Multiple sequence alignment - TraesCS3A01G064700

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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 TraesCS3A01G064700 chr3A 100.000 5241 0 0 1 5241 38293351 38288111 0.000000e+00 9679
1 TraesCS3A01G064700 chr3A 86.893 206 24 1 1974 2179 502268077 502268279 1.470000e-55 228
2 TraesCS3A01G064700 chr3D 94.835 2207 67 6 2599 4770 28744945 28747139 0.000000e+00 3400
3 TraesCS3A01G064700 chr3D 94.373 2186 75 8 2599 4748 28733649 28735822 0.000000e+00 3312
4 TraesCS3A01G064700 chr3D 90.076 393 16 6 4859 5241 28747781 28748160 6.100000e-134 488
5 TraesCS3A01G064700 chr3D 82.342 521 59 21 2089 2596 561098959 561098459 6.280000e-114 422
6 TraesCS3A01G064700 chr3D 80.418 526 72 21 2089 2598 368291938 368291428 6.410000e-99 372
7 TraesCS3A01G064700 chr3D 81.562 461 65 17 317 763 28732492 28732946 3.860000e-96 363
8 TraesCS3A01G064700 chr3D 92.917 240 14 2 2360 2598 558707090 558707327 3.890000e-91 346
9 TraesCS3A01G064700 chr3D 87.742 310 17 4 823 1118 28733087 28733389 5.030000e-90 342
10 TraesCS3A01G064700 chr3D 92.444 225 12 5 1309 1530 558707316 558707094 3.050000e-82 316
11 TraesCS3A01G064700 chr3D 87.681 276 26 7 317 587 28743485 28743757 1.100000e-81 315
12 TraesCS3A01G064700 chr3D 91.630 227 16 3 1309 1533 368292560 368292335 1.420000e-80 311
13 TraesCS3A01G064700 chr3D 84.951 206 28 1 1974 2179 378143079 378143281 6.880000e-49 206
14 TraesCS3A01G064700 chr3D 84.071 226 9 3 4860 5062 28736018 28736239 5.360000e-45 193
15 TraesCS3A01G064700 chr3D 96.190 105 4 0 1110 1214 28733420 28733524 6.980000e-39 172
16 TraesCS3A01G064700 chr3B 94.102 2221 68 10 2599 4770 49117005 49119211 0.000000e+00 3317
17 TraesCS3A01G064700 chr3B 94.087 1945 67 7 2599 4505 47683201 47681267 0.000000e+00 2911
18 TraesCS3A01G064700 chr3B 93.885 1946 70 9 2599 4505 48026219 48024284 0.000000e+00 2889
19 TraesCS3A01G064700 chr3B 87.018 986 79 18 156 1116 49115788 49116749 0.000000e+00 1066
20 TraesCS3A01G064700 chr3B 87.879 396 30 9 732 1116 48101249 48100861 2.880000e-122 449
21 TraesCS3A01G064700 chr3B 87.626 396 31 8 732 1116 47696267 47695879 1.340000e-120 444
22 TraesCS3A01G064700 chr3B 87.657 397 29 9 732 1116 47830584 47830196 1.340000e-120 444
23 TraesCS3A01G064700 chr3B 87.121 396 33 7 732 1116 47769264 47768876 2.900000e-117 433
24 TraesCS3A01G064700 chr3B 87.121 396 32 8 732 1116 47701404 47701017 1.040000e-116 431
25 TraesCS3A01G064700 chr3B 95.506 267 8 1 4504 4770 47681185 47680923 1.740000e-114 424
26 TraesCS3A01G064700 chr3B 94.757 267 10 1 4504 4770 48024202 48023940 3.780000e-111 412
27 TraesCS3A01G064700 chr3B 88.530 279 24 7 317 590 48027339 48027064 1.090000e-86 331
28 TraesCS3A01G064700 chr3B 87.455 279 27 7 317 590 47684357 47684082 1.100000e-81 315
29 TraesCS3A01G064700 chr3B 93.939 165 10 0 4 168 48042825 48042661 3.130000e-62 250
30 TraesCS3A01G064700 chr3B 93.333 165 11 0 4 168 47772819 47772655 1.460000e-60 244
31 TraesCS3A01G064700 chr3B 92.727 165 12 0 4 168 47834140 47833976 6.780000e-59 239
32 TraesCS3A01G064700 chr3B 92.727 165 12 0 4 168 48104803 48104639 6.780000e-59 239
33 TraesCS3A01G064700 chr3B 92.121 165 13 0 4 168 47704959 47704795 3.160000e-57 233
34 TraesCS3A01G064700 chr3B 90.909 165 15 0 1 165 49115385 49115549 6.830000e-54 222
35 TraesCS3A01G064700 chr3B 94.495 109 5 1 1110 1217 47683430 47683322 3.250000e-37 167
36 TraesCS3A01G064700 chr3B 94.495 109 5 1 1110 1217 48026448 48026340 3.250000e-37 167
37 TraesCS3A01G064700 chr3B 95.238 105 5 0 1110 1214 49116776 49116880 3.250000e-37 167
38 TraesCS3A01G064700 chr3B 92.929 99 3 4 646 743 47704181 47704086 1.970000e-29 141
39 TraesCS3A01G064700 chr3B 92.929 99 3 4 646 743 48042047 48041952 1.970000e-29 141
40 TraesCS3A01G064700 chr3B 92.929 99 3 4 646 743 48104025 48103930 1.970000e-29 141
41 TraesCS3A01G064700 chr3B 92.929 99 2 4 646 743 47699044 47698950 7.080000e-29 139
42 TraesCS3A01G064700 chr3B 91.919 99 5 3 646 743 47766903 47766807 9.150000e-28 135
43 TraesCS3A01G064700 chr3B 89.796 98 10 0 664 761 47683975 47683878 5.510000e-25 126
44 TraesCS3A01G064700 chr3B 80.556 180 18 5 664 827 48026988 48026810 7.130000e-24 122
45 TraesCS3A01G064700 chr3B 94.444 72 4 0 97 168 47767588 47767517 1.540000e-20 111
46 TraesCS3A01G064700 chr3B 93.056 72 5 0 97 168 47699729 47699658 7.180000e-19 106
47 TraesCS3A01G064700 chr6B 96.123 1986 61 4 2785 4770 131222536 131220567 0.000000e+00 3227
48 TraesCS3A01G064700 chr6B 90.932 397 22 5 4856 5241 131220023 131219630 6.010000e-144 521
49 TraesCS3A01G064700 chr6B 88.312 308 18 6 822 1118 131223234 131222934 2.320000e-93 353
50 TraesCS3A01G064700 chr6B 96.183 131 5 0 2599 2729 131222674 131222544 1.140000e-51 215
51 TraesCS3A01G064700 chr6B 95.238 105 5 0 1110 1214 131222903 131222799 3.250000e-37 167
52 TraesCS3A01G064700 chr2D 84.399 1705 168 36 2604 4249 648386126 648387791 0.000000e+00 1585
53 TraesCS3A01G064700 chr2D 93.277 238 14 1 2361 2598 520037637 520037872 3.000000e-92 350
54 TraesCS3A01G064700 chr2D 85.792 183 20 5 1032 1214 648385826 648386002 6.930000e-44 189
55 TraesCS3A01G064700 chr7D 94.586 942 45 6 1660 2598 566942170 566941232 0.000000e+00 1452
56 TraesCS3A01G064700 chr7D 81.524 525 60 23 2089 2598 610560883 610560381 1.060000e-106 398
57 TraesCS3A01G064700 chr5D 83.648 954 127 22 1660 2598 242648855 242649794 0.000000e+00 870
58 TraesCS3A01G064700 chr5D 92.562 242 13 4 2360 2599 331897710 331897472 5.030000e-90 342
59 TraesCS3A01G064700 chr5D 92.478 226 9 7 1308 1530 121073098 121073318 3.050000e-82 316
60 TraesCS3A01G064700 chr5D 92.411 224 13 4 1309 1530 436603851 436603630 3.050000e-82 316
61 TraesCS3A01G064700 chrUn 82.167 1043 117 16 2604 3595 30961806 30960782 0.000000e+00 832
62 TraesCS3A01G064700 chrUn 95.000 320 10 2 4186 4505 479036147 479036460 1.010000e-136 497
63 TraesCS3A01G064700 chr2B 79.600 951 147 24 1658 2593 790201613 790202531 5.720000e-179 638
64 TraesCS3A01G064700 chr6A 81.250 480 74 8 1748 2225 74732267 74732732 1.780000e-99 374
65 TraesCS3A01G064700 chr6A 98.387 124 2 0 1536 1659 107177406 107177529 8.840000e-53 219
66 TraesCS3A01G064700 chr4D 94.167 240 11 2 2360 2598 456276195 456275958 3.860000e-96 363
67 TraesCS3A01G064700 chr4D 92.946 241 14 3 2360 2599 29863156 29863394 1.080000e-91 348
68 TraesCS3A01G064700 chr4D 93.333 225 10 5 1309 1530 456275969 456276191 1.410000e-85 327
69 TraesCS3A01G064700 chr1D 94.167 240 11 2 2360 2598 38791404 38791167 3.860000e-96 363
70 TraesCS3A01G064700 chr1D 92.000 250 16 4 2360 2607 442450547 442450794 1.080000e-91 348
71 TraesCS3A01G064700 chr1D 93.333 225 10 5 1309 1530 38791178 38791400 1.410000e-85 327
72 TraesCS3A01G064700 chr1D 92.444 225 13 4 1309 1530 430065863 430066086 8.470000e-83 318
73 TraesCS3A01G064700 chr1D 92.105 228 12 5 1309 1533 442450773 442450549 3.050000e-82 316
74 TraesCS3A01G064700 chr2A 92.437 238 16 2 2361 2598 18292630 18292865 6.500000e-89 339
75 TraesCS3A01G064700 chr2A 98.374 123 2 0 1537 1659 120760532 120760410 3.180000e-52 217
76 TraesCS3A01G064700 chr6D 92.444 225 12 5 1309 1530 283809938 283810160 3.050000e-82 316
77 TraesCS3A01G064700 chr7A 99.200 125 1 0 1536 1660 607549733 607549857 5.280000e-55 226
78 TraesCS3A01G064700 chr7A 97.638 127 3 0 1534 1660 638815500 638815626 8.840000e-53 219
79 TraesCS3A01G064700 chr5B 97.656 128 3 0 1532 1659 397406949 397407076 2.460000e-53 220
80 TraesCS3A01G064700 chr5B 96.241 133 5 0 1537 1669 701545343 701545475 8.840000e-53 219
81 TraesCS3A01G064700 chr4A 98.387 124 2 0 1536 1659 615120066 615119943 8.840000e-53 219
82 TraesCS3A01G064700 chr1B 98.374 123 2 0 1537 1659 648709628 648709750 3.180000e-52 217
83 TraesCS3A01G064700 chr5A 96.875 128 3 1 1534 1660 635453583 635453456 4.110000e-51 213


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 TraesCS3A01G064700 chr3A 38288111 38293351 5240 True 9679.000000 9679 100.000000 1 5241 1 chr3A.!!$R1 5240
1 TraesCS3A01G064700 chr3D 28743485 28748160 4675 False 1401.000000 3400 90.864000 317 5241 3 chr3D.!!$F4 4924
2 TraesCS3A01G064700 chr3D 28732492 28736239 3747 False 876.400000 3312 88.787600 317 5062 5 chr3D.!!$F3 4745
3 TraesCS3A01G064700 chr3D 561098459 561098959 500 True 422.000000 422 82.342000 2089 2596 1 chr3D.!!$R2 507
4 TraesCS3A01G064700 chr3D 368291428 368292560 1132 True 341.500000 372 86.024000 1309 2598 2 chr3D.!!$R3 1289
5 TraesCS3A01G064700 chr3B 49115385 49119211 3826 False 1193.000000 3317 91.816750 1 4770 4 chr3B.!!$F1 4769
6 TraesCS3A01G064700 chr3B 47680923 47684357 3434 True 788.600000 2911 92.267800 317 4770 5 chr3B.!!$R1 4453
7 TraesCS3A01G064700 chr3B 48023940 48027339 3399 True 784.200000 2889 90.444600 317 4770 5 chr3B.!!$R5 4453
8 TraesCS3A01G064700 chr3B 47830196 47834140 3944 True 341.500000 444 90.192000 4 1116 2 chr3B.!!$R4 1112
9 TraesCS3A01G064700 chr3B 48100861 48104803 3942 True 276.333333 449 91.178333 4 1116 3 chr3B.!!$R7 1112
10 TraesCS3A01G064700 chr3B 47695879 47704959 9080 True 249.000000 444 90.963667 4 1116 6 chr3B.!!$R2 1112
11 TraesCS3A01G064700 chr3B 47766807 47772819 6012 True 230.750000 433 91.704250 4 1116 4 chr3B.!!$R3 1112
12 TraesCS3A01G064700 chr6B 131219630 131223234 3604 True 896.600000 3227 93.357600 822 5241 5 chr6B.!!$R1 4419
13 TraesCS3A01G064700 chr2D 648385826 648387791 1965 False 887.000000 1585 85.095500 1032 4249 2 chr2D.!!$F2 3217
14 TraesCS3A01G064700 chr7D 566941232 566942170 938 True 1452.000000 1452 94.586000 1660 2598 1 chr7D.!!$R1 938
15 TraesCS3A01G064700 chr7D 610560381 610560883 502 True 398.000000 398 81.524000 2089 2598 1 chr7D.!!$R2 509
16 TraesCS3A01G064700 chr5D 242648855 242649794 939 False 870.000000 870 83.648000 1660 2598 1 chr5D.!!$F2 938
17 TraesCS3A01G064700 chrUn 30960782 30961806 1024 True 832.000000 832 82.167000 2604 3595 1 chrUn.!!$R1 991
18 TraesCS3A01G064700 chr2B 790201613 790202531 918 False 638.000000 638 79.600000 1658 2593 1 chr2B.!!$F1 935

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
206 455 0.036164 TAGTGTTGCAATGGAGCGGT 59.964 50.0 0.59 0.0 37.31 5.68 F
207 456 0.036164 AGTGTTGCAATGGAGCGGTA 59.964 50.0 0.59 0.0 37.31 4.02 F
1537 4932 0.107017 AGCAATCAACCCCTCATCGG 60.107 55.0 0.00 0.0 0.00 4.18 F
1600 4995 0.105246 ACATGTGGGCCTTTTGGGAA 60.105 50.0 4.53 0.0 40.82 3.97 F
2018 5790 0.179100 CGTGCGTCATCTGGGATCTT 60.179 55.0 0.00 0.0 0.00 2.40 F
3597 8536 0.106708 AAAGGCAGCGTCAAGTCTCA 59.893 50.0 0.00 0.0 0.00 3.27 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1543 4938 0.029567 CTGCCGTACGTCAGAGGATC 59.970 60.000 21.01 0.00 32.26 3.36 R
1581 4976 0.105246 TTCCCAAAAGGCCCACATGT 60.105 50.000 0.00 0.00 34.51 3.21 R
3523 8462 0.713883 CGTACAAAACAGCGCGAGAT 59.286 50.000 12.10 0.00 0.00 2.75 R
3597 8536 1.296715 GTGATCAACGGCCTGTCCT 59.703 57.895 0.00 0.00 0.00 3.85 R
3922 8861 4.141482 TGCCTTGACAGATAAAGGTATCCC 60.141 45.833 3.58 0.00 44.13 3.85 R
4686 10311 0.038983 GCAAGTGTGTCATGCATGCA 60.039 50.000 25.04 25.04 40.05 3.96 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
55 56 0.039256 GAGCCGCTGATGCAAAAACA 60.039 50.000 0.00 0.00 39.64 2.83
61 62 2.221517 CGCTGATGCAAAAACAAAAGGG 59.778 45.455 0.00 0.00 39.64 3.95
63 64 2.208431 TGATGCAAAAACAAAAGGGCG 58.792 42.857 0.00 0.00 0.00 6.13
66 67 0.574922 GCAAAAACAAAAGGGCGACG 59.425 50.000 0.00 0.00 0.00 5.12
123 124 1.378119 GGGGGTCATTGTCGGTTCC 60.378 63.158 0.00 0.00 0.00 3.62
169 418 1.471119 CTGGAAGTGCTGCAATGGAT 58.529 50.000 2.77 0.00 0.00 3.41
187 436 4.421479 CGCTTGCCGACGACTCCT 62.421 66.667 0.00 0.00 40.02 3.69
204 453 0.729116 CCTAGTGTTGCAATGGAGCG 59.271 55.000 0.59 0.00 37.31 5.03
205 454 0.729116 CTAGTGTTGCAATGGAGCGG 59.271 55.000 0.59 0.00 37.31 5.52
206 455 0.036164 TAGTGTTGCAATGGAGCGGT 59.964 50.000 0.59 0.00 37.31 5.68
207 456 0.036164 AGTGTTGCAATGGAGCGGTA 59.964 50.000 0.59 0.00 37.31 4.02
249 498 1.809619 GCGATGCAGTACTCGGCAA 60.810 57.895 11.48 0.00 46.31 4.52
250 499 1.999051 CGATGCAGTACTCGGCAAC 59.001 57.895 11.48 8.36 46.31 4.17
277 526 1.155042 GGAGATGCGATGGAATGCTC 58.845 55.000 0.00 0.00 0.00 4.26
352 602 2.113986 GGCTGCTCCTGGTGTTGT 59.886 61.111 0.00 0.00 0.00 3.32
409 659 0.388907 GCGAATGCATGTTGTTGCCT 60.389 50.000 0.00 0.00 42.06 4.75
424 674 3.274288 GTTGCCTTTGCTACTGCTAGAT 58.726 45.455 0.00 0.00 39.67 1.98
461 711 1.060553 GCTGATTGACGCGATTCGAAA 59.939 47.619 15.93 0.00 41.67 3.46
471 721 2.148057 GCGATTCGAAAAAGAACGACG 58.852 47.619 10.88 0.00 38.24 5.12
544 797 2.284331 TGGTTGAGGCCTAGGCGA 60.284 61.111 27.24 11.10 43.06 5.54
618 871 8.729805 TTTTTGCAACTAAATTTGTCATCCTT 57.270 26.923 0.00 0.00 0.00 3.36
620 873 6.403866 TGCAACTAAATTTGTCATCCTTGT 57.596 33.333 0.00 0.00 0.00 3.16
630 883 7.765695 ATTTGTCATCCTTGTGTCACTAAAT 57.234 32.000 4.27 0.00 0.00 1.40
635 888 4.846779 TCCTTGTGTCACTAAATTTGCC 57.153 40.909 4.27 0.00 0.00 4.52
763 3751 7.234166 GGGCCTATAGAGTACTAATAACAACCA 59.766 40.741 0.84 0.00 32.04 3.67
764 3752 8.305317 GGCCTATAGAGTACTAATAACAACCAG 58.695 40.741 0.00 0.00 32.04 4.00
793 3821 1.961394 TCTCGATCTATTTGTCCGGGG 59.039 52.381 0.00 0.00 0.00 5.73
828 3897 4.084276 GGCTGAGAGAGAAACGAAAAGTTC 60.084 45.833 0.00 0.00 43.37 3.01
852 3921 4.201724 CCCTAGAATCGCTCAAGAAAAACG 60.202 45.833 0.00 0.00 0.00 3.60
853 3922 3.813529 AGAATCGCTCAAGAAAAACGG 57.186 42.857 0.00 0.00 0.00 4.44
994 4085 1.592223 GGGACTCGTGAGTTGGAGG 59.408 63.158 3.69 0.00 42.66 4.30
1013 4104 0.463474 GTGCAGATGGAAGAGGAGGC 60.463 60.000 0.00 0.00 0.00 4.70
1055 4146 1.150567 CGCAAGAGGAATCGAGCTGG 61.151 60.000 0.00 0.00 43.02 4.85
1194 4330 4.028852 TCTCGACAATCGTATCAAGGTG 57.971 45.455 0.00 0.00 41.35 4.00
1197 4333 5.124297 TCTCGACAATCGTATCAAGGTGTTA 59.876 40.000 0.00 0.00 41.35 2.41
1222 4418 0.962356 GCGGATGGGGAAGCATATGG 60.962 60.000 4.56 0.00 0.00 2.74
1249 4445 3.560902 TCAGTGATCTGAGTTCGACAC 57.439 47.619 0.00 0.00 44.58 3.67
1278 4477 4.514441 GCAGATCCAATTTCAGACGATGAT 59.486 41.667 0.00 0.00 37.89 2.45
1279 4478 5.560375 GCAGATCCAATTTCAGACGATGATG 60.560 44.000 0.00 0.00 37.89 3.07
1280 4479 5.756833 CAGATCCAATTTCAGACGATGATGA 59.243 40.000 0.00 0.00 37.89 2.92
1285 4484 6.204108 TCCAATTTCAGACGATGATGATGATG 59.796 38.462 0.00 0.00 37.89 3.07
1286 4485 6.371389 CAATTTCAGACGATGATGATGATGG 58.629 40.000 0.00 0.00 37.89 3.51
1287 4486 4.677673 TTCAGACGATGATGATGATGGT 57.322 40.909 0.00 0.00 37.89 3.55
1288 4487 3.986277 TCAGACGATGATGATGATGGTG 58.014 45.455 0.00 0.00 31.12 4.17
1290 4489 3.493503 CAGACGATGATGATGATGGTGTG 59.506 47.826 0.00 0.00 0.00 3.82
1291 4490 3.385755 AGACGATGATGATGATGGTGTGA 59.614 43.478 0.00 0.00 0.00 3.58
1293 4492 3.133542 ACGATGATGATGATGGTGTGAGT 59.866 43.478 0.00 0.00 0.00 3.41
1294 4493 3.739810 CGATGATGATGATGGTGTGAGTC 59.260 47.826 0.00 0.00 0.00 3.36
1295 4494 4.700700 GATGATGATGATGGTGTGAGTCA 58.299 43.478 0.00 0.00 0.00 3.41
1296 4495 4.556592 TGATGATGATGGTGTGAGTCAA 57.443 40.909 0.00 0.00 0.00 3.18
1297 4496 5.106876 TGATGATGATGGTGTGAGTCAAT 57.893 39.130 0.00 0.00 0.00 2.57
1299 4498 5.355910 TGATGATGATGGTGTGAGTCAATTG 59.644 40.000 0.00 0.00 0.00 2.32
1300 4499 3.441222 TGATGATGGTGTGAGTCAATTGC 59.559 43.478 0.00 0.00 0.00 3.56
1301 4500 2.861274 TGATGGTGTGAGTCAATTGCA 58.139 42.857 0.00 0.00 0.00 4.08
1303 4502 3.253921 TGATGGTGTGAGTCAATTGCAAG 59.746 43.478 4.94 0.00 0.00 4.01
1305 4504 3.286353 TGGTGTGAGTCAATTGCAAGAA 58.714 40.909 4.94 0.00 0.00 2.52
1307 4506 4.202040 TGGTGTGAGTCAATTGCAAGAAAG 60.202 41.667 4.94 0.00 0.00 2.62
1333 4580 1.656818 CCACCACATTTGCGGCTAGG 61.657 60.000 0.00 0.00 0.00 3.02
1341 4588 0.536233 TTTGCGGCTAGGTTTGCAGA 60.536 50.000 0.00 0.00 38.75 4.26
1368 4615 1.801771 CCAACTCGTTAATCCGTTGCA 59.198 47.619 0.00 0.00 36.36 4.08
1382 4629 2.542824 CCGTTGCAGAAAACACCGAATT 60.543 45.455 0.00 0.00 0.00 2.17
1383 4630 3.112580 CGTTGCAGAAAACACCGAATTT 58.887 40.909 0.00 0.00 0.00 1.82
1385 4632 4.032331 CGTTGCAGAAAACACCGAATTTTT 59.968 37.500 0.00 0.00 29.44 1.94
1438 4685 4.039124 GGATGATTTGGCCCGTTTAATCAT 59.961 41.667 18.81 18.81 45.47 2.45
1469 4716 0.918983 TGGGGCCAGATTGTAAGGAG 59.081 55.000 4.39 0.00 0.00 3.69
1477 4724 4.154918 GCCAGATTGTAAGGAGTTGACTTG 59.845 45.833 0.00 0.00 0.00 3.16
1533 4928 2.676748 ACAAAAGCAATCAACCCCTCA 58.323 42.857 0.00 0.00 0.00 3.86
1534 4929 3.242011 ACAAAAGCAATCAACCCCTCAT 58.758 40.909 0.00 0.00 0.00 2.90
1535 4930 3.259123 ACAAAAGCAATCAACCCCTCATC 59.741 43.478 0.00 0.00 0.00 2.92
1536 4931 1.755179 AAGCAATCAACCCCTCATCG 58.245 50.000 0.00 0.00 0.00 3.84
1537 4932 0.107017 AGCAATCAACCCCTCATCGG 60.107 55.000 0.00 0.00 0.00 4.18
1540 4935 2.224606 CAATCAACCCCTCATCGGATG 58.775 52.381 11.79 11.79 33.16 3.51
1541 4936 1.806496 ATCAACCCCTCATCGGATGA 58.194 50.000 18.96 18.96 37.76 2.92
1551 4946 2.523245 TCATCGGATGAGGATCCTCTG 58.477 52.381 35.84 25.91 45.68 3.35
1552 4947 2.108952 TCATCGGATGAGGATCCTCTGA 59.891 50.000 35.84 27.46 46.68 3.27
1553 4948 1.988293 TCGGATGAGGATCCTCTGAC 58.012 55.000 35.84 26.12 45.68 3.51
1555 4950 1.698506 GGATGAGGATCCTCTGACGT 58.301 55.000 35.84 19.66 44.58 4.34
1556 4951 2.810767 CGGATGAGGATCCTCTGACGTA 60.811 54.545 35.84 19.46 45.68 3.57
1557 4952 2.554893 GGATGAGGATCCTCTGACGTAC 59.445 54.545 35.84 20.15 44.58 3.67
1558 4953 1.664873 TGAGGATCCTCTGACGTACG 58.335 55.000 35.84 15.01 43.12 3.67
1559 4954 0.945813 GAGGATCCTCTGACGTACGG 59.054 60.000 31.11 1.50 39.80 4.02
1560 4955 1.102222 AGGATCCTCTGACGTACGGC 61.102 60.000 21.06 18.72 0.00 5.68
1566 4961 3.193757 CTGACGTACGGCAGCCTA 58.806 61.111 36.08 8.17 45.01 3.93
1567 4962 1.226603 CTGACGTACGGCAGCCTAC 60.227 63.158 36.08 10.07 45.01 3.18
1574 4969 2.509336 CGGCAGCCTACCGTTCTG 60.509 66.667 10.54 0.00 45.70 3.02
1575 4970 2.663196 GGCAGCCTACCGTTCTGT 59.337 61.111 3.29 0.00 0.00 3.41
1576 4971 1.448013 GGCAGCCTACCGTTCTGTC 60.448 63.158 3.29 0.00 0.00 3.51
1577 4972 1.292223 GCAGCCTACCGTTCTGTCA 59.708 57.895 0.00 0.00 0.00 3.58
1579 4974 0.603569 CAGCCTACCGTTCTGTCACT 59.396 55.000 0.00 0.00 0.00 3.41
1580 4975 0.603569 AGCCTACCGTTCTGTCACTG 59.396 55.000 0.00 0.00 0.00 3.66
1581 4976 0.601558 GCCTACCGTTCTGTCACTGA 59.398 55.000 0.00 0.00 0.00 3.41
1582 4977 1.669211 GCCTACCGTTCTGTCACTGAC 60.669 57.143 1.86 1.86 0.00 3.51
1584 4979 2.231478 CCTACCGTTCTGTCACTGACAT 59.769 50.000 12.34 0.00 41.94 3.06
1585 4980 2.154854 ACCGTTCTGTCACTGACATG 57.845 50.000 12.34 7.20 41.94 3.21
1586 4981 1.412710 ACCGTTCTGTCACTGACATGT 59.587 47.619 12.34 0.00 41.94 3.21
1587 4982 1.794701 CCGTTCTGTCACTGACATGTG 59.205 52.381 12.34 1.75 41.94 3.21
1589 4984 2.146342 GTTCTGTCACTGACATGTGGG 58.854 52.381 12.34 1.04 41.94 4.61
1591 4986 0.957395 CTGTCACTGACATGTGGGCC 60.957 60.000 12.34 0.00 41.94 5.80
1592 4987 1.376466 GTCACTGACATGTGGGCCT 59.624 57.895 1.15 0.00 38.40 5.19
1593 4988 0.250901 GTCACTGACATGTGGGCCTT 60.251 55.000 1.15 0.00 38.40 4.35
1595 4990 1.133513 TCACTGACATGTGGGCCTTTT 60.134 47.619 1.15 0.00 38.40 2.27
1596 4991 1.000060 CACTGACATGTGGGCCTTTTG 60.000 52.381 1.15 1.57 34.56 2.44
1598 4993 0.831288 TGACATGTGGGCCTTTTGGG 60.831 55.000 1.15 0.00 40.82 4.12
1599 4994 0.541764 GACATGTGGGCCTTTTGGGA 60.542 55.000 1.15 0.00 40.82 4.37
1600 4995 0.105246 ACATGTGGGCCTTTTGGGAA 60.105 50.000 4.53 0.00 40.82 3.97
1601 4996 0.321346 CATGTGGGCCTTTTGGGAAC 59.679 55.000 4.53 0.00 40.82 3.62
1614 5009 2.440599 GGAACCTGGCCCACATGT 59.559 61.111 0.00 0.00 0.00 3.21
1615 5010 1.678970 GGAACCTGGCCCACATGTC 60.679 63.158 0.00 0.00 0.00 3.06
1616 5011 1.074775 GAACCTGGCCCACATGTCA 59.925 57.895 0.00 0.00 0.00 3.58
1618 5013 1.719063 AACCTGGCCCACATGTCAGT 61.719 55.000 0.00 0.00 0.00 3.41
1625 5020 4.498346 CACATGTCAGTGGCCCAA 57.502 55.556 0.00 0.00 35.88 4.12
1626 5021 1.959085 CACATGTCAGTGGCCCAAC 59.041 57.895 0.00 0.00 35.88 3.77
1627 5022 1.600636 ACATGTCAGTGGCCCAACG 60.601 57.895 0.00 0.00 0.00 4.10
1628 5023 2.034066 ATGTCAGTGGCCCAACGG 59.966 61.111 0.00 0.00 0.00 4.44
1690 5296 4.088762 CCACGCACACACCATCGC 62.089 66.667 0.00 0.00 0.00 4.58
1801 5573 3.785499 TCGTCGTCGTCTGAGCCG 61.785 66.667 1.33 0.00 38.33 5.52
1896 5668 2.674033 GTGGCAGCCATGAGTGCA 60.674 61.111 19.75 0.00 41.75 4.57
1901 5673 4.025858 AGCCATGAGTGCAGCCGT 62.026 61.111 0.00 0.00 0.00 5.68
2015 5787 2.202932 GCGTGCGTCATCTGGGAT 60.203 61.111 0.00 0.00 0.00 3.85
2018 5790 0.179100 CGTGCGTCATCTGGGATCTT 60.179 55.000 0.00 0.00 0.00 2.40
2214 5998 1.915078 CGCTTCCTTGTCCTCCCCAT 61.915 60.000 0.00 0.00 0.00 4.00
2548 6401 2.995258 GCAACGGATTAACGAGTTGGTA 59.005 45.455 15.80 0.00 42.80 3.25
2783 6823 1.148867 TCCCATTCCCACCAACACAAT 59.851 47.619 0.00 0.00 0.00 2.71
2792 6832 1.598601 CACCAACACAATGGCAAAAGC 59.401 47.619 0.00 0.00 44.75 3.51
2952 7007 4.007644 CGTGACTGGGAGGCTGCA 62.008 66.667 8.68 0.00 0.00 4.41
3256 7858 0.890996 AGGTGAAAGGCGGCTTCAAG 60.891 55.000 25.70 0.00 34.68 3.02
3423 8362 0.323725 TTGGGGATCTTCTTGCCTGC 60.324 55.000 0.00 0.00 0.00 4.85
3471 8410 7.987750 TTATTAATTAATGCGGTGGCTGATA 57.012 32.000 18.98 0.00 40.82 2.15
3472 8411 8.574251 TTATTAATTAATGCGGTGGCTGATAT 57.426 30.769 18.98 0.00 40.82 1.63
3473 8412 9.674068 TTATTAATTAATGCGGTGGCTGATATA 57.326 29.630 18.98 0.00 40.82 0.86
3474 8413 5.880054 AATTAATGCGGTGGCTGATATAC 57.120 39.130 0.00 0.00 40.82 1.47
3541 8480 1.201921 CCATCTCGCGCTGTTTTGTAC 60.202 52.381 5.56 0.00 0.00 2.90
3597 8536 0.106708 AAAGGCAGCGTCAAGTCTCA 59.893 50.000 0.00 0.00 0.00 3.27
3922 8861 1.480137 AGAAGACCTGCGGATTCAGAG 59.520 52.381 0.00 0.00 36.19 3.35
3959 8898 4.095782 TGTCAAGGCAAGTTGTTTCTGTAC 59.904 41.667 4.48 0.00 0.00 2.90
4063 9002 3.019564 AGCCCAAGAATGCAACATAGAC 58.980 45.455 0.00 0.00 0.00 2.59
4125 9331 0.818040 GTTGCTTGGTCCCGTCTTGT 60.818 55.000 0.00 0.00 0.00 3.16
4224 9430 3.205784 GCTGAATGGAGAGCCTTACAT 57.794 47.619 0.00 0.00 34.31 2.29
4274 9480 9.629878 TTGGTATTAGTTTGTTGAAGTTCCTAA 57.370 29.630 0.00 0.40 0.00 2.69
4491 10033 6.988580 TGATTAATCTGCTATGGTCTGTTCTG 59.011 38.462 16.24 0.00 0.00 3.02
4686 10311 4.363991 AGCAAGTGAATCTTCTTCAGGT 57.636 40.909 0.00 0.00 33.63 4.00
4687 10312 4.070716 AGCAAGTGAATCTTCTTCAGGTG 58.929 43.478 0.00 0.00 33.63 4.00
4688 10313 3.365767 GCAAGTGAATCTTCTTCAGGTGC 60.366 47.826 6.90 6.90 34.43 5.01
4689 10314 3.777106 AGTGAATCTTCTTCAGGTGCA 57.223 42.857 0.00 0.00 0.00 4.57
4770 10395 9.988815 AGTTATCTGTAAACTGAAGCCATATAG 57.011 33.333 0.00 0.00 35.87 1.31
4771 10396 9.209175 GTTATCTGTAAACTGAAGCCATATAGG 57.791 37.037 0.00 0.00 41.84 2.57
4772 10397 6.174720 TCTGTAAACTGAAGCCATATAGGG 57.825 41.667 0.00 0.00 38.09 3.53
4783 10408 1.949525 CCATATAGGGCACACAACTGC 59.050 52.381 0.00 0.00 36.33 4.40
4784 10409 2.421952 CCATATAGGGCACACAACTGCT 60.422 50.000 0.00 0.00 37.33 4.24
4786 10411 2.403252 ATAGGGCACACAACTGCTAC 57.597 50.000 0.00 0.00 37.33 3.58
4788 10413 0.250467 AGGGCACACAACTGCTACAG 60.250 55.000 0.00 0.00 37.33 2.74
4791 10416 2.489971 GGCACACAACTGCTACAGTAA 58.510 47.619 0.00 0.00 44.62 2.24
4794 10419 4.092968 GGCACACAACTGCTACAGTAATAC 59.907 45.833 0.00 0.00 44.62 1.89
4795 10420 4.688879 GCACACAACTGCTACAGTAATACA 59.311 41.667 0.00 0.00 44.62 2.29
4799 10424 5.120208 CACAACTGCTACAGTAATACACACC 59.880 44.000 0.00 0.00 44.62 4.16
4803 10428 5.897824 ACTGCTACAGTAATACACACCCTAT 59.102 40.000 0.00 0.00 43.46 2.57
4805 10430 7.093024 ACTGCTACAGTAATACACACCCTATTT 60.093 37.037 0.00 0.00 43.46 1.40
4806 10431 8.308851 TGCTACAGTAATACACACCCTATTTA 57.691 34.615 0.00 0.00 0.00 1.40
4807 10432 8.760735 TGCTACAGTAATACACACCCTATTTAA 58.239 33.333 0.00 0.00 0.00 1.52
4808 10433 9.774413 GCTACAGTAATACACACCCTATTTAAT 57.226 33.333 0.00 0.00 0.00 1.40
4811 10436 9.832445 ACAGTAATACACACCCTATTTAATCAG 57.168 33.333 0.00 0.00 0.00 2.90
4814 10439 9.826574 GTAATACACACCCTATTTAATCAGACA 57.173 33.333 0.00 0.00 0.00 3.41
4816 10441 8.964476 ATACACACCCTATTTAATCAGACAAG 57.036 34.615 0.00 0.00 0.00 3.16
4817 10442 7.016153 ACACACCCTATTTAATCAGACAAGA 57.984 36.000 0.00 0.00 0.00 3.02
4818 10443 7.458397 ACACACCCTATTTAATCAGACAAGAA 58.542 34.615 0.00 0.00 0.00 2.52
4820 10445 8.454106 CACACCCTATTTAATCAGACAAGAAAG 58.546 37.037 0.00 0.00 0.00 2.62
4821 10446 7.121315 ACACCCTATTTAATCAGACAAGAAAGC 59.879 37.037 0.00 0.00 0.00 3.51
4822 10447 7.121168 CACCCTATTTAATCAGACAAGAAAGCA 59.879 37.037 0.00 0.00 0.00 3.91
4823 10448 7.337942 ACCCTATTTAATCAGACAAGAAAGCAG 59.662 37.037 0.00 0.00 0.00 4.24
4824 10449 7.201767 CCCTATTTAATCAGACAAGAAAGCAGG 60.202 40.741 0.00 0.00 0.00 4.85
4826 10451 9.383519 CTATTTAATCAGACAAGAAAGCAGGTA 57.616 33.333 0.00 0.00 0.00 3.08
4828 10453 5.948992 AATCAGACAAGAAAGCAGGTAAC 57.051 39.130 0.00 0.00 0.00 2.50
4829 10454 4.415881 TCAGACAAGAAAGCAGGTAACA 57.584 40.909 0.00 0.00 41.41 2.41
4830 10455 4.380531 TCAGACAAGAAAGCAGGTAACAG 58.619 43.478 0.00 0.00 41.41 3.16
4843 10468 4.827692 CAGGTAACAGCAGGTGTGTATTA 58.172 43.478 5.89 0.00 40.26 0.98
4844 10469 4.630069 CAGGTAACAGCAGGTGTGTATTAC 59.370 45.833 5.89 4.98 40.26 1.89
4848 10473 4.826274 ACAGCAGGTGTGTATTACTGAT 57.174 40.909 3.92 0.00 38.28 2.90
4849 10474 5.165961 ACAGCAGGTGTGTATTACTGATT 57.834 39.130 3.92 0.00 38.28 2.57
4850 10475 5.560724 ACAGCAGGTGTGTATTACTGATTT 58.439 37.500 3.92 0.00 38.28 2.17
4854 10479 8.124823 CAGCAGGTGTGTATTACTGATTTTATG 58.875 37.037 0.00 0.00 32.86 1.90
4929 11132 5.154932 CAGTCAGTAGTCTGGTTTTACTCG 58.845 45.833 0.00 0.00 41.59 4.18
4986 11221 3.309848 CCCCTTATTTGTTCCCATCAGGT 60.310 47.826 0.00 0.00 36.75 4.00
5000 11235 4.818546 CCCATCAGGTGATTGTCTGATTAC 59.181 45.833 3.40 0.00 45.32 1.89
5001 11236 5.430886 CCATCAGGTGATTGTCTGATTACA 58.569 41.667 3.40 0.00 45.32 2.41
5003 11238 6.017357 CCATCAGGTGATTGTCTGATTACATG 60.017 42.308 3.40 0.00 45.32 3.21
5009 11244 3.326836 TTGTCTGATTACATGGCGTCA 57.673 42.857 0.00 0.00 0.00 4.35
5010 11245 3.541996 TGTCTGATTACATGGCGTCAT 57.458 42.857 0.00 0.00 0.00 3.06
5125 11506 2.819019 TGCATTATGACCACAGGTGTTG 59.181 45.455 0.00 0.00 35.25 3.33
5164 11545 6.438741 TGGTTGGATAATGATGCCAGTTTAAA 59.561 34.615 0.00 0.00 32.47 1.52
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
2 3 1.126948 TCCTCCAGATGGTGCACACA 61.127 55.000 20.43 14.54 36.34 3.72
63 64 3.103911 CAACGGTGAGCGGTCGTC 61.104 66.667 9.43 5.63 36.01 4.20
66 67 1.433837 AACAACAACGGTGAGCGGTC 61.434 55.000 7.88 7.89 0.00 4.79
78 79 1.202313 GCACCCGCACTAAAACAACAA 60.202 47.619 0.00 0.00 38.36 2.83
169 418 4.415332 GGAGTCGTCGGCAAGCGA 62.415 66.667 0.00 0.00 34.54 4.93
187 436 0.036164 ACCGCTCCATTGCAACACTA 59.964 50.000 0.00 0.00 0.00 2.74
205 454 4.908877 GAGCCGCCGACGAGCTAC 62.909 72.222 7.04 0.00 43.03 3.58
246 495 1.880340 CATCTCCGAGAGCCGTTGC 60.880 63.158 4.07 0.00 36.31 4.17
249 498 3.893763 CGCATCTCCGAGAGCCGT 61.894 66.667 4.07 0.00 36.31 5.68
250 499 2.913765 ATCGCATCTCCGAGAGCCG 61.914 63.158 4.07 8.85 40.97 5.52
277 526 0.877649 AGCGCTCCATTGCAGTATCG 60.878 55.000 2.64 0.00 0.00 2.92
349 599 1.634757 CGGCAAGCGCTACATCACAA 61.635 55.000 12.05 0.00 38.60 3.33
352 602 0.387565 TATCGGCAAGCGCTACATCA 59.612 50.000 12.05 0.00 38.60 3.07
409 659 5.859205 TGATCTCATCTAGCAGTAGCAAA 57.141 39.130 0.00 0.00 45.49 3.68
424 674 1.304282 GCCCCCTGCTTTGATCTCA 59.696 57.895 0.00 0.00 36.87 3.27
449 699 1.788308 TCGTTCTTTTTCGAATCGCGT 59.212 42.857 5.77 0.00 41.80 6.01
461 711 1.079875 ACGCACACACGTCGTTCTTT 61.080 50.000 0.00 0.00 44.43 2.52
471 721 1.790755 TGGATAGTCAACGCACACAC 58.209 50.000 0.00 0.00 0.00 3.82
597 850 6.183360 ACACAAGGATGACAAATTTAGTTGCA 60.183 34.615 0.00 0.00 31.29 4.08
598 851 6.215845 ACACAAGGATGACAAATTTAGTTGC 58.784 36.000 0.00 0.00 31.29 4.17
607 860 7.581213 AATTTAGTGACACAAGGATGACAAA 57.419 32.000 8.59 0.00 0.00 2.83
618 871 5.781210 TCAATGGCAAATTTAGTGACACA 57.219 34.783 8.59 0.00 36.66 3.72
620 873 7.271511 AGTTTTCAATGGCAAATTTAGTGACA 58.728 30.769 0.00 0.00 38.70 3.58
651 941 7.695480 TGATAAATTCCGAACTTTTGATGGA 57.305 32.000 0.00 0.00 0.00 3.41
763 3751 7.278868 GGACAAATAGATCGAGAATGACAAACT 59.721 37.037 0.00 0.00 0.00 2.66
764 3752 7.402640 GGACAAATAGATCGAGAATGACAAAC 58.597 38.462 0.00 0.00 0.00 2.93
767 3755 5.281727 CGGACAAATAGATCGAGAATGACA 58.718 41.667 0.00 0.00 0.00 3.58
768 3756 4.681942 CCGGACAAATAGATCGAGAATGAC 59.318 45.833 0.00 0.00 0.00 3.06
769 3757 4.262036 CCCGGACAAATAGATCGAGAATGA 60.262 45.833 0.73 0.00 0.00 2.57
828 3897 3.543680 TTTCTTGAGCGATTCTAGGGG 57.456 47.619 0.00 0.00 30.73 4.79
852 3921 3.190744 GGTTTTCACGAAAGAGGGATTCC 59.809 47.826 0.00 0.00 0.00 3.01
853 3922 3.190744 GGGTTTTCACGAAAGAGGGATTC 59.809 47.826 0.00 0.00 0.00 2.52
973 4056 1.213013 CCAACTCACGAGTCCCGAG 59.787 63.158 0.00 2.61 41.58 4.63
977 4068 0.038159 CACCTCCAACTCACGAGTCC 60.038 60.000 0.00 0.00 41.58 3.85
994 4085 0.463474 GCCTCCTCTTCCATCTGCAC 60.463 60.000 0.00 0.00 0.00 4.57
1029 4120 0.173708 GATTCCTCTTGCGACGAGGT 59.826 55.000 15.21 2.38 46.49 3.85
1131 4267 2.684927 GCCCAGACTACGGTAGGAGTTA 60.685 54.545 18.73 0.00 0.00 2.24
1194 4330 2.469516 CCCCATCCGCTTGCGTAAC 61.470 63.158 13.97 0.00 0.00 2.50
1197 4333 3.976701 CTTCCCCATCCGCTTGCGT 62.977 63.158 13.97 0.00 0.00 5.24
1249 4445 5.055812 GTCTGAAATTGGATCTGCTCCTAG 58.944 45.833 0.00 0.00 45.21 3.02
1272 4468 3.725490 ACTCACACCATCATCATCATCG 58.275 45.455 0.00 0.00 0.00 3.84
1278 4477 3.441222 GCAATTGACTCACACCATCATCA 59.559 43.478 10.34 0.00 0.00 3.07
1279 4478 3.441222 TGCAATTGACTCACACCATCATC 59.559 43.478 10.34 0.00 0.00 2.92
1280 4479 3.423749 TGCAATTGACTCACACCATCAT 58.576 40.909 10.34 0.00 0.00 2.45
1285 4484 3.988379 TTCTTGCAATTGACTCACACC 57.012 42.857 10.34 0.00 0.00 4.16
1286 4485 5.173774 TCTTTCTTGCAATTGACTCACAC 57.826 39.130 10.34 0.00 0.00 3.82
1287 4486 5.589855 TCTTCTTTCTTGCAATTGACTCACA 59.410 36.000 10.34 0.00 0.00 3.58
1288 4487 6.064846 TCTTCTTTCTTGCAATTGACTCAC 57.935 37.500 10.34 0.00 0.00 3.51
1290 4489 6.419116 GGTTTCTTCTTTCTTGCAATTGACTC 59.581 38.462 10.34 0.00 0.00 3.36
1291 4490 6.127366 TGGTTTCTTCTTTCTTGCAATTGACT 60.127 34.615 10.34 0.00 0.00 3.41
1293 4492 6.042143 GTGGTTTCTTCTTTCTTGCAATTGA 58.958 36.000 10.34 0.00 0.00 2.57
1294 4493 5.234972 GGTGGTTTCTTCTTTCTTGCAATTG 59.765 40.000 0.00 0.00 0.00 2.32
1295 4494 5.104982 TGGTGGTTTCTTCTTTCTTGCAATT 60.105 36.000 0.00 0.00 0.00 2.32
1296 4495 4.405358 TGGTGGTTTCTTCTTTCTTGCAAT 59.595 37.500 0.00 0.00 0.00 3.56
1297 4496 3.766591 TGGTGGTTTCTTCTTTCTTGCAA 59.233 39.130 0.00 0.00 0.00 4.08
1299 4498 3.130340 TGTGGTGGTTTCTTCTTTCTTGC 59.870 43.478 0.00 0.00 0.00 4.01
1300 4499 4.981806 TGTGGTGGTTTCTTCTTTCTTG 57.018 40.909 0.00 0.00 0.00 3.02
1301 4500 6.340522 CAAATGTGGTGGTTTCTTCTTTCTT 58.659 36.000 0.00 0.00 0.00 2.52
1303 4502 4.507756 GCAAATGTGGTGGTTTCTTCTTTC 59.492 41.667 0.00 0.00 0.00 2.62
1305 4504 3.490761 CGCAAATGTGGTGGTTTCTTCTT 60.491 43.478 0.00 0.00 0.00 2.52
1307 4506 2.393764 CGCAAATGTGGTGGTTTCTTC 58.606 47.619 0.00 0.00 0.00 2.87
1333 4580 3.186909 GAGTTGGTGGTTTTCTGCAAAC 58.813 45.455 0.00 0.00 43.78 2.93
1341 4588 3.251487 CGGATTAACGAGTTGGTGGTTTT 59.749 43.478 0.00 0.00 35.47 2.43
1438 4685 2.175931 TCTGGCCCCACTTGTAAGAAAA 59.824 45.455 0.00 0.00 0.00 2.29
1537 4932 2.224549 CGTACGTCAGAGGATCCTCATC 59.775 54.545 37.28 25.61 44.99 2.92
1540 4935 0.945813 CCGTACGTCAGAGGATCCTC 59.054 60.000 31.27 31.27 43.03 3.71
1541 4936 1.102222 GCCGTACGTCAGAGGATCCT 61.102 60.000 16.13 16.13 33.66 3.24
1542 4937 1.359475 GCCGTACGTCAGAGGATCC 59.641 63.158 15.21 2.48 33.66 3.36
1543 4938 0.029567 CTGCCGTACGTCAGAGGATC 59.970 60.000 21.01 0.00 32.26 3.36
1544 4939 2.005960 GCTGCCGTACGTCAGAGGAT 62.006 60.000 28.71 0.00 32.26 3.24
1545 4940 2.697761 GCTGCCGTACGTCAGAGGA 61.698 63.158 28.71 6.50 32.26 3.71
1546 4941 2.202623 GCTGCCGTACGTCAGAGG 60.203 66.667 28.71 5.06 32.26 3.69
1548 4943 1.377594 TAGGCTGCCGTACGTCAGA 60.378 57.895 28.71 6.29 32.26 3.27
1551 4946 2.103736 GGTAGGCTGCCGTACGTC 59.896 66.667 15.21 0.71 34.08 4.34
1552 4947 3.818787 CGGTAGGCTGCCGTACGT 61.819 66.667 32.20 0.00 43.84 3.57
1558 4953 1.448013 GACAGAACGGTAGGCTGCC 60.448 63.158 11.65 11.65 33.03 4.85
1559 4954 1.014564 GTGACAGAACGGTAGGCTGC 61.015 60.000 0.00 0.00 33.03 5.25
1560 4955 0.603569 AGTGACAGAACGGTAGGCTG 59.396 55.000 0.00 0.00 35.81 4.85
1563 4958 1.611977 TGTCAGTGACAGAACGGTAGG 59.388 52.381 22.06 0.00 37.67 3.18
1564 4959 3.245797 CATGTCAGTGACAGAACGGTAG 58.754 50.000 28.54 9.07 46.04 3.18
1565 4960 2.626266 ACATGTCAGTGACAGAACGGTA 59.374 45.455 28.54 5.17 46.04 4.02
1566 4961 1.412710 ACATGTCAGTGACAGAACGGT 59.587 47.619 28.54 18.14 46.04 4.83
1567 4962 1.794701 CACATGTCAGTGACAGAACGG 59.205 52.381 28.54 17.59 46.04 4.44
1569 4964 2.146342 CCCACATGTCAGTGACAGAAC 58.854 52.381 28.54 1.97 46.04 3.01
1572 4967 0.957395 GGCCCACATGTCAGTGACAG 60.957 60.000 28.54 21.75 46.04 3.51
1573 4968 1.073025 GGCCCACATGTCAGTGACA 59.927 57.895 27.35 27.35 46.90 3.58
1574 4969 0.250901 AAGGCCCACATGTCAGTGAC 60.251 55.000 16.68 16.68 42.05 3.67
1575 4970 0.478072 AAAGGCCCACATGTCAGTGA 59.522 50.000 0.00 0.00 42.05 3.41
1576 4971 1.000060 CAAAAGGCCCACATGTCAGTG 60.000 52.381 0.00 0.00 39.21 3.66
1577 4972 1.331214 CAAAAGGCCCACATGTCAGT 58.669 50.000 0.00 0.00 0.00 3.41
1579 4974 0.831288 CCCAAAAGGCCCACATGTCA 60.831 55.000 0.00 0.00 0.00 3.58
1580 4975 0.541764 TCCCAAAAGGCCCACATGTC 60.542 55.000 0.00 0.00 34.51 3.06
1581 4976 0.105246 TTCCCAAAAGGCCCACATGT 60.105 50.000 0.00 0.00 34.51 3.21
1582 4977 0.321346 GTTCCCAAAAGGCCCACATG 59.679 55.000 0.00 0.00 34.51 3.21
1584 4979 1.458588 GGTTCCCAAAAGGCCCACA 60.459 57.895 0.00 0.00 34.51 4.17
1585 4980 1.152333 AGGTTCCCAAAAGGCCCAC 60.152 57.895 0.00 0.00 34.51 4.61
1586 4981 1.152355 CAGGTTCCCAAAAGGCCCA 60.152 57.895 0.00 0.00 34.51 5.36
1587 4982 1.913262 CCAGGTTCCCAAAAGGCCC 60.913 63.158 0.00 0.00 34.51 5.80
1589 4984 2.583441 GGCCAGGTTCCCAAAAGGC 61.583 63.158 0.00 0.00 41.29 4.35
1591 4986 3.791640 GGGCCAGGTTCCCAAAAG 58.208 61.111 4.39 0.00 43.37 2.27
1596 4991 2.362889 CATGTGGGCCAGGTTCCC 60.363 66.667 6.40 0.00 44.17 3.97
1598 4993 0.962356 CTGACATGTGGGCCAGGTTC 60.962 60.000 6.40 1.46 38.40 3.62
1599 4994 1.075482 CTGACATGTGGGCCAGGTT 59.925 57.895 6.40 0.00 38.40 3.50
1600 4995 2.156098 ACTGACATGTGGGCCAGGT 61.156 57.895 6.40 5.66 41.63 4.00
1601 4996 1.676635 CACTGACATGTGGGCCAGG 60.677 63.158 6.40 1.59 34.56 4.45
1608 5003 1.855213 CGTTGGGCCACTGACATGTG 61.855 60.000 5.23 0.00 37.66 3.21
1610 5005 2.334946 CCGTTGGGCCACTGACATG 61.335 63.158 5.23 0.00 0.00 3.21
1623 5018 4.424430 GTGCGCTACGTGCCGTTG 62.424 66.667 9.73 5.36 41.54 4.10
1632 5027 4.129737 TCCTCTGCCGTGCGCTAC 62.130 66.667 9.73 4.27 38.78 3.58
1633 5028 3.826754 CTCCTCTGCCGTGCGCTA 61.827 66.667 9.73 0.00 38.78 4.26
1638 5033 4.803426 GGACGCTCCTCTGCCGTG 62.803 72.222 0.00 0.00 32.53 4.94
1690 5296 1.100510 TCGACAGTAGGGATTGTCCG 58.899 55.000 0.00 0.00 38.71 4.79
1801 5573 2.591715 ACCGTGTGCTCTGCCAAC 60.592 61.111 0.00 0.00 0.00 3.77
2040 5812 0.905357 CCGTGGACAAGGAAGAGGAT 59.095 55.000 0.00 0.00 31.21 3.24
2203 5987 3.627332 TACGGCCATGGGGAGGACA 62.627 63.158 15.13 0.00 31.91 4.02
2312 6099 4.444024 CGCCGTGTTGTGCCATCG 62.444 66.667 0.00 0.00 0.00 3.84
2548 6401 1.880027 CGGCTAGGTTTGCAGAAAACT 59.120 47.619 3.88 0.00 46.27 2.66
2673 6526 1.306997 GGTGATCCTCTGGACCCCA 60.307 63.158 0.00 0.00 32.98 4.96
2783 6823 1.957177 TGTTTATGGACGCTTTTGCCA 59.043 42.857 0.00 0.00 43.93 4.92
2792 6832 5.411361 TCAAGGACTTCATTGTTTATGGACG 59.589 40.000 3.74 0.00 38.61 4.79
2952 7007 2.890474 CCGCTGCGTCGGCTAAAT 60.890 61.111 21.59 0.00 43.18 1.40
3256 7858 3.078837 ACCATACACGGACAATGGAAAC 58.921 45.455 13.26 0.00 42.36 2.78
3523 8462 0.713883 CGTACAAAACAGCGCGAGAT 59.286 50.000 12.10 0.00 0.00 2.75
3541 8480 7.091443 GGACCTCATAATTAACATAGTCCTCG 58.909 42.308 13.60 0.00 38.55 4.63
3597 8536 1.296715 GTGATCAACGGCCTGTCCT 59.703 57.895 0.00 0.00 0.00 3.85
3922 8861 4.141482 TGCCTTGACAGATAAAGGTATCCC 60.141 45.833 3.58 0.00 44.13 3.85
4125 9331 2.358957 CAAGCATCTCCATGTCCGAAA 58.641 47.619 0.00 0.00 31.86 3.46
4220 9426 8.717821 CAGTTCTTAAAAGATTCGTTCCATGTA 58.282 33.333 0.00 0.00 34.49 2.29
4224 9430 5.763204 AGCAGTTCTTAAAAGATTCGTTCCA 59.237 36.000 0.00 0.00 34.49 3.53
4274 9480 8.462811 CACGATGCAGAAATACTACTATAGGAT 58.537 37.037 4.43 0.00 0.00 3.24
4491 10033 9.931210 GCAACCACAAGTATAGTAATTAATCAC 57.069 33.333 0.00 0.00 0.00 3.06
4662 10287 4.142945 CCTGAAGAAGATTCACTTGCTTCG 60.143 45.833 0.00 0.00 42.07 3.79
4686 10311 0.038983 GCAAGTGTGTCATGCATGCA 60.039 50.000 25.04 25.04 40.05 3.96
4687 10312 0.242825 AGCAAGTGTGTCATGCATGC 59.757 50.000 22.25 11.82 42.35 4.06
4688 10313 2.717580 AAGCAAGTGTGTCATGCATG 57.282 45.000 21.07 21.07 42.35 4.06
4689 10314 5.165676 CAAATAAGCAAGTGTGTCATGCAT 58.834 37.500 0.00 0.00 42.35 3.96
4770 10395 0.535102 ACTGTAGCAGTTGTGTGCCC 60.535 55.000 0.00 0.00 42.59 5.36
4771 10396 2.163818 TACTGTAGCAGTTGTGTGCC 57.836 50.000 7.11 0.00 42.59 5.01
4772 10397 4.688879 TGTATTACTGTAGCAGTTGTGTGC 59.311 41.667 7.11 0.00 42.59 4.57
4773 10398 5.694458 TGTGTATTACTGTAGCAGTTGTGTG 59.306 40.000 7.11 0.00 42.59 3.82
4778 10403 4.530946 AGGGTGTGTATTACTGTAGCAGTT 59.469 41.667 7.11 0.00 42.59 3.16
4780 10405 4.737855 AGGGTGTGTATTACTGTAGCAG 57.262 45.455 0.00 0.00 37.52 4.24
4788 10413 9.826574 TGTCTGATTAAATAGGGTGTGTATTAC 57.173 33.333 0.00 0.00 0.00 1.89
4791 10416 8.768397 TCTTGTCTGATTAAATAGGGTGTGTAT 58.232 33.333 0.00 0.00 0.00 2.29
4794 10419 7.921786 TTCTTGTCTGATTAAATAGGGTGTG 57.078 36.000 0.00 0.00 0.00 3.82
4795 10420 7.121315 GCTTTCTTGTCTGATTAAATAGGGTGT 59.879 37.037 0.00 0.00 0.00 4.16
4799 10424 7.337942 ACCTGCTTTCTTGTCTGATTAAATAGG 59.662 37.037 0.00 0.00 0.00 2.57
4803 10428 7.500892 TGTTACCTGCTTTCTTGTCTGATTAAA 59.499 33.333 0.00 0.00 0.00 1.52
4805 10430 6.530120 TGTTACCTGCTTTCTTGTCTGATTA 58.470 36.000 0.00 0.00 0.00 1.75
4806 10431 5.376625 TGTTACCTGCTTTCTTGTCTGATT 58.623 37.500 0.00 0.00 0.00 2.57
4807 10432 4.973168 TGTTACCTGCTTTCTTGTCTGAT 58.027 39.130 0.00 0.00 0.00 2.90
4808 10433 4.380531 CTGTTACCTGCTTTCTTGTCTGA 58.619 43.478 0.00 0.00 0.00 3.27
4809 10434 3.058639 GCTGTTACCTGCTTTCTTGTCTG 60.059 47.826 0.00 0.00 33.16 3.51
4811 10436 2.878406 TGCTGTTACCTGCTTTCTTGTC 59.122 45.455 0.00 0.00 36.57 3.18
4812 10437 2.880890 CTGCTGTTACCTGCTTTCTTGT 59.119 45.455 0.00 0.00 36.57 3.16
4813 10438 2.227388 CCTGCTGTTACCTGCTTTCTTG 59.773 50.000 0.00 0.00 36.57 3.02
4814 10439 2.158608 ACCTGCTGTTACCTGCTTTCTT 60.159 45.455 0.00 0.00 36.57 2.52
4815 10440 1.421646 ACCTGCTGTTACCTGCTTTCT 59.578 47.619 0.00 0.00 36.57 2.52
4816 10441 1.537202 CACCTGCTGTTACCTGCTTTC 59.463 52.381 0.00 0.00 36.57 2.62
4817 10442 1.133792 ACACCTGCTGTTACCTGCTTT 60.134 47.619 0.00 0.00 36.57 3.51
4818 10443 0.474184 ACACCTGCTGTTACCTGCTT 59.526 50.000 0.00 0.00 36.57 3.91
4820 10445 0.535102 ACACACCTGCTGTTACCTGC 60.535 55.000 0.00 0.00 36.19 4.85
4821 10446 2.831685 TACACACCTGCTGTTACCTG 57.168 50.000 0.00 0.00 0.00 4.00
4822 10447 4.530946 AGTAATACACACCTGCTGTTACCT 59.469 41.667 0.00 0.00 0.00 3.08
4823 10448 4.630069 CAGTAATACACACCTGCTGTTACC 59.370 45.833 0.00 0.00 0.00 2.85
4824 10449 5.475719 TCAGTAATACACACCTGCTGTTAC 58.524 41.667 0.00 0.00 0.00 2.50
4826 10451 4.617253 TCAGTAATACACACCTGCTGTT 57.383 40.909 0.00 0.00 0.00 3.16
4828 10453 6.500684 AAAATCAGTAATACACACCTGCTG 57.499 37.500 0.00 0.00 0.00 4.41
4829 10454 7.283127 CCATAAAATCAGTAATACACACCTGCT 59.717 37.037 0.00 0.00 0.00 4.24
4830 10455 7.282224 TCCATAAAATCAGTAATACACACCTGC 59.718 37.037 0.00 0.00 0.00 4.85
4834 10459 9.988350 CAAGTCCATAAAATCAGTAATACACAC 57.012 33.333 0.00 0.00 0.00 3.82
4843 10468 9.959721 AGTACAATACAAGTCCATAAAATCAGT 57.040 29.630 0.00 0.00 0.00 3.41
4848 10473 9.158233 GTAGCAGTACAATACAAGTCCATAAAA 57.842 33.333 0.00 0.00 0.00 1.52
4849 10474 8.537016 AGTAGCAGTACAATACAAGTCCATAAA 58.463 33.333 0.00 0.00 0.00 1.40
4850 10475 8.074613 AGTAGCAGTACAATACAAGTCCATAA 57.925 34.615 0.00 0.00 0.00 1.90
4854 10479 6.096564 AGGTAGTAGCAGTACAATACAAGTCC 59.903 42.308 1.58 0.00 0.00 3.85
4929 11132 6.072452 CCTGAGGTAAATTCACTTGTTTCCTC 60.072 42.308 0.00 0.00 35.08 3.71
4986 11221 3.871006 GACGCCATGTAATCAGACAATCA 59.129 43.478 0.00 0.00 31.83 2.57
5001 11236 2.168521 ACTACTTACTGCATGACGCCAT 59.831 45.455 0.00 0.00 41.33 4.40
5003 11238 2.194271 GACTACTTACTGCATGACGCC 58.806 52.381 0.00 0.00 41.33 5.68
5009 11244 7.928307 AAATGACAATGACTACTTACTGCAT 57.072 32.000 0.00 0.00 0.00 3.96
5010 11245 7.744087 AAAATGACAATGACTACTTACTGCA 57.256 32.000 0.00 0.00 0.00 4.41
5114 11495 1.287815 CATGCAGCAACACCTGTGG 59.712 57.895 0.00 0.00 35.28 4.17
5125 11506 1.537348 CCAACCATACATGCATGCAGC 60.537 52.381 26.69 0.00 45.96 5.25
5164 11545 7.388224 TGCATGCAGATGTTATGTTTTGAAATT 59.612 29.630 18.46 0.00 31.50 1.82


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

AutoCloner maintained by Alex Coulton.