Multiple sequence alignment - TraesCS2D01G322300

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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 TraesCS2D01G322300 chr2D 100.000 5335 0 0 1 5335 413770726 413776060 0.000000e+00 9852.0
1 TraesCS2D01G322300 chr2D 90.297 1010 92 5 3331 4339 413690940 413691944 0.000000e+00 1317.0
2 TraesCS2D01G322300 chr2D 91.242 628 52 1 3707 4334 413724931 413725555 0.000000e+00 852.0
3 TraesCS2D01G322300 chr2D 81.105 344 56 4 2095 2432 109706739 109707079 3.170000e-67 267.0
4 TraesCS2D01G322300 chr2D 74.419 645 136 19 3704 4330 413290572 413291205 3.190000e-62 250.0
5 TraesCS2D01G322300 chr2D 87.302 189 24 0 1620 1808 185199207 185199395 3.240000e-52 217.0
6 TraesCS2D01G322300 chr2D 78.981 314 54 9 3314 3621 413724557 413724864 2.520000e-48 204.0
7 TraesCS2D01G322300 chr2A 92.343 1737 62 29 3082 4790 580848533 580850226 0.000000e+00 2405.0
8 TraesCS2D01G322300 chr2A 90.198 1010 93 3 3331 4339 580721122 580722126 0.000000e+00 1312.0
9 TraesCS2D01G322300 chr2A 86.423 1230 128 18 413 1613 580846986 580848205 0.000000e+00 1310.0
10 TraesCS2D01G322300 chr2A 85.967 848 95 16 3502 4334 580760273 580761111 0.000000e+00 885.0
11 TraesCS2D01G322300 chr2A 91.358 567 35 8 4776 5335 580850259 580850818 0.000000e+00 763.0
12 TraesCS2D01G322300 chr2A 78.605 631 116 13 3707 4329 580253389 580254008 2.990000e-107 399.0
13 TraesCS2D01G322300 chr2A 75.587 639 130 17 3704 4330 580324438 580325062 5.230000e-75 292.0
14 TraesCS2D01G322300 chr2A 82.919 322 29 16 2796 3096 580848198 580848514 3.170000e-67 267.0
15 TraesCS2D01G322300 chr2A 84.000 250 35 3 1 248 580846554 580846800 8.930000e-58 235.0
16 TraesCS2D01G322300 chr2A 90.226 133 13 0 277 409 580846801 580846933 1.980000e-39 174.0
17 TraesCS2D01G322300 chr2B 95.007 1382 47 12 3082 4459 486976198 486977561 0.000000e+00 2150.0
18 TraesCS2D01G322300 chr2B 89.552 1005 99 4 3331 4334 486952132 486953131 0.000000e+00 1269.0
19 TraesCS2D01G322300 chr2B 87.761 1103 104 16 410 1498 486974507 486975592 0.000000e+00 1260.0
20 TraesCS2D01G322300 chr2B 82.948 1038 144 22 3314 4334 486965660 486966681 0.000000e+00 905.0
21 TraesCS2D01G322300 chr2B 90.592 574 38 7 4776 5335 486983426 486983997 0.000000e+00 747.0
22 TraesCS2D01G322300 chr2B 84.185 411 60 3 2 410 486974052 486974459 1.390000e-105 394.0
23 TraesCS2D01G322300 chr2B 81.651 327 30 15 2796 3096 486975848 486976170 1.480000e-60 244.0
24 TraesCS2D01G322300 chr2B 88.953 172 8 4 4578 4749 486983014 486983174 9.060000e-48 202.0
25 TraesCS2D01G322300 chr2B 93.750 80 5 0 4485 4564 486977556 486977635 2.610000e-23 121.0
26 TraesCS2D01G322300 chr2B 93.103 58 4 0 1536 1593 486975793 486975850 9.520000e-13 86.1
27 TraesCS2D01G322300 chr2B 89.796 49 5 0 4740 4788 486983355 486983403 4.460000e-06 63.9
28 TraesCS2D01G322300 chr1D 95.922 1079 29 4 1737 2802 319430735 319431811 0.000000e+00 1735.0
29 TraesCS2D01G322300 chr1D 97.222 144 4 0 1621 1764 319430592 319430735 1.480000e-60 244.0
30 TraesCS2D01G322300 chr1D 88.770 187 21 0 1622 1808 477795099 477795285 4.160000e-56 230.0
31 TraesCS2D01G322300 chr1D 88.235 187 22 0 1622 1808 474229053 474229239 1.930000e-54 224.0
32 TraesCS2D01G322300 chr5A 90.013 751 70 5 2056 2802 568324539 568323790 0.000000e+00 966.0
33 TraesCS2D01G322300 chr5A 89.342 441 25 7 1622 2047 568325068 568324635 7.860000e-148 534.0
34 TraesCS2D01G322300 chr7B 88.652 749 81 4 2056 2802 717179894 717179148 0.000000e+00 909.0
35 TraesCS2D01G322300 chr7B 88.652 749 81 4 2056 2802 717254547 717253801 0.000000e+00 909.0
36 TraesCS2D01G322300 chr4D 86.174 311 40 3 2494 2802 119418551 119418242 3.080000e-87 333.0
37 TraesCS2D01G322300 chr4D 90.957 188 17 0 1621 1808 119418241 119418428 2.470000e-63 254.0
38 TraesCS2D01G322300 chr4D 87.701 187 23 0 1622 1808 193873000 193872814 9.000000e-53 219.0
39 TraesCS2D01G322300 chr7D 85.079 315 44 3 2494 2806 450264203 450264516 8.620000e-83 318.0
40 TraesCS2D01G322300 chr7D 90.909 187 17 0 1622 1808 450264512 450264326 8.870000e-63 252.0
41 TraesCS2D01G322300 chr7D 90.374 187 17 1 1622 1808 575812762 575812947 1.480000e-60 244.0
42 TraesCS2D01G322300 chr6D 89.958 239 24 0 2564 2802 404188279 404188517 5.190000e-80 309.0
43 TraesCS2D01G322300 chr6D 78.009 432 62 15 2095 2516 255525248 255524840 1.920000e-59 241.0
44 TraesCS2D01G322300 chr5D 74.664 892 130 51 1622 2435 362041406 362040533 1.870000e-79 307.0
45 TraesCS2D01G322300 chr5D 84.244 311 46 3 2494 2802 495075267 495074958 3.120000e-77 300.0
46 TraesCS2D01G322300 chr5D 83.923 311 44 4 2494 2802 383082915 383083221 5.230000e-75 292.0
47 TraesCS2D01G322300 chr5D 89.947 189 19 0 1620 1808 495074956 495075144 1.480000e-60 244.0
48 TraesCS2D01G322300 chr5D 93.878 49 3 0 1995 2043 3589437 3589485 2.060000e-09 75.0
49 TraesCS2D01G322300 chr3D 80.000 230 33 8 2102 2325 566074412 566074190 1.990000e-34 158.0
50 TraesCS2D01G322300 chr3B 79.386 228 27 11 2068 2289 754619236 754619023 5.570000e-30 143.0


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 TraesCS2D01G322300 chr2D 413770726 413776060 5334 False 9852.000000 9852 100.000000 1 5335 1 chr2D.!!$F5 5334
1 TraesCS2D01G322300 chr2D 413690940 413691944 1004 False 1317.000000 1317 90.297000 3331 4339 1 chr2D.!!$F4 1008
2 TraesCS2D01G322300 chr2D 413724557 413725555 998 False 528.000000 852 85.111500 3314 4334 2 chr2D.!!$F6 1020
3 TraesCS2D01G322300 chr2D 413290572 413291205 633 False 250.000000 250 74.419000 3704 4330 1 chr2D.!!$F3 626
4 TraesCS2D01G322300 chr2A 580721122 580722126 1004 False 1312.000000 1312 90.198000 3331 4339 1 chr2A.!!$F3 1008
5 TraesCS2D01G322300 chr2A 580760273 580761111 838 False 885.000000 885 85.967000 3502 4334 1 chr2A.!!$F4 832
6 TraesCS2D01G322300 chr2A 580846554 580850818 4264 False 859.000000 2405 87.878167 1 5335 6 chr2A.!!$F5 5334
7 TraesCS2D01G322300 chr2A 580253389 580254008 619 False 399.000000 399 78.605000 3707 4329 1 chr2A.!!$F1 622
8 TraesCS2D01G322300 chr2A 580324438 580325062 624 False 292.000000 292 75.587000 3704 4330 1 chr2A.!!$F2 626
9 TraesCS2D01G322300 chr2B 486952132 486953131 999 False 1269.000000 1269 89.552000 3331 4334 1 chr2B.!!$F1 1003
10 TraesCS2D01G322300 chr2B 486965660 486966681 1021 False 905.000000 905 82.948000 3314 4334 1 chr2B.!!$F2 1020
11 TraesCS2D01G322300 chr2B 486974052 486977635 3583 False 709.183333 2150 89.242833 2 4564 6 chr2B.!!$F3 4562
12 TraesCS2D01G322300 chr2B 486983014 486983997 983 False 337.633333 747 89.780333 4578 5335 3 chr2B.!!$F4 757
13 TraesCS2D01G322300 chr1D 319430592 319431811 1219 False 989.500000 1735 96.572000 1621 2802 2 chr1D.!!$F3 1181
14 TraesCS2D01G322300 chr5A 568323790 568325068 1278 True 750.000000 966 89.677500 1622 2802 2 chr5A.!!$R1 1180
15 TraesCS2D01G322300 chr7B 717179148 717179894 746 True 909.000000 909 88.652000 2056 2802 1 chr7B.!!$R1 746
16 TraesCS2D01G322300 chr7B 717253801 717254547 746 True 909.000000 909 88.652000 2056 2802 1 chr7B.!!$R2 746
17 TraesCS2D01G322300 chr5D 362040533 362041406 873 True 307.000000 307 74.664000 1622 2435 1 chr5D.!!$R1 813

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
207 209 0.103937 TGGCGCCTTTTTCCTGTTTG 59.896 50.000 29.70 0.0 0.00 2.93 F
208 210 0.104120 GGCGCCTTTTTCCTGTTTGT 59.896 50.000 22.15 0.0 0.00 2.83 F
801 869 0.179140 GCCAACCAACCGTGCATATG 60.179 55.000 0.00 0.0 0.00 1.78 F
1779 2049 0.331616 GGTTTATGACAGGTGGGGCT 59.668 55.000 0.00 0.0 0.00 5.19 F
2211 2623 2.852075 TCCAGGCGGAGGTGGTTT 60.852 61.111 0.00 0.0 35.91 3.27 F
3102 3589 2.590821 AGCTTCCTTCATTTGCTGTGT 58.409 42.857 0.00 0.0 32.32 3.72 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1016 1085 0.029300 GCACAAGAGCGCAAGAAACA 59.971 50.000 11.47 0.00 43.02 2.83 R
1366 1436 0.381445 TCATCGAATTTGCGCATGGG 59.619 50.000 12.75 5.19 0.00 4.00 R
2507 2925 0.967380 GAAACTCGACCGGGTCCCTA 60.967 60.000 21.06 6.48 0.00 3.53 R
2964 3390 0.909623 ACTCAGGGTTGGTAATCCGG 59.090 55.000 0.00 0.00 36.30 5.14 R
4139 4655 1.222936 GGTGTAGAGCTGCATGGCT 59.777 57.895 1.02 0.00 46.11 4.75 R
4354 4875 0.107214 TCGATGGGAATGGAGCCAAC 60.107 55.000 0.00 0.00 0.00 3.77 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
18 19 3.935371 AACATGTGGGTCCCAACAA 57.065 47.368 13.78 1.36 34.18 2.83
63 64 1.000843 ACCCTTTCTGAAATTTGGCGC 59.999 47.619 0.00 0.00 0.00 6.53
64 65 1.000731 CCCTTTCTGAAATTTGGCGCA 59.999 47.619 10.83 0.00 0.00 6.09
80 81 1.613437 GCGCATTGGGTGGCTTAATAT 59.387 47.619 0.30 0.00 0.00 1.28
105 107 1.299541 GTAGCATGACCCCAACATCG 58.700 55.000 0.00 0.00 0.00 3.84
108 110 0.676466 GCATGACCCCAACATCGTCA 60.676 55.000 0.00 0.00 40.58 4.35
115 117 2.021457 CCCCAACATCGTCAAATACCC 58.979 52.381 0.00 0.00 0.00 3.69
117 119 2.619332 CCCAACATCGTCAAATACCCCA 60.619 50.000 0.00 0.00 0.00 4.96
124 126 1.560611 CGTCAAATACCCCAACCCCTA 59.439 52.381 0.00 0.00 0.00 3.53
126 128 3.562182 GTCAAATACCCCAACCCCTATG 58.438 50.000 0.00 0.00 0.00 2.23
144 146 4.038763 CCTATGAATAGTGCGGTTGTCCTA 59.961 45.833 0.00 0.00 0.00 2.94
148 150 4.081365 TGAATAGTGCGGTTGTCCTATGAA 60.081 41.667 0.00 0.00 0.00 2.57
160 162 9.450807 CGGTTGTCCTATGAATCAAATAAAATC 57.549 33.333 0.00 0.00 0.00 2.17
191 193 6.481954 TCTTAGAGTCTTCGAAAAATTGGC 57.518 37.500 0.00 0.00 0.00 4.52
202 204 2.928801 AAAATTGGCGCCTTTTTCCT 57.071 40.000 29.70 10.15 0.00 3.36
203 205 2.168326 AAATTGGCGCCTTTTTCCTG 57.832 45.000 29.70 0.00 0.00 3.86
207 209 0.103937 TGGCGCCTTTTTCCTGTTTG 59.896 50.000 29.70 0.00 0.00 2.93
208 210 0.104120 GGCGCCTTTTTCCTGTTTGT 59.896 50.000 22.15 0.00 0.00 2.83
210 212 2.029380 GGCGCCTTTTTCCTGTTTGTAT 60.029 45.455 22.15 0.00 0.00 2.29
212 214 4.321378 GGCGCCTTTTTCCTGTTTGTATTA 60.321 41.667 22.15 0.00 0.00 0.98
213 215 4.857037 GCGCCTTTTTCCTGTTTGTATTAG 59.143 41.667 0.00 0.00 0.00 1.73
214 216 4.857037 CGCCTTTTTCCTGTTTGTATTAGC 59.143 41.667 0.00 0.00 0.00 3.09
215 217 5.335661 CGCCTTTTTCCTGTTTGTATTAGCT 60.336 40.000 0.00 0.00 0.00 3.32
216 218 6.128117 CGCCTTTTTCCTGTTTGTATTAGCTA 60.128 38.462 0.00 0.00 0.00 3.32
221 223 3.714798 TCCTGTTTGTATTAGCTAGGGGG 59.285 47.826 0.00 0.00 0.00 5.40
241 243 1.086696 CAACCATGCCCGTAGACAAG 58.913 55.000 0.00 0.00 0.00 3.16
244 246 1.206371 ACCATGCCCGTAGACAAGTAC 59.794 52.381 0.00 0.00 0.00 2.73
249 251 1.134560 GCCCGTAGACAAGTACTGAGG 59.865 57.143 0.00 0.00 0.00 3.86
253 255 2.458620 GTAGACAAGTACTGAGGGGCT 58.541 52.381 0.00 0.00 0.00 5.19
264 266 1.415659 CTGAGGGGCTAATGTCCTGAG 59.584 57.143 0.00 0.00 38.23 3.35
272 274 5.059833 GGGCTAATGTCCTGAGATAAACTG 58.940 45.833 0.00 0.00 34.49 3.16
288 290 8.888579 AGATAAACTGGATAAACGACATTAGG 57.111 34.615 0.00 0.00 0.00 2.69
322 324 4.691685 CCCATTGTCATCAACACCAAAATG 59.308 41.667 0.00 0.00 37.70 2.32
324 326 3.010624 TGTCATCAACACCAAAATGCG 57.989 42.857 0.00 0.00 31.20 4.73
359 361 9.705290 AACAACACACTTTCAAGTTAAAAATCT 57.295 25.926 0.00 0.00 37.08 2.40
360 362 9.139174 ACAACACACTTTCAAGTTAAAAATCTG 57.861 29.630 0.00 0.00 37.08 2.90
378 380 8.641499 AAAATCTGAAAATGTTTTTACTCGCA 57.359 26.923 0.00 0.00 0.00 5.10
410 412 9.520204 CAAATATGATTTATGACCCAACTTCAC 57.480 33.333 0.00 0.00 0.00 3.18
413 415 5.067273 TGATTTATGACCCAACTTCACGTT 58.933 37.500 0.00 0.00 35.88 3.99
414 416 5.180492 TGATTTATGACCCAACTTCACGTTC 59.820 40.000 0.00 0.00 32.27 3.95
459 510 9.818270 AAAGTTGTCATCCCATGATATATGAAT 57.182 29.630 0.00 0.00 42.04 2.57
466 517 6.839124 TCCCATGATATATGAATTTGGCAC 57.161 37.500 0.00 0.00 0.00 5.01
488 539 6.704050 GCACTGTATTGGTACCAAAATTGTTT 59.296 34.615 30.31 14.91 39.55 2.83
499 550 7.436970 GGTACCAAAATTGTTTAACAACCTGAG 59.563 37.037 13.01 5.26 41.40 3.35
506 557 3.623960 TGTTTAACAACCTGAGAACCACG 59.376 43.478 0.00 0.00 31.02 4.94
510 561 3.764237 ACAACCTGAGAACCACGTTAT 57.236 42.857 0.00 0.00 0.00 1.89
511 562 4.081322 ACAACCTGAGAACCACGTTATT 57.919 40.909 0.00 0.00 0.00 1.40
514 565 5.008316 ACAACCTGAGAACCACGTTATTTTC 59.992 40.000 0.00 0.00 0.00 2.29
519 570 6.872020 CCTGAGAACCACGTTATTTTCTCTAA 59.128 38.462 18.71 6.17 42.96 2.10
525 576 7.417496 ACCACGTTATTTTCTCTAACAAGTC 57.583 36.000 0.00 0.00 0.00 3.01
550 601 0.529378 AACCTAGCAAGTACCGACGG 59.471 55.000 13.61 13.61 0.00 4.79
621 672 9.480053 AAGATTTCACTGTGTAAAATCCAAATG 57.520 29.630 21.68 0.00 0.00 2.32
631 682 8.200792 TGTGTAAAATCCAAATGTAAAAGCAGT 58.799 29.630 0.00 0.00 0.00 4.40
700 753 9.912634 TCAAAATTGAAGGTTAATGTCATTCTC 57.087 29.630 0.07 0.00 33.55 2.87
799 867 1.974343 GGCCAACCAACCGTGCATA 60.974 57.895 0.00 0.00 35.26 3.14
801 869 0.179140 GCCAACCAACCGTGCATATG 60.179 55.000 0.00 0.00 0.00 1.78
805 873 3.553922 CCAACCAACCGTGCATATGTTTT 60.554 43.478 4.29 0.00 0.00 2.43
807 875 2.230266 ACCAACCGTGCATATGTTTTCC 59.770 45.455 4.29 0.00 0.00 3.13
825 893 1.202806 TCCACAGGTTCTTGAAGCCAG 60.203 52.381 8.68 5.32 0.00 4.85
836 904 4.569943 TCTTGAAGCCAGTAGTCATCAAC 58.430 43.478 0.00 0.00 0.00 3.18
843 911 3.548770 CCAGTAGTCATCAACCATGCAT 58.451 45.455 0.00 0.00 31.70 3.96
898 966 4.500545 CCTCACTTCCTCGATAATGAGTGG 60.501 50.000 11.86 0.00 33.28 4.00
924 993 2.303022 AGTGATATAACTGCCCATCCGG 59.697 50.000 0.00 0.00 0.00 5.14
926 995 2.708861 TGATATAACTGCCCATCCGGTT 59.291 45.455 0.00 0.00 37.94 4.44
927 996 3.904965 TGATATAACTGCCCATCCGGTTA 59.095 43.478 0.00 0.00 39.95 2.85
954 1023 1.461127 GTGTGATTCACTCGGTTCAGC 59.539 52.381 17.26 0.00 43.13 4.26
968 1037 1.022982 TTCAGCGCCTGCATCTTCTG 61.023 55.000 2.29 0.00 46.23 3.02
987 1056 2.690497 CTGAGCCATCGTCTTCTTCCTA 59.310 50.000 0.00 0.00 0.00 2.94
1010 1079 1.786049 GCTAACGCAATGGCTAGGGC 61.786 60.000 0.00 0.00 38.10 5.19
1016 1085 0.761802 GCAATGGCTAGGGCTCTAGT 59.238 55.000 21.71 0.00 43.68 2.57
1023 1092 2.502130 GGCTAGGGCTCTAGTGTTTCTT 59.498 50.000 21.71 0.00 43.68 2.52
1042 1111 2.253758 GCGCTCTTGTGCCTTGTGA 61.254 57.895 0.00 0.00 43.34 3.58
1113 1182 4.162651 ACATGCTCAAGAAAGGGGATTTT 58.837 39.130 0.00 0.00 0.00 1.82
1116 1185 4.222336 TGCTCAAGAAAGGGGATTTTTCA 58.778 39.130 1.21 0.00 37.08 2.69
1159 1228 3.257393 GCCACTATCATGTCGATCATCC 58.743 50.000 0.00 0.00 35.39 3.51
1169 1238 0.823769 TCGATCATCCTCCCCGACAG 60.824 60.000 0.00 0.00 0.00 3.51
1184 1253 3.470709 CCGACAGCAAAGGTATGATGAT 58.529 45.455 0.00 0.00 38.99 2.45
1189 1258 5.121811 ACAGCAAAGGTATGATGATCAGAC 58.878 41.667 11.52 11.52 38.99 3.51
1213 1282 7.343357 ACGATGTTCCTCCCTTTCAATATAAA 58.657 34.615 0.00 0.00 0.00 1.40
1244 1313 8.110860 ACCAGACATTATTCTTTTGTTGGTAG 57.889 34.615 0.00 0.00 35.23 3.18
1257 1326 4.032960 TGTTGGTAGCCAGAAATCATGT 57.967 40.909 0.00 0.00 33.81 3.21
1272 1341 6.328672 AGAAATCATGTAGCCTCTTAGGATGT 59.671 38.462 0.00 0.00 37.67 3.06
1279 1348 2.158842 AGCCTCTTAGGATGTCACATGC 60.159 50.000 0.00 0.00 37.67 4.06
1283 1352 1.945394 CTTAGGATGTCACATGCTGGC 59.055 52.381 21.37 0.00 0.00 4.85
1347 1416 9.295825 GGTGTTGATATCAATGAATATACCCAA 57.704 33.333 20.65 0.00 38.24 4.12
1356 1425 8.463930 TCAATGAATATACCCAAAGATGAACC 57.536 34.615 0.00 0.00 0.00 3.62
1399 1474 7.697710 GCAAATTCGATGAGTATTCACAATTGA 59.302 33.333 13.59 0.00 35.83 2.57
1410 1485 8.561738 AGTATTCACAATTGAGTTTTATCGGT 57.438 30.769 13.59 0.00 31.71 4.69
1415 1490 7.577979 TCACAATTGAGTTTTATCGGTGTAAC 58.422 34.615 13.59 0.00 0.00 2.50
1528 1607 8.616076 GCATATATAGATGATGTTTTAGGCACC 58.384 37.037 11.53 0.00 0.00 5.01
1613 1855 2.556144 TGCAGCTCTCTTTCATGTGT 57.444 45.000 0.00 0.00 0.00 3.72
1614 1856 2.148768 TGCAGCTCTCTTTCATGTGTG 58.851 47.619 0.00 0.00 0.00 3.82
1615 1857 2.149578 GCAGCTCTCTTTCATGTGTGT 58.850 47.619 0.00 0.00 0.00 3.72
1616 1858 2.159234 GCAGCTCTCTTTCATGTGTGTC 59.841 50.000 0.00 0.00 0.00 3.67
1617 1859 2.740981 CAGCTCTCTTTCATGTGTGTCC 59.259 50.000 0.00 0.00 0.00 4.02
1618 1860 2.369860 AGCTCTCTTTCATGTGTGTCCA 59.630 45.455 0.00 0.00 0.00 4.02
1619 1861 3.008813 AGCTCTCTTTCATGTGTGTCCAT 59.991 43.478 0.00 0.00 0.00 3.41
1779 2049 0.331616 GGTTTATGACAGGTGGGGCT 59.668 55.000 0.00 0.00 0.00 5.19
2211 2623 2.852075 TCCAGGCGGAGGTGGTTT 60.852 61.111 0.00 0.00 35.91 3.27
2277 2693 3.877450 GGATCCTCCATGGCGGCA 61.877 66.667 16.49 16.34 36.28 5.69
2397 2813 4.129737 GGCTCGTCACAGCGGCTA 62.130 66.667 0.26 0.00 40.68 3.93
2733 3152 3.060602 GCCGATTCTGGTAGTTATCAGC 58.939 50.000 0.00 0.00 34.44 4.26
2802 3221 8.475331 AGTGGTAGTTTTATGTTATTCACTCG 57.525 34.615 0.00 0.00 0.00 4.18
2803 3222 8.092687 AGTGGTAGTTTTATGTTATTCACTCGT 58.907 33.333 0.00 0.00 0.00 4.18
2804 3223 8.166706 GTGGTAGTTTTATGTTATTCACTCGTG 58.833 37.037 0.00 0.00 0.00 4.35
2805 3224 7.874016 TGGTAGTTTTATGTTATTCACTCGTGT 59.126 33.333 0.00 0.00 0.00 4.49
2821 3240 9.491675 TTCACTCGTGTCCATTATTAGTAAAAA 57.508 29.630 0.00 0.00 0.00 1.94
2895 3314 6.575162 AGGGTTGTGTGATAAATCTTTGAC 57.425 37.500 0.00 0.00 0.00 3.18
2898 3317 5.048991 GGTTGTGTGATAAATCTTTGACGGT 60.049 40.000 0.00 0.00 0.00 4.83
2907 3327 7.827236 TGATAAATCTTTGACGGTCCAATAACT 59.173 33.333 5.55 0.00 0.00 2.24
2918 3338 5.361571 ACGGTCCAATAACTGAAAGGTTTTT 59.638 36.000 0.00 0.00 39.30 1.94
3006 3451 5.396057 TTTGCCCCATACCTATACACATT 57.604 39.130 0.00 0.00 0.00 2.71
3007 3452 4.365514 TGCCCCATACCTATACACATTG 57.634 45.455 0.00 0.00 0.00 2.82
3097 3584 7.223387 CCATGTTTAATAGCTTCCTTCATTTGC 59.777 37.037 0.00 0.00 0.00 3.68
3102 3589 2.590821 AGCTTCCTTCATTTGCTGTGT 58.409 42.857 0.00 0.00 32.32 3.72
3231 3718 4.901849 TCGAATCCCATCTTCTCCAACTAT 59.098 41.667 0.00 0.00 0.00 2.12
3232 3719 6.075315 TCGAATCCCATCTTCTCCAACTATA 58.925 40.000 0.00 0.00 0.00 1.31
3236 3723 6.688073 TCCCATCTTCTCCAACTATAATCC 57.312 41.667 0.00 0.00 0.00 3.01
3239 3726 6.043706 CCCATCTTCTCCAACTATAATCCACT 59.956 42.308 0.00 0.00 0.00 4.00
3465 3953 3.002246 TGCAGTGTTCGATTCTGTCAAAC 59.998 43.478 11.59 0.00 0.00 2.93
3656 4153 5.183228 ACGACCCAATTCTTTACCATACAG 58.817 41.667 0.00 0.00 0.00 2.74
4262 4778 4.612412 GACGCCGTGAACCACCCA 62.612 66.667 0.00 0.00 0.00 4.51
4342 4863 7.385478 CCTCAAGTTCTCCTTCTAACTTTGTAC 59.615 40.741 0.00 0.00 41.89 2.90
4344 4865 7.926555 TCAAGTTCTCCTTCTAACTTTGTACTG 59.073 37.037 0.00 0.00 41.89 2.74
4346 4867 5.148651 TCTCCTTCTAACTTTGTACTGGC 57.851 43.478 0.00 0.00 0.00 4.85
4348 4869 4.638304 TCCTTCTAACTTTGTACTGGCAC 58.362 43.478 0.00 0.00 0.00 5.01
4360 4881 4.514585 TGGCACGGTTGGTTGGCT 62.515 61.111 0.00 0.00 0.00 4.75
4361 4882 3.670377 GGCACGGTTGGTTGGCTC 61.670 66.667 0.00 0.00 0.00 4.70
4379 4900 3.016736 GCTCCATTCCCATCGAGAAAAA 58.983 45.455 0.00 0.00 0.00 1.94
4380 4901 3.633986 GCTCCATTCCCATCGAGAAAAAT 59.366 43.478 0.00 0.00 0.00 1.82
4381 4902 4.821805 GCTCCATTCCCATCGAGAAAAATA 59.178 41.667 0.00 0.00 0.00 1.40
4407 4928 8.831000 AAAATAAAAATTAGGCGTGTACGATC 57.169 30.769 8.82 0.00 43.02 3.69
4408 4929 7.542534 AATAAAAATTAGGCGTGTACGATCA 57.457 32.000 8.82 0.00 43.02 2.92
4450 4971 4.384208 CCAGGACATCGGGTATCTTCTTTT 60.384 45.833 0.00 0.00 0.00 2.27
4482 5003 1.825191 CTGGCCCGTATGCTGCAAT 60.825 57.895 6.36 0.00 0.00 3.56
4487 5008 0.027979 CCCGTATGCTGCAATCAACG 59.972 55.000 6.36 13.87 0.00 4.10
4518 5042 6.223120 ACTTGTTCAAGCAAAAAGTTGACTT 58.777 32.000 11.79 0.00 36.83 3.01
4575 5099 2.809601 GCACCGAATGCGACGAGT 60.810 61.111 0.00 0.00 46.55 4.18
4576 5100 3.071459 GCACCGAATGCGACGAGTG 62.071 63.158 0.00 0.00 46.55 3.51
4577 5101 1.443702 CACCGAATGCGACGAGTGA 60.444 57.895 0.00 0.00 40.82 3.41
4578 5102 1.154016 ACCGAATGCGACGAGTGAG 60.154 57.895 0.00 0.00 40.82 3.51
4579 5103 2.508891 CCGAATGCGACGAGTGAGC 61.509 63.158 0.00 0.00 40.82 4.26
4580 5104 1.801512 CGAATGCGACGAGTGAGCA 60.802 57.895 0.00 5.66 45.46 4.26
4590 5135 4.405671 AGTGAGCAGCGCAGGCAT 62.406 61.111 23.22 10.42 43.41 4.40
4623 5168 0.385974 CCAAGAACCGAAAGCGCAAG 60.386 55.000 11.47 0.00 35.83 4.01
4626 5171 2.978018 GAACCGAAAGCGCAAGGGG 61.978 63.158 11.47 8.21 35.83 4.79
4693 5238 2.432456 GCGCATCAGGTGACACGA 60.432 61.111 0.30 0.00 0.00 4.35
4709 5254 4.409218 GACGACCCGCTACGTGCA 62.409 66.667 0.00 0.00 42.74 4.57
4774 5509 1.876263 CATGACGCGCGACACCATA 60.876 57.895 39.36 14.74 0.00 2.74
4905 5687 1.817941 GGTCACCAGTGCACGTTGT 60.818 57.895 12.01 7.17 0.00 3.32
4909 5691 2.096174 GTCACCAGTGCACGTTGTTAAA 59.904 45.455 12.01 0.00 0.00 1.52
4947 5729 2.186826 ACGCAAGAGGGTTGTGTGC 61.187 57.895 3.26 0.00 41.07 4.57
5002 5790 2.350772 GCTGCGTTTTCAGTTATGTGCT 60.351 45.455 0.00 0.00 36.49 4.40
5031 5819 4.206843 GCGAAATGCTATCGTGATTTCTG 58.793 43.478 0.00 0.00 42.15 3.02
5074 5862 6.091713 GTGGCTTGAAGATTGGATTTTTCATG 59.908 38.462 0.00 0.00 30.45 3.07
5149 5942 9.809096 GAAATATCTAGGCATTCGATGAATAGA 57.191 33.333 0.00 0.00 35.07 1.98
5213 6006 0.450482 GACACGCATTGGAACGAACG 60.450 55.000 0.00 0.00 0.00 3.95
5222 6015 4.912766 GCATTGGAACGAACGAAATAAACA 59.087 37.500 0.14 0.00 0.00 2.83
5226 6019 4.334759 TGGAACGAACGAAATAAACACCAA 59.665 37.500 0.14 0.00 0.00 3.67
5267 6061 0.179148 TCGTTCGGTGGATCATCACG 60.179 55.000 0.00 0.00 38.46 4.35
5306 6100 5.420409 GTCCCTCTTAGGTTCACATACAAG 58.580 45.833 0.00 0.00 31.93 3.16
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
11 12 2.632512 ACCTTAATGTGCCTTTGTTGGG 59.367 45.455 0.00 0.00 0.00 4.12
18 19 3.190439 ACCCTAGACCTTAATGTGCCTT 58.810 45.455 0.00 0.00 0.00 4.35
50 51 1.338011 ACCCAATGCGCCAAATTTCAG 60.338 47.619 4.18 0.00 0.00 3.02
59 60 1.675720 ATTAAGCCACCCAATGCGCC 61.676 55.000 4.18 0.00 0.00 6.53
60 61 1.028905 TATTAAGCCACCCAATGCGC 58.971 50.000 0.00 0.00 0.00 6.09
63 64 4.279169 CCACTCATATTAAGCCACCCAATG 59.721 45.833 0.00 0.00 0.00 2.82
64 65 4.079212 ACCACTCATATTAAGCCACCCAAT 60.079 41.667 0.00 0.00 0.00 3.16
76 77 3.073062 GGGGTCATGCTACCACTCATATT 59.927 47.826 5.97 0.00 40.05 1.28
80 81 0.546507 TGGGGTCATGCTACCACTCA 60.547 55.000 7.31 0.00 43.88 3.41
105 107 3.203487 TCATAGGGGTTGGGGTATTTGAC 59.797 47.826 0.00 0.00 0.00 3.18
108 110 5.679606 ACTATTCATAGGGGTTGGGGTATTT 59.320 40.000 0.00 0.00 34.69 1.40
115 117 2.494059 CGCACTATTCATAGGGGTTGG 58.506 52.381 0.00 0.00 34.35 3.77
117 119 2.124411 ACCGCACTATTCATAGGGGTT 58.876 47.619 0.00 0.00 34.35 4.11
124 126 4.100963 TCATAGGACAACCGCACTATTCAT 59.899 41.667 0.00 0.00 41.83 2.57
126 128 4.054780 TCATAGGACAACCGCACTATTC 57.945 45.455 0.00 0.00 41.83 1.75
164 166 9.899226 CCAATTTTTCGAAGACTCTAAGATTTT 57.101 29.630 0.00 0.00 34.32 1.82
172 174 2.095718 GCGCCAATTTTTCGAAGACTCT 60.096 45.455 0.00 0.00 34.32 3.24
181 183 3.058983 CAGGAAAAAGGCGCCAATTTTTC 60.059 43.478 35.70 35.70 46.97 2.29
182 184 2.877786 CAGGAAAAAGGCGCCAATTTTT 59.122 40.909 31.07 30.08 40.37 1.94
187 189 0.827368 AAACAGGAAAAAGGCGCCAA 59.173 45.000 31.54 0.00 0.00 4.52
191 193 4.857037 GCTAATACAAACAGGAAAAAGGCG 59.143 41.667 0.00 0.00 0.00 5.52
202 204 2.847449 TGCCCCCTAGCTAATACAAACA 59.153 45.455 0.00 0.00 0.00 2.83
203 205 3.570912 TGCCCCCTAGCTAATACAAAC 57.429 47.619 0.00 0.00 0.00 2.93
207 209 1.772453 TGGTTGCCCCCTAGCTAATAC 59.228 52.381 0.00 0.00 0.00 1.89
208 210 2.199927 TGGTTGCCCCCTAGCTAATA 57.800 50.000 0.00 0.00 0.00 0.98
210 212 0.550914 CATGGTTGCCCCCTAGCTAA 59.449 55.000 0.00 0.00 0.00 3.09
212 214 3.010144 CATGGTTGCCCCCTAGCT 58.990 61.111 0.00 0.00 0.00 3.32
213 215 2.834968 GCATGGTTGCCCCCTAGC 60.835 66.667 0.00 0.00 43.38 3.42
230 232 1.749634 CCCTCAGTACTTGTCTACGGG 59.250 57.143 0.00 0.00 0.00 5.28
241 243 2.103263 CAGGACATTAGCCCCTCAGTAC 59.897 54.545 0.00 0.00 0.00 2.73
244 246 1.415659 CTCAGGACATTAGCCCCTCAG 59.584 57.143 0.00 0.00 0.00 3.35
249 251 5.059833 CAGTTTATCTCAGGACATTAGCCC 58.940 45.833 0.00 0.00 0.00 5.19
253 255 9.832445 GTTTATCCAGTTTATCTCAGGACATTA 57.168 33.333 0.00 0.00 0.00 1.90
264 266 7.307811 GGCCTAATGTCGTTTATCCAGTTTATC 60.308 40.741 0.00 0.00 0.00 1.75
272 274 3.808174 GTGAGGCCTAATGTCGTTTATCC 59.192 47.826 4.42 0.00 0.00 2.59
288 290 0.603065 GACAATGGGGTTTGTGAGGC 59.397 55.000 0.00 0.00 39.85 4.70
322 324 2.290641 AGTGTGTTGTTCCTTCAATCGC 59.709 45.455 0.00 0.00 0.00 4.58
324 326 5.890334 TGAAAGTGTGTTGTTCCTTCAATC 58.110 37.500 0.00 0.00 0.00 2.67
359 361 7.489435 TGTGATTTGCGAGTAAAAACATTTTCA 59.511 29.630 0.00 0.00 0.00 2.69
360 362 7.836512 TGTGATTTGCGAGTAAAAACATTTTC 58.163 30.769 0.00 0.00 0.00 2.29
400 402 1.292061 TTGTCGAACGTGAAGTTGGG 58.708 50.000 0.00 0.00 44.35 4.12
404 406 6.849305 GTGAATTTTATTGTCGAACGTGAAGT 59.151 34.615 0.00 0.00 0.00 3.01
410 412 8.716619 TTTAAGGTGAATTTTATTGTCGAACG 57.283 30.769 0.00 0.00 0.00 3.95
413 415 9.672086 CAACTTTAAGGTGAATTTTATTGTCGA 57.328 29.630 3.55 0.00 33.95 4.20
414 416 9.458374 ACAACTTTAAGGTGAATTTTATTGTCG 57.542 29.630 17.62 0.00 33.95 4.35
459 510 3.510531 TGGTACCAATACAGTGCCAAA 57.489 42.857 13.60 0.00 45.50 3.28
466 517 9.751542 TGTTAAACAATTTTGGTACCAATACAG 57.248 29.630 27.57 19.20 35.70 2.74
488 539 6.056884 AAATAACGTGGTTCTCAGGTTGTTA 58.943 36.000 12.43 0.00 46.83 2.41
499 550 7.858583 ACTTGTTAGAGAAAATAACGTGGTTC 58.141 34.615 0.00 0.00 36.18 3.62
510 561 8.019656 AGGTTACTCTGACTTGTTAGAGAAAA 57.980 34.615 23.34 15.59 42.34 2.29
511 562 7.598759 AGGTTACTCTGACTTGTTAGAGAAA 57.401 36.000 23.34 11.73 42.34 2.52
514 565 6.151312 TGCTAGGTTACTCTGACTTGTTAGAG 59.849 42.308 17.37 17.37 44.63 2.43
519 570 4.589374 ACTTGCTAGGTTACTCTGACTTGT 59.411 41.667 0.00 0.00 0.00 3.16
525 576 3.693085 TCGGTACTTGCTAGGTTACTCTG 59.307 47.826 0.00 0.00 0.00 3.35
603 654 8.200792 TGCTTTTACATTTGGATTTTACACAGT 58.799 29.630 0.00 0.00 0.00 3.55
606 657 8.587952 ACTGCTTTTACATTTGGATTTTACAC 57.412 30.769 0.00 0.00 0.00 2.90
619 670 4.323417 TGATTGACGGACTGCTTTTACAT 58.677 39.130 0.00 0.00 0.00 2.29
620 671 3.734463 TGATTGACGGACTGCTTTTACA 58.266 40.909 0.00 0.00 0.00 2.41
621 672 3.125316 CCTGATTGACGGACTGCTTTTAC 59.875 47.826 0.00 0.00 0.00 2.01
631 682 4.771114 AACCATTATCCTGATTGACGGA 57.229 40.909 0.00 0.00 0.00 4.69
675 728 9.695526 TGAGAATGACATTAACCTTCAATTTTG 57.304 29.630 0.00 0.00 0.00 2.44
682 735 5.888161 ACCCATGAGAATGACATTAACCTTC 59.112 40.000 0.00 0.00 0.00 3.46
686 739 6.949352 ATGACCCATGAGAATGACATTAAC 57.051 37.500 0.00 0.00 0.00 2.01
687 740 6.891361 ACAATGACCCATGAGAATGACATTAA 59.109 34.615 0.00 0.00 0.00 1.40
697 750 2.583024 TGCAACAATGACCCATGAGA 57.417 45.000 0.00 0.00 0.00 3.27
699 752 1.205179 GCATGCAACAATGACCCATGA 59.795 47.619 14.21 0.00 36.32 3.07
700 753 1.066787 TGCATGCAACAATGACCCATG 60.067 47.619 20.30 0.00 37.07 3.66
732 785 1.203187 AGTGGACTAGGGAGAAGTGCA 60.203 52.381 0.00 0.00 42.18 4.57
737 790 3.562108 AAAGGAGTGGACTAGGGAGAA 57.438 47.619 0.00 0.00 0.00 2.87
761 814 4.037803 GGCCGTTAAAGGAAAACAAGGTTA 59.962 41.667 12.01 0.00 0.00 2.85
781 849 1.319614 ATATGCACGGTTGGTTGGCC 61.320 55.000 0.00 0.00 0.00 5.36
799 867 4.202151 GCTTCAAGAACCTGTGGAAAACAT 60.202 41.667 0.00 0.00 38.39 2.71
801 869 3.490933 GGCTTCAAGAACCTGTGGAAAAC 60.491 47.826 0.00 0.00 0.00 2.43
805 873 0.843309 TGGCTTCAAGAACCTGTGGA 59.157 50.000 0.00 0.00 0.00 4.02
807 875 1.972872 ACTGGCTTCAAGAACCTGTG 58.027 50.000 0.00 0.00 34.72 3.66
825 893 6.462500 AGAGATATGCATGGTTGATGACTAC 58.538 40.000 10.16 0.00 33.31 2.73
836 904 6.994496 TGGACTTTTTCTAGAGATATGCATGG 59.006 38.462 10.16 0.00 0.00 3.66
843 911 8.045507 TCGTCTAGTGGACTTTTTCTAGAGATA 58.954 37.037 5.02 0.00 42.44 1.98
898 966 5.337652 GGATGGGCAGTTATATCACTAGGAC 60.338 48.000 0.00 0.00 0.00 3.85
954 1023 2.178890 GGCTCAGAAGATGCAGGCG 61.179 63.158 0.00 0.00 0.00 5.52
968 1037 2.541999 CGTAGGAAGAAGACGATGGCTC 60.542 54.545 0.00 0.00 38.88 4.70
997 1066 0.761802 ACTAGAGCCCTAGCCATTGC 59.238 55.000 1.54 0.00 44.87 3.56
1010 1079 2.953020 AGAGCGCAAGAAACACTAGAG 58.047 47.619 11.47 0.00 43.02 2.43
1016 1085 0.029300 GCACAAGAGCGCAAGAAACA 59.971 50.000 11.47 0.00 43.02 2.83
1023 1092 2.203195 ACAAGGCACAAGAGCGCA 60.203 55.556 11.47 0.00 34.64 6.09
1042 1111 2.980233 GCAAACCAGCGCAGAGGT 60.980 61.111 11.47 12.18 39.08 3.85
1128 1197 1.077716 GATAGTGGCGCCCCAGTTT 60.078 57.895 26.77 3.85 42.21 2.66
1159 1228 0.541863 ATACCTTTGCTGTCGGGGAG 59.458 55.000 0.00 0.00 0.00 4.30
1169 1238 4.371786 TCGTCTGATCATCATACCTTTGC 58.628 43.478 0.00 0.00 0.00 3.68
1184 1253 1.938585 AAGGGAGGAACATCGTCTGA 58.061 50.000 0.77 0.00 32.33 3.27
1189 1258 7.801716 TTTATATTGAAAGGGAGGAACATCG 57.198 36.000 0.00 0.00 0.00 3.84
1220 1289 7.029563 GCTACCAACAAAAGAATAATGTCTGG 58.970 38.462 0.00 0.00 34.40 3.86
1244 1313 3.205784 AGAGGCTACATGATTTCTGGC 57.794 47.619 0.00 0.00 0.00 4.85
1257 1326 3.070159 GCATGTGACATCCTAAGAGGCTA 59.930 47.826 0.00 0.00 34.61 3.93
1319 1388 9.466497 GGGTATATTCATTGATATCAACACCAT 57.534 33.333 20.19 12.00 38.86 3.55
1330 1399 9.082313 GGTTCATCTTTGGGTATATTCATTGAT 57.918 33.333 0.00 0.00 0.00 2.57
1333 1402 8.837099 TTGGTTCATCTTTGGGTATATTCATT 57.163 30.769 0.00 0.00 0.00 2.57
1366 1436 0.381445 TCATCGAATTTGCGCATGGG 59.619 50.000 12.75 5.19 0.00 4.00
1446 1521 7.450323 TCCCCTAGGTTCTTGTAAAAAGAAATG 59.550 37.037 8.29 0.00 37.93 2.32
1451 1530 5.877491 ACTCCCCTAGGTTCTTGTAAAAAG 58.123 41.667 8.29 0.00 0.00 2.27
1502 1581 8.616076 GGTGCCTAAAACATCATCTATATATGC 58.384 37.037 0.00 0.00 0.00 3.14
1528 1607 5.475273 AATGCACATTAGAGATCGTGTTG 57.525 39.130 0.00 0.00 0.00 3.33
1589 1831 4.156190 CACATGAAAGAGAGCTGCAAGAAT 59.844 41.667 0.00 0.00 34.07 2.40
1590 1832 3.501062 CACATGAAAGAGAGCTGCAAGAA 59.499 43.478 0.00 0.00 34.07 2.52
1598 1840 2.771089 TGGACACACATGAAAGAGAGC 58.229 47.619 0.00 0.00 0.00 4.09
1613 1855 4.284829 TGTGCTATTCACTCAATGGACA 57.715 40.909 0.00 0.00 45.81 4.02
1614 1856 5.627499 TTTGTGCTATTCACTCAATGGAC 57.373 39.130 0.00 0.00 45.81 4.02
1615 1857 5.769662 AGTTTTGTGCTATTCACTCAATGGA 59.230 36.000 0.00 0.00 45.81 3.41
1616 1858 6.017400 AGTTTTGTGCTATTCACTCAATGG 57.983 37.500 0.00 0.00 45.81 3.16
1617 1859 7.023575 GGTAGTTTTGTGCTATTCACTCAATG 58.976 38.462 0.00 0.00 45.81 2.82
1618 1860 6.714810 TGGTAGTTTTGTGCTATTCACTCAAT 59.285 34.615 0.00 0.00 45.81 2.57
1619 1861 6.017440 GTGGTAGTTTTGTGCTATTCACTCAA 60.017 38.462 0.00 0.00 45.81 3.02
1691 1933 2.287427 ACGCCGATTCTGGTAGTTATCG 60.287 50.000 0.00 0.00 39.52 2.92
1779 2049 3.897936 CGGTTCATTTAGCCGCCA 58.102 55.556 0.00 0.00 45.41 5.69
1975 2298 1.447838 GATTTCGTCGCCCTGCTGA 60.448 57.895 0.00 0.00 0.00 4.26
2023 2346 4.332543 AGGTGGAAGGAGGGGCGA 62.333 66.667 0.00 0.00 0.00 5.54
2262 2678 4.575973 GCTGCCGCCATGGAGGAT 62.576 66.667 36.03 0.00 42.00 3.24
2507 2925 0.967380 GAAACTCGACCGGGTCCCTA 60.967 60.000 21.06 6.48 0.00 3.53
2829 3248 9.625747 TGACTTTCTAATATGCATATTTGGACA 57.374 29.630 31.30 21.36 34.91 4.02
2895 3314 5.447624 AAAACCTTTCAGTTATTGGACCG 57.552 39.130 0.00 0.00 0.00 4.79
2941 3367 9.595823 CCGGTTATTTATTGGTCGATATAGAAT 57.404 33.333 0.00 0.00 0.00 2.40
2943 3369 8.352137 TCCGGTTATTTATTGGTCGATATAGA 57.648 34.615 0.00 0.00 0.00 1.98
2946 3372 9.374838 GTAATCCGGTTATTTATTGGTCGATAT 57.625 33.333 0.00 0.00 0.00 1.63
2947 3373 7.818930 GGTAATCCGGTTATTTATTGGTCGATA 59.181 37.037 0.00 0.00 0.00 2.92
2948 3374 6.652062 GGTAATCCGGTTATTTATTGGTCGAT 59.348 38.462 0.00 0.00 0.00 3.59
2949 3375 5.990996 GGTAATCCGGTTATTTATTGGTCGA 59.009 40.000 0.00 0.00 0.00 4.20
2950 3376 5.759273 TGGTAATCCGGTTATTTATTGGTCG 59.241 40.000 0.00 0.00 36.30 4.79
2951 3377 7.420002 GTTGGTAATCCGGTTATTTATTGGTC 58.580 38.462 0.00 0.00 36.30 4.02
2952 3378 6.321945 GGTTGGTAATCCGGTTATTTATTGGT 59.678 38.462 0.00 0.00 36.30 3.67
2955 3381 6.548251 CAGGGTTGGTAATCCGGTTATTTATT 59.452 38.462 0.00 0.00 36.30 1.40
2964 3390 0.909623 ACTCAGGGTTGGTAATCCGG 59.090 55.000 0.00 0.00 36.30 5.14
3064 3509 6.036470 GGAAGCTATTAAACATGGCAGTTTC 58.964 40.000 15.15 2.95 41.58 2.78
3097 3584 3.121611 CACACACAAAAACAAGCACACAG 59.878 43.478 0.00 0.00 0.00 3.66
3102 3589 2.673610 GCCTCACACACAAAAACAAGCA 60.674 45.455 0.00 0.00 0.00 3.91
3214 3701 6.043706 AGTGGATTATAGTTGGAGAAGATGGG 59.956 42.308 0.00 0.00 0.00 4.00
3231 3718 3.199071 ACGTTGGGCTCATAAGTGGATTA 59.801 43.478 0.00 0.00 0.00 1.75
3232 3719 2.026262 ACGTTGGGCTCATAAGTGGATT 60.026 45.455 0.00 0.00 0.00 3.01
3236 3723 2.386661 AGACGTTGGGCTCATAAGTG 57.613 50.000 0.00 0.00 0.00 3.16
3239 3726 2.742348 TCCTAGACGTTGGGCTCATAA 58.258 47.619 0.00 0.00 0.00 1.90
3465 3953 1.528586 GCATGTTATCGCAGGTAGCTG 59.471 52.381 17.67 17.67 42.61 4.24
3656 4153 3.244345 TGATCAACGACACGACAGTTTTC 59.756 43.478 0.00 0.00 0.00 2.29
3716 4217 1.909781 GTACACGTCCAGGTCCCCA 60.910 63.158 0.00 0.00 0.00 4.96
3719 4220 2.126189 GCGTACACGTCCAGGTCC 60.126 66.667 3.44 0.00 42.22 4.46
3878 4379 4.200283 GACGCGGAGAGCTGGAGG 62.200 72.222 12.47 0.00 45.59 4.30
4139 4655 1.222936 GGTGTAGAGCTGCATGGCT 59.777 57.895 1.02 0.00 46.11 4.75
4262 4778 3.363351 GTCACCGACGGGAACTCT 58.637 61.111 20.00 0.00 36.97 3.24
4342 4863 3.977244 GCCAACCAACCGTGCCAG 61.977 66.667 0.00 0.00 0.00 4.85
4344 4865 3.670377 GAGCCAACCAACCGTGCC 61.670 66.667 0.00 0.00 0.00 5.01
4346 4867 1.178534 AATGGAGCCAACCAACCGTG 61.179 55.000 0.00 0.00 43.47 4.94
4348 4869 1.595093 GGAATGGAGCCAACCAACCG 61.595 60.000 9.99 0.00 43.47 4.44
4353 4874 1.103398 CGATGGGAATGGAGCCAACC 61.103 60.000 0.00 0.53 0.00 3.77
4354 4875 0.107214 TCGATGGGAATGGAGCCAAC 60.107 55.000 0.00 0.00 0.00 3.77
4355 4876 0.181114 CTCGATGGGAATGGAGCCAA 59.819 55.000 0.00 0.00 0.00 4.52
4356 4877 0.690744 TCTCGATGGGAATGGAGCCA 60.691 55.000 0.00 0.00 0.00 4.75
4357 4878 0.469917 TTCTCGATGGGAATGGAGCC 59.530 55.000 0.00 0.00 0.00 4.70
4358 4879 2.332063 TTTCTCGATGGGAATGGAGC 57.668 50.000 0.00 0.00 0.00 4.70
4360 4881 7.710676 TTTTATTTTTCTCGATGGGAATGGA 57.289 32.000 0.00 0.00 0.00 3.41
4361 4882 8.947055 ATTTTTATTTTTCTCGATGGGAATGG 57.053 30.769 0.00 0.00 0.00 3.16
4381 4902 9.281075 GATCGTACACGCCTAATTTTTATTTTT 57.719 29.630 0.00 0.00 39.60 1.94
4403 4924 3.427909 CCAAACCCAACACATCATGATCG 60.428 47.826 4.86 2.53 0.00 3.69
4404 4925 3.119029 CCCAAACCCAACACATCATGATC 60.119 47.826 4.86 0.00 0.00 2.92
4405 4926 2.833338 CCCAAACCCAACACATCATGAT 59.167 45.455 1.18 1.18 0.00 2.45
4406 4927 2.246469 CCCAAACCCAACACATCATGA 58.754 47.619 0.00 0.00 0.00 3.07
4407 4928 1.338011 GCCCAAACCCAACACATCATG 60.338 52.381 0.00 0.00 0.00 3.07
4408 4929 0.975887 GCCCAAACCCAACACATCAT 59.024 50.000 0.00 0.00 0.00 2.45
4450 4971 4.659172 CCAGCCAGCCCCGTTTGA 62.659 66.667 0.00 0.00 0.00 2.69
4482 5003 1.305201 GAACAAGTTGGGCTCGTTGA 58.695 50.000 7.96 0.00 0.00 3.18
4487 5008 1.032014 TGCTTGAACAAGTTGGGCTC 58.968 50.000 14.62 1.64 40.45 4.70
4500 5024 5.184864 TCCTCAAAGTCAACTTTTTGCTTGA 59.815 36.000 5.41 0.00 43.07 3.02
4501 5025 5.410067 TCCTCAAAGTCAACTTTTTGCTTG 58.590 37.500 5.41 0.00 43.07 4.01
4565 5089 2.507992 GCTGCTCACTCGTCGCAT 60.508 61.111 0.00 0.00 32.62 4.73
4574 5098 1.442526 ATAATGCCTGCGCTGCTCAC 61.443 55.000 20.27 6.09 35.36 3.51
4575 5099 1.153107 ATAATGCCTGCGCTGCTCA 60.153 52.632 20.27 14.69 35.36 4.26
4576 5100 1.281960 CATAATGCCTGCGCTGCTC 59.718 57.895 20.27 10.10 35.36 4.26
4577 5101 2.842256 GCATAATGCCTGCGCTGCT 61.842 57.895 20.27 6.73 37.42 4.24
4578 5102 2.354305 GCATAATGCCTGCGCTGC 60.354 61.111 9.73 12.54 37.42 5.25
4590 5135 2.435762 TTGGCTGCTCGCGCATAA 60.436 55.556 8.75 0.00 46.74 1.90
4598 5143 0.519077 CTTTCGGTTCTTGGCTGCTC 59.481 55.000 0.00 0.00 0.00 4.26
4769 5504 3.531538 CAACCGATGTTGTAGCTATGGT 58.468 45.455 0.00 0.00 45.51 3.55
4886 5668 1.817520 CAACGTGCACTGGTGACCA 60.818 57.895 18.02 3.40 0.00 4.02
4905 5687 7.642194 CGTGTTCTTGCTTAAGTTCATGTTTAA 59.358 33.333 4.02 0.00 0.00 1.52
4909 5691 4.554723 GCGTGTTCTTGCTTAAGTTCATGT 60.555 41.667 4.02 0.00 0.00 3.21
4965 5747 2.417924 CGCAGCACCATCTCCTATATCC 60.418 54.545 0.00 0.00 0.00 2.59
5031 5819 3.330267 CCACACTCTCTAGCAAAGAACC 58.670 50.000 0.00 0.00 32.46 3.62
5074 5862 2.818130 TTCACATTTGGAAGCCTTGC 57.182 45.000 0.00 0.00 0.00 4.01
5130 5923 4.623167 CGGTTCTATTCATCGAATGCCTAG 59.377 45.833 0.00 0.00 33.95 3.02
5131 5924 4.556233 CGGTTCTATTCATCGAATGCCTA 58.444 43.478 0.00 0.00 33.95 3.93
5149 5942 4.690719 TCCGATGTTGGCGCGGTT 62.691 61.111 8.83 0.00 45.02 4.44
5222 6015 6.210584 ACCATCCATTTCGTTTAATCTTTGGT 59.789 34.615 0.00 0.00 0.00 3.67
5226 6019 6.551736 CGAACCATCCATTTCGTTTAATCTT 58.448 36.000 0.00 0.00 39.79 2.40
5250 6044 0.810031 CCCGTGATGATCCACCGAAC 60.810 60.000 0.00 0.00 33.67 3.95
5267 6061 1.425694 GGACCTGTATTCCTCCTCCC 58.574 60.000 0.00 0.00 0.00 4.30
5306 6100 1.136872 TCGCGTGTTTGTTTGCTTGC 61.137 50.000 5.77 0.00 0.00 4.01


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

AutoCloner maintained by Alex Coulton.