Multiple sequence alignment - TraesCS2B01G088400

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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 TraesCS2B01G088400 chr2B 100.000 3319 0 0 1 3319 49908237 49911555 0.000000e+00 6130.0
1 TraesCS2B01G088400 chr2B 92.557 2163 84 23 469 2580 50195570 50193434 0.000000e+00 3031.0
2 TraesCS2B01G088400 chr2B 98.913 552 6 0 2580 3131 49917673 49918224 0.000000e+00 987.0
3 TraesCS2B01G088400 chr2B 98.913 552 6 0 2580 3131 708303754 708304305 0.000000e+00 987.0
4 TraesCS2B01G088400 chr2B 99.432 176 1 0 3144 3319 523165855 523166030 1.490000e-83 320.0
5 TraesCS2B01G088400 chr2B 76.220 328 58 14 917 1236 35124487 35124802 4.430000e-34 156.0
6 TraesCS2B01G088400 chr2B 92.063 63 3 2 398 458 50195665 50195603 1.640000e-13 87.9
7 TraesCS2B01G088400 chr2D 87.037 1890 160 43 469 2309 30456080 30457933 0.000000e+00 2054.0
8 TraesCS2B01G088400 chr2D 77.518 427 63 13 1500 1900 21097356 21097775 3.330000e-55 226.0
9 TraesCS2B01G088400 chr2D 73.162 272 67 6 968 1236 22151186 22151454 3.530000e-15 93.5
10 TraesCS2B01G088400 chr2D 89.474 57 2 2 398 450 30455980 30456036 5.940000e-08 69.4
11 TraesCS2B01G088400 chr2A 90.731 917 71 6 1494 2408 32455854 32456758 0.000000e+00 1210.0
12 TraesCS2B01G088400 chr2A 83.763 1047 70 35 317 1305 32454758 32455762 0.000000e+00 900.0
13 TraesCS2B01G088400 chr2A 92.340 470 33 3 1880 2346 32458748 32459217 0.000000e+00 665.0
14 TraesCS2B01G088400 chr2A 84.259 216 15 10 96 298 32453934 32454143 3.380000e-45 193.0
15 TraesCS2B01G088400 chr2A 100.000 58 0 0 2415 2472 32456886 32456943 1.260000e-19 108.0
16 TraesCS2B01G088400 chr2A 75.566 221 39 10 1020 1236 23967769 23967978 9.800000e-16 95.3
17 TraesCS2B01G088400 chr2A 88.889 54 6 0 2506 2559 23940164 23940111 2.140000e-07 67.6
18 TraesCS2B01G088400 chr1B 99.275 552 4 0 2580 3131 662818219 662817668 0.000000e+00 998.0
19 TraesCS2B01G088400 chr1B 99.432 176 1 0 3144 3319 662798277 662798102 1.490000e-83 320.0
20 TraesCS2B01G088400 chr1B 99.432 176 1 0 3144 3319 677019326 677019501 1.490000e-83 320.0
21 TraesCS2B01G088400 chr1B 99.429 175 1 0 3144 3318 531632323 531632497 5.340000e-83 318.0
22 TraesCS2B01G088400 chr1B 84.127 63 7 2 26 88 16526890 16526831 1.290000e-04 58.4
23 TraesCS2B01G088400 chr5B 99.094 552 5 0 2580 3131 34701969 34701418 0.000000e+00 992.0
24 TraesCS2B01G088400 chr5B 99.094 552 5 0 2580 3131 44171437 44171988 0.000000e+00 992.0
25 TraesCS2B01G088400 chr5B 99.094 552 5 0 2580 3131 404299807 404299256 0.000000e+00 992.0
26 TraesCS2B01G088400 chr5B 99.432 176 1 0 3144 3319 676895396 676895221 1.490000e-83 320.0
27 TraesCS2B01G088400 chr5B 82.353 68 12 0 1175 1242 489575015 489575082 3.580000e-05 60.2
28 TraesCS2B01G088400 chr5B 94.286 35 2 0 2523 2557 84658483 84658517 2.000000e-03 54.7
29 TraesCS2B01G088400 chr7B 98.913 552 6 0 2580 3131 463446555 463447106 0.000000e+00 987.0
30 TraesCS2B01G088400 chr7B 98.913 552 6 0 2580 3131 528323272 528323823 0.000000e+00 987.0
31 TraesCS2B01G088400 chr7B 90.554 307 20 7 867 1173 585518345 585518642 6.670000e-107 398.0
32 TraesCS2B01G088400 chr7B 99.432 176 1 0 3144 3319 150785437 150785262 1.490000e-83 320.0
33 TraesCS2B01G088400 chr7B 99.429 175 1 0 3144 3318 36574874 36575048 5.340000e-83 318.0
34 TraesCS2B01G088400 chr7B 99.429 175 1 0 3144 3318 154383770 154383596 5.340000e-83 318.0
35 TraesCS2B01G088400 chr6B 98.913 552 6 0 2580 3131 692753154 692752603 0.000000e+00 987.0
36 TraesCS2B01G088400 chr1A 93.220 354 24 0 911 1264 211990522 211990169 3.790000e-144 521.0
37 TraesCS2B01G088400 chr4B 99.429 175 1 0 3144 3318 626426746 626426920 5.340000e-83 318.0
38 TraesCS2B01G088400 chr5D 74.830 147 31 6 1099 1242 408219553 408219696 9.940000e-06 62.1
39 TraesCS2B01G088400 chr5D 94.286 35 2 0 2523 2557 75998817 75998851 2.000000e-03 54.7
40 TraesCS2B01G088400 chr5A 94.286 35 2 0 2523 2557 71454603 71454637 2.000000e-03 54.7


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

query scaffold start end length rev.comp avg.bitscore max.bitscore avg.percent.identical query.start query.end num_hsp groupid homo_length
0 TraesCS2B01G088400 chr2B 49908237 49911555 3318 False 6130.00 6130 100.0000 1 3319 1 chr2B.!!$F2 3318
1 TraesCS2B01G088400 chr2B 50193434 50195665 2231 True 1559.45 3031 92.3100 398 2580 2 chr2B.!!$R1 2182
2 TraesCS2B01G088400 chr2B 49917673 49918224 551 False 987.00 987 98.9130 2580 3131 1 chr2B.!!$F3 551
3 TraesCS2B01G088400 chr2B 708303754 708304305 551 False 987.00 987 98.9130 2580 3131 1 chr2B.!!$F5 551
4 TraesCS2B01G088400 chr2D 30455980 30457933 1953 False 1061.70 2054 88.2555 398 2309 2 chr2D.!!$F3 1911
5 TraesCS2B01G088400 chr2A 32453934 32459217 5283 False 615.20 1210 90.2186 96 2472 5 chr2A.!!$F2 2376
6 TraesCS2B01G088400 chr1B 662817668 662818219 551 True 998.00 998 99.2750 2580 3131 1 chr1B.!!$R3 551
7 TraesCS2B01G088400 chr5B 34701418 34701969 551 True 992.00 992 99.0940 2580 3131 1 chr5B.!!$R1 551
8 TraesCS2B01G088400 chr5B 44171437 44171988 551 False 992.00 992 99.0940 2580 3131 1 chr5B.!!$F1 551
9 TraesCS2B01G088400 chr5B 404299256 404299807 551 True 992.00 992 99.0940 2580 3131 1 chr5B.!!$R2 551
10 TraesCS2B01G088400 chr7B 463446555 463447106 551 False 987.00 987 98.9130 2580 3131 1 chr7B.!!$F2 551
11 TraesCS2B01G088400 chr7B 528323272 528323823 551 False 987.00 987 98.9130 2580 3131 1 chr7B.!!$F3 551
12 TraesCS2B01G088400 chr6B 692752603 692753154 551 True 987.00 987 98.9130 2580 3131 1 chr6B.!!$R1 551

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
499 1144 0.036732 CAGCTAACCACTCCCAAGCA 59.963 55.0 0.00 0.00 35.63 3.91 F
574 1219 0.741221 CTTAGTCCAAGGCCAGCGAC 60.741 60.0 5.01 6.77 0.00 5.19 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1695 2406 1.684450 TGTGTCGAGTCAAGGTTAGCA 59.316 47.619 0.0 0.0 0.0 3.49 R
2563 3398 2.162208 CCAACAACTAATGCATCGCTGT 59.838 45.455 0.0 0.0 0.0 4.40 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
17 18 2.659610 AGACAACGAGCCCTCTGC 59.340 61.111 0.00 0.00 41.71 4.26
18 19 2.435059 GACAACGAGCCCTCTGCC 60.435 66.667 0.00 0.00 42.71 4.85
19 20 3.240134 GACAACGAGCCCTCTGCCA 62.240 63.158 0.00 0.00 42.71 4.92
20 21 2.270205 CAACGAGCCCTCTGCCAT 59.730 61.111 0.00 0.00 42.71 4.40
21 22 1.377725 CAACGAGCCCTCTGCCATT 60.378 57.895 0.00 0.00 42.71 3.16
22 23 0.962356 CAACGAGCCCTCTGCCATTT 60.962 55.000 0.00 0.00 42.71 2.32
23 24 0.251341 AACGAGCCCTCTGCCATTTT 60.251 50.000 0.00 0.00 42.71 1.82
24 25 0.251341 ACGAGCCCTCTGCCATTTTT 60.251 50.000 0.00 0.00 42.71 1.94
25 26 0.171903 CGAGCCCTCTGCCATTTTTG 59.828 55.000 0.00 0.00 42.71 2.44
26 27 0.108472 GAGCCCTCTGCCATTTTTGC 60.108 55.000 0.00 0.00 42.71 3.68
27 28 1.078918 GCCCTCTGCCATTTTTGCC 60.079 57.895 0.00 0.00 0.00 4.52
28 29 1.829523 GCCCTCTGCCATTTTTGCCA 61.830 55.000 0.00 0.00 0.00 4.92
29 30 0.906775 CCCTCTGCCATTTTTGCCAT 59.093 50.000 0.00 0.00 0.00 4.40
30 31 1.406341 CCCTCTGCCATTTTTGCCATG 60.406 52.381 0.00 0.00 0.00 3.66
31 32 1.276989 CCTCTGCCATTTTTGCCATGT 59.723 47.619 0.00 0.00 0.00 3.21
32 33 2.496871 CCTCTGCCATTTTTGCCATGTA 59.503 45.455 0.00 0.00 0.00 2.29
33 34 3.514645 CTCTGCCATTTTTGCCATGTAC 58.485 45.455 0.00 0.00 0.00 2.90
34 35 2.233431 TCTGCCATTTTTGCCATGTACC 59.767 45.455 0.00 0.00 0.00 3.34
35 36 1.067283 TGCCATTTTTGCCATGTACCG 60.067 47.619 0.00 0.00 0.00 4.02
36 37 1.639280 CCATTTTTGCCATGTACCGC 58.361 50.000 0.00 0.00 0.00 5.68
37 38 1.639280 CATTTTTGCCATGTACCGCC 58.361 50.000 0.00 0.00 0.00 6.13
38 39 1.067283 CATTTTTGCCATGTACCGCCA 60.067 47.619 0.00 0.00 0.00 5.69
39 40 0.315568 TTTTTGCCATGTACCGCCAC 59.684 50.000 0.00 0.00 0.00 5.01
40 41 1.528292 TTTTGCCATGTACCGCCACC 61.528 55.000 0.00 0.00 0.00 4.61
41 42 4.769063 TGCCATGTACCGCCACCG 62.769 66.667 0.00 0.00 0.00 4.94
43 44 4.467084 CCATGTACCGCCACCGCT 62.467 66.667 0.00 0.00 0.00 5.52
44 45 3.195002 CATGTACCGCCACCGCTG 61.195 66.667 0.00 0.00 0.00 5.18
53 54 4.147449 CCACCGCTGCCGAGATGA 62.147 66.667 0.00 0.00 36.29 2.92
54 55 2.887568 CACCGCTGCCGAGATGAC 60.888 66.667 0.00 0.00 36.29 3.06
55 56 3.381983 ACCGCTGCCGAGATGACA 61.382 61.111 0.00 0.00 36.29 3.58
56 57 2.125552 CCGCTGCCGAGATGACAA 60.126 61.111 0.00 0.00 36.29 3.18
57 58 2.169789 CCGCTGCCGAGATGACAAG 61.170 63.158 0.00 0.00 36.29 3.16
58 59 2.169789 CGCTGCCGAGATGACAAGG 61.170 63.158 0.00 0.00 36.29 3.61
59 60 1.817099 GCTGCCGAGATGACAAGGG 60.817 63.158 0.00 0.00 0.00 3.95
60 61 1.153289 CTGCCGAGATGACAAGGGG 60.153 63.158 0.00 0.00 0.00 4.79
61 62 1.612146 TGCCGAGATGACAAGGGGA 60.612 57.895 0.00 0.00 0.00 4.81
62 63 1.198094 TGCCGAGATGACAAGGGGAA 61.198 55.000 0.00 0.00 0.00 3.97
63 64 0.462759 GCCGAGATGACAAGGGGAAG 60.463 60.000 0.00 0.00 0.00 3.46
64 65 0.179000 CCGAGATGACAAGGGGAAGG 59.821 60.000 0.00 0.00 0.00 3.46
65 66 0.179000 CGAGATGACAAGGGGAAGGG 59.821 60.000 0.00 0.00 0.00 3.95
66 67 0.106967 GAGATGACAAGGGGAAGGGC 60.107 60.000 0.00 0.00 0.00 5.19
67 68 0.846427 AGATGACAAGGGGAAGGGCA 60.846 55.000 0.00 0.00 0.00 5.36
68 69 0.039618 GATGACAAGGGGAAGGGCAA 59.960 55.000 0.00 0.00 0.00 4.52
69 70 0.040204 ATGACAAGGGGAAGGGCAAG 59.960 55.000 0.00 0.00 0.00 4.01
70 71 1.304464 GACAAGGGGAAGGGCAAGG 60.304 63.158 0.00 0.00 0.00 3.61
71 72 2.681421 CAAGGGGAAGGGCAAGGC 60.681 66.667 0.00 0.00 0.00 4.35
72 73 3.192630 AAGGGGAAGGGCAAGGCA 61.193 61.111 0.00 0.00 0.00 4.75
73 74 3.529835 AAGGGGAAGGGCAAGGCAC 62.530 63.158 0.00 0.00 0.00 5.01
93 94 4.436998 CGCCGGTGACTCCTGTCC 62.437 72.222 10.20 0.00 42.28 4.02
94 95 2.997897 GCCGGTGACTCCTGTCCT 60.998 66.667 1.90 0.00 42.28 3.85
111 112 5.282055 TGTCCTATCATGTCATGTCCTTC 57.718 43.478 12.54 2.26 0.00 3.46
117 118 6.996879 CCTATCATGTCATGTCCTTCAATTCT 59.003 38.462 12.54 0.00 0.00 2.40
118 119 6.694877 ATCATGTCATGTCCTTCAATTCTG 57.305 37.500 12.54 0.00 0.00 3.02
119 120 5.563592 TCATGTCATGTCCTTCAATTCTGT 58.436 37.500 12.54 0.00 0.00 3.41
120 121 5.413523 TCATGTCATGTCCTTCAATTCTGTG 59.586 40.000 12.54 0.00 0.00 3.66
126 127 9.764363 GTCATGTCCTTCAATTCTGTGTATATA 57.236 33.333 0.00 0.00 0.00 0.86
168 169 4.577834 CCCTTTTGGTTGTCATACGTTT 57.422 40.909 0.00 0.00 38.10 3.60
233 247 4.744570 TCTACGTATGCTCTTTGTTCCTG 58.255 43.478 0.00 0.00 0.00 3.86
235 249 1.061131 CGTATGCTCTTTGTTCCTGCG 59.939 52.381 0.00 0.00 0.00 5.18
236 250 2.076863 GTATGCTCTTTGTTCCTGCGT 58.923 47.619 0.00 0.00 0.00 5.24
262 276 5.008911 TGCATGAATTCGTATGGATTTGAGG 59.991 40.000 0.00 0.00 0.00 3.86
267 281 1.488812 TCGTATGGATTTGAGGGGTGG 59.511 52.381 0.00 0.00 0.00 4.61
275 289 4.033009 GGATTTGAGGGGTGGAAAATGAT 58.967 43.478 0.00 0.00 0.00 2.45
277 291 3.824001 TTGAGGGGTGGAAAATGATGA 57.176 42.857 0.00 0.00 0.00 2.92
278 292 3.370840 TGAGGGGTGGAAAATGATGAG 57.629 47.619 0.00 0.00 0.00 2.90
279 293 2.918934 TGAGGGGTGGAAAATGATGAGA 59.081 45.455 0.00 0.00 0.00 3.27
286 300 4.695455 GGTGGAAAATGATGAGAAAGACGA 59.305 41.667 0.00 0.00 0.00 4.20
309 354 3.393360 GACAGGGTCCAGGGACAG 58.607 66.667 19.43 11.09 46.20 3.51
310 355 2.203998 ACAGGGTCCAGGGACAGG 60.204 66.667 19.43 10.46 46.20 4.00
315 360 3.017581 GTCCAGGGACAGGGCCAT 61.018 66.667 13.49 0.00 44.02 4.40
352 962 3.881688 ACGGTAGATGCTCTTGTACGTAT 59.118 43.478 0.00 0.00 0.00 3.06
361 971 8.982685 AGATGCTCTTGTACGTATCAAAATATG 58.017 33.333 0.00 0.00 0.00 1.78
362 972 6.943981 TGCTCTTGTACGTATCAAAATATGC 58.056 36.000 0.00 6.11 0.00 3.14
368 978 7.835634 TGTACGTATCAAAATATGCTGACAA 57.164 32.000 0.00 0.00 0.00 3.18
385 995 1.352352 ACAAGCCTTGTGTGCCTCTAT 59.648 47.619 9.77 0.00 43.48 1.98
386 996 1.741706 CAAGCCTTGTGTGCCTCTATG 59.258 52.381 0.00 0.00 0.00 2.23
389 999 2.169352 AGCCTTGTGTGCCTCTATGTAG 59.831 50.000 0.00 0.00 0.00 2.74
395 1005 4.286707 TGTGTGCCTCTATGTAGTGGTAT 58.713 43.478 9.24 0.00 38.78 2.73
443 1057 2.663119 GTGCACCAATTCAAAGCGAATC 59.337 45.455 5.22 0.00 43.83 2.52
445 1059 3.755905 TGCACCAATTCAAAGCGAATCTA 59.244 39.130 0.00 0.00 43.83 1.98
452 1067 7.040409 ACCAATTCAAAGCGAATCTAAACTCTT 60.040 33.333 0.00 0.00 43.83 2.85
484 1124 2.568623 ACATTTCTTTCCCGTCAGCT 57.431 45.000 0.00 0.00 0.00 4.24
499 1144 0.036732 CAGCTAACCACTCCCAAGCA 59.963 55.000 0.00 0.00 35.63 3.91
519 1164 2.500183 GAAGAACTTGCGCGCCACTC 62.500 60.000 30.77 19.03 0.00 3.51
533 1178 1.479323 GCCACTCCACCGTATCACTTA 59.521 52.381 0.00 0.00 0.00 2.24
534 1179 2.737679 GCCACTCCACCGTATCACTTAC 60.738 54.545 0.00 0.00 0.00 2.34
536 1181 3.181489 CCACTCCACCGTATCACTTACTC 60.181 52.174 0.00 0.00 0.00 2.59
537 1182 3.022406 ACTCCACCGTATCACTTACTCC 58.978 50.000 0.00 0.00 0.00 3.85
540 1185 5.057843 TCCACCGTATCACTTACTCCTAT 57.942 43.478 0.00 0.00 0.00 2.57
541 1186 6.183361 ACTCCACCGTATCACTTACTCCTATA 60.183 42.308 0.00 0.00 0.00 1.31
542 1187 6.000219 TCCACCGTATCACTTACTCCTATAC 59.000 44.000 0.00 0.00 0.00 1.47
543 1188 6.002704 CCACCGTATCACTTACTCCTATACT 58.997 44.000 0.00 0.00 0.00 2.12
545 1190 7.361127 CACCGTATCACTTACTCCTATACTTG 58.639 42.308 0.00 0.00 0.00 3.16
547 1192 7.943447 ACCGTATCACTTACTCCTATACTTGAT 59.057 37.037 0.00 0.00 0.00 2.57
574 1219 0.741221 CTTAGTCCAAGGCCAGCGAC 60.741 60.000 5.01 6.77 0.00 5.19
575 1220 1.192146 TTAGTCCAAGGCCAGCGACT 61.192 55.000 18.92 18.92 38.97 4.18
576 1221 1.888436 TAGTCCAAGGCCAGCGACTG 61.888 60.000 22.16 4.06 36.31 3.51
577 1222 4.704833 TCCAAGGCCAGCGACTGC 62.705 66.667 5.01 0.00 43.24 4.40
583 1228 4.521062 GCCAGCGACTGCCGAGAT 62.521 66.667 0.00 0.00 44.31 2.75
584 1229 2.279120 CCAGCGACTGCCGAGATC 60.279 66.667 0.00 0.00 44.31 2.75
585 1230 2.491621 CAGCGACTGCCGAGATCA 59.508 61.111 0.00 0.00 44.31 2.92
586 1231 1.875813 CAGCGACTGCCGAGATCAC 60.876 63.158 0.00 0.00 44.31 3.06
587 1232 2.049185 AGCGACTGCCGAGATCACT 61.049 57.895 0.00 0.00 44.31 3.41
588 1233 1.587613 GCGACTGCCGAGATCACTC 60.588 63.158 0.00 0.00 41.76 3.51
621 1273 1.002990 CAGCTCACCATGGACAGCA 60.003 57.895 29.52 7.34 34.08 4.41
704 1368 3.751246 CACGCCAACCCCATGCTG 61.751 66.667 0.00 0.00 0.00 4.41
778 1442 2.973899 CCACGTCCTCTCCACCAG 59.026 66.667 0.00 0.00 0.00 4.00
780 1444 3.374402 ACGTCCTCTCCACCAGCG 61.374 66.667 0.00 0.00 0.00 5.18
909 1608 3.745803 GACGACGGCGAGGAACCT 61.746 66.667 22.49 0.00 41.64 3.50
913 1612 2.915659 ACGGCGAGGAACCTGTCA 60.916 61.111 16.62 0.00 0.00 3.58
1894 2605 1.271926 ACAGGGCCACAGGTATGAAAC 60.272 52.381 6.18 0.00 0.00 2.78
1908 2620 7.446013 ACAGGTATGAAACGAACCAAATTTCTA 59.554 33.333 0.00 0.00 35.64 2.10
1917 2629 7.499321 ACGAACCAAATTTCTACACATACAA 57.501 32.000 0.00 0.00 0.00 2.41
1930 2642 7.564793 TCTACACATACAACAATAAGGCTGAT 58.435 34.615 0.00 0.00 0.00 2.90
1973 2685 5.745294 ACAATGAATAAAAGCTAAGCATGCG 59.255 36.000 13.01 0.00 35.28 4.73
2106 2818 2.735478 CGACCGCCGCAAAGTACA 60.735 61.111 0.00 0.00 0.00 2.90
2117 2829 1.725641 CAAAGTACATGGAGAGCGCA 58.274 50.000 11.47 0.00 0.00 6.09
2392 3106 6.530534 CGACTCTATTGTTGTAAAATCCGAGT 59.469 38.462 0.00 0.00 33.85 4.18
2472 3307 6.096705 TGAATTTTGTGATGTTCTCCTGTGTT 59.903 34.615 0.00 0.00 0.00 3.32
2513 3348 7.155655 TGAACATGAATAAGTGCATGCTTTA 57.844 32.000 20.33 16.91 44.30 1.85
3131 5242 5.746307 TCATCATAATGAGCTCAAAGTGC 57.254 39.130 22.50 0.00 36.98 4.40
3132 5243 5.187687 TCATCATAATGAGCTCAAAGTGCA 58.812 37.500 22.50 9.59 36.98 4.57
3133 5244 5.826208 TCATCATAATGAGCTCAAAGTGCAT 59.174 36.000 22.50 11.18 36.98 3.96
3134 5245 5.746307 TCATAATGAGCTCAAAGTGCATC 57.254 39.130 22.50 0.00 0.00 3.91
3135 5246 5.187687 TCATAATGAGCTCAAAGTGCATCA 58.812 37.500 22.50 1.05 0.00 3.07
3136 5247 5.826208 TCATAATGAGCTCAAAGTGCATCAT 59.174 36.000 22.50 0.00 33.31 2.45
3139 5250 2.745821 TGAGCTCAAAGTGCATCATCAC 59.254 45.455 15.67 0.00 37.24 3.06
3142 5253 2.726989 GCTCAAAGTGCATCATCACACG 60.727 50.000 0.00 0.00 41.72 4.49
3143 5254 1.805943 TCAAAGTGCATCATCACACGG 59.194 47.619 0.00 0.00 41.72 4.94
3144 5255 1.805943 CAAAGTGCATCATCACACGGA 59.194 47.619 0.00 0.00 41.72 4.69
3146 5257 1.945387 AGTGCATCATCACACGGATC 58.055 50.000 0.00 0.00 41.72 3.36
3147 5258 0.578683 GTGCATCATCACACGGATCG 59.421 55.000 0.00 0.00 36.97 3.69
3148 5259 0.459489 TGCATCATCACACGGATCGA 59.541 50.000 0.00 0.00 32.57 3.59
3151 5262 2.389059 CATCATCACACGGATCGAGTC 58.611 52.381 0.00 0.00 32.57 3.36
3152 5263 1.751437 TCATCACACGGATCGAGTCT 58.249 50.000 0.00 0.00 32.57 3.24
3153 5264 1.671328 TCATCACACGGATCGAGTCTC 59.329 52.381 0.00 0.00 32.57 3.36
3155 5266 1.062685 CACACGGATCGAGTCTCGG 59.937 63.158 21.63 8.41 40.88 4.63
3156 5267 2.113433 ACACGGATCGAGTCTCGGG 61.113 63.158 21.63 11.23 40.88 5.14
3157 5268 3.210528 ACGGATCGAGTCTCGGGC 61.211 66.667 21.63 13.40 40.88 6.13
3158 5269 3.209812 CGGATCGAGTCTCGGGCA 61.210 66.667 21.63 3.43 40.88 5.36
3161 5272 1.668101 GGATCGAGTCTCGGGCAAGT 61.668 60.000 21.63 2.22 40.88 3.16
3162 5273 1.022735 GATCGAGTCTCGGGCAAGTA 58.977 55.000 21.63 1.13 40.88 2.24
3163 5274 1.404391 GATCGAGTCTCGGGCAAGTAA 59.596 52.381 21.63 0.37 40.88 2.24
3164 5275 0.524862 TCGAGTCTCGGGCAAGTAAC 59.475 55.000 21.63 0.00 40.88 2.50
3165 5276 0.242825 CGAGTCTCGGGCAAGTAACA 59.757 55.000 14.68 0.00 36.00 2.41
3167 5278 2.098607 CGAGTCTCGGGCAAGTAACATA 59.901 50.000 14.68 0.00 36.00 2.29
3169 5280 2.167900 AGTCTCGGGCAAGTAACATACC 59.832 50.000 0.00 0.00 0.00 2.73
3170 5281 1.135527 TCTCGGGCAAGTAACATACCG 59.864 52.381 0.00 0.00 42.45 4.02
3171 5282 0.896923 TCGGGCAAGTAACATACCGT 59.103 50.000 0.00 0.00 41.82 4.83
3172 5283 1.135024 TCGGGCAAGTAACATACCGTC 60.135 52.381 0.00 0.00 41.82 4.79
3173 5284 1.134907 CGGGCAAGTAACATACCGTCT 60.135 52.381 0.00 0.00 36.78 4.18
3175 5286 2.093869 GGGCAAGTAACATACCGTCTGA 60.094 50.000 0.00 0.00 0.00 3.27
3176 5287 2.928116 GGCAAGTAACATACCGTCTGAC 59.072 50.000 0.00 0.00 0.00 3.51
3177 5288 3.581755 GCAAGTAACATACCGTCTGACA 58.418 45.455 8.73 0.00 0.00 3.58
3178 5289 3.991773 GCAAGTAACATACCGTCTGACAA 59.008 43.478 8.73 0.00 0.00 3.18
3179 5290 4.449743 GCAAGTAACATACCGTCTGACAAA 59.550 41.667 8.73 0.00 0.00 2.83
3180 5291 5.389516 GCAAGTAACATACCGTCTGACAAAG 60.390 44.000 8.73 0.00 0.00 2.77
3184 5295 2.635915 ACATACCGTCTGACAAAGGGAA 59.364 45.455 8.73 0.00 0.00 3.97
3185 5296 3.263425 ACATACCGTCTGACAAAGGGAAT 59.737 43.478 8.73 0.00 0.00 3.01
3186 5297 4.468510 ACATACCGTCTGACAAAGGGAATA 59.531 41.667 8.73 0.00 0.00 1.75
3187 5298 3.611766 ACCGTCTGACAAAGGGAATAG 57.388 47.619 8.73 0.00 0.00 1.73
3188 5299 2.904434 ACCGTCTGACAAAGGGAATAGT 59.096 45.455 8.73 0.00 0.00 2.12
3189 5300 4.091549 ACCGTCTGACAAAGGGAATAGTA 58.908 43.478 8.73 0.00 0.00 1.82
3191 5302 5.895534 ACCGTCTGACAAAGGGAATAGTATA 59.104 40.000 8.73 0.00 0.00 1.47
3192 5303 6.183360 ACCGTCTGACAAAGGGAATAGTATAC 60.183 42.308 8.73 0.00 0.00 1.47
3193 5304 5.913514 CGTCTGACAAAGGGAATAGTATACG 59.086 44.000 8.73 0.00 0.00 3.06
3194 5305 6.214399 GTCTGACAAAGGGAATAGTATACGG 58.786 44.000 2.24 0.00 0.00 4.02
3195 5306 5.303589 TCTGACAAAGGGAATAGTATACGGG 59.696 44.000 0.00 0.00 0.00 5.28
3196 5307 4.345837 TGACAAAGGGAATAGTATACGGGG 59.654 45.833 0.00 0.00 0.00 5.73
3197 5308 4.301205 ACAAAGGGAATAGTATACGGGGT 58.699 43.478 0.00 0.00 0.00 4.95
3200 5311 2.636403 AGGGAATAGTATACGGGGTTGC 59.364 50.000 0.00 0.00 0.00 4.17
3201 5312 2.636403 GGGAATAGTATACGGGGTTGCT 59.364 50.000 0.00 0.00 0.00 3.91
3202 5313 3.072038 GGGAATAGTATACGGGGTTGCTT 59.928 47.826 0.00 0.00 0.00 3.91
3203 5314 4.062991 GGAATAGTATACGGGGTTGCTTG 58.937 47.826 0.00 0.00 0.00 4.01
3207 5318 3.805207 AGTATACGGGGTTGCTTGAATC 58.195 45.455 0.00 0.00 0.00 2.52
3208 5319 2.052782 ATACGGGGTTGCTTGAATCC 57.947 50.000 0.00 0.00 33.39 3.01
3209 5320 0.988832 TACGGGGTTGCTTGAATCCT 59.011 50.000 0.00 0.00 34.80 3.24
3211 5322 1.369091 CGGGGTTGCTTGAATCCTCG 61.369 60.000 0.00 0.00 34.80 4.63
3212 5323 0.035439 GGGGTTGCTTGAATCCTCGA 60.035 55.000 0.00 0.00 34.80 4.04
3214 5325 1.610624 GGGTTGCTTGAATCCTCGACA 60.611 52.381 0.00 0.00 31.10 4.35
3215 5326 2.359900 GGTTGCTTGAATCCTCGACAT 58.640 47.619 0.00 0.00 0.00 3.06
3216 5327 2.352960 GGTTGCTTGAATCCTCGACATC 59.647 50.000 0.00 0.00 0.00 3.06
3219 5330 1.590238 GCTTGAATCCTCGACATCGTG 59.410 52.381 0.54 0.00 40.80 4.35
3225 5336 3.741029 CCTCGACATCGTGGTTCAT 57.259 52.632 13.02 0.00 45.02 2.57
3226 5337 1.560923 CCTCGACATCGTGGTTCATC 58.439 55.000 13.02 0.00 45.02 2.92
3227 5338 1.560923 CTCGACATCGTGGTTCATCC 58.439 55.000 0.54 0.00 40.80 3.51
3228 5339 0.179148 TCGACATCGTGGTTCATCCG 60.179 55.000 0.54 0.00 40.80 4.18
3229 5340 0.179148 CGACATCGTGGTTCATCCGA 60.179 55.000 0.00 0.00 39.52 4.55
3230 5341 1.536072 CGACATCGTGGTTCATCCGAT 60.536 52.381 0.00 0.00 41.64 4.18
3233 5344 2.515926 ATCGTGGTTCATCCGATGAG 57.484 50.000 10.91 0.32 40.94 2.90
3235 5346 2.031870 TCGTGGTTCATCCGATGAGAT 58.968 47.619 10.91 0.00 40.94 2.75
3237 5348 2.223805 CGTGGTTCATCCGATGAGATCA 60.224 50.000 10.91 8.28 40.94 2.92
3238 5349 3.553715 CGTGGTTCATCCGATGAGATCAT 60.554 47.826 10.91 0.00 40.94 2.45
3239 5350 3.993081 GTGGTTCATCCGATGAGATCATC 59.007 47.826 10.91 11.98 46.93 2.92
3250 5361 5.895636 GATGAGATCATCGAGGAGTATGT 57.104 43.478 5.80 0.00 42.66 2.29
3251 5362 5.639757 GATGAGATCATCGAGGAGTATGTG 58.360 45.833 5.80 0.00 42.66 3.21
3252 5363 3.823304 TGAGATCATCGAGGAGTATGTGG 59.177 47.826 5.80 0.00 0.00 4.17
3253 5364 3.161067 AGATCATCGAGGAGTATGTGGG 58.839 50.000 5.80 0.00 0.00 4.61
3254 5365 2.748209 TCATCGAGGAGTATGTGGGA 57.252 50.000 0.00 0.00 0.00 4.37
3255 5366 2.587522 TCATCGAGGAGTATGTGGGAG 58.412 52.381 0.00 0.00 0.00 4.30
3256 5367 1.000283 CATCGAGGAGTATGTGGGAGC 60.000 57.143 0.00 0.00 0.00 4.70
3258 5369 1.043116 CGAGGAGTATGTGGGAGCCA 61.043 60.000 0.00 0.00 0.00 4.75
3261 5372 0.618458 GGAGTATGTGGGAGCCAACA 59.382 55.000 0.00 0.00 34.18 3.33
3262 5373 1.212935 GGAGTATGTGGGAGCCAACAT 59.787 52.381 13.75 13.75 34.18 2.71
3263 5374 2.292267 GAGTATGTGGGAGCCAACATG 58.708 52.381 17.84 0.00 34.18 3.21
3264 5375 1.064463 AGTATGTGGGAGCCAACATGG 60.064 52.381 17.84 0.00 41.55 3.66
3265 5376 0.258484 TATGTGGGAGCCAACATGGG 59.742 55.000 17.84 0.00 38.19 4.00
3280 5391 1.235989 TGGGTATCCAGATCCCGCT 59.764 57.895 0.00 0.00 43.75 5.52
3281 5392 1.121407 TGGGTATCCAGATCCCGCTG 61.121 60.000 0.00 0.00 43.75 5.18
3282 5393 1.122019 GGGTATCCAGATCCCGCTGT 61.122 60.000 0.00 0.00 34.06 4.40
3284 5395 1.270358 GGTATCCAGATCCCGCTGTTC 60.270 57.143 0.00 0.00 34.06 3.18
3286 5397 1.330655 ATCCAGATCCCGCTGTTCGT 61.331 55.000 0.00 0.00 36.19 3.85
3287 5398 1.079127 CCAGATCCCGCTGTTCGTT 60.079 57.895 0.00 0.00 36.19 3.85
3288 5399 0.174845 CCAGATCCCGCTGTTCGTTA 59.825 55.000 0.00 0.00 36.19 3.18
3289 5400 1.202533 CCAGATCCCGCTGTTCGTTAT 60.203 52.381 0.00 0.00 36.19 1.89
3291 5402 2.285220 CAGATCCCGCTGTTCGTTATTG 59.715 50.000 0.00 0.00 36.19 1.90
3292 5403 2.167693 AGATCCCGCTGTTCGTTATTGA 59.832 45.455 0.00 0.00 36.19 2.57
3293 5404 1.717194 TCCCGCTGTTCGTTATTGAC 58.283 50.000 0.00 0.00 36.19 3.18
3295 5406 0.368907 CCGCTGTTCGTTATTGACCG 59.631 55.000 0.00 0.00 36.19 4.79
3296 5407 0.368907 CGCTGTTCGTTATTGACCGG 59.631 55.000 0.00 0.00 0.00 5.28
3297 5408 1.717194 GCTGTTCGTTATTGACCGGA 58.283 50.000 9.46 0.00 0.00 5.14
3298 5409 1.659098 GCTGTTCGTTATTGACCGGAG 59.341 52.381 9.46 0.00 0.00 4.63
3299 5410 2.673043 GCTGTTCGTTATTGACCGGAGA 60.673 50.000 9.46 0.00 0.00 3.71
3300 5411 3.179830 CTGTTCGTTATTGACCGGAGAG 58.820 50.000 9.46 0.00 0.00 3.20
3301 5412 1.925185 GTTCGTTATTGACCGGAGAGC 59.075 52.381 9.46 0.00 0.00 4.09
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 2.659610 GCAGAGGGCTCGTTGTCT 59.340 61.111 0.00 0.00 40.25 3.41
1 2 2.435059 GGCAGAGGGCTCGTTGTC 60.435 66.667 0.00 0.00 44.01 3.18
2 3 2.129555 AATGGCAGAGGGCTCGTTGT 62.130 55.000 0.00 0.00 44.01 3.32
3 4 0.962356 AAATGGCAGAGGGCTCGTTG 60.962 55.000 0.00 0.00 44.01 4.10
4 5 0.251341 AAAATGGCAGAGGGCTCGTT 60.251 50.000 0.00 0.00 44.01 3.85
5 6 0.251341 AAAAATGGCAGAGGGCTCGT 60.251 50.000 0.00 0.00 44.01 4.18
6 7 0.171903 CAAAAATGGCAGAGGGCTCG 59.828 55.000 0.00 0.00 44.01 5.03
7 8 0.108472 GCAAAAATGGCAGAGGGCTC 60.108 55.000 0.00 0.00 44.01 4.70
8 9 1.547472 GGCAAAAATGGCAGAGGGCT 61.547 55.000 0.00 0.00 44.01 5.19
9 10 1.078918 GGCAAAAATGGCAGAGGGC 60.079 57.895 0.00 0.00 43.74 5.19
10 11 2.364353 TGGCAAAAATGGCAGAGGG 58.636 52.632 0.51 0.00 39.51 4.30
16 17 1.639280 CGGTACATGGCAAAAATGGC 58.361 50.000 0.00 0.00 0.00 4.40
17 18 1.639280 GCGGTACATGGCAAAAATGG 58.361 50.000 0.00 0.00 0.00 3.16
18 19 1.067283 TGGCGGTACATGGCAAAAATG 60.067 47.619 10.55 0.00 39.13 2.32
19 20 1.067213 GTGGCGGTACATGGCAAAAAT 60.067 47.619 13.90 0.00 44.01 1.82
20 21 0.315568 GTGGCGGTACATGGCAAAAA 59.684 50.000 13.90 0.00 44.01 1.94
21 22 1.528292 GGTGGCGGTACATGGCAAAA 61.528 55.000 13.90 0.00 44.01 2.44
22 23 1.974343 GGTGGCGGTACATGGCAAA 60.974 57.895 13.90 0.00 44.01 3.68
23 24 2.360600 GGTGGCGGTACATGGCAA 60.361 61.111 13.90 0.00 44.01 4.52
24 25 4.769063 CGGTGGCGGTACATGGCA 62.769 66.667 9.15 9.15 39.86 4.92
26 27 4.467084 AGCGGTGGCGGTACATGG 62.467 66.667 0.00 0.00 46.35 3.66
27 28 3.195002 CAGCGGTGGCGGTACATG 61.195 66.667 6.74 0.00 46.35 3.21
36 37 4.147449 TCATCTCGGCAGCGGTGG 62.147 66.667 17.54 0.04 0.00 4.61
37 38 2.887568 GTCATCTCGGCAGCGGTG 60.888 66.667 10.98 10.98 0.00 4.94
38 39 2.842394 CTTGTCATCTCGGCAGCGGT 62.842 60.000 0.00 0.00 0.00 5.68
39 40 2.125552 TTGTCATCTCGGCAGCGG 60.126 61.111 0.00 0.00 0.00 5.52
40 41 2.169789 CCTTGTCATCTCGGCAGCG 61.170 63.158 0.00 0.00 0.00 5.18
41 42 1.817099 CCCTTGTCATCTCGGCAGC 60.817 63.158 0.00 0.00 0.00 5.25
42 43 1.153289 CCCCTTGTCATCTCGGCAG 60.153 63.158 0.00 0.00 0.00 4.85
43 44 1.198094 TTCCCCTTGTCATCTCGGCA 61.198 55.000 0.00 0.00 0.00 5.69
44 45 0.462759 CTTCCCCTTGTCATCTCGGC 60.463 60.000 0.00 0.00 0.00 5.54
45 46 0.179000 CCTTCCCCTTGTCATCTCGG 59.821 60.000 0.00 0.00 0.00 4.63
46 47 0.179000 CCCTTCCCCTTGTCATCTCG 59.821 60.000 0.00 0.00 0.00 4.04
47 48 0.106967 GCCCTTCCCCTTGTCATCTC 60.107 60.000 0.00 0.00 0.00 2.75
48 49 0.846427 TGCCCTTCCCCTTGTCATCT 60.846 55.000 0.00 0.00 0.00 2.90
49 50 0.039618 TTGCCCTTCCCCTTGTCATC 59.960 55.000 0.00 0.00 0.00 2.92
50 51 0.040204 CTTGCCCTTCCCCTTGTCAT 59.960 55.000 0.00 0.00 0.00 3.06
51 52 1.460255 CTTGCCCTTCCCCTTGTCA 59.540 57.895 0.00 0.00 0.00 3.58
52 53 1.304464 CCTTGCCCTTCCCCTTGTC 60.304 63.158 0.00 0.00 0.00 3.18
53 54 2.854076 CCTTGCCCTTCCCCTTGT 59.146 61.111 0.00 0.00 0.00 3.16
54 55 2.681421 GCCTTGCCCTTCCCCTTG 60.681 66.667 0.00 0.00 0.00 3.61
55 56 3.192630 TGCCTTGCCCTTCCCCTT 61.193 61.111 0.00 0.00 0.00 3.95
56 57 3.984732 GTGCCTTGCCCTTCCCCT 61.985 66.667 0.00 0.00 0.00 4.79
76 77 4.436998 GGACAGGAGTCACCGGCG 62.437 72.222 0.00 0.00 46.80 6.46
77 78 1.043673 ATAGGACAGGAGTCACCGGC 61.044 60.000 0.00 0.00 46.80 6.13
78 79 1.033574 GATAGGACAGGAGTCACCGG 58.966 60.000 0.00 0.00 46.80 5.28
79 80 1.763968 TGATAGGACAGGAGTCACCG 58.236 55.000 0.00 0.00 46.80 4.94
80 81 3.034635 ACATGATAGGACAGGAGTCACC 58.965 50.000 0.00 0.00 46.80 4.02
81 82 3.701542 TGACATGATAGGACAGGAGTCAC 59.298 47.826 0.00 0.00 46.80 3.67
82 83 3.981212 TGACATGATAGGACAGGAGTCA 58.019 45.455 0.00 0.00 46.80 3.41
83 84 4.343526 ACATGACATGATAGGACAGGAGTC 59.656 45.833 22.19 0.00 44.21 3.36
84 85 4.293494 ACATGACATGATAGGACAGGAGT 58.707 43.478 22.19 0.00 0.00 3.85
85 86 4.262377 GGACATGACATGATAGGACAGGAG 60.262 50.000 22.19 0.00 0.00 3.69
86 87 3.643320 GGACATGACATGATAGGACAGGA 59.357 47.826 22.19 0.00 0.00 3.86
87 88 3.645212 AGGACATGACATGATAGGACAGG 59.355 47.826 22.19 0.00 0.00 4.00
88 89 4.952071 AGGACATGACATGATAGGACAG 57.048 45.455 22.19 0.00 0.00 3.51
89 90 4.716287 TGAAGGACATGACATGATAGGACA 59.284 41.667 22.19 11.00 0.00 4.02
90 91 5.282055 TGAAGGACATGACATGATAGGAC 57.718 43.478 22.19 8.83 0.00 3.85
91 92 5.955961 TTGAAGGACATGACATGATAGGA 57.044 39.130 22.19 0.00 0.00 2.94
92 93 6.996879 AGAATTGAAGGACATGACATGATAGG 59.003 38.462 22.19 0.00 0.00 2.57
93 94 7.498239 ACAGAATTGAAGGACATGACATGATAG 59.502 37.037 22.19 0.00 0.00 2.08
94 95 7.281549 CACAGAATTGAAGGACATGACATGATA 59.718 37.037 22.19 0.00 0.00 2.15
126 127 9.533831 AAAGGGTCTTAAGTTCATCACATAAAT 57.466 29.630 1.63 0.00 0.00 1.40
128 129 8.792633 CAAAAGGGTCTTAAGTTCATCACATAA 58.207 33.333 1.63 0.00 0.00 1.90
160 161 7.141100 AGGACAACCAAAAGATAAACGTATG 57.859 36.000 0.00 0.00 38.94 2.39
161 162 8.889717 CATAGGACAACCAAAAGATAAACGTAT 58.110 33.333 0.00 0.00 38.94 3.06
162 163 8.095792 TCATAGGACAACCAAAAGATAAACGTA 58.904 33.333 0.00 0.00 38.94 3.57
168 169 8.877864 ACATTTCATAGGACAACCAAAAGATA 57.122 30.769 0.00 0.00 38.94 1.98
207 221 5.581085 GGAACAAAGAGCATACGTAGAACAT 59.419 40.000 0.08 0.00 0.00 2.71
213 227 3.259064 GCAGGAACAAAGAGCATACGTA 58.741 45.455 0.00 0.00 0.00 3.57
215 229 1.061131 CGCAGGAACAAAGAGCATACG 59.939 52.381 0.00 0.00 0.00 3.06
233 247 2.365948 CATACGAATTCATGCACACGC 58.634 47.619 6.22 0.00 39.24 5.34
235 249 4.818534 ATCCATACGAATTCATGCACAC 57.181 40.909 6.22 0.00 0.00 3.82
236 250 5.356470 TCAAATCCATACGAATTCATGCACA 59.644 36.000 6.22 0.00 0.00 4.57
248 262 1.488812 TCCACCCCTCAAATCCATACG 59.511 52.381 0.00 0.00 0.00 3.06
262 276 4.142600 CGTCTTTCTCATCATTTTCCACCC 60.143 45.833 0.00 0.00 0.00 4.61
267 281 5.319931 GCAGTCGTCTTTCTCATCATTTTC 58.680 41.667 0.00 0.00 0.00 2.29
275 289 0.039437 GTCCGCAGTCGTCTTTCTCA 60.039 55.000 0.00 0.00 0.00 3.27
277 291 0.039074 CTGTCCGCAGTCGTCTTTCT 60.039 55.000 0.00 0.00 37.92 2.52
278 292 1.009389 CCTGTCCGCAGTCGTCTTTC 61.009 60.000 0.00 0.00 41.02 2.62
279 293 1.006102 CCTGTCCGCAGTCGTCTTT 60.006 57.895 0.00 0.00 41.02 2.52
303 348 3.131850 CCAAATATGGCCCTGTCCC 57.868 57.895 0.00 0.00 40.58 4.46
315 360 2.799126 ACCGTCAGGATTGCCAAATA 57.201 45.000 0.00 0.00 41.02 1.40
361 971 1.008079 GCACACAAGGCTTGTCAGC 60.008 57.895 29.07 28.07 43.23 4.26
362 972 0.820891 AGGCACACAAGGCTTGTCAG 60.821 55.000 29.07 23.33 43.23 3.51
373 983 2.536066 ACCACTACATAGAGGCACACA 58.464 47.619 2.60 0.00 37.54 3.72
376 986 3.895656 TCCATACCACTACATAGAGGCAC 59.104 47.826 2.60 0.00 37.54 5.01
378 988 3.511934 CCTCCATACCACTACATAGAGGC 59.488 52.174 2.60 0.00 37.54 4.70
385 995 2.827755 TGCTTCCTCCATACCACTACA 58.172 47.619 0.00 0.00 0.00 2.74
386 996 3.244249 GGATGCTTCCTCCATACCACTAC 60.244 52.174 11.34 0.00 39.14 2.73
389 999 1.490490 TGGATGCTTCCTCCATACCAC 59.510 52.381 18.67 0.00 43.07 4.16
395 1005 2.586245 CGCTGGATGCTTCCTCCA 59.414 61.111 18.67 8.59 43.07 3.86
443 1057 9.454859 AATGTTATCTTTGGAGGAAGAGTTTAG 57.545 33.333 0.00 0.00 38.90 1.85
445 1059 8.712228 AAATGTTATCTTTGGAGGAAGAGTTT 57.288 30.769 0.00 0.00 38.90 2.66
452 1067 6.663523 GGGAAAGAAATGTTATCTTTGGAGGA 59.336 38.462 6.27 0.00 44.81 3.71
484 1124 2.334977 TCTTCTGCTTGGGAGTGGTTA 58.665 47.619 0.00 0.00 0.00 2.85
499 1144 2.280797 TGGCGCGCAAGTTCTTCT 60.281 55.556 34.42 0.00 41.68 2.85
519 1164 6.002704 AGTATAGGAGTAAGTGATACGGTGG 58.997 44.000 0.00 0.00 39.62 4.61
567 1212 2.279120 GATCTCGGCAGTCGCTGG 60.279 66.667 8.57 0.00 45.28 4.85
568 1213 1.875813 GTGATCTCGGCAGTCGCTG 60.876 63.158 0.00 2.92 46.70 5.18
569 1214 1.999071 GAGTGATCTCGGCAGTCGCT 61.999 60.000 0.00 0.00 39.05 4.93
570 1215 1.587613 GAGTGATCTCGGCAGTCGC 60.588 63.158 0.00 0.00 39.05 5.19
571 1216 4.700037 GAGTGATCTCGGCAGTCG 57.300 61.111 0.00 0.00 40.90 4.18
579 1224 1.520342 GCAGGTGCCGAGTGATCTC 60.520 63.158 0.00 0.00 37.35 2.75
580 1225 2.581354 GCAGGTGCCGAGTGATCT 59.419 61.111 0.00 0.00 34.31 2.75
581 1226 2.887568 CGCAGGTGCCGAGTGATC 60.888 66.667 0.00 0.00 37.91 2.92
600 1245 2.821366 GTCCATGGTGAGCTGCCG 60.821 66.667 12.58 0.00 0.00 5.69
621 1273 3.515316 CTTGGACGGTGGCGTCTGT 62.515 63.158 0.00 0.00 38.76 3.41
653 1317 1.079057 GAACGGCAGGAAGAGGACC 60.079 63.158 0.00 0.00 0.00 4.46
899 1598 2.266055 CCCTGACAGGTTCCTCGC 59.734 66.667 20.24 0.00 31.93 5.03
900 1599 1.293498 CACCCTGACAGGTTCCTCG 59.707 63.158 20.24 6.21 38.39 4.63
901 1600 1.003233 GCACCCTGACAGGTTCCTC 60.003 63.158 20.24 1.24 38.39 3.71
906 1605 2.524394 ACGAGCACCCTGACAGGT 60.524 61.111 20.24 5.80 42.40 4.00
909 1608 1.663739 GTACACGAGCACCCTGACA 59.336 57.895 0.00 0.00 0.00 3.58
1695 2406 1.684450 TGTGTCGAGTCAAGGTTAGCA 59.316 47.619 0.00 0.00 0.00 3.49
1894 2605 7.356540 TGTTGTATGTGTAGAAATTTGGTTCG 58.643 34.615 0.00 0.00 32.50 3.95
1908 2620 6.179756 TCATCAGCCTTATTGTTGTATGTGT 58.820 36.000 0.00 0.00 0.00 3.72
1917 2629 6.769822 CCACTAAGAATCATCAGCCTTATTGT 59.230 38.462 0.00 0.00 0.00 2.71
1930 2642 8.634335 TCATTGTCAAATTCCACTAAGAATCA 57.366 30.769 0.00 0.00 35.40 2.57
2106 2818 3.882326 CCCCCATGCGCTCTCCAT 61.882 66.667 9.73 0.00 0.00 3.41
2337 3049 6.719829 TCAGTGTAGTAGGAACAATCTCTCAA 59.280 38.462 0.00 0.00 0.00 3.02
2472 3307 9.665719 TTCATGTTCAAATATACTCTGTTAGCA 57.334 29.630 0.00 0.00 0.00 3.49
2513 3348 9.896645 CCATTACTTTGCATATATCCAGTAGAT 57.103 33.333 0.00 0.00 39.15 1.98
2563 3398 2.162208 CCAACAACTAATGCATCGCTGT 59.838 45.455 0.00 0.00 0.00 4.40
2568 3403 6.421801 GGCATATTTCCAACAACTAATGCATC 59.578 38.462 0.00 0.00 40.10 3.91
3131 5242 2.033927 AGACTCGATCCGTGTGATGATG 59.966 50.000 0.00 0.00 33.78 3.07
3132 5243 2.292016 GAGACTCGATCCGTGTGATGAT 59.708 50.000 0.00 0.00 33.78 2.45
3133 5244 1.671328 GAGACTCGATCCGTGTGATGA 59.329 52.381 0.00 0.00 33.78 2.92
3134 5245 1.595732 CGAGACTCGATCCGTGTGATG 60.596 57.143 20.25 0.00 43.74 3.07
3135 5246 0.658368 CGAGACTCGATCCGTGTGAT 59.342 55.000 20.25 0.00 43.74 3.06
3136 5247 1.366854 CCGAGACTCGATCCGTGTGA 61.367 60.000 26.11 0.00 43.74 3.58
3139 5250 2.716244 CCCGAGACTCGATCCGTG 59.284 66.667 26.11 7.94 43.74 4.94
3142 5253 1.066587 CTTGCCCGAGACTCGATCC 59.933 63.158 26.11 13.29 43.74 3.36
3143 5254 1.022735 TACTTGCCCGAGACTCGATC 58.977 55.000 26.11 16.24 43.74 3.69
3144 5255 1.134560 GTTACTTGCCCGAGACTCGAT 59.865 52.381 26.11 6.68 43.74 3.59
3146 5257 0.242825 TGTTACTTGCCCGAGACTCG 59.757 55.000 18.08 18.08 40.07 4.18
3147 5258 2.674796 ATGTTACTTGCCCGAGACTC 57.325 50.000 0.00 0.00 0.00 3.36
3148 5259 2.167900 GGTATGTTACTTGCCCGAGACT 59.832 50.000 0.00 0.00 0.00 3.24
3151 5262 1.134907 ACGGTATGTTACTTGCCCGAG 60.135 52.381 14.52 0.00 38.75 4.63
3152 5263 0.896923 ACGGTATGTTACTTGCCCGA 59.103 50.000 14.52 0.00 38.75 5.14
3153 5264 1.134907 AGACGGTATGTTACTTGCCCG 60.135 52.381 8.72 8.72 41.09 6.13
3155 5266 2.928116 GTCAGACGGTATGTTACTTGCC 59.072 50.000 2.34 0.00 0.00 4.52
3156 5267 3.581755 TGTCAGACGGTATGTTACTTGC 58.418 45.455 2.34 0.00 0.00 4.01
3157 5268 5.120208 CCTTTGTCAGACGGTATGTTACTTG 59.880 44.000 2.34 0.00 0.00 3.16
3158 5269 5.235516 CCTTTGTCAGACGGTATGTTACTT 58.764 41.667 2.34 0.00 0.00 2.24
3161 5272 3.833650 TCCCTTTGTCAGACGGTATGTTA 59.166 43.478 2.34 0.00 0.00 2.41
3162 5273 2.635915 TCCCTTTGTCAGACGGTATGTT 59.364 45.455 2.34 0.00 0.00 2.71
3163 5274 2.253610 TCCCTTTGTCAGACGGTATGT 58.746 47.619 2.34 0.00 0.00 2.29
3164 5275 3.328382 TTCCCTTTGTCAGACGGTATG 57.672 47.619 0.00 0.00 0.00 2.39
3165 5276 4.715297 ACTATTCCCTTTGTCAGACGGTAT 59.285 41.667 0.00 0.00 0.00 2.73
3167 5278 2.904434 ACTATTCCCTTTGTCAGACGGT 59.096 45.455 0.00 0.00 0.00 4.83
3169 5280 5.913514 CGTATACTATTCCCTTTGTCAGACG 59.086 44.000 0.56 0.00 0.00 4.18
3170 5281 6.214399 CCGTATACTATTCCCTTTGTCAGAC 58.786 44.000 0.56 0.00 0.00 3.51
3171 5282 5.303589 CCCGTATACTATTCCCTTTGTCAGA 59.696 44.000 0.56 0.00 0.00 3.27
3172 5283 5.510861 CCCCGTATACTATTCCCTTTGTCAG 60.511 48.000 0.56 0.00 0.00 3.51
3173 5284 4.345837 CCCCGTATACTATTCCCTTTGTCA 59.654 45.833 0.56 0.00 0.00 3.58
3175 5286 4.301205 ACCCCGTATACTATTCCCTTTGT 58.699 43.478 0.56 0.00 0.00 2.83
3176 5287 4.968971 ACCCCGTATACTATTCCCTTTG 57.031 45.455 0.56 0.00 0.00 2.77
3177 5288 4.445305 GCAACCCCGTATACTATTCCCTTT 60.445 45.833 0.56 0.00 0.00 3.11
3178 5289 3.072038 GCAACCCCGTATACTATTCCCTT 59.928 47.826 0.56 0.00 0.00 3.95
3179 5290 2.636403 GCAACCCCGTATACTATTCCCT 59.364 50.000 0.56 0.00 0.00 4.20
3180 5291 2.636403 AGCAACCCCGTATACTATTCCC 59.364 50.000 0.56 0.00 0.00 3.97
3184 5295 5.512576 GGATTCAAGCAACCCCGTATACTAT 60.513 44.000 0.56 0.00 0.00 2.12
3185 5296 4.202284 GGATTCAAGCAACCCCGTATACTA 60.202 45.833 0.56 0.00 0.00 1.82
3186 5297 3.433173 GGATTCAAGCAACCCCGTATACT 60.433 47.826 0.56 0.00 0.00 2.12
3187 5298 2.876550 GGATTCAAGCAACCCCGTATAC 59.123 50.000 0.00 0.00 0.00 1.47
3188 5299 2.775384 AGGATTCAAGCAACCCCGTATA 59.225 45.455 0.00 0.00 0.00 1.47
3189 5300 1.564348 AGGATTCAAGCAACCCCGTAT 59.436 47.619 0.00 0.00 0.00 3.06
3191 5302 0.322546 GAGGATTCAAGCAACCCCGT 60.323 55.000 0.00 0.00 0.00 5.28
3192 5303 1.369091 CGAGGATTCAAGCAACCCCG 61.369 60.000 0.00 0.00 0.00 5.73
3193 5304 0.035439 TCGAGGATTCAAGCAACCCC 60.035 55.000 0.00 0.00 0.00 4.95
3194 5305 1.087501 GTCGAGGATTCAAGCAACCC 58.912 55.000 0.00 0.00 0.00 4.11
3195 5306 1.808411 TGTCGAGGATTCAAGCAACC 58.192 50.000 0.00 0.00 0.00 3.77
3196 5307 2.029728 CGATGTCGAGGATTCAAGCAAC 59.970 50.000 0.00 0.00 43.02 4.17
3197 5308 2.270923 CGATGTCGAGGATTCAAGCAA 58.729 47.619 0.00 0.00 43.02 3.91
3208 5319 1.560923 GGATGAACCACGATGTCGAG 58.439 55.000 9.67 0.82 43.39 4.04
3209 5320 0.179148 CGGATGAACCACGATGTCGA 60.179 55.000 9.67 0.00 43.39 4.20
3211 5322 2.225068 ATCGGATGAACCACGATGTC 57.775 50.000 0.00 0.00 44.66 3.06
3215 5326 1.470051 TCTCATCGGATGAACCACGA 58.530 50.000 20.29 11.52 39.11 4.35
3216 5327 2.223805 TGATCTCATCGGATGAACCACG 60.224 50.000 20.29 9.50 39.11 4.94
3228 5339 5.392919 CCACATACTCCTCGATGATCTCATC 60.393 48.000 9.66 9.66 46.93 2.92
3229 5340 4.462132 CCACATACTCCTCGATGATCTCAT 59.538 45.833 0.00 0.00 39.70 2.90
3230 5341 3.823304 CCACATACTCCTCGATGATCTCA 59.177 47.826 0.00 0.00 0.00 3.27
3231 5342 3.192422 CCCACATACTCCTCGATGATCTC 59.808 52.174 0.00 0.00 0.00 2.75
3233 5344 3.157881 TCCCACATACTCCTCGATGATC 58.842 50.000 0.00 0.00 0.00 2.92
3235 5346 2.587522 CTCCCACATACTCCTCGATGA 58.412 52.381 0.00 0.00 0.00 2.92
3237 5348 1.333177 GCTCCCACATACTCCTCGAT 58.667 55.000 0.00 0.00 0.00 3.59
3238 5349 0.755698 GGCTCCCACATACTCCTCGA 60.756 60.000 0.00 0.00 0.00 4.04
3239 5350 1.043116 TGGCTCCCACATACTCCTCG 61.043 60.000 0.00 0.00 0.00 4.63
3240 5351 1.134371 GTTGGCTCCCACATACTCCTC 60.134 57.143 0.00 0.00 30.78 3.71
3241 5352 0.912486 GTTGGCTCCCACATACTCCT 59.088 55.000 0.00 0.00 30.78 3.69
3244 5355 1.064463 CCATGTTGGCTCCCACATACT 60.064 52.381 5.44 0.00 30.78 2.12
3245 5356 1.392589 CCATGTTGGCTCCCACATAC 58.607 55.000 5.44 0.00 30.78 2.39
3246 5357 0.258484 CCCATGTTGGCTCCCACATA 59.742 55.000 5.44 0.00 35.79 2.29
3247 5358 1.000739 CCCATGTTGGCTCCCACAT 59.999 57.895 0.24 0.24 35.79 3.21
3248 5359 1.136961 TACCCATGTTGGCTCCCACA 61.137 55.000 0.00 0.00 35.79 4.17
3249 5360 0.258774 ATACCCATGTTGGCTCCCAC 59.741 55.000 0.00 0.00 35.79 4.61
3250 5361 0.550914 GATACCCATGTTGGCTCCCA 59.449 55.000 0.00 0.00 35.79 4.37
3251 5362 0.178990 GGATACCCATGTTGGCTCCC 60.179 60.000 0.00 0.00 35.79 4.30
3252 5363 0.550914 TGGATACCCATGTTGGCTCC 59.449 55.000 0.00 0.00 37.58 4.70
3253 5364 1.490490 TCTGGATACCCATGTTGGCTC 59.510 52.381 0.00 0.00 42.59 4.70
3254 5365 1.595311 TCTGGATACCCATGTTGGCT 58.405 50.000 0.00 0.00 42.59 4.75
3255 5366 2.508526 GATCTGGATACCCATGTTGGC 58.491 52.381 0.00 0.00 42.59 4.52
3256 5367 2.224867 GGGATCTGGATACCCATGTTGG 60.225 54.545 0.39 0.00 42.59 3.77
3258 5369 1.699634 CGGGATCTGGATACCCATGTT 59.300 52.381 6.28 0.00 42.59 2.71
3261 5372 0.178891 AGCGGGATCTGGATACCCAT 60.179 55.000 6.28 0.00 42.59 4.00
3262 5373 1.121407 CAGCGGGATCTGGATACCCA 61.121 60.000 6.28 0.00 43.40 4.51
3263 5374 1.122019 ACAGCGGGATCTGGATACCC 61.122 60.000 6.28 7.03 38.66 3.69
3264 5375 0.759346 AACAGCGGGATCTGGATACC 59.241 55.000 1.81 1.81 38.49 2.73
3265 5376 1.603172 CGAACAGCGGGATCTGGATAC 60.603 57.143 0.00 0.00 38.36 2.24
3266 5377 0.673985 CGAACAGCGGGATCTGGATA 59.326 55.000 0.00 0.00 38.36 2.59
3267 5378 1.330655 ACGAACAGCGGGATCTGGAT 61.331 55.000 0.00 0.00 46.49 3.41
3269 5380 0.174845 TAACGAACAGCGGGATCTGG 59.825 55.000 0.00 0.00 46.49 3.86
3270 5381 2.225068 ATAACGAACAGCGGGATCTG 57.775 50.000 0.00 0.00 46.49 2.90
3271 5382 2.167693 TCAATAACGAACAGCGGGATCT 59.832 45.455 0.00 0.00 46.49 2.75
3272 5383 2.284417 GTCAATAACGAACAGCGGGATC 59.716 50.000 0.00 0.00 46.49 3.36
3273 5384 2.277084 GTCAATAACGAACAGCGGGAT 58.723 47.619 0.00 0.00 46.49 3.85
3274 5385 1.673626 GGTCAATAACGAACAGCGGGA 60.674 52.381 0.00 0.00 46.49 5.14
3275 5386 0.725117 GGTCAATAACGAACAGCGGG 59.275 55.000 0.00 0.00 46.49 6.13
3276 5387 0.368907 CGGTCAATAACGAACAGCGG 59.631 55.000 0.00 0.00 46.49 5.52
3280 5391 2.673043 GCTCTCCGGTCAATAACGAACA 60.673 50.000 0.00 0.00 0.00 3.18
3281 5392 1.925185 GCTCTCCGGTCAATAACGAAC 59.075 52.381 0.00 0.00 0.00 3.95
3282 5393 1.134907 GGCTCTCCGGTCAATAACGAA 60.135 52.381 0.00 0.00 0.00 3.85
3284 5395 2.973420 GGCTCTCCGGTCAATAACG 58.027 57.895 0.00 0.00 0.00 3.18


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

AutoCloner maintained by Alex Coulton.