Multiple sequence alignment - TraesCS6D01G147500

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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 TraesCS6D01G147500 chr6D 100.000 5777 0 0 1709 7485 120647651 120653427 0.000000e+00 10669.0
1 TraesCS6D01G147500 chr6D 100.000 1526 0 0 1 1526 120645943 120647468 0.000000e+00 2819.0
2 TraesCS6D01G147500 chr6D 82.590 1907 269 38 4553 6422 427483218 427485098 0.000000e+00 1624.0
3 TraesCS6D01G147500 chr6D 97.872 94 2 0 1287 1380 437180548 437180641 6.010000e-36 163.0
4 TraesCS6D01G147500 chr6D 97.826 46 0 1 1467 1511 120647362 120647407 2.240000e-10 78.7
5 TraesCS6D01G147500 chr6D 97.826 46 0 1 1420 1465 120647409 120647453 2.240000e-10 78.7
6 TraesCS6D01G147500 chr6A 96.603 3297 90 8 3831 7122 158908636 158911915 0.000000e+00 5448.0
7 TraesCS6D01G147500 chr6A 96.126 1523 33 9 2326 3828 158907064 158908580 0.000000e+00 2462.0
8 TraesCS6D01G147500 chr6A 83.001 1906 273 33 4553 6422 572136563 572138453 0.000000e+00 1677.0
9 TraesCS6D01G147500 chr6A 89.514 1049 74 18 1 1028 158904365 158905398 0.000000e+00 1295.0
10 TraesCS6D01G147500 chr6A 94.355 372 17 4 7116 7485 158911954 158912323 1.090000e-157 568.0
11 TraesCS6D01G147500 chr6A 91.811 403 16 4 1711 2113 158906131 158906516 5.110000e-151 545.0
12 TraesCS6D01G147500 chr6A 95.437 263 10 2 1032 1294 158905666 158905926 1.160000e-112 418.0
13 TraesCS6D01G147500 chr6A 95.706 163 7 0 2110 2272 158906599 158906761 5.760000e-66 263.0
14 TraesCS6D01G147500 chr6A 93.706 143 9 0 1384 1526 158905934 158906076 1.640000e-51 215.0
15 TraesCS6D01G147500 chr6A 90.435 115 11 0 3660 3774 50348989 50348875 1.300000e-32 152.0
16 TraesCS6D01G147500 chr6B 96.273 3300 99 9 3831 7122 212627908 212624625 0.000000e+00 5391.0
17 TraesCS6D01G147500 chr6B 94.109 1341 60 4 2489 3828 212629286 212627964 0.000000e+00 2021.0
18 TraesCS6D01G147500 chr6B 91.062 1309 72 19 1 1294 212632158 212630880 0.000000e+00 1727.0
19 TraesCS6D01G147500 chr6B 82.984 1481 210 26 4978 6422 643264124 643265598 0.000000e+00 1301.0
20 TraesCS6D01G147500 chr6B 94.271 576 21 5 1717 2281 212630681 212630107 0.000000e+00 870.0
21 TraesCS6D01G147500 chr6B 94.022 368 21 1 7116 7483 212624586 212624220 2.360000e-154 556.0
22 TraesCS6D01G147500 chr6B 93.365 211 6 2 2288 2498 212629520 212629318 9.440000e-79 305.0
23 TraesCS6D01G147500 chr6B 89.865 148 7 1 1379 1526 212630881 212630742 4.610000e-42 183.0
24 TraesCS6D01G147500 chr6B 86.188 181 7 4 1931 2111 212630102 212629940 5.970000e-41 180.0
25 TraesCS6D01G147500 chr6B 94.175 103 3 3 1291 1393 79369212 79369113 3.620000e-33 154.0
26 TraesCS6D01G147500 chrUn 80.485 1732 293 23 4727 6422 108321537 108323259 0.000000e+00 1284.0
27 TraesCS6D01G147500 chrUn 80.037 1087 195 15 5359 6425 331495126 331496210 0.000000e+00 785.0
28 TraesCS6D01G147500 chrUn 78.018 1019 156 30 2498 3475 108319406 108320397 5.040000e-161 579.0
29 TraesCS6D01G147500 chrUn 76.972 938 149 35 2498 3394 134255062 134254151 2.440000e-129 473.0
30 TraesCS6D01G147500 chrUn 76.972 938 149 35 2498 3394 134266768 134267679 2.440000e-129 473.0
31 TraesCS6D01G147500 chrUn 76.819 591 101 23 3262 3846 354242343 354242903 4.390000e-77 300.0
32 TraesCS6D01G147500 chrUn 81.818 253 44 2 3916 4167 354243093 354243344 2.120000e-50 211.0
33 TraesCS6D01G147500 chrUn 75.658 152 28 8 285 427 384243765 384243614 4.850000e-07 67.6
34 TraesCS6D01G147500 chr3D 78.786 1796 324 42 4663 6422 561172060 561173834 0.000000e+00 1153.0
35 TraesCS6D01G147500 chr3D 77.858 1793 333 43 4663 6422 561375572 561377333 0.000000e+00 1053.0
36 TraesCS6D01G147500 chr3D 80.168 595 94 18 3262 3846 561374160 561374740 2.500000e-114 424.0
37 TraesCS6D01G147500 chr3D 79.899 592 99 17 3263 3846 561170594 561171173 4.180000e-112 416.0
38 TraesCS6D01G147500 chr3D 96.875 96 3 0 1289 1384 137484267 137484172 2.160000e-35 161.0
39 TraesCS6D01G147500 chr3D 75.591 254 52 8 61 309 38901571 38901323 4.750000e-22 117.0
40 TraesCS6D01G147500 chr3B 78.181 1902 344 48 4553 6425 747822317 747824176 0.000000e+00 1147.0
41 TraesCS6D01G147500 chr3B 78.146 1899 350 43 4553 6425 747834793 747836652 0.000000e+00 1147.0
42 TraesCS6D01G147500 chr3B 78.105 1900 349 45 4553 6425 747838845 747840704 0.000000e+00 1142.0
43 TraesCS6D01G147500 chr3B 78.128 1902 345 42 4553 6425 747851320 747853179 0.000000e+00 1142.0
44 TraesCS6D01G147500 chr3B 77.862 1057 191 27 2778 3815 748451658 748452690 3.840000e-172 616.0
45 TraesCS6D01G147500 chr3B 77.157 591 99 23 3262 3846 747833450 747834010 2.030000e-80 311.0
46 TraesCS6D01G147500 chr3B 76.988 591 100 23 3262 3846 747820973 747821533 9.440000e-79 305.0
47 TraesCS6D01G147500 chr3B 76.650 591 102 23 3262 3846 747849977 747850537 2.040000e-75 294.0
48 TraesCS6D01G147500 chr3B 76.701 485 86 18 4058 4537 748453009 748453471 2.090000e-60 244.0
49 TraesCS6D01G147500 chr3B 81.818 253 44 2 3916 4167 747821723 747821974 2.120000e-50 211.0
50 TraesCS6D01G147500 chr3B 81.818 253 44 2 3916 4167 747850726 747850977 2.120000e-50 211.0
51 TraesCS6D01G147500 chr3B 74.897 486 91 23 4058 4537 748413408 748413868 7.660000e-45 193.0
52 TraesCS6D01G147500 chr3B 94.175 103 3 3 1291 1393 553867814 553867913 3.620000e-33 154.0
53 TraesCS6D01G147500 chr5B 79.662 1598 267 41 4846 6408 419998332 419999906 0.000000e+00 1098.0
54 TraesCS6D01G147500 chr3A 77.757 1061 189 29 2778 3815 697275396 697276432 6.420000e-170 608.0
55 TraesCS6D01G147500 chr3A 79.754 568 100 12 3262 3822 697260156 697260715 1.510000e-106 398.0
56 TraesCS6D01G147500 chr3A 76.289 485 88 16 4058 4537 697276751 697277213 4.520000e-57 233.0
57 TraesCS6D01G147500 chr3A 82.800 250 43 0 5639 5888 678425205 678424956 2.720000e-54 224.0
58 TraesCS6D01G147500 chr4B 78.187 1004 150 25 2514 3475 665879432 665878456 1.810000e-160 577.0
59 TraesCS6D01G147500 chr4B 75.701 856 141 28 2530 3346 665552536 665553363 4.270000e-97 366.0
60 TraesCS6D01G147500 chr5A 78.068 994 149 25 2514 3465 705846412 705845446 1.410000e-156 564.0
61 TraesCS6D01G147500 chr5A 77.825 938 146 25 2498 3396 706081937 706082851 2.390000e-144 523.0
62 TraesCS6D01G147500 chr5A 78.882 161 25 7 3668 3828 705071811 705071962 4.780000e-17 100.0
63 TraesCS6D01G147500 chr5A 78.882 161 25 7 3668 3828 705085651 705085802 4.780000e-17 100.0
64 TraesCS6D01G147500 chr4A 75.878 655 108 27 3145 3790 658402609 658401996 9.500000e-74 289.0
65 TraesCS6D01G147500 chr4A 94.175 103 3 2 1275 1377 542276075 542275976 3.620000e-33 154.0
66 TraesCS6D01G147500 chr4D 96.939 98 2 1 1286 1382 447129604 447129507 6.010000e-36 163.0
67 TraesCS6D01G147500 chr7A 95.098 102 3 2 1284 1385 44739844 44739943 7.770000e-35 159.0
68 TraesCS6D01G147500 chr2A 93.458 107 7 0 1281 1387 177665297 177665191 7.770000e-35 159.0
69 TraesCS6D01G147500 chr2A 97.368 38 1 0 2458 2495 177658362 177658325 1.740000e-06 65.8
70 TraesCS6D01G147500 chr7D 95.000 100 5 0 1285 1384 611865510 611865411 2.800000e-34 158.0
71 TraesCS6D01G147500 chr2B 76.842 285 48 13 62 337 750365746 750365471 2.180000e-30 145.0
72 TraesCS6D01G147500 chr1D 100.000 38 0 0 2458 2495 316619703 316619666 3.750000e-08 71.3
73 TraesCS6D01G147500 chr1A 100.000 37 0 0 2458 2494 397738760 397738724 1.350000e-07 69.4
74 TraesCS6D01G147500 chr1B 97.436 39 1 0 2458 2496 4516636 4516674 4.850000e-07 67.6
75 TraesCS6D01G147500 chr1B 97.368 38 1 0 2458 2495 428723303 428723266 1.740000e-06 65.8
76 TraesCS6D01G147500 chr2D 95.122 41 2 0 2455 2495 172409710 172409750 1.740000e-06 65.8
77 TraesCS6D01G147500 chr2D 92.857 42 3 0 2458 2499 27924491 27924450 2.260000e-05 62.1


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 TraesCS6D01G147500 chr6D 120645943 120653427 7484 False 3411.350000 10669 98.913000 1 7485 4 chr6D.!!$F3 7484
1 TraesCS6D01G147500 chr6D 427483218 427485098 1880 False 1624.000000 1624 82.590000 4553 6422 1 chr6D.!!$F1 1869
2 TraesCS6D01G147500 chr6A 572136563 572138453 1890 False 1677.000000 1677 83.001000 4553 6422 1 chr6A.!!$F1 1869
3 TraesCS6D01G147500 chr6A 158904365 158912323 7958 False 1401.750000 5448 94.157250 1 7485 8 chr6A.!!$F2 7484
4 TraesCS6D01G147500 chr6B 212624220 212632158 7938 True 1404.125000 5391 92.394375 1 7483 8 chr6B.!!$R2 7482
5 TraesCS6D01G147500 chr6B 643264124 643265598 1474 False 1301.000000 1301 82.984000 4978 6422 1 chr6B.!!$F1 1444
6 TraesCS6D01G147500 chrUn 108319406 108323259 3853 False 931.500000 1284 79.251500 2498 6422 2 chrUn.!!$F3 3924
7 TraesCS6D01G147500 chrUn 331495126 331496210 1084 False 785.000000 785 80.037000 5359 6425 1 chrUn.!!$F2 1066
8 TraesCS6D01G147500 chrUn 134254151 134255062 911 True 473.000000 473 76.972000 2498 3394 1 chrUn.!!$R1 896
9 TraesCS6D01G147500 chrUn 134266768 134267679 911 False 473.000000 473 76.972000 2498 3394 1 chrUn.!!$F1 896
10 TraesCS6D01G147500 chrUn 354242343 354243344 1001 False 255.500000 300 79.318500 3262 4167 2 chrUn.!!$F4 905
11 TraesCS6D01G147500 chr3D 561170594 561173834 3240 False 784.500000 1153 79.342500 3263 6422 2 chr3D.!!$F1 3159
12 TraesCS6D01G147500 chr3D 561374160 561377333 3173 False 738.500000 1053 79.013000 3262 6422 2 chr3D.!!$F2 3160
13 TraesCS6D01G147500 chr3B 747833450 747840704 7254 False 866.666667 1147 77.802667 3262 6425 3 chr3B.!!$F4 3163
14 TraesCS6D01G147500 chr3B 747820973 747824176 3203 False 554.333333 1147 78.995667 3262 6425 3 chr3B.!!$F3 3163
15 TraesCS6D01G147500 chr3B 747849977 747853179 3202 False 549.000000 1142 78.865333 3262 6425 3 chr3B.!!$F5 3163
16 TraesCS6D01G147500 chr3B 748451658 748453471 1813 False 430.000000 616 77.281500 2778 4537 2 chr3B.!!$F6 1759
17 TraesCS6D01G147500 chr5B 419998332 419999906 1574 False 1098.000000 1098 79.662000 4846 6408 1 chr5B.!!$F1 1562
18 TraesCS6D01G147500 chr3A 697275396 697277213 1817 False 420.500000 608 77.023000 2778 4537 2 chr3A.!!$F2 1759
19 TraesCS6D01G147500 chr3A 697260156 697260715 559 False 398.000000 398 79.754000 3262 3822 1 chr3A.!!$F1 560
20 TraesCS6D01G147500 chr4B 665878456 665879432 976 True 577.000000 577 78.187000 2514 3475 1 chr4B.!!$R1 961
21 TraesCS6D01G147500 chr4B 665552536 665553363 827 False 366.000000 366 75.701000 2530 3346 1 chr4B.!!$F1 816
22 TraesCS6D01G147500 chr5A 705845446 705846412 966 True 564.000000 564 78.068000 2514 3465 1 chr5A.!!$R1 951
23 TraesCS6D01G147500 chr5A 706081937 706082851 914 False 523.000000 523 77.825000 2498 3396 1 chr5A.!!$F3 898
24 TraesCS6D01G147500 chr4A 658401996 658402609 613 True 289.000000 289 75.878000 3145 3790 1 chr4A.!!$R2 645

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
432 439 0.319383 TTCGTAAAGCGTGCGGGTTA 60.319 50.0 1.6 0.0 42.13 2.85 F
1043 1341 0.324460 TCTCCGTCCTCCCTTCTTCC 60.324 60.0 0.0 0.0 0.00 3.46 F
1478 1776 1.890876 TGTGGTTTGTTCGATGGGAG 58.109 50.0 0.0 0.0 0.00 4.30 F
2556 3604 0.975040 TTGTGGCTGTTGTGGGCTTT 60.975 50.0 0.0 0.0 0.00 3.51 F
3815 4972 2.549754 CGGGATGGTATGAGCAAATCAC 59.450 50.0 0.0 0.0 41.91 3.06 F
4841 6218 0.179020 TTCTTGGGTGGTCTGTGCTG 60.179 55.0 0.0 0.0 0.00 4.41 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1708 2006 0.106819 AGATGCCTGGTCTGCCATTC 60.107 55.000 0.00 0.00 45.05 2.67 R
1980 2292 0.800012 CCGAAATCCCGAAAGCGAAA 59.200 50.000 0.00 0.00 40.82 3.46 R
3418 4549 1.689984 TGCATGGCAAAGACTTCACA 58.310 45.000 0.00 0.00 34.76 3.58 R
3979 5283 1.462616 TCCAACCATCCTTGCATTCG 58.537 50.000 0.00 0.00 0.00 3.34 R
4862 6239 3.054802 AGAAATGAAGGGGACTACAGCTG 60.055 47.826 13.48 13.48 42.68 4.24 R
6761 8243 1.416030 TGTACAGCTCAGCCAGACAAA 59.584 47.619 0.00 0.00 0.00 2.83 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
59 61 9.622004 ATTACTTGTTACGAGGTCATATATTCG 57.378 33.333 4.48 3.55 38.88 3.34
64 66 9.537192 TTGTTACGAGGTCATATATTCGAAAAT 57.463 29.630 0.00 0.00 36.89 1.82
81 83 5.298276 TCGAAAATATAAAGGTGGACATGGC 59.702 40.000 0.00 0.00 0.00 4.40
186 191 7.644490 ACTTGATCGATCATTCTACTCAGTAC 58.356 38.462 27.75 0.00 36.56 2.73
187 192 6.561737 TGATCGATCATTCTACTCAGTACC 57.438 41.667 23.99 0.00 0.00 3.34
211 216 5.391312 AGTTTAATGAAGCATTGACACCC 57.609 39.130 3.07 0.00 35.54 4.61
214 219 2.885135 ATGAAGCATTGACACCCTGA 57.115 45.000 0.00 0.00 0.00 3.86
319 325 4.955811 TGCCTAGAATATCACGGATGTT 57.044 40.909 0.00 0.00 0.00 2.71
324 330 6.280643 CCTAGAATATCACGGATGTTGTTCA 58.719 40.000 0.00 0.00 31.46 3.18
330 336 0.320421 ACGGATGTTGTTCACTCGGG 60.320 55.000 0.00 0.00 32.14 5.14
335 341 2.702592 TGTTGTTCACTCGGGAAACT 57.297 45.000 0.00 0.00 0.00 2.66
336 342 2.993937 TGTTGTTCACTCGGGAAACTT 58.006 42.857 0.00 0.00 0.00 2.66
346 352 4.152759 CACTCGGGAAACTTTTTATACGCA 59.847 41.667 0.00 0.00 0.00 5.24
375 382 9.715123 CATCGACTATGCATGTTACAAATAAAA 57.285 29.630 10.16 0.00 0.00 1.52
377 384 9.929722 TCGACTATGCATGTTACAAATAAAATC 57.070 29.630 10.16 0.00 0.00 2.17
378 385 9.715123 CGACTATGCATGTTACAAATAAAATCA 57.285 29.630 10.16 0.00 0.00 2.57
428 435 4.440851 TTATAATTCGTAAAGCGTGCGG 57.559 40.909 1.60 0.00 42.13 5.69
432 439 0.319383 TTCGTAAAGCGTGCGGGTTA 60.319 50.000 1.60 0.00 42.13 2.85
454 461 4.910195 AGACAATATTCACCAACTCTGCA 58.090 39.130 0.00 0.00 0.00 4.41
581 597 2.244695 TGAGAAGACCGGTCAAAGCTA 58.755 47.619 35.00 14.52 0.00 3.32
587 603 2.567615 AGACCGGTCAAAGCTATCAAGT 59.432 45.455 35.00 7.87 0.00 3.16
590 606 2.420022 CCGGTCAAAGCTATCAAGTTGG 59.580 50.000 2.34 0.00 0.00 3.77
635 655 4.388773 CCATCATTATTATCACCACCGACG 59.611 45.833 0.00 0.00 0.00 5.12
636 656 3.985008 TCATTATTATCACCACCGACGG 58.015 45.455 13.61 13.61 0.00 4.79
637 657 2.894763 TTATTATCACCACCGACGGG 57.105 50.000 20.00 7.12 40.11 5.28
640 660 2.233605 TTATCACCACCGACGGGCTG 62.234 60.000 20.00 8.25 36.48 4.85
661 681 1.374758 CCGCTTTTCTCACGCCTCT 60.375 57.895 0.00 0.00 0.00 3.69
673 701 1.548269 CACGCCTCTCTCTTTTCCTCT 59.452 52.381 0.00 0.00 0.00 3.69
674 702 1.548269 ACGCCTCTCTCTTTTCCTCTG 59.452 52.381 0.00 0.00 0.00 3.35
675 703 1.738700 CGCCTCTCTCTTTTCCTCTGC 60.739 57.143 0.00 0.00 0.00 4.26
676 704 1.406751 GCCTCTCTCTTTTCCTCTGCC 60.407 57.143 0.00 0.00 0.00 4.85
677 705 2.187100 CCTCTCTCTTTTCCTCTGCCT 58.813 52.381 0.00 0.00 0.00 4.75
678 706 2.093553 CCTCTCTCTTTTCCTCTGCCTG 60.094 54.545 0.00 0.00 0.00 4.85
679 707 1.277557 TCTCTCTTTTCCTCTGCCTGC 59.722 52.381 0.00 0.00 0.00 4.85
680 708 1.278699 CTCTCTTTTCCTCTGCCTGCT 59.721 52.381 0.00 0.00 0.00 4.24
681 709 1.277557 TCTCTTTTCCTCTGCCTGCTC 59.722 52.381 0.00 0.00 0.00 4.26
919 953 2.837291 CCTCCTCCGCCTCCTCTG 60.837 72.222 0.00 0.00 0.00 3.35
920 954 3.535962 CTCCTCCGCCTCCTCTGC 61.536 72.222 0.00 0.00 0.00 4.26
921 955 4.067512 TCCTCCGCCTCCTCTGCT 62.068 66.667 0.00 0.00 0.00 4.24
971 1005 1.415659 CACTGCAAGGAGATAGAGGGG 59.584 57.143 0.00 0.00 39.30 4.79
998 1032 1.211457 GGGGCATCTTCTGACATCAGT 59.789 52.381 8.70 0.00 44.12 3.41
1043 1341 0.324460 TCTCCGTCCTCCCTTCTTCC 60.324 60.000 0.00 0.00 0.00 3.46
1095 1393 7.208080 ACGGATTTGCTACAAGTTATACTAGG 58.792 38.462 0.00 0.00 0.00 3.02
1249 1547 4.518970 TGTTTTTCCCTACTGCTCAATCAC 59.481 41.667 0.00 0.00 0.00 3.06
1294 1592 5.463724 CGGAGGAAGCTCTCATGTTTATTAC 59.536 44.000 4.93 0.00 35.58 1.89
1296 1594 6.704050 GGAGGAAGCTCTCATGTTTATTACTC 59.296 42.308 4.93 0.00 35.58 2.59
1297 1595 6.587273 AGGAAGCTCTCATGTTTATTACTCC 58.413 40.000 0.00 0.00 0.00 3.85
1298 1596 5.760743 GGAAGCTCTCATGTTTATTACTCCC 59.239 44.000 0.00 0.00 0.00 4.30
1299 1597 6.408662 GGAAGCTCTCATGTTTATTACTCCCT 60.409 42.308 0.00 0.00 0.00 4.20
1300 1598 6.168270 AGCTCTCATGTTTATTACTCCCTC 57.832 41.667 0.00 0.00 0.00 4.30
1301 1599 5.902431 AGCTCTCATGTTTATTACTCCCTCT 59.098 40.000 0.00 0.00 0.00 3.69
1303 1601 6.407525 GCTCTCATGTTTATTACTCCCTCTGT 60.408 42.308 0.00 0.00 0.00 3.41
1304 1602 7.201920 GCTCTCATGTTTATTACTCCCTCTGTA 60.202 40.741 0.00 0.00 0.00 2.74
1305 1603 8.603898 TCTCATGTTTATTACTCCCTCTGTAA 57.396 34.615 0.00 0.00 34.87 2.41
1306 1604 9.042450 TCTCATGTTTATTACTCCCTCTGTAAA 57.958 33.333 0.00 0.00 34.20 2.01
1307 1605 9.099454 CTCATGTTTATTACTCCCTCTGTAAAC 57.901 37.037 0.00 0.00 34.20 2.01
1308 1606 8.822805 TCATGTTTATTACTCCCTCTGTAAACT 58.177 33.333 0.00 0.00 34.70 2.66
1319 1617 8.862085 ACTCCCTCTGTAAACTAATATAAGAGC 58.138 37.037 0.00 0.00 0.00 4.09
1320 1618 7.883217 TCCCTCTGTAAACTAATATAAGAGCG 58.117 38.462 0.00 0.00 0.00 5.03
1321 1619 7.504911 TCCCTCTGTAAACTAATATAAGAGCGT 59.495 37.037 0.00 0.00 0.00 5.07
1322 1620 8.142551 CCCTCTGTAAACTAATATAAGAGCGTT 58.857 37.037 0.00 0.00 0.00 4.84
1323 1621 9.530633 CCTCTGTAAACTAATATAAGAGCGTTT 57.469 33.333 0.00 0.00 0.00 3.60
1338 1636 9.953697 ATAAGAGCGTTTAGATCACTACTTTAG 57.046 33.333 0.00 0.00 37.82 1.85
1339 1637 7.393841 AGAGCGTTTAGATCACTACTTTAGT 57.606 36.000 0.00 0.00 37.82 2.24
1340 1638 8.503458 AGAGCGTTTAGATCACTACTTTAGTA 57.497 34.615 0.00 0.00 37.82 1.82
1341 1639 8.954350 AGAGCGTTTAGATCACTACTTTAGTAA 58.046 33.333 0.00 0.00 37.82 2.24
1342 1640 9.733219 GAGCGTTTAGATCACTACTTTAGTAAT 57.267 33.333 0.00 0.00 37.23 1.89
1343 1641 9.733219 AGCGTTTAGATCACTACTTTAGTAATC 57.267 33.333 0.00 0.00 37.23 1.75
1344 1642 9.733219 GCGTTTAGATCACTACTTTAGTAATCT 57.267 33.333 4.72 4.72 37.23 2.40
1350 1648 9.733219 AGATCACTACTTTAGTAATCTAAACGC 57.267 33.333 0.00 0.00 40.05 4.84
1351 1649 9.733219 GATCACTACTTTAGTAATCTAAACGCT 57.267 33.333 0.00 0.00 40.05 5.07
1352 1650 9.733219 ATCACTACTTTAGTAATCTAAACGCTC 57.267 33.333 0.00 0.00 40.05 5.03
1353 1651 8.954350 TCACTACTTTAGTAATCTAAACGCTCT 58.046 33.333 0.00 0.00 40.05 4.09
1354 1652 9.570488 CACTACTTTAGTAATCTAAACGCTCTT 57.430 33.333 0.00 0.00 40.05 2.85
1368 1666 9.669353 TCTAAACGCTCTTATATTAGTTTACGG 57.331 33.333 0.00 0.00 34.29 4.02
1369 1667 9.669353 CTAAACGCTCTTATATTAGTTTACGGA 57.331 33.333 0.00 0.00 34.29 4.69
1370 1668 8.571461 AAACGCTCTTATATTAGTTTACGGAG 57.429 34.615 0.00 0.00 31.14 4.63
1371 1669 6.675987 ACGCTCTTATATTAGTTTACGGAGG 58.324 40.000 0.00 0.00 0.00 4.30
1372 1670 6.091437 CGCTCTTATATTAGTTTACGGAGGG 58.909 44.000 0.00 0.00 0.00 4.30
1373 1671 6.072286 CGCTCTTATATTAGTTTACGGAGGGA 60.072 42.308 0.00 0.00 34.63 4.20
1374 1672 7.314393 GCTCTTATATTAGTTTACGGAGGGAG 58.686 42.308 0.00 0.00 0.00 4.30
1375 1673 7.039853 GCTCTTATATTAGTTTACGGAGGGAGT 60.040 40.741 0.00 0.00 0.00 3.85
1376 1674 9.512588 CTCTTATATTAGTTTACGGAGGGAGTA 57.487 37.037 0.00 0.00 0.00 2.59
1377 1675 9.512588 TCTTATATTAGTTTACGGAGGGAGTAG 57.487 37.037 0.00 0.00 0.00 2.57
1378 1676 9.294614 CTTATATTAGTTTACGGAGGGAGTAGT 57.705 37.037 0.00 0.00 0.00 2.73
1381 1679 9.819754 ATATTAGTTTACGGAGGGAGTAGTATT 57.180 33.333 0.00 0.00 0.00 1.89
1382 1680 7.573968 TTAGTTTACGGAGGGAGTAGTATTC 57.426 40.000 0.00 0.00 0.00 1.75
1431 1729 5.817296 TCTGTTTTCATATGTTCGATGGGAG 59.183 40.000 1.90 0.00 0.00 4.30
1435 1733 7.175816 TGTTTTCATATGTTCGATGGGAGAAAA 59.824 33.333 1.90 0.00 32.15 2.29
1436 1734 7.695480 TTTCATATGTTCGATGGGAGAAAAA 57.305 32.000 1.90 0.00 0.00 1.94
1478 1776 1.890876 TGTGGTTTGTTCGATGGGAG 58.109 50.000 0.00 0.00 0.00 4.30
1803 2103 2.642171 TTGGTCAGGTATCAGGGTCT 57.358 50.000 0.00 0.00 0.00 3.85
1822 2122 2.133553 CTCACCAGATAAGATGCTGCG 58.866 52.381 0.00 0.00 0.00 5.18
1889 2189 4.260375 CCGGCTAAACTCTCATTTGAATCG 60.260 45.833 0.00 0.00 0.00 3.34
1926 2226 7.806487 TCCATTTGATCTGATATACGTACGTTC 59.194 37.037 27.92 18.33 0.00 3.95
1979 2291 3.758755 AGAGTTGAATGACACTGCTGA 57.241 42.857 0.00 0.00 0.00 4.26
1980 2292 4.283363 AGAGTTGAATGACACTGCTGAT 57.717 40.909 0.00 0.00 0.00 2.90
1981 2293 4.649692 AGAGTTGAATGACACTGCTGATT 58.350 39.130 0.00 0.00 0.00 2.57
1982 2294 5.068636 AGAGTTGAATGACACTGCTGATTT 58.931 37.500 0.00 0.00 0.00 2.17
1983 2295 5.180868 AGAGTTGAATGACACTGCTGATTTC 59.819 40.000 0.00 0.00 0.00 2.17
1984 2296 4.083643 AGTTGAATGACACTGCTGATTTCG 60.084 41.667 0.00 0.00 0.00 3.46
1985 2297 2.160219 TGAATGACACTGCTGATTTCGC 59.840 45.455 0.00 0.00 0.00 4.70
1986 2298 2.105006 ATGACACTGCTGATTTCGCT 57.895 45.000 0.00 0.00 0.00 4.93
1987 2299 1.882912 TGACACTGCTGATTTCGCTT 58.117 45.000 0.00 0.00 0.00 4.68
1988 2300 2.221169 TGACACTGCTGATTTCGCTTT 58.779 42.857 0.00 0.00 0.00 3.51
1989 2301 2.224079 TGACACTGCTGATTTCGCTTTC 59.776 45.455 0.00 0.00 0.00 2.62
1990 2302 1.195448 ACACTGCTGATTTCGCTTTCG 59.805 47.619 0.00 0.00 0.00 3.46
2036 2348 9.195411 GTCATTTGTTTCATATGTTGTTCATGT 57.805 29.630 1.90 0.00 37.91 3.21
2048 2360 5.107824 TGTTGTTCATGTTTGACACATTGG 58.892 37.500 0.00 0.00 44.40 3.16
2080 2398 1.879380 TCACACACAGCATTAACAGGC 59.121 47.619 0.00 0.00 0.00 4.85
2151 2555 5.633601 CGCACTTCAGTTAGTACATTTGAGA 59.366 40.000 0.00 0.00 0.00 3.27
2164 2568 8.048534 AGTACATTTGAGATGTTCATTTGGAG 57.951 34.615 0.00 0.00 35.27 3.86
2244 2648 8.092687 TGTTTGGTTAGTCTTATTCTAGGTGAC 58.907 37.037 0.00 0.00 0.00 3.67
2278 2682 5.602978 ACCTGGTCGATCTAATCACCTATTT 59.397 40.000 0.00 0.00 34.02 1.40
2279 2683 6.781014 ACCTGGTCGATCTAATCACCTATTTA 59.219 38.462 0.00 0.00 34.02 1.40
2280 2684 7.039644 ACCTGGTCGATCTAATCACCTATTTAG 60.040 40.741 0.00 0.00 34.02 1.85
2281 2685 7.176865 CCTGGTCGATCTAATCACCTATTTAGA 59.823 40.741 0.00 0.00 34.02 2.10
2282 2686 8.651589 TGGTCGATCTAATCACCTATTTAGAT 57.348 34.615 0.00 5.18 34.02 1.98
2284 2688 9.930693 GGTCGATCTAATCACCTATTTAGATTT 57.069 33.333 6.63 0.00 34.19 2.17
2324 3309 8.873144 CATCCCCATAACTGGAAATTGAATTAT 58.127 33.333 0.00 0.00 46.37 1.28
2361 3346 5.525745 TGATGTACAGTATATGTTTTGCCCG 59.474 40.000 0.33 0.00 39.96 6.13
2440 3436 9.189723 GAGATGGTCTTTTCTTCTTCATTTTTG 57.810 33.333 0.00 0.00 0.00 2.44
2556 3604 0.975040 TTGTGGCTGTTGTGGGCTTT 60.975 50.000 0.00 0.00 0.00 3.51
2868 3949 5.708736 TGTCTAAAGGATTCTAATGGGCA 57.291 39.130 0.00 0.00 0.00 5.36
3120 4215 4.032960 TGTCCATGTGCTTTATCTTGGT 57.967 40.909 0.00 0.00 32.84 3.67
3411 4542 9.788889 TGAGAATTCTTTGATCATATATGTGCT 57.211 29.630 9.87 0.00 0.00 4.40
3413 4544 9.570468 AGAATTCTTTGATCATATATGTGCTGT 57.430 29.630 12.42 0.00 0.00 4.40
3471 4602 6.151144 GCACCCTCTTTATGTATTGTTTGAGT 59.849 38.462 0.00 0.00 0.00 3.41
3815 4972 2.549754 CGGGATGGTATGAGCAAATCAC 59.450 50.000 0.00 0.00 41.91 3.06
3828 4992 6.114767 TGAGCAAATCACATTACAGATGCTA 58.885 36.000 0.00 0.00 31.12 3.49
3829 4993 6.598850 TGAGCAAATCACATTACAGATGCTAA 59.401 34.615 0.00 0.00 31.12 3.09
3838 5085 9.278978 TCACATTACAGATGCTAAACTTTGTAA 57.721 29.630 0.00 0.00 36.02 2.41
3979 5283 2.686915 CCCAGCTCATCACTTTTCCATC 59.313 50.000 0.00 0.00 0.00 3.51
4015 5320 2.944129 TGGAAACTAGCTTGCTGGTTT 58.056 42.857 28.26 28.26 40.00 3.27
4126 5432 7.333423 GGAAAAGTACATCACATACTGCACTAA 59.667 37.037 0.00 0.00 33.11 2.24
4150 5456 2.421424 GCATCAAACTTCGCTCCAAGAT 59.579 45.455 0.00 0.00 0.00 2.40
4308 5614 3.676172 TGATTTTCGTGTAGGTTACGCAG 59.324 43.478 0.00 0.00 41.08 5.18
4614 5988 9.382244 GATACAACAAACTTGAACATGTACTTC 57.618 33.333 0.00 0.00 0.00 3.01
4841 6218 0.179020 TTCTTGGGTGGTCTGTGCTG 60.179 55.000 0.00 0.00 0.00 4.41
4862 6239 5.795441 GCTGTTCATTTCTTTACCGTTGATC 59.205 40.000 0.00 0.00 0.00 2.92
5081 6465 2.795231 TGGGCTTTCCTGAAGATGAG 57.205 50.000 0.00 0.00 37.57 2.90
5111 6495 5.632244 TTGCTATTACGAGATGCGGTATA 57.368 39.130 0.00 0.00 46.49 1.47
5585 7006 2.818432 AGAATGCTTCCTGAACAAGCTG 59.182 45.455 6.03 0.00 45.59 4.24
5778 7199 1.080329 AGCTCTTCTCCCTTTCCCTCT 59.920 52.381 0.00 0.00 0.00 3.69
6380 7813 5.123344 GCATCGTTAGTTGGTAGATTTGGTT 59.877 40.000 0.00 0.00 0.00 3.67
6641 8122 4.137116 ACCGCAGCTTCATCTATGTTTA 57.863 40.909 0.00 0.00 0.00 2.01
6646 8127 5.961843 CGCAGCTTCATCTATGTTTAAACAG 59.038 40.000 24.22 13.11 43.04 3.16
6652 8133 6.985188 TCATCTATGTTTAAACAGTGAGGC 57.015 37.500 24.22 0.00 43.04 4.70
6719 8201 4.724399 TCCAAATTCTGTTTAGTGCTGGA 58.276 39.130 0.00 0.00 0.00 3.86
6720 8202 4.518970 TCCAAATTCTGTTTAGTGCTGGAC 59.481 41.667 0.00 0.00 0.00 4.02
6721 8203 4.278170 CCAAATTCTGTTTAGTGCTGGACA 59.722 41.667 1.24 0.00 0.00 4.02
6722 8204 5.221224 CCAAATTCTGTTTAGTGCTGGACAA 60.221 40.000 1.24 0.00 0.00 3.18
6723 8205 6.272318 CAAATTCTGTTTAGTGCTGGACAAA 58.728 36.000 1.24 0.00 0.00 2.83
6724 8206 4.893424 TTCTGTTTAGTGCTGGACAAAC 57.107 40.909 15.10 15.10 0.00 2.93
6725 8207 3.879998 TCTGTTTAGTGCTGGACAAACA 58.120 40.909 19.84 19.84 35.79 2.83
6726 8208 4.265893 TCTGTTTAGTGCTGGACAAACAA 58.734 39.130 20.69 13.71 36.25 2.83
6755 8237 1.097232 TGCACTGCCTTACATGATGC 58.903 50.000 0.00 0.00 0.00 3.91
6760 8242 3.064958 CACTGCCTTACATGATGCTCTTG 59.935 47.826 0.00 0.00 0.00 3.02
6761 8243 3.276857 CTGCCTTACATGATGCTCTTGT 58.723 45.455 0.00 8.81 38.20 3.16
6770 8252 1.881973 TGATGCTCTTGTTTGTCTGGC 59.118 47.619 0.00 0.00 0.00 4.85
6778 8260 0.181114 TGTTTGTCTGGCTGAGCTGT 59.819 50.000 3.72 0.00 0.00 4.40
6788 8270 1.938577 GGCTGAGCTGTACATGTCATG 59.061 52.381 11.41 11.41 0.00 3.07
6895 8378 7.568349 TCATATCATTTCCTCTGCTTACACTT 58.432 34.615 0.00 0.00 0.00 3.16
7011 8684 9.574516 AAGCCTATATAGGAAGGTAAAAATGTG 57.425 33.333 29.64 0.70 46.63 3.21
7012 8685 8.164070 AGCCTATATAGGAAGGTAAAAATGTGG 58.836 37.037 29.64 1.08 46.63 4.17
7067 8741 6.014669 AGCAGGGTGTTTAATTTGCTATTTCA 60.015 34.615 0.00 0.00 39.85 2.69
7083 8757 5.105997 GCTATTTCACACAGCATCTTTCCTT 60.106 40.000 0.00 0.00 35.35 3.36
7149 8879 2.042842 TGGGATGGGATGCAAAAGAAGA 59.957 45.455 0.00 0.00 0.00 2.87
7222 8952 1.525197 CGTTTCGCACACTAAGCTTGA 59.475 47.619 9.86 0.00 0.00 3.02
7301 10002 0.883833 CCCACAGCACACTTCATTCC 59.116 55.000 0.00 0.00 0.00 3.01
7325 10300 8.160765 TCCTTGGTAGTGATGAAAAGAATGTAA 58.839 33.333 0.00 0.00 0.00 2.41
7350 10326 2.026822 ACTGGTATTTCACTCAGGGCAG 60.027 50.000 0.00 0.00 32.66 4.85
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
59 61 6.239036 GGAGCCATGTCCACCTTTATATTTTC 60.239 42.308 0.00 0.00 36.51 2.29
64 66 2.104111 CGGAGCCATGTCCACCTTTATA 59.896 50.000 3.48 0.00 36.23 0.98
81 83 2.434884 ATGTTGGTGCTCGCGGAG 60.435 61.111 6.13 3.47 0.00 4.63
153 157 9.469807 GTAGAATGATCGATCAAGTTCAATACT 57.530 33.333 29.73 18.16 40.69 2.12
186 191 5.634859 GGTGTCAATGCTTCATTAAACTTGG 59.365 40.000 0.00 0.00 32.35 3.61
187 192 5.634859 GGGTGTCAATGCTTCATTAAACTTG 59.365 40.000 0.00 0.00 32.35 3.16
319 325 6.073657 CGTATAAAAAGTTTCCCGAGTGAACA 60.074 38.462 0.00 0.00 0.00 3.18
324 330 4.317488 TGCGTATAAAAAGTTTCCCGAGT 58.683 39.130 0.00 0.00 0.00 4.18
330 336 6.019152 TCGATGCTTGCGTATAAAAAGTTTC 58.981 36.000 0.00 0.00 0.00 2.78
335 341 6.645705 CATAGTCGATGCTTGCGTATAAAAA 58.354 36.000 0.00 0.00 0.00 1.94
336 342 6.210396 CATAGTCGATGCTTGCGTATAAAA 57.790 37.500 0.00 0.00 0.00 1.52
428 435 6.183360 GCAGAGTTGGTGAATATTGTCTAACC 60.183 42.308 0.00 0.00 0.00 2.85
432 439 4.910195 TGCAGAGTTGGTGAATATTGTCT 58.090 39.130 0.00 0.00 0.00 3.41
545 561 8.383619 CGGTCTTCTCATTTAAGTTAATGACTG 58.616 37.037 0.00 0.00 39.07 3.51
555 571 5.390991 GCTTTGACCGGTCTTCTCATTTAAG 60.391 44.000 33.39 20.34 0.00 1.85
564 580 3.247006 TGATAGCTTTGACCGGTCTTC 57.753 47.619 33.39 19.19 0.00 2.87
581 597 6.349280 CGGTCATAATTGTCAACCAACTTGAT 60.349 38.462 4.72 0.00 41.10 2.57
587 603 3.754323 GACCGGTCATAATTGTCAACCAA 59.246 43.478 29.75 0.00 37.49 3.67
590 606 3.126343 GTGGACCGGTCATAATTGTCAAC 59.874 47.826 34.40 13.83 0.00 3.18
597 617 2.123589 TGATGGTGGACCGGTCATAAT 58.876 47.619 34.40 21.36 39.43 1.28
598 618 1.574263 TGATGGTGGACCGGTCATAA 58.426 50.000 34.40 17.57 39.43 1.90
635 655 2.982744 GAGAAAAGCGGTGCAGCCC 61.983 63.158 10.90 0.25 38.01 5.19
636 656 2.260869 TGAGAAAAGCGGTGCAGCC 61.261 57.895 10.90 3.18 38.01 4.85
637 657 1.081840 GTGAGAAAAGCGGTGCAGC 60.082 57.895 5.64 5.64 37.41 5.25
640 660 2.127232 GCGTGAGAAAAGCGGTGC 60.127 61.111 0.00 0.00 0.00 5.01
661 681 1.277557 GAGCAGGCAGAGGAAAAGAGA 59.722 52.381 0.00 0.00 0.00 3.10
673 701 1.746470 CACATCTCAATGAGCAGGCA 58.254 50.000 5.18 0.00 36.67 4.75
674 702 0.381089 GCACATCTCAATGAGCAGGC 59.619 55.000 5.18 3.08 45.49 4.85
675 703 0.656259 CGCACATCTCAATGAGCAGG 59.344 55.000 5.18 0.00 46.21 4.85
676 704 0.027716 GCGCACATCTCAATGAGCAG 59.972 55.000 5.18 2.90 46.21 4.24
677 705 0.392060 AGCGCACATCTCAATGAGCA 60.392 50.000 11.47 0.00 46.21 4.26
678 706 0.027716 CAGCGCACATCTCAATGAGC 59.972 55.000 11.47 0.00 43.54 4.26
679 707 0.027716 GCAGCGCACATCTCAATGAG 59.972 55.000 11.47 3.38 36.67 2.90
680 708 1.698714 CGCAGCGCACATCTCAATGA 61.699 55.000 11.47 0.00 36.67 2.57
681 709 1.297378 CGCAGCGCACATCTCAATG 60.297 57.895 11.47 0.00 38.93 2.82
733 761 1.442769 ATGTGTTCTGTCGATGTGCC 58.557 50.000 0.00 0.00 0.00 5.01
919 953 2.046120 AGGAAGAGCAGCAGCAGC 60.046 61.111 3.17 0.46 45.49 5.25
920 954 1.810441 CGAGGAAGAGCAGCAGCAG 60.810 63.158 3.17 0.00 45.49 4.24
921 955 2.223200 CTCGAGGAAGAGCAGCAGCA 62.223 60.000 3.91 0.00 45.49 4.41
971 1005 4.570874 GAAGATGCCCCGCCCCTC 62.571 72.222 0.00 0.00 0.00 4.30
998 1032 1.133450 AGAGAGAGCCTACCGCCATTA 60.133 52.381 0.00 0.00 38.78 1.90
1043 1341 0.535102 ATGGGGCTCTAAAATCGCCG 60.535 55.000 0.00 0.00 44.68 6.46
1249 1547 2.415893 GCATCGGGATGGAAACTTTGTG 60.416 50.000 10.44 0.00 39.16 3.33
1294 1592 8.024285 CGCTCTTATATTAGTTTACAGAGGGAG 58.976 40.741 4.76 0.00 40.49 4.30
1296 1594 7.659186 ACGCTCTTATATTAGTTTACAGAGGG 58.341 38.462 8.36 8.36 42.53 4.30
1297 1595 9.530633 AAACGCTCTTATATTAGTTTACAGAGG 57.469 33.333 0.00 0.00 31.14 3.69
1312 1610 9.953697 CTAAAGTAGTGATCTAAACGCTCTTAT 57.046 33.333 0.00 0.00 0.00 1.73
1313 1611 8.954350 ACTAAAGTAGTGATCTAAACGCTCTTA 58.046 33.333 0.00 0.00 37.69 2.10
1314 1612 7.828712 ACTAAAGTAGTGATCTAAACGCTCTT 58.171 34.615 0.00 0.00 37.69 2.85
1315 1613 7.393841 ACTAAAGTAGTGATCTAAACGCTCT 57.606 36.000 0.00 0.00 37.69 4.09
1316 1614 9.733219 ATTACTAAAGTAGTGATCTAAACGCTC 57.267 33.333 0.00 0.00 39.81 5.03
1317 1615 9.733219 GATTACTAAAGTAGTGATCTAAACGCT 57.267 33.333 11.11 0.00 44.10 5.07
1325 1623 9.733219 AGCGTTTAGATTACTAAAGTAGTGATC 57.267 33.333 10.62 10.62 46.38 2.92
1326 1624 9.733219 GAGCGTTTAGATTACTAAAGTAGTGAT 57.267 33.333 0.00 0.00 45.42 3.06
1327 1625 8.954350 AGAGCGTTTAGATTACTAAAGTAGTGA 58.046 33.333 0.00 0.00 45.42 3.41
1328 1626 9.570488 AAGAGCGTTTAGATTACTAAAGTAGTG 57.430 33.333 0.00 0.00 45.42 2.74
1342 1640 9.669353 CCGTAAACTAATATAAGAGCGTTTAGA 57.331 33.333 0.00 0.00 30.36 2.10
1343 1641 9.669353 TCCGTAAACTAATATAAGAGCGTTTAG 57.331 33.333 0.00 0.00 30.36 1.85
1344 1642 9.669353 CTCCGTAAACTAATATAAGAGCGTTTA 57.331 33.333 0.00 0.00 0.00 2.01
1345 1643 7.650903 CCTCCGTAAACTAATATAAGAGCGTTT 59.349 37.037 0.00 0.00 0.00 3.60
1346 1644 7.144000 CCTCCGTAAACTAATATAAGAGCGTT 58.856 38.462 0.00 0.00 0.00 4.84
1347 1645 6.294397 CCCTCCGTAAACTAATATAAGAGCGT 60.294 42.308 0.00 0.00 0.00 5.07
1348 1646 6.072286 TCCCTCCGTAAACTAATATAAGAGCG 60.072 42.308 0.00 0.00 0.00 5.03
1349 1647 7.039853 ACTCCCTCCGTAAACTAATATAAGAGC 60.040 40.741 0.00 0.00 0.00 4.09
1350 1648 8.406730 ACTCCCTCCGTAAACTAATATAAGAG 57.593 38.462 0.00 0.00 0.00 2.85
1351 1649 9.512588 CTACTCCCTCCGTAAACTAATATAAGA 57.487 37.037 0.00 0.00 0.00 2.10
1352 1650 9.294614 ACTACTCCCTCCGTAAACTAATATAAG 57.705 37.037 0.00 0.00 0.00 1.73
1355 1653 9.819754 AATACTACTCCCTCCGTAAACTAATAT 57.180 33.333 0.00 0.00 0.00 1.28
1356 1654 9.289782 GAATACTACTCCCTCCGTAAACTAATA 57.710 37.037 0.00 0.00 0.00 0.98
1357 1655 8.003629 AGAATACTACTCCCTCCGTAAACTAAT 58.996 37.037 0.00 0.00 0.00 1.73
1358 1656 7.349598 AGAATACTACTCCCTCCGTAAACTAA 58.650 38.462 0.00 0.00 0.00 2.24
1359 1657 6.904626 AGAATACTACTCCCTCCGTAAACTA 58.095 40.000 0.00 0.00 0.00 2.24
1360 1658 5.764432 AGAATACTACTCCCTCCGTAAACT 58.236 41.667 0.00 0.00 0.00 2.66
1361 1659 6.096001 TCAAGAATACTACTCCCTCCGTAAAC 59.904 42.308 0.00 0.00 0.00 2.01
1362 1660 6.096001 GTCAAGAATACTACTCCCTCCGTAAA 59.904 42.308 0.00 0.00 0.00 2.01
1363 1661 5.591877 GTCAAGAATACTACTCCCTCCGTAA 59.408 44.000 0.00 0.00 0.00 3.18
1364 1662 5.128919 GTCAAGAATACTACTCCCTCCGTA 58.871 45.833 0.00 0.00 0.00 4.02
1365 1663 3.952967 GTCAAGAATACTACTCCCTCCGT 59.047 47.826 0.00 0.00 0.00 4.69
1366 1664 3.003482 CGTCAAGAATACTACTCCCTCCG 59.997 52.174 0.00 0.00 0.00 4.63
1367 1665 3.952967 ACGTCAAGAATACTACTCCCTCC 59.047 47.826 0.00 0.00 0.00 4.30
1368 1666 6.485984 TGATACGTCAAGAATACTACTCCCTC 59.514 42.308 0.00 0.00 0.00 4.30
1369 1667 6.363065 TGATACGTCAAGAATACTACTCCCT 58.637 40.000 0.00 0.00 0.00 4.20
1370 1668 6.262720 ACTGATACGTCAAGAATACTACTCCC 59.737 42.308 0.00 0.00 33.05 4.30
1371 1669 7.227116 AGACTGATACGTCAAGAATACTACTCC 59.773 40.741 0.00 0.00 36.38 3.85
1372 1670 8.065407 CAGACTGATACGTCAAGAATACTACTC 58.935 40.741 0.00 0.00 36.38 2.59
1373 1671 7.553402 ACAGACTGATACGTCAAGAATACTACT 59.447 37.037 10.08 0.00 36.38 2.57
1374 1672 7.640630 CACAGACTGATACGTCAAGAATACTAC 59.359 40.741 10.08 0.00 36.38 2.73
1375 1673 7.678927 GCACAGACTGATACGTCAAGAATACTA 60.679 40.741 10.08 0.00 36.38 1.82
1376 1674 6.556212 CACAGACTGATACGTCAAGAATACT 58.444 40.000 10.08 0.00 36.38 2.12
1377 1675 5.230306 GCACAGACTGATACGTCAAGAATAC 59.770 44.000 10.08 0.00 36.38 1.89
1378 1676 5.340803 GCACAGACTGATACGTCAAGAATA 58.659 41.667 10.08 0.00 36.38 1.75
1379 1677 4.177026 GCACAGACTGATACGTCAAGAAT 58.823 43.478 10.08 0.00 36.38 2.40
1380 1678 3.575630 GCACAGACTGATACGTCAAGAA 58.424 45.455 10.08 0.00 36.38 2.52
1381 1679 2.414161 CGCACAGACTGATACGTCAAGA 60.414 50.000 10.08 0.00 36.38 3.02
1382 1680 1.914051 CGCACAGACTGATACGTCAAG 59.086 52.381 10.08 0.00 36.38 3.02
1435 1733 6.670695 AAACCTCCAATATGCAGAAAGTTT 57.329 33.333 0.00 0.00 0.00 2.66
1436 1734 6.041979 ACAAAACCTCCAATATGCAGAAAGTT 59.958 34.615 0.00 0.00 0.00 2.66
1441 1739 3.763360 CCACAAAACCTCCAATATGCAGA 59.237 43.478 0.00 0.00 0.00 4.26
1447 1745 5.450688 CGAACAAACCACAAAACCTCCAATA 60.451 40.000 0.00 0.00 0.00 1.90
1708 2006 0.106819 AGATGCCTGGTCTGCCATTC 60.107 55.000 0.00 0.00 45.05 2.67
1709 2007 1.216064 TAGATGCCTGGTCTGCCATT 58.784 50.000 0.00 0.00 45.05 3.16
1712 2010 0.471617 ACATAGATGCCTGGTCTGCC 59.528 55.000 0.00 0.00 0.00 4.85
1803 2103 1.202568 CCGCAGCATCTTATCTGGTGA 60.203 52.381 6.67 0.00 43.12 4.02
1822 2122 2.349580 GCCGGTATTTTGACTAACGACC 59.650 50.000 1.90 0.00 30.93 4.79
1979 2291 1.400494 CCGAAATCCCGAAAGCGAAAT 59.600 47.619 0.00 0.00 40.82 2.17
1980 2292 0.800012 CCGAAATCCCGAAAGCGAAA 59.200 50.000 0.00 0.00 40.82 3.46
1981 2293 1.641123 GCCGAAATCCCGAAAGCGAA 61.641 55.000 0.00 0.00 40.82 4.70
1982 2294 2.104253 GCCGAAATCCCGAAAGCGA 61.104 57.895 0.00 0.00 40.82 4.93
1983 2295 2.106683 AGCCGAAATCCCGAAAGCG 61.107 57.895 0.00 0.00 37.24 4.68
1984 2296 1.429423 CAGCCGAAATCCCGAAAGC 59.571 57.895 0.00 0.00 0.00 3.51
1985 2297 1.429423 GCAGCCGAAATCCCGAAAG 59.571 57.895 0.00 0.00 0.00 2.62
1986 2298 2.043980 GGCAGCCGAAATCCCGAAA 61.044 57.895 0.00 0.00 0.00 3.46
1987 2299 2.437716 GGCAGCCGAAATCCCGAA 60.438 61.111 0.00 0.00 0.00 4.30
2007 2319 7.651304 TGAACAACATATGAAACAAATGACCAC 59.349 33.333 10.38 0.00 0.00 4.16
2036 2348 3.023119 ACAAGAGTGCCAATGTGTCAAA 58.977 40.909 0.00 0.00 0.00 2.69
2151 2555 4.942761 AGTTTGCACTCCAAATGAACAT 57.057 36.364 0.00 0.00 44.61 2.71
2164 2568 4.023878 TGGATAAACAACGGTAGTTTGCAC 60.024 41.667 10.13 2.95 39.36 4.57
2244 2648 0.893270 TCGACCAGGTTTGCCCATTG 60.893 55.000 0.00 0.00 34.66 2.82
2278 2682 8.161425 GGGGATGCTAAATAACTGGTAAATCTA 58.839 37.037 0.00 0.00 0.00 1.98
2279 2683 7.004691 GGGGATGCTAAATAACTGGTAAATCT 58.995 38.462 0.00 0.00 0.00 2.40
2280 2684 6.775629 TGGGGATGCTAAATAACTGGTAAATC 59.224 38.462 0.00 0.00 0.00 2.17
2281 2685 6.678547 TGGGGATGCTAAATAACTGGTAAAT 58.321 36.000 0.00 0.00 0.00 1.40
2282 2686 6.080969 TGGGGATGCTAAATAACTGGTAAA 57.919 37.500 0.00 0.00 0.00 2.01
2284 2688 5.922960 ATGGGGATGCTAAATAACTGGTA 57.077 39.130 0.00 0.00 0.00 3.25
2286 2690 6.306987 AGTTATGGGGATGCTAAATAACTGG 58.693 40.000 14.24 0.00 40.67 4.00
2361 3346 6.954944 TGTCACAACAAGACATTAAGCTAAC 58.045 36.000 0.00 0.00 40.80 2.34
2440 3436 7.421530 TTTGCAGTACAGTTTAGAGAACATC 57.578 36.000 0.00 0.00 0.00 3.06
2556 3604 6.091305 CGCACAGAGAAGAATTATTCTGTCAA 59.909 38.462 19.59 0.00 44.71 3.18
3410 4541 6.741992 TGGCAAAGACTTCACATATAACAG 57.258 37.500 0.00 0.00 0.00 3.16
3411 4542 6.404623 GCATGGCAAAGACTTCACATATAACA 60.405 38.462 0.00 0.00 0.00 2.41
3412 4543 5.973565 GCATGGCAAAGACTTCACATATAAC 59.026 40.000 0.00 0.00 0.00 1.89
3413 4544 5.651576 TGCATGGCAAAGACTTCACATATAA 59.348 36.000 0.00 0.00 34.76 0.98
3414 4545 5.192176 TGCATGGCAAAGACTTCACATATA 58.808 37.500 0.00 0.00 34.76 0.86
3415 4546 4.018490 TGCATGGCAAAGACTTCACATAT 58.982 39.130 0.00 0.00 34.76 1.78
3416 4547 3.419943 TGCATGGCAAAGACTTCACATA 58.580 40.909 0.00 0.00 34.76 2.29
3417 4548 2.241160 TGCATGGCAAAGACTTCACAT 58.759 42.857 0.00 0.00 34.76 3.21
3418 4549 1.689984 TGCATGGCAAAGACTTCACA 58.310 45.000 0.00 0.00 34.76 3.58
3419 4550 3.428045 GGTATGCATGGCAAAGACTTCAC 60.428 47.826 10.16 0.00 43.62 3.18
3420 4551 2.754552 GGTATGCATGGCAAAGACTTCA 59.245 45.455 10.16 0.00 43.62 3.02
3421 4552 3.019564 AGGTATGCATGGCAAAGACTTC 58.980 45.455 10.16 0.00 43.62 3.01
3677 4824 6.222389 TCATAAAAATCACAAACAAGCAGGG 58.778 36.000 0.00 0.00 0.00 4.45
3815 4972 9.722056 GGATTACAAAGTTTAGCATCTGTAATG 57.278 33.333 10.21 0.00 39.08 1.90
3838 5085 7.451877 AGTCCGATTGTACACTATATCTTGGAT 59.548 37.037 0.00 0.00 0.00 3.41
3979 5283 1.462616 TCCAACCATCCTTGCATTCG 58.537 50.000 0.00 0.00 0.00 3.34
4126 5432 2.161855 TGGAGCGAAGTTTGATGCAAT 58.838 42.857 0.00 0.00 0.00 3.56
4150 5456 6.305272 AGATATTGCTCTTCTTGAGGTTGA 57.695 37.500 0.00 0.00 42.87 3.18
4382 5697 5.682730 GCACTCCATACTCTTTCCCTACTTC 60.683 48.000 0.00 0.00 0.00 3.01
4614 5988 3.947834 GGTGATGGACAGGAATAAACTGG 59.052 47.826 0.00 0.00 40.23 4.00
4841 6218 5.795441 GCTGATCAACGGTAAAGAAATGAAC 59.205 40.000 0.00 0.00 0.00 3.18
4862 6239 3.054802 AGAAATGAAGGGGACTACAGCTG 60.055 47.826 13.48 13.48 42.68 4.24
5081 6465 9.919559 CCGCATCTCGTAATAGCAATATTTGCC 62.920 44.444 8.52 0.00 46.90 4.52
5111 6495 7.065803 TGTCGAGACAAAAATTTCAGAAAGAGT 59.934 33.333 3.11 0.00 38.56 3.24
5778 7199 5.298276 GGGAATGCATCAAATACGGTCTTTA 59.702 40.000 0.00 0.00 0.00 1.85
6380 7813 1.522668 CCAATCACCAAGTCGAAGCA 58.477 50.000 0.00 0.00 0.00 3.91
6641 8122 1.594293 CCACGTCGCCTCACTGTTT 60.594 57.895 0.00 0.00 0.00 2.83
6646 8127 3.296709 ATCCACCACGTCGCCTCAC 62.297 63.158 0.00 0.00 0.00 3.51
6652 8133 3.742786 CAAATAAACATCCACCACGTCG 58.257 45.455 0.00 0.00 0.00 5.12
6692 8174 7.094205 CCAGCACTAAACAGAATTTGGATACTT 60.094 37.037 0.00 0.00 37.61 2.24
6719 8201 3.946558 AGTGCATGGCAAAATTTGTTTGT 59.053 34.783 7.60 0.00 41.47 2.83
6720 8202 4.283678 CAGTGCATGGCAAAATTTGTTTG 58.716 39.130 7.60 4.36 41.47 2.93
6721 8203 3.243134 GCAGTGCATGGCAAAATTTGTTT 60.243 39.130 11.09 0.00 41.47 2.83
6722 8204 2.291190 GCAGTGCATGGCAAAATTTGTT 59.709 40.909 11.09 0.00 41.47 2.83
6723 8205 1.874872 GCAGTGCATGGCAAAATTTGT 59.125 42.857 11.09 0.00 41.47 2.83
6724 8206 2.604969 GCAGTGCATGGCAAAATTTG 57.395 45.000 11.09 0.57 41.47 2.32
6755 8237 1.534595 GCTCAGCCAGACAAACAAGAG 59.465 52.381 0.00 0.00 0.00 2.85
6760 8242 1.801178 GTACAGCTCAGCCAGACAAAC 59.199 52.381 0.00 0.00 0.00 2.93
6761 8243 1.416030 TGTACAGCTCAGCCAGACAAA 59.584 47.619 0.00 0.00 0.00 2.83
6770 8252 5.290400 CAGTTACATGACATGTACAGCTCAG 59.710 44.000 24.63 10.61 44.79 3.35
6778 8260 5.793817 ACTGAAGCAGTTACATGACATGTA 58.206 37.500 21.76 21.76 42.59 2.29
6941 8427 4.602340 AACCTTATCGTGTTCACTCACT 57.398 40.909 1.53 0.00 36.33 3.41
6942 8428 6.774354 TTTAACCTTATCGTGTTCACTCAC 57.226 37.500 1.53 0.00 35.28 3.51
6943 8429 7.211573 TCTTTTAACCTTATCGTGTTCACTCA 58.788 34.615 1.53 0.00 0.00 3.41
6944 8430 7.148623 CCTCTTTTAACCTTATCGTGTTCACTC 60.149 40.741 1.53 0.00 0.00 3.51
7011 8684 2.680339 GTTAACAGCAGAAGATCAGGCC 59.320 50.000 0.00 0.00 0.00 5.19
7012 8685 2.680339 GGTTAACAGCAGAAGATCAGGC 59.320 50.000 8.10 0.00 0.00 4.85
7067 8741 3.754965 TGCTAAAGGAAAGATGCTGTGT 58.245 40.909 0.00 0.00 0.00 3.72
7083 8757 6.315144 TCGTCTATGCTAAAATGCTTTGCTAA 59.685 34.615 0.00 0.00 0.00 3.09
7222 8952 4.644685 ACATTGGTACTTGTTTCAGCTTGT 59.355 37.500 0.00 0.00 0.00 3.16
7301 10002 9.003658 ACTTACATTCTTTTCATCACTACCAAG 57.996 33.333 0.00 0.00 0.00 3.61
7325 10300 4.323562 GCCCTGAGTGAAATACCAGTTACT 60.324 45.833 0.00 0.00 0.00 2.24


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

AutoCloner maintained by Alex Coulton.