Multiple sequence alignment - TraesCS5B01G370300

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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 TraesCS5B01G370300 chr5B 100.000 3734 0 0 1 3734 549083930 549080197 0.000000e+00 6896.0
1 TraesCS5B01G370300 chr5B 87.097 279 34 2 3083 3360 487061720 487061443 7.790000e-82 315.0
2 TraesCS5B01G370300 chr5B 76.623 462 69 28 130 563 266633333 266632883 6.280000e-53 219.0
3 TraesCS5B01G370300 chr5B 82.278 237 39 3 3496 3730 578648368 578648603 6.320000e-48 202.0
4 TraesCS5B01G370300 chr5B 92.199 141 10 1 3361 3501 419312706 419312845 8.180000e-47 198.0
5 TraesCS5B01G370300 chr5B 90.566 106 4 1 1 100 676407138 676407033 6.510000e-28 135.0
6 TraesCS5B01G370300 chr5D 91.044 2021 129 22 998 3010 449014907 449016883 0.000000e+00 2682.0
7 TraesCS5B01G370300 chr5D 89.691 97 9 1 1 97 430046033 430045938 5.060000e-24 122.0
8 TraesCS5B01G370300 chr5A 90.295 1762 111 19 998 2741 567781155 567782874 0.000000e+00 2252.0
9 TraesCS5B01G370300 chr5A 93.500 1477 67 10 891 2358 567896361 567897817 0.000000e+00 2169.0
10 TraesCS5B01G370300 chr5A 90.756 714 58 5 2351 3056 567900013 567900726 0.000000e+00 946.0
11 TraesCS5B01G370300 chr5A 85.965 741 76 14 36 756 567894437 567895169 0.000000e+00 767.0
12 TraesCS5B01G370300 chr5A 84.615 273 41 1 3083 3355 707530322 707530051 1.710000e-68 270.0
13 TraesCS5B01G370300 chr5A 74.318 440 79 25 132 551 486727900 486727475 4.990000e-34 156.0
14 TraesCS5B01G370300 chr5A 90.000 100 4 3 1 94 177540671 177540770 1.410000e-24 124.0
15 TraesCS5B01G370300 chr5A 71.456 515 92 31 126 613 335489029 335489515 6.640000e-13 86.1
16 TraesCS5B01G370300 chr7B 78.242 1650 226 83 1108 2698 643338897 643340472 0.000000e+00 935.0
17 TraesCS5B01G370300 chr7B 77.492 662 110 17 127 773 750137580 750138217 9.860000e-96 361.0
18 TraesCS5B01G370300 chr7B 74.711 779 134 37 1055 1812 42778719 42777983 4.720000e-74 289.0
19 TraesCS5B01G370300 chr7B 88.053 226 26 1 3506 3730 100713025 100712800 2.210000e-67 267.0
20 TraesCS5B01G370300 chr7B 88.426 216 21 3 3518 3729 525196599 525196814 1.330000e-64 257.0
21 TraesCS5B01G370300 chr7B 92.086 139 10 1 3363 3501 525194979 525195116 1.060000e-45 195.0
22 TraesCS5B01G370300 chr7B 91.489 141 11 1 3361 3501 100714424 100714285 3.810000e-45 193.0
23 TraesCS5B01G370300 chr7B 89.109 101 7 4 1 97 612037170 612037070 5.060000e-24 122.0
24 TraesCS5B01G370300 chr7D 87.161 553 62 2 2138 2681 579142646 579143198 1.470000e-173 619.0
25 TraesCS5B01G370300 chr7D 79.429 700 83 31 95 761 536593334 536594005 4.430000e-119 438.0
26 TraesCS5B01G370300 chr7D 78.514 740 98 41 1108 1806 579141628 579142347 2.660000e-116 429.0
27 TraesCS5B01G370300 chr7D 87.336 229 27 2 3503 3730 160492635 160492862 1.030000e-65 261.0
28 TraesCS5B01G370300 chr7D 86.017 236 32 1 3496 3730 610935994 610936229 6.190000e-63 252.0
29 TraesCS5B01G370300 chr7D 89.691 97 7 1 1 97 277349213 277349120 1.820000e-23 121.0
30 TraesCS5B01G370300 chr2D 79.913 692 86 14 95 761 605448188 605448851 3.400000e-125 459.0
31 TraesCS5B01G370300 chr2D 83.641 379 48 6 408 773 168451076 168451453 9.930000e-91 344.0
32 TraesCS5B01G370300 chr2D 82.328 232 38 3 3496 3726 475785554 475785783 8.180000e-47 198.0
33 TraesCS5B01G370300 chr3D 79.830 704 81 22 95 773 253141386 253140719 1.220000e-124 457.0
34 TraesCS5B01G370300 chr3D 85.612 278 37 3 3084 3360 99850855 99850580 4.720000e-74 289.0
35 TraesCS5B01G370300 chr3B 80.868 622 84 16 165 773 304514383 304514982 1.220000e-124 457.0
36 TraesCS5B01G370300 chr3B 88.261 230 21 6 3502 3729 644559646 644559871 1.710000e-68 270.0
37 TraesCS5B01G370300 chr3B 92.199 141 10 1 3361 3501 644557785 644557924 8.180000e-47 198.0
38 TraesCS5B01G370300 chr3B 91.489 141 11 1 3361 3501 1038494 1038355 3.810000e-45 193.0
39 TraesCS5B01G370300 chr1D 89.209 278 27 3 3084 3360 39507489 39507214 9.930000e-91 344.0
40 TraesCS5B01G370300 chr1D 89.252 214 22 1 3517 3729 39505559 39505346 2.210000e-67 267.0
41 TraesCS5B01G370300 chr6D 85.252 278 40 1 3083 3360 2532185 2532461 6.100000e-73 285.0
42 TraesCS5B01G370300 chr4D 84.946 279 40 2 3083 3360 491343136 491342859 7.900000e-72 281.0
43 TraesCS5B01G370300 chr4D 85.470 234 33 1 3498 3730 466539950 466540183 3.730000e-60 243.0
44 TraesCS5B01G370300 chr4D 90.099 101 3 4 1 94 108180123 108180023 1.410000e-24 124.0
45 TraesCS5B01G370300 chr7A 74.454 779 136 37 1055 1812 93488356 93489092 1.020000e-70 278.0
46 TraesCS5B01G370300 chr7A 82.609 230 40 0 3501 3730 683254024 683254253 1.760000e-48 204.0
47 TraesCS5B01G370300 chr3A 87.773 229 26 2 3502 3730 524787783 524787557 2.210000e-67 267.0
48 TraesCS5B01G370300 chr3A 92.908 141 9 1 3361 3501 525114278 525114139 1.760000e-48 204.0
49 TraesCS5B01G370300 chr3A 92.632 95 7 0 1 95 304294313 304294219 1.810000e-28 137.0
50 TraesCS5B01G370300 chr4B 83.154 279 43 3 3083 3360 560682751 560682476 6.190000e-63 252.0
51 TraesCS5B01G370300 chr1A 84.170 259 40 1 3083 3341 20207821 20207564 2.230000e-62 250.0
52 TraesCS5B01G370300 chr1A 86.344 227 31 0 3503 3729 579434097 579434323 8.010000e-62 248.0
53 TraesCS5B01G370300 chr1A 92.199 141 10 1 3361 3501 579432481 579432620 8.180000e-47 198.0
54 TraesCS5B01G370300 chr1A 87.006 177 22 1 2525 2700 582704199 582704375 8.180000e-47 198.0
55 TraesCS5B01G370300 chr1A 89.691 97 7 1 1 97 181125390 181125483 1.820000e-23 121.0
56 TraesCS5B01G370300 chr6B 83.784 259 40 2 3103 3360 4975889 4976146 1.040000e-60 244.0
57 TraesCS5B01G370300 chr6B 82.759 232 37 3 3501 3730 663101128 663101358 1.760000e-48 204.0
58 TraesCS5B01G370300 chr6B 82.759 232 37 3 3501 3730 672411756 672411986 1.760000e-48 204.0
59 TraesCS5B01G370300 chr1B 83.761 234 37 1 3496 3728 18373576 18373343 1.750000e-53 220.0
60 TraesCS5B01G370300 chr1B 83.333 234 38 1 3498 3730 601084546 601084313 8.120000e-52 215.0
61 TraesCS5B01G370300 chr2B 94.444 144 5 3 3361 3501 562680113 562679970 6.280000e-53 219.0
62 TraesCS5B01G370300 chr2B 91.096 146 8 2 3361 3501 11659030 11658885 3.810000e-45 193.0
63 TraesCS5B01G370300 chr2B 88.785 107 3 8 1 99 380244853 380244958 5.060000e-24 122.0
64 TraesCS5B01G370300 chr2A 76.151 478 77 28 136 588 39886930 39886465 2.260000e-52 217.0
65 TraesCS5B01G370300 chr2A 77.291 251 36 17 353 588 39590903 39591147 1.090000e-25 128.0
66 TraesCS5B01G370300 chr2A 75.089 281 57 10 159 431 76499856 76500131 6.550000e-23 119.0
67 TraesCS5B01G370300 chr4A 94.891 137 7 0 3360 3496 702517426 702517290 8.120000e-52 215.0


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 TraesCS5B01G370300 chr5B 549080197 549083930 3733 True 6896.0 6896 100.000000 1 3734 1 chr5B.!!$R3 3733
1 TraesCS5B01G370300 chr5D 449014907 449016883 1976 False 2682.0 2682 91.044000 998 3010 1 chr5D.!!$F1 2012
2 TraesCS5B01G370300 chr5A 567781155 567782874 1719 False 2252.0 2252 90.295000 998 2741 1 chr5A.!!$F3 1743
3 TraesCS5B01G370300 chr5A 567894437 567900726 6289 False 1294.0 2169 90.073667 36 3056 3 chr5A.!!$F4 3020
4 TraesCS5B01G370300 chr7B 643338897 643340472 1575 False 935.0 935 78.242000 1108 2698 1 chr7B.!!$F1 1590
5 TraesCS5B01G370300 chr7B 750137580 750138217 637 False 361.0 361 77.492000 127 773 1 chr7B.!!$F2 646
6 TraesCS5B01G370300 chr7B 42777983 42778719 736 True 289.0 289 74.711000 1055 1812 1 chr7B.!!$R1 757
7 TraesCS5B01G370300 chr7B 100712800 100714424 1624 True 230.0 267 89.771000 3361 3730 2 chr7B.!!$R3 369
8 TraesCS5B01G370300 chr7B 525194979 525196814 1835 False 226.0 257 90.256000 3363 3729 2 chr7B.!!$F3 366
9 TraesCS5B01G370300 chr7D 579141628 579143198 1570 False 524.0 619 82.837500 1108 2681 2 chr7D.!!$F4 1573
10 TraesCS5B01G370300 chr7D 536593334 536594005 671 False 438.0 438 79.429000 95 761 1 chr7D.!!$F2 666
11 TraesCS5B01G370300 chr2D 605448188 605448851 663 False 459.0 459 79.913000 95 761 1 chr2D.!!$F3 666
12 TraesCS5B01G370300 chr3D 253140719 253141386 667 True 457.0 457 79.830000 95 773 1 chr3D.!!$R2 678
13 TraesCS5B01G370300 chr3B 304514383 304514982 599 False 457.0 457 80.868000 165 773 1 chr3B.!!$F1 608
14 TraesCS5B01G370300 chr3B 644557785 644559871 2086 False 234.0 270 90.230000 3361 3729 2 chr3B.!!$F2 368
15 TraesCS5B01G370300 chr1D 39505346 39507489 2143 True 305.5 344 89.230500 3084 3729 2 chr1D.!!$R1 645
16 TraesCS5B01G370300 chr7A 93488356 93489092 736 False 278.0 278 74.454000 1055 1812 1 chr7A.!!$F1 757
17 TraesCS5B01G370300 chr1A 579432481 579434323 1842 False 223.0 248 89.271500 3361 3729 2 chr1A.!!$F3 368

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
727 770 0.033601 TGTTGTGCTTGGGTGTCCTT 60.034 50.0 0.00 0.0 0.00 3.36 F
837 1291 0.299003 GCTCGAGCACGCAGAATTAC 59.701 55.0 31.91 0.0 41.59 1.89 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1621 2766 0.037326 GAGTGACATGTCGCCTGGAA 60.037 55.0 30.72 5.76 40.77 3.53 R
2754 6156 0.032267 TTCGCATACACACGGACACA 59.968 50.0 0.00 0.00 0.00 3.72 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
28 29 9.783256 AGTCCGAAAACTAATATAAAATGTTGC 57.217 29.630 0.00 0.00 0.00 4.17
29 30 9.016623 GTCCGAAAACTAATATAAAATGTTGCC 57.983 33.333 0.00 0.00 0.00 4.52
30 31 8.740906 TCCGAAAACTAATATAAAATGTTGCCA 58.259 29.630 0.00 0.00 0.00 4.92
31 32 9.360093 CCGAAAACTAATATAAAATGTTGCCAA 57.640 29.630 0.00 0.00 0.00 4.52
134 154 5.872963 TCATGGATATGCAGTATTCTTGCT 58.127 37.500 2.55 0.00 34.21 3.91
144 164 4.210955 GCAGTATTCTTGCTAGTGAGATGC 59.789 45.833 0.00 0.00 0.00 3.91
245 266 8.375493 ACTACACATCCATAAGTAGAAAGGAA 57.625 34.615 0.00 0.00 37.84 3.36
246 267 8.822805 ACTACACATCCATAAGTAGAAAGGAAA 58.177 33.333 0.00 0.00 37.84 3.13
276 297 3.432252 GCACATCAACTACTACGCAGTTT 59.568 43.478 0.00 0.00 37.78 2.66
280 301 3.314553 TCAACTACTACGCAGTTTGCTC 58.685 45.455 0.00 0.00 37.78 4.26
300 321 1.798813 CGAACACCAGACTAAGTTGCC 59.201 52.381 0.00 0.00 0.00 4.52
315 336 3.305720 AGTTGCCCATATCTTCGGTAGA 58.694 45.455 0.00 0.00 37.28 2.59
318 339 2.249139 GCCCATATCTTCGGTAGAGGT 58.751 52.381 0.00 0.00 36.02 3.85
319 340 3.181426 TGCCCATATCTTCGGTAGAGGTA 60.181 47.826 0.00 0.00 36.02 3.08
320 341 3.193056 GCCCATATCTTCGGTAGAGGTAC 59.807 52.174 0.00 0.00 36.02 3.34
352 373 1.739667 GGTGTGCCAGTGAAAACCC 59.260 57.895 0.00 0.00 34.09 4.11
360 381 2.890945 GCCAGTGAAAACCCACAAGTAT 59.109 45.455 0.00 0.00 39.42 2.12
364 385 4.766891 CAGTGAAAACCCACAAGTATGGAT 59.233 41.667 0.00 0.00 43.02 3.41
412 433 5.834204 AGTTGACCTAGACAACAGACTAGTT 59.166 40.000 23.89 7.70 46.58 2.24
414 435 7.175293 AGTTGACCTAGACAACAGACTAGTTAG 59.825 40.741 23.89 0.00 46.58 2.34
433 455 6.729187 AGTTAGACATCACAAAAAGTTGCTC 58.271 36.000 0.00 0.00 38.39 4.26
436 458 3.709987 ACATCACAAAAAGTTGCTCTGC 58.290 40.909 0.00 0.00 38.39 4.26
438 460 1.065401 TCACAAAAAGTTGCTCTGCCG 59.935 47.619 0.00 0.00 38.39 5.69
467 489 7.172361 GCTAATCCTCATAGAAAGTTGGATCAC 59.828 40.741 0.00 0.00 33.70 3.06
477 500 1.553704 AGTTGGATCACGGGGTCTAAC 59.446 52.381 18.62 18.62 36.45 2.34
485 509 4.088056 TCACGGGGTCTAACAAAATTGA 57.912 40.909 0.00 0.00 0.00 2.57
491 515 5.407502 GGGGTCTAACAAAATTGATTTCGG 58.592 41.667 0.00 0.00 0.00 4.30
635 674 4.021192 AGCGAATTCCAACCATGAAAACAT 60.021 37.500 0.00 0.00 0.00 2.71
647 686 9.123902 CAACCATGAAAACATATCTGGATTCTA 57.876 33.333 0.00 0.00 0.00 2.10
660 699 7.721286 ATCTGGATTCTAACATTCGATTGTC 57.279 36.000 12.96 0.56 0.00 3.18
727 770 0.033601 TGTTGTGCTTGGGTGTCCTT 60.034 50.000 0.00 0.00 0.00 3.36
750 793 2.296471 CTCATATACGTGGACCCAGGTC 59.704 54.545 16.53 8.40 42.92 3.85
767 1138 0.448990 GTCGCATGCAGCTTTGATCA 59.551 50.000 19.57 0.00 42.61 2.92
773 1144 4.426416 GCATGCAGCTTTGATCATTTGTA 58.574 39.130 14.21 0.00 41.15 2.41
781 1156 5.047872 AGCTTTGATCATTTGTACACATGCA 60.048 36.000 15.73 7.49 0.00 3.96
797 1172 2.367377 CAGCCCCATCCCTCCTCA 60.367 66.667 0.00 0.00 0.00 3.86
802 1177 1.759881 CCCATCCCTCCTCATGCTC 59.240 63.158 0.00 0.00 0.00 4.26
806 1181 1.053264 ATCCCTCCTCATGCTCGCTT 61.053 55.000 0.00 0.00 0.00 4.68
807 1182 1.523258 CCCTCCTCATGCTCGCTTG 60.523 63.158 0.00 0.00 0.00 4.01
819 1194 1.721804 GCTCGCTTGTTGTCGTTTAGC 60.722 52.381 0.00 0.00 0.00 3.09
820 1195 1.792949 CTCGCTTGTTGTCGTTTAGCT 59.207 47.619 0.00 0.00 0.00 3.32
821 1196 1.790623 TCGCTTGTTGTCGTTTAGCTC 59.209 47.619 0.00 0.00 0.00 4.09
826 1201 1.269361 TGTTGTCGTTTAGCTCGAGCA 60.269 47.619 36.87 21.06 45.16 4.26
831 1285 1.704582 GTTTAGCTCGAGCACGCAG 59.295 57.895 36.87 0.00 45.16 5.18
837 1291 0.299003 GCTCGAGCACGCAGAATTAC 59.701 55.000 31.91 0.00 41.59 1.89
870 1324 9.914834 AGGATATATCTTAACTGCTACTCCTAG 57.085 37.037 12.42 0.00 0.00 3.02
871 1325 9.908747 GGATATATCTTAACTGCTACTCCTAGA 57.091 37.037 12.42 0.00 0.00 2.43
874 1328 5.776173 TCTTAACTGCTACTCCTAGATGC 57.224 43.478 0.00 0.00 0.00 3.91
875 1329 4.585162 TCTTAACTGCTACTCCTAGATGCC 59.415 45.833 0.00 0.00 0.00 4.40
876 1330 2.765689 ACTGCTACTCCTAGATGCCT 57.234 50.000 0.00 0.00 0.00 4.75
878 1332 3.761897 ACTGCTACTCCTAGATGCCTAG 58.238 50.000 0.00 0.00 41.58 3.02
879 1333 3.396276 ACTGCTACTCCTAGATGCCTAGA 59.604 47.826 0.00 0.00 44.00 2.43
880 1334 4.044065 ACTGCTACTCCTAGATGCCTAGAT 59.956 45.833 0.00 0.00 44.00 1.98
881 1335 4.594970 TGCTACTCCTAGATGCCTAGATC 58.405 47.826 0.00 0.00 44.00 2.75
882 1336 3.951680 GCTACTCCTAGATGCCTAGATCC 59.048 52.174 0.00 0.00 44.00 3.36
883 1337 4.325030 GCTACTCCTAGATGCCTAGATCCT 60.325 50.000 0.00 0.00 44.00 3.24
884 1338 4.757997 ACTCCTAGATGCCTAGATCCTT 57.242 45.455 0.00 0.00 44.00 3.36
887 1987 5.553953 ACTCCTAGATGCCTAGATCCTTCTA 59.446 44.000 0.00 0.00 44.00 2.10
889 1989 4.638421 CCTAGATGCCTAGATCCTTCTACG 59.362 50.000 0.00 0.00 44.00 3.51
916 2018 8.964476 ATATATAGTAGTACCATTGCCATTGC 57.036 34.615 0.00 0.00 38.26 3.56
929 2031 1.001020 CATTGCCCAGGTAGCCACA 60.001 57.895 0.00 0.00 0.00 4.17
936 2038 1.376466 CAGGTAGCCACAGCAACCT 59.624 57.895 0.00 0.00 43.56 3.50
937 2039 0.674895 CAGGTAGCCACAGCAACCTC 60.675 60.000 0.00 0.00 43.56 3.85
993 2096 1.174783 GGTAGAGGTGAGCGACTGAA 58.825 55.000 0.00 0.00 0.00 3.02
1026 2132 1.742761 CCTCCGATCAACAACAGCAT 58.257 50.000 0.00 0.00 0.00 3.79
1560 2705 1.686325 GGAAGTCCGCTCATGGCCTA 61.686 60.000 3.32 0.00 37.74 3.93
1621 2766 0.821711 CTTCCTCCTCCGCGAGATCT 60.822 60.000 8.23 0.00 30.97 2.75
1713 2867 1.743252 GAAGGAGCTCTGCCCGTTG 60.743 63.158 14.64 0.00 0.00 4.10
1879 3054 0.877743 TGATATCGAGGAGCAGCGAG 59.122 55.000 0.00 0.00 40.14 5.03
1880 3055 0.878416 GATATCGAGGAGCAGCGAGT 59.122 55.000 0.00 0.00 40.14 4.18
1890 3071 4.498520 CAGCGAGTGGACGGCGAT 62.499 66.667 16.62 0.00 0.00 4.58
1891 3072 4.498520 AGCGAGTGGACGGCGATG 62.499 66.667 16.62 0.00 0.00 3.84
1941 3128 4.112341 ACCGGCAGCGAGTACGTC 62.112 66.667 0.00 0.00 41.98 4.34
1982 3169 3.501548 GAGAGTCGCGTCGAGGCT 61.502 66.667 25.75 1.69 36.23 4.58
1983 3170 3.443261 GAGAGTCGCGTCGAGGCTC 62.443 68.421 25.75 21.08 36.23 4.70
1984 3171 3.800863 GAGTCGCGTCGAGGCTCA 61.801 66.667 23.19 11.07 36.23 4.26
1985 3172 4.104417 AGTCGCGTCGAGGCTCAC 62.104 66.667 25.75 20.86 36.23 3.51
1992 3179 2.089349 GTCGAGGCTCACGCTCAAC 61.089 63.158 15.95 0.00 36.09 3.18
2065 3252 2.293318 TGGAAGATGCTCACCGGCT 61.293 57.895 0.00 0.00 0.00 5.52
2598 6000 1.355066 GCAAGTACGTGCTCAGCTCC 61.355 60.000 24.08 0.00 41.51 4.70
2629 6031 1.613630 ACCTTCCTCGCCACCATCT 60.614 57.895 0.00 0.00 0.00 2.90
2711 6113 3.632107 TGACGTTGTTGTCGCGGC 61.632 61.111 2.29 2.29 41.87 6.53
2746 6148 2.735663 AGACAGTAGATCGGTATACGCG 59.264 50.000 3.53 3.53 43.86 6.01
2747 6149 1.802960 ACAGTAGATCGGTATACGCGG 59.197 52.381 12.47 0.00 43.86 6.46
2748 6150 0.801251 AGTAGATCGGTATACGCGGC 59.199 55.000 12.47 0.00 43.86 6.53
2750 6152 0.606130 TAGATCGGTATACGCGGCCA 60.606 55.000 12.47 0.00 43.86 5.36
2751 6153 1.731969 GATCGGTATACGCGGCCAC 60.732 63.158 12.47 4.18 43.86 5.01
2752 6154 3.547249 ATCGGTATACGCGGCCACG 62.547 63.158 12.53 12.53 43.86 4.94
2773 6178 0.032267 TGTGTCCGTGTGTATGCGAA 59.968 50.000 0.00 0.00 0.00 4.70
2774 6179 1.141645 GTGTCCGTGTGTATGCGAAA 58.858 50.000 0.00 0.00 0.00 3.46
2782 6187 3.181525 CGTGTGTATGCGAAAACATAGCA 60.182 43.478 0.00 0.00 44.07 3.49
2806 6215 4.579753 TGATCATGCTGTTGTCTTGTTTGA 59.420 37.500 0.00 0.00 0.00 2.69
2816 6225 3.199677 TGTCTTGTTTGAACCTACGGTG 58.800 45.455 0.00 0.00 35.34 4.94
2819 6228 4.095334 GTCTTGTTTGAACCTACGGTGTTT 59.905 41.667 0.00 0.00 35.34 2.83
2820 6229 4.095185 TCTTGTTTGAACCTACGGTGTTTG 59.905 41.667 0.00 0.00 35.34 2.93
2844 6253 2.859273 CTTGCCGGCGAGTCCTCATT 62.859 60.000 32.28 0.00 0.00 2.57
2866 6275 2.857744 CGATCTCGGTGGTAGGGGC 61.858 68.421 0.00 0.00 35.37 5.80
2932 6342 0.034574 TGATGTTGCCTTATGCCGGT 60.035 50.000 1.90 0.00 40.16 5.28
2936 6346 1.377987 TTGCCTTATGCCGGTGTCC 60.378 57.895 1.90 0.00 40.16 4.02
3036 6446 3.292492 AGTTCTTCGGGTCTGGTTTTT 57.708 42.857 0.00 0.00 0.00 1.94
3048 6458 5.128205 GGTCTGGTTTTTACTTGTGTAGGT 58.872 41.667 0.00 0.00 0.00 3.08
3056 6466 7.148689 GGTTTTTACTTGTGTAGGTATGTCTCG 60.149 40.741 0.00 0.00 0.00 4.04
3057 6467 3.505464 ACTTGTGTAGGTATGTCTCGC 57.495 47.619 0.00 0.00 0.00 5.03
3058 6468 3.090037 ACTTGTGTAGGTATGTCTCGCT 58.910 45.455 0.00 0.00 0.00 4.93
3059 6469 4.267536 ACTTGTGTAGGTATGTCTCGCTA 58.732 43.478 0.00 0.00 0.00 4.26
3060 6470 4.335874 ACTTGTGTAGGTATGTCTCGCTAG 59.664 45.833 0.00 0.00 0.00 3.42
3061 6471 3.882444 TGTGTAGGTATGTCTCGCTAGT 58.118 45.455 0.00 0.00 0.00 2.57
3062 6472 5.027293 TGTGTAGGTATGTCTCGCTAGTA 57.973 43.478 0.00 0.00 0.00 1.82
3063 6473 5.055144 TGTGTAGGTATGTCTCGCTAGTAG 58.945 45.833 0.00 0.00 0.00 2.57
3064 6474 5.163374 TGTGTAGGTATGTCTCGCTAGTAGA 60.163 44.000 0.00 0.00 0.00 2.59
3065 6475 5.757320 GTGTAGGTATGTCTCGCTAGTAGAA 59.243 44.000 0.00 0.00 0.00 2.10
3066 6476 6.259608 GTGTAGGTATGTCTCGCTAGTAGAAA 59.740 42.308 0.00 0.00 0.00 2.52
3067 6477 6.825213 TGTAGGTATGTCTCGCTAGTAGAAAA 59.175 38.462 0.00 0.00 0.00 2.29
3068 6478 6.134040 AGGTATGTCTCGCTAGTAGAAAAC 57.866 41.667 0.00 0.00 0.00 2.43
3069 6479 4.968788 GGTATGTCTCGCTAGTAGAAAACG 59.031 45.833 0.00 0.00 0.00 3.60
3070 6480 3.482722 TGTCTCGCTAGTAGAAAACGG 57.517 47.619 0.00 0.00 0.00 4.44
3071 6481 2.163010 TGTCTCGCTAGTAGAAAACGGG 59.837 50.000 0.00 0.00 0.00 5.28
3072 6482 2.421424 GTCTCGCTAGTAGAAAACGGGA 59.579 50.000 0.00 0.00 0.00 5.14
3073 6483 3.066481 GTCTCGCTAGTAGAAAACGGGAT 59.934 47.826 0.00 0.00 35.43 3.85
3074 6484 3.698040 TCTCGCTAGTAGAAAACGGGATT 59.302 43.478 0.00 0.00 0.00 3.01
3075 6485 4.159135 TCTCGCTAGTAGAAAACGGGATTT 59.841 41.667 0.00 0.00 0.00 2.17
3076 6486 4.824289 TCGCTAGTAGAAAACGGGATTTT 58.176 39.130 0.00 0.00 43.44 1.82
3096 6506 1.134007 TCCTACGTTCTAGCCGGATCA 60.134 52.381 5.05 0.00 0.00 2.92
3097 6507 1.679680 CCTACGTTCTAGCCGGATCAA 59.320 52.381 5.05 0.00 0.00 2.57
3099 6509 2.981859 ACGTTCTAGCCGGATCAAAT 57.018 45.000 5.05 0.00 0.00 2.32
3116 6526 0.828022 AATCAATAGTCCCGGTCGCA 59.172 50.000 0.00 0.00 0.00 5.10
3159 6569 0.174845 CATTAGTCCCGGTTCGAGCA 59.825 55.000 0.00 0.00 0.00 4.26
3161 6571 1.601419 TTAGTCCCGGTTCGAGCAGG 61.601 60.000 11.42 11.42 0.00 4.85
3194 6604 2.894387 GGCTCGGCAGACATCAGC 60.894 66.667 0.00 0.00 0.00 4.26
3202 6612 1.002134 CAGACATCAGCCCCGGTTT 60.002 57.895 0.00 0.00 0.00 3.27
3203 6613 0.251916 CAGACATCAGCCCCGGTTTA 59.748 55.000 0.00 0.00 0.00 2.01
3207 6617 3.201266 AGACATCAGCCCCGGTTTAAATA 59.799 43.478 0.00 0.00 0.00 1.40
3243 6653 3.180449 TGGAGACACCAACTGGGAT 57.820 52.632 0.00 0.00 46.75 3.85
3245 6655 2.626785 TGGAGACACCAACTGGGATTA 58.373 47.619 0.00 0.00 46.75 1.75
3251 6661 3.506398 ACACCAACTGGGATTAAAAGGG 58.494 45.455 0.00 0.00 41.15 3.95
3276 6686 1.227438 GCAGGCGCGATACCCTTTA 60.227 57.895 12.10 0.00 0.00 1.85
3283 6693 1.035139 GCGATACCCTTTAGTCCCGA 58.965 55.000 0.00 0.00 0.00 5.14
3286 6696 3.860002 GCGATACCCTTTAGTCCCGATTC 60.860 52.174 0.00 0.00 0.00 2.52
3293 6703 3.368116 CCTTTAGTCCCGATTCGTGTCTT 60.368 47.826 5.20 0.00 0.00 3.01
3303 6713 0.464870 TTCGTGTCTTCAACCGGGAA 59.535 50.000 6.32 0.00 0.00 3.97
3326 6736 0.112606 AGGTCTGTCTTCAGTCCCGA 59.887 55.000 7.61 0.00 46.08 5.14
3327 6737 0.244178 GGTCTGTCTTCAGTCCCGAC 59.756 60.000 0.00 0.00 41.63 4.79
3331 6741 3.255149 GTCTGTCTTCAGTCCCGACTTTA 59.745 47.826 0.00 0.00 40.20 1.85
3335 6745 3.255149 GTCTTCAGTCCCGACTTTAGACA 59.745 47.826 20.71 0.00 42.69 3.41
3336 6746 4.082136 GTCTTCAGTCCCGACTTTAGACAT 60.082 45.833 20.71 0.00 42.69 3.06
3355 6765 5.183140 AGACATCAACCGGGACTAAAAATTG 59.817 40.000 6.32 0.00 0.00 2.32
3356 6766 3.926821 TCAACCGGGACTAAAAATTGC 57.073 42.857 6.32 0.00 0.00 3.56
3358 6768 2.560981 CAACCGGGACTAAAAATTGCCT 59.439 45.455 6.32 0.00 0.00 4.75
3359 6769 3.724732 ACCGGGACTAAAAATTGCCTA 57.275 42.857 6.32 0.00 0.00 3.93
3365 6834 4.381612 GGGACTAAAAATTGCCTAAGGTGC 60.382 45.833 0.00 0.00 0.00 5.01
3376 6845 2.675889 GCCTAAGGTGCGTGCTAGTTTA 60.676 50.000 0.00 0.00 0.00 2.01
3445 6914 3.144657 TGATGCCACTTGAGTTCACAT 57.855 42.857 0.00 0.00 0.00 3.21
3484 6953 0.255890 ATGCCCGAGCCACACTTAAT 59.744 50.000 0.00 0.00 38.69 1.40
3501 6970 8.307483 CACACTTAATCTTTCTCCTCTGTTCTA 58.693 37.037 0.00 0.00 0.00 2.10
3504 8812 8.871125 ACTTAATCTTTCTCCTCTGTTCTACAA 58.129 33.333 0.00 0.00 0.00 2.41
3510 8818 6.978674 TTCTCCTCTGTTCTACAAAGAGAA 57.021 37.500 0.54 9.77 39.91 2.87
3512 8820 6.750148 TCTCCTCTGTTCTACAAAGAGAAAC 58.250 40.000 0.54 0.00 39.91 2.78
3514 8822 6.750148 TCCTCTGTTCTACAAAGAGAAACTC 58.250 40.000 0.54 0.00 39.91 3.01
3520 8828 6.819649 TGTTCTACAAAGAGAAACTCCGAAAA 59.180 34.615 0.00 0.00 37.20 2.29
3542 8850 8.533569 AAAATGAAAAGGAGAGGTTGAAGTTA 57.466 30.769 0.00 0.00 0.00 2.24
3555 8863 4.332819 GGTTGAAGTTAGAGCGCATGTTAT 59.667 41.667 11.47 0.00 0.00 1.89
3594 8903 3.680490 TGTACCCAAATTGCGAAGATGA 58.320 40.909 0.00 0.00 0.00 2.92
3595 8904 4.269183 TGTACCCAAATTGCGAAGATGAT 58.731 39.130 0.00 0.00 0.00 2.45
3598 8907 5.505173 ACCCAAATTGCGAAGATGATAAG 57.495 39.130 0.00 0.00 0.00 1.73
3600 8909 5.652014 ACCCAAATTGCGAAGATGATAAGAA 59.348 36.000 0.00 0.00 0.00 2.52
3625 8934 8.983702 AAAAACTAGTTACCACACTGGAATTA 57.016 30.769 8.92 0.00 40.96 1.40
3638 8947 4.701651 CACTGGAATTACTGCAATGGAAGA 59.298 41.667 0.00 0.00 0.00 2.87
3648 8957 4.828939 ACTGCAATGGAAGACAAAGAATGA 59.171 37.500 0.00 0.00 0.00 2.57
3730 9041 2.094762 ACGAATTGCCTGACAGTACC 57.905 50.000 0.93 0.00 0.00 3.34
3731 9042 1.346395 ACGAATTGCCTGACAGTACCA 59.654 47.619 0.93 0.00 0.00 3.25
3732 9043 1.732259 CGAATTGCCTGACAGTACCAC 59.268 52.381 0.93 0.00 0.00 4.16
3733 9044 2.612972 CGAATTGCCTGACAGTACCACT 60.613 50.000 0.93 0.00 0.00 4.00
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
2 3 9.783256 GCAACATTTTATATTAGTTTTCGGACT 57.217 29.630 0.00 0.00 0.00 3.85
3 4 9.016623 GGCAACATTTTATATTAGTTTTCGGAC 57.983 33.333 0.00 0.00 0.00 4.79
4 5 8.740906 TGGCAACATTTTATATTAGTTTTCGGA 58.259 29.630 0.00 0.00 46.17 4.55
5 6 8.918961 TGGCAACATTTTATATTAGTTTTCGG 57.081 30.769 0.00 0.00 46.17 4.30
24 25 9.341899 CTACAACTTTCATATACTTTTGGCAAC 57.658 33.333 0.00 0.00 0.00 4.17
25 26 9.290988 TCTACAACTTTCATATACTTTTGGCAA 57.709 29.630 0.00 0.00 0.00 4.52
26 27 8.856153 TCTACAACTTTCATATACTTTTGGCA 57.144 30.769 0.00 0.00 0.00 4.92
40 41 9.076596 GTTTCATGCCAATATTCTACAACTTTC 57.923 33.333 0.00 0.00 0.00 2.62
41 42 8.584157 TGTTTCATGCCAATATTCTACAACTTT 58.416 29.630 0.00 0.00 0.00 2.66
72 73 6.573434 TGCTGATATGTCTCTGTCGTATTTT 58.427 36.000 0.00 0.00 0.00 1.82
76 77 4.640647 AGTTGCTGATATGTCTCTGTCGTA 59.359 41.667 0.00 0.00 0.00 3.43
77 78 3.445450 AGTTGCTGATATGTCTCTGTCGT 59.555 43.478 0.00 0.00 0.00 4.34
78 79 4.039151 AGTTGCTGATATGTCTCTGTCG 57.961 45.455 0.00 0.00 0.00 4.35
79 80 6.593382 AGAAAAGTTGCTGATATGTCTCTGTC 59.407 38.462 0.00 0.00 0.00 3.51
81 82 6.817641 AGAGAAAAGTTGCTGATATGTCTCTG 59.182 38.462 0.00 0.00 38.26 3.35
88 96 6.156949 TGAGGGTAGAGAAAAGTTGCTGATAT 59.843 38.462 0.00 0.00 0.00 1.63
134 154 1.629013 CGAAGTTGCGCATCTCACTA 58.371 50.000 20.62 0.00 0.00 2.74
198 218 0.320374 TAGTTGGCAAGGACGACAGG 59.680 55.000 0.00 0.00 0.00 4.00
239 260 3.960102 TGATGTGCAACTCCTTTTCCTTT 59.040 39.130 0.00 0.00 38.04 3.11
276 297 1.961394 ACTTAGTCTGGTGTTCGAGCA 59.039 47.619 0.00 0.00 0.00 4.26
280 301 1.798813 GGCAACTTAGTCTGGTGTTCG 59.201 52.381 0.00 0.00 0.00 3.95
300 321 6.319152 CCTATGTACCTCTACCGAAGATATGG 59.681 46.154 0.00 0.00 32.41 2.74
315 336 0.694444 CCTGCCCCACCTATGTACCT 60.694 60.000 0.00 0.00 0.00 3.08
318 339 0.986019 CACCCTGCCCCACCTATGTA 60.986 60.000 0.00 0.00 0.00 2.29
319 340 2.127297 ACCCTGCCCCACCTATGT 59.873 61.111 0.00 0.00 0.00 2.29
320 341 2.308722 ACACCCTGCCCCACCTATG 61.309 63.158 0.00 0.00 0.00 2.23
352 373 1.340893 TGCACCCCATCCATACTTGTG 60.341 52.381 0.00 0.00 0.00 3.33
360 381 2.271821 CGATGTGCACCCCATCCA 59.728 61.111 15.69 0.00 36.23 3.41
364 385 0.902984 AGTAGTCGATGTGCACCCCA 60.903 55.000 15.69 0.00 0.00 4.96
412 433 5.277974 GCAGAGCAACTTTTTGTGATGTCTA 60.278 40.000 0.00 0.00 34.90 2.59
414 435 3.732721 GCAGAGCAACTTTTTGTGATGTC 59.267 43.478 0.00 0.00 34.90 3.06
433 455 0.107456 ATGAGGATTAGCCACGGCAG 59.893 55.000 11.35 0.00 44.88 4.85
436 458 4.202264 ACTTTCTATGAGGATTAGCCACGG 60.202 45.833 0.00 0.00 40.02 4.94
438 460 5.529060 CCAACTTTCTATGAGGATTAGCCAC 59.471 44.000 0.00 0.00 40.02 5.01
467 489 5.092781 CGAAATCAATTTTGTTAGACCCCG 58.907 41.667 0.00 0.00 0.00 5.73
477 500 9.209297 GTTCAACTTTTTCCGAAATCAATTTTG 57.791 29.630 0.00 0.00 0.00 2.44
485 509 8.194769 ACAGTATTGTTCAACTTTTTCCGAAAT 58.805 29.630 0.00 0.00 32.28 2.17
551 578 5.806654 AAAAATTATGCCAACTCTGGTGT 57.193 34.783 0.00 0.00 45.53 4.16
635 674 7.595130 CGACAATCGAATGTTAGAATCCAGATA 59.405 37.037 7.70 0.00 43.74 1.98
669 708 8.806429 ACTGGATTTTCAAATTTTCAAAAGGT 57.194 26.923 9.55 5.02 0.00 3.50
718 758 2.963782 ACGTATATGAGGAAGGACACCC 59.036 50.000 0.00 0.00 0.00 4.61
727 770 2.594131 CTGGGTCCACGTATATGAGGA 58.406 52.381 7.00 7.00 0.00 3.71
767 1138 1.185315 GGGGCTGCATGTGTACAAAT 58.815 50.000 0.00 0.00 0.00 2.32
773 1144 2.043652 GGATGGGGCTGCATGTGT 60.044 61.111 0.50 0.00 0.00 3.72
781 1156 1.773391 CATGAGGAGGGATGGGGCT 60.773 63.158 0.00 0.00 0.00 5.19
797 1172 0.944386 AAACGACAACAAGCGAGCAT 59.056 45.000 0.00 0.00 0.00 3.79
802 1177 1.460267 CGAGCTAAACGACAACAAGCG 60.460 52.381 0.00 0.00 38.23 4.68
806 1181 1.269361 TGCTCGAGCTAAACGACAACA 60.269 47.619 35.27 10.22 42.66 3.33
807 1182 1.124477 GTGCTCGAGCTAAACGACAAC 59.876 52.381 35.27 19.27 42.66 3.32
819 1194 0.567968 CGTAATTCTGCGTGCTCGAG 59.432 55.000 13.13 8.45 39.71 4.04
820 1195 0.800683 CCGTAATTCTGCGTGCTCGA 60.801 55.000 13.13 0.00 39.71 4.04
821 1196 1.076533 ACCGTAATTCTGCGTGCTCG 61.077 55.000 3.31 3.31 40.37 5.03
826 1201 3.929094 TCCTAAAACCGTAATTCTGCGT 58.071 40.909 0.00 0.00 0.00 5.24
864 1318 4.934356 AGAAGGATCTAGGCATCTAGGAG 58.066 47.826 0.00 0.00 42.42 3.69
865 1319 5.571862 CGTAGAAGGATCTAGGCATCTAGGA 60.572 48.000 0.00 0.00 42.42 2.94
866 1320 4.638421 CGTAGAAGGATCTAGGCATCTAGG 59.362 50.000 0.00 0.00 42.42 3.02
867 1321 5.250200 ACGTAGAAGGATCTAGGCATCTAG 58.750 45.833 5.69 0.00 44.26 2.43
869 1323 4.107127 ACGTAGAAGGATCTAGGCATCT 57.893 45.455 5.69 0.00 44.26 2.90
870 1324 7.811117 ATATACGTAGAAGGATCTAGGCATC 57.189 40.000 0.08 0.00 44.26 3.91
872 1326 9.999660 CTATATATACGTAGAAGGATCTAGGCA 57.000 37.037 0.08 0.00 44.26 4.75
887 1987 8.812513 TGGCAATGGTACTACTATATATACGT 57.187 34.615 0.00 0.00 0.00 3.57
901 2001 0.461135 CTGGGCAATGGCAATGGTAC 59.539 55.000 9.51 0.00 43.71 3.34
907 2007 1.682005 GCTACCTGGGCAATGGCAA 60.682 57.895 9.51 0.00 43.71 4.52
916 2018 1.675641 GTTGCTGTGGCTACCTGGG 60.676 63.158 0.00 0.00 38.03 4.45
929 2031 2.093447 GTGCACTAGGTATGAGGTTGCT 60.093 50.000 10.32 0.00 0.00 3.91
936 2038 1.435925 CGCGGTGCACTAGGTATGA 59.564 57.895 17.98 0.00 0.00 2.15
937 2039 2.237751 GCGCGGTGCACTAGGTATG 61.238 63.158 17.98 1.36 45.45 2.39
1554 2699 2.443203 TCGCGGAGGATTAGGCCA 60.443 61.111 6.13 0.00 0.00 5.36
1621 2766 0.037326 GAGTGACATGTCGCCTGGAA 60.037 55.000 30.72 5.76 40.77 3.53
1713 2867 1.683319 GGGAAGTTGCCCTCCATCTTC 60.683 57.143 1.04 5.86 45.12 2.87
1941 3128 2.177531 GTGGCGAGCAGTTGCATG 59.822 61.111 6.90 0.00 45.16 4.06
1982 3169 4.373116 GGCCTCCGTTGAGCGTGA 62.373 66.667 0.00 0.00 37.29 4.35
2250 3449 4.671590 TCGAGGGTCACTGCCGGA 62.672 66.667 5.05 0.00 0.00 5.14
2256 3455 1.367840 GTTGCAGTCGAGGGTCACT 59.632 57.895 0.00 0.00 0.00 3.41
2511 5913 3.729698 ACGTCGTCGATGACCGCA 61.730 61.111 27.63 0.00 40.62 5.69
2667 6069 0.887836 ACCGAGAGCACGTGTAGACA 60.888 55.000 18.38 0.00 0.00 3.41
2728 6130 1.465354 GCCGCGTATACCGATCTACTG 60.465 57.143 4.92 0.00 39.56 2.74
2748 6150 2.686956 TACACACGGACACAGCGTGG 62.687 60.000 0.93 0.00 37.94 4.94
2750 6152 0.666274 CATACACACGGACACAGCGT 60.666 55.000 0.00 0.00 0.00 5.07
2751 6153 1.955529 GCATACACACGGACACAGCG 61.956 60.000 0.00 0.00 0.00 5.18
2752 6154 1.787847 GCATACACACGGACACAGC 59.212 57.895 0.00 0.00 0.00 4.40
2754 6156 0.032267 TTCGCATACACACGGACACA 59.968 50.000 0.00 0.00 0.00 3.72
2755 6157 1.141645 TTTCGCATACACACGGACAC 58.858 50.000 0.00 0.00 0.00 3.67
2756 6158 1.527736 GTTTTCGCATACACACGGACA 59.472 47.619 0.00 0.00 0.00 4.02
2758 6160 1.867166 TGTTTTCGCATACACACGGA 58.133 45.000 0.00 0.00 0.00 4.69
2761 6163 4.335082 TGCTATGTTTTCGCATACACAC 57.665 40.909 0.00 0.00 0.00 3.82
2762 6164 4.633565 TCATGCTATGTTTTCGCATACACA 59.366 37.500 0.00 0.00 42.03 3.72
2782 6187 5.242171 TCAAACAAGACAACAGCATGATCAT 59.758 36.000 1.18 1.18 39.69 2.45
2816 6225 2.338620 GCCGGCAAGGAACCAAAC 59.661 61.111 24.80 0.00 45.00 2.93
2819 6228 4.697756 CTCGCCGGCAAGGAACCA 62.698 66.667 28.98 0.00 45.00 3.67
2820 6229 4.699522 ACTCGCCGGCAAGGAACC 62.700 66.667 28.98 0.00 45.00 3.62
2844 6253 1.676746 CCTACCACCGAGATCGAAGA 58.323 55.000 3.31 0.00 43.02 2.87
2866 6275 3.382227 ACCAAACCTTAAACTTGTTCCCG 59.618 43.478 0.00 0.00 0.00 5.14
2932 6342 2.158957 GGCGAGGATGACTTATTGGACA 60.159 50.000 0.00 0.00 0.00 4.02
2936 6346 2.223829 ACGAGGCGAGGATGACTTATTG 60.224 50.000 0.00 0.00 0.00 1.90
3026 6436 7.443272 ACATACCTACACAAGTAAAAACCAGAC 59.557 37.037 0.00 0.00 0.00 3.51
3036 6446 4.267536 AGCGAGACATACCTACACAAGTA 58.732 43.478 0.00 0.00 0.00 2.24
3048 6458 4.036027 CCCGTTTTCTACTAGCGAGACATA 59.964 45.833 0.00 0.00 0.00 2.29
3064 6474 4.392047 AGAACGTAGGAAAATCCCGTTTT 58.608 39.130 12.48 6.54 41.91 2.43
3065 6475 4.011966 AGAACGTAGGAAAATCCCGTTT 57.988 40.909 12.48 3.80 41.91 3.60
3066 6476 3.690475 AGAACGTAGGAAAATCCCGTT 57.310 42.857 11.48 11.48 43.58 4.44
3067 6477 3.429960 GCTAGAACGTAGGAAAATCCCGT 60.430 47.826 0.00 0.00 37.19 5.28
3068 6478 3.121544 GCTAGAACGTAGGAAAATCCCG 58.878 50.000 0.00 0.00 37.19 5.14
3069 6479 3.464907 GGCTAGAACGTAGGAAAATCCC 58.535 50.000 0.00 0.00 37.19 3.85
3070 6480 3.121544 CGGCTAGAACGTAGGAAAATCC 58.878 50.000 0.00 0.00 36.58 3.01
3071 6481 3.121544 CCGGCTAGAACGTAGGAAAATC 58.878 50.000 0.00 0.00 0.00 2.17
3072 6482 2.762327 TCCGGCTAGAACGTAGGAAAAT 59.238 45.455 0.00 0.00 0.00 1.82
3073 6483 2.170166 TCCGGCTAGAACGTAGGAAAA 58.830 47.619 0.00 0.00 0.00 2.29
3074 6484 1.838112 TCCGGCTAGAACGTAGGAAA 58.162 50.000 0.00 0.00 0.00 3.13
3075 6485 1.952296 GATCCGGCTAGAACGTAGGAA 59.048 52.381 0.00 0.00 0.00 3.36
3076 6486 1.134007 TGATCCGGCTAGAACGTAGGA 60.134 52.381 0.00 0.00 0.00 2.94
3077 6487 1.315690 TGATCCGGCTAGAACGTAGG 58.684 55.000 0.00 0.00 0.00 3.18
3078 6488 3.431922 TTTGATCCGGCTAGAACGTAG 57.568 47.619 0.00 0.00 0.00 3.51
3079 6489 3.382227 TGATTTGATCCGGCTAGAACGTA 59.618 43.478 0.00 0.00 0.00 3.57
3080 6490 2.167693 TGATTTGATCCGGCTAGAACGT 59.832 45.455 0.00 0.00 0.00 3.99
3081 6491 2.821546 TGATTTGATCCGGCTAGAACG 58.178 47.619 0.00 0.00 0.00 3.95
3082 6492 5.992217 ACTATTGATTTGATCCGGCTAGAAC 59.008 40.000 0.00 0.00 0.00 3.01
3096 6506 1.208535 TGCGACCGGGACTATTGATTT 59.791 47.619 6.32 0.00 0.00 2.17
3097 6507 0.828022 TGCGACCGGGACTATTGATT 59.172 50.000 6.32 0.00 0.00 2.57
3099 6509 0.828022 AATGCGACCGGGACTATTGA 59.172 50.000 6.32 0.00 0.00 2.57
3116 6526 5.026038 TCACATTAATCCCGGTTCGTAAT 57.974 39.130 0.00 0.00 0.00 1.89
3130 6540 3.199071 ACCGGGACTAATGCTCACATTAA 59.801 43.478 6.32 0.00 45.73 1.40
3159 6569 4.415150 TCGTCCGGCGTCCTACCT 62.415 66.667 16.00 0.00 42.13 3.08
3161 6571 3.885521 CCTCGTCCGGCGTCCTAC 61.886 72.222 16.00 0.00 42.13 3.18
3176 6586 2.898738 CTGATGTCTGCCGAGCCT 59.101 61.111 0.00 0.00 0.00 4.58
3187 6597 2.525105 ATTTAAACCGGGGCTGATGT 57.475 45.000 6.32 0.00 0.00 3.06
3194 6604 3.657398 AAGGTCCTATTTAAACCGGGG 57.343 47.619 6.32 0.00 38.14 5.73
3227 6637 4.459337 CCTTTTAATCCCAGTTGGTGTCTC 59.541 45.833 0.00 0.00 34.77 3.36
3238 6648 1.551452 CGCAACCCCTTTTAATCCCA 58.449 50.000 0.00 0.00 0.00 4.37
3243 6653 1.182385 CCTGCCGCAACCCCTTTTAA 61.182 55.000 0.00 0.00 0.00 1.52
3245 6655 2.917227 CCTGCCGCAACCCCTTTT 60.917 61.111 0.00 0.00 0.00 2.27
3276 6686 1.254026 TGAAGACACGAATCGGGACT 58.746 50.000 13.47 8.26 36.81 3.85
3283 6693 0.682852 TCCCGGTTGAAGACACGAAT 59.317 50.000 0.00 0.00 0.00 3.34
3286 6696 2.373540 TATTCCCGGTTGAAGACACG 57.626 50.000 0.00 0.00 0.00 4.49
3293 6703 2.640826 ACAGACCTTTATTCCCGGTTGA 59.359 45.455 0.00 0.00 0.00 3.18
3326 6736 2.904434 AGTCCCGGTTGATGTCTAAAGT 59.096 45.455 0.00 0.00 0.00 2.66
3327 6737 3.611766 AGTCCCGGTTGATGTCTAAAG 57.388 47.619 0.00 0.00 0.00 1.85
3331 6741 4.360951 TTTTTAGTCCCGGTTGATGTCT 57.639 40.909 0.00 0.00 0.00 3.41
3335 6745 3.194755 GGCAATTTTTAGTCCCGGTTGAT 59.805 43.478 0.00 0.00 0.00 2.57
3336 6746 2.559231 GGCAATTTTTAGTCCCGGTTGA 59.441 45.455 0.00 0.00 0.00 3.18
3355 6765 0.391263 AACTAGCACGCACCTTAGGC 60.391 55.000 0.00 0.00 0.00 3.93
3356 6766 2.094762 AAACTAGCACGCACCTTAGG 57.905 50.000 0.00 0.00 0.00 2.69
3358 6768 5.122711 GGAAAATAAACTAGCACGCACCTTA 59.877 40.000 0.00 0.00 0.00 2.69
3359 6769 4.082949 GGAAAATAAACTAGCACGCACCTT 60.083 41.667 0.00 0.00 0.00 3.50
3365 6834 4.941873 AGGAAGGGAAAATAAACTAGCACG 59.058 41.667 0.00 0.00 0.00 5.34
3376 6845 4.934356 TCTTGTGCATAGGAAGGGAAAAT 58.066 39.130 0.00 0.00 0.00 1.82
3445 6914 7.468494 CGGGCATCTCATATCATGTTTGTTTTA 60.468 37.037 0.00 0.00 0.00 1.52
3465 6934 0.255890 ATTAAGTGTGGCTCGGGCAT 59.744 50.000 10.74 0.00 40.92 4.40
3484 6953 6.778069 TCTCTTTGTAGAACAGAGGAGAAAGA 59.222 38.462 10.02 0.00 31.85 2.52
3501 6970 6.693315 TTCATTTTCGGAGTTTCTCTTTGT 57.307 33.333 0.00 0.00 0.00 2.83
3504 8812 6.546034 TCCTTTTCATTTTCGGAGTTTCTCTT 59.454 34.615 0.00 0.00 0.00 2.85
3510 8818 4.762251 CCTCTCCTTTTCATTTTCGGAGTT 59.238 41.667 0.00 0.00 41.50 3.01
3512 8820 4.327680 ACCTCTCCTTTTCATTTTCGGAG 58.672 43.478 0.00 0.00 42.00 4.63
3514 8822 4.518970 TCAACCTCTCCTTTTCATTTTCGG 59.481 41.667 0.00 0.00 0.00 4.30
3520 8828 7.079451 TCTAACTTCAACCTCTCCTTTTCAT 57.921 36.000 0.00 0.00 0.00 2.57
3532 8840 2.076863 ACATGCGCTCTAACTTCAACC 58.923 47.619 9.73 0.00 0.00 3.77
3542 8850 3.321968 TGTGATCCTATAACATGCGCTCT 59.678 43.478 9.73 0.00 0.00 4.09
3555 8863 9.535170 TTGGGTACAATAATTTTTGTGATCCTA 57.465 29.630 20.41 15.05 40.00 2.94
3600 8909 7.891498 AATTCCAGTGTGGTAACTAGTTTTT 57.109 32.000 14.49 0.00 39.03 1.94
3604 8913 6.698380 CAGTAATTCCAGTGTGGTAACTAGT 58.302 40.000 0.00 0.00 39.03 2.57
3607 8916 4.202419 TGCAGTAATTCCAGTGTGGTAACT 60.202 41.667 0.00 0.00 39.03 2.24
3609 8918 4.359434 TGCAGTAATTCCAGTGTGGTAA 57.641 40.909 0.00 0.00 39.03 2.85
3625 8934 4.828939 TCATTCTTTGTCTTCCATTGCAGT 59.171 37.500 0.00 0.00 0.00 4.40
3638 8947 6.095440 CCCTTGTCGGATAAATCATTCTTTGT 59.905 38.462 0.00 0.00 33.16 2.83
3648 8957 4.018779 TCTCAAACCCCTTGTCGGATAAAT 60.019 41.667 0.00 0.00 36.34 1.40


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

AutoCloner maintained by Alex Coulton.