Multiple sequence alignment - TraesCS1D01G272500

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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 TraesCS1D01G272500 chr1D 100.000 7750 0 0 1 7750 366250262 366242513 0.000000e+00 14312.0
1 TraesCS1D01G272500 chr1D 93.039 1609 98 6 1551 3158 471207061 471205466 0.000000e+00 2338.0
2 TraesCS1D01G272500 chr1B 92.498 4692 196 60 3154 7748 491238767 491243399 0.000000e+00 6571.0
3 TraesCS1D01G272500 chr1B 89.831 944 34 26 599 1514 491237862 491238771 0.000000e+00 1155.0
4 TraesCS1D01G272500 chr1B 84.691 614 72 16 1 606 491236641 491237240 1.860000e-165 593.0
5 TraesCS1D01G272500 chr1A 94.486 2974 109 24 4378 7322 465503027 465505974 0.000000e+00 4532.0
6 TraesCS1D01G272500 chr1A 91.683 1022 53 20 504 1514 465501180 465502180 0.000000e+00 1387.0
7 TraesCS1D01G272500 chr1A 92.767 871 40 10 3154 4024 465502176 465503023 0.000000e+00 1238.0
8 TraesCS1D01G272500 chr1A 92.254 426 30 3 1 426 465500668 465501090 1.110000e-167 601.0
9 TraesCS1D01G272500 chr1A 89.899 99 5 3 4047 4142 14236972 14236876 1.060000e-23 122.0
10 TraesCS1D01G272500 chr2D 93.012 1660 95 8 1511 3158 511532372 511530722 0.000000e+00 2403.0
11 TraesCS1D01G272500 chr2D 93.217 1607 96 4 1548 3154 201456569 201454976 0.000000e+00 2351.0
12 TraesCS1D01G272500 chr7D 92.993 1627 90 9 1531 3154 593682303 593680698 0.000000e+00 2351.0
13 TraesCS1D01G272500 chr7D 93.333 60 4 0 1512 1571 155748797 155748738 1.070000e-13 89.8
14 TraesCS1D01G272500 chrUn 93.065 1615 94 5 1548 3154 100847321 100848925 0.000000e+00 2346.0
15 TraesCS1D01G272500 chrUn 85.973 663 57 18 4887 5530 37333312 37333957 0.000000e+00 676.0
16 TraesCS1D01G272500 chrUn 83.461 653 57 12 6581 7230 37334273 37334877 1.890000e-155 560.0
17 TraesCS1D01G272500 chrUn 81.553 412 54 15 5919 6322 255438563 255438960 3.490000e-83 320.0
18 TraesCS1D01G272500 chrUn 89.873 79 6 1 6238 6314 255440188 255440266 4.950000e-17 100.0
19 TraesCS1D01G272500 chrUn 89.610 77 6 2 6238 6312 318688448 318688372 6.400000e-16 97.1
20 TraesCS1D01G272500 chr5A 91.988 1660 110 7 1512 3158 634469225 634467576 0.000000e+00 2307.0
21 TraesCS1D01G272500 chr5A 89.128 1674 140 18 1512 3158 585212327 585210669 0.000000e+00 2045.0
22 TraesCS1D01G272500 chr5A 87.666 527 56 8 5799 6323 5427740 5427221 8.600000e-169 604.0
23 TraesCS1D01G272500 chr3A 91.692 1613 117 9 1548 3154 703638971 703637370 0.000000e+00 2220.0
24 TraesCS1D01G272500 chr3A 86.047 688 60 18 4862 5530 26004114 26003444 0.000000e+00 706.0
25 TraesCS1D01G272500 chr3A 86.217 653 62 7 6581 7230 26002860 26002233 0.000000e+00 682.0
26 TraesCS1D01G272500 chr3A 88.132 514 54 6 5799 6309 671349290 671349799 8.600000e-169 604.0
27 TraesCS1D01G272500 chr3A 87.571 177 22 0 4511 4687 629219180 629219004 1.020000e-48 206.0
28 TraesCS1D01G272500 chr3A 75.000 264 49 10 3726 3981 629224070 629223816 1.060000e-18 106.0
29 TraesCS1D01G272500 chr7A 90.849 1661 128 11 1512 3160 685448476 685450124 0.000000e+00 2204.0
30 TraesCS1D01G272500 chr7A 83.575 414 51 10 5919 6322 88933967 88933561 9.500000e-99 372.0
31 TraesCS1D01G272500 chr7A 94.253 87 3 1 4047 4133 527538093 527538177 1.750000e-26 132.0
32 TraesCS1D01G272500 chr4A 90.942 1656 124 16 1514 3156 11807921 11806279 0.000000e+00 2204.0
33 TraesCS1D01G272500 chr4A 90.506 158 14 1 6429 6586 460230801 460230645 2.830000e-49 207.0
34 TraesCS1D01G272500 chr4A 89.691 97 8 2 4046 4140 590902898 590902802 1.060000e-23 122.0
35 TraesCS1D01G272500 chr3D 91.595 809 35 13 1512 2303 50542651 50541859 0.000000e+00 1086.0
36 TraesCS1D01G272500 chr3D 86.107 691 58 20 4860 5530 18426781 18427453 0.000000e+00 710.0
37 TraesCS1D01G272500 chr3D 84.755 715 85 8 6581 7292 534127571 534128264 0.000000e+00 695.0
38 TraesCS1D01G272500 chr3D 85.452 653 67 10 6581 7230 18428034 18428661 0.000000e+00 654.0
39 TraesCS1D01G272500 chr3D 86.161 224 19 5 5440 5661 534127146 534127359 1.680000e-56 231.0
40 TraesCS1D01G272500 chr3D 88.136 177 21 0 4511 4687 486043740 486043564 2.190000e-50 211.0
41 TraesCS1D01G272500 chr3D 89.873 79 6 2 6238 6314 36244665 36244587 4.950000e-17 100.0
42 TraesCS1D01G272500 chr5D 86.246 618 54 14 5055 5660 61698670 61698072 6.560000e-180 641.0
43 TraesCS1D01G272500 chr5D 82.963 540 59 12 6581 7116 61697850 61697340 2.550000e-124 457.0
44 TraesCS1D01G272500 chr5D 85.714 406 43 9 5924 6321 179649748 179650146 1.560000e-111 414.0
45 TraesCS1D01G272500 chr3B 85.460 619 58 14 5055 5660 720194084 720194683 3.970000e-172 616.0
46 TraesCS1D01G272500 chr3B 89.119 193 17 3 4511 4700 648741216 648741025 3.610000e-58 237.0
47 TraesCS1D01G272500 chr3B 93.333 90 3 1 4047 4133 62394194 62394283 6.310000e-26 130.0
48 TraesCS1D01G272500 chr5B 85.299 619 59 14 5055 5660 703732177 703732776 1.850000e-170 610.0
49 TraesCS1D01G272500 chr5B 84.967 459 53 8 6581 7036 703732998 703733443 1.190000e-122 451.0
50 TraesCS1D01G272500 chr5B 91.489 94 4 2 4048 4138 21154007 21154099 8.160000e-25 126.0
51 TraesCS1D01G272500 chr5B 94.737 57 3 0 1515 1571 536428283 536428339 1.070000e-13 89.8
52 TraesCS1D01G272500 chr6D 84.814 619 62 15 5055 5660 4982718 4982119 1.860000e-165 593.0
53 TraesCS1D01G272500 chr6D 87.963 108 3 7 4046 4148 1551884 1551782 1.370000e-22 119.0
54 TraesCS1D01G272500 chr6A 83.117 539 59 12 6581 7116 504346843 504346334 5.480000e-126 462.0
55 TraesCS1D01G272500 chr6A 97.917 48 1 0 1512 1559 94263027 94263074 4.980000e-12 84.2
56 TraesCS1D01G272500 chr2A 81.311 412 54 17 5919 6322 361210693 361210297 5.840000e-81 313.0
57 TraesCS1D01G272500 chr2A 92.857 154 10 1 6429 6582 141506318 141506470 1.010000e-53 222.0
58 TraesCS1D01G272500 chr2A 91.139 158 12 2 6429 6586 79316157 79316002 6.090000e-51 213.0
59 TraesCS1D01G272500 chr2A 89.873 79 6 1 6238 6314 361209069 361208991 4.950000e-17 100.0
60 TraesCS1D01G272500 chr4D 94.839 155 8 0 6429 6583 74079504 74079350 7.770000e-60 243.0
61 TraesCS1D01G272500 chr4D 88.073 109 6 5 4047 4151 252173788 252173683 1.060000e-23 122.0
62 TraesCS1D01G272500 chr4D 91.935 62 5 0 1511 1572 6801639 6801700 3.850000e-13 87.9
63 TraesCS1D01G272500 chr4D 94.444 54 3 0 1512 1565 363691385 363691438 4.980000e-12 84.2
64 TraesCS1D01G272500 chr4B 92.763 152 9 2 6431 6582 510827662 510827811 1.310000e-52 219.0
65 TraesCS1D01G272500 chr4B 91.613 155 12 1 6432 6586 146469365 146469212 6.090000e-51 213.0
66 TraesCS1D01G272500 chr4B 95.918 49 2 0 1514 1562 102408798 102408750 6.450000e-11 80.5
67 TraesCS1D01G272500 chr7B 91.250 160 12 2 6423 6582 44939711 44939554 4.710000e-52 217.0
68 TraesCS1D01G272500 chr6B 90.000 100 5 3 4042 4138 13827615 13827518 2.940000e-24 124.0
69 TraesCS1D01G272500 chr6B 88.073 109 6 4 4047 4151 76149749 76149854 1.060000e-23 122.0


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 TraesCS1D01G272500 chr1D 366242513 366250262 7749 True 14312.0 14312 100.000000 1 7750 1 chr1D.!!$R1 7749
1 TraesCS1D01G272500 chr1D 471205466 471207061 1595 True 2338.0 2338 93.039000 1551 3158 1 chr1D.!!$R2 1607
2 TraesCS1D01G272500 chr1B 491236641 491243399 6758 False 2773.0 6571 89.006667 1 7748 3 chr1B.!!$F1 7747
3 TraesCS1D01G272500 chr1A 465500668 465505974 5306 False 1939.5 4532 92.797500 1 7322 4 chr1A.!!$F1 7321
4 TraesCS1D01G272500 chr2D 511530722 511532372 1650 True 2403.0 2403 93.012000 1511 3158 1 chr2D.!!$R2 1647
5 TraesCS1D01G272500 chr2D 201454976 201456569 1593 True 2351.0 2351 93.217000 1548 3154 1 chr2D.!!$R1 1606
6 TraesCS1D01G272500 chr7D 593680698 593682303 1605 True 2351.0 2351 92.993000 1531 3154 1 chr7D.!!$R2 1623
7 TraesCS1D01G272500 chrUn 100847321 100848925 1604 False 2346.0 2346 93.065000 1548 3154 1 chrUn.!!$F1 1606
8 TraesCS1D01G272500 chrUn 37333312 37334877 1565 False 618.0 676 84.717000 4887 7230 2 chrUn.!!$F2 2343
9 TraesCS1D01G272500 chrUn 255438563 255440266 1703 False 210.0 320 85.713000 5919 6322 2 chrUn.!!$F3 403
10 TraesCS1D01G272500 chr5A 634467576 634469225 1649 True 2307.0 2307 91.988000 1512 3158 1 chr5A.!!$R3 1646
11 TraesCS1D01G272500 chr5A 585210669 585212327 1658 True 2045.0 2045 89.128000 1512 3158 1 chr5A.!!$R2 1646
12 TraesCS1D01G272500 chr5A 5427221 5427740 519 True 604.0 604 87.666000 5799 6323 1 chr5A.!!$R1 524
13 TraesCS1D01G272500 chr3A 703637370 703638971 1601 True 2220.0 2220 91.692000 1548 3154 1 chr3A.!!$R3 1606
14 TraesCS1D01G272500 chr3A 26002233 26004114 1881 True 694.0 706 86.132000 4862 7230 2 chr3A.!!$R4 2368
15 TraesCS1D01G272500 chr3A 671349290 671349799 509 False 604.0 604 88.132000 5799 6309 1 chr3A.!!$F1 510
16 TraesCS1D01G272500 chr7A 685448476 685450124 1648 False 2204.0 2204 90.849000 1512 3160 1 chr7A.!!$F2 1648
17 TraesCS1D01G272500 chr4A 11806279 11807921 1642 True 2204.0 2204 90.942000 1514 3156 1 chr4A.!!$R1 1642
18 TraesCS1D01G272500 chr3D 50541859 50542651 792 True 1086.0 1086 91.595000 1512 2303 1 chr3D.!!$R2 791
19 TraesCS1D01G272500 chr3D 18426781 18428661 1880 False 682.0 710 85.779500 4860 7230 2 chr3D.!!$F1 2370
20 TraesCS1D01G272500 chr3D 534127146 534128264 1118 False 463.0 695 85.458000 5440 7292 2 chr3D.!!$F2 1852
21 TraesCS1D01G272500 chr5D 61697340 61698670 1330 True 549.0 641 84.604500 5055 7116 2 chr5D.!!$R1 2061
22 TraesCS1D01G272500 chr3B 720194084 720194683 599 False 616.0 616 85.460000 5055 5660 1 chr3B.!!$F2 605
23 TraesCS1D01G272500 chr5B 703732177 703733443 1266 False 530.5 610 85.133000 5055 7036 2 chr5B.!!$F3 1981
24 TraesCS1D01G272500 chr6D 4982119 4982718 599 True 593.0 593 84.814000 5055 5660 1 chr6D.!!$R2 605
25 TraesCS1D01G272500 chr6A 504346334 504346843 509 True 462.0 462 83.117000 6581 7116 1 chr6A.!!$R1 535
26 TraesCS1D01G272500 chr2A 361208991 361210693 1702 True 206.5 313 85.592000 5919 6322 2 chr2A.!!$R2 403

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
510 544 1.106285 GGCCCAAATGGACTCATGAC 58.894 55.000 0.00 0.0 40.11 3.06 F
1158 1840 1.078143 CCTTGCCACTCCCTGTAGC 60.078 63.158 0.00 0.0 33.90 3.58 F
1566 2288 0.101579 CGCTTTTGTCCGTTTGGGTT 59.898 50.000 0.00 0.0 37.00 4.11 F
3246 4013 1.204467 ACAACAGTGTGCTTGGTTTGG 59.796 47.619 0.00 0.0 36.31 3.28 F
3428 4195 1.063492 AGGTTTTTGGAACCCGGAACT 60.063 47.619 0.73 0.0 41.18 3.01 F
4424 5193 0.612744 GAGGAAGAAGCAGCCTCAGT 59.387 55.000 0.00 0.0 45.89 3.41 F
4427 5196 1.675415 GGAAGAAGCAGCCTCAGTCTG 60.675 57.143 0.00 0.0 34.79 3.51 F
5244 6032 1.769098 CTGCAGATGGATTGACGGCG 61.769 60.000 8.42 4.8 0.00 6.46 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1348 2038 0.514255 CATCTGACCAACAGCACACG 59.486 55.000 0.00 0.00 45.38 4.49 R
2509 3269 2.123251 TCCGGAGAGGATCCCAGC 60.123 66.667 8.55 0.00 46.50 4.85 R
3412 4179 0.551879 TGGAGTTCCGGGTTCCAAAA 59.448 50.000 16.79 0.00 38.03 2.44 R
4348 5117 1.068741 CACCATAAGGAGCTCGGTACC 59.931 57.143 7.83 0.16 38.69 3.34 R
5227 6015 1.766143 GACGCCGTCAATCCATCTGC 61.766 60.000 13.23 0.00 32.09 4.26 R
5624 6424 2.827921 CCCCATAAACTTGAAGCAGCTT 59.172 45.455 7.60 7.60 0.00 3.74 R
5713 6522 3.245087 TGGCCTTATGCAAACTTACCAGA 60.245 43.478 3.32 0.00 43.89 3.86 R
6789 9226 1.066071 GCCTGGAGTACTGGGAAGTTC 60.066 57.143 0.00 0.00 38.54 3.01 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
133 134 2.639839 AGAAGCTTTAGCACCTTCCAGA 59.360 45.455 0.00 0.00 45.16 3.86
181 182 3.328050 CCCAAACCTCCTAGAACACTTCT 59.672 47.826 0.00 0.00 43.72 2.85
190 191 5.087323 TCCTAGAACACTTCTGAGGTCATT 58.913 41.667 0.00 0.00 40.94 2.57
202 203 7.281100 ACTTCTGAGGTCATTCGAAATATTTCC 59.719 37.037 20.01 7.09 33.68 3.13
213 214 2.430248 AATATTTCCGGAGCCCGTTT 57.570 45.000 3.34 0.00 46.80 3.60
244 245 5.055265 TCTATGACCTTCTAGTCCTCCTG 57.945 47.826 0.00 0.00 35.83 3.86
249 250 3.961408 GACCTTCTAGTCCTCCTGCATAA 59.039 47.826 0.00 0.00 0.00 1.90
268 269 3.631145 AACGCTAGTTAGTGAACGTGA 57.369 42.857 6.71 0.00 40.76 4.35
320 321 7.539710 CGGAACACCTTTCGATCGATAATTATA 59.460 37.037 20.18 0.00 0.00 0.98
325 326 8.708742 CACCTTTCGATCGATAATTATAAGCAA 58.291 33.333 20.18 4.50 0.00 3.91
399 400 9.316730 TCAAGCCATCATCTTTTTATTTATTGC 57.683 29.630 0.00 0.00 0.00 3.56
400 401 9.321562 CAAGCCATCATCTTTTTATTTATTGCT 57.678 29.630 0.00 0.00 0.00 3.91
429 430 7.051623 ACAATCGCATACAATTCCCTTTACTA 58.948 34.615 0.00 0.00 0.00 1.82
430 431 7.012044 ACAATCGCATACAATTCCCTTTACTAC 59.988 37.037 0.00 0.00 0.00 2.73
431 432 5.045215 TCGCATACAATTCCCTTTACTACG 58.955 41.667 0.00 0.00 0.00 3.51
432 433 4.210537 CGCATACAATTCCCTTTACTACGG 59.789 45.833 0.00 0.00 0.00 4.02
437 471 5.121105 ACAATTCCCTTTACTACGGCATAC 58.879 41.667 0.00 0.00 0.00 2.39
510 544 1.106285 GGCCCAAATGGACTCATGAC 58.894 55.000 0.00 0.00 40.11 3.06
515 549 1.739466 CAAATGGACTCATGACCACGG 59.261 52.381 7.18 0.00 40.48 4.94
534 568 2.028925 GGCCCAAACGCAAACAGG 59.971 61.111 0.00 0.00 0.00 4.00
537 571 1.659794 CCCAAACGCAAACAGGAGG 59.340 57.895 0.00 0.00 0.00 4.30
559 595 2.182030 GGCCCGTCGACTCAGAAG 59.818 66.667 14.70 0.00 0.00 2.85
785 1457 2.270257 CCGTAGACCCCACGTCACA 61.270 63.158 0.00 0.00 44.66 3.58
811 1483 3.687102 CACGGGCCCACGAGTACA 61.687 66.667 24.92 0.00 37.61 2.90
813 1485 2.433664 CGGGCCCACGAGTACAAC 60.434 66.667 24.92 0.00 35.47 3.32
869 1541 3.695825 GTCCCTCCCTCCCTCCCA 61.696 72.222 0.00 0.00 0.00 4.37
967 1639 4.816984 TCGCCGTCCTCCTCCTCC 62.817 72.222 0.00 0.00 0.00 4.30
970 1642 4.824515 CCGTCCTCCTCCTCCGCT 62.825 72.222 0.00 0.00 0.00 5.52
971 1643 3.213402 CGTCCTCCTCCTCCGCTC 61.213 72.222 0.00 0.00 0.00 5.03
972 1644 2.835895 GTCCTCCTCCTCCGCTCC 60.836 72.222 0.00 0.00 0.00 4.70
973 1645 4.507916 TCCTCCTCCTCCGCTCCG 62.508 72.222 0.00 0.00 0.00 4.63
1158 1840 1.078143 CCTTGCCACTCCCTGTAGC 60.078 63.158 0.00 0.00 33.90 3.58
1197 1879 2.625737 GCTTAGAGTTACCGAAACCCC 58.374 52.381 0.00 0.00 39.03 4.95
1221 1903 1.078214 TTGCTTGCTCGGATCTGGG 60.078 57.895 0.62 0.00 0.00 4.45
1224 1906 3.376935 CTTGCTCGGATCTGGGCGT 62.377 63.158 21.39 0.00 0.00 5.68
1230 1912 4.899239 GGATCTGGGCGTGCCTCG 62.899 72.222 11.25 2.33 43.12 4.63
1348 2038 2.218759 CCGCTTACTTGTCATGCGTATC 59.781 50.000 0.00 0.00 44.32 2.24
1483 2183 2.290367 CAGATGCCTGTGTTCGACAAAA 59.710 45.455 0.00 0.00 35.70 2.44
1566 2288 0.101579 CGCTTTTGTCCGTTTGGGTT 59.898 50.000 0.00 0.00 37.00 4.11
1614 2336 2.975799 GTTTGGGTCGGCGCAAGA 60.976 61.111 19.17 4.98 45.95 3.02
1776 2513 1.494824 AAAAACTAGACGACGCGCTT 58.505 45.000 5.73 0.00 0.00 4.68
2055 2811 2.685017 AGCCAGATCGGTGGAGCA 60.685 61.111 5.19 0.00 40.44 4.26
2936 3701 1.514087 GTCGTAGTTGGATGGCCGA 59.486 57.895 0.00 0.00 36.79 5.54
3163 3928 5.422012 CCCATTGGAGTTGCTTTTATAACCT 59.578 40.000 3.62 0.00 0.00 3.50
3166 3931 4.993028 TGGAGTTGCTTTTATAACCTGGT 58.007 39.130 0.00 0.00 0.00 4.00
3227 3992 3.673594 CGTGTGTCTGAATGACCTCCTAC 60.674 52.174 0.00 0.00 44.75 3.18
3232 3997 4.021104 TGTCTGAATGACCTCCTACAACAG 60.021 45.833 0.00 0.00 44.75 3.16
3246 4013 1.204467 ACAACAGTGTGCTTGGTTTGG 59.796 47.619 0.00 0.00 36.31 3.28
3261 4028 6.572119 GCTTGGTTTGGTCATGATATTGAACA 60.572 38.462 0.00 0.00 41.47 3.18
3265 4032 6.406177 GGTTTGGTCATGATATTGAACATGCT 60.406 38.462 0.00 0.00 42.63 3.79
3270 4037 7.040961 TGGTCATGATATTGAACATGCTGTATG 60.041 37.037 0.00 4.09 38.39 2.39
3412 4179 2.755686 ACTGCCCCGTAGTATTAGGTT 58.244 47.619 0.00 0.00 0.00 3.50
3422 4189 5.355071 CCGTAGTATTAGGTTTTTGGAACCC 59.645 44.000 4.41 0.00 41.18 4.11
3423 4190 5.063817 CGTAGTATTAGGTTTTTGGAACCCG 59.936 44.000 4.41 0.00 41.18 5.28
3424 4191 4.338012 AGTATTAGGTTTTTGGAACCCGG 58.662 43.478 0.00 0.00 41.18 5.73
3425 4192 3.529216 ATTAGGTTTTTGGAACCCGGA 57.471 42.857 0.73 0.00 41.18 5.14
3426 4193 3.309600 TTAGGTTTTTGGAACCCGGAA 57.690 42.857 0.73 0.00 41.18 4.30
3427 4194 1.405872 AGGTTTTTGGAACCCGGAAC 58.594 50.000 0.73 0.00 41.18 3.62
3428 4195 1.063492 AGGTTTTTGGAACCCGGAACT 60.063 47.619 0.73 0.00 41.18 3.01
3468 4236 5.133221 ACACTAAAACTTGACAGCATCCTT 58.867 37.500 0.00 0.00 0.00 3.36
3536 4304 6.928979 TTTCCATCTTGAAGTGTCGTTTAA 57.071 33.333 0.00 0.00 0.00 1.52
3538 4306 7.504924 TTCCATCTTGAAGTGTCGTTTAATT 57.495 32.000 0.00 0.00 0.00 1.40
3555 4323 6.903479 CGTTTAATTAACCATCGGTTCTTAGC 59.097 38.462 0.72 0.36 43.05 3.09
3565 4333 1.534175 CGGTTCTTAGCCACTAGAGCG 60.534 57.143 0.00 0.00 34.64 5.03
3574 4342 4.473477 AGCCACTAGAGCGTAAAGATTT 57.527 40.909 0.00 0.00 34.64 2.17
3610 4378 4.595781 AGACAACACTTGGACCCAGTATTA 59.404 41.667 0.00 0.00 34.12 0.98
3616 4384 7.266905 ACACTTGGACCCAGTATTATTACTT 57.733 36.000 0.00 0.00 36.50 2.24
3817 4585 7.934855 AGAACTGATTCATAGAAGTTGCAAT 57.065 32.000 0.59 0.00 37.29 3.56
3922 4690 7.142680 TCACTTGGTGGTTTATTCGATTTTTC 58.857 34.615 0.00 0.00 33.87 2.29
3961 4729 3.755378 CACTCTATGCAAAGCTTGGAGTT 59.245 43.478 17.11 5.03 46.31 3.01
4079 4847 9.754382 TCCGTAAAGAAATATAAGAGCGTTTAT 57.246 29.630 2.15 2.15 0.00 1.40
4093 4861 8.635877 AAGAGCGTTTATAGATCACTAAAGTG 57.364 34.615 3.64 3.64 46.91 3.16
4128 4896 7.386573 GCTCTTATATTTCTTTACAGAGGGAGC 59.613 40.741 0.00 0.00 33.61 4.70
4253 5022 5.183713 TCTCCAAAAGGATTAACACATGCAG 59.816 40.000 0.00 0.00 0.00 4.41
4275 5044 6.164876 CAGATTTGAGTTCAGAGAGATGTGT 58.835 40.000 0.00 0.00 0.00 3.72
4278 5047 6.851222 TTTGAGTTCAGAGAGATGTGTTTC 57.149 37.500 0.00 0.00 0.00 2.78
4301 5070 1.195115 CTGTGGGACTGCTAAGGCTA 58.805 55.000 0.00 0.00 39.59 3.93
4339 5108 4.633126 ACTGCTCTCGTTAGTTGTACGATA 59.367 41.667 0.00 0.00 45.76 2.92
4362 5131 3.434940 AAAAATGGTACCGAGCTCCTT 57.565 42.857 8.47 0.00 0.00 3.36
4411 5180 7.854557 TGAAATCATTGAGTACATGAGGAAG 57.145 36.000 0.00 0.00 0.00 3.46
4424 5193 0.612744 GAGGAAGAAGCAGCCTCAGT 59.387 55.000 0.00 0.00 45.89 3.41
4427 5196 1.675415 GGAAGAAGCAGCCTCAGTCTG 60.675 57.143 0.00 0.00 34.79 3.51
4496 5267 8.841300 TGATTTGCTCTATACTGAGTACTACAG 58.159 37.037 16.19 16.19 40.68 2.74
4806 5578 4.876107 TCTTGAAGAAAAGTGTCAGTGGAC 59.124 41.667 0.00 0.00 44.57 4.02
5227 6015 5.630680 ACTTGTTTATGCAAATCGCTTTCTG 59.369 36.000 0.00 0.00 43.06 3.02
5244 6032 1.769098 CTGCAGATGGATTGACGGCG 61.769 60.000 8.42 4.80 0.00 6.46
5338 6136 7.161404 TCATAAGCTACACAAAGATTCACACT 58.839 34.615 0.00 0.00 0.00 3.55
5430 6228 6.945435 ACCCATTAGTTGTGATTTGTGACATA 59.055 34.615 0.00 0.00 0.00 2.29
5616 6416 9.727859 AAATTTGTTGTGTAAACCCTAAAAAGT 57.272 25.926 0.00 0.00 0.00 2.66
5624 6424 6.487668 GTGTAAACCCTAAAAAGTCCAGCTAA 59.512 38.462 0.00 0.00 0.00 3.09
5678 6479 5.815581 ACATTAGAGTCACAAGGCCAAATA 58.184 37.500 5.01 0.00 0.00 1.40
5713 6522 7.449704 ACTTGGCTCTGTCTCAAAGATTATTTT 59.550 33.333 0.00 0.00 0.00 1.82
5940 6749 2.036475 ACACTGACAGAAGCGATGAACT 59.964 45.455 10.08 0.00 0.00 3.01
5980 6789 6.883744 TGTCTATGTTCACATGGTTAGCATA 58.116 36.000 2.50 0.00 37.15 3.14
5987 6796 8.518430 TGTTCACATGGTTAGCATATTAATGT 57.482 30.769 0.00 0.00 35.38 2.71
6134 6944 6.150140 GTGATATCTTTTTGGTGAACTCTGCT 59.850 38.462 3.98 0.00 0.00 4.24
6315 8441 7.225538 AGCACTTGTGAATACTATATGCTGTTC 59.774 37.037 4.79 0.00 34.79 3.18
6351 8786 5.119931 TGCTGGCAGTTTATTTGTAACAG 57.880 39.130 17.16 0.00 0.00 3.16
6365 8800 3.689347 TGTAACAGCTCAATCCAGCATT 58.311 40.909 0.00 0.00 42.40 3.56
6384 8819 6.331369 GCATTAGCTTATTTTGAGGGCATA 57.669 37.500 0.00 0.00 37.91 3.14
6391 8826 6.489361 AGCTTATTTTGAGGGCATATCTCTTG 59.511 38.462 0.00 0.00 32.78 3.02
6418 8853 9.438228 TTGTGGTCGTTAAGTTTGATATGATAA 57.562 29.630 0.00 0.00 0.00 1.75
6419 8854 8.875803 TGTGGTCGTTAAGTTTGATATGATAAC 58.124 33.333 0.00 0.00 0.00 1.89
6442 8878 5.005094 CCTTTTTAATACTCCCACCGTTCA 58.995 41.667 0.00 0.00 0.00 3.18
6443 8879 5.474189 CCTTTTTAATACTCCCACCGTTCAA 59.526 40.000 0.00 0.00 0.00 2.69
6755 9192 5.063691 CAGAATGATGACTGTCTGAAGCTTC 59.936 44.000 19.89 19.89 39.94 3.86
6787 9224 4.944317 CCAGCATATCTCAGGTATAGTCGA 59.056 45.833 0.00 0.00 0.00 4.20
6789 9226 6.404184 CCAGCATATCTCAGGTATAGTCGAAG 60.404 46.154 0.00 0.00 0.00 3.79
6801 9240 5.591877 GGTATAGTCGAAGAACTTCCCAGTA 59.408 44.000 8.66 4.33 39.69 2.74
6923 9368 2.610438 AGGAATGCCAAAGTCATGGT 57.390 45.000 0.00 0.00 42.75 3.55
6976 9421 1.771255 AGAAGCTGGAACACAAGGACT 59.229 47.619 0.00 0.00 0.00 3.85
6977 9422 1.876156 GAAGCTGGAACACAAGGACTG 59.124 52.381 0.00 0.00 0.00 3.51
7233 9690 8.755018 CATTGTTTTGTCAGAAGGATAAACAAC 58.245 33.333 11.64 3.55 45.29 3.32
7239 9696 6.282167 TGTCAGAAGGATAAACAACGTGTTA 58.718 36.000 0.00 0.00 40.14 2.41
7299 9756 0.037975 GGATGGCTGCCTGTTGTTTG 60.038 55.000 21.03 0.00 0.00 2.93
7308 9765 2.159014 TGCCTGTTGTTTGTCGTAGTCT 60.159 45.455 0.00 0.00 0.00 3.24
7325 9806 1.734465 GTCTTATCTGTGCGCTTTGCT 59.266 47.619 9.73 0.00 46.63 3.91
7331 9812 1.959899 CTGTGCGCTTTGCTCTACCG 61.960 60.000 9.73 0.00 46.63 4.02
7355 9836 1.976474 GGGCGACAATTGGCTTGGA 60.976 57.895 10.18 0.00 39.30 3.53
7362 9843 4.119136 CGACAATTGGCTTGGAAAACTTT 58.881 39.130 10.18 0.00 39.30 2.66
7364 9845 5.502220 CGACAATTGGCTTGGAAAACTTTTG 60.502 40.000 10.18 0.00 39.30 2.44
7369 9850 2.212652 GCTTGGAAAACTTTTGCCCAG 58.787 47.619 3.57 0.00 34.75 4.45
7377 9858 6.183361 TGGAAAACTTTTGCCCAGTGAATTAT 60.183 34.615 3.57 0.00 34.75 1.28
7390 9871 5.586243 CCAGTGAATTATGTACCCTCACTTG 59.414 44.000 0.41 0.00 43.14 3.16
7410 9891 9.562408 TCACTTGACAAATTATTTGGTACTACA 57.438 29.630 20.00 8.52 44.81 2.74
7431 9915 2.156343 ACTTTGAGAGAGCACGGTTC 57.844 50.000 0.00 0.00 0.00 3.62
7444 9928 1.098050 ACGGTTCTATTACGAGGCGT 58.902 50.000 0.00 0.00 44.35 5.68
7447 9931 3.316308 ACGGTTCTATTACGAGGCGTTAT 59.684 43.478 0.00 0.00 41.54 1.89
7449 9933 3.910767 GGTTCTATTACGAGGCGTTATCG 59.089 47.826 0.00 4.83 45.54 2.92
7463 9948 5.458891 GGCGTTATCGACATCTACAATACT 58.541 41.667 0.00 0.00 45.53 2.12
7464 9949 5.342525 GGCGTTATCGACATCTACAATACTG 59.657 44.000 0.00 0.00 45.53 2.74
7512 10026 8.911247 ATTGTTTTGTTCTCAGTAAACTTGAC 57.089 30.769 0.00 0.00 32.99 3.18
7526 10040 8.865001 CAGTAAACTTGACTAAAGATAGACAGC 58.135 37.037 0.00 0.00 39.38 4.40
7538 10052 2.417339 TAGACAGCGGATTATCGTGC 57.583 50.000 0.00 0.67 0.00 5.34
7556 10070 0.250209 GCATCGGGAGCTGTGATGAT 60.250 55.000 18.66 1.74 41.54 2.45
7560 10074 0.316522 CGGGAGCTGTGATGATCGAT 59.683 55.000 0.00 0.00 0.00 3.59
7562 10076 1.342496 GGGAGCTGTGATGATCGATGA 59.658 52.381 0.54 0.00 0.00 2.92
7609 10124 2.029649 GGCAGGGCAATATAGTGCATTG 60.030 50.000 24.93 21.12 46.81 2.82
7610 10125 2.624838 GCAGGGCAATATAGTGCATTGT 59.375 45.455 24.93 4.93 46.81 2.71
7623 10152 1.080366 CATTGTGCAATGCCGCTGT 60.080 52.632 11.33 0.00 41.27 4.40
7646 10175 1.629013 TGCGATCGAGCAAGTTACAG 58.371 50.000 21.57 0.00 45.06 2.74
7659 10188 7.010339 AGCAAGTTACAGAAGGAAGTATTCT 57.990 36.000 0.00 0.00 46.56 2.40
7668 10197 2.555199 AGGAAGTATTCTGATGCGTGC 58.445 47.619 0.00 0.00 46.56 5.34
7669 10198 1.599542 GGAAGTATTCTGATGCGTGCC 59.400 52.381 0.00 0.00 46.56 5.01
7678 10207 1.396648 CTGATGCGTGCCGTGATAAAA 59.603 47.619 0.00 0.00 0.00 1.52
7693 10222 7.281549 GCCGTGATAAAACTCCTAATTTCCTTA 59.718 37.037 0.00 0.00 0.00 2.69
7703 10232 6.330514 ACTCCTAATTTCCTTATTCCTCCTCC 59.669 42.308 0.00 0.00 0.00 4.30
7722 10251 5.833667 TCCTCCTGTAACAGATATGATCGTT 59.166 40.000 0.00 0.00 32.44 3.85
7748 10277 9.886132 TGTTTAATAAAGGTTGCCAAAGTTTTA 57.114 25.926 0.00 0.00 0.00 1.52
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
90 91 3.181449 TGAAAGACCCCGAAATGTTCTCA 60.181 43.478 0.00 0.00 0.00 3.27
133 134 1.133792 CCCGGATTTACCTGGAATGCT 60.134 52.381 0.73 0.00 44.39 3.79
162 163 4.284746 CCTCAGAAGTGTTCTAGGAGGTTT 59.715 45.833 12.06 0.00 41.55 3.27
163 164 3.835395 CCTCAGAAGTGTTCTAGGAGGTT 59.165 47.826 12.06 0.00 41.55 3.50
181 182 4.814234 CCGGAAATATTTCGAATGACCTCA 59.186 41.667 19.41 0.00 38.06 3.86
185 186 4.319549 GGCTCCGGAAATATTTCGAATGAC 60.320 45.833 19.41 10.03 38.06 3.06
190 191 1.539496 CGGGCTCCGGAAATATTTCGA 60.539 52.381 19.41 12.25 44.15 3.71
213 214 7.504238 GGACTAGAAGGTCATAGAGAATGAGAA 59.496 40.741 0.00 0.00 45.34 2.87
244 245 3.855950 ACGTTCACTAACTAGCGTTATGC 59.144 43.478 0.00 0.00 35.23 3.14
249 250 2.810274 TCTCACGTTCACTAACTAGCGT 59.190 45.455 0.00 0.00 33.15 5.07
320 321 1.000396 GGGTGCCCAGATCTTGCTT 60.000 57.895 13.60 0.00 35.81 3.91
342 343 3.865224 CCGTTGGTATGCGGTTATTAC 57.135 47.619 0.00 0.00 42.73 1.89
395 396 8.023128 GGAATTGTATGCGATTGTATAAGCAAT 58.977 33.333 0.37 0.00 43.19 3.56
396 397 7.359595 GGAATTGTATGCGATTGTATAAGCAA 58.640 34.615 0.37 0.00 43.19 3.91
398 399 6.149474 AGGGAATTGTATGCGATTGTATAAGC 59.851 38.462 0.37 0.00 0.00 3.09
399 400 7.672983 AGGGAATTGTATGCGATTGTATAAG 57.327 36.000 0.37 0.00 0.00 1.73
400 401 8.458573 AAAGGGAATTGTATGCGATTGTATAA 57.541 30.769 0.37 0.00 0.00 0.98
429 430 2.420722 CCGGTTTTGTAATGTATGCCGT 59.579 45.455 0.00 0.00 36.63 5.68
430 431 2.678836 TCCGGTTTTGTAATGTATGCCG 59.321 45.455 0.00 0.00 37.92 5.69
431 432 3.066203 CCTCCGGTTTTGTAATGTATGCC 59.934 47.826 0.00 0.00 0.00 4.40
432 433 3.488553 GCCTCCGGTTTTGTAATGTATGC 60.489 47.826 0.00 0.00 0.00 3.14
437 471 0.815095 GGGCCTCCGGTTTTGTAATG 59.185 55.000 0.84 0.00 0.00 1.90
468 502 6.767423 GCCTCCGGTTACACCTAAAATAATAA 59.233 38.462 0.00 0.00 35.66 1.40
470 504 5.128205 GCCTCCGGTTACACCTAAAATAAT 58.872 41.667 0.00 0.00 35.66 1.28
471 505 4.516323 GCCTCCGGTTACACCTAAAATAA 58.484 43.478 0.00 0.00 35.66 1.40
474 508 1.003464 GGCCTCCGGTTACACCTAAAA 59.997 52.381 0.00 0.00 35.66 1.52
475 509 0.614812 GGCCTCCGGTTACACCTAAA 59.385 55.000 0.00 0.00 35.66 1.85
476 510 1.266867 GGGCCTCCGGTTACACCTAA 61.267 60.000 0.84 0.00 35.66 2.69
477 511 1.686800 GGGCCTCCGGTTACACCTA 60.687 63.158 0.84 0.00 35.66 3.08
478 512 3.007323 GGGCCTCCGGTTACACCT 61.007 66.667 0.84 0.00 35.66 4.00
479 513 2.414658 TTTGGGCCTCCGGTTACACC 62.415 60.000 4.53 0.00 35.24 4.16
480 514 0.323087 ATTTGGGCCTCCGGTTACAC 60.323 55.000 4.53 0.00 35.24 2.90
481 515 0.322997 CATTTGGGCCTCCGGTTACA 60.323 55.000 4.53 0.00 35.24 2.41
482 516 1.035385 CCATTTGGGCCTCCGGTTAC 61.035 60.000 4.53 0.00 35.24 2.50
483 517 1.208844 TCCATTTGGGCCTCCGGTTA 61.209 55.000 4.53 0.00 36.21 2.85
484 518 2.037208 CCATTTGGGCCTCCGGTT 59.963 61.111 4.53 0.00 35.24 4.44
485 519 2.938798 TCCATTTGGGCCTCCGGT 60.939 61.111 4.53 0.00 36.21 5.28
486 520 2.440247 GTCCATTTGGGCCTCCGG 60.440 66.667 4.53 0.00 36.21 5.14
487 521 1.452108 GAGTCCATTTGGGCCTCCG 60.452 63.158 4.53 0.00 41.83 4.63
488 522 0.259938 ATGAGTCCATTTGGGCCTCC 59.740 55.000 4.53 0.00 41.83 4.30
489 523 1.064463 TCATGAGTCCATTTGGGCCTC 60.064 52.381 4.53 4.25 41.83 4.70
490 524 1.002069 TCATGAGTCCATTTGGGCCT 58.998 50.000 4.53 0.00 41.83 5.19
491 525 1.106285 GTCATGAGTCCATTTGGGCC 58.894 55.000 0.00 0.00 41.83 5.80
492 526 1.106285 GGTCATGAGTCCATTTGGGC 58.894 55.000 0.00 0.00 40.99 5.36
493 527 2.094675 GTGGTCATGAGTCCATTTGGG 58.905 52.381 8.20 0.00 35.43 4.12
494 528 1.739466 CGTGGTCATGAGTCCATTTGG 59.261 52.381 8.20 0.00 35.43 3.28
499 533 2.662596 GCCGTGGTCATGAGTCCA 59.337 61.111 0.00 0.00 0.00 4.02
500 534 2.509336 CGCCGTGGTCATGAGTCC 60.509 66.667 0.00 0.00 0.00 3.85
502 536 4.760047 GCCGCCGTGGTCATGAGT 62.760 66.667 0.00 0.00 41.21 3.41
537 571 4.773117 GAGTCGACGGGCCGTGTC 62.773 72.222 39.41 24.37 41.37 3.67
559 595 0.387239 GCCCACTGTTTGTTCGATGC 60.387 55.000 0.00 0.00 0.00 3.91
700 1363 2.328589 TGGGAGGAGGAGGAGGAGG 61.329 68.421 0.00 0.00 0.00 4.30
701 1364 1.075600 GTGGGAGGAGGAGGAGGAG 60.076 68.421 0.00 0.00 0.00 3.69
702 1365 1.862138 TGTGGGAGGAGGAGGAGGA 60.862 63.158 0.00 0.00 0.00 3.71
803 1475 1.335324 GCTACCGTGTGTTGTACTCGT 60.335 52.381 0.00 0.00 42.88 4.18
804 1476 1.334054 GCTACCGTGTGTTGTACTCG 58.666 55.000 0.00 0.00 43.74 4.18
805 1477 1.334054 CGCTACCGTGTGTTGTACTC 58.666 55.000 0.00 0.00 0.00 2.59
806 1478 3.484524 CGCTACCGTGTGTTGTACT 57.515 52.632 0.00 0.00 0.00 2.73
955 1627 2.835895 GGAGCGGAGGAGGAGGAC 60.836 72.222 0.00 0.00 0.00 3.85
1170 1852 1.619807 GGTAACTCTAAGCCCCGCCA 61.620 60.000 0.00 0.00 0.00 5.69
1197 1879 2.100584 AGATCCGAGCAAGCAACTAGAG 59.899 50.000 0.00 0.00 0.00 2.43
1275 1964 3.173167 AACCTCGGTGACAACCCCG 62.173 63.158 0.00 0.00 44.42 5.73
1310 1999 0.893270 CGGACCTCCAATGCAACCAA 60.893 55.000 0.00 0.00 35.14 3.67
1348 2038 0.514255 CATCTGACCAACAGCACACG 59.486 55.000 0.00 0.00 45.38 4.49
1483 2183 2.543861 CGGCGTGCATCTGAATAGTAGT 60.544 50.000 0.00 0.00 0.00 2.73
1776 2513 2.124403 GACGAGGACGCCTAGGGA 60.124 66.667 11.72 0.00 43.96 4.20
2049 2805 2.574018 CGAGTGGGTCAGTGCTCCA 61.574 63.158 6.54 3.87 0.00 3.86
2055 2811 4.664677 GTGCGCGAGTGGGTCAGT 62.665 66.667 12.10 0.00 0.00 3.41
2368 3128 3.479269 GTTCGCCTTCGAGCACGG 61.479 66.667 3.11 0.00 46.34 4.94
2464 3224 2.304056 CCCATGTGGAGGAGGTGCT 61.304 63.158 0.00 0.00 37.39 4.40
2509 3269 2.123251 TCCGGAGAGGATCCCAGC 60.123 66.667 8.55 0.00 46.50 4.85
2672 3432 4.516326 ATTCCCCCTCCCTCCCCG 62.516 72.222 0.00 0.00 0.00 5.73
2673 3433 2.778717 CATTCCCCCTCCCTCCCC 60.779 72.222 0.00 0.00 0.00 4.81
3227 3992 1.204467 ACCAAACCAAGCACACTGTTG 59.796 47.619 0.00 0.00 0.00 3.33
3232 3997 1.680735 TCATGACCAAACCAAGCACAC 59.319 47.619 0.00 0.00 0.00 3.82
3412 4179 0.551879 TGGAGTTCCGGGTTCCAAAA 59.448 50.000 16.79 0.00 38.03 2.44
3422 4189 1.539827 GTTCATGGGTTTGGAGTTCCG 59.460 52.381 0.00 0.00 39.43 4.30
3423 4190 2.558359 CAGTTCATGGGTTTGGAGTTCC 59.442 50.000 0.00 0.00 0.00 3.62
3424 4191 3.253432 GTCAGTTCATGGGTTTGGAGTTC 59.747 47.826 0.00 0.00 0.00 3.01
3425 4192 3.222603 GTCAGTTCATGGGTTTGGAGTT 58.777 45.455 0.00 0.00 0.00 3.01
3426 4193 2.174639 TGTCAGTTCATGGGTTTGGAGT 59.825 45.455 0.00 0.00 0.00 3.85
3427 4194 2.554032 GTGTCAGTTCATGGGTTTGGAG 59.446 50.000 0.00 0.00 0.00 3.86
3428 4195 2.174639 AGTGTCAGTTCATGGGTTTGGA 59.825 45.455 0.00 0.00 0.00 3.53
3468 4236 1.123077 AAGCAGTATGATCGCCCAGA 58.877 50.000 0.00 0.00 39.69 3.86
3504 4272 7.974675 ACACTTCAAGATGGAAAATATGTACG 58.025 34.615 0.00 0.00 0.00 3.67
3536 4304 4.080526 AGTGGCTAAGAACCGATGGTTAAT 60.081 41.667 0.34 0.00 46.95 1.40
3538 4306 2.835764 AGTGGCTAAGAACCGATGGTTA 59.164 45.455 0.34 0.00 46.95 2.85
3555 4323 5.575606 TCGAAAAATCTTTACGCTCTAGTGG 59.424 40.000 0.00 0.00 0.00 4.00
3574 4342 6.018262 CCAAGTGTTGTCTACTTTGATCGAAA 60.018 38.462 0.00 0.00 36.29 3.46
3610 4378 8.658499 AGAACAGAACAAGAACGTAAAGTAAT 57.342 30.769 0.00 0.00 0.00 1.89
3616 4384 5.898174 TGAGAGAACAGAACAAGAACGTAA 58.102 37.500 0.00 0.00 0.00 3.18
3715 4483 5.258456 CAAAGCATGCCTATTGAATGAGT 57.742 39.130 15.66 0.00 0.00 3.41
3922 4690 4.256920 AGAGTGGACTGAAAAATCCATCG 58.743 43.478 0.00 0.00 46.55 3.84
4051 4819 7.035840 ACGCTCTTATATTTCTTTACGGAGA 57.964 36.000 0.00 0.00 0.00 3.71
4098 4866 9.099454 CCTCTGTAAAGAAATATAAGAGCGTTT 57.901 33.333 0.00 0.00 0.00 3.60
4099 4867 7.711339 CCCTCTGTAAAGAAATATAAGAGCGTT 59.289 37.037 0.00 0.00 0.00 4.84
4100 4868 7.069578 TCCCTCTGTAAAGAAATATAAGAGCGT 59.930 37.037 0.00 0.00 0.00 5.07
4244 5013 4.392047 TCTGAACTCAAATCTGCATGTGT 58.608 39.130 0.00 0.00 0.00 3.72
4253 5022 7.387397 AGAAACACATCTCTCTGAACTCAAATC 59.613 37.037 0.00 0.00 0.00 2.17
4275 5044 4.389374 CTTAGCAGTCCCACAGAAAGAAA 58.611 43.478 0.00 0.00 0.00 2.52
4278 5047 2.704572 CCTTAGCAGTCCCACAGAAAG 58.295 52.381 0.00 0.00 0.00 2.62
4348 5117 1.068741 CACCATAAGGAGCTCGGTACC 59.931 57.143 7.83 0.16 38.69 3.34
4362 5131 3.388024 GGATCTCAGTAACTGGCACCATA 59.612 47.826 0.00 0.00 31.51 2.74
4411 5180 2.751166 TAACAGACTGAGGCTGCTTC 57.249 50.000 16.77 4.63 36.86 3.86
4496 5267 4.309933 CAAGGCCTGGAATCAAGAAAAAC 58.690 43.478 5.69 0.00 0.00 2.43
4724 5495 6.908820 ACGGAAATTTAAGAAAGAACGAACAC 59.091 34.615 0.00 0.00 0.00 3.32
4806 5578 6.730960 ATGGGTTTGTATATTTATACGCCG 57.269 37.500 3.89 0.00 41.04 6.46
4909 5683 9.890629 ATCAACTTCATAAGCTGATGTAACTTA 57.109 29.630 11.02 0.00 41.44 2.24
4919 5693 9.160496 GGATTATCCTATCAACTTCATAAGCTG 57.840 37.037 3.59 0.00 32.53 4.24
4933 5707 7.009179 TGGTCTTCATGTGGATTATCCTATC 57.991 40.000 12.91 4.11 37.46 2.08
4988 5762 5.653330 TGTCAATGATGTGGTGCATAGAAAT 59.347 36.000 0.00 0.00 38.06 2.17
5227 6015 1.766143 GACGCCGTCAATCCATCTGC 61.766 60.000 13.23 0.00 32.09 4.26
5430 6228 9.588096 ACACTCTTGAGATTTAAAAGGGTTTAT 57.412 29.630 4.49 0.00 32.26 1.40
5554 6353 5.546499 AGGAGTGACTGATTTAAACCACCTA 59.454 40.000 0.00 0.00 0.00 3.08
5624 6424 2.827921 CCCCATAAACTTGAAGCAGCTT 59.172 45.455 7.60 7.60 0.00 3.74
5654 6454 4.901197 TTGGCCTTGTGACTCTAATGTA 57.099 40.909 3.32 0.00 0.00 2.29
5678 6479 4.093011 AGACAGAGCCAAGTGAGTCTATT 58.907 43.478 0.00 0.00 34.83 1.73
5713 6522 3.245087 TGGCCTTATGCAAACTTACCAGA 60.245 43.478 3.32 0.00 43.89 3.86
5965 6774 8.744568 TCAACATTAATATGCTAACCATGTGA 57.255 30.769 0.00 0.00 35.03 3.58
5980 6789 7.558604 ACAAAGCATATTGGCTCAACATTAAT 58.441 30.769 0.00 0.00 45.07 1.40
5987 6796 6.054295 ACAAAAACAAAGCATATTGGCTCAA 58.946 32.000 0.00 0.00 45.07 3.02
5999 6808 6.258507 ACATCAGAATCCAACAAAAACAAAGC 59.741 34.615 0.00 0.00 0.00 3.51
6134 6944 5.833131 GGACAGATTGGGCCTTATAATTTCA 59.167 40.000 4.53 0.00 0.00 2.69
6315 8441 4.240096 CTGCCAGCAAGAAAATAACAAGG 58.760 43.478 0.00 0.00 0.00 3.61
6365 8800 7.321717 AGAGATATGCCCTCAAAATAAGCTA 57.678 36.000 0.00 0.00 33.25 3.32
6384 8819 4.957296 ACTTAACGACCACAACAAGAGAT 58.043 39.130 0.00 0.00 0.00 2.75
6391 8826 7.124347 TCATATCAAACTTAACGACCACAAC 57.876 36.000 0.00 0.00 0.00 3.32
6418 8853 4.645863 ACGGTGGGAGTATTAAAAAGGT 57.354 40.909 0.00 0.00 0.00 3.50
6419 8854 5.005094 TGAACGGTGGGAGTATTAAAAAGG 58.995 41.667 0.00 0.00 0.00 3.11
6435 8871 9.418045 CCAAAACATCTTATATTTTTGAACGGT 57.582 29.630 8.83 0.00 40.04 4.83
6464 8900 9.093970 CAGTTCGTATGTAGTCCATATTGAAAA 57.906 33.333 0.00 0.00 38.29 2.29
6551 8987 6.370442 CCTCCGTTCACAAATACAAGATGTTA 59.630 38.462 0.00 0.00 0.00 2.41
6553 8989 4.695455 CCTCCGTTCACAAATACAAGATGT 59.305 41.667 0.00 0.00 0.00 3.06
6560 8996 3.329929 ACTCCCTCCGTTCACAAATAC 57.670 47.619 0.00 0.00 0.00 1.89
6755 9192 4.361420 CTGAGATATGCTGGCGATATCTG 58.639 47.826 20.76 10.69 41.31 2.90
6757 9194 3.131933 ACCTGAGATATGCTGGCGATATC 59.868 47.826 12.57 12.57 34.30 1.63
6787 9224 2.907042 CCTGGAGTACTGGGAAGTTCTT 59.093 50.000 0.00 0.00 34.73 2.52
6789 9226 1.066071 GCCTGGAGTACTGGGAAGTTC 60.066 57.143 0.00 0.00 38.54 3.01
6909 9354 1.273048 GCATCAACCATGACTTTGGCA 59.727 47.619 0.00 0.00 40.68 4.92
6923 9368 8.400186 CAAATTGTACATCAGATGTAGCATCAA 58.600 33.333 21.60 20.21 45.62 2.57
6976 9421 2.416296 CCGGTGTTTACTCTATCGCACA 60.416 50.000 0.00 0.00 0.00 4.57
6977 9422 2.190981 CCGGTGTTTACTCTATCGCAC 58.809 52.381 0.00 0.00 0.00 5.34
7233 9690 2.609759 GCACGTTGGGGGTAACACG 61.610 63.158 0.00 0.00 46.14 4.49
7293 9750 5.404366 GCACAGATAAGACTACGACAAACAA 59.596 40.000 0.00 0.00 0.00 2.83
7294 9751 4.921515 GCACAGATAAGACTACGACAAACA 59.078 41.667 0.00 0.00 0.00 2.83
7299 9756 2.110226 GCGCACAGATAAGACTACGAC 58.890 52.381 0.30 0.00 0.00 4.34
7308 9765 2.099141 AGAGCAAAGCGCACAGATAA 57.901 45.000 11.47 0.00 46.13 1.75
7325 9806 1.252215 TGTCGCCCATGTTCGGTAGA 61.252 55.000 4.39 0.00 0.00 2.59
7331 9812 0.458370 GCCAATTGTCGCCCATGTTC 60.458 55.000 4.43 0.00 0.00 3.18
7355 9836 6.591001 ACATAATTCACTGGGCAAAAGTTTT 58.409 32.000 0.00 0.00 0.00 2.43
7362 9843 3.268334 AGGGTACATAATTCACTGGGCAA 59.732 43.478 0.00 0.00 0.00 4.52
7364 9845 3.118038 TGAGGGTACATAATTCACTGGGC 60.118 47.826 0.00 0.00 0.00 5.36
7369 9850 6.170506 TGTCAAGTGAGGGTACATAATTCAC 58.829 40.000 0.00 1.17 38.68 3.18
7377 9858 7.040062 CCAAATAATTTGTCAAGTGAGGGTACA 60.040 37.037 0.00 0.00 38.98 2.90
7410 9891 2.622064 ACCGTGCTCTCTCAAAGTTT 57.378 45.000 0.00 0.00 0.00 2.66
7414 9895 4.537135 AATAGAACCGTGCTCTCTCAAA 57.463 40.909 0.00 0.00 0.00 2.69
7431 9915 4.137849 TGTCGATAACGCCTCGTAATAG 57.862 45.455 0.00 0.00 39.99 1.73
7493 10007 9.832445 ATCTTTAGTCAAGTTTACTGAGAACAA 57.168 29.630 0.00 0.00 33.66 2.83
7502 10016 7.009357 CCGCTGTCTATCTTTAGTCAAGTTTAC 59.991 40.741 0.00 0.00 33.66 2.01
7512 10026 6.524933 CACGATAATCCGCTGTCTATCTTTAG 59.475 42.308 0.00 0.00 0.00 1.85
7526 10040 0.038618 TCCCGATGCACGATAATCCG 60.039 55.000 9.75 0.00 45.77 4.18
7538 10052 1.793258 GATCATCACAGCTCCCGATG 58.207 55.000 9.34 9.34 38.29 3.84
7556 10070 1.455773 ATCTCCCGGCAGTCATCGA 60.456 57.895 0.00 0.00 0.00 3.59
7560 10074 0.687427 TCATCATCTCCCGGCAGTCA 60.687 55.000 0.00 0.00 0.00 3.41
7562 10076 0.689080 ACTCATCATCTCCCGGCAGT 60.689 55.000 0.00 0.00 0.00 4.40
7623 10152 3.181290 CTTGCTCGATCGCACGCA 61.181 61.111 18.16 18.16 40.09 5.24
7626 10155 1.321743 CTGTAACTTGCTCGATCGCAC 59.678 52.381 11.09 5.18 40.09 5.34
7646 10175 3.001736 GCACGCATCAGAATACTTCCTTC 59.998 47.826 0.00 0.00 0.00 3.46
7668 10197 7.625828 AAGGAAATTAGGAGTTTTATCACGG 57.374 36.000 0.00 0.00 0.00 4.94
7678 10207 6.330514 GGAGGAGGAATAAGGAAATTAGGAGT 59.669 42.308 0.00 0.00 0.00 3.85
7693 10222 6.385443 TCATATCTGTTACAGGAGGAGGAAT 58.615 40.000 12.79 0.00 31.51 3.01
7722 10251 8.794335 AAAACTTTGGCAACCTTTATTAAACA 57.206 26.923 0.00 0.00 0.00 2.83


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

AutoCloner maintained by Alex Coulton.