Multiple sequence alignment - TraesCS7D01G304600

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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 TraesCS7D01G304600 chr7D 100.000 6542 0 0 1 6542 386518414 386511873 0.000000e+00 12081.0
1 TraesCS7D01G304600 chr7D 92.825 1352 37 22 728 2057 617831948 617830635 0.000000e+00 1905.0
2 TraesCS7D01G304600 chr7D 95.735 1149 37 5 2040 3177 617830616 617829469 0.000000e+00 1840.0
3 TraesCS7D01G304600 chr7D 89.189 111 7 3 684 790 511155487 511155378 4.120000e-27 134.0
4 TraesCS7D01G304600 chr7D 89.189 111 7 3 684 790 511157904 511157795 4.120000e-27 134.0
5 TraesCS7D01G304600 chr1D 94.042 2031 85 14 3188 5208 420203917 420205921 0.000000e+00 3048.0
6 TraesCS7D01G304600 chr1D 83.796 1117 108 36 3625 4699 420076558 420077643 0.000000e+00 992.0
7 TraesCS7D01G304600 chr1D 83.865 502 70 10 219 713 483442048 483441551 9.930000e-128 468.0
8 TraesCS7D01G304600 chr1D 91.343 335 28 1 5027 5361 420080144 420080477 2.150000e-124 457.0
9 TraesCS7D01G304600 chr1D 86.189 391 44 9 4959 5347 420077884 420078266 1.310000e-111 414.0
10 TraesCS7D01G304600 chr1D 78.291 433 60 18 3713 4127 421871636 421872052 1.410000e-61 248.0
11 TraesCS7D01G304600 chr1D 84.861 251 30 6 3251 3498 420075730 420075975 5.070000e-61 246.0
12 TraesCS7D01G304600 chr1D 91.034 145 9 2 5191 5333 420205936 420206078 6.690000e-45 193.0
13 TraesCS7D01G304600 chr1D 89.706 136 12 1 5529 5662 420206090 420206225 8.720000e-39 172.0
14 TraesCS7D01G304600 chr1D 90.816 98 9 0 6245 6342 421528539 421528636 1.480000e-26 132.0
15 TraesCS7D01G304600 chr1B 89.766 1456 111 14 4218 5662 567212149 567213577 0.000000e+00 1829.0
16 TraesCS7D01G304600 chr1B 89.002 1273 99 23 3225 4481 567855663 567856910 0.000000e+00 1537.0
17 TraesCS7D01G304600 chr1B 92.575 835 47 9 5718 6542 567969443 567970272 0.000000e+00 1184.0
18 TraesCS7D01G304600 chr1B 86.667 1110 96 22 5383 6468 567856911 567857992 0.000000e+00 1182.0
19 TraesCS7D01G304600 chr1B 91.257 835 60 5 4909 5731 567964531 567965364 0.000000e+00 1125.0
20 TraesCS7D01G304600 chr1B 87.553 474 49 7 3640 4109 567114402 567114869 2.080000e-149 540.0
21 TraesCS7D01G304600 chr1B 82.308 650 63 35 5884 6506 567974576 567975200 3.500000e-142 516.0
22 TraesCS7D01G304600 chr1B 88.832 394 32 3 4732 5115 567115642 567116033 2.130000e-129 473.0
23 TraesCS7D01G304600 chr1B 93.189 323 20 2 3815 4137 567211830 567212150 2.130000e-129 473.0
24 TraesCS7D01G304600 chr1B 89.492 295 26 1 3295 3589 567211234 567211523 1.040000e-97 368.0
25 TraesCS7D01G304600 chr1B 86.072 359 29 10 4332 4672 567114998 567115353 3.730000e-97 366.0
26 TraesCS7D01G304600 chr1B 87.307 323 31 7 5034 5352 567116066 567116382 1.730000e-95 361.0
27 TraesCS7D01G304600 chr1B 84.211 380 47 9 6094 6468 567236919 567237290 2.240000e-94 357.0
28 TraesCS7D01G304600 chr1B 89.163 203 8 2 5737 5925 567236716 567236918 2.360000e-59 241.0
29 TraesCS7D01G304600 chr1B 84.314 255 28 7 3251 3498 567113883 567114132 8.480000e-59 239.0
30 TraesCS7D01G304600 chr1B 80.000 310 48 8 6005 6307 567860049 567860351 3.970000e-52 217.0
31 TraesCS7D01G304600 chr1B 81.443 194 29 5 3624 3814 571694295 571694106 1.140000e-32 152.0
32 TraesCS7D01G304600 chr1B 94.805 77 3 1 3188 3264 567855260 567855335 1.150000e-22 119.0
33 TraesCS7D01G304600 chr1B 98.462 65 0 1 3583 3646 567211779 567211843 5.360000e-21 113.0
34 TraesCS7D01G304600 chr1B 80.180 111 22 0 5552 5662 567119648 567119758 4.200000e-12 84.2
35 TraesCS7D01G304600 chr1A 91.545 1100 72 11 4732 5822 516714385 516715472 0.000000e+00 1496.0
36 TraesCS7D01G304600 chr1A 95.307 618 27 1 3799 4416 516712745 516713360 0.000000e+00 979.0
37 TraesCS7D01G304600 chr1A 88.291 632 56 8 4732 5352 516626629 516627253 0.000000e+00 741.0
38 TraesCS7D01G304600 chr1A 89.002 491 42 9 3625 4110 516624407 516624890 1.210000e-166 597.0
39 TraesCS7D01G304600 chr1A 90.571 350 28 1 3293 3642 516701851 516702195 5.980000e-125 459.0
40 TraesCS7D01G304600 chr1A 89.602 327 27 5 6017 6338 516720685 516721009 6.110000e-110 409.0
41 TraesCS7D01G304600 chr1A 88.757 338 20 7 4410 4737 516714025 516714354 1.320000e-106 398.0
42 TraesCS7D01G304600 chr1A 85.588 340 34 7 4332 4659 516625027 516625363 6.280000e-90 342.0
43 TraesCS7D01G304600 chr1A 84.615 325 36 7 6154 6468 516715723 516716043 1.770000e-80 311.0
44 TraesCS7D01G304600 chr1A 85.668 307 28 7 5027 5332 516661784 516662075 6.370000e-80 309.0
45 TraesCS7D01G304600 chr1A 80.119 337 48 13 3251 3578 516623730 516624056 3.940000e-57 233.0
46 TraesCS7D01G304600 chr1A 80.392 306 31 14 3818 4114 517891843 517892128 8.600000e-49 206.0
47 TraesCS7D01G304600 chr1A 89.441 161 10 5 3647 3807 516708274 516708427 5.180000e-46 196.0
48 TraesCS7D01G304600 chr1A 82.990 194 26 4 3624 3814 518770010 518769821 1.130000e-37 169.0
49 TraesCS7D01G304600 chr1A 85.345 116 16 1 5503 5618 516721579 516721693 1.150000e-22 119.0
50 TraesCS7D01G304600 chr7A 90.909 814 56 7 1252 2050 75358830 75359640 0.000000e+00 1077.0
51 TraesCS7D01G304600 chr7A 93.465 658 38 5 2044 2697 75359669 75360325 0.000000e+00 972.0
52 TraesCS7D01G304600 chr7A 88.339 626 65 7 98 717 2425724 2426347 0.000000e+00 745.0
53 TraesCS7D01G304600 chr7A 88.339 626 65 7 98 717 2460809 2461432 0.000000e+00 745.0
54 TraesCS7D01G304600 chr7A 89.605 481 39 5 2693 3171 75360354 75360825 9.390000e-168 601.0
55 TraesCS7D01G304600 chr3B 90.652 813 59 6 1252 2050 9888580 9887771 0.000000e+00 1064.0
56 TraesCS7D01G304600 chr3B 92.956 653 40 6 2050 2697 9887736 9887085 0.000000e+00 946.0
57 TraesCS7D01G304600 chr3B 87.398 492 47 7 2693 3177 9887056 9886573 9.590000e-153 551.0
58 TraesCS7D01G304600 chr3B 83.268 514 71 14 218 726 688398654 688398151 5.980000e-125 459.0
59 TraesCS7D01G304600 chr6A 90.283 813 62 6 1252 2050 590675437 590674628 0.000000e+00 1048.0
60 TraesCS7D01G304600 chr6A 92.945 652 41 5 2050 2697 590674593 590673943 0.000000e+00 944.0
61 TraesCS7D01G304600 chr6A 87.526 489 49 6 2693 3177 590673914 590673434 7.410000e-154 555.0
62 TraesCS7D01G304600 chr2A 93.865 652 35 5 2050 2697 698197049 698196399 0.000000e+00 977.0
63 TraesCS7D01G304600 chr2A 89.773 616 48 4 1447 2050 698197696 698197084 0.000000e+00 774.0
64 TraesCS7D01G304600 chr2A 84.912 623 67 19 98 713 44439200 44439802 7.260000e-169 604.0
65 TraesCS7D01G304600 chr2A 84.395 628 84 13 93 713 335174938 335175558 7.260000e-169 604.0
66 TraesCS7D01G304600 chr2A 88.139 489 46 6 2693 3177 698196370 698195890 7.360000e-159 571.0
67 TraesCS7D01G304600 chr2A 86.059 373 45 6 351 721 20344586 20344219 1.710000e-105 394.0
68 TraesCS7D01G304600 chr2A 89.493 276 26 2 1690 1965 256890179 256890451 4.860000e-91 346.0
69 TraesCS7D01G304600 chr2A 90.476 63 6 0 2044 2106 257014277 257014339 4.200000e-12 84.2
70 TraesCS7D01G304600 chr2A 95.652 46 2 0 3 48 335174762 335174807 2.530000e-09 75.0
71 TraesCS7D01G304600 chr5A 87.360 625 67 10 101 714 344321989 344321366 0.000000e+00 706.0
72 TraesCS7D01G304600 chr5A 82.883 111 10 3 3061 3171 692544292 692544393 2.510000e-14 91.6
73 TraesCS7D01G304600 chr5A 85.870 92 4 5 3 85 344322421 344322330 9.040000e-14 89.8
74 TraesCS7D01G304600 chr2D 91.185 363 28 4 1690 2050 207480309 207479949 2.120000e-134 490.0
75 TraesCS7D01G304600 chr2D 81.173 324 31 12 787 1108 582555570 582555275 3.940000e-57 233.0
76 TraesCS7D01G304600 chr2D 95.000 60 3 0 2050 2109 207479914 207479855 1.940000e-15 95.3
77 TraesCS7D01G304600 chr4D 82.815 547 76 16 223 759 105231969 105232507 2.130000e-129 473.0
78 TraesCS7D01G304600 chr4D 89.286 112 9 3 3061 3171 499724578 499724687 3.180000e-28 137.0
79 TraesCS7D01G304600 chr4D 89.189 111 11 1 3061 3171 508478467 508478576 3.180000e-28 137.0
80 TraesCS7D01G304600 chr6D 83.034 501 69 14 223 713 43955101 43955595 2.170000e-119 440.0
81 TraesCS7D01G304600 chr6D 80.061 326 33 16 796 1119 379094593 379094298 5.140000e-51 213.0
82 TraesCS7D01G304600 chr6D 89.222 167 12 5 1220 1384 175422276 175422438 3.090000e-48 204.0
83 TraesCS7D01G304600 chr6D 88.288 111 12 1 3061 3171 337762314 337762423 1.480000e-26 132.0
84 TraesCS7D01G304600 chr7B 83.191 351 48 10 713 1058 418200398 418200054 1.770000e-80 311.0
85 TraesCS7D01G304600 chr7B 85.263 95 5 1 1 86 655570100 655570006 9.040000e-14 89.8
86 TraesCS7D01G304600 chr5D 86.842 228 16 5 1399 1612 238665896 238666123 6.550000e-60 243.0
87 TraesCS7D01G304600 chr5D 83.108 148 17 5 6211 6351 382260256 382260110 1.910000e-25 128.0
88 TraesCS7D01G304600 chr5D 81.457 151 18 8 6211 6352 382086685 382086536 1.490000e-21 115.0
89 TraesCS7D01G304600 chr4B 90.854 164 9 5 1223 1384 349109920 349110079 1.430000e-51 215.0
90 TraesCS7D01G304600 chr4B 90.244 164 11 4 1223 1384 240182681 240182841 6.650000e-50 209.0
91 TraesCS7D01G304600 chr5B 89.634 164 11 5 1223 1384 42168222 42168381 3.090000e-48 204.0
92 TraesCS7D01G304600 chr5B 89.634 164 12 4 1223 1384 42188093 42188253 3.090000e-48 204.0
93 TraesCS7D01G304600 chr5B 88.966 145 13 3 91 233 159722275 159722132 6.740000e-40 176.0
94 TraesCS7D01G304600 chr5B 80.337 178 23 11 684 851 2043965 2043790 2.480000e-24 124.0
95 TraesCS7D01G304600 chr5B 86.316 95 4 1 1 86 239338243 239338149 1.940000e-15 95.3
96 TraesCS7D01G304600 chrUn 88.966 145 13 3 91 233 236707580 236707437 6.740000e-40 176.0
97 TraesCS7D01G304600 chrUn 88.966 145 13 3 91 233 478280937 478281080 6.740000e-40 176.0
98 TraesCS7D01G304600 chrUn 86.842 114 7 4 684 790 393326480 393326368 3.200000e-23 121.0
99 TraesCS7D01G304600 chr3A 89.855 138 11 3 98 233 12147194 12147058 2.420000e-39 174.0
100 TraesCS7D01G304600 chr3D 84.211 95 6 1 1 86 120279637 120279543 4.200000e-12 84.2


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 TraesCS7D01G304600 chr7D 386511873 386518414 6541 True 12081.000000 12081 100.000000 1 6542 1 chr7D.!!$R1 6541
1 TraesCS7D01G304600 chr7D 617829469 617831948 2479 True 1872.500000 1905 94.280000 728 3177 2 chr7D.!!$R3 2449
2 TraesCS7D01G304600 chr1D 420203917 420206225 2308 False 1137.666667 3048 91.594000 3188 5662 3 chr1D.!!$F4 2474
3 TraesCS7D01G304600 chr1D 420075730 420080477 4747 False 527.250000 992 86.547250 3251 5361 4 chr1D.!!$F3 2110
4 TraesCS7D01G304600 chr1B 567969443 567970272 829 False 1184.000000 1184 92.575000 5718 6542 1 chr1B.!!$F2 824
5 TraesCS7D01G304600 chr1B 567964531 567965364 833 False 1125.000000 1125 91.257000 4909 5731 1 chr1B.!!$F1 822
6 TraesCS7D01G304600 chr1B 567855260 567860351 5091 False 763.750000 1537 87.618500 3188 6468 4 chr1B.!!$F7 3280
7 TraesCS7D01G304600 chr1B 567211234 567213577 2343 False 695.750000 1829 92.727250 3295 5662 4 chr1B.!!$F5 2367
8 TraesCS7D01G304600 chr1B 567974576 567975200 624 False 516.000000 516 82.308000 5884 6506 1 chr1B.!!$F3 622
9 TraesCS7D01G304600 chr1B 567113883 567119758 5875 False 343.866667 540 85.709667 3251 5662 6 chr1B.!!$F4 2411
10 TraesCS7D01G304600 chr1B 567236716 567237290 574 False 299.000000 357 86.687000 5737 6468 2 chr1B.!!$F6 731
11 TraesCS7D01G304600 chr1A 516712745 516716043 3298 False 796.000000 1496 90.056000 3799 6468 4 chr1A.!!$F6 2669
12 TraesCS7D01G304600 chr1A 516623730 516627253 3523 False 478.250000 741 85.750000 3251 5352 4 chr1A.!!$F5 2101
13 TraesCS7D01G304600 chr1A 516720685 516721693 1008 False 264.000000 409 87.473500 5503 6338 2 chr1A.!!$F7 835
14 TraesCS7D01G304600 chr7A 75358830 75360825 1995 False 883.333333 1077 91.326333 1252 3171 3 chr7A.!!$F3 1919
15 TraesCS7D01G304600 chr7A 2425724 2426347 623 False 745.000000 745 88.339000 98 717 1 chr7A.!!$F1 619
16 TraesCS7D01G304600 chr7A 2460809 2461432 623 False 745.000000 745 88.339000 98 717 1 chr7A.!!$F2 619
17 TraesCS7D01G304600 chr3B 9886573 9888580 2007 True 853.666667 1064 90.335333 1252 3177 3 chr3B.!!$R2 1925
18 TraesCS7D01G304600 chr3B 688398151 688398654 503 True 459.000000 459 83.268000 218 726 1 chr3B.!!$R1 508
19 TraesCS7D01G304600 chr6A 590673434 590675437 2003 True 849.000000 1048 90.251333 1252 3177 3 chr6A.!!$R1 1925
20 TraesCS7D01G304600 chr2A 698195890 698197696 1806 True 774.000000 977 90.592333 1447 3177 3 chr2A.!!$R2 1730
21 TraesCS7D01G304600 chr2A 44439200 44439802 602 False 604.000000 604 84.912000 98 713 1 chr2A.!!$F1 615
22 TraesCS7D01G304600 chr2A 335174762 335175558 796 False 339.500000 604 90.023500 3 713 2 chr2A.!!$F4 710
23 TraesCS7D01G304600 chr5A 344321366 344322421 1055 True 397.900000 706 86.615000 3 714 2 chr5A.!!$R1 711
24 TraesCS7D01G304600 chr4D 105231969 105232507 538 False 473.000000 473 82.815000 223 759 1 chr4D.!!$F1 536

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
974 1327 0.037447 ACTCCTGCTTCCTTTCCAGC 59.963 55.0 0.0 0.0 36.49 4.85 F
1007 1360 0.673956 GAGAAGTTGAGGGGCGGAAC 60.674 60.0 0.0 0.0 0.00 3.62 F
2831 3287 1.108727 CAGCTCCCCTGCACACAAAA 61.109 55.0 0.0 0.0 34.21 2.44 F
3378 4218 0.660005 GATACGCTCGCTCTGCTCTG 60.660 60.0 0.0 0.0 0.00 3.35 F
4532 6777 0.969409 GCATCTTGGGCAGGAGCTTT 60.969 55.0 0.0 0.0 41.70 3.51 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2804 3260 1.692042 CAGGGGAGCTGTGGGAGAT 60.692 63.158 0.00 0.0 0.00 2.75 R
2891 3353 1.961793 TGACCTAACGCTTGCACTTT 58.038 45.000 0.00 0.0 0.00 2.66 R
4664 6917 0.035152 CCACCAAGCATGCCTACTCA 60.035 55.000 15.66 0.0 0.00 3.41 R
4665 6918 0.253044 TCCACCAAGCATGCCTACTC 59.747 55.000 15.66 0.0 0.00 2.59 R
6215 10085 0.108567 GAGGCTCGAACTCTCAACCC 60.109 60.000 0.00 0.0 32.28 4.11 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
85 95 5.357878 TCCGGCTCGACTAGATTAGTTTTAA 59.642 40.000 0.00 0.00 39.59 1.52
86 96 5.458126 CCGGCTCGACTAGATTAGTTTTAAC 59.542 44.000 0.00 0.00 39.59 2.01
88 98 6.696148 CGGCTCGACTAGATTAGTTTTAACAT 59.304 38.462 0.00 0.00 39.59 2.71
89 99 7.306051 CGGCTCGACTAGATTAGTTTTAACATG 60.306 40.741 0.00 0.00 39.59 3.21
90 100 7.042658 GGCTCGACTAGATTAGTTTTAACATGG 60.043 40.741 0.00 0.00 39.59 3.66
91 101 7.516943 GCTCGACTAGATTAGTTTTAACATGGC 60.517 40.741 0.00 0.00 39.59 4.40
96 432 6.335781 AGATTAGTTTTAACATGGCCCCTA 57.664 37.500 0.00 0.00 0.00 3.53
125 461 4.495422 AGCTGTCGAATAACCTGTGTTAG 58.505 43.478 0.00 0.00 40.16 2.34
220 558 7.678837 TGTGATATGCATATGTTGGTCTATGA 58.321 34.615 23.76 0.00 0.00 2.15
260 598 9.646522 ACCAAAGCACCTATAATGATTAGAATT 57.353 29.630 0.00 0.00 0.00 2.17
339 679 2.743636 ATACTGACCACCACAAGTCG 57.256 50.000 0.00 0.00 35.71 4.18
347 687 0.943673 CACCACAAGTCGATGTTGCA 59.056 50.000 9.69 0.00 0.00 4.08
576 927 8.459521 TTTTTATCATTTTGTTAGCACCATCG 57.540 30.769 0.00 0.00 0.00 3.84
669 1021 6.757010 ACAAACCGTATTGCATTGTTACAAAA 59.243 30.769 0.66 0.00 33.52 2.44
670 1022 7.277981 ACAAACCGTATTGCATTGTTACAAAAA 59.722 29.630 0.66 0.00 33.52 1.94
776 1128 1.589716 AAAGCACGGATTGAGGCTGC 61.590 55.000 0.00 0.00 36.58 5.25
779 1131 3.390521 ACGGATTGAGGCTGCCGA 61.391 61.111 13.96 3.85 46.29 5.54
780 1132 2.587194 CGGATTGAGGCTGCCGAG 60.587 66.667 13.96 0.00 46.29 4.63
781 1133 2.586792 GGATTGAGGCTGCCGAGT 59.413 61.111 13.96 0.29 0.00 4.18
790 1142 2.805353 CTGCCGAGTTCACCGTCG 60.805 66.667 0.00 0.00 35.91 5.12
809 1161 0.571197 GCGGCGTTTTTGCGTAAAAA 59.429 45.000 18.44 18.44 41.96 1.94
810 1162 1.190543 GCGGCGTTTTTGCGTAAAAAT 59.809 42.857 23.73 0.00 44.80 1.82
818 1170 5.859648 CGTTTTTGCGTAAAAATCCCTGTAT 59.140 36.000 23.73 0.00 44.80 2.29
821 1173 7.644986 TTTTGCGTAAAAATCCCTGTATTTG 57.355 32.000 9.06 0.00 32.72 2.32
824 1176 7.450124 TGCGTAAAAATCCCTGTATTTGTTA 57.550 32.000 0.00 0.00 0.00 2.41
825 1177 7.306953 TGCGTAAAAATCCCTGTATTTGTTAC 58.693 34.615 0.00 0.00 0.00 2.50
826 1178 7.040617 TGCGTAAAAATCCCTGTATTTGTTACA 60.041 33.333 0.00 0.00 38.50 2.41
906 1259 3.703286 AAACCCTGCGTTTGTAAGAAC 57.297 42.857 0.00 0.00 43.21 3.01
913 1266 1.001048 GCGTTTGTAAGAACCCAACCC 60.001 52.381 0.00 0.00 0.00 4.11
915 1268 2.300433 GTTTGTAAGAACCCAACCCGT 58.700 47.619 0.00 0.00 0.00 5.28
921 1274 0.037734 AGAACCCAACCCGTGATTCC 59.962 55.000 0.00 0.00 0.00 3.01
922 1275 0.037734 GAACCCAACCCGTGATTCCT 59.962 55.000 0.00 0.00 0.00 3.36
923 1276 0.481128 AACCCAACCCGTGATTCCTT 59.519 50.000 0.00 0.00 0.00 3.36
924 1277 0.037734 ACCCAACCCGTGATTCCTTC 59.962 55.000 0.00 0.00 0.00 3.46
925 1278 0.679960 CCCAACCCGTGATTCCTTCC 60.680 60.000 0.00 0.00 0.00 3.46
926 1279 0.328258 CCAACCCGTGATTCCTTCCT 59.672 55.000 0.00 0.00 0.00 3.36
956 1309 5.700832 TCTGTTTCATCTTATCCACACACAC 59.299 40.000 0.00 0.00 0.00 3.82
957 1310 5.620206 TGTTTCATCTTATCCACACACACT 58.380 37.500 0.00 0.00 0.00 3.55
958 1311 5.700832 TGTTTCATCTTATCCACACACACTC 59.299 40.000 0.00 0.00 0.00 3.51
959 1312 4.471904 TCATCTTATCCACACACACTCC 57.528 45.455 0.00 0.00 0.00 3.85
960 1313 4.096681 TCATCTTATCCACACACACTCCT 58.903 43.478 0.00 0.00 0.00 3.69
961 1314 3.961480 TCTTATCCACACACACTCCTG 57.039 47.619 0.00 0.00 0.00 3.86
962 1315 2.028112 TCTTATCCACACACACTCCTGC 60.028 50.000 0.00 0.00 0.00 4.85
963 1316 1.644509 TATCCACACACACTCCTGCT 58.355 50.000 0.00 0.00 0.00 4.24
964 1317 0.767375 ATCCACACACACTCCTGCTT 59.233 50.000 0.00 0.00 0.00 3.91
965 1318 0.106708 TCCACACACACTCCTGCTTC 59.893 55.000 0.00 0.00 0.00 3.86
966 1319 0.886490 CCACACACACTCCTGCTTCC 60.886 60.000 0.00 0.00 0.00 3.46
967 1320 0.107456 CACACACACTCCTGCTTCCT 59.893 55.000 0.00 0.00 0.00 3.36
968 1321 0.839946 ACACACACTCCTGCTTCCTT 59.160 50.000 0.00 0.00 0.00 3.36
969 1322 1.212935 ACACACACTCCTGCTTCCTTT 59.787 47.619 0.00 0.00 0.00 3.11
970 1323 1.876156 CACACACTCCTGCTTCCTTTC 59.124 52.381 0.00 0.00 0.00 2.62
971 1324 1.202818 ACACACTCCTGCTTCCTTTCC 60.203 52.381 0.00 0.00 0.00 3.13
972 1325 1.140312 ACACTCCTGCTTCCTTTCCA 58.860 50.000 0.00 0.00 0.00 3.53
973 1326 1.072965 ACACTCCTGCTTCCTTTCCAG 59.927 52.381 0.00 0.00 0.00 3.86
974 1327 0.037447 ACTCCTGCTTCCTTTCCAGC 59.963 55.000 0.00 0.00 36.49 4.85
975 1328 0.679321 CTCCTGCTTCCTTTCCAGCC 60.679 60.000 0.00 0.00 34.91 4.85
976 1329 1.075482 CCTGCTTCCTTTCCAGCCA 59.925 57.895 0.00 0.00 34.91 4.75
1006 1359 1.677552 GAGAAGTTGAGGGGCGGAA 59.322 57.895 0.00 0.00 0.00 4.30
1007 1360 0.673956 GAGAAGTTGAGGGGCGGAAC 60.674 60.000 0.00 0.00 0.00 3.62
1042 1395 2.691779 GGTCGGAGAGGGAGGGAGA 61.692 68.421 0.00 0.00 36.95 3.71
1110 1467 1.739049 GAGTGGATGAGCGAGGAGG 59.261 63.158 0.00 0.00 0.00 4.30
1214 1571 3.172106 TTCAACTCCGGGGTGGCA 61.172 61.111 8.37 0.00 37.80 4.92
1217 1574 3.175710 AACTCCGGGGTGGCAAGT 61.176 61.111 8.37 0.00 37.80 3.16
1284 1643 1.627297 GCACGGGAGGGAAGGAGAAT 61.627 60.000 0.00 0.00 32.31 2.40
1496 1859 1.203300 CCCCAAAATCCACCCCTTCTT 60.203 52.381 0.00 0.00 0.00 2.52
1636 2010 6.642950 CGGTATGGATCTGACTCTTATGAAAC 59.357 42.308 0.00 0.00 0.00 2.78
1768 2143 6.748132 TGGTGATTCTTTTCAATGAAAGACC 58.252 36.000 8.51 9.37 43.32 3.85
1852 2227 6.769512 ACTGAAGACCAGCAAGTATTTAAGA 58.230 36.000 0.00 0.00 46.81 2.10
1960 2335 2.692557 CCAATGGCCATCGATTAAACCA 59.307 45.455 21.08 1.22 0.00 3.67
2003 2378 6.999272 TGTGGTAACTCTTGCCTATAAAAACA 59.001 34.615 0.00 0.00 36.27 2.83
2046 2457 6.100404 TGCTTCAGGTGAATTTTTGCTTAT 57.900 33.333 0.00 0.00 33.01 1.73
2048 2459 6.158598 GCTTCAGGTGAATTTTTGCTTATCA 58.841 36.000 0.00 0.00 33.01 2.15
2059 2470 9.597999 GAATTTTTGCTTATCATTTGTGGTTTC 57.402 29.630 0.00 0.00 0.00 2.78
2222 2633 1.374560 TGCCCAACCGATAATGAACG 58.625 50.000 0.00 0.00 0.00 3.95
2395 2809 3.071312 TGCTTTGGTCAATTTCTGCCATT 59.929 39.130 0.00 0.00 33.15 3.16
2476 2897 6.220930 TGACACTAAATAATACTCCATCCGC 58.779 40.000 0.00 0.00 0.00 5.54
2538 2959 3.118261 TCTCTTCTTCAGTTGTTGGCTGT 60.118 43.478 0.00 0.00 35.60 4.40
2609 3032 9.696917 AACTTTCTAATTTTGTTCCATGACATC 57.303 29.630 0.00 0.00 0.00 3.06
2804 3260 5.562298 AGCTCTTACCAACTAAGGTTTGA 57.438 39.130 0.00 0.00 43.08 2.69
2827 3283 2.670934 CACAGCTCCCCTGCACAC 60.671 66.667 0.00 0.00 45.78 3.82
2831 3287 1.108727 CAGCTCCCCTGCACACAAAA 61.109 55.000 0.00 0.00 34.21 2.44
2980 3442 4.860907 GCACAATTCTAGATTGTTGGCAAG 59.139 41.667 14.21 6.94 39.94 4.01
2984 3446 7.115378 CACAATTCTAGATTGTTGGCAAGAAAC 59.885 37.037 14.12 11.38 39.94 2.78
2986 3448 5.947228 TCTAGATTGTTGGCAAGAAACTG 57.053 39.130 23.99 15.85 38.10 3.16
3130 3595 9.376075 TCTCACTGAAAGAATATTTGATCTGTC 57.624 33.333 0.00 0.00 37.43 3.51
3173 3638 8.774890 TTATTATTAAGTACTGTCGTTTGCCA 57.225 30.769 0.00 0.00 0.00 4.92
3177 3642 1.623811 AGTACTGTCGTTTGCCATCCT 59.376 47.619 0.00 0.00 0.00 3.24
3178 3643 2.000447 GTACTGTCGTTTGCCATCCTC 59.000 52.381 0.00 0.00 0.00 3.71
3179 3644 0.687354 ACTGTCGTTTGCCATCCTCT 59.313 50.000 0.00 0.00 0.00 3.69
3180 3645 1.072331 ACTGTCGTTTGCCATCCTCTT 59.928 47.619 0.00 0.00 0.00 2.85
3181 3646 1.734465 CTGTCGTTTGCCATCCTCTTC 59.266 52.381 0.00 0.00 0.00 2.87
3182 3647 1.347707 TGTCGTTTGCCATCCTCTTCT 59.652 47.619 0.00 0.00 0.00 2.85
3183 3648 2.565391 TGTCGTTTGCCATCCTCTTCTA 59.435 45.455 0.00 0.00 0.00 2.10
3184 3649 3.197766 TGTCGTTTGCCATCCTCTTCTAT 59.802 43.478 0.00 0.00 0.00 1.98
3185 3650 4.192317 GTCGTTTGCCATCCTCTTCTATT 58.808 43.478 0.00 0.00 0.00 1.73
3186 3651 4.271291 GTCGTTTGCCATCCTCTTCTATTC 59.729 45.833 0.00 0.00 0.00 1.75
3354 4194 3.286694 ATGCCACCTGCGGGAATGT 62.287 57.895 21.41 0.00 45.60 2.71
3376 4216 1.724234 CGATACGCTCGCTCTGCTC 60.724 63.158 0.00 0.00 41.14 4.26
3377 4217 1.652012 GATACGCTCGCTCTGCTCT 59.348 57.895 0.00 0.00 0.00 4.09
3378 4218 0.660005 GATACGCTCGCTCTGCTCTG 60.660 60.000 0.00 0.00 0.00 3.35
3379 4219 2.676016 ATACGCTCGCTCTGCTCTGC 62.676 60.000 0.00 0.00 0.00 4.26
3380 4220 4.495336 CGCTCGCTCTGCTCTGCT 62.495 66.667 0.00 0.00 0.00 4.24
4153 5714 1.068948 TGAGGAATCACCGGGGAAAA 58.931 50.000 12.35 0.00 44.74 2.29
4326 5897 2.159114 TGATCAATGTCGCGGAAGATGA 60.159 45.455 6.13 5.61 0.00 2.92
4396 5967 3.582998 ATGCCATACTGTTGCTGGTAT 57.417 42.857 5.87 4.38 31.49 2.73
4405 5978 5.470047 ACTGTTGCTGGTATAGGTATAGC 57.530 43.478 0.00 0.00 37.23 2.97
4425 6667 1.540267 CGGTTGCACCTCCCAAATAA 58.460 50.000 0.00 0.00 35.66 1.40
4427 6669 2.159254 CGGTTGCACCTCCCAAATAATG 60.159 50.000 0.00 0.00 35.66 1.90
4519 6764 2.629656 GGTGCGCAGTTGGCATCTT 61.630 57.895 12.22 0.00 45.17 2.40
4532 6777 0.969409 GCATCTTGGGCAGGAGCTTT 60.969 55.000 0.00 0.00 41.70 3.51
4636 6889 2.556114 CCTTGCTTTCCCAGATTGAGGT 60.556 50.000 0.00 0.00 0.00 3.85
4641 6894 1.488705 TTCCCAGATTGAGGTGGCGT 61.489 55.000 0.00 0.00 31.85 5.68
4659 6912 2.917933 CGTTTTGGATCTATGGCCTCA 58.082 47.619 3.32 0.00 0.00 3.86
4661 6914 3.251729 CGTTTTGGATCTATGGCCTCATG 59.748 47.826 3.32 0.00 34.96 3.07
4662 6915 2.574006 TTGGATCTATGGCCTCATGC 57.426 50.000 3.32 0.00 40.16 4.06
4663 6916 1.437397 TGGATCTATGGCCTCATGCA 58.563 50.000 3.32 0.00 43.89 3.96
4664 6917 1.990327 TGGATCTATGGCCTCATGCAT 59.010 47.619 3.32 0.00 43.89 3.96
4665 6918 2.290705 TGGATCTATGGCCTCATGCATG 60.291 50.000 21.07 21.07 43.89 4.06
4835 8325 2.310779 TTAGGCTCAGTGGAGTGAGT 57.689 50.000 12.12 0.00 45.07 3.41
4881 8381 2.693074 TGATGACGCCAAGTATCTAGCA 59.307 45.455 0.00 0.00 0.00 3.49
4897 8397 4.096681 TCTAGCAAGAAGAAGGTGGATCA 58.903 43.478 0.00 0.00 0.00 2.92
5002 8502 8.158169 TGTAAGATGCCATCAGAATATTGTTC 57.842 34.615 7.56 0.00 0.00 3.18
5186 8810 4.857130 TGCTCCAGTACTAGTTCTCCTA 57.143 45.455 0.00 0.00 0.00 2.94
5192 8816 6.309357 TCCAGTACTAGTTCTCCTACACAAA 58.691 40.000 0.00 0.00 0.00 2.83
5194 8818 7.039923 TCCAGTACTAGTTCTCCTACACAAAAG 60.040 40.741 0.00 0.00 0.00 2.27
5201 8825 7.009179 AGTTCTCCTACACAAAAGATGATCA 57.991 36.000 0.00 0.00 0.00 2.92
5204 8862 6.768483 TCTCCTACACAAAAGATGATCACAA 58.232 36.000 0.00 0.00 0.00 3.33
5347 9005 7.224297 AGAAATTCTGTGAAGGCTACAGTTAA 58.776 34.615 15.20 5.86 44.49 2.01
5366 9073 6.814644 CAGTTAACTGTAACCGGATGATTACA 59.185 38.462 24.70 11.89 40.55 2.41
5374 9081 6.882140 TGTAACCGGATGATTACAATGTTCTT 59.118 34.615 9.46 0.00 38.13 2.52
5400 9107 7.013178 TGTGATTGCTGACAAGAATTTTACTCA 59.987 33.333 0.00 0.00 39.69 3.41
5437 9144 1.426751 TAAGGTGTTCCCCGTCTTGT 58.573 50.000 0.00 0.00 0.00 3.16
5450 9157 3.044986 CCGTCTTGTTTTTCATGTGCAG 58.955 45.455 0.00 0.00 0.00 4.41
5469 9177 3.375299 GCAGTTTCTGGCCTACTATGTTG 59.625 47.826 3.32 0.00 31.21 3.33
5702 9472 5.688807 CATTGATCTGTCCATTACTCCCTT 58.311 41.667 0.00 0.00 0.00 3.95
5727 9497 5.451039 GTCCCGAATAACTCGTCTTAGATC 58.549 45.833 0.00 0.00 46.65 2.75
5742 9515 8.957466 TCGTCTTAGATCTTTCTAGACAATGAA 58.043 33.333 18.73 0.00 35.88 2.57
6080 9902 5.422666 TCATCCATGATTTGTATTCGTGC 57.577 39.130 0.00 0.00 0.00 5.34
6189 10048 1.056700 AGAGGTGGTGGAGCAGTTGT 61.057 55.000 0.00 0.00 0.00 3.32
6192 10051 0.179018 GGTGGTGGAGCAGTTGTCTT 60.179 55.000 0.00 0.00 0.00 3.01
6215 10085 0.108804 TCGCTAAGAAACGCTCCTGG 60.109 55.000 0.00 0.00 0.00 4.45
6338 10268 0.250467 TGAGCAAGTCTGAACCTGGC 60.250 55.000 0.00 0.00 0.00 4.85
6339 10269 0.957888 GAGCAAGTCTGAACCTGGCC 60.958 60.000 0.00 0.00 0.00 5.36
6340 10270 1.073897 GCAAGTCTGAACCTGGCCT 59.926 57.895 3.32 0.00 0.00 5.19
6341 10271 0.957888 GCAAGTCTGAACCTGGCCTC 60.958 60.000 3.32 0.00 0.00 4.70
6342 10272 0.322008 CAAGTCTGAACCTGGCCTCC 60.322 60.000 3.32 0.00 0.00 4.30
6343 10273 0.474660 AAGTCTGAACCTGGCCTCCT 60.475 55.000 3.32 0.00 0.00 3.69
6344 10274 0.474660 AGTCTGAACCTGGCCTCCTT 60.475 55.000 3.32 0.00 0.00 3.36
6345 10275 0.402121 GTCTGAACCTGGCCTCCTTT 59.598 55.000 3.32 0.00 0.00 3.11
6346 10276 1.149101 TCTGAACCTGGCCTCCTTTT 58.851 50.000 3.32 0.00 0.00 2.27
6347 10277 1.499007 TCTGAACCTGGCCTCCTTTTT 59.501 47.619 3.32 0.00 0.00 1.94
6375 10305 9.816354 TCTTTTCCTTTTTGTTTTGAGATAAGG 57.184 29.630 0.00 0.00 33.61 2.69
6376 10306 9.816354 CTTTTCCTTTTTGTTTTGAGATAAGGA 57.184 29.630 0.00 0.00 38.24 3.36
6492 10473 3.811497 CGATGCTCATTCATGGCTCTTTA 59.189 43.478 0.00 0.00 0.00 1.85
6495 10476 3.887110 TGCTCATTCATGGCTCTTTATGG 59.113 43.478 0.00 0.00 0.00 2.74
6536 10524 1.442526 GGCGCGGTGAGCTAGTACTA 61.443 60.000 8.83 1.89 45.59 1.82
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 1.884235 CCCCTCATAATCCAACTCGC 58.116 55.000 0.00 0.00 0.00 5.03
1 2 1.873903 CGCCCCTCATAATCCAACTCG 60.874 57.143 0.00 0.00 0.00 4.18
59 69 2.219458 CTAATCTAGTCGAGCCGGACA 58.781 52.381 5.05 0.00 39.42 4.02
85 95 2.459555 CTCCAATTTAGGGGCCATGT 57.540 50.000 4.39 0.00 0.00 3.21
91 101 1.209504 TCGACAGCTCCAATTTAGGGG 59.790 52.381 0.00 0.00 0.00 4.79
96 432 4.396166 CAGGTTATTCGACAGCTCCAATTT 59.604 41.667 0.00 0.00 0.00 1.82
125 461 6.738114 TCACAAGATGGATCAAGAAACAAAC 58.262 36.000 0.00 0.00 0.00 2.93
267 605 9.956720 ACATGCATGATTAAAATCTTACTTAGC 57.043 29.630 32.75 0.00 36.39 3.09
324 664 0.756294 ACATCGACTTGTGGTGGTCA 59.244 50.000 0.00 0.00 33.19 4.02
339 679 4.871993 ATTTCTCATCGAGTGCAACATC 57.128 40.909 0.00 0.00 41.43 3.06
571 922 4.201724 GCTGCTCTAAACTTGTAACGATGG 60.202 45.833 0.00 0.00 0.00 3.51
576 927 4.467735 GCTTGCTGCTCTAAACTTGTAAC 58.532 43.478 0.00 0.00 38.95 2.50
636 988 5.690997 TGCAATACGGTTTGTATGAAACA 57.309 34.783 0.00 0.00 43.04 2.83
746 1098 9.268268 CCTCAATCCGTGCTTTACTATTAATTA 57.732 33.333 0.00 0.00 0.00 1.40
748 1100 6.204882 GCCTCAATCCGTGCTTTACTATTAAT 59.795 38.462 0.00 0.00 0.00 1.40
749 1101 5.526111 GCCTCAATCCGTGCTTTACTATTAA 59.474 40.000 0.00 0.00 0.00 1.40
755 1107 1.398390 CAGCCTCAATCCGTGCTTTAC 59.602 52.381 0.00 0.00 30.08 2.01
766 1118 0.674895 GTGAACTCGGCAGCCTCAAT 60.675 55.000 10.54 0.00 0.00 2.57
790 1142 0.571197 TTTTTACGCAAAAACGCCGC 59.429 45.000 2.11 0.00 38.42 6.53
794 1146 4.045783 ACAGGGATTTTTACGCAAAAACG 58.954 39.130 8.41 0.00 44.26 3.60
809 1161 7.093509 GGGTTCAATTGTAACAAATACAGGGAT 60.094 37.037 17.03 0.00 45.00 3.85
810 1162 6.209788 GGGTTCAATTGTAACAAATACAGGGA 59.790 38.462 17.03 0.00 45.00 4.20
818 1170 3.381908 ACTGCGGGTTCAATTGTAACAAA 59.618 39.130 17.03 0.00 0.00 2.83
821 1173 2.095415 GGACTGCGGGTTCAATTGTAAC 60.095 50.000 5.13 8.49 0.00 2.50
824 1176 0.893727 GGGACTGCGGGTTCAATTGT 60.894 55.000 5.13 0.00 0.00 2.71
825 1177 0.609131 AGGGACTGCGGGTTCAATTG 60.609 55.000 0.00 0.00 37.18 2.32
826 1178 0.322546 GAGGGACTGCGGGTTCAATT 60.323 55.000 0.00 0.00 41.55 2.32
895 1248 2.033675 CACGGGTTGGGTTCTTACAAAC 59.966 50.000 0.00 0.00 33.63 2.93
906 1259 0.679960 GGAAGGAATCACGGGTTGGG 60.680 60.000 0.00 0.00 0.00 4.12
913 1266 2.763448 AGAGGAAGAGGAAGGAATCACG 59.237 50.000 0.00 0.00 0.00 4.35
915 1268 3.796111 ACAGAGGAAGAGGAAGGAATCA 58.204 45.455 0.00 0.00 0.00 2.57
921 1274 5.419239 AGATGAAACAGAGGAAGAGGAAG 57.581 43.478 0.00 0.00 0.00 3.46
922 1275 5.832539 AAGATGAAACAGAGGAAGAGGAA 57.167 39.130 0.00 0.00 0.00 3.36
923 1276 6.098982 GGATAAGATGAAACAGAGGAAGAGGA 59.901 42.308 0.00 0.00 0.00 3.71
924 1277 6.126940 TGGATAAGATGAAACAGAGGAAGAGG 60.127 42.308 0.00 0.00 0.00 3.69
925 1278 6.760770 GTGGATAAGATGAAACAGAGGAAGAG 59.239 42.308 0.00 0.00 0.00 2.85
926 1279 6.213397 TGTGGATAAGATGAAACAGAGGAAGA 59.787 38.462 0.00 0.00 0.00 2.87
956 1309 0.679321 GGCTGGAAAGGAAGCAGGAG 60.679 60.000 0.00 0.00 41.36 3.69
957 1310 1.380302 GGCTGGAAAGGAAGCAGGA 59.620 57.895 0.00 0.00 41.36 3.86
958 1311 0.324091 ATGGCTGGAAAGGAAGCAGG 60.324 55.000 0.00 0.00 41.36 4.85
959 1312 0.815734 CATGGCTGGAAAGGAAGCAG 59.184 55.000 0.00 0.00 41.36 4.24
960 1313 0.612732 CCATGGCTGGAAAGGAAGCA 60.613 55.000 0.00 0.00 46.37 3.91
961 1314 1.953231 GCCATGGCTGGAAAGGAAGC 61.953 60.000 29.98 0.00 46.37 3.86
962 1315 1.660560 CGCCATGGCTGGAAAGGAAG 61.661 60.000 33.07 10.74 46.37 3.46
963 1316 1.678635 CGCCATGGCTGGAAAGGAA 60.679 57.895 33.07 0.00 46.37 3.36
964 1317 2.045045 CGCCATGGCTGGAAAGGA 60.045 61.111 33.07 0.00 46.37 3.36
965 1318 3.142838 CCGCCATGGCTGGAAAGG 61.143 66.667 31.65 22.51 46.37 3.11
966 1319 2.045045 TCCGCCATGGCTGGAAAG 60.045 61.111 33.81 20.08 46.37 2.62
967 1320 2.045045 CTCCGCCATGGCTGGAAA 60.045 61.111 34.39 22.02 46.37 3.13
968 1321 4.802051 GCTCCGCCATGGCTGGAA 62.802 66.667 34.39 23.95 46.37 3.53
974 1327 2.937379 CTTCTCCTGCTCCGCCATGG 62.937 65.000 7.63 7.63 40.09 3.66
975 1328 1.523258 CTTCTCCTGCTCCGCCATG 60.523 63.158 0.00 0.00 0.00 3.66
976 1329 1.557269 AACTTCTCCTGCTCCGCCAT 61.557 55.000 0.00 0.00 0.00 4.40
988 1341 0.673956 GTTCCGCCCCTCAACTTCTC 60.674 60.000 0.00 0.00 0.00 2.87
1042 1395 1.977129 ACTTTCTGCTGCTCTCCTTCT 59.023 47.619 0.00 0.00 0.00 2.85
1110 1467 4.168291 CCTCTTCCTCCAGCGCCC 62.168 72.222 2.29 0.00 0.00 6.13
1214 1571 2.105477 TGCTCTCTCAGGAAGCAAACTT 59.895 45.455 0.00 0.00 39.43 2.66
1217 1574 2.936919 TTGCTCTCTCAGGAAGCAAA 57.063 45.000 11.01 0.00 41.65 3.68
1636 2010 2.329379 GCACGTCCTGTCTAAGAAGTG 58.671 52.381 0.00 0.00 42.89 3.16
2046 2457 7.069331 ACAATCTTGTTAGGAAACCACAAATGA 59.931 33.333 0.00 0.00 38.47 2.57
2048 2459 7.360113 ACAATCTTGTTAGGAAACCACAAAT 57.640 32.000 0.00 0.00 38.47 2.32
2329 2740 6.299023 TGTTGACTTGCTGTACACAATAAG 57.701 37.500 10.10 6.69 0.00 1.73
2395 2809 3.565482 GGTCACATTTTCACAGAAGCTCA 59.435 43.478 0.00 0.00 0.00 4.26
2476 2897 8.779354 AAGCTAAAAGGTCTTACATTAGTGAG 57.221 34.615 0.00 0.00 32.96 3.51
2538 2959 5.955488 TGGTTCAAGAAAAATTGTTGACGA 58.045 33.333 2.56 0.00 41.85 4.20
2609 3032 6.434018 TTTTGAATGGAAGGTTGCAAAAAG 57.566 33.333 0.00 0.00 33.78 2.27
2651 3074 9.791801 AAACAAAGGTAAAATTTATTGCCATCT 57.208 25.926 0.00 0.00 37.51 2.90
2804 3260 1.692042 CAGGGGAGCTGTGGGAGAT 60.692 63.158 0.00 0.00 0.00 2.75
2891 3353 1.961793 TGACCTAACGCTTGCACTTT 58.038 45.000 0.00 0.00 0.00 2.66
2980 3442 4.681483 GCATGCAACTAAAACTCCAGTTTC 59.319 41.667 14.21 0.00 46.47 2.78
2984 3446 3.503363 TGAGCATGCAACTAAAACTCCAG 59.497 43.478 21.98 0.00 0.00 3.86
2986 3448 4.479619 CTTGAGCATGCAACTAAAACTCC 58.520 43.478 21.98 0.00 0.00 3.85
3164 3629 4.442706 GAATAGAAGAGGATGGCAAACGA 58.557 43.478 0.00 0.00 0.00 3.85
3171 3636 5.903198 AAGGAAGGAATAGAAGAGGATGG 57.097 43.478 0.00 0.00 0.00 3.51
3173 3638 5.071115 CGGAAAGGAAGGAATAGAAGAGGAT 59.929 44.000 0.00 0.00 0.00 3.24
3177 3642 5.338137 GGAACGGAAAGGAAGGAATAGAAGA 60.338 44.000 0.00 0.00 0.00 2.87
3178 3643 4.876679 GGAACGGAAAGGAAGGAATAGAAG 59.123 45.833 0.00 0.00 0.00 2.85
3179 3644 4.534897 AGGAACGGAAAGGAAGGAATAGAA 59.465 41.667 0.00 0.00 0.00 2.10
3180 3645 4.081087 CAGGAACGGAAAGGAAGGAATAGA 60.081 45.833 0.00 0.00 0.00 1.98
3181 3646 4.081087 TCAGGAACGGAAAGGAAGGAATAG 60.081 45.833 0.00 0.00 0.00 1.73
3182 3647 3.841845 TCAGGAACGGAAAGGAAGGAATA 59.158 43.478 0.00 0.00 0.00 1.75
3183 3648 2.642807 TCAGGAACGGAAAGGAAGGAAT 59.357 45.455 0.00 0.00 0.00 3.01
3184 3649 2.051692 TCAGGAACGGAAAGGAAGGAA 58.948 47.619 0.00 0.00 0.00 3.36
3185 3650 1.724545 TCAGGAACGGAAAGGAAGGA 58.275 50.000 0.00 0.00 0.00 3.36
3186 3651 2.561478 TTCAGGAACGGAAAGGAAGG 57.439 50.000 0.00 0.00 40.01 3.46
3376 4216 0.035725 TCAGCCACCATCTTGAGCAG 60.036 55.000 0.00 0.00 0.00 4.24
3377 4217 0.622136 ATCAGCCACCATCTTGAGCA 59.378 50.000 0.00 0.00 0.00 4.26
3378 4218 1.022735 CATCAGCCACCATCTTGAGC 58.977 55.000 0.00 0.00 0.00 4.26
3379 4219 2.704464 TCATCAGCCACCATCTTGAG 57.296 50.000 0.00 0.00 0.00 3.02
3380 4220 3.349927 CTTTCATCAGCCACCATCTTGA 58.650 45.455 0.00 0.00 0.00 3.02
4153 5714 0.704076 TAACTGGCCTTGGCCATCTT 59.296 50.000 30.78 24.83 39.34 2.40
4326 5897 2.307496 TGGGATGCAAGGAATGTGTT 57.693 45.000 0.00 0.00 0.00 3.32
4425 6667 7.816513 CGATCTACATCAACAGGATATCAACAT 59.183 37.037 4.83 0.00 33.95 2.71
4427 6669 7.371159 TCGATCTACATCAACAGGATATCAAC 58.629 38.462 4.83 0.00 33.95 3.18
4519 6764 0.905357 GACTCTAAAGCTCCTGCCCA 59.095 55.000 0.00 0.00 40.80 5.36
4532 6777 9.435570 AAGCTAAACCTATTCCTTATGACTCTA 57.564 33.333 0.00 0.00 0.00 2.43
4636 6889 1.388547 GCCATAGATCCAAAACGCCA 58.611 50.000 0.00 0.00 0.00 5.69
4641 6894 3.225104 GCATGAGGCCATAGATCCAAAA 58.775 45.455 5.01 0.00 36.11 2.44
4662 6915 1.674441 CACCAAGCATGCCTACTCATG 59.326 52.381 15.66 0.11 44.93 3.07
4663 6916 1.409241 CCACCAAGCATGCCTACTCAT 60.409 52.381 15.66 0.00 0.00 2.90
4664 6917 0.035152 CCACCAAGCATGCCTACTCA 60.035 55.000 15.66 0.00 0.00 3.41
4665 6918 0.253044 TCCACCAAGCATGCCTACTC 59.747 55.000 15.66 0.00 0.00 2.59
4711 7915 3.751175 CAGCTTGGTAAAGACGGATGAAA 59.249 43.478 0.00 0.00 35.19 2.69
4713 7917 2.935238 GCAGCTTGGTAAAGACGGATGA 60.935 50.000 0.00 0.00 35.19 2.92
4714 7918 1.398390 GCAGCTTGGTAAAGACGGATG 59.602 52.381 0.00 0.00 35.19 3.51
4715 7919 1.003118 TGCAGCTTGGTAAAGACGGAT 59.997 47.619 0.00 0.00 35.19 4.18
4835 8325 7.222000 ACTACCGCTTTTCCAAATATTTTCA 57.778 32.000 0.00 0.00 0.00 2.69
4881 8381 1.988107 TGGCTGATCCACCTTCTTCTT 59.012 47.619 3.06 0.00 40.72 2.52
4897 8397 1.764723 TCGTCATGATGAAGGATGGCT 59.235 47.619 15.35 0.00 0.00 4.75
5186 8810 5.047802 GTGGGATTGTGATCATCTTTTGTGT 60.048 40.000 0.00 0.00 33.77 3.72
5192 8816 4.849813 TCAGTGGGATTGTGATCATCTT 57.150 40.909 0.00 0.00 33.77 2.40
5194 8818 3.314635 GCTTCAGTGGGATTGTGATCATC 59.685 47.826 0.00 0.00 33.77 2.92
5201 8825 1.067295 TGGAGCTTCAGTGGGATTGT 58.933 50.000 0.00 0.00 0.00 2.71
5204 8862 1.004044 CTTGTGGAGCTTCAGTGGGAT 59.996 52.381 0.00 0.00 0.00 3.85
5311 8969 9.712305 CCTTCACAGAATTTCTTTCTCTAACTA 57.288 33.333 0.00 0.00 42.98 2.24
5347 9005 5.741011 ACATTGTAATCATCCGGTTACAGT 58.259 37.500 13.26 9.33 40.63 3.55
5366 9073 5.518848 TTGTCAGCAATCACAAGAACATT 57.481 34.783 0.00 0.00 0.00 2.71
5374 9081 7.013178 TGAGTAAAATTCTTGTCAGCAATCACA 59.987 33.333 0.00 0.00 33.65 3.58
5437 9144 3.456280 GCCAGAAACTGCACATGAAAAA 58.544 40.909 0.00 0.00 0.00 1.94
5450 9157 4.631813 CAGTCAACATAGTAGGCCAGAAAC 59.368 45.833 5.01 0.00 0.00 2.78
5469 9177 7.906160 ACATATACTTACGCAACATTTCAGTC 58.094 34.615 0.00 0.00 0.00 3.51
5727 9497 9.757227 CTATTACCTCCTTCATTGTCTAGAAAG 57.243 37.037 0.00 0.00 0.00 2.62
5742 9515 3.467863 AGGCAGTACTCCTATTACCTCCT 59.532 47.826 10.96 0.00 30.79 3.69
6080 9902 9.305925 GCTCTTGTTTCCTGATTTTTATATTGG 57.694 33.333 0.00 0.00 0.00 3.16
6127 9978 0.393077 ACGTCCTTGTAAGCTGCAGT 59.607 50.000 16.64 0.00 0.00 4.40
6189 10048 1.393539 GCGTTTCTTAGCGATGCAAGA 59.606 47.619 0.00 0.00 0.00 3.02
6192 10051 0.999406 GAGCGTTTCTTAGCGATGCA 59.001 50.000 0.00 0.00 38.61 3.96
6215 10085 0.108567 GAGGCTCGAACTCTCAACCC 60.109 60.000 0.00 0.00 32.28 4.11
6312 10199 4.518211 AGGTTCAGACTTGCTCAATTTCAG 59.482 41.667 0.00 0.00 0.00 3.02
6349 10279 9.816354 CCTTATCTCAAAACAAAAAGGAAAAGA 57.184 29.630 0.00 0.00 35.14 2.52
6350 10280 9.816354 TCCTTATCTCAAAACAAAAAGGAAAAG 57.184 29.630 0.00 0.00 38.39 2.27
6355 10285 9.807649 CCATATCCTTATCTCAAAACAAAAAGG 57.192 33.333 0.00 0.00 34.60 3.11
6359 10289 8.748412 CCAACCATATCCTTATCTCAAAACAAA 58.252 33.333 0.00 0.00 0.00 2.83
6360 10290 7.893302 ACCAACCATATCCTTATCTCAAAACAA 59.107 33.333 0.00 0.00 0.00 2.83
6361 10291 7.410174 ACCAACCATATCCTTATCTCAAAACA 58.590 34.615 0.00 0.00 0.00 2.83
6362 10292 7.881775 ACCAACCATATCCTTATCTCAAAAC 57.118 36.000 0.00 0.00 0.00 2.43
6363 10293 7.719633 GCTACCAACCATATCCTTATCTCAAAA 59.280 37.037 0.00 0.00 0.00 2.44
6364 10294 7.072454 AGCTACCAACCATATCCTTATCTCAAA 59.928 37.037 0.00 0.00 0.00 2.69
6365 10295 6.558775 AGCTACCAACCATATCCTTATCTCAA 59.441 38.462 0.00 0.00 0.00 3.02
6366 10296 6.084738 AGCTACCAACCATATCCTTATCTCA 58.915 40.000 0.00 0.00 0.00 3.27
6367 10297 6.351456 GGAGCTACCAACCATATCCTTATCTC 60.351 46.154 0.00 0.00 38.79 2.75
6368 10298 5.485708 GGAGCTACCAACCATATCCTTATCT 59.514 44.000 0.00 0.00 38.79 1.98
6369 10299 5.248477 TGGAGCTACCAACCATATCCTTATC 59.752 44.000 0.00 0.00 46.75 1.75
6370 10300 5.162637 TGGAGCTACCAACCATATCCTTAT 58.837 41.667 0.00 0.00 46.75 1.73
6371 10301 4.562767 TGGAGCTACCAACCATATCCTTA 58.437 43.478 0.00 0.00 46.75 2.69
6372 10302 3.393687 TGGAGCTACCAACCATATCCTT 58.606 45.455 0.00 0.00 46.75 3.36
6373 10303 3.060479 TGGAGCTACCAACCATATCCT 57.940 47.619 0.00 0.00 46.75 3.24
6464 10445 1.027357 ATGAATGAGCATCGGCAACC 58.973 50.000 0.00 0.00 44.61 3.77
6492 10473 1.004745 AGGCGTTGAATGTCCTTCCAT 59.995 47.619 0.00 0.00 32.49 3.41
6495 10476 2.412847 CGAAAGGCGTTGAATGTCCTTC 60.413 50.000 11.61 2.69 37.91 3.46
6519 10503 1.012086 TGTAGTACTAGCTCACCGCG 58.988 55.000 1.87 0.00 45.59 6.46
6520 10504 2.015587 AGTGTAGTACTAGCTCACCGC 58.984 52.381 15.06 5.32 38.04 5.68


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

AutoCloner maintained by Alex Coulton.