Multiple sequence alignment - TraesCS4A01G279200

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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 TraesCS4A01G279200 chr4A 100.000 2675 0 0 1 2675 586700897 586698223 0.000000e+00 4940
1 TraesCS4A01G279200 chr4A 93.727 1897 90 14 65 1950 456456848 456454970 0.000000e+00 2817
2 TraesCS4A01G279200 chr4A 86.478 1590 136 48 726 2276 586683022 586681473 0.000000e+00 1672
3 TraesCS4A01G279200 chr4A 90.746 389 24 4 2289 2675 323261707 323262085 2.380000e-140 508
4 TraesCS4A01G279200 chr4A 92.021 188 13 2 530 715 586683172 586682985 2.040000e-66 263
5 TraesCS4A01G279200 chr4A 91.579 190 12 3 530 715 456437579 456437390 2.640000e-65 259
6 TraesCS4A01G279200 chr4A 81.731 208 19 12 2072 2276 456420488 456420297 3.570000e-34 156
7 TraesCS4A01G279200 chr4A 100.000 65 0 0 1 65 586705768 586705704 1.300000e-23 121
8 TraesCS4A01G279200 chr4D 90.718 1993 155 20 301 2278 14850638 14852615 0.000000e+00 2628
9 TraesCS4A01G279200 chr4D 93.500 1523 76 13 791 2291 14862580 14864101 0.000000e+00 2242
10 TraesCS4A01G279200 chr4D 88.406 1587 123 27 726 2278 14914333 14915892 0.000000e+00 1855
11 TraesCS4A01G279200 chr4D 89.515 1278 101 19 711 1964 14857609 14858877 0.000000e+00 1587
12 TraesCS4A01G279200 chr4D 84.573 901 117 15 792 1688 14517460 14518342 0.000000e+00 874
13 TraesCS4A01G279200 chr4D 93.269 208 12 2 65 271 14850434 14850640 3.350000e-79 305
14 TraesCS4A01G279200 chr4D 86.275 255 21 6 466 715 14914124 14914369 5.680000e-67 265
15 TraesCS4A01G279200 chr4D 88.298 188 17 3 530 715 14460186 14460002 1.250000e-53 220
16 TraesCS4A01G279200 chr4D 85.714 210 18 4 466 670 14862340 14862542 7.500000e-51 211
17 TraesCS4A01G279200 chr4D 91.089 101 9 0 886 986 14557404 14557304 1.290000e-28 137
18 TraesCS4A01G279200 chr4D 87.500 120 11 4 881 998 14514237 14514354 4.650000e-28 135
19 TraesCS4A01G279200 chr4B 88.228 1580 135 29 731 2278 24759151 24760711 0.000000e+00 1840
20 TraesCS4A01G279200 chr4B 89.229 1439 108 19 711 2132 24732969 24734377 0.000000e+00 1755
21 TraesCS4A01G279200 chr4B 85.579 1588 154 36 726 2278 24745500 24747047 0.000000e+00 1594
22 TraesCS4A01G279200 chr4B 86.130 1168 136 14 880 2028 24690641 24689481 0.000000e+00 1236
23 TraesCS4A01G279200 chr4B 85.079 382 34 18 2288 2660 570889825 570890192 4.210000e-98 368
24 TraesCS4A01G279200 chr4B 87.616 323 25 12 2290 2608 527955595 527955906 7.040000e-96 361
25 TraesCS4A01G279200 chr4B 89.437 284 23 6 2287 2567 608059806 608060085 4.240000e-93 351
26 TraesCS4A01G279200 chr4B 80.966 352 37 24 2290 2616 538704863 538704517 4.420000e-63 252
27 TraesCS4A01G279200 chr4B 89.840 187 16 3 532 715 24741226 24741412 1.240000e-58 237
28 TraesCS4A01G279200 chr4B 84.100 239 29 8 2290 2524 622946832 622947065 3.470000e-54 222
29 TraesCS4A01G279200 chr4B 83.051 236 35 5 2289 2521 664161447 664161680 2.700000e-50 209
30 TraesCS4A01G279200 chr4B 82.692 156 22 5 2294 2446 628443621 628443468 1.670000e-27 134
31 TraesCS4A01G279200 chr1A 93.573 389 19 4 2289 2675 29220184 29220568 2.310000e-160 575
32 TraesCS4A01G279200 chr1A 92.268 388 21 4 2290 2675 555841680 555841300 2.340000e-150 542
33 TraesCS4A01G279200 chr1A 89.389 311 26 6 2288 2596 543716641 543716336 4.180000e-103 385
34 TraesCS4A01G279200 chr1B 89.815 324 25 7 2289 2610 633194232 633193915 2.480000e-110 409
35 TraesCS4A01G279200 chr1B 87.616 323 32 7 2290 2610 507839398 507839082 4.210000e-98 368
36 TraesCS4A01G279200 chr1B 87.898 314 34 4 2290 2600 526248310 526247998 1.510000e-97 366
37 TraesCS4A01G279200 chr1B 86.486 333 36 9 2290 2619 225449628 225449954 9.110000e-95 357
38 TraesCS4A01G279200 chr1B 85.757 337 34 10 2285 2616 16938702 16938375 7.090000e-91 344
39 TraesCS4A01G279200 chr1B 88.571 280 28 4 2290 2567 6239577 6239300 1.190000e-88 337
40 TraesCS4A01G279200 chr5A 90.032 311 24 6 2288 2596 475352182 475352487 1.930000e-106 396
41 TraesCS4A01G279200 chr5A 100.000 65 0 0 1 65 81498155 81498091 1.300000e-23 121
42 TraesCS4A01G279200 chr5A 98.438 64 1 0 1 64 81493282 81493219 2.180000e-21 113
43 TraesCS4A01G279200 chr7A 89.935 308 25 5 2290 2595 192610632 192610935 2.500000e-105 392
44 TraesCS4A01G279200 chr7A 88.764 89 9 1 259 346 9657465 9657377 1.010000e-19 108
45 TraesCS4A01G279200 chr6B 87.834 337 30 8 2288 2620 42365569 42365898 4.180000e-103 385
46 TraesCS4A01G279200 chr6B 88.889 90 9 1 257 345 639915410 639915321 2.820000e-20 110
47 TraesCS4A01G279200 chr5B 87.926 323 31 5 2290 2610 314955158 314954842 9.040000e-100 374
48 TraesCS4A01G279200 chr5B 88.816 304 28 5 2290 2591 588641241 588640942 4.210000e-98 368
49 TraesCS4A01G279200 chr5B 84.085 377 44 11 2290 2659 56553349 56553716 1.520000e-92 350
50 TraesCS4A01G279200 chr2B 83.463 387 50 13 2290 2671 29080916 29080539 5.480000e-92 348
51 TraesCS4A01G279200 chr2B 88.764 89 9 1 256 343 474356132 474356044 1.010000e-19 108
52 TraesCS4A01G279200 chr3B 88.083 193 20 3 524 713 452728484 452728676 2.680000e-55 226
53 TraesCS4A01G279200 chr3B 96.970 66 1 1 1 65 772364890 772364825 2.820000e-20 110
54 TraesCS4A01G279200 chr3B 96.970 66 1 1 1 65 772375021 772374956 2.820000e-20 110
55 TraesCS4A01G279200 chr7B 90.110 91 8 1 254 343 22814067 22813977 1.680000e-22 117
56 TraesCS4A01G279200 chr7B 98.462 65 0 1 1 64 27299309 27299373 2.180000e-21 113
57 TraesCS4A01G279200 chr7B 96.923 65 1 1 1 64 648391986 648391922 1.010000e-19 108
58 TraesCS4A01G279200 chr7B 95.455 66 2 1 1 65 27294436 27294501 1.310000e-18 104
59 TraesCS4A01G279200 chr3D 90.110 91 5 3 259 345 185070510 185070600 6.050000e-22 115
60 TraesCS4A01G279200 chr2D 89.888 89 8 1 256 343 154900262 154900350 2.180000e-21 113
61 TraesCS4A01G279200 chr5D 89.773 88 8 1 259 345 10524838 10524925 7.830000e-21 111


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 TraesCS4A01G279200 chr4A 586698223 586700897 2674 True 4940.000000 4940 100.000000 1 2675 1 chr4A.!!$R4 2674
1 TraesCS4A01G279200 chr4A 456454970 456456848 1878 True 2817.000000 2817 93.727000 65 1950 1 chr4A.!!$R3 1885
2 TraesCS4A01G279200 chr4A 586681473 586683172 1699 True 967.500000 1672 89.249500 530 2276 2 chr4A.!!$R6 1746
3 TraesCS4A01G279200 chr4D 14850434 14852615 2181 False 1466.500000 2628 91.993500 65 2278 2 chr4D.!!$F2 2213
4 TraesCS4A01G279200 chr4D 14857609 14864101 6492 False 1346.666667 2242 89.576333 466 2291 3 chr4D.!!$F3 1825
5 TraesCS4A01G279200 chr4D 14914124 14915892 1768 False 1060.000000 1855 87.340500 466 2278 2 chr4D.!!$F4 1812
6 TraesCS4A01G279200 chr4D 14514237 14518342 4105 False 504.500000 874 86.036500 792 1688 2 chr4D.!!$F1 896
7 TraesCS4A01G279200 chr4B 24759151 24760711 1560 False 1840.000000 1840 88.228000 731 2278 1 chr4B.!!$F4 1547
8 TraesCS4A01G279200 chr4B 24732969 24734377 1408 False 1755.000000 1755 89.229000 711 2132 1 chr4B.!!$F1 1421
9 TraesCS4A01G279200 chr4B 24745500 24747047 1547 False 1594.000000 1594 85.579000 726 2278 1 chr4B.!!$F3 1552
10 TraesCS4A01G279200 chr4B 24689481 24690641 1160 True 1236.000000 1236 86.130000 880 2028 1 chr4B.!!$R1 1148

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
23 24 0.033011 CCGGGAGAGGAAGGAAGAGA 60.033 60.0 0.0 0.0 0.0 3.10 F
713 4989 0.249073 CAAGCTACCTCATCCCGACG 60.249 60.0 0.0 0.0 0.0 5.12 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1275 5925 0.110486 GGTTCATGGACACACCCAGT 59.890 55.0 6.44 0.00 39.97 4.00 R
2493 8297 0.037017 TACCCCCACCACGTGAAATG 59.963 55.0 19.30 12.04 35.23 2.32 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
17 18 4.463043 AGAACCGGGAGAGGAAGG 57.537 61.111 6.32 0.00 34.73 3.46
18 19 1.781676 AGAACCGGGAGAGGAAGGA 59.218 57.895 6.32 0.00 34.73 3.36
19 20 0.116541 AGAACCGGGAGAGGAAGGAA 59.883 55.000 6.32 0.00 34.73 3.36
20 21 0.537653 GAACCGGGAGAGGAAGGAAG 59.462 60.000 6.32 0.00 34.73 3.46
21 22 0.116541 AACCGGGAGAGGAAGGAAGA 59.883 55.000 6.32 0.00 34.73 2.87
22 23 0.324830 ACCGGGAGAGGAAGGAAGAG 60.325 60.000 6.32 0.00 34.73 2.85
23 24 0.033011 CCGGGAGAGGAAGGAAGAGA 60.033 60.000 0.00 0.00 0.00 3.10
25 26 2.158445 CCGGGAGAGGAAGGAAGAGATA 60.158 54.545 0.00 0.00 0.00 1.98
26 27 3.153919 CGGGAGAGGAAGGAAGAGATAG 58.846 54.545 0.00 0.00 0.00 2.08
27 28 3.435890 CGGGAGAGGAAGGAAGAGATAGT 60.436 52.174 0.00 0.00 0.00 2.12
28 29 4.552674 GGGAGAGGAAGGAAGAGATAGTT 58.447 47.826 0.00 0.00 0.00 2.24
29 30 4.343814 GGGAGAGGAAGGAAGAGATAGTTG 59.656 50.000 0.00 0.00 0.00 3.16
30 31 5.205056 GGAGAGGAAGGAAGAGATAGTTGA 58.795 45.833 0.00 0.00 0.00 3.18
31 32 5.301805 GGAGAGGAAGGAAGAGATAGTTGAG 59.698 48.000 0.00 0.00 0.00 3.02
32 33 6.086011 AGAGGAAGGAAGAGATAGTTGAGA 57.914 41.667 0.00 0.00 0.00 3.27
33 34 6.682537 AGAGGAAGGAAGAGATAGTTGAGAT 58.317 40.000 0.00 0.00 0.00 2.75
34 35 7.132128 AGAGGAAGGAAGAGATAGTTGAGATT 58.868 38.462 0.00 0.00 0.00 2.40
35 36 8.285891 AGAGGAAGGAAGAGATAGTTGAGATTA 58.714 37.037 0.00 0.00 0.00 1.75
36 37 8.846423 AGGAAGGAAGAGATAGTTGAGATTAA 57.154 34.615 0.00 0.00 0.00 1.40
37 38 9.273137 AGGAAGGAAGAGATAGTTGAGATTAAA 57.727 33.333 0.00 0.00 0.00 1.52
63 64 9.347240 ACTACAACTACTACTCAAACTCTAACA 57.653 33.333 0.00 0.00 0.00 2.41
273 275 5.394333 GCTGAGAAGTACTCCCTTCGTAAAT 60.394 44.000 0.00 0.00 44.46 1.40
380 383 2.887783 CAGCGACAGGTAGTATGGATCT 59.112 50.000 0.00 0.00 0.00 2.75
459 466 3.244422 ACATCAACGGAGCAAAGGACTTA 60.244 43.478 0.00 0.00 0.00 2.24
463 470 1.079503 CGGAGCAAAGGACTTAGTGC 58.920 55.000 0.00 0.00 37.26 4.40
623 4899 5.546499 AGAAACACCTCCTGGTTTATCTGTA 59.454 40.000 0.00 0.00 46.05 2.74
713 4989 0.249073 CAAGCTACCTCATCCCGACG 60.249 60.000 0.00 0.00 0.00 5.12
1028 5676 3.118738 TGCTCTAAAACCCTAGTAGCTGC 60.119 47.826 0.00 0.00 0.00 5.25
1032 5680 1.205055 AAACCCTAGTAGCTGCCCTC 58.795 55.000 0.00 0.00 0.00 4.30
1054 5702 0.745845 CGCCATGCTGTTCCTAGCTT 60.746 55.000 0.00 0.00 44.01 3.74
1245 5893 3.978723 CTCGGCTGTGACGGAGCTG 62.979 68.421 0.00 0.00 43.19 4.24
1275 5925 3.169242 TGGCCCGGTACCAACACA 61.169 61.111 13.54 2.36 33.12 3.72
1473 6123 3.411517 CTCATCCCACGGGGCCTT 61.412 66.667 0.00 0.00 43.94 4.35
1545 6195 2.852075 AACAGCCAGAACCCCGGA 60.852 61.111 0.73 0.00 0.00 5.14
1979 6664 8.792831 AACATATTCTATAGTTTACGTCACGG 57.207 34.615 0.35 0.00 0.00 4.94
1984 6669 2.139888 TAGTTTACGTCACGGCGGCA 62.140 55.000 13.24 0.00 35.98 5.69
1985 6670 2.048033 TTTACGTCACGGCGGCAT 60.048 55.556 13.24 0.00 35.98 4.40
2291 8044 1.585521 CTCACGGTCACGGCGTATC 60.586 63.158 14.22 8.75 46.48 2.24
2292 8045 2.581409 CACGGTCACGGCGTATCC 60.581 66.667 14.22 16.94 46.48 2.59
2293 8046 3.063704 ACGGTCACGGCGTATCCA 61.064 61.111 24.59 5.06 46.48 3.41
2294 8047 2.278596 CGGTCACGGCGTATCCAG 60.279 66.667 24.59 16.43 36.18 3.86
2295 8048 2.767445 CGGTCACGGCGTATCCAGA 61.767 63.158 24.59 12.07 36.18 3.86
2296 8049 1.514087 GGTCACGGCGTATCCAGAA 59.486 57.895 14.22 0.00 34.01 3.02
2297 8050 0.108520 GGTCACGGCGTATCCAGAAA 60.109 55.000 14.22 0.00 34.01 2.52
2298 8051 1.472728 GGTCACGGCGTATCCAGAAAT 60.473 52.381 14.22 0.00 34.01 2.17
2300 8053 3.450578 GTCACGGCGTATCCAGAAATAA 58.549 45.455 14.22 0.00 34.01 1.40
2301 8054 3.489785 GTCACGGCGTATCCAGAAATAAG 59.510 47.826 14.22 0.00 34.01 1.73
2302 8055 3.382227 TCACGGCGTATCCAGAAATAAGA 59.618 43.478 14.22 0.00 34.01 2.10
2304 8057 3.635373 ACGGCGTATCCAGAAATAAGAGA 59.365 43.478 12.58 0.00 34.01 3.10
2305 8058 4.098960 ACGGCGTATCCAGAAATAAGAGAA 59.901 41.667 12.58 0.00 34.01 2.87
2306 8059 4.681942 CGGCGTATCCAGAAATAAGAGAAG 59.318 45.833 0.00 0.00 34.01 2.85
2307 8060 4.449405 GGCGTATCCAGAAATAAGAGAAGC 59.551 45.833 0.00 0.00 34.01 3.86
2308 8061 5.050490 GCGTATCCAGAAATAAGAGAAGCA 58.950 41.667 0.00 0.00 0.00 3.91
2311 8064 6.146837 CGTATCCAGAAATAAGAGAAGCATGG 59.853 42.308 0.00 0.00 0.00 3.66
2312 8065 5.698741 TCCAGAAATAAGAGAAGCATGGA 57.301 39.130 0.00 0.00 32.10 3.41
2330 8083 1.375098 GATGCACAAGCCTCCTCAGC 61.375 60.000 0.00 0.00 41.13 4.26
2331 8084 3.123620 GCACAAGCCTCCTCAGCG 61.124 66.667 0.00 0.00 34.64 5.18
2332 8085 2.659016 CACAAGCCTCCTCAGCGA 59.341 61.111 0.00 0.00 34.64 4.93
2336 8089 3.438017 AAGCCTCCTCAGCGATCGC 62.438 63.158 32.15 32.15 42.33 4.58
2346 8099 3.706668 GCGATCGCGATTCTGGGC 61.707 66.667 26.12 16.90 40.82 5.36
2347 8100 3.038417 CGATCGCGATTCTGGGCC 61.038 66.667 24.55 7.36 40.82 5.80
2348 8101 3.038417 GATCGCGATTCTGGGCCG 61.038 66.667 24.55 0.00 0.00 6.13
2349 8102 3.792053 GATCGCGATTCTGGGCCGT 62.792 63.158 24.55 0.00 0.00 5.68
2350 8103 3.385749 ATCGCGATTCTGGGCCGTT 62.386 57.895 17.62 0.00 0.00 4.44
2351 8104 3.864686 CGCGATTCTGGGCCGTTG 61.865 66.667 0.00 0.00 0.00 4.10
2352 8105 3.508840 GCGATTCTGGGCCGTTGG 61.509 66.667 0.00 0.00 0.00 3.77
2353 8106 2.267642 CGATTCTGGGCCGTTGGA 59.732 61.111 0.00 0.00 0.00 3.53
2354 8107 1.153168 CGATTCTGGGCCGTTGGAT 60.153 57.895 0.00 0.00 0.00 3.41
2355 8108 1.160329 CGATTCTGGGCCGTTGGATC 61.160 60.000 0.00 0.49 0.00 3.36
2356 8109 1.153168 ATTCTGGGCCGTTGGATCG 60.153 57.895 0.00 0.00 0.00 3.69
2363 8116 2.987125 CCGTTGGATCGGTTCCCT 59.013 61.111 2.74 0.00 44.77 4.20
2364 8117 1.298667 CCGTTGGATCGGTTCCCTT 59.701 57.895 2.74 0.00 44.77 3.95
2365 8118 1.024579 CCGTTGGATCGGTTCCCTTG 61.025 60.000 2.74 0.00 44.77 3.61
2366 8119 0.036765 CGTTGGATCGGTTCCCTTGA 60.037 55.000 2.74 0.00 44.77 3.02
2367 8120 1.406887 CGTTGGATCGGTTCCCTTGAT 60.407 52.381 2.74 0.00 44.77 2.57
2369 8122 0.107214 TGGATCGGTTCCCTTGATGC 60.107 55.000 2.74 0.00 44.77 3.91
2370 8123 1.160329 GGATCGGTTCCCTTGATGCG 61.160 60.000 0.00 0.00 38.75 4.73
2371 8124 0.462047 GATCGGTTCCCTTGATGCGT 60.462 55.000 0.00 0.00 0.00 5.24
2372 8125 0.035439 ATCGGTTCCCTTGATGCGTT 60.035 50.000 0.00 0.00 0.00 4.84
2373 8126 0.250553 TCGGTTCCCTTGATGCGTTT 60.251 50.000 0.00 0.00 0.00 3.60
2375 8128 1.000717 CGGTTCCCTTGATGCGTTTTT 60.001 47.619 0.00 0.00 0.00 1.94
2376 8129 2.403259 GGTTCCCTTGATGCGTTTTTG 58.597 47.619 0.00 0.00 0.00 2.44
2378 8131 3.049912 GTTCCCTTGATGCGTTTTTGTC 58.950 45.455 0.00 0.00 0.00 3.18
2379 8132 1.611491 TCCCTTGATGCGTTTTTGTCC 59.389 47.619 0.00 0.00 0.00 4.02
2380 8133 1.665735 CCCTTGATGCGTTTTTGTCCG 60.666 52.381 0.00 0.00 0.00 4.79
2381 8134 1.001815 CCTTGATGCGTTTTTGTCCGT 60.002 47.619 0.00 0.00 0.00 4.69
2382 8135 2.542824 CCTTGATGCGTTTTTGTCCGTT 60.543 45.455 0.00 0.00 0.00 4.44
2383 8136 2.112475 TGATGCGTTTTTGTCCGTTG 57.888 45.000 0.00 0.00 0.00 4.10
2385 8138 1.002251 GATGCGTTTTTGTCCGTTGGA 60.002 47.619 0.00 0.00 0.00 3.53
2386 8139 1.025812 TGCGTTTTTGTCCGTTGGAT 58.974 45.000 0.00 0.00 32.73 3.41
2387 8140 1.002251 TGCGTTTTTGTCCGTTGGATC 60.002 47.619 0.00 0.00 32.73 3.36
2389 8142 1.527736 CGTTTTTGTCCGTTGGATCGA 59.472 47.619 0.00 0.00 32.73 3.59
2390 8143 2.411031 CGTTTTTGTCCGTTGGATCGAG 60.411 50.000 0.00 0.00 32.73 4.04
2391 8144 2.803956 GTTTTTGTCCGTTGGATCGAGA 59.196 45.455 0.00 0.00 32.73 4.04
2392 8145 2.363788 TTTGTCCGTTGGATCGAGAG 57.636 50.000 0.00 0.00 32.73 3.20
2393 8146 0.530744 TTGTCCGTTGGATCGAGAGG 59.469 55.000 0.00 0.00 32.73 3.69
2394 8147 0.611062 TGTCCGTTGGATCGAGAGGT 60.611 55.000 0.00 0.00 32.73 3.85
2396 8149 1.141881 CCGTTGGATCGAGAGGTGG 59.858 63.158 0.00 0.00 0.00 4.61
2397 8150 1.141881 CGTTGGATCGAGAGGTGGG 59.858 63.158 0.00 0.00 0.00 4.61
2403 8156 1.253100 GATCGAGAGGTGGGAGGATC 58.747 60.000 0.00 0.00 0.00 3.36
2404 8157 0.856982 ATCGAGAGGTGGGAGGATCT 59.143 55.000 0.00 0.00 33.73 2.75
2405 8158 0.106469 TCGAGAGGTGGGAGGATCTG 60.106 60.000 0.00 0.00 33.73 2.90
2406 8159 1.112315 CGAGAGGTGGGAGGATCTGG 61.112 65.000 0.00 0.00 33.73 3.86
2407 8160 0.762461 GAGAGGTGGGAGGATCTGGG 60.762 65.000 0.00 0.00 33.73 4.45
2408 8161 2.367512 AGGTGGGAGGATCTGGGC 60.368 66.667 0.00 0.00 33.73 5.36
2409 8162 3.493303 GGTGGGAGGATCTGGGCC 61.493 72.222 0.00 0.00 33.73 5.80
2410 8163 3.866582 GTGGGAGGATCTGGGCCG 61.867 72.222 0.00 0.00 33.73 6.13
2411 8164 4.414956 TGGGAGGATCTGGGCCGT 62.415 66.667 0.00 0.00 33.73 5.68
2412 8165 3.551407 GGGAGGATCTGGGCCGTC 61.551 72.222 0.00 0.00 33.73 4.79
2413 8166 3.917760 GGAGGATCTGGGCCGTCG 61.918 72.222 0.00 0.00 33.73 5.12
2415 8168 4.458829 AGGATCTGGGCCGTCGGA 62.459 66.667 17.49 0.00 0.00 4.55
2416 8169 3.234730 GGATCTGGGCCGTCGGAT 61.235 66.667 17.49 3.18 35.61 4.18
2417 8170 2.340443 GATCTGGGCCGTCGGATC 59.660 66.667 17.49 13.21 40.85 3.36
2418 8171 2.123251 ATCTGGGCCGTCGGATCT 60.123 61.111 17.49 0.00 0.00 2.75
2419 8172 2.427540 GATCTGGGCCGTCGGATCTG 62.428 65.000 17.49 9.87 42.99 2.90
2420 8173 4.227134 CTGGGCCGTCGGATCTGG 62.227 72.222 17.49 0.00 0.00 3.86
2421 8174 4.770362 TGGGCCGTCGGATCTGGA 62.770 66.667 17.49 0.00 0.00 3.86
2422 8175 3.467226 GGGCCGTCGGATCTGGAA 61.467 66.667 17.49 0.00 0.00 3.53
2423 8176 2.107141 GGCCGTCGGATCTGGAAG 59.893 66.667 17.49 0.00 0.00 3.46
2435 8188 2.260844 TCTGGAAGAAACACTGCTGG 57.739 50.000 0.00 0.00 42.31 4.85
2436 8189 1.768275 TCTGGAAGAAACACTGCTGGA 59.232 47.619 0.00 0.00 42.31 3.86
2437 8190 2.172505 TCTGGAAGAAACACTGCTGGAA 59.827 45.455 0.00 0.00 42.31 3.53
2438 8191 3.152341 CTGGAAGAAACACTGCTGGAAT 58.848 45.455 0.00 0.00 34.07 3.01
2439 8192 2.886523 TGGAAGAAACACTGCTGGAATG 59.113 45.455 0.00 0.00 0.00 2.67
2440 8193 3.149196 GGAAGAAACACTGCTGGAATGA 58.851 45.455 0.00 0.00 0.00 2.57
2444 8248 6.404074 GGAAGAAACACTGCTGGAATGAATAG 60.404 42.308 0.00 0.00 0.00 1.73
2447 8251 7.168219 AGAAACACTGCTGGAATGAATAGTAA 58.832 34.615 0.00 0.00 0.00 2.24
2473 8277 7.463469 GGCAACAAAATGTAAATACTATGCC 57.537 36.000 0.00 0.00 41.25 4.40
2474 8278 6.478673 GGCAACAAAATGTAAATACTATGCCC 59.521 38.462 0.00 0.00 41.88 5.36
2475 8279 6.478673 GCAACAAAATGTAAATACTATGCCCC 59.521 38.462 0.00 0.00 0.00 5.80
2476 8280 6.724893 ACAAAATGTAAATACTATGCCCCC 57.275 37.500 0.00 0.00 0.00 5.40
2479 8283 3.868619 TGTAAATACTATGCCCCCACC 57.131 47.619 0.00 0.00 0.00 4.61
2481 8285 3.137544 TGTAAATACTATGCCCCCACCAG 59.862 47.826 0.00 0.00 0.00 4.00
2482 8286 1.149101 AATACTATGCCCCCACCAGG 58.851 55.000 0.00 0.00 0.00 4.45
2492 8296 4.850193 CCACCAGGGCATTTCAGT 57.150 55.556 0.00 0.00 0.00 3.41
2493 8297 2.571548 CCACCAGGGCATTTCAGTC 58.428 57.895 0.00 0.00 0.00 3.51
2494 8298 0.251297 CCACCAGGGCATTTCAGTCA 60.251 55.000 0.00 0.00 0.00 3.41
2496 8300 2.173519 CACCAGGGCATTTCAGTCATT 58.826 47.619 0.00 0.00 0.00 2.57
2497 8301 2.564062 CACCAGGGCATTTCAGTCATTT 59.436 45.455 0.00 0.00 0.00 2.32
2498 8302 2.827921 ACCAGGGCATTTCAGTCATTTC 59.172 45.455 0.00 0.00 0.00 2.17
2500 8304 3.367703 CCAGGGCATTTCAGTCATTTCAC 60.368 47.826 0.00 0.00 0.00 3.18
2501 8305 2.489329 AGGGCATTTCAGTCATTTCACG 59.511 45.455 0.00 0.00 0.00 4.35
2502 8306 2.228822 GGGCATTTCAGTCATTTCACGT 59.771 45.455 0.00 0.00 0.00 4.49
2503 8307 3.236816 GGCATTTCAGTCATTTCACGTG 58.763 45.455 9.94 9.94 0.00 4.49
2504 8308 3.236816 GCATTTCAGTCATTTCACGTGG 58.763 45.455 17.00 0.00 0.00 4.94
2505 8309 3.304659 GCATTTCAGTCATTTCACGTGGT 60.305 43.478 17.00 0.00 0.00 4.16
2507 8311 1.877637 TCAGTCATTTCACGTGGTGG 58.122 50.000 17.00 3.42 33.87 4.61
2508 8312 0.874390 CAGTCATTTCACGTGGTGGG 59.126 55.000 17.00 3.80 33.87 4.61
2510 8314 1.074072 TCATTTCACGTGGTGGGGG 59.926 57.895 17.00 1.19 33.87 5.40
2511 8315 1.228429 CATTTCACGTGGTGGGGGT 60.228 57.895 17.00 0.00 33.87 4.95
2513 8317 0.996583 ATTTCACGTGGTGGGGGTAT 59.003 50.000 17.00 0.00 33.87 2.73
2514 8318 1.654159 TTTCACGTGGTGGGGGTATA 58.346 50.000 17.00 0.00 33.87 1.47
2515 8319 1.654159 TTCACGTGGTGGGGGTATAA 58.346 50.000 17.00 0.00 33.87 0.98
2516 8320 1.654159 TCACGTGGTGGGGGTATAAA 58.346 50.000 17.00 0.00 33.87 1.40
2517 8321 1.983691 TCACGTGGTGGGGGTATAAAA 59.016 47.619 17.00 0.00 33.87 1.52
2518 8322 2.027007 TCACGTGGTGGGGGTATAAAAG 60.027 50.000 17.00 0.00 33.87 2.27
2526 8437 1.529948 GGGTATAAAAGGGCCGGCC 60.530 63.158 38.57 38.57 0.00 6.13
2528 8439 2.203238 TATAAAAGGGCCGGCCGC 60.203 61.111 38.22 29.61 36.85 6.53
2541 8452 4.814294 GCCGCCCCTGTGACGTAG 62.814 72.222 0.00 0.00 0.00 3.51
2546 8457 0.682209 GCCCCTGTGACGTAGACCTA 60.682 60.000 0.00 0.00 0.00 3.08
2550 8461 0.377554 CTGTGACGTAGACCTAGCCG 59.622 60.000 0.00 0.00 0.00 5.52
2553 8464 1.823041 GACGTAGACCTAGCCGCCT 60.823 63.158 0.00 0.00 0.00 5.52
2554 8465 1.784036 GACGTAGACCTAGCCGCCTC 61.784 65.000 0.00 0.00 0.00 4.70
2559 8470 3.742248 GACCTAGCCGCCTCCTCCT 62.742 68.421 0.00 0.00 0.00 3.69
2560 8471 2.915137 CCTAGCCGCCTCCTCCTC 60.915 72.222 0.00 0.00 0.00 3.71
2562 8473 1.901464 CTAGCCGCCTCCTCCTCTC 60.901 68.421 0.00 0.00 0.00 3.20
2563 8474 2.351924 CTAGCCGCCTCCTCCTCTCT 62.352 65.000 0.00 0.00 0.00 3.10
2565 8476 2.520741 CCGCCTCCTCCTCTCTCC 60.521 72.222 0.00 0.00 0.00 3.71
2566 8477 2.520741 CGCCTCCTCCTCTCTCCC 60.521 72.222 0.00 0.00 0.00 4.30
2567 8478 3.024217 GCCTCCTCCTCTCTCCCT 58.976 66.667 0.00 0.00 0.00 4.20
2568 8479 1.152546 GCCTCCTCCTCTCTCCCTC 60.153 68.421 0.00 0.00 0.00 4.30
2570 8481 1.541672 CTCCTCCTCTCTCCCTCCC 59.458 68.421 0.00 0.00 0.00 4.30
2571 8482 0.998945 CTCCTCCTCTCTCCCTCCCT 60.999 65.000 0.00 0.00 0.00 4.20
2572 8483 0.996762 TCCTCCTCTCTCCCTCCCTC 60.997 65.000 0.00 0.00 0.00 4.30
2575 8486 1.232792 CCTCTCTCCCTCCCTCCTG 59.767 68.421 0.00 0.00 0.00 3.86
2576 8487 1.457455 CTCTCTCCCTCCCTCCTGC 60.457 68.421 0.00 0.00 0.00 4.85
2577 8488 2.235602 CTCTCTCCCTCCCTCCTGCA 62.236 65.000 0.00 0.00 0.00 4.41
2578 8489 1.761667 CTCTCCCTCCCTCCTGCAG 60.762 68.421 6.78 6.78 0.00 4.41
2579 8490 3.478274 CTCCCTCCCTCCTGCAGC 61.478 72.222 8.66 0.00 0.00 5.25
2598 8509 4.890306 GCCTCCCTCCCTCCCCTC 62.890 77.778 0.00 0.00 0.00 4.30
2600 8511 4.179599 CTCCCTCCCTCCCCTCCC 62.180 77.778 0.00 0.00 0.00 4.30
2624 8773 2.780693 CTCCTCTCCTCCCACCCA 59.219 66.667 0.00 0.00 0.00 4.51
2626 8775 2.122729 CCTCTCCTCCCACCCACA 59.877 66.667 0.00 0.00 0.00 4.17
2632 8781 4.838152 CTCCCACCCACATCGCCG 62.838 72.222 0.00 0.00 0.00 6.46
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 0.116541 TTCCTTCCTCTCCCGGTTCT 59.883 55.000 0.00 0.00 0.00 3.01
1 2 0.537653 CTTCCTTCCTCTCCCGGTTC 59.462 60.000 0.00 0.00 0.00 3.62
2 3 0.116541 TCTTCCTTCCTCTCCCGGTT 59.883 55.000 0.00 0.00 0.00 4.44
7 8 5.205056 TCAACTATCTCTTCCTTCCTCTCC 58.795 45.833 0.00 0.00 0.00 3.71
8 9 6.126409 TCTCAACTATCTCTTCCTTCCTCTC 58.874 44.000 0.00 0.00 0.00 3.20
9 10 6.086011 TCTCAACTATCTCTTCCTTCCTCT 57.914 41.667 0.00 0.00 0.00 3.69
10 11 6.976934 ATCTCAACTATCTCTTCCTTCCTC 57.023 41.667 0.00 0.00 0.00 3.71
11 12 8.846423 TTAATCTCAACTATCTCTTCCTTCCT 57.154 34.615 0.00 0.00 0.00 3.36
37 38 9.347240 TGTTAGAGTTTGAGTAGTAGTTGTAGT 57.653 33.333 0.00 0.00 0.00 2.73
39 40 9.123902 TGTGTTAGAGTTTGAGTAGTAGTTGTA 57.876 33.333 0.00 0.00 0.00 2.41
40 41 7.919621 GTGTGTTAGAGTTTGAGTAGTAGTTGT 59.080 37.037 0.00 0.00 0.00 3.32
42 43 7.432059 GGTGTGTTAGAGTTTGAGTAGTAGTT 58.568 38.462 0.00 0.00 0.00 2.24
43 44 6.015603 GGGTGTGTTAGAGTTTGAGTAGTAGT 60.016 42.308 0.00 0.00 0.00 2.73
44 45 6.015688 TGGGTGTGTTAGAGTTTGAGTAGTAG 60.016 42.308 0.00 0.00 0.00 2.57
45 46 5.834742 TGGGTGTGTTAGAGTTTGAGTAGTA 59.165 40.000 0.00 0.00 0.00 1.82
46 47 4.652421 TGGGTGTGTTAGAGTTTGAGTAGT 59.348 41.667 0.00 0.00 0.00 2.73
48 49 5.362263 GTTGGGTGTGTTAGAGTTTGAGTA 58.638 41.667 0.00 0.00 0.00 2.59
49 50 4.196971 GTTGGGTGTGTTAGAGTTTGAGT 58.803 43.478 0.00 0.00 0.00 3.41
50 51 3.247648 CGTTGGGTGTGTTAGAGTTTGAG 59.752 47.826 0.00 0.00 0.00 3.02
51 52 3.199677 CGTTGGGTGTGTTAGAGTTTGA 58.800 45.455 0.00 0.00 0.00 2.69
53 54 2.567985 CCGTTGGGTGTGTTAGAGTTT 58.432 47.619 0.00 0.00 0.00 2.66
54 55 1.812708 GCCGTTGGGTGTGTTAGAGTT 60.813 52.381 0.00 0.00 34.97 3.01
56 57 0.034896 AGCCGTTGGGTGTGTTAGAG 59.965 55.000 0.00 0.00 34.97 2.43
57 58 0.250124 CAGCCGTTGGGTGTGTTAGA 60.250 55.000 6.86 0.00 45.06 2.10
58 59 2.244000 CAGCCGTTGGGTGTGTTAG 58.756 57.895 6.86 0.00 45.06 2.34
59 60 4.466133 CAGCCGTTGGGTGTGTTA 57.534 55.556 6.86 0.00 45.06 2.41
380 383 0.324091 GGTACTCCTTCGGTCCCTCA 60.324 60.000 0.00 0.00 0.00 3.86
459 466 0.181114 TGCCAGTGTCTTCAAGCACT 59.819 50.000 8.24 8.24 45.69 4.40
463 470 3.304928 GGTGAAATGCCAGTGTCTTCAAG 60.305 47.826 0.00 0.00 0.00 3.02
623 4899 2.878526 GCTAAGGAAATGGGACCAACGT 60.879 50.000 0.00 0.00 0.00 3.99
713 4989 1.145819 GGAGATGCTCAGGGTCAGC 59.854 63.158 0.00 0.00 37.40 4.26
959 5301 5.426689 TCAGCTAGAGTTTGTTGATGGAT 57.573 39.130 0.00 0.00 0.00 3.41
1028 5676 1.372087 GAACAGCATGGCGAAGAGGG 61.372 60.000 0.00 0.00 43.62 4.30
1032 5680 1.293924 CTAGGAACAGCATGGCGAAG 58.706 55.000 0.00 0.00 43.62 3.79
1054 5702 2.753043 GGTGGCTAGGACGGTCGA 60.753 66.667 1.43 0.00 0.00 4.20
1275 5925 0.110486 GGTTCATGGACACACCCAGT 59.890 55.000 6.44 0.00 39.97 4.00
1545 6195 1.218316 GAGGGGCACGAAGACGATT 59.782 57.895 0.00 0.00 42.66 3.34
1874 6537 5.063438 TCAGTGAAAAGAACAAAGACGACAG 59.937 40.000 0.00 0.00 0.00 3.51
1959 6644 4.285292 CGCCGTGACGTAAACTATAGAAT 58.715 43.478 6.78 0.00 0.00 2.40
1979 6664 0.164647 GATCGCTCAACATATGCCGC 59.835 55.000 1.58 0.00 0.00 6.53
1984 6669 5.532557 TGATTTCGAGATCGCTCAACATAT 58.467 37.500 10.98 0.00 41.36 1.78
1985 6670 4.932146 TGATTTCGAGATCGCTCAACATA 58.068 39.130 10.98 0.00 41.36 2.29
2118 6816 1.868997 CGGGATATTCCGTGCATGC 59.131 57.895 14.83 11.82 44.60 4.06
2231 6946 5.447624 TGATACACTTCGTCACAAGAGAA 57.552 39.130 0.00 0.00 0.00 2.87
2232 6947 5.183140 TGATGATACACTTCGTCACAAGAGA 59.817 40.000 0.00 0.00 36.87 3.10
2233 6948 5.402398 TGATGATACACTTCGTCACAAGAG 58.598 41.667 0.00 0.00 36.87 2.85
2234 6949 5.385509 TGATGATACACTTCGTCACAAGA 57.614 39.130 0.00 0.00 36.87 3.02
2240 6955 6.754209 ACTGAAAGATGATGATACACTTCGTC 59.246 38.462 0.00 0.00 38.30 4.20
2291 8044 6.315091 CATCCATGCTTCTCTTATTTCTGG 57.685 41.667 0.00 0.00 0.00 3.86
2312 8065 1.378250 GCTGAGGAGGCTTGTGCAT 60.378 57.895 0.00 0.00 41.91 3.96
2316 8069 1.519719 GATCGCTGAGGAGGCTTGT 59.480 57.895 0.00 0.00 0.00 3.16
2317 8070 1.591059 CGATCGCTGAGGAGGCTTG 60.591 63.158 0.26 0.00 0.00 4.01
2318 8071 2.811101 CGATCGCTGAGGAGGCTT 59.189 61.111 0.26 0.00 0.00 4.35
2319 8072 3.910490 GCGATCGCTGAGGAGGCT 61.910 66.667 31.94 0.00 38.26 4.58
2321 8074 2.413437 AATCGCGATCGCTGAGGAGG 62.413 60.000 34.69 19.03 39.32 4.30
2323 8076 1.008424 GAATCGCGATCGCTGAGGA 60.008 57.895 34.69 25.08 39.32 3.71
2324 8077 1.007964 AGAATCGCGATCGCTGAGG 60.008 57.895 34.69 20.81 39.32 3.86
2326 8079 1.299392 CCAGAATCGCGATCGCTGA 60.299 57.895 34.72 30.70 39.32 4.26
2327 8080 2.305853 CCCAGAATCGCGATCGCTG 61.306 63.158 34.69 30.06 39.32 5.18
2328 8081 2.028190 CCCAGAATCGCGATCGCT 59.972 61.111 34.69 19.08 39.32 4.93
2330 8083 3.038417 GGCCCAGAATCGCGATCG 61.038 66.667 23.92 11.69 0.00 3.69
2331 8084 3.038417 CGGCCCAGAATCGCGATC 61.038 66.667 23.92 15.49 0.00 3.69
2332 8085 3.385749 AACGGCCCAGAATCGCGAT 62.386 57.895 17.62 17.62 0.00 4.58
2336 8089 1.153168 ATCCAACGGCCCAGAATCG 60.153 57.895 0.00 0.00 0.00 3.34
2337 8090 1.160329 CGATCCAACGGCCCAGAATC 61.160 60.000 0.00 0.00 0.00 2.52
2338 8091 1.153168 CGATCCAACGGCCCAGAAT 60.153 57.895 0.00 0.00 0.00 2.40
2357 8110 3.049912 GACAAAAACGCATCAAGGGAAC 58.950 45.455 0.00 0.00 0.00 3.62
2359 8112 1.611491 GGACAAAAACGCATCAAGGGA 59.389 47.619 0.00 0.00 0.00 4.20
2361 8114 1.001815 ACGGACAAAAACGCATCAAGG 60.002 47.619 0.00 0.00 0.00 3.61
2362 8115 2.399396 ACGGACAAAAACGCATCAAG 57.601 45.000 0.00 0.00 0.00 3.02
2363 8116 2.455032 CAACGGACAAAAACGCATCAA 58.545 42.857 0.00 0.00 0.00 2.57
2364 8117 1.268794 CCAACGGACAAAAACGCATCA 60.269 47.619 0.00 0.00 0.00 3.07
2365 8118 1.002251 TCCAACGGACAAAAACGCATC 60.002 47.619 0.00 0.00 0.00 3.91
2366 8119 1.025812 TCCAACGGACAAAAACGCAT 58.974 45.000 0.00 0.00 0.00 4.73
2367 8120 1.002251 GATCCAACGGACAAAAACGCA 60.002 47.619 0.00 0.00 32.98 5.24
2369 8122 1.527736 TCGATCCAACGGACAAAAACG 59.472 47.619 0.00 0.00 32.98 3.60
2370 8123 2.803956 TCTCGATCCAACGGACAAAAAC 59.196 45.455 0.00 0.00 32.98 2.43
2371 8124 3.064207 CTCTCGATCCAACGGACAAAAA 58.936 45.455 0.00 0.00 32.98 1.94
2372 8125 2.611971 CCTCTCGATCCAACGGACAAAA 60.612 50.000 0.00 0.00 32.98 2.44
2373 8126 1.067142 CCTCTCGATCCAACGGACAAA 60.067 52.381 0.00 0.00 32.98 2.83
2375 8128 0.611062 ACCTCTCGATCCAACGGACA 60.611 55.000 0.00 0.00 32.98 4.02
2376 8129 0.179134 CACCTCTCGATCCAACGGAC 60.179 60.000 0.00 0.00 32.98 4.79
2378 8131 1.141881 CCACCTCTCGATCCAACGG 59.858 63.158 0.00 0.00 0.00 4.44
2379 8132 1.141881 CCCACCTCTCGATCCAACG 59.858 63.158 0.00 0.00 0.00 4.10
2380 8133 0.461961 CTCCCACCTCTCGATCCAAC 59.538 60.000 0.00 0.00 0.00 3.77
2381 8134 0.687757 CCTCCCACCTCTCGATCCAA 60.688 60.000 0.00 0.00 0.00 3.53
2382 8135 1.075970 CCTCCCACCTCTCGATCCA 60.076 63.158 0.00 0.00 0.00 3.41
2383 8136 0.178947 ATCCTCCCACCTCTCGATCC 60.179 60.000 0.00 0.00 0.00 3.36
2385 8138 0.856982 AGATCCTCCCACCTCTCGAT 59.143 55.000 0.00 0.00 0.00 3.59
2386 8139 0.106469 CAGATCCTCCCACCTCTCGA 60.106 60.000 0.00 0.00 0.00 4.04
2387 8140 1.112315 CCAGATCCTCCCACCTCTCG 61.112 65.000 0.00 0.00 0.00 4.04
2389 8142 1.316266 CCCAGATCCTCCCACCTCT 59.684 63.158 0.00 0.00 0.00 3.69
2390 8143 2.447714 GCCCAGATCCTCCCACCTC 61.448 68.421 0.00 0.00 0.00 3.85
2391 8144 2.367512 GCCCAGATCCTCCCACCT 60.368 66.667 0.00 0.00 0.00 4.00
2392 8145 3.493303 GGCCCAGATCCTCCCACC 61.493 72.222 0.00 0.00 0.00 4.61
2393 8146 3.866582 CGGCCCAGATCCTCCCAC 61.867 72.222 0.00 0.00 0.00 4.61
2394 8147 4.414956 ACGGCCCAGATCCTCCCA 62.415 66.667 0.00 0.00 0.00 4.37
2396 8149 3.917760 CGACGGCCCAGATCCTCC 61.918 72.222 0.00 0.00 0.00 4.30
2397 8150 3.917760 CCGACGGCCCAGATCCTC 61.918 72.222 0.00 0.00 0.00 3.71
2403 8156 4.227134 CCAGATCCGACGGCCCAG 62.227 72.222 9.66 0.00 0.00 4.45
2404 8157 4.770362 TCCAGATCCGACGGCCCA 62.770 66.667 9.66 0.00 0.00 5.36
2405 8158 3.447025 CTTCCAGATCCGACGGCCC 62.447 68.421 9.66 2.91 0.00 5.80
2406 8159 1.956629 TTCTTCCAGATCCGACGGCC 61.957 60.000 9.66 3.31 0.00 6.13
2407 8160 0.108329 TTTCTTCCAGATCCGACGGC 60.108 55.000 9.66 0.00 0.00 5.68
2408 8161 1.067142 TGTTTCTTCCAGATCCGACGG 60.067 52.381 7.84 7.84 0.00 4.79
2409 8162 1.993370 GTGTTTCTTCCAGATCCGACG 59.007 52.381 0.00 0.00 0.00 5.12
2410 8163 2.996621 CAGTGTTTCTTCCAGATCCGAC 59.003 50.000 0.00 0.00 0.00 4.79
2411 8164 2.612972 GCAGTGTTTCTTCCAGATCCGA 60.613 50.000 0.00 0.00 0.00 4.55
2412 8165 1.734465 GCAGTGTTTCTTCCAGATCCG 59.266 52.381 0.00 0.00 0.00 4.18
2413 8166 2.746362 CAGCAGTGTTTCTTCCAGATCC 59.254 50.000 0.00 0.00 0.00 3.36
2415 8168 2.373169 TCCAGCAGTGTTTCTTCCAGAT 59.627 45.455 0.00 0.00 0.00 2.90
2416 8169 1.768275 TCCAGCAGTGTTTCTTCCAGA 59.232 47.619 0.00 0.00 0.00 3.86
2417 8170 2.260844 TCCAGCAGTGTTTCTTCCAG 57.739 50.000 0.00 0.00 0.00 3.86
2418 8171 2.727123 TTCCAGCAGTGTTTCTTCCA 57.273 45.000 0.00 0.00 0.00 3.53
2419 8172 3.149196 TCATTCCAGCAGTGTTTCTTCC 58.851 45.455 0.00 0.00 0.00 3.46
2420 8173 4.836125 TTCATTCCAGCAGTGTTTCTTC 57.164 40.909 0.00 0.00 0.00 2.87
2421 8174 6.006449 ACTATTCATTCCAGCAGTGTTTCTT 58.994 36.000 0.00 0.00 0.00 2.52
2422 8175 5.564550 ACTATTCATTCCAGCAGTGTTTCT 58.435 37.500 0.00 0.00 0.00 2.52
2423 8176 5.886960 ACTATTCATTCCAGCAGTGTTTC 57.113 39.130 0.00 0.00 0.00 2.78
2425 8178 6.319658 CCATTACTATTCATTCCAGCAGTGTT 59.680 38.462 0.00 0.00 0.00 3.32
2426 8179 5.824624 CCATTACTATTCATTCCAGCAGTGT 59.175 40.000 0.00 0.00 0.00 3.55
2427 8180 5.278169 GCCATTACTATTCATTCCAGCAGTG 60.278 44.000 0.00 0.00 0.00 3.66
2428 8181 4.823989 GCCATTACTATTCATTCCAGCAGT 59.176 41.667 0.00 0.00 0.00 4.40
2429 8182 4.823442 TGCCATTACTATTCATTCCAGCAG 59.177 41.667 0.00 0.00 0.00 4.24
2431 8184 5.067674 TGTTGCCATTACTATTCATTCCAGC 59.932 40.000 0.00 0.00 0.00 4.85
2432 8185 6.698008 TGTTGCCATTACTATTCATTCCAG 57.302 37.500 0.00 0.00 0.00 3.86
2433 8186 7.473735 TTTGTTGCCATTACTATTCATTCCA 57.526 32.000 0.00 0.00 0.00 3.53
2434 8187 8.819974 CATTTTGTTGCCATTACTATTCATTCC 58.180 33.333 0.00 0.00 0.00 3.01
2435 8188 9.369904 ACATTTTGTTGCCATTACTATTCATTC 57.630 29.630 0.00 0.00 0.00 2.67
2447 8251 7.710475 GGCATAGTATTTACATTTTGTTGCCAT 59.290 33.333 9.61 0.00 35.51 4.40
2457 8261 4.169068 TGGTGGGGGCATAGTATTTACATT 59.831 41.667 0.00 0.00 0.00 2.71
2458 8262 3.724738 TGGTGGGGGCATAGTATTTACAT 59.275 43.478 0.00 0.00 0.00 2.29
2459 8263 3.124066 TGGTGGGGGCATAGTATTTACA 58.876 45.455 0.00 0.00 0.00 2.41
2460 8264 3.497942 CCTGGTGGGGGCATAGTATTTAC 60.498 52.174 0.00 0.00 0.00 2.01
2462 8266 1.499007 CCTGGTGGGGGCATAGTATTT 59.501 52.381 0.00 0.00 0.00 1.40
2463 8267 1.149101 CCTGGTGGGGGCATAGTATT 58.851 55.000 0.00 0.00 0.00 1.89
2465 8269 4.411164 CCTGGTGGGGGCATAGTA 57.589 61.111 0.00 0.00 0.00 1.82
2475 8279 0.251297 TGACTGAAATGCCCTGGTGG 60.251 55.000 0.00 0.00 37.09 4.61
2476 8280 1.843368 ATGACTGAAATGCCCTGGTG 58.157 50.000 0.00 0.00 0.00 4.17
2479 8283 3.671433 CGTGAAATGACTGAAATGCCCTG 60.671 47.826 0.00 0.00 0.00 4.45
2481 8285 2.228822 ACGTGAAATGACTGAAATGCCC 59.771 45.455 0.00 0.00 0.00 5.36
2482 8286 3.236816 CACGTGAAATGACTGAAATGCC 58.763 45.455 10.90 0.00 0.00 4.40
2484 8288 4.221342 CACCACGTGAAATGACTGAAATG 58.779 43.478 19.30 0.00 35.23 2.32
2486 8290 2.616376 CCACCACGTGAAATGACTGAAA 59.384 45.455 19.30 0.00 35.23 2.69
2488 8292 1.542328 CCCACCACGTGAAATGACTGA 60.542 52.381 19.30 0.00 35.23 3.41
2490 8294 0.250727 CCCCACCACGTGAAATGACT 60.251 55.000 19.30 0.00 35.23 3.41
2491 8295 1.241315 CCCCCACCACGTGAAATGAC 61.241 60.000 19.30 0.00 35.23 3.06
2492 8296 1.074072 CCCCCACCACGTGAAATGA 59.926 57.895 19.30 0.00 35.23 2.57
2493 8297 0.037017 TACCCCCACCACGTGAAATG 59.963 55.000 19.30 12.04 35.23 2.32
2494 8298 0.996583 ATACCCCCACCACGTGAAAT 59.003 50.000 19.30 0.00 35.23 2.17
2496 8300 1.654159 TTATACCCCCACCACGTGAA 58.346 50.000 19.30 0.00 35.23 3.18
2497 8301 1.654159 TTTATACCCCCACCACGTGA 58.346 50.000 19.30 0.00 35.23 4.35
2498 8302 2.361789 CTTTTATACCCCCACCACGTG 58.638 52.381 9.08 9.08 0.00 4.49
2500 8304 1.409101 CCCTTTTATACCCCCACCACG 60.409 57.143 0.00 0.00 0.00 4.94
2501 8305 1.687054 GCCCTTTTATACCCCCACCAC 60.687 57.143 0.00 0.00 0.00 4.16
2502 8306 0.632294 GCCCTTTTATACCCCCACCA 59.368 55.000 0.00 0.00 0.00 4.17
2503 8307 0.105862 GGCCCTTTTATACCCCCACC 60.106 60.000 0.00 0.00 0.00 4.61
2504 8308 0.466739 CGGCCCTTTTATACCCCCAC 60.467 60.000 0.00 0.00 0.00 4.61
2505 8309 1.647334 CCGGCCCTTTTATACCCCCA 61.647 60.000 0.00 0.00 0.00 4.96
2507 8311 1.529948 GCCGGCCCTTTTATACCCC 60.530 63.158 18.11 0.00 0.00 4.95
2508 8312 1.529948 GGCCGGCCCTTTTATACCC 60.530 63.158 36.64 4.38 0.00 3.69
2510 8314 2.549198 GCGGCCGGCCCTTTTATAC 61.549 63.158 39.24 14.57 34.80 1.47
2511 8315 2.203238 GCGGCCGGCCCTTTTATA 60.203 61.111 39.24 0.00 34.80 0.98
2526 8437 2.181021 GTCTACGTCACAGGGGCG 59.819 66.667 0.00 0.00 0.00 6.13
2528 8439 1.390565 CTAGGTCTACGTCACAGGGG 58.609 60.000 0.00 0.00 0.00 4.79
2529 8440 0.739561 GCTAGGTCTACGTCACAGGG 59.260 60.000 0.00 0.00 0.00 4.45
2530 8441 0.739561 GGCTAGGTCTACGTCACAGG 59.260 60.000 0.00 0.00 0.00 4.00
2532 8443 1.651240 GCGGCTAGGTCTACGTCACA 61.651 60.000 0.00 0.00 0.00 3.58
2533 8444 1.063811 GCGGCTAGGTCTACGTCAC 59.936 63.158 0.00 0.00 0.00 3.67
2538 8449 1.152715 AGGAGGCGGCTAGGTCTAC 60.153 63.158 13.24 0.00 0.00 2.59
2539 8450 1.150992 GAGGAGGCGGCTAGGTCTA 59.849 63.158 13.24 0.00 0.00 2.59
2540 8451 2.123640 GAGGAGGCGGCTAGGTCT 60.124 66.667 13.24 7.43 0.00 3.85
2541 8452 3.228017 GGAGGAGGCGGCTAGGTC 61.228 72.222 13.24 8.87 0.00 3.85
2546 8457 3.731766 GAGAGAGGAGGAGGCGGCT 62.732 68.421 13.09 13.09 0.00 5.52
2550 8461 1.152546 GAGGGAGAGAGGAGGAGGC 60.153 68.421 0.00 0.00 0.00 4.70
2553 8464 0.996762 GAGGGAGGGAGAGAGGAGGA 60.997 65.000 0.00 0.00 0.00 3.71
2554 8465 1.541672 GAGGGAGGGAGAGAGGAGG 59.458 68.421 0.00 0.00 0.00 4.30
2559 8470 2.235602 CTGCAGGAGGGAGGGAGAGA 62.236 65.000 5.57 0.00 0.00 3.10
2560 8471 1.761667 CTGCAGGAGGGAGGGAGAG 60.762 68.421 5.57 0.00 0.00 3.20
2562 8473 3.478274 GCTGCAGGAGGGAGGGAG 61.478 72.222 17.12 0.00 35.12 4.30
2581 8492 4.890306 GAGGGGAGGGAGGGAGGC 62.890 77.778 0.00 0.00 0.00 4.70
2604 8515 3.151022 GTGGGAGGAGAGGAGGCG 61.151 72.222 0.00 0.00 0.00 5.52
2605 8516 2.766229 GGTGGGAGGAGAGGAGGC 60.766 72.222 0.00 0.00 0.00 4.70
2606 8517 2.041405 GGGTGGGAGGAGAGGAGG 60.041 72.222 0.00 0.00 0.00 4.30
2609 8758 1.307343 ATGTGGGTGGGAGGAGAGG 60.307 63.158 0.00 0.00 0.00 3.69
2613 8762 3.399181 GCGATGTGGGTGGGAGGA 61.399 66.667 0.00 0.00 0.00 3.71
2614 8763 4.489771 GGCGATGTGGGTGGGAGG 62.490 72.222 0.00 0.00 0.00 4.30


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

AutoCloner maintained by Alex Coulton.