Multiple sequence alignment - TraesCS5A01G253100

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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 TraesCS5A01G253100 chr5A 100.000 5289 0 0 1 5289 469058627 469053339 0.000000e+00 9768.0
1 TraesCS5A01G253100 chr5A 82.769 1625 249 19 2408 4020 469063900 469062295 0.000000e+00 1421.0
2 TraesCS5A01G253100 chr5A 95.062 81 4 0 541 621 469057985 469057905 1.550000e-25 128.0
3 TraesCS5A01G253100 chr5A 95.062 81 4 0 643 723 469058087 469058007 1.550000e-25 128.0
4 TraesCS5A01G253100 chr5B 95.806 3553 127 9 1684 5228 434417859 434414321 0.000000e+00 5716.0
5 TraesCS5A01G253100 chr5B 94.234 1561 62 11 50 1603 434419397 434417858 0.000000e+00 2359.0
6 TraesCS5A01G253100 chr5B 94.885 1310 59 5 1684 2990 434674170 434672866 0.000000e+00 2041.0
7 TraesCS5A01G253100 chr5B 93.453 1222 48 15 386 1603 434675362 434674169 0.000000e+00 1784.0
8 TraesCS5A01G253100 chr5B 82.801 1628 243 23 2408 4020 434700174 434698569 0.000000e+00 1421.0
9 TraesCS5A01G253100 chr5B 82.985 1581 235 23 2451 4020 434425195 434423638 0.000000e+00 1399.0
10 TraesCS5A01G253100 chr5B 88.932 515 55 2 757 1270 434615425 434614912 7.470000e-178 634.0
11 TraesCS5A01G253100 chr5B 81.781 741 100 25 870 1599 434702147 434701431 5.900000e-164 588.0
12 TraesCS5A01G253100 chr5B 89.234 483 20 13 1684 2165 434568408 434567957 4.590000e-160 575.0
13 TraesCS5A01G253100 chr5B 80.564 674 107 15 870 1538 434427364 434426710 1.020000e-136 497.0
14 TraesCS5A01G253100 chr5B 89.506 324 31 3 1281 1603 434568728 434568407 1.770000e-109 407.0
15 TraesCS5A01G253100 chr5B 91.732 254 6 6 5051 5289 434672860 434672607 6.560000e-89 339.0
16 TraesCS5A01G253100 chr5B 88.696 230 10 4 50 276 434675836 434675620 3.140000e-67 267.0
17 TraesCS5A01G253100 chr5B 89.326 178 19 0 2178 2355 434567431 434567254 1.920000e-54 224.0
18 TraesCS5A01G253100 chr5B 95.556 90 4 0 5200 5289 434414322 434414233 1.540000e-30 145.0
19 TraesCS5A01G253100 chr5B 95.062 81 4 0 541 621 434675133 434675053 1.550000e-25 128.0
20 TraesCS5A01G253100 chr5B 93.827 81 5 0 643 723 434418923 434418843 7.190000e-24 122.0
21 TraesCS5A01G253100 chr5B 95.455 66 3 0 658 723 434675202 434675137 7.240000e-19 106.0
22 TraesCS5A01G253100 chr5D 94.273 3073 143 15 1684 4736 367241948 367238889 0.000000e+00 4669.0
23 TraesCS5A01G253100 chr5D 82.862 1628 241 25 2408 4020 367415111 367413507 0.000000e+00 1426.0
24 TraesCS5A01G253100 chr5D 83.112 1581 233 21 2451 4020 367251670 367250113 0.000000e+00 1410.0
25 TraesCS5A01G253100 chr5D 95.401 848 30 3 756 1603 367242785 367241947 0.000000e+00 1341.0
26 TraesCS5A01G253100 chr5D 89.988 849 81 4 757 1603 367344688 367343842 0.000000e+00 1094.0
27 TraesCS5A01G253100 chr5D 92.258 465 22 7 164 624 367243550 367243096 0.000000e+00 647.0
28 TraesCS5A01G253100 chr5D 81.326 739 114 15 870 1603 367253710 367252991 3.550000e-161 579.0
29 TraesCS5A01G253100 chr5D 80.676 740 116 18 870 1603 367384223 367383505 2.780000e-152 549.0
30 TraesCS5A01G253100 chr5D 87.603 484 29 13 1684 2165 367343843 367343389 2.800000e-147 532.0
31 TraesCS5A01G253100 chr5D 91.398 186 16 0 2167 2352 367312739 367312554 6.800000e-64 255.0
32 TraesCS5A01G253100 chr5D 88.827 179 9 1 1 179 367243887 367243720 5.370000e-50 209.0
33 TraesCS5A01G253100 chr5D 94.186 86 4 1 1601 1685 373214657 373214572 4.300000e-26 130.0
34 TraesCS5A01G253100 chr5D 90.909 88 7 1 643 730 367243179 367243093 3.350000e-22 117.0
35 TraesCS5A01G253100 chr5D 100.000 32 0 0 491 522 22839600 22839631 5.720000e-05 60.2
36 TraesCS5A01G253100 chr5D 100.000 32 0 0 491 522 437262501 437262532 5.720000e-05 60.2
37 TraesCS5A01G253100 chr6D 83.717 1652 225 23 2451 4088 78352984 78354605 0.000000e+00 1520.0
38 TraesCS5A01G253100 chr6D 79.128 436 70 15 1683 2107 78352223 78352648 1.120000e-71 281.0
39 TraesCS5A01G253100 chr6B 94.898 98 3 2 1593 1688 526034150 526034247 9.170000e-33 152.0
40 TraesCS5A01G253100 chr6B 91.489 94 7 1 1593 1685 717901630 717901537 1.550000e-25 128.0
41 TraesCS5A01G253100 chr6B 85.714 119 10 6 1571 1685 183717307 183717422 9.300000e-23 119.0
42 TraesCS5A01G253100 chr7D 93.478 92 4 2 1598 1688 510397845 510397755 9.240000e-28 135.0
43 TraesCS5A01G253100 chr7D 92.222 90 4 3 1602 1689 448337046 448336958 2.000000e-24 124.0
44 TraesCS5A01G253100 chr6A 93.258 89 4 2 1602 1688 557970048 557970136 4.300000e-26 130.0
45 TraesCS5A01G253100 chr2D 93.258 89 5 1 1598 1685 15192970 15192882 4.300000e-26 130.0
46 TraesCS5A01G253100 chr3D 94.118 85 4 1 1602 1685 602250813 602250729 1.550000e-25 128.0
47 TraesCS5A01G253100 chr7B 100.000 32 0 0 491 522 20206578 20206609 5.720000e-05 60.2
48 TraesCS5A01G253100 chr2A 100.000 32 0 0 491 522 191434533 191434564 5.720000e-05 60.2
49 TraesCS5A01G253100 chr2A 97.143 35 1 0 491 525 384035295 384035261 5.720000e-05 60.2
50 TraesCS5A01G253100 chr1D 97.143 35 1 0 491 525 9369230 9369196 5.720000e-05 60.2
51 TraesCS5A01G253100 chr3A 100.000 30 0 0 5047 5076 727992725 727992754 7.400000e-04 56.5


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 TraesCS5A01G253100 chr5A 469053339 469058627 5288 True 3341.333333 9768 96.708000 1 5289 3 chr5A.!!$R2 5288
1 TraesCS5A01G253100 chr5A 469062295 469063900 1605 True 1421.000000 1421 82.769000 2408 4020 1 chr5A.!!$R1 1612
2 TraesCS5A01G253100 chr5B 434414233 434419397 5164 True 2085.500000 5716 94.855750 50 5289 4 chr5B.!!$R2 5239
3 TraesCS5A01G253100 chr5B 434698569 434702147 3578 True 1004.500000 1421 82.291000 870 4020 2 chr5B.!!$R6 3150
4 TraesCS5A01G253100 chr5B 434423638 434427364 3726 True 948.000000 1399 81.774500 870 4020 2 chr5B.!!$R3 3150
5 TraesCS5A01G253100 chr5B 434672607 434675836 3229 True 777.500000 2041 93.213833 50 5289 6 chr5B.!!$R5 5239
6 TraesCS5A01G253100 chr5B 434614912 434615425 513 True 634.000000 634 88.932000 757 1270 1 chr5B.!!$R1 513
7 TraesCS5A01G253100 chr5B 434567254 434568728 1474 True 402.000000 575 89.355333 1281 2355 3 chr5B.!!$R4 1074
8 TraesCS5A01G253100 chr5D 367413507 367415111 1604 True 1426.000000 1426 82.862000 2408 4020 1 chr5D.!!$R3 1612
9 TraesCS5A01G253100 chr5D 367238889 367243887 4998 True 1396.600000 4669 92.333600 1 4736 5 chr5D.!!$R5 4735
10 TraesCS5A01G253100 chr5D 367250113 367253710 3597 True 994.500000 1410 82.219000 870 4020 2 chr5D.!!$R6 3150
11 TraesCS5A01G253100 chr5D 367343389 367344688 1299 True 813.000000 1094 88.795500 757 2165 2 chr5D.!!$R7 1408
12 TraesCS5A01G253100 chr5D 367383505 367384223 718 True 549.000000 549 80.676000 870 1603 1 chr5D.!!$R2 733
13 TraesCS5A01G253100 chr6D 78352223 78354605 2382 False 900.500000 1520 81.422500 1683 4088 2 chr6D.!!$F1 2405

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
137 138 1.066430 TGTACTTCAACGAGATGGCCC 60.066 52.381 0.00 0.0 0.0 5.80 F
1611 2385 0.531532 CTTGCATGCTACTCCCTCCG 60.532 60.000 20.33 0.0 0.0 4.63 F
1618 2392 0.749454 GCTACTCCCTCCGTCCGTAA 60.749 60.000 0.00 0.0 0.0 3.18 F
2994 5069 0.247736 AGTCTTTAGCAGCCTCCACG 59.752 55.000 0.00 0.0 0.0 4.94 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1789 2563 0.179045 GCTTCTCCCGTGCCATGTAT 60.179 55.000 0.00 0.00 0.00 2.29 R
2994 5069 3.436704 CCCACTGTGTGTCATGTTCATAC 59.563 47.826 7.08 11.18 0.00 2.39 R
3276 5351 3.662148 TGGGTGCCCATAATCCATAGATT 59.338 43.478 5.73 0.00 42.41 2.40 R
4982 7081 0.455633 CAGCAATTGGAAGTCGCTGC 60.456 55.000 7.72 0.00 43.09 5.25 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
62 63 9.281371 ACTCCTTTTGTAACTTAATGTAAGACC 57.719 33.333 2.11 0.00 39.09 3.85
135 136 3.724295 GTTGTACTTCAACGAGATGGC 57.276 47.619 0.00 0.00 45.23 4.40
136 137 2.380084 TGTACTTCAACGAGATGGCC 57.620 50.000 0.00 0.00 0.00 5.36
137 138 1.066430 TGTACTTCAACGAGATGGCCC 60.066 52.381 0.00 0.00 0.00 5.80
138 139 1.066430 GTACTTCAACGAGATGGCCCA 60.066 52.381 0.00 0.00 0.00 5.36
193 381 4.564041 ACACTAAGTGCACTGAGAATCTG 58.436 43.478 33.89 23.69 36.98 2.90
229 420 1.676006 GCTACGCAGGCCAAATAACAT 59.324 47.619 5.01 0.00 0.00 2.71
230 421 2.875933 GCTACGCAGGCCAAATAACATA 59.124 45.455 5.01 0.00 0.00 2.29
231 422 3.502211 GCTACGCAGGCCAAATAACATAT 59.498 43.478 5.01 0.00 0.00 1.78
414 753 3.501445 GGGCTTACATTGATGATCAGAGC 59.499 47.826 0.09 2.39 0.00 4.09
451 790 9.549078 AGAAGGTAAATAAATAAGCTAGAGTGC 57.451 33.333 0.00 0.00 0.00 4.40
452 791 9.549078 GAAGGTAAATAAATAAGCTAGAGTGCT 57.451 33.333 0.00 0.00 46.40 4.40
461 800 2.297701 AGCTAGAGTGCTAGACTGAGC 58.702 52.381 4.23 5.95 45.71 4.26
522 861 4.579647 TCCGGTTTAAAGGGCTTATCTT 57.420 40.909 0.00 0.00 0.00 2.40
588 927 8.760103 TTATTATTTTTGCGGTTTAAAGGGTC 57.240 30.769 0.00 0.00 0.00 4.46
589 928 3.455990 TTTTTGCGGTTTAAAGGGTCC 57.544 42.857 0.00 0.00 0.00 4.46
590 929 2.068834 TTTGCGGTTTAAAGGGTCCA 57.931 45.000 0.00 0.00 0.00 4.02
591 930 2.296073 TTGCGGTTTAAAGGGTCCAT 57.704 45.000 0.00 0.00 0.00 3.41
592 931 1.828979 TGCGGTTTAAAGGGTCCATC 58.171 50.000 0.00 0.00 0.00 3.51
593 932 1.353022 TGCGGTTTAAAGGGTCCATCT 59.647 47.619 0.00 0.00 0.00 2.90
594 933 2.014857 GCGGTTTAAAGGGTCCATCTC 58.985 52.381 0.00 0.00 0.00 2.75
595 934 2.640184 CGGTTTAAAGGGTCCATCTCC 58.360 52.381 0.00 0.00 0.00 3.71
596 935 2.026636 CGGTTTAAAGGGTCCATCTCCA 60.027 50.000 0.00 0.00 0.00 3.86
597 936 3.371595 CGGTTTAAAGGGTCCATCTCCAT 60.372 47.826 0.00 0.00 0.00 3.41
598 937 4.207955 GGTTTAAAGGGTCCATCTCCATC 58.792 47.826 0.00 0.00 0.00 3.51
599 938 4.325030 GGTTTAAAGGGTCCATCTCCATCA 60.325 45.833 0.00 0.00 0.00 3.07
600 939 5.449553 GTTTAAAGGGTCCATCTCCATCAT 58.550 41.667 0.00 0.00 0.00 2.45
601 940 3.872459 AAAGGGTCCATCTCCATCATC 57.128 47.619 0.00 0.00 0.00 2.92
602 941 2.811322 AGGGTCCATCTCCATCATCT 57.189 50.000 0.00 0.00 0.00 2.90
603 942 2.336891 AGGGTCCATCTCCATCATCTG 58.663 52.381 0.00 0.00 0.00 2.90
604 943 2.053244 GGGTCCATCTCCATCATCTGT 58.947 52.381 0.00 0.00 0.00 3.41
605 944 2.441001 GGGTCCATCTCCATCATCTGTT 59.559 50.000 0.00 0.00 0.00 3.16
606 945 3.117738 GGGTCCATCTCCATCATCTGTTT 60.118 47.826 0.00 0.00 0.00 2.83
607 946 4.103153 GGGTCCATCTCCATCATCTGTTTA 59.897 45.833 0.00 0.00 0.00 2.01
608 947 5.303971 GGTCCATCTCCATCATCTGTTTAG 58.696 45.833 0.00 0.00 0.00 1.85
609 948 5.070981 GGTCCATCTCCATCATCTGTTTAGA 59.929 44.000 0.00 0.00 37.35 2.10
610 949 6.239829 GGTCCATCTCCATCATCTGTTTAGAT 60.240 42.308 0.00 0.00 44.45 1.98
611 950 7.222872 GTCCATCTCCATCATCTGTTTAGATT 58.777 38.462 0.00 0.00 41.71 2.40
612 951 7.718753 GTCCATCTCCATCATCTGTTTAGATTT 59.281 37.037 0.00 0.00 41.71 2.17
613 952 8.937835 TCCATCTCCATCATCTGTTTAGATTTA 58.062 33.333 0.00 0.00 41.71 1.40
614 953 9.217278 CCATCTCCATCATCTGTTTAGATTTAG 57.783 37.037 0.00 0.00 41.71 1.85
615 954 9.993454 CATCTCCATCATCTGTTTAGATTTAGA 57.007 33.333 0.00 0.00 41.71 2.10
617 956 9.426534 TCTCCATCATCTGTTTAGATTTAGAGA 57.573 33.333 0.00 0.00 41.71 3.10
618 957 9.474920 CTCCATCATCTGTTTAGATTTAGAGAC 57.525 37.037 0.00 0.00 41.71 3.36
619 958 8.981659 TCCATCATCTGTTTAGATTTAGAGACA 58.018 33.333 0.00 0.00 41.71 3.41
620 959 9.039870 CCATCATCTGTTTAGATTTAGAGACAC 57.960 37.037 0.00 0.00 41.71 3.67
621 960 9.591792 CATCATCTGTTTAGATTTAGAGACACA 57.408 33.333 0.00 0.00 41.71 3.72
628 967 8.721478 TGTTTAGATTTAGAGACACATTTCTGC 58.279 33.333 0.00 0.00 0.00 4.26
629 968 8.721478 GTTTAGATTTAGAGACACATTTCTGCA 58.279 33.333 0.00 0.00 0.00 4.41
630 969 6.734104 AGATTTAGAGACACATTTCTGCAC 57.266 37.500 0.00 0.00 0.00 4.57
631 970 6.471146 AGATTTAGAGACACATTTCTGCACT 58.529 36.000 0.00 0.00 0.00 4.40
632 971 5.929697 TTTAGAGACACATTTCTGCACTG 57.070 39.130 0.00 0.00 0.00 3.66
633 972 3.758755 AGAGACACATTTCTGCACTGA 57.241 42.857 0.00 0.00 0.00 3.41
634 973 3.661944 AGAGACACATTTCTGCACTGAG 58.338 45.455 0.00 0.00 0.00 3.35
635 974 2.740981 GAGACACATTTCTGCACTGAGG 59.259 50.000 0.00 0.00 0.00 3.86
636 975 2.105477 AGACACATTTCTGCACTGAGGT 59.895 45.455 0.00 0.00 0.00 3.85
637 976 2.880890 GACACATTTCTGCACTGAGGTT 59.119 45.455 0.00 0.00 0.00 3.50
638 977 3.290710 ACACATTTCTGCACTGAGGTTT 58.709 40.909 0.00 0.00 0.00 3.27
639 978 4.460263 ACACATTTCTGCACTGAGGTTTA 58.540 39.130 0.00 0.00 0.00 2.01
640 979 4.887071 ACACATTTCTGCACTGAGGTTTAA 59.113 37.500 0.00 0.00 0.00 1.52
641 980 5.009010 ACACATTTCTGCACTGAGGTTTAAG 59.991 40.000 0.00 0.00 0.00 1.85
642 981 4.520492 ACATTTCTGCACTGAGGTTTAAGG 59.480 41.667 0.00 0.00 0.00 2.69
643 982 2.859165 TCTGCACTGAGGTTTAAGGG 57.141 50.000 0.00 0.00 0.00 3.95
644 983 2.054799 TCTGCACTGAGGTTTAAGGGT 58.945 47.619 0.00 0.00 0.00 4.34
645 984 2.154462 CTGCACTGAGGTTTAAGGGTG 58.846 52.381 0.00 0.00 0.00 4.61
646 985 1.493022 TGCACTGAGGTTTAAGGGTGT 59.507 47.619 0.00 0.00 0.00 4.16
647 986 2.706723 TGCACTGAGGTTTAAGGGTGTA 59.293 45.455 0.00 0.00 0.00 2.90
648 987 3.136809 TGCACTGAGGTTTAAGGGTGTAA 59.863 43.478 0.00 0.00 0.00 2.41
649 988 3.751698 GCACTGAGGTTTAAGGGTGTAAG 59.248 47.826 0.00 0.00 0.00 2.34
650 989 4.324267 CACTGAGGTTTAAGGGTGTAAGG 58.676 47.826 0.00 0.00 0.00 2.69
651 990 3.329814 ACTGAGGTTTAAGGGTGTAAGGG 59.670 47.826 0.00 0.00 0.00 3.95
652 991 3.585732 CTGAGGTTTAAGGGTGTAAGGGA 59.414 47.826 0.00 0.00 0.00 4.20
653 992 3.328637 TGAGGTTTAAGGGTGTAAGGGAC 59.671 47.826 0.00 0.00 0.00 4.46
654 993 2.646297 AGGTTTAAGGGTGTAAGGGACC 59.354 50.000 0.00 0.00 0.00 4.46
655 994 2.646297 GGTTTAAGGGTGTAAGGGACCT 59.354 50.000 0.00 0.00 33.58 3.85
656 995 3.845992 GGTTTAAGGGTGTAAGGGACCTA 59.154 47.826 0.00 0.00 33.58 3.08
657 996 4.476113 GGTTTAAGGGTGTAAGGGACCTAT 59.524 45.833 0.00 0.00 33.58 2.57
658 997 5.667172 GGTTTAAGGGTGTAAGGGACCTATA 59.333 44.000 0.00 0.00 33.58 1.31
659 998 6.331042 GGTTTAAGGGTGTAAGGGACCTATAT 59.669 42.308 0.00 0.00 33.58 0.86
660 999 7.448420 GTTTAAGGGTGTAAGGGACCTATATC 58.552 42.308 0.00 0.00 33.58 1.63
661 1000 4.845530 AGGGTGTAAGGGACCTATATCA 57.154 45.455 0.00 0.00 33.58 2.15
662 1001 5.166013 AGGGTGTAAGGGACCTATATCAA 57.834 43.478 0.00 0.00 33.58 2.57
663 1002 5.738401 AGGGTGTAAGGGACCTATATCAAT 58.262 41.667 0.00 0.00 33.58 2.57
664 1003 6.882155 AGGGTGTAAGGGACCTATATCAATA 58.118 40.000 0.00 0.00 33.58 1.90
665 1004 7.496922 AGGGTGTAAGGGACCTATATCAATAT 58.503 38.462 0.00 0.00 33.58 1.28
666 1005 7.967747 AGGGTGTAAGGGACCTATATCAATATT 59.032 37.037 0.00 0.00 33.58 1.28
667 1006 9.275572 GGGTGTAAGGGACCTATATCAATATTA 57.724 37.037 0.00 0.00 33.58 0.98
826 1463 5.126384 TGTTTTGAAGGTTTAAGGGTGTCAG 59.874 40.000 0.00 0.00 0.00 3.51
832 1469 3.914435 AGGTTTAAGGGTGTCAGGTGTAT 59.086 43.478 0.00 0.00 0.00 2.29
857 1494 7.867752 TGGTTCTACTGCTTTAAAACATGTAC 58.132 34.615 0.00 0.00 0.00 2.90
893 1530 7.330946 TGAGCATTAACACAGTTACTATGTCAC 59.669 37.037 0.00 0.00 0.00 3.67
907 1544 6.875972 ACTATGTCACTTGGAGAAGGTATT 57.124 37.500 0.00 0.00 32.95 1.89
1201 1838 1.250328 TCAAGATTTGTGCAGCCCAG 58.750 50.000 0.00 0.00 0.00 4.45
1344 1987 1.078708 TTAAGTGCAGCCTACCCGC 60.079 57.895 0.00 0.00 0.00 6.13
1407 2056 1.141657 TGGGCAGGAGATGTATGAAGC 59.858 52.381 0.00 0.00 0.00 3.86
1418 2067 6.208402 GGAGATGTATGAAGCTATGACTGAGA 59.792 42.308 0.00 0.00 0.00 3.27
1472 2121 2.813754 TCGGAGGAAGTCAAAGCAAATG 59.186 45.455 0.00 0.00 0.00 2.32
1552 2326 0.547712 AGGTAGCTTTCCTGCCCTCA 60.548 55.000 8.99 0.00 46.57 3.86
1603 2377 6.538742 TCTGGAGTAAATAACTTGCATGCTAC 59.461 38.462 20.33 10.10 39.07 3.58
1604 2378 6.414732 TGGAGTAAATAACTTGCATGCTACT 58.585 36.000 20.33 14.77 39.07 2.57
1605 2379 6.538742 TGGAGTAAATAACTTGCATGCTACTC 59.461 38.462 21.99 21.99 39.07 2.59
1606 2380 6.017852 GGAGTAAATAACTTGCATGCTACTCC 60.018 42.308 28.34 28.34 44.01 3.85
1607 2381 5.823045 AGTAAATAACTTGCATGCTACTCCC 59.177 40.000 20.33 0.00 33.35 4.30
1608 2382 4.510167 AATAACTTGCATGCTACTCCCT 57.490 40.909 20.33 0.00 0.00 4.20
1609 2383 2.409948 AACTTGCATGCTACTCCCTC 57.590 50.000 20.33 0.00 0.00 4.30
1610 2384 0.543749 ACTTGCATGCTACTCCCTCC 59.456 55.000 20.33 0.00 0.00 4.30
1611 2385 0.531532 CTTGCATGCTACTCCCTCCG 60.532 60.000 20.33 0.00 0.00 4.63
1612 2386 1.264749 TTGCATGCTACTCCCTCCGT 61.265 55.000 20.33 0.00 0.00 4.69
1613 2387 1.068250 GCATGCTACTCCCTCCGTC 59.932 63.158 11.37 0.00 0.00 4.79
1614 2388 1.742768 CATGCTACTCCCTCCGTCC 59.257 63.158 0.00 0.00 0.00 4.79
1615 2389 1.828660 ATGCTACTCCCTCCGTCCG 60.829 63.158 0.00 0.00 0.00 4.79
1616 2390 2.439883 GCTACTCCCTCCGTCCGT 60.440 66.667 0.00 0.00 0.00 4.69
1617 2391 1.153086 GCTACTCCCTCCGTCCGTA 60.153 63.158 0.00 0.00 0.00 4.02
1618 2392 0.749454 GCTACTCCCTCCGTCCGTAA 60.749 60.000 0.00 0.00 0.00 3.18
1619 2393 1.978454 CTACTCCCTCCGTCCGTAAT 58.022 55.000 0.00 0.00 0.00 1.89
1620 2394 2.811873 GCTACTCCCTCCGTCCGTAATA 60.812 54.545 0.00 0.00 0.00 0.98
1621 2395 2.671896 ACTCCCTCCGTCCGTAATAT 57.328 50.000 0.00 0.00 0.00 1.28
1622 2396 3.795688 ACTCCCTCCGTCCGTAATATA 57.204 47.619 0.00 0.00 0.00 0.86
1623 2397 4.104383 ACTCCCTCCGTCCGTAATATAA 57.896 45.455 0.00 0.00 0.00 0.98
1624 2398 4.077822 ACTCCCTCCGTCCGTAATATAAG 58.922 47.826 0.00 0.00 0.00 1.73
1625 2399 4.202503 ACTCCCTCCGTCCGTAATATAAGA 60.203 45.833 0.00 0.00 0.00 2.10
1626 2400 4.330250 TCCCTCCGTCCGTAATATAAGAG 58.670 47.826 0.00 0.00 0.00 2.85
1627 2401 4.077822 CCCTCCGTCCGTAATATAAGAGT 58.922 47.826 0.00 0.00 0.00 3.24
1628 2402 4.082895 CCCTCCGTCCGTAATATAAGAGTG 60.083 50.000 0.00 0.00 0.00 3.51
1629 2403 4.518211 CCTCCGTCCGTAATATAAGAGTGT 59.482 45.833 0.00 0.00 0.00 3.55
1630 2404 5.009410 CCTCCGTCCGTAATATAAGAGTGTT 59.991 44.000 0.00 0.00 0.00 3.32
1631 2405 6.455360 TCCGTCCGTAATATAAGAGTGTTT 57.545 37.500 0.00 0.00 0.00 2.83
1632 2406 6.866480 TCCGTCCGTAATATAAGAGTGTTTT 58.134 36.000 0.00 0.00 0.00 2.43
1633 2407 7.322664 TCCGTCCGTAATATAAGAGTGTTTTT 58.677 34.615 0.00 0.00 0.00 1.94
1660 2434 6.071463 CACTAATGTAGTGTCAAAAACGCTC 58.929 40.000 7.17 0.00 45.69 5.03
1661 2435 5.989777 ACTAATGTAGTGTCAAAAACGCTCT 59.010 36.000 0.00 0.00 45.69 4.09
1662 2436 5.751243 AATGTAGTGTCAAAAACGCTCTT 57.249 34.783 0.00 0.00 45.69 2.85
1663 2437 6.854496 AATGTAGTGTCAAAAACGCTCTTA 57.146 33.333 0.00 0.00 45.69 2.10
1664 2438 7.435068 AATGTAGTGTCAAAAACGCTCTTAT 57.565 32.000 0.00 0.00 45.69 1.73
1665 2439 8.542497 AATGTAGTGTCAAAAACGCTCTTATA 57.458 30.769 0.00 0.00 45.69 0.98
1666 2440 8.718102 ATGTAGTGTCAAAAACGCTCTTATAT 57.282 30.769 0.00 0.00 45.69 0.86
1667 2441 8.542497 TGTAGTGTCAAAAACGCTCTTATATT 57.458 30.769 0.00 0.00 45.69 1.28
1668 2442 9.642327 TGTAGTGTCAAAAACGCTCTTATATTA 57.358 29.630 0.00 0.00 45.69 0.98
1671 2445 9.378551 AGTGTCAAAAACGCTCTTATATTATGA 57.621 29.630 0.00 0.00 45.69 2.15
1672 2446 9.638300 GTGTCAAAAACGCTCTTATATTATGAG 57.362 33.333 0.00 0.00 35.42 2.90
1673 2447 9.594478 TGTCAAAAACGCTCTTATATTATGAGA 57.406 29.630 0.00 0.00 33.20 3.27
1674 2448 9.851043 GTCAAAAACGCTCTTATATTATGAGAC 57.149 33.333 0.00 0.00 33.20 3.36
1675 2449 8.752254 TCAAAAACGCTCTTATATTATGAGACG 58.248 33.333 13.57 13.57 36.53 4.18
1676 2450 7.639162 AAAACGCTCTTATATTATGAGACGG 57.361 36.000 16.71 7.11 35.72 4.79
1677 2451 6.570672 AACGCTCTTATATTATGAGACGGA 57.429 37.500 16.71 0.00 35.72 4.69
1678 2452 6.761099 ACGCTCTTATATTATGAGACGGAT 57.239 37.500 16.71 3.68 35.72 4.18
1679 2453 6.556212 ACGCTCTTATATTATGAGACGGATG 58.444 40.000 16.71 3.20 35.72 3.51
1680 2454 5.974158 CGCTCTTATATTATGAGACGGATGG 59.026 44.000 0.00 0.00 33.20 3.51
1681 2455 6.183360 CGCTCTTATATTATGAGACGGATGGA 60.183 42.308 0.00 0.00 33.20 3.41
1682 2456 7.199766 GCTCTTATATTATGAGACGGATGGAG 58.800 42.308 0.00 0.00 33.20 3.86
1683 2457 7.147983 GCTCTTATATTATGAGACGGATGGAGT 60.148 40.741 0.00 0.00 33.20 3.85
1684 2458 9.397280 CTCTTATATTATGAGACGGATGGAGTA 57.603 37.037 0.00 0.00 33.20 2.59
1789 2563 4.517453 GGAAATGTGCTACCAACACTTGTA 59.483 41.667 0.00 0.00 38.86 2.41
1876 2654 2.754552 GGTGCACTCAATAATCTTGCCA 59.245 45.455 17.98 0.00 31.94 4.92
1964 2747 8.206867 ACTGATTCTTAGCAGCATATTAGTTGA 58.793 33.333 0.00 0.00 41.49 3.18
2083 2877 6.780031 TCCTTTGAGAAAATTGTACCATGGAA 59.220 34.615 21.47 2.07 0.00 3.53
2140 3054 6.295688 GGATTGTTTGTAGAGTTGAGGGAGTA 60.296 42.308 0.00 0.00 0.00 2.59
2165 3079 6.700520 ACAAAACTCTCCACTTCTTTAGTACG 59.299 38.462 0.00 0.00 34.56 3.67
2166 3080 6.645790 AAACTCTCCACTTCTTTAGTACGA 57.354 37.500 0.00 0.00 34.56 3.43
2167 3081 5.883503 ACTCTCCACTTCTTTAGTACGAG 57.116 43.478 0.00 0.00 34.56 4.18
2186 3613 5.854157 ACGAGTAGCATTTTGTGAAATACG 58.146 37.500 0.00 0.00 33.78 3.06
2189 3616 6.554334 AGTAGCATTTTGTGAAATACGTGT 57.446 33.333 0.00 0.00 33.78 4.49
2294 3986 3.865302 GCACCCAATTGCACATCATTTGA 60.865 43.478 0.00 0.00 42.49 2.69
2414 4472 7.605449 AGAACTTATTCACAATTGTTCCATGG 58.395 34.615 8.77 4.97 37.29 3.66
2647 4707 9.196139 CAATTCCCCCAGAACTATAACAATTTA 57.804 33.333 0.00 0.00 37.29 1.40
2820 4892 4.251169 AGGTATTGATGGGTGGTATGGAT 58.749 43.478 0.00 0.00 0.00 3.41
2948 5023 7.122650 AGGAATCAAAGACAAAACACAAGAGAA 59.877 33.333 0.00 0.00 0.00 2.87
2994 5069 0.247736 AGTCTTTAGCAGCCTCCACG 59.752 55.000 0.00 0.00 0.00 4.94
3189 5264 2.416747 CAACACAAGAGATGGAGCGAA 58.583 47.619 0.00 0.00 0.00 4.70
3276 5351 1.746861 CGGCATCAAATGGGCTACTCA 60.747 52.381 0.00 0.00 0.00 3.41
3379 5455 3.256704 TCCTTGTTCCCAGAGGTAATGT 58.743 45.455 0.00 0.00 32.33 2.71
3380 5456 3.655777 TCCTTGTTCCCAGAGGTAATGTT 59.344 43.478 0.00 0.00 32.33 2.71
3402 5480 8.415950 TGTTTTCATAATAGGAAAAGCCTCAA 57.584 30.769 12.33 0.00 46.97 3.02
3475 5557 4.215109 TCAGATTACGAGTCCATGGATCA 58.785 43.478 19.62 1.92 0.00 2.92
3823 5905 1.909700 TCAAATTCTGACAGGTGGCC 58.090 50.000 1.81 0.00 0.00 5.36
3910 5995 6.770746 ATATCCCATTCTATGAAGCAATGC 57.229 37.500 0.00 0.00 0.00 3.56
3987 6072 1.300971 TTGCGATGTTGGCTCTGCTC 61.301 55.000 0.00 0.00 0.00 4.26
4140 6229 5.186021 CCTTGAGACTATCACTTGGTACTGT 59.814 44.000 0.00 0.00 37.77 3.55
4141 6230 5.644977 TGAGACTATCACTTGGTACTGTG 57.355 43.478 0.00 0.52 35.59 3.66
4213 6304 3.181443 GGGCCTACCTAATACACATGCTT 60.181 47.826 0.84 0.00 35.85 3.91
4242 6333 1.900486 AGCAGGTACAACTCCAGGTAC 59.100 52.381 0.00 0.00 39.25 3.34
4391 6482 0.814457 CAGAGCGCAGAAGACTACCT 59.186 55.000 11.47 0.00 0.00 3.08
4414 6505 7.100409 CCTTCTTCTAAGAAACTGTAAGAGGG 58.900 42.308 6.61 0.00 43.84 4.30
4474 6566 7.340232 TCTTGAAGGGGAAATTCAGTTCATATG 59.660 37.037 0.00 0.00 37.91 1.78
4528 6624 8.821894 GTTCTTCTTATGCTCACCTAATTGTAG 58.178 37.037 0.00 0.00 0.00 2.74
4720 6816 7.048629 AGACTACATGATTAGATGTCAGTGG 57.951 40.000 0.00 0.00 37.70 4.00
4754 6850 6.932356 ACATGCAATAATCACTGAGTAAGG 57.068 37.500 0.00 0.00 0.00 2.69
4763 6859 8.779354 ATAATCACTGAGTAAGGAAAGAACAC 57.221 34.615 0.00 0.00 0.00 3.32
4764 6860 4.617959 TCACTGAGTAAGGAAAGAACACG 58.382 43.478 0.00 0.00 0.00 4.49
4769 6865 6.202954 ACTGAGTAAGGAAAGAACACGAAATG 59.797 38.462 0.00 0.00 0.00 2.32
4891 6990 9.052759 AGTTACAGATAAAACAAGTGTTACAGG 57.947 33.333 0.00 0.00 37.25 4.00
4893 6992 9.787435 TTACAGATAAAACAAGTGTTACAGGAT 57.213 29.630 0.00 0.00 37.25 3.24
4898 6997 6.952773 AAAACAAGTGTTACAGGATGCTTA 57.047 33.333 0.00 0.00 37.02 3.09
4913 7012 8.421002 ACAGGATGCTTAAATGTGTAAACTTTT 58.579 29.630 2.75 2.75 42.53 2.27
4952 7051 7.575365 TGTGCAGCTATATCATTGTTAAATCG 58.425 34.615 0.00 0.00 0.00 3.34
4971 7070 3.305720 TCGGAACTGAGGGCTAACATAT 58.694 45.455 0.00 0.00 0.00 1.78
4980 7079 5.162637 TGAGGGCTAACATATAGTGGGAAT 58.837 41.667 0.00 0.00 0.00 3.01
4982 7081 4.289672 AGGGCTAACATATAGTGGGAATGG 59.710 45.833 0.00 0.00 0.00 3.16
4987 7086 2.079158 CATATAGTGGGAATGGCAGCG 58.921 52.381 0.00 0.00 0.00 5.18
4989 7088 0.179045 ATAGTGGGAATGGCAGCGAC 60.179 55.000 0.00 0.00 0.00 5.19
4990 7089 1.264749 TAGTGGGAATGGCAGCGACT 61.265 55.000 0.00 0.00 0.00 4.18
4991 7090 1.675641 GTGGGAATGGCAGCGACTT 60.676 57.895 0.00 0.00 0.00 3.01
4992 7091 1.377202 TGGGAATGGCAGCGACTTC 60.377 57.895 0.00 0.00 0.00 3.01
4993 7092 2.115291 GGGAATGGCAGCGACTTCC 61.115 63.158 8.06 8.06 37.11 3.46
4994 7093 1.377202 GGAATGGCAGCGACTTCCA 60.377 57.895 11.08 1.38 37.65 3.53
4995 7094 0.960364 GGAATGGCAGCGACTTCCAA 60.960 55.000 11.08 0.00 37.65 3.53
5019 7118 4.191544 TGCTGGATAAGGATTGAAGTTCG 58.808 43.478 0.00 0.00 0.00 3.95
5041 7140 6.403049 TCGGTTCATGCTATGACTAAAAGAA 58.597 36.000 0.00 0.00 39.39 2.52
5059 7158 3.236896 AGAAAACTACTCCCTCCGTTCA 58.763 45.455 0.00 0.00 0.00 3.18
5076 7175 6.107343 TCCGTTCAATAATTATTGTCGTGGA 58.893 36.000 30.63 27.51 42.70 4.02
5114 7213 9.476202 GAATTTTGGTGATAATAATACTTGGGC 57.524 33.333 0.00 0.00 0.00 5.36
5209 7308 9.060347 TGCCTAGATCAATTGAATATTGAGTTC 57.940 33.333 13.09 2.01 40.80 3.01
5233 7359 5.050769 CGTATCTTTTGTGAAGGATCGATGG 60.051 44.000 0.54 0.00 34.00 3.51
5241 7367 7.880160 TTGTGAAGGATCGATGGATAATTTT 57.120 32.000 0.54 0.00 31.51 1.82
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
43 44 8.780249 GCAGAAAGGTCTTACATTAAGTTACAA 58.220 33.333 0.00 0.00 37.10 2.41
128 129 1.072852 GCCATCTCTGGGCCATCTC 59.927 63.158 6.72 0.00 45.87 2.75
129 130 3.248764 GCCATCTCTGGGCCATCT 58.751 61.111 6.72 0.00 45.87 2.90
135 136 0.036448 CATAGGCTGCCATCTCTGGG 59.964 60.000 22.65 0.00 43.36 4.45
136 137 1.002201 CTCATAGGCTGCCATCTCTGG 59.998 57.143 22.65 2.92 46.17 3.86
137 138 1.693062 ACTCATAGGCTGCCATCTCTG 59.307 52.381 22.65 10.16 0.00 3.35
138 139 2.100128 ACTCATAGGCTGCCATCTCT 57.900 50.000 22.65 1.45 0.00 3.10
292 483 2.584835 TAGAAACCCTTGTGCTGCAT 57.415 45.000 5.27 0.00 0.00 3.96
361 603 6.580041 CGTTGATAATGCCTTATCTTGCAATC 59.420 38.462 18.74 0.00 42.49 2.67
375 617 2.208326 CCCTTTGGCGTTGATAATGC 57.792 50.000 0.00 0.00 42.68 3.56
448 787 2.202810 GGCCGCTCAGTCTAGCAC 60.203 66.667 0.00 0.00 42.91 4.40
449 788 1.544825 AAAGGCCGCTCAGTCTAGCA 61.545 55.000 0.00 0.00 42.91 3.49
450 789 0.391793 AAAAGGCCGCTCAGTCTAGC 60.392 55.000 0.00 0.00 39.21 3.42
451 790 1.205893 AGAAAAGGCCGCTCAGTCTAG 59.794 52.381 0.00 0.00 0.00 2.43
452 791 1.267121 AGAAAAGGCCGCTCAGTCTA 58.733 50.000 0.00 0.00 0.00 2.59
453 792 1.267121 TAGAAAAGGCCGCTCAGTCT 58.733 50.000 0.00 0.00 0.00 3.24
454 793 2.317530 ATAGAAAAGGCCGCTCAGTC 57.682 50.000 0.00 0.00 0.00 3.51
455 794 3.031736 TCTATAGAAAAGGCCGCTCAGT 58.968 45.455 0.00 0.00 0.00 3.41
489 828 0.400594 AAACCGGAAAGGAGGGAGTG 59.599 55.000 9.46 0.00 45.00 3.51
566 905 5.070047 TGGACCCTTTAAACCGCAAAAATAA 59.930 36.000 0.00 0.00 0.00 1.40
581 920 3.137913 CAGATGATGGAGATGGACCCTTT 59.862 47.826 0.00 0.00 0.00 3.11
582 921 2.709934 CAGATGATGGAGATGGACCCTT 59.290 50.000 0.00 0.00 0.00 3.95
583 922 2.336891 CAGATGATGGAGATGGACCCT 58.663 52.381 0.00 0.00 0.00 4.34
584 923 2.053244 ACAGATGATGGAGATGGACCC 58.947 52.381 0.00 0.00 0.00 4.46
585 924 3.853355 AACAGATGATGGAGATGGACC 57.147 47.619 0.00 0.00 0.00 4.46
586 925 6.166984 TCTAAACAGATGATGGAGATGGAC 57.833 41.667 0.00 0.00 0.00 4.02
587 926 7.384524 AATCTAAACAGATGATGGAGATGGA 57.615 36.000 0.00 0.00 31.22 3.41
588 927 9.217278 CTAAATCTAAACAGATGATGGAGATGG 57.783 37.037 0.00 0.00 31.22 3.51
589 928 9.993454 TCTAAATCTAAACAGATGATGGAGATG 57.007 33.333 0.00 0.00 31.22 2.90
591 930 9.426534 TCTCTAAATCTAAACAGATGATGGAGA 57.573 33.333 10.24 10.24 33.97 3.71
592 931 9.474920 GTCTCTAAATCTAAACAGATGATGGAG 57.525 37.037 7.30 7.30 31.26 3.86
593 932 8.981659 TGTCTCTAAATCTAAACAGATGATGGA 58.018 33.333 0.00 0.00 0.00 3.41
594 933 9.039870 GTGTCTCTAAATCTAAACAGATGATGG 57.960 37.037 0.00 0.00 0.00 3.51
595 934 9.591792 TGTGTCTCTAAATCTAAACAGATGATG 57.408 33.333 0.00 0.00 0.00 3.07
602 941 8.721478 GCAGAAATGTGTCTCTAAATCTAAACA 58.279 33.333 0.00 0.00 0.00 2.83
603 942 8.721478 TGCAGAAATGTGTCTCTAAATCTAAAC 58.279 33.333 0.00 0.00 0.00 2.01
604 943 8.721478 GTGCAGAAATGTGTCTCTAAATCTAAA 58.279 33.333 0.00 0.00 0.00 1.85
605 944 8.097038 AGTGCAGAAATGTGTCTCTAAATCTAA 58.903 33.333 0.00 0.00 0.00 2.10
606 945 7.547019 CAGTGCAGAAATGTGTCTCTAAATCTA 59.453 37.037 0.00 0.00 0.00 1.98
607 946 6.370994 CAGTGCAGAAATGTGTCTCTAAATCT 59.629 38.462 0.00 0.00 0.00 2.40
608 947 6.369890 TCAGTGCAGAAATGTGTCTCTAAATC 59.630 38.462 0.00 0.00 0.00 2.17
609 948 6.233434 TCAGTGCAGAAATGTGTCTCTAAAT 58.767 36.000 0.00 0.00 0.00 1.40
610 949 5.610398 TCAGTGCAGAAATGTGTCTCTAAA 58.390 37.500 0.00 0.00 0.00 1.85
611 950 5.213891 TCAGTGCAGAAATGTGTCTCTAA 57.786 39.130 0.00 0.00 0.00 2.10
612 951 4.322273 CCTCAGTGCAGAAATGTGTCTCTA 60.322 45.833 0.00 0.00 0.00 2.43
613 952 3.556633 CCTCAGTGCAGAAATGTGTCTCT 60.557 47.826 0.00 0.00 0.00 3.10
614 953 2.740981 CCTCAGTGCAGAAATGTGTCTC 59.259 50.000 0.00 0.00 0.00 3.36
615 954 2.105477 ACCTCAGTGCAGAAATGTGTCT 59.895 45.455 0.00 0.00 0.00 3.41
616 955 2.498167 ACCTCAGTGCAGAAATGTGTC 58.502 47.619 0.00 0.00 0.00 3.67
617 956 2.645838 ACCTCAGTGCAGAAATGTGT 57.354 45.000 0.00 0.00 0.00 3.72
618 957 3.996150 AAACCTCAGTGCAGAAATGTG 57.004 42.857 0.00 0.00 0.00 3.21
619 958 4.520492 CCTTAAACCTCAGTGCAGAAATGT 59.480 41.667 0.00 0.00 0.00 2.71
620 959 4.082571 CCCTTAAACCTCAGTGCAGAAATG 60.083 45.833 0.00 0.00 0.00 2.32
621 960 4.082125 CCCTTAAACCTCAGTGCAGAAAT 58.918 43.478 0.00 0.00 0.00 2.17
622 961 3.117663 ACCCTTAAACCTCAGTGCAGAAA 60.118 43.478 0.00 0.00 0.00 2.52
623 962 2.441750 ACCCTTAAACCTCAGTGCAGAA 59.558 45.455 0.00 0.00 0.00 3.02
624 963 2.054799 ACCCTTAAACCTCAGTGCAGA 58.945 47.619 0.00 0.00 0.00 4.26
625 964 2.154462 CACCCTTAAACCTCAGTGCAG 58.846 52.381 0.00 0.00 0.00 4.41
626 965 1.493022 ACACCCTTAAACCTCAGTGCA 59.507 47.619 0.00 0.00 0.00 4.57
627 966 2.271944 ACACCCTTAAACCTCAGTGC 57.728 50.000 0.00 0.00 0.00 4.40
628 967 4.324267 CCTTACACCCTTAAACCTCAGTG 58.676 47.826 0.00 0.00 0.00 3.66
629 968 3.329814 CCCTTACACCCTTAAACCTCAGT 59.670 47.826 0.00 0.00 0.00 3.41
630 969 3.585732 TCCCTTACACCCTTAAACCTCAG 59.414 47.826 0.00 0.00 0.00 3.35
631 970 3.328637 GTCCCTTACACCCTTAAACCTCA 59.671 47.826 0.00 0.00 0.00 3.86
632 971 3.307975 GGTCCCTTACACCCTTAAACCTC 60.308 52.174 0.00 0.00 0.00 3.85
633 972 2.646297 GGTCCCTTACACCCTTAAACCT 59.354 50.000 0.00 0.00 0.00 3.50
634 973 2.646297 AGGTCCCTTACACCCTTAAACC 59.354 50.000 0.00 0.00 33.96 3.27
635 974 5.705397 ATAGGTCCCTTACACCCTTAAAC 57.295 43.478 0.00 0.00 33.96 2.01
636 975 7.140990 TGATATAGGTCCCTTACACCCTTAAA 58.859 38.462 0.00 0.00 33.96 1.52
637 976 6.695624 TGATATAGGTCCCTTACACCCTTAA 58.304 40.000 0.00 0.00 33.96 1.85
638 977 6.297830 TGATATAGGTCCCTTACACCCTTA 57.702 41.667 0.00 0.00 33.96 2.69
639 978 5.166013 TGATATAGGTCCCTTACACCCTT 57.834 43.478 0.00 0.00 33.96 3.95
640 979 4.845530 TGATATAGGTCCCTTACACCCT 57.154 45.455 0.00 0.00 33.96 4.34
641 980 7.750947 ATATTGATATAGGTCCCTTACACCC 57.249 40.000 0.00 0.00 33.96 4.61
665 1004 9.713713 GGACCCTTTAAACTGCAAAAATAATAA 57.286 29.630 0.00 0.00 0.00 1.40
666 1005 8.871125 TGGACCCTTTAAACTGCAAAAATAATA 58.129 29.630 0.00 0.00 0.00 0.98
667 1006 7.740805 TGGACCCTTTAAACTGCAAAAATAAT 58.259 30.769 0.00 0.00 0.00 1.28
668 1007 7.125792 TGGACCCTTTAAACTGCAAAAATAA 57.874 32.000 0.00 0.00 0.00 1.40
669 1008 6.732896 TGGACCCTTTAAACTGCAAAAATA 57.267 33.333 0.00 0.00 0.00 1.40
670 1009 5.622346 TGGACCCTTTAAACTGCAAAAAT 57.378 34.783 0.00 0.00 0.00 1.82
671 1010 5.365314 AGATGGACCCTTTAAACTGCAAAAA 59.635 36.000 0.00 0.00 0.00 1.94
672 1011 4.898861 AGATGGACCCTTTAAACTGCAAAA 59.101 37.500 0.00 0.00 0.00 2.44
673 1012 4.479158 AGATGGACCCTTTAAACTGCAAA 58.521 39.130 0.00 0.00 0.00 3.68
674 1013 4.079253 GAGATGGACCCTTTAAACTGCAA 58.921 43.478 0.00 0.00 0.00 4.08
675 1014 3.561313 GGAGATGGACCCTTTAAACTGCA 60.561 47.826 0.00 0.00 0.00 4.41
676 1015 3.017442 GGAGATGGACCCTTTAAACTGC 58.983 50.000 0.00 0.00 0.00 4.40
677 1016 4.301072 TGGAGATGGACCCTTTAAACTG 57.699 45.455 0.00 0.00 0.00 3.16
678 1017 4.540099 TGATGGAGATGGACCCTTTAAACT 59.460 41.667 0.00 0.00 0.00 2.66
679 1018 4.855340 TGATGGAGATGGACCCTTTAAAC 58.145 43.478 0.00 0.00 0.00 2.01
680 1019 5.433051 AGATGATGGAGATGGACCCTTTAAA 59.567 40.000 0.00 0.00 0.00 1.52
681 1020 4.977739 AGATGATGGAGATGGACCCTTTAA 59.022 41.667 0.00 0.00 0.00 1.52
682 1021 4.349048 CAGATGATGGAGATGGACCCTTTA 59.651 45.833 0.00 0.00 0.00 1.85
826 1463 7.040961 TGTTTTAAAGCAGTAGAACCATACACC 60.041 37.037 0.00 0.00 0.00 4.16
832 1469 6.952773 ACATGTTTTAAAGCAGTAGAACCA 57.047 33.333 10.59 0.00 0.00 3.67
857 1494 1.398390 GTTAATGCTCAGTGCGGGAAG 59.602 52.381 0.00 0.00 46.63 3.46
893 1530 4.442753 GCCTCTCTCAATACCTTCTCCAAG 60.443 50.000 0.00 0.00 0.00 3.61
907 1544 1.895798 CACACAAGGTAGCCTCTCTCA 59.104 52.381 0.00 0.00 30.89 3.27
945 1582 0.461693 GCTCTGAGTGTGGATCTGCC 60.462 60.000 6.53 0.00 37.10 4.85
1044 1681 0.525029 GAATCGAACCTCCGTCGTCC 60.525 60.000 0.00 0.00 0.00 4.79
1201 1838 3.456277 ACCCTGATAAGTGACCATTCCTC 59.544 47.826 0.00 0.00 0.00 3.71
1313 1955 5.269313 GCTGCACTTAACATTAAGCATCTC 58.731 41.667 10.64 0.00 42.98 2.75
1344 1987 0.530744 ATGCCAAATGCTGAGCACTG 59.469 50.000 10.33 10.46 43.04 3.66
1407 2056 7.595875 CAGCTGTATCAATTCTCTCAGTCATAG 59.404 40.741 5.25 0.00 0.00 2.23
1418 2067 6.072286 CCTGACAAAACAGCTGTATCAATTCT 60.072 38.462 22.01 0.00 36.67 2.40
1472 2121 8.413309 TGATCCCATTCATGAAATCCTTTATC 57.587 34.615 13.09 9.62 0.00 1.75
1522 2171 2.938956 AAGCTACCTGAACAGTTGCT 57.061 45.000 0.00 4.79 0.00 3.91
1523 2172 2.226674 GGAAAGCTACCTGAACAGTTGC 59.773 50.000 0.00 2.80 0.00 4.17
1552 2326 8.907222 ATCATGCAAACCTTTACTCAAATTTT 57.093 26.923 0.00 0.00 0.00 1.82
1603 2377 4.330250 TCTTATATTACGGACGGAGGGAG 58.670 47.826 0.00 0.00 0.00 4.30
1604 2378 4.202503 ACTCTTATATTACGGACGGAGGGA 60.203 45.833 0.00 0.00 0.00 4.20
1605 2379 4.077822 ACTCTTATATTACGGACGGAGGG 58.922 47.826 0.00 0.00 0.00 4.30
1606 2380 4.518211 ACACTCTTATATTACGGACGGAGG 59.482 45.833 0.00 0.00 0.00 4.30
1607 2381 5.686159 ACACTCTTATATTACGGACGGAG 57.314 43.478 0.00 0.00 0.00 4.63
1608 2382 6.455360 AAACACTCTTATATTACGGACGGA 57.545 37.500 0.00 0.00 0.00 4.69
1609 2383 7.529880 AAAAACACTCTTATATTACGGACGG 57.470 36.000 0.00 0.00 0.00 4.79
1637 2411 5.989777 AGAGCGTTTTTGACACTACATTAGT 59.010 36.000 0.00 0.00 40.28 2.24
1638 2412 6.467723 AGAGCGTTTTTGACACTACATTAG 57.532 37.500 0.00 0.00 0.00 1.73
1639 2413 6.854496 AAGAGCGTTTTTGACACTACATTA 57.146 33.333 0.00 0.00 0.00 1.90
1640 2414 5.751243 AAGAGCGTTTTTGACACTACATT 57.249 34.783 0.00 0.00 0.00 2.71
1641 2415 8.718102 ATATAAGAGCGTTTTTGACACTACAT 57.282 30.769 0.00 0.00 0.00 2.29
1642 2416 8.542497 AATATAAGAGCGTTTTTGACACTACA 57.458 30.769 0.00 0.00 0.00 2.74
1645 2419 9.378551 TCATAATATAAGAGCGTTTTTGACACT 57.621 29.630 0.00 0.00 0.00 3.55
1646 2420 9.638300 CTCATAATATAAGAGCGTTTTTGACAC 57.362 33.333 0.00 0.00 0.00 3.67
1647 2421 9.594478 TCTCATAATATAAGAGCGTTTTTGACA 57.406 29.630 0.00 0.00 0.00 3.58
1648 2422 9.851043 GTCTCATAATATAAGAGCGTTTTTGAC 57.149 33.333 0.00 0.00 0.00 3.18
1649 2423 8.752254 CGTCTCATAATATAAGAGCGTTTTTGA 58.248 33.333 0.00 0.00 0.00 2.69
1650 2424 8.004344 CCGTCTCATAATATAAGAGCGTTTTTG 58.996 37.037 0.00 0.00 31.69 2.44
1651 2425 7.924412 TCCGTCTCATAATATAAGAGCGTTTTT 59.076 33.333 0.00 0.00 31.69 1.94
1652 2426 7.431249 TCCGTCTCATAATATAAGAGCGTTTT 58.569 34.615 0.00 0.00 31.69 2.43
1653 2427 6.978338 TCCGTCTCATAATATAAGAGCGTTT 58.022 36.000 0.00 0.00 31.69 3.60
1654 2428 6.570672 TCCGTCTCATAATATAAGAGCGTT 57.429 37.500 0.00 0.00 31.69 4.84
1655 2429 6.404844 CCATCCGTCTCATAATATAAGAGCGT 60.405 42.308 0.00 0.00 31.69 5.07
1656 2430 5.974158 CCATCCGTCTCATAATATAAGAGCG 59.026 44.000 0.00 0.00 0.00 5.03
1657 2431 7.101652 TCCATCCGTCTCATAATATAAGAGC 57.898 40.000 0.00 0.00 0.00 4.09
1658 2432 8.287439 ACTCCATCCGTCTCATAATATAAGAG 57.713 38.462 0.00 0.00 0.00 2.85
1659 2433 9.922477 ATACTCCATCCGTCTCATAATATAAGA 57.078 33.333 0.00 0.00 0.00 2.10
1663 2437 8.260818 CCAAATACTCCATCCGTCTCATAATAT 58.739 37.037 0.00 0.00 0.00 1.28
1664 2438 7.310423 CCCAAATACTCCATCCGTCTCATAATA 60.310 40.741 0.00 0.00 0.00 0.98
1665 2439 6.467677 CCAAATACTCCATCCGTCTCATAAT 58.532 40.000 0.00 0.00 0.00 1.28
1666 2440 5.221641 CCCAAATACTCCATCCGTCTCATAA 60.222 44.000 0.00 0.00 0.00 1.90
1667 2441 4.283467 CCCAAATACTCCATCCGTCTCATA 59.717 45.833 0.00 0.00 0.00 2.15
1668 2442 3.071602 CCCAAATACTCCATCCGTCTCAT 59.928 47.826 0.00 0.00 0.00 2.90
1669 2443 2.434336 CCCAAATACTCCATCCGTCTCA 59.566 50.000 0.00 0.00 0.00 3.27
1670 2444 2.698797 TCCCAAATACTCCATCCGTCTC 59.301 50.000 0.00 0.00 0.00 3.36
1671 2445 2.700897 CTCCCAAATACTCCATCCGTCT 59.299 50.000 0.00 0.00 0.00 4.18
1672 2446 2.434702 ACTCCCAAATACTCCATCCGTC 59.565 50.000 0.00 0.00 0.00 4.79
1673 2447 2.478292 ACTCCCAAATACTCCATCCGT 58.522 47.619 0.00 0.00 0.00 4.69
1674 2448 3.560636 AACTCCCAAATACTCCATCCG 57.439 47.619 0.00 0.00 0.00 4.18
1675 2449 4.855340 TGAAACTCCCAAATACTCCATCC 58.145 43.478 0.00 0.00 0.00 3.51
1676 2450 5.946377 ACTTGAAACTCCCAAATACTCCATC 59.054 40.000 0.00 0.00 0.00 3.51
1677 2451 5.892348 ACTTGAAACTCCCAAATACTCCAT 58.108 37.500 0.00 0.00 0.00 3.41
1678 2452 5.319043 ACTTGAAACTCCCAAATACTCCA 57.681 39.130 0.00 0.00 0.00 3.86
1679 2453 7.939784 ATAACTTGAAACTCCCAAATACTCC 57.060 36.000 0.00 0.00 0.00 3.85
1717 2491 3.831333 TGCCCTCTATCAGAATCTAGCAG 59.169 47.826 0.00 0.00 0.00 4.24
1789 2563 0.179045 GCTTCTCCCGTGCCATGTAT 60.179 55.000 0.00 0.00 0.00 2.29
2083 2877 9.874205 CACAAAATGAATTATTAGGGTGTGAAT 57.126 29.630 0.00 0.00 33.61 2.57
2140 3054 6.700520 CGTACTAAAGAAGTGGAGAGTTTTGT 59.299 38.462 0.00 0.00 39.39 2.83
2165 3079 6.599437 ACACGTATTTCACAAAATGCTACTC 58.401 36.000 0.00 0.00 35.89 2.59
2166 3080 6.554334 ACACGTATTTCACAAAATGCTACT 57.446 33.333 0.00 0.00 35.89 2.57
2167 3081 8.785101 CATTACACGTATTTCACAAAATGCTAC 58.215 33.333 0.00 0.00 35.89 3.58
2312 4004 0.033642 TGTTGTTGGACGACGCCATA 59.966 50.000 11.00 2.84 37.86 2.74
2802 4874 4.665009 ACACTATCCATACCACCCATCAAT 59.335 41.667 0.00 0.00 0.00 2.57
2803 4875 4.044308 ACACTATCCATACCACCCATCAA 58.956 43.478 0.00 0.00 0.00 2.57
2948 5023 6.700960 CGCTTTCTCTTCAATCTCATCTATGT 59.299 38.462 0.00 0.00 0.00 2.29
2994 5069 3.436704 CCCACTGTGTGTCATGTTCATAC 59.563 47.826 7.08 11.18 0.00 2.39
3189 5264 7.823745 TGAAAGAAAAATTGAGAAGCTACCT 57.176 32.000 0.00 0.00 0.00 3.08
3276 5351 3.662148 TGGGTGCCCATAATCCATAGATT 59.338 43.478 5.73 0.00 42.41 2.40
3475 5557 7.933577 CACACATAAGACATATATGAAGGGTGT 59.066 37.037 19.63 18.53 35.28 4.16
3685 5767 5.500931 GCTCGTATCTCTTGGATTCGTTTTG 60.501 44.000 0.00 0.00 42.87 2.44
3910 5995 1.941668 GCCTTTGTCCTTCCTCACGAG 60.942 57.143 0.00 0.00 0.00 4.18
3987 6072 4.996788 AGGACCTTACACTATTGGTACG 57.003 45.455 0.00 0.00 38.40 3.67
4045 6134 8.598041 AGTGTACTTCAAGAGAACCATAATTCT 58.402 33.333 0.00 0.00 41.74 2.40
4099 6188 9.593565 AGTCTCAAGGTAGATGATCATACATAA 57.406 33.333 8.54 0.00 0.00 1.90
4124 6213 4.627467 GTCTTGCACAGTACCAAGTGATAG 59.373 45.833 13.11 9.27 39.47 2.08
4213 6304 3.958798 GAGTTGTACCTGCTGGATACCTA 59.041 47.826 17.64 0.00 37.04 3.08
4242 6333 6.915544 ATAATGTGTGTTGTGAGCTAGATG 57.084 37.500 0.00 0.00 0.00 2.90
4295 6386 3.262915 GCTGAGGTCATCCTTATAGGCAT 59.737 47.826 0.00 0.00 45.24 4.40
4321 6412 8.491152 CATGCAGTAAGTTGTATAATAGACAGC 58.509 37.037 0.00 0.00 0.00 4.40
4391 6482 7.850935 TCCCTCTTACAGTTTCTTAGAAGAA 57.149 36.000 0.46 0.46 42.91 2.52
4414 6505 7.362662 TGACACATGCTGTAAAAATTCTCTTC 58.637 34.615 0.00 0.00 31.03 2.87
4497 6589 5.574188 AGGTGAGCATAAGAAGAACCAAAT 58.426 37.500 0.00 0.00 0.00 2.32
4528 6624 1.134371 GGTCAATGCACTAGGACTCCC 60.134 57.143 0.00 0.00 0.00 4.30
4697 6793 7.043961 TCCACTGACATCTAATCATGTAGTC 57.956 40.000 0.00 0.00 37.11 2.59
4700 6796 7.365497 ACATCCACTGACATCTAATCATGTA 57.635 36.000 0.00 0.00 37.11 2.29
4763 6859 7.565848 TCAAAAGAATGCAATGAAACATTTCG 58.434 30.769 0.00 0.00 40.01 3.46
4764 6860 9.887406 AATCAAAAGAATGCAATGAAACATTTC 57.113 25.926 0.00 0.00 36.65 2.17
4797 6893 7.819415 TGTTCACTGTCCAAATCAGTTCTATAG 59.181 37.037 0.00 0.00 43.14 1.31
4798 6894 7.676004 TGTTCACTGTCCAAATCAGTTCTATA 58.324 34.615 0.00 0.00 43.14 1.31
4799 6895 6.533730 TGTTCACTGTCCAAATCAGTTCTAT 58.466 36.000 0.00 0.00 43.14 1.98
4842 6941 8.954950 ACTGAACAGTCTATTATCATTTCTGG 57.045 34.615 1.32 0.00 36.92 3.86
4859 6958 8.612619 ACACTTGTTTTATCTGTAACTGAACAG 58.387 33.333 8.09 8.09 46.78 3.16
4872 6971 7.145932 AGCATCCTGTAACACTTGTTTTATC 57.854 36.000 0.00 0.00 39.31 1.75
4913 7012 4.144297 AGCTGCACATTTAACTCTCCAAA 58.856 39.130 1.02 0.00 0.00 3.28
4915 7014 3.423539 AGCTGCACATTTAACTCTCCA 57.576 42.857 1.02 0.00 0.00 3.86
4952 7051 5.511545 CCACTATATGTTAGCCCTCAGTTCC 60.512 48.000 0.00 0.00 0.00 3.62
4971 7070 1.220749 GTCGCTGCCATTCCCACTA 59.779 57.895 0.00 0.00 0.00 2.74
4980 7079 1.865788 GCAATTGGAAGTCGCTGCCA 61.866 55.000 7.72 2.72 37.41 4.92
4982 7081 0.455633 CAGCAATTGGAAGTCGCTGC 60.456 55.000 7.72 0.00 43.09 5.25
4993 7092 6.461110 ACTTCAATCCTTATCCAGCAATTG 57.539 37.500 0.00 0.00 0.00 2.32
4994 7093 6.183360 CGAACTTCAATCCTTATCCAGCAATT 60.183 38.462 0.00 0.00 0.00 2.32
4995 7094 5.297776 CGAACTTCAATCCTTATCCAGCAAT 59.702 40.000 0.00 0.00 0.00 3.56
5012 7111 4.184629 AGTCATAGCATGAACCGAACTTC 58.815 43.478 0.00 0.00 41.69 3.01
5015 7114 6.312918 TCTTTTAGTCATAGCATGAACCGAAC 59.687 38.462 0.00 0.00 41.69 3.95
5019 7118 8.515414 AGTTTTCTTTTAGTCATAGCATGAACC 58.485 33.333 0.00 0.00 41.69 3.62
5041 7140 5.750352 TTATTGAACGGAGGGAGTAGTTT 57.250 39.130 0.00 0.00 0.00 2.66
5059 7158 5.054477 CCTCCGTCCACGACAATAATTATT 58.946 41.667 4.81 4.81 43.02 1.40
5076 7175 2.910977 ACCAAAATTCTACTCCCTCCGT 59.089 45.455 0.00 0.00 0.00 4.69
5209 7308 5.050769 CCATCGATCCTTCACAAAAGATACG 60.051 44.000 0.00 0.00 0.00 3.06
5241 7367 5.542635 AGGCATCCGGTAAGAGTTCATATTA 59.457 40.000 0.00 0.00 0.00 0.98
5253 7379 1.271856 TGTTCAGAGGCATCCGGTAA 58.728 50.000 0.00 0.00 0.00 2.85


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

AutoCloner maintained by Alex Coulton.