Multiple sequence alignment - TraesCS4D01G126000

Loading Multiple Alignment...

Download Multiple Sequence Alignment: (Fasta) (Clustal)


BLAST Results


Shown here are the results of a BLAST search against the genome using the input sequence. The pipeline uses this to extract flanking regions for cloning. If the result of the multiple sequence alignment is not as expected, these results could be used for further investigation.

qseqid sseqid percentage.identical alignment.length no.mismatch no.gap.openings qstart qend sstart send evalue bitscore
0 TraesCS4D01G126000 chr4D 100.000 5045 0 0 972 6016 110083370 110088414 0.000000e+00 9317.0
1 TraesCS4D01G126000 chr4D 100.000 563 0 0 1 563 110082399 110082961 0.000000e+00 1040.0
2 TraesCS4D01G126000 chr4D 88.978 499 50 5 5522 6016 3354940 3354443 3.990000e-171 612.0
3 TraesCS4D01G126000 chr4D 86.486 111 11 3 5305 5413 251555243 251555351 1.060000e-22 119.0
4 TraesCS4D01G126000 chr4D 82.022 89 6 3 4094 4172 380598132 380598044 3.890000e-07 67.6
5 TraesCS4D01G126000 chr4D 94.737 38 2 0 4093 4130 224554271 224554308 6.510000e-05 60.2
6 TraesCS4D01G126000 chr4A 95.615 3307 108 18 2018 5300 466635758 466632465 0.000000e+00 5269.0
7 TraesCS4D01G126000 chr4A 89.585 1037 59 27 972 1991 466636759 466635755 0.000000e+00 1271.0
8 TraesCS4D01G126000 chr4A 84.967 459 28 22 123 563 466637204 466636769 1.550000e-115 427.0
9 TraesCS4D01G126000 chr4A 90.090 111 11 0 1 111 466637387 466637277 1.750000e-30 145.0
10 TraesCS4D01G126000 chr4A 85.714 119 16 1 1431 1549 641486878 641486761 2.280000e-24 124.0
11 TraesCS4D01G126000 chr4A 84.091 88 5 1 4094 4172 696150091 696150178 6.470000e-10 76.8
12 TraesCS4D01G126000 chr4A 100.000 33 0 0 3822 3854 466633755 466633723 1.810000e-05 62.1
13 TraesCS4D01G126000 chr4B 94.871 3256 104 19 2042 5271 171619779 171616561 0.000000e+00 5029.0
14 TraesCS4D01G126000 chr4B 90.390 1103 48 20 975 2044 171621056 171619979 0.000000e+00 1397.0
15 TraesCS4D01G126000 chr4B 85.470 468 27 13 111 563 171621498 171621057 3.310000e-122 449.0
16 TraesCS4D01G126000 chr4B 95.495 111 4 1 1 111 171621636 171621527 6.200000e-40 176.0
17 TraesCS4D01G126000 chr4B 84.091 88 5 1 4094 4172 179310361 179310448 6.470000e-10 76.8
18 TraesCS4D01G126000 chr4B 82.759 87 6 5 4093 4170 3828822 3828736 1.080000e-07 69.4
19 TraesCS4D01G126000 chr4B 81.522 92 8 1 4090 4172 586463924 586464015 3.890000e-07 67.6
20 TraesCS4D01G126000 chr5D 95.122 492 23 1 5526 6016 407693910 407693419 0.000000e+00 774.0
21 TraesCS4D01G126000 chr5D 96.262 107 4 0 5423 5529 407693985 407693879 6.200000e-40 176.0
22 TraesCS4D01G126000 chr5D 91.453 117 10 0 4860 4976 242000004 241999888 1.740000e-35 161.0
23 TraesCS4D01G126000 chr5D 89.916 119 11 1 5303 5420 407694077 407693959 1.040000e-32 152.0
24 TraesCS4D01G126000 chr5D 74.279 416 77 18 2395 2806 242002615 242002226 1.350000e-31 148.0
25 TraesCS4D01G126000 chr5D 86.992 123 16 0 4617 4739 242000249 242000127 8.130000e-29 139.0
26 TraesCS4D01G126000 chr5D 84.146 82 11 2 4094 4175 301990119 301990040 1.800000e-10 78.7
27 TraesCS4D01G126000 chr5D 84.270 89 5 1 4093 4172 504792930 504793018 1.800000e-10 78.7
28 TraesCS4D01G126000 chr5D 90.476 42 4 0 4131 4172 43945871 43945830 8.420000e-04 56.5
29 TraesCS4D01G126000 chr5D 90.476 42 3 1 2307 2348 115410315 115410275 3.000000e-03 54.7
30 TraesCS4D01G126000 chr5D 79.545 88 9 1 4094 4172 446767254 446767167 3.000000e-03 54.7
31 TraesCS4D01G126000 chr5D 79.310 87 9 1 4095 4172 228786463 228786549 1.100000e-02 52.8
32 TraesCS4D01G126000 chr5D 100.000 28 0 0 4093 4120 535546974 535547001 1.100000e-02 52.8
33 TraesCS4D01G126000 chr5B 90.872 493 42 3 5526 6016 569830773 569830282 0.000000e+00 658.0
34 TraesCS4D01G126000 chr5B 89.858 493 47 3 5526 6016 144180873 144181364 1.100000e-176 630.0
35 TraesCS4D01G126000 chr5B 90.598 117 11 0 4860 4976 256943085 256942969 8.070000e-34 156.0
36 TraesCS4D01G126000 chr5B 90.566 106 10 0 4417 4522 256943625 256943520 2.260000e-29 141.0
37 TraesCS4D01G126000 chr5B 86.992 123 16 0 4617 4739 256943400 256943278 8.130000e-29 139.0
38 TraesCS4D01G126000 chr5B 73.850 413 80 17 2395 2806 256945275 256944890 8.130000e-29 139.0
39 TraesCS4D01G126000 chr7A 90.101 495 45 3 5526 6016 95269418 95268924 1.830000e-179 640.0
40 TraesCS4D01G126000 chr7A 85.345 116 16 1 5306 5420 436180547 436180432 1.060000e-22 119.0
41 TraesCS4D01G126000 chr3B 90.369 488 43 4 5532 6016 54764934 54764448 6.580000e-179 638.0
42 TraesCS4D01G126000 chr3B 90.385 468 42 3 5551 6016 507008786 507008320 3.990000e-171 612.0
43 TraesCS4D01G126000 chr3B 87.952 83 6 1 4094 4172 257512410 257512492 1.790000e-15 95.3
44 TraesCS4D01G126000 chr6D 89.837 492 45 4 5526 6016 78861419 78860932 1.420000e-175 627.0
45 TraesCS4D01G126000 chr6D 85.593 118 16 1 5304 5420 78861586 78861469 8.190000e-24 122.0
46 TraesCS4D01G126000 chr6D 100.000 32 0 0 2304 2335 468839907 468839938 6.510000e-05 60.2
47 TraesCS4D01G126000 chr2A 89.206 491 51 2 5527 6016 753062575 753062086 3.990000e-171 612.0
48 TraesCS4D01G126000 chr1A 84.520 323 21 16 5423 5744 582292128 582291834 5.900000e-75 292.0
49 TraesCS4D01G126000 chr1A 90.164 122 11 1 5300 5420 582292223 582292102 2.240000e-34 158.0
50 TraesCS4D01G126000 chr1A 100.000 32 0 0 2304 2335 58191719 58191688 6.510000e-05 60.2
51 TraesCS4D01G126000 chr5A 76.554 354 49 23 4417 4739 311975464 311975114 4.820000e-36 163.0
52 TraesCS4D01G126000 chr5A 91.453 117 10 0 4860 4976 311974991 311974875 1.740000e-35 161.0
53 TraesCS4D01G126000 chr5A 73.850 413 83 17 2395 2806 311977379 311976991 2.260000e-29 141.0
54 TraesCS4D01G126000 chr5A 86.364 110 13 2 5305 5413 24741825 24741717 1.060000e-22 119.0
55 TraesCS4D01G126000 chr7D 95.890 73 3 0 5304 5376 112955098 112955170 1.060000e-22 119.0
56 TraesCS4D01G126000 chr7D 86.747 83 7 4 4094 4176 479597486 479597564 8.300000e-14 89.8
57 TraesCS4D01G126000 chr7D 79.775 89 9 4 4094 4173 587384908 587384820 8.420000e-04 56.5
58 TraesCS4D01G126000 chr6A 84.874 119 17 1 1431 1549 530086113 530085996 1.060000e-22 119.0
59 TraesCS4D01G126000 chr6A 88.889 45 5 0 4131 4175 612190061 612190017 8.420000e-04 56.5
60 TraesCS4D01G126000 chrUn 85.714 112 14 2 5303 5413 79942168 79942278 3.810000e-22 117.0
61 TraesCS4D01G126000 chr2D 86.239 109 12 3 5306 5413 551933553 551933659 1.370000e-21 115.0
62 TraesCS4D01G126000 chr2D 83.516 91 6 1 4094 4175 12976017 12975927 6.470000e-10 76.8
63 TraesCS4D01G126000 chr2D 91.111 45 1 3 2304 2347 11861771 11861813 2.340000e-04 58.4
64 TraesCS4D01G126000 chr6B 83.333 126 18 3 1429 1554 17384279 17384401 4.930000e-21 113.0
65 TraesCS4D01G126000 chr6B 93.023 43 3 0 4131 4173 437477759 437477717 5.030000e-06 63.9
66 TraesCS4D01G126000 chr3A 86.842 76 8 2 4100 4175 729183925 729183852 3.860000e-12 84.2
67 TraesCS4D01G126000 chr3A 87.671 73 7 2 4100 4172 729577408 729577478 3.860000e-12 84.2
68 TraesCS4D01G126000 chr1B 85.542 83 8 3 4094 4172 474686768 474686686 3.860000e-12 84.2
69 TraesCS4D01G126000 chr1B 93.333 45 2 1 4086 4130 301588041 301588084 1.400000e-06 65.8
70 TraesCS4D01G126000 chr2B 93.333 45 3 0 4086 4130 264582701 264582657 3.890000e-07 67.6
71 TraesCS4D01G126000 chr1D 95.238 42 2 0 4131 4172 443834455 443834496 3.890000e-07 67.6
72 TraesCS4D01G126000 chr1D 80.682 88 7 5 4094 4172 299211474 299211560 6.510000e-05 60.2
73 TraesCS4D01G126000 chr7B 97.143 35 1 0 2304 2338 652133231 652133197 6.510000e-05 60.2
74 TraesCS4D01G126000 chr3D 97.059 34 1 0 2304 2337 7334008 7333975 2.340000e-04 58.4
75 TraesCS4D01G126000 chr3D 90.698 43 1 3 2303 2344 473829204 473829164 3.000000e-03 54.7
76 TraesCS4D01G126000 chr3D 96.875 32 0 1 4142 4173 450882690 450882660 1.100000e-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 TraesCS4D01G126000 chr4D 110082399 110088414 6015 False 5178.500000 9317 100.000000 1 6016 2 chr4D.!!$F3 6015
1 TraesCS4D01G126000 chr4A 466632465 466637387 4922 True 1434.820000 5269 92.051400 1 5300 5 chr4A.!!$R2 5299
2 TraesCS4D01G126000 chr4B 171616561 171621636 5075 True 1762.750000 5029 91.556500 1 5271 4 chr4B.!!$R2 5270
3 TraesCS4D01G126000 chr5D 407693419 407694077 658 True 367.333333 774 93.766667 5303 6016 3 chr5D.!!$R6 713
4 TraesCS4D01G126000 chr6D 78860932 78861586 654 True 374.500000 627 87.715000 5304 6016 2 chr6D.!!$R1 712

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
360 444 0.905357 GAGGAAGCAGGTAGGCAGAA 59.095 55.0 0.0 0.0 35.83 3.02 F
1303 1423 1.035385 TAGATGCCTGCCGAGACGAA 61.035 55.0 0.0 0.0 0.00 3.85 F
1306 1426 1.091771 ATGCCTGCCGAGACGAATTG 61.092 55.0 0.0 0.0 0.00 2.32 F
2950 3324 0.676782 GACTCCACACCCCAATTCCG 60.677 60.0 0.0 0.0 0.00 4.30 F
4112 4486 2.077687 TACTCCCTCCGTCCCATAAC 57.922 55.0 0.0 0.0 0.00 1.89 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1561 1682 0.981183 TACGAACAATGCCTCCCTGT 59.019 50.000 0.0 0.0 0.0 4.00 R
2932 3306 1.378762 CGGAATTGGGGTGTGGAGT 59.621 57.895 0.0 0.0 0.0 3.85 R
3391 3765 2.829720 TGTATCTACGTCCCAAGTGCTT 59.170 45.455 0.0 0.0 0.0 3.91 R
4803 5186 2.494059 ACAGCTCTTTACGCATGTTGT 58.506 42.857 0.0 0.0 0.0 3.32 R
5752 6139 0.259356 TTGGTCCCTTTGGTCGGTTT 59.741 50.000 0.0 0.0 0.0 3.27 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
34 35 8.572185 TCCAATTTTGTGTTCGATCTGAATTTA 58.428 29.630 3.86 0.00 39.21 1.40
40 41 7.591006 TGTGTTCGATCTGAATTTACCTTAC 57.409 36.000 3.86 0.00 39.21 2.34
117 118 6.741992 TTGAGCATCGAAATGTAAGAACAT 57.258 33.333 0.00 0.00 43.47 2.71
118 119 7.841915 TTGAGCATCGAAATGTAAGAACATA 57.158 32.000 0.00 0.00 41.60 2.29
119 120 8.437360 TTGAGCATCGAAATGTAAGAACATAT 57.563 30.769 0.00 0.00 41.60 1.78
121 122 8.892723 TGAGCATCGAAATGTAAGAACATATTT 58.107 29.630 0.00 0.00 41.60 1.40
189 251 2.806237 CGGAGGTAGGCGGAAGAC 59.194 66.667 0.00 0.00 42.06 3.01
332 410 3.118454 CAATGTCGGCGCGAGGTT 61.118 61.111 12.10 0.00 36.23 3.50
348 432 2.084546 AGGTTACAAATGCGAGGAAGC 58.915 47.619 0.00 0.00 37.71 3.86
355 439 3.298958 TGCGAGGAAGCAGGTAGG 58.701 61.111 0.00 0.00 42.92 3.18
356 440 2.202946 GCGAGGAAGCAGGTAGGC 60.203 66.667 0.00 0.00 37.05 3.93
357 441 3.019003 GCGAGGAAGCAGGTAGGCA 62.019 63.158 0.00 0.00 37.05 4.75
358 442 1.142748 CGAGGAAGCAGGTAGGCAG 59.857 63.158 0.00 0.00 35.83 4.85
359 443 1.323271 CGAGGAAGCAGGTAGGCAGA 61.323 60.000 0.00 0.00 35.83 4.26
360 444 0.905357 GAGGAAGCAGGTAGGCAGAA 59.095 55.000 0.00 0.00 35.83 3.02
361 445 1.279271 GAGGAAGCAGGTAGGCAGAAA 59.721 52.381 0.00 0.00 35.83 2.52
362 446 1.705186 AGGAAGCAGGTAGGCAGAAAA 59.295 47.619 0.00 0.00 35.83 2.29
363 447 2.108250 AGGAAGCAGGTAGGCAGAAAAA 59.892 45.455 0.00 0.00 35.83 1.94
364 448 2.489722 GGAAGCAGGTAGGCAGAAAAAG 59.510 50.000 0.00 0.00 35.83 2.27
365 449 1.539157 AGCAGGTAGGCAGAAAAAGC 58.461 50.000 0.00 0.00 35.83 3.51
373 457 2.620251 GGCAGAAAAAGCCCAAGTTT 57.380 45.000 0.00 0.00 46.50 2.66
374 458 2.483876 GGCAGAAAAAGCCCAAGTTTC 58.516 47.619 0.00 0.00 46.50 2.78
375 459 2.483876 GCAGAAAAAGCCCAAGTTTCC 58.516 47.619 0.00 0.00 32.74 3.13
383 467 1.971695 CCCAAGTTTCCACGAGGCC 60.972 63.158 0.00 0.00 33.74 5.19
395 479 4.785453 GAGGCCTGCTTGACGGGG 62.785 72.222 12.00 0.00 46.10 5.73
403 487 2.202932 CTTGACGGGGCCGAGATG 60.203 66.667 0.00 0.00 42.83 2.90
411 495 1.806542 CGGGGCCGAGATGAATAAATG 59.193 52.381 0.00 0.00 42.83 2.32
416 503 3.499918 GGCCGAGATGAATAAATGTCCTG 59.500 47.826 0.00 0.00 0.00 3.86
1090 1193 5.641709 CGGCTCTTCTTATTTCCTTTTTCC 58.358 41.667 0.00 0.00 0.00 3.13
1124 1235 5.416271 AGCTCTCCCTAATTTTCGTGTTA 57.584 39.130 0.00 0.00 0.00 2.41
1153 1264 1.682323 GGCGTTTGTTTGGTTAGGGAA 59.318 47.619 0.00 0.00 0.00 3.97
1253 1365 8.304138 GTCGTTCGTTTCAATGCTATTTTATTG 58.696 33.333 0.00 0.00 36.00 1.90
1297 1413 1.179174 AGCGTATAGATGCCTGCCGA 61.179 55.000 0.00 0.00 38.47 5.54
1303 1423 1.035385 TAGATGCCTGCCGAGACGAA 61.035 55.000 0.00 0.00 0.00 3.85
1306 1426 1.091771 ATGCCTGCCGAGACGAATTG 61.092 55.000 0.00 0.00 0.00 2.32
1325 1445 8.131100 ACGAATTGCTCCTATGATTAAATTGTG 58.869 33.333 0.00 0.00 0.00 3.33
1326 1446 8.131100 CGAATTGCTCCTATGATTAAATTGTGT 58.869 33.333 0.00 0.00 0.00 3.72
1327 1447 9.807649 GAATTGCTCCTATGATTAAATTGTGTT 57.192 29.630 0.00 0.00 0.00 3.32
1330 1450 8.984891 TGCTCCTATGATTAAATTGTGTTTTG 57.015 30.769 0.00 0.00 0.00 2.44
1331 1451 8.584157 TGCTCCTATGATTAAATTGTGTTTTGT 58.416 29.630 0.00 0.00 0.00 2.83
1337 1457 7.938563 TGATTAAATTGTGTTTTGTACCTGC 57.061 32.000 0.00 0.00 0.00 4.85
1338 1458 7.721402 TGATTAAATTGTGTTTTGTACCTGCT 58.279 30.769 0.00 0.00 0.00 4.24
1339 1459 8.200792 TGATTAAATTGTGTTTTGTACCTGCTT 58.799 29.630 0.00 0.00 0.00 3.91
1340 1460 9.685828 GATTAAATTGTGTTTTGTACCTGCTTA 57.314 29.630 0.00 0.00 0.00 3.09
1342 1462 9.522804 TTAAATTGTGTTTTGTACCTGCTTAAG 57.477 29.630 0.00 0.00 0.00 1.85
1343 1463 6.709018 ATTGTGTTTTGTACCTGCTTAAGT 57.291 33.333 4.02 0.00 0.00 2.24
1344 1464 6.518208 TTGTGTTTTGTACCTGCTTAAGTT 57.482 33.333 4.02 0.00 0.00 2.66
1345 1465 5.885881 TGTGTTTTGTACCTGCTTAAGTTG 58.114 37.500 4.02 0.00 0.00 3.16
1346 1466 5.416326 TGTGTTTTGTACCTGCTTAAGTTGT 59.584 36.000 4.02 1.99 0.00 3.32
1347 1467 5.741982 GTGTTTTGTACCTGCTTAAGTTGTG 59.258 40.000 4.02 0.00 0.00 3.33
1348 1468 4.561735 TTTGTACCTGCTTAAGTTGTGC 57.438 40.909 4.02 3.74 0.00 4.57
1523 1644 7.011382 ACTATCTCCGAGGATTTAGTATTGGT 58.989 38.462 10.55 0.00 0.00 3.67
1586 1718 3.445857 GGAGGCATTGTTCGTAGACTAC 58.554 50.000 2.24 2.24 34.32 2.73
1637 1771 4.752604 TCGCTTTGTAGCTTTGATGTTGTA 59.247 37.500 0.00 0.00 45.51 2.41
1767 1901 4.999950 AGGACTACTTCATGCTTTGTCTTG 59.000 41.667 0.00 0.00 0.00 3.02
1972 2109 5.041287 TCTGCTATTTTAGATGGAACGTCG 58.959 41.667 0.00 0.00 0.00 5.12
2010 2147 9.905713 ATGTTTATTAGTACAGATGAACCATGT 57.094 29.630 11.15 0.00 0.00 3.21
2024 2161 7.667219 AGATGAACCATGTCAGAAATTTAGTGT 59.333 33.333 0.00 0.00 0.00 3.55
2263 2602 7.678194 TTAGTGCATGAAAAGAAAGTTTTCG 57.322 32.000 0.00 0.00 41.92 3.46
2270 2609 7.547119 CATGAAAAGAAAGTTTTCGTACTTGC 58.453 34.615 4.96 0.00 41.92 4.01
2335 2677 7.760340 CGTCTTATATTTAGGAATGGAGGTAGC 59.240 40.741 0.00 0.00 0.00 3.58
2518 2892 5.541484 TGCTGACAGTGATATGGATAGTGAT 59.459 40.000 3.99 0.00 0.00 3.06
2694 3068 8.397575 TGTTGCTAATAGGTCAATTTTGTACA 57.602 30.769 0.00 0.00 0.00 2.90
2808 3182 5.122869 CACAGGTCATGTTCAGGTAATTCTG 59.877 44.000 0.00 0.00 41.41 3.02
2875 3249 5.076182 TCAACATTTGGTTAATCTCTGCCA 58.924 37.500 0.00 0.00 37.72 4.92
2950 3324 0.676782 GACTCCACACCCCAATTCCG 60.677 60.000 0.00 0.00 0.00 4.30
3459 3833 3.384789 AGCGTTGAAGATCTACAGGCATA 59.615 43.478 13.05 0.00 0.00 3.14
3637 4011 3.935828 GACAGAGAAGAAACCCTGTATGC 59.064 47.826 0.00 0.00 39.67 3.14
3670 4044 4.782156 TCACAATGCTGATGTTAACGTTG 58.218 39.130 11.99 0.00 35.61 4.10
3861 4235 3.808174 AGGTACTTTCGTCTTGACAAAGC 59.192 43.478 17.24 8.59 27.25 3.51
3881 4255 3.062639 AGCACATTTTTCTATGCTCGTCG 59.937 43.478 0.00 0.00 45.11 5.12
3917 4291 3.031013 ACTTCAAAGGGGTGTTTTCCTG 58.969 45.455 0.00 0.00 32.95 3.86
4084 4458 6.145535 GGCATGTTATTGCTAGTAGAATTGC 58.854 40.000 0.00 5.17 42.38 3.56
4112 4486 2.077687 TACTCCCTCCGTCCCATAAC 57.922 55.000 0.00 0.00 0.00 1.89
4239 4617 3.921119 CTGCCAAAATCACTGCAGTTA 57.079 42.857 18.94 10.56 44.69 2.24
4240 4618 3.568538 CTGCCAAAATCACTGCAGTTAC 58.431 45.455 18.94 0.00 44.69 2.50
4664 5047 2.168936 AGATGCAGAAGAGGAAGCTGAG 59.831 50.000 0.00 0.00 0.00 3.35
4745 5128 4.448210 TCTTTGTTCACCAGGTACTTGAC 58.552 43.478 6.55 0.00 34.60 3.18
4746 5129 3.916359 TTGTTCACCAGGTACTTGACA 57.084 42.857 6.55 0.00 34.60 3.58
4803 5186 2.642129 CATGTGTCGCGGCCAAAA 59.358 55.556 8.89 0.00 0.00 2.44
4811 5194 2.656807 CGCGGCCAAAACAACATGC 61.657 57.895 2.24 0.00 0.00 4.06
4884 5269 4.281941 AGGGCCAGAAAGATTTGAAAGAAC 59.718 41.667 6.18 0.00 0.00 3.01
4910 5295 0.109342 GGCATCCACAGATACCTGGG 59.891 60.000 0.00 0.00 44.60 4.45
4991 5376 0.465097 CCATAGCTGGGGCAGACAAG 60.465 60.000 0.00 0.00 41.70 3.16
5025 5410 3.620488 CCACTTGGCTAATTCAAGGCTA 58.380 45.455 9.45 0.00 44.13 3.93
5080 5465 6.373216 AGGACAATACTGCGAGTATCTATCTC 59.627 42.308 8.61 0.00 40.32 2.75
5119 5504 8.286800 TGTATTTTATGTTTCTCTGTTTCGTGG 58.713 33.333 0.00 0.00 0.00 4.94
5133 5518 1.924731 TCGTGGAGACAACCATCTCT 58.075 50.000 3.00 0.00 46.06 3.10
5134 5519 3.081710 TCGTGGAGACAACCATCTCTA 57.918 47.619 3.00 0.00 46.06 2.43
5139 5524 4.806247 GTGGAGACAACCATCTCTATTTCG 59.194 45.833 3.00 0.00 46.06 3.46
5195 5580 6.483640 GGATGATACTCACCAAATTACCTGAC 59.516 42.308 0.00 0.00 0.00 3.51
5228 5613 7.562454 TCTACTTTTGACACCGAAGAATTTT 57.438 32.000 0.00 0.00 0.00 1.82
5291 5676 2.224606 CGCTGATCACCAAATAGCCAT 58.775 47.619 0.00 0.00 0.00 4.40
5300 5685 6.357579 TCACCAAATAGCCATCAATTGTTT 57.642 33.333 5.13 0.00 0.00 2.83
5301 5686 6.767456 TCACCAAATAGCCATCAATTGTTTT 58.233 32.000 5.13 0.00 0.00 2.43
5380 5765 2.874701 GGCAGCATCCACACATACTTAG 59.125 50.000 0.00 0.00 0.00 2.18
5384 5769 3.123804 GCATCCACACATACTTAGGTCG 58.876 50.000 0.00 0.00 0.00 4.79
5387 5772 5.520632 CATCCACACATACTTAGGTCGTAG 58.479 45.833 0.00 0.00 0.00 3.51
5388 5773 3.949754 TCCACACATACTTAGGTCGTAGG 59.050 47.826 0.00 0.00 0.00 3.18
5389 5774 3.490419 CCACACATACTTAGGTCGTAGGC 60.490 52.174 0.00 0.00 0.00 3.93
5390 5775 3.380637 CACACATACTTAGGTCGTAGGCT 59.619 47.826 0.00 0.00 0.00 4.58
5391 5776 4.021916 ACACATACTTAGGTCGTAGGCTT 58.978 43.478 0.00 0.00 0.00 4.35
5392 5777 4.142227 ACACATACTTAGGTCGTAGGCTTG 60.142 45.833 0.00 0.00 0.00 4.01
5394 5779 4.708421 ACATACTTAGGTCGTAGGCTTGAA 59.292 41.667 0.00 0.00 0.00 2.69
5395 5780 5.363005 ACATACTTAGGTCGTAGGCTTGAAT 59.637 40.000 0.00 0.00 0.00 2.57
5396 5781 6.548622 ACATACTTAGGTCGTAGGCTTGAATA 59.451 38.462 0.00 0.00 0.00 1.75
5397 5782 5.927281 ACTTAGGTCGTAGGCTTGAATAA 57.073 39.130 0.00 0.00 0.00 1.40
5398 5783 6.290294 ACTTAGGTCGTAGGCTTGAATAAA 57.710 37.500 0.00 0.00 0.00 1.40
5399 5784 6.704310 ACTTAGGTCGTAGGCTTGAATAAAA 58.296 36.000 0.00 0.00 0.00 1.52
5400 5785 6.592994 ACTTAGGTCGTAGGCTTGAATAAAAC 59.407 38.462 0.00 0.00 0.00 2.43
5401 5786 4.901868 AGGTCGTAGGCTTGAATAAAACA 58.098 39.130 0.00 0.00 0.00 2.83
5402 5787 4.935808 AGGTCGTAGGCTTGAATAAAACAG 59.064 41.667 0.00 0.00 0.00 3.16
5403 5788 4.694037 GGTCGTAGGCTTGAATAAAACAGT 59.306 41.667 0.00 0.00 0.00 3.55
5404 5789 5.163884 GGTCGTAGGCTTGAATAAAACAGTC 60.164 44.000 0.00 0.00 0.00 3.51
5405 5790 5.407387 GTCGTAGGCTTGAATAAAACAGTCA 59.593 40.000 0.00 0.00 0.00 3.41
5406 5791 6.092259 GTCGTAGGCTTGAATAAAACAGTCAT 59.908 38.462 0.00 0.00 29.94 3.06
5407 5792 6.312918 TCGTAGGCTTGAATAAAACAGTCATC 59.687 38.462 0.00 0.00 29.94 2.92
5408 5793 5.551760 AGGCTTGAATAAAACAGTCATCG 57.448 39.130 0.00 0.00 29.94 3.84
5409 5794 5.245531 AGGCTTGAATAAAACAGTCATCGA 58.754 37.500 0.00 0.00 29.94 3.59
5410 5795 5.352569 AGGCTTGAATAAAACAGTCATCGAG 59.647 40.000 0.00 0.00 29.94 4.04
5411 5796 5.024555 GCTTGAATAAAACAGTCATCGAGC 58.975 41.667 0.00 0.00 37.21 5.03
5412 5797 5.545658 TTGAATAAAACAGTCATCGAGCC 57.454 39.130 0.00 0.00 29.94 4.70
5413 5798 3.616821 TGAATAAAACAGTCATCGAGCCG 59.383 43.478 0.00 0.00 0.00 5.52
5414 5799 2.736144 TAAAACAGTCATCGAGCCGT 57.264 45.000 0.00 0.00 0.00 5.68
5415 5800 2.736144 AAAACAGTCATCGAGCCGTA 57.264 45.000 0.00 0.00 0.00 4.02
5416 5801 2.279582 AAACAGTCATCGAGCCGTAG 57.720 50.000 0.00 0.00 0.00 3.51
5482 5868 6.720288 AGCTAAGAAGGAACAGACAGTAGTTA 59.280 38.462 0.00 0.00 0.00 2.24
5515 5901 2.662006 CGGAGCATCAAGAAGACAGA 57.338 50.000 0.00 0.00 36.25 3.41
5516 5902 3.176552 CGGAGCATCAAGAAGACAGAT 57.823 47.619 0.00 0.00 36.25 2.90
5517 5903 4.313277 CGGAGCATCAAGAAGACAGATA 57.687 45.455 0.00 0.00 36.25 1.98
5518 5904 4.297510 CGGAGCATCAAGAAGACAGATAG 58.702 47.826 0.00 0.00 36.25 2.08
5519 5905 4.057432 GGAGCATCAAGAAGACAGATAGC 58.943 47.826 0.00 0.00 36.25 2.97
5520 5906 4.202243 GGAGCATCAAGAAGACAGATAGCT 60.202 45.833 0.00 0.00 36.25 3.32
5521 5907 5.010516 GGAGCATCAAGAAGACAGATAGCTA 59.989 44.000 0.00 0.00 36.25 3.32
5522 5908 6.462207 GGAGCATCAAGAAGACAGATAGCTAA 60.462 42.308 0.00 0.00 36.25 3.09
5523 5909 6.882656 AGCATCAAGAAGACAGATAGCTAAA 58.117 36.000 0.00 0.00 30.24 1.85
5524 5910 7.334090 AGCATCAAGAAGACAGATAGCTAAAA 58.666 34.615 0.00 0.00 30.24 1.52
5525 5911 7.495279 AGCATCAAGAAGACAGATAGCTAAAAG 59.505 37.037 0.00 0.00 30.24 2.27
5526 5912 7.254727 GCATCAAGAAGACAGATAGCTAAAAGG 60.255 40.741 0.00 0.00 0.00 3.11
5527 5913 7.482169 TCAAGAAGACAGATAGCTAAAAGGA 57.518 36.000 0.00 0.00 0.00 3.36
5528 5914 7.551585 TCAAGAAGACAGATAGCTAAAAGGAG 58.448 38.462 0.00 0.00 0.00 3.69
5529 5915 5.912892 AGAAGACAGATAGCTAAAAGGAGC 58.087 41.667 0.00 0.00 43.19 4.70
5530 5916 5.423610 AGAAGACAGATAGCTAAAAGGAGCA 59.576 40.000 0.00 0.00 45.43 4.26
5531 5917 5.885449 AGACAGATAGCTAAAAGGAGCAT 57.115 39.130 0.00 0.00 45.43 3.79
5532 5918 5.852827 AGACAGATAGCTAAAAGGAGCATC 58.147 41.667 0.00 0.00 45.43 3.91
5533 5919 5.365025 AGACAGATAGCTAAAAGGAGCATCA 59.635 40.000 0.00 0.00 45.43 3.07
5534 5920 5.994250 ACAGATAGCTAAAAGGAGCATCAA 58.006 37.500 0.00 0.00 45.43 2.57
5535 5921 6.054295 ACAGATAGCTAAAAGGAGCATCAAG 58.946 40.000 0.00 0.00 45.43 3.02
5536 5922 6.126940 ACAGATAGCTAAAAGGAGCATCAAGA 60.127 38.462 0.00 0.00 45.43 3.02
5537 5923 6.765036 CAGATAGCTAAAAGGAGCATCAAGAA 59.235 38.462 0.00 0.00 45.43 2.52
5538 5924 6.991531 AGATAGCTAAAAGGAGCATCAAGAAG 59.008 38.462 0.00 0.00 45.43 2.85
5539 5925 5.171339 AGCTAAAAGGAGCATCAAGAAGA 57.829 39.130 0.00 0.00 45.43 2.87
5540 5926 4.940654 AGCTAAAAGGAGCATCAAGAAGAC 59.059 41.667 0.00 0.00 45.43 3.01
5541 5927 4.697352 GCTAAAAGGAGCATCAAGAAGACA 59.303 41.667 0.00 0.00 42.36 3.41
5542 5928 5.356470 GCTAAAAGGAGCATCAAGAAGACAT 59.644 40.000 0.00 0.00 42.36 3.06
5600 5986 0.108615 CCGTCTTGTCGAGCCTTCAT 60.109 55.000 0.00 0.00 0.00 2.57
5652 6038 1.733041 CATGCGTTCCTCGTCACGT 60.733 57.895 0.00 0.00 42.13 4.49
5661 6047 0.032952 CCTCGTCACGTTTCTTCCCA 59.967 55.000 0.00 0.00 0.00 4.37
5663 6049 1.525619 CTCGTCACGTTTCTTCCCAAC 59.474 52.381 0.00 0.00 0.00 3.77
5668 6054 1.281656 CGTTTCTTCCCAACGGTGC 59.718 57.895 0.00 0.00 42.68 5.01
5669 6055 1.440938 CGTTTCTTCCCAACGGTGCA 61.441 55.000 0.00 0.00 42.68 4.57
5674 6061 1.280710 TCTTCCCAACGGTGCACATAT 59.719 47.619 20.43 0.00 0.00 1.78
5720 6107 0.695462 TGATATCAGCAGGGTGGGCT 60.695 55.000 0.00 0.00 43.77 5.19
5752 6139 5.009110 TGTGCTCAATCGTAATTTTGTTCCA 59.991 36.000 0.00 0.00 0.00 3.53
5882 6269 5.236047 TGGATTCCAATTTTGTTTGAAAGCG 59.764 36.000 1.94 0.00 0.00 4.68
5915 6302 2.289694 ACTCCACGCAAATCTAGCAAGT 60.290 45.455 0.00 0.00 0.00 3.16
5965 6352 1.128809 TCCCCTAAACCGCAAGTGGA 61.129 55.000 6.67 0.00 0.00 4.02
5979 6366 3.228017 TGGAGCACGTTCCGTCCA 61.228 61.111 1.94 1.80 38.32 4.02
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
34 35 6.942576 TCTCTGTTTTACCTACTACGTAAGGT 59.057 38.462 20.04 20.04 46.39 3.50
40 41 5.041940 GCCATCTCTGTTTTACCTACTACG 58.958 45.833 0.00 0.00 0.00 3.51
121 122 9.529823 TCTGAGACTAAATCTTGGTTAGTTCTA 57.470 33.333 0.00 0.00 40.93 2.10
247 315 4.072088 CAACAGGAACGGCGCGAC 62.072 66.667 12.10 5.80 0.00 5.19
326 404 2.004583 TCCTCGCATTTGTAACCTCG 57.995 50.000 0.00 0.00 0.00 4.63
327 405 2.096013 GCTTCCTCGCATTTGTAACCTC 59.904 50.000 0.00 0.00 0.00 3.85
328 406 2.084546 GCTTCCTCGCATTTGTAACCT 58.915 47.619 0.00 0.00 0.00 3.50
329 407 1.810151 TGCTTCCTCGCATTTGTAACC 59.190 47.619 0.00 0.00 34.44 2.85
331 409 2.083774 CCTGCTTCCTCGCATTTGTAA 58.916 47.619 0.00 0.00 39.52 2.41
332 410 1.003118 ACCTGCTTCCTCGCATTTGTA 59.997 47.619 0.00 0.00 39.52 2.41
355 439 2.158971 TGGAAACTTGGGCTTTTTCTGC 60.159 45.455 0.00 0.00 31.21 4.26
356 440 3.457234 GTGGAAACTTGGGCTTTTTCTG 58.543 45.455 0.00 0.00 31.21 3.02
357 441 2.100749 CGTGGAAACTTGGGCTTTTTCT 59.899 45.455 0.00 0.00 31.21 2.52
358 442 2.100087 TCGTGGAAACTTGGGCTTTTTC 59.900 45.455 0.00 0.00 0.00 2.29
359 443 2.100749 CTCGTGGAAACTTGGGCTTTTT 59.899 45.455 0.00 0.00 0.00 1.94
360 444 1.681264 CTCGTGGAAACTTGGGCTTTT 59.319 47.619 0.00 0.00 0.00 2.27
361 445 1.318576 CTCGTGGAAACTTGGGCTTT 58.681 50.000 0.00 0.00 0.00 3.51
362 446 0.537371 CCTCGTGGAAACTTGGGCTT 60.537 55.000 0.00 0.00 34.57 4.35
363 447 1.073199 CCTCGTGGAAACTTGGGCT 59.927 57.895 0.00 0.00 34.57 5.19
364 448 2.626780 GCCTCGTGGAAACTTGGGC 61.627 63.158 7.92 0.00 34.57 5.36
365 449 1.971695 GGCCTCGTGGAAACTTGGG 60.972 63.158 7.92 0.00 34.57 4.12
366 450 1.073199 AGGCCTCGTGGAAACTTGG 59.927 57.895 7.92 0.00 34.57 3.61
367 451 1.856265 GCAGGCCTCGTGGAAACTTG 61.856 60.000 0.00 0.00 34.57 3.16
368 452 1.600916 GCAGGCCTCGTGGAAACTT 60.601 57.895 0.00 0.00 34.57 2.66
369 453 2.032681 GCAGGCCTCGTGGAAACT 59.967 61.111 0.00 0.00 34.57 2.66
370 454 1.600916 AAGCAGGCCTCGTGGAAAC 60.601 57.895 0.00 0.00 34.57 2.78
371 455 1.600636 CAAGCAGGCCTCGTGGAAA 60.601 57.895 0.00 0.00 34.57 3.13
372 456 2.032528 CAAGCAGGCCTCGTGGAA 59.967 61.111 0.00 0.00 34.57 3.53
373 457 2.922503 TCAAGCAGGCCTCGTGGA 60.923 61.111 0.00 0.00 34.57 4.02
374 458 2.743928 GTCAAGCAGGCCTCGTGG 60.744 66.667 0.00 0.00 0.00 4.94
375 459 3.114616 CGTCAAGCAGGCCTCGTG 61.115 66.667 0.00 7.05 0.00 4.35
395 479 4.380531 TCAGGACATTTATTCATCTCGGC 58.619 43.478 0.00 0.00 0.00 5.54
399 483 5.455899 GGGCTCTCAGGACATTTATTCATCT 60.456 44.000 0.00 0.00 0.00 2.90
403 487 3.879892 GTGGGCTCTCAGGACATTTATTC 59.120 47.826 0.00 0.00 0.00 1.75
411 495 2.262915 CACGTGGGCTCTCAGGAC 59.737 66.667 7.95 0.00 0.00 3.85
974 1073 0.179086 GCTAAGGCTGAGAGGTCTGC 60.179 60.000 2.00 0.00 44.73 4.26
1090 1193 2.971330 AGGGAGAGCTTATCATCAGTGG 59.029 50.000 0.00 0.00 0.00 4.00
1124 1235 1.460273 AAACAAACGCCGCCCAAGAT 61.460 50.000 0.00 0.00 0.00 2.40
1153 1264 1.002430 TGAAGCATCAGCCTTCTTCGT 59.998 47.619 0.00 0.00 43.56 3.85
1216 1327 1.226323 CGAACGACTAGTGCTCCCG 60.226 63.158 0.00 0.00 0.00 5.14
1227 1339 7.948513 ATAAAATAGCATTGAAACGAACGAC 57.051 32.000 0.14 0.00 0.00 4.34
1230 1342 9.937577 GAACAATAAAATAGCATTGAAACGAAC 57.062 29.630 0.00 0.00 36.00 3.95
1253 1365 8.991243 TCCAATCAATCAATCAATCAAAGAAC 57.009 30.769 0.00 0.00 0.00 3.01
1297 1413 8.562892 CAATTTAATCATAGGAGCAATTCGTCT 58.437 33.333 0.00 0.00 0.00 4.18
1306 1426 8.986477 ACAAAACACAATTTAATCATAGGAGC 57.014 30.769 0.00 0.00 0.00 4.70
1325 1445 4.738252 GCACAACTTAAGCAGGTACAAAAC 59.262 41.667 1.29 0.00 0.00 2.43
1326 1446 4.642885 AGCACAACTTAAGCAGGTACAAAA 59.357 37.500 1.29 0.00 0.00 2.44
1327 1447 4.204012 AGCACAACTTAAGCAGGTACAAA 58.796 39.130 1.29 0.00 0.00 2.83
1328 1448 3.815809 AGCACAACTTAAGCAGGTACAA 58.184 40.909 1.29 0.00 0.00 2.41
1329 1449 3.485463 AGCACAACTTAAGCAGGTACA 57.515 42.857 1.29 0.00 0.00 2.90
1330 1450 4.515567 AGAAAGCACAACTTAAGCAGGTAC 59.484 41.667 1.29 0.00 37.75 3.34
1331 1451 4.714632 AGAAAGCACAACTTAAGCAGGTA 58.285 39.130 1.29 0.00 37.75 3.08
1332 1452 3.555966 AGAAAGCACAACTTAAGCAGGT 58.444 40.909 1.29 0.00 37.75 4.00
1333 1453 4.276926 AGAAGAAAGCACAACTTAAGCAGG 59.723 41.667 1.29 0.00 37.75 4.85
1334 1454 5.210715 CAGAAGAAAGCACAACTTAAGCAG 58.789 41.667 1.29 0.00 37.75 4.24
1335 1455 4.640201 ACAGAAGAAAGCACAACTTAAGCA 59.360 37.500 1.29 0.00 37.75 3.91
1336 1456 5.175090 ACAGAAGAAAGCACAACTTAAGC 57.825 39.130 1.29 0.00 37.75 3.09
1337 1457 7.020914 AGAACAGAAGAAAGCACAACTTAAG 57.979 36.000 0.00 0.00 37.75 1.85
1338 1458 6.597672 TGAGAACAGAAGAAAGCACAACTTAA 59.402 34.615 0.00 0.00 37.75 1.85
1339 1459 6.112734 TGAGAACAGAAGAAAGCACAACTTA 58.887 36.000 0.00 0.00 37.75 2.24
1340 1460 4.943705 TGAGAACAGAAGAAAGCACAACTT 59.056 37.500 0.00 0.00 41.70 2.66
1341 1461 4.517285 TGAGAACAGAAGAAAGCACAACT 58.483 39.130 0.00 0.00 0.00 3.16
1342 1462 4.882671 TGAGAACAGAAGAAAGCACAAC 57.117 40.909 0.00 0.00 0.00 3.32
1343 1463 4.261322 GCATGAGAACAGAAGAAAGCACAA 60.261 41.667 0.00 0.00 0.00 3.33
1344 1464 3.251729 GCATGAGAACAGAAGAAAGCACA 59.748 43.478 0.00 0.00 0.00 4.57
1345 1465 3.501445 AGCATGAGAACAGAAGAAAGCAC 59.499 43.478 0.00 0.00 0.00 4.40
1346 1466 3.748083 AGCATGAGAACAGAAGAAAGCA 58.252 40.909 0.00 0.00 0.00 3.91
1347 1467 5.163774 CCTTAGCATGAGAACAGAAGAAAGC 60.164 44.000 0.00 0.00 0.00 3.51
1348 1468 6.169094 TCCTTAGCATGAGAACAGAAGAAAG 58.831 40.000 0.00 0.00 0.00 2.62
1523 1644 2.364002 GTTTTACCTCAAGCAAGGCCAA 59.636 45.455 5.01 0.00 40.34 4.52
1561 1682 0.981183 TACGAACAATGCCTCCCTGT 59.019 50.000 0.00 0.00 0.00 4.00
1586 1718 9.483062 GTGAATCTTTGAGAACAGATAATTTCG 57.517 33.333 0.00 0.00 0.00 3.46
1593 1725 5.121454 GCGAAGTGAATCTTTGAGAACAGAT 59.879 40.000 0.00 0.00 39.30 2.90
1597 1729 4.999751 AGCGAAGTGAATCTTTGAGAAC 57.000 40.909 0.00 0.00 39.30 3.01
1767 1901 4.756084 ACTGTAATCTCAGTTTTGCTGC 57.244 40.909 0.00 0.00 44.92 5.25
1791 1926 4.825422 TCTCTATGTGGCAGAACAGAAAG 58.175 43.478 0.00 0.00 32.52 2.62
2010 2147 5.335897 GCAAGCATCCACACTAAATTTCTGA 60.336 40.000 0.00 0.00 0.00 3.27
2024 2161 2.824689 TAAATGGGAGCAAGCATCCA 57.175 45.000 8.41 8.41 38.70 3.41
2262 2601 6.335777 AGGTAGTAAATGGTAAGCAAGTACG 58.664 40.000 0.00 0.00 0.00 3.67
2263 2602 9.657419 TTTAGGTAGTAAATGGTAAGCAAGTAC 57.343 33.333 0.00 0.00 0.00 2.73
2270 2609 7.107542 TGGCAGTTTAGGTAGTAAATGGTAAG 58.892 38.462 0.00 0.00 33.11 2.34
2335 2677 5.974158 TGTGTGGAAACGTAAATGAAACATG 59.026 36.000 0.00 0.00 0.00 3.21
2518 2892 4.221482 TCTTCTTCTTCATCACTGCTGCTA 59.779 41.667 0.00 0.00 0.00 3.49
2808 3182 9.561270 GTAAATAAAGAGAAATGAGAGCCAAAC 57.439 33.333 0.00 0.00 0.00 2.93
2875 3249 4.624913 TCTATCTGTTCCTGGGAAGATGT 58.375 43.478 11.87 2.96 34.49 3.06
2932 3306 1.378762 CGGAATTGGGGTGTGGAGT 59.621 57.895 0.00 0.00 0.00 3.85
3391 3765 2.829720 TGTATCTACGTCCCAAGTGCTT 59.170 45.455 0.00 0.00 0.00 3.91
3637 4011 4.454678 TCAGCATTGTGAGCCTTAATAGG 58.545 43.478 0.00 0.00 45.02 2.57
3670 4044 7.229581 AGTAAATATACCGATTCCAGGAGAC 57.770 40.000 0.00 0.00 32.08 3.36
3861 4235 3.370978 ACCGACGAGCATAGAAAAATGTG 59.629 43.478 0.00 0.00 0.00 3.21
3881 4255 3.343941 TGAAGTGGGTAGTATGCAACC 57.656 47.619 0.00 0.00 34.85 3.77
3917 4291 6.720012 ACAAATCAGAAAAACACAAACCAC 57.280 33.333 0.00 0.00 0.00 4.16
4084 4458 4.262506 GGGACGGAGGGAGTATCAAATTAG 60.263 50.000 0.00 0.00 36.25 1.73
4130 4506 7.696453 CCCATAATGTAAGTCATTTTTCGACAC 59.304 37.037 0.00 0.00 43.33 3.67
4143 4519 2.704065 CCCTCCGTCCCATAATGTAAGT 59.296 50.000 0.00 0.00 0.00 2.24
4239 4617 5.483685 ACATACTGATTGTGGTAGTGTGT 57.516 39.130 0.00 0.00 40.44 3.72
4240 4618 5.390885 GCAACATACTGATTGTGGTAGTGTG 60.391 44.000 0.00 0.00 38.84 3.82
4349 4727 4.929808 AGAGTTGACGTGAACATACCATTC 59.070 41.667 20.00 6.78 0.00 2.67
4664 5047 4.214971 TGCTCTTTCATCTTTGCTCTGAAC 59.785 41.667 0.00 0.00 0.00 3.18
4745 5128 5.656213 AGCCATCTTCAGGAGAAATTTTG 57.344 39.130 0.00 0.00 38.06 2.44
4746 5129 6.676990 AAAGCCATCTTCAGGAGAAATTTT 57.323 33.333 0.00 0.00 38.06 1.82
4803 5186 2.494059 ACAGCTCTTTACGCATGTTGT 58.506 42.857 0.00 0.00 0.00 3.32
4811 5194 5.177696 ACTTGCTTCTTTACAGCTCTTTACG 59.822 40.000 0.00 0.00 38.19 3.18
4895 5280 2.866923 TCATCCCAGGTATCTGTGGA 57.133 50.000 13.59 13.59 41.34 4.02
5115 5500 4.392921 AATAGAGATGGTTGTCTCCACG 57.607 45.455 0.59 0.00 44.55 4.94
5119 5504 5.411781 ACACGAAATAGAGATGGTTGTCTC 58.588 41.667 0.00 0.00 43.95 3.36
5356 5741 0.911053 TATGTGTGGATGCTGCCTGA 59.089 50.000 0.00 0.00 0.00 3.86
5380 5765 4.694037 ACTGTTTTATTCAAGCCTACGACC 59.306 41.667 0.00 0.00 0.00 4.79
5384 5769 6.312918 TCGATGACTGTTTTATTCAAGCCTAC 59.687 38.462 0.00 0.00 0.00 3.18
5387 5772 5.545658 TCGATGACTGTTTTATTCAAGCC 57.454 39.130 0.00 0.00 0.00 4.35
5388 5773 5.024555 GCTCGATGACTGTTTTATTCAAGC 58.975 41.667 0.00 0.00 0.00 4.01
5389 5774 5.563842 GGCTCGATGACTGTTTTATTCAAG 58.436 41.667 0.00 0.00 0.00 3.02
5390 5775 4.092821 CGGCTCGATGACTGTTTTATTCAA 59.907 41.667 0.00 0.00 0.00 2.69
5391 5776 3.616821 CGGCTCGATGACTGTTTTATTCA 59.383 43.478 0.00 0.00 0.00 2.57
5392 5777 3.617263 ACGGCTCGATGACTGTTTTATTC 59.383 43.478 1.50 0.00 0.00 1.75
5394 5779 3.247006 ACGGCTCGATGACTGTTTTAT 57.753 42.857 1.50 0.00 0.00 1.40
5395 5780 2.736144 ACGGCTCGATGACTGTTTTA 57.264 45.000 1.50 0.00 0.00 1.52
5396 5781 2.607187 CTACGGCTCGATGACTGTTTT 58.393 47.619 1.50 0.00 0.00 2.43
5397 5782 1.135083 CCTACGGCTCGATGACTGTTT 60.135 52.381 1.50 0.00 0.00 2.83
5398 5783 0.456221 CCTACGGCTCGATGACTGTT 59.544 55.000 1.50 0.00 0.00 3.16
5399 5784 2.005960 GCCTACGGCTCGATGACTGT 62.006 60.000 0.00 0.00 46.69 3.55
5400 5785 1.299468 GCCTACGGCTCGATGACTG 60.299 63.158 0.00 0.00 46.69 3.51
5401 5786 3.121019 GCCTACGGCTCGATGACT 58.879 61.111 0.00 0.00 46.69 3.41
5411 5796 4.693566 TGACTGTTTTATTGAAGCCTACGG 59.306 41.667 0.00 0.00 0.00 4.02
5412 5797 5.856126 TGACTGTTTTATTGAAGCCTACG 57.144 39.130 0.00 0.00 0.00 3.51
5413 5798 6.312918 TCGATGACTGTTTTATTGAAGCCTAC 59.687 38.462 0.00 0.00 0.00 3.18
5414 5799 6.403049 TCGATGACTGTTTTATTGAAGCCTA 58.597 36.000 0.00 0.00 0.00 3.93
5415 5800 5.245531 TCGATGACTGTTTTATTGAAGCCT 58.754 37.500 0.00 0.00 0.00 4.58
5416 5801 5.545658 TCGATGACTGTTTTATTGAAGCC 57.454 39.130 0.00 0.00 0.00 4.35
5417 5802 5.024555 GCTCGATGACTGTTTTATTGAAGC 58.975 41.667 0.00 0.00 0.00 3.86
5418 5803 5.563842 GGCTCGATGACTGTTTTATTGAAG 58.436 41.667 0.00 0.00 0.00 3.02
5419 5804 4.092821 CGGCTCGATGACTGTTTTATTGAA 59.907 41.667 0.00 0.00 0.00 2.69
5420 5805 3.616821 CGGCTCGATGACTGTTTTATTGA 59.383 43.478 0.00 0.00 0.00 2.57
5421 5806 3.370978 ACGGCTCGATGACTGTTTTATTG 59.629 43.478 1.50 0.00 0.00 1.90
5482 5868 3.266510 TGCTCCGCTTTTGTGATCTAT 57.733 42.857 0.00 0.00 0.00 1.98
5512 5898 6.286758 TCTTGATGCTCCTTTTAGCTATCTG 58.713 40.000 0.00 0.00 43.19 2.90
5515 5901 6.765512 GTCTTCTTGATGCTCCTTTTAGCTAT 59.234 38.462 0.00 0.00 43.19 2.97
5516 5902 6.109359 GTCTTCTTGATGCTCCTTTTAGCTA 58.891 40.000 0.00 0.00 43.19 3.32
5517 5903 4.940654 GTCTTCTTGATGCTCCTTTTAGCT 59.059 41.667 0.00 0.00 43.19 3.32
5518 5904 4.697352 TGTCTTCTTGATGCTCCTTTTAGC 59.303 41.667 0.00 0.00 43.08 3.09
5519 5905 6.998968 ATGTCTTCTTGATGCTCCTTTTAG 57.001 37.500 0.00 0.00 0.00 1.85
5520 5906 9.770097 CTATATGTCTTCTTGATGCTCCTTTTA 57.230 33.333 0.00 0.00 0.00 1.52
5521 5907 7.228308 GCTATATGTCTTCTTGATGCTCCTTTT 59.772 37.037 0.00 0.00 0.00 2.27
5522 5908 6.709846 GCTATATGTCTTCTTGATGCTCCTTT 59.290 38.462 0.00 0.00 0.00 3.11
5523 5909 6.043012 AGCTATATGTCTTCTTGATGCTCCTT 59.957 38.462 0.00 0.00 0.00 3.36
5524 5910 5.543405 AGCTATATGTCTTCTTGATGCTCCT 59.457 40.000 0.00 0.00 0.00 3.69
5525 5911 5.792741 AGCTATATGTCTTCTTGATGCTCC 58.207 41.667 0.00 0.00 0.00 4.70
5526 5912 8.824159 TTTAGCTATATGTCTTCTTGATGCTC 57.176 34.615 0.00 0.00 0.00 4.26
5527 5913 9.270640 CTTTTAGCTATATGTCTTCTTGATGCT 57.729 33.333 0.00 0.00 0.00 3.79
5528 5914 9.050601 ACTTTTAGCTATATGTCTTCTTGATGC 57.949 33.333 0.00 0.00 0.00 3.91
5542 5928 9.815306 ACCATGAGATCTCTACTTTTAGCTATA 57.185 33.333 22.95 0.00 0.00 1.31
5600 5986 3.181457 GGAGCTGATCAAGATGACCATGA 60.181 47.826 0.00 0.00 0.00 3.07
5652 6038 0.394488 TGTGCACCGTTGGGAAGAAA 60.394 50.000 15.69 0.00 36.97 2.52
5661 6047 2.236146 TCCTTCAGATATGTGCACCGTT 59.764 45.455 15.69 1.55 0.00 4.44
5663 6049 2.602257 TCCTTCAGATATGTGCACCG 57.398 50.000 15.69 0.00 0.00 4.94
5664 6050 5.126061 ACATTTTCCTTCAGATATGTGCACC 59.874 40.000 15.69 0.00 32.09 5.01
5666 6052 5.945191 TCACATTTTCCTTCAGATATGTGCA 59.055 36.000 0.00 0.00 42.25 4.57
5667 6053 6.127925 TGTCACATTTTCCTTCAGATATGTGC 60.128 38.462 0.00 0.00 42.25 4.57
5668 6054 7.381766 TGTCACATTTTCCTTCAGATATGTG 57.618 36.000 0.00 0.00 43.02 3.21
5669 6055 8.585471 AATGTCACATTTTCCTTCAGATATGT 57.415 30.769 0.00 0.00 32.97 2.29
5674 6061 6.957920 TCAAATGTCACATTTTCCTTCAGA 57.042 33.333 13.35 3.29 0.00 3.27
5720 6107 1.202758 ACGATTGAGCACAAGTTCCCA 60.203 47.619 2.37 0.00 39.46 4.37
5752 6139 0.259356 TTGGTCCCTTTGGTCGGTTT 59.741 50.000 0.00 0.00 0.00 3.27
5882 6269 0.456312 CGTGGAGTGCGGTTAGAGAC 60.456 60.000 0.00 0.00 0.00 3.36
5915 6302 1.333308 CACGTGTTCTTTGGATGTGCA 59.667 47.619 7.58 0.00 0.00 4.57
5979 6366 3.679738 CAAACGCAATGGGCCGGT 61.680 61.111 1.90 0.00 40.31 5.28


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

AutoCloner maintained by Alex Coulton.