Multiple sequence alignment - TraesCS7B01G367500

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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 TraesCS7B01G367500 chr7B 100.000 2979 0 0 2669 5647 632177227 632174249 0.000000e+00 5502.0
1 TraesCS7B01G367500 chr7B 100.000 1457 0 0 965 2421 632178931 632177475 0.000000e+00 2691.0
2 TraesCS7B01G367500 chr7B 100.000 477 0 0 1 477 632179895 632179419 0.000000e+00 881.0
3 TraesCS7B01G367500 chr7B 94.600 463 22 3 1 462 130269062 130268602 0.000000e+00 713.0
4 TraesCS7B01G367500 chr7B 97.872 47 1 0 3014 3060 632176837 632176791 1.300000e-11 82.4
5 TraesCS7B01G367500 chr7B 97.872 47 1 0 3059 3105 632176882 632176836 1.300000e-11 82.4
6 TraesCS7B01G367500 chr7B 100.000 29 0 0 3032 3060 7367600 7367572 3.000000e-03 54.7
7 TraesCS7B01G367500 chr7D 94.879 2187 66 16 3105 5257 573435197 573433023 0.000000e+00 3376.0
8 TraesCS7B01G367500 chr7D 94.902 1432 54 11 968 2392 573437068 573435649 0.000000e+00 2222.0
9 TraesCS7B01G367500 chr7D 94.444 468 21 5 1 465 219836554 219837019 0.000000e+00 715.0
10 TraesCS7B01G367500 chr7D 93.909 394 24 0 5254 5647 573432916 573432523 3.770000e-166 595.0
11 TraesCS7B01G367500 chr7D 98.524 271 4 0 2790 3060 573435490 573435220 3.960000e-131 479.0
12 TraesCS7B01G367500 chr7D 82.196 337 46 8 5259 5592 595737362 595737037 1.550000e-70 278.0
13 TraesCS7B01G367500 chr7D 80.769 338 54 6 5254 5589 83461396 83461724 2.610000e-63 254.0
14 TraesCS7B01G367500 chr7D 79.882 338 53 9 5254 5587 447945833 447946159 3.400000e-57 233.0
15 TraesCS7B01G367500 chr7D 98.889 90 1 0 2705 2794 573435611 573435522 1.630000e-35 161.0
16 TraesCS7B01G367500 chr7D 100.000 47 0 0 3059 3105 573435266 573435220 2.800000e-13 87.9
17 TraesCS7B01G367500 chr7D 100.000 31 0 0 3075 3105 514658916 514658886 2.200000e-04 58.4
18 TraesCS7B01G367500 chr7D 100.000 28 0 0 3033 3060 314966847 314966820 1.000000e-02 52.8
19 TraesCS7B01G367500 chr7D 100.000 28 0 0 4209 4236 573434156 573434129 1.000000e-02 52.8
20 TraesCS7B01G367500 chr7A 94.635 1957 69 18 3059 5000 663380212 663378277 0.000000e+00 3000.0
21 TraesCS7B01G367500 chr7A 94.850 1437 56 9 968 2397 663382321 663380896 0.000000e+00 2228.0
22 TraesCS7B01G367500 chr7A 95.248 463 20 2 1 463 301639176 301639636 0.000000e+00 732.0
23 TraesCS7B01G367500 chr7A 90.489 368 6 3 2705 3043 663380550 663380183 5.160000e-125 459.0
24 TraesCS7B01G367500 chr7A 100.000 31 0 0 4206 4236 663379141 663379111 2.200000e-04 58.4
25 TraesCS7B01G367500 chr7A 97.059 34 0 1 3073 3105 82192114 82192147 7.900000e-04 56.5
26 TraesCS7B01G367500 chr4B 94.972 1452 65 6 3367 4813 354349361 354350809 0.000000e+00 2270.0
27 TraesCS7B01G367500 chr4B 93.317 793 40 5 1621 2408 354347661 354348445 0.000000e+00 1158.0
28 TraesCS7B01G367500 chr4B 93.740 655 33 3 970 1624 354341500 354342146 0.000000e+00 976.0
29 TraesCS7B01G367500 chr4B 95.248 463 18 4 1 462 385954570 385954111 0.000000e+00 730.0
30 TraesCS7B01G367500 chr4B 88.952 353 20 10 2703 3036 354348771 354349123 8.750000e-113 418.0
31 TraesCS7B01G367500 chr4B 95.395 152 7 0 3131 3282 354349117 354349268 5.650000e-60 243.0
32 TraesCS7B01G367500 chr4B 84.699 183 12 6 4970 5151 354352779 354352946 9.730000e-38 169.0
33 TraesCS7B01G367500 chr4D 93.583 1387 75 9 970 2356 182070733 182069361 0.000000e+00 2056.0
34 TraesCS7B01G367500 chr4D 95.902 1098 37 6 3406 4499 182068513 182067420 0.000000e+00 1772.0
35 TraesCS7B01G367500 chr4D 95.341 279 12 1 3131 3408 182068974 182068696 5.190000e-120 442.0
36 TraesCS7B01G367500 chr4D 89.235 353 19 10 2703 3036 182069320 182068968 1.880000e-114 424.0
37 TraesCS7B01G367500 chr4D 90.875 263 21 2 4495 4755 182067341 182067080 3.240000e-92 350.0
38 TraesCS7B01G367500 chr4D 86.154 195 12 2 4966 5160 182065984 182065805 4.460000e-46 196.0
39 TraesCS7B01G367500 chr4D 100.000 30 0 0 3077 3106 261560009 261560038 7.900000e-04 56.5
40 TraesCS7B01G367500 chr4A 92.757 1422 83 6 965 2378 369539707 369541116 0.000000e+00 2037.0
41 TraesCS7B01G367500 chr4A 95.528 872 30 6 3131 3998 369541882 369542748 0.000000e+00 1386.0
42 TraesCS7B01G367500 chr4A 94.352 602 27 4 3899 4497 369542746 369543343 0.000000e+00 917.0
43 TraesCS7B01G367500 chr4A 90.582 361 31 2 4495 4852 369543502 369543862 5.120000e-130 475.0
44 TraesCS7B01G367500 chr4A 87.749 351 24 8 2705 3036 369541538 369541888 5.300000e-105 392.0
45 TraesCS7B01G367500 chr4A 81.953 338 44 11 5259 5592 557199398 557199074 2.590000e-68 270.0
46 TraesCS7B01G367500 chr4A 96.970 33 1 0 2670 2702 369541490 369541522 7.900000e-04 56.5
47 TraesCS7B01G367500 chr6A 95.896 463 19 0 1 463 105536741 105536279 0.000000e+00 750.0
48 TraesCS7B01G367500 chr6A 95.248 463 20 2 1 462 237919292 237919753 0.000000e+00 732.0
49 TraesCS7B01G367500 chr6A 100.000 31 0 0 3030 3060 287303969 287303999 2.200000e-04 58.4
50 TraesCS7B01G367500 chr6A 94.595 37 1 1 3031 3067 16074970 16075005 7.900000e-04 56.5
51 TraesCS7B01G367500 chr3A 95.680 463 18 2 1 462 209407683 209408144 0.000000e+00 743.0
52 TraesCS7B01G367500 chr3A 80.000 235 35 7 5260 5492 673256282 673256058 4.530000e-36 163.0
53 TraesCS7B01G367500 chr3A 85.714 63 6 2 4243 4302 57545753 57545815 4.720000e-06 63.9
54 TraesCS7B01G367500 chr3B 95.248 463 21 1 1 463 690854225 690854686 0.000000e+00 732.0
55 TraesCS7B01G367500 chr3B 81.250 336 50 9 5260 5592 113536350 113536025 5.610000e-65 259.0
56 TraesCS7B01G367500 chr3B 80.712 337 45 11 5258 5589 492223432 492223753 1.570000e-60 244.0
57 TraesCS7B01G367500 chr2B 95.248 463 19 3 1 462 679154996 679155456 0.000000e+00 730.0
58 TraesCS7B01G367500 chr2B 81.362 279 43 4 5310 5587 20359925 20359655 9.530000e-53 219.0
59 TraesCS7B01G367500 chr5D 84.615 338 39 7 5254 5589 273482514 273482188 1.960000e-84 324.0
60 TraesCS7B01G367500 chr5D 79.403 335 58 5 5260 5592 458196313 458195988 5.690000e-55 226.0
61 TraesCS7B01G367500 chr5B 83.036 336 46 7 5259 5592 308996441 308996115 1.540000e-75 294.0
62 TraesCS7B01G367500 chr5B 100.000 28 0 0 3078 3105 364132773 364132746 1.000000e-02 52.8
63 TraesCS7B01G367500 chr6D 84.190 253 32 6 4318 4565 254906117 254906366 7.310000e-59 239.0
64 TraesCS7B01G367500 chr6D 76.667 330 55 7 5259 5587 126514860 126515168 4.530000e-36 163.0
65 TraesCS7B01G367500 chr6D 100.000 31 0 0 3075 3105 168220631 168220601 2.200000e-04 58.4
66 TraesCS7B01G367500 chr1A 80.120 332 54 6 5260 5589 186209523 186209844 2.630000e-58 237.0
67 TraesCS7B01G367500 chr2D 79.456 331 47 16 5259 5580 586623167 586623485 1.230000e-51 215.0
68 TraesCS7B01G367500 chr2D 80.156 257 36 8 5259 5514 36437238 36437480 1.620000e-40 178.0
69 TraesCS7B01G367500 chr5A 97.143 35 0 1 3072 3105 645274896 645274862 2.200000e-04 58.4
70 TraesCS7B01G367500 chr6B 96.970 33 0 1 3029 3060 301608790 301608758 3.000000e-03 54.7
71 TraesCS7B01G367500 chr1D 100.000 28 0 0 3078 3105 476562497 476562470 1.000000e-02 52.8


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 TraesCS7B01G367500 chr7B 632174249 632179895 5646 True 1847.760000 5502 99.148800 1 5647 5 chr7B.!!$R3 5646
1 TraesCS7B01G367500 chr7D 573432523 573437068 4545 True 996.242857 3376 97.300429 968 5647 7 chr7D.!!$R4 4679
2 TraesCS7B01G367500 chr7A 663378277 663382321 4044 True 1436.350000 3000 94.993500 968 5000 4 chr7A.!!$R1 4032
3 TraesCS7B01G367500 chr4B 354341500 354342146 646 False 976.000000 976 93.740000 970 1624 1 chr4B.!!$F1 654
4 TraesCS7B01G367500 chr4B 354347661 354352946 5285 False 851.600000 2270 91.467000 1621 5151 5 chr4B.!!$F2 3530
5 TraesCS7B01G367500 chr4D 182065805 182070733 4928 True 873.333333 2056 91.848333 970 5160 6 chr4D.!!$R1 4190
6 TraesCS7B01G367500 chr4A 369539707 369543862 4155 False 877.250000 2037 92.989667 965 4852 6 chr4A.!!$F1 3887

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
388 389 0.033504 ATAGTAATCGTGCCCTGGCG 59.966 55.000 3.32 0.0 45.51 5.69 F
1086 1087 0.037303 CACACACCATCAAGCCCTCT 59.963 55.000 0.00 0.0 0.00 3.69 F
1594 1601 0.108585 AGTGTTACCCTGTGGCTGTG 59.891 55.000 0.00 0.0 33.59 3.66 F
1595 1602 0.889186 GTGTTACCCTGTGGCTGTGG 60.889 60.000 0.00 0.0 33.59 4.17 F
3092 3296 1.345415 TGTTTGTACTCCCTCCGTTCC 59.655 52.381 0.00 0.0 0.00 3.62 F
3094 3298 1.946984 TTGTACTCCCTCCGTTCCAT 58.053 50.000 0.00 0.0 0.00 3.41 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1883 1902 0.462047 GAACAGATACAGGTGCCCCG 60.462 60.000 0.0 0.0 35.12 5.73 R
2127 2147 0.740737 GAATTGCAGAACCATCGGGG 59.259 55.000 0.0 0.0 44.81 5.73 R
3573 3974 0.462047 CGGAGGCAACCCATCAGTAC 60.462 60.000 0.0 0.0 37.17 2.73 R
3924 4326 3.652274 ACCAGGCAATTTCGTTCATTTG 58.348 40.909 0.0 0.0 0.00 2.32 R
4058 4561 1.197721 ACTGAAAAGGCTGAAATCGCG 59.802 47.619 0.0 0.0 0.00 5.87 R
5138 7850 1.729586 AGGGGCTATTAGATTCGGCA 58.270 50.000 0.0 0.0 0.00 5.69 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
21 22 4.415783 GGCCAAATGGGTCGTCTT 57.584 55.556 0.00 0.00 39.65 3.01
22 23 2.653557 GGCCAAATGGGTCGTCTTT 58.346 52.632 0.00 0.00 39.65 2.52
23 24 0.966179 GGCCAAATGGGTCGTCTTTT 59.034 50.000 0.00 0.00 39.65 2.27
24 25 1.067846 GGCCAAATGGGTCGTCTTTTC 60.068 52.381 0.00 0.00 39.65 2.29
25 26 1.886542 GCCAAATGGGTCGTCTTTTCT 59.113 47.619 0.90 0.00 39.65 2.52
26 27 2.351738 GCCAAATGGGTCGTCTTTTCTG 60.352 50.000 0.90 0.00 39.65 3.02
27 28 2.228822 CCAAATGGGTCGTCTTTTCTGG 59.771 50.000 0.00 0.00 0.00 3.86
28 29 2.200373 AATGGGTCGTCTTTTCTGGG 57.800 50.000 0.00 0.00 0.00 4.45
29 30 0.322546 ATGGGTCGTCTTTTCTGGGC 60.323 55.000 0.00 0.00 0.00 5.36
30 31 1.674651 GGGTCGTCTTTTCTGGGCC 60.675 63.158 0.00 0.00 0.00 5.80
31 32 2.033194 GGTCGTCTTTTCTGGGCCG 61.033 63.158 0.00 0.00 0.00 6.13
32 33 2.033194 GTCGTCTTTTCTGGGCCGG 61.033 63.158 5.83 5.83 0.00 6.13
33 34 3.431725 CGTCTTTTCTGGGCCGGC 61.432 66.667 21.18 21.18 0.00 6.13
34 35 3.062466 GTCTTTTCTGGGCCGGCC 61.062 66.667 38.57 38.57 0.00 6.13
175 176 2.203153 GGCACGGCCCGATTACAT 60.203 61.111 11.71 0.00 44.06 2.29
176 177 1.822186 GGCACGGCCCGATTACATT 60.822 57.895 11.71 0.00 44.06 2.71
177 178 1.381165 GGCACGGCCCGATTACATTT 61.381 55.000 11.71 0.00 44.06 2.32
178 179 0.454196 GCACGGCCCGATTACATTTT 59.546 50.000 11.71 0.00 0.00 1.82
179 180 1.135228 GCACGGCCCGATTACATTTTT 60.135 47.619 11.71 0.00 0.00 1.94
230 231 9.830186 TGGCCCAATATATAAAAATAGGCTAAA 57.170 29.630 0.00 0.00 37.98 1.85
256 257 4.003519 GCTTAGTGCGTCAAATAACAGG 57.996 45.455 0.00 0.00 0.00 4.00
257 258 3.727970 GCTTAGTGCGTCAAATAACAGGC 60.728 47.826 0.00 0.00 0.00 4.85
258 259 2.185004 AGTGCGTCAAATAACAGGCT 57.815 45.000 0.00 0.00 0.00 4.58
259 260 3.328382 AGTGCGTCAAATAACAGGCTA 57.672 42.857 0.00 0.00 0.00 3.93
260 261 3.670625 AGTGCGTCAAATAACAGGCTAA 58.329 40.909 0.00 0.00 0.00 3.09
261 262 4.069304 AGTGCGTCAAATAACAGGCTAAA 58.931 39.130 0.00 0.00 0.00 1.85
262 263 4.517453 AGTGCGTCAAATAACAGGCTAAAA 59.483 37.500 0.00 0.00 0.00 1.52
263 264 5.009210 AGTGCGTCAAATAACAGGCTAAAAA 59.991 36.000 0.00 0.00 0.00 1.94
264 265 5.861787 GTGCGTCAAATAACAGGCTAAAAAT 59.138 36.000 0.00 0.00 0.00 1.82
265 266 7.024768 GTGCGTCAAATAACAGGCTAAAAATA 58.975 34.615 0.00 0.00 0.00 1.40
266 267 7.700656 GTGCGTCAAATAACAGGCTAAAAATAT 59.299 33.333 0.00 0.00 0.00 1.28
267 268 7.700234 TGCGTCAAATAACAGGCTAAAAATATG 59.300 33.333 0.00 0.00 0.00 1.78
268 269 7.305993 GCGTCAAATAACAGGCTAAAAATATGC 60.306 37.037 0.00 0.00 0.00 3.14
269 270 7.097047 CGTCAAATAACAGGCTAAAAATATGCG 60.097 37.037 0.00 0.00 0.00 4.73
270 271 7.167468 GTCAAATAACAGGCTAAAAATATGCGG 59.833 37.037 0.00 0.00 0.00 5.69
271 272 3.436700 AACAGGCTAAAAATATGCGGC 57.563 42.857 0.00 0.00 0.00 6.53
272 273 1.681264 ACAGGCTAAAAATATGCGGCC 59.319 47.619 0.00 0.00 39.82 6.13
273 274 1.000274 CAGGCTAAAAATATGCGGCCC 60.000 52.381 0.00 0.00 40.32 5.80
274 275 1.036707 GGCTAAAAATATGCGGCCCA 58.963 50.000 0.00 0.00 34.19 5.36
275 276 1.269569 GGCTAAAAATATGCGGCCCAC 60.270 52.381 0.00 0.00 34.19 4.61
276 277 1.269569 GCTAAAAATATGCGGCCCACC 60.270 52.381 0.00 0.00 0.00 4.61
294 295 2.559330 GTGCTAAACGGGCCAACG 59.441 61.111 4.39 1.48 40.31 4.10
308 309 4.622650 AACGTGCCGGCCCGTTTA 62.623 61.111 38.23 11.19 44.16 2.01
311 312 2.265424 GTGCCGGCCCGTTTACTA 59.735 61.111 26.77 0.00 0.00 1.82
312 313 1.375780 GTGCCGGCCCGTTTACTAA 60.376 57.895 26.77 0.00 0.00 2.24
313 314 1.375780 TGCCGGCCCGTTTACTAAC 60.376 57.895 26.77 0.00 0.00 2.34
314 315 2.108514 GCCGGCCCGTTTACTAACC 61.109 63.158 18.11 0.00 0.00 2.85
315 316 1.810853 CCGGCCCGTTTACTAACCG 60.811 63.158 0.85 0.00 40.30 4.44
316 317 1.810853 CGGCCCGTTTACTAACCGG 60.811 63.158 0.00 0.00 37.04 5.28
317 318 1.450134 GGCCCGTTTACTAACCGGG 60.450 63.158 17.40 17.40 44.21 5.73
318 319 4.206958 CCCGTTTACTAACCGGGC 57.793 61.111 10.59 0.00 39.48 6.13
319 320 1.450134 CCCGTTTACTAACCGGGCC 60.450 63.158 10.59 0.00 39.48 5.80
320 321 1.810853 CCGTTTACTAACCGGGCCG 60.811 63.158 21.46 21.46 0.00 6.13
321 322 1.079888 CGTTTACTAACCGGGCCGT 60.080 57.895 26.32 10.07 0.00 5.68
322 323 1.353609 CGTTTACTAACCGGGCCGTG 61.354 60.000 26.32 18.46 0.00 4.94
323 324 1.375780 TTTACTAACCGGGCCGTGC 60.376 57.895 26.32 0.00 0.00 5.34
371 372 2.497293 CACAGCACGGCCCGTATA 59.503 61.111 9.25 0.00 38.32 1.47
372 373 1.591594 CACAGCACGGCCCGTATAG 60.592 63.158 9.25 3.71 38.32 1.31
373 374 2.056223 ACAGCACGGCCCGTATAGT 61.056 57.895 9.25 4.46 38.32 2.12
374 375 0.752743 ACAGCACGGCCCGTATAGTA 60.753 55.000 9.25 0.00 38.32 1.82
375 376 0.386476 CAGCACGGCCCGTATAGTAA 59.614 55.000 9.25 0.00 38.32 2.24
376 377 1.000506 CAGCACGGCCCGTATAGTAAT 59.999 52.381 9.25 0.00 38.32 1.89
377 378 1.271656 AGCACGGCCCGTATAGTAATC 59.728 52.381 9.25 0.00 38.32 1.75
378 379 1.973138 CACGGCCCGTATAGTAATCG 58.027 55.000 9.25 0.00 38.32 3.34
379 380 1.267806 CACGGCCCGTATAGTAATCGT 59.732 52.381 9.25 0.00 38.32 3.73
380 381 1.267806 ACGGCCCGTATAGTAATCGTG 59.732 52.381 7.20 0.00 38.73 4.35
381 382 1.706443 GGCCCGTATAGTAATCGTGC 58.294 55.000 0.00 0.00 0.00 5.34
382 383 1.670967 GGCCCGTATAGTAATCGTGCC 60.671 57.143 7.70 7.70 40.23 5.01
383 384 1.670967 GCCCGTATAGTAATCGTGCCC 60.671 57.143 0.00 0.00 0.00 5.36
384 385 1.891150 CCCGTATAGTAATCGTGCCCT 59.109 52.381 0.00 0.00 0.00 5.19
385 386 2.352421 CCCGTATAGTAATCGTGCCCTG 60.352 54.545 0.00 0.00 0.00 4.45
386 387 2.352421 CCGTATAGTAATCGTGCCCTGG 60.352 54.545 0.00 0.00 0.00 4.45
387 388 2.685100 GTATAGTAATCGTGCCCTGGC 58.315 52.381 0.00 0.00 42.35 4.85
388 389 0.033504 ATAGTAATCGTGCCCTGGCG 59.966 55.000 3.32 0.00 45.51 5.69
389 390 2.023414 TAGTAATCGTGCCCTGGCGG 62.023 60.000 3.32 0.00 45.51 6.13
415 416 2.270850 GGGCCAGGCACGATTACA 59.729 61.111 15.19 0.00 0.00 2.41
416 417 1.377987 GGGCCAGGCACGATTACAA 60.378 57.895 15.19 0.00 0.00 2.41
417 418 0.751643 GGGCCAGGCACGATTACAAT 60.752 55.000 15.19 0.00 0.00 2.71
418 419 0.381801 GGCCAGGCACGATTACAATG 59.618 55.000 15.19 0.00 0.00 2.82
419 420 0.381801 GCCAGGCACGATTACAATGG 59.618 55.000 6.55 0.00 0.00 3.16
420 421 1.024271 CCAGGCACGATTACAATGGG 58.976 55.000 0.00 0.00 0.00 4.00
421 422 0.381801 CAGGCACGATTACAATGGGC 59.618 55.000 0.00 0.00 0.00 5.36
422 423 0.751643 AGGCACGATTACAATGGGCC 60.752 55.000 0.00 0.00 40.18 5.80
423 424 1.355210 GCACGATTACAATGGGCCG 59.645 57.895 0.00 0.00 0.00 6.13
424 425 2.021722 CACGATTACAATGGGCCGG 58.978 57.895 0.00 0.00 0.00 6.13
425 426 1.153046 ACGATTACAATGGGCCGGG 60.153 57.895 2.18 0.00 0.00 5.73
426 427 2.551912 CGATTACAATGGGCCGGGC 61.552 63.158 22.00 22.00 0.00 6.13
462 463 3.918544 CCCGTTTGGCCAGGTATG 58.081 61.111 5.11 0.95 0.00 2.39
463 464 2.414785 CCCGTTTGGCCAGGTATGC 61.415 63.158 5.11 0.00 0.00 3.14
464 465 1.378514 CCGTTTGGCCAGGTATGCT 60.379 57.895 5.11 0.00 0.00 3.79
465 466 0.965363 CCGTTTGGCCAGGTATGCTT 60.965 55.000 5.11 0.00 0.00 3.91
466 467 0.171007 CGTTTGGCCAGGTATGCTTG 59.829 55.000 5.11 0.00 0.00 4.01
467 468 0.532115 GTTTGGCCAGGTATGCTTGG 59.468 55.000 5.11 7.64 43.91 3.61
468 469 0.114168 TTTGGCCAGGTATGCTTGGT 59.886 50.000 13.42 0.00 43.10 3.67
469 470 0.114168 TTGGCCAGGTATGCTTGGTT 59.886 50.000 13.42 0.00 43.10 3.67
470 471 0.611618 TGGCCAGGTATGCTTGGTTG 60.612 55.000 13.42 0.00 43.10 3.77
471 472 0.611896 GGCCAGGTATGCTTGGTTGT 60.612 55.000 13.42 0.00 43.10 3.32
472 473 1.256812 GCCAGGTATGCTTGGTTGTT 58.743 50.000 13.42 0.00 43.10 2.83
473 474 1.202348 GCCAGGTATGCTTGGTTGTTC 59.798 52.381 13.42 0.00 43.10 3.18
474 475 1.818674 CCAGGTATGCTTGGTTGTTCC 59.181 52.381 3.61 0.00 37.12 3.62
475 476 1.818674 CAGGTATGCTTGGTTGTTCCC 59.181 52.381 0.00 0.00 34.77 3.97
476 477 1.427368 AGGTATGCTTGGTTGTTCCCA 59.573 47.619 0.00 0.00 34.77 4.37
1073 1074 3.044305 GCTCCCACTCGCACACAC 61.044 66.667 0.00 0.00 0.00 3.82
1086 1087 0.037303 CACACACCATCAAGCCCTCT 59.963 55.000 0.00 0.00 0.00 3.69
1336 1340 1.330234 GGATCTCGGGGGAGACTTAC 58.670 60.000 0.00 0.00 33.58 2.34
1563 1570 8.407832 TGATTAGCTCAAAATGTCCATAATGTG 58.592 33.333 0.00 0.00 0.00 3.21
1590 1597 3.412237 TCTTTAGTGTTACCCTGTGGC 57.588 47.619 0.00 0.00 33.59 5.01
1591 1598 2.976882 TCTTTAGTGTTACCCTGTGGCT 59.023 45.455 0.00 0.00 33.59 4.75
1592 1599 2.851263 TTAGTGTTACCCTGTGGCTG 57.149 50.000 0.00 0.00 33.59 4.85
1593 1600 1.724545 TAGTGTTACCCTGTGGCTGT 58.275 50.000 0.00 0.00 33.59 4.40
1594 1601 0.108585 AGTGTTACCCTGTGGCTGTG 59.891 55.000 0.00 0.00 33.59 3.66
1595 1602 0.889186 GTGTTACCCTGTGGCTGTGG 60.889 60.000 0.00 0.00 33.59 4.17
1660 1677 3.700038 AGAATACTTAGGTGAGTCCGGTG 59.300 47.826 0.00 0.00 41.99 4.94
1792 1809 8.267894 ACTTCTAGTAACATACAATGATGCCTT 58.732 33.333 0.00 0.00 0.00 4.35
1824 1841 4.319766 CCCATAATATGCTTGAACTGTCGC 60.320 45.833 0.00 0.00 0.00 5.19
1880 1899 9.413734 AGCTTATTTCCTGATTGTAGCTAAAAT 57.586 29.630 8.99 8.99 36.08 1.82
1981 2001 1.474077 GAGCATAACTGGGCTTGTTGG 59.526 52.381 6.06 1.15 41.22 3.77
2127 2147 9.118236 GACTGATTTAAGCACAATTTAAGTCAC 57.882 33.333 0.00 0.00 34.13 3.67
2211 2231 4.367450 GAATCACCAGAAGGAGAAGATCG 58.633 47.826 0.00 0.00 38.05 3.69
2229 2249 6.412362 AGATCGACATAGCCTAGTTTTGAT 57.588 37.500 0.00 0.00 0.00 2.57
2306 2326 2.704572 CATTCAGTGGAGAGGGTTCAC 58.295 52.381 0.00 0.00 0.00 3.18
2408 2433 2.095372 GGCGCCAACTATGTTTGTAGTC 59.905 50.000 24.80 0.00 33.92 2.59
2409 2434 2.739913 GCGCCAACTATGTTTGTAGTCA 59.260 45.455 0.00 0.00 33.92 3.41
2410 2435 3.187637 GCGCCAACTATGTTTGTAGTCAA 59.812 43.478 0.00 0.00 33.92 3.18
2411 2436 4.669197 GCGCCAACTATGTTTGTAGTCAAG 60.669 45.833 0.00 0.00 33.92 3.02
2412 2437 4.451096 CGCCAACTATGTTTGTAGTCAAGT 59.549 41.667 0.00 0.00 33.92 3.16
2413 2438 5.389516 CGCCAACTATGTTTGTAGTCAAGTC 60.390 44.000 0.00 0.00 33.92 3.01
2414 2439 5.389516 GCCAACTATGTTTGTAGTCAAGTCG 60.390 44.000 0.00 0.00 33.92 4.18
2415 2440 5.694910 CCAACTATGTTTGTAGTCAAGTCGT 59.305 40.000 0.00 0.00 33.92 4.34
2416 2441 6.202188 CCAACTATGTTTGTAGTCAAGTCGTT 59.798 38.462 0.00 0.00 33.92 3.85
2417 2442 7.383029 CCAACTATGTTTGTAGTCAAGTCGTTA 59.617 37.037 0.00 0.00 33.92 3.18
2418 2443 8.425491 CAACTATGTTTGTAGTCAAGTCGTTAG 58.575 37.037 0.00 0.00 33.92 2.34
2419 2444 5.840940 ATGTTTGTAGTCAAGTCGTTAGC 57.159 39.130 0.00 0.00 34.88 3.09
2420 2445 4.053295 TGTTTGTAGTCAAGTCGTTAGCC 58.947 43.478 0.00 0.00 34.88 3.93
2805 2925 5.627499 CAATGTACCATTGCACACTAACT 57.373 39.130 4.20 0.00 0.00 2.24
2806 2926 6.012658 CAATGTACCATTGCACACTAACTT 57.987 37.500 4.20 0.00 0.00 2.66
2807 2927 5.880054 ATGTACCATTGCACACTAACTTC 57.120 39.130 0.00 0.00 0.00 3.01
2808 2928 4.968259 TGTACCATTGCACACTAACTTCT 58.032 39.130 0.00 0.00 0.00 2.85
2812 2932 5.621193 ACCATTGCACACTAACTTCTAACT 58.379 37.500 0.00 0.00 0.00 2.24
2813 2933 6.062095 ACCATTGCACACTAACTTCTAACTT 58.938 36.000 0.00 0.00 0.00 2.66
2814 2934 7.221450 ACCATTGCACACTAACTTCTAACTTA 58.779 34.615 0.00 0.00 0.00 2.24
2815 2935 7.717875 ACCATTGCACACTAACTTCTAACTTAA 59.282 33.333 0.00 0.00 0.00 1.85
3043 3247 2.038557 GCTCTTGTTTGTACTCCCTCCA 59.961 50.000 0.00 0.00 0.00 3.86
3060 3264 5.073144 TCCCTCCATTCCATATTAGTTGTCC 59.927 44.000 0.00 0.00 0.00 4.02
3061 3265 5.316987 CCTCCATTCCATATTAGTTGTCCC 58.683 45.833 0.00 0.00 0.00 4.46
3062 3266 5.163099 CCTCCATTCCATATTAGTTGTCCCA 60.163 44.000 0.00 0.00 0.00 4.37
3063 3267 6.467775 CCTCCATTCCATATTAGTTGTCCCAT 60.468 42.308 0.00 0.00 0.00 4.00
3064 3268 6.306199 TCCATTCCATATTAGTTGTCCCATG 58.694 40.000 0.00 0.00 0.00 3.66
3065 3269 6.102468 TCCATTCCATATTAGTTGTCCCATGA 59.898 38.462 0.00 0.00 0.00 3.07
3066 3270 6.950041 CCATTCCATATTAGTTGTCCCATGAT 59.050 38.462 0.00 0.00 0.00 2.45
3067 3271 7.094075 CCATTCCATATTAGTTGTCCCATGATG 60.094 40.741 0.00 0.00 0.00 3.07
3069 3273 5.073554 TCCATATTAGTTGTCCCATGATGCT 59.926 40.000 0.00 0.00 0.00 3.79
3070 3274 5.413833 CCATATTAGTTGTCCCATGATGCTC 59.586 44.000 0.00 0.00 0.00 4.26
3071 3275 4.785346 ATTAGTTGTCCCATGATGCTCT 57.215 40.909 0.00 0.00 0.00 4.09
3073 3277 2.719739 AGTTGTCCCATGATGCTCTTG 58.280 47.619 0.00 0.00 0.00 3.02
3075 3279 2.821969 GTTGTCCCATGATGCTCTTGTT 59.178 45.455 0.00 0.00 0.00 2.83
3076 3280 3.159213 TGTCCCATGATGCTCTTGTTT 57.841 42.857 0.00 0.00 0.00 2.83
3078 3282 2.821969 GTCCCATGATGCTCTTGTTTGT 59.178 45.455 0.00 0.00 0.00 2.83
3079 3283 4.009675 GTCCCATGATGCTCTTGTTTGTA 58.990 43.478 0.00 0.00 0.00 2.41
3080 3284 4.009675 TCCCATGATGCTCTTGTTTGTAC 58.990 43.478 0.00 0.00 0.00 2.90
3081 3285 4.012374 CCCATGATGCTCTTGTTTGTACT 58.988 43.478 0.00 0.00 0.00 2.73
3083 3287 4.095483 CCATGATGCTCTTGTTTGTACTCC 59.905 45.833 0.00 0.00 0.00 3.85
3084 3288 3.674997 TGATGCTCTTGTTTGTACTCCC 58.325 45.455 0.00 0.00 0.00 4.30
3085 3289 3.327757 TGATGCTCTTGTTTGTACTCCCT 59.672 43.478 0.00 0.00 0.00 4.20
3086 3290 3.402628 TGCTCTTGTTTGTACTCCCTC 57.597 47.619 0.00 0.00 0.00 4.30
3087 3291 2.038557 TGCTCTTGTTTGTACTCCCTCC 59.961 50.000 0.00 0.00 0.00 4.30
3088 3292 2.931320 GCTCTTGTTTGTACTCCCTCCG 60.931 54.545 0.00 0.00 0.00 4.63
3089 3293 2.299297 CTCTTGTTTGTACTCCCTCCGT 59.701 50.000 0.00 0.00 0.00 4.69
3090 3294 2.701951 TCTTGTTTGTACTCCCTCCGTT 59.298 45.455 0.00 0.00 0.00 4.44
3091 3295 2.825861 TGTTTGTACTCCCTCCGTTC 57.174 50.000 0.00 0.00 0.00 3.95
3092 3296 1.345415 TGTTTGTACTCCCTCCGTTCC 59.655 52.381 0.00 0.00 0.00 3.62
3093 3297 1.345415 GTTTGTACTCCCTCCGTTCCA 59.655 52.381 0.00 0.00 0.00 3.53
3094 3298 1.946984 TTGTACTCCCTCCGTTCCAT 58.053 50.000 0.00 0.00 0.00 3.41
3095 3299 2.832643 TGTACTCCCTCCGTTCCATA 57.167 50.000 0.00 0.00 0.00 2.74
3096 3300 3.323774 TGTACTCCCTCCGTTCCATAT 57.676 47.619 0.00 0.00 0.00 1.78
3097 3301 3.649843 TGTACTCCCTCCGTTCCATATT 58.350 45.455 0.00 0.00 0.00 1.28
3098 3302 4.806892 TGTACTCCCTCCGTTCCATATTA 58.193 43.478 0.00 0.00 0.00 0.98
3099 3303 4.831155 TGTACTCCCTCCGTTCCATATTAG 59.169 45.833 0.00 0.00 0.00 1.73
3100 3304 3.924922 ACTCCCTCCGTTCCATATTAGT 58.075 45.455 0.00 0.00 0.00 2.24
3101 3305 4.296056 ACTCCCTCCGTTCCATATTAGTT 58.704 43.478 0.00 0.00 0.00 2.24
3102 3306 4.101119 ACTCCCTCCGTTCCATATTAGTTG 59.899 45.833 0.00 0.00 0.00 3.16
3103 3307 4.035112 TCCCTCCGTTCCATATTAGTTGT 58.965 43.478 0.00 0.00 0.00 3.32
3104 3308 4.100498 TCCCTCCGTTCCATATTAGTTGTC 59.900 45.833 0.00 0.00 0.00 3.18
3349 3554 7.944554 AGCCAATAAGTTATATGGTTGTGCTAT 59.055 33.333 17.83 0.00 35.34 2.97
3902 4304 8.469200 TGATTTGAATTCACCCTGTTATGAATC 58.531 33.333 7.89 10.72 43.21 2.52
3934 4437 7.780008 TTGAAGTTCTCTTACAAATGAACGA 57.220 32.000 4.17 0.00 42.29 3.85
4058 4561 5.694910 TGGATCAAAGAAAGTAACTCGTGAC 59.305 40.000 0.00 0.00 0.00 3.67
4070 4573 2.092291 TCGTGACGCGATTTCAGCC 61.092 57.895 15.93 0.00 45.68 4.85
4284 4801 6.414732 TCTTGGCATTGTTACTACATTAGCT 58.585 36.000 0.00 0.00 33.44 3.32
4361 4878 6.153851 TGAATTCCACAAATGCAATCTCTCAT 59.846 34.615 2.27 0.00 29.29 2.90
4362 4879 5.988310 TTCCACAAATGCAATCTCTCATT 57.012 34.783 0.00 0.00 34.66 2.57
4363 4880 5.319140 TCCACAAATGCAATCTCTCATTG 57.681 39.130 0.00 0.00 33.61 2.82
4374 4891 5.174398 GCAATCTCTCATTGTTGTTGTTGTG 59.826 40.000 0.00 0.00 0.00 3.33
4534 5213 4.513442 AGTATTCTGAAAACGGCTGCATA 58.487 39.130 0.50 0.00 0.00 3.14
4594 5273 6.002062 AGCTATTATACTCGCAATTTTGGC 57.998 37.500 0.00 0.00 0.00 4.52
4686 5365 6.365520 TCTACTGATATCTCACTGCTTACCA 58.634 40.000 3.98 0.00 0.00 3.25
4730 5413 7.778083 ACTGGAGATAAATGTTGTATCGTGTA 58.222 34.615 0.00 0.00 33.89 2.90
4754 5605 7.326968 AGGAGCTAGAGCAATTTTTGTATTC 57.673 36.000 4.01 0.00 45.16 1.75
4760 5611 6.029346 AGAGCAATTTTTGTATTCAGGTGG 57.971 37.500 0.00 0.00 0.00 4.61
4763 5614 6.825610 AGCAATTTTTGTATTCAGGTGGAAA 58.174 32.000 0.00 0.00 39.39 3.13
4794 5645 4.676924 GCTCAAAAACGTCCAGATCTTTTG 59.323 41.667 11.35 11.35 37.99 2.44
4852 5703 3.398406 CTGGTTTGTAAAATTGGTGGCC 58.602 45.455 0.00 0.00 0.00 5.36
4853 5704 2.771943 TGGTTTGTAAAATTGGTGGCCA 59.228 40.909 0.00 0.00 0.00 5.36
4855 5706 3.562141 GGTTTGTAAAATTGGTGGCCAAC 59.438 43.478 15.99 15.99 46.95 3.77
4856 5707 4.447290 GTTTGTAAAATTGGTGGCCAACT 58.553 39.130 24.13 2.98 46.95 3.16
4857 5708 3.742433 TGTAAAATTGGTGGCCAACTG 57.258 42.857 24.13 0.00 46.95 3.16
4964 7658 2.255252 CGGCTCAAAACAAGGGCG 59.745 61.111 0.00 0.00 40.84 6.13
5006 7700 8.603242 TCTGTGTAGAGAAACAAACTAATTCC 57.397 34.615 0.00 0.00 0.00 3.01
5121 7833 4.514401 CCCAAGAGTAGTATCAACCCAAC 58.486 47.826 0.00 0.00 0.00 3.77
5138 7850 6.435292 ACCCAACTGTAGTATGAAGAAAGT 57.565 37.500 0.00 0.00 0.00 2.66
5170 7882 2.768344 CCCCTATCCACCGCCACT 60.768 66.667 0.00 0.00 0.00 4.00
5178 7890 2.613506 CCACCGCCACTCCGTTTTC 61.614 63.158 0.00 0.00 0.00 2.29
5206 7918 8.885722 CCGTTTTTGTGCCTTTATATACTTCTA 58.114 33.333 0.00 0.00 0.00 2.10
5269 8091 3.062234 GCATACCGCTTGTGAGTAGTTTC 59.938 47.826 0.00 0.00 37.77 2.78
5270 8092 1.779569 ACCGCTTGTGAGTAGTTTCG 58.220 50.000 0.00 0.00 0.00 3.46
5272 8094 1.719780 CCGCTTGTGAGTAGTTTCGTC 59.280 52.381 0.00 0.00 0.00 4.20
5309 8131 6.435904 GTCCATAGCAGTAGTTAGATGATCCT 59.564 42.308 0.00 0.00 0.00 3.24
5346 8168 6.647229 TCTCAATACAAAGATCACATGAGCT 58.353 36.000 0.00 0.00 43.46 4.09
5351 8173 1.937278 AAGATCACATGAGCTGCTCG 58.063 50.000 23.35 13.28 40.30 5.03
5428 8250 7.667635 TGGGTTGTGATCAATTGTCACTTTATA 59.332 33.333 26.73 13.69 44.80 0.98
5509 8331 9.981460 TCTTATTCATATATGCTCTCTGGTCTA 57.019 33.333 7.92 0.00 0.00 2.59
5518 8340 8.900983 ATATGCTCTCTGGTCTATTCTTTTTC 57.099 34.615 0.00 0.00 0.00 2.29
5519 8341 6.114187 TGCTCTCTGGTCTATTCTTTTTCA 57.886 37.500 0.00 0.00 0.00 2.69
5527 8349 4.466015 GGTCTATTCTTTTTCATTGGGCCA 59.534 41.667 0.00 0.00 0.00 5.36
5552 8374 3.874383 TGGGGTTTGATCTTCAAGTGA 57.126 42.857 0.00 0.00 37.70 3.41
5573 8395 6.437477 AGTGAGAGTTGTGTATGATAGTTGGA 59.563 38.462 0.00 0.00 0.00 3.53
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 2.361610 CGACCCATTTGGCCAGCT 60.362 61.111 5.11 0.00 37.83 4.24
1 2 2.676471 ACGACCCATTTGGCCAGC 60.676 61.111 5.11 0.00 37.83 4.85
3 4 0.178975 AAAGACGACCCATTTGGCCA 60.179 50.000 0.00 0.00 37.83 5.36
4 5 0.966179 AAAAGACGACCCATTTGGCC 59.034 50.000 0.00 0.00 37.83 5.36
5 6 1.886542 AGAAAAGACGACCCATTTGGC 59.113 47.619 0.00 0.00 37.83 4.52
6 7 2.228822 CCAGAAAAGACGACCCATTTGG 59.771 50.000 0.00 0.00 41.37 3.28
7 8 2.228822 CCCAGAAAAGACGACCCATTTG 59.771 50.000 0.00 0.00 0.00 2.32
8 9 2.514803 CCCAGAAAAGACGACCCATTT 58.485 47.619 0.00 0.00 0.00 2.32
9 10 1.886655 GCCCAGAAAAGACGACCCATT 60.887 52.381 0.00 0.00 0.00 3.16
10 11 0.322546 GCCCAGAAAAGACGACCCAT 60.323 55.000 0.00 0.00 0.00 4.00
11 12 1.072505 GCCCAGAAAAGACGACCCA 59.927 57.895 0.00 0.00 0.00 4.51
12 13 1.674651 GGCCCAGAAAAGACGACCC 60.675 63.158 0.00 0.00 0.00 4.46
13 14 2.033194 CGGCCCAGAAAAGACGACC 61.033 63.158 0.00 0.00 0.00 4.79
14 15 2.033194 CCGGCCCAGAAAAGACGAC 61.033 63.158 0.00 0.00 0.00 4.34
15 16 2.345991 CCGGCCCAGAAAAGACGA 59.654 61.111 0.00 0.00 0.00 4.20
16 17 3.431725 GCCGGCCCAGAAAAGACG 61.432 66.667 18.11 0.00 0.00 4.18
17 18 3.062466 GGCCGGCCCAGAAAAGAC 61.062 66.667 36.64 5.01 0.00 3.01
70 71 4.097863 GTTTAGCCCGTGCCGTGC 62.098 66.667 0.00 0.00 38.69 5.34
71 72 3.784412 CGTTTAGCCCGTGCCGTG 61.784 66.667 0.00 0.00 38.69 4.94
159 160 0.454196 AAAATGTAATCGGGCCGTGC 59.546 50.000 27.32 11.97 0.00 5.34
160 161 2.931512 AAAAATGTAATCGGGCCGTG 57.068 45.000 27.32 0.00 0.00 4.94
204 205 9.830186 TTTAGCCTATTTTTATATATTGGGCCA 57.170 29.630 0.00 0.00 37.98 5.36
235 236 3.727970 GCCTGTTATTTGACGCACTAAGC 60.728 47.826 0.00 0.00 40.87 3.09
236 237 3.684788 AGCCTGTTATTTGACGCACTAAG 59.315 43.478 0.00 0.00 0.00 2.18
237 238 3.670625 AGCCTGTTATTTGACGCACTAA 58.329 40.909 0.00 0.00 0.00 2.24
238 239 3.328382 AGCCTGTTATTTGACGCACTA 57.672 42.857 0.00 0.00 0.00 2.74
239 240 2.185004 AGCCTGTTATTTGACGCACT 57.815 45.000 0.00 0.00 0.00 4.40
240 241 4.413495 TTTAGCCTGTTATTTGACGCAC 57.587 40.909 0.00 0.00 0.00 5.34
241 242 5.440234 TTTTTAGCCTGTTATTTGACGCA 57.560 34.783 0.00 0.00 0.00 5.24
242 243 7.305993 GCATATTTTTAGCCTGTTATTTGACGC 60.306 37.037 0.00 0.00 0.00 5.19
243 244 7.097047 CGCATATTTTTAGCCTGTTATTTGACG 60.097 37.037 0.00 0.00 0.00 4.35
244 245 7.167468 CCGCATATTTTTAGCCTGTTATTTGAC 59.833 37.037 0.00 0.00 0.00 3.18
245 246 7.199766 CCGCATATTTTTAGCCTGTTATTTGA 58.800 34.615 0.00 0.00 0.00 2.69
246 247 6.074356 GCCGCATATTTTTAGCCTGTTATTTG 60.074 38.462 0.00 0.00 0.00 2.32
247 248 5.983118 GCCGCATATTTTTAGCCTGTTATTT 59.017 36.000 0.00 0.00 0.00 1.40
248 249 5.508994 GGCCGCATATTTTTAGCCTGTTATT 60.509 40.000 0.00 0.00 37.42 1.40
249 250 4.022329 GGCCGCATATTTTTAGCCTGTTAT 60.022 41.667 0.00 0.00 37.42 1.89
250 251 3.316868 GGCCGCATATTTTTAGCCTGTTA 59.683 43.478 0.00 0.00 37.42 2.41
251 252 2.100749 GGCCGCATATTTTTAGCCTGTT 59.899 45.455 0.00 0.00 37.42 3.16
252 253 1.681264 GGCCGCATATTTTTAGCCTGT 59.319 47.619 0.00 0.00 37.42 4.00
253 254 1.000274 GGGCCGCATATTTTTAGCCTG 60.000 52.381 0.00 0.00 40.32 4.85
254 255 1.328279 GGGCCGCATATTTTTAGCCT 58.672 50.000 0.00 0.00 40.32 4.58
255 256 1.036707 TGGGCCGCATATTTTTAGCC 58.963 50.000 0.00 0.00 39.73 3.93
256 257 1.269569 GGTGGGCCGCATATTTTTAGC 60.270 52.381 20.39 0.00 0.00 3.09
257 258 2.793278 GGTGGGCCGCATATTTTTAG 57.207 50.000 20.39 0.00 0.00 1.85
269 270 3.428282 CGTTTAGCACGGTGGGCC 61.428 66.667 10.60 0.00 45.89 5.80
277 278 2.255881 ACGTTGGCCCGTTTAGCAC 61.256 57.895 0.00 0.00 37.96 4.40
278 279 2.111460 ACGTTGGCCCGTTTAGCA 59.889 55.556 0.00 0.00 37.96 3.49
279 280 2.559330 CACGTTGGCCCGTTTAGC 59.441 61.111 4.13 0.00 39.45 3.09
280 281 2.559330 GCACGTTGGCCCGTTTAG 59.441 61.111 4.13 0.00 39.45 1.85
294 295 1.375780 TTAGTAAACGGGCCGGCAC 60.376 57.895 31.78 26.77 0.00 5.01
295 296 1.375780 GTTAGTAAACGGGCCGGCA 60.376 57.895 31.78 11.85 0.00 5.69
296 297 2.108514 GGTTAGTAAACGGGCCGGC 61.109 63.158 31.78 21.18 36.39 6.13
297 298 1.810853 CGGTTAGTAAACGGGCCGG 60.811 63.158 31.78 12.53 36.39 6.13
298 299 1.810853 CCGGTTAGTAAACGGGCCG 60.811 63.158 28.35 27.06 45.62 6.13
299 300 4.206958 CCGGTTAGTAAACGGGCC 57.793 61.111 28.35 4.07 45.62 5.80
302 303 1.810853 CGGCCCGGTTAGTAAACGG 60.811 63.158 28.92 28.92 36.39 4.44
303 304 1.079888 ACGGCCCGGTTAGTAAACG 60.080 57.895 13.49 13.49 36.39 3.60
304 305 1.638388 GCACGGCCCGGTTAGTAAAC 61.638 60.000 8.57 0.00 34.66 2.01
305 306 1.375780 GCACGGCCCGGTTAGTAAA 60.376 57.895 8.57 0.00 0.00 2.01
306 307 2.265424 GCACGGCCCGGTTAGTAA 59.735 61.111 8.57 0.00 0.00 2.24
307 308 3.773404 GGCACGGCCCGGTTAGTA 61.773 66.667 8.57 0.00 44.06 1.82
353 354 3.726595 TATACGGGCCGTGCTGTGC 62.727 63.158 39.80 0.00 41.39 4.57
354 355 1.591594 CTATACGGGCCGTGCTGTG 60.592 63.158 39.80 20.81 41.39 3.66
355 356 0.752743 TACTATACGGGCCGTGCTGT 60.753 55.000 39.80 31.75 41.39 4.40
356 357 0.386476 TTACTATACGGGCCGTGCTG 59.614 55.000 39.80 28.38 41.39 4.41
357 358 1.271656 GATTACTATACGGGCCGTGCT 59.728 52.381 39.80 27.94 41.39 4.40
358 359 1.706443 GATTACTATACGGGCCGTGC 58.294 55.000 39.80 15.03 41.39 5.34
359 360 1.267806 ACGATTACTATACGGGCCGTG 59.732 52.381 39.80 26.05 41.39 4.94
360 361 1.267806 CACGATTACTATACGGGCCGT 59.732 52.381 35.91 35.91 44.35 5.68
361 362 1.973138 CACGATTACTATACGGGCCG 58.027 55.000 27.06 27.06 0.00 6.13
364 365 1.891150 AGGGCACGATTACTATACGGG 59.109 52.381 0.00 0.00 0.00 5.28
365 366 2.352421 CCAGGGCACGATTACTATACGG 60.352 54.545 0.00 0.00 0.00 4.02
366 367 2.925306 GCCAGGGCACGATTACTATACG 60.925 54.545 5.20 0.00 41.49 3.06
367 368 2.685100 GCCAGGGCACGATTACTATAC 58.315 52.381 5.20 0.00 41.49 1.47
368 369 1.271379 CGCCAGGGCACGATTACTATA 59.729 52.381 11.42 0.00 42.06 1.31
369 370 0.033504 CGCCAGGGCACGATTACTAT 59.966 55.000 11.42 0.00 42.06 2.12
370 371 1.440060 CGCCAGGGCACGATTACTA 59.560 57.895 11.42 0.00 42.06 1.82
371 372 2.186903 CGCCAGGGCACGATTACT 59.813 61.111 11.42 0.00 42.06 2.24
372 373 2.895372 CCGCCAGGGCACGATTAC 60.895 66.667 11.42 0.00 42.06 1.89
396 397 4.169696 TAATCGTGCCTGGCCCGG 62.170 66.667 22.84 9.24 0.00 5.73
397 398 2.895372 GTAATCGTGCCTGGCCCG 60.895 66.667 17.67 17.67 0.00 6.13
398 399 0.751643 ATTGTAATCGTGCCTGGCCC 60.752 55.000 17.53 2.94 0.00 5.80
399 400 0.381801 CATTGTAATCGTGCCTGGCC 59.618 55.000 17.53 6.66 0.00 5.36
400 401 0.381801 CCATTGTAATCGTGCCTGGC 59.618 55.000 12.87 12.87 0.00 4.85
401 402 1.024271 CCCATTGTAATCGTGCCTGG 58.976 55.000 0.00 0.00 0.00 4.45
402 403 0.381801 GCCCATTGTAATCGTGCCTG 59.618 55.000 0.00 0.00 0.00 4.85
403 404 0.751643 GGCCCATTGTAATCGTGCCT 60.752 55.000 0.00 0.00 34.61 4.75
404 405 1.733526 GGCCCATTGTAATCGTGCC 59.266 57.895 0.00 0.00 0.00 5.01
405 406 1.355210 CGGCCCATTGTAATCGTGC 59.645 57.895 0.00 0.00 0.00 5.34
406 407 1.444119 CCCGGCCCATTGTAATCGTG 61.444 60.000 0.00 0.00 0.00 4.35
407 408 1.153046 CCCGGCCCATTGTAATCGT 60.153 57.895 0.00 0.00 0.00 3.73
408 409 2.551912 GCCCGGCCCATTGTAATCG 61.552 63.158 0.00 0.00 0.00 3.34
409 410 2.200337 GGCCCGGCCCATTGTAATC 61.200 63.158 18.83 0.00 44.06 1.75
410 411 2.123468 GGCCCGGCCCATTGTAAT 60.123 61.111 18.83 0.00 44.06 1.89
445 446 2.414785 GCATACCTGGCCAAACGGG 61.415 63.158 7.01 7.12 42.81 5.28
446 447 0.965363 AAGCATACCTGGCCAAACGG 60.965 55.000 7.01 7.56 0.00 4.44
447 448 0.171007 CAAGCATACCTGGCCAAACG 59.829 55.000 7.01 0.00 0.00 3.60
448 449 0.532115 CCAAGCATACCTGGCCAAAC 59.468 55.000 7.01 0.00 0.00 2.93
449 450 0.114168 ACCAAGCATACCTGGCCAAA 59.886 50.000 7.01 0.00 0.00 3.28
450 451 0.114168 AACCAAGCATACCTGGCCAA 59.886 50.000 7.01 0.00 0.00 4.52
451 452 0.611618 CAACCAAGCATACCTGGCCA 60.612 55.000 4.71 4.71 0.00 5.36
452 453 0.611896 ACAACCAAGCATACCTGGCC 60.612 55.000 0.00 0.00 0.00 5.36
453 454 1.202348 GAACAACCAAGCATACCTGGC 59.798 52.381 0.00 0.00 0.00 4.85
454 455 1.818674 GGAACAACCAAGCATACCTGG 59.181 52.381 0.00 0.00 38.79 4.45
455 456 1.818674 GGGAACAACCAAGCATACCTG 59.181 52.381 0.00 0.00 41.20 4.00
456 457 1.427368 TGGGAACAACCAAGCATACCT 59.573 47.619 0.00 0.00 41.20 3.08
457 458 1.917872 TGGGAACAACCAAGCATACC 58.082 50.000 0.00 0.00 41.20 2.73
1073 1074 0.110104 GGATGGAGAGGGCTTGATGG 59.890 60.000 0.00 0.00 0.00 3.51
1128 1129 3.403558 GGAGGTGGGGAGGACAGC 61.404 72.222 0.00 0.00 36.64 4.40
1280 1284 4.704103 AGAGAGCGAGGGGGCACA 62.704 66.667 0.00 0.00 34.64 4.57
1336 1340 1.875813 GAGCGACAGATCAGCACGG 60.876 63.158 0.00 0.00 32.08 4.94
1464 1468 0.737715 CTCAAGTACCTGCAGCCGTC 60.738 60.000 8.66 0.00 0.00 4.79
1557 1564 4.827692 ACACTAAAGATCGCACCACATTA 58.172 39.130 0.00 0.00 0.00 1.90
1563 1570 2.934553 GGGTAACACTAAAGATCGCACC 59.065 50.000 0.00 0.00 39.74 5.01
1647 1662 2.932234 CGAAGCACCGGACTCACCT 61.932 63.158 9.46 0.00 36.31 4.00
1660 1677 1.084370 CACCCCTGATCGAACGAAGC 61.084 60.000 0.12 0.00 0.00 3.86
1792 1809 8.637986 GTTCAAGCATATTATGGGGTTATCAAA 58.362 33.333 5.84 0.00 0.00 2.69
1880 1899 1.306654 AGATACAGGTGCCCCGGAA 60.307 57.895 0.73 0.00 35.12 4.30
1883 1902 0.462047 GAACAGATACAGGTGCCCCG 60.462 60.000 0.00 0.00 35.12 5.73
1981 2001 4.504858 CAGTTCATCTACAGTAACACCCC 58.495 47.826 0.00 0.00 0.00 4.95
2127 2147 0.740737 GAATTGCAGAACCATCGGGG 59.259 55.000 0.00 0.00 44.81 5.73
2211 2231 7.600752 GGTCAGATATCAAAACTAGGCTATGTC 59.399 40.741 5.32 0.00 0.00 3.06
2229 2249 3.706594 CACTAAAGCCTCCTGGTCAGATA 59.293 47.826 0.00 0.00 35.27 1.98
2285 2305 1.003580 TGAACCCTCTCCACTGAATGC 59.996 52.381 0.00 0.00 0.00 3.56
2323 2343 7.436118 ACACTACAATACTTTCGTTTACCTCA 58.564 34.615 0.00 0.00 0.00 3.86
2342 2362 9.651718 GTAAGATAAGCAAATGCATAACACTAC 57.348 33.333 8.28 2.41 45.16 2.73
2397 2422 4.689345 GGCTAACGACTTGACTACAAACAT 59.311 41.667 0.00 0.00 35.49 2.71
2668 2693 2.104281 GGCCACCTCCATTACTACGAAT 59.896 50.000 0.00 0.00 0.00 3.34
2669 2694 1.483415 GGCCACCTCCATTACTACGAA 59.517 52.381 0.00 0.00 0.00 3.85
2670 2695 1.117150 GGCCACCTCCATTACTACGA 58.883 55.000 0.00 0.00 0.00 3.43
2671 2696 0.828022 TGGCCACCTCCATTACTACG 59.172 55.000 0.00 0.00 0.00 3.51
2794 2914 9.856488 CTAGATTAAGTTAGAAGTTAGTGTGCA 57.144 33.333 0.00 0.00 0.00 4.57
2795 2915 9.303537 CCTAGATTAAGTTAGAAGTTAGTGTGC 57.696 37.037 0.00 0.00 0.00 4.57
2815 2935 9.528489 TGTAAAATGCTTTTTAGGTTCCTAGAT 57.472 29.630 15.60 0.00 37.83 1.98
2961 3117 3.382865 TGCTTAACTGCAACCATTTGTCA 59.617 39.130 0.00 0.00 40.29 3.58
3060 3264 4.095483 GGAGTACAAACAAGAGCATCATGG 59.905 45.833 0.00 0.00 38.31 3.66
3061 3265 4.095483 GGGAGTACAAACAAGAGCATCATG 59.905 45.833 0.00 0.00 40.19 3.07
3062 3266 4.018960 AGGGAGTACAAACAAGAGCATCAT 60.019 41.667 0.00 0.00 37.82 2.45
3063 3267 3.327757 AGGGAGTACAAACAAGAGCATCA 59.672 43.478 0.00 0.00 37.82 3.07
3064 3268 3.935828 GAGGGAGTACAAACAAGAGCATC 59.064 47.826 0.00 0.00 0.00 3.91
3065 3269 3.307762 GGAGGGAGTACAAACAAGAGCAT 60.308 47.826 0.00 0.00 0.00 3.79
3066 3270 2.038557 GGAGGGAGTACAAACAAGAGCA 59.961 50.000 0.00 0.00 0.00 4.26
3067 3271 2.701107 GGAGGGAGTACAAACAAGAGC 58.299 52.381 0.00 0.00 0.00 4.09
3069 3273 2.322658 ACGGAGGGAGTACAAACAAGA 58.677 47.619 0.00 0.00 0.00 3.02
3070 3274 2.833631 ACGGAGGGAGTACAAACAAG 57.166 50.000 0.00 0.00 0.00 3.16
3071 3275 2.224354 GGAACGGAGGGAGTACAAACAA 60.224 50.000 0.00 0.00 0.00 2.83
3073 3277 1.345415 TGGAACGGAGGGAGTACAAAC 59.655 52.381 0.00 0.00 0.00 2.93
3075 3279 1.946984 ATGGAACGGAGGGAGTACAA 58.053 50.000 0.00 0.00 0.00 2.41
3076 3280 2.832643 TATGGAACGGAGGGAGTACA 57.167 50.000 0.00 0.00 0.00 2.90
3078 3282 5.070823 ACTAATATGGAACGGAGGGAGTA 57.929 43.478 0.00 0.00 0.00 2.59
3079 3283 3.924922 ACTAATATGGAACGGAGGGAGT 58.075 45.455 0.00 0.00 0.00 3.85
3080 3284 4.101119 ACAACTAATATGGAACGGAGGGAG 59.899 45.833 0.00 0.00 0.00 4.30
3081 3285 4.035112 ACAACTAATATGGAACGGAGGGA 58.965 43.478 0.00 0.00 0.00 4.20
3083 3287 5.277857 AGACAACTAATATGGAACGGAGG 57.722 43.478 0.00 0.00 0.00 4.30
3095 3299 8.386264 CCCTCCATTCCATATTAGACAACTAAT 58.614 37.037 0.00 0.00 46.79 1.73
3096 3300 7.570982 TCCCTCCATTCCATATTAGACAACTAA 59.429 37.037 0.00 0.00 41.87 2.24
3097 3301 7.079700 TCCCTCCATTCCATATTAGACAACTA 58.920 38.462 0.00 0.00 0.00 2.24
3098 3302 5.911178 TCCCTCCATTCCATATTAGACAACT 59.089 40.000 0.00 0.00 0.00 3.16
3099 3303 6.187727 TCCCTCCATTCCATATTAGACAAC 57.812 41.667 0.00 0.00 0.00 3.32
3100 3304 7.406620 AATCCCTCCATTCCATATTAGACAA 57.593 36.000 0.00 0.00 0.00 3.18
3101 3305 8.551440 CATAATCCCTCCATTCCATATTAGACA 58.449 37.037 0.00 0.00 0.00 3.41
3102 3306 8.552296 ACATAATCCCTCCATTCCATATTAGAC 58.448 37.037 0.00 0.00 0.00 2.59
3103 3307 8.700145 ACATAATCCCTCCATTCCATATTAGA 57.300 34.615 0.00 0.00 0.00 2.10
3104 3308 9.759473 AAACATAATCCCTCCATTCCATATTAG 57.241 33.333 0.00 0.00 0.00 1.73
3179 3384 8.223177 AGAATTTCCAGAAGATAATGAAGCAG 57.777 34.615 0.00 0.00 0.00 4.24
3254 3459 8.794335 AATGACAGAAAACCCTAGAATAACTC 57.206 34.615 0.00 0.00 0.00 3.01
3573 3974 0.462047 CGGAGGCAACCCATCAGTAC 60.462 60.000 0.00 0.00 37.17 2.73
3924 4326 3.652274 ACCAGGCAATTTCGTTCATTTG 58.348 40.909 0.00 0.00 0.00 2.32
3934 4437 4.706962 GGTCTCAGATTTACCAGGCAATTT 59.293 41.667 0.00 0.00 33.28 1.82
4058 4561 1.197721 ACTGAAAAGGCTGAAATCGCG 59.802 47.619 0.00 0.00 0.00 5.87
4202 4719 5.047021 TCTCTTGAACCTAGAACACTGATGG 60.047 44.000 0.00 0.00 0.00 3.51
4284 4801 9.063615 GGTACTAACCTTGAATCTTGAGAAAAA 57.936 33.333 0.00 0.00 43.08 1.94
4312 4829 3.601443 ACTAAAGCAGAACGAGAGCAT 57.399 42.857 0.00 0.00 0.00 3.79
4361 4878 8.787852 TGTTATATGATAGCACAACAACAACAA 58.212 29.630 3.03 0.00 0.00 2.83
4362 4879 8.329203 TGTTATATGATAGCACAACAACAACA 57.671 30.769 3.03 0.00 0.00 3.33
4363 4880 7.910162 CCTGTTATATGATAGCACAACAACAAC 59.090 37.037 6.22 0.00 0.00 3.32
4374 4891 3.691609 GCAAGGCCCTGTTATATGATAGC 59.308 47.826 0.00 0.00 0.00 2.97
4525 5204 4.067896 ACCTATCAGAAAATATGCAGCCG 58.932 43.478 0.00 0.00 0.00 5.52
4534 5213 7.293535 ACCAGAGGCTTATACCTATCAGAAAAT 59.706 37.037 0.00 0.00 41.32 1.82
4686 5365 7.782168 TCTCCAGTACAAGATCAGATAATCAGT 59.218 37.037 0.00 0.00 0.00 3.41
4730 5413 6.886459 TGAATACAAAAATTGCTCTAGCTCCT 59.114 34.615 3.26 0.00 42.66 3.69
4771 5622 4.489679 AAAGATCTGGACGTTTTTGAGC 57.510 40.909 0.00 0.00 0.00 4.26
4794 5645 5.769367 TCTTATACCAGCGTGACATGATAC 58.231 41.667 0.00 0.00 0.00 2.24
4964 7658 2.228059 CAGATCATGGAGCCAATGGAC 58.772 52.381 2.05 0.00 0.00 4.02
5006 7700 4.198530 AGAAAACCAAAATGCAAAGGGTG 58.801 39.130 0.00 0.00 30.91 4.61
5121 7833 4.744570 TCGGCACTTTCTTCATACTACAG 58.255 43.478 0.00 0.00 0.00 2.74
5138 7850 1.729586 AGGGGCTATTAGATTCGGCA 58.270 50.000 0.00 0.00 0.00 5.69
5170 7882 2.478200 GCACAAAAACGGAGAAAACGGA 60.478 45.455 0.00 0.00 35.23 4.69
5178 7890 7.316544 AGTATATAAAGGCACAAAAACGGAG 57.683 36.000 0.00 0.00 0.00 4.63
5206 7918 8.206126 AGGATGATAAATTCACAAAGGGTTTT 57.794 30.769 0.00 0.00 37.11 2.43
5287 8109 7.611467 AGAGAGGATCATCTAACTACTGCTATG 59.389 40.741 10.39 0.00 37.82 2.23
5288 8110 7.698912 AGAGAGGATCATCTAACTACTGCTAT 58.301 38.462 10.39 0.00 37.82 2.97
5298 8120 3.900601 GCAAGGGAGAGAGGATCATCTAA 59.099 47.826 10.39 0.00 37.82 2.10
5309 8131 4.096681 TGTATTGAGAAGCAAGGGAGAGA 58.903 43.478 0.00 0.00 40.42 3.10
5346 8168 3.598299 TGAATCACAATCATGTCGAGCA 58.402 40.909 0.00 0.00 37.82 4.26
5371 8193 9.730705 ACACATTAATAGATTACATCAGATGGG 57.269 33.333 15.13 0.00 33.60 4.00
5502 8324 5.394553 GGCCCAATGAAAAAGAATAGACCAG 60.395 44.000 0.00 0.00 0.00 4.00
5503 8325 4.466015 GGCCCAATGAAAAAGAATAGACCA 59.534 41.667 0.00 0.00 0.00 4.02
5504 8326 4.466015 TGGCCCAATGAAAAAGAATAGACC 59.534 41.667 0.00 0.00 0.00 3.85
5505 8327 5.659440 TGGCCCAATGAAAAAGAATAGAC 57.341 39.130 0.00 0.00 0.00 2.59
5509 8331 4.980339 ACTTGGCCCAATGAAAAAGAAT 57.020 36.364 0.00 0.00 0.00 2.40
5527 8349 4.962362 ACTTGAAGATCAAACCCCAAACTT 59.038 37.500 0.00 0.00 35.73 2.66
5552 8374 7.851228 TGAATCCAACTATCATACACAACTCT 58.149 34.615 0.00 0.00 0.00 3.24
5573 8395 7.725251 TCTTTTTATCACTTGCAAGGTTGAAT 58.275 30.769 29.18 16.27 0.00 2.57


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

AutoCloner maintained by Alex Coulton.