Multiple sequence alignment - TraesCS7A01G545000

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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 TraesCS7A01G545000 chr7A 100.000 5468 0 0 1 5468 721171023 721176490 0.000000e+00 10098.0
1 TraesCS7A01G545000 chr7A 88.656 1525 157 8 1766 3280 721165432 721163914 0.000000e+00 1844.0
2 TraesCS7A01G545000 chr7A 83.651 1101 124 35 3329 4413 721163914 721162854 0.000000e+00 985.0
3 TraesCS7A01G545000 chr7A 86.853 251 21 9 1000 1241 721166166 721165919 2.510000e-68 270.0
4 TraesCS7A01G545000 chr7A 76.763 241 34 16 1509 1736 2008342 2008573 1.240000e-21 115.0
5 TraesCS7A01G545000 chr7A 79.429 175 23 11 1509 1677 3219104 3219271 1.610000e-20 111.0
6 TraesCS7A01G545000 chr7D 93.853 3595 168 30 943 4512 625603019 625606585 0.000000e+00 5365.0
7 TraesCS7A01G545000 chr7D 87.698 2650 269 36 1783 4419 625599301 625596696 0.000000e+00 3035.0
8 TraesCS7A01G545000 chr7D 72.667 1972 436 74 1804 3733 483140434 483142344 1.330000e-155 560.0
9 TraesCS7A01G545000 chr7D 86.623 456 46 9 4678 5132 625607200 625607641 1.770000e-134 490.0
10 TraesCS7A01G545000 chr7D 90.800 250 22 1 5220 5468 625607725 625607974 3.160000e-87 333.0
11 TraesCS7A01G545000 chr7D 92.529 174 10 3 509 679 625602181 625602354 4.230000e-61 246.0
12 TraesCS7A01G545000 chr7D 92.727 165 12 0 5 169 625602485 625602649 7.080000e-59 239.0
13 TraesCS7A01G545000 chr7D 92.903 155 7 1 4512 4662 625606613 625606767 7.130000e-54 222.0
14 TraesCS7A01G545000 chr7D 78.788 231 27 18 1509 1724 3891202 3890979 9.550000e-28 135.0
15 TraesCS7A01G545000 chr7B 94.668 3151 137 18 1373 4505 725524051 725527188 0.000000e+00 4859.0
16 TraesCS7A01G545000 chr7B 86.858 2686 292 40 1766 4418 725519965 725517308 0.000000e+00 2948.0
17 TraesCS7A01G545000 chr7B 88.285 589 36 9 943 1513 725522685 725523258 0.000000e+00 675.0
18 TraesCS7A01G545000 chr7B 87.755 539 56 8 4679 5213 725527769 725528301 6.020000e-174 621.0
19 TraesCS7A01G545000 chr7B 89.643 280 19 5 409 678 725521736 725522015 1.130000e-91 348.0
20 TraesCS7A01G545000 chr7B 89.883 257 15 3 5220 5467 725528336 725528590 2.460000e-83 320.0
21 TraesCS7A01G545000 chr7B 84.980 253 24 11 1000 1241 725520644 725520395 1.520000e-60 244.0
22 TraesCS7A01G545000 chr7B 90.909 165 13 1 5 169 725522147 725522309 2.560000e-53 220.0
23 TraesCS7A01G545000 chr7B 93.750 144 8 1 5326 5468 682385770 682385627 1.190000e-51 215.0
24 TraesCS7A01G545000 chr7B 87.719 171 16 3 244 413 725521331 725521497 1.550000e-45 195.0
25 TraesCS7A01G545000 chr1B 86.955 2660 268 52 1765 4387 30544381 30546998 0.000000e+00 2916.0
26 TraesCS7A01G545000 chr1B 78.995 438 60 17 61 487 30542622 30543038 2.510000e-68 270.0
27 TraesCS7A01G545000 chr1B 73.477 558 122 21 3186 3733 626154405 626154946 2.600000e-43 187.0
28 TraesCS7A01G545000 chr1B 76.902 368 60 15 304 661 30525254 30525606 9.350000e-43 185.0
29 TraesCS7A01G545000 chr1D 87.145 2567 255 44 1781 4315 16610720 16613243 0.000000e+00 2843.0
30 TraesCS7A01G545000 chr1D 80.258 699 89 26 62 727 16609130 16609812 1.070000e-131 481.0
31 TraesCS7A01G545000 chr1A 86.688 2231 250 28 2049 4256 17008893 17011099 0.000000e+00 2431.0
32 TraesCS7A01G545000 chr1A 80.142 705 86 28 60 727 17006732 17007419 1.380000e-130 477.0
33 TraesCS7A01G545000 chr1A 92.562 242 14 2 1771 2008 17008649 17008890 1.460000e-90 344.0
34 TraesCS7A01G545000 chrUn 72.641 1992 435 76 1798 3741 156674884 156676813 4.780000e-155 558.0
35 TraesCS7A01G545000 chr5D 87.190 484 28 12 2552 3035 299063633 299064082 2.260000e-143 520.0
36 TraesCS7A01G545000 chr5D 90.164 61 2 3 4569 4625 422423737 422423797 5.870000e-10 76.8
37 TraesCS7A01G545000 chr4B 72.352 1964 422 81 1827 3737 660353091 660354986 1.760000e-139 507.0


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 TraesCS7A01G545000 chr7A 721171023 721176490 5467 False 10098.000000 10098 100.000000 1 5468 1 chr7A.!!$F3 5467
1 TraesCS7A01G545000 chr7A 721162854 721166166 3312 True 1033.000000 1844 86.386667 1000 4413 3 chr7A.!!$R1 3413
2 TraesCS7A01G545000 chr7D 625596696 625599301 2605 True 3035.000000 3035 87.698000 1783 4419 1 chr7D.!!$R2 2636
3 TraesCS7A01G545000 chr7D 625602181 625607974 5793 False 1149.166667 5365 91.572500 5 5468 6 chr7D.!!$F2 5463
4 TraesCS7A01G545000 chr7D 483140434 483142344 1910 False 560.000000 560 72.667000 1804 3733 1 chr7D.!!$F1 1929
5 TraesCS7A01G545000 chr7B 725517308 725520644 3336 True 1596.000000 2948 85.919000 1000 4418 2 chr7B.!!$R2 3418
6 TraesCS7A01G545000 chr7B 725521331 725528590 7259 False 1034.000000 4859 89.837429 5 5467 7 chr7B.!!$F1 5462
7 TraesCS7A01G545000 chr1B 30542622 30546998 4376 False 1593.000000 2916 82.975000 61 4387 2 chr1B.!!$F3 4326
8 TraesCS7A01G545000 chr1D 16609130 16613243 4113 False 1662.000000 2843 83.701500 62 4315 2 chr1D.!!$F1 4253
9 TraesCS7A01G545000 chr1A 17006732 17011099 4367 False 1084.000000 2431 86.464000 60 4256 3 chr1A.!!$F1 4196
10 TraesCS7A01G545000 chrUn 156674884 156676813 1929 False 558.000000 558 72.641000 1798 3741 1 chrUn.!!$F1 1943
11 TraesCS7A01G545000 chr4B 660353091 660354986 1895 False 507.000000 507 72.352000 1827 3737 1 chr4B.!!$F1 1910

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
519 1077 0.035439 CCAATTCGTGGGTGCTAGGT 60.035 55.0 0.00 0.0 44.64 3.08 F
838 2254 0.100503 GGCCGTGGCACATCATTAAC 59.899 55.0 19.09 0.0 44.52 2.01 F
839 2255 0.100503 GCCGTGGCACATCATTAACC 59.899 55.0 19.09 0.0 44.52 2.85 F
857 2273 0.390860 CCAACGAACCAATTGGCCAA 59.609 50.0 24.79 23.0 39.07 4.52 F
1093 2756 0.464373 CACCACATCCTCCATTCCCG 60.464 60.0 0.00 0.0 0.00 5.14 F
2637 5790 0.462047 CTGCCCGAGGAACATGTACC 60.462 60.0 0.00 0.0 0.00 3.34 F
3686 6860 0.107017 ACTATGCCAAGGCGCAGAAT 60.107 50.0 10.83 0.0 43.26 2.40 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2222 5351 2.352421 CGTCCTCTGCGAAAAGAAGGTA 60.352 50.000 0.00 0.00 0.00 3.08 R
2538 5685 0.107654 AAGAGGCCGGCTTCATACAC 60.108 55.000 36.38 13.98 0.00 2.90 R
2581 5731 1.574702 GCTGCCGCGGAAGTACTTTT 61.575 55.000 33.43 0.00 0.00 2.27 R
2582 5732 2.033194 GCTGCCGCGGAAGTACTTT 61.033 57.895 33.43 0.00 0.00 2.66 R
2993 6158 0.389391 CGCCTTGTATCCTCCATCGT 59.611 55.000 0.00 0.00 0.00 3.73 R
3756 6947 0.165079 GCAATGCAATGCAAGCACAC 59.835 50.000 21.74 8.06 45.95 3.82 R
5156 8955 0.107703 TCTGAATAACGGGGCTGCAG 60.108 55.000 10.11 10.11 0.00 4.41 R

All possible primers

Listed here are all possible primers based on the multiple sequence alignment and SNPs generated previously. A lower penalty score indicates a better primer. If the AutoCloner primers did not work during PCR or sequencing, these could be used as alternatives.

Download all possible primers: (Forward) (Reverse)
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
28 329 2.092753 CACCTCCTTATGGACACTGCAT 60.093 50.000 0.00 0.00 37.46 3.96
38 339 5.876651 ATGGACACTGCATATCTGAAGTA 57.123 39.130 0.00 0.00 39.43 2.24
45 346 8.067751 ACACTGCATATCTGAAGTAAGAGTTA 57.932 34.615 0.00 0.00 39.43 2.24
102 405 1.532505 GCAAGGTGCAGAATATGTGCG 60.533 52.381 5.98 0.00 44.26 5.34
105 408 0.248215 GGTGCAGAATATGTGCGTGC 60.248 55.000 5.98 0.00 44.35 5.34
141 445 4.215613 GGTTACCAAAGTCCTAGCAAACTG 59.784 45.833 0.00 0.00 0.00 3.16
190 494 7.308589 GCGTAGTAAAATTATGAATGCCCATCT 60.309 37.037 0.00 0.00 0.00 2.90
195 499 9.199982 GTAAAATTATGAATGCCCATCTCATTG 57.800 33.333 9.53 0.00 34.59 2.82
216 520 6.566079 TTGATGGATCTGGTCAACTAGATT 57.434 37.500 9.95 0.00 43.04 2.40
228 532 0.108804 ACTAGATTGACGGCACCACG 60.109 55.000 0.00 0.00 40.31 4.94
238 542 1.479323 ACGGCACCACGTAGTATGATT 59.521 47.619 0.00 0.00 46.58 2.57
239 543 2.093869 ACGGCACCACGTAGTATGATTT 60.094 45.455 0.00 0.00 46.58 2.17
240 544 3.130869 ACGGCACCACGTAGTATGATTTA 59.869 43.478 0.00 0.00 46.58 1.40
242 546 4.149922 CGGCACCACGTAGTATGATTTATG 59.850 45.833 0.00 0.00 41.61 1.90
243 547 5.054477 GGCACCACGTAGTATGATTTATGT 58.946 41.667 0.00 0.00 41.61 2.29
244 548 5.176958 GGCACCACGTAGTATGATTTATGTC 59.823 44.000 0.00 0.00 41.61 3.06
245 549 5.751509 GCACCACGTAGTATGATTTATGTCA 59.248 40.000 0.00 0.00 41.61 3.58
351 661 6.686630 TGTTTCCAATGATTTCCATGTGTAC 58.313 36.000 0.00 0.00 35.24 2.90
433 991 3.639094 AGGATGTAGCTAGCGTCAAGATT 59.361 43.478 9.55 0.00 0.00 2.40
462 1020 1.500512 GCACGGTTCGGTTTAGCACA 61.501 55.000 0.00 0.00 0.00 4.57
488 1046 0.994247 TGAGGGAAGTGGCACATGAT 59.006 50.000 21.41 2.45 44.52 2.45
498 1056 6.428159 GGAAGTGGCACATGATTAACCTATAG 59.572 42.308 21.41 0.00 44.52 1.31
506 1064 8.507249 GCACATGATTAACCTATAGACCAATTC 58.493 37.037 0.00 0.00 0.00 2.17
507 1065 8.712363 CACATGATTAACCTATAGACCAATTCG 58.288 37.037 0.00 0.00 0.00 3.34
508 1066 8.429641 ACATGATTAACCTATAGACCAATTCGT 58.570 33.333 0.00 0.00 0.00 3.85
509 1067 8.712363 CATGATTAACCTATAGACCAATTCGTG 58.288 37.037 0.00 0.00 0.00 4.35
519 1077 0.035439 CCAATTCGTGGGTGCTAGGT 60.035 55.000 0.00 0.00 44.64 3.08
523 1081 2.684001 TTCGTGGGTGCTAGGTTATG 57.316 50.000 0.00 0.00 0.00 1.90
530 1098 3.214328 GGGTGCTAGGTTATGTGAATGG 58.786 50.000 0.00 0.00 0.00 3.16
672 1508 6.398095 TCTGAAAGCAAGAATCGATGAACTA 58.602 36.000 0.00 0.00 0.00 2.24
700 1801 1.730902 CTCTCAGTCCACACGCACG 60.731 63.158 0.00 0.00 0.00 5.34
702 1803 1.591594 CTCAGTCCACACGCACGTT 60.592 57.895 0.00 0.00 0.00 3.99
730 1832 2.526304 TCTTTCTCGTTGGACCTGTG 57.474 50.000 0.00 0.00 0.00 3.66
732 1834 0.878523 TTTCTCGTTGGACCTGTGCG 60.879 55.000 0.00 0.00 0.00 5.34
733 1835 3.414700 CTCGTTGGACCTGTGCGC 61.415 66.667 0.00 0.00 0.00 6.09
734 1836 4.228567 TCGTTGGACCTGTGCGCA 62.229 61.111 5.66 5.66 0.00 6.09
735 1837 3.276091 CGTTGGACCTGTGCGCAA 61.276 61.111 14.00 1.19 0.00 4.85
736 1838 2.331451 GTTGGACCTGTGCGCAAC 59.669 61.111 14.00 7.43 0.00 4.17
775 2188 5.511386 AATTGGCCAATTGGTAATTTGGA 57.489 34.783 37.02 4.55 39.36 3.53
784 2200 9.393768 GCCAATTGGTAATTTGGATAGGATCCG 62.394 44.444 25.19 0.00 44.43 4.18
831 2247 2.985282 CAACTGGCCGTGGCACAT 60.985 61.111 19.09 0.00 44.52 3.21
832 2248 2.672996 AACTGGCCGTGGCACATC 60.673 61.111 19.09 7.99 44.52 3.06
833 2249 3.490031 AACTGGCCGTGGCACATCA 62.490 57.895 19.09 10.95 44.52 3.07
834 2250 2.438975 CTGGCCGTGGCACATCAT 60.439 61.111 19.09 0.00 44.52 2.45
835 2251 2.035469 TGGCCGTGGCACATCATT 59.965 55.556 19.09 0.00 44.52 2.57
836 2252 0.747644 CTGGCCGTGGCACATCATTA 60.748 55.000 19.09 0.00 44.52 1.90
837 2253 0.322906 TGGCCGTGGCACATCATTAA 60.323 50.000 19.09 0.00 44.52 1.40
838 2254 0.100503 GGCCGTGGCACATCATTAAC 59.899 55.000 19.09 0.00 44.52 2.01
839 2255 0.100503 GCCGTGGCACATCATTAACC 59.899 55.000 19.09 0.00 44.52 2.85
840 2256 1.458398 CCGTGGCACATCATTAACCA 58.542 50.000 19.09 0.00 44.52 3.67
841 2257 1.815613 CCGTGGCACATCATTAACCAA 59.184 47.619 19.09 0.00 44.52 3.67
842 2258 2.415357 CCGTGGCACATCATTAACCAAC 60.415 50.000 19.09 0.00 44.52 3.77
843 2259 2.727607 CGTGGCACATCATTAACCAACG 60.728 50.000 19.09 0.00 44.52 4.10
844 2260 2.486203 GTGGCACATCATTAACCAACGA 59.514 45.455 13.86 0.00 44.52 3.85
845 2261 3.057876 GTGGCACATCATTAACCAACGAA 60.058 43.478 13.86 0.00 44.52 3.85
846 2262 3.057876 TGGCACATCATTAACCAACGAAC 60.058 43.478 0.00 0.00 0.00 3.95
847 2263 3.498082 GCACATCATTAACCAACGAACC 58.502 45.455 0.00 0.00 0.00 3.62
848 2264 3.057876 GCACATCATTAACCAACGAACCA 60.058 43.478 0.00 0.00 0.00 3.67
849 2265 4.557695 GCACATCATTAACCAACGAACCAA 60.558 41.667 0.00 0.00 0.00 3.67
850 2266 5.708948 CACATCATTAACCAACGAACCAAT 58.291 37.500 0.00 0.00 0.00 3.16
851 2267 6.155827 CACATCATTAACCAACGAACCAATT 58.844 36.000 0.00 0.00 0.00 2.32
852 2268 6.089283 CACATCATTAACCAACGAACCAATTG 59.911 38.462 0.00 0.00 0.00 2.32
855 2271 4.985845 CCAACGAACCAATTGGCC 57.014 55.556 24.79 15.09 39.07 5.36
856 2272 2.045280 CCAACGAACCAATTGGCCA 58.955 52.632 24.79 0.00 39.07 5.36
857 2273 0.390860 CCAACGAACCAATTGGCCAA 59.609 50.000 24.79 23.00 39.07 4.52
858 2274 1.605202 CCAACGAACCAATTGGCCAAG 60.605 52.381 24.94 13.02 39.07 3.61
883 2299 5.353956 TGGCACTGACACATGATTAACATAC 59.646 40.000 0.00 0.00 37.46 2.39
923 2341 3.380320 GGGCGCTTGGTAATTTGAATAGT 59.620 43.478 7.64 0.00 0.00 2.12
924 2342 4.351192 GGCGCTTGGTAATTTGAATAGTG 58.649 43.478 7.64 0.00 0.00 2.74
925 2343 3.791353 GCGCTTGGTAATTTGAATAGTGC 59.209 43.478 0.00 0.00 0.00 4.40
967 2567 5.220815 GCTGGTCTTATCTGAAGCAAGAATG 60.221 44.000 0.00 0.00 30.50 2.67
996 2596 4.968080 ACTTAGCCTCCATCTCTCAATCTT 59.032 41.667 0.00 0.00 0.00 2.40
997 2597 3.842007 AGCCTCCATCTCTCAATCTTG 57.158 47.619 0.00 0.00 0.00 3.02
998 2598 3.113824 AGCCTCCATCTCTCAATCTTGT 58.886 45.455 0.00 0.00 0.00 3.16
1027 2660 1.301677 GCACTGCCTAGCAACACCTC 61.302 60.000 0.00 0.00 38.41 3.85
1028 2661 1.016130 CACTGCCTAGCAACACCTCG 61.016 60.000 0.00 0.00 38.41 4.63
1034 2668 1.066858 CCTAGCAACACCTCGTGACAT 60.067 52.381 0.00 0.00 36.96 3.06
1071 2726 4.699522 GCCCACCGGTCACCACTC 62.700 72.222 2.59 0.00 0.00 3.51
1072 2727 3.238497 CCCACCGGTCACCACTCA 61.238 66.667 2.59 0.00 0.00 3.41
1073 2728 2.030562 CCACCGGTCACCACTCAC 59.969 66.667 2.59 0.00 0.00 3.51
1074 2729 2.030562 CACCGGTCACCACTCACC 59.969 66.667 2.59 0.00 0.00 4.02
1075 2730 2.445085 ACCGGTCACCACTCACCA 60.445 61.111 0.00 0.00 32.33 4.17
1076 2731 2.030562 CCGGTCACCACTCACCAC 59.969 66.667 0.00 0.00 32.33 4.16
1093 2756 0.464373 CACCACATCCTCCATTCCCG 60.464 60.000 0.00 0.00 0.00 5.14
1297 2993 5.109903 CCAAAGTTAGCTTCGCTATAGTGT 58.890 41.667 12.89 0.00 41.01 3.55
1303 2999 6.318144 AGTTAGCTTCGCTATAGTGTCACTAA 59.682 38.462 16.50 14.04 41.01 2.24
1304 3000 5.776173 AGCTTCGCTATAGTGTCACTAAT 57.224 39.130 16.50 8.15 36.99 1.73
1319 3015 3.134081 TCACTAATTAAAGAGCCCTCCCG 59.866 47.826 0.00 0.00 0.00 5.14
1330 3026 1.631898 AGCCCTCCCGTTAAAGCTTTA 59.368 47.619 14.96 14.96 0.00 1.85
1335 3031 4.461431 CCCTCCCGTTAAAGCTTTACATTT 59.539 41.667 18.45 0.00 0.00 2.32
1342 3038 8.077386 CCCGTTAAAGCTTTACATTTTTAGTGA 58.923 33.333 18.45 0.00 0.00 3.41
1452 3148 4.037565 ACCAAAACTTTCTAGGCTTTTCGG 59.962 41.667 0.00 0.00 0.00 4.30
1482 3178 0.746659 GCAGCGGCCCAAATTTCTAT 59.253 50.000 0.00 0.00 0.00 1.98
1491 3187 5.997746 CGGCCCAAATTTCTATCTCATTCTA 59.002 40.000 0.00 0.00 0.00 2.10
1674 4411 9.822185 ATTTTAGAAATGCTAAATGGGCTTTAG 57.178 29.630 0.00 2.73 45.72 1.85
1898 5012 3.903282 GCCCGGACGCGTACCATA 61.903 66.667 17.51 0.00 0.00 2.74
1982 5096 2.648102 GCCGACGTCGTCATCTCG 60.648 66.667 33.49 18.76 37.74 4.04
2231 5360 1.382914 AGGTGCCCCATACCTTCTTT 58.617 50.000 0.00 0.00 46.13 2.52
2251 5380 4.329545 GCAGAGGACGGGGTGCAA 62.330 66.667 0.00 0.00 35.91 4.08
2538 5685 1.066587 GTCTCCTCCATCGAAGGCG 59.933 63.158 0.65 0.00 39.35 5.52
2570 5720 1.617947 GCCTCTTGGACACGAGGGAT 61.618 60.000 21.76 0.00 44.43 3.85
2581 5731 2.121538 CGAGGGATGAGCTGACGGA 61.122 63.158 0.00 0.00 0.00 4.69
2582 5732 1.667154 CGAGGGATGAGCTGACGGAA 61.667 60.000 0.00 0.00 0.00 4.30
2637 5790 0.462047 CTGCCCGAGGAACATGTACC 60.462 60.000 0.00 0.00 0.00 3.34
2666 5819 0.888619 ACATCTTCGACGCCAAGAGA 59.111 50.000 5.40 0.00 33.36 3.10
2740 5905 2.733593 GCTGCCTTCGTCGTCGTT 60.734 61.111 1.33 0.00 38.33 3.85
2893 6058 1.296715 CCAACTTCAGGGACGAGGG 59.703 63.158 0.00 0.00 0.00 4.30
2993 6158 2.616969 GCTCCACAACTTCGAGCAA 58.383 52.632 3.51 0.00 46.63 3.91
3377 6551 1.326213 ACACGATCCCCAGAGAGCTG 61.326 60.000 0.00 0.00 41.93 4.24
3380 6554 0.754957 CGATCCCCAGAGAGCTGTCT 60.755 60.000 7.74 7.74 40.63 3.41
3437 6611 2.202401 GCGGTCTACGTCGTGGTC 60.202 66.667 8.47 2.45 46.52 4.02
3686 6860 0.107017 ACTATGCCAAGGCGCAGAAT 60.107 50.000 10.83 0.00 43.26 2.40
3744 6922 9.344772 AGATGATGATAGGTACGTAATATCTCC 57.655 37.037 21.00 15.49 0.00 3.71
3749 6940 6.217074 TGATAGGTACGTAATATCTCCCCTCT 59.783 42.308 21.00 6.46 0.00 3.69
3756 6947 6.994221 ACGTAATATCTCCCCTCTGTTATTG 58.006 40.000 0.00 0.00 0.00 1.90
3758 6960 6.868864 CGTAATATCTCCCCTCTGTTATTGTG 59.131 42.308 0.00 0.00 0.00 3.33
3859 7103 0.911769 TCGGATCTGCCAACCTCAAT 59.088 50.000 0.00 0.00 35.94 2.57
3937 7181 1.079405 CCGCATCAACACCGGTACT 60.079 57.895 6.87 0.00 37.36 2.73
3985 7229 0.467474 TCCGGATGTCGCTCTGGTAT 60.467 55.000 0.00 0.00 41.67 2.73
4123 7370 2.936032 GACCTCCCAGGCCACCTT 60.936 66.667 5.01 0.00 39.63 3.50
4198 7445 4.508662 GATTCGAATTCTTCCCTGACACT 58.491 43.478 12.81 0.00 0.00 3.55
4334 7592 4.090210 GCACGTCAGCTTTCTTAGTTACTC 59.910 45.833 0.00 0.00 0.00 2.59
4335 7593 4.621886 CACGTCAGCTTTCTTAGTTACTCC 59.378 45.833 0.00 0.00 0.00 3.85
4397 7655 7.795482 TTTTCTGTTAGCTAGTTTGTTAGCA 57.205 32.000 7.66 0.00 46.69 3.49
4407 7665 1.069500 GTTTGTTAGCATGAACCGCGT 60.069 47.619 4.92 0.00 0.00 6.01
4453 7711 2.959357 GAGCAGGCAGTTCACACGC 61.959 63.158 0.00 0.00 0.00 5.34
4483 7741 7.342799 CCCTTTCATGAATAAATGGAGGAAGAA 59.657 37.037 17.85 0.00 35.23 2.52
4484 7742 8.752187 CCTTTCATGAATAAATGGAGGAAGAAA 58.248 33.333 9.40 0.00 35.23 2.52
4536 7822 1.915078 ATAGCTCCGGCCAACAGCTT 61.915 55.000 21.71 9.79 40.77 3.74
4541 7827 0.960364 TCCGGCCAACAGCTTGATTC 60.960 55.000 2.24 0.00 43.05 2.52
4569 7859 0.580104 CCGAACCAAAGTGTCGTGTC 59.420 55.000 0.00 0.00 0.00 3.67
4618 7908 6.496338 AAACCTCGACACTTATTTTGGATC 57.504 37.500 0.00 0.00 0.00 3.36
4621 7911 2.933906 TCGACACTTATTTTGGATCGGC 59.066 45.455 0.00 0.00 0.00 5.54
4626 7916 2.294074 CTTATTTTGGATCGGCGGGAA 58.706 47.619 7.21 0.00 0.00 3.97
4662 7952 2.942376 AGCTGTTGATGTCGTGTTTTGA 59.058 40.909 0.00 0.00 0.00 2.69
4663 7953 3.002656 AGCTGTTGATGTCGTGTTTTGAG 59.997 43.478 0.00 0.00 0.00 3.02
4665 7955 4.518217 CTGTTGATGTCGTGTTTTGAGTC 58.482 43.478 0.00 0.00 0.00 3.36
4666 7956 3.935828 TGTTGATGTCGTGTTTTGAGTCA 59.064 39.130 0.00 0.00 0.00 3.41
4667 7957 4.033932 TGTTGATGTCGTGTTTTGAGTCAG 59.966 41.667 0.00 0.00 0.00 3.51
4668 7958 4.053469 TGATGTCGTGTTTTGAGTCAGA 57.947 40.909 0.00 0.00 0.00 3.27
4669 7959 4.051237 TGATGTCGTGTTTTGAGTCAGAG 58.949 43.478 0.00 0.00 0.00 3.35
4670 7960 3.520290 TGTCGTGTTTTGAGTCAGAGT 57.480 42.857 0.00 0.00 0.00 3.24
4672 7962 4.357142 TGTCGTGTTTTGAGTCAGAGTAC 58.643 43.478 0.00 0.00 0.00 2.73
4673 7963 3.734735 GTCGTGTTTTGAGTCAGAGTACC 59.265 47.826 0.00 0.00 0.00 3.34
4675 7965 4.038763 TCGTGTTTTGAGTCAGAGTACCAT 59.961 41.667 0.00 0.00 0.00 3.55
4676 7966 4.750098 CGTGTTTTGAGTCAGAGTACCATT 59.250 41.667 0.00 0.00 0.00 3.16
4712 8507 1.728971 GTCAGAGTTTGTGCGATGGAG 59.271 52.381 0.00 0.00 0.00 3.86
4720 8515 3.885724 TTGTGCGATGGAGACTGATTA 57.114 42.857 0.00 0.00 0.00 1.75
4726 8521 4.507756 TGCGATGGAGACTGATTATTTTCG 59.492 41.667 0.00 0.00 0.00 3.46
4745 8540 2.350192 TCGCTACAAATACAACATGCCG 59.650 45.455 0.00 0.00 0.00 5.69
4762 8557 8.459635 CAACATGCCGACATAGTACTAGTATAT 58.540 37.037 5.75 0.94 33.67 0.86
4867 8665 5.814705 GTCATCACACCTTATTTCTCTGGAG 59.185 44.000 0.00 0.00 0.00 3.86
4893 8691 4.023707 GGGATTGAAATAGCGATGACCTTG 60.024 45.833 0.00 0.00 0.00 3.61
4907 8705 3.206150 TGACCTTGTTCTCTGCAGAAAC 58.794 45.455 18.85 21.86 40.49 2.78
4938 8736 3.863142 AAGAGATGCAATGTTTCCTGC 57.137 42.857 0.00 0.00 39.09 4.85
4943 8741 0.899717 TGCAATGTTTCCTGCCCTCC 60.900 55.000 0.00 0.00 37.79 4.30
4956 8754 1.376609 GCCCTCCCTGTTATGCAACG 61.377 60.000 0.00 0.00 37.48 4.10
5023 8821 4.813161 ACTTTCAGATATTCAGTGGCATCG 59.187 41.667 0.00 0.00 0.00 3.84
5029 8827 6.870439 TCAGATATTCAGTGGCATCGAATTAG 59.130 38.462 16.39 7.47 31.94 1.73
5066 8864 3.190744 TGCACAACCGAACAACTAAACAA 59.809 39.130 0.00 0.00 0.00 2.83
5074 8872 5.591067 ACCGAACAACTAAACAATTGAGGAA 59.409 36.000 13.59 0.00 0.00 3.36
5075 8873 6.142817 CCGAACAACTAAACAATTGAGGAAG 58.857 40.000 13.59 6.40 0.00 3.46
5076 8874 5.625311 CGAACAACTAAACAATTGAGGAAGC 59.375 40.000 13.59 0.00 0.00 3.86
5077 8875 6.513393 CGAACAACTAAACAATTGAGGAAGCT 60.513 38.462 13.59 0.00 0.00 3.74
5082 8880 6.947464 ACTAAACAATTGAGGAAGCTAGCTA 58.053 36.000 19.70 0.40 0.00 3.32
5100 8898 2.684927 GCTAGGCATTCTGACAACCCAT 60.685 50.000 0.00 0.00 0.00 4.00
5140 8938 0.596577 GCCGAAAGAGTTTGAACCCC 59.403 55.000 0.00 0.00 0.00 4.95
5141 8939 1.975660 CCGAAAGAGTTTGAACCCCA 58.024 50.000 0.00 0.00 0.00 4.96
5143 8941 2.034179 CCGAAAGAGTTTGAACCCCAAC 59.966 50.000 0.00 0.00 33.85 3.77
5156 8955 0.895559 CCCCAACCCTGAAAGCTGAC 60.896 60.000 0.00 0.00 0.00 3.51
5187 8986 5.050490 CCGTTATTCAGAGGATGTTACTGG 58.950 45.833 0.00 0.00 33.19 4.00
5249 9076 4.686191 TGGCAAGTGTGGATTTTCAATT 57.314 36.364 0.00 0.00 0.00 2.32
5281 9116 1.002315 GTCGTTGCCCCCAAGTAAGTA 59.998 52.381 0.00 0.00 0.00 2.24
5356 9192 9.264719 GCTGGACTGTTACTAAACTAAACTAAA 57.735 33.333 0.00 0.00 36.51 1.85
5412 9248 6.531021 AGCCACACTATAAACAACACTACTT 58.469 36.000 0.00 0.00 0.00 2.24
5439 9275 2.279502 GATCTCGTGCTGGCGGTGTA 62.280 60.000 0.00 0.00 0.00 2.90
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
4 5 1.556911 AGTGTCCATAAGGAGGTGCAG 59.443 52.381 0.00 0.00 46.92 4.41
5 6 1.278985 CAGTGTCCATAAGGAGGTGCA 59.721 52.381 0.00 0.00 46.92 4.57
7 8 1.278985 TGCAGTGTCCATAAGGAGGTG 59.721 52.381 0.00 0.00 46.92 4.00
38 339 6.632900 GCTGGAGGCTAAGGTAAATAACTCTT 60.633 42.308 0.00 0.00 38.06 2.85
102 405 3.063588 GGTAACCTAGATTTGCTTCGCAC 59.936 47.826 0.00 0.00 38.71 5.34
105 408 5.411669 ACTTTGGTAACCTAGATTTGCTTCG 59.588 40.000 0.00 0.00 0.00 3.79
119 423 4.215613 CCAGTTTGCTAGGACTTTGGTAAC 59.784 45.833 0.00 0.00 0.00 2.50
141 445 2.225491 TGTGATTACGAGCTGCAAAACC 59.775 45.455 1.02 0.00 0.00 3.27
190 494 4.849813 AGTTGACCAGATCCATCAATGA 57.150 40.909 7.05 0.00 34.98 2.57
195 499 6.166984 TCAATCTAGTTGACCAGATCCATC 57.833 41.667 4.31 0.00 41.79 3.51
206 510 1.621317 TGGTGCCGTCAATCTAGTTGA 59.379 47.619 4.31 4.31 44.36 3.18
207 511 1.732259 GTGGTGCCGTCAATCTAGTTG 59.268 52.381 0.00 0.00 39.25 3.16
216 520 0.171679 CATACTACGTGGTGCCGTCA 59.828 55.000 15.58 0.00 42.00 4.35
221 525 5.751509 TGACATAAATCATACTACGTGGTGC 59.248 40.000 15.58 0.00 0.00 5.01
351 661 4.026886 GCTTGTTTGGCTGTTACTTTTTCG 60.027 41.667 0.00 0.00 0.00 3.46
382 692 9.491675 TCCGACTTGTTACAAATAAAATAGTCA 57.508 29.630 0.00 0.00 30.76 3.41
396 707 5.690857 GCTACATCCTTATCCGACTTGTTAC 59.309 44.000 0.00 0.00 0.00 2.50
400 711 4.592485 AGCTACATCCTTATCCGACTTG 57.408 45.455 0.00 0.00 0.00 3.16
447 1005 0.179200 CGCATGTGCTAAACCGAACC 60.179 55.000 3.25 0.00 39.32 3.62
462 1020 1.599047 CCACTTCCCTCAGTCGCAT 59.401 57.895 0.00 0.00 0.00 4.73
488 1046 5.426185 ACCCACGAATTGGTCTATAGGTTAA 59.574 40.000 0.00 0.00 45.25 2.01
498 1056 1.369625 CTAGCACCCACGAATTGGTC 58.630 55.000 0.00 0.00 45.25 4.02
506 1064 1.206132 TCACATAACCTAGCACCCACG 59.794 52.381 0.00 0.00 0.00 4.94
507 1065 3.343941 TTCACATAACCTAGCACCCAC 57.656 47.619 0.00 0.00 0.00 4.61
508 1066 3.371487 CCATTCACATAACCTAGCACCCA 60.371 47.826 0.00 0.00 0.00 4.51
509 1067 3.214328 CCATTCACATAACCTAGCACCC 58.786 50.000 0.00 0.00 0.00 4.61
510 1068 2.618709 GCCATTCACATAACCTAGCACC 59.381 50.000 0.00 0.00 0.00 5.01
511 1069 3.278574 TGCCATTCACATAACCTAGCAC 58.721 45.455 0.00 0.00 0.00 4.40
513 1071 4.392940 AGATGCCATTCACATAACCTAGC 58.607 43.478 0.00 0.00 0.00 3.42
514 1072 5.641209 GCTAGATGCCATTCACATAACCTAG 59.359 44.000 0.00 0.00 35.15 3.02
515 1073 5.551233 GCTAGATGCCATTCACATAACCTA 58.449 41.667 0.00 0.00 35.15 3.08
516 1074 4.392940 GCTAGATGCCATTCACATAACCT 58.607 43.478 0.00 0.00 35.15 3.50
517 1075 4.756084 GCTAGATGCCATTCACATAACC 57.244 45.455 0.00 0.00 35.15 2.85
645 1294 4.813161 TCATCGATTCTTGCTTTCAGATCC 59.187 41.667 0.00 0.00 0.00 3.36
700 1801 4.676924 CCAACGAGAAAGATGCTTCAAAAC 59.323 41.667 2.07 0.00 0.00 2.43
702 1803 4.024048 GTCCAACGAGAAAGATGCTTCAAA 60.024 41.667 2.07 0.00 0.00 2.69
732 1834 1.663161 GGAAGTGTTGCTAAGCGTTGC 60.663 52.381 0.00 0.00 0.00 4.17
733 1835 1.601903 TGGAAGTGTTGCTAAGCGTTG 59.398 47.619 0.00 0.00 0.00 4.10
734 1836 1.961793 TGGAAGTGTTGCTAAGCGTT 58.038 45.000 0.00 0.00 0.00 4.84
735 1837 1.961793 TTGGAAGTGTTGCTAAGCGT 58.038 45.000 0.00 0.00 0.00 5.07
736 1838 3.236816 CAATTGGAAGTGTTGCTAAGCG 58.763 45.455 0.00 0.00 0.00 4.68
739 2107 2.298729 GGCCAATTGGAAGTGTTGCTAA 59.701 45.455 29.02 0.00 37.39 3.09
773 2186 2.808543 GTGCATTCAACGGATCCTATCC 59.191 50.000 10.75 0.00 46.22 2.59
774 2187 3.496130 CAGTGCATTCAACGGATCCTATC 59.504 47.826 10.75 0.00 0.00 2.08
775 2188 3.470709 CAGTGCATTCAACGGATCCTAT 58.529 45.455 10.75 0.00 0.00 2.57
784 2200 3.242543 CGATTCTAGGCAGTGCATTCAAC 60.243 47.826 18.61 0.00 0.00 3.18
785 2201 2.938451 CGATTCTAGGCAGTGCATTCAA 59.062 45.455 18.61 6.49 0.00 2.69
788 2204 2.169352 AGTCGATTCTAGGCAGTGCATT 59.831 45.455 18.61 7.04 0.00 3.56
819 2235 0.100503 GTTAATGATGTGCCACGGCC 59.899 55.000 5.42 0.00 41.09 6.13
823 2239 2.486203 TCGTTGGTTAATGATGTGCCAC 59.514 45.455 0.00 0.00 0.00 5.01
826 2242 3.057876 TGGTTCGTTGGTTAATGATGTGC 60.058 43.478 0.00 0.00 32.17 4.57
827 2243 4.757799 TGGTTCGTTGGTTAATGATGTG 57.242 40.909 0.00 0.00 32.17 3.21
828 2244 5.975693 ATTGGTTCGTTGGTTAATGATGT 57.024 34.783 0.00 0.00 32.17 3.06
829 2245 5.576384 CCAATTGGTTCGTTGGTTAATGATG 59.424 40.000 16.90 0.00 39.97 3.07
830 2246 5.719173 CCAATTGGTTCGTTGGTTAATGAT 58.281 37.500 16.90 0.00 39.97 2.45
831 2247 4.559704 GCCAATTGGTTCGTTGGTTAATGA 60.560 41.667 25.19 0.00 45.25 2.57
832 2248 3.677596 GCCAATTGGTTCGTTGGTTAATG 59.322 43.478 25.19 0.00 45.25 1.90
833 2249 3.306433 GGCCAATTGGTTCGTTGGTTAAT 60.306 43.478 25.19 0.00 45.25 1.40
834 2250 2.036089 GGCCAATTGGTTCGTTGGTTAA 59.964 45.455 25.19 0.00 45.25 2.01
835 2251 1.614413 GGCCAATTGGTTCGTTGGTTA 59.386 47.619 25.19 0.00 45.25 2.85
836 2252 0.391228 GGCCAATTGGTTCGTTGGTT 59.609 50.000 25.19 0.00 45.25 3.67
837 2253 0.757188 TGGCCAATTGGTTCGTTGGT 60.757 50.000 25.19 0.00 45.25 3.67
838 2254 0.390860 TTGGCCAATTGGTTCGTTGG 59.609 50.000 25.19 0.00 46.03 3.77
839 2255 1.068434 ACTTGGCCAATTGGTTCGTTG 59.932 47.619 25.19 13.04 37.57 4.10
840 2256 1.068434 CACTTGGCCAATTGGTTCGTT 59.932 47.619 24.39 5.36 37.57 3.85
841 2257 0.673437 CACTTGGCCAATTGGTTCGT 59.327 50.000 24.39 12.51 37.57 3.85
842 2258 0.038343 CCACTTGGCCAATTGGTTCG 60.038 55.000 35.47 19.18 36.66 3.95
843 2259 3.912899 CCACTTGGCCAATTGGTTC 57.087 52.632 35.47 17.58 36.66 3.62
854 2270 0.594602 CATGTGTCAGTGCCACTTGG 59.405 55.000 11.26 0.00 35.49 3.61
855 2271 1.596603 TCATGTGTCAGTGCCACTTG 58.403 50.000 12.55 12.55 38.58 3.16
856 2272 2.574006 ATCATGTGTCAGTGCCACTT 57.426 45.000 5.81 0.00 33.92 3.16
857 2273 2.574006 AATCATGTGTCAGTGCCACT 57.426 45.000 5.81 0.00 33.92 4.00
858 2274 3.501828 TGTTAATCATGTGTCAGTGCCAC 59.498 43.478 0.00 0.00 0.00 5.01
923 2341 2.425592 CGTCCACAAGGAGGTGCA 59.574 61.111 0.00 0.00 46.92 4.57
939 2367 2.200067 CTTCAGATAAGACCAGCAGCG 58.800 52.381 0.00 0.00 0.00 5.18
967 2567 3.645687 AGAGATGGAGGCTAAGTTCATCC 59.354 47.826 0.00 0.00 35.98 3.51
998 2598 3.141398 GCTAGGCAGTGCATTTATAGCA 58.859 45.455 18.61 0.00 40.19 3.49
1027 2660 2.094894 GCTTCACTTGGATGATGTCACG 59.905 50.000 0.00 0.00 0.00 4.35
1028 2661 3.076621 TGCTTCACTTGGATGATGTCAC 58.923 45.455 0.00 0.00 0.00 3.67
1034 2668 2.156917 CAAGCTGCTTCACTTGGATGA 58.843 47.619 12.82 0.00 39.67 2.92
1070 2725 1.281867 GAATGGAGGATGTGGTGGTGA 59.718 52.381 0.00 0.00 0.00 4.02
1071 2726 1.683011 GGAATGGAGGATGTGGTGGTG 60.683 57.143 0.00 0.00 0.00 4.17
1072 2727 0.625849 GGAATGGAGGATGTGGTGGT 59.374 55.000 0.00 0.00 0.00 4.16
1073 2728 0.106519 GGGAATGGAGGATGTGGTGG 60.107 60.000 0.00 0.00 0.00 4.61
1074 2729 0.464373 CGGGAATGGAGGATGTGGTG 60.464 60.000 0.00 0.00 0.00 4.17
1075 2730 0.914417 ACGGGAATGGAGGATGTGGT 60.914 55.000 0.00 0.00 0.00 4.16
1076 2731 0.255890 AACGGGAATGGAGGATGTGG 59.744 55.000 0.00 0.00 0.00 4.17
1297 2993 3.134081 CGGGAGGGCTCTTTAATTAGTGA 59.866 47.826 0.00 0.00 0.00 3.41
1303 2999 4.524053 CTTTAACGGGAGGGCTCTTTAAT 58.476 43.478 0.00 0.00 0.00 1.40
1304 3000 3.871074 GCTTTAACGGGAGGGCTCTTTAA 60.871 47.826 0.00 0.00 0.00 1.52
1335 3031 7.761409 AGCAGCATTTTCGATTTATCACTAAA 58.239 30.769 0.00 0.00 0.00 1.85
1342 3038 8.863049 CAAGTTTTAGCAGCATTTTCGATTTAT 58.137 29.630 0.00 0.00 0.00 1.40
1348 3044 3.983344 AGCAAGTTTTAGCAGCATTTTCG 59.017 39.130 0.00 0.00 0.00 3.46
1357 3053 6.151691 CAGCAGAAAATAGCAAGTTTTAGCA 58.848 36.000 14.43 0.00 34.65 3.49
1452 3148 3.470567 CCGCTGCGACGTGACTTC 61.471 66.667 25.45 0.00 0.00 3.01
1672 4409 7.822334 TGTCAAAAACTATAGCAAAGCTAGCTA 59.178 33.333 19.70 19.42 44.66 3.32
1673 4410 6.655003 TGTCAAAAACTATAGCAAAGCTAGCT 59.345 34.615 12.68 12.68 44.66 3.32
1674 4411 6.842163 TGTCAAAAACTATAGCAAAGCTAGC 58.158 36.000 6.62 6.62 44.66 3.42
1675 4412 8.256611 TCTGTCAAAAACTATAGCAAAGCTAG 57.743 34.615 0.00 0.00 44.66 3.42
1676 4413 7.878127 ACTCTGTCAAAAACTATAGCAAAGCTA 59.122 33.333 0.00 0.71 45.55 3.32
1682 4419 6.531594 CGATGACTCTGTCAAAAACTATAGCA 59.468 38.462 4.46 0.00 45.96 3.49
1982 5096 2.897780 GAGCTGCTCGATCATGACC 58.102 57.895 14.68 0.00 0.00 4.02
2222 5351 2.352421 CGTCCTCTGCGAAAAGAAGGTA 60.352 50.000 0.00 0.00 0.00 3.08
2231 5360 3.691342 CACCCCGTCCTCTGCGAA 61.691 66.667 0.00 0.00 0.00 4.70
2441 5570 2.747855 CCGAGGGTTTCCTGCTGC 60.748 66.667 0.00 0.00 45.05 5.25
2538 5685 0.107654 AAGAGGCCGGCTTCATACAC 60.108 55.000 36.38 13.98 0.00 2.90
2570 5720 3.554337 GGAAGTACTTTTCCGTCAGCTCA 60.554 47.826 10.02 0.00 37.48 4.26
2581 5731 1.574702 GCTGCCGCGGAAGTACTTTT 61.575 55.000 33.43 0.00 0.00 2.27
2582 5732 2.033194 GCTGCCGCGGAAGTACTTT 61.033 57.895 33.43 0.00 0.00 2.66
2637 5790 2.286713 CGTCGAAGATGTAGCCTCTGAG 60.287 54.545 0.00 0.00 40.67 3.35
2666 5819 4.091549 TGTAAAAGATGGAGTCGGTAGGT 58.908 43.478 0.00 0.00 0.00 3.08
2893 6058 2.876645 CCTTCTCGAGCGTCGCAC 60.877 66.667 21.09 12.75 40.21 5.34
2960 6125 3.899981 GAGCACGTCCCATGCCACA 62.900 63.158 0.00 0.00 44.53 4.17
2993 6158 0.389391 CGCCTTGTATCCTCCATCGT 59.611 55.000 0.00 0.00 0.00 3.73
3377 6551 3.692101 TCTTCCTCACGATCTTGAGAGAC 59.308 47.826 26.25 0.00 45.19 3.36
3380 6554 3.313803 CGATCTTCCTCACGATCTTGAGA 59.686 47.826 26.25 12.39 45.19 3.27
3437 6611 2.272146 CCTTCCGACCACATGGGG 59.728 66.667 14.08 14.08 42.91 4.96
3654 6828 2.031360 CATAGTCCGTCCCGTCCTC 58.969 63.158 0.00 0.00 0.00 3.71
3686 6860 2.046411 ATCATGAACCGGCGTGCA 60.046 55.556 6.01 0.50 0.00 4.57
3744 6922 2.095059 GCAAGCACACAATAACAGAGGG 60.095 50.000 0.00 0.00 0.00 4.30
3749 6940 3.058450 GCAATGCAAGCACACAATAACA 58.942 40.909 0.00 0.00 0.00 2.41
3756 6947 0.165079 GCAATGCAATGCAAGCACAC 59.835 50.000 21.74 8.06 45.95 3.82
3776 6978 6.427853 TGCATATTAGTTAGCGATCAAGCAAT 59.572 34.615 0.00 0.00 40.15 3.56
3985 7229 2.343758 GTCTTGCCGAGGTGCTCA 59.656 61.111 0.00 0.00 0.00 4.26
4031 7275 1.883084 CCCTCCGCACGCATTCTAC 60.883 63.158 0.00 0.00 0.00 2.59
4123 7370 2.753043 GCGACGGGGTAGGTGAGA 60.753 66.667 0.00 0.00 0.00 3.27
4198 7445 4.069232 CCAAGGACGCGAGCCTGA 62.069 66.667 22.11 0.00 37.62 3.86
4397 7655 4.626225 GCACAAAACGCGGTTCAT 57.374 50.000 11.17 0.00 0.00 2.57
4407 7665 1.462731 AAGGCATGGCTCGCACAAAA 61.463 50.000 23.56 0.00 0.00 2.44
4453 7711 7.342799 TCCTCCATTTATTCATGAAAGGGAAAG 59.657 37.037 13.09 7.32 43.88 2.62
4483 7741 7.882271 AGCTTGAGAGAGTGTTTTCTCATTATT 59.118 33.333 5.16 0.00 46.54 1.40
4484 7742 7.393216 AGCTTGAGAGAGTGTTTTCTCATTAT 58.607 34.615 5.16 0.00 46.54 1.28
4485 7743 6.763355 AGCTTGAGAGAGTGTTTTCTCATTA 58.237 36.000 5.16 0.00 46.54 1.90
4536 7822 2.291996 TGGTTCGGAGGGAGTAGAATCA 60.292 50.000 0.00 0.00 32.07 2.57
4541 7827 1.900486 ACTTTGGTTCGGAGGGAGTAG 59.100 52.381 0.00 0.00 0.00 2.57
4600 7890 2.933906 GCCGATCCAAAATAAGTGTCGA 59.066 45.455 0.00 0.00 0.00 4.20
4618 7908 3.053831 AGATAAATGGTATTCCCGCCG 57.946 47.619 0.00 0.00 35.15 6.46
4621 7911 5.180117 CAGCTGAAGATAAATGGTATTCCCG 59.820 44.000 8.42 0.00 35.15 5.14
4626 7916 7.776969 ACATCAACAGCTGAAGATAAATGGTAT 59.223 33.333 23.35 0.00 37.67 2.73
4662 7952 4.896482 CCCTAGCTAAATGGTACTCTGACT 59.104 45.833 0.00 0.00 0.00 3.41
4663 7953 4.650131 ACCCTAGCTAAATGGTACTCTGAC 59.350 45.833 7.34 0.00 0.00 3.51
4665 7955 5.615925 AACCCTAGCTAAATGGTACTCTG 57.384 43.478 9.10 0.00 0.00 3.35
4666 7956 6.214819 TCAAAACCCTAGCTAAATGGTACTCT 59.785 38.462 9.10 0.00 0.00 3.24
4667 7957 6.412214 TCAAAACCCTAGCTAAATGGTACTC 58.588 40.000 9.10 0.00 0.00 2.59
4668 7958 6.012771 ACTCAAAACCCTAGCTAAATGGTACT 60.013 38.462 9.10 0.00 0.00 2.73
4669 7959 6.178324 ACTCAAAACCCTAGCTAAATGGTAC 58.822 40.000 9.10 0.00 0.00 3.34
4670 7960 6.013206 TGACTCAAAACCCTAGCTAAATGGTA 60.013 38.462 9.10 0.00 0.00 3.25
4672 7962 5.253330 TGACTCAAAACCCTAGCTAAATGG 58.747 41.667 0.00 0.00 0.00 3.16
4673 7963 6.173339 TCTGACTCAAAACCCTAGCTAAATG 58.827 40.000 0.00 0.00 0.00 2.32
4675 7965 5.307196 ACTCTGACTCAAAACCCTAGCTAAA 59.693 40.000 0.00 0.00 0.00 1.85
4676 7966 4.838986 ACTCTGACTCAAAACCCTAGCTAA 59.161 41.667 0.00 0.00 0.00 3.09
4712 8507 9.982291 TTGTATTTGTAGCGAAAATAATCAGTC 57.018 29.630 0.00 0.00 32.71 3.51
4720 8515 5.804979 GGCATGTTGTATTTGTAGCGAAAAT 59.195 36.000 0.00 1.01 0.00 1.82
4726 8521 3.126171 TGTCGGCATGTTGTATTTGTAGC 59.874 43.478 0.00 0.00 0.00 3.58
4808 8606 8.358895 TGCATGTTTTCAGATTTATTTGTGAGA 58.641 29.630 0.00 0.00 0.00 3.27
4809 8607 8.523523 TGCATGTTTTCAGATTTATTTGTGAG 57.476 30.769 0.00 0.00 0.00 3.51
4829 8627 7.709947 AGGTGTGATGACTTATTTAATGCATG 58.290 34.615 0.00 0.00 0.00 4.06
4867 8665 4.214332 GGTCATCGCTATTTCAATCCCTTC 59.786 45.833 0.00 0.00 0.00 3.46
4893 8691 3.790212 GGTAACGTTTCTGCAGAGAAC 57.210 47.619 17.43 20.24 37.97 3.01
4938 8736 0.251916 TCGTTGCATAACAGGGAGGG 59.748 55.000 0.00 0.00 36.58 4.30
4943 8741 5.794687 TTGTAGAATCGTTGCATAACAGG 57.205 39.130 0.00 0.00 36.58 4.00
5014 8812 3.895232 ACTCACTAATTCGATGCCACT 57.105 42.857 0.00 0.00 0.00 4.00
5023 8821 9.529325 TGTGCATATACTGTAACTCACTAATTC 57.471 33.333 0.00 0.00 0.00 2.17
5029 8827 5.005394 CGGTTGTGCATATACTGTAACTCAC 59.995 44.000 0.00 0.00 0.00 3.51
5066 8864 2.402564 TGCCTAGCTAGCTTCCTCAAT 58.597 47.619 24.88 0.00 0.00 2.57
5074 8872 2.392662 TGTCAGAATGCCTAGCTAGCT 58.607 47.619 23.12 23.12 34.76 3.32
5075 8873 2.869192 GTTGTCAGAATGCCTAGCTAGC 59.131 50.000 15.74 6.62 34.76 3.42
5076 8874 3.462021 GGTTGTCAGAATGCCTAGCTAG 58.538 50.000 14.20 14.20 34.76 3.42
5077 8875 2.170607 GGGTTGTCAGAATGCCTAGCTA 59.829 50.000 0.00 0.00 34.76 3.32
5082 8880 1.617804 CCATGGGTTGTCAGAATGCCT 60.618 52.381 2.85 0.00 34.76 4.75
5100 8898 4.154556 GGCAAAGCAAATAACGTACTACCA 59.845 41.667 0.00 0.00 0.00 3.25
5140 8938 0.595095 GCAGTCAGCTTTCAGGGTTG 59.405 55.000 0.00 0.00 41.15 3.77
5141 8939 0.183492 TGCAGTCAGCTTTCAGGGTT 59.817 50.000 0.00 0.00 45.94 4.11
5143 8941 2.552802 CTGCAGTCAGCTTTCAGGG 58.447 57.895 5.25 0.00 45.94 4.45
5156 8955 0.107703 TCTGAATAACGGGGCTGCAG 60.108 55.000 10.11 10.11 0.00 4.41
5213 9012 4.021368 CACTTGCCAAGGTAGTACACTACT 60.021 45.833 16.84 0.51 46.06 2.57
5215 9014 3.899360 ACACTTGCCAAGGTAGTACACTA 59.101 43.478 9.64 0.00 0.00 2.74
5216 9015 2.704065 ACACTTGCCAAGGTAGTACACT 59.296 45.455 9.64 0.00 0.00 3.55
5218 9017 2.224426 CCACACTTGCCAAGGTAGTACA 60.224 50.000 9.64 0.00 0.00 2.90
5234 9061 6.680810 TGACTCATGAATTGAAAATCCACAC 58.319 36.000 0.00 0.00 32.78 3.82
5249 9076 2.143122 GGCAACGACTTTGACTCATGA 58.857 47.619 0.00 0.00 40.58 3.07
5281 9116 6.198237 AGATCTAAGGCTAATGGATGCTTT 57.802 37.500 0.00 0.00 33.25 3.51
5356 9192 8.612619 GCATGCTTTACTAACATATAACAGTGT 58.387 33.333 11.37 0.00 0.00 3.55
5412 9248 0.108472 CAGCACGAGATCTGAAGCCA 60.108 55.000 0.00 0.00 32.26 4.75
5439 9275 4.394712 CGGGCCTTGAAGACCGCT 62.395 66.667 13.59 0.00 39.85 5.52


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

AutoCloner maintained by Alex Coulton.