT 60.302 57.895 0.00 0.00 0.00 4.40
7482 9348 2.225019 CACATGTCACTGCTTTGAGGTC 59.775 50.000 0.00 0.00 0.00 3.85
7589 9455 0.810031 GTAGGGTGCCATGCTACACG 60.810 60.000 5.88 0.00 37.68 4.49
7947 9819 1.362717 CACCGTCGTGGAGTGTTCT 59.637 57.895 3.47 0.00 42.00 3.01
7991 9863 4.998671 TGAGGCATGTTTGAGAAAACAA 57.001 36.364 7.99 0.00 44.70 2.83
7992 9864 4.796946 GCATGAGGCATGTTTGAGAAAACA 60.797 41.667 6.50 6.50 45.48 2.83
8085 9958 2.623889 CCGATCCGAGACTTCCAGTTAT 59.376 50.000 0.00 0.00 0.00 1.89
8115 9988 3.499021 GGCCCAAACCTGAGTAACCTTTA 60.499 47.826 0.00 0.00 0.00 1.85
8123 9996 2.895424 CGGAGGCCCAAACCTGAGT 61.895 63.158 0.00 0.00 41.32 3.41
8124 9997 1.550130 TACGGAGGCCCAAACCTGAG 61.550 60.000 0.00 0.00 41.32 3.35
8125 9998 1.536907 TACGGAGGCCCAAACCTGA 60.537 57.895 0.00 0.00 41.32 3.86
8172 10047 5.544682 AGGTACCCCTCCACTATGAATAAA 58.455 41.667 8.74 0.00 35.62 1.40
8217 10092 4.408182 ACTTTCGCTAGCAACCTCATAT 57.592 40.909 16.45 0.00 0.00 1.78
8231 10106 5.980116 TCTAATCTCAGATAGCAACTTTCGC 59.020 40.000 0.00 0.00 0.00 4.70
8277 10152 6.331572 TGACCTCCTTGCCTATATAAATGGAA 59.668 38.462 0.00 0.00 0.00 3.53
8340 10215 1.376037 GACCTCCAAGACAAGGGCG 60.376 63.158 0.00 0.00 36.95 6.13


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

AutoCloner maintained by Alex Coulton.