Multiple sequence alignment - TraesCS5A01G485200

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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 TraesCS5A01G485200 chr5A 100.000 3878 0 0 1 3878 656493153 656497030 0.000000e+00 7162.0
1 TraesCS5A01G485200 chr5A 94.428 2082 75 13 755 2813 656670773 656672836 0.000000e+00 3164.0
2 TraesCS5A01G485200 chr5A 90.434 1704 149 11 1073 2773 656222595 656220903 0.000000e+00 2231.0
3 TraesCS5A01G485200 chr5A 92.734 578 28 6 3315 3878 323384984 323385561 0.000000e+00 822.0
4 TraesCS5A01G485200 chr5A 85.095 369 31 16 2962 3317 655092274 655092631 4.770000e-94 355.0
5 TraesCS5A01G485200 chr5A 88.235 187 10 4 575 751 656670615 656670799 3.040000e-51 213.0
6 TraesCS5A01G485200 chr5B 91.369 2549 141 32 310 2813 665538975 665541489 0.000000e+00 3415.0
7 TraesCS5A01G485200 chr5B 91.656 2385 122 35 592 2957 665173656 665171330 0.000000e+00 3230.0
8 TraesCS5A01G485200 chr5B 90.064 1711 152 11 1076 2773 665026431 665024726 0.000000e+00 2202.0
9 TraesCS5A01G485200 chr5B 85.169 445 39 13 31 451 665538524 665538965 7.700000e-117 431.0
10 TraesCS5A01G485200 chr5B 86.486 370 24 16 2962 3317 296042263 296041906 2.190000e-102 383.0
11 TraesCS5A01G485200 chr5B 83.416 404 35 13 31 409 665184613 665184217 2.870000e-91 346.0
12 TraesCS5A01G485200 chr5B 84.426 122 14 4 460 580 42705809 42705692 8.800000e-22 115.0
13 TraesCS5A01G485200 chr5D 93.822 2169 112 15 802 2956 528414969 528417129 0.000000e+00 3243.0
14 TraesCS5A01G485200 chr5D 94.019 2023 81 10 802 2813 528586955 528588948 0.000000e+00 3029.0
15 TraesCS5A01G485200 chr5D 90.245 1712 144 15 1076 2773 528296417 528294715 0.000000e+00 2215.0
16 TraesCS5A01G485200 chr5D 85.099 557 45 12 31 551 528586023 528586577 5.700000e-148 534.0
17 TraesCS5A01G485200 chr6A 94.326 564 27 4 3318 3878 29290190 29289629 0.000000e+00 859.0
18 TraesCS5A01G485200 chr6A 92.483 572 31 8 3318 3878 29243183 29243753 0.000000e+00 808.0
19 TraesCS5A01G485200 chr6A 91.711 567 34 11 3318 3878 374697639 374697080 0.000000e+00 774.0
20 TraesCS5A01G485200 chr7A 93.092 579 25 8 3311 3878 64067793 64068367 0.000000e+00 833.0
21 TraesCS5A01G485200 chr7A 93.428 563 34 3 3318 3878 666534551 666533990 0.000000e+00 832.0
22 TraesCS5A01G485200 chr7A 93.146 569 26 6 3318 3878 648884183 648883620 0.000000e+00 822.0
23 TraesCS5A01G485200 chr7A 86.875 320 30 8 3009 3317 541459529 541459847 7.970000e-92 348.0
24 TraesCS5A01G485200 chr3A 92.883 562 34 6 3321 3878 16128311 16127752 0.000000e+00 811.0
25 TraesCS5A01G485200 chr3A 92.063 567 30 11 3318 3878 28197359 28196802 0.000000e+00 784.0
26 TraesCS5A01G485200 chr7B 86.425 442 55 5 1629 2066 706991894 706991454 2.710000e-131 479.0
27 TraesCS5A01G485200 chr7B 93.636 110 7 0 2118 2227 706981773 706981664 8.620000e-37 165.0
28 TraesCS5A01G485200 chr2D 80.524 611 53 25 1629 2227 645597822 645598378 3.610000e-110 409.0
29 TraesCS5A01G485200 chr7D 86.243 378 31 12 2951 3317 596257737 596257370 1.310000e-104 390.0
30 TraesCS5A01G485200 chrUn 87.115 357 23 13 2956 3298 71414598 71414251 2.190000e-102 383.0
31 TraesCS5A01G485200 chrUn 88.820 322 20 10 3009 3317 28729201 28728883 7.860000e-102 381.0
32 TraesCS5A01G485200 chrUn 85.904 376 30 12 2956 3317 71473660 71473294 2.830000e-101 379.0
33 TraesCS5A01G485200 chr4A 87.059 340 28 10 2962 3291 575778151 575777818 1.700000e-98 370.0
34 TraesCS5A01G485200 chr2A 87.147 319 27 9 3000 3305 672443448 672443131 2.220000e-92 350.0
35 TraesCS5A01G485200 chr2A 90.000 50 5 0 1392 1441 569902530 569902579 8.990000e-07 65.8
36 TraesCS5A01G485200 chr2B 88.889 135 14 1 456 590 539342101 539341968 8.620000e-37 165.0
37 TraesCS5A01G485200 chr2B 88.148 135 15 1 456 590 539344058 539343925 4.010000e-35 159.0
38 TraesCS5A01G485200 chr2B 87.050 139 16 2 452 590 539344929 539344793 5.190000e-34 156.0
39 TraesCS5A01G485200 chr2B 86.667 135 17 1 456 590 539346673 539346540 8.680000e-32 148.0
40 TraesCS5A01G485200 chr2B 96.970 33 1 0 456 488 539378502 539378470 5.410000e-04 56.5
41 TraesCS5A01G485200 chr1D 83.654 104 15 1 485 588 422270932 422271033 3.190000e-16 97.1
42 TraesCS5A01G485200 chr1A 93.333 60 4 0 2057 2116 138785466 138785407 5.340000e-14 89.8
43 TraesCS5A01G485200 chr1A 93.333 60 4 0 2057 2116 357953137 357953078 5.340000e-14 89.8
44 TraesCS5A01G485200 chr3D 90.698 43 0 4 2050 2090 177347654 177347614 2.000000e-03 54.7


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 TraesCS5A01G485200 chr5A 656493153 656497030 3877 False 7162.0 7162 100.0000 1 3878 1 chr5A.!!$F3 3877
1 TraesCS5A01G485200 chr5A 656220903 656222595 1692 True 2231.0 2231 90.4340 1073 2773 1 chr5A.!!$R1 1700
2 TraesCS5A01G485200 chr5A 656670615 656672836 2221 False 1688.5 3164 91.3315 575 2813 2 chr5A.!!$F4 2238
3 TraesCS5A01G485200 chr5A 323384984 323385561 577 False 822.0 822 92.7340 3315 3878 1 chr5A.!!$F1 563
4 TraesCS5A01G485200 chr5B 665171330 665173656 2326 True 3230.0 3230 91.6560 592 2957 1 chr5B.!!$R4 2365
5 TraesCS5A01G485200 chr5B 665024726 665026431 1705 True 2202.0 2202 90.0640 1076 2773 1 chr5B.!!$R3 1697
6 TraesCS5A01G485200 chr5B 665538524 665541489 2965 False 1923.0 3415 88.2690 31 2813 2 chr5B.!!$F1 2782
7 TraesCS5A01G485200 chr5D 528414969 528417129 2160 False 3243.0 3243 93.8220 802 2956 1 chr5D.!!$F1 2154
8 TraesCS5A01G485200 chr5D 528294715 528296417 1702 True 2215.0 2215 90.2450 1076 2773 1 chr5D.!!$R1 1697
9 TraesCS5A01G485200 chr5D 528586023 528588948 2925 False 1781.5 3029 89.5590 31 2813 2 chr5D.!!$F2 2782
10 TraesCS5A01G485200 chr6A 29289629 29290190 561 True 859.0 859 94.3260 3318 3878 1 chr6A.!!$R1 560
11 TraesCS5A01G485200 chr6A 29243183 29243753 570 False 808.0 808 92.4830 3318 3878 1 chr6A.!!$F1 560
12 TraesCS5A01G485200 chr6A 374697080 374697639 559 True 774.0 774 91.7110 3318 3878 1 chr6A.!!$R2 560
13 TraesCS5A01G485200 chr7A 64067793 64068367 574 False 833.0 833 93.0920 3311 3878 1 chr7A.!!$F1 567
14 TraesCS5A01G485200 chr7A 666533990 666534551 561 True 832.0 832 93.4280 3318 3878 1 chr7A.!!$R2 560
15 TraesCS5A01G485200 chr7A 648883620 648884183 563 True 822.0 822 93.1460 3318 3878 1 chr7A.!!$R1 560
16 TraesCS5A01G485200 chr3A 16127752 16128311 559 True 811.0 811 92.8830 3321 3878 1 chr3A.!!$R1 557
17 TraesCS5A01G485200 chr3A 28196802 28197359 557 True 784.0 784 92.0630 3318 3878 1 chr3A.!!$R2 560
18 TraesCS5A01G485200 chr2D 645597822 645598378 556 False 409.0 409 80.5240 1629 2227 1 chr2D.!!$F1 598

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
751 1141 0.110010 TGCACACACAAACACACACG 60.110 50.0 0.0 0.0 0.0 4.49 F
1173 1591 0.261991 TCCGTAAGCTCCCTCCTGAT 59.738 55.0 0.0 0.0 0.0 2.90 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2724 3205 0.248289 GCACGTAGAAGCCCAGGTTA 59.752 55.0 0.0 0.0 0.00 2.85 R
2959 3445 0.107214 ATATGTGCCCAGGAACCACG 60.107 55.0 0.0 0.0 32.32 4.94 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
28 29 3.672293 CCGTGTTTGGCAGCTCAT 58.328 55.556 0.00 0.00 0.00 2.90
29 30 2.853159 CCGTGTTTGGCAGCTCATA 58.147 52.632 0.00 0.00 0.00 2.15
36 37 4.035675 GTGTTTGGCAGCTCATAATAGTCC 59.964 45.833 0.00 0.00 0.00 3.85
40 41 5.474578 TGGCAGCTCATAATAGTCCTAAG 57.525 43.478 0.00 0.00 0.00 2.18
64 65 9.590451 AAGAATATTATTGTGTTTGGCATCAAG 57.410 29.630 0.00 0.00 33.98 3.02
112 113 9.073475 ACAGTATCTCCAATGAGTAGTATCTTC 57.927 37.037 0.00 0.00 39.75 2.87
196 221 3.354948 ACTGGAATACCGGGGTTTTAC 57.645 47.619 6.32 0.00 46.20 2.01
244 269 5.665459 TGCTCTCAAACTAAGCCTAAGATC 58.335 41.667 0.00 0.00 35.12 2.75
251 276 6.442564 TCAAACTAAGCCTAAGATCCAACCTA 59.557 38.462 0.00 0.00 0.00 3.08
270 295 9.730420 CCAACCTATATAAAAACACTTGTATGC 57.270 33.333 0.00 0.00 0.00 3.14
276 301 4.846779 AAAAACACTTGTATGCGGATGT 57.153 36.364 0.00 0.00 0.00 3.06
303 328 6.641176 TTTAATGCATATCATACGGCGTAG 57.359 37.500 25.01 16.27 34.33 3.51
402 578 8.624367 AGAAGTTGTATCTACGCTAGATATGT 57.376 34.615 13.97 0.00 46.25 2.29
422 598 3.519510 TGTTGCATTTAGACCTCTAGGCT 59.480 43.478 0.00 0.00 39.32 4.58
424 600 2.158900 TGCATTTAGACCTCTAGGCTGC 60.159 50.000 0.00 0.00 39.32 5.25
445 621 2.167861 CGGAGCTTAGCGCAAGTCC 61.168 63.158 11.47 17.02 42.61 3.85
451 627 3.659089 TTAGCGCAAGTCCGAGGGC 62.659 63.158 11.47 0.00 43.19 5.19
531 732 3.855689 AATCAATTCTTTGTCCGCCTG 57.144 42.857 0.00 0.00 34.32 4.85
632 994 5.471797 TGAGTTGTGACACACTTCTGAAAAA 59.528 36.000 8.05 0.00 35.11 1.94
658 1048 1.270550 CGCCAGCAAATTCCTCAAACT 59.729 47.619 0.00 0.00 0.00 2.66
674 1064 5.105997 CCTCAAACTGATTCATTCCCTCAAC 60.106 44.000 0.00 0.00 0.00 3.18
688 1078 8.359642 TCATTCCCTCAACAACTTTGATAAAAG 58.640 33.333 0.52 0.52 35.93 2.27
707 1097 1.141053 AGTCACAAAAACGAGGCCTCT 59.859 47.619 29.73 14.52 0.00 3.69
713 1103 0.591659 AAAACGAGGCCTCTTTTCGC 59.408 50.000 30.91 6.49 37.84 4.70
751 1141 0.110010 TGCACACACAAACACACACG 60.110 50.000 0.00 0.00 0.00 4.49
752 1142 1.402479 GCACACACAAACACACACGC 61.402 55.000 0.00 0.00 0.00 5.34
753 1143 1.125274 CACACACAAACACACACGCG 61.125 55.000 3.53 3.53 0.00 6.01
754 1144 2.099446 ACACAAACACACACGCGC 59.901 55.556 5.73 0.00 0.00 6.86
755 1145 3.010692 CACAAACACACACGCGCG 61.011 61.111 30.96 30.96 0.00 6.86
756 1146 4.879686 ACAAACACACACGCGCGC 62.880 61.111 32.58 23.91 0.00 6.86
782 1178 2.324477 GCGCACACACACACAGAC 59.676 61.111 0.30 0.00 0.00 3.51
783 1179 2.620459 CGCACACACACACAGACG 59.380 61.111 0.00 0.00 0.00 4.18
829 1225 0.969149 GCCTTTCTTCCCCCAACTTG 59.031 55.000 0.00 0.00 0.00 3.16
839 1235 3.058160 CCAACTTGCCCTGCCTCG 61.058 66.667 0.00 0.00 0.00 4.63
841 1237 3.958860 AACTTGCCCTGCCTCGCT 61.959 61.111 0.00 0.00 0.00 4.93
843 1239 4.093291 CTTGCCCTGCCTCGCTCT 62.093 66.667 0.00 0.00 0.00 4.09
847 1244 3.898509 CCCTGCCTCGCTCTCTCG 61.899 72.222 0.00 0.00 0.00 4.04
881 1278 1.076533 CGCGCGGCTATATAACTGGG 61.077 60.000 24.84 4.98 0.00 4.45
909 1311 1.455849 CTCCCAGCCTCACACCAAA 59.544 57.895 0.00 0.00 0.00 3.28
928 1343 6.207417 CACCAAAAACCACAGATCAATCTACT 59.793 38.462 0.00 0.00 34.85 2.57
929 1344 7.390440 CACCAAAAACCACAGATCAATCTACTA 59.610 37.037 0.00 0.00 34.85 1.82
930 1345 7.607991 ACCAAAAACCACAGATCAATCTACTAG 59.392 37.037 0.00 0.00 34.85 2.57
1071 1489 0.324645 ATGGGGAGTGGGACAAATGC 60.325 55.000 0.00 0.00 44.16 3.56
1171 1589 0.390860 CATCCGTAAGCTCCCTCCTG 59.609 60.000 0.00 0.00 0.00 3.86
1173 1591 0.261991 TCCGTAAGCTCCCTCCTGAT 59.738 55.000 0.00 0.00 0.00 2.90
1174 1592 0.676736 CCGTAAGCTCCCTCCTGATC 59.323 60.000 0.00 0.00 0.00 2.92
1175 1593 1.698506 CGTAAGCTCCCTCCTGATCT 58.301 55.000 0.00 0.00 0.00 2.75
1198 1651 2.809119 TCTGTCTCTGTCTCTGTTCGTC 59.191 50.000 0.00 0.00 0.00 4.20
1224 1689 2.139917 GATGGCAGTGTGTGAACGTTA 58.860 47.619 0.00 0.00 0.00 3.18
1226 1691 2.566913 TGGCAGTGTGTGAACGTTATT 58.433 42.857 0.00 0.00 0.00 1.40
1227 1692 2.289274 TGGCAGTGTGTGAACGTTATTG 59.711 45.455 0.00 0.00 0.00 1.90
1228 1693 2.546368 GGCAGTGTGTGAACGTTATTGA 59.454 45.455 0.00 0.00 0.00 2.57
1229 1694 3.541711 GCAGTGTGTGAACGTTATTGAC 58.458 45.455 0.00 0.00 0.00 3.18
1230 1695 3.247648 GCAGTGTGTGAACGTTATTGACT 59.752 43.478 0.00 0.00 0.00 3.41
1425 1890 4.125695 GTCGCCGACGCCTACCTT 62.126 66.667 0.00 0.00 39.84 3.50
1707 2180 4.370066 AACTGCGCGCTCTGCTCT 62.370 61.111 33.29 6.61 43.27 4.09
1976 2453 0.744057 GGCAAGAAGAGGCTGCTCTC 60.744 60.000 0.00 4.83 32.47 3.20
2481 2962 3.550431 CTGATGGGGGTCGGCGAT 61.550 66.667 14.79 0.00 0.00 4.58
2851 3332 2.344441 CCGTACAATCACAAGTGCGTAG 59.656 50.000 0.00 0.00 41.27 3.51
2876 3357 1.407712 GGGGAGCGCTTTTGGTGTATA 60.408 52.381 13.26 0.00 0.00 1.47
2884 3365 5.413213 AGCGCTTTTGGTGTATAACATAACA 59.587 36.000 2.64 0.00 0.00 2.41
2941 3427 0.536915 GAGGAAGATGGCCAGGCATC 60.537 60.000 22.73 22.73 0.00 3.91
2957 3443 1.209019 GCATCAGCAGAGAAGGAAGGA 59.791 52.381 0.00 0.00 41.58 3.36
2958 3444 2.355513 GCATCAGCAGAGAAGGAAGGAA 60.356 50.000 0.00 0.00 41.58 3.36
2959 3445 3.269178 CATCAGCAGAGAAGGAAGGAAC 58.731 50.000 0.00 0.00 0.00 3.62
2960 3446 1.273606 TCAGCAGAGAAGGAAGGAACG 59.726 52.381 0.00 0.00 0.00 3.95
2961 3447 1.001406 CAGCAGAGAAGGAAGGAACGT 59.999 52.381 0.00 0.00 0.00 3.99
2962 3448 1.001406 AGCAGAGAAGGAAGGAACGTG 59.999 52.381 0.00 0.00 0.00 4.49
2963 3449 1.941668 GCAGAGAAGGAAGGAACGTGG 60.942 57.143 0.00 0.00 0.00 4.94
2964 3450 1.344763 CAGAGAAGGAAGGAACGTGGT 59.655 52.381 0.00 0.00 0.00 4.16
2965 3451 2.047830 AGAGAAGGAAGGAACGTGGTT 58.952 47.619 0.00 0.00 0.00 3.67
2966 3452 2.037381 AGAGAAGGAAGGAACGTGGTTC 59.963 50.000 0.00 0.00 41.32 3.62
2973 3459 2.112297 GAACGTGGTTCCTGGGCA 59.888 61.111 0.00 0.00 36.65 5.36
2974 3460 2.203294 AACGTGGTTCCTGGGCAC 60.203 61.111 0.00 0.00 0.00 5.01
2975 3461 2.951475 GAACGTGGTTCCTGGGCACA 62.951 60.000 0.00 0.00 36.65 4.57
2976 3462 2.034066 CGTGGTTCCTGGGCACAT 59.966 61.111 0.00 0.00 0.00 3.21
2977 3463 1.298340 CGTGGTTCCTGGGCACATA 59.702 57.895 0.00 0.00 0.00 2.29
2978 3464 0.107214 CGTGGTTCCTGGGCACATAT 60.107 55.000 0.00 0.00 0.00 1.78
2979 3465 1.392589 GTGGTTCCTGGGCACATATG 58.607 55.000 0.00 0.00 0.00 1.78
2980 3466 0.998928 TGGTTCCTGGGCACATATGT 59.001 50.000 1.41 1.41 0.00 2.29
2981 3467 2.092646 GTGGTTCCTGGGCACATATGTA 60.093 50.000 8.32 0.00 0.00 2.29
2982 3468 2.092646 TGGTTCCTGGGCACATATGTAC 60.093 50.000 8.32 2.21 0.00 2.90
2983 3469 2.572290 GTTCCTGGGCACATATGTACC 58.428 52.381 15.84 15.84 0.00 3.34
2984 3470 2.172717 GTTCCTGGGCACATATGTACCT 59.827 50.000 21.91 0.00 32.04 3.08
2985 3471 2.487775 TCCTGGGCACATATGTACCTT 58.512 47.619 21.91 0.00 32.04 3.50
2986 3472 3.659841 TCCTGGGCACATATGTACCTTA 58.340 45.455 21.91 12.12 32.04 2.69
2987 3473 4.239495 TCCTGGGCACATATGTACCTTAT 58.761 43.478 21.91 0.00 32.04 1.73
2988 3474 5.407936 TCCTGGGCACATATGTACCTTATA 58.592 41.667 21.91 7.97 32.04 0.98
2989 3475 6.029431 TCCTGGGCACATATGTACCTTATAT 58.971 40.000 21.91 0.00 32.04 0.86
2990 3476 7.193338 TCCTGGGCACATATGTACCTTATATA 58.807 38.462 21.91 5.01 32.04 0.86
2991 3477 7.344612 TCCTGGGCACATATGTACCTTATATAG 59.655 40.741 21.91 12.46 32.04 1.31
2992 3478 7.344612 CCTGGGCACATATGTACCTTATATAGA 59.655 40.741 21.91 3.83 32.04 1.98
2993 3479 8.673456 TGGGCACATATGTACCTTATATAGAA 57.327 34.615 21.91 1.51 32.04 2.10
2994 3480 9.106977 TGGGCACATATGTACCTTATATAGAAA 57.893 33.333 21.91 0.90 32.04 2.52
2995 3481 9.953565 GGGCACATATGTACCTTATATAGAAAA 57.046 33.333 21.91 0.00 32.04 2.29
3035 3521 9.911138 AGCAATTCAACAAAAAGTCAAAAATTT 57.089 22.222 0.00 0.00 0.00 1.82
3064 3550 9.611284 GAAAATATTTTTGAAATGAACTTGGCC 57.389 29.630 14.45 0.00 0.00 5.36
3065 3551 8.922931 AAATATTTTTGAAATGAACTTGGCCT 57.077 26.923 3.32 0.00 0.00 5.19
3066 3552 8.922931 AATATTTTTGAAATGAACTTGGCCTT 57.077 26.923 3.32 0.00 0.00 4.35
3067 3553 8.922931 ATATTTTTGAAATGAACTTGGCCTTT 57.077 26.923 3.32 0.00 0.00 3.11
3068 3554 6.676237 TTTTTGAAATGAACTTGGCCTTTC 57.324 33.333 3.32 4.26 0.00 2.62
3069 3555 5.350504 TTTGAAATGAACTTGGCCTTTCA 57.649 34.783 14.80 14.80 36.21 2.69
3070 3556 5.549742 TTGAAATGAACTTGGCCTTTCAT 57.450 34.783 17.28 17.28 42.95 2.57
3072 3558 5.299148 TGAAATGAACTTGGCCTTTCATTG 58.701 37.500 27.22 6.87 46.81 2.82
3073 3559 4.961438 AATGAACTTGGCCTTTCATTGT 57.039 36.364 26.51 13.18 46.11 2.71
3074 3560 4.961438 ATGAACTTGGCCTTTCATTGTT 57.039 36.364 17.28 6.99 38.99 2.83
3075 3561 4.320608 TGAACTTGGCCTTTCATTGTTC 57.679 40.909 3.32 8.40 34.35 3.18
3076 3562 3.960102 TGAACTTGGCCTTTCATTGTTCT 59.040 39.130 3.32 0.00 34.59 3.01
3077 3563 5.136828 TGAACTTGGCCTTTCATTGTTCTA 58.863 37.500 3.32 0.00 34.59 2.10
3078 3564 5.241506 TGAACTTGGCCTTTCATTGTTCTAG 59.758 40.000 3.32 0.00 34.59 2.43
3079 3565 4.729868 ACTTGGCCTTTCATTGTTCTAGT 58.270 39.130 3.32 0.00 0.00 2.57
3080 3566 4.520492 ACTTGGCCTTTCATTGTTCTAGTG 59.480 41.667 3.32 0.00 0.00 2.74
3081 3567 4.365514 TGGCCTTTCATTGTTCTAGTGA 57.634 40.909 3.32 0.00 0.00 3.41
3082 3568 4.326826 TGGCCTTTCATTGTTCTAGTGAG 58.673 43.478 3.32 0.00 0.00 3.51
3083 3569 4.041567 TGGCCTTTCATTGTTCTAGTGAGA 59.958 41.667 3.32 0.00 0.00 3.27
3084 3570 5.003804 GGCCTTTCATTGTTCTAGTGAGAA 58.996 41.667 0.00 0.00 39.47 2.87
3085 3571 5.473504 GGCCTTTCATTGTTCTAGTGAGAAA 59.526 40.000 0.00 0.00 43.38 2.52
3086 3572 6.016276 GGCCTTTCATTGTTCTAGTGAGAAAA 60.016 38.462 0.00 0.00 43.38 2.29
3087 3573 7.080724 GCCTTTCATTGTTCTAGTGAGAAAAG 58.919 38.462 0.00 0.00 43.38 2.27
3088 3574 7.255277 GCCTTTCATTGTTCTAGTGAGAAAAGT 60.255 37.037 0.00 0.00 43.38 2.66
3089 3575 8.624776 CCTTTCATTGTTCTAGTGAGAAAAGTT 58.375 33.333 0.00 0.00 43.38 2.66
3090 3576 9.657121 CTTTCATTGTTCTAGTGAGAAAAGTTC 57.343 33.333 0.00 0.00 43.38 3.01
3091 3577 7.730364 TCATTGTTCTAGTGAGAAAAGTTCC 57.270 36.000 0.00 0.00 43.38 3.62
3092 3578 7.279615 TCATTGTTCTAGTGAGAAAAGTTCCA 58.720 34.615 0.00 0.00 43.38 3.53
3093 3579 6.920569 TTGTTCTAGTGAGAAAAGTTCCAC 57.079 37.500 0.00 0.00 43.38 4.02
3094 3580 5.984725 TGTTCTAGTGAGAAAAGTTCCACA 58.015 37.500 0.00 0.00 43.38 4.17
3095 3581 6.411376 TGTTCTAGTGAGAAAAGTTCCACAA 58.589 36.000 0.00 0.00 43.38 3.33
3096 3582 6.882140 TGTTCTAGTGAGAAAAGTTCCACAAA 59.118 34.615 0.00 0.00 43.38 2.83
3097 3583 7.392113 TGTTCTAGTGAGAAAAGTTCCACAAAA 59.608 33.333 0.00 0.00 43.38 2.44
3098 3584 7.553881 TCTAGTGAGAAAAGTTCCACAAAAG 57.446 36.000 0.00 0.00 35.01 2.27
3099 3585 7.335627 TCTAGTGAGAAAAGTTCCACAAAAGA 58.664 34.615 0.00 0.00 35.01 2.52
3100 3586 6.834168 AGTGAGAAAAGTTCCACAAAAGAA 57.166 33.333 0.00 0.00 35.01 2.52
3101 3587 7.227049 AGTGAGAAAAGTTCCACAAAAGAAA 57.773 32.000 0.00 0.00 35.01 2.52
3102 3588 7.666623 AGTGAGAAAAGTTCCACAAAAGAAAA 58.333 30.769 0.00 0.00 35.01 2.29
3103 3589 8.314021 AGTGAGAAAAGTTCCACAAAAGAAAAT 58.686 29.630 0.00 0.00 35.01 1.82
3104 3590 8.935844 GTGAGAAAAGTTCCACAAAAGAAAATT 58.064 29.630 0.00 0.00 33.70 1.82
3105 3591 9.150348 TGAGAAAAGTTCCACAAAAGAAAATTC 57.850 29.630 0.00 0.00 0.00 2.17
3106 3592 9.371136 GAGAAAAGTTCCACAAAAGAAAATTCT 57.629 29.630 0.00 0.00 39.74 2.40
3108 3594 9.973246 GAAAAGTTCCACAAAAGAAAATTCTTC 57.027 29.630 8.74 0.00 46.22 2.87
3109 3595 9.500785 AAAAGTTCCACAAAAGAAAATTCTTCA 57.499 25.926 8.74 0.00 46.22 3.02
3110 3596 9.671279 AAAGTTCCACAAAAGAAAATTCTTCAT 57.329 25.926 8.74 0.00 46.22 2.57
3111 3597 9.671279 AAGTTCCACAAAAGAAAATTCTTCATT 57.329 25.926 8.74 0.00 46.22 2.57
3112 3598 9.101655 AGTTCCACAAAAGAAAATTCTTCATTG 57.898 29.630 8.74 12.10 46.22 2.82
3113 3599 9.097257 GTTCCACAAAAGAAAATTCTTCATTGA 57.903 29.630 19.57 8.27 46.22 2.57
3114 3600 8.647143 TCCACAAAAGAAAATTCTTCATTGAC 57.353 30.769 19.57 0.00 46.22 3.18
3115 3601 8.477256 TCCACAAAAGAAAATTCTTCATTGACT 58.523 29.630 19.57 3.84 46.22 3.41
3116 3602 9.101655 CCACAAAAGAAAATTCTTCATTGACTT 57.898 29.630 19.57 4.82 46.22 3.01
3123 3609 9.455847 AGAAAATTCTTCATTGACTTCTTTTCG 57.544 29.630 12.91 0.00 36.00 3.46
3124 3610 9.450807 GAAAATTCTTCATTGACTTCTTTTCGA 57.549 29.630 0.00 0.00 0.00 3.71
3125 3611 9.801873 AAAATTCTTCATTGACTTCTTTTCGAA 57.198 25.926 0.00 0.00 0.00 3.71
3126 3612 9.801873 AAATTCTTCATTGACTTCTTTTCGAAA 57.198 25.926 6.47 6.47 0.00 3.46
3127 3613 9.801873 AATTCTTCATTGACTTCTTTTCGAAAA 57.198 25.926 21.35 21.35 0.00 2.29
3128 3614 9.801873 ATTCTTCATTGACTTCTTTTCGAAAAA 57.198 25.926 22.67 9.49 0.00 1.94
3129 3615 8.841444 TCTTCATTGACTTCTTTTCGAAAAAG 57.159 30.769 22.67 19.56 0.00 2.27
3130 3616 8.673711 TCTTCATTGACTTCTTTTCGAAAAAGA 58.326 29.630 22.67 18.11 34.73 2.52
3131 3617 8.614994 TTCATTGACTTCTTTTCGAAAAAGAC 57.385 30.769 22.67 17.74 36.14 3.01
3132 3618 7.757526 TCATTGACTTCTTTTCGAAAAAGACA 58.242 30.769 22.67 19.73 36.14 3.41
3133 3619 8.240682 TCATTGACTTCTTTTCGAAAAAGACAA 58.759 29.630 26.75 26.75 36.14 3.18
3134 3620 8.859156 CATTGACTTCTTTTCGAAAAAGACAAA 58.141 29.630 27.55 18.06 36.14 2.83
3135 3621 8.980143 TTGACTTCTTTTCGAAAAAGACAAAT 57.020 26.923 24.55 9.79 36.14 2.32
3136 3622 8.980143 TGACTTCTTTTCGAAAAAGACAAATT 57.020 26.923 22.67 7.92 36.14 1.82
3137 3623 9.418045 TGACTTCTTTTCGAAAAAGACAAATTT 57.582 25.926 22.67 2.63 36.14 1.82
3151 3637 7.637709 AAGACAAATTTTCGGTCAAAATAGC 57.362 32.000 9.15 0.00 42.86 2.97
3152 3638 6.744112 AGACAAATTTTCGGTCAAAATAGCA 58.256 32.000 9.15 0.00 42.86 3.49
3153 3639 7.378181 AGACAAATTTTCGGTCAAAATAGCAT 58.622 30.769 9.15 0.00 42.86 3.79
3154 3640 7.329226 AGACAAATTTTCGGTCAAAATAGCATG 59.671 33.333 9.15 0.00 42.86 4.06
3155 3641 7.151308 ACAAATTTTCGGTCAAAATAGCATGA 58.849 30.769 0.00 0.00 42.86 3.07
3156 3642 7.655328 ACAAATTTTCGGTCAAAATAGCATGAA 59.345 29.630 0.00 0.00 42.86 2.57
3157 3643 8.658609 CAAATTTTCGGTCAAAATAGCATGAAT 58.341 29.630 0.00 0.00 42.86 2.57
3158 3644 9.868277 AAATTTTCGGTCAAAATAGCATGAATA 57.132 25.926 0.00 0.00 42.86 1.75
3159 3645 9.520204 AATTTTCGGTCAAAATAGCATGAATAG 57.480 29.630 0.00 0.00 42.86 1.73
3160 3646 7.624360 TTTCGGTCAAAATAGCATGAATAGT 57.376 32.000 0.00 0.00 0.00 2.12
3161 3647 6.603237 TCGGTCAAAATAGCATGAATAGTG 57.397 37.500 0.00 0.00 0.00 2.74
3162 3648 6.345298 TCGGTCAAAATAGCATGAATAGTGA 58.655 36.000 0.00 0.00 0.00 3.41
3163 3649 6.992123 TCGGTCAAAATAGCATGAATAGTGAT 59.008 34.615 0.00 0.00 0.00 3.06
3164 3650 7.171508 TCGGTCAAAATAGCATGAATAGTGATC 59.828 37.037 0.00 0.00 0.00 2.92
3165 3651 7.172190 CGGTCAAAATAGCATGAATAGTGATCT 59.828 37.037 0.00 0.00 0.00 2.75
3166 3652 9.494271 GGTCAAAATAGCATGAATAGTGATCTA 57.506 33.333 0.00 0.00 0.00 1.98
3207 3693 3.840890 TTTTTGCTGTGAAGTCAACGT 57.159 38.095 0.00 0.00 0.00 3.99
3208 3694 3.840890 TTTTGCTGTGAAGTCAACGTT 57.159 38.095 0.00 0.00 0.00 3.99
3209 3695 2.823196 TTGCTGTGAAGTCAACGTTG 57.177 45.000 22.35 22.35 0.00 4.10
3210 3696 1.013596 TGCTGTGAAGTCAACGTTGG 58.986 50.000 27.02 10.17 0.00 3.77
3211 3697 1.014352 GCTGTGAAGTCAACGTTGGT 58.986 50.000 27.02 12.89 0.00 3.67
3212 3698 1.400494 GCTGTGAAGTCAACGTTGGTT 59.600 47.619 27.02 20.09 36.63 3.67
3213 3699 2.159435 GCTGTGAAGTCAACGTTGGTTT 60.159 45.455 27.02 20.33 32.98 3.27
3214 3700 3.672241 GCTGTGAAGTCAACGTTGGTTTT 60.672 43.478 27.02 18.03 32.98 2.43
3215 3701 4.481463 CTGTGAAGTCAACGTTGGTTTTT 58.519 39.130 27.02 15.76 32.98 1.94
3241 3727 9.710979 TTTGTGAAAAATTATATACTAGTGCGC 57.289 29.630 5.39 0.00 0.00 6.09
3242 3728 8.426881 TGTGAAAAATTATATACTAGTGCGCA 57.573 30.769 5.66 5.66 0.00 6.09
3243 3729 8.884726 TGTGAAAAATTATATACTAGTGCGCAA 58.115 29.630 14.00 0.00 0.00 4.85
3244 3730 9.370126 GTGAAAAATTATATACTAGTGCGCAAG 57.630 33.333 14.00 10.16 43.44 4.01
3245 3731 9.104965 TGAAAAATTATATACTAGTGCGCAAGT 57.895 29.630 14.00 16.58 41.68 3.16
3246 3732 9.931210 GAAAAATTATATACTAGTGCGCAAGTT 57.069 29.630 19.11 7.73 41.68 2.66
3250 3736 9.760077 AATTATATACTAGTGCGCAAGTTAAGT 57.240 29.630 19.11 15.91 41.68 2.24
3251 3737 9.760077 ATTATATACTAGTGCGCAAGTTAAGTT 57.240 29.630 19.11 8.60 41.68 2.66
3252 3738 9.590451 TTATATACTAGTGCGCAAGTTAAGTTT 57.410 29.630 19.11 11.89 41.68 2.66
3254 3740 7.894376 ATACTAGTGCGCAAGTTAAGTTTAA 57.106 32.000 19.11 0.21 41.68 1.52
3255 3741 6.796705 ACTAGTGCGCAAGTTAAGTTTAAT 57.203 33.333 14.00 0.00 41.68 1.40
3256 3742 6.828672 ACTAGTGCGCAAGTTAAGTTTAATC 58.171 36.000 14.00 0.00 41.68 1.75
3257 3743 5.941948 AGTGCGCAAGTTAAGTTTAATCT 57.058 34.783 14.00 0.00 41.68 2.40
3258 3744 7.816031 ACTAGTGCGCAAGTTAAGTTTAATCTA 59.184 33.333 14.00 2.83 41.68 1.98
3259 3745 7.429636 AGTGCGCAAGTTAAGTTTAATCTAA 57.570 32.000 14.00 0.00 41.68 2.10
3260 3746 7.867752 AGTGCGCAAGTTAAGTTTAATCTAAA 58.132 30.769 14.00 0.00 41.68 1.85
3261 3747 8.347035 AGTGCGCAAGTTAAGTTTAATCTAAAA 58.653 29.630 14.00 0.00 41.68 1.52
3262 3748 8.960075 GTGCGCAAGTTAAGTTTAATCTAAAAA 58.040 29.630 14.00 0.00 41.68 1.94
3263 3749 9.685828 TGCGCAAGTTAAGTTTAATCTAAAAAT 57.314 25.926 8.16 0.00 41.68 1.82
3836 4395 3.784719 GGGGCGGTAGCGGGTAAA 61.785 66.667 17.08 0.00 46.35 2.01
3845 4404 3.800506 CGGTAGCGGGTAAAAGTATTCTG 59.199 47.826 6.39 0.00 0.00 3.02
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
11 12 1.164411 TTATGAGCTGCCAAACACGG 58.836 50.000 0.00 0.00 0.00 4.94
12 13 3.623060 ACTATTATGAGCTGCCAAACACG 59.377 43.478 0.00 0.00 0.00 4.49
13 14 4.035675 GGACTATTATGAGCTGCCAAACAC 59.964 45.833 0.00 0.00 0.00 3.32
14 15 4.080356 AGGACTATTATGAGCTGCCAAACA 60.080 41.667 0.00 0.00 0.00 2.83
15 16 4.455606 AGGACTATTATGAGCTGCCAAAC 58.544 43.478 0.00 0.00 0.00 2.93
16 17 4.778213 AGGACTATTATGAGCTGCCAAA 57.222 40.909 0.00 0.00 0.00 3.28
17 18 5.602561 TCTTAGGACTATTATGAGCTGCCAA 59.397 40.000 0.00 0.00 0.00 4.52
18 19 5.147767 TCTTAGGACTATTATGAGCTGCCA 58.852 41.667 0.00 0.00 0.00 4.92
19 20 5.730296 TCTTAGGACTATTATGAGCTGCC 57.270 43.478 0.00 0.00 0.00 4.85
20 21 9.883142 AATATTCTTAGGACTATTATGAGCTGC 57.117 33.333 0.00 0.00 29.43 5.25
40 41 9.585099 TTCTTGATGCCAAACACAATAATATTC 57.415 29.630 0.00 0.00 0.00 1.75
86 87 9.073475 GAAGATACTACTCATTGGAGATACTGT 57.927 37.037 0.00 0.00 44.26 3.55
87 88 8.233868 CGAAGATACTACTCATTGGAGATACTG 58.766 40.741 0.00 0.00 44.26 2.74
112 113 2.758423 AGGCCCCTTTTAAAATACTGCG 59.242 45.455 0.00 0.00 0.00 5.18
159 161 9.382275 GTATTCCAGTTTCTAAAACCCGTTATA 57.618 33.333 0.00 0.00 0.00 0.98
161 163 6.654582 GGTATTCCAGTTTCTAAAACCCGTTA 59.345 38.462 0.00 0.00 0.00 3.18
164 166 4.093850 CGGTATTCCAGTTTCTAAAACCCG 59.906 45.833 0.00 0.64 0.00 5.28
167 169 4.397103 CCCCGGTATTCCAGTTTCTAAAAC 59.603 45.833 0.00 0.00 0.00 2.43
219 244 5.482908 TCTTAGGCTTAGTTTGAGAGCAAG 58.517 41.667 0.00 0.00 38.14 4.01
220 245 5.483685 TCTTAGGCTTAGTTTGAGAGCAA 57.516 39.130 0.00 0.00 38.14 3.91
244 269 9.730420 GCATACAAGTGTTTTTATATAGGTTGG 57.270 33.333 0.00 0.00 0.00 3.77
251 276 8.220755 ACATCCGCATACAAGTGTTTTTATAT 57.779 30.769 0.00 0.00 0.00 0.86
262 287 8.450180 TGCATTAAATATACATCCGCATACAAG 58.550 33.333 0.00 0.00 0.00 3.16
268 293 8.729805 TGATATGCATTAAATATACATCCGCA 57.270 30.769 3.54 0.00 0.00 5.69
276 301 8.880878 ACGCCGTATGATATGCATTAAATATA 57.119 30.769 3.54 0.00 38.44 0.86
392 568 7.158021 AGAGGTCTAAATGCAACATATCTAGC 58.842 38.462 0.00 0.00 0.00 3.42
402 578 3.682718 GCAGCCTAGAGGTCTAAATGCAA 60.683 47.826 0.00 0.00 37.57 4.08
519 720 0.310854 GAACAACCAGGCGGACAAAG 59.689 55.000 2.43 0.00 35.59 2.77
524 725 2.799126 AATATGAACAACCAGGCGGA 57.201 45.000 2.43 0.00 35.59 5.54
527 728 3.119495 AGCGAAAATATGAACAACCAGGC 60.119 43.478 0.00 0.00 0.00 4.85
531 732 4.091365 GCCAAAGCGAAAATATGAACAACC 59.909 41.667 0.00 0.00 0.00 3.77
570 932 2.437359 GCAGTGCCGGAGCTTGAT 60.437 61.111 5.05 0.00 40.80 2.57
637 1027 1.000274 GTTTGAGGAATTTGCTGGCGT 60.000 47.619 0.00 0.00 0.00 5.68
643 1033 6.312180 GGAATGAATCAGTTTGAGGAATTTGC 59.688 38.462 0.00 0.00 0.00 3.68
658 1048 5.832595 TCAAAGTTGTTGAGGGAATGAATCA 59.167 36.000 0.00 0.00 0.00 2.57
688 1078 1.594331 AGAGGCCTCGTTTTTGTGAC 58.406 50.000 26.95 0.00 34.09 3.67
707 1097 0.025770 GCGAATCGAATCCGCGAAAA 59.974 50.000 8.23 0.00 44.22 2.29
713 1103 4.686257 GCGCGCGAATCGAATCCG 62.686 66.667 37.18 0.41 41.67 4.18
763 1153 4.943591 CTGTGTGTGTGTGCGCGC 62.944 66.667 27.26 27.26 36.27 6.86
764 1154 3.261216 TCTGTGTGTGTGTGCGCG 61.261 61.111 0.00 0.00 0.00 6.86
765 1155 2.324477 GTCTGTGTGTGTGTGCGC 59.676 61.111 0.00 0.00 0.00 6.09
766 1156 2.620459 CGTCTGTGTGTGTGTGCG 59.380 61.111 0.00 0.00 0.00 5.34
767 1157 1.490693 CTCCGTCTGTGTGTGTGTGC 61.491 60.000 0.00 0.00 0.00 4.57
768 1158 0.179111 ACTCCGTCTGTGTGTGTGTG 60.179 55.000 0.00 0.00 0.00 3.82
779 1169 4.017126 TGTGATGTGAAGATACTCCGTCT 58.983 43.478 0.00 0.00 0.00 4.18
782 1178 3.119291 GCTGTGATGTGAAGATACTCCG 58.881 50.000 0.00 0.00 0.00 4.63
783 1179 3.119291 CGCTGTGATGTGAAGATACTCC 58.881 50.000 0.00 0.00 0.00 3.85
795 1191 3.490759 GGCCACGTCGCTGTGATG 61.491 66.667 4.85 8.80 42.55 3.07
796 1192 2.731691 AAAGGCCACGTCGCTGTGAT 62.732 55.000 5.01 0.00 42.55 3.06
797 1193 3.454587 AAAGGCCACGTCGCTGTGA 62.455 57.895 5.01 0.00 42.55 3.58
829 1225 4.219999 GAGAGAGCGAGGCAGGGC 62.220 72.222 0.00 0.00 0.00 5.19
839 1235 2.107953 GGCATGGACCGAGAGAGC 59.892 66.667 0.00 0.00 0.00 4.09
841 1237 2.764128 GGGGCATGGACCGAGAGA 60.764 66.667 0.00 0.00 0.00 3.10
843 1239 3.399181 GTGGGGCATGGACCGAGA 61.399 66.667 0.00 0.00 0.00 4.04
881 1278 1.379176 GGCTGGGAGGAAAAGAGGC 60.379 63.158 0.00 0.00 0.00 4.70
909 1311 7.122353 ACGTACTAGTAGATTGATCTGTGGTTT 59.878 37.037 1.87 0.00 37.76 3.27
928 1343 1.000060 ACTGCGCTTTTGGACGTACTA 60.000 47.619 9.73 0.00 0.00 1.82
929 1344 0.249741 ACTGCGCTTTTGGACGTACT 60.250 50.000 9.73 0.00 0.00 2.73
930 1345 0.110823 CACTGCGCTTTTGGACGTAC 60.111 55.000 9.73 0.00 0.00 3.67
1046 1464 2.365635 CCCACTCCCCATCTCCGT 60.366 66.667 0.00 0.00 0.00 4.69
1049 1467 0.991920 TTTGTCCCACTCCCCATCTC 59.008 55.000 0.00 0.00 0.00 2.75
1050 1468 1.285962 CATTTGTCCCACTCCCCATCT 59.714 52.381 0.00 0.00 0.00 2.90
1071 1489 3.054503 ACGGAGGAGTCGTCCACG 61.055 66.667 27.00 17.88 46.80 4.94
1171 1589 4.517285 ACAGAGACAGAGACAGAGAGATC 58.483 47.826 0.00 0.00 0.00 2.75
1173 1591 4.323417 GAACAGAGACAGAGACAGAGAGA 58.677 47.826 0.00 0.00 0.00 3.10
1174 1592 3.125146 CGAACAGAGACAGAGACAGAGAG 59.875 52.174 0.00 0.00 0.00 3.20
1175 1593 3.070748 CGAACAGAGACAGAGACAGAGA 58.929 50.000 0.00 0.00 0.00 3.10
1198 1651 0.594602 CACACACTGCCATCAACCAG 59.405 55.000 0.00 0.00 35.26 4.00
1224 1689 5.659440 AAACCACACAACAAGAAGTCAAT 57.341 34.783 0.00 0.00 0.00 2.57
1226 1691 4.321601 CCAAAACCACACAACAAGAAGTCA 60.322 41.667 0.00 0.00 0.00 3.41
1227 1692 4.173256 CCAAAACCACACAACAAGAAGTC 58.827 43.478 0.00 0.00 0.00 3.01
1228 1693 3.616317 GCCAAAACCACACAACAAGAAGT 60.616 43.478 0.00 0.00 0.00 3.01
1229 1694 2.929398 GCCAAAACCACACAACAAGAAG 59.071 45.455 0.00 0.00 0.00 2.85
1230 1695 2.300152 TGCCAAAACCACACAACAAGAA 59.700 40.909 0.00 0.00 0.00 2.52
1797 2270 1.310933 GGTAGACGACGAGGGAGCAA 61.311 60.000 0.00 0.00 0.00 3.91
1976 2453 4.394712 GGAGCTGGTCGGTGTGGG 62.395 72.222 0.00 0.00 0.00 4.61
1997 2474 1.003839 ATTGCCGCCTTGTCGAGAA 60.004 52.632 0.00 0.00 0.00 2.87
2454 2935 2.434884 CCCATCAGCGCGAACTGT 60.435 61.111 12.10 0.00 38.84 3.55
2547 3028 3.849951 AGGTACAGCCCGATGCCG 61.850 66.667 0.00 0.00 42.71 5.69
2724 3205 0.248289 GCACGTAGAAGCCCAGGTTA 59.752 55.000 0.00 0.00 0.00 2.85
2821 3302 5.867716 ACTTGTGATTGTACGGACTATTGAC 59.132 40.000 0.00 0.00 0.00 3.18
2851 3332 2.985847 AAAAGCGCTCCCCTGTGC 60.986 61.111 12.06 0.00 43.09 4.57
2852 3333 2.629656 CCAAAAGCGCTCCCCTGTG 61.630 63.158 12.06 0.00 0.00 3.66
2876 3357 6.804677 TGTGTTGATGCTTCTTTGTTATGTT 58.195 32.000 0.88 0.00 0.00 2.71
2884 3365 3.814842 TGACGATGTGTTGATGCTTCTTT 59.185 39.130 0.88 0.00 0.00 2.52
2896 3382 5.506649 GGTGGTTAAAATGTTGACGATGTGT 60.507 40.000 0.00 0.00 0.00 3.72
2897 3383 4.915085 GGTGGTTAAAATGTTGACGATGTG 59.085 41.667 0.00 0.00 0.00 3.21
2941 3427 1.001406 ACGTTCCTTCCTTCTCTGCTG 59.999 52.381 0.00 0.00 0.00 4.41
2957 3443 2.203294 GTGCCCAGGAACCACGTT 60.203 61.111 0.00 0.00 0.00 3.99
2958 3444 1.485294 TATGTGCCCAGGAACCACGT 61.485 55.000 0.00 0.00 33.64 4.49
2959 3445 0.107214 ATATGTGCCCAGGAACCACG 60.107 55.000 0.00 0.00 32.32 4.94
2960 3446 1.340991 ACATATGTGCCCAGGAACCAC 60.341 52.381 7.78 0.00 0.00 4.16
2961 3447 0.998928 ACATATGTGCCCAGGAACCA 59.001 50.000 7.78 0.00 0.00 3.67
2962 3448 2.572290 GTACATATGTGCCCAGGAACC 58.428 52.381 18.81 0.00 0.00 3.62
2963 3449 2.572290 GGTACATATGTGCCCAGGAAC 58.428 52.381 27.46 11.36 43.79 3.62
3009 3495 9.911138 AAATTTTTGACTTTTTGTTGAATTGCT 57.089 22.222 0.00 0.00 0.00 3.91
3038 3524 9.611284 GGCCAAGTTCATTTCAAAAATATTTTC 57.389 29.630 13.68 0.00 0.00 2.29
3039 3525 9.353431 AGGCCAAGTTCATTTCAAAAATATTTT 57.647 25.926 5.01 7.64 0.00 1.82
3040 3526 8.922931 AGGCCAAGTTCATTTCAAAAATATTT 57.077 26.923 5.01 0.00 0.00 1.40
3041 3527 8.922931 AAGGCCAAGTTCATTTCAAAAATATT 57.077 26.923 5.01 0.00 0.00 1.28
3042 3528 8.922931 AAAGGCCAAGTTCATTTCAAAAATAT 57.077 26.923 5.01 0.00 0.00 1.28
3043 3529 7.989741 TGAAAGGCCAAGTTCATTTCAAAAATA 59.010 29.630 5.01 0.00 37.04 1.40
3044 3530 6.827762 TGAAAGGCCAAGTTCATTTCAAAAAT 59.172 30.769 5.01 0.00 37.04 1.82
3045 3531 6.176183 TGAAAGGCCAAGTTCATTTCAAAAA 58.824 32.000 5.01 0.00 37.04 1.94
3046 3532 5.738909 TGAAAGGCCAAGTTCATTTCAAAA 58.261 33.333 5.01 0.00 37.04 2.44
3047 3533 5.350504 TGAAAGGCCAAGTTCATTTCAAA 57.649 34.783 5.01 0.00 37.04 2.69
3048 3534 5.549742 ATGAAAGGCCAAGTTCATTTCAA 57.450 34.783 18.58 5.28 40.71 2.69
3053 3539 4.590222 AGAACAATGAAAGGCCAAGTTCAT 59.410 37.500 18.58 18.58 44.43 2.57
3054 3540 3.960102 AGAACAATGAAAGGCCAAGTTCA 59.040 39.130 16.15 16.15 37.48 3.18
3055 3541 4.590850 AGAACAATGAAAGGCCAAGTTC 57.409 40.909 5.01 6.18 36.38 3.01
3056 3542 5.010012 CACTAGAACAATGAAAGGCCAAGTT 59.990 40.000 5.01 0.00 0.00 2.66
3057 3543 4.520492 CACTAGAACAATGAAAGGCCAAGT 59.480 41.667 5.01 0.00 0.00 3.16
3058 3544 4.761739 TCACTAGAACAATGAAAGGCCAAG 59.238 41.667 5.01 0.00 0.00 3.61
3059 3545 4.724399 TCACTAGAACAATGAAAGGCCAA 58.276 39.130 5.01 0.00 0.00 4.52
3060 3546 4.041567 TCTCACTAGAACAATGAAAGGCCA 59.958 41.667 5.01 0.00 0.00 5.36
3061 3547 4.579869 TCTCACTAGAACAATGAAAGGCC 58.420 43.478 0.00 0.00 0.00 5.19
3062 3548 6.560253 TTTCTCACTAGAACAATGAAAGGC 57.440 37.500 0.00 0.00 41.48 4.35
3063 3549 8.159344 ACTTTTCTCACTAGAACAATGAAAGG 57.841 34.615 0.00 0.00 41.48 3.11
3064 3550 9.657121 GAACTTTTCTCACTAGAACAATGAAAG 57.343 33.333 0.00 1.14 41.48 2.62
3065 3551 8.621286 GGAACTTTTCTCACTAGAACAATGAAA 58.379 33.333 0.00 0.00 41.48 2.69
3066 3552 7.773224 TGGAACTTTTCTCACTAGAACAATGAA 59.227 33.333 0.00 0.00 41.48 2.57
3067 3553 7.226720 GTGGAACTTTTCTCACTAGAACAATGA 59.773 37.037 0.00 0.00 41.48 2.57
3068 3554 7.012327 TGTGGAACTTTTCTCACTAGAACAATG 59.988 37.037 0.00 0.00 38.58 2.82
3069 3555 7.054124 TGTGGAACTTTTCTCACTAGAACAAT 58.946 34.615 0.00 0.00 38.58 2.71
3070 3556 6.411376 TGTGGAACTTTTCTCACTAGAACAA 58.589 36.000 0.00 0.00 38.58 2.83
3071 3557 5.984725 TGTGGAACTTTTCTCACTAGAACA 58.015 37.500 0.00 0.00 38.58 3.18
3072 3558 6.920569 TTGTGGAACTTTTCTCACTAGAAC 57.079 37.500 0.00 0.00 38.58 3.01
3073 3559 7.827236 TCTTTTGTGGAACTTTTCTCACTAGAA 59.173 33.333 0.00 0.00 37.61 2.10
3074 3560 7.335627 TCTTTTGTGGAACTTTTCTCACTAGA 58.664 34.615 0.00 0.00 38.04 2.43
3075 3561 7.553881 TCTTTTGTGGAACTTTTCTCACTAG 57.446 36.000 0.00 0.00 38.04 2.57
3076 3562 7.931578 TTCTTTTGTGGAACTTTTCTCACTA 57.068 32.000 0.00 0.00 38.04 2.74
3077 3563 6.834168 TTCTTTTGTGGAACTTTTCTCACT 57.166 33.333 0.00 0.00 38.04 3.41
3078 3564 7.883229 TTTTCTTTTGTGGAACTTTTCTCAC 57.117 32.000 0.00 0.00 38.04 3.51
3079 3565 9.150348 GAATTTTCTTTTGTGGAACTTTTCTCA 57.850 29.630 0.00 0.00 38.04 3.27
3080 3566 9.371136 AGAATTTTCTTTTGTGGAACTTTTCTC 57.629 29.630 0.00 0.00 32.96 2.87
3081 3567 9.725019 AAGAATTTTCTTTTGTGGAACTTTTCT 57.275 25.926 0.00 0.00 44.70 2.52
3082 3568 9.973246 GAAGAATTTTCTTTTGTGGAACTTTTC 57.027 29.630 6.98 0.00 46.84 2.29
3083 3569 9.500785 TGAAGAATTTTCTTTTGTGGAACTTTT 57.499 25.926 6.98 0.00 46.84 2.27
3084 3570 9.671279 ATGAAGAATTTTCTTTTGTGGAACTTT 57.329 25.926 6.98 0.00 46.84 2.66
3085 3571 9.671279 AATGAAGAATTTTCTTTTGTGGAACTT 57.329 25.926 6.98 0.00 46.84 2.66
3086 3572 9.101655 CAATGAAGAATTTTCTTTTGTGGAACT 57.898 29.630 6.98 0.00 46.84 3.01
3087 3573 9.097257 TCAATGAAGAATTTTCTTTTGTGGAAC 57.903 29.630 6.98 0.00 46.84 3.62
3088 3574 9.097257 GTCAATGAAGAATTTTCTTTTGTGGAA 57.903 29.630 6.98 0.00 46.84 3.53
3089 3575 8.477256 AGTCAATGAAGAATTTTCTTTTGTGGA 58.523 29.630 6.98 0.80 46.84 4.02
3090 3576 8.652810 AGTCAATGAAGAATTTTCTTTTGTGG 57.347 30.769 6.98 0.00 46.84 4.17
3097 3583 9.455847 CGAAAAGAAGTCAATGAAGAATTTTCT 57.544 29.630 16.03 5.26 39.74 2.52
3098 3584 9.450807 TCGAAAAGAAGTCAATGAAGAATTTTC 57.549 29.630 11.62 11.62 33.15 2.29
3099 3585 9.801873 TTCGAAAAGAAGTCAATGAAGAATTTT 57.198 25.926 0.00 0.00 34.26 1.82
3100 3586 9.801873 TTTCGAAAAGAAGTCAATGAAGAATTT 57.198 25.926 8.44 0.00 40.40 1.82
3101 3587 9.801873 TTTTCGAAAAGAAGTCAATGAAGAATT 57.198 25.926 19.08 0.00 40.40 2.17
3102 3588 9.801873 TTTTTCGAAAAGAAGTCAATGAAGAAT 57.198 25.926 21.53 0.00 40.40 2.40
3103 3589 9.289303 CTTTTTCGAAAAGAAGTCAATGAAGAA 57.711 29.630 21.53 2.44 40.40 2.52
3104 3590 8.673711 TCTTTTTCGAAAAGAAGTCAATGAAGA 58.326 29.630 21.53 14.27 40.40 2.87
3105 3591 8.737648 GTCTTTTTCGAAAAGAAGTCAATGAAG 58.262 33.333 21.53 12.41 40.40 3.02
3106 3592 8.240682 TGTCTTTTTCGAAAAGAAGTCAATGAA 58.759 29.630 21.53 3.63 40.40 2.57
3107 3593 7.757526 TGTCTTTTTCGAAAAGAAGTCAATGA 58.242 30.769 21.53 5.19 40.40 2.57
3108 3594 7.969387 TGTCTTTTTCGAAAAGAAGTCAATG 57.031 32.000 21.53 3.04 40.40 2.82
3109 3595 8.980143 TTTGTCTTTTTCGAAAAGAAGTCAAT 57.020 26.923 23.23 0.00 40.40 2.57
3110 3596 8.980143 ATTTGTCTTTTTCGAAAAGAAGTCAA 57.020 26.923 21.53 21.13 40.40 3.18
3111 3597 8.980143 AATTTGTCTTTTTCGAAAAGAAGTCA 57.020 26.923 21.53 17.37 40.40 3.41
3125 3611 8.547894 GCTATTTTGACCGAAAATTTGTCTTTT 58.452 29.630 8.19 0.00 40.73 2.27
3126 3612 7.708752 TGCTATTTTGACCGAAAATTTGTCTTT 59.291 29.630 8.19 0.00 40.73 2.52
3127 3613 7.206687 TGCTATTTTGACCGAAAATTTGTCTT 58.793 30.769 8.19 0.00 40.73 3.01
3128 3614 6.744112 TGCTATTTTGACCGAAAATTTGTCT 58.256 32.000 8.19 0.00 40.73 3.41
3129 3615 7.328249 TCATGCTATTTTGACCGAAAATTTGTC 59.672 33.333 0.00 0.00 40.73 3.18
3130 3616 7.151308 TCATGCTATTTTGACCGAAAATTTGT 58.849 30.769 0.00 0.00 40.73 2.83
3131 3617 7.579589 TCATGCTATTTTGACCGAAAATTTG 57.420 32.000 0.00 0.00 40.73 2.32
3132 3618 8.776376 ATTCATGCTATTTTGACCGAAAATTT 57.224 26.923 0.00 0.00 40.73 1.82
3133 3619 9.520204 CTATTCATGCTATTTTGACCGAAAATT 57.480 29.630 0.00 0.00 40.73 1.82
3134 3620 8.686334 ACTATTCATGCTATTTTGACCGAAAAT 58.314 29.630 0.00 0.00 44.77 1.82
3135 3621 7.967854 CACTATTCATGCTATTTTGACCGAAAA 59.032 33.333 0.00 0.00 37.93 2.29
3136 3622 7.335673 TCACTATTCATGCTATTTTGACCGAAA 59.664 33.333 0.00 0.00 0.00 3.46
3137 3623 6.821160 TCACTATTCATGCTATTTTGACCGAA 59.179 34.615 0.00 0.00 0.00 4.30
3138 3624 6.345298 TCACTATTCATGCTATTTTGACCGA 58.655 36.000 0.00 0.00 0.00 4.69
3139 3625 6.603237 TCACTATTCATGCTATTTTGACCG 57.397 37.500 0.00 0.00 0.00 4.79
3140 3626 8.388484 AGATCACTATTCATGCTATTTTGACC 57.612 34.615 0.00 0.00 0.00 4.02
3187 3673 3.840890 ACGTTGACTTCACAGCAAAAA 57.159 38.095 0.00 0.00 0.00 1.94
3188 3674 3.497118 CAACGTTGACTTCACAGCAAAA 58.503 40.909 23.90 0.00 0.00 2.44
3189 3675 2.159448 CCAACGTTGACTTCACAGCAAA 60.159 45.455 29.35 0.00 0.00 3.68
3190 3676 1.400142 CCAACGTTGACTTCACAGCAA 59.600 47.619 29.35 0.00 0.00 3.91
3191 3677 1.013596 CCAACGTTGACTTCACAGCA 58.986 50.000 29.35 0.00 0.00 4.41
3192 3678 1.014352 ACCAACGTTGACTTCACAGC 58.986 50.000 29.35 0.00 0.00 4.40
3193 3679 3.757745 AAACCAACGTTGACTTCACAG 57.242 42.857 29.35 12.16 30.72 3.66
3194 3680 4.506886 AAAAACCAACGTTGACTTCACA 57.493 36.364 29.35 0.00 30.72 3.58
3215 3701 9.710979 GCGCACTAGTATATAATTTTTCACAAA 57.289 29.630 0.30 0.00 0.00 2.83
3216 3702 8.884726 TGCGCACTAGTATATAATTTTTCACAA 58.115 29.630 5.66 0.00 0.00 3.33
3217 3703 8.426881 TGCGCACTAGTATATAATTTTTCACA 57.573 30.769 5.66 0.00 0.00 3.58
3218 3704 9.370126 CTTGCGCACTAGTATATAATTTTTCAC 57.630 33.333 11.12 0.00 0.00 3.18
3219 3705 9.104965 ACTTGCGCACTAGTATATAATTTTTCA 57.895 29.630 11.12 0.00 29.61 2.69
3220 3706 9.931210 AACTTGCGCACTAGTATATAATTTTTC 57.069 29.630 11.12 0.00 31.28 2.29
3224 3710 9.760077 ACTTAACTTGCGCACTAGTATATAATT 57.240 29.630 11.12 0.00 31.28 1.40
3225 3711 9.760077 AACTTAACTTGCGCACTAGTATATAAT 57.240 29.630 11.12 0.00 31.28 1.28
3226 3712 9.590451 AAACTTAACTTGCGCACTAGTATATAA 57.410 29.630 11.12 7.11 31.28 0.98
3228 3714 9.590451 TTAAACTTAACTTGCGCACTAGTATAT 57.410 29.630 11.12 0.00 31.28 0.86
3229 3715 8.984891 TTAAACTTAACTTGCGCACTAGTATA 57.015 30.769 11.12 4.94 31.28 1.47
3230 3716 7.894376 TTAAACTTAACTTGCGCACTAGTAT 57.106 32.000 11.12 5.92 31.28 2.12
3231 3717 7.816031 AGATTAAACTTAACTTGCGCACTAGTA 59.184 33.333 11.12 0.00 31.28 1.82
3232 3718 6.649557 AGATTAAACTTAACTTGCGCACTAGT 59.350 34.615 11.12 9.81 32.98 2.57
3233 3719 7.061752 AGATTAAACTTAACTTGCGCACTAG 57.938 36.000 11.12 8.97 0.00 2.57
3234 3720 8.537049 TTAGATTAAACTTAACTTGCGCACTA 57.463 30.769 11.12 0.00 0.00 2.74
3235 3721 5.941948 AGATTAAACTTAACTTGCGCACT 57.058 34.783 11.12 0.00 0.00 4.40
3236 3722 8.496872 TTTTAGATTAAACTTAACTTGCGCAC 57.503 30.769 11.12 0.00 0.00 5.34
3237 3723 9.685828 ATTTTTAGATTAAACTTAACTTGCGCA 57.314 25.926 5.66 5.66 0.00 6.09
3295 3781 8.916628 AGTGTATACGGGGTAGTTTTTAAAAA 57.083 30.769 9.31 9.31 0.00 1.94
3296 3782 9.651913 CTAGTGTATACGGGGTAGTTTTTAAAA 57.348 33.333 0.00 0.00 0.00 1.52
3297 3783 8.811994 ACTAGTGTATACGGGGTAGTTTTTAAA 58.188 33.333 0.00 0.00 0.00 1.52
3298 3784 8.250332 CACTAGTGTATACGGGGTAGTTTTTAA 58.750 37.037 15.06 0.00 0.00 1.52
3299 3785 7.630513 GCACTAGTGTATACGGGGTAGTTTTTA 60.631 40.741 23.44 0.00 0.00 1.52
3300 3786 6.633856 CACTAGTGTATACGGGGTAGTTTTT 58.366 40.000 15.06 0.00 0.00 1.94
3301 3787 5.394553 GCACTAGTGTATACGGGGTAGTTTT 60.395 44.000 23.44 0.00 0.00 2.43
3302 3788 4.098501 GCACTAGTGTATACGGGGTAGTTT 59.901 45.833 23.44 0.00 0.00 2.66
3303 3789 3.633986 GCACTAGTGTATACGGGGTAGTT 59.366 47.826 23.44 0.00 0.00 2.24
3304 3790 3.217626 GCACTAGTGTATACGGGGTAGT 58.782 50.000 23.44 0.19 0.00 2.73
3305 3791 3.216800 TGCACTAGTGTATACGGGGTAG 58.783 50.000 23.44 0.00 0.00 3.18
3306 3792 3.117926 TCTGCACTAGTGTATACGGGGTA 60.118 47.826 23.44 0.00 0.00 3.69
3307 3793 2.029623 CTGCACTAGTGTATACGGGGT 58.970 52.381 23.44 0.00 0.00 4.95
3308 3794 2.304092 TCTGCACTAGTGTATACGGGG 58.696 52.381 23.44 6.98 0.00 5.73
3309 3795 3.490419 GGTTCTGCACTAGTGTATACGGG 60.490 52.174 23.44 7.68 0.00 5.28
3316 3802 1.671742 CCCGGTTCTGCACTAGTGT 59.328 57.895 23.44 0.00 0.00 3.55
3412 3898 2.231964 TCGTGCTGAACCGGTACTAAAT 59.768 45.455 8.00 0.00 0.00 1.40
3513 4004 1.752498 CCCCCAACCTTTTAATACCGC 59.248 52.381 0.00 0.00 0.00 5.68
3836 4395 6.995091 GTCATAGATCCCAAAGCAGAATACTT 59.005 38.462 0.00 0.00 0.00 2.24
3845 4404 2.173569 ACCAGGTCATAGATCCCAAAGC 59.826 50.000 0.00 0.00 0.00 3.51


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

AutoCloner maintained by Alex Coulton.