Multiple sequence alignment - TraesCS2B01G366600

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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 TraesCS2B01G366600 chr2B 100.000 3937 0 0 1 3937 522832788 522836724 0.000000e+00 7271.0
1 TraesCS2B01G366600 chr2B 92.857 98 5 2 3840 3937 514214628 514214533 1.470000e-29 141.0
2 TraesCS2B01G366600 chr2B 93.103 58 4 0 3043 3100 242381988 242381931 7.010000e-13 86.1
3 TraesCS2B01G366600 chr2B 93.220 59 3 1 3101 3159 793277957 793277900 7.010000e-13 86.1
4 TraesCS2B01G366600 chr2B 88.710 62 4 2 3095 3156 573198842 573198900 5.460000e-09 73.1
5 TraesCS2B01G366600 chr2B 75.281 178 26 12 368 542 522815296 522815458 7.060000e-08 69.4
6 TraesCS2B01G366600 chr2B 94.595 37 1 1 557 593 522815649 522815684 5.500000e-04 56.5
7 TraesCS2B01G366600 chr2A 88.985 2533 126 55 601 3039 587148064 587150537 0.000000e+00 2990.0
8 TraesCS2B01G366600 chr2A 95.398 565 19 3 3292 3849 587150860 587151424 0.000000e+00 893.0
9 TraesCS2B01G366600 chr2A 87.748 302 14 9 571 851 587145935 587146234 8.150000e-87 331.0
10 TraesCS2B01G366600 chr2A 91.503 153 12 1 3142 3293 587150546 587150698 3.990000e-50 209.0
11 TraesCS2B01G366600 chr2A 91.589 107 9 0 2594 2700 479256767 479256661 8.810000e-32 148.0
12 TraesCS2B01G366600 chr2A 86.111 72 7 3 3101 3171 124288501 124288432 1.520000e-09 75.0
13 TraesCS2B01G366600 chr2A 81.000 100 13 3 3043 3142 632257949 632258042 1.520000e-09 75.0
14 TraesCS2B01G366600 chr2A 80.000 100 14 3 3043 3142 49308999 49309092 7.060000e-08 69.4
15 TraesCS2B01G366600 chr2D 90.235 1915 62 46 632 2477 444385348 444387206 0.000000e+00 2385.0
16 TraesCS2B01G366600 chr2D 95.804 715 23 4 3142 3849 444387707 444388421 0.000000e+00 1147.0
17 TraesCS2B01G366600 chr2D 90.730 507 35 8 2542 3044 444387211 444387709 0.000000e+00 665.0
18 TraesCS2B01G366600 chr2D 86.429 560 30 25 1 542 444384527 444385058 4.410000e-159 571.0
19 TraesCS2B01G366600 chr2D 96.629 89 2 1 3848 3936 25037881 25037968 3.170000e-31 147.0
20 TraesCS2B01G366600 chr2D 90.654 107 10 0 2594 2700 240850587 240850481 4.100000e-30 143.0
21 TraesCS2B01G366600 chr2D 92.929 99 4 3 3840 3937 582628969 582629065 1.470000e-29 141.0
22 TraesCS2B01G366600 chr2D 87.356 87 2 3 571 649 444385263 444385348 1.510000e-14 91.6
23 TraesCS2B01G366600 chr2D 88.889 72 8 0 3043 3114 620018449 620018378 5.420000e-14 89.8
24 TraesCS2B01G366600 chr5A 91.589 107 9 0 2594 2700 287718861 287718755 8.810000e-32 148.0
25 TraesCS2B01G366600 chr5A 92.308 104 6 2 3833 3936 207681931 207681830 3.170000e-31 147.0
26 TraesCS2B01G366600 chr1A 92.308 104 8 0 2594 2697 479666364 479666467 8.810000e-32 148.0
27 TraesCS2B01G366600 chr1B 94.681 94 4 1 3844 3937 631232768 631232676 1.140000e-30 145.0
28 TraesCS2B01G366600 chr1B 94.828 58 1 2 3043 3099 607627153 607627209 5.420000e-14 89.8
29 TraesCS2B01G366600 chr1B 91.803 61 3 2 3041 3100 90314641 90314700 2.520000e-12 84.2
30 TraesCS2B01G366600 chr4B 94.624 93 4 1 3845 3937 178078810 178078901 4.100000e-30 143.0
31 TraesCS2B01G366600 chr3B 94.624 93 3 2 3844 3936 334313158 334313068 4.100000e-30 143.0
32 TraesCS2B01G366600 chr3B 89.706 68 6 1 3036 3102 229298932 229298999 7.010000e-13 86.1
33 TraesCS2B01G366600 chr3A 93.750 96 5 1 3842 3937 533623344 533623250 4.100000e-30 143.0
34 TraesCS2B01G366600 chr5D 89.720 107 11 0 2594 2700 120613021 120612915 1.910000e-28 137.0
35 TraesCS2B01G366600 chr5D 88.679 106 12 0 2595 2700 198468151 198468046 3.190000e-26 130.0
36 TraesCS2B01G366600 chr7A 89.720 107 10 1 3831 3937 155147880 155147985 6.860000e-28 135.0
37 TraesCS2B01G366600 chr6A 89.130 92 10 0 2609 2700 244455852 244455761 8.940000e-22 115.0
38 TraesCS2B01G366600 chr6A 84.722 72 11 0 2118 2189 598861391 598861462 5.460000e-09 73.1
39 TraesCS2B01G366600 chr1D 93.651 63 4 0 3040 3102 370219048 370219110 1.160000e-15 95.3
40 TraesCS2B01G366600 chr1D 97.959 49 1 0 3101 3149 18549228 18549180 7.010000e-13 86.1
41 TraesCS2B01G366600 chr5B 93.103 58 4 0 3043 3100 455291477 455291534 7.010000e-13 86.1
42 TraesCS2B01G366600 chr6D 96.000 50 2 0 3095 3144 309579596 309579645 9.070000e-12 82.4
43 TraesCS2B01G366600 chr6B 92.857 56 3 1 3101 3156 566034327 566034273 3.260000e-11 80.5
44 TraesCS2B01G366600 chr3D 94.118 51 3 0 3101 3151 172378759 172378709 1.170000e-10 78.7


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 TraesCS2B01G366600 chr2B 522832788 522836724 3936 False 7271.00 7271 100.0000 1 3937 1 chr2B.!!$F1 3936
1 TraesCS2B01G366600 chr2A 587145935 587151424 5489 False 1105.75 2990 90.9085 571 3849 4 chr2A.!!$F3 3278
2 TraesCS2B01G366600 chr2D 444384527 444388421 3894 False 971.92 2385 90.1108 1 3849 5 chr2D.!!$F3 3848

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
276 277 0.032130 CGGCAGGCGTGTCATATACT 59.968 55.0 12.03 0.0 0.00 2.12 F
896 3244 0.179111 TTCCCTGCGATACAAGAGCG 60.179 55.0 0.00 0.0 40.87 5.03 F
2146 4580 0.666913 ACAAGAGCGACGTGTACAGT 59.333 50.0 0.00 0.0 39.22 3.55 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1962 4390 0.039617 GGCGAGATGAGATGAGACGG 60.040 60.0 0.00 0.00 0.0 4.79 R
2158 4592 0.108424 CCGTCAAGAGCTCCAGAAGG 60.108 60.0 18.64 18.64 0.0 3.46 R
3659 6303 0.730265 TGCCGCGAACCACAAATATC 59.270 50.0 8.23 0.00 0.0 1.63 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
66 67 0.665369 CGCCGAACCACTACGAGTTT 60.665 55.000 0.00 0.00 0.00 2.66
78 79 6.483307 ACCACTACGAGTTTAGGGTTTAAAAC 59.517 38.462 0.00 0.00 36.13 2.43
83 84 4.751600 CGAGTTTAGGGTTTAAAACGGACT 59.248 41.667 0.00 0.00 39.90 3.85
88 89 8.965819 AGTTTAGGGTTTAAAACGGACTTTAAA 58.034 29.630 0.00 7.56 39.90 1.52
91 92 7.643569 AGGGTTTAAAACGGACTTTAAAGAA 57.356 32.000 21.92 0.08 39.95 2.52
140 141 3.181973 GCGCCTATTAAGTTAAGCGAGAC 59.818 47.826 23.88 8.98 46.03 3.36
276 277 0.032130 CGGCAGGCGTGTCATATACT 59.968 55.000 12.03 0.00 0.00 2.12
278 279 2.135933 GGCAGGCGTGTCATATACTTC 58.864 52.381 6.05 0.00 0.00 3.01
279 280 2.483013 GGCAGGCGTGTCATATACTTCA 60.483 50.000 6.05 0.00 0.00 3.02
280 281 3.194861 GCAGGCGTGTCATATACTTCAA 58.805 45.455 8.40 0.00 0.00 2.69
281 282 3.621268 GCAGGCGTGTCATATACTTCAAA 59.379 43.478 8.40 0.00 0.00 2.69
282 283 4.273480 GCAGGCGTGTCATATACTTCAAAT 59.727 41.667 8.40 0.00 0.00 2.32
283 284 5.559035 GCAGGCGTGTCATATACTTCAAATC 60.559 44.000 8.40 0.00 0.00 2.17
285 286 6.203530 CAGGCGTGTCATATACTTCAAATCAT 59.796 38.462 0.00 0.00 0.00 2.45
289 293 7.254761 GCGTGTCATATACTTCAAATCATTGGA 60.255 37.037 0.00 0.00 37.15 3.53
314 318 1.205657 GTCAAAACACAGACGCGAGA 58.794 50.000 15.93 0.00 0.00 4.04
315 319 1.190323 GTCAAAACACAGACGCGAGAG 59.810 52.381 15.93 3.66 0.00 3.20
330 334 1.239347 GAGAGGGCAACTGTTGGAAC 58.761 55.000 21.01 5.49 0.00 3.62
331 335 0.846693 AGAGGGCAACTGTTGGAACT 59.153 50.000 21.01 5.05 0.00 3.01
332 336 1.215423 AGAGGGCAACTGTTGGAACTT 59.785 47.619 21.01 0.00 0.00 2.66
333 337 1.338020 GAGGGCAACTGTTGGAACTTG 59.662 52.381 21.01 0.00 0.00 3.16
334 338 0.389025 GGGCAACTGTTGGAACTTGG 59.611 55.000 21.01 0.00 0.00 3.61
335 339 1.398692 GGCAACTGTTGGAACTTGGA 58.601 50.000 21.01 0.00 0.00 3.53
336 340 1.754226 GGCAACTGTTGGAACTTGGAA 59.246 47.619 21.01 0.00 0.00 3.53
337 341 2.223805 GGCAACTGTTGGAACTTGGAAG 60.224 50.000 21.01 0.00 0.00 3.46
338 342 2.799562 GCAACTGTTGGAACTTGGAAGC 60.800 50.000 21.01 0.00 0.00 3.86
339 343 1.308998 ACTGTTGGAACTTGGAAGCG 58.691 50.000 0.00 0.00 0.00 4.68
340 344 1.134220 ACTGTTGGAACTTGGAAGCGA 60.134 47.619 0.00 0.00 0.00 4.93
341 345 1.264288 CTGTTGGAACTTGGAAGCGAC 59.736 52.381 0.00 0.00 0.00 5.19
342 346 0.591659 GTTGGAACTTGGAAGCGACC 59.408 55.000 0.00 0.00 0.00 4.79
440 444 0.968405 GCAGAGGCAGATAGAGGGAG 59.032 60.000 0.00 0.00 40.72 4.30
441 445 1.631405 CAGAGGCAGATAGAGGGAGG 58.369 60.000 0.00 0.00 0.00 4.30
442 446 1.146774 CAGAGGCAGATAGAGGGAGGA 59.853 57.143 0.00 0.00 0.00 3.71
443 447 2.081043 AGAGGCAGATAGAGGGAGGAT 58.919 52.381 0.00 0.00 0.00 3.24
444 448 2.454381 AGAGGCAGATAGAGGGAGGATT 59.546 50.000 0.00 0.00 0.00 3.01
445 449 2.566724 GAGGCAGATAGAGGGAGGATTG 59.433 54.545 0.00 0.00 0.00 2.67
446 450 2.180973 AGGCAGATAGAGGGAGGATTGA 59.819 50.000 0.00 0.00 0.00 2.57
447 451 3.180507 GGCAGATAGAGGGAGGATTGAT 58.819 50.000 0.00 0.00 0.00 2.57
448 452 3.586618 GGCAGATAGAGGGAGGATTGATT 59.413 47.826 0.00 0.00 0.00 2.57
449 453 4.323409 GGCAGATAGAGGGAGGATTGATTC 60.323 50.000 0.00 0.00 0.00 2.52
450 454 4.285517 GCAGATAGAGGGAGGATTGATTCA 59.714 45.833 0.00 0.00 0.00 2.57
451 455 5.792741 CAGATAGAGGGAGGATTGATTCAC 58.207 45.833 0.00 0.00 0.00 3.18
452 456 4.843516 AGATAGAGGGAGGATTGATTCACC 59.156 45.833 0.00 0.00 0.00 4.02
453 457 2.131023 AGAGGGAGGATTGATTCACCC 58.869 52.381 0.00 0.00 40.57 4.61
537 562 3.062466 CGGCCGGAGTGTCTCTGA 61.062 66.667 20.10 0.00 39.05 3.27
542 567 2.701780 CGGAGTGTCTCTGACCGGG 61.702 68.421 6.32 0.00 39.05 5.73
543 568 1.304217 GGAGTGTCTCTGACCGGGA 60.304 63.158 6.32 0.00 0.00 5.14
558 770 2.833582 GGAGGCGATCCGGTCAGA 60.834 66.667 0.00 0.00 38.67 3.27
563 775 3.518998 CGATCCGGTCAGAGGCGT 61.519 66.667 0.00 0.00 0.00 5.68
564 776 2.105128 GATCCGGTCAGAGGCGTG 59.895 66.667 0.00 0.00 0.00 5.34
565 777 4.148825 ATCCGGTCAGAGGCGTGC 62.149 66.667 0.00 0.00 0.00 5.34
568 780 4.717629 CGGTCAGAGGCGTGCGAA 62.718 66.667 0.00 0.00 0.00 4.70
569 781 3.112709 GGTCAGAGGCGTGCGAAC 61.113 66.667 0.00 0.00 0.00 3.95
599 812 3.706373 CTAGCCAGCCACCGTGGT 61.706 66.667 18.95 3.28 40.46 4.16
615 834 4.906537 GTGTTGGCCGTTGGGGGT 62.907 66.667 0.00 0.00 35.78 4.95
616 835 4.904590 TGTTGGCCGTTGGGGGTG 62.905 66.667 0.00 0.00 35.78 4.61
626 852 1.607178 TTGGGGGTGCATGAAGCTG 60.607 57.895 2.20 0.00 45.94 4.24
651 880 1.816863 GAGACTCGGTCCAACTGCCA 61.817 60.000 1.06 0.00 32.18 4.92
716 967 1.875813 GTCTGCGGCGAGATGTCAG 60.876 63.158 12.98 7.42 0.00 3.51
718 969 3.068064 TGCGGCGAGATGTCAGGA 61.068 61.111 12.98 0.00 0.00 3.86
721 972 1.226802 CGGCGAGATGTCAGGACTG 60.227 63.158 0.00 0.00 0.00 3.51
793 1048 2.005370 ACTTCGTCCACTACTTCCCA 57.995 50.000 0.00 0.00 0.00 4.37
803 1058 0.462047 CTACTTCCCACCCATGTCGC 60.462 60.000 0.00 0.00 0.00 5.19
813 1068 1.429148 CCCATGTCGCCGTAAGCTTC 61.429 60.000 0.00 0.00 40.39 3.86
863 3211 1.343506 GCAGGAAAATTTCAGCAGCG 58.656 50.000 14.56 0.00 33.93 5.18
896 3244 0.179111 TTCCCTGCGATACAAGAGCG 60.179 55.000 0.00 0.00 40.87 5.03
1092 3463 3.083997 AAGGCGCCCGAGGATCTT 61.084 61.111 26.15 4.89 0.00 2.40
1130 3520 3.869832 GAGCCCGGTAATTAGTTCTTCAC 59.130 47.826 0.00 0.00 0.00 3.18
1137 3527 5.637810 CGGTAATTAGTTCTTCACTTGCTCA 59.362 40.000 0.00 0.00 36.88 4.26
1139 3529 7.307751 CGGTAATTAGTTCTTCACTTGCTCAAA 60.308 37.037 0.00 0.00 36.88 2.69
1140 3530 8.349983 GGTAATTAGTTCTTCACTTGCTCAAAA 58.650 33.333 0.00 0.00 36.88 2.44
1148 3564 3.963665 TCACTTGCTCAAAATTTCCGTG 58.036 40.909 0.00 0.00 0.00 4.94
1151 3567 2.132740 TGCTCAAAATTTCCGTGCAC 57.867 45.000 6.82 6.82 0.00 4.57
1157 3573 4.861210 TCAAAATTTCCGTGCACGTAATT 58.139 34.783 34.81 31.31 37.74 1.40
1158 3574 5.998553 TCAAAATTTCCGTGCACGTAATTA 58.001 33.333 31.88 21.73 37.74 1.40
1161 3577 8.235226 TCAAAATTTCCGTGCACGTAATTAATA 58.765 29.630 31.88 22.62 37.74 0.98
1165 3581 4.373527 TCCGTGCACGTAATTAATAGCAT 58.626 39.130 34.81 0.00 37.74 3.79
1172 3588 8.495949 GTGCACGTAATTAATAGCATCAACTAT 58.504 33.333 0.00 0.00 34.25 2.12
1173 3589 9.699703 TGCACGTAATTAATAGCATCAACTATA 57.300 29.630 0.00 0.00 32.49 1.31
1210 3626 2.050351 CGTCGTGTCCAGCGAAGT 60.050 61.111 0.00 0.00 40.19 3.01
1224 3640 1.708027 GAAGTGGAAACGATCGCGG 59.292 57.895 16.60 0.00 43.17 6.46
1225 3641 2.292802 GAAGTGGAAACGATCGCGGC 62.293 60.000 16.60 3.97 43.17 6.53
1612 4040 2.428890 CTCGCCATTCTAGACCTTGAGT 59.571 50.000 0.00 0.00 0.00 3.41
1616 4044 5.831525 TCGCCATTCTAGACCTTGAGTTATA 59.168 40.000 0.00 0.00 0.00 0.98
1645 4073 4.258932 TGACTGACACGCGACGCA 62.259 61.111 21.35 6.22 0.00 5.24
1955 4383 4.446413 CCCGAGTACGTGCCCCAC 62.446 72.222 0.00 0.00 37.88 4.61
1958 4386 3.001406 GAGTACGTGCCCCACCCT 61.001 66.667 0.00 0.00 0.00 4.34
1959 4387 3.001406 AGTACGTGCCCCACCCTC 61.001 66.667 0.00 0.00 0.00 4.30
1960 4388 4.091939 GTACGTGCCCCACCCTCC 62.092 72.222 0.00 0.00 0.00 4.30
1961 4389 4.642488 TACGTGCCCCACCCTCCA 62.642 66.667 0.00 0.00 0.00 3.86
2000 4429 3.039202 GCCGGCGTCCTTGTTGATG 62.039 63.158 12.58 0.00 0.00 3.07
2001 4430 1.375396 CCGGCGTCCTTGTTGATGA 60.375 57.895 6.01 0.00 0.00 2.92
2004 4433 1.202065 CGGCGTCCTTGTTGATGATTG 60.202 52.381 0.00 0.00 0.00 2.67
2005 4434 1.812571 GGCGTCCTTGTTGATGATTGT 59.187 47.619 0.00 0.00 0.00 2.71
2007 4436 3.438781 GGCGTCCTTGTTGATGATTGTTA 59.561 43.478 0.00 0.00 0.00 2.41
2008 4437 4.403453 GCGTCCTTGTTGATGATTGTTAC 58.597 43.478 0.00 0.00 0.00 2.50
2070 4500 5.911752 TGCTTAATTTGCTTGGTTTCTGAA 58.088 33.333 5.05 0.00 0.00 3.02
2071 4501 6.344500 TGCTTAATTTGCTTGGTTTCTGAAA 58.656 32.000 0.00 0.00 0.00 2.69
2146 4580 0.666913 ACAAGAGCGACGTGTACAGT 59.333 50.000 0.00 0.00 39.22 3.55
2155 4589 1.389106 GACGTGTACAGTTTCGGCATC 59.611 52.381 4.69 0.00 0.00 3.91
2158 4592 1.389106 GTGTACAGTTTCGGCATCGTC 59.611 52.381 0.00 0.00 37.69 4.20
2161 4595 0.034896 ACAGTTTCGGCATCGTCCTT 59.965 50.000 0.00 0.00 37.69 3.36
2320 4762 5.355910 TGGTGAAAAGGTTTAACAGACACTC 59.644 40.000 0.00 0.00 0.00 3.51
2485 4941 2.259012 ACAATGCAATCACCACCCATT 58.741 42.857 0.00 0.00 0.00 3.16
2486 4942 3.439154 ACAATGCAATCACCACCCATTA 58.561 40.909 0.00 0.00 0.00 1.90
2487 4943 3.195396 ACAATGCAATCACCACCCATTAC 59.805 43.478 0.00 0.00 0.00 1.89
2488 4944 1.458398 TGCAATCACCACCCATTACG 58.542 50.000 0.00 0.00 0.00 3.18
2489 4945 1.271652 TGCAATCACCACCCATTACGT 60.272 47.619 0.00 0.00 0.00 3.57
2490 4946 1.400494 GCAATCACCACCCATTACGTC 59.600 52.381 0.00 0.00 0.00 4.34
2491 4947 2.705730 CAATCACCACCCATTACGTCA 58.294 47.619 0.00 0.00 0.00 4.35
2492 4948 3.278574 CAATCACCACCCATTACGTCAT 58.721 45.455 0.00 0.00 0.00 3.06
2493 4949 2.684001 TCACCACCCATTACGTCATC 57.316 50.000 0.00 0.00 0.00 2.92
2494 4950 1.208535 TCACCACCCATTACGTCATCC 59.791 52.381 0.00 0.00 0.00 3.51
2495 4951 0.177141 ACCACCCATTACGTCATCCG 59.823 55.000 0.00 0.00 44.03 4.18
2496 4952 0.531974 CCACCCATTACGTCATCCGG 60.532 60.000 0.00 0.00 42.24 5.14
2497 4953 0.462375 CACCCATTACGTCATCCGGA 59.538 55.000 6.61 6.61 42.24 5.14
2498 4954 1.070134 CACCCATTACGTCATCCGGAT 59.930 52.381 12.38 12.38 42.24 4.18
2512 4968 0.933097 CCGGATGCAGAACATTCTCG 59.067 55.000 0.00 0.00 39.84 4.04
2529 4985 2.952978 TCTCGAAGGATCCAACTAGCTC 59.047 50.000 15.82 0.00 0.00 4.09
2531 4987 1.069358 CGAAGGATCCAACTAGCTCCC 59.931 57.143 15.82 0.00 0.00 4.30
2538 4994 3.806949 TCCAACTAGCTCCCAAACAAT 57.193 42.857 0.00 0.00 0.00 2.71
2539 4995 4.112634 TCCAACTAGCTCCCAAACAATT 57.887 40.909 0.00 0.00 0.00 2.32
2540 4996 3.826157 TCCAACTAGCTCCCAAACAATTG 59.174 43.478 3.24 3.24 36.25 2.32
2545 5001 5.385198 ACTAGCTCCCAAACAATTGAGAAA 58.615 37.500 13.59 0.00 38.94 2.52
2592 5049 3.810373 CGTTTTCCATTCCGTTCTCAAG 58.190 45.455 0.00 0.00 0.00 3.02
2725 5182 4.069232 CCGGAGCGCTCAAGGTCA 62.069 66.667 36.27 0.00 40.14 4.02
2726 5183 2.507992 CGGAGCGCTCAAGGTCAG 60.508 66.667 36.27 15.17 40.14 3.51
2746 5203 3.056821 CAGTCTCCACACGGTTTCATCTA 60.057 47.826 0.00 0.00 0.00 1.98
2748 5205 3.192844 GTCTCCACACGGTTTCATCTAGA 59.807 47.826 0.00 0.00 0.00 2.43
2760 5217 7.094506 ACGGTTTCATCTAGAATTTGTTTACCC 60.095 37.037 0.00 0.00 35.83 3.69
2773 5230 4.771114 TGTTTACCCGAATCCATCTCAT 57.229 40.909 0.00 0.00 0.00 2.90
2775 5232 6.241882 TGTTTACCCGAATCCATCTCATTA 57.758 37.500 0.00 0.00 0.00 1.90
2785 5242 6.259608 CGAATCCATCTCATTATAGCCCAATC 59.740 42.308 0.00 0.00 0.00 2.67
2804 5261 5.639082 CCAATCTAACAAACCCTGCAAAATC 59.361 40.000 0.00 0.00 0.00 2.17
2805 5262 4.864704 TCTAACAAACCCTGCAAAATCC 57.135 40.909 0.00 0.00 0.00 3.01
2939 5400 2.821366 CAGGGCGTGGTCTGATGC 60.821 66.667 0.00 0.00 33.11 3.91
2940 5401 4.457496 AGGGCGTGGTCTGATGCG 62.457 66.667 0.00 0.00 0.00 4.73
2941 5402 4.451150 GGGCGTGGTCTGATGCGA 62.451 66.667 0.00 0.00 0.00 5.10
2972 5439 4.137872 CCGGCGTACGTGTGGGAT 62.138 66.667 17.90 0.00 42.24 3.85
3011 5478 2.154462 CAGTGGTTCTTCCTGCGAATT 58.846 47.619 0.00 0.00 37.07 2.17
3041 5512 5.235186 GCATGTCTAGTTGCCTGTACTATTG 59.765 44.000 0.00 0.00 32.66 1.90
3042 5513 5.995565 TGTCTAGTTGCCTGTACTATTGT 57.004 39.130 0.00 0.00 0.00 2.71
3043 5514 7.489160 CATGTCTAGTTGCCTGTACTATTGTA 58.511 38.462 0.00 0.00 0.00 2.41
3044 5515 6.860080 TGTCTAGTTGCCTGTACTATTGTAC 58.140 40.000 10.11 10.11 46.74 2.90
3045 5516 6.662234 TGTCTAGTTGCCTGTACTATTGTACT 59.338 38.462 16.61 1.32 46.70 2.73
3046 5517 7.148120 TGTCTAGTTGCCTGTACTATTGTACTC 60.148 40.741 16.61 8.00 46.70 2.59
3047 5518 5.340439 AGTTGCCTGTACTATTGTACTCC 57.660 43.478 16.61 7.13 46.70 3.85
3048 5519 4.161754 AGTTGCCTGTACTATTGTACTCCC 59.838 45.833 16.61 6.85 46.70 4.30
3049 5520 3.990369 TGCCTGTACTATTGTACTCCCT 58.010 45.455 16.61 0.00 46.70 4.20
3050 5521 4.359105 TGCCTGTACTATTGTACTCCCTT 58.641 43.478 16.61 0.00 46.70 3.95
3051 5522 4.404715 TGCCTGTACTATTGTACTCCCTTC 59.595 45.833 16.61 3.57 46.70 3.46
3052 5523 4.650131 GCCTGTACTATTGTACTCCCTTCT 59.350 45.833 16.61 0.00 46.70 2.85
3053 5524 5.128991 GCCTGTACTATTGTACTCCCTTCTT 59.871 44.000 16.61 0.00 46.70 2.52
3054 5525 6.351966 GCCTGTACTATTGTACTCCCTTCTTT 60.352 42.308 16.61 0.00 46.70 2.52
3055 5526 7.266400 CCTGTACTATTGTACTCCCTTCTTTC 58.734 42.308 16.61 0.00 46.70 2.62
3056 5527 7.179076 TGTACTATTGTACTCCCTTCTTTCC 57.821 40.000 16.61 0.00 46.70 3.13
3057 5528 6.958192 TGTACTATTGTACTCCCTTCTTTCCT 59.042 38.462 16.61 0.00 46.70 3.36
3058 5529 8.117956 TGTACTATTGTACTCCCTTCTTTCCTA 58.882 37.037 16.61 0.00 46.70 2.94
3059 5530 8.975295 GTACTATTGTACTCCCTTCTTTCCTAA 58.025 37.037 9.81 0.00 44.08 2.69
3060 5531 8.445361 ACTATTGTACTCCCTTCTTTCCTAAA 57.555 34.615 0.00 0.00 0.00 1.85
3061 5532 9.059023 ACTATTGTACTCCCTTCTTTCCTAAAT 57.941 33.333 0.00 0.00 0.00 1.40
3062 5533 9.331282 CTATTGTACTCCCTTCTTTCCTAAATG 57.669 37.037 0.00 0.00 0.00 2.32
3063 5534 6.697641 TGTACTCCCTTCTTTCCTAAATGT 57.302 37.500 0.00 0.00 0.00 2.71
3064 5535 7.801893 TGTACTCCCTTCTTTCCTAAATGTA 57.198 36.000 0.00 0.00 0.00 2.29
3065 5536 8.209802 TGTACTCCCTTCTTTCCTAAATGTAA 57.790 34.615 0.00 0.00 0.00 2.41
3066 5537 8.319146 TGTACTCCCTTCTTTCCTAAATGTAAG 58.681 37.037 0.00 0.00 0.00 2.34
3067 5538 7.331089 ACTCCCTTCTTTCCTAAATGTAAGT 57.669 36.000 0.00 0.00 0.00 2.24
3068 5539 7.395617 ACTCCCTTCTTTCCTAAATGTAAGTC 58.604 38.462 0.00 0.00 0.00 3.01
3069 5540 7.237887 ACTCCCTTCTTTCCTAAATGTAAGTCT 59.762 37.037 0.00 0.00 0.00 3.24
3070 5541 7.985589 TCCCTTCTTTCCTAAATGTAAGTCTT 58.014 34.615 0.00 0.00 0.00 3.01
3071 5542 8.445588 TCCCTTCTTTCCTAAATGTAAGTCTTT 58.554 33.333 0.00 0.00 0.00 2.52
3072 5543 8.731605 CCCTTCTTTCCTAAATGTAAGTCTTTC 58.268 37.037 0.00 0.00 0.00 2.62
3073 5544 9.508642 CCTTCTTTCCTAAATGTAAGTCTTTCT 57.491 33.333 0.00 0.00 0.00 2.52
3087 5558 9.155975 TGTAAGTCTTTCTAGAGATTTCAATGC 57.844 33.333 0.00 0.00 29.76 3.56
3088 5559 9.155975 GTAAGTCTTTCTAGAGATTTCAATGCA 57.844 33.333 0.00 0.00 29.76 3.96
3089 5560 8.627208 AAGTCTTTCTAGAGATTTCAATGCAA 57.373 30.769 0.00 0.00 0.00 4.08
3090 5561 8.627208 AGTCTTTCTAGAGATTTCAATGCAAA 57.373 30.769 0.00 0.00 0.00 3.68
3091 5562 8.510505 AGTCTTTCTAGAGATTTCAATGCAAAC 58.489 33.333 0.00 0.00 0.00 2.93
3092 5563 8.510505 GTCTTTCTAGAGATTTCAATGCAAACT 58.489 33.333 0.00 0.00 0.00 2.66
3093 5564 9.725019 TCTTTCTAGAGATTTCAATGCAAACTA 57.275 29.630 0.00 0.00 0.00 2.24
3094 5565 9.766277 CTTTCTAGAGATTTCAATGCAAACTAC 57.234 33.333 0.00 0.00 0.00 2.73
3095 5566 8.846943 TTCTAGAGATTTCAATGCAAACTACA 57.153 30.769 0.00 0.00 0.00 2.74
3096 5567 9.453572 TTCTAGAGATTTCAATGCAAACTACAT 57.546 29.630 0.00 0.00 0.00 2.29
3099 5570 7.688372 AGAGATTTCAATGCAAACTACATACG 58.312 34.615 0.00 0.00 0.00 3.06
3100 5571 6.785191 AGATTTCAATGCAAACTACATACGG 58.215 36.000 0.00 0.00 0.00 4.02
3101 5572 6.597672 AGATTTCAATGCAAACTACATACGGA 59.402 34.615 0.00 0.00 0.00 4.69
3102 5573 6.561737 TTTCAATGCAAACTACATACGGAA 57.438 33.333 0.00 0.00 0.00 4.30
3103 5574 6.561737 TTCAATGCAAACTACATACGGAAA 57.438 33.333 0.00 0.00 0.00 3.13
3104 5575 6.751514 TCAATGCAAACTACATACGGAAAT 57.248 33.333 0.00 0.00 0.00 2.17
3105 5576 6.781138 TCAATGCAAACTACATACGGAAATC 58.219 36.000 0.00 0.00 0.00 2.17
3106 5577 6.597672 TCAATGCAAACTACATACGGAAATCT 59.402 34.615 0.00 0.00 0.00 2.40
3107 5578 6.604735 ATGCAAACTACATACGGAAATCTC 57.395 37.500 0.00 0.00 0.00 2.75
3108 5579 5.730550 TGCAAACTACATACGGAAATCTCT 58.269 37.500 0.00 0.00 0.00 3.10
3109 5580 6.869695 TGCAAACTACATACGGAAATCTCTA 58.130 36.000 0.00 0.00 0.00 2.43
3110 5581 6.978659 TGCAAACTACATACGGAAATCTCTAG 59.021 38.462 0.00 0.00 0.00 2.43
3111 5582 7.147966 TGCAAACTACATACGGAAATCTCTAGA 60.148 37.037 0.00 0.00 0.00 2.43
3112 5583 7.705325 GCAAACTACATACGGAAATCTCTAGAA 59.295 37.037 0.00 0.00 0.00 2.10
3113 5584 9.582431 CAAACTACATACGGAAATCTCTAGAAA 57.418 33.333 0.00 0.00 0.00 2.52
3114 5585 9.804758 AAACTACATACGGAAATCTCTAGAAAG 57.195 33.333 0.00 0.00 0.00 2.62
3115 5586 8.749026 ACTACATACGGAAATCTCTAGAAAGA 57.251 34.615 0.00 0.00 0.00 2.52
3116 5587 8.623030 ACTACATACGGAAATCTCTAGAAAGAC 58.377 37.037 0.00 0.00 0.00 3.01
3117 5588 7.648039 ACATACGGAAATCTCTAGAAAGACT 57.352 36.000 0.00 0.00 0.00 3.24
3118 5589 8.068892 ACATACGGAAATCTCTAGAAAGACTT 57.931 34.615 0.00 0.00 0.00 3.01
3119 5590 9.186837 ACATACGGAAATCTCTAGAAAGACTTA 57.813 33.333 0.00 0.00 0.00 2.24
3135 5606 9.819267 AGAAAGACTTATATTTAGAAACGGAGG 57.181 33.333 0.00 0.00 0.00 4.30
3136 5607 8.959705 AAAGACTTATATTTAGAAACGGAGGG 57.040 34.615 0.00 0.00 0.00 4.30
3137 5608 7.909485 AGACTTATATTTAGAAACGGAGGGA 57.091 36.000 0.00 0.00 0.00 4.20
3138 5609 7.953752 AGACTTATATTTAGAAACGGAGGGAG 58.046 38.462 0.00 0.00 0.00 4.30
3139 5610 7.564292 AGACTTATATTTAGAAACGGAGGGAGT 59.436 37.037 0.00 0.00 0.00 3.85
3140 5611 8.773033 ACTTATATTTAGAAACGGAGGGAGTA 57.227 34.615 0.00 0.00 0.00 2.59
3337 5980 4.338118 TCCTTCTGTTTTTGCGTCAAGAAT 59.662 37.500 0.46 0.00 0.00 2.40
3391 6034 3.320541 AGCTCGTCAGGGAAATCTGATAG 59.679 47.826 0.00 0.00 44.43 2.08
3433 6076 9.383519 GGTGAGTACATATGGATATACATTTGG 57.616 37.037 19.03 7.28 35.13 3.28
3453 6096 2.621055 GGTACAACATTGAGCACACCAA 59.379 45.455 0.00 0.00 0.00 3.67
3659 6303 7.624360 TTTGGTTTAATCTACCATGCTACAG 57.376 36.000 0.00 0.00 44.70 2.74
3849 6497 7.066374 TCTGTTGCCAAACAAAACAAATTAC 57.934 32.000 0.00 0.00 45.50 1.89
3850 6498 6.876257 TCTGTTGCCAAACAAAACAAATTACT 59.124 30.769 0.00 0.00 45.50 2.24
3851 6499 7.389053 TCTGTTGCCAAACAAAACAAATTACTT 59.611 29.630 0.00 0.00 45.50 2.24
3852 6500 7.522374 TGTTGCCAAACAAAACAAATTACTTC 58.478 30.769 0.00 0.00 43.32 3.01
3853 6501 7.389053 TGTTGCCAAACAAAACAAATTACTTCT 59.611 29.630 0.00 0.00 43.32 2.85
3854 6502 7.532682 TGCCAAACAAAACAAATTACTTCTC 57.467 32.000 0.00 0.00 0.00 2.87
3855 6503 6.536941 TGCCAAACAAAACAAATTACTTCTCC 59.463 34.615 0.00 0.00 0.00 3.71
3856 6504 6.018262 GCCAAACAAAACAAATTACTTCTCCC 60.018 38.462 0.00 0.00 0.00 4.30
3857 6505 7.272244 CCAAACAAAACAAATTACTTCTCCCT 58.728 34.615 0.00 0.00 0.00 4.20
3858 6506 7.438160 CCAAACAAAACAAATTACTTCTCCCTC 59.562 37.037 0.00 0.00 0.00 4.30
3859 6507 6.650427 ACAAAACAAATTACTTCTCCCTCC 57.350 37.500 0.00 0.00 0.00 4.30
3860 6508 5.240844 ACAAAACAAATTACTTCTCCCTCCG 59.759 40.000 0.00 0.00 0.00 4.63
3861 6509 4.635699 AACAAATTACTTCTCCCTCCGT 57.364 40.909 0.00 0.00 0.00 4.69
3862 6510 4.203654 ACAAATTACTTCTCCCTCCGTC 57.796 45.455 0.00 0.00 0.00 4.79
3863 6511 3.055312 ACAAATTACTTCTCCCTCCGTCC 60.055 47.826 0.00 0.00 0.00 4.79
3864 6512 1.790818 ATTACTTCTCCCTCCGTCCC 58.209 55.000 0.00 0.00 0.00 4.46
3865 6513 0.410663 TTACTTCTCCCTCCGTCCCA 59.589 55.000 0.00 0.00 0.00 4.37
3866 6514 0.635009 TACTTCTCCCTCCGTCCCAT 59.365 55.000 0.00 0.00 0.00 4.00
3867 6515 0.635009 ACTTCTCCCTCCGTCCCATA 59.365 55.000 0.00 0.00 0.00 2.74
3868 6516 1.007963 ACTTCTCCCTCCGTCCCATAA 59.992 52.381 0.00 0.00 0.00 1.90
3869 6517 2.330216 CTTCTCCCTCCGTCCCATAAT 58.670 52.381 0.00 0.00 0.00 1.28
3870 6518 1.717032 TCTCCCTCCGTCCCATAATG 58.283 55.000 0.00 0.00 0.00 1.90
3871 6519 1.062428 TCTCCCTCCGTCCCATAATGT 60.062 52.381 0.00 0.00 0.00 2.71
3872 6520 2.178325 TCTCCCTCCGTCCCATAATGTA 59.822 50.000 0.00 0.00 0.00 2.29
3873 6521 2.969950 CTCCCTCCGTCCCATAATGTAA 59.030 50.000 0.00 0.00 0.00 2.41
3874 6522 2.969950 TCCCTCCGTCCCATAATGTAAG 59.030 50.000 0.00 0.00 0.00 2.34
3875 6523 2.969950 CCCTCCGTCCCATAATGTAAGA 59.030 50.000 0.00 0.00 0.00 2.10
3876 6524 3.244112 CCCTCCGTCCCATAATGTAAGAC 60.244 52.174 0.00 0.00 0.00 3.01
3878 6526 3.025978 TCCGTCCCATAATGTAAGACGT 58.974 45.455 9.63 0.00 46.62 4.34
3879 6527 3.448301 TCCGTCCCATAATGTAAGACGTT 59.552 43.478 9.63 0.00 46.62 3.99
3880 6528 4.081531 TCCGTCCCATAATGTAAGACGTTT 60.082 41.667 9.63 0.00 46.62 3.60
3881 6529 4.632688 CCGTCCCATAATGTAAGACGTTTT 59.367 41.667 9.63 0.00 46.62 2.43
3882 6530 5.122711 CCGTCCCATAATGTAAGACGTTTTT 59.877 40.000 9.63 0.00 46.62 1.94
3928 6576 3.720949 CGTCTTACATTATGGGACGGA 57.279 47.619 20.50 2.30 43.69 4.69
3929 6577 3.639538 CGTCTTACATTATGGGACGGAG 58.360 50.000 20.50 2.74 43.69 4.63
3930 6578 3.552273 CGTCTTACATTATGGGACGGAGG 60.552 52.174 20.50 5.87 43.69 4.30
3931 6579 2.969950 TCTTACATTATGGGACGGAGGG 59.030 50.000 0.00 0.00 0.00 4.30
3932 6580 2.779429 TACATTATGGGACGGAGGGA 57.221 50.000 0.00 0.00 0.00 4.20
3933 6581 1.424638 ACATTATGGGACGGAGGGAG 58.575 55.000 0.00 0.00 0.00 4.30
3934 6582 1.344087 ACATTATGGGACGGAGGGAGT 60.344 52.381 0.00 0.00 0.00 3.85
3935 6583 2.090943 ACATTATGGGACGGAGGGAGTA 60.091 50.000 0.00 0.00 0.00 2.59
3936 6584 2.376695 TTATGGGACGGAGGGAGTAG 57.623 55.000 0.00 0.00 0.00 2.57
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
2 3 1.092348 GGTCGATTGCACCCTAAACC 58.908 55.000 0.00 0.00 0.00 3.27
35 36 1.330829 GGTTCGGCGGAATGAATTCTC 59.669 52.381 7.21 0.00 37.00 2.87
36 37 1.339631 TGGTTCGGCGGAATGAATTCT 60.340 47.619 7.21 0.00 37.00 2.40
37 38 1.091537 TGGTTCGGCGGAATGAATTC 58.908 50.000 7.21 0.00 34.05 2.17
38 39 0.808755 GTGGTTCGGCGGAATGAATT 59.191 50.000 7.21 0.00 34.05 2.17
66 67 8.744568 TTCTTTAAAGTCCGTTTTAAACCCTA 57.255 30.769 14.74 0.00 37.50 3.53
111 112 5.681543 GCTTAACTTAATAGGCGCATGTTTC 59.318 40.000 9.81 0.00 0.00 2.78
113 114 4.260620 CGCTTAACTTAATAGGCGCATGTT 60.261 41.667 10.83 10.04 42.94 2.71
114 115 3.247648 CGCTTAACTTAATAGGCGCATGT 59.752 43.478 10.83 0.00 42.94 3.21
115 116 3.493129 TCGCTTAACTTAATAGGCGCATG 59.507 43.478 10.83 0.00 46.91 4.06
116 117 3.724374 TCGCTTAACTTAATAGGCGCAT 58.276 40.909 10.83 3.98 46.91 4.73
117 118 3.120792 CTCGCTTAACTTAATAGGCGCA 58.879 45.455 10.83 0.00 46.91 6.09
123 124 4.107622 GCACCGTCTCGCTTAACTTAATA 58.892 43.478 0.00 0.00 0.00 0.98
140 141 2.674954 TGCTTTGAAAATCATGCACCG 58.325 42.857 0.00 0.00 33.55 4.94
280 281 7.052873 TGTGTTTTGACCAAAATCCAATGATT 58.947 30.769 10.61 0.00 43.08 2.57
281 282 6.590068 TGTGTTTTGACCAAAATCCAATGAT 58.410 32.000 10.61 0.00 41.64 2.45
282 283 5.982356 TGTGTTTTGACCAAAATCCAATGA 58.018 33.333 10.61 0.00 41.64 2.57
283 284 6.018832 GTCTGTGTTTTGACCAAAATCCAATG 60.019 38.462 10.61 3.46 41.64 2.82
285 286 5.415221 GTCTGTGTTTTGACCAAAATCCAA 58.585 37.500 10.61 0.00 41.64 3.53
289 293 3.443976 GCGTCTGTGTTTTGACCAAAAT 58.556 40.909 10.61 0.00 41.64 1.82
314 318 1.402787 CAAGTTCCAACAGTTGCCCT 58.597 50.000 7.88 0.15 0.00 5.19
315 319 0.389025 CCAAGTTCCAACAGTTGCCC 59.611 55.000 7.88 0.00 0.00 5.36
317 321 2.799562 GCTTCCAAGTTCCAACAGTTGC 60.800 50.000 7.88 0.00 0.00 4.17
319 323 1.676006 CGCTTCCAAGTTCCAACAGTT 59.324 47.619 0.00 0.00 0.00 3.16
320 324 1.134220 TCGCTTCCAAGTTCCAACAGT 60.134 47.619 0.00 0.00 0.00 3.55
322 326 1.305201 GTCGCTTCCAAGTTCCAACA 58.695 50.000 0.00 0.00 0.00 3.33
358 362 3.599285 TTGCCTAAGCGTGACCCGG 62.599 63.158 0.00 0.00 44.31 5.73
359 363 2.047655 TTGCCTAAGCGTGACCCG 60.048 61.111 0.00 0.00 44.31 5.28
360 364 0.248289 TAGTTGCCTAAGCGTGACCC 59.752 55.000 0.00 0.00 44.31 4.46
425 429 2.180973 TCAATCCTCCCTCTATCTGCCT 59.819 50.000 0.00 0.00 0.00 4.75
440 444 2.163613 GGTTGAACGGGTGAATCAATCC 59.836 50.000 0.00 0.00 35.70 3.01
441 445 3.081804 AGGTTGAACGGGTGAATCAATC 58.918 45.455 0.00 0.00 35.70 2.67
442 446 2.819608 CAGGTTGAACGGGTGAATCAAT 59.180 45.455 0.00 0.00 35.70 2.57
443 447 2.226330 CAGGTTGAACGGGTGAATCAA 58.774 47.619 0.00 0.00 0.00 2.57
444 448 1.890876 CAGGTTGAACGGGTGAATCA 58.109 50.000 0.00 0.00 0.00 2.57
445 449 0.521735 GCAGGTTGAACGGGTGAATC 59.478 55.000 0.00 0.00 0.00 2.52
446 450 1.234615 CGCAGGTTGAACGGGTGAAT 61.235 55.000 0.00 0.00 0.00 2.57
447 451 1.890041 CGCAGGTTGAACGGGTGAA 60.890 57.895 0.00 0.00 0.00 3.18
448 452 2.280524 CGCAGGTTGAACGGGTGA 60.281 61.111 0.00 0.00 0.00 4.02
475 479 1.600916 GTCAGGTGCAGGGTGTTCC 60.601 63.158 0.00 0.00 0.00 3.62
477 481 2.111043 CGTCAGGTGCAGGGTGTT 59.889 61.111 0.00 0.00 0.00 3.32
478 482 3.941188 CCGTCAGGTGCAGGGTGT 61.941 66.667 0.00 0.00 0.00 4.16
529 554 2.680352 GCCTCCCGGTCAGAGACA 60.680 66.667 7.69 0.00 33.68 3.41
530 555 3.827898 CGCCTCCCGGTCAGAGAC 61.828 72.222 7.69 0.00 32.86 3.36
542 567 2.725008 CTCTGACCGGATCGCCTC 59.275 66.667 9.46 0.00 0.00 4.70
543 568 2.835431 CCTCTGACCGGATCGCCT 60.835 66.667 9.46 0.00 0.00 5.52
545 570 4.933064 CGCCTCTGACCGGATCGC 62.933 72.222 9.46 0.00 0.00 4.58
572 784 2.103143 CTGGCTAGCTCGGTCACG 59.897 66.667 15.72 0.00 42.74 4.35
599 812 4.904590 CACCCCCAACGGCCAACA 62.905 66.667 2.24 0.00 0.00 3.33
605 824 2.282816 TTCATGCACCCCCAACGG 60.283 61.111 0.00 0.00 0.00 4.44
616 835 3.109612 CTCCGCTGCAGCTTCATGC 62.110 63.158 34.22 9.53 46.68 4.06
617 836 1.449070 TCTCCGCTGCAGCTTCATG 60.449 57.895 34.22 19.18 39.32 3.07
618 837 1.449246 GTCTCCGCTGCAGCTTCAT 60.449 57.895 34.22 0.00 39.32 2.57
619 838 2.047844 GTCTCCGCTGCAGCTTCA 60.048 61.111 34.22 17.61 39.32 3.02
620 839 1.809209 GAGTCTCCGCTGCAGCTTC 60.809 63.158 34.22 19.15 39.32 3.86
626 852 4.500116 GGACCGAGTCTCCGCTGC 62.500 72.222 0.00 0.00 32.47 5.25
685 936 3.175240 CAGACTTCCTCGCGTGCG 61.175 66.667 5.77 8.14 41.35 5.34
742 993 0.250901 AAACGAGCAGGCAGGTGATT 60.251 50.000 0.00 0.00 0.00 2.57
793 1048 2.125269 GCTTACGGCGACATGGGT 60.125 61.111 16.62 0.00 0.00 4.51
803 1058 1.796796 GCTGCAAGGAAGCTTACGG 59.203 57.895 2.17 0.65 37.69 4.02
813 1068 2.456119 GGACGACATCGCTGCAAGG 61.456 63.158 0.14 0.00 44.43 3.61
863 3211 0.674534 AGGGAATCTATCGACACCGC 59.325 55.000 0.00 0.00 35.37 5.68
896 3244 4.439057 TGACTGACTAGTTGTTGTTGTCC 58.561 43.478 0.00 0.00 37.25 4.02
1130 3520 2.472488 GTGCACGGAAATTTTGAGCAAG 59.528 45.455 14.62 0.00 31.78 4.01
1137 3527 7.219344 GCTATTAATTACGTGCACGGAAATTTT 59.781 33.333 37.14 30.30 46.21 1.82
1139 3529 6.183360 TGCTATTAATTACGTGCACGGAAATT 60.183 34.615 38.01 36.52 46.21 1.82
1140 3530 5.294799 TGCTATTAATTACGTGCACGGAAAT 59.705 36.000 38.01 32.15 46.21 2.17
1453 3869 4.007644 CAGCCTGGACGCCACAGA 62.008 66.667 0.00 0.00 38.20 3.41
1586 4002 2.091775 AGGTCTAGAATGGCGAGTAGGT 60.092 50.000 0.00 0.00 0.00 3.08
1587 4003 2.588620 AGGTCTAGAATGGCGAGTAGG 58.411 52.381 0.00 0.00 0.00 3.18
1589 4005 3.628008 TCAAGGTCTAGAATGGCGAGTA 58.372 45.455 0.00 0.00 0.00 2.59
1592 4008 2.457598 ACTCAAGGTCTAGAATGGCGA 58.542 47.619 0.00 0.00 0.00 5.54
1600 4028 7.337184 TCAGTCAGTGTATAACTCAAGGTCTAG 59.663 40.741 0.00 0.00 36.83 2.43
1602 4030 6.010850 TCAGTCAGTGTATAACTCAAGGTCT 58.989 40.000 0.00 0.00 36.83 3.85
1612 4040 5.768164 TGTCAGTCAGTCAGTCAGTGTATAA 59.232 40.000 0.00 0.00 0.00 0.98
1616 4044 2.099921 GTGTCAGTCAGTCAGTCAGTGT 59.900 50.000 0.00 0.00 0.00 3.55
1952 4380 1.961180 GATGAGACGGTGGAGGGTGG 61.961 65.000 0.00 0.00 0.00 4.61
1953 4381 0.972983 AGATGAGACGGTGGAGGGTG 60.973 60.000 0.00 0.00 0.00 4.61
1955 4383 0.684479 TGAGATGAGACGGTGGAGGG 60.684 60.000 0.00 0.00 0.00 4.30
1958 4386 2.302260 GAGATGAGATGAGACGGTGGA 58.698 52.381 0.00 0.00 0.00 4.02
1959 4387 1.001924 CGAGATGAGATGAGACGGTGG 60.002 57.143 0.00 0.00 0.00 4.61
1960 4388 1.599171 GCGAGATGAGATGAGACGGTG 60.599 57.143 0.00 0.00 0.00 4.94
1961 4389 0.665835 GCGAGATGAGATGAGACGGT 59.334 55.000 0.00 0.00 0.00 4.83
1962 4390 0.039617 GGCGAGATGAGATGAGACGG 60.040 60.000 0.00 0.00 0.00 4.79
1963 4391 0.385348 CGGCGAGATGAGATGAGACG 60.385 60.000 0.00 0.00 0.00 4.18
1964 4392 0.662970 GCGGCGAGATGAGATGAGAC 60.663 60.000 12.98 0.00 0.00 3.36
2000 4429 9.230932 GAATACGTGGAGTAGTAAGTAACAATC 57.769 37.037 0.00 0.00 38.94 2.67
2001 4430 7.912250 CGAATACGTGGAGTAGTAAGTAACAAT 59.088 37.037 0.00 0.00 38.94 2.71
2004 4433 7.005062 TCGAATACGTGGAGTAGTAAGTAAC 57.995 40.000 0.00 0.00 38.94 2.50
2005 4434 7.609760 TTCGAATACGTGGAGTAGTAAGTAA 57.390 36.000 0.00 0.00 38.94 2.24
2007 4436 6.690194 ATTCGAATACGTGGAGTAGTAAGT 57.310 37.500 9.39 0.00 38.94 2.24
2008 4437 7.699391 TCAAATTCGAATACGTGGAGTAGTAAG 59.301 37.037 11.83 0.00 38.94 2.34
2070 4500 4.021719 CCCAGTCAAATCAGCATTCAGTTT 60.022 41.667 0.00 0.00 0.00 2.66
2071 4501 3.508793 CCCAGTCAAATCAGCATTCAGTT 59.491 43.478 0.00 0.00 0.00 3.16
2146 4580 0.391130 CCAGAAGGACGATGCCGAAA 60.391 55.000 0.00 0.00 39.50 3.46
2155 4589 0.891373 TCAAGAGCTCCAGAAGGACG 59.109 55.000 10.93 0.00 39.61 4.79
2158 4592 0.108424 CCGTCAAGAGCTCCAGAAGG 60.108 60.000 18.64 18.64 0.00 3.46
2161 4595 2.650116 GCCCGTCAAGAGCTCCAGA 61.650 63.158 10.93 5.80 0.00 3.86
2405 4859 5.266733 AGAAGCTGTGCAAATGAAAAGAA 57.733 34.783 0.00 0.00 0.00 2.52
2413 4867 7.391554 TCAATTCTAGTTAGAAGCTGTGCAAAT 59.608 33.333 7.57 0.00 44.67 2.32
2475 4931 1.663695 GGATGACGTAATGGGTGGTG 58.336 55.000 0.00 0.00 0.00 4.17
2485 4941 1.107945 TTCTGCATCCGGATGACGTA 58.892 50.000 41.87 23.88 41.20 3.57
2486 4942 0.460284 GTTCTGCATCCGGATGACGT 60.460 55.000 41.87 8.91 41.20 4.34
2487 4943 0.460109 TGTTCTGCATCCGGATGACG 60.460 55.000 41.87 30.53 41.20 4.35
2488 4944 1.959042 ATGTTCTGCATCCGGATGAC 58.041 50.000 41.87 31.82 41.20 3.06
2489 4945 2.171237 AGAATGTTCTGCATCCGGATGA 59.829 45.455 41.87 26.64 40.44 2.92
2490 4946 2.547211 GAGAATGTTCTGCATCCGGATG 59.453 50.000 35.50 35.50 37.73 3.51
2491 4947 2.804572 CGAGAATGTTCTGCATCCGGAT 60.805 50.000 12.38 12.38 37.73 4.18
2492 4948 1.471501 CGAGAATGTTCTGCATCCGGA 60.472 52.381 6.61 6.61 37.73 5.14
2493 4949 0.933097 CGAGAATGTTCTGCATCCGG 59.067 55.000 0.00 0.00 37.73 5.14
2494 4950 1.926561 TCGAGAATGTTCTGCATCCG 58.073 50.000 0.00 0.00 37.73 4.18
2495 4951 2.611292 CCTTCGAGAATGTTCTGCATCC 59.389 50.000 0.00 0.00 37.73 3.51
2496 4952 3.525537 TCCTTCGAGAATGTTCTGCATC 58.474 45.455 0.00 0.00 37.73 3.91
2497 4953 3.616956 TCCTTCGAGAATGTTCTGCAT 57.383 42.857 0.00 0.00 37.73 3.96
2498 4954 3.525537 GATCCTTCGAGAATGTTCTGCA 58.474 45.455 0.00 0.00 37.73 4.41
2512 4968 2.119495 TGGGAGCTAGTTGGATCCTTC 58.881 52.381 14.23 5.98 41.12 3.46
2529 4985 7.540745 CGGTAACTTATTTCTCAATTGTTTGGG 59.459 37.037 5.13 0.00 34.39 4.12
2531 4987 8.901748 CACGGTAACTTATTTCTCAATTGTTTG 58.098 33.333 5.13 0.00 0.00 2.93
2538 4994 4.643463 TGCCACGGTAACTTATTTCTCAA 58.357 39.130 0.00 0.00 0.00 3.02
2539 4995 4.274602 TGCCACGGTAACTTATTTCTCA 57.725 40.909 0.00 0.00 0.00 3.27
2540 4996 5.049267 TGTTTGCCACGGTAACTTATTTCTC 60.049 40.000 0.00 0.00 0.00 2.87
2592 5049 0.247460 GGAGGCCCATCAAACTTTGC 59.753 55.000 0.00 0.00 0.00 3.68
2615 5072 4.547859 GCAGGTGCATCAGTAGGG 57.452 61.111 0.00 0.00 41.59 3.53
2725 5182 1.971357 AGATGAAACCGTGTGGAGACT 59.029 47.619 0.00 0.00 39.21 3.24
2726 5183 2.457366 AGATGAAACCGTGTGGAGAC 57.543 50.000 0.00 0.00 39.21 3.36
2746 5203 6.187682 AGATGGATTCGGGTAAACAAATTCT 58.812 36.000 0.00 0.00 0.00 2.40
2748 5205 5.949354 TGAGATGGATTCGGGTAAACAAATT 59.051 36.000 0.00 0.00 0.00 1.82
2760 5217 5.089970 TGGGCTATAATGAGATGGATTCG 57.910 43.478 0.00 0.00 0.00 3.34
2773 5230 6.126409 CAGGGTTTGTTAGATTGGGCTATAA 58.874 40.000 0.00 0.00 0.00 0.98
2775 5232 4.536765 CAGGGTTTGTTAGATTGGGCTAT 58.463 43.478 0.00 0.00 0.00 2.97
2785 5242 3.574614 CGGATTTTGCAGGGTTTGTTAG 58.425 45.455 0.00 0.00 0.00 2.34
2804 5261 2.859273 CTAGCTGCAAGGGACACCGG 62.859 65.000 0.00 0.00 43.47 5.28
2805 5262 1.448540 CTAGCTGCAAGGGACACCG 60.449 63.158 1.02 0.00 43.47 4.94
2883 5344 2.877360 TAGTTGATCACGCGGGCGAC 62.877 60.000 20.98 4.43 42.83 5.19
2939 5400 2.920869 GGTACGCGCACATCATCG 59.079 61.111 12.27 0.00 0.00 3.84
2972 5439 2.721231 GCAACGGCAGCAACTTCA 59.279 55.556 0.00 0.00 40.72 3.02
3011 5478 1.404986 GGCAACTAGACATGCACGGTA 60.405 52.381 17.23 0.00 44.32 4.02
3041 5512 8.319881 ACTTACATTTAGGAAAGAAGGGAGTAC 58.680 37.037 0.00 0.00 0.00 2.73
3042 5513 8.445361 ACTTACATTTAGGAAAGAAGGGAGTA 57.555 34.615 0.00 0.00 0.00 2.59
3043 5514 7.237887 AGACTTACATTTAGGAAAGAAGGGAGT 59.762 37.037 0.00 0.00 0.00 3.85
3044 5515 7.625469 AGACTTACATTTAGGAAAGAAGGGAG 58.375 38.462 0.00 0.00 0.00 4.30
3045 5516 7.569599 AGACTTACATTTAGGAAAGAAGGGA 57.430 36.000 0.00 0.00 0.00 4.20
3046 5517 8.637196 AAAGACTTACATTTAGGAAAGAAGGG 57.363 34.615 0.00 0.00 0.00 3.95
3047 5518 9.508642 AGAAAGACTTACATTTAGGAAAGAAGG 57.491 33.333 0.00 0.00 0.00 3.46
3061 5532 9.155975 GCATTGAAATCTCTAGAAAGACTTACA 57.844 33.333 0.00 0.00 0.00 2.41
3062 5533 9.155975 TGCATTGAAATCTCTAGAAAGACTTAC 57.844 33.333 0.00 0.00 0.00 2.34
3063 5534 9.725019 TTGCATTGAAATCTCTAGAAAGACTTA 57.275 29.630 0.00 0.00 0.00 2.24
3064 5535 8.627208 TTGCATTGAAATCTCTAGAAAGACTT 57.373 30.769 0.00 0.00 0.00 3.01
3065 5536 8.510505 GTTTGCATTGAAATCTCTAGAAAGACT 58.489 33.333 0.00 0.00 0.00 3.24
3066 5537 8.510505 AGTTTGCATTGAAATCTCTAGAAAGAC 58.489 33.333 0.00 0.00 0.00 3.01
3067 5538 8.627208 AGTTTGCATTGAAATCTCTAGAAAGA 57.373 30.769 0.00 0.00 0.00 2.52
3068 5539 9.766277 GTAGTTTGCATTGAAATCTCTAGAAAG 57.234 33.333 0.00 0.00 0.00 2.62
3069 5540 9.283768 TGTAGTTTGCATTGAAATCTCTAGAAA 57.716 29.630 0.00 0.00 0.00 2.52
3070 5541 8.846943 TGTAGTTTGCATTGAAATCTCTAGAA 57.153 30.769 0.00 0.00 0.00 2.10
3073 5544 8.817100 CGTATGTAGTTTGCATTGAAATCTCTA 58.183 33.333 0.00 0.00 0.00 2.43
3074 5545 7.201644 CCGTATGTAGTTTGCATTGAAATCTCT 60.202 37.037 0.00 0.00 0.00 3.10
3075 5546 6.907212 CCGTATGTAGTTTGCATTGAAATCTC 59.093 38.462 0.00 0.00 0.00 2.75
3076 5547 6.597672 TCCGTATGTAGTTTGCATTGAAATCT 59.402 34.615 0.00 0.00 0.00 2.40
3077 5548 6.781138 TCCGTATGTAGTTTGCATTGAAATC 58.219 36.000 0.00 0.00 0.00 2.17
3078 5549 6.751514 TCCGTATGTAGTTTGCATTGAAAT 57.248 33.333 0.00 0.00 0.00 2.17
3079 5550 6.561737 TTCCGTATGTAGTTTGCATTGAAA 57.438 33.333 0.00 0.00 0.00 2.69
3080 5551 6.561737 TTTCCGTATGTAGTTTGCATTGAA 57.438 33.333 0.00 0.00 0.00 2.69
3081 5552 6.597672 AGATTTCCGTATGTAGTTTGCATTGA 59.402 34.615 0.00 0.00 0.00 2.57
3082 5553 6.785191 AGATTTCCGTATGTAGTTTGCATTG 58.215 36.000 0.00 0.00 0.00 2.82
3083 5554 6.823689 AGAGATTTCCGTATGTAGTTTGCATT 59.176 34.615 0.00 0.00 0.00 3.56
3084 5555 6.349300 AGAGATTTCCGTATGTAGTTTGCAT 58.651 36.000 0.00 0.00 0.00 3.96
3085 5556 5.730550 AGAGATTTCCGTATGTAGTTTGCA 58.269 37.500 0.00 0.00 0.00 4.08
3086 5557 7.201145 TCTAGAGATTTCCGTATGTAGTTTGC 58.799 38.462 0.00 0.00 0.00 3.68
3087 5558 9.582431 TTTCTAGAGATTTCCGTATGTAGTTTG 57.418 33.333 0.00 0.00 0.00 2.93
3088 5559 9.804758 CTTTCTAGAGATTTCCGTATGTAGTTT 57.195 33.333 0.00 0.00 0.00 2.66
3089 5560 9.186837 TCTTTCTAGAGATTTCCGTATGTAGTT 57.813 33.333 0.00 0.00 0.00 2.24
3090 5561 8.623030 GTCTTTCTAGAGATTTCCGTATGTAGT 58.377 37.037 0.00 0.00 0.00 2.73
3091 5562 8.842280 AGTCTTTCTAGAGATTTCCGTATGTAG 58.158 37.037 0.00 0.00 0.00 2.74
3092 5563 8.749026 AGTCTTTCTAGAGATTTCCGTATGTA 57.251 34.615 0.00 0.00 0.00 2.29
3093 5564 7.648039 AGTCTTTCTAGAGATTTCCGTATGT 57.352 36.000 0.00 0.00 0.00 2.29
3109 5580 9.819267 CCTCCGTTTCTAAATATAAGTCTTTCT 57.181 33.333 0.00 0.00 0.00 2.52
3110 5581 9.043079 CCCTCCGTTTCTAAATATAAGTCTTTC 57.957 37.037 0.00 0.00 0.00 2.62
3111 5582 8.765517 TCCCTCCGTTTCTAAATATAAGTCTTT 58.234 33.333 0.00 0.00 0.00 2.52
3112 5583 8.315220 TCCCTCCGTTTCTAAATATAAGTCTT 57.685 34.615 0.00 0.00 0.00 3.01
3113 5584 7.564292 ACTCCCTCCGTTTCTAAATATAAGTCT 59.436 37.037 0.00 0.00 0.00 3.24
3114 5585 7.724287 ACTCCCTCCGTTTCTAAATATAAGTC 58.276 38.462 0.00 0.00 0.00 3.01
3115 5586 7.672122 ACTCCCTCCGTTTCTAAATATAAGT 57.328 36.000 0.00 0.00 0.00 2.24
3116 5587 8.858094 ACTACTCCCTCCGTTTCTAAATATAAG 58.142 37.037 0.00 0.00 0.00 1.73
3117 5588 8.773033 ACTACTCCCTCCGTTTCTAAATATAA 57.227 34.615 0.00 0.00 0.00 0.98
3118 5589 9.866655 TTACTACTCCCTCCGTTTCTAAATATA 57.133 33.333 0.00 0.00 0.00 0.86
3119 5590 8.637099 GTTACTACTCCCTCCGTTTCTAAATAT 58.363 37.037 0.00 0.00 0.00 1.28
3120 5591 7.836183 AGTTACTACTCCCTCCGTTTCTAAATA 59.164 37.037 0.00 0.00 0.00 1.40
3121 5592 6.666980 AGTTACTACTCCCTCCGTTTCTAAAT 59.333 38.462 0.00 0.00 0.00 1.40
3122 5593 6.012745 AGTTACTACTCCCTCCGTTTCTAAA 58.987 40.000 0.00 0.00 0.00 1.85
3123 5594 5.574188 AGTTACTACTCCCTCCGTTTCTAA 58.426 41.667 0.00 0.00 0.00 2.10
3124 5595 5.184892 AGTTACTACTCCCTCCGTTTCTA 57.815 43.478 0.00 0.00 0.00 2.10
3125 5596 4.044946 AGTTACTACTCCCTCCGTTTCT 57.955 45.455 0.00 0.00 0.00 2.52
3126 5597 4.797800 AAGTTACTACTCCCTCCGTTTC 57.202 45.455 0.00 0.00 31.99 2.78
3127 5598 5.557576 AAAAGTTACTACTCCCTCCGTTT 57.442 39.130 0.00 0.00 31.99 3.60
3128 5599 5.557576 AAAAAGTTACTACTCCCTCCGTT 57.442 39.130 0.00 0.00 31.99 4.44
3157 5628 7.197017 AGCTTACGAAGTTCAGATACACATAG 58.803 38.462 3.32 0.00 37.78 2.23
3226 5704 1.478510 CTTCTGTCGATGGGCTACAGT 59.521 52.381 0.00 0.00 40.25 3.55
3236 5714 8.893219 TGAATAAATAGAATGCTTCTGTCGAT 57.107 30.769 8.21 0.00 40.94 3.59
3337 5980 5.004448 TGTTTATTATCTGCCCACAAACGA 58.996 37.500 0.00 0.00 0.00 3.85
3391 6034 5.520376 ACTCACCATTATTAAATGCTGCC 57.480 39.130 0.00 0.00 41.06 4.85
3433 6076 3.980646 TTGGTGTGCTCAATGTTGTAC 57.019 42.857 0.00 0.00 0.00 2.90
3659 6303 0.730265 TGCCGCGAACCACAAATATC 59.270 50.000 8.23 0.00 0.00 1.63
3849 6497 1.789523 TTATGGGACGGAGGGAGAAG 58.210 55.000 0.00 0.00 0.00 2.85
3850 6498 2.047061 CATTATGGGACGGAGGGAGAA 58.953 52.381 0.00 0.00 0.00 2.87
3851 6499 1.062428 ACATTATGGGACGGAGGGAGA 60.062 52.381 0.00 0.00 0.00 3.71
3852 6500 1.424638 ACATTATGGGACGGAGGGAG 58.575 55.000 0.00 0.00 0.00 4.30
3853 6501 2.779429 TACATTATGGGACGGAGGGA 57.221 50.000 0.00 0.00 0.00 4.20
3854 6502 2.969950 TCTTACATTATGGGACGGAGGG 59.030 50.000 0.00 0.00 0.00 4.30
3855 6503 3.552273 CGTCTTACATTATGGGACGGAGG 60.552 52.174 20.50 5.87 43.69 4.30
3856 6504 3.639538 CGTCTTACATTATGGGACGGAG 58.360 50.000 20.50 2.74 43.69 4.63
3857 6505 3.720949 CGTCTTACATTATGGGACGGA 57.279 47.619 20.50 2.30 43.69 4.69
3903 6551 5.122711 CCGTCCCATAATGTAAGACGTTTTT 59.877 40.000 9.63 0.00 46.62 1.94
3904 6552 4.632688 CCGTCCCATAATGTAAGACGTTTT 59.367 41.667 9.63 0.00 46.62 2.43
3905 6553 4.081531 TCCGTCCCATAATGTAAGACGTTT 60.082 41.667 9.63 0.00 46.62 3.60
3906 6554 3.448301 TCCGTCCCATAATGTAAGACGTT 59.552 43.478 9.63 0.00 46.62 3.99
3907 6555 3.025978 TCCGTCCCATAATGTAAGACGT 58.974 45.455 9.63 0.00 46.62 4.34
3909 6557 3.244112 CCCTCCGTCCCATAATGTAAGAC 60.244 52.174 0.00 0.00 0.00 3.01
3910 6558 2.969950 CCCTCCGTCCCATAATGTAAGA 59.030 50.000 0.00 0.00 0.00 2.10
3911 6559 2.969950 TCCCTCCGTCCCATAATGTAAG 59.030 50.000 0.00 0.00 0.00 2.34
3912 6560 2.969950 CTCCCTCCGTCCCATAATGTAA 59.030 50.000 0.00 0.00 0.00 2.41
3913 6561 2.090943 ACTCCCTCCGTCCCATAATGTA 60.091 50.000 0.00 0.00 0.00 2.29
3914 6562 1.344087 ACTCCCTCCGTCCCATAATGT 60.344 52.381 0.00 0.00 0.00 2.71
3915 6563 1.424638 ACTCCCTCCGTCCCATAATG 58.575 55.000 0.00 0.00 0.00 1.90
3916 6564 2.890814 CTACTCCCTCCGTCCCATAAT 58.109 52.381 0.00 0.00 0.00 1.28
3917 6565 2.376695 CTACTCCCTCCGTCCCATAA 57.623 55.000 0.00 0.00 0.00 1.90


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

AutoCloner maintained by Alex Coulton.