Multiple sequence alignment - TraesCS1A01G341800

Loading Multiple Alignment...

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 TraesCS1A01G341800 chr1A 100.000 4550 0 0 1 4550 531238255 531242804 0.000000e+00 8403.0
1 TraesCS1A01G341800 chr1A 99.038 104 1 0 2545 2648 531240717 531240820 2.160000e-43 187.0
2 TraesCS1A01G341800 chr1A 99.038 104 1 0 2463 2566 531240799 531240902 2.160000e-43 187.0
3 TraesCS1A01G341800 chr1D 84.544 2478 186 107 126 2537 432797090 432799436 0.000000e+00 2272.0
4 TraesCS1A01G341800 chr1D 87.500 496 17 6 3364 3838 432801018 432801489 8.670000e-147 531.0
5 TraesCS1A01G341800 chr1D 97.810 274 5 1 3063 3335 432800685 432800958 5.330000e-129 472.0
6 TraesCS1A01G341800 chr1D 92.361 288 18 1 2693 2980 432800384 432800667 1.520000e-109 407.0
7 TraesCS1A01G341800 chr1D 85.965 114 6 8 4 117 432796950 432797053 3.720000e-21 113.0
8 TraesCS1A01G341800 chr1B 84.544 2051 145 89 188 2164 584157269 584159221 0.000000e+00 1873.0
9 TraesCS1A01G341800 chr1B 90.301 732 25 14 3076 3799 584160194 584160887 0.000000e+00 917.0
10 TraesCS1A01G341800 chr1B 93.208 265 13 2 2720 2983 584159910 584160170 7.140000e-103 385.0
11 TraesCS1A01G341800 chr1B 83.095 349 29 16 2178 2510 584159418 584159752 1.600000e-74 291.0
12 TraesCS1A01G341800 chr1B 97.368 38 1 0 1 38 584156981 584157018 1.060000e-06 65.8
13 TraesCS1A01G341800 chr3A 93.886 687 37 3 3865 4550 731170662 731171344 0.000000e+00 1031.0
14 TraesCS1A01G341800 chr5A 93.623 690 35 5 3864 4550 682355529 682354846 0.000000e+00 1022.0
15 TraesCS1A01G341800 chr5A 93.362 693 31 8 3865 4550 659067871 659068555 0.000000e+00 1011.0
16 TraesCS1A01G341800 chr5A 93.169 688 36 7 3865 4550 72942072 72941394 0.000000e+00 1000.0
17 TraesCS1A01G341800 chr6A 93.353 692 36 7 3865 4550 103896244 103896931 0.000000e+00 1014.0
18 TraesCS1A01G341800 chr6A 93.064 692 30 10 3865 4550 605975202 605975881 0.000000e+00 996.0
19 TraesCS1A01G341800 chr7A 92.939 694 39 6 3861 4550 595336025 595335338 0.000000e+00 1002.0
20 TraesCS1A01G341800 chr7A 92.970 697 31 8 3864 4550 698418777 698418089 0.000000e+00 1000.0
21 TraesCS1A01G341800 chr7A 92.806 695 36 6 3864 4550 673655430 673656118 0.000000e+00 994.0
22 TraesCS1A01G341800 chr2B 84.200 481 62 12 3076 3544 80557271 80557749 5.370000e-124 455.0
23 TraesCS1A01G341800 chr2B 80.242 496 80 15 1539 2026 80556277 80556762 1.560000e-94 357.0
24 TraesCS1A01G341800 chr2D 83.607 488 61 15 3070 3544 52043043 52043524 1.500000e-119 440.0
25 TraesCS1A01G341800 chr2D 83.023 483 62 15 3076 3544 42716305 42715829 1.960000e-113 420.0
26 TraesCS1A01G341800 chr2D 80.282 497 78 17 1540 2026 52042081 52042567 1.560000e-94 357.0
27 TraesCS1A01G341800 chr2D 88.584 219 25 0 1808 2026 42717001 42716783 2.700000e-67 267.0
28 TraesCS1A01G341800 chr2A 82.626 495 63 19 3070 3544 53442859 53443350 2.530000e-112 416.0
29 TraesCS1A01G341800 chr2A 89.091 220 22 2 1808 2026 53442190 53442408 5.800000e-69 272.0


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 TraesCS1A01G341800 chr1A 531238255 531242804 4549 False 2925.666667 8403 99.358667 1 4550 3 chr1A.!!$F1 4549
1 TraesCS1A01G341800 chr1D 432796950 432801489 4539 False 759.000000 2272 89.636000 4 3838 5 chr1D.!!$F1 3834
2 TraesCS1A01G341800 chr1B 584156981 584160887 3906 False 706.360000 1873 89.703200 1 3799 5 chr1B.!!$F1 3798
3 TraesCS1A01G341800 chr3A 731170662 731171344 682 False 1031.000000 1031 93.886000 3865 4550 1 chr3A.!!$F1 685
4 TraesCS1A01G341800 chr5A 682354846 682355529 683 True 1022.000000 1022 93.623000 3864 4550 1 chr5A.!!$R2 686
5 TraesCS1A01G341800 chr5A 659067871 659068555 684 False 1011.000000 1011 93.362000 3865 4550 1 chr5A.!!$F1 685
6 TraesCS1A01G341800 chr5A 72941394 72942072 678 True 1000.000000 1000 93.169000 3865 4550 1 chr5A.!!$R1 685
7 TraesCS1A01G341800 chr6A 103896244 103896931 687 False 1014.000000 1014 93.353000 3865 4550 1 chr6A.!!$F1 685
8 TraesCS1A01G341800 chr6A 605975202 605975881 679 False 996.000000 996 93.064000 3865 4550 1 chr6A.!!$F2 685
9 TraesCS1A01G341800 chr7A 595335338 595336025 687 True 1002.000000 1002 92.939000 3861 4550 1 chr7A.!!$R1 689
10 TraesCS1A01G341800 chr7A 698418089 698418777 688 True 1000.000000 1000 92.970000 3864 4550 1 chr7A.!!$R2 686
11 TraesCS1A01G341800 chr7A 673655430 673656118 688 False 994.000000 994 92.806000 3864 4550 1 chr7A.!!$F1 686
12 TraesCS1A01G341800 chr2B 80556277 80557749 1472 False 406.000000 455 82.221000 1539 3544 2 chr2B.!!$F1 2005
13 TraesCS1A01G341800 chr2D 52042081 52043524 1443 False 398.500000 440 81.944500 1540 3544 2 chr2D.!!$F1 2004
14 TraesCS1A01G341800 chr2D 42715829 42717001 1172 True 343.500000 420 85.803500 1808 3544 2 chr2D.!!$R1 1736
15 TraesCS1A01G341800 chr2A 53442190 53443350 1160 False 344.000000 416 85.858500 1808 3544 2 chr2A.!!$F1 1736

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
620 749 0.106167 TCCGGATAGGACACTGGGAG 60.106 60.0 0.00 0.00 45.98 4.3 F
2034 2231 0.179089 GAGGTGCGTGCATCATCTCT 60.179 55.0 19.11 7.92 38.36 3.1 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2618 3072 0.248825 GAGATCGTGTCTCGCAGCAT 60.249 55.0 0.00 0.0 43.65 3.79 R
3569 5157 0.108851 CATTAACTTGCGGTTGCCCC 60.109 55.0 5.33 0.0 41.78 5.80 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
53 104 2.846371 GGCACAAGCTGACAGTAGG 58.154 57.895 3.99 0.00 41.70 3.18
54 105 0.321671 GGCACAAGCTGACAGTAGGA 59.678 55.000 3.99 0.00 41.70 2.94
63 114 0.631753 TGACAGTAGGAGAGAGGGGG 59.368 60.000 0.00 0.00 0.00 5.40
93 144 0.723981 GACAGAGAATGTGCGCTTCC 59.276 55.000 9.73 0.00 44.17 3.46
124 178 3.547468 GCATGTTGATTGCATTTACGGAC 59.453 43.478 0.00 0.00 39.90 4.79
148 244 3.061831 CACAGAGATCACTTGATTGACGC 59.938 47.826 0.00 0.00 34.37 5.19
151 247 4.502282 CAGAGATCACTTGATTGACGCTAC 59.498 45.833 0.00 0.00 34.37 3.58
157 253 7.863375 AGATCACTTGATTGACGCTACTAATAC 59.137 37.037 0.00 0.00 34.37 1.89
158 254 5.969435 TCACTTGATTGACGCTACTAATACG 59.031 40.000 0.00 0.00 0.00 3.06
161 257 5.104562 TGATTGACGCTACTAATACGAGG 57.895 43.478 0.00 0.00 0.00 4.63
162 258 4.577693 TGATTGACGCTACTAATACGAGGT 59.422 41.667 0.00 0.00 0.00 3.85
163 259 5.759763 TGATTGACGCTACTAATACGAGGTA 59.240 40.000 0.00 0.00 0.00 3.08
165 261 5.602458 TGACGCTACTAATACGAGGTATG 57.398 43.478 0.00 0.00 0.00 2.39
166 262 4.453478 TGACGCTACTAATACGAGGTATGG 59.547 45.833 0.00 0.00 0.00 2.74
168 264 3.755378 CGCTACTAATACGAGGTATGGGT 59.245 47.826 0.00 0.00 0.00 4.51
169 265 4.379186 CGCTACTAATACGAGGTATGGGTG 60.379 50.000 0.00 0.00 0.00 4.61
171 267 2.631545 ACTAATACGAGGTATGGGTGGC 59.368 50.000 0.00 0.00 0.00 5.01
172 268 1.802553 AATACGAGGTATGGGTGGCT 58.197 50.000 0.00 0.00 0.00 4.75
173 269 1.048601 ATACGAGGTATGGGTGGCTG 58.951 55.000 0.00 0.00 0.00 4.85
174 270 0.324923 TACGAGGTATGGGTGGCTGT 60.325 55.000 0.00 0.00 0.00 4.40
175 271 0.324923 ACGAGGTATGGGTGGCTGTA 60.325 55.000 0.00 0.00 0.00 2.74
182 294 6.123045 AGGTATGGGTGGCTGTAATATAAC 57.877 41.667 0.00 0.00 0.00 1.89
186 298 4.776349 TGGGTGGCTGTAATATAACTGTG 58.224 43.478 0.00 0.00 0.00 3.66
206 320 1.135286 GTAAAGCTGCAAGGATGGTGC 60.135 52.381 1.02 0.00 42.55 5.01
210 324 4.402851 TGCAAGGATGGTGCAGAC 57.597 55.556 0.00 0.00 46.76 3.51
223 337 1.734465 GTGCAGACTGTACTTGATGGC 59.266 52.381 15.61 0.00 30.04 4.40
224 338 1.002366 GCAGACTGTACTTGATGGCG 58.998 55.000 3.99 0.00 0.00 5.69
287 401 5.577945 CGTACGACTTTTATGTATGGTTGGT 59.422 40.000 10.44 0.00 0.00 3.67
288 402 6.091169 CGTACGACTTTTATGTATGGTTGGTT 59.909 38.462 10.44 0.00 0.00 3.67
290 404 5.182380 ACGACTTTTATGTATGGTTGGTTGG 59.818 40.000 0.00 0.00 0.00 3.77
369 492 3.556004 GCTGGATATCTTCTTCCCGGAAG 60.556 52.174 19.80 19.80 42.72 3.46
371 494 3.388024 TGGATATCTTCTTCCCGGAAGTG 59.612 47.826 23.80 17.92 42.19 3.16
379 502 0.404040 TTCCCGGAAGTGGAAATGCT 59.596 50.000 0.73 0.00 37.45 3.79
410 533 4.262045 CCGTTTCAGAAAACACTGTTTTCG 59.738 41.667 29.15 24.77 44.13 3.46
451 574 4.704965 ACTGGAAGAAAAGGTGTGTCTAC 58.295 43.478 0.00 0.00 37.43 2.59
455 578 4.930405 GGAAGAAAAGGTGTGTCTACTAGC 59.070 45.833 0.00 0.00 0.00 3.42
459 582 0.811915 AGGTGTGTCTACTAGCAGCG 59.188 55.000 0.00 0.00 34.91 5.18
476 599 1.226802 CGCTCATCACCCACGAGAG 60.227 63.158 0.00 0.00 0.00 3.20
480 603 1.448540 CATCACCCACGAGAGCCAC 60.449 63.158 0.00 0.00 0.00 5.01
520 649 0.960364 CACGGAATGGAACCAGGGTG 60.960 60.000 0.00 1.72 0.00 4.61
522 651 2.046285 GGAATGGAACCAGGGTGCG 61.046 63.158 0.00 0.00 0.00 5.34
523 652 1.303317 GAATGGAACCAGGGTGCGT 60.303 57.895 0.00 0.00 0.00 5.24
620 749 0.106167 TCCGGATAGGACACTGGGAG 60.106 60.000 0.00 0.00 45.98 4.30
632 761 3.377656 TGGGAGACAGAGGCGAAC 58.622 61.111 0.00 0.00 0.00 3.95
634 763 2.341101 GGGAGACAGAGGCGAACGA 61.341 63.158 0.00 0.00 0.00 3.85
635 764 1.585006 GGAGACAGAGGCGAACGAA 59.415 57.895 0.00 0.00 0.00 3.85
637 766 0.456995 GAGACAGAGGCGAACGAAGG 60.457 60.000 0.00 0.00 0.00 3.46
639 768 2.815647 CAGAGGCGAACGAAGGGC 60.816 66.667 0.00 0.00 0.00 5.19
779 919 3.114616 CACGAACAGCGGGCTCTG 61.115 66.667 0.00 5.91 46.49 3.35
781 921 4.749310 CGAACAGCGGGCTCTGCT 62.749 66.667 2.97 2.97 45.31 4.24
782 922 2.817396 GAACAGCGGGCTCTGCTC 60.817 66.667 5.63 2.15 41.72 4.26
783 923 4.400961 AACAGCGGGCTCTGCTCC 62.401 66.667 5.63 0.00 41.72 4.70
785 925 4.834453 CAGCGGGCTCTGCTCCTG 62.834 72.222 5.63 0.00 41.72 3.86
788 928 4.527583 CGGGCTCTGCTCCTGCTC 62.528 72.222 0.00 0.00 40.48 4.26
789 929 4.527583 GGGCTCTGCTCCTGCTCG 62.528 72.222 0.00 0.00 40.48 5.03
936 1081 3.986006 GGTGAGTGACCACCGCGA 61.986 66.667 8.23 0.00 46.00 5.87
937 1082 2.733593 GTGAGTGACCACCGCGAC 60.734 66.667 8.23 0.00 0.00 5.19
938 1083 3.220658 TGAGTGACCACCGCGACA 61.221 61.111 8.23 0.00 0.00 4.35
939 1084 2.430921 GAGTGACCACCGCGACAG 60.431 66.667 8.23 0.00 0.00 3.51
940 1085 4.664677 AGTGACCACCGCGACAGC 62.665 66.667 8.23 0.00 40.74 4.40
943 1088 4.980805 GACCACCGCGACAGCCAA 62.981 66.667 8.23 0.00 41.18 4.52
1264 1419 4.922026 GGTTCACGCGGTGGGTGT 62.922 66.667 12.47 0.00 44.89 4.16
1281 1436 3.978193 TGGTTCATGGGCGGGCTT 61.978 61.111 0.26 0.00 0.00 4.35
1478 1633 1.859427 TACGTGCGTGACCTGACCTC 61.859 60.000 7.55 0.00 0.00 3.85
1481 1636 4.057428 GCGTGACCTGACCTCGCT 62.057 66.667 0.00 0.00 42.88 4.93
1488 1643 1.337387 GACCTGACCTCGCTACCATAC 59.663 57.143 0.00 0.00 0.00 2.39
1490 1645 1.609555 CCTGACCTCGCTACCATACTC 59.390 57.143 0.00 0.00 0.00 2.59
1491 1646 1.264557 CTGACCTCGCTACCATACTCG 59.735 57.143 0.00 0.00 0.00 4.18
1749 1936 4.409218 GGTGCGTGCGTACTCGGA 62.409 66.667 12.01 0.00 37.56 4.55
1750 1937 2.429571 GTGCGTGCGTACTCGGAA 60.430 61.111 1.24 0.00 39.39 4.30
1784 1971 1.289276 TGGCGACATGACATCGATTG 58.711 50.000 8.26 0.00 42.25 2.67
1785 1972 1.134848 TGGCGACATGACATCGATTGA 60.135 47.619 8.26 0.00 42.25 2.57
1787 1974 2.545526 GGCGACATGACATCGATTGATT 59.454 45.455 8.26 0.00 42.25 2.57
1788 1975 3.740832 GGCGACATGACATCGATTGATTA 59.259 43.478 8.26 0.00 42.25 1.75
1797 1984 6.794374 TGACATCGATTGATTAATTTGTGGG 58.206 36.000 0.00 0.00 30.49 4.61
2032 2229 1.520120 CGAGGTGCGTGCATCATCT 60.520 57.895 7.97 4.61 34.64 2.90
2034 2231 0.179089 GAGGTGCGTGCATCATCTCT 60.179 55.000 19.11 7.92 38.36 3.10
2036 2233 1.089920 GGTGCGTGCATCATCTCTTT 58.910 50.000 0.00 0.00 0.00 2.52
2037 2234 1.063174 GGTGCGTGCATCATCTCTTTC 59.937 52.381 0.00 0.00 0.00 2.62
2038 2235 2.005451 GTGCGTGCATCATCTCTTTCT 58.995 47.619 0.00 0.00 0.00 2.52
2039 2236 2.030213 GTGCGTGCATCATCTCTTTCTC 59.970 50.000 0.00 0.00 0.00 2.87
2040 2237 2.093816 TGCGTGCATCATCTCTTTCTCT 60.094 45.455 0.00 0.00 0.00 3.10
2042 2239 3.778618 CGTGCATCATCTCTTTCTCTCA 58.221 45.455 0.00 0.00 0.00 3.27
2043 2240 4.370049 CGTGCATCATCTCTTTCTCTCAT 58.630 43.478 0.00 0.00 0.00 2.90
2044 2241 4.809958 CGTGCATCATCTCTTTCTCTCATT 59.190 41.667 0.00 0.00 0.00 2.57
2047 2244 6.201425 GTGCATCATCTCTTTCTCTCATTCTC 59.799 42.308 0.00 0.00 0.00 2.87
2048 2245 5.697633 GCATCATCTCTTTCTCTCATTCTCC 59.302 44.000 0.00 0.00 0.00 3.71
2049 2246 5.512753 TCATCTCTTTCTCTCATTCTCCG 57.487 43.478 0.00 0.00 0.00 4.63
2050 2247 4.952957 TCATCTCTTTCTCTCATTCTCCGT 59.047 41.667 0.00 0.00 0.00 4.69
2051 2248 4.974368 TCTCTTTCTCTCATTCTCCGTC 57.026 45.455 0.00 0.00 0.00 4.79
2052 2249 4.594970 TCTCTTTCTCTCATTCTCCGTCT 58.405 43.478 0.00 0.00 0.00 4.18
2053 2250 4.638421 TCTCTTTCTCTCATTCTCCGTCTC 59.362 45.833 0.00 0.00 0.00 3.36
2054 2251 4.336280 TCTTTCTCTCATTCTCCGTCTCA 58.664 43.478 0.00 0.00 0.00 3.27
2055 2252 4.767409 TCTTTCTCTCATTCTCCGTCTCAA 59.233 41.667 0.00 0.00 0.00 3.02
2056 2253 4.710423 TTCTCTCATTCTCCGTCTCAAG 57.290 45.455 0.00 0.00 0.00 3.02
2057 2254 2.425312 TCTCTCATTCTCCGTCTCAAGC 59.575 50.000 0.00 0.00 0.00 4.01
2058 2255 2.165234 CTCTCATTCTCCGTCTCAAGCA 59.835 50.000 0.00 0.00 0.00 3.91
2059 2256 2.562738 TCTCATTCTCCGTCTCAAGCAA 59.437 45.455 0.00 0.00 0.00 3.91
2060 2257 2.928757 CTCATTCTCCGTCTCAAGCAAG 59.071 50.000 0.00 0.00 0.00 4.01
2061 2258 1.396301 CATTCTCCGTCTCAAGCAAGC 59.604 52.381 0.00 0.00 0.00 4.01
2164 2389 0.666577 GTGTCGACTGCCACTGTACC 60.667 60.000 17.92 0.00 0.00 3.34
2165 2390 0.826256 TGTCGACTGCCACTGTACCT 60.826 55.000 17.92 0.00 0.00 3.08
2167 2392 1.215647 CGACTGCCACTGTACCTCC 59.784 63.158 0.00 0.00 0.00 4.30
2170 2395 3.665675 CTGCCACTGTACCTCCGCC 62.666 68.421 0.00 0.00 0.00 6.13
2308 2749 4.295119 GTGTGCACGGGTCGGTCT 62.295 66.667 13.13 0.00 0.00 3.85
2334 2775 4.026407 GCGTTCTCACACTGTTAAAACAC 58.974 43.478 0.00 0.00 34.70 3.32
2336 2777 5.623335 CGTTCTCACACTGTTAAAACACAA 58.377 37.500 0.00 0.00 34.70 3.33
2339 2780 6.417191 TCTCACACTGTTAAAACACAAGAC 57.583 37.500 0.00 0.00 34.70 3.01
2388 2832 2.604046 CTGGAAGGGAATAGGACGTG 57.396 55.000 0.00 0.00 0.00 4.49
2421 2865 0.320374 TGAGCCCGTGACGAATCTTT 59.680 50.000 6.54 0.00 0.00 2.52
2460 2910 4.168291 GCCCTTCTCGCTCTGGGG 62.168 72.222 0.00 0.00 39.99 4.96
2505 2959 2.764128 ACCGCTCCCGATCCATGT 60.764 61.111 0.00 0.00 36.29 3.21
2510 2964 1.592669 CTCCCGATCCATGTCGTGC 60.593 63.158 5.17 0.00 39.89 5.34
2513 2967 2.202743 CGATCCATGTCGTGCCGT 60.203 61.111 0.00 0.00 36.88 5.68
2514 2968 2.516589 CGATCCATGTCGTGCCGTG 61.517 63.158 0.00 0.00 36.88 4.94
2515 2969 2.125147 ATCCATGTCGTGCCGTGG 60.125 61.111 0.00 4.92 41.96 4.94
2518 2972 3.792047 CATGTCGTGCCGTGGCTG 61.792 66.667 12.84 4.94 42.51 4.85
2545 2999 3.592814 CCCATGCCATGCTGCGAG 61.593 66.667 0.00 0.00 0.00 5.03
2546 3000 2.515290 CCATGCCATGCTGCGAGA 60.515 61.111 0.00 0.00 0.00 4.04
2549 3003 2.110967 ATGCCATGCTGCGAGACAC 61.111 57.895 0.00 0.00 0.00 3.67
2550 3004 3.857854 GCCATGCTGCGAGACACG 61.858 66.667 0.00 0.00 45.66 4.49
2552 3006 1.520120 CCATGCTGCGAGACACGAT 60.520 57.895 0.00 0.00 45.77 3.73
2553 3007 1.485838 CCATGCTGCGAGACACGATC 61.486 60.000 0.00 0.00 45.77 3.69
2554 3008 0.527169 CATGCTGCGAGACACGATCT 60.527 55.000 0.00 0.00 45.77 2.75
2566 3020 2.180769 CGATCTCGTTCCGTGGCA 59.819 61.111 0.00 0.00 34.11 4.92
2567 3021 1.874019 CGATCTCGTTCCGTGGCAG 60.874 63.158 0.00 0.00 34.11 4.85
2568 3022 1.519455 GATCTCGTTCCGTGGCAGG 60.519 63.158 0.00 0.00 0.00 4.85
2569 3023 3.665675 ATCTCGTTCCGTGGCAGGC 62.666 63.158 0.70 0.00 0.00 4.85
2570 3024 4.680237 CTCGTTCCGTGGCAGGCA 62.680 66.667 0.70 0.00 0.00 4.75
2571 3025 4.980805 TCGTTCCGTGGCAGGCAC 62.981 66.667 17.21 17.21 0.00 5.01
2582 3036 4.899239 CAGGCACCGCTCCCGATC 62.899 72.222 0.00 0.00 36.29 3.69
2585 3039 4.241555 GCACCGCTCCCGATCCAT 62.242 66.667 0.00 0.00 36.29 3.41
2586 3040 2.280389 CACCGCTCCCGATCCATG 60.280 66.667 0.00 0.00 36.29 3.66
2587 3041 2.764128 ACCGCTCCCGATCCATGT 60.764 61.111 0.00 0.00 36.29 3.21
2588 3042 2.029666 CCGCTCCCGATCCATGTC 59.970 66.667 0.00 0.00 36.29 3.06
2589 3043 2.355126 CGCTCCCGATCCATGTCG 60.355 66.667 0.00 0.00 41.13 4.35
2590 3044 2.815308 GCTCCCGATCCATGTCGT 59.185 61.111 5.17 0.00 39.89 4.34
2591 3045 1.592669 GCTCCCGATCCATGTCGTG 60.593 63.158 5.17 0.00 39.89 4.35
2592 3046 1.592669 CTCCCGATCCATGTCGTGC 60.593 63.158 5.17 0.00 39.89 5.34
2593 3047 2.588877 CCCGATCCATGTCGTGCC 60.589 66.667 5.17 0.00 39.89 5.01
2594 3048 2.961721 CCGATCCATGTCGTGCCG 60.962 66.667 5.17 0.00 39.89 5.69
2595 3049 2.202743 CGATCCATGTCGTGCCGT 60.203 61.111 0.00 0.00 36.88 5.68
2596 3050 2.516589 CGATCCATGTCGTGCCGTG 61.517 63.158 0.00 0.00 36.88 4.94
2597 3051 2.125147 ATCCATGTCGTGCCGTGG 60.125 61.111 0.00 4.92 41.96 4.94
2600 3054 3.792047 CATGTCGTGCCGTGGCTG 61.792 66.667 12.84 4.94 42.51 4.85
2632 3086 3.857854 GCCATGCTGCGAGACACG 61.858 66.667 0.00 0.00 45.66 4.49
2813 4201 2.780643 CAGTGAGCCATTGTCGCG 59.219 61.111 0.00 0.00 0.00 5.87
2837 4225 2.605818 GCTTGTATCGTTGCGGAATGTA 59.394 45.455 8.82 0.00 0.00 2.29
2951 4456 2.347490 CTAGTTGGTGCCGTGCCT 59.653 61.111 0.00 0.00 0.00 4.75
2980 4488 5.126067 TCTGCTTGCCCTTAGCTTAATTAG 58.874 41.667 0.00 0.00 44.23 1.73
2997 4505 9.000018 GCTTAATTAGCTCGACATAAAACTTTG 58.000 33.333 0.00 0.00 46.77 2.77
2999 4507 7.448748 AATTAGCTCGACATAAAACTTTGGT 57.551 32.000 0.00 0.00 0.00 3.67
3001 4509 7.591006 TTAGCTCGACATAAAACTTTGGTAG 57.409 36.000 0.00 0.00 0.00 3.18
3003 4511 4.436986 GCTCGACATAAAACTTTGGTAGCC 60.437 45.833 0.00 0.00 0.00 3.93
3005 4513 5.064558 TCGACATAAAACTTTGGTAGCCAA 58.935 37.500 0.00 0.00 42.29 4.52
3006 4514 5.708230 TCGACATAAAACTTTGGTAGCCAAT 59.292 36.000 1.09 0.00 43.55 3.16
3010 4518 6.493458 ACATAAAACTTTGGTAGCCAATCAGT 59.507 34.615 1.09 0.91 43.55 3.41
3011 4519 5.453567 AAAACTTTGGTAGCCAATCAGTC 57.546 39.130 1.09 0.00 43.55 3.51
3013 4521 3.679389 ACTTTGGTAGCCAATCAGTCAG 58.321 45.455 1.09 0.00 43.55 3.51
3014 4522 3.073062 ACTTTGGTAGCCAATCAGTCAGT 59.927 43.478 1.09 0.00 43.55 3.41
3016 4524 2.256306 TGGTAGCCAATCAGTCAGTCA 58.744 47.619 0.00 0.00 0.00 3.41
3018 4526 2.234908 GGTAGCCAATCAGTCAGTCACT 59.765 50.000 0.00 0.00 34.67 3.41
3019 4527 3.447586 GGTAGCCAATCAGTCAGTCACTA 59.552 47.826 0.00 0.00 32.21 2.74
3021 4529 2.093764 AGCCAATCAGTCAGTCACTAGC 60.094 50.000 0.00 0.00 32.21 3.42
3022 4530 2.093764 GCCAATCAGTCAGTCACTAGCT 60.094 50.000 0.00 0.00 32.21 3.32
3023 4531 3.131223 GCCAATCAGTCAGTCACTAGCTA 59.869 47.826 0.00 0.00 32.21 3.32
3024 4532 4.382040 GCCAATCAGTCAGTCACTAGCTAA 60.382 45.833 0.00 0.00 32.21 3.09
3039 4547 0.810426 GCTAAGCTAACCTGGGCGTC 60.810 60.000 0.00 0.00 0.00 5.19
3041 4549 0.905809 TAAGCTAACCTGGGCGTCCA 60.906 55.000 9.26 9.26 41.58 4.02
3042 4550 1.562672 AAGCTAACCTGGGCGTCCAT 61.563 55.000 10.40 0.00 43.11 3.41
3043 4551 1.819632 GCTAACCTGGGCGTCCATG 60.820 63.158 10.40 10.18 43.11 3.66
3044 4552 1.153168 CTAACCTGGGCGTCCATGG 60.153 63.158 10.40 16.17 43.11 3.66
3045 4553 3.338275 TAACCTGGGCGTCCATGGC 62.338 63.158 10.40 0.96 43.11 4.40
3335 4904 2.122783 ACGTCTCTCCCTCTCTTCTG 57.877 55.000 0.00 0.00 0.00 3.02
3336 4905 1.631388 ACGTCTCTCCCTCTCTTCTGA 59.369 52.381 0.00 0.00 0.00 3.27
3337 4906 2.040545 ACGTCTCTCCCTCTCTTCTGAA 59.959 50.000 0.00 0.00 0.00 3.02
3338 4907 3.287222 CGTCTCTCCCTCTCTTCTGAAT 58.713 50.000 0.00 0.00 0.00 2.57
3339 4908 3.066621 CGTCTCTCCCTCTCTTCTGAATG 59.933 52.174 0.00 0.00 0.00 2.67
3340 4909 3.030291 TCTCTCCCTCTCTTCTGAATGC 58.970 50.000 0.00 0.00 0.00 3.56
3341 4910 2.102925 CTCTCCCTCTCTTCTGAATGCC 59.897 54.545 0.00 0.00 0.00 4.40
3342 4911 1.836166 CTCCCTCTCTTCTGAATGCCA 59.164 52.381 0.00 0.00 0.00 4.92
3355 4924 4.657504 TCTGAATGCCATCTATGTTCCTCT 59.342 41.667 0.00 0.00 0.00 3.69
3357 4926 3.784511 ATGCCATCTATGTTCCTCTGG 57.215 47.619 0.00 0.00 0.00 3.86
3359 4928 1.875576 GCCATCTATGTTCCTCTGGCG 60.876 57.143 0.00 0.00 39.70 5.69
3361 4930 1.123077 ATCTATGTTCCTCTGGCGCA 58.877 50.000 10.83 0.00 0.00 6.09
3362 4931 0.901827 TCTATGTTCCTCTGGCGCAA 59.098 50.000 10.83 0.00 0.00 4.85
3557 5145 3.127533 CAGGTTGTAGCAGCGGCC 61.128 66.667 4.82 0.00 42.56 6.13
3558 5146 4.760047 AGGTTGTAGCAGCGGCCG 62.760 66.667 24.05 24.05 42.56 6.13
3560 5148 4.752879 GTTGTAGCAGCGGCCGGA 62.753 66.667 29.38 0.00 42.56 5.14
3561 5149 3.781307 TTGTAGCAGCGGCCGGAT 61.781 61.111 29.38 12.87 42.56 4.18
3563 5151 4.971125 GTAGCAGCGGCCGGATCC 62.971 72.222 29.38 10.23 42.56 3.36
3575 5163 3.743017 GGATCCAGGCAGGGGCAA 61.743 66.667 6.95 0.00 43.71 4.52
3576 5164 2.440980 GATCCAGGCAGGGGCAAC 60.441 66.667 0.00 0.00 43.71 4.17
3590 5178 2.262572 GGCAACCGCAAGTTAATGAG 57.737 50.000 0.00 0.00 41.24 2.90
3616 5206 3.056536 TGACTAGCAGCAGAGTAACTTGG 60.057 47.826 0.00 0.00 0.00 3.61
3657 5247 1.083806 TGAATCCATGACGAGCACGC 61.084 55.000 2.62 0.00 43.96 5.34
3659 5249 0.462581 AATCCATGACGAGCACGCAT 60.463 50.000 2.62 5.58 43.96 4.73
3799 5414 1.953559 TGCACCTTGTGTTCTCTGTC 58.046 50.000 0.00 0.00 35.75 3.51
3810 5425 4.588951 TGTGTTCTCTGTCCAGTGATACTT 59.411 41.667 0.00 0.00 31.90 2.24
3849 5464 4.516092 AAAAACAGTCGTGACGAGAAAG 57.484 40.909 8.41 0.87 36.23 2.62
3850 5465 3.431922 AAACAGTCGTGACGAGAAAGA 57.568 42.857 8.41 0.00 36.23 2.52
3851 5466 2.402640 ACAGTCGTGACGAGAAAGAC 57.597 50.000 8.41 0.00 36.23 3.01
3852 5467 1.948145 ACAGTCGTGACGAGAAAGACT 59.052 47.619 8.41 0.00 42.20 3.24
3853 5468 2.031857 ACAGTCGTGACGAGAAAGACTC 60.032 50.000 8.41 0.00 39.82 3.36
3854 5469 2.031944 CAGTCGTGACGAGAAAGACTCA 60.032 50.000 8.41 0.00 45.14 3.41
3855 5470 2.617308 AGTCGTGACGAGAAAGACTCAA 59.383 45.455 8.41 0.00 45.14 3.02
3856 5471 3.066342 AGTCGTGACGAGAAAGACTCAAA 59.934 43.478 8.41 0.00 45.14 2.69
3857 5472 3.795101 GTCGTGACGAGAAAGACTCAAAA 59.205 43.478 8.41 0.00 45.14 2.44
3858 5473 4.042398 TCGTGACGAGAAAGACTCAAAAG 58.958 43.478 2.39 0.00 45.14 2.27
3859 5474 4.042398 CGTGACGAGAAAGACTCAAAAGA 58.958 43.478 0.00 0.00 45.14 2.52
3890 5505 1.103398 GCAGAACCGGGCAATAGCAT 61.103 55.000 6.32 0.00 44.61 3.79
3935 5551 1.400113 GGTTTGTAACCGGCGCTAAAC 60.400 52.381 7.64 8.85 42.62 2.01
4012 5633 2.587753 CAACCACGTGGCACGAGT 60.588 61.111 42.65 33.51 46.05 4.18
4298 5942 0.871722 ACACACACACACACACACAC 59.128 50.000 0.00 0.00 0.00 3.82
4344 5996 2.922503 TGCCTTCGGAGCCAGTGA 60.923 61.111 0.00 0.00 0.00 3.41
4353 6005 0.543749 GGAGCCAGTGACATTAGCCT 59.456 55.000 0.00 0.00 0.00 4.58
4354 6006 1.762957 GGAGCCAGTGACATTAGCCTA 59.237 52.381 0.00 0.00 0.00 3.93
4479 6131 5.067283 GCAAAAATCCCGCTATTTCCTCTTA 59.933 40.000 0.00 0.00 0.00 2.10
4499 6151 1.299541 AATTGCTTCTATGCGGTCCG 58.700 50.000 6.99 6.99 35.36 4.79
4544 6196 6.542370 CACCTCTTTGAACTGTTAAGAAGGAA 59.458 38.462 18.24 0.00 0.00 3.36
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
2 3 3.057456 GTCAGGTCTCTCTCGCTTTTACA 60.057 47.826 0.00 0.00 0.00 2.41
43 94 1.410932 CCCCCTCTCTCCTACTGTCAG 60.411 61.905 0.00 0.00 0.00 3.51
44 95 0.631753 CCCCCTCTCTCCTACTGTCA 59.368 60.000 0.00 0.00 0.00 3.58
45 96 0.927767 TCCCCCTCTCTCCTACTGTC 59.072 60.000 0.00 0.00 0.00 3.51
46 97 1.007359 GTTCCCCCTCTCTCCTACTGT 59.993 57.143 0.00 0.00 0.00 3.55
47 98 1.689892 GGTTCCCCCTCTCTCCTACTG 60.690 61.905 0.00 0.00 0.00 2.74
48 99 0.637743 GGTTCCCCCTCTCTCCTACT 59.362 60.000 0.00 0.00 0.00 2.57
49 100 0.338814 TGGTTCCCCCTCTCTCCTAC 59.661 60.000 0.00 0.00 0.00 3.18
50 101 1.098589 TTGGTTCCCCCTCTCTCCTA 58.901 55.000 0.00 0.00 0.00 2.94
51 102 0.547954 GTTGGTTCCCCCTCTCTCCT 60.548 60.000 0.00 0.00 0.00 3.69
52 103 0.840722 TGTTGGTTCCCCCTCTCTCC 60.841 60.000 0.00 0.00 0.00 3.71
53 104 0.615850 CTGTTGGTTCCCCCTCTCTC 59.384 60.000 0.00 0.00 0.00 3.20
54 105 0.104409 ACTGTTGGTTCCCCCTCTCT 60.104 55.000 0.00 0.00 0.00 3.10
63 114 4.024556 CACATTCTCTGTCACTGTTGGTTC 60.025 45.833 0.00 0.00 35.29 3.62
67 118 2.096565 CGCACATTCTCTGTCACTGTTG 60.097 50.000 0.00 0.00 35.29 3.33
103 154 3.785521 CGTCCGTAAATGCAATCAACATG 59.214 43.478 0.00 0.00 0.00 3.21
121 175 1.067565 TCAAGTGATCTCTGTGCGTCC 60.068 52.381 0.00 0.00 0.00 4.79
124 178 3.061831 GTCAATCAAGTGATCTCTGTGCG 59.938 47.826 0.00 0.00 32.75 5.34
148 244 4.082354 GCCACCCATACCTCGTATTAGTAG 60.082 50.000 0.00 0.00 0.00 2.57
151 247 2.897969 AGCCACCCATACCTCGTATTAG 59.102 50.000 0.00 0.00 0.00 1.73
157 253 0.828022 TTACAGCCACCCATACCTCG 59.172 55.000 0.00 0.00 0.00 4.63
158 254 4.910458 ATATTACAGCCACCCATACCTC 57.090 45.455 0.00 0.00 0.00 3.85
161 257 6.426937 CACAGTTATATTACAGCCACCCATAC 59.573 42.308 0.00 0.00 0.00 2.39
162 258 6.100569 ACACAGTTATATTACAGCCACCCATA 59.899 38.462 0.00 0.00 0.00 2.74
163 259 5.104109 ACACAGTTATATTACAGCCACCCAT 60.104 40.000 0.00 0.00 0.00 4.00
165 261 4.777463 ACACAGTTATATTACAGCCACCC 58.223 43.478 0.00 0.00 0.00 4.61
166 262 7.466860 GCTTTACACAGTTATATTACAGCCACC 60.467 40.741 0.00 0.00 0.00 4.61
168 264 7.279981 CAGCTTTACACAGTTATATTACAGCCA 59.720 37.037 0.00 0.00 0.00 4.75
169 265 7.630924 CAGCTTTACACAGTTATATTACAGCC 58.369 38.462 0.00 0.00 0.00 4.85
171 267 8.196802 TGCAGCTTTACACAGTTATATTACAG 57.803 34.615 0.00 0.00 0.00 2.74
172 268 8.554835 TTGCAGCTTTACACAGTTATATTACA 57.445 30.769 0.00 0.00 0.00 2.41
173 269 8.122952 CCTTGCAGCTTTACACAGTTATATTAC 58.877 37.037 0.00 0.00 0.00 1.89
174 270 8.044309 TCCTTGCAGCTTTACACAGTTATATTA 58.956 33.333 0.00 0.00 0.00 0.98
175 271 6.884295 TCCTTGCAGCTTTACACAGTTATATT 59.116 34.615 0.00 0.00 0.00 1.28
182 294 2.163010 CCATCCTTGCAGCTTTACACAG 59.837 50.000 0.00 0.00 0.00 3.66
186 298 1.135286 GCACCATCCTTGCAGCTTTAC 60.135 52.381 0.00 0.00 39.93 2.01
206 320 2.534298 CTCGCCATCAAGTACAGTCTG 58.466 52.381 0.00 0.00 0.00 3.51
209 323 0.608130 TGCTCGCCATCAAGTACAGT 59.392 50.000 0.00 0.00 0.00 3.55
210 324 1.596260 CATGCTCGCCATCAAGTACAG 59.404 52.381 0.00 0.00 29.71 2.74
248 362 2.941064 TCGTACGGGAATGAGTGAGTAG 59.059 50.000 16.52 0.00 0.00 2.57
250 364 1.471684 GTCGTACGGGAATGAGTGAGT 59.528 52.381 16.52 0.00 0.00 3.41
251 365 1.743958 AGTCGTACGGGAATGAGTGAG 59.256 52.381 16.52 0.00 0.00 3.51
252 366 1.830279 AGTCGTACGGGAATGAGTGA 58.170 50.000 16.52 0.00 0.00 3.41
253 367 2.649331 AAGTCGTACGGGAATGAGTG 57.351 50.000 16.52 0.00 0.00 3.51
287 401 2.125310 ATGCGCGTCGATTCCCAA 60.125 55.556 8.43 0.00 0.00 4.12
288 402 2.889988 CATGCGCGTCGATTCCCA 60.890 61.111 8.43 0.00 0.00 4.37
290 404 2.378945 ATTGCATGCGCGTCGATTCC 62.379 55.000 14.09 0.00 42.97 3.01
348 471 3.643792 ACTTCCGGGAAGAAGATATCCAG 59.356 47.826 36.76 12.38 45.08 3.86
351 474 3.641906 TCCACTTCCGGGAAGAAGATATC 59.358 47.826 36.76 0.00 45.08 1.63
352 475 3.654273 TCCACTTCCGGGAAGAAGATAT 58.346 45.455 36.76 15.44 45.08 1.63
353 476 3.110293 TCCACTTCCGGGAAGAAGATA 57.890 47.619 36.76 18.91 45.08 1.98
354 477 1.952621 TCCACTTCCGGGAAGAAGAT 58.047 50.000 36.76 16.49 45.08 2.40
355 478 1.724545 TTCCACTTCCGGGAAGAAGA 58.275 50.000 36.76 28.27 45.08 2.87
356 479 2.561478 TTTCCACTTCCGGGAAGAAG 57.439 50.000 36.76 27.34 44.70 2.85
357 480 2.790433 CATTTCCACTTCCGGGAAGAA 58.210 47.619 36.76 23.13 44.70 2.52
369 492 1.736696 CGGATTTGCCAGCATTTCCAC 60.737 52.381 16.90 0.00 35.94 4.02
371 494 0.532115 ACGGATTTGCCAGCATTTCC 59.468 50.000 10.02 10.02 35.94 3.13
379 502 3.131223 TGTTTTCTGAAACGGATTTGCCA 59.869 39.130 1.58 0.00 46.44 4.92
421 544 7.778382 ACACACCTTTTCTTCCAGTAATAAACT 59.222 33.333 0.00 0.00 39.81 2.66
422 545 7.937649 ACACACCTTTTCTTCCAGTAATAAAC 58.062 34.615 0.00 0.00 0.00 2.01
428 551 5.601313 AGTAGACACACCTTTTCTTCCAGTA 59.399 40.000 0.00 0.00 0.00 2.74
429 552 3.933861 AGACACACCTTTTCTTCCAGT 57.066 42.857 0.00 0.00 0.00 4.00
430 553 4.962155 AGTAGACACACCTTTTCTTCCAG 58.038 43.478 0.00 0.00 0.00 3.86
431 554 5.510861 GCTAGTAGACACACCTTTTCTTCCA 60.511 44.000 0.00 0.00 0.00 3.53
432 555 4.930405 GCTAGTAGACACACCTTTTCTTCC 59.070 45.833 0.00 0.00 0.00 3.46
433 556 5.539048 TGCTAGTAGACACACCTTTTCTTC 58.461 41.667 0.00 0.00 0.00 2.87
451 574 1.593750 GGGTGATGAGCGCTGCTAG 60.594 63.158 18.48 0.00 39.88 3.42
455 578 3.190849 CGTGGGTGATGAGCGCTG 61.191 66.667 18.48 0.00 0.00 5.18
459 582 1.520342 GCTCTCGTGGGTGATGAGC 60.520 63.158 0.00 0.00 42.31 4.26
480 603 2.579787 GCATCACGACCTCCGACG 60.580 66.667 0.00 0.00 41.76 5.12
526 655 6.183360 GGTTTACTTTGTTTTGAGCAGTGTTG 60.183 38.462 0.00 0.00 0.00 3.33
579 708 2.327228 GCAAACCAGCCTTGTACGT 58.673 52.632 0.00 0.00 0.00 3.57
614 743 1.216710 GTTCGCCTCTGTCTCCCAG 59.783 63.158 0.00 0.00 42.97 4.45
620 749 1.446272 CCCTTCGTTCGCCTCTGTC 60.446 63.158 0.00 0.00 0.00 3.51
632 761 1.344942 CGTCTTCGTCTTGCCCTTCG 61.345 60.000 0.00 0.00 0.00 3.79
634 763 0.391597 TTCGTCTTCGTCTTGCCCTT 59.608 50.000 0.00 0.00 38.33 3.95
635 764 0.319641 GTTCGTCTTCGTCTTGCCCT 60.320 55.000 0.00 0.00 38.33 5.19
637 766 0.662374 TCGTTCGTCTTCGTCTTGCC 60.662 55.000 0.00 0.00 38.33 4.52
639 768 0.703466 GCTCGTTCGTCTTCGTCTTG 59.297 55.000 0.00 0.00 38.33 3.02
747 878 1.185618 TCGTGCTGGTTGGCTCTAGT 61.186 55.000 0.00 0.00 0.00 2.57
748 879 0.037326 TTCGTGCTGGTTGGCTCTAG 60.037 55.000 0.00 0.00 0.00 2.43
749 880 0.320421 GTTCGTGCTGGTTGGCTCTA 60.320 55.000 0.00 0.00 0.00 2.43
750 881 1.598130 GTTCGTGCTGGTTGGCTCT 60.598 57.895 0.00 0.00 0.00 4.09
751 882 1.845809 CTGTTCGTGCTGGTTGGCTC 61.846 60.000 0.00 0.00 0.00 4.70
778 918 4.426112 CGAGCACGAGCAGGAGCA 62.426 66.667 7.77 0.00 45.49 4.26
779 919 4.427661 ACGAGCACGAGCAGGAGC 62.428 66.667 11.40 0.00 45.49 4.70
780 920 2.505777 CACGAGCACGAGCAGGAG 60.506 66.667 11.40 0.00 45.49 3.69
781 921 2.982744 CTCACGAGCACGAGCAGGA 61.983 63.158 11.40 0.00 45.49 3.86
782 922 2.505777 CTCACGAGCACGAGCAGG 60.506 66.667 11.40 0.32 45.49 4.85
865 1006 2.081462 GGGGTGTGTCAGGTTTAATCG 58.919 52.381 0.00 0.00 0.00 3.34
934 1079 3.357079 GGGTGCTGTTGGCTGTCG 61.357 66.667 0.00 0.00 42.39 4.35
935 1080 1.589716 GATGGGTGCTGTTGGCTGTC 61.590 60.000 0.00 0.00 42.39 3.51
936 1081 1.604593 GATGGGTGCTGTTGGCTGT 60.605 57.895 0.00 0.00 42.39 4.40
937 1082 2.693762 CGATGGGTGCTGTTGGCTG 61.694 63.158 0.00 0.00 42.39 4.85
938 1083 2.360350 CGATGGGTGCTGTTGGCT 60.360 61.111 0.00 0.00 42.39 4.75
939 1084 3.443045 CCGATGGGTGCTGTTGGC 61.443 66.667 0.00 0.00 42.22 4.52
940 1085 3.443045 GCCGATGGGTGCTGTTGG 61.443 66.667 0.00 0.00 34.97 3.77
1151 1300 0.608856 CTTGGTATGCCTGTGTGCCA 60.609 55.000 0.16 0.00 35.27 4.92
1155 1304 1.000896 GCCCTTGGTATGCCTGTGT 60.001 57.895 0.16 0.00 35.27 3.72
1246 1401 4.619227 CACCCACCGCGTGAACCT 62.619 66.667 4.92 0.00 35.23 3.50
1264 1419 3.978193 AAGCCCGCCCATGAACCA 61.978 61.111 0.00 0.00 0.00 3.67
1478 1633 1.462051 CGATCGACGAGTATGGTAGCG 60.462 57.143 10.26 0.00 45.77 4.26
1481 1636 3.461061 AGAACGATCGACGAGTATGGTA 58.539 45.455 24.34 0.00 45.77 3.25
1488 1643 2.095128 CGAAAGAGAACGATCGACGAG 58.905 52.381 24.34 0.00 45.77 4.18
1491 1646 1.912110 CACCGAAAGAGAACGATCGAC 59.088 52.381 24.34 14.96 37.48 4.20
1572 1742 2.048503 CCTCCACCGTCACGAACC 60.049 66.667 0.00 0.00 0.00 3.62
1764 1951 1.869132 CAATCGATGTCATGTCGCCAT 59.131 47.619 0.00 0.00 38.88 4.40
1767 1954 3.867055 AATCAATCGATGTCATGTCGC 57.133 42.857 0.00 0.00 38.88 5.19
1772 1959 7.068593 ACCCACAAATTAATCAATCGATGTCAT 59.931 33.333 0.00 0.00 30.13 3.06
1774 1961 6.692681 CACCCACAAATTAATCAATCGATGTC 59.307 38.462 0.00 0.00 30.13 3.06
1776 1963 6.794374 TCACCCACAAATTAATCAATCGATG 58.206 36.000 0.00 0.00 30.13 3.84
1779 1966 7.062138 CAGTTTCACCCACAAATTAATCAATCG 59.938 37.037 0.00 0.00 0.00 3.34
1780 1967 7.872483 ACAGTTTCACCCACAAATTAATCAATC 59.128 33.333 0.00 0.00 0.00 2.67
1781 1968 7.656948 CACAGTTTCACCCACAAATTAATCAAT 59.343 33.333 0.00 0.00 0.00 2.57
1784 1971 5.405269 GCACAGTTTCACCCACAAATTAATC 59.595 40.000 0.00 0.00 0.00 1.75
1785 1972 5.163364 TGCACAGTTTCACCCACAAATTAAT 60.163 36.000 0.00 0.00 0.00 1.40
1787 1974 3.701542 TGCACAGTTTCACCCACAAATTA 59.298 39.130 0.00 0.00 0.00 1.40
1788 1975 2.499289 TGCACAGTTTCACCCACAAATT 59.501 40.909 0.00 0.00 0.00 1.82
2029 2226 5.200483 AGACGGAGAATGAGAGAAAGAGAT 58.800 41.667 0.00 0.00 0.00 2.75
2032 2229 4.336280 TGAGACGGAGAATGAGAGAAAGA 58.664 43.478 0.00 0.00 0.00 2.52
2034 2231 4.619394 GCTTGAGACGGAGAATGAGAGAAA 60.619 45.833 0.00 0.00 0.00 2.52
2036 2233 2.425312 GCTTGAGACGGAGAATGAGAGA 59.575 50.000 0.00 0.00 0.00 3.10
2037 2234 2.165234 TGCTTGAGACGGAGAATGAGAG 59.835 50.000 0.00 0.00 0.00 3.20
2038 2235 2.171003 TGCTTGAGACGGAGAATGAGA 58.829 47.619 0.00 0.00 0.00 3.27
2039 2236 2.662006 TGCTTGAGACGGAGAATGAG 57.338 50.000 0.00 0.00 0.00 2.90
2040 2237 2.932622 GCTTGCTTGAGACGGAGAATGA 60.933 50.000 0.00 0.00 0.00 2.57
2042 2239 1.277557 AGCTTGCTTGAGACGGAGAAT 59.722 47.619 0.00 0.00 0.00 2.40
2043 2240 0.681733 AGCTTGCTTGAGACGGAGAA 59.318 50.000 0.00 0.00 0.00 2.87
2044 2241 0.681733 AAGCTTGCTTGAGACGGAGA 59.318 50.000 7.09 0.00 0.00 3.71
2057 2254 1.884579 AGGAATGTCTGTGCAAGCTTG 59.115 47.619 22.44 22.44 0.00 4.01
2058 2255 2.157738 GAGGAATGTCTGTGCAAGCTT 58.842 47.619 0.00 0.00 0.00 3.74
2059 2256 1.350351 AGAGGAATGTCTGTGCAAGCT 59.650 47.619 0.00 0.00 0.00 3.74
2060 2257 1.818642 AGAGGAATGTCTGTGCAAGC 58.181 50.000 0.00 0.00 0.00 4.01
2061 2258 6.506500 AATTAAGAGGAATGTCTGTGCAAG 57.493 37.500 0.00 0.00 0.00 4.01
2067 2264 7.120285 TGCTTGAGAAATTAAGAGGAATGTCTG 59.880 37.037 0.00 0.00 34.16 3.51
2069 2266 7.383102 TGCTTGAGAAATTAAGAGGAATGTC 57.617 36.000 0.00 0.00 0.00 3.06
2074 2271 5.564550 AGCTTGCTTGAGAAATTAAGAGGA 58.435 37.500 0.00 0.00 0.00 3.71
2167 2392 4.976925 CTATGCAGGGCTCGGGCG 62.977 72.222 0.00 0.00 39.81 6.13
2170 2395 2.030262 GCTCTATGCAGGGCTCGG 59.970 66.667 0.00 0.00 45.60 4.63
2252 2667 4.838152 ACTGGTAGGCCATGCGCG 62.838 66.667 5.01 0.00 45.05 6.86
2253 2668 3.204827 CACTGGTAGGCCATGCGC 61.205 66.667 5.01 0.00 45.05 6.09
2254 2669 1.815421 GACACTGGTAGGCCATGCG 60.815 63.158 5.01 0.00 45.05 4.73
2255 2670 1.452108 GGACACTGGTAGGCCATGC 60.452 63.158 5.01 0.00 45.05 4.06
2256 2671 1.224592 GGGACACTGGTAGGCCATG 59.775 63.158 5.01 0.00 45.05 3.66
2257 2672 1.229820 TGGGACACTGGTAGGCCAT 60.230 57.895 5.01 0.00 45.05 4.40
2258 2673 2.205749 TGGGACACTGGTAGGCCA 59.794 61.111 5.01 0.00 43.73 5.36
2308 2749 7.779046 TGTTTTAACAGTGTGAGAACGCTCAA 61.779 38.462 9.00 0.00 42.19 3.02
2350 2791 3.006859 CCAGGAATGTACTGTCACTGTGA 59.993 47.826 6.36 6.36 34.16 3.58
2351 2792 3.006859 TCCAGGAATGTACTGTCACTGTG 59.993 47.826 0.17 0.17 34.16 3.66
2352 2793 3.239449 TCCAGGAATGTACTGTCACTGT 58.761 45.455 0.00 0.00 34.16 3.55
2353 2794 3.961480 TCCAGGAATGTACTGTCACTG 57.039 47.619 0.00 2.11 34.16 3.66
2354 2795 3.261897 CCTTCCAGGAATGTACTGTCACT 59.738 47.826 1.09 0.00 37.67 3.41
2355 2796 3.600388 CCTTCCAGGAATGTACTGTCAC 58.400 50.000 1.09 0.00 37.67 3.67
2383 2824 1.226603 CGGTGCTACTAGCCACGTC 60.227 63.158 5.58 0.00 41.51 4.34
2388 2832 1.227002 GCTCACGGTGCTACTAGCC 60.227 63.158 2.51 0.00 41.51 3.93
2446 2896 2.186384 CTGCCCCAGAGCGAGAAG 59.814 66.667 0.00 0.00 32.44 2.85
2535 2989 0.527169 AGATCGTGTCTCGCAGCATG 60.527 55.000 0.00 0.00 39.67 4.06
2538 2992 3.990141 GAGATCGTGTCTCGCAGC 58.010 61.111 5.16 0.00 43.65 5.25
2565 3019 4.899239 GATCGGGAGCGGTGCCTG 62.899 72.222 23.15 15.90 29.93 4.85
2568 3022 4.241555 ATGGATCGGGAGCGGTGC 62.242 66.667 0.00 0.00 0.00 5.01
2569 3023 2.280389 CATGGATCGGGAGCGGTG 60.280 66.667 0.00 0.00 0.00 4.94
2570 3024 2.764128 ACATGGATCGGGAGCGGT 60.764 61.111 0.00 0.00 0.00 5.68
2571 3025 2.029666 GACATGGATCGGGAGCGG 59.970 66.667 0.00 0.00 0.00 5.52
2572 3026 2.355126 CGACATGGATCGGGAGCG 60.355 66.667 0.00 0.00 38.47 5.03
2573 3027 2.815308 ACGACATGGATCGGGAGC 59.185 61.111 10.11 0.00 46.56 4.70
2606 3060 4.201679 CAGCATGGCATGGGCACG 62.202 66.667 27.48 7.15 41.84 5.34
2607 3061 4.524318 GCAGCATGGCATGGGCAC 62.524 66.667 27.48 11.73 41.84 5.01
2610 3064 3.592814 CTCGCAGCATGGCATGGG 61.593 66.667 27.48 12.98 35.86 4.00
2611 3065 2.515290 TCTCGCAGCATGGCATGG 60.515 61.111 27.48 13.79 35.86 3.66
2612 3066 2.110352 TGTCTCGCAGCATGGCATG 61.110 57.895 22.99 22.99 35.86 4.06
2613 3067 2.110967 GTGTCTCGCAGCATGGCAT 61.111 57.895 0.00 0.00 35.86 4.40
2614 3068 2.743538 GTGTCTCGCAGCATGGCA 60.744 61.111 0.00 0.00 35.86 4.92
2615 3069 3.857854 CGTGTCTCGCAGCATGGC 61.858 66.667 0.00 0.00 35.86 4.40
2616 3070 1.485838 GATCGTGTCTCGCAGCATGG 61.486 60.000 0.00 0.00 39.67 3.66
2617 3071 0.527169 AGATCGTGTCTCGCAGCATG 60.527 55.000 0.00 0.00 39.67 4.06
2618 3072 0.248825 GAGATCGTGTCTCGCAGCAT 60.249 55.000 0.00 0.00 43.65 3.79
2619 3073 1.137614 GAGATCGTGTCTCGCAGCA 59.862 57.895 0.00 0.00 43.65 4.41
2620 3074 3.990141 GAGATCGTGTCTCGCAGC 58.010 61.111 5.16 0.00 43.65 5.25
2679 3157 3.548793 GATACGTACGGGAGGCCGC 62.549 68.421 21.06 0.00 36.58 6.53
2806 4194 2.433491 ATACAAGCGGCGCGACAA 60.433 55.556 27.59 14.27 0.00 3.18
2813 4201 2.021380 CGCAACGATACAAGCGGC 59.979 61.111 0.00 0.00 45.83 6.53
2816 4204 1.396996 ACATTCCGCAACGATACAAGC 59.603 47.619 0.00 0.00 0.00 4.01
2951 4456 4.163427 AGCTAAGGGCAAGCAGATAGATA 58.837 43.478 8.20 0.00 42.62 1.98
2980 4488 4.436986 GGCTACCAAAGTTTTATGTCGAGC 60.437 45.833 0.00 0.00 0.00 5.03
2982 4490 4.643463 TGGCTACCAAAGTTTTATGTCGA 58.357 39.130 0.00 0.00 0.00 4.20
2983 4491 5.365403 TTGGCTACCAAAGTTTTATGTCG 57.635 39.130 0.00 0.00 40.92 4.35
2995 4503 5.786059 AGTGACTGACTGATTGGCTACCAA 61.786 45.833 0.77 0.77 39.85 3.67
2997 4505 2.234908 AGTGACTGACTGATTGGCTACC 59.765 50.000 0.00 0.00 31.75 3.18
2999 4507 3.131223 GCTAGTGACTGACTGATTGGCTA 59.869 47.826 0.00 0.00 35.96 3.93
3001 4509 2.093764 AGCTAGTGACTGACTGATTGGC 60.094 50.000 0.00 0.00 35.96 4.52
3003 4511 4.803088 GCTTAGCTAGTGACTGACTGATTG 59.197 45.833 0.00 0.00 35.96 2.67
3005 4513 4.277476 AGCTTAGCTAGTGACTGACTGAT 58.723 43.478 4.30 0.00 36.99 2.90
3006 4514 3.691575 AGCTTAGCTAGTGACTGACTGA 58.308 45.455 4.30 0.00 36.99 3.41
3010 4518 4.399618 CAGGTTAGCTTAGCTAGTGACTGA 59.600 45.833 20.91 3.87 42.34 3.41
3011 4519 4.440802 CCAGGTTAGCTTAGCTAGTGACTG 60.441 50.000 13.93 17.57 42.34 3.51
3013 4521 3.181474 CCCAGGTTAGCTTAGCTAGTGAC 60.181 52.174 13.93 9.67 42.34 3.67
3014 4522 3.031736 CCCAGGTTAGCTTAGCTAGTGA 58.968 50.000 13.93 0.00 42.34 3.41
3016 4524 1.763545 GCCCAGGTTAGCTTAGCTAGT 59.236 52.381 13.93 0.90 42.34 2.57
3018 4526 0.750850 CGCCCAGGTTAGCTTAGCTA 59.249 55.000 10.21 10.21 40.44 3.32
3019 4527 1.265454 ACGCCCAGGTTAGCTTAGCT 61.265 55.000 12.67 12.67 43.41 3.32
3021 4529 0.179081 GGACGCCCAGGTTAGCTTAG 60.179 60.000 0.00 0.00 0.00 2.18
3022 4530 0.905809 TGGACGCCCAGGTTAGCTTA 60.906 55.000 0.00 0.00 37.58 3.09
3023 4531 2.221299 TGGACGCCCAGGTTAGCTT 61.221 57.895 0.00 0.00 37.58 3.74
3024 4532 2.606519 TGGACGCCCAGGTTAGCT 60.607 61.111 0.00 0.00 37.58 3.32
3050 4558 2.224495 ATTCCCCAAAACGCATGCCG 62.224 55.000 13.15 10.04 44.21 5.69
3051 4559 0.740516 CATTCCCCAAAACGCATGCC 60.741 55.000 13.15 0.00 0.00 4.40
3057 4565 2.159254 CCTGTATGCATTCCCCAAAACG 60.159 50.000 3.54 0.00 0.00 3.60
3060 4568 1.360852 ACCCTGTATGCATTCCCCAAA 59.639 47.619 3.54 0.00 0.00 3.28
3335 4904 4.070716 CCAGAGGAACATAGATGGCATTC 58.929 47.826 0.00 0.00 0.00 2.67
3336 4905 4.096190 CCAGAGGAACATAGATGGCATT 57.904 45.455 0.00 0.00 0.00 3.56
3337 4906 3.784511 CCAGAGGAACATAGATGGCAT 57.215 47.619 0.00 0.00 0.00 4.40
3339 4908 1.889545 GCCAGAGGAACATAGATGGC 58.110 55.000 0.00 0.00 45.61 4.40
3340 4909 1.875576 GCGCCAGAGGAACATAGATGG 60.876 57.143 0.00 0.00 0.00 3.51
3341 4910 1.202568 TGCGCCAGAGGAACATAGATG 60.203 52.381 4.18 0.00 0.00 2.90
3342 4911 1.123077 TGCGCCAGAGGAACATAGAT 58.877 50.000 4.18 0.00 0.00 1.98
3355 4924 3.594775 CCAGTTGCACTTGCGCCA 61.595 61.111 4.18 0.00 45.83 5.69
3359 4928 2.195567 TCAGCCCAGTTGCACTTGC 61.196 57.895 0.00 0.00 42.50 4.01
3361 4930 1.893808 CGTCAGCCCAGTTGCACTT 60.894 57.895 0.00 0.00 0.00 3.16
3362 4931 2.281070 CGTCAGCCCAGTTGCACT 60.281 61.111 0.00 0.00 0.00 4.40
3558 5146 3.743017 TTGCCCCTGCCTGGATCC 61.743 66.667 4.20 4.20 38.35 3.36
3559 5147 2.440980 GTTGCCCCTGCCTGGATC 60.441 66.667 0.00 0.00 38.35 3.36
3560 5148 4.066139 GGTTGCCCCTGCCTGGAT 62.066 66.667 0.00 0.00 38.35 3.41
3567 5155 1.175983 TTAACTTGCGGTTGCCCCTG 61.176 55.000 5.33 0.00 41.78 4.45
3568 5156 0.251608 ATTAACTTGCGGTTGCCCCT 60.252 50.000 5.33 0.00 41.78 4.79
3569 5157 0.108851 CATTAACTTGCGGTTGCCCC 60.109 55.000 5.33 0.00 41.78 5.80
3570 5158 0.885196 TCATTAACTTGCGGTTGCCC 59.115 50.000 5.33 0.00 41.78 5.36
3571 5159 1.539827 ACTCATTAACTTGCGGTTGCC 59.460 47.619 5.33 0.00 41.78 4.52
3572 5160 2.989422 ACTCATTAACTTGCGGTTGC 57.011 45.000 5.33 0.00 38.75 4.17
3573 5161 6.021596 GTCATTACTCATTAACTTGCGGTTG 58.978 40.000 5.33 0.00 38.75 3.77
3574 5162 5.938125 AGTCATTACTCATTAACTTGCGGTT 59.062 36.000 0.81 0.81 41.54 4.44
3575 5163 5.488341 AGTCATTACTCATTAACTTGCGGT 58.512 37.500 0.00 0.00 0.00 5.68
3576 5164 6.292381 GCTAGTCATTACTCATTAACTTGCGG 60.292 42.308 0.00 0.00 37.15 5.69
3577 5165 6.255670 TGCTAGTCATTACTCATTAACTTGCG 59.744 38.462 0.00 0.00 37.99 4.85
3578 5166 7.539712 TGCTAGTCATTACTCATTAACTTGC 57.460 36.000 0.00 0.00 37.15 4.01
3579 5167 7.278646 TGCTGCTAGTCATTACTCATTAACTTG 59.721 37.037 0.00 0.00 37.15 3.16
3580 5168 7.331026 TGCTGCTAGTCATTACTCATTAACTT 58.669 34.615 0.00 0.00 37.15 2.66
3581 5169 6.878317 TGCTGCTAGTCATTACTCATTAACT 58.122 36.000 0.00 0.00 37.15 2.24
3582 5170 6.980978 TCTGCTGCTAGTCATTACTCATTAAC 59.019 38.462 0.00 0.00 37.15 2.01
3583 5171 7.112452 TCTGCTGCTAGTCATTACTCATTAA 57.888 36.000 0.00 0.00 37.15 1.40
3584 5172 6.322456 ACTCTGCTGCTAGTCATTACTCATTA 59.678 38.462 0.00 0.00 37.15 1.90
3585 5173 5.128499 ACTCTGCTGCTAGTCATTACTCATT 59.872 40.000 0.00 0.00 37.15 2.57
3586 5174 4.648762 ACTCTGCTGCTAGTCATTACTCAT 59.351 41.667 0.00 0.00 37.15 2.90
3587 5175 4.019858 ACTCTGCTGCTAGTCATTACTCA 58.980 43.478 0.00 0.00 37.15 3.41
3588 5176 4.647424 ACTCTGCTGCTAGTCATTACTC 57.353 45.455 0.00 0.00 37.15 2.59
3589 5177 5.654650 AGTTACTCTGCTGCTAGTCATTACT 59.345 40.000 10.72 8.34 39.91 2.24
3590 5178 5.897050 AGTTACTCTGCTGCTAGTCATTAC 58.103 41.667 10.72 6.73 0.00 1.89
3828 5443 4.032558 GTCTTTCTCGTCACGACTGTTTTT 59.967 41.667 0.00 0.00 0.00 1.94
3838 5453 5.174216 GTCTCTTTTGAGTCTTTCTCGTCAC 59.826 44.000 0.00 0.00 46.30 3.67
3839 5454 5.163550 TGTCTCTTTTGAGTCTTTCTCGTCA 60.164 40.000 0.00 0.00 46.30 4.35
3840 5455 5.174216 GTGTCTCTTTTGAGTCTTTCTCGTC 59.826 44.000 0.00 0.00 46.30 4.20
3841 5456 5.044558 GTGTCTCTTTTGAGTCTTTCTCGT 58.955 41.667 0.00 0.00 46.30 4.18
3842 5457 5.043903 TGTGTCTCTTTTGAGTCTTTCTCG 58.956 41.667 0.00 0.00 46.30 4.04
3843 5458 6.045955 AGTGTGTCTCTTTTGAGTCTTTCTC 58.954 40.000 0.00 0.00 46.30 2.87
3844 5459 5.983540 AGTGTGTCTCTTTTGAGTCTTTCT 58.016 37.500 0.00 0.00 46.30 2.52
3845 5460 6.981559 ACTAGTGTGTCTCTTTTGAGTCTTTC 59.018 38.462 0.00 0.00 46.30 2.62
3846 5461 6.758886 CACTAGTGTGTCTCTTTTGAGTCTTT 59.241 38.462 15.06 0.00 40.11 2.52
3847 5462 6.276847 CACTAGTGTGTCTCTTTTGAGTCTT 58.723 40.000 15.06 0.00 40.11 3.01
3848 5463 5.737635 GCACTAGTGTGTCTCTTTTGAGTCT 60.738 44.000 23.44 0.00 45.44 3.24
3849 5464 4.446051 GCACTAGTGTGTCTCTTTTGAGTC 59.554 45.833 23.44 0.00 45.44 3.36
3850 5465 4.141937 TGCACTAGTGTGTCTCTTTTGAGT 60.142 41.667 23.44 0.00 45.44 3.41
3851 5466 4.371786 TGCACTAGTGTGTCTCTTTTGAG 58.628 43.478 23.44 0.00 45.44 3.02
3852 5467 4.099419 TCTGCACTAGTGTGTCTCTTTTGA 59.901 41.667 23.44 5.36 45.44 2.69
3853 5468 4.371786 TCTGCACTAGTGTGTCTCTTTTG 58.628 43.478 23.44 0.00 45.44 2.44
3854 5469 4.672587 TCTGCACTAGTGTGTCTCTTTT 57.327 40.909 23.44 0.00 45.44 2.27
3855 5470 4.372656 GTTCTGCACTAGTGTGTCTCTTT 58.627 43.478 23.44 0.00 45.44 2.52
3856 5471 3.243907 GGTTCTGCACTAGTGTGTCTCTT 60.244 47.826 23.44 0.00 45.44 2.85
3857 5472 2.297597 GGTTCTGCACTAGTGTGTCTCT 59.702 50.000 23.44 0.00 45.44 3.10
3858 5473 2.678324 GGTTCTGCACTAGTGTGTCTC 58.322 52.381 23.44 11.66 45.44 3.36
3859 5474 1.000163 CGGTTCTGCACTAGTGTGTCT 60.000 52.381 23.44 0.00 45.44 3.41
3890 5505 1.205417 CTAAAGGGCCTTACGAACCGA 59.795 52.381 21.25 0.00 0.00 4.69
3987 5608 1.457009 GCCACGTGGTTGCCCTTTAA 61.457 55.000 33.92 0.00 37.57 1.52
4255 5889 8.085296 TGTGTGAATTAATTAATGGTGGTTGTC 58.915 33.333 11.42 3.85 0.00 3.18
4353 6005 4.002906 CCGAAGGCACCAATTAGCTATA 57.997 45.455 0.00 0.00 46.14 1.31
4354 6006 2.851195 CCGAAGGCACCAATTAGCTAT 58.149 47.619 0.00 0.00 46.14 2.97
4479 6131 1.670811 CGGACCGCATAGAAGCAATTT 59.329 47.619 0.00 0.00 0.00 1.82
4499 6151 1.222113 GGGACAAGCTCCTAGCACC 59.778 63.158 1.22 0.00 45.56 5.01


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

AutoCloner maintained by Alex Coulton.