Multiple sequence alignment - TraesCS3A01G360600

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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 TraesCS3A01G360600 chr3A 100.000 4127 0 0 1 4127 608349288 608345162 0.000000e+00 7622.0
1 TraesCS3A01G360600 chr3A 81.214 1219 191 31 1920 3123 608195759 608194564 0.000000e+00 948.0
2 TraesCS3A01G360600 chr3A 98.198 111 2 0 3811 3921 718043095 718042985 1.170000e-45 195.0
3 TraesCS3A01G360600 chr3A 98.165 109 2 0 3810 3918 661930651 661930759 1.510000e-44 191.0
4 TraesCS3A01G360600 chr3B 92.675 3522 154 42 67 3545 618444014 618440554 0.000000e+00 4979.0
5 TraesCS3A01G360600 chr3B 80.343 1226 201 34 1920 3123 618155767 618154560 0.000000e+00 893.0
6 TraesCS3A01G360600 chr3B 92.073 164 12 1 3915 4077 618440384 618440221 3.210000e-56 230.0
7 TraesCS3A01G360600 chr3B 79.851 134 27 0 1700 1833 618156440 618156307 9.440000e-17 99.0
8 TraesCS3A01G360600 chr3D 95.242 2375 78 18 1170 3539 465027901 465025557 0.000000e+00 3727.0
9 TraesCS3A01G360600 chr3D 85.393 1157 100 33 3 1136 465029015 465027905 0.000000e+00 1136.0
10 TraesCS3A01G360600 chr3D 81.669 1222 191 29 1920 3123 464808961 464807755 0.000000e+00 985.0
11 TraesCS3A01G360600 chr3D 75.556 990 201 26 1924 2903 465510082 465511040 2.260000e-122 449.0
12 TraesCS3A01G360600 chr3D 90.551 254 22 2 1358 1610 465509507 465509759 6.610000e-88 335.0
13 TraesCS3A01G360600 chr3D 89.243 251 24 3 1358 1605 464809975 464809725 1.110000e-80 311.0
14 TraesCS3A01G360600 chr3D 91.358 162 11 3 3916 4074 465025419 465025258 6.950000e-53 219.0
15 TraesCS3A01G360600 chr3D 79.641 167 23 5 2705 2870 472197773 472197929 4.360000e-20 110.0
16 TraesCS3A01G360600 chr3D 84.848 66 9 1 3925 3990 6461722 6461658 9.580000e-07 65.8
17 TraesCS3A01G360600 chr1D 83.317 1001 133 23 1926 2903 381019561 381020550 0.000000e+00 893.0
18 TraesCS3A01G360600 chr1D 83.247 388 63 2 1218 1604 381019047 381019433 5.070000e-94 355.0
19 TraesCS3A01G360600 chr1D 94.167 120 5 2 3799 3918 335497323 335497206 9.110000e-42 182.0
20 TraesCS3A01G360600 chr1B 83.267 998 139 18 1926 2903 510809344 510810333 0.000000e+00 893.0
21 TraesCS3A01G360600 chr7D 80.132 1213 215 20 1702 2903 149181675 149182872 0.000000e+00 881.0
22 TraesCS3A01G360600 chr7D 84.794 388 57 2 1218 1604 149181290 149181676 5.000000e-104 388.0
23 TraesCS3A01G360600 chr7D 84.615 377 55 3 1218 1593 149085763 149085389 5.040000e-99 372.0
24 TraesCS3A01G360600 chr1A 82.783 999 130 24 1926 2903 481674509 481675486 0.000000e+00 854.0
25 TraesCS3A01G360600 chr1A 82.469 405 65 5 1203 1604 481673980 481674381 2.360000e-92 350.0
26 TraesCS3A01G360600 chr2D 76.314 1465 279 55 1702 3127 165484966 165483531 0.000000e+00 721.0
27 TraesCS3A01G360600 chr2D 86.216 370 49 2 1218 1586 165485351 165484983 2.310000e-107 399.0
28 TraesCS3A01G360600 chr2D 85.405 370 52 2 1218 1586 165333643 165334011 2.330000e-102 383.0
29 TraesCS3A01G360600 chr2D 74.934 758 162 23 2379 3127 165340078 165340816 5.150000e-84 322.0
30 TraesCS3A01G360600 chr2D 94.167 120 5 2 3799 3918 473880261 473880144 9.110000e-42 182.0
31 TraesCS3A01G360600 chr2B 77.377 1220 241 28 1702 2903 232261908 232263110 0.000000e+00 691.0
32 TraesCS3A01G360600 chr2B 77.220 1216 243 24 1923 3127 232290701 232289509 0.000000e+00 680.0
33 TraesCS3A01G360600 chr2B 86.472 377 47 4 1218 1592 232291311 232290937 1.070000e-110 411.0
34 TraesCS3A01G360600 chr2B 85.984 371 48 4 1218 1586 232261523 232261891 1.080000e-105 394.0
35 TraesCS3A01G360600 chr5B 76.476 1016 178 36 1923 2903 679312548 679313537 2.870000e-136 496.0
36 TraesCS3A01G360600 chr5B 84.615 390 56 4 1218 1605 679311152 679311539 6.470000e-103 385.0
37 TraesCS3A01G360600 chr5B 87.879 132 16 0 1702 1833 679311537 679311668 5.520000e-34 156.0
38 TraesCS3A01G360600 chr7A 84.539 401 53 7 1197 1593 150021865 150022260 5.000000e-104 388.0
39 TraesCS3A01G360600 chr7A 98.718 156 2 0 3536 3691 679064098 679063943 1.130000e-70 278.0
40 TraesCS3A01G360600 chr7A 98.701 154 2 0 3536 3689 566530028 566529875 1.460000e-69 274.0
41 TraesCS3A01G360600 chr7A 98.693 153 2 0 3536 3688 80195662 80195814 5.260000e-69 272.0
42 TraesCS3A01G360600 chr7A 97.436 156 4 0 3536 3691 195840034 195839879 2.450000e-67 267.0
43 TraesCS3A01G360600 chr7A 97.419 155 4 0 3536 3690 232743957 232743803 8.800000e-67 265.0
44 TraesCS3A01G360600 chr5D 84.833 389 55 4 1219 1605 538255194 538255580 5.000000e-104 388.0
45 TraesCS3A01G360600 chr4A 75.153 652 126 23 1923 2546 631619286 631618643 1.460000e-69 274.0
46 TraesCS3A01G360600 chr4A 97.419 155 4 0 3536 3690 96473382 96473536 8.800000e-67 265.0
47 TraesCS3A01G360600 chr4A 95.690 116 5 0 3806 3921 179550741 179550626 1.960000e-43 187.0
48 TraesCS3A01G360600 chr6A 97.419 155 4 0 3536 3690 12370972 12371126 8.800000e-67 265.0
49 TraesCS3A01G360600 chr6A 92.857 126 8 1 3810 3934 613616703 613616578 9.110000e-42 182.0
50 TraesCS3A01G360600 chr6A 86.747 83 7 4 3905 3985 547633956 547633876 5.680000e-14 89.8
51 TraesCS3A01G360600 chr5A 96.875 160 2 2 3536 3692 598682969 598682810 8.800000e-67 265.0
52 TraesCS3A01G360600 chr5A 97.403 154 4 0 3536 3689 385383984 385384137 3.160000e-66 263.0
53 TraesCS3A01G360600 chr4B 83.534 249 37 3 1358 1604 445229495 445229741 3.210000e-56 230.0
54 TraesCS3A01G360600 chr4D 82.996 247 42 0 1358 1604 360451518 360451764 1.490000e-54 224.0
55 TraesCS3A01G360600 chr2A 95.798 119 4 1 3801 3919 183328340 183328457 1.510000e-44 191.0
56 TraesCS3A01G360600 chr2A 97.297 111 3 0 3811 3921 676458908 676459018 5.450000e-44 189.0
57 TraesCS3A01G360600 chr7B 90.370 135 9 2 3812 3942 654954528 654954662 1.520000e-39 174.0
58 TraesCS3A01G360600 chr6B 96.875 32 0 1 3713 3744 276229286 276229316 7.000000e-03 52.8


These results show the homologous regions that are presented in the multiple sequence alignment. HSPs from the BLAST search that are within 2000 bases of each other have been grouped together. Homologous regions that are purely upstream or downstream may be removed if they don't overlap both primers.

query scaffold start end length rev.comp avg.bitscore max.bitscore avg.percent.identical query.start query.end num_hsp groupid homo_length
0 TraesCS3A01G360600 chr3A 608345162 608349288 4126 True 7622.000000 7622 100.000000 1 4127 1 chr3A.!!$R2 4126
1 TraesCS3A01G360600 chr3A 608194564 608195759 1195 True 948.000000 948 81.214000 1920 3123 1 chr3A.!!$R1 1203
2 TraesCS3A01G360600 chr3B 618440221 618444014 3793 True 2604.500000 4979 92.374000 67 4077 2 chr3B.!!$R2 4010
3 TraesCS3A01G360600 chr3B 618154560 618156440 1880 True 496.000000 893 80.097000 1700 3123 2 chr3B.!!$R1 1423
4 TraesCS3A01G360600 chr3D 465025258 465029015 3757 True 1694.000000 3727 90.664333 3 4074 3 chr3D.!!$R3 4071
5 TraesCS3A01G360600 chr3D 464807755 464809975 2220 True 648.000000 985 85.456000 1358 3123 2 chr3D.!!$R2 1765
6 TraesCS3A01G360600 chr3D 465509507 465511040 1533 False 392.000000 449 83.053500 1358 2903 2 chr3D.!!$F2 1545
7 TraesCS3A01G360600 chr1D 381019047 381020550 1503 False 624.000000 893 83.282000 1218 2903 2 chr1D.!!$F1 1685
8 TraesCS3A01G360600 chr1B 510809344 510810333 989 False 893.000000 893 83.267000 1926 2903 1 chr1B.!!$F1 977
9 TraesCS3A01G360600 chr7D 149181290 149182872 1582 False 634.500000 881 82.463000 1218 2903 2 chr7D.!!$F1 1685
10 TraesCS3A01G360600 chr1A 481673980 481675486 1506 False 602.000000 854 82.626000 1203 2903 2 chr1A.!!$F1 1700
11 TraesCS3A01G360600 chr2D 165483531 165485351 1820 True 560.000000 721 81.265000 1218 3127 2 chr2D.!!$R2 1909
12 TraesCS3A01G360600 chr2D 165340078 165340816 738 False 322.000000 322 74.934000 2379 3127 1 chr2D.!!$F2 748
13 TraesCS3A01G360600 chr2B 232289509 232291311 1802 True 545.500000 680 81.846000 1218 3127 2 chr2B.!!$R1 1909
14 TraesCS3A01G360600 chr2B 232261523 232263110 1587 False 542.500000 691 81.680500 1218 2903 2 chr2B.!!$F1 1685
15 TraesCS3A01G360600 chr5B 679311152 679313537 2385 False 345.666667 496 82.990000 1218 2903 3 chr5B.!!$F1 1685
16 TraesCS3A01G360600 chr4A 631618643 631619286 643 True 274.000000 274 75.153000 1923 2546 1 chr4A.!!$R2 623

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
624 641 0.319125 GGTCAAGAGCCCGATCGATC 60.319 60.0 18.66 15.68 0.0 3.69 F
1184 1226 0.110823 GCCATTGACGACGTTGTGAC 60.111 55.0 14.59 0.00 0.0 3.67 F
2020 3413 0.683179 TCTTCTTCTCCATCGCCGGA 60.683 55.0 5.05 0.00 0.0 5.14 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1850 2834 1.067142 ACACACACGCATGTAGGTAGG 60.067 52.381 0.00 0.00 36.72 3.18 R
2086 3479 2.754254 GTTTGGCCCGGGGTGATC 60.754 66.667 25.28 4.19 0.00 2.92 R
3684 5143 0.251519 ACCCGGACGGAAGAAGTACT 60.252 55.000 13.13 0.00 37.50 2.73 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
82 85 2.552373 GGGGAATGATCAACCCGATACC 60.552 54.545 25.15 13.54 44.09 2.73
94 97 2.038557 ACCCGATACCATGGCAGAATAC 59.961 50.000 13.04 0.00 0.00 1.89
218 221 3.680169 TCCCCCTCTCCAAATATCATGT 58.320 45.455 0.00 0.00 0.00 3.21
239 242 1.407979 CATTCCTCAAATGCCAGGCTC 59.592 52.381 14.15 0.00 38.48 4.70
277 280 2.512885 CACGCACAAATCATCTGAAGC 58.487 47.619 0.00 0.00 0.00 3.86
278 281 1.470098 ACGCACAAATCATCTGAAGCC 59.530 47.619 0.00 0.00 0.00 4.35
280 283 2.223203 CGCACAAATCATCTGAAGCCTC 60.223 50.000 0.00 0.00 0.00 4.70
283 286 4.774124 CACAAATCATCTGAAGCCTCCTA 58.226 43.478 0.00 0.00 0.00 2.94
289 292 2.550277 TCTGAAGCCTCCTATGTCCA 57.450 50.000 0.00 0.00 0.00 4.02
298 301 3.503748 GCCTCCTATGTCCATGCAAATAC 59.496 47.826 0.00 0.00 0.00 1.89
307 310 2.034124 CCATGCAAATACTCCCTTGGG 58.966 52.381 0.00 0.00 0.00 4.12
317 320 6.419484 AATACTCCCTTGGGTTTTCTTTTG 57.581 37.500 5.51 0.00 0.00 2.44
375 378 3.302870 GGTACATGTAGCGTAAAATGGCG 60.303 47.826 18.52 0.00 0.00 5.69
380 383 4.201679 GCGTAAAATGGCGCCCCC 62.202 66.667 26.77 0.00 46.93 5.40
532 549 5.662674 ACTCCTAGTACACCAATCTTGAC 57.337 43.478 0.00 0.00 0.00 3.18
538 555 8.258007 TCCTAGTACACCAATCTTGACAATTAG 58.742 37.037 0.00 0.00 0.00 1.73
588 605 1.147153 GGAAAGGCCGGAGAGGATG 59.853 63.158 5.05 0.00 45.00 3.51
590 607 2.330924 GAAAGGCCGGAGAGGATGGG 62.331 65.000 5.05 0.00 45.00 4.00
622 639 3.207354 GGTCAAGAGCCCGATCGA 58.793 61.111 18.66 0.00 0.00 3.59
623 640 1.742768 GGTCAAGAGCCCGATCGAT 59.257 57.895 18.66 0.00 0.00 3.59
624 641 0.319125 GGTCAAGAGCCCGATCGATC 60.319 60.000 18.66 15.68 0.00 3.69
635 652 2.046283 CGATCGATCGGAAATTCGGA 57.954 50.000 34.54 5.72 45.93 4.55
636 653 2.390938 CGATCGATCGGAAATTCGGAA 58.609 47.619 34.54 0.00 45.93 4.30
637 654 2.987149 CGATCGATCGGAAATTCGGAAT 59.013 45.455 34.54 0.00 45.93 3.01
639 656 3.446310 TCGATCGGAAATTCGGAATGA 57.554 42.857 16.41 5.83 36.08 2.57
640 657 3.120792 TCGATCGGAAATTCGGAATGAC 58.879 45.455 16.41 1.85 36.08 3.06
641 658 2.863740 CGATCGGAAATTCGGAATGACA 59.136 45.455 7.38 0.00 29.49 3.58
642 659 3.494626 CGATCGGAAATTCGGAATGACAT 59.505 43.478 7.38 0.00 29.49 3.06
643 660 4.609113 CGATCGGAAATTCGGAATGACATG 60.609 45.833 7.38 0.00 29.49 3.21
644 661 2.354510 TCGGAAATTCGGAATGACATGC 59.645 45.455 3.59 0.00 0.00 4.06
695 712 3.201290 CTCCCAAGCTATAGCAACACAG 58.799 50.000 26.07 12.11 45.16 3.66
809 826 1.208052 TGGCTAGCTTGCTGAACTAGG 59.792 52.381 19.45 0.00 35.09 3.02
811 828 1.946745 CTAGCTTGCTGAACTAGGCC 58.053 55.000 5.26 0.00 31.65 5.19
826 843 3.493440 GCCGGGGTAAACGCTTCG 61.493 66.667 2.18 0.00 0.00 3.79
864 881 7.370383 TGACAAAAATGCTTCAACTAATCTCC 58.630 34.615 0.00 0.00 0.00 3.71
906 948 1.268283 ACCTCTAGGGCAAGCACCTC 61.268 60.000 0.20 0.00 39.54 3.85
914 956 2.806856 GCAAGCACCTCGCATCTCG 61.807 63.158 0.00 0.00 46.13 4.04
966 1008 1.631405 CTATCCAGAGCTCTCAGGGG 58.369 60.000 14.96 12.55 36.95 4.79
1087 1129 2.719739 TGGAGTACCAGTTCGAGGTAG 58.280 52.381 2.44 0.00 42.01 3.18
1093 1135 0.320374 CCAGTTCGAGGTAGGTTGCA 59.680 55.000 0.00 0.00 0.00 4.08
1098 1140 1.045407 TCGAGGTAGGTTGCACAGTT 58.955 50.000 0.00 0.00 0.00 3.16
1099 1141 2.241160 TCGAGGTAGGTTGCACAGTTA 58.759 47.619 0.00 0.00 0.00 2.24
1100 1142 2.230508 TCGAGGTAGGTTGCACAGTTAG 59.769 50.000 0.00 0.00 0.00 2.34
1101 1143 2.029290 CGAGGTAGGTTGCACAGTTAGT 60.029 50.000 0.00 0.00 0.00 2.24
1102 1144 3.586892 GAGGTAGGTTGCACAGTTAGTC 58.413 50.000 0.00 0.00 0.00 2.59
1103 1145 2.969950 AGGTAGGTTGCACAGTTAGTCA 59.030 45.455 0.00 0.00 0.00 3.41
1104 1146 3.006967 AGGTAGGTTGCACAGTTAGTCAG 59.993 47.826 0.00 0.00 0.00 3.51
1114 1156 4.342772 CACAGTTAGTCAGTTGTTGCAAC 58.657 43.478 22.83 22.83 0.00 4.17
1136 1178 1.135517 ACCGTTGTTCAGTTGTTGCAC 60.136 47.619 0.00 0.00 0.00 4.57
1147 1189 3.067180 CAGTTGTTGCACATTCAGGTTCT 59.933 43.478 0.00 0.00 0.00 3.01
1148 1190 3.067180 AGTTGTTGCACATTCAGGTTCTG 59.933 43.478 0.00 0.00 0.00 3.02
1184 1226 0.110823 GCCATTGACGACGTTGTGAC 60.111 55.000 14.59 0.00 0.00 3.67
1187 1229 0.859232 ATTGACGACGTTGTGACTGC 59.141 50.000 14.59 0.00 0.00 4.40
1195 1237 2.143122 ACGTTGTGACTGCTATGGTTG 58.857 47.619 0.00 0.00 0.00 3.77
1637 1686 2.165167 CCTACAAGGTGGTGACTCGTA 58.835 52.381 0.00 0.00 0.00 3.43
1647 1696 3.924686 GTGGTGACTCGTAATAAGTGTGG 59.075 47.826 0.00 0.00 0.00 4.17
1648 1697 2.928116 GGTGACTCGTAATAAGTGTGGC 59.072 50.000 0.00 0.00 0.00 5.01
1651 1700 4.032900 GTGACTCGTAATAAGTGTGGCATG 59.967 45.833 0.00 0.00 0.00 4.06
1652 1701 2.936498 ACTCGTAATAAGTGTGGCATGC 59.064 45.455 9.90 9.90 0.00 4.06
1680 1729 8.352201 TGCATGCATGGATTACTTAAGTTTATC 58.648 33.333 27.34 15.71 0.00 1.75
1681 1730 8.352201 GCATGCATGGATTACTTAAGTTTATCA 58.648 33.333 27.34 8.42 0.00 2.15
1850 2834 0.923911 GTTTGTGTCGTGTGCTTCGC 60.924 55.000 0.00 0.00 0.00 4.70
2020 3413 0.683179 TCTTCTTCTCCATCGCCGGA 60.683 55.000 5.05 0.00 0.00 5.14
2282 3699 1.073199 AACAAGAACCTCCCGCTGG 59.927 57.895 0.00 0.00 0.00 4.85
2476 3911 4.353437 GGCCCGACGAACGACAGT 62.353 66.667 0.00 0.00 45.77 3.55
3182 4637 1.441016 CGTCCGCTTTTGCTTGCTC 60.441 57.895 0.00 0.00 44.80 4.26
3296 4752 7.279615 TCTTTAACTTTCATGTCAAGTCCTCA 58.720 34.615 11.80 0.00 33.12 3.86
3328 4784 4.818546 ACTGTTGTGAGGTTTCTTGATCAG 59.181 41.667 0.00 0.00 0.00 2.90
3351 4807 2.003301 GCAAGAGGCTTAGGACTTTCG 58.997 52.381 0.00 0.00 40.25 3.46
3441 4900 7.147983 GCCTGTCCAATAATTTGTACCAACATA 60.148 37.037 0.00 0.00 34.97 2.29
3455 4914 6.550481 TGTACCAACATATGATTCATGGCAAT 59.450 34.615 10.38 0.00 0.00 3.56
3488 4947 9.394477 GTTATTGGTTATTTAATCGGCAGATTC 57.606 33.333 15.61 0.54 45.21 2.52
3524 4983 3.056107 TCATAGGACACAACTACTGCACC 60.056 47.826 0.00 0.00 0.00 5.01
3536 4995 0.251922 ACTGCACCAATTCCATGGCT 60.252 50.000 6.96 0.00 44.75 4.75
3539 4998 3.117550 ACTGCACCAATTCCATGGCTATA 60.118 43.478 6.96 0.00 44.75 1.31
3540 4999 4.084287 CTGCACCAATTCCATGGCTATAT 58.916 43.478 6.96 0.00 44.75 0.86
3541 5000 3.827876 TGCACCAATTCCATGGCTATATG 59.172 43.478 6.96 2.13 44.75 1.78
3545 5004 5.713389 CACCAATTCCATGGCTATATGATGT 59.287 40.000 6.96 0.00 44.75 3.06
3546 5005 5.713389 ACCAATTCCATGGCTATATGATGTG 59.287 40.000 6.96 0.00 44.75 3.21
3548 5007 6.434965 CCAATTCCATGGCTATATGATGTGAA 59.565 38.462 6.96 0.00 32.78 3.18
3549 5008 7.039574 CCAATTCCATGGCTATATGATGTGAAA 60.040 37.037 6.96 0.00 32.78 2.69
3550 5009 7.698506 ATTCCATGGCTATATGATGTGAAAG 57.301 36.000 6.96 0.00 0.00 2.62
3551 5010 6.191657 TCCATGGCTATATGATGTGAAAGT 57.808 37.500 6.96 0.00 0.00 2.66
3552 5011 7.315066 TCCATGGCTATATGATGTGAAAGTA 57.685 36.000 6.96 0.00 0.00 2.24
3553 5012 7.161404 TCCATGGCTATATGATGTGAAAGTAC 58.839 38.462 6.96 0.00 0.00 2.73
3554 5013 6.936335 CCATGGCTATATGATGTGAAAGTACA 59.064 38.462 0.00 0.00 34.63 2.90
3555 5014 7.609146 CCATGGCTATATGATGTGAAAGTACAT 59.391 37.037 0.00 0.00 43.61 2.29
3556 5015 9.006839 CATGGCTATATGATGTGAAAGTACATT 57.993 33.333 0.00 0.00 41.15 2.71
3557 5016 8.607441 TGGCTATATGATGTGAAAGTACATTC 57.393 34.615 3.88 3.88 41.15 2.67
3558 5017 8.210265 TGGCTATATGATGTGAAAGTACATTCA 58.790 33.333 9.38 9.38 41.15 2.57
3559 5018 9.056005 GGCTATATGATGTGAAAGTACATTCAA 57.944 33.333 14.64 6.63 41.15 2.69
3640 5099 8.911247 AACTTAGTCAAAACTTACAAAGCTTG 57.089 30.769 0.00 0.00 36.92 4.01
3641 5100 8.276252 ACTTAGTCAAAACTTACAAAGCTTGA 57.724 30.769 0.00 0.00 36.92 3.02
3642 5101 8.182227 ACTTAGTCAAAACTTACAAAGCTTGAC 58.818 33.333 18.45 18.45 45.61 3.18
3665 5124 6.757897 CTTTGACCAAAGCTAATATGTGGA 57.242 37.500 9.25 0.00 40.94 4.02
3666 5125 6.509418 TTTGACCAAAGCTAATATGTGGAC 57.491 37.500 0.00 0.00 33.39 4.02
3667 5126 5.435686 TGACCAAAGCTAATATGTGGACT 57.564 39.130 0.00 0.00 33.39 3.85
3668 5127 6.553953 TGACCAAAGCTAATATGTGGACTA 57.446 37.500 0.00 0.00 33.39 2.59
3669 5128 6.953101 TGACCAAAGCTAATATGTGGACTAA 58.047 36.000 0.00 0.00 33.39 2.24
3670 5129 7.398829 TGACCAAAGCTAATATGTGGACTAAA 58.601 34.615 0.00 0.00 33.39 1.85
3671 5130 8.052748 TGACCAAAGCTAATATGTGGACTAAAT 58.947 33.333 0.00 0.00 33.39 1.40
3672 5131 9.555727 GACCAAAGCTAATATGTGGACTAAATA 57.444 33.333 0.00 0.00 33.39 1.40
3673 5132 9.914834 ACCAAAGCTAATATGTGGACTAAATAA 57.085 29.630 0.00 0.00 33.39 1.40
3679 5138 9.659830 GCTAATATGTGGACTAAATAAAAACGG 57.340 33.333 0.00 0.00 0.00 4.44
3682 5141 6.753107 ATGTGGACTAAATAAAAACGGAGG 57.247 37.500 0.00 0.00 0.00 4.30
3683 5142 5.005094 TGTGGACTAAATAAAAACGGAGGG 58.995 41.667 0.00 0.00 0.00 4.30
3684 5143 5.221884 TGTGGACTAAATAAAAACGGAGGGA 60.222 40.000 0.00 0.00 0.00 4.20
3685 5144 5.353400 GTGGACTAAATAAAAACGGAGGGAG 59.647 44.000 0.00 0.00 0.00 4.30
3709 5168 2.678471 TCTTCCGTCCGGGTTTATTC 57.322 50.000 0.00 0.00 37.00 1.75
3711 5170 2.167075 TCTTCCGTCCGGGTTTATTCTC 59.833 50.000 0.00 0.00 37.00 2.87
3712 5171 0.457035 TCCGTCCGGGTTTATTCTCG 59.543 55.000 0.00 0.00 37.00 4.04
3714 5173 1.405105 CCGTCCGGGTTTATTCTCGTA 59.595 52.381 0.00 0.00 0.00 3.43
3725 5188 7.571613 CGGGTTTATTCTCGTATTTTTGTGTCA 60.572 37.037 0.00 0.00 0.00 3.58
3814 5279 9.679661 TCAATGATGTAATTTATGTGGTGTACT 57.320 29.630 0.00 0.00 0.00 2.73
3815 5280 9.935682 CAATGATGTAATTTATGTGGTGTACTC 57.064 33.333 0.00 0.00 0.00 2.59
3816 5281 8.677148 ATGATGTAATTTATGTGGTGTACTCC 57.323 34.615 7.03 7.03 0.00 3.85
3817 5282 7.051623 TGATGTAATTTATGTGGTGTACTCCC 58.948 38.462 11.36 3.51 0.00 4.30
3818 5283 6.630203 TGTAATTTATGTGGTGTACTCCCT 57.370 37.500 11.36 0.00 0.00 4.20
3819 5284 6.646267 TGTAATTTATGTGGTGTACTCCCTC 58.354 40.000 11.36 5.59 0.00 4.30
3820 5285 4.772886 ATTTATGTGGTGTACTCCCTCC 57.227 45.455 11.36 0.72 0.00 4.30
3821 5286 1.771565 TATGTGGTGTACTCCCTCCG 58.228 55.000 11.36 0.00 0.00 4.63
3822 5287 0.252103 ATGTGGTGTACTCCCTCCGT 60.252 55.000 11.36 0.00 0.00 4.69
3823 5288 0.470456 TGTGGTGTACTCCCTCCGTT 60.470 55.000 11.36 0.00 0.00 4.44
3824 5289 0.245813 GTGGTGTACTCCCTCCGTTC 59.754 60.000 11.36 0.00 0.00 3.95
3825 5290 1.246056 TGGTGTACTCCCTCCGTTCG 61.246 60.000 11.36 0.00 0.00 3.95
3826 5291 1.509923 GTGTACTCCCTCCGTTCGG 59.490 63.158 4.74 4.74 0.00 4.30
3827 5292 0.962356 GTGTACTCCCTCCGTTCGGA 60.962 60.000 13.34 13.34 0.00 4.55
3828 5293 0.251297 TGTACTCCCTCCGTTCGGAA 60.251 55.000 14.79 0.04 33.41 4.30
3829 5294 1.109609 GTACTCCCTCCGTTCGGAAT 58.890 55.000 14.79 2.09 33.41 3.01
3830 5295 1.479730 GTACTCCCTCCGTTCGGAATT 59.520 52.381 14.79 0.00 33.41 2.17
3831 5296 1.856629 ACTCCCTCCGTTCGGAATTA 58.143 50.000 14.79 2.82 33.41 1.40
3832 5297 1.479730 ACTCCCTCCGTTCGGAATTAC 59.520 52.381 14.79 0.00 33.41 1.89
3833 5298 1.755380 CTCCCTCCGTTCGGAATTACT 59.245 52.381 14.79 0.00 33.41 2.24
3834 5299 2.167900 CTCCCTCCGTTCGGAATTACTT 59.832 50.000 14.79 0.00 33.41 2.24
3835 5300 2.093869 TCCCTCCGTTCGGAATTACTTG 60.094 50.000 14.79 1.97 33.41 3.16
3836 5301 2.354403 CCCTCCGTTCGGAATTACTTGT 60.354 50.000 14.79 0.00 33.41 3.16
3837 5302 2.928116 CCTCCGTTCGGAATTACTTGTC 59.072 50.000 14.79 0.00 33.41 3.18
3838 5303 3.368116 CCTCCGTTCGGAATTACTTGTCT 60.368 47.826 14.79 0.00 33.41 3.41
3839 5304 4.243270 CTCCGTTCGGAATTACTTGTCTT 58.757 43.478 14.79 0.00 33.41 3.01
3840 5305 3.991773 TCCGTTCGGAATTACTTGTCTTG 59.008 43.478 11.66 0.00 0.00 3.02
3841 5306 3.991773 CCGTTCGGAATTACTTGTCTTGA 59.008 43.478 5.19 0.00 0.00 3.02
3842 5307 4.449743 CCGTTCGGAATTACTTGTCTTGAA 59.550 41.667 5.19 0.00 0.00 2.69
3843 5308 5.121768 CCGTTCGGAATTACTTGTCTTGAAT 59.878 40.000 5.19 0.00 0.00 2.57
3844 5309 6.311935 CCGTTCGGAATTACTTGTCTTGAATA 59.688 38.462 5.19 0.00 0.00 1.75
3845 5310 7.011109 CCGTTCGGAATTACTTGTCTTGAATAT 59.989 37.037 5.19 0.00 0.00 1.28
3846 5311 7.846107 CGTTCGGAATTACTTGTCTTGAATATG 59.154 37.037 0.00 0.00 0.00 1.78
3847 5312 7.786178 TCGGAATTACTTGTCTTGAATATGG 57.214 36.000 0.00 0.00 0.00 2.74
3848 5313 7.561251 TCGGAATTACTTGTCTTGAATATGGA 58.439 34.615 0.00 0.00 0.00 3.41
3849 5314 8.210946 TCGGAATTACTTGTCTTGAATATGGAT 58.789 33.333 0.00 0.00 0.00 3.41
3850 5315 8.285394 CGGAATTACTTGTCTTGAATATGGATG 58.715 37.037 0.00 0.00 0.00 3.51
3851 5316 9.125026 GGAATTACTTGTCTTGAATATGGATGT 57.875 33.333 0.00 0.00 0.00 3.06
3891 5356 7.194607 ACATCTAAATACATCCATTTCTGCG 57.805 36.000 0.00 0.00 30.84 5.18
3892 5357 6.992123 ACATCTAAATACATCCATTTCTGCGA 59.008 34.615 0.00 0.00 30.84 5.10
3893 5358 6.844696 TCTAAATACATCCATTTCTGCGAC 57.155 37.500 0.00 0.00 30.84 5.19
3894 5359 6.345298 TCTAAATACATCCATTTCTGCGACA 58.655 36.000 0.00 0.00 30.84 4.35
3895 5360 5.895636 AAATACATCCATTTCTGCGACAA 57.104 34.783 0.00 0.00 0.00 3.18
3896 5361 5.490139 AATACATCCATTTCTGCGACAAG 57.510 39.130 0.00 0.00 0.00 3.16
3897 5362 2.783135 ACATCCATTTCTGCGACAAGT 58.217 42.857 0.00 0.00 0.00 3.16
3898 5363 3.937814 ACATCCATTTCTGCGACAAGTA 58.062 40.909 0.00 0.00 0.00 2.24
3899 5364 4.323417 ACATCCATTTCTGCGACAAGTAA 58.677 39.130 0.00 0.00 0.00 2.24
3900 5365 4.943705 ACATCCATTTCTGCGACAAGTAAT 59.056 37.500 0.00 0.00 0.00 1.89
3901 5366 5.415701 ACATCCATTTCTGCGACAAGTAATT 59.584 36.000 0.00 0.00 0.00 1.40
3902 5367 5.545658 TCCATTTCTGCGACAAGTAATTC 57.454 39.130 0.00 0.00 0.00 2.17
3903 5368 4.394920 TCCATTTCTGCGACAAGTAATTCC 59.605 41.667 0.00 0.00 0.00 3.01
3904 5369 4.334443 CATTTCTGCGACAAGTAATTCCG 58.666 43.478 0.00 0.00 0.00 4.30
3905 5370 3.306917 TTCTGCGACAAGTAATTCCGA 57.693 42.857 0.00 0.00 0.00 4.55
3906 5371 3.306917 TCTGCGACAAGTAATTCCGAA 57.693 42.857 0.00 0.00 0.00 4.30
3907 5372 2.991190 TCTGCGACAAGTAATTCCGAAC 59.009 45.455 0.00 0.00 0.00 3.95
3908 5373 1.722464 TGCGACAAGTAATTCCGAACG 59.278 47.619 0.00 0.00 0.00 3.95
3909 5374 1.060122 GCGACAAGTAATTCCGAACGG 59.940 52.381 6.94 6.94 0.00 4.44
3910 5375 2.598589 CGACAAGTAATTCCGAACGGA 58.401 47.619 12.04 12.04 43.52 4.69
3911 5376 2.597305 CGACAAGTAATTCCGAACGGAG 59.403 50.000 15.34 5.60 46.06 4.63
3912 5377 2.928116 GACAAGTAATTCCGAACGGAGG 59.072 50.000 15.34 4.52 46.06 4.30
3913 5378 2.277084 CAAGTAATTCCGAACGGAGGG 58.723 52.381 15.34 0.00 46.06 4.30
3932 5397 9.151177 ACGGAGGGAGTATAACTTATATTTTGA 57.849 33.333 0.00 0.00 0.00 2.69
3992 5457 6.014840 ACAAGGAAGAACTATAAACGAGGACA 60.015 38.462 0.00 0.00 0.00 4.02
3993 5458 6.600882 AGGAAGAACTATAAACGAGGACAA 57.399 37.500 0.00 0.00 0.00 3.18
4071 5538 2.106684 GGTTCTCTCCAGGGTGAAAACT 59.893 50.000 6.56 0.00 0.00 2.66
4072 5539 3.326880 GGTTCTCTCCAGGGTGAAAACTA 59.673 47.826 6.56 0.00 0.00 2.24
4073 5540 4.019231 GGTTCTCTCCAGGGTGAAAACTAT 60.019 45.833 6.56 0.00 0.00 2.12
4075 5542 6.296259 GGTTCTCTCCAGGGTGAAAACTATTA 60.296 42.308 6.56 0.00 0.00 0.98
4076 5543 6.546428 TCTCTCCAGGGTGAAAACTATTAG 57.454 41.667 0.00 0.00 0.00 1.73
4078 5545 4.080526 TCTCCAGGGTGAAAACTATTAGGC 60.081 45.833 0.00 0.00 0.00 3.93
4079 5546 3.053917 TCCAGGGTGAAAACTATTAGGCC 60.054 47.826 0.00 0.00 0.00 5.19
4080 5547 3.308832 CCAGGGTGAAAACTATTAGGCCA 60.309 47.826 5.01 0.00 0.00 5.36
4081 5548 4.340617 CAGGGTGAAAACTATTAGGCCAA 58.659 43.478 5.01 0.00 0.00 4.52
4082 5549 4.157840 CAGGGTGAAAACTATTAGGCCAAC 59.842 45.833 5.01 0.00 0.00 3.77
4083 5550 4.044191 AGGGTGAAAACTATTAGGCCAACT 59.956 41.667 5.01 0.00 0.00 3.16
4084 5551 4.398358 GGGTGAAAACTATTAGGCCAACTC 59.602 45.833 5.01 0.00 0.00 3.01
4085 5552 5.254115 GGTGAAAACTATTAGGCCAACTCT 58.746 41.667 5.01 0.00 0.00 3.24
4086 5553 6.412214 GGTGAAAACTATTAGGCCAACTCTA 58.588 40.000 5.01 0.00 0.00 2.43
4087 5554 6.539103 GGTGAAAACTATTAGGCCAACTCTAG 59.461 42.308 5.01 0.77 0.00 2.43
4088 5555 6.037281 GTGAAAACTATTAGGCCAACTCTAGC 59.963 42.308 5.01 0.00 0.00 3.42
4095 5562 3.102090 GCCAACTCTAGCCAATCCC 57.898 57.895 0.00 0.00 0.00 3.85
4096 5563 0.255890 GCCAACTCTAGCCAATCCCA 59.744 55.000 0.00 0.00 0.00 4.37
4097 5564 1.133668 GCCAACTCTAGCCAATCCCAT 60.134 52.381 0.00 0.00 0.00 4.00
4098 5565 2.106511 GCCAACTCTAGCCAATCCCATA 59.893 50.000 0.00 0.00 0.00 2.74
4099 5566 3.245052 GCCAACTCTAGCCAATCCCATAT 60.245 47.826 0.00 0.00 0.00 1.78
4100 5567 4.019321 GCCAACTCTAGCCAATCCCATATA 60.019 45.833 0.00 0.00 0.00 0.86
4101 5568 5.514834 GCCAACTCTAGCCAATCCCATATAA 60.515 44.000 0.00 0.00 0.00 0.98
4102 5569 5.940470 CCAACTCTAGCCAATCCCATATAAC 59.060 44.000 0.00 0.00 0.00 1.89
4103 5570 5.763876 ACTCTAGCCAATCCCATATAACC 57.236 43.478 0.00 0.00 0.00 2.85
4104 5571 4.223032 ACTCTAGCCAATCCCATATAACCG 59.777 45.833 0.00 0.00 0.00 4.44
4105 5572 2.879103 AGCCAATCCCATATAACCGG 57.121 50.000 0.00 0.00 0.00 5.28
4106 5573 2.062636 AGCCAATCCCATATAACCGGT 58.937 47.619 0.00 0.00 0.00 5.28
4107 5574 2.445525 AGCCAATCCCATATAACCGGTT 59.554 45.455 25.64 25.64 0.00 4.44
4108 5575 3.653836 AGCCAATCCCATATAACCGGTTA 59.346 43.478 28.40 28.40 0.00 2.85
4109 5576 4.007659 GCCAATCCCATATAACCGGTTAG 58.992 47.826 29.49 17.30 0.00 2.34
4110 5577 4.263156 GCCAATCCCATATAACCGGTTAGA 60.263 45.833 29.49 26.37 0.00 2.10
4111 5578 5.488341 CCAATCCCATATAACCGGTTAGAG 58.512 45.833 29.49 20.76 0.00 2.43
4112 5579 5.012768 CCAATCCCATATAACCGGTTAGAGT 59.987 44.000 29.49 18.02 0.00 3.24
4113 5580 6.211986 CCAATCCCATATAACCGGTTAGAGTA 59.788 42.308 29.49 18.66 0.00 2.59
4114 5581 7.321153 CAATCCCATATAACCGGTTAGAGTAG 58.679 42.308 29.49 18.89 0.00 2.57
4115 5582 5.957132 TCCCATATAACCGGTTAGAGTAGT 58.043 41.667 29.49 15.77 0.00 2.73
4116 5583 7.090319 TCCCATATAACCGGTTAGAGTAGTA 57.910 40.000 29.49 17.32 0.00 1.82
4117 5584 7.526041 TCCCATATAACCGGTTAGAGTAGTAA 58.474 38.462 29.49 8.13 0.00 2.24
4118 5585 8.004215 TCCCATATAACCGGTTAGAGTAGTAAA 58.996 37.037 29.49 7.37 0.00 2.01
4119 5586 8.641541 CCCATATAACCGGTTAGAGTAGTAAAA 58.358 37.037 29.49 6.83 0.00 1.52
4124 5591 5.654497 ACCGGTTAGAGTAGTAAAAATCCG 58.346 41.667 0.00 0.00 35.02 4.18
4125 5592 5.045872 CCGGTTAGAGTAGTAAAAATCCGG 58.954 45.833 0.00 0.00 45.77 5.14
4126 5593 4.505556 CGGTTAGAGTAGTAAAAATCCGGC 59.494 45.833 0.00 0.00 0.00 6.13
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
52 55 5.535030 GGGTTGATCATTCCCCTACAATTAC 59.465 44.000 19.85 1.48 35.52 1.89
57 60 1.488812 CGGGTTGATCATTCCCCTACA 59.511 52.381 22.74 0.00 38.09 2.74
58 61 1.766496 TCGGGTTGATCATTCCCCTAC 59.234 52.381 22.74 6.85 38.09 3.18
60 63 1.522900 ATCGGGTTGATCATTCCCCT 58.477 50.000 22.74 12.66 38.09 4.79
82 85 1.035139 GGCAAGGGTATTCTGCCATG 58.965 55.000 7.42 0.00 44.42 3.66
94 97 2.263153 CCAACGGTAAAGGCAAGGG 58.737 57.895 0.00 0.00 0.00 3.95
139 142 5.661759 AGAATTATTGGTCTTCCTACTCGGT 59.338 40.000 0.00 0.00 34.23 4.69
218 221 1.006281 AGCCTGGCATTTGAGGAATGA 59.994 47.619 22.65 0.00 46.59 2.57
277 280 4.978099 AGTATTTGCATGGACATAGGAGG 58.022 43.478 0.00 0.00 0.00 4.30
278 281 4.999950 GGAGTATTTGCATGGACATAGGAG 59.000 45.833 0.00 0.00 0.00 3.69
280 283 4.074970 GGGAGTATTTGCATGGACATAGG 58.925 47.826 0.00 0.00 0.00 2.57
283 286 3.956199 CAAGGGAGTATTTGCATGGACAT 59.044 43.478 0.00 0.00 0.00 3.06
289 292 3.473113 AACCCAAGGGAGTATTTGCAT 57.527 42.857 13.15 0.00 38.96 3.96
298 301 3.069586 GGACAAAAGAAAACCCAAGGGAG 59.930 47.826 13.15 0.00 38.96 4.30
307 310 7.008901 CGGTTTACTCAAAGGACAAAAGAAAAC 59.991 37.037 0.00 0.00 0.00 2.43
317 320 2.490991 AGTGCGGTTTACTCAAAGGAC 58.509 47.619 0.00 0.00 0.00 3.85
515 532 8.038944 GTCCTAATTGTCAAGATTGGTGTACTA 58.961 37.037 0.00 0.00 0.00 1.82
517 534 6.093633 GGTCCTAATTGTCAAGATTGGTGTAC 59.906 42.308 0.00 0.00 0.00 2.90
523 540 4.332819 GTCCGGTCCTAATTGTCAAGATTG 59.667 45.833 0.00 0.00 0.00 2.67
532 549 2.614057 GCAGAATGTCCGGTCCTAATTG 59.386 50.000 0.00 0.00 39.31 2.32
538 555 2.100631 CACGCAGAATGTCCGGTCC 61.101 63.158 0.00 0.00 39.31 4.46
579 596 1.834822 CGTCCTCCCCATCCTCTCC 60.835 68.421 0.00 0.00 0.00 3.71
621 638 4.776743 CATGTCATTCCGAATTTCCGATC 58.223 43.478 0.00 0.00 0.00 3.69
622 639 3.003689 GCATGTCATTCCGAATTTCCGAT 59.996 43.478 0.00 0.00 0.00 4.18
623 640 2.354510 GCATGTCATTCCGAATTTCCGA 59.645 45.455 0.00 0.00 0.00 4.55
624 641 2.097304 TGCATGTCATTCCGAATTTCCG 59.903 45.455 0.00 0.00 0.00 4.30
625 642 3.781079 TGCATGTCATTCCGAATTTCC 57.219 42.857 0.00 0.00 0.00 3.13
628 645 2.824936 TGGTTGCATGTCATTCCGAATT 59.175 40.909 0.00 0.00 0.00 2.17
629 646 2.424601 CTGGTTGCATGTCATTCCGAAT 59.575 45.455 0.00 0.00 0.00 3.34
630 647 1.811965 CTGGTTGCATGTCATTCCGAA 59.188 47.619 0.00 0.00 0.00 4.30
631 648 1.003003 TCTGGTTGCATGTCATTCCGA 59.997 47.619 0.00 0.49 0.00 4.55
632 649 1.131126 GTCTGGTTGCATGTCATTCCG 59.869 52.381 0.00 0.00 0.00 4.30
634 651 1.466360 GCGTCTGGTTGCATGTCATTC 60.466 52.381 0.00 0.00 0.00 2.67
635 652 0.523072 GCGTCTGGTTGCATGTCATT 59.477 50.000 0.00 0.00 0.00 2.57
636 653 1.638388 CGCGTCTGGTTGCATGTCAT 61.638 55.000 0.00 0.00 0.00 3.06
637 654 2.316867 CGCGTCTGGTTGCATGTCA 61.317 57.895 0.00 0.00 0.00 3.58
639 656 3.726517 GCGCGTCTGGTTGCATGT 61.727 61.111 8.43 0.00 0.00 3.21
640 657 4.799473 CGCGCGTCTGGTTGCATG 62.799 66.667 24.19 0.00 0.00 4.06
809 826 3.493440 CGAAGCGTTTACCCCGGC 61.493 66.667 0.00 0.00 0.00 6.13
811 828 1.080298 ACTCGAAGCGTTTACCCCG 60.080 57.895 0.00 0.00 0.00 5.73
826 843 1.295792 TTTGTCAAGACGTGGCACTC 58.704 50.000 16.72 11.95 43.07 3.51
864 881 4.159693 TGCCTATATATAACCAGTGGCGAG 59.840 45.833 9.78 0.00 41.73 5.03
906 948 0.025898 CTGCATGTGTTCGAGATGCG 59.974 55.000 12.99 0.00 44.52 4.73
914 956 2.503375 GCGCTGCTGCATGTGTTC 60.503 61.111 16.29 0.00 39.64 3.18
962 1004 1.629297 CTAGCTCCCCTTCTCCCCT 59.371 63.158 0.00 0.00 0.00 4.79
966 1008 0.966179 GCTAGCTAGCTCCCCTTCTC 59.034 60.000 33.71 5.30 45.62 2.87
1065 1107 0.170561 CCTCGAACTGGTACTCCACG 59.829 60.000 0.00 0.00 39.03 4.94
1083 1125 3.244112 ACTGACTAACTGTGCAACCTACC 60.244 47.826 0.00 0.00 34.36 3.18
1087 1129 2.943033 ACAACTGACTAACTGTGCAACC 59.057 45.455 0.00 0.00 34.36 3.77
1093 1135 4.261801 AGTTGCAACAACTGACTAACTGT 58.738 39.130 30.11 2.33 0.00 3.55
1098 1140 3.181473 ACGGTAGTTGCAACAACTGACTA 60.181 43.478 30.11 10.09 0.00 2.59
1099 1141 2.210116 CGGTAGTTGCAACAACTGACT 58.790 47.619 30.11 11.14 0.00 3.41
1100 1142 1.937899 ACGGTAGTTGCAACAACTGAC 59.062 47.619 30.11 18.08 0.00 3.51
1101 1143 2.319136 ACGGTAGTTGCAACAACTGA 57.681 45.000 30.11 8.06 0.00 3.41
1114 1156 2.353269 TGCAACAACTGAACAACGGTAG 59.647 45.455 0.00 0.00 37.07 3.18
1136 1178 1.009829 GTAGGCGCAGAACCTGAATG 58.990 55.000 10.83 0.00 38.26 2.67
1184 1226 1.679153 TGCATGCATCAACCATAGCAG 59.321 47.619 18.46 0.00 40.71 4.24
1187 1229 2.034179 CACCTGCATGCATCAACCATAG 59.966 50.000 22.97 5.79 0.00 2.23
1195 1237 2.825387 TCGCCACCTGCATGCATC 60.825 61.111 22.97 7.34 41.33 3.91
1680 1729 1.795872 TGAGCACGTCCGTAAACAATG 59.204 47.619 0.00 0.00 0.00 2.82
1681 1730 2.066262 CTGAGCACGTCCGTAAACAAT 58.934 47.619 0.00 0.00 0.00 2.71
1691 1740 2.456119 CCATTCGCCTGAGCACGTC 61.456 63.158 0.00 0.00 39.83 4.34
1850 2834 1.067142 ACACACACGCATGTAGGTAGG 60.067 52.381 0.00 0.00 36.72 3.18
2020 3413 3.296709 GACGATGGTGAGCGGGTGT 62.297 63.158 0.00 0.00 34.48 4.16
2086 3479 2.754254 GTTTGGCCCGGGGTGATC 60.754 66.667 25.28 4.19 0.00 2.92
3202 4657 2.995258 CACACACAAGCAAAAGCAGTTT 59.005 40.909 0.00 0.00 0.00 2.66
3233 4688 2.203408 TTGATGGCACCAACCGCA 60.203 55.556 0.00 0.00 0.00 5.69
3296 4752 7.227156 AGAAACCTCACAACAGTTAATCAGAT 58.773 34.615 0.00 0.00 0.00 2.90
3351 4807 3.424962 GCGACTAATCAGCAGTCCAAAAC 60.425 47.826 0.00 0.00 39.43 2.43
3510 4969 2.884012 TGGAATTGGTGCAGTAGTTGTG 59.116 45.455 0.00 0.00 0.00 3.33
3514 4973 2.726821 CCATGGAATTGGTGCAGTAGT 58.273 47.619 5.56 0.00 31.74 2.73
3524 4983 7.457024 TTCACATCATATAGCCATGGAATTG 57.543 36.000 18.40 5.11 0.00 2.32
3614 5073 9.353999 CAAGCTTTGTAAGTTTTGACTAAGTTT 57.646 29.630 0.00 0.00 34.21 2.66
3615 5074 8.736244 TCAAGCTTTGTAAGTTTTGACTAAGTT 58.264 29.630 0.00 0.00 32.90 2.66
3616 5075 8.182227 GTCAAGCTTTGTAAGTTTTGACTAAGT 58.818 33.333 19.73 0.00 43.65 2.24
3617 5076 8.548433 GTCAAGCTTTGTAAGTTTTGACTAAG 57.452 34.615 19.73 5.96 43.65 2.18
3621 5080 7.812309 AAAGTCAAGCTTTGTAAGTTTTGAC 57.188 32.000 19.57 19.57 45.00 3.18
3643 5102 6.245408 AGTCCACATATTAGCTTTGGTCAAA 58.755 36.000 0.00 0.00 0.00 2.69
3644 5103 5.815581 AGTCCACATATTAGCTTTGGTCAA 58.184 37.500 0.00 0.00 0.00 3.18
3645 5104 5.435686 AGTCCACATATTAGCTTTGGTCA 57.564 39.130 0.00 0.00 0.00 4.02
3646 5105 7.859325 TTTAGTCCACATATTAGCTTTGGTC 57.141 36.000 0.00 0.00 0.00 4.02
3647 5106 9.914834 TTATTTAGTCCACATATTAGCTTTGGT 57.085 29.630 0.00 0.00 0.00 3.67
3653 5112 9.659830 CCGTTTTTATTTAGTCCACATATTAGC 57.340 33.333 0.00 0.00 0.00 3.09
3656 5115 8.899771 CCTCCGTTTTTATTTAGTCCACATATT 58.100 33.333 0.00 0.00 0.00 1.28
3657 5116 7.501225 CCCTCCGTTTTTATTTAGTCCACATAT 59.499 37.037 0.00 0.00 0.00 1.78
3658 5117 6.824704 CCCTCCGTTTTTATTTAGTCCACATA 59.175 38.462 0.00 0.00 0.00 2.29
3659 5118 5.650703 CCCTCCGTTTTTATTTAGTCCACAT 59.349 40.000 0.00 0.00 0.00 3.21
3660 5119 5.005094 CCCTCCGTTTTTATTTAGTCCACA 58.995 41.667 0.00 0.00 0.00 4.17
3661 5120 5.247862 TCCCTCCGTTTTTATTTAGTCCAC 58.752 41.667 0.00 0.00 0.00 4.02
3662 5121 5.013391 ACTCCCTCCGTTTTTATTTAGTCCA 59.987 40.000 0.00 0.00 0.00 4.02
3663 5122 5.494724 ACTCCCTCCGTTTTTATTTAGTCC 58.505 41.667 0.00 0.00 0.00 3.85
3664 5123 7.326454 AGTACTCCCTCCGTTTTTATTTAGTC 58.674 38.462 0.00 0.00 0.00 2.59
3665 5124 7.250032 AGTACTCCCTCCGTTTTTATTTAGT 57.750 36.000 0.00 0.00 0.00 2.24
3666 5125 8.039538 AGAAGTACTCCCTCCGTTTTTATTTAG 58.960 37.037 0.00 0.00 0.00 1.85
3667 5126 7.910584 AGAAGTACTCCCTCCGTTTTTATTTA 58.089 34.615 0.00 0.00 0.00 1.40
3668 5127 6.776744 AGAAGTACTCCCTCCGTTTTTATTT 58.223 36.000 0.00 0.00 0.00 1.40
3669 5128 6.370186 AGAAGTACTCCCTCCGTTTTTATT 57.630 37.500 0.00 0.00 0.00 1.40
3670 5129 6.370186 AAGAAGTACTCCCTCCGTTTTTAT 57.630 37.500 0.00 0.00 0.00 1.40
3671 5130 5.279657 GGAAGAAGTACTCCCTCCGTTTTTA 60.280 44.000 0.00 0.00 0.00 1.52
3672 5131 4.504514 GGAAGAAGTACTCCCTCCGTTTTT 60.505 45.833 0.00 0.00 0.00 1.94
3673 5132 3.007723 GGAAGAAGTACTCCCTCCGTTTT 59.992 47.826 0.00 0.00 0.00 2.43
3674 5133 2.566279 GGAAGAAGTACTCCCTCCGTTT 59.434 50.000 0.00 0.00 0.00 3.60
3675 5134 2.177734 GGAAGAAGTACTCCCTCCGTT 58.822 52.381 0.00 0.00 0.00 4.44
3676 5135 1.849977 GGAAGAAGTACTCCCTCCGT 58.150 55.000 0.00 0.00 0.00 4.69
3677 5136 0.739561 CGGAAGAAGTACTCCCTCCG 59.260 60.000 19.16 19.16 41.27 4.63
3678 5137 1.750206 GACGGAAGAAGTACTCCCTCC 59.250 57.143 0.00 1.40 0.00 4.30
3679 5138 1.750206 GGACGGAAGAAGTACTCCCTC 59.250 57.143 0.00 0.00 0.00 4.30
3680 5139 1.849977 GGACGGAAGAAGTACTCCCT 58.150 55.000 0.00 0.00 0.00 4.20
3681 5140 0.455005 CGGACGGAAGAAGTACTCCC 59.545 60.000 0.00 0.00 0.00 4.30
3682 5141 0.455005 CCGGACGGAAGAAGTACTCC 59.545 60.000 4.40 0.00 37.50 3.85
3683 5142 0.455005 CCCGGACGGAAGAAGTACTC 59.545 60.000 13.13 0.00 37.50 2.59
3684 5143 0.251519 ACCCGGACGGAAGAAGTACT 60.252 55.000 13.13 0.00 37.50 2.73
3685 5144 0.605083 AACCCGGACGGAAGAAGTAC 59.395 55.000 13.13 0.00 37.50 2.73
3788 5253 9.679661 AGTACACCACATAAATTACATCATTGA 57.320 29.630 0.00 0.00 0.00 2.57
3796 5261 6.053650 GGAGGGAGTACACCACATAAATTAC 58.946 44.000 11.69 0.00 0.00 1.89
3813 5278 1.755380 AGTAATTCCGAACGGAGGGAG 59.245 52.381 15.34 0.00 46.06 4.30
3814 5279 1.856629 AGTAATTCCGAACGGAGGGA 58.143 50.000 15.34 2.49 46.06 4.20
3815 5280 2.277084 CAAGTAATTCCGAACGGAGGG 58.723 52.381 15.34 0.00 46.06 4.30
3816 5281 2.928116 GACAAGTAATTCCGAACGGAGG 59.072 50.000 15.34 4.52 46.06 4.30
3817 5282 3.846360 AGACAAGTAATTCCGAACGGAG 58.154 45.455 15.34 5.60 46.06 4.63
3818 5283 3.947910 AGACAAGTAATTCCGAACGGA 57.052 42.857 12.04 12.04 43.52 4.69
3819 5284 3.991773 TCAAGACAAGTAATTCCGAACGG 59.008 43.478 6.94 6.94 0.00 4.44
3820 5285 5.585500 TTCAAGACAAGTAATTCCGAACG 57.415 39.130 0.00 0.00 0.00 3.95
3821 5286 8.122952 CCATATTCAAGACAAGTAATTCCGAAC 58.877 37.037 0.00 0.00 0.00 3.95
3822 5287 8.044309 TCCATATTCAAGACAAGTAATTCCGAA 58.956 33.333 0.00 0.00 0.00 4.30
3823 5288 7.561251 TCCATATTCAAGACAAGTAATTCCGA 58.439 34.615 0.00 0.00 0.00 4.55
3824 5289 7.786178 TCCATATTCAAGACAAGTAATTCCG 57.214 36.000 0.00 0.00 0.00 4.30
3825 5290 9.125026 ACATCCATATTCAAGACAAGTAATTCC 57.875 33.333 0.00 0.00 0.00 3.01
3865 5330 8.939929 CGCAGAAATGGATGTATTTAGATGTAT 58.060 33.333 0.00 0.00 30.78 2.29
3866 5331 8.147704 TCGCAGAAATGGATGTATTTAGATGTA 58.852 33.333 0.00 0.00 30.78 2.29
3867 5332 6.992123 TCGCAGAAATGGATGTATTTAGATGT 59.008 34.615 0.00 0.00 30.78 3.06
3868 5333 7.041848 TGTCGCAGAAATGGATGTATTTAGATG 60.042 37.037 0.00 0.00 39.69 2.90
3869 5334 6.992123 TGTCGCAGAAATGGATGTATTTAGAT 59.008 34.615 0.00 0.00 39.69 1.98
3870 5335 6.345298 TGTCGCAGAAATGGATGTATTTAGA 58.655 36.000 0.00 0.00 39.69 2.10
3871 5336 6.603237 TGTCGCAGAAATGGATGTATTTAG 57.397 37.500 0.00 0.00 39.69 1.85
3872 5337 6.597672 ACTTGTCGCAGAAATGGATGTATTTA 59.402 34.615 0.00 0.00 39.69 1.40
3873 5338 5.415701 ACTTGTCGCAGAAATGGATGTATTT 59.584 36.000 0.00 0.00 39.69 1.40
3874 5339 4.943705 ACTTGTCGCAGAAATGGATGTATT 59.056 37.500 0.00 0.00 39.69 1.89
3875 5340 4.517285 ACTTGTCGCAGAAATGGATGTAT 58.483 39.130 0.00 0.00 39.69 2.29
3876 5341 3.937814 ACTTGTCGCAGAAATGGATGTA 58.062 40.909 0.00 0.00 39.69 2.29
3877 5342 2.783135 ACTTGTCGCAGAAATGGATGT 58.217 42.857 0.00 0.00 39.69 3.06
3878 5343 4.944962 TTACTTGTCGCAGAAATGGATG 57.055 40.909 0.00 0.00 39.69 3.51
3879 5344 5.066505 GGAATTACTTGTCGCAGAAATGGAT 59.933 40.000 0.00 0.00 39.69 3.41
3880 5345 4.394920 GGAATTACTTGTCGCAGAAATGGA 59.605 41.667 0.00 0.00 39.69 3.41
3881 5346 4.662145 GGAATTACTTGTCGCAGAAATGG 58.338 43.478 0.00 0.00 39.69 3.16
3882 5347 4.092821 TCGGAATTACTTGTCGCAGAAATG 59.907 41.667 0.00 0.00 39.69 2.32
3883 5348 4.250464 TCGGAATTACTTGTCGCAGAAAT 58.750 39.130 0.00 0.00 39.69 2.17
3884 5349 3.655486 TCGGAATTACTTGTCGCAGAAA 58.345 40.909 0.00 0.00 39.69 2.52
3885 5350 3.306917 TCGGAATTACTTGTCGCAGAA 57.693 42.857 0.00 0.00 39.69 3.02
3886 5351 2.991190 GTTCGGAATTACTTGTCGCAGA 59.009 45.455 0.00 0.00 0.00 4.26
3887 5352 2.222508 CGTTCGGAATTACTTGTCGCAG 60.223 50.000 0.00 0.00 0.00 5.18
3888 5353 1.722464 CGTTCGGAATTACTTGTCGCA 59.278 47.619 0.00 0.00 0.00 5.10
3889 5354 1.060122 CCGTTCGGAATTACTTGTCGC 59.940 52.381 5.19 0.00 0.00 5.19
3890 5355 2.597305 CTCCGTTCGGAATTACTTGTCG 59.403 50.000 14.79 0.00 33.41 4.35
3891 5356 2.928116 CCTCCGTTCGGAATTACTTGTC 59.072 50.000 14.79 0.00 33.41 3.18
3892 5357 2.354403 CCCTCCGTTCGGAATTACTTGT 60.354 50.000 14.79 0.00 33.41 3.16
3893 5358 2.093869 TCCCTCCGTTCGGAATTACTTG 60.094 50.000 14.79 1.97 33.41 3.16
3894 5359 2.167900 CTCCCTCCGTTCGGAATTACTT 59.832 50.000 14.79 0.00 33.41 2.24
3895 5360 1.755380 CTCCCTCCGTTCGGAATTACT 59.245 52.381 14.79 0.00 33.41 2.24
3896 5361 1.479730 ACTCCCTCCGTTCGGAATTAC 59.520 52.381 14.79 0.00 33.41 1.89
3897 5362 1.856629 ACTCCCTCCGTTCGGAATTA 58.143 50.000 14.79 2.82 33.41 1.40
3898 5363 1.856629 TACTCCCTCCGTTCGGAATT 58.143 50.000 14.79 0.00 33.41 2.17
3899 5364 2.083628 ATACTCCCTCCGTTCGGAAT 57.916 50.000 14.79 2.14 33.41 3.01
3900 5365 2.689983 GTTATACTCCCTCCGTTCGGAA 59.310 50.000 14.79 0.00 33.41 4.30
3901 5366 2.092212 AGTTATACTCCCTCCGTTCGGA 60.092 50.000 13.34 13.34 0.00 4.55
3902 5367 2.305009 AGTTATACTCCCTCCGTTCGG 58.695 52.381 4.74 4.74 0.00 4.30
3903 5368 5.702349 ATAAGTTATACTCCCTCCGTTCG 57.298 43.478 0.00 0.00 0.00 3.95
3904 5369 9.993454 AAAATATAAGTTATACTCCCTCCGTTC 57.007 33.333 4.71 0.00 0.00 3.95
3905 5370 9.774413 CAAAATATAAGTTATACTCCCTCCGTT 57.226 33.333 4.71 0.00 0.00 4.44
3906 5371 9.151177 TCAAAATATAAGTTATACTCCCTCCGT 57.849 33.333 4.71 0.00 0.00 4.69
3986 5451 5.678955 ATGTACCTACTTCCTTTGTCCTC 57.321 43.478 0.00 0.00 0.00 3.71
3992 5457 5.045797 GGAGTGGAATGTACCTACTTCCTTT 60.046 44.000 12.19 4.05 39.36 3.11
3993 5458 4.470304 GGAGTGGAATGTACCTACTTCCTT 59.530 45.833 12.19 4.30 39.36 3.36
4078 5545 4.647564 ATATGGGATTGGCTAGAGTTGG 57.352 45.455 0.00 0.00 0.00 3.77
4079 5546 5.940470 GGTTATATGGGATTGGCTAGAGTTG 59.060 44.000 0.00 0.00 0.00 3.16
4080 5547 5.280011 CGGTTATATGGGATTGGCTAGAGTT 60.280 44.000 0.00 0.00 0.00 3.01
4081 5548 4.223032 CGGTTATATGGGATTGGCTAGAGT 59.777 45.833 0.00 0.00 0.00 3.24
4082 5549 4.383118 CCGGTTATATGGGATTGGCTAGAG 60.383 50.000 0.00 0.00 0.00 2.43
4083 5550 3.517901 CCGGTTATATGGGATTGGCTAGA 59.482 47.826 0.00 0.00 0.00 2.43
4084 5551 3.263425 ACCGGTTATATGGGATTGGCTAG 59.737 47.826 0.00 0.00 0.00 3.42
4085 5552 3.253220 ACCGGTTATATGGGATTGGCTA 58.747 45.455 0.00 0.00 0.00 3.93
4086 5553 2.062636 ACCGGTTATATGGGATTGGCT 58.937 47.619 0.00 0.00 0.00 4.75
4087 5554 2.579410 ACCGGTTATATGGGATTGGC 57.421 50.000 0.00 0.00 0.00 4.52
4088 5555 5.012768 ACTCTAACCGGTTATATGGGATTGG 59.987 44.000 26.70 11.45 0.00 3.16
4089 5556 6.110411 ACTCTAACCGGTTATATGGGATTG 57.890 41.667 26.70 12.15 0.00 2.67
4090 5557 7.015064 ACTACTCTAACCGGTTATATGGGATT 58.985 38.462 26.70 15.84 0.00 3.01
4091 5558 6.559429 ACTACTCTAACCGGTTATATGGGAT 58.441 40.000 26.70 11.06 0.00 3.85
4092 5559 5.957132 ACTACTCTAACCGGTTATATGGGA 58.043 41.667 26.70 18.16 0.00 4.37
4093 5560 7.765695 TTACTACTCTAACCGGTTATATGGG 57.234 40.000 26.70 17.60 0.00 4.00
4098 5565 7.922811 CGGATTTTTACTACTCTAACCGGTTAT 59.077 37.037 26.70 15.12 34.27 1.89
4099 5566 7.257722 CGGATTTTTACTACTCTAACCGGTTA 58.742 38.462 25.09 25.09 34.27 2.85
4100 5567 6.101997 CGGATTTTTACTACTCTAACCGGTT 58.898 40.000 25.64 25.64 34.27 4.44
4101 5568 5.654497 CGGATTTTTACTACTCTAACCGGT 58.346 41.667 0.00 0.00 34.27 5.28
4103 5570 4.505556 GCCGGATTTTTACTACTCTAACCG 59.494 45.833 5.05 0.00 37.02 4.44
4104 5571 5.980698 GCCGGATTTTTACTACTCTAACC 57.019 43.478 5.05 0.00 0.00 2.85


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

AutoCloner maintained by Alex Coulton.