Multiple sequence alignment - TraesCS2D01G027700

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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 TraesCS2D01G027700 chr2D 100.000 3328 0 0 1 3328 11479047 11475720 0.000000e+00 6146.0
1 TraesCS2D01G027700 chr2D 92.927 1230 76 6 1308 2532 11509647 11508424 0.000000e+00 1779.0
2 TraesCS2D01G027700 chr2D 92.344 1071 82 0 1310 2380 13421721 13422791 0.000000e+00 1524.0
3 TraesCS2D01G027700 chr2D 81.724 580 63 19 709 1255 11510215 11509646 8.470000e-121 444.0
4 TraesCS2D01G027700 chr2D 95.238 273 13 0 993 1265 11496552 11496280 1.830000e-117 433.0
5 TraesCS2D01G027700 chr2D 78.947 152 19 10 700 844 617051017 617051162 1.270000e-14 91.6
6 TraesCS2D01G027700 chr2A 91.412 2026 139 15 1309 3323 12048330 12046329 0.000000e+00 2745.0
7 TraesCS2D01G027700 chr2A 93.039 1063 73 1 1321 2382 15395155 15396217 0.000000e+00 1552.0
8 TraesCS2D01G027700 chr2A 92.644 1074 71 1 1308 2381 12103039 12101974 0.000000e+00 1539.0
9 TraesCS2D01G027700 chr2A 92.551 1074 72 4 1308 2381 12073222 12072157 0.000000e+00 1533.0
10 TraesCS2D01G027700 chr2A 84.588 850 72 27 415 1246 12049150 12048342 0.000000e+00 789.0
11 TraesCS2D01G027700 chr2A 94.258 418 23 1 1 418 12094839 12094423 3.620000e-179 638.0
12 TraesCS2D01G027700 chr2A 88.391 491 23 7 407 881 12080327 12079855 8.060000e-156 560.0
13 TraesCS2D01G027700 chr2A 92.810 306 16 3 955 1255 12073525 12073221 3.940000e-119 438.0
14 TraesCS2D01G027700 chr2A 90.476 315 15 6 955 1255 12103351 12103038 5.170000e-108 401.0
15 TraesCS2D01G027700 chr2A 91.016 256 17 4 995 1246 15394873 15395126 1.140000e-89 340.0
16 TraesCS2D01G027700 chr2A 85.492 193 20 4 4 195 567084957 567085142 9.420000e-46 195.0
17 TraesCS2D01G027700 chr2A 85.492 193 20 4 4 195 567193829 567194014 9.420000e-46 195.0
18 TraesCS2D01G027700 chr2A 86.207 174 16 4 23 195 547666714 547666548 7.330000e-42 182.0
19 TraesCS2D01G027700 chr2A 86.806 144 12 3 8 151 12049436 12049300 1.600000e-33 154.0
20 TraesCS2D01G027700 chr2A 84.444 135 13 5 710 844 12103611 12103485 3.490000e-25 126.0
21 TraesCS2D01G027700 chr2A 77.041 196 34 10 2534 2724 688224804 688224993 5.870000e-18 102.0
22 TraesCS2D01G027700 chr2A 76.531 196 35 9 2534 2724 688203322 688203511 2.730000e-16 97.1
23 TraesCS2D01G027700 chr2A 76.410 195 37 7 2534 2724 688214065 688214254 2.730000e-16 97.1
24 TraesCS2D01G027700 chr2A 78.289 152 19 9 700 844 747086733 747086877 5.920000e-13 86.1
25 TraesCS2D01G027700 chr2B 90.403 1240 86 17 1324 2532 17873746 17872509 0.000000e+00 1600.0
26 TraesCS2D01G027700 chr2B 91.031 1115 92 4 1267 2381 17882965 17881859 0.000000e+00 1498.0
27 TraesCS2D01G027700 chr2B 91.682 1070 87 2 1321 2388 24089826 24090895 0.000000e+00 1482.0
28 TraesCS2D01G027700 chr2B 89.597 471 23 6 415 883 17874513 17874067 2.880000e-160 575.0
29 TraesCS2D01G027700 chr2B 94.774 287 12 2 981 1265 17883316 17883031 8.470000e-121 444.0
30 TraesCS2D01G027700 chr2B 93.561 264 14 3 995 1255 17874034 17873771 1.120000e-104 390.0
31 TraesCS2D01G027700 chr2B 93.254 252 13 4 960 1209 24089496 24089745 5.250000e-98 368.0
32 TraesCS2D01G027700 chr2B 89.286 252 23 2 2 249 17874815 17874564 2.490000e-81 313.0
33 TraesCS2D01G027700 chr2B 87.500 272 29 4 2715 2982 474908662 474908392 3.220000e-80 309.0
34 TraesCS2D01G027700 chr2B 83.824 136 13 6 709 844 17883567 17883441 1.620000e-23 121.0
35 TraesCS2D01G027700 chr2B 80.882 136 14 10 700 828 752784835 752784965 2.730000e-16 97.1
36 TraesCS2D01G027700 chrUn 86.989 269 30 4 2715 2979 93409422 93409689 6.980000e-77 298.0
37 TraesCS2D01G027700 chrUn 86.989 269 30 4 2715 2979 216521781 216522048 6.980000e-77 298.0
38 TraesCS2D01G027700 chrUn 86.716 271 30 5 2715 2981 422745264 422744996 2.510000e-76 296.0
39 TraesCS2D01G027700 chr6D 86.765 272 31 4 2715 2982 168255135 168254865 6.980000e-77 298.0
40 TraesCS2D01G027700 chr4A 86.989 269 30 4 2715 2979 73812299 73812566 6.980000e-77 298.0
41 TraesCS2D01G027700 chr5D 86.397 272 32 4 2715 2982 6189149 6188879 3.250000e-75 292.0
42 TraesCS2D01G027700 chr1A 86.397 272 32 4 2715 2982 554512457 554512187 3.250000e-75 292.0
43 TraesCS2D01G027700 chr1D 81.176 340 60 4 4 340 16394443 16394105 1.520000e-68 270.0
44 TraesCS2D01G027700 chr3A 88.083 193 15 4 4 195 569717679 569717494 4.320000e-54 222.0
45 TraesCS2D01G027700 chr3A 87.047 193 17 4 4 195 723631773 723631958 9.350000e-51 211.0
46 TraesCS2D01G027700 chr5A 81.507 146 14 8 2570 2713 657983585 657983719 1.260000e-19 108.0
47 TraesCS2D01G027700 chr7D 79.195 149 21 5 2570 2714 163200915 163201057 9.830000e-16 95.3
48 TraesCS2D01G027700 chr5B 82.407 108 16 3 2569 2673 700858003 700858110 1.270000e-14 91.6
49 TraesCS2D01G027700 chr7B 76.374 182 34 7 2538 2716 623502349 623502524 4.570000e-14 89.8
50 TraesCS2D01G027700 chr7B 75.275 182 38 5 2538 2716 623264164 623264341 2.750000e-11 80.5
51 TraesCS2D01G027700 chr7B 90.000 60 4 2 2664 2723 682374604 682374661 3.560000e-10 76.8


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 TraesCS2D01G027700 chr2D 11475720 11479047 3327 True 6146.000000 6146 100.000000 1 3328 1 chr2D.!!$R1 3327
1 TraesCS2D01G027700 chr2D 13421721 13422791 1070 False 1524.000000 1524 92.344000 1310 2380 1 chr2D.!!$F1 1070
2 TraesCS2D01G027700 chr2D 11508424 11510215 1791 True 1111.500000 1779 87.325500 709 2532 2 chr2D.!!$R3 1823
3 TraesCS2D01G027700 chr2A 12046329 12049436 3107 True 1229.333333 2745 87.602000 8 3323 3 chr2A.!!$R4 3315
4 TraesCS2D01G027700 chr2A 12072157 12073525 1368 True 985.500000 1533 92.680500 955 2381 2 chr2A.!!$R5 1426
5 TraesCS2D01G027700 chr2A 15394873 15396217 1344 False 946.000000 1552 92.027500 995 2382 2 chr2A.!!$F7 1387
6 TraesCS2D01G027700 chr2A 12101974 12103611 1637 True 688.666667 1539 89.188000 710 2381 3 chr2A.!!$R6 1671
7 TraesCS2D01G027700 chr2B 24089496 24090895 1399 False 925.000000 1482 92.468000 960 2388 2 chr2B.!!$F2 1428
8 TraesCS2D01G027700 chr2B 17872509 17874815 2306 True 719.500000 1600 90.711750 2 2532 4 chr2B.!!$R2 2530
9 TraesCS2D01G027700 chr2B 17881859 17883567 1708 True 687.666667 1498 89.876333 709 2381 3 chr2B.!!$R3 1672

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
924 983 0.179000 CCTGCTCTATCCCGCAAACT 59.821 55.0 0.00 0.0 35.46 2.66 F
2024 2188 0.114954 AAGCCTTCAAGCCATTGGGA 59.885 50.0 4.53 0.0 37.02 4.37 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2228 2392 0.036388 TCATTCCCTCGCCAGTTGTC 60.036 55.0 0.0 0.0 0.00 3.18 R
2904 3102 0.249911 GCACTTTCGGTCCTGTGAGT 60.250 55.0 0.0 0.0 32.72 3.41 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
82 83 9.675464 TCCTAAGTCGGTTCAATATTTACAAAT 57.325 29.630 0.00 0.00 0.00 2.32
109 110 9.944663 TTATTATTGATTTCTAACGGCAACATC 57.055 29.630 0.00 0.00 0.00 3.06
121 125 8.091449 TCTAACGGCAACATCCAATTAAAAATT 58.909 29.630 0.00 0.00 0.00 1.82
165 169 5.816777 CCGGTTTATATTTTCCAAGGTCGTA 59.183 40.000 0.00 0.00 0.00 3.43
249 254 4.168760 GTGGCATTGTGTTATCTTGCTTC 58.831 43.478 0.00 0.00 33.86 3.86
250 255 4.081406 TGGCATTGTGTTATCTTGCTTCT 58.919 39.130 0.00 0.00 33.86 2.85
251 256 5.123820 GTGGCATTGTGTTATCTTGCTTCTA 59.876 40.000 0.00 0.00 33.86 2.10
254 260 6.038603 GGCATTGTGTTATCTTGCTTCTATGA 59.961 38.462 0.00 0.00 33.86 2.15
256 262 8.133627 GCATTGTGTTATCTTGCTTCTATGATT 58.866 33.333 0.00 0.00 0.00 2.57
262 268 9.269453 TGTTATCTTGCTTCTATGATTCTCATG 57.731 33.333 0.00 0.00 37.70 3.07
263 269 9.270640 GTTATCTTGCTTCTATGATTCTCATGT 57.729 33.333 0.00 0.00 37.70 3.21
264 270 7.731882 ATCTTGCTTCTATGATTCTCATGTG 57.268 36.000 0.00 0.00 37.70 3.21
272 278 9.551734 CTTCTATGATTCTCATGTGTTATTCCA 57.448 33.333 0.00 0.00 37.70 3.53
326 332 9.561069 TTATCTAAATCTAAGGCAACATTCTCC 57.439 33.333 0.00 0.00 41.41 3.71
327 333 7.200434 TCTAAATCTAAGGCAACATTCTCCT 57.800 36.000 0.00 0.00 41.41 3.69
328 334 7.275920 TCTAAATCTAAGGCAACATTCTCCTC 58.724 38.462 0.00 0.00 41.41 3.71
329 335 3.914426 TCTAAGGCAACATTCTCCTCC 57.086 47.619 0.00 0.00 41.41 4.30
330 336 3.454858 TCTAAGGCAACATTCTCCTCCT 58.545 45.455 0.00 0.00 41.41 3.69
331 337 2.797177 AAGGCAACATTCTCCTCCTC 57.203 50.000 0.00 0.00 41.41 3.71
332 338 1.661463 AGGCAACATTCTCCTCCTCA 58.339 50.000 0.00 0.00 41.41 3.86
333 339 2.203584 AGGCAACATTCTCCTCCTCAT 58.796 47.619 0.00 0.00 41.41 2.90
334 340 3.387962 AGGCAACATTCTCCTCCTCATA 58.612 45.455 0.00 0.00 41.41 2.15
335 341 3.979347 AGGCAACATTCTCCTCCTCATAT 59.021 43.478 0.00 0.00 41.41 1.78
336 342 5.158141 AGGCAACATTCTCCTCCTCATATA 58.842 41.667 0.00 0.00 41.41 0.86
337 343 5.012561 AGGCAACATTCTCCTCCTCATATAC 59.987 44.000 0.00 0.00 41.41 1.47
338 344 5.012561 GGCAACATTCTCCTCCTCATATACT 59.987 44.000 0.00 0.00 0.00 2.12
339 345 6.211584 GGCAACATTCTCCTCCTCATATACTA 59.788 42.308 0.00 0.00 0.00 1.82
340 346 7.093992 GCAACATTCTCCTCCTCATATACTAC 58.906 42.308 0.00 0.00 0.00 2.73
341 347 7.607250 CAACATTCTCCTCCTCATATACTACC 58.393 42.308 0.00 0.00 0.00 3.18
342 348 6.257586 ACATTCTCCTCCTCATATACTACCC 58.742 44.000 0.00 0.00 0.00 3.69
343 349 4.949966 TCTCCTCCTCATATACTACCCC 57.050 50.000 0.00 0.00 0.00 4.95
344 350 4.524312 TCTCCTCCTCATATACTACCCCT 58.476 47.826 0.00 0.00 0.00 4.79
345 351 4.926987 TCTCCTCCTCATATACTACCCCTT 59.073 45.833 0.00 0.00 0.00 3.95
346 352 5.015391 TCTCCTCCTCATATACTACCCCTTC 59.985 48.000 0.00 0.00 0.00 3.46
347 353 4.045590 TCCTCCTCATATACTACCCCTTCC 59.954 50.000 0.00 0.00 0.00 3.46
348 354 4.017808 CTCCTCATATACTACCCCTTCCG 58.982 52.174 0.00 0.00 0.00 4.30
349 355 3.400322 TCCTCATATACTACCCCTTCCGT 59.600 47.826 0.00 0.00 0.00 4.69
350 356 3.762823 CCTCATATACTACCCCTTCCGTC 59.237 52.174 0.00 0.00 0.00 4.79
351 357 3.762823 CTCATATACTACCCCTTCCGTCC 59.237 52.174 0.00 0.00 0.00 4.79
352 358 2.683211 TATACTACCCCTTCCGTCCC 57.317 55.000 0.00 0.00 0.00 4.46
353 359 0.638292 ATACTACCCCTTCCGTCCCA 59.362 55.000 0.00 0.00 0.00 4.37
354 360 0.638292 TACTACCCCTTCCGTCCCAT 59.362 55.000 0.00 0.00 0.00 4.00
355 361 0.638292 ACTACCCCTTCCGTCCCATA 59.362 55.000 0.00 0.00 0.00 2.74
356 362 1.008693 ACTACCCCTTCCGTCCCATAA 59.991 52.381 0.00 0.00 0.00 1.90
357 363 2.335933 CTACCCCTTCCGTCCCATAAT 58.664 52.381 0.00 0.00 0.00 1.28
358 364 2.500269 ACCCCTTCCGTCCCATAATA 57.500 50.000 0.00 0.00 0.00 0.98
359 365 2.999928 ACCCCTTCCGTCCCATAATAT 58.000 47.619 0.00 0.00 0.00 1.28
360 366 4.150516 ACCCCTTCCGTCCCATAATATA 57.849 45.455 0.00 0.00 0.00 0.86
361 367 4.505367 ACCCCTTCCGTCCCATAATATAA 58.495 43.478 0.00 0.00 0.00 0.98
362 368 4.534897 ACCCCTTCCGTCCCATAATATAAG 59.465 45.833 0.00 0.00 0.00 1.73
363 369 4.781087 CCCCTTCCGTCCCATAATATAAGA 59.219 45.833 0.00 0.00 0.00 2.10
364 370 5.249852 CCCCTTCCGTCCCATAATATAAGAA 59.750 44.000 0.00 0.00 0.00 2.52
365 371 6.069615 CCCCTTCCGTCCCATAATATAAGAAT 60.070 42.308 0.00 0.00 0.00 2.40
366 372 7.126726 CCCCTTCCGTCCCATAATATAAGAATA 59.873 40.741 0.00 0.00 0.00 1.75
367 373 8.545472 CCCTTCCGTCCCATAATATAAGAATAA 58.455 37.037 0.00 0.00 0.00 1.40
404 410 8.539770 AACATTCTTATATTATGAGACCGCTG 57.460 34.615 0.00 0.00 0.00 5.18
405 411 7.099764 ACATTCTTATATTATGAGACCGCTGG 58.900 38.462 0.00 0.00 0.00 4.85
406 412 6.911250 TTCTTATATTATGAGACCGCTGGA 57.089 37.500 1.50 0.00 0.00 3.86
407 413 6.516739 TCTTATATTATGAGACCGCTGGAG 57.483 41.667 1.50 0.00 0.00 3.86
408 414 6.010850 TCTTATATTATGAGACCGCTGGAGT 58.989 40.000 1.50 0.00 0.00 3.85
409 415 7.173032 TCTTATATTATGAGACCGCTGGAGTA 58.827 38.462 1.50 0.00 0.00 2.59
410 416 7.834681 TCTTATATTATGAGACCGCTGGAGTAT 59.165 37.037 1.50 0.00 0.00 2.12
411 417 9.121658 CTTATATTATGAGACCGCTGGAGTATA 57.878 37.037 1.50 0.00 0.00 1.47
412 418 9.642343 TTATATTATGAGACCGCTGGAGTATAT 57.358 33.333 1.50 0.00 0.00 0.86
413 419 5.644977 TTATGAGACCGCTGGAGTATATG 57.355 43.478 1.50 0.00 0.00 1.78
417 423 3.085533 AGACCGCTGGAGTATATGCTAG 58.914 50.000 0.00 0.00 0.00 3.42
439 445 7.961827 GCTAGCTGTGCAAAAGATTATGATATC 59.038 37.037 7.70 0.00 0.00 1.63
454 460 0.973632 ATATCTATGGCCCGTGCGAA 59.026 50.000 0.00 0.00 38.85 4.70
467 473 4.983090 GCGAATGCACGGATTCAG 57.017 55.556 11.19 5.70 42.15 3.02
487 493 6.443934 TCAGAACTAGTGATGCTCTAACTC 57.556 41.667 0.00 0.00 0.00 3.01
488 494 5.946377 TCAGAACTAGTGATGCTCTAACTCA 59.054 40.000 0.00 0.00 0.00 3.41
489 495 6.605194 TCAGAACTAGTGATGCTCTAACTCAT 59.395 38.462 0.00 0.00 0.00 2.90
490 496 7.775561 TCAGAACTAGTGATGCTCTAACTCATA 59.224 37.037 0.00 0.00 0.00 2.15
491 497 8.409371 CAGAACTAGTGATGCTCTAACTCATAA 58.591 37.037 0.00 0.00 0.00 1.90
492 498 8.410141 AGAACTAGTGATGCTCTAACTCATAAC 58.590 37.037 0.00 0.00 0.00 1.89
493 499 7.889873 ACTAGTGATGCTCTAACTCATAACT 57.110 36.000 0.00 0.00 37.90 2.24
504 510 6.062749 TCTAACTCATAACTCATAGCGAGGT 58.937 40.000 0.00 0.00 46.98 3.85
671 684 1.135689 CGGTTCAAGCACATAACTGGC 60.136 52.381 0.00 0.00 0.00 4.85
777 791 2.374504 CCATCCATGCATCTCCTACCTT 59.625 50.000 0.00 0.00 0.00 3.50
825 859 2.230660 CAACTGACCAAACCCCTTCTC 58.769 52.381 0.00 0.00 0.00 2.87
831 865 1.299976 CAAACCCCTTCTCCCCGAG 59.700 63.158 0.00 0.00 0.00 4.63
911 965 3.386078 TGTCATTCATCTACCTCCTGCTC 59.614 47.826 0.00 0.00 0.00 4.26
924 983 0.179000 CCTGCTCTATCCCGCAAACT 59.821 55.000 0.00 0.00 35.46 2.66
926 985 2.158957 CCTGCTCTATCCCGCAAACTTA 60.159 50.000 0.00 0.00 35.46 2.24
929 988 3.124560 GCTCTATCCCGCAAACTTAGAC 58.875 50.000 0.00 0.00 0.00 2.59
930 989 3.372954 CTCTATCCCGCAAACTTAGACG 58.627 50.000 0.00 0.00 0.00 4.18
938 997 1.459592 GCAAACTTAGACGTCGCACAT 59.540 47.619 10.46 0.00 0.00 3.21
943 1006 1.065701 CTTAGACGTCGCACATAGCCT 59.934 52.381 10.46 0.00 41.38 4.58
984 1047 2.103042 GCTTGTCAGCCGCTGGTAG 61.103 63.158 20.23 14.74 40.61 3.18
986 1050 2.513026 CTTGTCAGCCGCTGGTAGCT 62.513 60.000 20.23 0.00 39.60 3.32
1202 1279 7.856145 AGAGGATGTGTAAGTTCAATGAATC 57.144 36.000 0.00 0.00 0.00 2.52
1260 1350 0.912486 GGACATGCAACCTACTCCCT 59.088 55.000 0.00 0.00 0.00 4.20
1284 1403 5.065474 TCTGTAACTAGCTTGCAAAAACGTT 59.935 36.000 0.00 0.00 0.00 3.99
1298 1417 8.500837 TGCAAAAACGTTTTATATTGTGAGAG 57.499 30.769 25.44 6.35 0.00 3.20
1300 1419 7.061789 GCAAAAACGTTTTATATTGTGAGAGGG 59.938 37.037 25.44 0.00 0.00 4.30
1302 1421 7.611213 AAACGTTTTATATTGTGAGAGGGAG 57.389 36.000 7.96 0.00 0.00 4.30
1303 1422 5.671493 ACGTTTTATATTGTGAGAGGGAGG 58.329 41.667 0.00 0.00 0.00 4.30
1306 1460 6.631766 CGTTTTATATTGTGAGAGGGAGGGAA 60.632 42.308 0.00 0.00 0.00 3.97
1349 1513 2.234661 AGGTGACAAATCGCAGATCAGA 59.765 45.455 0.00 0.00 45.12 3.27
1406 1570 3.669344 AACCCCAACATGTGCGCG 61.669 61.111 0.00 0.00 0.00 6.86
1466 1630 2.352805 GTGGAGGTCCCCAAGCTG 59.647 66.667 0.99 0.00 38.06 4.24
1955 2119 1.273098 GGTCTCACCTTCCACCTCCTA 60.273 57.143 0.00 0.00 34.73 2.94
1982 2146 1.304282 GCCTGGCCTCATCTCCAAA 59.696 57.895 7.66 0.00 30.98 3.28
2024 2188 0.114954 AAGCCTTCAAGCCATTGGGA 59.885 50.000 4.53 0.00 37.02 4.37
2090 2254 1.617804 CCAGCCATCCTTGACATGGTT 60.618 52.381 7.22 0.00 42.68 3.67
2102 2266 0.251341 ACATGGTTGAGGCCAAGGTC 60.251 55.000 5.01 0.00 42.48 3.85
2228 2392 4.082523 ACCGAGGATGGCCACACG 62.083 66.667 8.16 11.67 36.29 4.49
2247 2411 0.036388 GACAACTGGCGAGGGAATGA 60.036 55.000 0.00 0.00 0.00 2.57
2390 2554 6.459024 CGTGGAAAAATCTACTGTTGTTGGAA 60.459 38.462 0.00 0.00 0.00 3.53
2431 2623 2.355009 GTTGGCGTGCTTTGCTGG 60.355 61.111 0.00 0.00 0.00 4.85
2450 2642 2.194056 CCACCTGGGCCATAGCTG 59.806 66.667 6.72 0.00 39.73 4.24
2460 2652 1.064389 GGCCATAGCTGTTCCTTCCTT 60.064 52.381 0.00 0.00 39.73 3.36
2476 2670 3.643199 TCCTTTGTGCTATGCATACCA 57.357 42.857 1.16 0.00 41.91 3.25
2536 2730 7.295201 TGATTTGCGTAATTGAAAGTACAGTC 58.705 34.615 0.00 0.00 30.42 3.51
2544 2738 8.492748 CGTAATTGAAAGTACAGTCTTGCTAAA 58.507 33.333 0.00 0.00 30.42 1.85
2545 2739 9.595357 GTAATTGAAAGTACAGTCTTGCTAAAC 57.405 33.333 0.00 0.00 30.42 2.01
2558 2752 5.578727 GTCTTGCTAAACCTCAGTCACTATG 59.421 44.000 0.00 0.00 0.00 2.23
2577 2771 8.321353 TCACTATGACTTGGTTATGTCTCAATT 58.679 33.333 0.00 0.00 33.44 2.32
2578 2772 8.393366 CACTATGACTTGGTTATGTCTCAATTG 58.607 37.037 0.00 0.00 33.44 2.32
2580 2774 6.801539 TGACTTGGTTATGTCTCAATTGAC 57.198 37.500 3.38 0.00 37.47 3.18
2605 2799 8.727910 ACGCTATATTCGTGAGATCTTACATTA 58.272 33.333 16.95 6.15 41.60 1.90
2611 2805 6.145338 TCGTGAGATCTTACATTAAGGTCC 57.855 41.667 16.95 0.00 45.02 4.46
2620 2814 5.531659 TCTTACATTAAGGTCCGTGCAAAAA 59.468 36.000 0.00 0.00 36.45 1.94
2669 2867 6.545504 ACATGTTATGTCACTTGACTTGAC 57.454 37.500 10.63 10.96 44.99 3.18
2670 2868 6.291377 ACATGTTATGTCACTTGACTTGACT 58.709 36.000 16.26 4.95 44.99 3.41
2671 2869 6.203530 ACATGTTATGTCACTTGACTTGACTG 59.796 38.462 16.26 14.15 44.99 3.51
2672 2870 5.912892 TGTTATGTCACTTGACTTGACTGA 58.087 37.500 16.26 1.22 44.99 3.41
2673 2871 5.985530 TGTTATGTCACTTGACTTGACTGAG 59.014 40.000 16.26 0.00 44.99 3.35
2674 2872 4.944619 ATGTCACTTGACTTGACTGAGA 57.055 40.909 10.63 0.00 44.99 3.27
2675 2873 4.046938 TGTCACTTGACTTGACTGAGAC 57.953 45.455 10.63 0.00 44.99 3.36
2676 2874 3.701542 TGTCACTTGACTTGACTGAGACT 59.298 43.478 10.63 0.00 44.99 3.24
2677 2875 4.160439 TGTCACTTGACTTGACTGAGACTT 59.840 41.667 10.63 0.00 44.99 3.01
2678 2876 4.505922 GTCACTTGACTTGACTGAGACTTG 59.494 45.833 1.92 0.00 40.30 3.16
2679 2877 3.806521 CACTTGACTTGACTGAGACTTGG 59.193 47.826 0.00 0.00 0.00 3.61
2680 2878 3.452627 ACTTGACTTGACTGAGACTTGGT 59.547 43.478 0.00 0.00 0.00 3.67
2702 2900 6.208007 TGGTTAAGTCTCAATCGACTAAGACA 59.792 38.462 19.29 3.45 43.14 3.41
2790 2988 2.523657 CTACCCCCGGCTAGACCC 60.524 72.222 0.00 0.00 33.26 4.46
2841 3039 8.747538 ACCAAAGTGATTGAGTTTAGTAGTTT 57.252 30.769 0.00 0.00 41.85 2.66
2912 3110 6.205464 ACAAAATTGTCTGATACACTCACAGG 59.795 38.462 0.00 0.00 38.00 4.00
2929 3127 0.838987 AGGACCGAAAGTGCCCCTTA 60.839 55.000 0.00 0.00 37.58 2.69
2960 3158 2.434702 GAGGAGGACGGGTTATTCACAT 59.565 50.000 0.00 0.00 0.00 3.21
2981 3179 7.395772 TCACATTTAATTTAATGGCCAGAGACA 59.604 33.333 13.05 0.00 39.33 3.41
2993 3191 2.740055 GAGACAGTGGCTGGTGCG 60.740 66.667 1.10 0.00 40.82 5.34
3009 3207 1.427819 GCGTTAGGCGTTCATTGGG 59.572 57.895 0.00 0.00 43.66 4.12
3013 3211 2.280628 GTTAGGCGTTCATTGGGAGAG 58.719 52.381 0.00 0.00 0.00 3.20
3016 3214 2.398588 AGGCGTTCATTGGGAGAGATA 58.601 47.619 0.00 0.00 0.00 1.98
3019 3217 2.481952 GCGTTCATTGGGAGAGATATGC 59.518 50.000 0.00 0.00 0.00 3.14
3030 3228 1.134699 AGAGATATGCGTGTGTGGGTG 60.135 52.381 0.00 0.00 0.00 4.61
3042 3240 4.181578 GTGTGTGGGTGTAGTCATATGAC 58.818 47.826 25.47 25.47 45.08 3.06
3065 3263 3.806949 TGGCCTCTATGAAAACACCTT 57.193 42.857 3.32 0.00 0.00 3.50
3095 3294 6.698766 GGCATTCTTTTCCACATATGATGAAC 59.301 38.462 10.38 0.00 0.00 3.18
3137 3336 6.757897 AACAGCGAGATATTTGATGGAAAA 57.242 33.333 0.00 0.00 30.53 2.29
3176 3375 4.668576 CTTGCGAGCAATCTCACTTTAA 57.331 40.909 11.15 0.00 39.30 1.52
3177 3376 4.645956 CTTGCGAGCAATCTCACTTTAAG 58.354 43.478 11.15 0.00 39.30 1.85
3178 3377 3.925379 TGCGAGCAATCTCACTTTAAGA 58.075 40.909 0.00 0.00 39.30 2.10
3179 3378 4.314961 TGCGAGCAATCTCACTTTAAGAA 58.685 39.130 0.00 0.00 39.30 2.52
3180 3379 4.937620 TGCGAGCAATCTCACTTTAAGAAT 59.062 37.500 0.00 0.00 39.30 2.40
3181 3380 5.412594 TGCGAGCAATCTCACTTTAAGAATT 59.587 36.000 0.00 0.00 39.30 2.17
3182 3381 6.593770 TGCGAGCAATCTCACTTTAAGAATTA 59.406 34.615 0.00 0.00 39.30 1.40
3183 3382 7.119116 TGCGAGCAATCTCACTTTAAGAATTAA 59.881 33.333 0.00 0.00 37.73 1.40
3184 3383 7.637907 GCGAGCAATCTCACTTTAAGAATTAAG 59.362 37.037 0.00 0.00 39.36 1.85
3188 3387 7.912773 GCAATCTCACTTTAAGAATTAAGAGCC 59.087 37.037 0.00 0.00 42.24 4.70
3193 3392 9.823647 CTCACTTTAAGAATTAAGAGCCTATGA 57.176 33.333 0.00 0.00 42.24 2.15
3220 3419 6.069556 AGTCCACTAGTGAGTACAATAGGAGA 60.070 42.308 24.68 5.06 45.30 3.71
3223 3422 6.773200 CCACTAGTGAGTACAATAGGAGATGA 59.227 42.308 24.68 0.00 45.30 2.92
3232 3431 9.959749 GAGTACAATAGGAGATGAAAAGTCTAG 57.040 37.037 0.00 0.00 0.00 2.43
3257 3456 7.396339 AGGATTCGGCTACACTGATATTATGTA 59.604 37.037 0.00 0.00 32.28 2.29
3258 3457 7.702772 GGATTCGGCTACACTGATATTATGTAG 59.297 40.741 13.62 13.62 45.67 2.74
3259 3458 7.520451 TTCGGCTACACTGATATTATGTAGT 57.480 36.000 16.87 0.00 45.02 2.73
3306 3505 7.921786 TTCTCAAGAACTGAAAACTCTCAAA 57.078 32.000 0.00 0.00 32.17 2.69
3323 3522 5.531634 TCTCAAAATCTGGAATGTTGCAAC 58.468 37.500 22.83 22.83 0.00 4.17
3324 3523 4.297510 TCAAAATCTGGAATGTTGCAACG 58.702 39.130 23.79 9.15 0.00 4.10
3325 3524 3.302365 AAATCTGGAATGTTGCAACGG 57.698 42.857 23.79 5.81 0.00 4.44
3326 3525 2.198827 ATCTGGAATGTTGCAACGGA 57.801 45.000 23.79 11.17 0.00 4.69
3327 3526 1.522668 TCTGGAATGTTGCAACGGAG 58.477 50.000 23.79 14.14 0.00 4.63
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 7.543756 TGCTGGCAAGAAACCTATAAATAAAC 58.456 34.615 0.00 0.00 0.00 2.01
47 48 5.235516 TGAACCGACTTAGGATGTTTTCTC 58.764 41.667 0.00 0.00 34.73 2.87
121 125 4.638421 CCGGCCAAAATTTGTCTCTATGTA 59.362 41.667 2.24 0.00 0.00 2.29
135 139 5.740290 TGGAAAATATAAACCGGCCAAAA 57.260 34.783 0.00 0.00 0.00 2.44
218 223 3.052455 ACACAATGCCACGTCATCTAA 57.948 42.857 0.00 0.00 0.00 2.10
221 226 3.623060 AGATAACACAATGCCACGTCATC 59.377 43.478 0.00 0.00 0.00 2.92
226 231 2.162208 AGCAAGATAACACAATGCCACG 59.838 45.455 0.00 0.00 37.73 4.94
315 321 6.107901 AGTATATGAGGAGGAGAATGTTGC 57.892 41.667 0.00 0.00 0.00 4.17
318 324 6.257586 GGGTAGTATATGAGGAGGAGAATGT 58.742 44.000 0.00 0.00 0.00 2.71
323 329 4.957606 AGGGGTAGTATATGAGGAGGAG 57.042 50.000 0.00 0.00 0.00 3.69
326 332 4.017808 CGGAAGGGGTAGTATATGAGGAG 58.982 52.174 0.00 0.00 0.00 3.69
327 333 3.400322 ACGGAAGGGGTAGTATATGAGGA 59.600 47.826 0.00 0.00 0.00 3.71
328 334 3.762823 GACGGAAGGGGTAGTATATGAGG 59.237 52.174 0.00 0.00 0.00 3.86
329 335 3.762823 GGACGGAAGGGGTAGTATATGAG 59.237 52.174 0.00 0.00 0.00 2.90
330 336 3.501019 GGGACGGAAGGGGTAGTATATGA 60.501 52.174 0.00 0.00 0.00 2.15
331 337 2.830321 GGGACGGAAGGGGTAGTATATG 59.170 54.545 0.00 0.00 0.00 1.78
332 338 2.452047 TGGGACGGAAGGGGTAGTATAT 59.548 50.000 0.00 0.00 0.00 0.86
333 339 1.858910 TGGGACGGAAGGGGTAGTATA 59.141 52.381 0.00 0.00 0.00 1.47
334 340 0.638292 TGGGACGGAAGGGGTAGTAT 59.362 55.000 0.00 0.00 0.00 2.12
335 341 0.638292 ATGGGACGGAAGGGGTAGTA 59.362 55.000 0.00 0.00 0.00 1.82
336 342 0.638292 TATGGGACGGAAGGGGTAGT 59.362 55.000 0.00 0.00 0.00 2.73
337 343 1.797320 TTATGGGACGGAAGGGGTAG 58.203 55.000 0.00 0.00 0.00 3.18
338 344 2.500269 ATTATGGGACGGAAGGGGTA 57.500 50.000 0.00 0.00 0.00 3.69
339 345 2.500269 TATTATGGGACGGAAGGGGT 57.500 50.000 0.00 0.00 0.00 4.95
340 346 4.781087 TCTTATATTATGGGACGGAAGGGG 59.219 45.833 0.00 0.00 0.00 4.79
341 347 6.368779 TTCTTATATTATGGGACGGAAGGG 57.631 41.667 0.00 0.00 0.00 3.95
378 384 8.993121 CAGCGGTCTCATAATATAAGAATGTTT 58.007 33.333 0.00 0.00 0.00 2.83
379 385 7.604164 CCAGCGGTCTCATAATATAAGAATGTT 59.396 37.037 0.00 0.00 0.00 2.71
380 386 7.039011 TCCAGCGGTCTCATAATATAAGAATGT 60.039 37.037 0.00 0.00 0.00 2.71
381 387 7.323420 TCCAGCGGTCTCATAATATAAGAATG 58.677 38.462 0.00 0.00 0.00 2.67
382 388 7.179338 ACTCCAGCGGTCTCATAATATAAGAAT 59.821 37.037 0.00 0.00 0.00 2.40
383 389 6.493802 ACTCCAGCGGTCTCATAATATAAGAA 59.506 38.462 0.00 0.00 0.00 2.52
384 390 6.010850 ACTCCAGCGGTCTCATAATATAAGA 58.989 40.000 0.00 0.00 0.00 2.10
385 391 6.274157 ACTCCAGCGGTCTCATAATATAAG 57.726 41.667 0.00 0.00 0.00 1.73
386 392 7.956328 ATACTCCAGCGGTCTCATAATATAA 57.044 36.000 0.00 0.00 0.00 0.98
387 393 9.067986 CATATACTCCAGCGGTCTCATAATATA 57.932 37.037 0.00 0.00 0.00 0.86
388 394 7.470702 GCATATACTCCAGCGGTCTCATAATAT 60.471 40.741 0.00 0.00 0.00 1.28
389 395 6.183360 GCATATACTCCAGCGGTCTCATAATA 60.183 42.308 0.00 0.00 0.00 0.98
390 396 5.394663 GCATATACTCCAGCGGTCTCATAAT 60.395 44.000 0.00 0.00 0.00 1.28
391 397 4.082190 GCATATACTCCAGCGGTCTCATAA 60.082 45.833 0.00 0.00 0.00 1.90
392 398 3.444034 GCATATACTCCAGCGGTCTCATA 59.556 47.826 0.00 0.00 0.00 2.15
393 399 2.232452 GCATATACTCCAGCGGTCTCAT 59.768 50.000 0.00 0.00 0.00 2.90
394 400 1.613925 GCATATACTCCAGCGGTCTCA 59.386 52.381 0.00 0.00 0.00 3.27
395 401 1.889829 AGCATATACTCCAGCGGTCTC 59.110 52.381 0.00 0.00 0.00 3.36
396 402 2.002505 AGCATATACTCCAGCGGTCT 57.997 50.000 0.00 0.00 0.00 3.85
397 403 2.416162 GCTAGCATATACTCCAGCGGTC 60.416 54.545 10.63 0.00 0.00 4.79
398 404 1.546476 GCTAGCATATACTCCAGCGGT 59.454 52.381 10.63 0.00 0.00 5.68
399 405 1.821753 AGCTAGCATATACTCCAGCGG 59.178 52.381 18.83 0.00 34.26 5.52
400 406 2.230025 ACAGCTAGCATATACTCCAGCG 59.770 50.000 18.83 0.00 34.26 5.18
401 407 3.583806 CACAGCTAGCATATACTCCAGC 58.416 50.000 18.83 0.00 0.00 4.85
402 408 3.006217 TGCACAGCTAGCATATACTCCAG 59.994 47.826 18.83 0.00 37.02 3.86
403 409 2.965147 TGCACAGCTAGCATATACTCCA 59.035 45.455 18.83 0.00 37.02 3.86
404 410 3.667497 TGCACAGCTAGCATATACTCC 57.333 47.619 18.83 0.00 37.02 3.85
405 411 5.755375 TCTTTTGCACAGCTAGCATATACTC 59.245 40.000 18.83 0.00 42.33 2.59
406 412 5.674525 TCTTTTGCACAGCTAGCATATACT 58.325 37.500 18.83 0.00 42.33 2.12
407 413 5.991328 TCTTTTGCACAGCTAGCATATAC 57.009 39.130 18.83 2.61 42.33 1.47
408 414 8.724229 CATAATCTTTTGCACAGCTAGCATATA 58.276 33.333 18.83 0.00 42.33 0.86
409 415 7.446319 TCATAATCTTTTGCACAGCTAGCATAT 59.554 33.333 18.83 0.00 42.33 1.78
410 416 6.767423 TCATAATCTTTTGCACAGCTAGCATA 59.233 34.615 18.83 6.61 42.33 3.14
411 417 5.591472 TCATAATCTTTTGCACAGCTAGCAT 59.409 36.000 18.83 0.78 42.33 3.79
412 418 4.943093 TCATAATCTTTTGCACAGCTAGCA 59.057 37.500 18.83 8.79 40.85 3.49
413 419 5.490139 TCATAATCTTTTGCACAGCTAGC 57.510 39.130 6.62 6.62 0.00 3.42
417 423 9.770503 CATAGATATCATAATCTTTTGCACAGC 57.229 33.333 5.32 0.00 37.41 4.40
439 445 2.896801 GCATTCGCACGGGCCATAG 61.897 63.158 2.82 0.00 38.36 2.23
454 460 3.195610 TCACTAGTTCTGAATCCGTGCAT 59.804 43.478 0.00 0.00 0.00 3.96
462 468 7.123397 TGAGTTAGAGCATCACTAGTTCTGAAT 59.877 37.037 4.58 0.00 37.82 2.57
467 473 8.410141 AGTTATGAGTTAGAGCATCACTAGTTC 58.590 37.037 0.00 0.00 37.82 3.01
487 493 3.570125 TCAGGACCTCGCTATGAGTTATG 59.430 47.826 0.00 0.00 43.64 1.90
488 494 3.833732 TCAGGACCTCGCTATGAGTTAT 58.166 45.455 0.00 0.00 43.64 1.89
489 495 3.292492 TCAGGACCTCGCTATGAGTTA 57.708 47.619 0.00 0.00 43.64 2.24
490 496 2.145397 TCAGGACCTCGCTATGAGTT 57.855 50.000 0.00 0.00 43.64 3.01
491 497 2.145397 TTCAGGACCTCGCTATGAGT 57.855 50.000 0.00 0.00 43.64 3.41
492 498 2.801342 GCTTTCAGGACCTCGCTATGAG 60.801 54.545 0.00 0.00 44.83 2.90
493 499 1.137086 GCTTTCAGGACCTCGCTATGA 59.863 52.381 0.00 0.00 0.00 2.15
504 510 0.608130 TTGCTCTAGCGCTTTCAGGA 59.392 50.000 18.68 7.73 45.83 3.86
671 684 2.926200 CTCGTGTGCTTAATCTGTCCAG 59.074 50.000 0.00 0.00 0.00 3.86
707 720 4.856801 CAATCCGGCCGAGTGGGG 62.857 72.222 30.73 8.93 32.83 4.96
777 791 2.354343 TGGATGGCCACGAATGCA 59.646 55.556 8.16 0.00 39.92 3.96
831 865 1.339644 TATACGTGGGAAGGGTGGCC 61.340 60.000 0.00 0.00 0.00 5.36
911 965 3.114065 GACGTCTAAGTTTGCGGGATAG 58.886 50.000 8.70 0.00 0.00 2.08
924 983 1.065102 GAGGCTATGTGCGACGTCTAA 59.935 52.381 14.70 0.00 44.05 2.10
926 985 1.032657 AGAGGCTATGTGCGACGTCT 61.033 55.000 14.70 0.00 44.05 4.18
929 988 0.458543 AACAGAGGCTATGTGCGACG 60.459 55.000 16.52 0.00 44.05 5.12
930 989 1.002366 CAACAGAGGCTATGTGCGAC 58.998 55.000 16.52 0.00 44.05 5.19
943 1006 5.589452 GCTAGCTAGTAGTTACCTCAACAGA 59.411 44.000 21.62 0.00 39.81 3.41
984 1047 2.139118 GCCATTGATCTCTCGGTAAGC 58.861 52.381 0.00 0.00 0.00 3.09
986 1050 1.068588 CCGCCATTGATCTCTCGGTAA 59.931 52.381 0.00 0.00 32.93 2.85
990 1054 2.305853 CGCCGCCATTGATCTCTCG 61.306 63.158 0.00 0.00 0.00 4.04
991 1055 1.068083 TCGCCGCCATTGATCTCTC 59.932 57.895 0.00 0.00 0.00 3.20
1101 1168 1.831286 CGGGTAGTCGGCCTGGTAT 60.831 63.158 0.00 0.00 0.00 2.73
1202 1279 1.740025 GAGACGGCAAAGAAGAATGGG 59.260 52.381 0.00 0.00 0.00 4.00
1260 1350 4.573201 ACGTTTTTGCAAGCTAGTTACAGA 59.427 37.500 0.00 0.00 0.00 3.41
1284 1403 8.437575 GTTATTCCCTCCCTCTCACAATATAAA 58.562 37.037 0.00 0.00 0.00 1.40
1298 1417 2.101415 GCATTGCTTGTTATTCCCTCCC 59.899 50.000 0.16 0.00 0.00 4.30
1322 1485 4.574892 TCTGCGATTTGTCACCTGAAATA 58.425 39.130 0.00 0.00 0.00 1.40
1370 1534 0.041684 TGTCCTGCAGGATCTCCTCA 59.958 55.000 37.07 25.51 46.65 3.86
1406 1570 1.878522 CAGAGACGGCGCCATGTAC 60.879 63.158 28.98 14.02 0.00 2.90
1937 2101 3.173965 CTTTAGGAGGTGGAAGGTGAGA 58.826 50.000 0.00 0.00 0.00 3.27
1955 2119 1.000396 GAGGCCAGGCACATCCTTT 60.000 57.895 15.19 0.00 44.75 3.11
1970 2134 3.064545 GCTCGATGTTTTTGGAGATGAGG 59.935 47.826 0.00 0.00 0.00 3.86
1982 2146 4.760047 AGGGCGCGCTCGATGTTT 62.760 61.111 32.29 6.70 38.10 2.83
2001 2165 1.203994 CAATGGCTTGAAGGCTTCCTG 59.796 52.381 23.68 16.59 41.96 3.86
2006 2170 0.114954 TTCCCAATGGCTTGAAGGCT 59.885 50.000 19.72 2.75 41.96 4.58
2024 2188 3.543680 ACGGAGTTCCAATCATCGATT 57.456 42.857 0.00 0.00 37.78 3.34
2075 2239 1.747355 GCCTCAACCATGTCAAGGATG 59.253 52.381 0.00 0.00 0.00 3.51
2090 2254 1.059584 TCAGGTTGACCTTGGCCTCA 61.060 55.000 3.32 0.00 46.09 3.86
2102 2266 1.961793 TCCGTTCCTTGTTCAGGTTG 58.038 50.000 0.00 0.00 44.37 3.77
2228 2392 0.036388 TCATTCCCTCGCCAGTTGTC 60.036 55.000 0.00 0.00 0.00 3.18
2247 2411 1.004918 CGAAGAGAACGCCCCAGTT 60.005 57.895 0.00 0.00 36.99 3.16
2449 2641 2.819608 GCATAGCACAAAGGAAGGAACA 59.180 45.455 0.00 0.00 0.00 3.18
2450 2642 2.819608 TGCATAGCACAAAGGAAGGAAC 59.180 45.455 0.00 0.00 31.71 3.62
2460 2652 4.462132 ACAAACATGGTATGCATAGCACAA 59.538 37.500 34.19 17.04 43.04 3.33
2476 2670 4.214119 CACCTCGATCTCAACAACAAACAT 59.786 41.667 0.00 0.00 0.00 2.71
2536 2730 5.578727 GTCATAGTGACTGAGGTTTAGCAAG 59.421 44.000 0.00 0.00 43.73 4.01
2558 2752 5.671329 GCGTCAATTGAGACATAACCAAGTC 60.671 44.000 8.80 0.00 38.43 3.01
2577 2771 5.690997 AAGATCTCACGAATATAGCGTCA 57.309 39.130 0.00 0.00 40.44 4.35
2578 2772 6.600350 TGTAAGATCTCACGAATATAGCGTC 58.400 40.000 0.00 0.00 40.44 5.19
2580 2774 9.556030 TTAATGTAAGATCTCACGAATATAGCG 57.444 33.333 0.00 0.00 0.00 4.26
2690 2888 4.142004 GGGTGTGGTTATGTCTTAGTCGAT 60.142 45.833 0.00 0.00 0.00 3.59
2702 2900 5.074804 GGTTACTTTCAAGGGTGTGGTTAT 58.925 41.667 0.00 0.00 0.00 1.89
2790 2988 5.091910 GTTACTCAACGGTTTTCTTCTGG 57.908 43.478 0.00 0.00 0.00 3.86
2816 3014 8.747538 AAACTACTAAACTCAATCACTTTGGT 57.252 30.769 0.00 0.00 35.92 3.67
2893 3091 3.258372 GGTCCTGTGAGTGTATCAGACAA 59.742 47.826 0.00 0.00 40.66 3.18
2895 3093 2.159366 CGGTCCTGTGAGTGTATCAGAC 60.159 54.545 0.00 0.00 39.07 3.51
2896 3094 2.092323 CGGTCCTGTGAGTGTATCAGA 58.908 52.381 0.00 0.00 39.07 3.27
2897 3095 2.092323 TCGGTCCTGTGAGTGTATCAG 58.908 52.381 0.00 0.00 39.07 2.90
2898 3096 2.209690 TCGGTCCTGTGAGTGTATCA 57.790 50.000 0.00 0.00 34.79 2.15
2899 3097 3.056749 ACTTTCGGTCCTGTGAGTGTATC 60.057 47.826 0.00 0.00 0.00 2.24
2900 3098 2.897969 ACTTTCGGTCCTGTGAGTGTAT 59.102 45.455 0.00 0.00 0.00 2.29
2901 3099 2.035449 CACTTTCGGTCCTGTGAGTGTA 59.965 50.000 0.00 0.00 32.12 2.90
2903 3101 1.502231 CACTTTCGGTCCTGTGAGTG 58.498 55.000 0.00 0.00 32.72 3.51
2904 3102 0.249911 GCACTTTCGGTCCTGTGAGT 60.250 55.000 0.00 0.00 32.72 3.41
2905 3103 0.951040 GGCACTTTCGGTCCTGTGAG 60.951 60.000 0.00 0.00 32.72 3.51
2906 3104 1.070786 GGCACTTTCGGTCCTGTGA 59.929 57.895 0.00 0.00 32.72 3.58
2907 3105 1.966451 GGGCACTTTCGGTCCTGTG 60.966 63.158 0.00 0.00 0.00 3.66
2912 3110 2.124277 AATAAGGGGCACTTTCGGTC 57.876 50.000 7.60 0.00 40.64 4.79
2929 3127 2.237392 CCCGTCCTCCTCTCTTTGAAAT 59.763 50.000 0.00 0.00 0.00 2.17
2960 3158 6.152661 CCACTGTCTCTGGCCATTAAATTAAA 59.847 38.462 5.51 0.00 0.00 1.52
2981 3179 2.347490 CCTAACGCACCAGCCACT 59.653 61.111 0.00 0.00 37.52 4.00
2993 3191 2.093658 TCTCTCCCAATGAACGCCTAAC 60.094 50.000 0.00 0.00 0.00 2.34
3000 3198 3.496130 CACGCATATCTCTCCCAATGAAC 59.504 47.826 0.00 0.00 0.00 3.18
3005 3203 1.831106 ACACACGCATATCTCTCCCAA 59.169 47.619 0.00 0.00 0.00 4.12
3009 3207 1.137086 ACCCACACACGCATATCTCTC 59.863 52.381 0.00 0.00 0.00 3.20
3013 3211 2.201732 CTACACCCACACACGCATATC 58.798 52.381 0.00 0.00 0.00 1.63
3016 3214 0.320421 GACTACACCCACACACGCAT 60.320 55.000 0.00 0.00 0.00 4.73
3019 3217 3.119280 TCATATGACTACACCCACACACG 60.119 47.826 0.00 0.00 0.00 4.49
3030 3228 3.508012 AGAGGCCATCGTCATATGACTAC 59.492 47.826 28.51 15.12 42.66 2.73
3042 3240 2.614057 GGTGTTTTCATAGAGGCCATCG 59.386 50.000 5.01 0.00 0.00 3.84
3109 3308 8.450578 TCCATCAAATATCTCGCTGTTTTAAT 57.549 30.769 0.00 0.00 0.00 1.40
3110 3309 7.857734 TCCATCAAATATCTCGCTGTTTTAA 57.142 32.000 0.00 0.00 0.00 1.52
3137 3336 7.330700 GCTCGCAAGCTATATCTTATTCTTTCT 59.669 37.037 0.00 0.00 45.55 2.52
3167 3366 9.823647 TCATAGGCTCTTAATTCTTAAAGTGAG 57.176 33.333 0.00 0.00 0.00 3.51
3168 3367 9.601217 GTCATAGGCTCTTAATTCTTAAAGTGA 57.399 33.333 0.00 0.00 0.00 3.41
3169 3368 9.383519 TGTCATAGGCTCTTAATTCTTAAAGTG 57.616 33.333 0.00 0.00 0.00 3.16
3175 3374 6.156949 TGGACTGTCATAGGCTCTTAATTCTT 59.843 38.462 10.38 0.00 33.66 2.52
3176 3375 5.663106 TGGACTGTCATAGGCTCTTAATTCT 59.337 40.000 10.38 0.00 33.66 2.40
3177 3376 5.755861 GTGGACTGTCATAGGCTCTTAATTC 59.244 44.000 10.38 0.00 33.66 2.17
3178 3377 5.426833 AGTGGACTGTCATAGGCTCTTAATT 59.573 40.000 10.38 0.00 33.66 1.40
3179 3378 4.965532 AGTGGACTGTCATAGGCTCTTAAT 59.034 41.667 10.38 0.00 33.66 1.40
3180 3379 4.353777 AGTGGACTGTCATAGGCTCTTAA 58.646 43.478 10.38 0.00 33.66 1.85
3181 3380 3.982516 AGTGGACTGTCATAGGCTCTTA 58.017 45.455 10.38 0.00 33.66 2.10
3182 3381 2.826488 AGTGGACTGTCATAGGCTCTT 58.174 47.619 10.38 0.00 33.66 2.85
3183 3382 2.541233 AGTGGACTGTCATAGGCTCT 57.459 50.000 10.38 0.00 33.66 4.09
3184 3383 3.067461 CACTAGTGGACTGTCATAGGCTC 59.933 52.174 15.49 0.00 33.66 4.70
3188 3387 5.880887 TGTACTCACTAGTGGACTGTCATAG 59.119 44.000 22.48 11.32 36.36 2.23
3193 3392 5.652891 CCTATTGTACTCACTAGTGGACTGT 59.347 44.000 22.48 16.89 36.36 3.55
3220 3419 4.762289 AGCCGAATCCTAGACTTTTCAT 57.238 40.909 0.00 0.00 0.00 2.57
3223 3422 4.466726 AGTGTAGCCGAATCCTAGACTTTT 59.533 41.667 0.00 0.00 36.38 2.27
3232 3431 6.398918 ACATAATATCAGTGTAGCCGAATCC 58.601 40.000 0.00 0.00 0.00 3.01
3278 3477 7.554118 TGAGAGTTTTCAGTTCTTGAGAATGTT 59.446 33.333 0.00 0.00 37.07 2.71
3288 3487 7.056635 TCCAGATTTTGAGAGTTTTCAGTTCT 58.943 34.615 0.00 0.00 0.00 3.01
3294 3493 7.095899 GCAACATTCCAGATTTTGAGAGTTTTC 60.096 37.037 0.00 0.00 0.00 2.29
3306 3505 2.489329 CTCCGTTGCAACATTCCAGATT 59.511 45.455 28.01 0.00 0.00 2.40


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

AutoCloner maintained by Alex Coulton.