Multiple sequence alignment - TraesCS6A01G122400

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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 TraesCS6A01G122400 chr6A 100.000 2657 0 0 1 2657 94378482 94375826 0.000000e+00 4907.0
1 TraesCS6A01G122400 chr6A 82.216 1164 113 45 1301 2413 95795373 95794253 0.000000e+00 917.0
2 TraesCS6A01G122400 chr6A 80.152 660 62 22 754 1361 95795994 95795352 1.890000e-116 429.0
3 TraesCS6A01G122400 chr6A 78.995 219 30 10 473 678 613258656 613258871 4.610000e-28 135.0
4 TraesCS6A01G122400 chr6D 94.581 1384 47 9 971 2336 79171605 79170232 0.000000e+00 2115.0
5 TraesCS6A01G122400 chr6D 83.651 1101 115 33 1301 2355 79620554 79619473 0.000000e+00 976.0
6 TraesCS6A01G122400 chr6D 89.711 554 28 7 357 900 79172294 79171760 0.000000e+00 680.0
7 TraesCS6A01G122400 chr6D 86.373 499 61 7 1447 1939 79704038 79703541 3.010000e-149 538.0
8 TraesCS6A01G122400 chr6D 80.699 658 67 18 754 1361 79621297 79620650 8.670000e-125 457.0
9 TraesCS6A01G122400 chr6D 83.908 435 44 15 1930 2355 79703142 79702725 2.480000e-105 392.0
10 TraesCS6A01G122400 chr6D 88.927 289 19 3 2323 2611 79170028 79169753 7.040000e-91 344.0
11 TraesCS6A01G122400 chr6D 92.073 164 13 0 80 243 79172456 79172293 5.720000e-57 231.0
12 TraesCS6A01G122400 chr6D 92.126 127 9 1 237 362 366701101 366701227 7.560000e-41 178.0
13 TraesCS6A01G122400 chr6D 92.063 126 9 1 237 361 142147464 142147589 2.720000e-40 176.0
14 TraesCS6A01G122400 chr6D 81.897 116 21 0 533 648 41514839 41514724 6.050000e-17 99.0
15 TraesCS6A01G122400 chr6D 90.476 63 6 0 404 466 463797313 463797251 1.690000e-12 84.2
16 TraesCS6A01G122400 chr6D 95.652 46 2 0 2417 2462 79702723 79702678 1.020000e-09 75.0
17 TraesCS6A01G122400 chr6B 84.534 1041 106 25 1353 2355 151821329 151820306 0.000000e+00 979.0
18 TraesCS6A01G122400 chr6B 92.742 124 9 0 240 363 618132662 618132539 2.100000e-41 180.0
19 TraesCS6A01G122400 chr6B 95.652 46 2 0 2417 2462 151820304 151820259 1.020000e-09 75.0
20 TraesCS6A01G122400 chr6B 87.719 57 7 0 473 529 616865487 616865431 1.710000e-07 67.6
21 TraesCS6A01G122400 chr2A 92.248 129 10 0 242 370 560689352 560689224 1.620000e-42 183.0
22 TraesCS6A01G122400 chr2A 85.430 151 14 8 533 680 13009333 13009478 1.650000e-32 150.0
23 TraesCS6A01G122400 chr2A 79.793 193 26 6 473 655 4999719 4999908 7.720000e-26 128.0
24 TraesCS6A01G122400 chr2A 80.000 155 20 4 484 629 708312029 708312181 1.300000e-18 104.0
25 TraesCS6A01G122400 chr2A 96.364 55 2 0 412 466 445022218 445022272 1.010000e-14 91.6
26 TraesCS6A01G122400 chr4B 90.000 140 12 2 228 365 517059880 517059741 2.100000e-41 180.0
27 TraesCS6A01G122400 chr4B 81.560 141 15 7 501 634 637347555 637347419 3.620000e-19 106.0
28 TraesCS6A01G122400 chr1B 93.388 121 8 0 241 361 16170944 16171064 2.100000e-41 180.0
29 TraesCS6A01G122400 chr7D 90.769 130 11 1 241 370 253793468 253793596 3.520000e-39 172.0
30 TraesCS6A01G122400 chr7D 88.652 141 11 5 234 371 45626683 45626821 1.640000e-37 167.0
31 TraesCS6A01G122400 chr7D 78.804 184 24 8 473 646 123454646 123454824 2.800000e-20 110.0
32 TraesCS6A01G122400 chr7D 76.712 219 35 9 472 678 569606072 569605858 1.010000e-19 108.0
33 TraesCS6A01G122400 chr7D 94.643 56 3 0 411 466 429243274 429243329 1.310000e-13 87.9
34 TraesCS6A01G122400 chr1D 90.769 130 11 1 233 361 408872529 408872400 3.520000e-39 172.0
35 TraesCS6A01G122400 chr1D 75.627 279 48 15 411 676 203264865 203265136 1.290000e-23 121.0
36 TraesCS6A01G122400 chr5D 80.829 193 24 5 473 656 365124239 365124427 3.570000e-29 139.0
37 TraesCS6A01G122400 chr2B 80.749 187 25 4 501 678 263811230 263811414 4.610000e-28 135.0
38 TraesCS6A01G122400 chr5B 78.636 220 33 6 473 681 505606675 505606459 1.660000e-27 134.0
39 TraesCS6A01G122400 chr7A 78.756 193 30 8 473 656 559184168 559184358 4.650000e-23 119.0
40 TraesCS6A01G122400 chr5A 78.155 206 32 6 484 678 616911601 616911398 4.650000e-23 119.0
41 TraesCS6A01G122400 chr4D 79.167 192 25 6 475 656 54385850 54386036 4.650000e-23 119.0
42 TraesCS6A01G122400 chr4A 77.626 219 34 9 473 682 16996509 16996297 4.650000e-23 119.0
43 TraesCS6A01G122400 chr4A 81.905 105 19 0 104 208 706671798 706671694 3.640000e-14 89.8
44 TraesCS6A01G122400 chr3B 96.429 56 2 0 411 466 143311479 143311424 2.820000e-15 93.5
45 TraesCS6A01G122400 chr3B 90.476 63 5 1 411 473 764132230 764132291 6.100000e-12 82.4
46 TraesCS6A01G122400 chr7B 93.548 62 3 1 412 473 531683736 531683796 1.010000e-14 91.6
47 TraesCS6A01G122400 chr2D 94.643 56 3 0 411 466 365445023 365445078 1.310000e-13 87.9
48 TraesCS6A01G122400 chr2D 77.011 174 15 11 501 663 61314980 61314821 2.840000e-10 76.8


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 TraesCS6A01G122400 chr6A 94375826 94378482 2656 True 4907.0 4907 100.000000 1 2657 1 chr6A.!!$R1 2656
1 TraesCS6A01G122400 chr6A 95794253 95795994 1741 True 673.0 917 81.184000 754 2413 2 chr6A.!!$R2 1659
2 TraesCS6A01G122400 chr6D 79169753 79172456 2703 True 842.5 2115 91.323000 80 2611 4 chr6D.!!$R3 2531
3 TraesCS6A01G122400 chr6D 79619473 79621297 1824 True 716.5 976 82.175000 754 2355 2 chr6D.!!$R4 1601
4 TraesCS6A01G122400 chr6D 79702678 79704038 1360 True 335.0 538 88.644333 1447 2462 3 chr6D.!!$R5 1015
5 TraesCS6A01G122400 chr6B 151820259 151821329 1070 True 527.0 979 90.093000 1353 2462 2 chr6B.!!$R3 1109

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
68 69 0.17924 CACGCGAGCACAACTTCATC 60.179 55.0 15.93 0.0 0.0 2.92 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1826 2187 0.103026 CGATCAGATCCTTGCGGACA 59.897 55.0 4.73 0.0 43.51 4.02 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
21 22 3.648009 GTGAGATTAGGATGCGAGAAGG 58.352 50.000 0.00 0.00 0.00 3.46
22 23 2.630098 TGAGATTAGGATGCGAGAAGGG 59.370 50.000 0.00 0.00 0.00 3.95
23 24 2.630580 GAGATTAGGATGCGAGAAGGGT 59.369 50.000 0.00 0.00 0.00 4.34
24 25 2.630580 AGATTAGGATGCGAGAAGGGTC 59.369 50.000 0.00 0.00 0.00 4.46
25 26 1.860641 TTAGGATGCGAGAAGGGTCA 58.139 50.000 0.00 0.00 0.00 4.02
26 27 1.860641 TAGGATGCGAGAAGGGTCAA 58.139 50.000 0.00 0.00 0.00 3.18
27 28 0.984230 AGGATGCGAGAAGGGTCAAA 59.016 50.000 0.00 0.00 0.00 2.69
28 29 1.065854 AGGATGCGAGAAGGGTCAAAG 60.066 52.381 0.00 0.00 0.00 2.77
29 30 1.339151 GGATGCGAGAAGGGTCAAAGT 60.339 52.381 0.00 0.00 0.00 2.66
30 31 2.427506 GATGCGAGAAGGGTCAAAGTT 58.572 47.619 0.00 0.00 0.00 2.66
31 32 1.878953 TGCGAGAAGGGTCAAAGTTC 58.121 50.000 0.00 0.00 0.00 3.01
32 33 1.140052 TGCGAGAAGGGTCAAAGTTCA 59.860 47.619 0.00 0.00 0.00 3.18
33 34 2.224523 TGCGAGAAGGGTCAAAGTTCAT 60.225 45.455 0.00 0.00 0.00 2.57
34 35 2.416893 GCGAGAAGGGTCAAAGTTCATC 59.583 50.000 0.00 0.00 0.00 2.92
35 36 3.866449 GCGAGAAGGGTCAAAGTTCATCT 60.866 47.826 0.00 0.00 0.00 2.90
36 37 3.929610 CGAGAAGGGTCAAAGTTCATCTC 59.070 47.826 0.00 0.00 0.00 2.75
37 38 4.561530 CGAGAAGGGTCAAAGTTCATCTCA 60.562 45.833 0.00 0.00 33.40 3.27
38 39 5.495640 GAGAAGGGTCAAAGTTCATCTCAT 58.504 41.667 0.00 0.00 33.87 2.90
39 40 6.627087 AGAAGGGTCAAAGTTCATCTCATA 57.373 37.500 0.00 0.00 0.00 2.15
40 41 6.410540 AGAAGGGTCAAAGTTCATCTCATAC 58.589 40.000 0.00 0.00 0.00 2.39
41 42 5.762179 AGGGTCAAAGTTCATCTCATACA 57.238 39.130 0.00 0.00 0.00 2.29
42 43 5.491982 AGGGTCAAAGTTCATCTCATACAC 58.508 41.667 0.00 0.00 0.00 2.90
43 44 5.013079 AGGGTCAAAGTTCATCTCATACACA 59.987 40.000 0.00 0.00 0.00 3.72
44 45 5.122396 GGGTCAAAGTTCATCTCATACACAC 59.878 44.000 0.00 0.00 0.00 3.82
45 46 5.122396 GGTCAAAGTTCATCTCATACACACC 59.878 44.000 0.00 0.00 0.00 4.16
46 47 5.122396 GTCAAAGTTCATCTCATACACACCC 59.878 44.000 0.00 0.00 0.00 4.61
47 48 4.908601 AAGTTCATCTCATACACACCCA 57.091 40.909 0.00 0.00 0.00 4.51
48 49 4.908601 AGTTCATCTCATACACACCCAA 57.091 40.909 0.00 0.00 0.00 4.12
49 50 4.579869 AGTTCATCTCATACACACCCAAC 58.420 43.478 0.00 0.00 0.00 3.77
50 51 4.041567 AGTTCATCTCATACACACCCAACA 59.958 41.667 0.00 0.00 0.00 3.33
51 52 3.937814 TCATCTCATACACACCCAACAC 58.062 45.455 0.00 0.00 0.00 3.32
52 53 2.448926 TCTCATACACACCCAACACG 57.551 50.000 0.00 0.00 0.00 4.49
53 54 0.796312 CTCATACACACCCAACACGC 59.204 55.000 0.00 0.00 0.00 5.34
54 55 0.946700 TCATACACACCCAACACGCG 60.947 55.000 3.53 3.53 0.00 6.01
55 56 0.946700 CATACACACCCAACACGCGA 60.947 55.000 15.93 0.00 0.00 5.87
56 57 0.669318 ATACACACCCAACACGCGAG 60.669 55.000 15.93 7.88 0.00 5.03
57 58 4.012895 CACACCCAACACGCGAGC 62.013 66.667 15.93 0.00 0.00 5.03
58 59 4.539083 ACACCCAACACGCGAGCA 62.539 61.111 15.93 0.00 0.00 4.26
59 60 4.012895 CACCCAACACGCGAGCAC 62.013 66.667 15.93 0.00 0.00 4.40
60 61 4.539083 ACCCAACACGCGAGCACA 62.539 61.111 15.93 0.00 0.00 4.57
61 62 3.276091 CCCAACACGCGAGCACAA 61.276 61.111 15.93 0.00 0.00 3.33
62 63 2.052237 CCAACACGCGAGCACAAC 60.052 61.111 15.93 0.00 0.00 3.32
63 64 2.534019 CCAACACGCGAGCACAACT 61.534 57.895 15.93 0.00 0.00 3.16
64 65 1.351707 CAACACGCGAGCACAACTT 59.648 52.632 15.93 0.00 0.00 2.66
65 66 0.654472 CAACACGCGAGCACAACTTC 60.654 55.000 15.93 0.00 0.00 3.01
66 67 1.087202 AACACGCGAGCACAACTTCA 61.087 50.000 15.93 0.00 0.00 3.02
67 68 0.880278 ACACGCGAGCACAACTTCAT 60.880 50.000 15.93 0.00 0.00 2.57
68 69 0.179240 CACGCGAGCACAACTTCATC 60.179 55.000 15.93 0.00 0.00 2.92
69 70 0.319900 ACGCGAGCACAACTTCATCT 60.320 50.000 15.93 0.00 0.00 2.90
70 71 0.368227 CGCGAGCACAACTTCATCTC 59.632 55.000 0.00 0.00 0.00 2.75
71 72 1.432514 GCGAGCACAACTTCATCTCA 58.567 50.000 0.00 0.00 0.00 3.27
72 73 2.005451 GCGAGCACAACTTCATCTCAT 58.995 47.619 0.00 0.00 0.00 2.90
73 74 3.190079 GCGAGCACAACTTCATCTCATA 58.810 45.455 0.00 0.00 0.00 2.15
74 75 3.000724 GCGAGCACAACTTCATCTCATAC 59.999 47.826 0.00 0.00 0.00 2.39
75 76 4.428209 CGAGCACAACTTCATCTCATACT 58.572 43.478 0.00 0.00 0.00 2.12
76 77 4.867047 CGAGCACAACTTCATCTCATACTT 59.133 41.667 0.00 0.00 0.00 2.24
77 78 5.349817 CGAGCACAACTTCATCTCATACTTT 59.650 40.000 0.00 0.00 0.00 2.66
78 79 6.128445 CGAGCACAACTTCATCTCATACTTTT 60.128 38.462 0.00 0.00 0.00 2.27
112 113 4.188462 TGTTGGTAGCCAATTATCACTCG 58.812 43.478 3.77 0.00 45.80 4.18
142 143 1.112315 TTGTGTGCCATCACCAACCC 61.112 55.000 0.00 0.00 42.46 4.11
153 154 5.630069 GCCATCACCAACCCTCCATATATAG 60.630 48.000 0.00 0.00 0.00 1.31
158 159 3.189606 CAACCCTCCATATATAGCCCCA 58.810 50.000 0.00 0.00 0.00 4.96
189 190 6.281405 ACTTCAAGACCCGACATAATACATC 58.719 40.000 0.00 0.00 0.00 3.06
207 208 5.679734 ACATCGCCTTGTGAATAATGATC 57.320 39.130 0.00 0.00 0.00 2.92
215 216 7.099120 GCCTTGTGAATAATGATCCACTTTTT 58.901 34.615 0.00 0.00 0.00 1.94
229 230 9.905713 TGATCCACTTTTTAGTTTAGATGCTAT 57.094 29.630 0.00 0.00 0.00 2.97
255 256 7.775397 TTTTTAATAATACTTCCTCCGTCCG 57.225 36.000 0.00 0.00 0.00 4.79
256 257 6.713762 TTTAATAATACTTCCTCCGTCCGA 57.286 37.500 0.00 0.00 0.00 4.55
257 258 6.713762 TTAATAATACTTCCTCCGTCCGAA 57.286 37.500 0.00 0.00 0.00 4.30
258 259 5.603170 AATAATACTTCCTCCGTCCGAAA 57.397 39.130 0.00 0.00 0.00 3.46
259 260 3.967332 AATACTTCCTCCGTCCGAAAA 57.033 42.857 0.00 0.00 0.00 2.29
260 261 4.482952 AATACTTCCTCCGTCCGAAAAT 57.517 40.909 0.00 0.00 0.00 1.82
261 262 5.603170 AATACTTCCTCCGTCCGAAAATA 57.397 39.130 0.00 0.00 0.00 1.40
262 263 3.242549 ACTTCCTCCGTCCGAAAATAC 57.757 47.619 0.00 0.00 0.00 1.89
263 264 2.830321 ACTTCCTCCGTCCGAAAATACT 59.170 45.455 0.00 0.00 0.00 2.12
264 265 3.260128 ACTTCCTCCGTCCGAAAATACTT 59.740 43.478 0.00 0.00 0.00 2.24
265 266 3.241067 TCCTCCGTCCGAAAATACTTG 57.759 47.619 0.00 0.00 0.00 3.16
266 267 2.564062 TCCTCCGTCCGAAAATACTTGT 59.436 45.455 0.00 0.00 0.00 3.16
267 268 2.928116 CCTCCGTCCGAAAATACTTGTC 59.072 50.000 0.00 0.00 0.00 3.18
268 269 2.597305 CTCCGTCCGAAAATACTTGTCG 59.403 50.000 0.00 0.00 34.58 4.35
269 270 2.228582 TCCGTCCGAAAATACTTGTCGA 59.771 45.455 1.13 0.00 36.92 4.20
270 271 2.988493 CCGTCCGAAAATACTTGTCGAA 59.012 45.455 1.13 0.00 36.92 3.71
271 272 3.060363 CCGTCCGAAAATACTTGTCGAAG 59.940 47.826 1.13 0.00 36.92 3.79
272 273 3.916172 CGTCCGAAAATACTTGTCGAAGA 59.084 43.478 1.13 0.00 36.92 2.87
273 274 4.383649 CGTCCGAAAATACTTGTCGAAGAA 59.616 41.667 1.13 0.00 39.69 2.52
274 275 5.107760 CGTCCGAAAATACTTGTCGAAGAAA 60.108 40.000 1.13 0.00 39.69 2.52
275 276 6.400727 CGTCCGAAAATACTTGTCGAAGAAAT 60.401 38.462 1.13 0.00 39.69 2.17
276 277 6.736853 GTCCGAAAATACTTGTCGAAGAAATG 59.263 38.462 1.13 0.00 39.69 2.32
277 278 6.021596 CCGAAAATACTTGTCGAAGAAATGG 58.978 40.000 1.13 0.00 39.69 3.16
278 279 6.021596 CGAAAATACTTGTCGAAGAAATGGG 58.978 40.000 0.00 0.00 39.69 4.00
279 280 6.348213 CGAAAATACTTGTCGAAGAAATGGGT 60.348 38.462 0.00 0.00 39.69 4.51
280 281 7.148540 CGAAAATACTTGTCGAAGAAATGGGTA 60.149 37.037 0.00 0.00 39.69 3.69
281 282 7.989416 AAATACTTGTCGAAGAAATGGGTAA 57.011 32.000 0.00 0.00 39.69 2.85
282 283 7.989416 AATACTTGTCGAAGAAATGGGTAAA 57.011 32.000 0.00 0.00 39.69 2.01
283 284 7.989416 ATACTTGTCGAAGAAATGGGTAAAA 57.011 32.000 0.00 0.00 39.69 1.52
284 285 6.702716 ACTTGTCGAAGAAATGGGTAAAAA 57.297 33.333 0.00 0.00 39.69 1.94
285 286 7.284919 ACTTGTCGAAGAAATGGGTAAAAAT 57.715 32.000 0.00 0.00 39.69 1.82
286 287 7.145323 ACTTGTCGAAGAAATGGGTAAAAATG 58.855 34.615 0.00 0.00 39.69 2.32
287 288 6.885952 TGTCGAAGAAATGGGTAAAAATGA 57.114 33.333 0.00 0.00 39.69 2.57
288 289 7.278461 TGTCGAAGAAATGGGTAAAAATGAA 57.722 32.000 0.00 0.00 39.69 2.57
289 290 7.891561 TGTCGAAGAAATGGGTAAAAATGAAT 58.108 30.769 0.00 0.00 39.69 2.57
290 291 7.812191 TGTCGAAGAAATGGGTAAAAATGAATG 59.188 33.333 0.00 0.00 39.69 2.67
291 292 7.812669 GTCGAAGAAATGGGTAAAAATGAATGT 59.187 33.333 0.00 0.00 39.69 2.71
292 293 9.015367 TCGAAGAAATGGGTAAAAATGAATGTA 57.985 29.630 0.00 0.00 0.00 2.29
293 294 9.801873 CGAAGAAATGGGTAAAAATGAATGTAT 57.198 29.630 0.00 0.00 0.00 2.29
333 334 8.952278 ACGTCTAGATATATCCATTTCTCTGAC 58.048 37.037 9.18 2.98 31.02 3.51
334 335 8.951243 CGTCTAGATATATCCATTTCTCTGACA 58.049 37.037 9.18 0.00 32.24 3.58
344 345 7.912056 TCCATTTCTCTGACAAGTATTTCTG 57.088 36.000 0.00 0.00 0.00 3.02
345 346 6.881065 TCCATTTCTCTGACAAGTATTTCTGG 59.119 38.462 0.00 0.00 0.00 3.86
346 347 6.881065 CCATTTCTCTGACAAGTATTTCTGGA 59.119 38.462 0.00 0.00 0.00 3.86
347 348 7.148340 CCATTTCTCTGACAAGTATTTCTGGAC 60.148 40.741 0.00 0.00 0.00 4.02
348 349 5.060662 TCTCTGACAAGTATTTCTGGACG 57.939 43.478 0.00 0.00 0.00 4.79
349 350 4.082190 TCTCTGACAAGTATTTCTGGACGG 60.082 45.833 0.00 0.00 0.00 4.79
350 351 3.830178 TCTGACAAGTATTTCTGGACGGA 59.170 43.478 0.00 0.00 0.00 4.69
351 352 4.082190 TCTGACAAGTATTTCTGGACGGAG 60.082 45.833 0.00 0.00 0.00 4.63
352 353 3.056107 TGACAAGTATTTCTGGACGGAGG 60.056 47.826 0.00 0.00 0.00 4.30
353 354 3.170717 ACAAGTATTTCTGGACGGAGGA 58.829 45.455 0.00 0.00 0.00 3.71
354 355 3.581332 ACAAGTATTTCTGGACGGAGGAA 59.419 43.478 0.00 0.00 0.00 3.36
355 356 4.184629 CAAGTATTTCTGGACGGAGGAAG 58.815 47.826 0.00 0.00 0.00 3.46
373 374 6.488006 GGAGGAAGTATATGATTGTGTGCATT 59.512 38.462 0.00 0.00 0.00 3.56
417 420 6.741992 TGACAATATCAGAATTTGCGAACT 57.258 33.333 0.00 0.00 31.91 3.01
420 423 8.175069 TGACAATATCAGAATTTGCGAACTAAC 58.825 33.333 0.00 0.00 31.91 2.34
421 424 7.472543 ACAATATCAGAATTTGCGAACTAACC 58.527 34.615 0.00 0.00 0.00 2.85
422 425 7.336931 ACAATATCAGAATTTGCGAACTAACCT 59.663 33.333 0.00 0.00 0.00 3.50
423 426 8.826710 CAATATCAGAATTTGCGAACTAACCTA 58.173 33.333 0.00 0.00 0.00 3.08
424 427 9.561069 AATATCAGAATTTGCGAACTAACCTAT 57.439 29.630 0.00 0.00 0.00 2.57
425 428 6.662414 TCAGAATTTGCGAACTAACCTATG 57.338 37.500 0.00 0.00 0.00 2.23
426 429 5.584649 TCAGAATTTGCGAACTAACCTATGG 59.415 40.000 0.00 0.00 0.00 2.74
427 430 5.354234 CAGAATTTGCGAACTAACCTATGGT 59.646 40.000 0.00 0.00 37.65 3.55
429 432 5.560966 ATTTGCGAACTAACCTATGGTTG 57.439 39.130 11.78 5.16 46.35 3.77
430 433 2.980568 TGCGAACTAACCTATGGTTGG 58.019 47.619 11.78 11.16 46.35 3.77
431 434 2.568062 TGCGAACTAACCTATGGTTGGA 59.432 45.455 17.52 0.00 45.18 3.53
432 435 3.199071 TGCGAACTAACCTATGGTTGGAT 59.801 43.478 17.52 7.46 45.18 3.41
433 436 3.560068 GCGAACTAACCTATGGTTGGATG 59.440 47.826 17.52 8.78 45.18 3.51
434 437 4.127171 CGAACTAACCTATGGTTGGATGG 58.873 47.826 17.52 5.52 45.18 3.51
435 438 4.383770 CGAACTAACCTATGGTTGGATGGT 60.384 45.833 17.52 2.78 45.18 3.55
436 439 5.506708 GAACTAACCTATGGTTGGATGGTT 58.493 41.667 17.52 11.06 45.18 3.67
446 449 2.092914 GGTTGGATGGTTAGGAGGACAG 60.093 54.545 0.00 0.00 0.00 3.51
456 459 1.019650 AGGAGGACAGTGGTATCCCT 58.980 55.000 0.00 0.00 34.82 4.20
467 470 0.693092 GGTATCCCTAGCCCACCACA 60.693 60.000 0.00 0.00 0.00 4.17
479 482 2.166254 GCCCACCACAGGTCATTTATTG 59.834 50.000 0.00 0.00 31.02 1.90
482 485 3.257873 CCACCACAGGTCATTTATTGCAA 59.742 43.478 0.00 0.00 31.02 4.08
488 491 6.875195 CCACAGGTCATTTATTGCAAGATTTT 59.125 34.615 4.94 0.00 0.00 1.82
514 517 1.067776 GTACGTGTTCAGTGGGAGGAG 60.068 57.143 0.00 0.00 0.00 3.69
520 523 1.070289 GTTCAGTGGGAGGAGACGTTT 59.930 52.381 0.00 0.00 0.00 3.60
567 578 5.862924 AAAATCTCAATATGATACGCCGG 57.137 39.130 0.00 0.00 0.00 6.13
571 582 1.616374 TCAATATGATACGCCGGCTCA 59.384 47.619 26.68 21.93 0.00 4.26
574 585 1.037493 TATGATACGCCGGCTCAGTT 58.963 50.000 26.68 10.03 0.00 3.16
579 590 2.537792 TACGCCGGCTCAGTTTCTCG 62.538 60.000 26.68 7.01 0.00 4.04
583 594 0.243907 CCGGCTCAGTTTCTCGAAGA 59.756 55.000 0.00 0.00 0.00 2.87
589 600 4.177026 GCTCAGTTTCTCGAAGATGCTTA 58.823 43.478 0.00 0.00 33.89 3.09
594 605 6.096987 TCAGTTTCTCGAAGATGCTTATAGGT 59.903 38.462 0.00 0.00 33.89 3.08
600 611 5.382616 TCGAAGATGCTTATAGGTGTAGGA 58.617 41.667 0.00 0.00 0.00 2.94
608 619 2.890808 ATAGGTGTAGGATGTGCGTG 57.109 50.000 0.00 0.00 0.00 5.34
660 671 8.833493 ACATGTATATATATGAGCGCTTACGTA 58.167 33.333 22.13 5.86 42.83 3.57
704 715 3.808728 TCAGGATTTTTCTATCAGGCCG 58.191 45.455 0.00 0.00 0.00 6.13
840 856 0.758734 CTCGACCTAATGGGCCATGA 59.241 55.000 22.01 12.44 38.45 3.07
841 857 1.140852 CTCGACCTAATGGGCCATGAA 59.859 52.381 22.01 10.77 38.45 2.57
900 924 1.209621 AGGGTTAGCATCCGCCTTTA 58.790 50.000 0.00 0.00 39.83 1.85
901 925 1.774856 AGGGTTAGCATCCGCCTTTAT 59.225 47.619 0.00 0.00 39.83 1.40
902 926 2.976882 AGGGTTAGCATCCGCCTTTATA 59.023 45.455 0.00 0.00 39.83 0.98
906 933 4.760204 GGTTAGCATCCGCCTTTATATGTT 59.240 41.667 0.00 0.00 39.83 2.71
910 937 4.455877 AGCATCCGCCTTTATATGTTTAGC 59.544 41.667 0.00 0.00 39.83 3.09
938 965 4.106925 GCCCTCCTCCTGCCACAG 62.107 72.222 0.00 0.00 0.00 3.66
944 971 2.750657 CCTCCTGCCACAGATCCCC 61.751 68.421 0.00 0.00 32.44 4.81
951 978 0.769873 GCCACAGATCCCCATCAGAT 59.230 55.000 0.00 0.00 0.00 2.90
1297 1447 1.028868 GCAGGACATCTCCAAGGCAC 61.029 60.000 0.00 0.00 39.39 5.01
1313 1463 1.738099 CACCGGTTTCTGAGCCTCG 60.738 63.158 2.97 0.00 0.00 4.63
1348 1498 0.891373 CGAGGAGCCTGTTTCTGAGA 59.109 55.000 0.00 0.00 0.00 3.27
1383 1695 5.471456 GGACCAGGATGTTTATGATGATGAC 59.529 44.000 0.00 0.00 0.00 3.06
1605 1962 1.682684 GGAGAGGGTCCTCGAGCAA 60.683 63.158 6.99 0.00 46.90 3.91
1628 1986 2.643232 GCCCGAGTACCAGGACGTT 61.643 63.158 5.84 0.00 0.00 3.99
1685 2043 3.461085 ACATAAGTCTGATCTTGGCCCAT 59.539 43.478 0.00 0.00 0.00 4.00
1717 2075 1.382522 CCAATCACCCATGACCTTCG 58.617 55.000 0.00 0.00 37.79 3.79
1797 2158 1.376812 CCGGTGTACAAGAAGGCCC 60.377 63.158 0.00 0.00 0.00 5.80
1826 2187 3.321968 GGTTTGAGAAGTTTCAGGCCAAT 59.678 43.478 5.01 0.00 0.00 3.16
1907 2269 2.310052 AGGGACAGATTTTGGGAAGAGG 59.690 50.000 0.00 0.00 0.00 3.69
1990 2760 3.307059 GGATCATCCGTTATTCTGGAGGG 60.307 52.174 0.00 0.00 37.76 4.30
2017 2790 6.001460 TGGGGATTATAAACGATGATGAACC 58.999 40.000 0.00 0.00 0.00 3.62
2018 2791 6.183361 TGGGGATTATAAACGATGATGAACCT 60.183 38.462 0.00 0.00 0.00 3.50
2058 2831 7.716612 TCATGTCTGTCCATGTATACAAGTAG 58.283 38.462 10.14 7.93 42.29 2.57
2059 2832 7.342026 TCATGTCTGTCCATGTATACAAGTAGT 59.658 37.037 10.14 0.00 42.29 2.73
2060 2833 8.630037 CATGTCTGTCCATGTATACAAGTAGTA 58.370 37.037 10.14 0.00 37.91 1.82
2070 2843 2.474410 ACAAGTAGTACAAGCAGGCC 57.526 50.000 2.52 0.00 0.00 5.19
2198 2974 1.369091 GGTATGTGTTCGCCTGGCTG 61.369 60.000 17.92 10.52 0.00 4.85
2269 3047 5.416013 TGTTCATGTGTGTTTGGTTTACTGA 59.584 36.000 0.00 0.00 0.00 3.41
2279 3057 9.689976 TGTGTTTGGTTTACTGATATTTGATTG 57.310 29.630 0.00 0.00 0.00 2.67
2287 3065 5.456921 ACTGATATTTGATTGGGACCACT 57.543 39.130 0.00 0.00 0.00 4.00
2291 3069 6.934056 TGATATTTGATTGGGACCACTTTTG 58.066 36.000 0.00 0.00 0.00 2.44
2304 3082 0.781278 ACTTTTGGGGGAAATCGGGA 59.219 50.000 0.00 0.00 0.00 5.14
2307 3085 2.632763 TTTGGGGGAAATCGGGAATT 57.367 45.000 0.00 0.00 0.00 2.17
2364 3359 7.394016 TCTACCATCTGCATCTTAAAAGTTCA 58.606 34.615 0.00 0.00 0.00 3.18
2368 3363 7.341256 ACCATCTGCATCTTAAAAGTTCATCAT 59.659 33.333 0.00 0.00 0.00 2.45
2378 3373 7.502226 TCTTAAAAGTTCATCATCCTGTGTTGT 59.498 33.333 0.00 0.00 0.00 3.32
2391 3386 1.542030 TGTGTTGTTTTGTGGCTCGTT 59.458 42.857 0.00 0.00 0.00 3.85
2404 3399 2.024414 GGCTCGTTCCTATTGGCATTT 58.976 47.619 0.00 0.00 0.00 2.32
2413 3408 6.198966 CGTTCCTATTGGCATTTAAGATTTGC 59.801 38.462 0.00 0.00 35.64 3.68
2462 3457 5.919755 TGATCTGTATTGCCGGTTGTAATA 58.080 37.500 1.90 1.00 31.27 0.98
2463 3458 6.350103 TGATCTGTATTGCCGGTTGTAATAA 58.650 36.000 1.90 0.00 33.98 1.40
2464 3459 6.995686 TGATCTGTATTGCCGGTTGTAATAAT 59.004 34.615 1.90 0.00 33.98 1.28
2505 3500 4.882671 TTCTGCTGAAGTTCACTTGTTC 57.117 40.909 0.08 0.00 36.11 3.18
2506 3501 4.142609 TCTGCTGAAGTTCACTTGTTCT 57.857 40.909 0.08 0.00 36.11 3.01
2523 3518 7.908082 CACTTGTTCTTTACAGAAAAATCGTGA 59.092 33.333 7.63 0.00 40.90 4.35
2532 3527 9.925268 TTTACAGAAAAATCGTGAACTTCTAAC 57.075 29.630 0.00 0.00 0.00 2.34
2614 3609 3.281727 TGGACCTTGATCCATGTTAGC 57.718 47.619 0.00 0.00 44.14 3.09
2615 3610 2.846206 TGGACCTTGATCCATGTTAGCT 59.154 45.455 0.00 0.00 44.14 3.32
2616 3611 4.037222 TGGACCTTGATCCATGTTAGCTA 58.963 43.478 0.00 0.00 44.14 3.32
2617 3612 4.473196 TGGACCTTGATCCATGTTAGCTAA 59.527 41.667 0.86 0.86 44.14 3.09
2618 3613 5.132648 TGGACCTTGATCCATGTTAGCTAAT 59.867 40.000 9.88 0.00 44.14 1.73
2619 3614 6.064717 GGACCTTGATCCATGTTAGCTAATT 58.935 40.000 9.88 0.00 38.77 1.40
2620 3615 6.547510 GGACCTTGATCCATGTTAGCTAATTT 59.452 38.462 9.88 0.00 38.77 1.82
2621 3616 7.068716 GGACCTTGATCCATGTTAGCTAATTTT 59.931 37.037 9.88 0.00 38.77 1.82
2622 3617 8.366359 ACCTTGATCCATGTTAGCTAATTTTT 57.634 30.769 9.88 0.00 0.00 1.94
2641 3636 4.695217 TTTTTCCATATTGCTCGGTGAC 57.305 40.909 0.00 0.00 0.00 3.67
2642 3637 3.342377 TTTCCATATTGCTCGGTGACA 57.658 42.857 0.00 0.00 0.00 3.58
2643 3638 2.309528 TCCATATTGCTCGGTGACAC 57.690 50.000 0.00 0.00 0.00 3.67
2644 3639 1.552792 TCCATATTGCTCGGTGACACA 59.447 47.619 8.08 0.00 0.00 3.72
2645 3640 2.027653 TCCATATTGCTCGGTGACACAA 60.028 45.455 8.08 0.00 0.00 3.33
2646 3641 2.945008 CCATATTGCTCGGTGACACAAT 59.055 45.455 8.08 0.89 36.70 2.71
2647 3642 4.126437 CCATATTGCTCGGTGACACAATA 58.874 43.478 8.08 3.17 38.82 1.90
2648 3643 4.756642 CCATATTGCTCGGTGACACAATAT 59.243 41.667 8.08 5.34 43.18 1.28
2649 3644 5.929697 ATATTGCTCGGTGACACAATATG 57.070 39.130 8.08 0.00 41.68 1.78
2650 3645 2.022764 TGCTCGGTGACACAATATGG 57.977 50.000 8.08 0.00 0.00 2.74
2651 3646 1.552792 TGCTCGGTGACACAATATGGA 59.447 47.619 8.08 0.00 0.00 3.41
2652 3647 1.933853 GCTCGGTGACACAATATGGAC 59.066 52.381 8.08 0.00 0.00 4.02
2653 3648 2.550978 CTCGGTGACACAATATGGACC 58.449 52.381 8.08 0.00 33.47 4.46
2654 3649 2.168521 CTCGGTGACACAATATGGACCT 59.831 50.000 8.08 0.00 34.27 3.85
2655 3650 2.569853 TCGGTGACACAATATGGACCTT 59.430 45.455 8.08 0.00 34.27 3.50
2656 3651 2.677836 CGGTGACACAATATGGACCTTG 59.322 50.000 8.08 0.00 34.27 3.61
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 3.553922 CCCTTCTCGCATCCTAATCTCAC 60.554 52.174 0.00 0.00 0.00 3.51
1 2 2.630098 CCCTTCTCGCATCCTAATCTCA 59.370 50.000 0.00 0.00 0.00 3.27
2 3 2.630580 ACCCTTCTCGCATCCTAATCTC 59.369 50.000 0.00 0.00 0.00 2.75
4 5 2.365617 TGACCCTTCTCGCATCCTAATC 59.634 50.000 0.00 0.00 0.00 1.75
5 6 2.398588 TGACCCTTCTCGCATCCTAAT 58.601 47.619 0.00 0.00 0.00 1.73
6 7 1.860641 TGACCCTTCTCGCATCCTAA 58.139 50.000 0.00 0.00 0.00 2.69
7 8 1.860641 TTGACCCTTCTCGCATCCTA 58.139 50.000 0.00 0.00 0.00 2.94
8 9 0.984230 TTTGACCCTTCTCGCATCCT 59.016 50.000 0.00 0.00 0.00 3.24
9 10 1.339151 ACTTTGACCCTTCTCGCATCC 60.339 52.381 0.00 0.00 0.00 3.51
10 11 2.100605 ACTTTGACCCTTCTCGCATC 57.899 50.000 0.00 0.00 0.00 3.91
11 12 2.224523 TGAACTTTGACCCTTCTCGCAT 60.225 45.455 0.00 0.00 0.00 4.73
12 13 1.140052 TGAACTTTGACCCTTCTCGCA 59.860 47.619 0.00 0.00 0.00 5.10
13 14 1.878953 TGAACTTTGACCCTTCTCGC 58.121 50.000 0.00 0.00 0.00 5.03
14 15 3.929610 GAGATGAACTTTGACCCTTCTCG 59.070 47.826 0.00 0.00 0.00 4.04
15 16 4.899502 TGAGATGAACTTTGACCCTTCTC 58.100 43.478 0.00 0.00 33.24 2.87
16 17 4.982241 TGAGATGAACTTTGACCCTTCT 57.018 40.909 0.00 0.00 0.00 2.85
17 18 6.092807 GTGTATGAGATGAACTTTGACCCTTC 59.907 42.308 0.00 0.00 0.00 3.46
18 19 5.940470 GTGTATGAGATGAACTTTGACCCTT 59.060 40.000 0.00 0.00 0.00 3.95
19 20 5.013079 TGTGTATGAGATGAACTTTGACCCT 59.987 40.000 0.00 0.00 0.00 4.34
20 21 5.122396 GTGTGTATGAGATGAACTTTGACCC 59.878 44.000 0.00 0.00 0.00 4.46
21 22 5.122396 GGTGTGTATGAGATGAACTTTGACC 59.878 44.000 0.00 0.00 0.00 4.02
22 23 5.122396 GGGTGTGTATGAGATGAACTTTGAC 59.878 44.000 0.00 0.00 0.00 3.18
23 24 5.221823 TGGGTGTGTATGAGATGAACTTTGA 60.222 40.000 0.00 0.00 0.00 2.69
24 25 5.003160 TGGGTGTGTATGAGATGAACTTTG 58.997 41.667 0.00 0.00 0.00 2.77
25 26 5.241403 TGGGTGTGTATGAGATGAACTTT 57.759 39.130 0.00 0.00 0.00 2.66
26 27 4.908601 TGGGTGTGTATGAGATGAACTT 57.091 40.909 0.00 0.00 0.00 2.66
27 28 4.041567 TGTTGGGTGTGTATGAGATGAACT 59.958 41.667 0.00 0.00 0.00 3.01
28 29 4.154195 GTGTTGGGTGTGTATGAGATGAAC 59.846 45.833 0.00 0.00 0.00 3.18
29 30 4.323417 GTGTTGGGTGTGTATGAGATGAA 58.677 43.478 0.00 0.00 0.00 2.57
30 31 3.616317 CGTGTTGGGTGTGTATGAGATGA 60.616 47.826 0.00 0.00 0.00 2.92
31 32 2.672874 CGTGTTGGGTGTGTATGAGATG 59.327 50.000 0.00 0.00 0.00 2.90
32 33 2.935238 GCGTGTTGGGTGTGTATGAGAT 60.935 50.000 0.00 0.00 0.00 2.75
33 34 1.606994 GCGTGTTGGGTGTGTATGAGA 60.607 52.381 0.00 0.00 0.00 3.27
34 35 0.796312 GCGTGTTGGGTGTGTATGAG 59.204 55.000 0.00 0.00 0.00 2.90
35 36 0.946700 CGCGTGTTGGGTGTGTATGA 60.947 55.000 0.00 0.00 0.00 2.15
36 37 0.946700 TCGCGTGTTGGGTGTGTATG 60.947 55.000 5.77 0.00 0.00 2.39
37 38 0.669318 CTCGCGTGTTGGGTGTGTAT 60.669 55.000 5.77 0.00 0.00 2.29
38 39 1.300311 CTCGCGTGTTGGGTGTGTA 60.300 57.895 5.77 0.00 0.00 2.90
39 40 2.587753 CTCGCGTGTTGGGTGTGT 60.588 61.111 5.77 0.00 0.00 3.72
40 41 4.012895 GCTCGCGTGTTGGGTGTG 62.013 66.667 5.77 0.00 0.00 3.82
41 42 4.539083 TGCTCGCGTGTTGGGTGT 62.539 61.111 5.77 0.00 0.00 4.16
42 43 4.012895 GTGCTCGCGTGTTGGGTG 62.013 66.667 5.77 0.00 0.00 4.61
43 44 4.539083 TGTGCTCGCGTGTTGGGT 62.539 61.111 5.77 0.00 0.00 4.51
44 45 3.276091 TTGTGCTCGCGTGTTGGG 61.276 61.111 5.77 0.00 0.00 4.12
45 46 2.047151 AAGTTGTGCTCGCGTGTTGG 62.047 55.000 5.77 0.00 0.00 3.77
46 47 0.654472 GAAGTTGTGCTCGCGTGTTG 60.654 55.000 5.77 0.00 0.00 3.33
47 48 1.087202 TGAAGTTGTGCTCGCGTGTT 61.087 50.000 5.77 0.00 0.00 3.32
48 49 0.880278 ATGAAGTTGTGCTCGCGTGT 60.880 50.000 5.77 0.00 0.00 4.49
49 50 0.179240 GATGAAGTTGTGCTCGCGTG 60.179 55.000 5.77 4.44 0.00 5.34
50 51 0.319900 AGATGAAGTTGTGCTCGCGT 60.320 50.000 5.77 0.00 0.00 6.01
51 52 0.368227 GAGATGAAGTTGTGCTCGCG 59.632 55.000 0.00 0.00 0.00 5.87
52 53 1.432514 TGAGATGAAGTTGTGCTCGC 58.567 50.000 0.00 0.00 0.00 5.03
53 54 4.428209 AGTATGAGATGAAGTTGTGCTCG 58.572 43.478 0.00 0.00 0.00 5.03
54 55 6.734104 AAAGTATGAGATGAAGTTGTGCTC 57.266 37.500 0.00 0.00 0.00 4.26
55 56 7.516198 AAAAAGTATGAGATGAAGTTGTGCT 57.484 32.000 0.00 0.00 0.00 4.40
76 77 7.556844 TGGCTACCAACAAATTTAGTGAAAAA 58.443 30.769 0.00 0.00 0.00 1.94
77 78 7.113658 TGGCTACCAACAAATTTAGTGAAAA 57.886 32.000 0.00 0.00 0.00 2.29
78 79 6.716934 TGGCTACCAACAAATTTAGTGAAA 57.283 33.333 0.00 0.00 0.00 2.69
87 88 6.183360 CGAGTGATAATTGGCTACCAACAAAT 60.183 38.462 0.17 0.00 46.95 2.32
93 94 3.958147 TCTCGAGTGATAATTGGCTACCA 59.042 43.478 13.13 0.00 0.00 3.25
112 113 3.921119 TGGCACACAAATTGATGTCTC 57.079 42.857 0.00 0.00 0.00 3.36
142 143 5.762179 TTCAAGTGGGGCTATATATGGAG 57.238 43.478 0.00 0.00 0.00 3.86
172 173 2.029290 AGGCGATGTATTATGTCGGGTC 60.029 50.000 0.00 0.00 36.00 4.46
176 177 4.048504 TCACAAGGCGATGTATTATGTCG 58.951 43.478 0.00 0.00 38.34 4.35
189 190 3.879295 AGTGGATCATTATTCACAAGGCG 59.121 43.478 1.18 0.00 43.24 5.52
241 242 4.019174 AGTATTTTCGGACGGAGGAAGTA 58.981 43.478 0.00 0.00 0.00 2.24
242 243 2.830321 AGTATTTTCGGACGGAGGAAGT 59.170 45.455 0.00 0.00 0.00 3.01
243 244 3.521947 AGTATTTTCGGACGGAGGAAG 57.478 47.619 0.00 0.00 0.00 3.46
244 245 3.007182 ACAAGTATTTTCGGACGGAGGAA 59.993 43.478 0.00 0.00 0.00 3.36
245 246 2.564062 ACAAGTATTTTCGGACGGAGGA 59.436 45.455 0.00 0.00 0.00 3.71
246 247 2.928116 GACAAGTATTTTCGGACGGAGG 59.072 50.000 0.00 0.00 0.00 4.30
247 248 2.597305 CGACAAGTATTTTCGGACGGAG 59.403 50.000 0.00 0.00 0.00 4.63
248 249 2.228582 TCGACAAGTATTTTCGGACGGA 59.771 45.455 0.00 0.00 33.50 4.69
249 250 2.598589 TCGACAAGTATTTTCGGACGG 58.401 47.619 0.00 0.00 33.50 4.79
250 251 3.916172 TCTTCGACAAGTATTTTCGGACG 59.084 43.478 0.00 0.00 33.50 4.79
251 252 5.834239 TTCTTCGACAAGTATTTTCGGAC 57.166 39.130 0.00 0.00 33.50 4.79
252 253 6.128391 CCATTTCTTCGACAAGTATTTTCGGA 60.128 38.462 0.00 0.00 33.50 4.55
253 254 6.021596 CCATTTCTTCGACAAGTATTTTCGG 58.978 40.000 0.00 0.00 33.50 4.30
254 255 6.021596 CCCATTTCTTCGACAAGTATTTTCG 58.978 40.000 0.00 0.00 0.00 3.46
255 256 6.909909 ACCCATTTCTTCGACAAGTATTTTC 58.090 36.000 0.00 0.00 0.00 2.29
256 257 6.894339 ACCCATTTCTTCGACAAGTATTTT 57.106 33.333 0.00 0.00 0.00 1.82
257 258 7.989416 TTACCCATTTCTTCGACAAGTATTT 57.011 32.000 0.00 0.00 0.00 1.40
258 259 7.989416 TTTACCCATTTCTTCGACAAGTATT 57.011 32.000 0.00 0.00 0.00 1.89
259 260 7.989416 TTTTACCCATTTCTTCGACAAGTAT 57.011 32.000 0.00 0.00 0.00 2.12
260 261 7.804843 TTTTTACCCATTTCTTCGACAAGTA 57.195 32.000 0.00 0.00 0.00 2.24
261 262 6.702716 TTTTTACCCATTTCTTCGACAAGT 57.297 33.333 0.00 0.00 0.00 3.16
262 263 7.367285 TCATTTTTACCCATTTCTTCGACAAG 58.633 34.615 0.00 0.00 0.00 3.16
263 264 7.278461 TCATTTTTACCCATTTCTTCGACAA 57.722 32.000 0.00 0.00 0.00 3.18
264 265 6.885952 TCATTTTTACCCATTTCTTCGACA 57.114 33.333 0.00 0.00 0.00 4.35
265 266 7.812669 ACATTCATTTTTACCCATTTCTTCGAC 59.187 33.333 0.00 0.00 0.00 4.20
266 267 7.891561 ACATTCATTTTTACCCATTTCTTCGA 58.108 30.769 0.00 0.00 0.00 3.71
267 268 9.801873 ATACATTCATTTTTACCCATTTCTTCG 57.198 29.630 0.00 0.00 0.00 3.79
307 308 8.952278 GTCAGAGAAATGGATATATCTAGACGT 58.048 37.037 12.42 0.00 0.00 4.34
308 309 8.951243 TGTCAGAGAAATGGATATATCTAGACG 58.049 37.037 12.42 0.00 33.34 4.18
318 319 9.605275 CAGAAATACTTGTCAGAGAAATGGATA 57.395 33.333 0.00 0.00 0.00 2.59
319 320 7.555554 CCAGAAATACTTGTCAGAGAAATGGAT 59.444 37.037 0.00 0.00 0.00 3.41
320 321 6.881065 CCAGAAATACTTGTCAGAGAAATGGA 59.119 38.462 0.00 0.00 0.00 3.41
321 322 6.881065 TCCAGAAATACTTGTCAGAGAAATGG 59.119 38.462 0.00 0.00 0.00 3.16
322 323 7.412346 CGTCCAGAAATACTTGTCAGAGAAATG 60.412 40.741 0.00 0.00 0.00 2.32
323 324 6.591834 CGTCCAGAAATACTTGTCAGAGAAAT 59.408 38.462 0.00 0.00 0.00 2.17
324 325 5.926542 CGTCCAGAAATACTTGTCAGAGAAA 59.073 40.000 0.00 0.00 0.00 2.52
325 326 5.470368 CGTCCAGAAATACTTGTCAGAGAA 58.530 41.667 0.00 0.00 0.00 2.87
326 327 4.082190 CCGTCCAGAAATACTTGTCAGAGA 60.082 45.833 0.00 0.00 0.00 3.10
327 328 4.082190 TCCGTCCAGAAATACTTGTCAGAG 60.082 45.833 0.00 0.00 0.00 3.35
328 329 3.830178 TCCGTCCAGAAATACTTGTCAGA 59.170 43.478 0.00 0.00 0.00 3.27
329 330 4.177026 CTCCGTCCAGAAATACTTGTCAG 58.823 47.826 0.00 0.00 0.00 3.51
330 331 3.056107 CCTCCGTCCAGAAATACTTGTCA 60.056 47.826 0.00 0.00 0.00 3.58
331 332 3.194968 TCCTCCGTCCAGAAATACTTGTC 59.805 47.826 0.00 0.00 0.00 3.18
332 333 3.170717 TCCTCCGTCCAGAAATACTTGT 58.829 45.455 0.00 0.00 0.00 3.16
333 334 3.887621 TCCTCCGTCCAGAAATACTTG 57.112 47.619 0.00 0.00 0.00 3.16
334 335 3.838903 ACTTCCTCCGTCCAGAAATACTT 59.161 43.478 0.00 0.00 0.00 2.24
335 336 3.442076 ACTTCCTCCGTCCAGAAATACT 58.558 45.455 0.00 0.00 0.00 2.12
336 337 3.889520 ACTTCCTCCGTCCAGAAATAC 57.110 47.619 0.00 0.00 0.00 1.89
337 338 7.008332 TCATATACTTCCTCCGTCCAGAAATA 58.992 38.462 0.00 0.00 0.00 1.40
338 339 5.839063 TCATATACTTCCTCCGTCCAGAAAT 59.161 40.000 0.00 0.00 0.00 2.17
339 340 5.205821 TCATATACTTCCTCCGTCCAGAAA 58.794 41.667 0.00 0.00 0.00 2.52
340 341 4.800023 TCATATACTTCCTCCGTCCAGAA 58.200 43.478 0.00 0.00 0.00 3.02
341 342 4.448720 TCATATACTTCCTCCGTCCAGA 57.551 45.455 0.00 0.00 0.00 3.86
342 343 5.011125 ACAATCATATACTTCCTCCGTCCAG 59.989 44.000 0.00 0.00 0.00 3.86
343 344 4.899457 ACAATCATATACTTCCTCCGTCCA 59.101 41.667 0.00 0.00 0.00 4.02
344 345 5.221461 ACACAATCATATACTTCCTCCGTCC 60.221 44.000 0.00 0.00 0.00 4.79
345 346 5.692204 CACACAATCATATACTTCCTCCGTC 59.308 44.000 0.00 0.00 0.00 4.79
346 347 5.601662 CACACAATCATATACTTCCTCCGT 58.398 41.667 0.00 0.00 0.00 4.69
347 348 4.449068 GCACACAATCATATACTTCCTCCG 59.551 45.833 0.00 0.00 0.00 4.63
348 349 5.368145 TGCACACAATCATATACTTCCTCC 58.632 41.667 0.00 0.00 0.00 4.30
349 350 7.502120 AATGCACACAATCATATACTTCCTC 57.498 36.000 0.00 0.00 0.00 3.71
350 351 7.886629 AAATGCACACAATCATATACTTCCT 57.113 32.000 0.00 0.00 0.00 3.36
351 352 8.931385 AAAAATGCACACAATCATATACTTCC 57.069 30.769 0.00 0.00 0.00 3.46
395 398 7.640240 GGTTAGTTCGCAAATTCTGATATTGTC 59.360 37.037 5.28 0.00 0.00 3.18
417 420 5.290335 TCCTAACCATCCAACCATAGGTTA 58.710 41.667 0.40 0.00 45.01 2.85
420 423 3.073062 CCTCCTAACCATCCAACCATAGG 59.927 52.174 0.00 0.00 32.90 2.57
421 424 3.973973 TCCTCCTAACCATCCAACCATAG 59.026 47.826 0.00 0.00 0.00 2.23
422 425 3.714798 GTCCTCCTAACCATCCAACCATA 59.285 47.826 0.00 0.00 0.00 2.74
423 426 2.509964 GTCCTCCTAACCATCCAACCAT 59.490 50.000 0.00 0.00 0.00 3.55
424 427 1.913419 GTCCTCCTAACCATCCAACCA 59.087 52.381 0.00 0.00 0.00 3.67
425 428 1.913419 TGTCCTCCTAACCATCCAACC 59.087 52.381 0.00 0.00 0.00 3.77
426 429 2.572104 ACTGTCCTCCTAACCATCCAAC 59.428 50.000 0.00 0.00 0.00 3.77
427 430 2.571653 CACTGTCCTCCTAACCATCCAA 59.428 50.000 0.00 0.00 0.00 3.53
428 431 2.187958 CACTGTCCTCCTAACCATCCA 58.812 52.381 0.00 0.00 0.00 3.41
429 432 1.486726 CCACTGTCCTCCTAACCATCC 59.513 57.143 0.00 0.00 0.00 3.51
430 433 2.188817 ACCACTGTCCTCCTAACCATC 58.811 52.381 0.00 0.00 0.00 3.51
431 434 2.344093 ACCACTGTCCTCCTAACCAT 57.656 50.000 0.00 0.00 0.00 3.55
432 435 3.371965 GATACCACTGTCCTCCTAACCA 58.628 50.000 0.00 0.00 0.00 3.67
433 436 2.699321 GGATACCACTGTCCTCCTAACC 59.301 54.545 0.00 0.00 0.00 2.85
456 459 1.072266 AAATGACCTGTGGTGGGCTA 58.928 50.000 0.00 0.00 35.25 3.93
467 470 7.029563 GTCGAAAATCTTGCAATAAATGACCT 58.970 34.615 0.00 0.00 0.00 3.85
479 482 1.723003 ACGTACCGTCGAAAATCTTGC 59.277 47.619 0.00 0.00 33.69 4.01
482 485 2.712057 ACACGTACCGTCGAAAATCT 57.288 45.000 0.00 0.00 38.32 2.40
488 491 0.041047 CACTGAACACGTACCGTCGA 60.041 55.000 0.00 0.00 38.32 4.20
499 502 0.469331 ACGTCTCCTCCCACTGAACA 60.469 55.000 0.00 0.00 0.00 3.18
514 517 0.438830 GTGCAGTCGATGGAAACGTC 59.561 55.000 0.00 0.00 43.20 4.34
520 523 2.261361 CACCGTGCAGTCGATGGA 59.739 61.111 0.00 0.00 0.00 3.41
567 578 2.615869 AGCATCTTCGAGAAACTGAGC 58.384 47.619 0.00 0.00 0.00 4.26
571 582 6.127310 ACACCTATAAGCATCTTCGAGAAACT 60.127 38.462 0.00 0.00 0.00 2.66
574 585 5.854010 ACACCTATAAGCATCTTCGAGAA 57.146 39.130 0.00 0.00 0.00 2.87
579 590 6.870965 CACATCCTACACCTATAAGCATCTTC 59.129 42.308 0.00 0.00 0.00 2.87
583 594 4.561530 CGCACATCCTACACCTATAAGCAT 60.562 45.833 0.00 0.00 0.00 3.79
589 600 2.108168 ACACGCACATCCTACACCTAT 58.892 47.619 0.00 0.00 0.00 2.57
594 605 0.391228 ACACACACGCACATCCTACA 59.609 50.000 0.00 0.00 0.00 2.74
600 611 0.534877 ATGACCACACACACGCACAT 60.535 50.000 0.00 0.00 0.00 3.21
608 619 3.928992 CACTCACTCATATGACCACACAC 59.071 47.826 0.00 0.00 0.00 3.82
646 657 1.209128 GTGCATACGTAAGCGCTCAT 58.791 50.000 24.57 0.00 42.83 2.90
647 658 2.660944 GTGCATACGTAAGCGCTCA 58.339 52.632 24.57 0.00 42.83 4.26
694 705 1.550976 GGATACCTTCCGGCCTGATAG 59.449 57.143 0.00 0.36 33.93 2.08
704 715 9.031537 TTTTATGGAAAAAGAAGGATACCTTCC 57.968 33.333 21.95 10.76 43.32 3.46
840 856 1.806496 TGGGATCAGGATCGGATGTT 58.194 50.000 0.00 0.00 38.69 2.71
841 857 1.806496 TTGGGATCAGGATCGGATGT 58.194 50.000 0.00 0.00 38.69 3.06
900 924 1.959226 CGGCGGCGGCTAAACATAT 60.959 57.895 30.65 0.00 39.81 1.78
901 925 2.586635 CGGCGGCGGCTAAACATA 60.587 61.111 30.65 0.00 39.81 2.29
921 948 4.106925 CTGTGGCAGGAGGAGGGC 62.107 72.222 0.00 0.00 0.00 5.19
934 961 5.688807 AGTTTAATCTGATGGGGATCTGTG 58.311 41.667 0.00 0.00 0.00 3.66
938 965 5.506317 CGCAAAGTTTAATCTGATGGGGATC 60.506 44.000 0.00 0.00 0.00 3.36
944 971 4.346129 GCCTCGCAAAGTTTAATCTGATG 58.654 43.478 0.00 0.00 0.00 3.07
951 978 1.873698 ACTCGCCTCGCAAAGTTTAA 58.126 45.000 0.00 0.00 0.00 1.52
1074 1191 1.811266 CCCGTCGATGGCTGACTTG 60.811 63.158 18.81 0.00 34.17 3.16
1290 1440 1.856265 GCTCAGAAACCGGTGCCTTG 61.856 60.000 8.52 4.98 0.00 3.61
1297 1447 2.125512 CCGAGGCTCAGAAACCGG 60.126 66.667 15.95 0.00 0.00 5.28
1325 1475 1.079057 GAAACAGGCTCCTCGGTCC 60.079 63.158 0.00 0.00 0.00 4.46
1328 1478 0.108424 CTCAGAAACAGGCTCCTCGG 60.108 60.000 0.00 0.00 0.00 4.63
1348 1498 1.611851 CCTGGTCCTCAGCCTGAGT 60.612 63.158 19.89 0.00 42.80 3.41
1383 1695 6.892310 TCTTGATAATCATAATCGGCATCG 57.108 37.500 0.00 0.00 37.82 3.84
1605 1962 0.325296 TCCTGGTACTCGGGCTTGAT 60.325 55.000 4.73 0.00 41.78 2.57
1670 2028 1.767088 CTCTCATGGGCCAAGATCAGA 59.233 52.381 11.89 4.55 0.00 3.27
1717 2075 4.150897 TCAGCTGGGTATATTGTGGAAC 57.849 45.455 15.13 0.00 37.35 3.62
1797 2158 4.199310 TGAAACTTCTCAAACCTGTCCTG 58.801 43.478 0.00 0.00 0.00 3.86
1826 2187 0.103026 CGATCAGATCCTTGCGGACA 59.897 55.000 4.73 0.00 43.51 4.02
1907 2269 4.086706 TCTTTTTCCACTCTTCCTCCAC 57.913 45.455 0.00 0.00 0.00 4.02
1990 2760 3.395639 TCATCGTTTATAATCCCCACGC 58.604 45.455 2.47 0.00 0.00 5.34
2017 2790 2.485426 ACATGATGTTTGACGGCAAGAG 59.515 45.455 2.76 0.00 35.04 2.85
2018 2791 2.483877 GACATGATGTTTGACGGCAAGA 59.516 45.455 2.76 0.00 35.04 3.02
2058 2831 3.536956 TGTATACAGGCCTGCTTGTAC 57.463 47.619 33.06 25.78 40.43 2.90
2059 2832 3.370103 GGTTGTATACAGGCCTGCTTGTA 60.370 47.826 33.06 18.48 41.52 2.41
2060 2833 2.618045 GGTTGTATACAGGCCTGCTTGT 60.618 50.000 33.06 16.72 39.57 3.16
2198 2974 4.666928 TTTTAGGCGTCGAATTTACCAC 57.333 40.909 0.00 0.00 0.00 4.16
2269 3047 5.189539 CCCAAAAGTGGTCCCAATCAAATAT 59.810 40.000 0.00 0.00 44.30 1.28
2279 3057 0.105401 TTTCCCCCAAAAGTGGTCCC 60.105 55.000 0.00 0.00 44.30 4.46
2287 3065 2.569404 CAATTCCCGATTTCCCCCAAAA 59.431 45.455 0.00 0.00 0.00 2.44
2291 3069 1.860641 AACAATTCCCGATTTCCCCC 58.139 50.000 0.00 0.00 0.00 5.40
2304 3082 2.482721 CGACCGCAACTAGGAAACAATT 59.517 45.455 0.00 0.00 0.00 2.32
2307 3085 0.675083 TCGACCGCAACTAGGAAACA 59.325 50.000 0.00 0.00 0.00 2.83
2318 3096 6.085555 AGATAGAAGATTAATTCGACCGCA 57.914 37.500 0.00 0.00 34.27 5.69
2364 3359 3.243839 GCCACAAAACAACACAGGATGAT 60.244 43.478 0.00 0.00 39.69 2.45
2368 3363 1.748493 GAGCCACAAAACAACACAGGA 59.252 47.619 0.00 0.00 0.00 3.86
2378 3373 2.817258 CCAATAGGAACGAGCCACAAAA 59.183 45.455 0.00 0.00 36.89 2.44
2391 3386 8.710749 ATAGCAAATCTTAAATGCCAATAGGA 57.289 30.769 0.00 0.00 40.93 2.94
2404 3399 9.979897 ATAGATGCCCAAATATAGCAAATCTTA 57.020 29.630 0.00 0.00 40.46 2.10
2478 3473 7.945134 ACAAGTGAACTTCAGCAGAAAATAAT 58.055 30.769 0.00 0.00 33.11 1.28
2484 3479 4.517285 AGAACAAGTGAACTTCAGCAGAA 58.483 39.130 0.00 0.00 33.11 3.02
2506 3501 9.925268 GTTAGAAGTTCACGATTTTTCTGTAAA 57.075 29.630 5.50 0.00 31.19 2.01
2575 3570 2.754552 CCAACCACAGGGACACAATATG 59.245 50.000 0.00 0.00 38.05 1.78
2579 3574 2.312323 TCCAACCACAGGGACACAA 58.688 52.632 0.00 0.00 38.05 3.33
2620 3615 4.075682 TGTCACCGAGCAATATGGAAAAA 58.924 39.130 0.00 0.00 0.00 1.94
2621 3616 3.438781 GTGTCACCGAGCAATATGGAAAA 59.561 43.478 0.00 0.00 0.00 2.29
2622 3617 3.006940 GTGTCACCGAGCAATATGGAAA 58.993 45.455 0.00 0.00 0.00 3.13
2623 3618 2.027653 TGTGTCACCGAGCAATATGGAA 60.028 45.455 0.00 0.00 0.00 3.53
2624 3619 1.552792 TGTGTCACCGAGCAATATGGA 59.447 47.619 0.00 0.00 0.00 3.41
2625 3620 2.022764 TGTGTCACCGAGCAATATGG 57.977 50.000 0.00 0.00 0.00 2.74
2626 3621 5.682869 CATATTGTGTCACCGAGCAATATG 58.317 41.667 16.49 16.49 46.44 1.78
2627 3622 4.756642 CCATATTGTGTCACCGAGCAATAT 59.243 41.667 0.00 0.71 42.05 1.28
2628 3623 4.126437 CCATATTGTGTCACCGAGCAATA 58.874 43.478 0.00 0.00 37.93 1.90
2629 3624 2.945008 CCATATTGTGTCACCGAGCAAT 59.055 45.455 0.00 0.00 35.90 3.56
2630 3625 2.027653 TCCATATTGTGTCACCGAGCAA 60.028 45.455 0.00 0.00 0.00 3.91
2631 3626 1.552792 TCCATATTGTGTCACCGAGCA 59.447 47.619 0.00 0.00 0.00 4.26
2632 3627 1.933853 GTCCATATTGTGTCACCGAGC 59.066 52.381 0.00 0.00 0.00 5.03
2633 3628 2.168521 AGGTCCATATTGTGTCACCGAG 59.831 50.000 0.00 0.00 35.15 4.63
2634 3629 2.184533 AGGTCCATATTGTGTCACCGA 58.815 47.619 0.00 0.00 35.15 4.69
2635 3630 2.677836 CAAGGTCCATATTGTGTCACCG 59.322 50.000 0.00 0.00 35.15 4.94


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

AutoCloner maintained by Alex Coulton.