Multiple sequence alignment - TraesCS3D01G491900

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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 TraesCS3D01G491900 chr3D 100.000 7328 0 0 1 7328 585716285 585708958 0.000000e+00 13533.0
1 TraesCS3D01G491900 chr3D 83.723 1837 193 52 4792 6597 585652653 585654414 0.000000e+00 1639.0
2 TraesCS3D01G491900 chr3D 83.487 1841 201 50 4792 6599 585433227 585431457 0.000000e+00 1620.0
3 TraesCS3D01G491900 chr3D 83.241 1629 165 47 4999 6597 585617344 585618894 0.000000e+00 1397.0
4 TraesCS3D01G491900 chr3D 87.287 1172 130 10 3620 4787 585912211 585911055 0.000000e+00 1321.0
5 TraesCS3D01G491900 chr3D 83.677 1262 154 23 1790 3014 585635619 585636865 0.000000e+00 1142.0
6 TraesCS3D01G491900 chr3D 87.097 1023 97 14 1702 2708 585630762 585631765 0.000000e+00 1125.0
7 TraesCS3D01G491900 chr3D 83.888 1142 136 27 1595 2708 585435964 585434843 0.000000e+00 1046.0
8 TraesCS3D01G491900 chr3D 86.224 980 98 18 1673 2635 585612914 585613873 0.000000e+00 1027.0
9 TraesCS3D01G491900 chr3D 84.804 1020 105 20 1702 2706 585649964 585650948 0.000000e+00 979.0
10 TraesCS3D01G491900 chr3D 84.962 931 109 18 1793 2708 585402080 585401166 0.000000e+00 915.0
11 TraesCS3D01G491900 chr3D 84.174 575 59 13 4251 4795 585433834 585433262 5.030000e-146 529.0
12 TraesCS3D01G491900 chr3D 78.977 899 96 33 5729 6599 585467968 585467135 1.810000e-145 527.0
13 TraesCS3D01G491900 chr3D 84.877 529 58 10 1793 2308 585664788 585665307 1.410000e-141 514.0
14 TraesCS3D01G491900 chr3D 85.569 492 58 10 2710 3200 585615242 585615721 3.050000e-138 503.0
15 TraesCS3D01G491900 chr3D 84.242 495 61 10 2710 3200 585631798 585632279 4.000000e-127 466.0
16 TraesCS3D01G491900 chr3D 83.943 492 66 8 2710 3200 585650983 585651462 6.700000e-125 459.0
17 TraesCS3D01G491900 chr3D 77.625 581 63 39 807 1361 585611346 585611885 2.590000e-74 291.0
18 TraesCS3D01G491900 chr3D 85.252 278 22 10 1541 1817 585629823 585630082 1.210000e-67 268.0
19 TraesCS3D01G491900 chr3D 82.174 230 26 7 1589 1817 585612152 585612367 4.520000e-42 183.0
20 TraesCS3D01G491900 chr3D 89.231 130 9 1 1589 1713 585915545 585915416 2.740000e-34 158.0
21 TraesCS3D01G491900 chr3D 88.333 120 9 2 6480 6599 585655166 585655280 9.910000e-29 139.0
22 TraesCS3D01G491900 chr3D 97.619 42 1 0 3173 3214 585912692 585912651 1.020000e-08 73.1
23 TraesCS3D01G491900 chr3D 94.737 38 0 2 1380 1415 585611932 585611969 2.860000e-04 58.4
24 TraesCS3D01G491900 chr3B 91.922 4692 278 52 1840 6464 781556625 781551968 0.000000e+00 6471.0
25 TraesCS3D01G491900 chr3B 96.538 2513 72 9 3456 5957 782115039 782112531 0.000000e+00 4145.0
26 TraesCS3D01G491900 chr3B 82.539 2056 242 55 4251 6241 781671748 781669745 0.000000e+00 1700.0
27 TraesCS3D01G491900 chr3B 84.213 1837 192 45 4792 6598 781837192 781835424 0.000000e+00 1696.0
28 TraesCS3D01G491900 chr3B 83.279 1836 235 47 4792 6599 782341818 782340027 0.000000e+00 1624.0
29 TraesCS3D01G491900 chr3B 97.517 886 18 3 2587 3470 782115935 782115052 0.000000e+00 1511.0
30 TraesCS3D01G491900 chr3B 88.354 1288 67 29 805 2044 782117896 782116644 0.000000e+00 1471.0
31 TraesCS3D01G491900 chr3B 88.642 1171 124 8 3619 4785 782483046 782481881 0.000000e+00 1417.0
32 TraesCS3D01G491900 chr3B 83.736 1574 168 44 1672 3200 781839914 781838384 0.000000e+00 1408.0
33 TraesCS3D01G491900 chr3B 82.606 1696 193 58 1690 3333 782344570 782342925 0.000000e+00 1404.0
34 TraesCS3D01G491900 chr3B 87.380 1046 100 13 3778 4795 782342894 782341853 0.000000e+00 1171.0
35 TraesCS3D01G491900 chr3B 98.545 550 8 0 2039 2588 782116566 782116017 0.000000e+00 972.0
36 TraesCS3D01G491900 chr3B 83.816 933 113 23 1793 2708 781810313 781809402 0.000000e+00 852.0
37 TraesCS3D01G491900 chr3B 82.952 962 89 33 2312 3217 781854193 781853251 0.000000e+00 798.0
38 TraesCS3D01G491900 chr3B 84.085 754 75 22 6463 7205 782112051 782111332 0.000000e+00 686.0
39 TraesCS3D01G491900 chr3B 89.516 496 36 3 2738 3217 782484094 782483599 1.350000e-171 614.0
40 TraesCS3D01G491900 chr3B 92.644 435 13 11 6050 6465 782112524 782112090 6.290000e-170 608.0
41 TraesCS3D01G491900 chr3B 92.429 317 17 3 1 312 782118735 782118421 5.220000e-121 446.0
42 TraesCS3D01G491900 chr3B 90.149 335 16 9 479 804 782118277 782117951 3.160000e-113 420.0
43 TraesCS3D01G491900 chr3B 91.837 294 22 1 4502 4795 781837518 781837227 6.840000e-110 409.0
44 TraesCS3D01G491900 chr3B 78.397 574 64 35 805 1361 781843777 781843247 1.190000e-82 318.0
45 TraesCS3D01G491900 chr3B 90.805 174 12 2 150 322 781844266 781844096 5.720000e-56 230.0
46 TraesCS3D01G491900 chr3B 80.117 342 21 18 6278 6599 781669745 781669431 2.070000e-50 211.0
47 TraesCS3D01G491900 chr3B 91.379 116 10 0 43 158 781844402 781844287 7.610000e-35 159.0
48 TraesCS3D01G491900 chr3B 86.885 122 14 2 7011 7131 461732979 461733099 1.280000e-27 135.0
49 TraesCS3D01G491900 chr3B 84.106 151 10 6 1670 1820 781840692 781840556 4.610000e-27 134.0
50 TraesCS3D01G491900 chr3B 90.588 85 7 1 232 315 781859911 781859827 2.160000e-20 111.0
51 TraesCS3D01G491900 chr3B 93.478 46 1 2 1380 1423 781843201 781843156 4.740000e-07 67.6
52 TraesCS3D01G491900 chrUn 83.303 1629 164 47 4999 6597 321264022 321265572 0.000000e+00 1402.0
53 TraesCS3D01G491900 chrUn 82.526 1362 133 45 5264 6597 300190850 300192134 0.000000e+00 1099.0
54 TraesCS3D01G491900 chrUn 85.569 492 58 10 2710 3200 358608604 358609083 3.050000e-138 503.0
55 TraesCS3D01G491900 chrUn 83.784 74 5 6 6844 6913 322970906 322970836 6.140000e-06 63.9
56 TraesCS3D01G491900 chrUn 83.784 74 5 6 6844 6913 322980578 322980508 6.140000e-06 63.9
57 TraesCS3D01G491900 chrUn 85.075 67 5 5 6844 6908 338433511 338433574 6.140000e-06 63.9
58 TraesCS3D01G491900 chrUn 83.784 74 5 6 6844 6913 373634435 373634365 6.140000e-06 63.9
59 TraesCS3D01G491900 chr4D 90.019 1042 90 9 4954 5990 340550106 340549074 0.000000e+00 1336.0
60 TraesCS3D01G491900 chr4D 86.087 1150 123 16 3672 4789 340552118 340550974 0.000000e+00 1203.0
61 TraesCS3D01G491900 chr4D 87.526 481 43 7 2710 3184 340552597 340552128 2.330000e-149 540.0
62 TraesCS3D01G491900 chr4D 84.064 251 30 9 6131 6372 340548861 340548612 4.420000e-57 233.0
63 TraesCS3D01G491900 chr4B 89.215 1057 100 9 4954 6006 422031713 422030667 0.000000e+00 1308.0
64 TraesCS3D01G491900 chr4B 86.580 1155 121 17 3671 4795 422033736 422032586 0.000000e+00 1243.0
65 TraesCS3D01G491900 chr4B 87.318 481 44 7 2710 3184 422034214 422033745 1.080000e-147 534.0
66 TraesCS3D01G491900 chr4B 85.141 249 30 4 6131 6372 422030375 422030127 1.580000e-61 248.0
67 TraesCS3D01G491900 chr4B 96.970 33 1 0 3273 3305 3579188 3579156 1.000000e-03 56.5
68 TraesCS3D01G491900 chr4A 87.247 839 100 6 3671 4504 127484022 127484858 0.000000e+00 950.0
69 TraesCS3D01G491900 chr4A 86.038 838 111 6 3671 4504 127288727 127287892 0.000000e+00 894.0
70 TraesCS3D01G491900 chr4A 83.115 918 92 32 2309 3184 127289632 127288736 0.000000e+00 778.0
71 TraesCS3D01G491900 chr4A 87.344 482 43 9 2710 3184 127483543 127484013 3.010000e-148 536.0
72 TraesCS3D01G491900 chr4A 91.873 283 22 1 4507 4789 127484915 127485196 1.920000e-105 394.0
73 TraesCS3D01G491900 chr4A 84.462 251 29 7 6131 6372 127487297 127487546 9.500000e-59 239.0
74 TraesCS3D01G491900 chr4A 84.431 167 22 4 7011 7175 484242834 484242998 2.120000e-35 161.0
75 TraesCS3D01G491900 chr7B 77.474 293 52 11 6926 7212 700440988 700441272 5.880000e-36 163.0
76 TraesCS3D01G491900 chr5A 77.689 251 41 13 6991 7232 505285515 505285271 9.910000e-29 139.0


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 TraesCS3D01G491900 chr3D 585708958 585716285 7327 True 13533.000000 13533 100.000000 1 7328 1 chr3D.!!$R3 7327
1 TraesCS3D01G491900 chr3D 585431457 585435964 4507 True 1065.000000 1620 83.849667 1595 6599 3 chr3D.!!$R4 5004
2 TraesCS3D01G491900 chr3D 585401166 585402080 914 True 915.000000 915 84.962000 1793 2708 1 chr3D.!!$R1 915
3 TraesCS3D01G491900 chr3D 585649964 585655280 5316 False 804.000000 1639 85.200750 1702 6599 4 chr3D.!!$F4 4897
4 TraesCS3D01G491900 chr3D 585629823 585636865 7042 False 750.250000 1142 85.067000 1541 3200 4 chr3D.!!$F3 1659
5 TraesCS3D01G491900 chr3D 585611346 585618894 7548 False 576.566667 1397 84.928333 807 6597 6 chr3D.!!$F2 5790
6 TraesCS3D01G491900 chr3D 585467135 585467968 833 True 527.000000 527 78.977000 5729 6599 1 chr3D.!!$R2 870
7 TraesCS3D01G491900 chr3D 585911055 585915545 4490 True 517.366667 1321 91.379000 1589 4787 3 chr3D.!!$R5 3198
8 TraesCS3D01G491900 chr3D 585664788 585665307 519 False 514.000000 514 84.877000 1793 2308 1 chr3D.!!$F1 515
9 TraesCS3D01G491900 chr3B 781551968 781556625 4657 True 6471.000000 6471 91.922000 1840 6464 1 chr3B.!!$R1 4624
10 TraesCS3D01G491900 chr3B 782340027 782344570 4543 True 1399.666667 1624 84.421667 1690 6599 3 chr3B.!!$R8 4909
11 TraesCS3D01G491900 chr3B 782111332 782118735 7403 True 1282.375000 4145 92.532625 1 7205 8 chr3B.!!$R7 7204
12 TraesCS3D01G491900 chr3B 782481881 782484094 2213 True 1015.500000 1417 89.079000 2738 4785 2 chr3B.!!$R9 2047
13 TraesCS3D01G491900 chr3B 781669431 781671748 2317 True 955.500000 1700 81.328000 4251 6599 2 chr3B.!!$R5 2348
14 TraesCS3D01G491900 chr3B 781809402 781810313 911 True 852.000000 852 83.816000 1793 2708 1 chr3B.!!$R2 915
15 TraesCS3D01G491900 chr3B 781853251 781854193 942 True 798.000000 798 82.952000 2312 3217 1 chr3B.!!$R3 905
16 TraesCS3D01G491900 chr3B 781835424 781844402 8978 True 552.700000 1696 87.243875 43 6598 8 chr3B.!!$R6 6555
17 TraesCS3D01G491900 chrUn 321264022 321265572 1550 False 1402.000000 1402 83.303000 4999 6597 1 chrUn.!!$F2 1598
18 TraesCS3D01G491900 chrUn 300190850 300192134 1284 False 1099.000000 1099 82.526000 5264 6597 1 chrUn.!!$F1 1333
19 TraesCS3D01G491900 chr4D 340548612 340552597 3985 True 828.000000 1336 86.924000 2710 6372 4 chr4D.!!$R1 3662
20 TraesCS3D01G491900 chr4B 422030127 422034214 4087 True 833.250000 1308 87.063500 2710 6372 4 chr4B.!!$R2 3662
21 TraesCS3D01G491900 chr4A 127287892 127289632 1740 True 836.000000 894 84.576500 2309 4504 2 chr4A.!!$R1 2195
22 TraesCS3D01G491900 chr4A 127483543 127487546 4003 False 529.750000 950 87.731500 2710 6372 4 chr4A.!!$F2 3662

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
318 353 0.105224 TACACCTTGTCACACCACGG 59.895 55.000 0.00 0.00 0.00 4.94 F
357 392 0.108585 AGCGCAGTTCTTTTCCCTCA 59.891 50.000 11.47 0.00 0.00 3.86 F
1133 1310 0.173708 GAAGAGAACGACCAGCCGAT 59.826 55.000 0.00 0.00 0.00 4.18 F
1134 1311 0.173708 AAGAGAACGACCAGCCGATC 59.826 55.000 0.00 0.00 0.00 3.69 F
1276 1475 0.179056 CAATTCTCGCCGGGGTGTAT 60.179 55.000 19.13 12.35 0.00 2.29 F
1483 1761 0.394352 AACATTCACCTCATCCGGCC 60.394 55.000 0.00 0.00 0.00 6.13 F
3499 10244 0.033504 GGAGTTGACTTCTGGCGACA 59.966 55.000 0.00 0.00 39.59 4.35 F
4435 11476 4.478317 AGGATGACAATATTCCCAACCTGA 59.522 41.667 12.03 0.00 31.79 3.86 F
5507 13712 0.537371 GCTTGCGGCCATATTACCCT 60.537 55.000 2.24 0.00 34.27 4.34 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1276 1475 0.781787 CAACGACGACGCAGAATCAA 59.218 50.0 7.3 0.0 43.96 2.57 R
1481 1759 1.172812 ACTTTCAAGTCCAAGCGGGC 61.173 55.0 0.0 0.0 32.86 6.13 R
2662 7759 3.274288 CTGATTTAAGTGGGAGTCAGGC 58.726 50.0 0.0 0.0 31.77 4.85 R
2699 7804 6.560253 AAACAAGGTGAACTGCTAATGTAG 57.440 37.5 0.0 0.0 0.00 2.74 R
3499 10244 2.958355 GAGCCTGACTTCTCTGCTAGAT 59.042 50.0 0.0 0.0 33.05 1.98 R
3614 10360 2.484742 AACATGACCCGTTACCTTCC 57.515 50.0 0.0 0.0 0.00 3.46 R
4533 11632 0.744771 GGGCGTCAAATCTCCAGACC 60.745 60.0 0.0 0.0 0.00 3.85 R
5763 14214 0.886563 AGAGCCATCAACAAAGCTGC 59.113 50.0 0.0 0.0 35.23 5.25 R
6660 17767 1.523758 ATGAAAAGCTGGTGGTCGTC 58.476 50.0 0.0 0.0 0.00 4.20 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
57 59 4.451150 GCCATCCCACGACGCTCA 62.451 66.667 0.00 0.00 0.00 4.26
217 248 4.967575 CCGTTTATTTTGCCAAGTATAGCG 59.032 41.667 0.00 0.00 0.00 4.26
221 252 7.519328 CGTTTATTTTGCCAAGTATAGCGGTAT 60.519 37.037 12.42 12.42 0.00 2.73
222 253 8.776470 GTTTATTTTGCCAAGTATAGCGGTATA 58.224 33.333 10.22 10.22 0.00 1.47
225 256 6.653526 TTTGCCAAGTATAGCGGTATAGTA 57.346 37.500 19.48 4.41 0.00 1.82
226 257 6.845758 TTGCCAAGTATAGCGGTATAGTAT 57.154 37.500 19.48 9.40 0.00 2.12
228 259 6.860080 TGCCAAGTATAGCGGTATAGTATTC 58.140 40.000 19.48 12.54 0.00 1.75
229 260 6.662234 TGCCAAGTATAGCGGTATAGTATTCT 59.338 38.462 19.48 8.68 0.00 2.40
230 261 7.177921 TGCCAAGTATAGCGGTATAGTATTCTT 59.822 37.037 19.48 13.34 0.00 2.52
315 350 1.474320 GCAGTACACCTTGTCACACCA 60.474 52.381 0.00 0.00 0.00 4.17
316 351 2.210116 CAGTACACCTTGTCACACCAC 58.790 52.381 0.00 0.00 0.00 4.16
317 352 1.202486 AGTACACCTTGTCACACCACG 60.202 52.381 0.00 0.00 0.00 4.94
318 353 0.105224 TACACCTTGTCACACCACGG 59.895 55.000 0.00 0.00 0.00 4.94
319 354 1.145156 CACCTTGTCACACCACGGA 59.855 57.895 0.00 0.00 0.00 4.69
320 355 0.880278 CACCTTGTCACACCACGGAG 60.880 60.000 0.00 0.00 0.00 4.63
322 357 0.677288 CCTTGTCACACCACGGAGTA 59.323 55.000 0.00 0.00 41.61 2.59
323 358 1.275291 CCTTGTCACACCACGGAGTAT 59.725 52.381 0.00 0.00 41.61 2.12
324 359 2.494471 CCTTGTCACACCACGGAGTATA 59.506 50.000 0.00 0.00 41.61 1.47
325 360 3.132289 CCTTGTCACACCACGGAGTATAT 59.868 47.826 0.00 0.00 41.61 0.86
326 361 4.340097 CCTTGTCACACCACGGAGTATATA 59.660 45.833 0.00 0.00 41.61 0.86
327 362 5.507482 CCTTGTCACACCACGGAGTATATAG 60.507 48.000 0.00 0.00 41.61 1.31
328 363 4.529897 TGTCACACCACGGAGTATATAGT 58.470 43.478 0.00 0.00 41.61 2.12
329 364 4.951715 TGTCACACCACGGAGTATATAGTT 59.048 41.667 0.00 0.00 41.61 2.24
330 365 5.419788 TGTCACACCACGGAGTATATAGTTT 59.580 40.000 0.00 0.00 41.61 2.66
331 366 5.975939 GTCACACCACGGAGTATATAGTTTC 59.024 44.000 0.00 0.00 41.61 2.78
332 367 5.889853 TCACACCACGGAGTATATAGTTTCT 59.110 40.000 0.00 0.00 41.61 2.52
333 368 7.012704 GTCACACCACGGAGTATATAGTTTCTA 59.987 40.741 0.00 0.00 41.61 2.10
334 369 7.557358 TCACACCACGGAGTATATAGTTTCTAA 59.443 37.037 0.00 0.00 41.61 2.10
335 370 7.646922 CACACCACGGAGTATATAGTTTCTAAC 59.353 40.741 0.00 0.00 41.61 2.34
336 371 6.854892 CACCACGGAGTATATAGTTTCTAACG 59.145 42.308 0.00 0.00 41.61 3.18
337 372 6.767902 ACCACGGAGTATATAGTTTCTAACGA 59.232 38.462 0.00 0.00 41.61 3.85
338 373 7.283127 ACCACGGAGTATATAGTTTCTAACGAA 59.717 37.037 0.00 0.00 41.61 3.85
339 374 7.802251 CCACGGAGTATATAGTTTCTAACGAAG 59.198 40.741 0.00 0.00 41.61 3.79
340 375 7.323177 CACGGAGTATATAGTTTCTAACGAAGC 59.677 40.741 0.00 0.00 41.61 3.86
341 376 6.519078 CGGAGTATATAGTTTCTAACGAAGCG 59.481 42.308 0.00 0.00 35.75 4.68
342 377 6.305160 GGAGTATATAGTTTCTAACGAAGCGC 59.695 42.308 0.00 0.00 35.75 5.92
343 378 6.732154 AGTATATAGTTTCTAACGAAGCGCA 58.268 36.000 11.47 0.00 35.75 6.09
344 379 6.856938 AGTATATAGTTTCTAACGAAGCGCAG 59.143 38.462 11.47 2.53 35.75 5.18
345 380 2.150397 AGTTTCTAACGAAGCGCAGT 57.850 45.000 11.47 3.31 35.75 4.40
346 381 2.480845 AGTTTCTAACGAAGCGCAGTT 58.519 42.857 11.47 15.31 35.75 3.16
347 382 2.475487 AGTTTCTAACGAAGCGCAGTTC 59.525 45.455 11.47 4.49 35.75 3.01
348 383 2.433868 TTCTAACGAAGCGCAGTTCT 57.566 45.000 11.47 0.00 0.00 3.01
349 384 2.433868 TCTAACGAAGCGCAGTTCTT 57.566 45.000 11.47 4.95 0.00 2.52
350 385 2.750948 TCTAACGAAGCGCAGTTCTTT 58.249 42.857 11.47 8.25 0.00 2.52
351 386 3.128349 TCTAACGAAGCGCAGTTCTTTT 58.872 40.909 11.47 4.44 0.00 2.27
352 387 2.384899 AACGAAGCGCAGTTCTTTTC 57.615 45.000 11.47 1.08 0.00 2.29
353 388 0.586802 ACGAAGCGCAGTTCTTTTCC 59.413 50.000 11.47 0.00 0.00 3.13
354 389 0.110192 CGAAGCGCAGTTCTTTTCCC 60.110 55.000 11.47 0.00 0.00 3.97
355 390 1.239347 GAAGCGCAGTTCTTTTCCCT 58.761 50.000 11.47 0.00 0.00 4.20
356 391 1.197949 GAAGCGCAGTTCTTTTCCCTC 59.802 52.381 11.47 0.00 0.00 4.30
357 392 0.108585 AGCGCAGTTCTTTTCCCTCA 59.891 50.000 11.47 0.00 0.00 3.86
358 393 0.951558 GCGCAGTTCTTTTCCCTCAA 59.048 50.000 0.30 0.00 0.00 3.02
359 394 1.336755 GCGCAGTTCTTTTCCCTCAAA 59.663 47.619 0.30 0.00 0.00 2.69
360 395 2.223711 GCGCAGTTCTTTTCCCTCAAAA 60.224 45.455 0.30 0.00 32.77 2.44
361 396 3.736740 GCGCAGTTCTTTTCCCTCAAAAA 60.737 43.478 0.30 0.00 33.40 1.94
398 433 3.414700 CACCTTCACGCTCACGGC 61.415 66.667 0.00 0.00 46.04 5.68
399 434 4.681978 ACCTTCACGCTCACGGCC 62.682 66.667 0.00 0.00 46.04 6.13
401 436 4.680237 CTTCACGCTCACGGCCCA 62.680 66.667 0.00 0.00 46.04 5.36
402 437 4.980805 TTCACGCTCACGGCCCAC 62.981 66.667 0.00 0.00 46.04 4.61
471 511 0.675837 CGGAGTAGACCCTCACACGA 60.676 60.000 0.00 0.00 32.91 4.35
472 512 1.096416 GGAGTAGACCCTCACACGAG 58.904 60.000 0.00 0.00 39.16 4.18
474 514 0.966370 AGTAGACCCTCACACGAGCC 60.966 60.000 0.00 0.00 38.00 4.70
475 515 0.966370 GTAGACCCTCACACGAGCCT 60.966 60.000 0.00 0.00 38.00 4.58
494 572 2.705220 CGCATGCATCACACCTCG 59.295 61.111 19.57 0.00 0.00 4.63
510 595 1.733416 CTCGTCGCGCATGTACACAG 61.733 60.000 8.75 0.00 0.00 3.66
554 639 6.433847 TCCAGAGAAAACACCAATTCTAGA 57.566 37.500 0.00 0.00 36.08 2.43
582 667 4.342772 CACGCGAAAATTAATAAGCAGCT 58.657 39.130 15.93 0.00 0.00 4.24
608 693 0.738762 CAGGATCGTGACTGGTGCAG 60.739 60.000 9.87 0.00 37.52 4.41
714 799 4.637483 GCGCATGCACCCAATATATTAT 57.363 40.909 19.57 0.00 42.15 1.28
715 800 4.353737 GCGCATGCACCCAATATATTATG 58.646 43.478 19.57 0.00 42.15 1.90
755 840 3.776656 GCAATAGCGACGTTCCGT 58.223 55.556 0.00 0.00 45.10 4.69
756 841 2.075761 GCAATAGCGACGTTCCGTT 58.924 52.632 0.00 0.00 41.37 4.44
909 1060 2.165437 CGACAGAGGAGAAAGAGGAAGG 59.835 54.545 0.00 0.00 0.00 3.46
1017 1181 3.160557 GATGGTGATGCTGACGCGC 62.161 63.158 5.73 0.00 39.65 6.86
1024 1194 2.862436 TGCTGACGCGCATCTTTG 59.138 55.556 5.73 0.00 39.65 2.77
1027 1197 3.386867 CTGACGCGCATCTTTGCCC 62.387 63.158 5.73 0.00 46.57 5.36
1030 1200 2.200170 GACGCGCATCTTTGCCCTTT 62.200 55.000 5.73 0.00 46.57 3.11
1040 1210 0.410270 TTTGCCCTTTCCCCGGTTAT 59.590 50.000 0.00 0.00 0.00 1.89
1059 1234 3.728373 CCGCCCCCACCTAAGCTT 61.728 66.667 3.48 3.48 0.00 3.74
1060 1235 2.438434 CGCCCCCACCTAAGCTTG 60.438 66.667 9.86 0.00 0.00 4.01
1062 1237 2.763215 CCCCCACCTAAGCTTGCA 59.237 61.111 9.86 0.00 0.00 4.08
1063 1238 1.379044 CCCCCACCTAAGCTTGCAG 60.379 63.158 9.86 0.00 0.00 4.41
1064 1239 2.048603 CCCCACCTAAGCTTGCAGC 61.049 63.158 9.86 0.47 42.84 5.25
1073 1248 4.885426 GCTTGCAGCTATGGCCTA 57.115 55.556 3.32 0.00 38.45 3.93
1074 1249 3.336122 GCTTGCAGCTATGGCCTAT 57.664 52.632 3.32 0.00 38.45 2.57
1075 1250 0.879765 GCTTGCAGCTATGGCCTATG 59.120 55.000 3.32 0.00 38.45 2.23
1132 1309 0.894184 AGAAGAGAACGACCAGCCGA 60.894 55.000 0.00 0.00 0.00 5.54
1133 1310 0.173708 GAAGAGAACGACCAGCCGAT 59.826 55.000 0.00 0.00 0.00 4.18
1134 1311 0.173708 AAGAGAACGACCAGCCGATC 59.826 55.000 0.00 0.00 0.00 3.69
1135 1312 1.586564 GAGAACGACCAGCCGATCG 60.587 63.158 8.51 8.51 43.97 3.69
1136 1313 1.989966 GAGAACGACCAGCCGATCGA 61.990 60.000 18.66 0.00 40.86 3.59
1137 1314 1.065928 GAACGACCAGCCGATCGAT 59.934 57.895 18.66 0.00 40.86 3.59
1138 1315 0.935366 GAACGACCAGCCGATCGATC 60.935 60.000 18.66 15.68 40.86 3.69
1187 1364 3.827898 CCGTCCTCCGCTCCACTC 61.828 72.222 0.00 0.00 34.38 3.51
1188 1365 2.752238 CGTCCTCCGCTCCACTCT 60.752 66.667 0.00 0.00 0.00 3.24
1190 1367 2.363018 TCCTCCGCTCCACTCTGG 60.363 66.667 0.00 0.00 39.43 3.86
1205 1401 0.322816 TCTGGATTTGGTGAGGCTGC 60.323 55.000 0.00 0.00 0.00 5.25
1228 1424 1.318576 CGGGATTTGGCCAGGTAATC 58.681 55.000 17.08 17.08 0.00 1.75
1232 1428 2.101415 GGATTTGGCCAGGTAATCAAGC 59.899 50.000 23.68 10.18 31.47 4.01
1240 1439 2.016318 CAGGTAATCAAGCCAATCGCA 58.984 47.619 0.00 0.00 41.38 5.10
1251 1450 0.935898 CCAATCGCACTGCTCATCTC 59.064 55.000 0.00 0.00 0.00 2.75
1255 1454 2.514871 CGCACTGCTCATCTCTGCG 61.515 63.158 0.00 0.00 44.06 5.18
1273 1472 3.508840 GCAATTCTCGCCGGGGTG 61.509 66.667 19.13 16.40 0.00 4.61
1276 1475 0.179056 CAATTCTCGCCGGGGTGTAT 60.179 55.000 19.13 12.35 0.00 2.29
1427 1663 4.424711 GGATTGCGGTGCCCCTGA 62.425 66.667 0.00 0.00 0.00 3.86
1480 1758 2.009774 GACCAACATTCACCTCATCCG 58.990 52.381 0.00 0.00 0.00 4.18
1481 1759 1.340017 ACCAACATTCACCTCATCCGG 60.340 52.381 0.00 0.00 0.00 5.14
1482 1760 0.734889 CAACATTCACCTCATCCGGC 59.265 55.000 0.00 0.00 0.00 6.13
1483 1761 0.394352 AACATTCACCTCATCCGGCC 60.394 55.000 0.00 0.00 0.00 6.13
1535 1813 9.666626 CTGAGTACTGACTTATCGGTTAATTAG 57.333 37.037 0.00 0.00 42.10 1.73
1556 1834 8.924511 ATTAGATGGTTTATTGATTGATCGGT 57.075 30.769 0.00 0.00 0.00 4.69
1643 1977 4.248691 TCTGATTCTGATGCTCATACCG 57.751 45.455 0.00 0.00 0.00 4.02
1679 4185 6.013842 TGTGTCTACAGTCATTGAGTAGTG 57.986 41.667 10.97 0.34 37.20 2.74
1719 4253 4.855388 GTGTTAGCTCATTCATTGTTGCAG 59.145 41.667 0.00 0.00 0.00 4.41
1720 4254 2.649331 AGCTCATTCATTGTTGCAGC 57.351 45.000 0.00 0.00 0.00 5.25
1721 4255 1.890489 AGCTCATTCATTGTTGCAGCA 59.110 42.857 0.00 0.00 0.00 4.41
1865 5403 4.686839 TCTATGTGTCGTCTCTGTCTTG 57.313 45.455 0.00 0.00 0.00 3.02
1896 5435 3.286751 GCACCCAAAGCACGAGCA 61.287 61.111 7.77 0.00 45.49 4.26
2159 5802 1.681780 CCTTTAATTGCCCTCGCCAGA 60.682 52.381 0.00 0.00 0.00 3.86
2548 6266 8.770322 TCATCAAATGGAAATTATGGAAATGGT 58.230 29.630 0.00 0.00 0.00 3.55
2662 7759 1.162698 CTCAGACTTGTGGGCATGTG 58.837 55.000 0.00 0.00 33.81 3.21
2679 7784 1.771854 TGTGCCTGACTCCCACTTAAA 59.228 47.619 0.00 0.00 0.00 1.52
2690 7795 6.269077 TGACTCCCACTTAAATCAGTTAGTCA 59.731 38.462 0.00 0.00 36.76 3.41
3390 10106 3.067106 TCAGCTACTTTCTTTCCTTGCG 58.933 45.455 0.00 0.00 0.00 4.85
3445 10161 2.873133 AGCACCGTAGCTGATACTTC 57.127 50.000 0.00 0.00 44.66 3.01
3499 10244 0.033504 GGAGTTGACTTCTGGCGACA 59.966 55.000 0.00 0.00 39.59 4.35
3624 10404 5.992729 TGATTTTCTTTTCGGAAGGTAACG 58.007 37.500 0.00 0.00 46.39 3.18
3704 10484 5.181245 AGACTTGTACCACATATTGTTGCAC 59.819 40.000 0.00 0.00 0.00 4.57
3728 10508 5.918011 CGCTTTCAAAGGTAATTGCTTTGTA 59.082 36.000 0.00 0.00 38.69 2.41
3994 10825 4.934075 TCTTTCTGATTCACTGAATGCG 57.066 40.909 9.08 0.55 36.59 4.73
4435 11476 4.478317 AGGATGACAATATTCCCAACCTGA 59.522 41.667 12.03 0.00 31.79 3.86
4480 11521 8.378172 ACATAACGTATGTAGATCAATTTGGG 57.622 34.615 8.34 0.00 46.90 4.12
4562 11662 2.022240 TTTGACGCCCCCTTGTTTGC 62.022 55.000 0.00 0.00 0.00 3.68
5399 13604 4.061131 TGAGTGGATGGTTCTCTAGGAA 57.939 45.455 0.00 0.00 0.00 3.36
5462 13667 6.603599 GGCCAAGTACCAAGAATTATCTTCTT 59.396 38.462 0.00 0.00 44.11 2.52
5507 13712 0.537371 GCTTGCGGCCATATTACCCT 60.537 55.000 2.24 0.00 34.27 4.34
5763 14214 4.212004 CAGTGATATGTTAGATGCCAACCG 59.788 45.833 0.00 0.00 0.00 4.44
5983 15845 0.823356 TGGAGCAAAGACTGGCCAAC 60.823 55.000 7.01 3.90 0.00 3.77
6057 16148 1.962807 TGCAGCTGCCAACAAGTAATT 59.037 42.857 34.64 0.00 41.18 1.40
6061 16166 4.797275 GCAGCTGCCAACAAGTAATTTCTT 60.797 41.667 28.76 0.00 34.31 2.52
6154 16320 2.908626 GCTTGAGGTTTTACAATTCGCG 59.091 45.455 0.00 0.00 0.00 5.87
6161 16332 1.454201 TTTACAATTCGCGGGCATGA 58.546 45.000 6.13 0.00 0.00 3.07
6315 16493 0.676782 CGGCCTTCCTTACCAACCTG 60.677 60.000 0.00 0.00 0.00 4.00
6413 16610 4.206404 CGTCGCAATGGTGTGTAAGTATAG 59.794 45.833 0.00 0.00 36.58 1.31
6465 16668 0.250858 CCCTGACAGTGAACCATGCA 60.251 55.000 0.00 0.00 0.00 3.96
6467 16670 2.165167 CCTGACAGTGAACCATGCATT 58.835 47.619 0.00 0.00 0.00 3.56
6470 16673 4.218200 CCTGACAGTGAACCATGCATTTTA 59.782 41.667 0.00 0.00 0.00 1.52
6471 16674 5.119931 TGACAGTGAACCATGCATTTTAC 57.880 39.130 0.00 0.00 0.00 2.01
6472 16675 4.022416 TGACAGTGAACCATGCATTTTACC 60.022 41.667 0.00 0.00 0.00 2.85
6473 16676 3.057596 ACAGTGAACCATGCATTTTACCG 60.058 43.478 0.00 0.00 0.00 4.02
6474 16677 3.190327 CAGTGAACCATGCATTTTACCGA 59.810 43.478 0.00 0.00 0.00 4.69
6475 16678 3.823873 AGTGAACCATGCATTTTACCGAA 59.176 39.130 0.00 0.00 0.00 4.30
6508 16751 3.386768 TGTTTGAGTGACTAGTCCTGC 57.613 47.619 20.11 10.25 0.00 4.85
6616 17723 2.328099 CGAACAAGCCAGCTCCCAC 61.328 63.158 0.00 0.00 0.00 4.61
6617 17724 1.973812 GAACAAGCCAGCTCCCACC 60.974 63.158 0.00 0.00 0.00 4.61
6665 17772 2.660064 ATGGACAGGGCTGGACGAC 61.660 63.158 0.00 0.00 34.19 4.34
6677 17784 0.534203 TGGACGACCACCAGCTTTTC 60.534 55.000 1.37 0.00 41.77 2.29
6680 17787 1.880027 GACGACCACCAGCTTTTCATT 59.120 47.619 0.00 0.00 0.00 2.57
6817 17926 3.845775 CGTATTGGCAAAATGTTCGTGAG 59.154 43.478 3.01 0.00 0.00 3.51
6824 17933 4.564769 GGCAAAATGTTCGTGAGTTTGAAA 59.435 37.500 0.00 0.00 32.18 2.69
6967 18083 8.716646 AAAACAATTTTCTGGAATTTCGAACT 57.283 26.923 0.00 0.00 0.00 3.01
6968 18084 7.698836 AACAATTTTCTGGAATTTCGAACTG 57.301 32.000 0.00 0.00 0.00 3.16
7016 18132 8.994429 ATGTTCACAAAACTCAAACAATGTTA 57.006 26.923 0.00 0.00 33.92 2.41
7028 18144 8.196771 ACTCAAACAATGTTAGCTGATTCAAAA 58.803 29.630 0.00 0.00 0.00 2.44
7029 18145 8.351495 TCAAACAATGTTAGCTGATTCAAAAC 57.649 30.769 0.00 0.00 0.00 2.43
7030 18146 7.978414 TCAAACAATGTTAGCTGATTCAAAACA 59.022 29.630 0.00 0.00 34.81 2.83
7031 18147 8.602328 CAAACAATGTTAGCTGATTCAAAACAA 58.398 29.630 0.00 0.23 34.08 2.83
7032 18148 8.891671 AACAATGTTAGCTGATTCAAAACAAT 57.108 26.923 0.00 3.35 34.08 2.71
7033 18149 9.979578 AACAATGTTAGCTGATTCAAAACAATA 57.020 25.926 0.00 0.00 34.08 1.90
7059 18175 6.733145 TCATGAATTCAAACAATGTTCGTCA 58.267 32.000 13.09 0.00 0.00 4.35
7066 18182 5.568482 TCAAACAATGTTCGTCAAAGACAG 58.432 37.500 0.00 0.00 32.09 3.51
7069 18185 5.409643 ACAATGTTCGTCAAAGACAGAAG 57.590 39.130 0.00 0.00 30.67 2.85
7070 18186 4.273480 ACAATGTTCGTCAAAGACAGAAGG 59.727 41.667 0.00 0.00 30.67 3.46
7098 18214 5.587289 TCTGAATTTCAAAAGTTGTTCCCG 58.413 37.500 0.01 0.00 0.00 5.14
7109 18225 8.198109 TCAAAAGTTGTTCCCGAATTTCAATAA 58.802 29.630 0.00 0.00 0.00 1.40
7115 18231 6.626302 TGTTCCCGAATTTCAATAATTGTCC 58.374 36.000 0.00 0.00 0.00 4.02
7122 18238 6.578545 CGAATTTCAATAATTGTCCGCCTATG 59.421 38.462 0.00 0.00 0.00 2.23
7123 18239 4.829064 TTCAATAATTGTCCGCCTATGC 57.171 40.909 0.00 0.00 0.00 3.14
7125 18241 4.203226 TCAATAATTGTCCGCCTATGCAA 58.797 39.130 0.00 0.00 37.32 4.08
7196 18313 2.414058 TCGTGCAATGCGAAAATGTT 57.586 40.000 0.00 0.00 35.28 2.71
7199 18316 2.089427 CGTGCAATGCGAAAATGTTCAG 59.911 45.455 0.00 0.00 32.89 3.02
7205 18322 4.853924 ATGCGAAAATGTTCAGGAGTTT 57.146 36.364 0.00 0.00 32.89 2.66
7206 18323 5.957842 ATGCGAAAATGTTCAGGAGTTTA 57.042 34.783 0.00 0.00 32.89 2.01
7207 18324 5.759506 TGCGAAAATGTTCAGGAGTTTAA 57.240 34.783 0.00 0.00 32.89 1.52
7208 18325 6.137794 TGCGAAAATGTTCAGGAGTTTAAA 57.862 33.333 0.00 0.00 32.89 1.52
7209 18326 6.565234 TGCGAAAATGTTCAGGAGTTTAAAA 58.435 32.000 0.00 0.00 32.89 1.52
7210 18327 7.036220 TGCGAAAATGTTCAGGAGTTTAAAAA 58.964 30.769 0.00 0.00 32.89 1.94
7233 18350 7.734538 AAAGGTTCGCAATTTCAAATATACG 57.265 32.000 0.00 0.00 0.00 3.06
7234 18351 6.671614 AGGTTCGCAATTTCAAATATACGA 57.328 33.333 0.00 0.00 0.00 3.43
7235 18352 7.259290 AGGTTCGCAATTTCAAATATACGAT 57.741 32.000 0.00 0.00 0.00 3.73
7236 18353 8.373048 AGGTTCGCAATTTCAAATATACGATA 57.627 30.769 0.00 0.00 0.00 2.92
7237 18354 8.832521 AGGTTCGCAATTTCAAATATACGATAA 58.167 29.630 0.00 0.00 0.00 1.75
7238 18355 9.440784 GGTTCGCAATTTCAAATATACGATAAA 57.559 29.630 0.00 0.00 0.00 1.40
7240 18357 9.989869 TTCGCAATTTCAAATATACGATAAACA 57.010 25.926 0.00 0.00 0.00 2.83
7268 18385 7.789202 TTTAAATCCAGAAATGTTCATCCCA 57.211 32.000 0.00 0.00 0.00 4.37
7269 18386 7.789202 TTAAATCCAGAAATGTTCATCCCAA 57.211 32.000 0.00 0.00 0.00 4.12
7270 18387 6.684897 AAATCCAGAAATGTTCATCCCAAA 57.315 33.333 0.00 0.00 0.00 3.28
7271 18388 6.879367 AATCCAGAAATGTTCATCCCAAAT 57.121 33.333 0.00 0.00 0.00 2.32
7272 18389 6.879367 ATCCAGAAATGTTCATCCCAAATT 57.121 33.333 0.00 0.00 0.00 1.82
7273 18390 6.684897 TCCAGAAATGTTCATCCCAAATTT 57.315 33.333 0.00 0.00 0.00 1.82
7274 18391 7.077050 TCCAGAAATGTTCATCCCAAATTTT 57.923 32.000 0.00 0.00 0.00 1.82
7275 18392 8.200024 TCCAGAAATGTTCATCCCAAATTTTA 57.800 30.769 0.00 0.00 0.00 1.52
7276 18393 8.654997 TCCAGAAATGTTCATCCCAAATTTTAA 58.345 29.630 0.00 0.00 0.00 1.52
7277 18394 9.282569 CCAGAAATGTTCATCCCAAATTTTAAA 57.717 29.630 0.00 0.00 0.00 1.52
7306 18423 9.585099 TGTTCATGAATTTAGGAAATTGTATGC 57.415 29.630 12.12 0.00 40.97 3.14
7307 18424 9.585099 GTTCATGAATTTAGGAAATTGTATGCA 57.415 29.630 12.12 0.00 40.97 3.96
7323 18440 8.795842 ATTGTATGCAATTTCCAAAATGTGAT 57.204 26.923 2.84 0.00 42.19 3.06
7324 18441 7.598189 TGTATGCAATTTCCAAAATGTGATG 57.402 32.000 0.00 0.00 0.00 3.07
7325 18442 7.384477 TGTATGCAATTTCCAAAATGTGATGA 58.616 30.769 0.00 0.00 0.00 2.92
7326 18443 7.876582 TGTATGCAATTTCCAAAATGTGATGAA 59.123 29.630 0.00 0.00 0.00 2.57
7327 18444 6.542574 TGCAATTTCCAAAATGTGATGAAC 57.457 33.333 0.00 0.00 0.00 3.18
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
57 59 0.323360 ATACGCACCTTGCCCACATT 60.323 50.000 0.00 0.00 41.12 2.71
187 218 1.738908 GGCAAAATAAACGGCCGACTA 59.261 47.619 35.90 22.11 36.58 2.59
225 256 9.660180 CAGCTAGTTTCCTTTAAGTAGAAGAAT 57.340 33.333 0.00 0.00 34.40 2.40
226 257 8.867097 TCAGCTAGTTTCCTTTAAGTAGAAGAA 58.133 33.333 0.00 0.00 34.40 2.52
228 259 9.660180 ATTCAGCTAGTTTCCTTTAAGTAGAAG 57.340 33.333 0.00 0.00 34.40 2.85
236 267 6.892658 TGCAAATTCAGCTAGTTTCCTTTA 57.107 33.333 4.71 0.00 0.00 1.85
315 350 7.358830 GCTTCGTTAGAAACTATATACTCCGT 58.641 38.462 0.00 0.00 35.71 4.69
316 351 6.519078 CGCTTCGTTAGAAACTATATACTCCG 59.481 42.308 0.00 0.00 35.71 4.63
317 352 6.305160 GCGCTTCGTTAGAAACTATATACTCC 59.695 42.308 0.00 0.00 35.71 3.85
318 353 6.854892 TGCGCTTCGTTAGAAACTATATACTC 59.145 38.462 9.73 0.00 35.71 2.59
319 354 6.732154 TGCGCTTCGTTAGAAACTATATACT 58.268 36.000 9.73 0.00 35.71 2.12
320 355 6.636044 ACTGCGCTTCGTTAGAAACTATATAC 59.364 38.462 9.73 0.00 35.71 1.47
321 356 6.732154 ACTGCGCTTCGTTAGAAACTATATA 58.268 36.000 9.73 0.00 35.71 0.86
322 357 5.589192 ACTGCGCTTCGTTAGAAACTATAT 58.411 37.500 9.73 0.00 35.71 0.86
323 358 4.990257 ACTGCGCTTCGTTAGAAACTATA 58.010 39.130 9.73 0.00 35.71 1.31
324 359 3.846360 ACTGCGCTTCGTTAGAAACTAT 58.154 40.909 9.73 0.00 35.71 2.12
325 360 3.293311 ACTGCGCTTCGTTAGAAACTA 57.707 42.857 9.73 0.00 35.71 2.24
326 361 2.150397 ACTGCGCTTCGTTAGAAACT 57.850 45.000 9.73 0.00 35.71 2.66
327 362 2.475487 AGAACTGCGCTTCGTTAGAAAC 59.525 45.455 9.73 0.00 35.71 2.78
328 363 2.750948 AGAACTGCGCTTCGTTAGAAA 58.249 42.857 9.73 0.00 35.71 2.52
329 364 2.433868 AGAACTGCGCTTCGTTAGAA 57.566 45.000 9.73 0.00 34.76 2.10
330 365 2.433868 AAGAACTGCGCTTCGTTAGA 57.566 45.000 9.73 0.00 0.00 2.10
331 366 3.470562 GAAAAGAACTGCGCTTCGTTAG 58.529 45.455 9.73 0.00 0.00 2.34
332 367 2.222445 GGAAAAGAACTGCGCTTCGTTA 59.778 45.455 9.73 0.00 0.00 3.18
333 368 1.002792 GGAAAAGAACTGCGCTTCGTT 60.003 47.619 9.73 9.55 0.00 3.85
334 369 0.586802 GGAAAAGAACTGCGCTTCGT 59.413 50.000 9.73 0.00 0.00 3.85
335 370 0.110192 GGGAAAAGAACTGCGCTTCG 60.110 55.000 9.73 0.00 0.00 3.79
336 371 1.197949 GAGGGAAAAGAACTGCGCTTC 59.802 52.381 9.73 4.91 0.00 3.86
337 372 1.239347 GAGGGAAAAGAACTGCGCTT 58.761 50.000 9.73 0.00 0.00 4.68
338 373 0.108585 TGAGGGAAAAGAACTGCGCT 59.891 50.000 9.73 0.00 0.00 5.92
339 374 0.951558 TTGAGGGAAAAGAACTGCGC 59.048 50.000 0.00 0.00 0.00 6.09
340 375 3.708563 TTTTGAGGGAAAAGAACTGCG 57.291 42.857 0.00 0.00 0.00 5.18
364 399 1.533129 GGTGAACTGCGCTTCGTTTTT 60.533 47.619 9.73 0.00 0.00 1.94
365 400 0.028902 GGTGAACTGCGCTTCGTTTT 59.971 50.000 9.73 0.00 0.00 2.43
366 401 0.814010 AGGTGAACTGCGCTTCGTTT 60.814 50.000 9.73 0.00 0.00 3.60
367 402 0.814010 AAGGTGAACTGCGCTTCGTT 60.814 50.000 9.73 9.55 0.00 3.85
368 403 1.222115 GAAGGTGAACTGCGCTTCGT 61.222 55.000 9.73 0.00 0.00 3.85
398 433 1.378882 TACTCCGTCCGATTCGTGGG 61.379 60.000 5.20 3.38 0.00 4.61
399 434 0.248377 GTACTCCGTCCGATTCGTGG 60.248 60.000 5.20 4.28 0.00 4.94
400 435 0.448990 TGTACTCCGTCCGATTCGTG 59.551 55.000 5.20 0.00 0.00 4.35
401 436 1.332997 GATGTACTCCGTCCGATTCGT 59.667 52.381 5.20 0.00 0.00 3.85
402 437 1.602851 AGATGTACTCCGTCCGATTCG 59.397 52.381 0.00 0.00 0.00 3.34
403 438 3.066342 TCAAGATGTACTCCGTCCGATTC 59.934 47.826 0.00 0.00 0.00 2.52
404 439 3.021695 TCAAGATGTACTCCGTCCGATT 58.978 45.455 0.00 0.00 0.00 3.34
405 440 2.358267 GTCAAGATGTACTCCGTCCGAT 59.642 50.000 0.00 0.00 0.00 4.18
406 441 1.741706 GTCAAGATGTACTCCGTCCGA 59.258 52.381 0.00 0.00 0.00 4.55
407 442 1.531264 CGTCAAGATGTACTCCGTCCG 60.531 57.143 0.00 0.00 0.00 4.79
408 443 1.798079 GCGTCAAGATGTACTCCGTCC 60.798 57.143 0.00 0.00 0.00 4.79
409 444 1.135489 TGCGTCAAGATGTACTCCGTC 60.135 52.381 0.00 0.00 0.00 4.79
410 445 0.885879 TGCGTCAAGATGTACTCCGT 59.114 50.000 0.00 0.00 0.00 4.69
494 572 2.395690 GCTGTGTACATGCGCGAC 59.604 61.111 12.10 0.88 0.00 5.19
554 639 2.999507 TTAATTTTCGCGTGGCACAT 57.000 40.000 19.09 0.00 44.52 3.21
582 667 2.298610 CAGTCACGATCCTGGTAGCTA 58.701 52.381 0.00 0.00 0.00 3.32
623 708 2.036346 CTGCCAACTCAAAAAGGGGAAG 59.964 50.000 0.00 0.00 0.00 3.46
626 711 1.069049 CACTGCCAACTCAAAAAGGGG 59.931 52.381 0.00 0.00 0.00 4.79
627 712 1.538849 GCACTGCCAACTCAAAAAGGG 60.539 52.381 0.00 0.00 0.00 3.95
628 713 1.856802 GCACTGCCAACTCAAAAAGG 58.143 50.000 0.00 0.00 0.00 3.11
629 714 1.202290 ACGCACTGCCAACTCAAAAAG 60.202 47.619 0.00 0.00 0.00 2.27
710 795 0.032678 CGAGGACGCTGGCTCATAAT 59.967 55.000 0.00 0.00 0.00 1.28
711 796 1.320344 ACGAGGACGCTGGCTCATAA 61.320 55.000 0.00 0.00 43.96 1.90
712 797 1.725557 GACGAGGACGCTGGCTCATA 61.726 60.000 0.00 0.00 43.96 2.15
713 798 3.069980 GACGAGGACGCTGGCTCAT 62.070 63.158 0.00 0.00 43.96 2.90
714 799 3.749064 GACGAGGACGCTGGCTCA 61.749 66.667 0.00 0.00 43.96 4.26
715 800 4.838486 CGACGAGGACGCTGGCTC 62.838 72.222 0.00 0.00 43.96 4.70
754 839 3.119743 GCGTGGGTGGGATTAACTTAAAC 60.120 47.826 0.00 0.00 0.00 2.01
755 840 3.083293 GCGTGGGTGGGATTAACTTAAA 58.917 45.455 0.00 0.00 0.00 1.52
756 841 2.618559 GGCGTGGGTGGGATTAACTTAA 60.619 50.000 0.00 0.00 0.00 1.85
801 888 0.794473 GTCGGTTGATTTGGACGACC 59.206 55.000 0.00 0.00 45.70 4.79
909 1060 1.372128 CGTTTGGCTTTCTGGCTGC 60.372 57.895 0.00 0.00 42.34 5.25
1017 1181 1.322538 CCGGGGAAAGGGCAAAGATG 61.323 60.000 0.00 0.00 0.00 2.90
1019 1183 2.014033 AACCGGGGAAAGGGCAAAGA 62.014 55.000 6.32 0.00 0.00 2.52
1024 1194 2.125326 GCATAACCGGGGAAAGGGC 61.125 63.158 6.32 0.00 0.00 5.19
1059 1234 1.073722 GCCATAGGCCATAGCTGCA 59.926 57.895 5.01 0.00 44.06 4.41
1060 1235 3.993535 GCCATAGGCCATAGCTGC 58.006 61.111 5.01 0.00 44.06 5.25
1139 1316 4.772687 GAGGTTTCGGCCGGGGTC 62.773 72.222 27.83 13.12 0.00 4.46
1141 1318 4.468689 GAGAGGTTTCGGCCGGGG 62.469 72.222 27.83 0.00 0.00 5.73
1142 1319 3.372554 GAGAGAGGTTTCGGCCGGG 62.373 68.421 27.83 0.00 0.00 5.73
1145 1322 3.285371 TCGAGAGAGGTTTCGGCC 58.715 61.111 0.00 0.00 37.42 6.13
1146 1323 4.392644 TCGAATCGAGAGAGGTTTCGGC 62.393 54.545 13.29 0.00 45.24 5.54
1187 1364 1.318158 GGCAGCCTCACCAAATCCAG 61.318 60.000 3.29 0.00 0.00 3.86
1188 1365 1.304381 GGCAGCCTCACCAAATCCA 60.304 57.895 3.29 0.00 0.00 3.41
1190 1367 1.304381 TGGGCAGCCTCACCAAATC 60.304 57.895 12.43 0.00 0.00 2.17
1192 1369 2.203480 GTGGGCAGCCTCACCAAA 60.203 61.111 12.43 0.00 35.77 3.28
1193 1370 4.641645 CGTGGGCAGCCTCACCAA 62.642 66.667 21.07 0.00 35.77 3.67
1199 1395 3.661648 AAATCCCGTGGGCAGCCT 61.662 61.111 12.43 0.00 34.68 4.58
1205 1401 2.755469 CTGGCCAAATCCCGTGGG 60.755 66.667 7.01 0.00 36.58 4.61
1228 1424 1.136147 GAGCAGTGCGATTGGCTTG 59.864 57.895 10.00 0.00 44.05 4.01
1232 1428 0.935898 GAGATGAGCAGTGCGATTGG 59.064 55.000 10.00 0.00 0.00 3.16
1240 1439 2.176314 TTGCCGCAGAGATGAGCAGT 62.176 55.000 0.00 0.00 34.45 4.40
1270 1469 2.268298 ACGACGCAGAATCAATACACC 58.732 47.619 0.00 0.00 0.00 4.16
1273 1472 2.182825 ACGACGACGCAGAATCAATAC 58.817 47.619 7.30 0.00 43.96 1.89
1276 1475 0.781787 CAACGACGACGCAGAATCAA 59.218 50.000 7.30 0.00 43.96 2.57
1426 1662 4.398319 TCTGTTGGAGGGAAGAAACAATC 58.602 43.478 0.00 0.00 32.50 2.67
1427 1663 4.104738 TCTCTGTTGGAGGGAAGAAACAAT 59.895 41.667 0.00 0.00 42.10 2.71
1480 1758 1.866853 CTTTCAAGTCCAAGCGGGCC 61.867 60.000 0.00 0.00 37.79 5.80
1481 1759 1.172812 ACTTTCAAGTCCAAGCGGGC 61.173 55.000 0.00 0.00 32.86 6.13
1482 1760 3.021451 ACTTTCAAGTCCAAGCGGG 57.979 52.632 0.00 0.00 32.86 6.13
1513 1791 9.408069 CCATCTAATTAACCGATAAGTCAGTAC 57.592 37.037 0.00 0.00 0.00 2.73
1514 1792 9.139734 ACCATCTAATTAACCGATAAGTCAGTA 57.860 33.333 0.00 0.00 0.00 2.74
1515 1793 8.019656 ACCATCTAATTAACCGATAAGTCAGT 57.980 34.615 0.00 0.00 0.00 3.41
1535 1813 5.334105 CCGACCGATCAATCAATAAACCATC 60.334 44.000 0.00 0.00 0.00 3.51
1556 1834 2.132089 ATTTGGGGAAAGTCGGCCGA 62.132 55.000 27.28 27.28 0.00 5.54
1643 1977 5.461078 ACTGTAGACACAACAATTACACGAC 59.539 40.000 0.00 0.00 33.22 4.34
1679 4185 5.176590 GCTAACACATGAATCTGCTACTAGC 59.823 44.000 0.00 0.61 42.82 3.42
1720 4254 3.058016 ACACGAAAGGAAATGCAGTCATG 60.058 43.478 0.00 0.00 32.23 3.07
1721 4255 3.149196 ACACGAAAGGAAATGCAGTCAT 58.851 40.909 0.00 0.00 33.53 3.06
1734 4268 2.972625 TGGAAGAGCCATACACGAAAG 58.027 47.619 0.00 0.00 43.33 2.62
1762 4406 5.955488 ACGATGACTAGGCATATATGTGTC 58.045 41.667 12.18 15.40 0.00 3.67
1896 5435 7.450074 TGGGATAACAACTATCGATAATGCTT 58.550 34.615 14.61 11.37 37.83 3.91
2159 5802 5.227569 TGAAAGACCACTATGTGACATGT 57.772 39.130 8.61 0.00 35.23 3.21
2662 7759 3.274288 CTGATTTAAGTGGGAGTCAGGC 58.726 50.000 0.00 0.00 31.77 4.85
2690 7795 7.982354 GGTGAACTGCTAATGTAGTTTATCTCT 59.018 37.037 1.53 0.00 46.42 3.10
2699 7804 6.560253 AAACAAGGTGAACTGCTAATGTAG 57.440 37.500 0.00 0.00 0.00 2.74
3499 10244 2.958355 GAGCCTGACTTCTCTGCTAGAT 59.042 50.000 0.00 0.00 33.05 1.98
3614 10360 2.484742 AACATGACCCGTTACCTTCC 57.515 50.000 0.00 0.00 0.00 3.46
3655 10435 8.691661 TTGAGCTAAAACCTAAAATGTCTTCT 57.308 30.769 0.00 0.00 0.00 2.85
3656 10436 8.784043 TCTTGAGCTAAAACCTAAAATGTCTTC 58.216 33.333 0.00 0.00 0.00 2.87
3728 10508 6.295462 CCTGGTTGATCAGTTCAATCCAAAAT 60.295 38.462 12.69 0.00 45.77 1.82
4253 11264 5.986135 GTGTGCGAAGAAGTATGAGGATAAT 59.014 40.000 0.00 0.00 0.00 1.28
4533 11632 0.744771 GGGCGTCAAATCTCCAGACC 60.745 60.000 0.00 0.00 0.00 3.85
4562 11662 8.792456 AAGGATATAGAAACCTCCCTGGAACAG 61.792 44.444 0.00 0.00 43.90 3.16
4729 11833 3.423162 TTGCTGTGGCGTGTTTGGC 62.423 57.895 0.00 0.00 42.25 4.52
4921 12101 1.917872 TTATGAAACCCAGGGCACAC 58.082 50.000 4.91 0.00 0.00 3.82
5024 13222 5.575606 GCAAATCAGCATATCATTGCCATAC 59.424 40.000 0.00 0.00 43.83 2.39
5074 13273 8.450578 TTGACAATGTCTTGAAGTGTATCTTT 57.549 30.769 14.97 0.00 36.20 2.52
5507 13712 3.243359 AGAGCCCATTTCCTTTGAACA 57.757 42.857 0.00 0.00 0.00 3.18
5763 14214 0.886563 AGAGCCATCAACAAAGCTGC 59.113 50.000 0.00 0.00 35.23 5.25
5903 15751 4.218417 GGCAACATTGAGTACACAATCCTT 59.782 41.667 14.65 7.39 38.25 3.36
5910 15758 3.563808 TGTGAAGGCAACATTGAGTACAC 59.436 43.478 0.00 0.00 41.41 2.90
6042 16133 5.010012 ACCAGAAGAAATTACTTGTTGGCAG 59.990 40.000 0.00 0.00 36.00 4.85
6154 16320 5.046304 AGACACCATATACAGTATCATGCCC 60.046 44.000 0.00 0.00 0.00 5.36
6161 16332 6.055588 GCCAAACAGACACCATATACAGTAT 58.944 40.000 0.00 0.00 0.00 2.12
6315 16493 5.123979 CCAAAACAAGCACTATAGAACCCTC 59.876 44.000 6.78 0.00 0.00 4.30
6413 16610 3.058914 CCGAAGATGAAACACACAACCTC 60.059 47.826 0.00 0.00 0.00 3.85
6553 17660 8.999895 ACCACCTCAAACTATTTATACCATACT 58.000 33.333 0.00 0.00 0.00 2.12
6593 17700 1.633852 GAGCTGGCTTGTTCGCAGAG 61.634 60.000 0.00 0.00 38.43 3.35
6617 17724 2.681273 AATAGGCGAGAGGGGAGGGG 62.681 65.000 0.00 0.00 0.00 4.79
6651 17758 3.626924 GTGGTCGTCCAGCCCTGT 61.627 66.667 0.19 0.00 45.24 4.00
6660 17767 1.523758 ATGAAAAGCTGGTGGTCGTC 58.476 50.000 0.00 0.00 0.00 4.20
6747 17854 9.696917 ACACTTTATGATTTCTGGAACAATTTC 57.303 29.630 0.00 0.00 38.70 2.17
6748 17855 9.696917 GACACTTTATGATTTCTGGAACAATTT 57.303 29.630 0.00 0.00 38.70 1.82
6749 17856 8.306761 GGACACTTTATGATTTCTGGAACAATT 58.693 33.333 0.00 0.00 38.70 2.32
6750 17857 7.362056 CGGACACTTTATGATTTCTGGAACAAT 60.362 37.037 0.00 0.00 38.70 2.71
6751 17858 6.072728 CGGACACTTTATGATTTCTGGAACAA 60.073 38.462 0.00 0.00 38.70 2.83
6752 17859 5.411361 CGGACACTTTATGATTTCTGGAACA 59.589 40.000 0.00 0.00 0.00 3.18
6753 17860 5.411669 ACGGACACTTTATGATTTCTGGAAC 59.588 40.000 0.00 0.00 0.00 3.62
6755 17862 4.935205 CACGGACACTTTATGATTTCTGGA 59.065 41.667 0.00 0.00 0.00 3.86
6756 17863 4.695455 ACACGGACACTTTATGATTTCTGG 59.305 41.667 0.00 0.00 0.00 3.86
6878 17994 8.735692 ATTGTGAACAATTTTTGGAAATCACT 57.264 26.923 2.80 0.00 43.48 3.41
6986 18102 9.651913 ATTGTTTGAGTTTTGTGAACATTACTT 57.348 25.926 0.00 0.00 31.15 2.24
6988 18104 8.868916 ACATTGTTTGAGTTTTGTGAACATTAC 58.131 29.630 0.00 0.00 31.15 1.89
6989 18105 8.994429 ACATTGTTTGAGTTTTGTGAACATTA 57.006 26.923 0.00 0.00 31.15 1.90
7031 18147 9.859427 ACGAACATTGTTTGAATTCATGAATAT 57.141 25.926 21.00 11.35 0.00 1.28
7032 18148 9.340695 GACGAACATTGTTTGAATTCATGAATA 57.659 29.630 21.00 4.04 0.00 1.75
7033 18149 7.866898 TGACGAACATTGTTTGAATTCATGAAT 59.133 29.630 21.08 15.36 0.00 2.57
7034 18150 7.199078 TGACGAACATTGTTTGAATTCATGAA 58.801 30.769 21.08 11.26 0.00 2.57
7035 18151 6.733145 TGACGAACATTGTTTGAATTCATGA 58.267 32.000 21.08 0.00 0.00 3.07
7036 18152 6.989796 TGACGAACATTGTTTGAATTCATG 57.010 33.333 21.08 6.71 0.00 3.07
7037 18153 7.920151 TCTTTGACGAACATTGTTTGAATTCAT 59.080 29.630 21.08 0.04 0.00 2.57
7038 18154 7.219917 GTCTTTGACGAACATTGTTTGAATTCA 59.780 33.333 21.08 3.38 0.00 2.57
7039 18155 7.219917 TGTCTTTGACGAACATTGTTTGAATTC 59.780 33.333 21.08 10.35 34.95 2.17
7040 18156 7.032580 TGTCTTTGACGAACATTGTTTGAATT 58.967 30.769 21.08 1.40 34.95 2.17
7041 18157 6.559810 TGTCTTTGACGAACATTGTTTGAAT 58.440 32.000 21.08 2.09 34.95 2.57
7042 18158 5.944013 TGTCTTTGACGAACATTGTTTGAA 58.056 33.333 21.08 7.98 34.95 2.69
7043 18159 5.352846 TCTGTCTTTGACGAACATTGTTTGA 59.647 36.000 21.08 0.00 34.95 2.69
7044 18160 5.568482 TCTGTCTTTGACGAACATTGTTTG 58.432 37.500 14.08 14.08 34.95 2.93
7045 18161 5.811399 TCTGTCTTTGACGAACATTGTTT 57.189 34.783 3.08 0.00 34.95 2.83
7046 18162 5.220854 CCTTCTGTCTTTGACGAACATTGTT 60.221 40.000 0.63 0.63 34.95 2.83
7047 18163 4.273480 CCTTCTGTCTTTGACGAACATTGT 59.727 41.667 0.00 0.00 34.95 2.71
7066 18182 8.382875 CAACTTTTGAAATTCAGAAACACCTTC 58.617 33.333 0.70 0.00 0.00 3.46
7069 18185 7.595311 ACAACTTTTGAAATTCAGAAACACC 57.405 32.000 0.70 0.00 0.00 4.16
7070 18186 8.168626 GGAACAACTTTTGAAATTCAGAAACAC 58.831 33.333 0.70 0.00 0.00 3.32
7084 18200 6.843069 ATTGAAATTCGGGAACAACTTTTG 57.157 33.333 0.00 0.00 0.00 2.44
7089 18205 7.062956 GGACAATTATTGAAATTCGGGAACAAC 59.937 37.037 12.28 0.00 0.00 3.32
7098 18214 6.363357 GCATAGGCGGACAATTATTGAAATTC 59.637 38.462 12.28 0.00 0.00 2.17
7141 18257 9.130312 GTAATTGCGTAAATTTGTTATGGAACA 57.870 29.630 0.00 0.00 43.94 3.18
7176 18293 2.414058 ACATTTTCGCATTGCACGAA 57.586 40.000 9.69 6.54 46.91 3.85
7178 18295 2.049959 TGAACATTTTCGCATTGCACG 58.950 42.857 9.69 0.00 34.04 5.34
7181 18298 2.919229 CTCCTGAACATTTTCGCATTGC 59.081 45.455 0.00 0.00 34.04 3.56
7207 18324 8.643752 CGTATATTTGAAATTGCGAACCTTTTT 58.356 29.630 0.00 0.00 0.00 1.94
7208 18325 8.024285 TCGTATATTTGAAATTGCGAACCTTTT 58.976 29.630 0.00 0.00 0.00 2.27
7209 18326 7.531716 TCGTATATTTGAAATTGCGAACCTTT 58.468 30.769 0.00 0.00 0.00 3.11
7210 18327 7.079182 TCGTATATTTGAAATTGCGAACCTT 57.921 32.000 0.00 0.00 0.00 3.50
7211 18328 6.671614 TCGTATATTTGAAATTGCGAACCT 57.328 33.333 0.00 0.00 0.00 3.50
7212 18329 8.996988 TTATCGTATATTTGAAATTGCGAACC 57.003 30.769 13.38 0.00 0.00 3.62
7214 18331 9.989869 TGTTTATCGTATATTTGAAATTGCGAA 57.010 25.926 13.38 0.00 0.00 4.70
7242 18359 8.654997 TGGGATGAACATTTCTGGATTTAAAAA 58.345 29.630 0.00 0.00 0.00 1.94
7243 18360 8.200024 TGGGATGAACATTTCTGGATTTAAAA 57.800 30.769 0.00 0.00 0.00 1.52
7244 18361 7.789202 TGGGATGAACATTTCTGGATTTAAA 57.211 32.000 0.00 0.00 0.00 1.52
7245 18362 7.789202 TTGGGATGAACATTTCTGGATTTAA 57.211 32.000 0.00 0.00 0.00 1.52
7246 18363 7.789202 TTTGGGATGAACATTTCTGGATTTA 57.211 32.000 0.00 0.00 0.00 1.40
7247 18364 6.684897 TTTGGGATGAACATTTCTGGATTT 57.315 33.333 0.00 0.00 0.00 2.17
7248 18365 6.879367 ATTTGGGATGAACATTTCTGGATT 57.121 33.333 0.00 0.00 0.00 3.01
7249 18366 6.879367 AATTTGGGATGAACATTTCTGGAT 57.121 33.333 0.00 0.00 0.00 3.41
7250 18367 6.684897 AAATTTGGGATGAACATTTCTGGA 57.315 33.333 0.00 0.00 0.00 3.86
7251 18368 8.845413 TTAAAATTTGGGATGAACATTTCTGG 57.155 30.769 0.00 0.00 0.00 3.86
7280 18397 9.585099 GCATACAATTTCCTAAATTCATGAACA 57.415 29.630 11.07 0.00 38.97 3.18
7281 18398 9.585099 TGCATACAATTTCCTAAATTCATGAAC 57.415 29.630 11.07 0.00 38.97 3.18
7299 18416 7.876582 TCATCACATTTTGGAAATTGCATACAA 59.123 29.630 0.00 0.00 40.87 2.41
7300 18417 7.384477 TCATCACATTTTGGAAATTGCATACA 58.616 30.769 0.00 0.00 0.00 2.29
7301 18418 7.830940 TCATCACATTTTGGAAATTGCATAC 57.169 32.000 0.00 0.00 0.00 2.39
7302 18419 8.254178 GTTCATCACATTTTGGAAATTGCATA 57.746 30.769 0.00 0.00 0.00 3.14
7303 18420 7.136289 GTTCATCACATTTTGGAAATTGCAT 57.864 32.000 0.00 0.00 0.00 3.96
7304 18421 6.542574 GTTCATCACATTTTGGAAATTGCA 57.457 33.333 0.00 0.00 0.00 4.08


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

AutoCloner maintained by Alex Coulton.