Multiple sequence alignment - TraesCS4A01G353500

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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 TraesCS4A01G353500 chr4A 100.000 5954 0 0 1 5954 628502027 628507980 0.000000e+00 10996.0
1 TraesCS4A01G353500 chr4A 88.525 366 39 3 2798 3162 627752163 627751800 1.970000e-119 440.0
2 TraesCS4A01G353500 chr4A 87.549 257 27 5 2581 2834 627752433 627752179 5.840000e-75 292.0
3 TraesCS4A01G353500 chr4A 88.115 244 24 4 3156 3394 627751779 627751536 9.770000e-73 285.0
4 TraesCS4A01G353500 chr4A 76.757 370 53 26 5608 5950 628693523 628693886 6.130000e-40 176.0
5 TraesCS4A01G353500 chr5B 91.534 2079 106 35 2908 4946 681962052 681960004 0.000000e+00 2800.0
6 TraesCS4A01G353500 chr5B 95.181 913 31 6 5045 5954 681959899 681958997 0.000000e+00 1430.0
7 TraesCS4A01G353500 chr5B 82.738 1344 129 53 3391 4671 682850941 682852244 0.000000e+00 1101.0
8 TraesCS4A01G353500 chr5B 93.875 702 26 8 837 1523 681963985 681963286 0.000000e+00 1042.0
9 TraesCS4A01G353500 chr5B 89.851 739 68 4 27 760 681964821 681964085 0.000000e+00 942.0
10 TraesCS4A01G353500 chr5B 89.035 684 45 16 1521 2187 681963239 681962569 0.000000e+00 821.0
11 TraesCS4A01G353500 chr5B 81.956 593 71 19 3400 3981 683975296 683974729 2.510000e-128 470.0
12 TraesCS4A01G353500 chr5B 89.041 365 25 3 2798 3162 682850301 682850650 7.080000e-119 438.0
13 TraesCS4A01G353500 chr5B 86.352 403 40 9 1742 2137 682848846 682849240 5.520000e-115 425.0
14 TraesCS4A01G353500 chr5B 88.760 258 26 3 2579 2833 681962407 681962150 4.480000e-81 313.0
15 TraesCS4A01G353500 chr5B 86.786 280 15 9 969 1226 682848232 682848511 5.840000e-75 292.0
16 TraesCS4A01G353500 chr5B 83.051 236 27 9 3154 3385 682850670 682850896 1.010000e-47 202.0
17 TraesCS4A01G353500 chr5B 86.826 167 13 5 2614 2779 682850087 682850245 1.710000e-40 178.0
18 TraesCS4A01G353500 chr5B 92.793 111 8 0 1406 1516 683974717 683974607 1.720000e-35 161.0
19 TraesCS4A01G353500 chr5B 78.007 291 35 19 4183 4451 683973870 683973587 7.990000e-34 156.0
20 TraesCS4A01G353500 chr5B 75.871 373 49 31 5608 5943 681662858 681663226 1.030000e-32 152.0
21 TraesCS4A01G353500 chr5B 88.095 126 15 0 2179 2304 682849069 682849194 3.720000e-32 150.0
22 TraesCS4A01G353500 chr5B 94.737 95 5 0 2296 2390 602263878 602263972 1.340000e-31 148.0
23 TraesCS4A01G353500 chr5B 81.690 142 17 3 4810 4946 683973444 683973307 6.310000e-20 110.0
24 TraesCS4A01G353500 chr5B 95.455 44 2 0 2849 2892 681962094 681962051 2.980000e-08 71.3
25 TraesCS4A01G353500 chr5D 91.906 1705 78 28 4297 5954 539872594 539870903 0.000000e+00 2329.0
26 TraesCS4A01G353500 chr5D 88.091 1545 129 34 1 1523 539876915 539875404 0.000000e+00 1783.0
27 TraesCS4A01G353500 chr5D 93.044 1107 63 12 2849 3950 539874263 539873166 0.000000e+00 1605.0
28 TraesCS4A01G353500 chr5D 83.280 1555 154 48 3154 4671 540587663 540589148 0.000000e+00 1334.0
29 TraesCS4A01G353500 chr5D 82.444 1555 160 49 3154 4671 540832205 540833683 0.000000e+00 1254.0
30 TraesCS4A01G353500 chr5D 82.598 1224 93 58 969 2137 540585067 540586225 0.000000e+00 970.0
31 TraesCS4A01G353500 chr5D 83.965 923 96 27 3157 4061 541909693 541908805 0.000000e+00 837.0
32 TraesCS4A01G353500 chr5D 83.440 936 93 34 3154 4061 541807164 541806263 0.000000e+00 813.0
33 TraesCS4A01G353500 chr5D 85.950 605 49 21 2579 3159 540831590 540832182 1.100000e-171 614.0
34 TraesCS4A01G353500 chr5D 87.570 539 31 13 1652 2187 539875252 539874747 5.140000e-165 592.0
35 TraesCS4A01G353500 chr5D 85.124 605 54 21 2579 3159 540587048 540587640 2.390000e-163 586.0
36 TraesCS4A01G353500 chr5D 84.746 590 58 19 1560 2137 541809266 541808697 4.030000e-156 562.0
37 TraesCS4A01G353500 chr5D 84.654 593 59 19 1560 2140 541911733 541911161 4.030000e-156 562.0
38 TraesCS4A01G353500 chr5D 86.939 490 40 10 1665 2137 540830285 540830767 4.090000e-146 529.0
39 TraesCS4A01G353500 chr5D 94.186 344 17 3 3956 4299 539873049 539872709 6.840000e-144 521.0
40 TraesCS4A01G353500 chr5D 84.677 496 36 16 1651 2140 540614890 540615351 5.440000e-125 459.0
41 TraesCS4A01G353500 chr5D 91.098 337 19 5 1191 1523 540829785 540830114 4.230000e-121 446.0
42 TraesCS4A01G353500 chr5D 88.525 366 39 3 2798 3162 540615878 540616241 1.970000e-119 440.0
43 TraesCS4A01G353500 chr5D 82.420 529 69 11 997 1522 541809879 541809372 1.970000e-119 440.0
44 TraesCS4A01G353500 chr5D 82.897 497 66 11 1652 2140 541911084 541910599 4.260000e-116 429.0
45 TraesCS4A01G353500 chr5D 82.794 494 67 13 1652 2140 540586308 540586788 5.520000e-115 425.0
46 TraesCS4A01G353500 chr5D 82.389 494 69 13 1652 2140 540830850 540831330 1.190000e-111 414.0
47 TraesCS4A01G353500 chr5D 87.879 363 28 8 2800 3162 541910063 541909717 4.290000e-111 412.0
48 TraesCS4A01G353500 chr5D 87.052 363 36 4 2800 3162 541807535 541807184 3.340000e-107 399.0
49 TraesCS4A01G353500 chr5D 80.110 543 68 23 4059 4570 541908718 541908185 9.430000e-98 368.0
50 TraesCS4A01G353500 chr5D 80.800 500 69 17 4059 4537 541806183 541805690 3.390000e-97 366.0
51 TraesCS4A01G353500 chr5D 90.038 261 21 5 2579 2834 541910341 541910081 3.440000e-87 333.0
52 TraesCS4A01G353500 chr5D 89.412 255 23 4 2579 2829 541807812 541807558 9.630000e-83 318.0
53 TraesCS4A01G353500 chr5D 87.903 248 29 1 2581 2828 540615610 540615856 2.100000e-74 291.0
54 TraesCS4A01G353500 chr5D 88.306 248 21 7 3154 3395 540616261 540616506 2.100000e-74 291.0
55 TraesCS4A01G353500 chr5D 81.793 368 46 8 1160 1522 541912190 541911839 7.550000e-74 289.0
56 TraesCS4A01G353500 chr5D 87.395 238 25 5 2579 2812 539874585 539874349 9.840000e-68 268.0
57 TraesCS4A01G353500 chr5D 92.258 155 9 1 969 1120 540829426 540829580 3.610000e-52 217.0
58 TraesCS4A01G353500 chr5D 77.717 368 47 28 5611 5950 539725982 539725622 6.090000e-45 193.0
59 TraesCS4A01G353500 chr5D 83.417 199 25 4 5033 5223 541805235 541805037 1.710000e-40 178.0
60 TraesCS4A01G353500 chr5D 88.079 151 15 3 2157 2306 540586592 540586740 6.130000e-40 176.0
61 TraesCS4A01G353500 chr5D 88.079 151 15 3 2157 2306 540831134 540831282 6.130000e-40 176.0
62 TraesCS4A01G353500 chr5D 88.889 135 14 1 2172 2306 541910780 541910647 1.330000e-36 165.0
63 TraesCS4A01G353500 chr5D 88.889 126 14 0 2179 2304 540586054 540586179 7.990000e-34 156.0
64 TraesCS4A01G353500 chr5D 83.562 146 13 4 4810 4948 541908138 541907997 6.260000e-25 126.0
65 TraesCS4A01G353500 chr5D 95.918 49 0 1 1548 1594 540830181 540830229 1.780000e-10 78.7
66 TraesCS4A01G353500 chr5D 92.593 54 3 1 2387 2439 539874844 539874791 6.400000e-10 76.8
67 TraesCS4A01G353500 chr5D 92.453 53 3 1 2388 2439 541910084 541910032 2.300000e-09 75.0
68 TraesCS4A01G353500 chr5D 90.741 54 4 1 2387 2439 541807557 541807504 2.980000e-08 71.3
69 TraesCS4A01G353500 chr6B 90.337 445 33 6 5517 5954 713923350 713922909 5.180000e-160 575.0
70 TraesCS4A01G353500 chr7A 98.837 86 1 0 2304 2389 138960742 138960827 2.870000e-33 154.0
71 TraesCS4A01G353500 chr6A 98.837 86 1 0 2304 2389 172113267 172113182 2.870000e-33 154.0
72 TraesCS4A01G353500 chr1D 96.703 91 3 0 2299 2389 64325912 64326002 1.030000e-32 152.0
73 TraesCS4A01G353500 chr2D 95.699 93 4 0 2297 2389 165009228 165009320 3.720000e-32 150.0
74 TraesCS4A01G353500 chr2D 93.878 98 5 1 2293 2389 51248216 51248119 4.810000e-31 147.0
75 TraesCS4A01G353500 chr2D 88.136 118 10 4 2276 2391 649141946 649142061 2.890000e-28 137.0
76 TraesCS4A01G353500 chr2B 92.079 101 8 0 2303 2403 12015689 12015789 6.220000e-30 143.0
77 TraesCS4A01G353500 chr1B 94.565 92 5 0 2298 2389 666824309 666824400 6.220000e-30 143.0


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 TraesCS4A01G353500 chr4A 628502027 628507980 5953 False 10996.000000 10996 100.000000 1 5954 1 chr4A.!!$F1 5953
1 TraesCS4A01G353500 chr4A 627751536 627752433 897 True 339.000000 440 88.063000 2581 3394 3 chr4A.!!$R1 813
2 TraesCS4A01G353500 chr5B 681958997 681964821 5824 True 1059.900000 2800 91.955857 27 5954 7 chr5B.!!$R1 5927
3 TraesCS4A01G353500 chr5B 682848232 682852244 4012 False 398.000000 1101 86.127000 969 4671 7 chr5B.!!$F3 3702
4 TraesCS4A01G353500 chr5B 683973307 683975296 1989 True 224.250000 470 83.611500 1406 4946 4 chr5B.!!$R2 3540
5 TraesCS4A01G353500 chr5D 539870903 539876915 6012 True 1024.971429 2329 90.683571 1 5954 7 chr5D.!!$R2 5953
6 TraesCS4A01G353500 chr5D 540585067 540589148 4081 False 607.833333 1334 85.127333 969 4671 6 chr5D.!!$F1 3702
7 TraesCS4A01G353500 chr5D 540829426 540833683 4257 False 466.087500 1254 88.134375 969 4671 8 chr5D.!!$F3 3702
8 TraesCS4A01G353500 chr5D 541805037 541809879 4842 True 393.412500 813 85.253500 997 5223 8 chr5D.!!$R3 4226
9 TraesCS4A01G353500 chr5D 540614890 540616506 1616 False 370.250000 459 87.352750 1651 3395 4 chr5D.!!$F2 1744
10 TraesCS4A01G353500 chr5D 541907997 541912190 4193 True 359.600000 837 85.624000 1160 4948 10 chr5D.!!$R4 3788

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
437 443 0.472898 GGAGCCCCTTGTATACCCAC 59.527 60.0 0.00 0.00 0.00 4.61 F
559 565 0.734889 GACGCCACCATTCAAGATGG 59.265 55.0 3.58 3.58 44.54 3.51 F
1504 1732 0.109412 ACGTTTCTCCACGGTCGATC 60.109 55.0 0.00 0.00 44.82 3.69 F
2519 3458 0.179000 AGCCTGCTGTATGCCTGTAC 59.821 55.0 0.00 0.00 42.00 2.90 F
3869 5195 1.123077 TGCGAGGATGAGCCAGTATT 58.877 50.0 0.00 0.00 40.02 1.89 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1486 1714 0.170561 AGATCGACCGTGGAGAAACG 59.829 55.0 0.0 0.0 43.20 3.60 R
1822 2392 0.250295 TTCACTCTGAACAAGGCGGG 60.250 55.0 0.0 0.0 30.26 6.13 R
2659 3780 0.603569 GACTCCGAAGTCCTTGCAGA 59.396 55.0 0.0 0.0 45.26 4.26 R
4243 5791 0.178995 TGATGCAGGGTGCTGAACAA 60.179 50.0 0.0 0.0 45.31 2.83 R
5567 7434 0.107654 CCCCTACTACAACAGCAGCC 60.108 60.0 0.0 0.0 0.00 4.85 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
47 48 2.730094 CACAACCTGGGCAACTGC 59.270 61.111 0.00 0.00 41.14 4.40
69 70 5.600484 TGCCTTGTTTAAAATCTCTTCCCAA 59.400 36.000 0.00 0.00 0.00 4.12
149 150 6.441093 TTCAGATATGCAAACACTCCATTC 57.559 37.500 0.00 0.00 0.00 2.67
187 188 5.570205 TCAGCCGGTAATCCCAAATATTA 57.430 39.130 1.90 0.00 0.00 0.98
278 279 6.662234 AGCCCTTACCAAAGTAAATAAAGGAC 59.338 38.462 0.00 0.00 37.99 3.85
338 339 1.538047 TTTGCACTGAATCTCTGGCC 58.462 50.000 0.00 0.00 0.00 5.36
343 344 1.153005 CTGAATCTCTGGCCCAGGC 60.153 63.158 11.68 0.00 41.06 4.85
437 443 0.472898 GGAGCCCCTTGTATACCCAC 59.527 60.000 0.00 0.00 0.00 4.61
440 446 1.834301 CCCCTTGTATACCCACCGG 59.166 63.158 0.00 0.00 0.00 5.28
466 472 5.581085 GTCACTTCCTCACGCTTTAACATAT 59.419 40.000 0.00 0.00 0.00 1.78
473 479 6.874664 TCCTCACGCTTTAACATATAACACAA 59.125 34.615 0.00 0.00 0.00 3.33
474 480 7.551262 TCCTCACGCTTTAACATATAACACAAT 59.449 33.333 0.00 0.00 0.00 2.71
558 564 1.667724 GAGACGCCACCATTCAAGATG 59.332 52.381 0.00 0.00 0.00 2.90
559 565 0.734889 GACGCCACCATTCAAGATGG 59.265 55.000 3.58 3.58 44.54 3.51
610 620 1.809567 GAGCTGCACAAACCTTGGGG 61.810 60.000 1.02 0.00 33.68 4.96
611 621 2.871253 GCTGCACAAACCTTGGGGG 61.871 63.158 0.00 0.00 41.89 5.40
612 622 2.841988 TGCACAAACCTTGGGGGC 60.842 61.111 0.00 0.00 39.10 5.80
613 623 3.989787 GCACAAACCTTGGGGGCG 61.990 66.667 0.00 0.00 39.10 6.13
630 640 3.056179 GGGGCGAATCCAATTTTCTTCAA 60.056 43.478 0.00 0.00 36.21 2.69
662 672 5.303078 TCCAGATAACTCCATTCTACTCTGC 59.697 44.000 0.00 0.00 0.00 4.26
669 679 3.900601 CTCCATTCTACTCTGCCATAGGT 59.099 47.826 0.00 0.00 0.00 3.08
699 709 8.604035 CATCGTATCTAACTTAACTGCACAATT 58.396 33.333 0.00 0.00 0.00 2.32
755 765 5.872635 GTGCAGACATTTATATGCGCATAT 58.127 37.500 37.15 37.15 45.90 1.78
763 786 7.639039 ACATTTATATGCGCATATTTATCCGG 58.361 34.615 39.32 25.51 35.71 5.14
776 799 7.764443 GCATATTTATCCGGAATAAGCAGAGTA 59.236 37.037 9.01 0.00 35.13 2.59
780 803 4.585955 TCCGGAATAAGCAGAGTATGTC 57.414 45.455 0.00 0.00 0.00 3.06
783 833 5.128827 TCCGGAATAAGCAGAGTATGTCTTT 59.871 40.000 0.00 0.00 30.64 2.52
784 834 5.817816 CCGGAATAAGCAGAGTATGTCTTTT 59.182 40.000 0.00 0.00 30.64 2.27
785 835 6.316390 CCGGAATAAGCAGAGTATGTCTTTTT 59.684 38.462 0.00 0.49 30.64 1.94
897 948 3.611674 CACCACCGCAAAACCCCC 61.612 66.667 0.00 0.00 0.00 5.40
913 968 1.296715 CCCTTCTCCCCTTCACACG 59.703 63.158 0.00 0.00 0.00 4.49
917 972 2.358737 CTCCCCTTCACACGCACC 60.359 66.667 0.00 0.00 0.00 5.01
929 984 3.582120 CGCACCCACACACACACC 61.582 66.667 0.00 0.00 0.00 4.16
1172 1258 4.825679 CCTCCCCCTCCTCCCACC 62.826 77.778 0.00 0.00 0.00 4.61
1236 1445 1.521681 GTTGCTCGGATCGAAGGGG 60.522 63.158 0.00 0.00 34.74 4.79
1299 1526 2.450345 GGCGGTTCGTGTCGGATTC 61.450 63.158 0.00 0.00 0.00 2.52
1364 1591 4.363990 CGATGGGATCCGCCGAGG 62.364 72.222 5.45 0.00 42.97 4.63
1486 1714 2.286121 TCCCATCCACCTCCCCAC 60.286 66.667 0.00 0.00 0.00 4.61
1495 1723 1.460689 ACCTCCCCACGTTTCTCCA 60.461 57.895 0.00 0.00 0.00 3.86
1504 1732 0.109412 ACGTTTCTCCACGGTCGATC 60.109 55.000 0.00 0.00 44.82 3.69
1517 1745 0.781191 GTCGATCTCGCAATGCTAGC 59.219 55.000 8.10 8.10 39.60 3.42
1538 1821 1.523938 GCGGTAGGATTCAGTGGCC 60.524 63.158 0.00 0.00 0.00 5.36
1596 1927 2.477825 CCTATCTGAACCTGATGTGCG 58.522 52.381 0.00 0.00 0.00 5.34
1601 1956 0.950555 TGAACCTGATGTGCGCTGTC 60.951 55.000 9.73 4.54 0.00 3.51
1614 1969 1.135139 GCGCTGTCTCTGAACCTGATA 59.865 52.381 0.00 0.00 0.00 2.15
1618 1973 5.106118 GCGCTGTCTCTGAACCTGATATATA 60.106 44.000 0.00 0.00 0.00 0.86
1619 1974 6.570571 GCGCTGTCTCTGAACCTGATATATAA 60.571 42.308 0.00 0.00 0.00 0.98
1620 1975 7.026562 CGCTGTCTCTGAACCTGATATATAAG 58.973 42.308 0.00 0.00 0.00 1.73
1622 1977 7.812191 GCTGTCTCTGAACCTGATATATAAGTG 59.188 40.741 0.00 0.00 0.00 3.16
1623 1978 7.661968 TGTCTCTGAACCTGATATATAAGTGC 58.338 38.462 0.00 0.00 0.00 4.40
1625 1980 7.596995 GTCTCTGAACCTGATATATAAGTGCAC 59.403 40.741 9.40 9.40 0.00 4.57
1626 1981 7.507277 TCTCTGAACCTGATATATAAGTGCACT 59.493 37.037 15.25 15.25 0.00 4.40
1628 1983 7.069950 TCTGAACCTGATATATAAGTGCACTGT 59.930 37.037 22.49 14.96 0.00 3.55
1629 1984 8.245195 TGAACCTGATATATAAGTGCACTGTA 57.755 34.615 22.49 16.73 0.00 2.74
1630 1985 8.870116 TGAACCTGATATATAAGTGCACTGTAT 58.130 33.333 22.49 21.98 0.00 2.29
1631 1986 9.360093 GAACCTGATATATAAGTGCACTGTATC 57.640 37.037 22.49 22.34 0.00 2.24
1632 1987 8.657387 ACCTGATATATAAGTGCACTGTATCT 57.343 34.615 22.49 13.96 0.00 1.98
1634 1989 9.935241 CCTGATATATAAGTGCACTGTATCTTT 57.065 33.333 22.49 5.01 0.00 2.52
1732 2278 5.340403 GTGTCATGTTGTTTGTGAATGATCG 59.660 40.000 0.00 0.00 30.52 3.69
1745 2298 0.684153 ATGATCGGGTGCCCTTTTGG 60.684 55.000 5.64 0.00 39.97 3.28
1822 2392 4.533222 CCAGTTGGTTCAACACGATTTAC 58.467 43.478 12.46 0.00 45.66 2.01
1825 2395 2.144730 TGGTTCAACACGATTTACCCG 58.855 47.619 0.00 0.00 0.00 5.28
1888 2461 2.910360 CATCGCATCCACCTCCCA 59.090 61.111 0.00 0.00 0.00 4.37
1895 2468 2.178580 GCATCCACCTCCCAATTTTGA 58.821 47.619 0.00 0.00 0.00 2.69
1906 2479 2.568509 CCCAATTTTGACCTTGGCTCAT 59.431 45.455 0.00 0.00 40.51 2.90
1912 2485 3.726557 TTGACCTTGGCTCATTCTCAT 57.273 42.857 0.00 0.00 0.00 2.90
1961 2534 4.447290 TGTTAGTGCTTCTGTTTACTGCA 58.553 39.130 0.00 0.00 0.00 4.41
1962 2535 5.063204 TGTTAGTGCTTCTGTTTACTGCAT 58.937 37.500 0.00 0.00 36.04 3.96
2044 2620 3.192422 CCTTGTTGTCAGGTGTTTGTGAA 59.808 43.478 0.00 0.00 0.00 3.18
2141 2722 3.684305 TGTGGCAGTTGATCATAAACTCG 59.316 43.478 0.00 0.00 35.70 4.18
2159 2790 3.573110 ACTCGTTTACCAGTGCTTCTAGT 59.427 43.478 0.00 0.00 0.00 2.57
2160 2791 3.909430 TCGTTTACCAGTGCTTCTAGTG 58.091 45.455 0.00 0.00 0.00 2.74
2220 3155 6.494893 TCTATGTTTGCATCACCAAAGTAC 57.505 37.500 0.00 0.00 35.55 2.73
2226 3161 2.084546 GCATCACCAAAGTACCAGGAC 58.915 52.381 0.00 0.00 0.00 3.85
2227 3162 2.552155 GCATCACCAAAGTACCAGGACA 60.552 50.000 0.00 0.00 0.00 4.02
2237 3172 3.115390 AGTACCAGGACAGCATACCATT 58.885 45.455 0.00 0.00 0.00 3.16
2238 3173 4.295201 AGTACCAGGACAGCATACCATTA 58.705 43.478 0.00 0.00 0.00 1.90
2253 3188 6.751888 GCATACCATTATTGTCAGGTTGTTTC 59.248 38.462 0.00 0.00 35.62 2.78
2284 3219 6.687105 GCTTAGGTCTTGTATGTAATTTTGCG 59.313 38.462 0.00 0.00 0.00 4.85
2306 3241 5.050972 GCGCCAGTAGATCATAAACTTGTAC 60.051 44.000 0.00 0.00 0.00 2.90
2307 3242 6.273825 CGCCAGTAGATCATAAACTTGTACT 58.726 40.000 0.00 0.00 0.00 2.73
2308 3243 6.418226 CGCCAGTAGATCATAAACTTGTACTC 59.582 42.308 0.00 0.00 0.00 2.59
2309 3244 6.702282 GCCAGTAGATCATAAACTTGTACTCC 59.298 42.308 0.00 0.00 0.00 3.85
2310 3245 7.210873 CCAGTAGATCATAAACTTGTACTCCC 58.789 42.308 0.00 0.00 0.00 4.30
2311 3246 7.070074 CCAGTAGATCATAAACTTGTACTCCCT 59.930 40.741 0.00 0.00 0.00 4.20
2312 3247 8.138712 CAGTAGATCATAAACTTGTACTCCCTC 58.861 40.741 0.00 0.00 0.00 4.30
2313 3248 6.487299 AGATCATAAACTTGTACTCCCTCC 57.513 41.667 0.00 0.00 0.00 4.30
2314 3249 4.730949 TCATAAACTTGTACTCCCTCCG 57.269 45.455 0.00 0.00 0.00 4.63
2315 3250 4.091549 TCATAAACTTGTACTCCCTCCGT 58.908 43.478 0.00 0.00 0.00 4.69
2316 3251 5.263599 TCATAAACTTGTACTCCCTCCGTA 58.736 41.667 0.00 0.00 0.00 4.02
2317 3252 5.716228 TCATAAACTTGTACTCCCTCCGTAA 59.284 40.000 0.00 0.00 0.00 3.18
2318 3253 4.961438 AAACTTGTACTCCCTCCGTAAA 57.039 40.909 0.00 0.00 0.00 2.01
2319 3254 3.949842 ACTTGTACTCCCTCCGTAAAC 57.050 47.619 0.00 0.00 0.00 2.01
2320 3255 3.504375 ACTTGTACTCCCTCCGTAAACT 58.496 45.455 0.00 0.00 0.00 2.66
2321 3256 4.666512 ACTTGTACTCCCTCCGTAAACTA 58.333 43.478 0.00 0.00 0.00 2.24
2322 3257 5.079643 ACTTGTACTCCCTCCGTAAACTAA 58.920 41.667 0.00 0.00 0.00 2.24
2323 3258 5.718607 ACTTGTACTCCCTCCGTAAACTAAT 59.281 40.000 0.00 0.00 0.00 1.73
2324 3259 6.891908 ACTTGTACTCCCTCCGTAAACTAATA 59.108 38.462 0.00 0.00 0.00 0.98
2325 3260 7.562821 ACTTGTACTCCCTCCGTAAACTAATAT 59.437 37.037 0.00 0.00 0.00 1.28
2326 3261 8.995027 TTGTACTCCCTCCGTAAACTAATATA 57.005 34.615 0.00 0.00 0.00 0.86
2327 3262 8.995027 TGTACTCCCTCCGTAAACTAATATAA 57.005 34.615 0.00 0.00 0.00 0.98
2328 3263 9.071276 TGTACTCCCTCCGTAAACTAATATAAG 57.929 37.037 0.00 0.00 0.00 1.73
2329 3264 9.289782 GTACTCCCTCCGTAAACTAATATAAGA 57.710 37.037 0.00 0.00 0.00 2.10
2330 3265 8.406730 ACTCCCTCCGTAAACTAATATAAGAG 57.593 38.462 0.00 0.00 0.00 2.85
2331 3266 8.003629 ACTCCCTCCGTAAACTAATATAAGAGT 58.996 37.037 0.00 0.00 0.00 3.24
2332 3267 8.174733 TCCCTCCGTAAACTAATATAAGAGTG 57.825 38.462 0.00 0.00 0.00 3.51
2333 3268 7.781693 TCCCTCCGTAAACTAATATAAGAGTGT 59.218 37.037 0.00 0.00 0.00 3.55
2334 3269 8.419442 CCCTCCGTAAACTAATATAAGAGTGTT 58.581 37.037 0.00 0.00 0.00 3.32
2335 3270 9.813446 CCTCCGTAAACTAATATAAGAGTGTTT 57.187 33.333 0.00 0.00 0.00 2.83
2351 3286 8.653036 AAGAGTGTTTAGATCACTACCTTAGT 57.347 34.615 0.00 0.00 44.68 2.24
2365 3300 7.906199 ACTACCTTAGTGATCTAAATGCTCT 57.094 36.000 0.00 0.00 37.69 4.09
2366 3301 8.312669 ACTACCTTAGTGATCTAAATGCTCTT 57.687 34.615 0.00 0.00 37.69 2.85
2367 3302 9.422681 ACTACCTTAGTGATCTAAATGCTCTTA 57.577 33.333 0.00 0.00 37.69 2.10
2385 3320 8.777578 TGCTCTTATATTAGTTTACAGAGGGA 57.222 34.615 0.00 0.00 0.00 4.20
2386 3321 8.861086 TGCTCTTATATTAGTTTACAGAGGGAG 58.139 37.037 0.00 0.00 0.00 4.30
2387 3322 8.862085 GCTCTTATATTAGTTTACAGAGGGAGT 58.138 37.037 0.00 0.00 0.00 3.85
2410 3345 6.998673 AGTAAGAGACATTTTAGGCACTTTGT 59.001 34.615 0.00 0.00 41.75 2.83
2431 3367 5.701855 TGTAATGTTGTGCAGTTGATCATG 58.298 37.500 0.00 0.00 0.00 3.07
2436 3372 4.023792 TGTTGTGCAGTTGATCATGAACTC 60.024 41.667 8.56 0.00 31.05 3.01
2469 3408 4.599041 TGTTCCCTTCAATGGTAGGATTG 58.401 43.478 0.00 0.00 33.64 2.67
2496 3435 6.256757 GGAGTTATGAGTGTTATCAGTGCTTC 59.743 42.308 0.00 0.00 31.44 3.86
2497 3436 6.940739 AGTTATGAGTGTTATCAGTGCTTCT 58.059 36.000 0.00 0.00 31.44 2.85
2498 3437 8.067751 AGTTATGAGTGTTATCAGTGCTTCTA 57.932 34.615 0.00 0.00 31.44 2.10
2519 3458 0.179000 AGCCTGCTGTATGCCTGTAC 59.821 55.000 0.00 0.00 42.00 2.90
2525 3464 2.304470 TGCTGTATGCCTGTACCTGAAA 59.696 45.455 0.00 0.00 42.00 2.69
2529 3468 5.765182 GCTGTATGCCTGTACCTGAAATTAT 59.235 40.000 0.00 0.00 35.15 1.28
2539 3478 7.393234 CCTGTACCTGAAATTATGTTCCAGAAA 59.607 37.037 0.00 0.00 0.00 2.52
2558 3497 7.821359 TCCAGAAATCTGTAGTTTGATGAGAAG 59.179 37.037 9.43 0.00 42.27 2.85
2568 3507 9.871238 TGTAGTTTGATGAGAAGTAGGATTTAC 57.129 33.333 0.00 0.00 0.00 2.01
2612 3733 7.905493 GGAACAAATACTTCTGTTGATCGAATC 59.095 37.037 0.00 0.00 35.93 2.52
2630 3751 2.196742 TCTATGCATCCACCTTCCCT 57.803 50.000 0.19 0.00 0.00 4.20
2659 3780 6.007076 TCTTCTGACTCACTCTCACAATAGT 58.993 40.000 0.00 0.00 0.00 2.12
2666 3787 4.814147 TCACTCTCACAATAGTCTGCAAG 58.186 43.478 0.00 0.00 0.00 4.01
2692 3814 3.921677 TCGGAGTCATGTTACTGTTTCC 58.078 45.455 0.00 0.00 0.00 3.13
2796 3920 4.093743 TGGTCATGACTGCTTAGGTCTTA 58.906 43.478 24.50 0.00 35.04 2.10
2798 3922 5.163405 TGGTCATGACTGCTTAGGTCTTATC 60.163 44.000 24.50 3.51 35.04 1.75
2830 3980 7.333423 TGTTGTGCCAGTAGATCATAAACTTAC 59.667 37.037 0.00 0.00 0.00 2.34
2920 4136 2.751259 CAGTGTGCATATTCAGTGGCTT 59.249 45.455 0.00 0.00 33.09 4.35
2950 4166 3.214328 GAGCCTTTCCTGTCTGACAAAA 58.786 45.455 12.16 9.35 0.00 2.44
2958 4174 3.138283 TCCTGTCTGACAAAAGTCCCAAT 59.862 43.478 12.16 0.00 0.00 3.16
2965 4181 7.721842 TGTCTGACAAAAGTCCCAATTTATGTA 59.278 33.333 8.27 0.00 0.00 2.29
3114 4332 2.038387 ACCGAACTGTTTCACTTGCT 57.962 45.000 0.00 0.00 0.00 3.91
3134 4354 7.335924 ACTTGCTTTTAACTTTCTGTGTGTAGA 59.664 33.333 0.00 0.00 0.00 2.59
3171 4421 6.238593 CCTGCTATCCTTTTTACTCATTGCTC 60.239 42.308 0.00 0.00 0.00 4.26
3194 4446 9.219603 GCTCCAACATGAACATATATAAGCTAA 57.780 33.333 0.00 0.00 0.00 3.09
3329 4585 8.239998 CCAAAGAGGTTTGAACTTCTATTGATC 58.760 37.037 19.68 0.00 43.53 2.92
3336 4592 7.970614 GGTTTGAACTTCTATTGATCCAATGAC 59.029 37.037 2.71 0.00 35.54 3.06
3339 4595 8.812513 TGAACTTCTATTGATCCAATGACATT 57.187 30.769 0.00 0.00 35.54 2.71
3385 4641 5.920273 CACAGTTTGGTTACCAGCTTTAATG 59.080 40.000 3.65 1.95 33.81 1.90
3428 4724 4.304110 GTTCATTGAAGACCGAGTACACA 58.696 43.478 0.00 0.00 0.00 3.72
3499 4813 4.024048 CGTACAGAATTTCAAAGGTGTGCT 60.024 41.667 0.00 0.00 0.00 4.40
3537 4851 7.907389 TCTACCACATTTTCTGAAGTCTATGT 58.093 34.615 0.00 0.00 0.00 2.29
3778 5098 4.830600 TCCTTGTTAACCTTTAAAGCTGGG 59.169 41.667 9.86 0.00 0.00 4.45
3818 5139 6.680625 TTTTACGAAAAATTGTGCTACTGGCA 60.681 34.615 0.00 0.00 37.88 4.92
3869 5195 1.123077 TGCGAGGATGAGCCAGTATT 58.877 50.000 0.00 0.00 40.02 1.89
3897 5231 7.069950 TCAGGTTATACTTGTGCATACTGAGAT 59.930 37.037 0.00 0.00 0.00 2.75
3924 5265 6.150976 TGAATTTGTAGTTTCCTGCCACATAG 59.849 38.462 0.00 0.00 0.00 2.23
3954 5404 5.466432 TCTCTGTTGTCGACTACTTATCG 57.534 43.478 26.27 12.93 41.00 2.92
4096 5640 5.163663 TGCTGTCACTTGTCTTTTAAACAGG 60.164 40.000 0.00 0.00 34.80 4.00
4103 5647 7.825270 TCACTTGTCTTTTAAACAGGTCTTGTA 59.175 33.333 0.00 0.00 39.73 2.41
4108 5652 6.856426 GTCTTTTAAACAGGTCTTGTATGTGC 59.144 38.462 0.00 0.00 39.73 4.57
4243 5791 4.133078 CTCTGAAGAAGTTGAAGCAGGTT 58.867 43.478 0.00 0.00 0.00 3.50
4286 5838 1.072505 GGAACCGCCTTTCTGGTCA 59.927 57.895 0.00 0.00 37.54 4.02
4333 6009 1.682740 TCGATGCGTATCAGTACCCA 58.317 50.000 14.06 0.00 32.67 4.51
4337 6016 3.365064 CGATGCGTATCAGTACCCAGTAG 60.365 52.174 14.06 0.00 32.67 2.57
4338 6017 2.304092 TGCGTATCAGTACCCAGTAGG 58.696 52.381 0.00 0.00 43.78 3.18
4497 6200 2.520979 GTCTTTCAGATCGACGTGGAG 58.479 52.381 6.39 0.00 0.00 3.86
4498 6201 1.472878 TCTTTCAGATCGACGTGGAGG 59.527 52.381 6.39 0.00 0.00 4.30
4499 6202 1.472878 CTTTCAGATCGACGTGGAGGA 59.527 52.381 6.39 1.07 0.00 3.71
4575 6291 2.029649 TCTGTAGCGTTTCGGTAGCTTT 60.030 45.455 0.00 0.00 40.42 3.51
4689 6418 4.196971 GCACGTAGGTTCCATAGGATTTT 58.803 43.478 0.00 0.00 0.00 1.82
4707 6436 5.418840 GGATTTTGAATAGCTTCTTCACCCA 59.581 40.000 10.08 0.56 32.57 4.51
4808 6544 1.298264 TTGCTTTCTTGCACGCACG 60.298 52.632 0.00 0.00 43.20 5.34
4874 6610 7.759489 TCCAACATGTAAATTCTTTAGCAGT 57.241 32.000 0.00 0.00 0.00 4.40
4976 6812 7.228590 AGGTTTACATCTACTGCAAGGTTTTA 58.771 34.615 0.00 0.00 39.30 1.52
5001 6857 3.683847 GCTACTCCACATTGCATCCTTCT 60.684 47.826 0.00 0.00 0.00 2.85
5008 6864 2.092538 ACATTGCATCCTTCTCTGGAGG 60.093 50.000 0.00 0.00 39.78 4.30
5016 6872 3.858135 TCCTTCTCTGGAGGTTGTAACT 58.142 45.455 0.00 0.00 0.00 2.24
5017 6873 3.833070 TCCTTCTCTGGAGGTTGTAACTC 59.167 47.826 0.00 0.00 0.00 3.01
5032 6888 5.970317 TGTAACTCGAAGTGGTAATCTGA 57.030 39.130 0.00 0.00 0.00 3.27
5055 6911 3.706698 TCTGAACTCTGAAGACGTTGTG 58.293 45.455 0.00 0.00 0.00 3.33
5061 6917 1.483004 TCTGAAGACGTTGTGGTTCCA 59.517 47.619 0.00 0.00 0.00 3.53
5070 6928 1.063469 GTTGTGGTTCCACTTCACGTG 59.937 52.381 20.48 9.94 43.41 4.49
5271 7138 2.264794 GGCACCTGGTGGTACGAG 59.735 66.667 27.02 1.19 46.60 4.18
5299 7166 1.572085 CGTCCACACGTACGTCCTCT 61.572 60.000 19.94 0.00 41.42 3.69
5314 7181 1.603236 CCTCTTCTGCTCCTGCTCGT 61.603 60.000 0.00 0.00 40.48 4.18
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
11 12 2.730928 GTGCCAACATTTTCAATGTCCG 59.269 45.455 2.65 0.00 0.00 4.79
47 48 6.041523 TGGTTGGGAAGAGATTTTAAACAAGG 59.958 38.462 0.00 0.00 0.00 3.61
77 78 5.770162 AGGGTGGATAGAAAAACTCTTGTTG 59.230 40.000 0.00 0.00 36.39 3.33
149 150 2.137523 GCTGATGTTGGTTGGCAAAAG 58.862 47.619 0.00 0.00 0.00 2.27
229 230 6.845302 TGCTCTGAAAATAACTTACATGCAG 58.155 36.000 0.00 0.00 0.00 4.41
338 339 1.070445 CTATCGAAGGGCTGCCTGG 59.930 63.158 19.68 0.66 0.00 4.45
343 344 2.540265 AAGCATCTATCGAAGGGCTG 57.460 50.000 0.00 0.00 36.68 4.85
392 398 3.316029 GGCACTTACCGTTAAACACCTTT 59.684 43.478 0.00 0.00 0.00 3.11
399 405 2.106166 TCCCTTGGCACTTACCGTTAAA 59.894 45.455 0.00 0.00 0.00 1.52
405 411 1.378646 GGCTCCCTTGGCACTTACC 60.379 63.158 0.00 0.00 0.00 2.85
437 443 1.372997 CGTGAGGAAGTGACACCGG 60.373 63.158 0.00 0.00 0.00 5.28
440 446 1.583054 AAAGCGTGAGGAAGTGACAC 58.417 50.000 0.00 0.00 0.00 3.67
466 472 4.832248 CTGGTAGCTGAAGGATTGTGTTA 58.168 43.478 0.00 0.00 0.00 2.41
473 479 3.439857 TTTTGCTGGTAGCTGAAGGAT 57.560 42.857 0.00 0.00 42.97 3.24
474 480 2.949177 TTTTGCTGGTAGCTGAAGGA 57.051 45.000 0.00 0.00 42.97 3.36
529 535 0.951040 GGTGGCGTCTCAAAGGAGTG 60.951 60.000 0.00 0.00 42.05 3.51
558 564 0.111639 TGACCTTGGTTACCTTGGCC 59.888 55.000 2.07 0.00 0.00 5.36
559 565 1.244816 GTGACCTTGGTTACCTTGGC 58.755 55.000 2.07 2.59 0.00 4.52
610 620 5.059404 TCTTGAAGAAAATTGGATTCGCC 57.941 39.130 0.00 0.00 37.10 5.54
611 621 6.416161 GCTATCTTGAAGAAAATTGGATTCGC 59.584 38.462 0.00 0.00 32.04 4.70
612 622 7.701445 AGCTATCTTGAAGAAAATTGGATTCG 58.299 34.615 0.00 0.00 32.04 3.34
613 623 9.513727 GAAGCTATCTTGAAGAAAATTGGATTC 57.486 33.333 0.00 0.00 31.48 2.52
630 640 6.786959 AGAATGGAGTTATCTGGAAGCTATCT 59.213 38.462 0.00 0.00 0.00 1.98
662 672 8.888579 AAGTTAGATACGATGAAAACCTATGG 57.111 34.615 0.00 0.00 0.00 2.74
669 679 8.653338 GTGCAGTTAAGTTAGATACGATGAAAA 58.347 33.333 0.00 0.00 0.00 2.29
755 765 7.015292 AGACATACTCTGCTTATTCCGGATAAA 59.985 37.037 4.15 1.32 30.07 1.40
817 867 8.253113 CCCAAAATTACAAATGATAGCAAGTCT 58.747 33.333 0.00 0.00 0.00 3.24
818 868 7.010460 GCCCAAAATTACAAATGATAGCAAGTC 59.990 37.037 0.00 0.00 0.00 3.01
819 869 6.818142 GCCCAAAATTACAAATGATAGCAAGT 59.182 34.615 0.00 0.00 0.00 3.16
820 870 7.010738 CAGCCCAAAATTACAAATGATAGCAAG 59.989 37.037 0.00 0.00 0.00 4.01
821 871 6.817641 CAGCCCAAAATTACAAATGATAGCAA 59.182 34.615 0.00 0.00 0.00 3.91
822 872 6.154192 TCAGCCCAAAATTACAAATGATAGCA 59.846 34.615 0.00 0.00 0.00 3.49
823 873 6.572519 TCAGCCCAAAATTACAAATGATAGC 58.427 36.000 0.00 0.00 0.00 2.97
824 874 7.999679 TCTCAGCCCAAAATTACAAATGATAG 58.000 34.615 0.00 0.00 0.00 2.08
825 875 7.953005 TCTCAGCCCAAAATTACAAATGATA 57.047 32.000 0.00 0.00 0.00 2.15
826 876 6.855763 TCTCAGCCCAAAATTACAAATGAT 57.144 33.333 0.00 0.00 0.00 2.45
827 877 6.127366 GGATCTCAGCCCAAAATTACAAATGA 60.127 38.462 0.00 0.00 0.00 2.57
828 878 6.044682 GGATCTCAGCCCAAAATTACAAATG 58.955 40.000 0.00 0.00 0.00 2.32
829 879 5.721000 TGGATCTCAGCCCAAAATTACAAAT 59.279 36.000 0.00 0.00 0.00 2.32
830 880 5.083122 TGGATCTCAGCCCAAAATTACAAA 58.917 37.500 0.00 0.00 0.00 2.83
831 881 4.671831 TGGATCTCAGCCCAAAATTACAA 58.328 39.130 0.00 0.00 0.00 2.41
832 882 4.272489 CTGGATCTCAGCCCAAAATTACA 58.728 43.478 0.00 0.00 36.60 2.41
833 883 4.907879 CTGGATCTCAGCCCAAAATTAC 57.092 45.455 0.00 0.00 36.60 1.89
897 948 0.951040 GTGCGTGTGAAGGGGAGAAG 60.951 60.000 0.00 0.00 0.00 2.85
913 968 3.582120 CGGTGTGTGTGTGGGTGC 61.582 66.667 0.00 0.00 0.00 5.01
917 972 2.821810 TGTGCGGTGTGTGTGTGG 60.822 61.111 0.00 0.00 0.00 4.17
1299 1526 0.443869 AATCAGTTAAGCGCACGCAG 59.556 50.000 18.24 0.00 44.88 5.18
1364 1591 0.373024 GATCTGCTTGAAGTCGCTGC 59.627 55.000 0.00 0.00 0.00 5.25
1486 1714 0.170561 AGATCGACCGTGGAGAAACG 59.829 55.000 0.00 0.00 43.20 3.60
1495 1723 1.878522 GCATTGCGAGATCGACCGT 60.879 57.895 6.39 0.00 43.02 4.83
1517 1745 0.806102 CCACTGAATCCTACCGCACG 60.806 60.000 0.00 0.00 0.00 5.34
1538 1821 5.447954 TGGAAACACAAATAACACACTCGTG 60.448 40.000 0.00 0.00 42.23 4.35
1596 1927 7.812191 CACTTATATATCAGGTTCAGAGACAGC 59.188 40.741 0.00 0.00 0.00 4.40
1601 1956 7.598118 CAGTGCACTTATATATCAGGTTCAGAG 59.402 40.741 18.94 0.00 0.00 3.35
1642 1997 8.150945 GCCTAAATTCAGATACAGTATCCTCAA 58.849 37.037 15.87 7.67 35.79 3.02
1643 1998 7.510685 AGCCTAAATTCAGATACAGTATCCTCA 59.489 37.037 15.87 1.94 35.79 3.86
1644 1999 7.902087 AGCCTAAATTCAGATACAGTATCCTC 58.098 38.462 15.87 0.00 35.79 3.71
1645 2000 7.863901 AGCCTAAATTCAGATACAGTATCCT 57.136 36.000 15.87 2.49 35.79 3.24
1646 2001 8.150945 TGAAGCCTAAATTCAGATACAGTATCC 58.849 37.037 15.87 0.31 35.79 2.59
1745 2298 5.927281 TTGGTACCTACTACTCCAATCAC 57.073 43.478 14.36 0.00 33.95 3.06
1810 2380 1.135803 CAAGGCGGGTAAATCGTGTTG 60.136 52.381 0.00 0.00 0.00 3.33
1822 2392 0.250295 TTCACTCTGAACAAGGCGGG 60.250 55.000 0.00 0.00 30.26 6.13
1888 2461 4.834496 TGAGAATGAGCCAAGGTCAAAATT 59.166 37.500 0.04 0.00 43.29 1.82
1895 2468 5.312079 GCTATTATGAGAATGAGCCAAGGT 58.688 41.667 0.00 0.00 0.00 3.50
1906 2479 5.994250 AGTCTTTGCAGGCTATTATGAGAA 58.006 37.500 0.00 0.00 31.00 2.87
1912 2485 3.620488 CCCAAGTCTTTGCAGGCTATTA 58.380 45.455 0.00 0.00 31.87 0.98
2044 2620 6.902771 AGATTACATACGAGACCTAAGCAT 57.097 37.500 0.00 0.00 0.00 3.79
2106 2684 5.590663 TCAACTGCCACAACATTACAAAGTA 59.409 36.000 0.00 0.00 0.00 2.24
2141 2722 3.186613 GCACACTAGAAGCACTGGTAAAC 59.813 47.826 0.00 0.00 38.24 2.01
2220 3155 4.464008 ACAATAATGGTATGCTGTCCTGG 58.536 43.478 0.00 0.00 0.00 4.45
2226 3161 5.357878 ACAACCTGACAATAATGGTATGCTG 59.642 40.000 0.00 0.00 31.82 4.41
2227 3162 5.509498 ACAACCTGACAATAATGGTATGCT 58.491 37.500 0.00 0.00 31.82 3.79
2253 3188 5.078411 ACATACAAGACCTAAGCAGTCAG 57.922 43.478 0.00 0.00 36.68 3.51
2284 3219 6.702282 GGAGTACAAGTTTATGATCTACTGGC 59.298 42.308 0.00 0.00 0.00 4.85
2306 3241 8.298140 CACTCTTATATTAGTTTACGGAGGGAG 58.702 40.741 0.00 0.00 0.00 4.30
2307 3242 7.781693 ACACTCTTATATTAGTTTACGGAGGGA 59.218 37.037 0.00 0.00 0.00 4.20
2308 3243 7.949434 ACACTCTTATATTAGTTTACGGAGGG 58.051 38.462 0.00 0.00 0.00 4.30
2309 3244 9.813446 AAACACTCTTATATTAGTTTACGGAGG 57.187 33.333 0.00 0.00 0.00 4.30
2325 3260 9.750783 ACTAAGGTAGTGATCTAAACACTCTTA 57.249 33.333 0.00 0.00 45.58 2.10
2326 3261 8.653036 ACTAAGGTAGTGATCTAAACACTCTT 57.347 34.615 0.00 0.00 45.58 2.85
2341 3276 7.906199 AGAGCATTTAGATCACTAAGGTAGT 57.094 36.000 0.00 0.00 39.36 2.73
2359 3294 9.381038 TCCCTCTGTAAACTAATATAAGAGCAT 57.619 33.333 0.00 0.00 0.00 3.79
2360 3295 8.777578 TCCCTCTGTAAACTAATATAAGAGCA 57.222 34.615 0.00 0.00 0.00 4.26
2361 3296 8.862085 ACTCCCTCTGTAAACTAATATAAGAGC 58.138 37.037 0.00 0.00 0.00 4.09
2368 3303 9.406113 GTCTCTTACTCCCTCTGTAAACTAATA 57.594 37.037 0.00 0.00 30.72 0.98
2369 3304 7.894364 TGTCTCTTACTCCCTCTGTAAACTAAT 59.106 37.037 0.00 0.00 30.72 1.73
2370 3305 7.236529 TGTCTCTTACTCCCTCTGTAAACTAA 58.763 38.462 0.00 0.00 30.72 2.24
2371 3306 6.787170 TGTCTCTTACTCCCTCTGTAAACTA 58.213 40.000 0.00 0.00 30.72 2.24
2372 3307 5.642165 TGTCTCTTACTCCCTCTGTAAACT 58.358 41.667 0.00 0.00 30.72 2.66
2373 3308 5.979288 TGTCTCTTACTCCCTCTGTAAAC 57.021 43.478 0.00 0.00 30.72 2.01
2374 3309 7.554959 AAATGTCTCTTACTCCCTCTGTAAA 57.445 36.000 0.00 0.00 30.72 2.01
2375 3310 7.554959 AAAATGTCTCTTACTCCCTCTGTAA 57.445 36.000 0.00 0.00 0.00 2.41
2376 3311 7.342284 CCTAAAATGTCTCTTACTCCCTCTGTA 59.658 40.741 0.00 0.00 0.00 2.74
2377 3312 6.155393 CCTAAAATGTCTCTTACTCCCTCTGT 59.845 42.308 0.00 0.00 0.00 3.41
2378 3313 6.578023 CCTAAAATGTCTCTTACTCCCTCTG 58.422 44.000 0.00 0.00 0.00 3.35
2379 3314 5.129650 GCCTAAAATGTCTCTTACTCCCTCT 59.870 44.000 0.00 0.00 0.00 3.69
2380 3315 5.104900 TGCCTAAAATGTCTCTTACTCCCTC 60.105 44.000 0.00 0.00 0.00 4.30
2381 3316 4.783227 TGCCTAAAATGTCTCTTACTCCCT 59.217 41.667 0.00 0.00 0.00 4.20
2382 3317 4.876679 GTGCCTAAAATGTCTCTTACTCCC 59.123 45.833 0.00 0.00 0.00 4.30
2383 3318 5.735766 AGTGCCTAAAATGTCTCTTACTCC 58.264 41.667 0.00 0.00 0.00 3.85
2384 3319 7.173390 ACAAAGTGCCTAAAATGTCTCTTACTC 59.827 37.037 0.00 0.00 0.00 2.59
2385 3320 6.998673 ACAAAGTGCCTAAAATGTCTCTTACT 59.001 34.615 0.00 0.00 0.00 2.24
2386 3321 7.203255 ACAAAGTGCCTAAAATGTCTCTTAC 57.797 36.000 0.00 0.00 0.00 2.34
2387 3322 8.911918 TTACAAAGTGCCTAAAATGTCTCTTA 57.088 30.769 0.00 0.00 0.00 2.10
2388 3323 7.817418 TTACAAAGTGCCTAAAATGTCTCTT 57.183 32.000 0.00 0.00 0.00 2.85
2410 3345 6.207221 AGTTCATGATCAACTGCACAACATTA 59.793 34.615 0.00 0.00 32.65 1.90
2431 3367 4.972514 GGAACAAATCTCCCATGAGTTC 57.027 45.455 0.00 0.00 39.75 3.01
2469 3408 5.292101 GCACTGATAACACTCATAACTCCAC 59.708 44.000 0.00 0.00 0.00 4.02
2539 3478 7.962995 TCCTACTTCTCATCAAACTACAGAT 57.037 36.000 0.00 0.00 0.00 2.90
2546 3485 7.760340 ACTCGTAAATCCTACTTCTCATCAAAC 59.240 37.037 0.00 0.00 0.00 2.93
2549 3488 6.377429 ACACTCGTAAATCCTACTTCTCATCA 59.623 38.462 0.00 0.00 0.00 3.07
2558 3497 7.829378 AAGAAATGACACTCGTAAATCCTAC 57.171 36.000 0.00 0.00 0.00 3.18
2568 3507 4.035091 TGTTCCACAAAGAAATGACACTCG 59.965 41.667 0.00 0.00 0.00 4.18
2596 3717 6.128607 GGATGCATAGATTCGATCAACAGAAG 60.129 42.308 0.00 0.00 0.00 2.85
2599 3720 4.992951 TGGATGCATAGATTCGATCAACAG 59.007 41.667 0.00 0.00 0.00 3.16
2612 3733 3.303351 AAAGGGAAGGTGGATGCATAG 57.697 47.619 0.00 0.00 0.00 2.23
2638 3759 5.414144 CAGACTATTGTGAGAGTGAGTCAGA 59.586 44.000 0.00 0.00 36.59 3.27
2659 3780 0.603569 GACTCCGAAGTCCTTGCAGA 59.396 55.000 0.00 0.00 45.26 4.26
2796 3920 3.832490 TCTACTGGCACAACACTACAGAT 59.168 43.478 0.00 0.00 38.70 2.90
2798 3922 3.660501 TCTACTGGCACAACACTACAG 57.339 47.619 0.00 0.00 38.70 2.74
2830 3980 7.916914 TGATCATGTATGATATGCTTCCTTG 57.083 36.000 7.31 0.00 46.84 3.61
2842 4046 6.603940 TCATACCGGAATGATCATGTATGA 57.396 37.500 26.95 26.95 41.70 2.15
2920 4136 5.649395 CAGACAGGAAAGGCTCAAAATATCA 59.351 40.000 0.00 0.00 0.00 2.15
2950 4166 7.779798 AGTGTGCAATATACATAAATTGGGACT 59.220 33.333 0.00 0.00 34.37 3.85
2965 4181 5.404946 CAGCAGCTAAAAAGTGTGCAATAT 58.595 37.500 0.00 0.00 36.57 1.28
2980 4196 7.848128 AGTAAAGTAAATTCTACCAGCAGCTA 58.152 34.615 0.00 0.00 0.00 3.32
3147 4367 6.238593 GGAGCAATGAGTAAAAAGGATAGCAG 60.239 42.308 0.00 0.00 0.00 4.24
3225 4478 8.618677 CATTTGTCAGCAATCAGAGTACATATT 58.381 33.333 0.00 0.00 34.18 1.28
3339 4595 9.671279 CTGTGGCAATATTATATAACCTGATGA 57.329 33.333 0.00 0.00 0.00 2.92
3385 4641 3.057315 ACCTTCACACTGCATTGCATAAC 60.057 43.478 12.53 0.00 38.13 1.89
3428 4724 3.953612 TGTCATGAGTGGCTTGAAACTTT 59.046 39.130 0.00 0.00 33.09 2.66
3499 4813 2.571202 TGTGGTAGAGGATGCACATTCA 59.429 45.455 0.00 0.00 0.00 2.57
3562 4877 5.726397 TGCCACGTGTAGAGTATGTATTTT 58.274 37.500 15.65 0.00 0.00 1.82
3841 5167 3.487544 GGCTCATCCTCGCAAACAAATAC 60.488 47.826 0.00 0.00 0.00 1.89
3852 5178 3.797039 TGAAAATACTGGCTCATCCTCG 58.203 45.455 0.00 0.00 35.26 4.63
3853 5179 4.133078 CCTGAAAATACTGGCTCATCCTC 58.867 47.826 0.00 0.00 35.26 3.71
3869 5195 7.390823 TCAGTATGCACAAGTATAACCTGAAA 58.609 34.615 0.00 0.00 34.76 2.69
3897 5231 4.518970 GTGGCAGGAAACTACAAATTCAGA 59.481 41.667 0.00 0.00 40.21 3.27
3924 5265 4.489810 AGTCGACAACAGAGATGATTCAC 58.510 43.478 19.50 0.00 0.00 3.18
3954 5404 4.378774 AGATCTGCAGCATACAAGATGTC 58.621 43.478 9.47 0.00 0.00 3.06
3959 5409 5.353400 TGAGAAAAGATCTGCAGCATACAAG 59.647 40.000 9.47 0.00 38.96 3.16
3961 5411 4.835678 TGAGAAAAGATCTGCAGCATACA 58.164 39.130 9.47 0.00 38.96 2.29
3964 5414 4.765856 ACTTTGAGAAAAGATCTGCAGCAT 59.234 37.500 9.47 3.41 38.96 3.79
4108 5652 9.766277 GTATTTGAGTAAGAGCAAAGAATCTTG 57.234 33.333 0.00 0.00 37.41 3.02
4243 5791 0.178995 TGATGCAGGGTGCTGAACAA 60.179 50.000 0.00 0.00 45.31 2.83
4268 5817 0.322546 ATGACCAGAAAGGCGGTTCC 60.323 55.000 1.01 0.00 43.14 3.62
4333 6009 6.627087 TGTCAAAGAGAATTCCATCCTACT 57.373 37.500 0.65 0.00 0.00 2.57
4337 6016 7.362142 GGTTACTTGTCAAAGAGAATTCCATCC 60.362 40.741 0.65 0.00 36.84 3.51
4338 6017 7.362142 GGGTTACTTGTCAAAGAGAATTCCATC 60.362 40.741 0.65 0.00 36.84 3.51
4497 6200 9.832445 TCTGTTCTTCAAAACCATATACTATCC 57.168 33.333 0.00 0.00 0.00 2.59
4689 6418 3.674997 GTGTGGGTGAAGAAGCTATTCA 58.325 45.455 9.60 9.60 37.94 2.57
4707 6436 2.281484 AAACCGCATGAGCCGTGT 60.281 55.556 0.00 0.00 37.52 4.49
4874 6610 0.476771 GTTGTTGGTCCAGGGGAAGA 59.523 55.000 0.00 0.00 31.38 2.87
4927 6677 9.888878 CCTTTCTGTATTTGCTTGATATATGTG 57.111 33.333 0.00 0.00 0.00 3.21
4943 6698 7.620880 TGCAGTAGATGTAAACCTTTCTGTAT 58.379 34.615 0.00 0.00 0.00 2.29
4946 6701 6.128172 CCTTGCAGTAGATGTAAACCTTTCTG 60.128 42.308 0.00 0.00 32.74 3.02
4947 6702 5.940470 CCTTGCAGTAGATGTAAACCTTTCT 59.060 40.000 0.00 0.00 32.74 2.52
4976 6812 3.019564 GGATGCAATGTGGAGTAGCTTT 58.980 45.455 0.00 0.00 0.00 3.51
5001 6857 3.005472 CACTTCGAGTTACAACCTCCAGA 59.995 47.826 0.00 0.00 0.00 3.86
5008 6864 6.154445 TCAGATTACCACTTCGAGTTACAAC 58.846 40.000 0.00 0.00 0.00 3.32
5016 6872 5.914898 TCAGATTCAGATTACCACTTCGA 57.085 39.130 0.00 0.00 0.00 3.71
5017 6873 6.102663 AGTTCAGATTCAGATTACCACTTCG 58.897 40.000 0.00 0.00 0.00 3.79
5032 6888 4.747108 CACAACGTCTTCAGAGTTCAGATT 59.253 41.667 0.00 0.00 0.00 2.40
5151 7015 0.319555 AGTTCACGTCCATGGTGTCG 60.320 55.000 12.58 16.69 36.76 4.35
5241 7105 2.892425 GTGCCCAGCGAGAATCCG 60.892 66.667 0.00 0.00 0.00 4.18
5244 7111 2.270205 CAGGTGCCCAGCGAGAAT 59.730 61.111 0.00 0.00 0.00 2.40
5299 7166 2.047844 GCACGAGCAGGAGCAGAA 60.048 61.111 0.00 0.00 45.49 3.02
5314 7181 2.899838 GTGCCAGACCGTGTTGCA 60.900 61.111 0.00 0.00 0.00 4.08
5567 7434 0.107654 CCCCTACTACAACAGCAGCC 60.108 60.000 0.00 0.00 0.00 4.85
5568 7435 0.902531 TCCCCTACTACAACAGCAGC 59.097 55.000 0.00 0.00 0.00 5.25
5569 7436 1.135083 CGTCCCCTACTACAACAGCAG 60.135 57.143 0.00 0.00 0.00 4.24
5570 7437 0.892755 CGTCCCCTACTACAACAGCA 59.107 55.000 0.00 0.00 0.00 4.41
5754 7621 2.809601 GGCTACTGGCACGACGTG 60.810 66.667 23.43 23.43 44.01 4.49


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

AutoCloner maintained by Alex Coulton.