Multiple sequence alignment - TraesCS3D01G035700

Loading Multiple Alignment...

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 TraesCS3D01G035700 chr3D 100.000 2981 0 0 1 2981 12883281 12886261 0.000000e+00 5505.0
1 TraesCS3D01G035700 chr3B 85.957 883 81 23 1397 2239 18503377 18504256 0.000000e+00 904.0
2 TraesCS3D01G035700 chr3B 82.362 635 69 19 1000 1603 18559608 18558986 2.050000e-141 512.0
3 TraesCS3D01G035700 chr3B 89.216 306 22 2 948 1244 18502627 18502930 3.630000e-99 372.0
4 TraesCS3D01G035700 chr3B 75.768 879 133 43 1408 2246 18559560 18558722 1.310000e-98 370.0
5 TraesCS3D01G035700 chr3B 83.196 363 41 8 1 347 18561230 18560872 6.200000e-82 315.0
6 TraesCS3D01G035700 chr3B 77.580 562 80 30 387 918 18560277 18559732 6.250000e-77 298.0
7 TraesCS3D01G035700 chr3B 78.641 515 53 25 2432 2909 604771796 604772290 3.760000e-74 289.0
8 TraesCS3D01G035700 chr3B 97.059 34 0 1 2347 2379 7335771 7335804 4.150000e-04 56.5
9 TraesCS3D01G035700 chr3A 79.447 1085 130 42 1405 2432 24511008 24509960 0.000000e+00 682.0
10 TraesCS3D01G035700 chr3A 83.713 571 49 22 323 868 24511802 24511251 1.600000e-137 499.0
11 TraesCS3D01G035700 chr3A 81.260 635 63 26 1003 1600 24511037 24510422 2.090000e-126 462.0
12 TraesCS3D01G035700 chr3A 97.059 34 0 1 2347 2379 218727093 218727126 4.150000e-04 56.5
13 TraesCS3D01G035700 chr2B 88.107 412 44 5 2571 2981 131838778 131839185 4.470000e-133 484.0
14 TraesCS3D01G035700 chr2B 80.142 141 24 3 2432 2571 131838610 131838747 5.260000e-18 102.0
15 TraesCS3D01G035700 chr1B 81.663 409 52 17 2432 2826 57044412 57044013 4.800000e-83 318.0
16 TraesCS3D01G035700 chr5B 80.605 397 64 6 2590 2981 664726364 664725976 8.080000e-76 294.0
17 TraesCS3D01G035700 chr5B 78.488 344 53 12 2638 2981 598612894 598613216 3.890000e-49 206.0
18 TraesCS3D01G035700 chr2D 77.368 570 73 32 2432 2980 88311443 88310909 1.350000e-73 287.0
19 TraesCS3D01G035700 chr2D 86.640 247 28 5 2432 2676 385158984 385158741 4.900000e-68 268.0
20 TraesCS3D01G035700 chr6A 77.348 543 73 24 2463 2981 73657656 73657140 2.930000e-70 276.0
21 TraesCS3D01G035700 chr6A 97.059 34 0 1 2347 2379 483734823 483734790 4.150000e-04 56.5
22 TraesCS3D01G035700 chr7B 79.442 394 67 12 2595 2980 37125166 37125553 1.760000e-67 267.0
23 TraesCS3D01G035700 chrUn 79.787 282 56 1 2699 2980 31478631 31478351 1.400000e-48 204.0
24 TraesCS3D01G035700 chr6B 79.783 277 46 5 2713 2980 433924926 433924651 3.030000e-45 193.0
25 TraesCS3D01G035700 chr6B 84.615 65 7 3 2316 2378 255522216 255522279 8.920000e-06 62.1
26 TraesCS3D01G035700 chr6B 83.333 66 6 4 2318 2378 378287130 378287065 4.150000e-04 56.5
27 TraesCS3D01G035700 chr7D 97.059 34 0 1 2347 2379 550241504 550241471 4.150000e-04 56.5
28 TraesCS3D01G035700 chr7A 97.059 34 0 1 2347 2379 485742948 485742981 4.150000e-04 56.5
29 TraesCS3D01G035700 chr1D 97.059 34 0 1 2347 2379 480528471 480528504 4.150000e-04 56.5
30 TraesCS3D01G035700 chr1D 90.476 42 3 1 2338 2378 246951953 246951994 1.000000e-03 54.7


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 TraesCS3D01G035700 chr3D 12883281 12886261 2980 False 5505.000000 5505 100.000000 1 2981 1 chr3D.!!$F1 2980
1 TraesCS3D01G035700 chr3B 18502627 18504256 1629 False 638.000000 904 87.586500 948 2239 2 chr3B.!!$F3 1291
2 TraesCS3D01G035700 chr3B 18558722 18561230 2508 True 373.750000 512 79.726500 1 2246 4 chr3B.!!$R1 2245
3 TraesCS3D01G035700 chr3A 24509960 24511802 1842 True 547.666667 682 81.473333 323 2432 3 chr3A.!!$R1 2109
4 TraesCS3D01G035700 chr2B 131838610 131839185 575 False 293.000000 484 84.124500 2432 2981 2 chr2B.!!$F1 549
5 TraesCS3D01G035700 chr2D 88310909 88311443 534 True 287.000000 287 77.368000 2432 2980 1 chr2D.!!$R1 548
6 TraesCS3D01G035700 chr6A 73657140 73657656 516 True 276.000000 276 77.348000 2463 2981 1 chr6A.!!$R1 518

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
918 1535 0.038067 CGACCGTGTGGACACCATTA 60.038 55.0 4.34 0.0 43.66 1.90 F
1536 2562 0.317020 GCAACAAGTGCGACAAGGAC 60.317 55.0 0.00 0.0 45.10 3.85 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1740 2779 0.037326 TAACAGCTGCTTCCTGACCG 60.037 55.0 15.27 0.0 34.47 4.79 R
2935 4142 0.178967 TGTGGCTCAAATGCTTCCCA 60.179 50.0 0.00 0.0 0.00 4.37 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
25 26 5.540719 TGTTTTCGTGATAAATTCCCCCTTT 59.459 36.000 0.00 0.00 0.00 3.11
32 33 5.127194 GTGATAAATTCCCCCTTTCTCAACC 59.873 44.000 0.00 0.00 0.00 3.77
35 36 1.541275 TTCCCCCTTTCTCAACCCTT 58.459 50.000 0.00 0.00 0.00 3.95
40 41 3.576861 CCCCTTTCTCAACCCTTTTCTT 58.423 45.455 0.00 0.00 0.00 2.52
47 48 6.894339 TTCTCAACCCTTTTCTTTACCATC 57.106 37.500 0.00 0.00 0.00 3.51
49 50 4.412843 TCAACCCTTTTCTTTACCATCCC 58.587 43.478 0.00 0.00 0.00 3.85
52 53 1.749063 CCTTTTCTTTACCATCCCGCC 59.251 52.381 0.00 0.00 0.00 6.13
61 62 4.481112 CATCCCGCCGCTTTGCAC 62.481 66.667 0.00 0.00 0.00 4.57
67 68 4.090057 GCCGCTTTGCACCGTCTC 62.090 66.667 0.00 0.00 0.00 3.36
82 83 4.832608 CTCGGGGGTAAGGCGTGC 62.833 72.222 0.00 0.00 0.00 5.34
112 113 6.462487 GCACCTTGCACTTGTAGGAGTATATA 60.462 42.308 8.39 0.00 44.26 0.86
113 114 7.671302 CACCTTGCACTTGTAGGAGTATATAT 58.329 38.462 8.39 0.00 33.21 0.86
130 131 7.697691 AGTATATATTGCATAAAATCAGCCGC 58.302 34.615 0.00 0.00 0.00 6.53
159 160 3.469899 TTGCATAAACACTCGCATCAC 57.530 42.857 0.00 0.00 33.71 3.06
162 163 2.672874 GCATAAACACTCGCATCACTCA 59.327 45.455 0.00 0.00 0.00 3.41
174 190 2.286872 CATCACTCAGGAGGTGAATGC 58.713 52.381 0.83 0.00 45.09 3.56
175 191 1.351076 TCACTCAGGAGGTGAATGCA 58.649 50.000 0.83 0.00 40.21 3.96
180 196 2.486982 CTCAGGAGGTGAATGCAACTTG 59.513 50.000 0.00 0.00 43.61 3.16
190 206 0.601558 ATGCAACTTGAGCAGCCAAG 59.398 50.000 17.41 17.41 46.36 3.61
199 215 1.681666 AGCAGCCAAGCTAGCTCAA 59.318 52.632 19.65 0.00 44.50 3.02
224 240 3.130516 TGCTAGATCCAGAAAGTACCGTG 59.869 47.826 0.00 0.00 0.00 4.94
242 258 1.540617 GGTAACCCACCTGACCCCT 60.541 63.158 0.00 0.00 44.79 4.79
254 270 3.019564 CCTGACCCCTTGCAATTTAGAG 58.980 50.000 0.00 0.00 0.00 2.43
259 275 1.401905 CCCTTGCAATTTAGAGCGGAC 59.598 52.381 0.00 0.00 0.00 4.79
260 276 1.062587 CCTTGCAATTTAGAGCGGACG 59.937 52.381 0.00 0.00 0.00 4.79
261 277 1.062587 CTTGCAATTTAGAGCGGACGG 59.937 52.381 0.00 0.00 0.00 4.79
297 313 3.596214 AGTGATTAAGTTGCAGTACCCG 58.404 45.455 0.00 0.00 0.00 5.28
317 333 5.054477 CCCGGTTGTACATCTACTAATTGG 58.946 45.833 0.00 0.00 0.00 3.16
321 338 6.053650 GGTTGTACATCTACTAATTGGACCC 58.946 44.000 0.00 0.00 0.00 4.46
323 340 5.202765 TGTACATCTACTAATTGGACCCGA 58.797 41.667 0.00 0.00 0.00 5.14
325 342 5.215252 ACATCTACTAATTGGACCCGATG 57.785 43.478 0.00 4.72 34.69 3.84
355 372 9.998106 ACTAAAATGCGTCTTATTATCCAGTAT 57.002 29.630 0.00 0.00 0.00 2.12
357 374 7.907214 AAATGCGTCTTATTATCCAGTATCC 57.093 36.000 0.00 0.00 0.00 2.59
385 453 4.537965 AGTTGTAGTATGCGAATCTAGCG 58.462 43.478 0.00 0.00 37.44 4.26
393 461 0.778815 GCGAATCTAGCGTCATTCCG 59.221 55.000 0.00 0.00 0.00 4.30
413 481 6.935240 TCCGAGTGGATTATGGAATCTATT 57.065 37.500 0.00 0.00 40.17 1.73
436 504 4.873129 CGCCGGTGACCAGATCCG 62.873 72.222 10.20 0.00 43.30 4.18
467 536 3.622455 GCATGTCTACCCTAAGCCACTTT 60.622 47.826 0.00 0.00 0.00 2.66
484 553 8.118976 AGCCACTTTCTAATTTTAGGTTAACC 57.881 34.615 17.41 17.41 0.00 2.85
553 632 9.199982 GCATCAGTTTAAATATTATGCAAGCAT 57.800 29.630 12.66 12.66 38.44 3.79
555 634 9.918630 ATCAGTTTAAATATTATGCAAGCATCC 57.081 29.630 11.32 0.00 37.82 3.51
556 635 8.911965 TCAGTTTAAATATTATGCAAGCATCCA 58.088 29.630 11.32 0.00 37.82 3.41
557 636 9.701098 CAGTTTAAATATTATGCAAGCATCCAT 57.299 29.630 11.32 7.70 37.82 3.41
569 648 3.831729 CATCCATACATGCACGCAC 57.168 52.632 0.00 0.00 0.00 5.34
608 687 2.094182 AGTAGTCCACCACGTATGCTTG 60.094 50.000 0.00 0.00 0.00 4.01
675 1266 2.146724 TCGGGGGCATCTGGGTATG 61.147 63.158 0.00 0.00 0.00 2.39
678 1269 0.400594 GGGGGCATCTGGGTATGTAC 59.599 60.000 0.00 0.00 0.00 2.90
680 1271 1.705186 GGGGCATCTGGGTATGTACAT 59.295 52.381 13.93 13.93 0.00 2.29
683 1274 4.202524 GGGGCATCTGGGTATGTACATAAA 60.203 45.833 17.07 5.70 0.00 1.40
685 1276 6.010219 GGGCATCTGGGTATGTACATAAAAT 58.990 40.000 17.07 4.46 0.00 1.82
686 1277 7.172342 GGGCATCTGGGTATGTACATAAAATA 58.828 38.462 17.07 3.35 0.00 1.40
688 1279 8.512138 GGCATCTGGGTATGTACATAAAATAAC 58.488 37.037 17.07 6.40 0.00 1.89
689 1280 9.284968 GCATCTGGGTATGTACATAAAATAACT 57.715 33.333 17.07 0.00 0.00 2.24
705 1314 0.610232 AACTGAACATCCTGCAGCCC 60.610 55.000 8.66 0.00 33.03 5.19
706 1315 1.751927 CTGAACATCCTGCAGCCCC 60.752 63.158 8.66 0.00 0.00 5.80
729 1338 1.005037 AGCAACGGCAAGATCGTCA 60.005 52.632 0.00 0.00 44.61 4.35
731 1340 1.134818 AGCAACGGCAAGATCGTCATA 60.135 47.619 0.00 0.00 44.61 2.15
732 1341 1.867233 GCAACGGCAAGATCGTCATAT 59.133 47.619 0.00 0.00 40.18 1.78
734 1343 3.493129 GCAACGGCAAGATCGTCATATAA 59.507 43.478 0.00 0.00 40.18 0.98
735 1344 4.025229 GCAACGGCAAGATCGTCATATAAA 60.025 41.667 0.00 0.00 40.18 1.40
737 1346 6.299604 CAACGGCAAGATCGTCATATAAATC 58.700 40.000 0.00 0.00 40.18 2.17
738 1347 5.784177 ACGGCAAGATCGTCATATAAATCT 58.216 37.500 0.00 0.00 35.87 2.40
739 1348 6.223852 ACGGCAAGATCGTCATATAAATCTT 58.776 36.000 0.00 0.00 38.64 2.40
782 1393 3.051479 CCGGCGCCCGTAAGTTTT 61.051 61.111 23.46 0.00 46.80 2.43
785 1396 0.302589 CGGCGCCCGTAAGTTTTATC 59.697 55.000 23.46 0.00 42.73 1.75
792 1403 3.506844 GCCCGTAAGTTTTATCCACCAAA 59.493 43.478 0.00 0.00 0.00 3.28
796 1407 5.158494 CGTAAGTTTTATCCACCAAAAGCC 58.842 41.667 0.00 0.00 0.00 4.35
820 1437 0.879400 GATCGACCTGCAGCCATGAG 60.879 60.000 8.66 0.00 0.00 2.90
918 1535 0.038067 CGACCGTGTGGACACCATTA 60.038 55.000 4.34 0.00 43.66 1.90
919 1536 1.435577 GACCGTGTGGACACCATTAC 58.564 55.000 4.34 0.00 43.66 1.89
920 1537 0.759959 ACCGTGTGGACACCATTACA 59.240 50.000 4.34 0.00 43.66 2.41
921 1538 1.349688 ACCGTGTGGACACCATTACAT 59.650 47.619 4.34 0.00 43.66 2.29
922 1539 1.737236 CCGTGTGGACACCATTACATG 59.263 52.381 4.34 0.00 43.66 3.21
923 1540 2.614229 CCGTGTGGACACCATTACATGA 60.614 50.000 0.00 0.00 43.66 3.07
924 1541 3.070748 CGTGTGGACACCATTACATGAA 58.929 45.455 0.00 0.00 43.66 2.57
925 1542 3.689161 CGTGTGGACACCATTACATGAAT 59.311 43.478 0.00 0.00 43.66 2.57
926 1543 4.201812 CGTGTGGACACCATTACATGAATC 60.202 45.833 0.00 0.00 43.66 2.52
927 1544 4.096382 GTGTGGACACCATTACATGAATCC 59.904 45.833 0.00 0.00 40.85 3.01
928 1545 4.263683 TGTGGACACCATTACATGAATCCA 60.264 41.667 0.00 0.00 35.28 3.41
929 1546 4.889409 GTGGACACCATTACATGAATCCAT 59.111 41.667 0.00 0.00 37.53 3.41
931 1548 6.716628 GTGGACACCATTACATGAATCCATAT 59.283 38.462 0.00 0.00 37.53 1.78
932 1549 7.882791 GTGGACACCATTACATGAATCCATATA 59.117 37.037 0.00 0.00 37.53 0.86
933 1550 8.443979 TGGACACCATTACATGAATCCATATAA 58.556 33.333 0.00 0.00 33.38 0.98
934 1551 9.466497 GGACACCATTACATGAATCCATATAAT 57.534 33.333 0.00 0.00 33.84 1.28
936 1553 9.812347 ACACCATTACATGAATCCATATAATGT 57.188 29.630 0.00 0.00 43.50 2.71
944 1561 9.293404 ACATGAATCCATATAATGTTGGAAGAG 57.707 33.333 0.00 0.00 44.83 2.85
945 1562 7.750229 TGAATCCATATAATGTTGGAAGAGC 57.250 36.000 0.00 0.00 44.83 4.09
946 1563 7.289310 TGAATCCATATAATGTTGGAAGAGCA 58.711 34.615 0.00 0.00 44.83 4.26
955 1617 3.295093 TGTTGGAAGAGCAAATGTTGGA 58.705 40.909 0.00 0.00 0.00 3.53
993 1655 3.188048 GCTAGCTGCATGTGATAATCACC 59.812 47.826 7.70 0.00 43.13 4.02
998 1660 4.520111 GCTGCATGTGATAATCACCCAATA 59.480 41.667 0.00 0.00 46.40 1.90
1095 1815 3.716006 CCGTTGTGCAGCAGGTCG 61.716 66.667 0.00 0.31 0.00 4.79
1134 1854 4.796231 ATGGACGCCGTCGAGCAC 62.796 66.667 11.60 0.00 39.41 4.40
1177 1897 4.680537 AGGCGTCCCAGTCCGACT 62.681 66.667 0.00 0.00 37.68 4.18
1187 1907 0.318441 CAGTCCGACTCTTCCAAGCA 59.682 55.000 0.00 0.00 0.00 3.91
1189 1909 1.009389 GTCCGACTCTTCCAAGCACG 61.009 60.000 0.00 0.00 0.00 5.34
1254 1980 2.511600 CCCGACGACATCCCAAGC 60.512 66.667 0.00 0.00 0.00 4.01
1275 2001 3.788333 GGTACGTACTGATGCTAACCA 57.212 47.619 24.07 0.00 0.00 3.67
1276 2002 4.114058 GGTACGTACTGATGCTAACCAA 57.886 45.455 24.07 0.00 0.00 3.67
1277 2003 4.497300 GGTACGTACTGATGCTAACCAAA 58.503 43.478 24.07 0.00 0.00 3.28
1278 2004 4.328169 GGTACGTACTGATGCTAACCAAAC 59.672 45.833 24.07 0.00 0.00 2.93
1279 2005 4.267349 ACGTACTGATGCTAACCAAACT 57.733 40.909 0.00 0.00 0.00 2.66
1288 2032 3.323243 TGCTAACCAAACTACTCGAAGC 58.677 45.455 0.00 0.00 0.00 3.86
1290 2034 3.368236 GCTAACCAAACTACTCGAAGCAG 59.632 47.826 0.00 0.00 0.00 4.24
1313 2057 4.628333 GCTCGCTAGGTATCTCTACTAGTG 59.372 50.000 5.39 0.00 0.00 2.74
1328 2088 2.895404 ACTAGTGTCCATGTAACGGTGT 59.105 45.455 0.00 0.00 0.00 4.16
1329 2089 2.163818 AGTGTCCATGTAACGGTGTG 57.836 50.000 0.00 0.00 0.00 3.82
1330 2090 0.515564 GTGTCCATGTAACGGTGTGC 59.484 55.000 0.00 0.00 0.00 4.57
1341 2106 4.927782 GGTGTGCGTGCAGGTCCA 62.928 66.667 8.40 2.31 0.00 4.02
1343 2108 4.624364 TGTGCGTGCAGGTCCAGG 62.624 66.667 8.40 0.00 0.00 4.45
1348 2113 2.930562 GTGCAGGTCCAGGGGTCT 60.931 66.667 0.00 0.00 0.00 3.85
1349 2114 2.607750 TGCAGGTCCAGGGGTCTC 60.608 66.667 0.00 0.00 0.00 3.36
1356 2121 3.077556 CCAGGGGTCTCTGGTCCG 61.078 72.222 8.69 0.00 46.89 4.79
1357 2122 3.775654 CAGGGGTCTCTGGTCCGC 61.776 72.222 0.00 0.00 37.01 5.54
1362 2127 3.692406 GTCTCTGGTCCGCCGGTT 61.692 66.667 1.63 0.00 41.89 4.44
1363 2128 3.691342 TCTCTGGTCCGCCGGTTG 61.691 66.667 1.63 0.00 41.89 3.77
1364 2129 4.003788 CTCTGGTCCGCCGGTTGT 62.004 66.667 1.63 0.00 41.89 3.32
1365 2130 3.934391 CTCTGGTCCGCCGGTTGTC 62.934 68.421 1.63 0.00 41.89 3.18
1366 2131 4.308458 CTGGTCCGCCGGTTGTCA 62.308 66.667 1.63 0.00 36.39 3.58
1367 2132 4.308458 TGGTCCGCCGGTTGTCAG 62.308 66.667 1.63 0.00 37.67 3.51
1373 2138 2.946762 GCCGGTTGTCAGTCAAGC 59.053 61.111 1.90 0.02 46.96 4.01
1401 2166 3.462678 GGGGAGGAGACCAGCGTC 61.463 72.222 0.00 0.00 39.50 5.19
1419 2445 4.856607 GTCGGCGGCGAGGAGAAG 62.857 72.222 35.53 1.41 0.00 2.85
1428 2454 4.214327 GAGGAGAAGCCGAGGCCG 62.214 72.222 10.95 0.00 43.43 6.13
1433 2459 4.388499 GAAGCCGAGGCCGTGGAA 62.388 66.667 19.28 0.00 43.17 3.53
1447 2473 2.811317 GGAAGTGCTGCGACGAGG 60.811 66.667 0.00 0.00 0.00 4.63
1536 2562 0.317020 GCAACAAGTGCGACAAGGAC 60.317 55.000 0.00 0.00 45.10 3.85
1587 2613 3.081409 TCCTACTTCGGCTGGCCC 61.081 66.667 0.00 0.00 0.00 5.80
1608 2634 3.902112 CCCAGGTGCACCAACCCT 61.902 66.667 36.39 14.05 41.54 4.34
1616 2645 2.357034 CACCAACCCTGACGACGG 60.357 66.667 0.00 0.00 0.00 4.79
1620 2649 4.309950 AACCCTGACGACGGCCAC 62.310 66.667 2.24 0.00 0.00 5.01
1653 2682 0.888619 CTGGTACCAGACTCGAAGCA 59.111 55.000 34.54 0.00 46.30 3.91
1654 2683 0.601558 TGGTACCAGACTCGAAGCAC 59.398 55.000 11.60 0.00 0.00 4.40
1657 2686 0.888619 TACCAGACTCGAAGCACCTG 59.111 55.000 0.00 0.00 0.00 4.00
1658 2687 1.115930 ACCAGACTCGAAGCACCTGT 61.116 55.000 0.00 0.00 0.00 4.00
1659 2688 0.389166 CCAGACTCGAAGCACCTGTC 60.389 60.000 0.00 0.00 0.00 3.51
1660 2689 0.600557 CAGACTCGAAGCACCTGTCT 59.399 55.000 0.00 0.00 38.36 3.41
1682 2711 8.258007 TGTCTAGGAATTTCTACTTGTATGTGG 58.742 37.037 0.00 0.00 0.00 4.17
1684 2713 8.258007 TCTAGGAATTTCTACTTGTATGTGGTG 58.742 37.037 0.00 0.00 0.00 4.17
1685 2714 5.648092 AGGAATTTCTACTTGTATGTGGTGC 59.352 40.000 0.00 0.00 0.00 5.01
1695 2730 7.695480 ACTTGTATGTGGTGCAATGTTTATA 57.305 32.000 0.00 0.00 31.82 0.98
1697 2732 9.402320 ACTTGTATGTGGTGCAATGTTTATATA 57.598 29.630 0.00 0.00 31.82 0.86
1698 2733 9.882996 CTTGTATGTGGTGCAATGTTTATATAG 57.117 33.333 0.00 0.00 31.82 1.31
1701 2740 9.051679 GTATGTGGTGCAATGTTTATATAGTGA 57.948 33.333 0.00 0.00 0.00 3.41
1704 2743 7.279981 TGTGGTGCAATGTTTATATAGTGAGTC 59.720 37.037 0.00 0.00 0.00 3.36
1705 2744 7.495934 GTGGTGCAATGTTTATATAGTGAGTCT 59.504 37.037 0.00 0.00 0.00 3.24
1751 2838 2.126031 GGTCGTCGGTCAGGAAGC 60.126 66.667 0.00 0.00 0.00 3.86
1884 2977 0.106708 TGAAGAAGTGCGCCAAGACT 59.893 50.000 4.18 0.00 0.00 3.24
1932 3025 3.231736 ACTTCCCTCCGCGTGTGT 61.232 61.111 4.92 0.00 0.00 3.72
1980 3073 2.436417 GCCAAGTGCCACAAGATCTAA 58.564 47.619 0.00 0.00 0.00 2.10
1987 3080 1.656652 CCACAAGATCTAACCTGGCG 58.343 55.000 0.00 0.00 0.00 5.69
1991 3084 1.984288 AAGATCTAACCTGGCGGCCC 61.984 60.000 17.97 0.00 0.00 5.80
2154 3265 0.243907 CACTGTAGTAGGTGCGCACT 59.756 55.000 36.84 25.16 0.00 4.40
2186 3297 0.178533 TCTTCCGGGTTGTCGTTGTT 59.821 50.000 0.00 0.00 0.00 2.83
2187 3298 0.306533 CTTCCGGGTTGTCGTTGTTG 59.693 55.000 0.00 0.00 0.00 3.33
2188 3299 0.392729 TTCCGGGTTGTCGTTGTTGT 60.393 50.000 0.00 0.00 0.00 3.32
2195 3306 0.579630 TTGTCGTTGTTGTAGCGCTG 59.420 50.000 22.90 0.00 32.60 5.18
2205 3316 1.790755 TGTAGCGCTGGTAGTGTTTG 58.209 50.000 22.90 0.00 0.00 2.93
2230 3341 2.870835 GCATGGTCTCAGCATCGATGAT 60.871 50.000 29.20 20.98 33.46 2.45
2233 3344 4.879197 TGGTCTCAGCATCGATGATTAT 57.121 40.909 29.20 8.22 0.00 1.28
2259 3370 9.500785 TGATAAGTTGTGTTAATCAGACAATCA 57.499 29.630 0.00 0.00 0.00 2.57
2282 3393 2.416431 GCCATCTTTGTTGATGCTGGAC 60.416 50.000 0.00 0.00 41.65 4.02
2284 3395 3.366679 CCATCTTTGTTGATGCTGGACAC 60.367 47.826 0.00 0.00 41.65 3.67
2288 3399 1.511850 TGTTGATGCTGGACACTTCG 58.488 50.000 0.00 0.00 0.00 3.79
2319 3443 4.768968 GGTGGTCACTACCTCTTTACTGTA 59.231 45.833 2.32 0.00 46.91 2.74
2393 3526 0.250597 AGTAGGTTGGTTTCGTGGGC 60.251 55.000 0.00 0.00 0.00 5.36
2394 3527 0.535553 GTAGGTTGGTTTCGTGGGCA 60.536 55.000 0.00 0.00 0.00 5.36
2423 3556 4.579340 GCATGACTGATTGATGTTGGAGAT 59.421 41.667 0.00 0.00 0.00 2.75
2425 3558 3.943381 TGACTGATTGATGTTGGAGATGC 59.057 43.478 0.00 0.00 0.00 3.91
2437 3570 4.695455 TGTTGGAGATGCACTTAGCTAAAC 59.305 41.667 7.74 0.99 45.94 2.01
2455 3588 5.449999 GCTAAACAAGTGTTTACAGTGCCTT 60.450 40.000 11.65 0.00 45.47 4.35
2461 3594 3.069158 AGTGTTTACAGTGCCTTCGTAGT 59.931 43.478 0.00 0.00 0.00 2.73
2508 3642 2.049248 CAGCGGCCGTTGCAAAAT 60.049 55.556 29.17 0.78 40.13 1.82
2515 3649 2.287547 CGGCCGTTGCAAAATATAGCAT 60.288 45.455 19.50 0.00 40.94 3.79
2521 3655 1.601430 TGCAAAATATAGCATGCGCGA 59.399 42.857 12.10 1.83 45.49 5.87
2522 3656 2.236690 GCAAAATATAGCATGCGCGAG 58.763 47.619 12.10 0.00 45.49 5.03
2585 3763 7.831690 ACTCTGATTCGAGGCATAGATAGATAA 59.168 37.037 8.35 0.00 35.33 1.75
2665 3843 3.527507 TCATAGCCTCCTCCTACGATT 57.472 47.619 0.00 0.00 0.00 3.34
2669 3847 2.683768 AGCCTCCTCCTACGATTGATT 58.316 47.619 0.00 0.00 0.00 2.57
2672 3850 5.580998 AGCCTCCTCCTACGATTGATTATA 58.419 41.667 0.00 0.00 0.00 0.98
2678 3856 9.542462 CTCCTCCTACGATTGATTATAAAAACA 57.458 33.333 0.00 0.00 0.00 2.83
2729 3927 1.849975 TTCTCCTCCTCCGACTCCGT 61.850 60.000 0.00 0.00 0.00 4.69
2749 3947 0.684479 CTCGGTGATGTCCTCCTCCA 60.684 60.000 0.00 0.00 0.00 3.86
2756 3954 2.291346 TGATGTCCTCCTCCAACGTCTA 60.291 50.000 0.00 0.00 31.62 2.59
2757 3955 2.297698 TGTCCTCCTCCAACGTCTAA 57.702 50.000 0.00 0.00 0.00 2.10
2761 3959 4.041198 TGTCCTCCTCCAACGTCTAAAATT 59.959 41.667 0.00 0.00 0.00 1.82
2764 3962 6.652062 GTCCTCCTCCAACGTCTAAAATTAAA 59.348 38.462 0.00 0.00 0.00 1.52
2800 3998 1.605058 CGTCGTTGGAGTCCCAGGAT 61.605 60.000 6.74 0.00 44.60 3.24
2837 4035 1.098050 GATGTTGAATTGAGCGGCCT 58.902 50.000 0.00 0.00 0.00 5.19
2843 4041 1.432270 GAATTGAGCGGCCTCCTTCG 61.432 60.000 0.00 0.00 37.29 3.79
2867 4065 1.873863 CGCCTATCATCGCGGTAGA 59.126 57.895 6.13 1.86 44.57 2.59
2868 4066 0.452184 CGCCTATCATCGCGGTAGAT 59.548 55.000 6.13 10.08 44.57 1.98
2902 4109 2.586792 CTCTCCGCCCTCCTTTGG 59.413 66.667 0.00 0.00 0.00 3.28
2920 4127 2.886124 GCGTAGAACTGGCGCTCC 60.886 66.667 7.64 0.00 46.55 4.70
2934 4141 0.738975 CGCTCCTTGATGACGTCCTA 59.261 55.000 14.12 0.00 0.00 2.94
2935 4142 1.338337 CGCTCCTTGATGACGTCCTAT 59.662 52.381 14.12 0.00 0.00 2.57
2946 4153 2.238646 TGACGTCCTATGGGAAGCATTT 59.761 45.455 14.12 0.00 44.15 2.32
2948 4155 2.238646 ACGTCCTATGGGAAGCATTTGA 59.761 45.455 10.93 0.00 44.15 2.69
2955 4162 0.968405 GGGAAGCATTTGAGCCACAA 59.032 50.000 0.00 0.00 36.65 3.33
2960 4167 1.959085 CATTTGAGCCACAACGCCT 59.041 52.632 0.00 0.00 38.29 5.52
2971 4178 1.600636 CAACGCCTTGGCTTCCTCA 60.601 57.895 10.12 0.00 0.00 3.86
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
7 8 4.523083 TGAGAAAGGGGGAATTTATCACG 58.477 43.478 0.00 0.00 34.06 4.35
14 15 2.081855 AGGGTTGAGAAAGGGGGAATT 58.918 47.619 0.00 0.00 0.00 2.17
25 26 5.321927 GGATGGTAAAGAAAAGGGTTGAGA 58.678 41.667 0.00 0.00 0.00 3.27
32 33 1.749063 GGCGGGATGGTAAAGAAAAGG 59.251 52.381 0.00 0.00 0.00 3.11
35 36 1.027792 GCGGCGGGATGGTAAAGAAA 61.028 55.000 9.78 0.00 0.00 2.52
40 41 1.747367 CAAAGCGGCGGGATGGTAA 60.747 57.895 9.78 0.00 0.00 2.85
52 53 3.777925 CCGAGACGGTGCAAAGCG 61.778 66.667 1.80 0.00 42.73 4.68
59 60 2.718073 CCTTACCCCCGAGACGGTG 61.718 68.421 9.28 0.00 46.80 4.94
103 104 8.338259 CGGCTGATTTTATGCAATATATACTCC 58.662 37.037 0.00 0.00 0.00 3.85
112 113 1.069049 GGGCGGCTGATTTTATGCAAT 59.931 47.619 9.56 0.00 0.00 3.56
113 114 0.459489 GGGCGGCTGATTTTATGCAA 59.541 50.000 9.56 0.00 0.00 4.08
122 123 1.611673 GCAATATACTGGGCGGCTGAT 60.612 52.381 9.56 0.00 0.00 2.90
130 131 5.334105 GCGAGTGTTTATGCAATATACTGGG 60.334 44.000 0.00 0.00 32.80 4.45
159 160 2.486472 AGTTGCATTCACCTCCTGAG 57.514 50.000 0.00 0.00 0.00 3.35
162 163 2.787994 CTCAAGTTGCATTCACCTCCT 58.212 47.619 0.00 0.00 0.00 3.69
174 190 1.467734 CTAGCTTGGCTGCTCAAGTTG 59.532 52.381 22.79 0.00 44.26 3.16
175 191 1.818642 CTAGCTTGGCTGCTCAAGTT 58.181 50.000 22.79 20.60 44.26 2.66
180 196 4.123300 GAGCTAGCTTGGCTGCTC 57.877 61.111 20.42 19.38 44.87 4.26
199 215 4.202161 CGGTACTTTCTGGATCTAGCATGT 60.202 45.833 0.23 2.01 0.00 3.21
242 258 1.083489 CCGTCCGCTCTAAATTGCAA 58.917 50.000 0.00 0.00 0.00 4.08
254 270 4.166011 GCAATCACAGCCGTCCGC 62.166 66.667 0.00 0.00 37.98 5.54
259 275 1.014044 ACTACGTGCAATCACAGCCG 61.014 55.000 0.00 0.00 43.28 5.52
260 276 0.443869 CACTACGTGCAATCACAGCC 59.556 55.000 0.00 0.00 43.28 4.85
261 277 1.428448 TCACTACGTGCAATCACAGC 58.572 50.000 0.00 0.00 43.28 4.40
265 281 5.390461 GCAACTTAATCACTACGTGCAATCA 60.390 40.000 0.00 0.00 32.98 2.57
275 291 4.382254 CCGGGTACTGCAACTTAATCACTA 60.382 45.833 0.00 0.00 0.00 2.74
297 313 6.053650 GGGTCCAATTAGTAGATGTACAACC 58.946 44.000 0.00 0.00 0.00 3.77
317 333 3.489785 CGCATTTTAGTAGTCATCGGGTC 59.510 47.826 0.00 0.00 0.00 4.46
321 338 5.950965 AAGACGCATTTTAGTAGTCATCG 57.049 39.130 0.00 0.00 34.56 3.84
325 342 9.472361 TGGATAATAAGACGCATTTTAGTAGTC 57.528 33.333 0.00 0.00 0.00 2.59
355 372 3.697542 TCGCATACTACAACTAGCTTGGA 59.302 43.478 0.00 1.38 33.66 3.53
357 374 5.980116 AGATTCGCATACTACAACTAGCTTG 59.020 40.000 0.00 0.00 35.77 4.01
393 461 7.393216 AGCTCAATAGATTCCATAATCCACTC 58.607 38.462 0.00 0.00 42.20 3.51
436 504 0.170339 GGTAGACATGCGGCAAAACC 59.830 55.000 6.82 6.78 0.00 3.27
447 516 4.104831 AGAAAGTGGCTTAGGGTAGACAT 58.895 43.478 0.00 0.00 35.17 3.06
452 521 8.050930 CCTAAAATTAGAAAGTGGCTTAGGGTA 58.949 37.037 1.75 0.00 33.50 3.69
467 536 9.457436 CTAGGCTTTGGTTAACCTAAAATTAGA 57.543 33.333 24.78 6.85 34.44 2.10
484 553 5.934625 ACAGATCACTTGTAACTAGGCTTTG 59.065 40.000 0.00 0.00 0.00 2.77
539 618 6.802608 GCATGTATGGATGCTTGCATAATAT 58.197 36.000 14.14 9.74 44.57 1.28
553 632 2.460275 GCGTGCGTGCATGTATGGA 61.460 57.895 16.65 0.00 35.52 3.41
554 633 2.023181 GCGTGCGTGCATGTATGG 59.977 61.111 16.65 6.09 35.52 2.74
555 634 2.783935 TGCGTGCGTGCATGTATG 59.216 55.556 14.92 11.49 40.62 2.39
569 648 1.129251 ACTTTTGAGTCGATGCATGCG 59.871 47.619 14.09 8.11 0.00 4.73
581 660 3.107642 ACGTGGTGGACTACTTTTGAG 57.892 47.619 0.00 0.00 0.00 3.02
608 687 1.327460 ACATGTCGTGCACGCATAATC 59.673 47.619 32.96 20.50 39.60 1.75
675 1266 8.673711 TGCAGGATGTTCAGTTATTTTATGTAC 58.326 33.333 0.00 0.00 39.31 2.90
678 1269 6.694411 GCTGCAGGATGTTCAGTTATTTTATG 59.306 38.462 17.12 0.00 39.31 1.90
680 1271 5.125417 GGCTGCAGGATGTTCAGTTATTTTA 59.875 40.000 17.12 0.00 39.31 1.52
683 1274 3.019564 GGCTGCAGGATGTTCAGTTATT 58.980 45.455 17.12 0.00 39.31 1.40
685 1276 1.340017 GGGCTGCAGGATGTTCAGTTA 60.340 52.381 17.12 0.00 39.31 2.24
686 1277 0.610232 GGGCTGCAGGATGTTCAGTT 60.610 55.000 17.12 0.00 39.31 3.16
688 1279 1.751927 GGGGCTGCAGGATGTTCAG 60.752 63.158 17.12 0.00 39.31 3.02
689 1280 1.866483 ATGGGGCTGCAGGATGTTCA 61.866 55.000 17.12 0.00 39.31 3.18
690 1281 1.076485 ATGGGGCTGCAGGATGTTC 60.076 57.895 17.12 0.00 39.31 3.18
698 1307 3.982111 TTGCTGGATGGGGCTGCA 61.982 61.111 0.50 0.00 0.00 4.41
705 1314 1.033746 ATCTTGCCGTTGCTGGATGG 61.034 55.000 0.00 0.00 38.71 3.51
706 1315 0.379669 GATCTTGCCGTTGCTGGATG 59.620 55.000 0.00 0.00 38.71 3.51
729 1338 3.657537 GCGCGCGCAAGATTTATAT 57.342 47.368 46.11 0.00 41.49 0.86
751 1362 1.336240 GCGCCGGTCCGTATTTATAGT 60.336 52.381 11.06 0.00 0.00 2.12
774 1385 6.091718 TGGCTTTTGGTGGATAAAACTTAC 57.908 37.500 0.00 0.00 0.00 2.34
782 1393 1.354031 TCAGCTGGCTTTTGGTGGATA 59.646 47.619 15.13 0.00 33.13 2.59
785 1396 0.529378 GATCAGCTGGCTTTTGGTGG 59.471 55.000 15.13 0.00 33.13 4.61
792 1403 1.220206 CAGGTCGATCAGCTGGCTT 59.780 57.895 15.13 0.00 45.53 4.35
820 1437 2.056481 GACGGCAGCAATGCATCTCC 62.056 60.000 8.35 1.50 36.33 3.71
904 1521 4.096382 GGATTCATGTAATGGTGTCCACAC 59.904 45.833 0.85 0.85 46.73 3.82
918 1535 9.293404 CTCTTCCAACATTATATGGATTCATGT 57.707 33.333 0.00 0.00 44.83 3.21
919 1536 8.242053 GCTCTTCCAACATTATATGGATTCATG 58.758 37.037 0.00 0.00 44.83 3.07
920 1537 7.946219 TGCTCTTCCAACATTATATGGATTCAT 59.054 33.333 0.00 0.00 44.83 2.57
921 1538 7.289310 TGCTCTTCCAACATTATATGGATTCA 58.711 34.615 0.00 0.00 44.83 2.57
922 1539 7.750229 TGCTCTTCCAACATTATATGGATTC 57.250 36.000 0.00 0.00 44.83 2.52
923 1540 8.537728 TTTGCTCTTCCAACATTATATGGATT 57.462 30.769 0.00 0.00 44.83 3.01
924 1541 8.582437 CATTTGCTCTTCCAACATTATATGGAT 58.418 33.333 0.00 0.00 44.83 3.41
925 1542 7.560991 ACATTTGCTCTTCCAACATTATATGGA 59.439 33.333 0.00 0.00 43.84 3.41
926 1543 7.719483 ACATTTGCTCTTCCAACATTATATGG 58.281 34.615 0.00 0.00 38.09 2.74
927 1544 9.027129 CAACATTTGCTCTTCCAACATTATATG 57.973 33.333 0.00 0.00 0.00 1.78
928 1545 8.199449 CCAACATTTGCTCTTCCAACATTATAT 58.801 33.333 0.00 0.00 0.00 0.86
929 1546 7.395772 TCCAACATTTGCTCTTCCAACATTATA 59.604 33.333 0.00 0.00 0.00 0.98
931 1548 5.538053 TCCAACATTTGCTCTTCCAACATTA 59.462 36.000 0.00 0.00 0.00 1.90
932 1549 4.344679 TCCAACATTTGCTCTTCCAACATT 59.655 37.500 0.00 0.00 0.00 2.71
933 1550 3.896888 TCCAACATTTGCTCTTCCAACAT 59.103 39.130 0.00 0.00 0.00 2.71
934 1551 3.295093 TCCAACATTTGCTCTTCCAACA 58.705 40.909 0.00 0.00 0.00 3.33
935 1552 4.037923 TCTTCCAACATTTGCTCTTCCAAC 59.962 41.667 0.00 0.00 0.00 3.77
936 1553 4.214310 TCTTCCAACATTTGCTCTTCCAA 58.786 39.130 0.00 0.00 0.00 3.53
937 1554 3.822735 CTCTTCCAACATTTGCTCTTCCA 59.177 43.478 0.00 0.00 0.00 3.53
938 1555 3.366781 GCTCTTCCAACATTTGCTCTTCC 60.367 47.826 0.00 0.00 0.00 3.46
939 1556 3.254166 TGCTCTTCCAACATTTGCTCTTC 59.746 43.478 0.00 0.00 0.00 2.87
940 1557 3.225104 TGCTCTTCCAACATTTGCTCTT 58.775 40.909 0.00 0.00 0.00 2.85
941 1558 2.867624 TGCTCTTCCAACATTTGCTCT 58.132 42.857 0.00 0.00 0.00 4.09
942 1559 3.648339 TTGCTCTTCCAACATTTGCTC 57.352 42.857 0.00 0.00 0.00 4.26
944 1561 4.060205 ACATTTGCTCTTCCAACATTTGC 58.940 39.130 0.00 0.00 0.00 3.68
945 1562 6.607735 AAACATTTGCTCTTCCAACATTTG 57.392 33.333 0.00 0.00 0.00 2.32
946 1563 7.474190 CAAAAACATTTGCTCTTCCAACATTT 58.526 30.769 0.00 0.00 0.00 2.32
985 1647 6.950041 CCTGGATTCATGTATTGGGTGATTAT 59.050 38.462 0.00 0.00 0.00 1.28
993 1655 4.037208 GCAAGACCTGGATTCATGTATTGG 59.963 45.833 15.77 0.00 39.45 3.16
998 1660 2.306805 TCAGCAAGACCTGGATTCATGT 59.693 45.455 0.00 0.00 33.64 3.21
1052 1772 4.021925 AGCACTTCCACGGCCTCC 62.022 66.667 0.00 0.00 0.00 4.30
1189 1909 1.735559 GGTACCGGTCGTTGCAGAC 60.736 63.158 12.40 0.00 40.25 3.51
1254 1980 2.097954 TGGTTAGCATCAGTACGTACCG 59.902 50.000 21.80 12.46 0.00 4.02
1260 1986 5.515626 CGAGTAGTTTGGTTAGCATCAGTAC 59.484 44.000 0.00 0.00 0.00 2.73
1261 1987 5.416639 TCGAGTAGTTTGGTTAGCATCAGTA 59.583 40.000 0.00 0.00 0.00 2.74
1262 1988 4.219944 TCGAGTAGTTTGGTTAGCATCAGT 59.780 41.667 0.00 0.00 0.00 3.41
1263 1989 4.744570 TCGAGTAGTTTGGTTAGCATCAG 58.255 43.478 0.00 0.00 0.00 2.90
1265 1991 4.033014 GCTTCGAGTAGTTTGGTTAGCATC 59.967 45.833 0.00 0.00 0.00 3.91
1266 1992 3.933332 GCTTCGAGTAGTTTGGTTAGCAT 59.067 43.478 0.00 0.00 0.00 3.79
1267 1993 3.243941 TGCTTCGAGTAGTTTGGTTAGCA 60.244 43.478 0.00 0.00 34.10 3.49
1268 1994 3.323243 TGCTTCGAGTAGTTTGGTTAGC 58.677 45.455 0.00 0.00 0.00 3.09
1270 1996 3.006537 AGCTGCTTCGAGTAGTTTGGTTA 59.993 43.478 0.00 0.00 30.12 2.85
1272 1998 1.344763 AGCTGCTTCGAGTAGTTTGGT 59.655 47.619 0.00 0.00 30.12 3.67
1275 2001 1.983972 CGAGCTGCTTCGAGTAGTTT 58.016 50.000 2.53 0.00 43.03 2.66
1276 2002 0.456995 GCGAGCTGCTTCGAGTAGTT 60.457 55.000 20.23 0.00 43.03 2.24
1277 2003 1.137825 GCGAGCTGCTTCGAGTAGT 59.862 57.895 20.23 0.00 43.03 2.73
1278 2004 3.990141 GCGAGCTGCTTCGAGTAG 58.010 61.111 20.23 0.00 43.03 2.57
1288 2032 3.670625 AGTAGAGATACCTAGCGAGCTG 58.329 50.000 7.99 0.00 0.00 4.24
1290 2034 4.628333 CACTAGTAGAGATACCTAGCGAGC 59.372 50.000 3.59 0.00 0.00 5.03
1300 2044 6.709397 CCGTTACATGGACACTAGTAGAGATA 59.291 42.308 3.59 0.00 0.00 1.98
1313 2057 1.785321 CGCACACCGTTACATGGAC 59.215 57.895 0.00 0.00 0.00 4.02
1330 2090 4.394712 GACCCCTGGACCTGCACG 62.395 72.222 0.00 0.00 0.00 5.34
1348 2113 3.998672 GACAACCGGCGGACCAGA 61.999 66.667 35.78 0.00 34.57 3.86
1349 2114 4.308458 TGACAACCGGCGGACCAG 62.308 66.667 35.78 20.21 34.57 4.00
1352 2117 2.737376 GACTGACAACCGGCGGAC 60.737 66.667 35.78 19.84 0.00 4.79
1355 2120 2.954753 GCTTGACTGACAACCGGCG 61.955 63.158 0.00 0.00 34.56 6.46
1356 2121 2.946762 GCTTGACTGACAACCGGC 59.053 61.111 0.00 0.00 34.56 6.13
1357 2122 1.300620 TCGCTTGACTGACAACCGG 60.301 57.895 0.00 0.00 37.91 5.28
1358 2123 1.853319 GTCGCTTGACTGACAACCG 59.147 57.895 2.03 2.03 39.61 4.44
1359 2124 1.557443 CCGTCGCTTGACTGACAACC 61.557 60.000 0.00 0.00 40.61 3.77
1360 2125 0.596600 TCCGTCGCTTGACTGACAAC 60.597 55.000 0.00 0.00 40.61 3.32
1361 2126 0.318699 CTCCGTCGCTTGACTGACAA 60.319 55.000 0.00 0.00 40.61 3.18
1362 2127 1.285950 CTCCGTCGCTTGACTGACA 59.714 57.895 0.00 0.00 40.61 3.58
1363 2128 1.444553 CCTCCGTCGCTTGACTGAC 60.445 63.158 0.00 0.00 40.61 3.51
1364 2129 2.962569 CCTCCGTCGCTTGACTGA 59.037 61.111 0.00 0.00 40.61 3.41
1365 2130 2.811317 GCCTCCGTCGCTTGACTG 60.811 66.667 0.00 0.00 40.61 3.51
1366 2131 4.421479 CGCCTCCGTCGCTTGACT 62.421 66.667 0.00 0.00 40.61 3.41
1385 2150 3.827898 CGACGCTGGTCTCCTCCC 61.828 72.222 0.00 0.00 41.16 4.30
1428 2454 2.355837 TCGTCGCAGCACTTCCAC 60.356 61.111 0.00 0.00 0.00 4.02
1447 2473 1.002468 GAACGACATGGTGCATATGGC 60.002 52.381 15.57 12.54 45.13 4.40
1536 2562 4.831307 CGGGAAGCGTCGGACTCG 62.831 72.222 6.57 0.00 37.82 4.18
1599 2625 2.357034 CCGTCGTCAGGGTTGGTG 60.357 66.667 0.00 0.00 0.00 4.17
1634 2663 0.888619 TGCTTCGAGTCTGGTACCAG 59.111 55.000 32.61 32.61 44.86 4.00
1643 2672 1.133407 CCTAGACAGGTGCTTCGAGTC 59.867 57.143 0.00 0.00 37.15 3.36
1644 2673 1.178276 CCTAGACAGGTGCTTCGAGT 58.822 55.000 0.00 0.00 37.15 4.18
1645 2674 1.464734 TCCTAGACAGGTGCTTCGAG 58.535 55.000 0.00 0.00 43.18 4.04
1647 2676 2.969628 ATTCCTAGACAGGTGCTTCG 57.030 50.000 0.00 0.00 43.18 3.79
1648 2677 4.837972 AGAAATTCCTAGACAGGTGCTTC 58.162 43.478 0.00 0.00 43.18 3.86
1649 2678 4.917906 AGAAATTCCTAGACAGGTGCTT 57.082 40.909 0.00 0.00 43.18 3.91
1653 2682 6.936968 ACAAGTAGAAATTCCTAGACAGGT 57.063 37.500 0.00 0.00 43.18 4.00
1654 2683 8.478877 ACATACAAGTAGAAATTCCTAGACAGG 58.521 37.037 0.00 0.00 44.17 4.00
1657 2686 8.258708 ACCACATACAAGTAGAAATTCCTAGAC 58.741 37.037 0.00 0.00 0.00 2.59
1658 2687 8.258007 CACCACATACAAGTAGAAATTCCTAGA 58.742 37.037 0.00 0.00 0.00 2.43
1659 2688 7.011482 GCACCACATACAAGTAGAAATTCCTAG 59.989 40.741 0.00 0.00 0.00 3.02
1660 2689 6.821665 GCACCACATACAAGTAGAAATTCCTA 59.178 38.462 0.00 0.00 0.00 2.94
1669 2698 5.627499 AACATTGCACCACATACAAGTAG 57.373 39.130 0.00 0.00 0.00 2.57
1674 2703 8.835439 CACTATATAAACATTGCACCACATACA 58.165 33.333 0.00 0.00 0.00 2.29
1675 2704 9.051679 TCACTATATAAACATTGCACCACATAC 57.948 33.333 0.00 0.00 0.00 2.39
1678 2707 7.109501 ACTCACTATATAAACATTGCACCACA 58.890 34.615 0.00 0.00 0.00 4.17
1679 2708 7.495934 AGACTCACTATATAAACATTGCACCAC 59.504 37.037 0.00 0.00 0.00 4.16
1680 2709 7.495606 CAGACTCACTATATAAACATTGCACCA 59.504 37.037 0.00 0.00 0.00 4.17
1682 2711 8.331022 CACAGACTCACTATATAAACATTGCAC 58.669 37.037 0.00 0.00 0.00 4.57
1684 2713 7.011389 TGCACAGACTCACTATATAAACATTGC 59.989 37.037 0.00 0.00 0.00 3.56
1685 2714 8.424274 TGCACAGACTCACTATATAAACATTG 57.576 34.615 0.00 0.00 0.00 2.82
1695 2730 1.827969 GGACCTGCACAGACTCACTAT 59.172 52.381 0.00 0.00 0.00 2.12
1697 2732 0.760567 TGGACCTGCACAGACTCACT 60.761 55.000 0.00 0.00 0.00 3.41
1698 2733 0.320247 CTGGACCTGCACAGACTCAC 60.320 60.000 0.00 0.00 36.86 3.51
1701 2740 1.152247 TCCTGGACCTGCACAGACT 60.152 57.895 3.73 0.00 36.86 3.24
1704 2743 0.109342 AAACTCCTGGACCTGCACAG 59.891 55.000 0.00 0.00 34.54 3.66
1705 2744 0.108585 GAAACTCCTGGACCTGCACA 59.891 55.000 0.00 0.00 0.00 4.57
1740 2779 0.037326 TAACAGCTGCTTCCTGACCG 60.037 55.000 15.27 0.00 34.47 4.79
1751 2838 1.599171 CGATCTCCTCGCTAACAGCTG 60.599 57.143 13.48 13.48 41.14 4.24
1848 2941 0.179234 TCACCTTGTCGTGGCAGAAA 59.821 50.000 0.00 0.00 34.36 2.52
1932 3025 2.975536 CCGAAGTAAGGGTCGCCA 59.024 61.111 0.00 0.00 35.93 5.69
1941 3034 4.090588 CCGGGCCAGCCGAAGTAA 62.091 66.667 4.39 0.00 36.85 2.24
1960 3053 2.113860 TAGATCTTGTGGCACTTGGC 57.886 50.000 19.83 4.70 43.74 4.52
2004 3097 4.202620 TGGACATCCTAGCTAGCTAGTCAT 60.203 45.833 37.50 28.75 43.22 3.06
2007 3100 3.885976 TGGACATCCTAGCTAGCTAGT 57.114 47.619 37.50 26.12 43.22 2.57
2097 3208 1.935300 GCTCGGTACACAAGGTCACTG 60.935 57.143 0.00 0.00 0.00 3.66
2098 3209 0.317479 GCTCGGTACACAAGGTCACT 59.683 55.000 0.00 0.00 0.00 3.41
2099 3210 0.669625 GGCTCGGTACACAAGGTCAC 60.670 60.000 0.00 0.00 0.00 3.67
2100 3211 1.116536 TGGCTCGGTACACAAGGTCA 61.117 55.000 0.00 0.00 0.00 4.02
2101 3212 0.669625 GTGGCTCGGTACACAAGGTC 60.670 60.000 0.00 0.00 37.54 3.85
2102 3213 1.370064 GTGGCTCGGTACACAAGGT 59.630 57.895 0.00 0.00 37.54 3.50
2103 3214 1.736645 CGTGGCTCGGTACACAAGG 60.737 63.158 0.13 0.00 37.45 3.61
2104 3215 3.856508 CGTGGCTCGGTACACAAG 58.143 61.111 0.13 0.00 37.45 3.16
2154 3265 2.613133 CCCGGAAGAAAACAACACGTAA 59.387 45.455 0.73 0.00 0.00 3.18
2186 3297 1.606994 CCAAACACTACCAGCGCTACA 60.607 52.381 10.99 0.00 0.00 2.74
2187 3298 1.076332 CCAAACACTACCAGCGCTAC 58.924 55.000 10.99 0.00 0.00 3.58
2188 3299 0.682852 ACCAAACACTACCAGCGCTA 59.317 50.000 10.99 0.00 0.00 4.26
2195 3306 1.960689 ACCATGCAACCAAACACTACC 59.039 47.619 0.00 0.00 0.00 3.18
2205 3316 0.737219 GATGCTGAGACCATGCAACC 59.263 55.000 0.00 0.00 40.24 3.77
2233 3344 9.500785 TGATTGTCTGATTAACACAACTTATCA 57.499 29.630 0.00 0.00 0.00 2.15
2247 3358 5.421056 ACAAAGATGGCATGATTGTCTGATT 59.579 36.000 17.27 0.24 28.61 2.57
2256 3367 3.704566 AGCATCAACAAAGATGGCATGAT 59.295 39.130 3.81 0.00 44.33 2.45
2259 3370 2.167693 CCAGCATCAACAAAGATGGCAT 59.832 45.455 0.00 0.00 44.33 4.40
2282 3393 2.135933 GACCACCTCAAACTCGAAGTG 58.864 52.381 0.00 0.00 0.00 3.16
2284 3395 2.135933 GTGACCACCTCAAACTCGAAG 58.864 52.381 0.00 0.00 0.00 3.79
2288 3399 3.041508 GGTAGTGACCACCTCAAACTC 57.958 52.381 0.00 0.00 46.12 3.01
2357 3482 8.432805 CCAACCTACTCCTCTGTATCAAAATAT 58.567 37.037 0.00 0.00 0.00 1.28
2365 3490 4.159879 CGAAACCAACCTACTCCTCTGTAT 59.840 45.833 0.00 0.00 0.00 2.29
2370 3495 2.612221 CCACGAAACCAACCTACTCCTC 60.612 54.545 0.00 0.00 0.00 3.71
2372 3497 1.609841 CCCACGAAACCAACCTACTCC 60.610 57.143 0.00 0.00 0.00 3.85
2394 3527 3.636764 ACATCAATCAGTCATGCATGCAT 59.363 39.130 27.46 27.46 37.08 3.96
2407 3540 3.959293 AGTGCATCTCCAACATCAATCA 58.041 40.909 0.00 0.00 0.00 2.57
2409 3542 4.337555 GCTAAGTGCATCTCCAACATCAAT 59.662 41.667 0.00 0.00 42.31 2.57
2437 3570 2.612212 ACGAAGGCACTGTAAACACTTG 59.388 45.455 0.00 0.00 40.86 3.16
2455 3588 0.435769 GCGCGCAAAAACTACTACGA 59.564 50.000 29.10 0.00 0.00 3.43
2500 3634 2.032675 TCGCGCATGCTATATTTTGCAA 59.967 40.909 17.13 0.00 42.74 4.08
2508 3642 2.430751 CGGCTCGCGCATGCTATA 60.431 61.111 17.13 0.00 39.65 1.31
2521 3655 1.361993 CGCATCTTCTAGAGCGGCT 59.638 57.895 14.44 0.00 45.83 5.52
2522 3656 3.929389 CGCATCTTCTAGAGCGGC 58.071 61.111 14.44 6.88 45.83 6.53
2532 3666 6.107901 AGGAGAAGAAATATAGCGCATCTT 57.892 37.500 11.47 9.11 33.28 2.40
2536 3670 5.537300 AGAAGGAGAAGAAATATAGCGCA 57.463 39.130 11.47 0.00 0.00 6.09
2566 3713 7.210718 TCGTTTTATCTATCTATGCCTCGAA 57.789 36.000 0.00 0.00 0.00 3.71
2630 3808 7.782644 AGGAGGCTATGAACTATCTATGTATCC 59.217 40.741 0.00 0.00 0.00 2.59
2729 3927 0.395862 GGAGGAGGACATCACCGAGA 60.396 60.000 0.00 0.00 34.73 4.04
2749 3947 6.017687 ACCTTGACGCTTTAATTTTAGACGTT 60.018 34.615 0.00 0.00 31.63 3.99
2756 3954 4.756135 TCGGTACCTTGACGCTTTAATTTT 59.244 37.500 10.90 0.00 0.00 1.82
2757 3955 4.317488 TCGGTACCTTGACGCTTTAATTT 58.683 39.130 10.90 0.00 0.00 1.82
2761 3959 2.478370 CGATCGGTACCTTGACGCTTTA 60.478 50.000 10.90 0.00 0.00 1.85
2764 3962 1.310933 ACGATCGGTACCTTGACGCT 61.311 55.000 20.98 0.00 0.00 5.07
2800 3998 0.898326 TCAACCTAGGAGCAGCGTCA 60.898 55.000 17.98 0.00 0.00 4.35
2854 4052 0.244994 GAGCCATCTACCGCGATGAT 59.755 55.000 8.23 5.06 42.63 2.45
2920 4127 3.722147 CTTCCCATAGGACGTCATCAAG 58.278 50.000 18.91 3.72 43.90 3.02
2934 4141 1.188863 GTGGCTCAAATGCTTCCCAT 58.811 50.000 0.00 0.00 35.06 4.00
2935 4142 0.178967 TGTGGCTCAAATGCTTCCCA 60.179 50.000 0.00 0.00 0.00 4.37
2960 4167 1.139654 CGAGATGGATGAGGAAGCCAA 59.860 52.381 0.00 0.00 34.95 4.52


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

AutoCloner maintained by Alex Coulton.