Multiple sequence alignment - TraesCS7B01G410800

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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 TraesCS7B01G410800 chr7B 100.000 3062 0 0 2280 5341 679712136 679709075 0.000000e+00 5655.0
1 TraesCS7B01G410800 chr7B 100.000 2099 0 0 1 2099 679714415 679712317 0.000000e+00 3877.0
2 TraesCS7B01G410800 chr7B 96.960 987 27 3 4357 5341 693345619 693346604 0.000000e+00 1653.0
3 TraesCS7B01G410800 chr7B 96.496 742 26 0 2300 3041 464102656 464101915 0.000000e+00 1227.0
4 TraesCS7B01G410800 chr7B 89.171 434 32 5 740 1163 679684442 679684014 1.320000e-145 527.0
5 TraesCS7B01G410800 chr7B 83.162 582 73 13 1194 1770 679684022 679683461 4.770000e-140 508.0
6 TraesCS7B01G410800 chr7D 89.279 2136 142 41 1 2099 599885873 599883788 0.000000e+00 2595.0
7 TraesCS7B01G410800 chr7D 89.581 739 67 3 2300 3038 603769786 603769058 0.000000e+00 929.0
8 TraesCS7B01G410800 chr7D 87.759 531 39 13 3836 4353 599883327 599882810 9.900000e-167 597.0
9 TraesCS7B01G410800 chr7D 90.852 317 25 3 3067 3383 599883635 599883323 6.400000e-114 422.0
10 TraesCS7B01G410800 chr7D 90.708 226 19 2 1271 1495 618679795 618680019 3.130000e-77 300.0
11 TraesCS7B01G410800 chr7D 89.326 178 19 0 1582 1759 110891194 110891371 1.940000e-54 224.0
12 TraesCS7B01G410800 chr7D 82.126 207 32 5 415 619 436988343 436988140 7.110000e-39 172.0
13 TraesCS7B01G410800 chr7D 78.528 163 29 6 416 574 498535516 498535676 9.460000e-18 102.0
14 TraesCS7B01G410800 chr7D 95.000 40 2 0 3039 3078 599883693 599883654 4.470000e-06 63.9
15 TraesCS7B01G410800 chr5B 98.278 987 14 3 4357 5341 517629395 517630380 0.000000e+00 1725.0
16 TraesCS7B01G410800 chr5B 96.973 991 23 6 4357 5341 443262904 443261915 0.000000e+00 1657.0
17 TraesCS7B01G410800 chr5B 91.009 456 31 7 3384 3835 544984170 544983721 1.650000e-169 606.0
18 TraesCS7B01G410800 chr5B 80.851 235 39 6 375 606 397962785 397962554 4.250000e-41 180.0
19 TraesCS7B01G410800 chr1B 97.972 986 19 1 4357 5341 298716085 298717070 0.000000e+00 1709.0
20 TraesCS7B01G410800 chr1B 95.805 739 31 0 2300 3038 611576296 611577034 0.000000e+00 1194.0
21 TraesCS7B01G410800 chr1B 81.377 494 79 11 1271 1758 608996280 608995794 1.800000e-104 390.0
22 TraesCS7B01G410800 chr1B 90.809 272 17 7 3565 3835 7598151 7598415 1.830000e-94 357.0
23 TraesCS7B01G410800 chr1B 83.898 118 16 3 1066 1180 608996436 608996319 5.660000e-20 110.0
24 TraesCS7B01G410800 chr1B 77.966 118 24 2 430 545 542573937 542574054 7.420000e-09 73.1
25 TraesCS7B01G410800 chr7A 88.827 1441 76 32 699 2099 692131301 692129906 0.000000e+00 1690.0
26 TraesCS7B01G410800 chr7A 91.396 709 54 6 1 706 692132180 692131476 0.000000e+00 965.0
27 TraesCS7B01G410800 chr7A 93.043 345 20 2 3039 3383 692129812 692129472 7.990000e-138 501.0
28 TraesCS7B01G410800 chr7A 81.445 609 78 20 1214 1801 692155831 692155237 2.910000e-127 466.0
29 TraesCS7B01G410800 chr7A 87.838 370 23 10 4000 4353 692128990 692128627 1.070000e-111 414.0
30 TraesCS7B01G410800 chr7A 84.106 453 34 16 724 1162 692056826 692056398 2.320000e-108 403.0
31 TraesCS7B01G410800 chr7A 87.085 271 32 3 1225 1495 692056380 692056113 2.420000e-78 303.0
32 TraesCS7B01G410800 chr7A 89.823 226 21 2 1271 1495 712307268 712307492 6.770000e-74 289.0
33 TraesCS7B01G410800 chr7A 87.701 187 23 0 1584 1770 692056020 692055834 9.010000e-53 219.0
34 TraesCS7B01G410800 chr6B 97.068 989 23 5 4357 5341 66709326 66710312 0.000000e+00 1661.0
35 TraesCS7B01G410800 chr6B 96.612 738 23 2 2301 3037 123238898 123238162 0.000000e+00 1223.0
36 TraesCS7B01G410800 chr6B 95.794 737 30 1 2298 3034 20831273 20830538 0.000000e+00 1188.0
37 TraesCS7B01G410800 chr6B 95.670 739 28 1 2300 3038 712569377 712570111 0.000000e+00 1184.0
38 TraesCS7B01G410800 chr6B 88.776 98 9 2 1066 1161 548948685 548948782 9.400000e-23 119.0
39 TraesCS7B01G410800 chr3B 97.068 989 24 4 4357 5341 29476601 29475614 0.000000e+00 1661.0
40 TraesCS7B01G410800 chr3B 96.973 991 23 6 4357 5341 823350489 823349500 0.000000e+00 1657.0
41 TraesCS7B01G410800 chr3B 96.960 987 28 2 4357 5341 63790858 63791844 0.000000e+00 1655.0
42 TraesCS7B01G410800 chrUn 96.960 987 27 3 4357 5341 310459497 310458512 0.000000e+00 1653.0
43 TraesCS7B01G410800 chrUn 88.776 98 9 2 1066 1161 426294984 426295081 9.400000e-23 119.0
44 TraesCS7B01G410800 chrUn 76.650 197 37 9 422 616 476057221 476057410 3.400000e-17 100.0
45 TraesCS7B01G410800 chr2B 95.946 740 18 2 2300 3039 43617821 43618548 0.000000e+00 1190.0
46 TraesCS7B01G410800 chr2B 95.129 739 36 0 2300 3038 435825639 435824901 0.000000e+00 1166.0
47 TraesCS7B01G410800 chr2B 85.650 223 14 14 3603 3819 767422810 767422600 9.010000e-53 219.0
48 TraesCS7B01G410800 chr2B 81.095 201 32 6 422 620 646452828 646453024 7.160000e-34 156.0
49 TraesCS7B01G410800 chr4B 95.436 745 33 1 2295 3038 466287379 466288123 0.000000e+00 1186.0
50 TraesCS7B01G410800 chr4D 91.240 742 55 3 2294 3035 341027362 341028093 0.000000e+00 1002.0
51 TraesCS7B01G410800 chr1D 90.364 467 26 13 3384 3838 485811752 485811293 3.560000e-166 595.0
52 TraesCS7B01G410800 chr1D 90.150 467 27 13 3384 3838 485810427 485809968 1.660000e-164 590.0
53 TraesCS7B01G410800 chr1D 89.722 467 29 13 3384 3838 485807782 485807323 3.590000e-161 579.0
54 TraesCS7B01G410800 chr1D 89.507 467 30 13 3384 3838 485809105 485808646 1.670000e-159 573.0
55 TraesCS7B01G410800 chr1D 89.056 466 34 11 3384 3838 485813077 485812618 3.610000e-156 562.0
56 TraesCS7B01G410800 chr1D 89.103 468 28 14 3384 3835 485806460 485806000 1.300000e-155 560.0
57 TraesCS7B01G410800 chr1D 80.963 436 62 14 1066 1495 445642716 445642296 5.160000e-85 326.0
58 TraesCS7B01G410800 chr1D 87.931 174 21 0 1585 1758 445642207 445642034 7.010000e-49 206.0
59 TraesCS7B01G410800 chr1D 83.193 119 15 2 489 606 464612436 464612550 2.630000e-18 104.0
60 TraesCS7B01G410800 chr1A 79.915 707 107 25 1066 1758 541895707 541895022 2.240000e-133 486.0
61 TraesCS7B01G410800 chr5A 85.238 420 50 4 2621 3039 564558441 564558033 6.400000e-114 422.0
62 TraesCS7B01G410800 chr2D 79.268 246 44 7 375 617 575434364 575434123 1.190000e-36 165.0


These results show the homologous regions that are presented in the multiple sequence alignment. HSPs from the BLAST search that are within 2000 bases of each other have been grouped together. Homologous regions that are purely upstream or downstream may be removed if they don't overlap both primers.

query scaffold start end length rev.comp avg.bitscore max.bitscore avg.percent.identical query.start query.end num_hsp groupid homo_length
0 TraesCS7B01G410800 chr7B 679709075 679714415 5340 True 4766.000000 5655 100.000000 1 5341 2 chr7B.!!$R3 5340
1 TraesCS7B01G410800 chr7B 693345619 693346604 985 False 1653.000000 1653 96.960000 4357 5341 1 chr7B.!!$F1 984
2 TraesCS7B01G410800 chr7B 464101915 464102656 741 True 1227.000000 1227 96.496000 2300 3041 1 chr7B.!!$R1 741
3 TraesCS7B01G410800 chr7B 679683461 679684442 981 True 517.500000 527 86.166500 740 1770 2 chr7B.!!$R2 1030
4 TraesCS7B01G410800 chr7D 603769058 603769786 728 True 929.000000 929 89.581000 2300 3038 1 chr7D.!!$R2 738
5 TraesCS7B01G410800 chr7D 599882810 599885873 3063 True 919.475000 2595 90.722500 1 4353 4 chr7D.!!$R3 4352
6 TraesCS7B01G410800 chr5B 517629395 517630380 985 False 1725.000000 1725 98.278000 4357 5341 1 chr5B.!!$F1 984
7 TraesCS7B01G410800 chr5B 443261915 443262904 989 True 1657.000000 1657 96.973000 4357 5341 1 chr5B.!!$R2 984
8 TraesCS7B01G410800 chr1B 298716085 298717070 985 False 1709.000000 1709 97.972000 4357 5341 1 chr1B.!!$F2 984
9 TraesCS7B01G410800 chr1B 611576296 611577034 738 False 1194.000000 1194 95.805000 2300 3038 1 chr1B.!!$F4 738
10 TraesCS7B01G410800 chr1B 608995794 608996436 642 True 250.000000 390 82.637500 1066 1758 2 chr1B.!!$R1 692
11 TraesCS7B01G410800 chr7A 692128627 692132180 3553 True 892.500000 1690 90.276000 1 4353 4 chr7A.!!$R3 4352
12 TraesCS7B01G410800 chr7A 692155237 692155831 594 True 466.000000 466 81.445000 1214 1801 1 chr7A.!!$R1 587
13 TraesCS7B01G410800 chr7A 692055834 692056826 992 True 308.333333 403 86.297333 724 1770 3 chr7A.!!$R2 1046
14 TraesCS7B01G410800 chr6B 66709326 66710312 986 False 1661.000000 1661 97.068000 4357 5341 1 chr6B.!!$F1 984
15 TraesCS7B01G410800 chr6B 123238162 123238898 736 True 1223.000000 1223 96.612000 2301 3037 1 chr6B.!!$R2 736
16 TraesCS7B01G410800 chr6B 20830538 20831273 735 True 1188.000000 1188 95.794000 2298 3034 1 chr6B.!!$R1 736
17 TraesCS7B01G410800 chr6B 712569377 712570111 734 False 1184.000000 1184 95.670000 2300 3038 1 chr6B.!!$F3 738
18 TraesCS7B01G410800 chr3B 29475614 29476601 987 True 1661.000000 1661 97.068000 4357 5341 1 chr3B.!!$R1 984
19 TraesCS7B01G410800 chr3B 823349500 823350489 989 True 1657.000000 1657 96.973000 4357 5341 1 chr3B.!!$R2 984
20 TraesCS7B01G410800 chr3B 63790858 63791844 986 False 1655.000000 1655 96.960000 4357 5341 1 chr3B.!!$F1 984
21 TraesCS7B01G410800 chrUn 310458512 310459497 985 True 1653.000000 1653 96.960000 4357 5341 1 chrUn.!!$R1 984
22 TraesCS7B01G410800 chr2B 43617821 43618548 727 False 1190.000000 1190 95.946000 2300 3039 1 chr2B.!!$F1 739
23 TraesCS7B01G410800 chr2B 435824901 435825639 738 True 1166.000000 1166 95.129000 2300 3038 1 chr2B.!!$R1 738
24 TraesCS7B01G410800 chr4B 466287379 466288123 744 False 1186.000000 1186 95.436000 2295 3038 1 chr4B.!!$F1 743
25 TraesCS7B01G410800 chr4D 341027362 341028093 731 False 1002.000000 1002 91.240000 2294 3035 1 chr4D.!!$F1 741
26 TraesCS7B01G410800 chr1D 485806000 485813077 7077 True 576.500000 595 89.650333 3384 3838 6 chr1D.!!$R2 454
27 TraesCS7B01G410800 chr1D 445642034 445642716 682 True 266.000000 326 84.447000 1066 1758 2 chr1D.!!$R1 692
28 TraesCS7B01G410800 chr1A 541895022 541895707 685 True 486.000000 486 79.915000 1066 1758 1 chr1A.!!$R1 692

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
40 41 0.107165 GGCACCCCTTGTATCTGGTC 60.107 60.0 0.00 0.00 0.00 4.02 F
462 467 0.250295 TTTTGTCTGGCTCCGGTGAG 60.250 55.0 7.92 0.00 41.84 3.51 F
1998 2303 0.105658 TCGGCTGCTATAGGGGAACT 60.106 55.0 1.04 0.00 0.00 3.01 F
3082 3455 0.027979 CATCAATGTAGCGGCCGTTG 59.972 55.0 28.70 21.98 0.00 4.10 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1063 1262 1.011131 GCGTCGGCGGAAATCATTC 60.011 57.895 13.05 0.0 38.78 2.67 R
2056 2365 0.457853 GCTAGGCACGTTCGTGATGA 60.458 55.000 25.87 10.4 38.30 2.92 R
3245 3618 0.400213 TCGAGGGACCAAAAGCACAT 59.600 50.000 0.00 0.0 0.00 3.21 R
4652 8697 1.007721 CAGAGAGGAGAGGGGAAAGGA 59.992 57.143 0.00 0.0 0.00 3.36 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
40 41 0.107165 GGCACCCCTTGTATCTGGTC 60.107 60.000 0.00 0.00 0.00 4.02
144 149 6.592607 GTCGATTAGGGTTTATGTCTGTTCAA 59.407 38.462 0.00 0.00 0.00 2.69
170 175 6.721843 AGATAAGGTAGTGATAGCTCCCTA 57.278 41.667 0.00 0.00 0.00 3.53
172 177 6.949463 AGATAAGGTAGTGATAGCTCCCTAAC 59.051 42.308 0.00 0.00 0.00 2.34
199 204 0.970937 TGAGGTCTCCCGCCTAACTG 60.971 60.000 0.00 0.00 36.29 3.16
221 226 1.487976 CATCCCTGTGGTGCATCTAGT 59.512 52.381 0.00 0.00 0.00 2.57
227 232 1.343142 TGTGGTGCATCTAGTGTCGTT 59.657 47.619 0.00 0.00 0.00 3.85
245 250 1.118965 TTCAGAGGGCGTGTGAAGGA 61.119 55.000 14.76 0.00 33.59 3.36
352 357 2.758979 TGGTCGGATTCTTCCACTCTAC 59.241 50.000 0.00 0.00 42.74 2.59
353 358 2.758979 GGTCGGATTCTTCCACTCTACA 59.241 50.000 0.00 0.00 42.74 2.74
354 359 3.194968 GGTCGGATTCTTCCACTCTACAA 59.805 47.826 0.00 0.00 42.74 2.41
372 377 4.713824 ACAATTCTCTCCGTCGATAACA 57.286 40.909 0.00 0.00 0.00 2.41
373 378 5.068234 ACAATTCTCTCCGTCGATAACAA 57.932 39.130 0.00 0.00 0.00 2.83
405 410 2.787567 GCGCTGGTCCTCTAGGGTC 61.788 68.421 0.00 0.00 37.41 4.46
410 415 3.243724 GCTGGTCCTCTAGGGTCATTAT 58.756 50.000 0.00 0.00 36.25 1.28
413 418 4.890988 TGGTCCTCTAGGGTCATTATCAA 58.109 43.478 0.00 0.00 36.25 2.57
462 467 0.250295 TTTTGTCTGGCTCCGGTGAG 60.250 55.000 7.92 0.00 41.84 3.51
474 479 2.070039 CGGTGAGGGAGGGGCAATA 61.070 63.158 0.00 0.00 0.00 1.90
485 490 1.437160 GGGCAATAATGGTGGTGCG 59.563 57.895 0.00 0.00 37.89 5.34
498 503 1.443872 GGTGCGACGTCGTCTCATT 60.444 57.895 35.48 0.00 42.22 2.57
543 548 4.163458 GGTGGTCTATGAACCTGGATGTAA 59.837 45.833 0.00 0.00 40.20 2.41
583 588 8.180706 TGGTGTTACTTGTACTACTATGACAA 57.819 34.615 0.00 0.00 0.00 3.18
611 616 8.289618 TGATGAATAGGTTGAAAGTTTTTCTCG 58.710 33.333 3.53 0.00 0.00 4.04
616 621 9.516314 AATAGGTTGAAAGTTTTTCTCGAAAAG 57.484 29.630 5.15 0.00 40.83 2.27
634 639 5.228012 CGAAAAGAAGATATTTGCTTTCGCC 59.772 40.000 0.00 0.00 34.43 5.54
635 640 5.904362 AAAGAAGATATTTGCTTTCGCCT 57.096 34.783 0.00 0.00 34.43 5.52
636 641 5.904362 AAGAAGATATTTGCTTTCGCCTT 57.096 34.783 0.00 0.00 34.43 4.35
688 693 1.521423 GCCAACTCGTACATATCACGC 59.479 52.381 0.00 0.00 39.23 5.34
691 696 2.486951 ACTCGTACATATCACGCCAC 57.513 50.000 0.00 0.00 39.23 5.01
697 702 2.533266 ACATATCACGCCACATCCTC 57.467 50.000 0.00 0.00 0.00 3.71
706 711 2.290260 ACGCCACATCCTCTTTCATTCA 60.290 45.455 0.00 0.00 0.00 2.57
714 900 7.451732 CACATCCTCTTTCATTCATCTATCCT 58.548 38.462 0.00 0.00 0.00 3.24
715 901 8.591940 CACATCCTCTTTCATTCATCTATCCTA 58.408 37.037 0.00 0.00 0.00 2.94
716 902 8.592809 ACATCCTCTTTCATTCATCTATCCTAC 58.407 37.037 0.00 0.00 0.00 3.18
846 1035 1.273048 ACACCCAACGCGTATGACTTA 59.727 47.619 14.46 0.00 0.00 2.24
895 1084 2.240162 CTTACCCAGCCACGAGGACC 62.240 65.000 1.86 0.00 36.89 4.46
903 1092 1.418637 AGCCACGAGGACCAGTAAAAA 59.581 47.619 1.86 0.00 36.89 1.94
908 1097 2.173143 ACGAGGACCAGTAAAAACCCAA 59.827 45.455 0.00 0.00 0.00 4.12
927 1116 5.432060 ACCCAATCTAACTAACCATTAGCCT 59.568 40.000 0.00 0.00 36.71 4.58
974 1171 1.593479 GAACCCGGCCACGCTATAC 60.593 63.158 2.24 0.00 39.22 1.47
1059 1258 3.382832 CAGTCTCCTTCCCGGCGT 61.383 66.667 6.01 0.00 0.00 5.68
1068 1267 3.247056 TTCCCGGCGTGCAGAATGA 62.247 57.895 6.01 0.00 39.69 2.57
1106 1305 1.858458 CGTAACATCGTCGGCATCATT 59.142 47.619 0.00 0.00 0.00 2.57
1189 1404 4.473520 CCGCCGCCCTCTTCACAT 62.474 66.667 0.00 0.00 0.00 3.21
1210 1425 6.209788 CACATCCTCCTCCTCTTACCTATAAC 59.790 46.154 0.00 0.00 0.00 1.89
1310 1542 2.281484 TGCAAGGCCAAGGACGTC 60.281 61.111 7.13 7.13 0.00 4.34
1317 1549 2.182030 CCAAGGACGTCGAGGAGC 59.818 66.667 12.85 3.27 0.00 4.70
1379 1611 0.252103 TCTGGGTCTTCTACGGCCTT 60.252 55.000 0.00 0.00 0.00 4.35
1497 1729 1.611491 CCAACAACAAGCGGGTACATT 59.389 47.619 0.00 0.00 0.00 2.71
1655 1927 4.367023 GTGGTGGTCGGCGTGCTA 62.367 66.667 6.85 0.00 0.00 3.49
1817 2089 9.863845 TTTAATTCTTTCTTTCCGTTTCTTGTT 57.136 25.926 0.00 0.00 0.00 2.83
1821 2093 6.090129 TCTTTCTTTCCGTTTCTTGTTGTTG 58.910 36.000 0.00 0.00 0.00 3.33
1822 2094 4.364415 TCTTTCCGTTTCTTGTTGTTGG 57.636 40.909 0.00 0.00 0.00 3.77
1823 2095 3.759618 TCTTTCCGTTTCTTGTTGTTGGT 59.240 39.130 0.00 0.00 0.00 3.67
1824 2096 3.495670 TTCCGTTTCTTGTTGTTGGTG 57.504 42.857 0.00 0.00 0.00 4.17
1827 2099 4.008330 TCCGTTTCTTGTTGTTGGTGTTA 58.992 39.130 0.00 0.00 0.00 2.41
1829 2101 4.142556 CCGTTTCTTGTTGTTGGTGTTAGT 60.143 41.667 0.00 0.00 0.00 2.24
1830 2102 5.395642 CGTTTCTTGTTGTTGGTGTTAGTT 58.604 37.500 0.00 0.00 0.00 2.24
1831 2103 6.403418 CCGTTTCTTGTTGTTGGTGTTAGTTA 60.403 38.462 0.00 0.00 0.00 2.24
1832 2104 6.685403 CGTTTCTTGTTGTTGGTGTTAGTTAG 59.315 38.462 0.00 0.00 0.00 2.34
1833 2105 7.532571 GTTTCTTGTTGTTGGTGTTAGTTAGT 58.467 34.615 0.00 0.00 0.00 2.24
1834 2106 7.690952 TTCTTGTTGTTGGTGTTAGTTAGTT 57.309 32.000 0.00 0.00 0.00 2.24
1835 2107 7.690952 TCTTGTTGTTGGTGTTAGTTAGTTT 57.309 32.000 0.00 0.00 0.00 2.66
1836 2108 7.754625 TCTTGTTGTTGGTGTTAGTTAGTTTC 58.245 34.615 0.00 0.00 0.00 2.78
1837 2109 7.608761 TCTTGTTGTTGGTGTTAGTTAGTTTCT 59.391 33.333 0.00 0.00 0.00 2.52
1838 2110 7.079182 TGTTGTTGGTGTTAGTTAGTTTCTG 57.921 36.000 0.00 0.00 0.00 3.02
1839 2111 6.094325 TGTTGTTGGTGTTAGTTAGTTTCTGG 59.906 38.462 0.00 0.00 0.00 3.86
1840 2112 4.577283 TGTTGGTGTTAGTTAGTTTCTGGC 59.423 41.667 0.00 0.00 0.00 4.85
1841 2113 3.746940 TGGTGTTAGTTAGTTTCTGGCC 58.253 45.455 0.00 0.00 0.00 5.36
1842 2114 3.079578 GGTGTTAGTTAGTTTCTGGCCC 58.920 50.000 0.00 0.00 0.00 5.80
1843 2115 3.244805 GGTGTTAGTTAGTTTCTGGCCCT 60.245 47.826 0.00 0.00 0.00 5.19
1844 2116 4.019950 GGTGTTAGTTAGTTTCTGGCCCTA 60.020 45.833 0.00 0.00 0.00 3.53
1845 2117 5.513614 GGTGTTAGTTAGTTTCTGGCCCTAA 60.514 44.000 0.00 0.00 0.00 2.69
1846 2118 5.642491 GTGTTAGTTAGTTTCTGGCCCTAAG 59.358 44.000 0.00 0.00 0.00 2.18
1847 2119 5.544948 TGTTAGTTAGTTTCTGGCCCTAAGA 59.455 40.000 0.00 0.00 0.00 2.10
1848 2120 6.214819 TGTTAGTTAGTTTCTGGCCCTAAGAT 59.785 38.462 0.00 0.00 0.00 2.40
1849 2121 5.360649 AGTTAGTTTCTGGCCCTAAGATC 57.639 43.478 0.00 0.00 0.00 2.75
1850 2122 4.783227 AGTTAGTTTCTGGCCCTAAGATCA 59.217 41.667 0.00 0.00 0.00 2.92
1851 2123 5.430089 AGTTAGTTTCTGGCCCTAAGATCAT 59.570 40.000 0.00 0.00 0.00 2.45
1852 2124 4.429854 AGTTTCTGGCCCTAAGATCATC 57.570 45.455 0.00 0.00 0.00 2.92
1853 2125 3.134458 GTTTCTGGCCCTAAGATCATCG 58.866 50.000 0.00 0.00 0.00 3.84
1889 2161 2.280457 TGTTGATGCCGCACGTGA 60.280 55.556 22.23 0.00 0.00 4.35
1907 2212 2.424246 GTGAGGCTAACTAACGCTCTCT 59.576 50.000 0.00 0.00 0.00 3.10
1918 2223 6.452494 ACTAACGCTCTCTTCTGCTTATAA 57.548 37.500 0.00 0.00 0.00 0.98
1929 2234 9.809096 TCTCTTCTGCTTATAAATCTGTACTTG 57.191 33.333 0.00 0.00 0.00 3.16
1930 2235 8.948631 TCTTCTGCTTATAAATCTGTACTTGG 57.051 34.615 0.00 0.00 0.00 3.61
1931 2236 7.987458 TCTTCTGCTTATAAATCTGTACTTGGG 59.013 37.037 0.00 0.00 0.00 4.12
1932 2237 6.591935 TCTGCTTATAAATCTGTACTTGGGG 58.408 40.000 0.00 0.00 0.00 4.96
1933 2238 6.157994 TCTGCTTATAAATCTGTACTTGGGGT 59.842 38.462 0.00 0.00 0.00 4.95
1934 2239 6.119536 TGCTTATAAATCTGTACTTGGGGTG 58.880 40.000 0.00 0.00 0.00 4.61
1935 2240 6.120220 GCTTATAAATCTGTACTTGGGGTGT 58.880 40.000 0.00 0.00 0.00 4.16
1936 2241 7.092802 TGCTTATAAATCTGTACTTGGGGTGTA 60.093 37.037 0.00 0.00 0.00 2.90
1937 2242 7.937394 GCTTATAAATCTGTACTTGGGGTGTAT 59.063 37.037 0.00 0.00 0.00 2.29
1940 2245 6.886178 AAATCTGTACTTGGGGTGTATAGT 57.114 37.500 0.00 0.00 33.05 2.12
1964 2269 3.318017 CATTCCGCGTATTTAGCTAGCT 58.682 45.455 23.12 23.12 0.00 3.32
1981 2286 3.982576 AGCTAACCAACCAAACTTTCG 57.017 42.857 0.00 0.00 0.00 3.46
1998 2303 0.105658 TCGGCTGCTATAGGGGAACT 60.106 55.000 1.04 0.00 0.00 3.01
2015 2323 8.943594 AGGGGAACTACATTTACAAATTACAA 57.056 30.769 0.00 0.00 0.00 2.41
2056 2365 0.110486 AAACCTGTGGTCCATCGCTT 59.890 50.000 0.00 0.00 33.12 4.68
2063 2372 0.460109 TGGTCCATCGCTTCATCACG 60.460 55.000 0.00 0.00 0.00 4.35
2415 2734 4.400884 AGATCGAGCTGTAGAACATGACTT 59.599 41.667 0.39 0.00 0.00 3.01
2462 2803 2.284684 TCGATCTCGAGCTAGTTTCGAC 59.715 50.000 7.81 7.31 44.22 4.20
2591 2932 3.320626 CGAGCACATCTTTGTCTCTTGA 58.679 45.455 0.00 0.00 32.34 3.02
2610 2951 7.283354 TCTCTTGAGCGAACTAGAAATAGATGA 59.717 37.037 0.00 0.00 0.00 2.92
2655 2996 5.990120 AGAAAAAGAAGGTGCATATGCTT 57.010 34.783 27.13 14.27 42.66 3.91
2656 2997 6.350629 AGAAAAAGAAGGTGCATATGCTTT 57.649 33.333 27.13 18.21 42.66 3.51
3078 3451 1.599542 GAGTTCATCAATGTAGCGGCC 59.400 52.381 0.00 0.00 0.00 6.13
3082 3455 0.027979 CATCAATGTAGCGGCCGTTG 59.972 55.000 28.70 21.98 0.00 4.10
3085 3458 0.304705 CAATGTAGCGGCCGTTGATC 59.695 55.000 28.70 15.82 31.83 2.92
3108 3481 8.664669 ATCAACCAGGGAATTTGTTTACTTAT 57.335 30.769 0.00 0.00 0.00 1.73
3158 3531 8.887036 GTTTTCCAAAACAAAAGATAGGTCAT 57.113 30.769 9.58 0.00 45.72 3.06
3179 3552 8.607441 GTCATACATATTTTATGACTCAGCCA 57.393 34.615 18.93 0.00 46.70 4.75
3308 3681 1.519408 ACCAGAACCGGTTTTCATCG 58.481 50.000 23.22 8.58 34.91 3.84
3350 3723 2.570415 TTGCGGAATGGTCCTTACAA 57.430 45.000 0.00 0.00 42.44 2.41
3357 3730 5.190677 CGGAATGGTCCTTACAATTTACCT 58.809 41.667 0.00 0.00 42.44 3.08
3363 3736 5.073965 TGGTCCTTACAATTTACCTGAACCT 59.926 40.000 0.00 0.00 0.00 3.50
3458 3831 1.880027 CGGCTGGGATTACTATTTGGC 59.120 52.381 0.00 0.00 0.00 4.52
3465 5163 4.103469 TGGGATTACTATTTGGCCGTATGT 59.897 41.667 0.00 0.00 0.00 2.29
3486 5184 2.914059 ACACGTGTTAGAGTTGGCTTT 58.086 42.857 17.22 0.00 0.00 3.51
3516 5214 3.392285 TGGTGCTAGCTGATTCCATGTAT 59.608 43.478 17.23 0.00 0.00 2.29
3573 5275 1.226746 GTCAAGGTGAGTCCGGTTTG 58.773 55.000 0.00 0.00 41.99 2.93
3699 5401 7.402071 GGGTATAGGGGTCATGTAATATCAGAA 59.598 40.741 0.00 0.00 0.00 3.02
3701 5403 9.877178 GTATAGGGGTCATGTAATATCAGAAAG 57.123 37.037 0.00 0.00 0.00 2.62
3704 5406 8.331931 AGGGGTCATGTAATATCAGAAAGTAA 57.668 34.615 0.00 0.00 0.00 2.24
3706 5408 7.990886 GGGGTCATGTAATATCAGAAAGTAACA 59.009 37.037 0.00 0.00 0.00 2.41
3712 5414 9.905713 ATGTAATATCAGAAAGTAACATGGTGT 57.094 29.630 0.00 0.00 0.00 4.16
3714 5416 7.630242 AATATCAGAAAGTAACATGGTGTGG 57.370 36.000 0.00 0.00 0.00 4.17
3715 5417 3.750371 TCAGAAAGTAACATGGTGTGGG 58.250 45.455 0.00 0.00 0.00 4.61
3722 6745 4.398319 AGTAACATGGTGTGGGAGAAAAG 58.602 43.478 0.00 0.00 0.00 2.27
3723 6746 2.292828 ACATGGTGTGGGAGAAAAGG 57.707 50.000 0.00 0.00 0.00 3.11
3724 6747 1.780309 ACATGGTGTGGGAGAAAAGGA 59.220 47.619 0.00 0.00 0.00 3.36
3725 6748 2.224867 ACATGGTGTGGGAGAAAAGGAG 60.225 50.000 0.00 0.00 0.00 3.69
3729 6752 3.053245 TGGTGTGGGAGAAAAGGAGAAAA 60.053 43.478 0.00 0.00 0.00 2.29
3745 6772 9.513906 AAAGGAGAAAAGAAATAAAGAGAGGAG 57.486 33.333 0.00 0.00 0.00 3.69
3779 6806 2.364632 GCCTTTGGCCAAAGTTTTTGT 58.635 42.857 41.82 0.00 44.66 2.83
3780 6807 2.097304 GCCTTTGGCCAAAGTTTTTGTG 59.903 45.455 41.82 30.18 44.66 3.33
3781 6808 3.342719 CCTTTGGCCAAAGTTTTTGTGT 58.657 40.909 41.82 0.00 44.66 3.72
3782 6809 3.126686 CCTTTGGCCAAAGTTTTTGTGTG 59.873 43.478 41.82 26.40 44.66 3.82
3783 6810 1.731720 TGGCCAAAGTTTTTGTGTGC 58.268 45.000 0.61 0.00 0.00 4.57
3784 6811 0.649993 GGCCAAAGTTTTTGTGTGCG 59.350 50.000 0.00 0.00 0.00 5.34
3785 6812 0.026156 GCCAAAGTTTTTGTGTGCGC 59.974 50.000 0.00 0.00 0.00 6.09
3786 6813 1.354040 CCAAAGTTTTTGTGTGCGCA 58.646 45.000 5.66 5.66 0.00 6.09
3787 6814 1.060409 CCAAAGTTTTTGTGTGCGCAC 59.940 47.619 33.11 33.11 45.44 5.34
3795 6822 2.717190 GTGTGCGCACGTTTGTCG 60.717 61.111 33.22 0.00 46.00 4.35
3823 6851 1.264045 TGTGATCGATCCTGTGGGCA 61.264 55.000 22.31 7.31 0.00 5.36
3853 6881 4.974645 ACAGTTTACCCATTGTCTCTGA 57.025 40.909 0.00 0.00 0.00 3.27
3864 6892 5.010922 CCCATTGTCTCTGATTTTGGACAAA 59.989 40.000 11.76 0.00 46.77 2.83
3865 6893 6.462768 CCCATTGTCTCTGATTTTGGACAAAA 60.463 38.462 12.07 12.07 46.77 2.44
3899 6927 2.162681 GTGACTTGAGGGACCAAATGG 58.837 52.381 0.00 0.00 42.17 3.16
3901 6929 0.609131 ACTTGAGGGACCAAATGGCG 60.609 55.000 0.00 0.00 39.32 5.69
3908 6936 1.111277 GGACCAAATGGCGCCTAAAT 58.889 50.000 29.70 10.42 39.32 1.40
3942 6970 4.899502 ACCAGATGTAGACTTTTGGTGAG 58.100 43.478 9.24 0.00 37.20 3.51
3949 6977 2.576615 AGACTTTTGGTGAGCTTGACC 58.423 47.619 8.59 8.59 0.00 4.02
3953 6981 0.534203 TTTGGTGAGCTTGACCGACC 60.534 55.000 10.42 0.00 36.12 4.79
3970 6999 6.068473 ACCGACCAAAACATACTTTTCTTC 57.932 37.500 0.00 0.00 0.00 2.87
3987 7318 4.602340 TCTTCAGAAAAAGTAGCGAGGT 57.398 40.909 0.00 0.00 0.00 3.85
4008 7359 7.201444 CGAGGTCCTTAAAATATGCTATTAGCG 60.201 40.741 10.94 0.00 46.26 4.26
4068 7419 5.279384 CAGGACATTGCTCAAAATGCTATC 58.721 41.667 0.00 0.00 40.54 2.08
4136 7502 1.872952 CTTGCAGGTTCGTGTGATCAA 59.127 47.619 0.00 0.00 0.00 2.57
4179 7545 0.674581 CATTCTTCCTGTCGCTGGCA 60.675 55.000 0.00 0.00 0.00 4.92
4191 7557 0.590195 CGCTGGCAATATTCCTCAGC 59.410 55.000 17.52 17.52 45.01 4.26
4298 8343 3.973135 GCTTTGATGCGATGATGTCAATC 59.027 43.478 0.00 0.00 31.39 2.67
4299 8344 4.261072 GCTTTGATGCGATGATGTCAATCT 60.261 41.667 0.00 0.00 33.61 2.40
4303 8348 6.034161 TGATGCGATGATGTCAATCTATCT 57.966 37.500 0.00 0.00 33.61 1.98
4306 8351 6.331369 TGCGATGATGTCAATCTATCTACA 57.669 37.500 0.00 0.00 33.61 2.74
4315 8360 7.543947 TGTCAATCTATCTACACTTTGCATG 57.456 36.000 0.00 0.00 0.00 4.06
4320 8365 6.737720 TCTATCTACACTTTGCATGGATCT 57.262 37.500 0.00 0.00 0.00 2.75
4322 8367 8.250143 TCTATCTACACTTTGCATGGATCTAA 57.750 34.615 0.00 0.00 0.00 2.10
4323 8368 8.874156 TCTATCTACACTTTGCATGGATCTAAT 58.126 33.333 0.00 0.00 0.00 1.73
4324 8369 7.976135 ATCTACACTTTGCATGGATCTAATC 57.024 36.000 0.00 0.00 0.00 1.75
4353 8398 7.816995 TCAATTGTGATGCCCACTTTTAATTAC 59.183 33.333 5.13 0.00 45.86 1.89
4354 8399 5.652994 TGTGATGCCCACTTTTAATTACC 57.347 39.130 7.67 0.00 45.86 2.85
4355 8400 4.464597 TGTGATGCCCACTTTTAATTACCC 59.535 41.667 7.67 0.00 45.86 3.69
4425 8470 3.447918 TTAGAGCCGGCACTAATGTAC 57.552 47.619 33.78 12.66 0.00 2.90
4496 8541 3.007635 GTTCGTGGCTAACCTTTAGCAT 58.992 45.455 17.42 0.00 42.06 3.79
4614 8659 4.723309 ACCGATACTAAAGGTCGTCCTAT 58.277 43.478 0.37 0.00 44.35 2.57
4652 8697 0.170116 CGAGCTCGCTCTGTTCTTCT 59.830 55.000 25.07 0.00 40.69 2.85
4855 8904 6.195600 TGTGAGTTTAGTAATTTGGGAGGT 57.804 37.500 0.00 0.00 0.00 3.85
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
24 25 0.617820 AGCGACCAGATACAAGGGGT 60.618 55.000 0.00 0.00 36.05 4.95
87 88 2.755952 AAAACAGAGCAGGAACCCTT 57.244 45.000 0.00 0.00 0.00 3.95
109 110 6.997239 AAACCCTAATCGACCTAAAACATC 57.003 37.500 0.00 0.00 0.00 3.06
110 111 8.050930 ACATAAACCCTAATCGACCTAAAACAT 58.949 33.333 0.00 0.00 0.00 2.71
111 112 7.396418 ACATAAACCCTAATCGACCTAAAACA 58.604 34.615 0.00 0.00 0.00 2.83
112 113 7.767659 AGACATAAACCCTAATCGACCTAAAAC 59.232 37.037 0.00 0.00 0.00 2.43
144 149 6.014012 GGGAGCTATCACTACCTTATCTTCT 58.986 44.000 0.00 0.00 37.72 2.85
199 204 2.043652 ATGCACCACAGGGATGGC 60.044 61.111 0.00 0.00 44.33 4.40
221 226 2.338620 CACGCCCTCTGAACGACA 59.661 61.111 0.00 0.00 0.00 4.35
227 232 1.533033 TCCTTCACACGCCCTCTGA 60.533 57.895 0.00 0.00 0.00 3.27
352 357 6.036083 ACAATTGTTATCGACGGAGAGAATTG 59.964 38.462 4.92 17.52 38.04 2.32
353 358 6.106673 ACAATTGTTATCGACGGAGAGAATT 58.893 36.000 4.92 0.00 0.00 2.17
354 359 5.661458 ACAATTGTTATCGACGGAGAGAAT 58.339 37.500 4.92 0.00 0.00 2.40
372 377 2.462889 CAGCGCAACAGAACAACAATT 58.537 42.857 11.47 0.00 0.00 2.32
373 378 1.269206 CCAGCGCAACAGAACAACAAT 60.269 47.619 11.47 0.00 0.00 2.71
405 410 7.012704 AGACAATGGGAAATCGTCTTGATAATG 59.987 37.037 0.00 0.00 35.84 1.90
410 415 4.286297 AGACAATGGGAAATCGTCTTGA 57.714 40.909 0.00 0.00 33.20 3.02
413 418 5.046591 TGAAGTAGACAATGGGAAATCGTCT 60.047 40.000 0.00 0.00 40.03 4.18
462 467 0.469892 CCACCATTATTGCCCCTCCC 60.470 60.000 0.00 0.00 0.00 4.30
472 477 0.804544 CGACGTCGCACCACCATTAT 60.805 55.000 26.59 0.00 0.00 1.28
474 479 2.736995 CGACGTCGCACCACCATT 60.737 61.111 26.59 0.00 0.00 3.16
485 490 2.263077 AGCATTGAATGAGACGACGTC 58.737 47.619 20.25 20.25 0.00 4.34
498 503 3.319137 AGCGACAACTAGAAGCATTGA 57.681 42.857 0.00 0.00 0.00 2.57
688 693 6.654161 GGATAGATGAATGAAAGAGGATGTGG 59.346 42.308 0.00 0.00 0.00 4.17
691 696 8.040132 GGTAGGATAGATGAATGAAAGAGGATG 58.960 40.741 0.00 0.00 0.00 3.51
697 702 6.809196 GCGTAGGTAGGATAGATGAATGAAAG 59.191 42.308 0.00 0.00 0.00 2.62
706 711 3.810721 ACCAGCGTAGGTAGGATAGAT 57.189 47.619 0.00 0.00 40.98 1.98
714 900 0.742505 CATCCGAACCAGCGTAGGTA 59.257 55.000 1.30 0.00 42.25 3.08
715 901 0.968901 TCATCCGAACCAGCGTAGGT 60.969 55.000 0.00 0.00 45.91 3.08
716 902 0.249073 CTCATCCGAACCAGCGTAGG 60.249 60.000 0.00 0.00 0.00 3.18
846 1035 0.396417 AGCTCGTGGGATAGACTGCT 60.396 55.000 0.00 0.00 0.00 4.24
895 1084 8.398878 TGGTTAGTTAGATTGGGTTTTTACTG 57.601 34.615 0.00 0.00 0.00 2.74
903 1092 5.432060 AGGCTAATGGTTAGTTAGATTGGGT 59.568 40.000 0.00 0.00 35.66 4.51
908 1097 9.381038 TGATTAGAGGCTAATGGTTAGTTAGAT 57.619 33.333 4.55 0.00 35.66 1.98
924 1113 4.946157 CACCCAATGGATATGATTAGAGGC 59.054 45.833 0.00 0.00 34.81 4.70
1063 1262 1.011131 GCGTCGGCGGAAATCATTC 60.011 57.895 13.05 0.00 38.78 2.67
1106 1305 2.028420 CGAAGGAGATGACATTGCCA 57.972 50.000 9.40 0.00 0.00 4.92
1187 1402 5.717654 GGTTATAGGTAAGAGGAGGAGGATG 59.282 48.000 0.00 0.00 0.00 3.51
1188 1403 5.622204 AGGTTATAGGTAAGAGGAGGAGGAT 59.378 44.000 0.00 0.00 0.00 3.24
1189 1404 4.989545 AGGTTATAGGTAAGAGGAGGAGGA 59.010 45.833 0.00 0.00 0.00 3.71
1210 1425 8.646004 CAATCACCCTCCATATACATAGATAGG 58.354 40.741 0.00 0.00 0.00 2.57
1310 1542 4.069232 TCCGGCTTGTGCTCCTCG 62.069 66.667 0.00 0.00 39.59 4.63
1317 1549 2.267961 GTAGGGGTCCGGCTTGTG 59.732 66.667 0.00 0.00 0.00 3.33
1379 1611 2.204013 TTGGGGTGGACGATGGGA 60.204 61.111 0.00 0.00 0.00 4.37
1497 1729 3.068024 ACGATTAGGGGACGCGTTTATAA 59.932 43.478 15.53 11.15 0.00 0.98
1663 1935 2.280797 GCTTCTCGTGGGTGTGCA 60.281 61.111 0.00 0.00 0.00 4.57
1776 2048 9.141400 GAAAGAATTAAAGAGTAGACACGATGT 57.859 33.333 0.00 0.00 0.00 3.06
1817 2089 4.577283 GCCAGAAACTAACTAACACCAACA 59.423 41.667 0.00 0.00 0.00 3.33
1821 2093 3.079578 GGGCCAGAAACTAACTAACACC 58.920 50.000 4.39 0.00 0.00 4.16
1822 2094 4.017177 AGGGCCAGAAACTAACTAACAC 57.983 45.455 6.18 0.00 0.00 3.32
1823 2095 5.544948 TCTTAGGGCCAGAAACTAACTAACA 59.455 40.000 6.18 0.00 0.00 2.41
1824 2096 6.046290 TCTTAGGGCCAGAAACTAACTAAC 57.954 41.667 6.18 0.00 0.00 2.34
1827 2099 4.783227 TGATCTTAGGGCCAGAAACTAACT 59.217 41.667 6.18 0.00 0.00 2.24
1829 2101 5.453339 CGATGATCTTAGGGCCAGAAACTAA 60.453 44.000 6.18 1.28 0.00 2.24
1830 2102 4.039245 CGATGATCTTAGGGCCAGAAACTA 59.961 45.833 6.18 0.00 0.00 2.24
1831 2103 3.181461 CGATGATCTTAGGGCCAGAAACT 60.181 47.826 6.18 0.00 0.00 2.66
1832 2104 3.134458 CGATGATCTTAGGGCCAGAAAC 58.866 50.000 6.18 0.63 0.00 2.78
1833 2105 3.038280 TCGATGATCTTAGGGCCAGAAA 58.962 45.455 6.18 0.00 0.00 2.52
1834 2106 2.365617 GTCGATGATCTTAGGGCCAGAA 59.634 50.000 6.18 0.00 0.00 3.02
1835 2107 1.964223 GTCGATGATCTTAGGGCCAGA 59.036 52.381 6.18 0.00 0.00 3.86
1836 2108 1.967066 AGTCGATGATCTTAGGGCCAG 59.033 52.381 6.18 0.00 0.00 4.85
1837 2109 1.964223 GAGTCGATGATCTTAGGGCCA 59.036 52.381 6.18 0.00 0.00 5.36
1838 2110 1.964223 TGAGTCGATGATCTTAGGGCC 59.036 52.381 0.00 0.00 0.00 5.80
1839 2111 2.625790 ACTGAGTCGATGATCTTAGGGC 59.374 50.000 0.00 0.00 0.00 5.19
1840 2112 4.927978 AACTGAGTCGATGATCTTAGGG 57.072 45.455 0.00 0.00 0.00 3.53
1841 2113 6.627395 ACTAACTGAGTCGATGATCTTAGG 57.373 41.667 0.00 0.00 29.95 2.69
1842 2114 7.476667 ACAACTAACTGAGTCGATGATCTTAG 58.523 38.462 0.00 0.00 37.44 2.18
1843 2115 7.392494 ACAACTAACTGAGTCGATGATCTTA 57.608 36.000 0.00 0.00 37.44 2.10
1844 2116 6.274157 ACAACTAACTGAGTCGATGATCTT 57.726 37.500 0.00 0.00 37.44 2.40
1845 2117 5.906113 ACAACTAACTGAGTCGATGATCT 57.094 39.130 0.00 0.00 37.44 2.75
1846 2118 5.220303 GCAACAACTAACTGAGTCGATGATC 60.220 44.000 0.00 0.00 37.44 2.92
1847 2119 4.627467 GCAACAACTAACTGAGTCGATGAT 59.373 41.667 0.00 0.00 37.44 2.45
1848 2120 3.987868 GCAACAACTAACTGAGTCGATGA 59.012 43.478 0.00 0.00 37.44 2.92
1849 2121 3.181540 CGCAACAACTAACTGAGTCGATG 60.182 47.826 0.00 0.00 37.44 3.84
1850 2122 2.987149 CGCAACAACTAACTGAGTCGAT 59.013 45.455 0.00 0.00 37.44 3.59
1851 2123 2.223641 ACGCAACAACTAACTGAGTCGA 60.224 45.455 0.00 0.00 37.44 4.20
1852 2124 2.097396 CACGCAACAACTAACTGAGTCG 60.097 50.000 0.00 0.00 37.44 4.18
1853 2125 2.864343 ACACGCAACAACTAACTGAGTC 59.136 45.455 0.00 0.00 37.44 3.36
1889 2161 3.129638 CAGAAGAGAGCGTTAGTTAGCCT 59.870 47.826 0.00 0.00 0.00 4.58
1901 2206 8.141268 AGTACAGATTTATAAGCAGAAGAGAGC 58.859 37.037 0.00 0.00 0.00 4.09
1907 2212 7.054124 CCCCAAGTACAGATTTATAAGCAGAA 58.946 38.462 0.00 0.00 0.00 3.02
1918 2223 6.650120 CAACTATACACCCCAAGTACAGATT 58.350 40.000 0.00 0.00 0.00 2.40
1928 2233 2.420827 CGGAATGCAACTATACACCCCA 60.421 50.000 0.00 0.00 0.00 4.96
1929 2234 2.218603 CGGAATGCAACTATACACCCC 58.781 52.381 0.00 0.00 0.00 4.95
1930 2235 1.602377 GCGGAATGCAACTATACACCC 59.398 52.381 0.00 0.00 45.45 4.61
1931 2236 1.260561 CGCGGAATGCAACTATACACC 59.739 52.381 0.00 0.00 46.97 4.16
1932 2237 1.931172 ACGCGGAATGCAACTATACAC 59.069 47.619 12.47 0.00 46.97 2.90
1933 2238 2.303163 ACGCGGAATGCAACTATACA 57.697 45.000 12.47 0.00 46.97 2.29
1934 2239 4.985044 AATACGCGGAATGCAACTATAC 57.015 40.909 12.47 0.00 46.97 1.47
1935 2240 5.119588 GCTAAATACGCGGAATGCAACTATA 59.880 40.000 12.47 0.00 46.97 1.31
1936 2241 4.084013 GCTAAATACGCGGAATGCAACTAT 60.084 41.667 12.47 0.00 46.97 2.12
1937 2242 3.246699 GCTAAATACGCGGAATGCAACTA 59.753 43.478 12.47 0.00 46.97 2.24
1938 2243 2.031683 GCTAAATACGCGGAATGCAACT 59.968 45.455 12.47 0.00 46.97 3.16
1939 2244 2.031683 AGCTAAATACGCGGAATGCAAC 59.968 45.455 12.47 0.00 46.97 4.17
1940 2245 2.285083 AGCTAAATACGCGGAATGCAA 58.715 42.857 12.47 0.00 46.97 4.08
1964 2269 2.359531 CAGCCGAAAGTTTGGTTGGTTA 59.640 45.455 6.32 0.00 38.77 2.85
1981 2286 2.326428 TGTAGTTCCCCTATAGCAGCC 58.674 52.381 0.00 0.00 0.00 4.85
2047 2356 1.640428 GTTCGTGATGAAGCGATGGA 58.360 50.000 0.00 0.00 37.23 3.41
2056 2365 0.457853 GCTAGGCACGTTCGTGATGA 60.458 55.000 25.87 10.40 38.30 2.92
2063 2372 1.041447 TCCCCTAGCTAGGCACGTTC 61.041 60.000 31.33 0.00 42.26 3.95
2291 2610 4.628074 TCGTTTGCAGCCCTAACTATATC 58.372 43.478 0.00 0.00 0.00 1.63
2292 2611 4.101119 ACTCGTTTGCAGCCCTAACTATAT 59.899 41.667 0.00 0.00 0.00 0.86
2293 2612 3.449737 ACTCGTTTGCAGCCCTAACTATA 59.550 43.478 0.00 0.00 0.00 1.31
2415 2734 0.608130 ATCGGTACAAGCTGAGCACA 59.392 50.000 7.39 0.00 0.00 4.57
2501 2842 7.152645 GTGTTGTGTCCTTATCTAGTCTGAAA 58.847 38.462 0.00 0.00 0.00 2.69
2591 2932 6.266558 AGACCATCATCTATTTCTAGTTCGCT 59.733 38.462 0.00 0.00 0.00 4.93
3078 3451 3.255642 ACAAATTCCCTGGTTGATCAACG 59.744 43.478 27.69 17.06 42.02 4.10
3082 3455 6.590234 AGTAAACAAATTCCCTGGTTGATC 57.410 37.500 2.18 0.00 0.00 2.92
3133 3506 8.887036 ATGACCTATCTTTTGTTTTGGAAAAC 57.113 30.769 7.86 7.86 46.40 2.43
3134 3507 9.974980 GTATGACCTATCTTTTGTTTTGGAAAA 57.025 29.630 0.00 0.00 0.00 2.29
3136 3509 8.698973 TGTATGACCTATCTTTTGTTTTGGAA 57.301 30.769 0.00 0.00 0.00 3.53
3137 3510 8.877864 ATGTATGACCTATCTTTTGTTTTGGA 57.122 30.769 0.00 0.00 0.00 3.53
3158 3531 7.041167 GCACATGGCTGAGTCATAAAATATGTA 60.041 37.037 0.00 0.00 40.25 2.29
3245 3618 0.400213 TCGAGGGACCAAAAGCACAT 59.600 50.000 0.00 0.00 0.00 3.21
3250 3623 2.143925 GTGAAGTCGAGGGACCAAAAG 58.856 52.381 0.00 0.00 44.54 2.27
3254 3627 0.761323 TTGGTGAAGTCGAGGGACCA 60.761 55.000 0.00 2.21 44.54 4.02
3350 3723 2.514803 GTGGCACAGGTTCAGGTAAAT 58.485 47.619 13.86 0.00 41.80 1.40
3382 3755 9.975218 ACCAATTTAGACAAGATTACCTAACAT 57.025 29.630 0.00 0.00 0.00 2.71
3404 3777 4.281688 ACTTAGGCGACACTAACTAACCAA 59.718 41.667 0.00 0.00 0.00 3.67
3465 5163 3.738830 AAGCCAACTCTAACACGTGTA 57.261 42.857 23.69 5.42 0.00 2.90
3486 5184 5.485620 GAATCAGCTAGCACCATGATATGA 58.514 41.667 18.83 8.72 32.25 2.15
3516 5214 3.688694 ACTTCGGCACTAACCAATACA 57.311 42.857 0.00 0.00 0.00 2.29
3573 5275 2.329379 CACGTACTTGCTCTTGAGTCC 58.671 52.381 0.00 0.00 0.00 3.85
3577 5279 1.272490 CCTCCACGTACTTGCTCTTGA 59.728 52.381 0.00 0.00 0.00 3.02
3579 5281 1.339097 ACCTCCACGTACTTGCTCTT 58.661 50.000 0.00 0.00 0.00 2.85
3699 5401 4.447138 TTTCTCCCACACCATGTTACTT 57.553 40.909 0.00 0.00 0.00 2.24
3701 5403 3.506067 CCTTTTCTCCCACACCATGTTAC 59.494 47.826 0.00 0.00 0.00 2.50
3704 5406 1.780309 TCCTTTTCTCCCACACCATGT 59.220 47.619 0.00 0.00 0.00 3.21
3706 5408 2.348472 TCTCCTTTTCTCCCACACCAT 58.652 47.619 0.00 0.00 0.00 3.55
3710 5412 4.788925 TCTTTTCTCCTTTTCTCCCACA 57.211 40.909 0.00 0.00 0.00 4.17
3711 5413 6.656632 ATTTCTTTTCTCCTTTTCTCCCAC 57.343 37.500 0.00 0.00 0.00 4.61
3712 5414 8.776061 TTTATTTCTTTTCTCCTTTTCTCCCA 57.224 30.769 0.00 0.00 0.00 4.37
3722 6745 7.768582 CCTCTCCTCTCTTTATTTCTTTTCTCC 59.231 40.741 0.00 0.00 0.00 3.71
3723 6746 7.279981 GCCTCTCCTCTCTTTATTTCTTTTCTC 59.720 40.741 0.00 0.00 0.00 2.87
3724 6747 7.109501 GCCTCTCCTCTCTTTATTTCTTTTCT 58.890 38.462 0.00 0.00 0.00 2.52
3725 6748 6.881602 TGCCTCTCCTCTCTTTATTTCTTTTC 59.118 38.462 0.00 0.00 0.00 2.29
3729 6752 4.142049 CGTGCCTCTCCTCTCTTTATTTCT 60.142 45.833 0.00 0.00 0.00 2.52
3741 6764 2.597805 ACGTGTCGTGCCTCTCCT 60.598 61.111 0.00 0.00 39.18 3.69
3768 6795 2.417964 GTGCGCACACAAAAACTTTG 57.582 45.000 34.52 0.00 46.61 2.77
3778 6805 2.717190 CGACAAACGTGCGCACAC 60.717 61.111 37.03 19.47 43.76 3.82
3788 6815 4.651994 GATCACATCCAATCACGACAAAC 58.348 43.478 0.00 0.00 0.00 2.93
3789 6816 3.370672 CGATCACATCCAATCACGACAAA 59.629 43.478 0.00 0.00 0.00 2.83
3792 6819 2.809446 TCGATCACATCCAATCACGAC 58.191 47.619 0.00 0.00 0.00 4.34
3793 6820 3.552890 GGATCGATCACATCCAATCACGA 60.553 47.826 25.93 0.00 39.88 4.35
3794 6821 2.733552 GGATCGATCACATCCAATCACG 59.266 50.000 25.93 0.00 39.88 4.35
3795 6822 3.744942 CAGGATCGATCACATCCAATCAC 59.255 47.826 25.93 4.90 42.28 3.06
3796 6823 3.389002 ACAGGATCGATCACATCCAATCA 59.611 43.478 25.93 0.00 42.28 2.57
3797 6824 3.744942 CACAGGATCGATCACATCCAATC 59.255 47.826 25.93 6.11 42.28 2.67
3800 6827 1.413812 CCACAGGATCGATCACATCCA 59.586 52.381 25.93 0.00 42.28 3.41
3801 6828 1.270518 CCCACAGGATCGATCACATCC 60.271 57.143 25.93 10.79 40.37 3.51
3804 6832 1.264045 TGCCCACAGGATCGATCACA 61.264 55.000 25.93 9.54 33.47 3.58
3823 6851 5.423931 ACAATGGGTAAACTGTTGGAACTTT 59.576 36.000 0.00 0.00 0.00 2.66
3865 6893 5.066505 CCTCAAGTCACAAAACTAAGCAAGT 59.933 40.000 0.00 0.00 41.49 3.16
3877 6905 3.221771 CATTTGGTCCCTCAAGTCACAA 58.778 45.455 0.00 0.00 0.00 3.33
3942 6970 2.812011 AGTATGTTTTGGTCGGTCAAGC 59.188 45.455 0.00 0.00 0.00 4.01
3949 6977 6.954944 TCTGAAGAAAAGTATGTTTTGGTCG 58.045 36.000 0.00 0.00 0.00 4.79
3970 6999 3.320673 AGGACCTCGCTACTTTTTCTG 57.679 47.619 0.00 0.00 0.00 3.02
3978 7309 5.298347 AGCATATTTTAAGGACCTCGCTAC 58.702 41.667 0.00 0.00 0.00 3.58
4047 7398 4.285292 CGATAGCATTTTGAGCAATGTCC 58.715 43.478 0.00 0.00 36.63 4.02
4106 7472 3.173599 CGAACCTGCAAGCAATACAATG 58.826 45.455 0.00 0.00 0.00 2.82
4153 7519 1.399440 CGACAGGAAGAATGGCATGTG 59.601 52.381 0.00 0.00 0.00 3.21
4179 7545 3.012560 GCAGCCGCTGAGGAATATT 57.987 52.632 24.80 0.00 45.00 1.28
4202 7568 2.427540 GATGAGCGCATAGGCCGTCT 62.428 60.000 11.47 0.00 34.11 4.18
4231 7597 1.287815 CACTGACCGCCACGTAGAA 59.712 57.895 0.00 0.00 0.00 2.10
4257 8302 2.360483 AGCTAGATCGATGGAGTGTGTG 59.640 50.000 0.54 0.00 0.00 3.82
4298 8343 9.149225 GATTAGATCCATGCAAAGTGTAGATAG 57.851 37.037 0.00 0.00 0.00 2.08
4299 8344 8.650490 TGATTAGATCCATGCAAAGTGTAGATA 58.350 33.333 0.00 0.00 0.00 1.98
4303 8348 7.774625 TGATTGATTAGATCCATGCAAAGTGTA 59.225 33.333 0.00 0.00 0.00 2.90
4306 8351 7.649533 TTGATTGATTAGATCCATGCAAAGT 57.350 32.000 0.00 0.00 0.00 2.66
4315 8360 7.088905 GGCATCACAATTGATTGATTAGATCC 58.911 38.462 13.59 4.46 40.79 3.36
4320 8365 5.904941 GTGGGCATCACAATTGATTGATTA 58.095 37.500 13.59 0.00 45.39 1.75
4322 8367 4.395959 GTGGGCATCACAATTGATTGAT 57.604 40.909 13.59 9.05 45.39 2.57
4323 8368 3.872511 GTGGGCATCACAATTGATTGA 57.127 42.857 13.59 6.84 45.39 2.57
4353 8398 3.585732 TGACCCTTTTTCTACTAGTGGGG 59.414 47.826 14.80 11.65 37.56 4.96
4354 8399 4.903045 TGACCCTTTTTCTACTAGTGGG 57.097 45.455 5.39 8.16 39.06 4.61
4355 8400 5.178809 CGTTTGACCCTTTTTCTACTAGTGG 59.821 44.000 5.39 1.87 0.00 4.00
4425 8470 1.199097 GTTGGAACCGGCACTAATGTG 59.801 52.381 0.00 0.00 46.37 3.21
4614 8659 1.481772 CGGGTGGACGAAGGGTTTATA 59.518 52.381 0.00 0.00 35.47 0.98
4652 8697 1.007721 CAGAGAGGAGAGGGGAAAGGA 59.992 57.143 0.00 0.00 0.00 3.36


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

AutoCloner maintained by Alex Coulton.