Multiple sequence alignment - TraesCS2B01G626000

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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 TraesCS2B01G626000 chr2B 100.000 6841 0 0 1 6841 798577293 798584133 0.000000e+00 12634.0
1 TraesCS2B01G626000 chr2B 90.394 3248 214 42 3631 6817 798745287 798742077 0.000000e+00 4180.0
2 TraesCS2B01G626000 chr2B 95.980 796 31 1 6046 6841 798591800 798592594 0.000000e+00 1291.0
3 TraesCS2B01G626000 chr2B 93.042 891 42 9 726 1605 798746457 798745576 0.000000e+00 1284.0
4 TraesCS2B01G626000 chr2B 83.442 1383 215 8 4530 5909 798590226 798591597 0.000000e+00 1273.0
5 TraesCS2B01G626000 chr2B 94.110 730 41 2 1 729 798749516 798748788 0.000000e+00 1109.0
6 TraesCS2B01G626000 chr2B 95.338 665 30 1 6177 6841 798738452 798737789 0.000000e+00 1055.0
7 TraesCS2B01G626000 chr2B 91.727 278 19 3 1356 1629 798732741 798732464 3.870000e-102 383.0
8 TraesCS2B01G626000 chr2B 88.106 227 25 2 1356 1581 793380139 793379914 1.130000e-67 268.0
9 TraesCS2B01G626000 chr2B 86.809 235 29 2 1348 1581 793367810 793367577 1.890000e-65 261.0
10 TraesCS2B01G626000 chr2B 95.489 133 6 0 1815 1947 798745464 798745332 5.370000e-51 213.0
11 TraesCS2B01G626000 chr2B 86.364 154 18 3 6191 6343 799001671 799001520 1.530000e-36 165.0
12 TraesCS2B01G626000 chr2B 85.714 154 19 3 6191 6343 798993423 798993272 7.100000e-35 159.0
13 TraesCS2B01G626000 chr2B 91.579 95 3 3 5907 5998 798591701 798591793 7.200000e-25 126.0
14 TraesCS2B01G626000 chr2B 92.000 50 4 0 3532 3581 798745342 798745293 3.420000e-08 71.3
15 TraesCS2B01G626000 chr2B 95.000 40 2 0 1822 1861 798610674 798610713 5.730000e-06 63.9
16 TraesCS2B01G626000 chr2B 85.965 57 6 2 2068 2122 243791320 243791376 7.410000e-05 60.2
17 TraesCS2B01G626000 chr2A 89.535 2561 208 32 4306 6841 765054422 765051897 0.000000e+00 3190.0
18 TraesCS2B01G626000 chr2A 82.508 949 90 33 703 1605 765056851 765055933 0.000000e+00 763.0
19 TraesCS2B01G626000 chr2A 81.885 541 50 18 3555 4088 765055643 765055144 4.940000e-111 412.0
20 TraesCS2B01G626000 chr2A 76.860 242 50 6 6431 6671 17812691 17812455 1.550000e-26 132.0
21 TraesCS2B01G626000 chr2D 90.064 2194 130 37 4225 6358 639679569 639677404 0.000000e+00 2763.0
22 TraesCS2B01G626000 chr2D 88.901 892 58 7 757 1617 639680825 639679944 0.000000e+00 1061.0
23 TraesCS2B01G626000 chr2D 81.684 879 153 5 4514 5388 639674733 639673859 0.000000e+00 725.0
24 TraesCS2B01G626000 chr2D 85.070 355 40 6 5612 5964 639673861 639673518 3.930000e-92 350.0
25 TraesCS2B01G626000 chr2D 79.132 484 66 28 1114 1581 643761756 643762220 1.120000e-77 302.0
26 TraesCS2B01G626000 chr2D 96.154 182 7 0 3575 3756 639679747 639679566 1.440000e-76 298.0
27 TraesCS2B01G626000 chr2D 88.000 225 27 0 1357 1581 643674996 643675220 4.070000e-67 267.0
28 TraesCS2B01G626000 chr2D 87.773 229 25 2 1356 1581 643662186 643661958 1.460000e-66 265.0
29 TraesCS2B01G626000 chr2D 96.124 129 5 0 1786 1914 639679873 639679745 1.930000e-50 211.0
30 TraesCS2B01G626000 chr2D 78.862 246 47 4 6423 6667 15837621 15837380 1.970000e-35 161.0
31 TraesCS2B01G626000 chr4D 88.185 1532 170 9 1967 3496 47111011 47109489 0.000000e+00 1816.0
32 TraesCS2B01G626000 chr4D 91.667 288 23 1 3242 3529 220418093 220417807 1.380000e-106 398.0
33 TraesCS2B01G626000 chr4D 96.491 57 2 0 3473 3529 490953351 490953295 2.030000e-15 95.3
34 TraesCS2B01G626000 chr1D 81.180 1610 266 29 1942 3529 449843460 449841866 0.000000e+00 1260.0
35 TraesCS2B01G626000 chr7A 80.485 1609 272 31 1945 3529 266583301 266581711 0.000000e+00 1194.0
36 TraesCS2B01G626000 chr1A 82.192 1314 228 6 2219 3529 147674134 147672824 0.000000e+00 1125.0
37 TraesCS2B01G626000 chr4B 86.516 1016 113 9 1957 2967 315631959 315632955 0.000000e+00 1096.0
38 TraesCS2B01G626000 chr4B 88.414 561 62 3 2969 3529 315643440 315643997 0.000000e+00 673.0
39 TraesCS2B01G626000 chr3B 80.205 1364 254 13 2173 3529 439017007 439018361 0.000000e+00 1009.0
40 TraesCS2B01G626000 chr5B 79.821 1343 261 8 2190 3529 656797669 656799004 0.000000e+00 970.0
41 TraesCS2B01G626000 chr5B 80.058 346 57 10 81 420 402745008 402744669 5.300000e-61 246.0
42 TraesCS2B01G626000 chr7D 81.156 1125 185 21 1945 3054 124641919 124643031 0.000000e+00 878.0
43 TraesCS2B01G626000 chr7D 75.740 338 69 10 5442 5774 89311280 89310951 2.550000e-34 158.0
44 TraesCS2B01G626000 chr6D 79.156 1209 249 3 2190 3397 3058149 3056943 0.000000e+00 833.0
45 TraesCS2B01G626000 chr6D 85.294 102 13 1 324 425 417901254 417901353 3.370000e-18 104.0
46 TraesCS2B01G626000 chr4A 83.333 186 25 5 6494 6678 676541755 676541575 4.240000e-37 167.0
47 TraesCS2B01G626000 chr5D 79.116 249 38 8 120 361 434455742 434455501 7.100000e-35 159.0
48 TraesCS2B01G626000 chr7B 75.522 335 69 10 5442 5771 40275936 40275610 1.190000e-32 152.0


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 TraesCS2B01G626000 chr2B 798577293 798584133 6840 False 12634.000000 12634 100.000000 1 6841 1 chr2B.!!$F2 6840
1 TraesCS2B01G626000 chr2B 798737789 798749516 11727 True 1318.716667 4180 93.395500 1 6841 6 chr2B.!!$R6 6840
2 TraesCS2B01G626000 chr2B 798590226 798592594 2368 False 896.666667 1291 90.333667 4530 6841 3 chr2B.!!$F4 2311
3 TraesCS2B01G626000 chr2A 765051897 765056851 4954 True 1455.000000 3190 84.642667 703 6841 3 chr2A.!!$R2 6138
4 TraesCS2B01G626000 chr2D 639673518 639680825 7307 True 901.333333 2763 89.666167 757 6358 6 chr2D.!!$R3 5601
5 TraesCS2B01G626000 chr4D 47109489 47111011 1522 True 1816.000000 1816 88.185000 1967 3496 1 chr4D.!!$R1 1529
6 TraesCS2B01G626000 chr1D 449841866 449843460 1594 True 1260.000000 1260 81.180000 1942 3529 1 chr1D.!!$R1 1587
7 TraesCS2B01G626000 chr7A 266581711 266583301 1590 True 1194.000000 1194 80.485000 1945 3529 1 chr7A.!!$R1 1584
8 TraesCS2B01G626000 chr1A 147672824 147674134 1310 True 1125.000000 1125 82.192000 2219 3529 1 chr1A.!!$R1 1310
9 TraesCS2B01G626000 chr4B 315631959 315632955 996 False 1096.000000 1096 86.516000 1957 2967 1 chr4B.!!$F1 1010
10 TraesCS2B01G626000 chr4B 315643440 315643997 557 False 673.000000 673 88.414000 2969 3529 1 chr4B.!!$F2 560
11 TraesCS2B01G626000 chr3B 439017007 439018361 1354 False 1009.000000 1009 80.205000 2173 3529 1 chr3B.!!$F1 1356
12 TraesCS2B01G626000 chr5B 656797669 656799004 1335 False 970.000000 970 79.821000 2190 3529 1 chr5B.!!$F1 1339
13 TraesCS2B01G626000 chr7D 124641919 124643031 1112 False 878.000000 878 81.156000 1945 3054 1 chr7D.!!$F1 1109
14 TraesCS2B01G626000 chr6D 3056943 3058149 1206 True 833.000000 833 79.156000 2190 3397 1 chr6D.!!$R1 1207

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
698 700 0.238289 CGGTGACTGAAACATGTGCC 59.762 55.0 0.00 0.00 0.00 5.01 F
1098 3493 0.178992 ATCCGAGAGCAGAGGAGAGG 60.179 60.0 0.00 0.00 37.49 3.69 F
1720 4121 0.028770 ACACATGAAACACGCGGTTG 59.971 50.0 12.47 2.37 40.35 3.77 F
3010 5440 0.469705 ACCAAAAGCACATGGCCTCA 60.470 50.0 3.32 0.00 46.50 3.86 F
4710 7787 0.467384 CATTCCTCTCGCACAGGGAT 59.533 55.0 0.00 0.00 27.63 3.85 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1589 3990 0.250770 ACGGGAAGCAAAAGGAGGAC 60.251 55.0 0.00 0.0 0.00 3.85 R
2987 5417 0.106521 GCCATGTGCTTTTGGTTGGT 59.893 50.0 0.00 0.0 35.34 3.67 R
3683 6122 0.250467 ATGGCGATGGATACCAGCAC 60.250 55.0 6.83 0.0 40.32 4.40 R
4943 8020 0.759436 CATAGAGGCGGTAGGTGGGT 60.759 60.0 0.00 0.0 0.00 4.51 R
6045 9292 0.388649 CCGTCACAGCACCTGTCTAC 60.389 60.0 0.00 0.0 43.43 2.59 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
30 31 2.082366 GCGCATTGACAAACAGCCG 61.082 57.895 0.30 0.00 0.00 5.52
107 108 4.942852 TCGCAGAAAACACATTTGGAAAT 58.057 34.783 0.00 0.00 0.00 2.17
108 109 5.233902 TTCGCAGAAAACACATTTGGAAATG 59.766 36.000 10.01 10.01 46.35 2.32
109 110 4.744137 CGCAGAAAACACATTTGGAAATGA 59.256 37.500 17.07 0.00 46.72 2.57
112 113 7.127686 GCAGAAAACACATTTGGAAATGAAAG 58.872 34.615 17.07 9.62 46.72 2.62
114 115 6.260714 AGAAAACACATTTGGAAATGAAAGGC 59.739 34.615 17.07 4.19 46.72 4.35
116 117 4.886579 ACACATTTGGAAATGAAAGGCTC 58.113 39.130 17.07 0.00 46.72 4.70
163 165 4.217767 GGTTTTTGCAAAGGGAGGTAGTAG 59.782 45.833 12.41 0.00 0.00 2.57
197 199 5.699839 AGAAAACCTTGCTAAGCGTAATTG 58.300 37.500 0.00 0.00 0.00 2.32
201 203 4.261801 ACCTTGCTAAGCGTAATTGACAT 58.738 39.130 0.00 0.00 0.00 3.06
246 248 5.105351 TGTGATCACGAGGAGACAATACATT 60.105 40.000 20.54 0.00 0.00 2.71
282 284 7.560991 TGTCATATCCATTTACTGCCTTGATTT 59.439 33.333 0.00 0.00 0.00 2.17
308 310 5.510323 GCACGCCACTAATTTTGTATACAAC 59.490 40.000 17.85 2.77 35.28 3.32
322 324 5.995446 TGTATACAACCATCACAGCCAATA 58.005 37.500 2.20 0.00 0.00 1.90
361 363 5.327737 TTGGAAACTAGTTGGGTGGTATT 57.672 39.130 9.34 0.00 0.00 1.89
367 369 8.434392 GGAAACTAGTTGGGTGGTATTATCATA 58.566 37.037 9.34 0.00 0.00 2.15
368 370 9.841295 GAAACTAGTTGGGTGGTATTATCATAA 57.159 33.333 9.34 0.00 0.00 1.90
378 380 6.206829 GGTGGTATTATCATAAGTTGAAGGGC 59.793 42.308 0.00 0.00 38.03 5.19
405 407 3.820467 TCCATGTGGAAGTTTGTGTCATC 59.180 43.478 0.00 0.00 42.18 2.92
410 412 3.748568 GTGGAAGTTTGTGTCATCCTCTC 59.251 47.826 0.00 0.00 0.00 3.20
429 431 5.527214 CCTCTCGGCAATATGTAATTGTCAA 59.473 40.000 3.54 0.00 33.56 3.18
475 477 7.482654 TCATCTATTGTCCTAATTTCTTGCG 57.517 36.000 0.00 0.00 0.00 4.85
476 478 6.483307 TCATCTATTGTCCTAATTTCTTGCGG 59.517 38.462 0.00 0.00 0.00 5.69
485 487 4.827284 CCTAATTTCTTGCGGGTTATCCAT 59.173 41.667 0.00 0.00 34.36 3.41
486 488 4.654091 AATTTCTTGCGGGTTATCCATG 57.346 40.909 0.00 0.00 34.36 3.66
497 499 2.104792 GGTTATCCATGGAGCTACTGCA 59.895 50.000 21.33 0.00 42.74 4.41
541 543 2.494059 ACAACATGTAGATATGCGGGC 58.506 47.619 0.00 0.00 0.00 6.13
586 588 5.675684 AGGTTTGTTCAATCAGTTTGGTT 57.324 34.783 0.00 0.00 35.92 3.67
598 600 2.426738 CAGTTTGGTTGACAAGCCAAGA 59.573 45.455 14.49 7.32 44.43 3.02
698 700 0.238289 CGGTGACTGAAACATGTGCC 59.762 55.000 0.00 0.00 0.00 5.01
751 3087 2.457813 TGTATAGGCCGGGTACTTCA 57.542 50.000 2.18 0.00 0.00 3.02
755 3099 2.773993 TAGGCCGGGTACTTCAAAAG 57.226 50.000 2.18 0.00 0.00 2.27
785 3129 2.534396 AATTGACGAGGCCCCCACA 61.534 57.895 0.00 0.00 0.00 4.17
860 3204 1.379527 AAATCGGCAGTTTCGGATCC 58.620 50.000 0.00 0.00 0.00 3.36
1020 3405 4.935495 CGCCCATATGCCGGCTGT 62.935 66.667 29.70 18.80 43.38 4.40
1070 3461 2.044848 AGCGAGCCGAGAGAGGAA 60.045 61.111 0.00 0.00 0.00 3.36
1098 3493 0.178992 ATCCGAGAGCAGAGGAGAGG 60.179 60.000 0.00 0.00 37.49 3.69
1111 3506 0.398381 GGAGAGGGGCAGAGAGATGT 60.398 60.000 0.00 0.00 0.00 3.06
1148 3543 4.039092 GGCTCCCTTCCTGCTGCA 62.039 66.667 0.88 0.88 0.00 4.41
1273 3668 2.755929 GGTACGTACTCTCGGTCGT 58.244 57.895 24.07 0.00 36.37 4.34
1332 3727 5.561532 CGTCCGTCAAGTAACAGTCTTCTTA 60.562 44.000 0.00 0.00 0.00 2.10
1349 3745 1.001974 CTTAATCGATCCGGCATGGGA 59.998 52.381 0.00 0.00 41.17 4.37
1589 3990 2.358939 ACGTCCTGGTACGCTAAAAG 57.641 50.000 15.37 0.00 46.71 2.27
1612 4013 1.953686 CTCCTTTTGCTTCCCGTTCAA 59.046 47.619 0.00 0.00 0.00 2.69
1613 4014 2.558359 CTCCTTTTGCTTCCCGTTCAAT 59.442 45.455 0.00 0.00 0.00 2.57
1614 4015 2.962421 TCCTTTTGCTTCCCGTTCAATT 59.038 40.909 0.00 0.00 0.00 2.32
1615 4016 3.386402 TCCTTTTGCTTCCCGTTCAATTT 59.614 39.130 0.00 0.00 0.00 1.82
1616 4017 4.126437 CCTTTTGCTTCCCGTTCAATTTT 58.874 39.130 0.00 0.00 0.00 1.82
1617 4018 4.211164 CCTTTTGCTTCCCGTTCAATTTTC 59.789 41.667 0.00 0.00 0.00 2.29
1618 4019 3.378911 TTGCTTCCCGTTCAATTTTCC 57.621 42.857 0.00 0.00 0.00 3.13
1619 4020 2.593026 TGCTTCCCGTTCAATTTTCCT 58.407 42.857 0.00 0.00 0.00 3.36
1620 4021 2.556622 TGCTTCCCGTTCAATTTTCCTC 59.443 45.455 0.00 0.00 0.00 3.71
1621 4022 2.094700 GCTTCCCGTTCAATTTTCCTCC 60.095 50.000 0.00 0.00 0.00 4.30
1622 4023 3.421844 CTTCCCGTTCAATTTTCCTCCT 58.578 45.455 0.00 0.00 0.00 3.69
1623 4024 3.518992 TCCCGTTCAATTTTCCTCCTT 57.481 42.857 0.00 0.00 0.00 3.36
1624 4025 3.839778 TCCCGTTCAATTTTCCTCCTTT 58.160 40.909 0.00 0.00 0.00 3.11
1625 4026 4.219919 TCCCGTTCAATTTTCCTCCTTTT 58.780 39.130 0.00 0.00 0.00 2.27
1626 4027 4.038642 TCCCGTTCAATTTTCCTCCTTTTG 59.961 41.667 0.00 0.00 0.00 2.44
1627 4028 3.740832 CCGTTCAATTTTCCTCCTTTTGC 59.259 43.478 0.00 0.00 0.00 3.68
1628 4029 4.501400 CCGTTCAATTTTCCTCCTTTTGCT 60.501 41.667 0.00 0.00 0.00 3.91
1629 4030 5.049828 CGTTCAATTTTCCTCCTTTTGCTT 58.950 37.500 0.00 0.00 0.00 3.91
1630 4031 5.175673 CGTTCAATTTTCCTCCTTTTGCTTC 59.824 40.000 0.00 0.00 0.00 3.86
1631 4032 5.213891 TCAATTTTCCTCCTTTTGCTTCC 57.786 39.130 0.00 0.00 0.00 3.46
1632 4033 4.040339 TCAATTTTCCTCCTTTTGCTTCCC 59.960 41.667 0.00 0.00 0.00 3.97
1633 4034 1.616159 TTTCCTCCTTTTGCTTCCCG 58.384 50.000 0.00 0.00 0.00 5.14
1634 4035 0.476771 TTCCTCCTTTTGCTTCCCGT 59.523 50.000 0.00 0.00 0.00 5.28
1635 4036 0.476771 TCCTCCTTTTGCTTCCCGTT 59.523 50.000 0.00 0.00 0.00 4.44
1636 4037 0.881796 CCTCCTTTTGCTTCCCGTTC 59.118 55.000 0.00 0.00 0.00 3.95
1637 4038 1.604604 CTCCTTTTGCTTCCCGTTCA 58.395 50.000 0.00 0.00 0.00 3.18
1638 4039 1.953686 CTCCTTTTGCTTCCCGTTCAA 59.046 47.619 0.00 0.00 0.00 2.69
1674 4075 2.476051 CGTTCGCTGCACCATCAC 59.524 61.111 0.00 0.00 0.00 3.06
1676 4077 1.965930 GTTCGCTGCACCATCACCA 60.966 57.895 0.00 0.00 0.00 4.17
1677 4078 1.228094 TTCGCTGCACCATCACCAA 60.228 52.632 0.00 0.00 0.00 3.67
1678 4079 0.608856 TTCGCTGCACCATCACCAAT 60.609 50.000 0.00 0.00 0.00 3.16
1679 4080 1.026182 TCGCTGCACCATCACCAATC 61.026 55.000 0.00 0.00 0.00 2.67
1680 4081 1.307355 CGCTGCACCATCACCAATCA 61.307 55.000 0.00 0.00 0.00 2.57
1681 4082 0.171903 GCTGCACCATCACCAATCAC 59.828 55.000 0.00 0.00 0.00 3.06
1682 4083 0.813184 CTGCACCATCACCAATCACC 59.187 55.000 0.00 0.00 0.00 4.02
1683 4084 0.112025 TGCACCATCACCAATCACCA 59.888 50.000 0.00 0.00 0.00 4.17
1705 4106 5.511888 CCATCATGGTAGATGCTATCACACA 60.512 44.000 0.00 0.00 43.15 3.72
1709 4110 5.612725 TGGTAGATGCTATCACACATGAA 57.387 39.130 0.00 0.00 38.69 2.57
1711 4112 5.817296 TGGTAGATGCTATCACACATGAAAC 59.183 40.000 0.00 0.00 38.69 2.78
1720 4121 0.028770 ACACATGAAACACGCGGTTG 59.971 50.000 12.47 2.37 40.35 3.77
1747 4151 7.499321 AAATAAGATGAGATCTAGTCGTCGT 57.501 36.000 0.00 0.00 39.08 4.34
1748 4152 6.715344 ATAAGATGAGATCTAGTCGTCGTC 57.285 41.667 0.00 0.00 39.08 4.20
1749 4153 3.054166 AGATGAGATCTAGTCGTCGTCG 58.946 50.000 0.00 0.00 38.00 5.12
1750 4154 2.290531 TGAGATCTAGTCGTCGTCGT 57.709 50.000 0.00 0.00 38.33 4.34
1751 4155 2.191802 TGAGATCTAGTCGTCGTCGTC 58.808 52.381 0.00 0.00 38.33 4.20
1752 4156 1.187704 GAGATCTAGTCGTCGTCGTCG 59.812 57.143 5.50 5.50 38.33 5.12
1768 4180 1.227147 TCGCCGTGGTAATGCTAGC 60.227 57.895 8.10 8.10 0.00 3.42
1771 4183 0.880718 GCCGTGGTAATGCTAGCCTC 60.881 60.000 13.29 0.00 0.00 4.70
1776 4188 3.467803 GTGGTAATGCTAGCCTCGAATT 58.532 45.455 13.29 7.35 0.00 2.17
1941 4356 5.531122 ACAGTAGTGACTTTTCTAGCACA 57.469 39.130 4.09 0.00 35.01 4.57
1942 4357 6.102897 ACAGTAGTGACTTTTCTAGCACAT 57.897 37.500 4.09 0.00 35.01 3.21
1943 4358 5.928839 ACAGTAGTGACTTTTCTAGCACATG 59.071 40.000 4.09 0.00 35.01 3.21
1993 4408 3.607741 GCCTTAAACTGAGACCCTTACC 58.392 50.000 0.00 0.00 0.00 2.85
2036 4451 3.493699 CGACCAGGTCCAAAGTACAGAAA 60.494 47.826 14.46 0.00 0.00 2.52
2041 4456 5.301805 CCAGGTCCAAAGTACAGAAAAACAT 59.698 40.000 0.00 0.00 0.00 2.71
2054 4469 9.908152 GTACAGAAAAACATAGCAAAAAGGTAT 57.092 29.630 0.00 0.00 41.43 2.73
2065 4488 5.466819 AGCAAAAAGGTATAAGAAAACGGC 58.533 37.500 0.00 0.00 0.00 5.68
2066 4493 5.243060 AGCAAAAAGGTATAAGAAAACGGCT 59.757 36.000 0.00 0.00 0.00 5.52
2069 4496 6.887626 AAAAGGTATAAGAAAACGGCTGAA 57.112 33.333 0.00 0.00 0.00 3.02
2073 4500 5.180680 AGGTATAAGAAAACGGCTGAAACAC 59.819 40.000 0.00 0.00 0.00 3.32
2100 4528 1.663388 CGGATACATAGCGGCGCAA 60.663 57.895 35.02 13.79 0.00 4.85
2128 4556 3.479006 CAAAGGCGAGTAAAACATCGTG 58.521 45.455 0.00 0.00 40.97 4.35
2222 4650 3.253838 ACCTTGCCCGCACCCTTA 61.254 61.111 0.00 0.00 0.00 2.69
2335 4763 4.263243 GCTGGATGCCTGATAAATACTCCT 60.263 45.833 0.00 0.00 35.15 3.69
2355 4783 6.716628 ACTCCTTCTATCAATGCTTTGTTTCA 59.283 34.615 11.67 0.00 34.32 2.69
2410 4838 3.217626 CCCAAGCCATGTAATCCTCTTC 58.782 50.000 0.00 0.00 0.00 2.87
2420 4848 5.149584 TGTAATCCTCTTCTCCCTCTCAT 57.850 43.478 0.00 0.00 0.00 2.90
2434 4862 2.492012 CTCTCATAAGTGGATGCTGCC 58.508 52.381 0.00 0.00 0.00 4.85
2524 4952 5.149273 CACATAAATCGAGCCATAATGCAC 58.851 41.667 0.00 0.00 0.00 4.57
2566 4994 0.764890 CTTCACTCTCCCCACACCAA 59.235 55.000 0.00 0.00 0.00 3.67
2752 5181 4.275810 ACAAGGATCATGTGGAGAATTGG 58.724 43.478 2.87 0.00 0.00 3.16
2761 5190 2.513897 GAGAATTGGCCGGACGGG 60.514 66.667 5.05 3.74 39.58 5.28
2827 5257 4.469657 ACCCTCTCAATTTAGTGTGCAAA 58.530 39.130 0.00 0.00 0.00 3.68
2880 5310 3.687102 TCGCCGGAATCGTGGTGT 61.687 61.111 5.05 0.00 37.07 4.16
2905 5335 1.746615 CCCCTGTCACCAGCAATCG 60.747 63.158 0.00 0.00 37.38 3.34
2906 5336 1.296392 CCCTGTCACCAGCAATCGA 59.704 57.895 0.00 0.00 37.38 3.59
2943 5373 1.083489 TTCTCGGCGATCGCAAAAAT 58.917 45.000 38.00 0.00 44.11 1.82
2986 5416 0.911769 TCCCATCCTCACACCACATC 59.088 55.000 0.00 0.00 0.00 3.06
2987 5417 0.620030 CCCATCCTCACACCACATCA 59.380 55.000 0.00 0.00 0.00 3.07
3009 5439 0.681175 AACCAAAAGCACATGGCCTC 59.319 50.000 3.32 0.00 46.50 4.70
3010 5440 0.469705 ACCAAAAGCACATGGCCTCA 60.470 50.000 3.32 0.00 46.50 3.86
3031 5461 6.127366 CCTCACCATTATGCACAATAAACCTT 60.127 38.462 0.00 0.00 34.41 3.50
3103 5533 4.819630 TGCGACAATTTAGTGTTCCTTCTT 59.180 37.500 0.00 0.00 0.00 2.52
3118 5548 2.421529 CCTTCTTAATTCCACCCCTCCG 60.422 54.545 0.00 0.00 0.00 4.63
3181 5611 2.176045 CCCTGGCCGGTTAGAATTTTT 58.824 47.619 11.58 0.00 0.00 1.94
3216 5646 5.786401 GTCATGAGACACCAGTTCATTAC 57.214 43.478 0.00 0.00 44.34 1.89
3248 5678 2.935481 CCCCAAGCCCACCTCTCA 60.935 66.667 0.00 0.00 0.00 3.27
3281 5711 6.184789 TCACAAATATTCTCCCAACTAACCC 58.815 40.000 0.00 0.00 0.00 4.11
3322 5752 3.242016 CGTTTTCTTTCGCCCAGAAAAAC 59.758 43.478 14.17 7.34 46.71 2.43
3325 5755 0.948678 CTTTCGCCCAGAAAAACCGA 59.051 50.000 0.00 0.00 46.98 4.69
3529 5960 0.737219 TAGTTAAGGCTCTCGCGGAC 59.263 55.000 6.13 0.00 36.88 4.79
3530 5961 1.518792 GTTAAGGCTCTCGCGGACC 60.519 63.158 6.13 2.53 36.88 4.46
3563 5994 8.567948 TGTTTGATACTTGATTTCTTCTGGTTC 58.432 33.333 0.00 0.00 0.00 3.62
3570 6001 7.684529 ACTTGATTTCTTCTGGTTCTCTGTAT 58.315 34.615 0.00 0.00 0.00 2.29
3619 6058 7.418337 AGAAATTACACCCTTTGAACTTTGT 57.582 32.000 0.00 0.00 0.00 2.83
3700 6139 1.956170 CGTGCTGGTATCCATCGCC 60.956 63.158 0.00 0.00 30.82 5.54
3817 6261 5.105752 GTCAACAAAATGCACAAGTTACCA 58.894 37.500 0.00 0.00 0.00 3.25
3843 6287 2.457366 ACTTGTCTACTTGGCGGAAG 57.543 50.000 0.00 0.00 37.73 3.46
3852 6296 5.291371 GTCTACTTGGCGGAAGAATAGTTTC 59.709 44.000 1.34 0.00 35.42 2.78
3863 6307 7.622672 GCGGAAGAATAGTTTCGTTTGATGTAA 60.623 37.037 0.00 0.00 36.93 2.41
3885 6329 3.695830 ATCTCTTTCGCTTGTGGGTTA 57.304 42.857 0.00 0.00 0.00 2.85
4008 6464 1.387084 CGCTTGAAGTCGTGTCTTAGC 59.613 52.381 0.00 0.00 0.00 3.09
4050 6506 7.280876 CCTTGCAGCTCATAGTTATTTTGACTA 59.719 37.037 0.00 0.00 34.38 2.59
4106 6562 1.840635 GACTCCTAGGGTGCTGGAAAT 59.159 52.381 9.46 0.00 0.00 2.17
4167 6625 0.813821 GCCATTCCTGAAAGCCTCAC 59.186 55.000 0.00 0.00 0.00 3.51
4168 6626 1.887956 GCCATTCCTGAAAGCCTCACA 60.888 52.381 0.00 0.00 0.00 3.58
4169 6627 2.731572 CCATTCCTGAAAGCCTCACAT 58.268 47.619 0.00 0.00 0.00 3.21
4170 6628 2.686915 CCATTCCTGAAAGCCTCACATC 59.313 50.000 0.00 0.00 0.00 3.06
4171 6629 3.618351 CATTCCTGAAAGCCTCACATCT 58.382 45.455 0.00 0.00 0.00 2.90
4172 6630 4.384537 CCATTCCTGAAAGCCTCACATCTA 60.385 45.833 0.00 0.00 0.00 1.98
4173 6631 3.895232 TCCTGAAAGCCTCACATCTAC 57.105 47.619 0.00 0.00 0.00 2.59
4174 6632 3.445008 TCCTGAAAGCCTCACATCTACT 58.555 45.455 0.00 0.00 0.00 2.57
4175 6633 3.840666 TCCTGAAAGCCTCACATCTACTT 59.159 43.478 0.00 0.00 0.00 2.24
4176 6634 5.023452 TCCTGAAAGCCTCACATCTACTTA 58.977 41.667 0.00 0.00 0.00 2.24
4177 6635 5.483937 TCCTGAAAGCCTCACATCTACTTAA 59.516 40.000 0.00 0.00 0.00 1.85
4178 6636 6.013725 TCCTGAAAGCCTCACATCTACTTAAA 60.014 38.462 0.00 0.00 0.00 1.52
4179 6637 6.092807 CCTGAAAGCCTCACATCTACTTAAAC 59.907 42.308 0.00 0.00 0.00 2.01
4180 6638 5.637810 TGAAAGCCTCACATCTACTTAAACG 59.362 40.000 0.00 0.00 0.00 3.60
4181 6639 4.124851 AGCCTCACATCTACTTAAACGG 57.875 45.455 0.00 0.00 0.00 4.44
4182 6640 3.514309 AGCCTCACATCTACTTAAACGGT 59.486 43.478 0.00 0.00 0.00 4.83
4183 6641 3.864003 GCCTCACATCTACTTAAACGGTC 59.136 47.826 0.00 0.00 0.00 4.79
4184 6642 4.430908 CCTCACATCTACTTAAACGGTCC 58.569 47.826 0.00 0.00 0.00 4.46
4185 6643 4.081862 CCTCACATCTACTTAAACGGTCCA 60.082 45.833 0.00 0.00 0.00 4.02
4186 6644 4.813027 TCACATCTACTTAAACGGTCCAC 58.187 43.478 0.00 0.00 0.00 4.02
4187 6645 4.525487 TCACATCTACTTAAACGGTCCACT 59.475 41.667 0.00 0.00 0.00 4.00
4188 6646 5.711506 TCACATCTACTTAAACGGTCCACTA 59.288 40.000 0.00 0.00 0.00 2.74
4189 6647 6.209192 TCACATCTACTTAAACGGTCCACTAA 59.791 38.462 0.00 0.00 0.00 2.24
4257 6716 6.038714 GGTCAAGTTTCAGAGACAACTCAATT 59.961 38.462 0.00 0.00 44.79 2.32
4480 7554 7.561021 TTGGGCAAGAAAATTAAAAACTTCC 57.439 32.000 0.00 0.00 0.00 3.46
4512 7586 5.066634 TCGCTTTGTCCTTTACATTGAACAA 59.933 36.000 0.00 0.00 38.10 2.83
4542 7619 7.436376 ACGTTAAGTAGACACTAACCAAGTTTC 59.564 37.037 0.00 0.00 35.76 2.78
4589 7666 5.395103 GGGATATGGCATGATGACTCTAGTC 60.395 48.000 10.98 3.08 44.97 2.59
4656 7733 3.755628 CTTCCGGCCCTTCGTCGA 61.756 66.667 0.00 0.00 0.00 4.20
4710 7787 0.467384 CATTCCTCTCGCACAGGGAT 59.533 55.000 0.00 0.00 27.63 3.85
4898 7975 1.300931 GATCGGCTTCGGCATGCTA 60.301 57.895 18.92 3.12 43.96 3.49
4943 8020 1.533033 TGTCTTCCTCTCCGGCACA 60.533 57.895 0.00 0.00 0.00 4.57
4964 8041 1.399744 CCACCTACCGCCTCTATGCA 61.400 60.000 0.00 0.00 0.00 3.96
5069 8149 2.859165 AAGGATGCCAAGACGAAGAA 57.141 45.000 0.00 0.00 0.00 2.52
5084 8164 2.357034 GAAGTCGCGGCCAAGTCA 60.357 61.111 7.31 0.00 0.00 3.41
5117 8197 2.262915 GTGCTGCGACTGCTACCT 59.737 61.111 0.00 0.00 43.34 3.08
5258 8338 3.774528 CAGACGCTAGGGCCAGCA 61.775 66.667 22.09 1.19 41.88 4.41
5345 8425 3.382832 CCGTCGGGGCTGACTCTT 61.383 66.667 2.34 0.00 36.71 2.85
5642 8722 2.045926 GGCGGGTTCATCAGCAGT 60.046 61.111 0.00 0.00 0.00 4.40
5675 8755 1.446099 CATCGACCGTGTCACCAGG 60.446 63.158 0.00 0.00 32.09 4.45
5711 8791 0.031178 GCTGGTTTGCTGACAACCTG 59.969 55.000 9.15 9.36 34.87 4.00
5735 8815 1.590147 CGCCCACCTCGACTACTTT 59.410 57.895 0.00 0.00 0.00 2.66
5813 8893 3.326747 CAGCTCCTACACCTACAACAAC 58.673 50.000 0.00 0.00 0.00 3.32
5814 8894 2.969950 AGCTCCTACACCTACAACAACA 59.030 45.455 0.00 0.00 0.00 3.33
5815 8895 3.389983 AGCTCCTACACCTACAACAACAA 59.610 43.478 0.00 0.00 0.00 2.83
5835 8915 1.490490 ACAACCACAAGAGGCTTCAGA 59.510 47.619 0.00 0.00 0.00 3.27
5850 8930 3.063180 GCTTCAGAAATGAGTGATCACCG 59.937 47.826 22.21 3.29 0.00 4.94
5851 8931 3.961480 TCAGAAATGAGTGATCACCGT 57.039 42.857 22.21 12.03 0.00 4.83
5852 8932 3.849911 TCAGAAATGAGTGATCACCGTC 58.150 45.455 22.21 14.44 0.00 4.79
5853 8933 3.258123 TCAGAAATGAGTGATCACCGTCA 59.742 43.478 22.21 19.45 0.00 4.35
5854 8934 3.369147 CAGAAATGAGTGATCACCGTCAC 59.631 47.826 22.21 8.74 46.90 3.67
5990 9206 1.735973 GGCGAGCCCATTGGAAATC 59.264 57.895 3.62 0.00 0.00 2.17
5991 9207 0.753111 GGCGAGCCCATTGGAAATCT 60.753 55.000 3.62 0.00 0.00 2.40
5992 9208 0.383231 GCGAGCCCATTGGAAATCTG 59.617 55.000 3.62 0.00 0.00 2.90
5993 9209 2.018644 GCGAGCCCATTGGAAATCTGA 61.019 52.381 3.62 0.00 0.00 3.27
5994 9210 1.945394 CGAGCCCATTGGAAATCTGAG 59.055 52.381 3.62 0.00 0.00 3.35
5995 9211 2.681976 CGAGCCCATTGGAAATCTGAGT 60.682 50.000 3.62 0.00 0.00 3.41
5996 9212 2.686915 GAGCCCATTGGAAATCTGAGTG 59.313 50.000 3.62 0.00 0.00 3.51
5999 9215 3.119352 GCCCATTGGAAATCTGAGTGTTC 60.119 47.826 3.62 0.00 0.00 3.18
6449 13987 7.494952 CCCTCCTTTTATTTTTACTCCTCGTAG 59.505 40.741 0.00 0.00 0.00 3.51
6492 14030 8.925700 CAAGCTTTATAAGGTTTGACCAAATTC 58.074 33.333 16.07 0.00 46.23 2.17
6679 14220 2.554462 GAGTGAAAAGAAACAGAGGGGC 59.446 50.000 0.00 0.00 0.00 5.80
6703 15186 8.361592 GCTAATAAAGAGCCGAAATACAGTTA 57.638 34.615 0.00 0.00 33.60 2.24
6746 15229 3.859961 CCAAAAATTGCACACGTACACAA 59.140 39.130 0.00 0.00 0.00 3.33
6824 17433 9.244292 TCCTCATAGTGGTTAGCTATATGTTAG 57.756 37.037 9.88 3.51 0.00 2.34
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
8 9 0.730155 CTGTTTGTCAATGCGCGCAT 60.730 50.000 39.13 39.13 38.46 4.73
16 17 2.625823 CGGCCGGCTGTTTGTCAAT 61.626 57.895 27.83 0.00 0.00 2.57
30 31 2.125512 ACGTCAATGCTCTCGGCC 60.126 61.111 0.00 0.00 40.92 6.13
77 78 8.119226 CCAAATGTGTTTTCTGCGAAAAATAAA 58.881 29.630 14.87 2.78 31.29 1.40
107 108 3.843422 TGATTTTGGAAGGAGCCTTTCA 58.157 40.909 6.14 6.14 39.58 2.69
108 109 4.871933 TTGATTTTGGAAGGAGCCTTTC 57.128 40.909 2.85 1.55 36.26 2.62
109 110 4.655649 ACTTTGATTTTGGAAGGAGCCTTT 59.344 37.500 2.85 0.00 36.26 3.11
112 113 4.607293 AACTTTGATTTTGGAAGGAGCC 57.393 40.909 0.00 0.00 0.00 4.70
114 115 8.981647 CACATAAAACTTTGATTTTGGAAGGAG 58.018 33.333 0.00 0.00 33.80 3.69
116 117 7.714813 ACCACATAAAACTTTGATTTTGGAAGG 59.285 33.333 0.00 0.00 33.80 3.46
180 182 4.094887 ACATGTCAATTACGCTTAGCAAGG 59.905 41.667 4.70 0.00 0.00 3.61
197 199 9.180678 CAAAACCACTATTTTCTGTTACATGTC 57.819 33.333 0.00 0.00 29.17 3.06
201 203 8.282455 TCACAAAACCACTATTTTCTGTTACA 57.718 30.769 0.00 0.00 29.17 2.41
282 284 1.323412 ACAAAATTAGTGGCGTGCCA 58.677 45.000 10.06 10.06 45.02 4.92
288 290 7.700656 GTGATGGTTGTATACAAAATTAGTGGC 59.299 37.037 19.63 4.43 37.63 5.01
308 310 5.132502 TGGAATACTTATTGGCTGTGATGG 58.867 41.667 0.00 0.00 0.00 3.51
361 363 5.833131 GGATTTGGCCCTTCAACTTATGATA 59.167 40.000 0.00 0.00 38.03 2.15
367 369 2.397044 TGGATTTGGCCCTTCAACTT 57.603 45.000 0.00 0.00 0.00 2.66
368 370 2.181975 CATGGATTTGGCCCTTCAACT 58.818 47.619 0.00 0.00 0.00 3.16
378 380 4.202243 ACACAAACTTCCACATGGATTTGG 60.202 41.667 22.24 16.13 43.41 3.28
410 412 7.984002 TCATTTTGACAATTACATATTGCCG 57.016 32.000 0.00 0.00 32.55 5.69
449 451 8.226448 CGCAAGAAATTAGGACAATAGATGATC 58.774 37.037 0.00 0.00 43.02 2.92
453 455 5.765182 CCCGCAAGAAATTAGGACAATAGAT 59.235 40.000 0.00 0.00 43.02 1.98
475 477 2.551071 GCAGTAGCTCCATGGATAACCC 60.551 54.545 16.63 2.70 37.91 4.11
476 478 2.104792 TGCAGTAGCTCCATGGATAACC 59.895 50.000 16.63 4.21 42.74 2.85
485 487 2.026915 ACACATTCATGCAGTAGCTCCA 60.027 45.455 0.00 0.00 42.74 3.86
486 488 2.636830 ACACATTCATGCAGTAGCTCC 58.363 47.619 0.00 0.00 42.74 4.70
540 542 9.612620 CCTTACTTTTATCATTTCGATAATGGC 57.387 33.333 15.56 0.00 44.29 4.40
566 568 5.866633 TGTCAACCAAACTGATTGAACAAAC 59.133 36.000 0.00 0.00 41.85 2.93
570 572 4.504097 GCTTGTCAACCAAACTGATTGAAC 59.496 41.667 0.00 0.00 41.85 3.18
586 588 4.299586 TCCACATAATCTTGGCTTGTCA 57.700 40.909 0.00 0.00 32.37 3.58
622 624 3.963129 GACCATAGTCCATCAAACCCAA 58.037 45.455 0.00 0.00 37.00 4.12
698 700 6.307558 TGCACACAATGATTTTATTAAGCGTG 59.692 34.615 0.00 0.00 0.00 5.34
785 3129 4.846940 AGTAGTCTCTTTTGGATGGTTCCT 59.153 41.667 0.00 0.00 43.07 3.36
787 3131 4.865365 CGAGTAGTCTCTTTTGGATGGTTC 59.135 45.833 0.00 0.00 38.45 3.62
860 3204 1.670087 GGTGATCCAGTCAGACGTGTG 60.670 57.143 6.31 6.31 37.56 3.82
1098 3493 2.107953 GCCGACATCTCTCTGCCC 59.892 66.667 0.00 0.00 0.00 5.36
1128 3523 2.690510 AGCAGGAAGGGAGCCTCC 60.691 66.667 0.73 0.73 32.12 4.30
1148 3543 2.561885 CCTCGTCGTCTTCAGCGT 59.438 61.111 0.00 0.00 0.00 5.07
1273 3668 4.124351 AGCTTGCGCGCGTAGGTA 62.124 61.111 32.35 11.45 42.32 3.08
1282 3677 2.821810 GGGGAAGAGAGCTTGCGC 60.822 66.667 0.00 0.00 45.22 6.09
1286 3681 0.327591 CAAGCAGGGGAAGAGAGCTT 59.672 55.000 0.00 0.00 45.54 3.74
1287 3682 1.989620 CAAGCAGGGGAAGAGAGCT 59.010 57.895 0.00 0.00 37.08 4.09
1332 3727 0.401738 AATCCCATGCCGGATCGATT 59.598 50.000 5.05 0.93 42.05 3.34
1349 3745 2.885135 TCTCCACCACTGCAATCAAT 57.115 45.000 0.00 0.00 0.00 2.57
1466 3867 4.754667 GTCCCCGACCAGGCGTTC 62.755 72.222 0.00 0.00 39.21 3.95
1589 3990 0.250770 ACGGGAAGCAAAAGGAGGAC 60.251 55.000 0.00 0.00 0.00 3.85
1612 4013 2.562738 CGGGAAGCAAAAGGAGGAAAAT 59.437 45.455 0.00 0.00 0.00 1.82
1613 4014 1.960689 CGGGAAGCAAAAGGAGGAAAA 59.039 47.619 0.00 0.00 0.00 2.29
1614 4015 1.133606 ACGGGAAGCAAAAGGAGGAAA 60.134 47.619 0.00 0.00 0.00 3.13
1615 4016 0.476771 ACGGGAAGCAAAAGGAGGAA 59.523 50.000 0.00 0.00 0.00 3.36
1616 4017 0.476771 AACGGGAAGCAAAAGGAGGA 59.523 50.000 0.00 0.00 0.00 3.71
1617 4018 0.881796 GAACGGGAAGCAAAAGGAGG 59.118 55.000 0.00 0.00 0.00 4.30
1618 4019 1.604604 TGAACGGGAAGCAAAAGGAG 58.395 50.000 0.00 0.00 0.00 3.69
1619 4020 2.060050 TTGAACGGGAAGCAAAAGGA 57.940 45.000 0.00 0.00 0.00 3.36
1620 4021 3.385193 AATTGAACGGGAAGCAAAAGG 57.615 42.857 0.00 0.00 0.00 3.11
1621 4022 5.733226 AAAAATTGAACGGGAAGCAAAAG 57.267 34.783 0.00 0.00 0.00 2.27
1622 4023 5.524281 GGTAAAAATTGAACGGGAAGCAAAA 59.476 36.000 0.00 0.00 0.00 2.44
1623 4024 5.051153 GGTAAAAATTGAACGGGAAGCAAA 58.949 37.500 0.00 0.00 0.00 3.68
1624 4025 4.501743 GGGTAAAAATTGAACGGGAAGCAA 60.502 41.667 0.00 0.00 0.00 3.91
1625 4026 3.006003 GGGTAAAAATTGAACGGGAAGCA 59.994 43.478 0.00 0.00 0.00 3.91
1626 4027 3.257375 AGGGTAAAAATTGAACGGGAAGC 59.743 43.478 0.00 0.00 0.00 3.86
1627 4028 4.765339 AGAGGGTAAAAATTGAACGGGAAG 59.235 41.667 0.00 0.00 0.00 3.46
1628 4029 4.732065 AGAGGGTAAAAATTGAACGGGAA 58.268 39.130 0.00 0.00 0.00 3.97
1629 4030 4.042435 AGAGAGGGTAAAAATTGAACGGGA 59.958 41.667 0.00 0.00 0.00 5.14
1630 4031 4.156008 CAGAGAGGGTAAAAATTGAACGGG 59.844 45.833 0.00 0.00 0.00 5.28
1631 4032 4.760204 ACAGAGAGGGTAAAAATTGAACGG 59.240 41.667 0.00 0.00 0.00 4.44
1632 4033 5.941948 ACAGAGAGGGTAAAAATTGAACG 57.058 39.130 0.00 0.00 0.00 3.95
1633 4034 6.567891 CGGAACAGAGAGGGTAAAAATTGAAC 60.568 42.308 0.00 0.00 0.00 3.18
1634 4035 5.472137 CGGAACAGAGAGGGTAAAAATTGAA 59.528 40.000 0.00 0.00 0.00 2.69
1635 4036 5.001232 CGGAACAGAGAGGGTAAAAATTGA 58.999 41.667 0.00 0.00 0.00 2.57
1636 4037 4.760204 ACGGAACAGAGAGGGTAAAAATTG 59.240 41.667 0.00 0.00 0.00 2.32
1637 4038 4.981812 ACGGAACAGAGAGGGTAAAAATT 58.018 39.130 0.00 0.00 0.00 1.82
1638 4039 4.635699 ACGGAACAGAGAGGGTAAAAAT 57.364 40.909 0.00 0.00 0.00 1.82
1681 4082 4.934001 GTGTGATAGCATCTACCATGATGG 59.066 45.833 10.53 10.53 42.82 3.51
1682 4083 5.544650 TGTGTGATAGCATCTACCATGATG 58.455 41.667 0.00 0.00 44.72 3.07
1683 4084 5.813513 TGTGTGATAGCATCTACCATGAT 57.186 39.130 0.00 0.00 0.00 2.45
1705 4106 3.694535 TTTTACAACCGCGTGTTTCAT 57.305 38.095 7.72 1.80 34.00 2.57
1709 4110 5.179742 TCATCTTATTTTACAACCGCGTGTT 59.820 36.000 7.72 7.38 37.80 3.32
1711 4112 5.062934 TCTCATCTTATTTTACAACCGCGTG 59.937 40.000 4.92 0.00 0.00 5.34
1720 4121 9.320406 CGACGACTAGATCTCATCTTATTTTAC 57.680 37.037 0.00 0.00 40.76 2.01
1749 4153 1.488261 GCTAGCATTACCACGGCGAC 61.488 60.000 16.62 0.00 0.00 5.19
1750 4154 1.227147 GCTAGCATTACCACGGCGA 60.227 57.895 16.62 0.00 0.00 5.54
1751 4155 2.244651 GGCTAGCATTACCACGGCG 61.245 63.158 18.24 4.80 0.00 6.46
1752 4156 0.880718 GAGGCTAGCATTACCACGGC 60.881 60.000 18.24 0.00 0.00 5.68
1756 4168 3.133901 TCAATTCGAGGCTAGCATTACCA 59.866 43.478 18.24 0.00 0.00 3.25
1758 4170 5.050490 TCTTCAATTCGAGGCTAGCATTAC 58.950 41.667 18.24 0.00 0.00 1.89
1768 4180 2.283617 CGAGCACATCTTCAATTCGAGG 59.716 50.000 0.00 0.00 0.00 4.63
1771 4183 2.926200 ACTCGAGCACATCTTCAATTCG 59.074 45.455 13.61 0.00 0.00 3.34
1776 4188 0.881796 ACGACTCGAGCACATCTTCA 59.118 50.000 13.61 0.00 0.00 3.02
1965 4380 0.394352 CTCAGTTTAAGGCCGGGCAT 60.394 55.000 31.59 22.05 0.00 4.40
2041 4456 6.431852 AGCCGTTTTCTTATACCTTTTTGCTA 59.568 34.615 0.00 0.00 0.00 3.49
2050 4465 5.388111 GTGTTTCAGCCGTTTTCTTATACC 58.612 41.667 0.00 0.00 0.00 2.73
2054 4469 2.286536 GCGTGTTTCAGCCGTTTTCTTA 60.287 45.455 0.00 0.00 0.00 2.10
2107 4535 3.059188 ACACGATGTTTTACTCGCCTTTG 60.059 43.478 0.00 0.00 38.42 2.77
2128 4556 0.380378 CTCAGCTACCTCGAGAGCAC 59.620 60.000 23.49 7.88 41.36 4.40
2159 4587 0.457035 GGACACCGCCGACATAACTA 59.543 55.000 0.00 0.00 0.00 2.24
2162 4590 0.683828 TAGGGACACCGCCGACATAA 60.684 55.000 0.00 0.00 43.47 1.90
2222 4650 1.378646 TCGTGGAGGAGCTCGTCAT 60.379 57.895 31.29 8.72 32.79 3.06
2273 4701 4.551702 TGGTGTCTTTCTTGCAGCTATA 57.448 40.909 0.00 0.00 0.00 1.31
2335 4763 6.899393 ACCTGAAACAAAGCATTGATAGAA 57.101 33.333 8.96 0.00 38.94 2.10
2355 4783 1.893801 CGTGGTCTCTTTGGACTACCT 59.106 52.381 5.75 0.00 42.22 3.08
2392 4820 3.137360 GGGAGAAGAGGATTACATGGCTT 59.863 47.826 0.00 0.00 0.00 4.35
2410 4838 2.971330 AGCATCCACTTATGAGAGGGAG 59.029 50.000 1.13 0.00 34.70 4.30
2420 4848 2.124736 GCCGGCAGCATCCACTTA 60.125 61.111 24.80 0.00 42.97 2.24
2434 4862 3.127030 GGTTCTCAGAATTTTACTGGCCG 59.873 47.826 0.00 0.00 36.22 6.13
2524 4952 4.134563 ACCGGGATCATATTCTTTTTCGG 58.865 43.478 6.32 0.00 39.59 4.30
2566 4994 1.591183 GGGCGATGGCAAATGTGTT 59.409 52.632 1.01 0.00 42.47 3.32
2752 5181 2.027169 CGATTAGACCCGTCCGGC 59.973 66.667 0.00 0.00 33.26 6.13
2827 5257 2.372172 AGAAAACACCGAGTGGGAAGAT 59.628 45.455 0.00 0.00 40.75 2.40
2880 5310 3.399181 GGTGACAGGGGCGATGGA 61.399 66.667 0.00 0.00 0.00 3.41
2905 5335 1.620822 ACCAGAATGCCAAAGTGGTC 58.379 50.000 0.00 0.00 40.46 4.02
2906 5336 1.963515 GAACCAGAATGCCAAAGTGGT 59.036 47.619 0.00 0.00 43.54 4.16
2986 5416 1.868469 CCATGTGCTTTTGGTTGGTG 58.132 50.000 0.00 0.00 0.00 4.17
2987 5417 0.106521 GCCATGTGCTTTTGGTTGGT 59.893 50.000 0.00 0.00 35.34 3.67
3009 5439 6.397272 ACAAGGTTTATTGTGCATAATGGTG 58.603 36.000 17.97 9.14 41.76 4.17
3010 5440 6.350949 GGACAAGGTTTATTGTGCATAATGGT 60.351 38.462 17.97 5.45 46.98 3.55
3031 5461 0.395862 CTCTTCTCCGGCTAGGGACA 60.396 60.000 0.00 0.00 41.52 4.02
3103 5533 1.887797 ATGACGGAGGGGTGGAATTA 58.112 50.000 0.00 0.00 0.00 1.40
3181 5611 4.772100 TGTCTCATGACTAAGTGGACATGA 59.228 41.667 0.00 0.00 44.05 3.07
3216 5646 3.131046 GCTTGGGGTGATCAATACCAAAG 59.869 47.826 20.78 19.68 40.36 2.77
3248 5678 5.016831 GGAGAATATTTGTGAACCCAAGGT 58.983 41.667 0.00 0.00 37.65 3.50
3281 5711 0.250513 GGGAAGCAGAGGTACCACAG 59.749 60.000 15.94 5.97 0.00 3.66
3322 5752 6.570058 CGAAATTAAATAAAGTGCGATCTCGG 59.430 38.462 1.34 0.00 36.26 4.63
3325 5755 6.781138 TGCGAAATTAAATAAAGTGCGATCT 58.219 32.000 0.00 0.00 36.26 2.75
3356 5786 5.001874 GGGTTTTTATCTCCTTCAAGACGT 58.998 41.667 0.00 0.00 0.00 4.34
3477 5908 4.122046 ACAACCCGTAGTAGACAAAACAC 58.878 43.478 0.00 0.00 0.00 3.32
3529 5960 5.571784 ATCAAGTATCAAACATGTGCTGG 57.428 39.130 0.00 0.00 0.00 4.85
3530 5961 7.310664 AGAAATCAAGTATCAAACATGTGCTG 58.689 34.615 0.00 0.00 0.00 4.41
3683 6122 0.250467 ATGGCGATGGATACCAGCAC 60.250 55.000 6.83 0.00 40.32 4.40
3700 6139 6.072286 ACCAGTTGCTCTCAGAAATGTTTATG 60.072 38.462 0.00 0.00 0.00 1.90
3817 6261 2.224548 GCCAAGTAGACAAGTTGACCCT 60.225 50.000 10.54 6.19 40.44 4.34
3852 6296 7.166628 AGCGAAAGAGATATTACATCAAACG 57.833 36.000 0.00 0.00 0.00 3.60
3863 6307 3.914426 ACCCACAAGCGAAAGAGATAT 57.086 42.857 0.00 0.00 0.00 1.63
3963 6419 8.119845 CGACGAACACAATGAATCCATAATTAA 58.880 33.333 0.00 0.00 31.59 1.40
4008 6464 7.938715 AGCTGCAAGGAAAATGATAATCTTAG 58.061 34.615 1.02 0.00 0.00 2.18
4024 6480 6.094603 AGTCAAAATAACTATGAGCTGCAAGG 59.905 38.462 1.02 0.00 0.00 3.61
4050 6506 9.638239 AAATAATGATAACATTTGCAAAGTCGT 57.362 25.926 18.19 11.43 43.17 4.34
4092 6548 1.080638 AACCCATTTCCAGCACCCTA 58.919 50.000 0.00 0.00 0.00 3.53
4106 6562 5.010314 CCTCGTAGCACTAATATACAACCCA 59.990 44.000 0.00 0.00 0.00 4.51
4154 6612 3.902881 AGTAGATGTGAGGCTTTCAGG 57.097 47.619 0.00 0.00 36.21 3.86
4155 6613 6.183360 CGTTTAAGTAGATGTGAGGCTTTCAG 60.183 42.308 0.00 0.00 36.21 3.02
4167 6625 7.377928 CGTATTAGTGGACCGTTTAAGTAGATG 59.622 40.741 0.00 0.00 0.00 2.90
4168 6626 7.283127 TCGTATTAGTGGACCGTTTAAGTAGAT 59.717 37.037 0.00 0.00 0.00 1.98
4169 6627 6.597672 TCGTATTAGTGGACCGTTTAAGTAGA 59.402 38.462 0.00 0.00 0.00 2.59
4170 6628 6.785191 TCGTATTAGTGGACCGTTTAAGTAG 58.215 40.000 0.00 0.00 0.00 2.57
4171 6629 6.751514 TCGTATTAGTGGACCGTTTAAGTA 57.248 37.500 0.00 0.00 0.00 2.24
4172 6630 5.643379 TCGTATTAGTGGACCGTTTAAGT 57.357 39.130 0.00 0.00 0.00 2.24
4173 6631 6.587608 AGTTTCGTATTAGTGGACCGTTTAAG 59.412 38.462 0.00 0.00 0.00 1.85
4174 6632 6.454795 AGTTTCGTATTAGTGGACCGTTTAA 58.545 36.000 0.00 0.00 0.00 1.52
4175 6633 6.024552 AGTTTCGTATTAGTGGACCGTTTA 57.975 37.500 0.00 0.00 0.00 2.01
4176 6634 4.886579 AGTTTCGTATTAGTGGACCGTTT 58.113 39.130 0.00 0.00 0.00 3.60
4177 6635 4.488879 GAGTTTCGTATTAGTGGACCGTT 58.511 43.478 0.00 0.00 0.00 4.44
4178 6636 3.119352 GGAGTTTCGTATTAGTGGACCGT 60.119 47.826 0.00 0.00 0.00 4.83
4179 6637 3.119388 TGGAGTTTCGTATTAGTGGACCG 60.119 47.826 0.00 0.00 0.00 4.79
4180 6638 4.460948 TGGAGTTTCGTATTAGTGGACC 57.539 45.455 0.00 0.00 0.00 4.46
4181 6639 6.790285 TTTTGGAGTTTCGTATTAGTGGAC 57.210 37.500 0.00 0.00 0.00 4.02
4182 6640 7.162761 TGATTTTGGAGTTTCGTATTAGTGGA 58.837 34.615 0.00 0.00 0.00 4.02
4183 6641 7.372451 TGATTTTGGAGTTTCGTATTAGTGG 57.628 36.000 0.00 0.00 0.00 4.00
4184 6642 9.840427 ATTTGATTTTGGAGTTTCGTATTAGTG 57.160 29.630 0.00 0.00 0.00 2.74
4230 6689 3.456277 AGTTGTCTCTGAAACTTGACCCT 59.544 43.478 0.00 0.00 32.75 4.34
4242 6701 3.062763 ACGAGCAATTGAGTTGTCTCTG 58.937 45.455 10.34 4.64 40.98 3.35
4257 6716 6.247727 TGCAATTTACTCAAATTACGAGCA 57.752 33.333 5.02 0.00 41.41 4.26
4294 6754 9.787435 ACTAATGTCAGGTTTAACATGAAGTAA 57.213 29.630 14.04 1.69 40.81 2.24
4480 7554 7.591006 TGTAAAGGACAAAGCGAAACTATAG 57.409 36.000 0.00 0.00 34.15 1.31
4512 7586 9.415544 CTTGGTTAGTGTCTACTTAACGTTTAT 57.584 33.333 5.91 0.00 38.36 1.40
4542 7619 4.410448 TGCACGCATACACACATATTTTG 58.590 39.130 0.00 0.00 0.00 2.44
4589 7666 4.662961 TGCGTCTGGAGCGTGGTG 62.663 66.667 0.00 0.00 37.44 4.17
4630 7707 1.147153 GGGCCGGAAGAGGAATGAG 59.853 63.158 5.05 0.00 0.00 2.90
4793 7870 3.057734 CGAGAAGTACCACCAGTTGAAC 58.942 50.000 0.00 0.00 0.00 3.18
4925 8002 1.533033 TGTGCCGGAGAGGAAGACA 60.533 57.895 5.05 0.00 45.00 3.41
4943 8020 0.759436 CATAGAGGCGGTAGGTGGGT 60.759 60.000 0.00 0.00 0.00 4.51
5042 8122 3.071479 GTCTTGGCATCCTTTTGTACGA 58.929 45.455 0.00 0.00 0.00 3.43
5069 8149 3.288308 CTCTGACTTGGCCGCGACT 62.288 63.158 8.23 0.00 0.00 4.18
5114 8194 3.849951 CACGCCGCCCAGATAGGT 61.850 66.667 0.00 0.00 34.66 3.08
5144 8224 1.882625 GATCTGCGCGTATGCCACA 60.883 57.895 8.43 0.00 38.08 4.17
5150 8230 1.278172 GCGTCATGATCTGCGCGTAT 61.278 55.000 8.43 0.00 39.37 3.06
5249 8329 3.345028 AGGATGCTTGCTGGCCCT 61.345 61.111 0.00 0.00 0.00 5.19
5258 8338 1.523758 GGACGAACAACAGGATGCTT 58.476 50.000 0.00 0.00 42.53 3.91
5549 8629 3.129638 GCATCTGGTCGTAGAAGAACTCT 59.870 47.826 0.00 0.00 39.69 3.24
5642 8722 0.755079 CGATGAAGGAGATGAGGGCA 59.245 55.000 0.00 0.00 0.00 5.36
5687 8767 2.281484 TCAGCAAACCAGCCGTCC 60.281 61.111 0.00 0.00 34.23 4.79
5735 8815 2.027073 CGCTGCGAGCAACCAGTAA 61.027 57.895 18.66 0.00 42.58 2.24
5813 8893 2.023673 TGAAGCCTCTTGTGGTTGTTG 58.976 47.619 0.00 0.00 0.00 3.33
5814 8894 2.092429 TCTGAAGCCTCTTGTGGTTGTT 60.092 45.455 0.00 0.00 0.00 2.83
5815 8895 1.490490 TCTGAAGCCTCTTGTGGTTGT 59.510 47.619 0.00 0.00 0.00 3.32
5835 8915 2.337583 CGTGACGGTGATCACTCATTT 58.662 47.619 24.50 5.48 45.73 2.32
5990 9206 8.960351 ATGAGATGCATTGAACTGAACACTCAG 61.960 40.741 0.00 0.59 43.98 3.35
5991 9207 4.392047 AGATGCATTGAACTGAACACTCA 58.608 39.130 0.00 0.00 0.00 3.41
5992 9208 4.453478 TGAGATGCATTGAACTGAACACTC 59.547 41.667 0.00 0.00 0.00 3.51
5993 9209 4.392047 TGAGATGCATTGAACTGAACACT 58.608 39.130 0.00 0.00 0.00 3.55
5994 9210 4.754372 TGAGATGCATTGAACTGAACAC 57.246 40.909 0.00 0.00 0.00 3.32
5995 9211 5.123344 CAGATGAGATGCATTGAACTGAACA 59.877 40.000 0.00 0.00 37.34 3.18
5996 9212 5.353400 TCAGATGAGATGCATTGAACTGAAC 59.647 40.000 16.23 0.00 37.34 3.18
5999 9215 5.760743 AGATCAGATGAGATGCATTGAACTG 59.239 40.000 0.00 7.92 37.34 3.16
6045 9292 0.388649 CCGTCACAGCACCTGTCTAC 60.389 60.000 0.00 0.00 43.43 2.59
6449 13987 5.582689 AGCTTGACTTTGGGCAAATATAC 57.417 39.130 0.00 0.00 0.00 1.47
6619 14160 9.862371 TTGTCTGAAATCATACTCTCTAAAGTC 57.138 33.333 1.42 0.00 0.00 3.01
6697 15180 5.209818 TGTGTCCTCGAAGAAATAACTGT 57.790 39.130 0.00 0.00 34.09 3.55
6703 15186 3.512680 GACGATGTGTCCTCGAAGAAAT 58.487 45.455 0.00 0.00 42.04 2.17
6746 15229 5.935789 CCATTCCTTTTTCATTGTGCAGAAT 59.064 36.000 2.67 2.67 0.00 2.40


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

AutoCloner maintained by Alex Coulton.