Multiple sequence alignment - TraesCS2B01G481500

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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 TraesCS2B01G481500 chr2B 100.000 5613 0 0 1 5613 679819978 679814366 0.000000e+00 10366.0
1 TraesCS2B01G481500 chr2B 92.400 750 33 6 3882 4629 679885942 679885215 0.000000e+00 1048.0
2 TraesCS2B01G481500 chr2B 86.981 699 67 18 452 1139 679887202 679886517 0.000000e+00 765.0
3 TraesCS2B01G481500 chr2B 87.500 504 32 11 1713 2195 567180765 567180272 2.290000e-153 553.0
4 TraesCS2B01G481500 chr2B 90.215 419 27 8 1289 1707 567181131 567180727 8.280000e-148 534.0
5 TraesCS2B01G481500 chr2B 95.556 270 12 0 2191 2460 589732560 589732829 3.110000e-117 433.0
6 TraesCS2B01G481500 chr2B 96.183 262 10 0 2192 2453 517503462 517503723 4.020000e-116 429.0
7 TraesCS2B01G481500 chr2B 90.847 295 19 5 2572 2864 567180179 567179891 6.820000e-104 388.0
8 TraesCS2B01G481500 chr2B 92.661 109 6 1 2452 2558 567180275 567180167 7.530000e-34 156.0
9 TraesCS2B01G481500 chr2B 100.000 53 0 0 1655 1707 679818280 679818228 1.290000e-16 99.0
10 TraesCS2B01G481500 chr2B 79.851 134 19 8 3747 3877 751255869 751255741 2.150000e-14 91.6
11 TraesCS2B01G481500 chr2B 92.727 55 3 1 3125 3178 22021750 22021804 1.680000e-10 78.7
12 TraesCS2B01G481500 chr2B 95.745 47 2 0 3125 3171 46071831 46071785 6.030000e-10 76.8
13 TraesCS2B01G481500 chr2B 95.652 46 2 0 3125 3170 784975581 784975626 2.170000e-09 75.0
14 TraesCS2B01G481500 chr2D 94.242 1754 74 16 3125 4855 566836813 566835064 0.000000e+00 2654.0
15 TraesCS2B01G481500 chr2D 93.377 1223 71 9 83 1302 566838647 566837432 0.000000e+00 1801.0
16 TraesCS2B01G481500 chr2D 92.339 744 33 8 3885 4626 566980592 566979871 0.000000e+00 1037.0
17 TraesCS2B01G481500 chr2D 92.049 742 33 18 4877 5613 566835082 566834362 0.000000e+00 1020.0
18 TraesCS2B01G481500 chr2D 86.305 701 59 21 452 1139 566982004 566981328 0.000000e+00 728.0
19 TraesCS2B01G481500 chr2D 91.045 268 15 4 2865 3132 566837371 566837113 2.490000e-93 353.0
20 TraesCS2B01G481500 chr2A 93.869 1207 60 7 83 1288 706646043 706644850 0.000000e+00 1807.0
21 TraesCS2B01G481500 chr2A 93.739 1182 40 11 3877 5032 706644628 706643455 0.000000e+00 1742.0
22 TraesCS2B01G481500 chr2A 92.236 747 34 6 3885 4629 706742072 706741348 0.000000e+00 1037.0
23 TraesCS2B01G481500 chr2A 87.278 676 58 16 480 1139 706743312 706742649 0.000000e+00 747.0
24 TraesCS2B01G481500 chr2A 91.569 510 35 4 5111 5613 706642470 706641962 0.000000e+00 697.0
25 TraesCS2B01G481500 chr2A 96.212 264 10 0 2190 2453 438519181 438519444 3.110000e-117 433.0
26 TraesCS2B01G481500 chr2A 95.833 264 11 0 2190 2453 199580216 199580479 1.450000e-115 427.0
27 TraesCS2B01G481500 chr2A 87.879 264 28 3 2597 2859 310063088 310063348 1.960000e-79 307.0
28 TraesCS2B01G481500 chr2A 88.356 146 15 2 1699 1844 718386135 718386278 2.080000e-39 174.0
29 TraesCS2B01G481500 chr2A 80.000 145 20 8 3740 3877 733663757 733663615 1.290000e-16 99.0
30 TraesCS2B01G481500 chr6D 87.844 436 49 3 1702 2134 4147158 4146724 5.020000e-140 508.0
31 TraesCS2B01G481500 chr6D 88.283 367 41 2 1699 2064 310431904 310431539 6.680000e-119 438.0
32 TraesCS2B01G481500 chr6D 85.959 292 33 5 2574 2861 4146608 4146321 7.060000e-79 305.0
33 TraesCS2B01G481500 chr5B 98.479 263 4 0 2191 2453 547158012 547158274 1.100000e-126 464.0
34 TraesCS2B01G481500 chr5B 95.556 270 11 1 2184 2453 92370387 92370655 1.120000e-116 431.0
35 TraesCS2B01G481500 chr5B 85.567 97 10 4 3774 3867 485886393 485886488 1.290000e-16 99.0
36 TraesCS2B01G481500 chr4B 87.192 406 47 5 1699 2102 312231825 312232227 1.840000e-124 457.0
37 TraesCS2B01G481500 chr4B 83.911 404 49 9 1302 1705 312231488 312231875 6.870000e-99 372.0
38 TraesCS2B01G481500 chr4B 88.372 258 27 2 2600 2857 238612250 238611996 1.960000e-79 307.0
39 TraesCS2B01G481500 chr4B 82.270 141 18 7 3741 3877 367334653 367334790 1.280000e-21 115.0
40 TraesCS2B01G481500 chr3B 86.881 404 48 5 1699 2100 491410427 491410027 1.110000e-121 448.0
41 TraesCS2B01G481500 chr3B 85.407 418 47 11 1298 1707 491410787 491410376 6.720000e-114 422.0
42 TraesCS2B01G481500 chr3B 81.967 122 18 4 3741 3858 537657822 537657701 3.580000e-17 100.0
43 TraesCS2B01G481500 chr3B 88.333 60 5 2 3116 3175 77066669 77066612 2.810000e-08 71.3
44 TraesCS2B01G481500 chr3B 95.122 41 2 0 3784 3824 160272508 160272468 1.310000e-06 65.8
45 TraesCS2B01G481500 chr3B 95.122 41 2 0 3131 3171 263277948 263277988 1.310000e-06 65.8
46 TraesCS2B01G481500 chr7B 95.522 268 11 1 2191 2458 372681194 372681460 1.450000e-115 427.0
47 TraesCS2B01G481500 chr7B 78.797 349 61 9 1361 1707 282529842 282530179 7.320000e-54 222.0
48 TraesCS2B01G481500 chr1B 95.489 266 12 0 2192 2457 657321041 657321306 5.200000e-115 425.0
49 TraesCS2B01G481500 chr7A 93.357 286 13 6 2170 2453 726689626 726689907 8.700000e-113 418.0
50 TraesCS2B01G481500 chr7A 97.872 47 1 0 3125 3171 725196878 725196924 1.300000e-11 82.4
51 TraesCS2B01G481500 chr7A 97.674 43 1 0 3129 3171 732577436 732577394 2.170000e-09 75.0
52 TraesCS2B01G481500 chr3A 86.322 329 40 3 1699 2027 8287110 8287433 2.490000e-93 353.0
53 TraesCS2B01G481500 chr3A 88.390 267 27 3 2597 2862 636837161 636837424 9.070000e-83 318.0
54 TraesCS2B01G481500 chrUn 89.015 264 25 3 2597 2859 268672214 268671954 1.950000e-84 324.0
55 TraesCS2B01G481500 chrUn 79.412 204 32 9 1511 1707 53283454 53283254 9.810000e-28 135.0
56 TraesCS2B01G481500 chr4A 89.015 264 25 3 2597 2859 720522949 720522689 1.950000e-84 324.0
57 TraesCS2B01G481500 chr4A 88.258 264 27 3 2600 2862 888871 888611 4.220000e-81 313.0
58 TraesCS2B01G481500 chr1A 88.846 260 26 2 2600 2859 535885520 535885264 3.260000e-82 316.0
59 TraesCS2B01G481500 chr1A 89.726 146 15 0 1702 1847 535886494 535886349 2.670000e-43 187.0
60 TraesCS2B01G481500 chr5A 91.096 146 11 2 1699 1844 255783134 255783277 4.440000e-46 196.0
61 TraesCS2B01G481500 chr5A 82.258 124 14 6 3751 3870 509722443 509722324 3.580000e-17 100.0
62 TraesCS2B01G481500 chr6B 83.571 140 20 3 3740 3877 633550834 633550972 1.640000e-25 128.0
63 TraesCS2B01G481500 chr4D 92.157 51 3 1 1302 1351 215441197 215441247 2.810000e-08 71.3


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 TraesCS2B01G481500 chr2B 679814366 679819978 5612 True 5232.500000 10366 100.00000 1 5613 2 chr2B.!!$R4 5612
1 TraesCS2B01G481500 chr2B 679885215 679887202 1987 True 906.500000 1048 89.69050 452 4629 2 chr2B.!!$R5 4177
2 TraesCS2B01G481500 chr2B 567179891 567181131 1240 True 407.750000 553 90.30575 1289 2864 4 chr2B.!!$R3 1575
3 TraesCS2B01G481500 chr2D 566834362 566838647 4285 True 1457.000000 2654 92.67825 83 5613 4 chr2D.!!$R1 5530
4 TraesCS2B01G481500 chr2D 566979871 566982004 2133 True 882.500000 1037 89.32200 452 4626 2 chr2D.!!$R2 4174
5 TraesCS2B01G481500 chr2A 706641962 706646043 4081 True 1415.333333 1807 93.05900 83 5613 3 chr2A.!!$R2 5530
6 TraesCS2B01G481500 chr2A 706741348 706743312 1964 True 892.000000 1037 89.75700 480 4629 2 chr2A.!!$R3 4149
7 TraesCS2B01G481500 chr6D 4146321 4147158 837 True 406.500000 508 86.90150 1702 2861 2 chr6D.!!$R2 1159
8 TraesCS2B01G481500 chr4B 312231488 312232227 739 False 414.500000 457 85.55150 1302 2102 2 chr4B.!!$F2 800
9 TraesCS2B01G481500 chr3B 491410027 491410787 760 True 435.000000 448 86.14400 1298 2100 2 chr3B.!!$R4 802
10 TraesCS2B01G481500 chr1A 535885264 535886494 1230 True 251.500000 316 89.28600 1702 2859 2 chr1A.!!$R1 1157

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
225 227 0.816825 CAGATCCGGTGGGCAGAATG 60.817 60.000 0.00 0.00 40.87 2.67 F
1045 1078 0.401738 ACTGCTTGCTGTGGTGGTAT 59.598 50.000 4.40 0.00 0.00 2.73 F
1681 2048 0.236449 GCCGGGTCACACTTTTAACG 59.764 55.000 2.18 0.00 0.00 3.18 F
1682 2049 0.869730 CCGGGTCACACTTTTAACGG 59.130 55.000 0.00 0.00 0.00 4.44 F
2955 3887 1.268539 GCAGCCCGGTATTTTTCATCG 60.269 52.381 0.00 0.00 0.00 3.84 F
3446 4693 2.290260 TGCTCTGGAATTGTCGGACATT 60.290 45.455 12.26 5.65 0.00 2.71 F
3453 4700 4.226761 GGAATTGTCGGACATTGTTTCAC 58.773 43.478 12.26 4.69 0.00 3.18 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1662 2029 0.236449 CGTTAAAAGTGTGACCCGGC 59.764 55.000 0.00 0.00 0.00 6.13 R
2435 3271 0.702902 AGTACTCCCTCCGTTCCTCA 59.297 55.000 0.00 0.00 0.00 3.86 R
3335 4574 1.876156 CAGCTCTCTTCGCCTTTTTGT 59.124 47.619 0.00 0.00 0.00 2.83 R
3563 4814 5.368256 AGAAAGCTACAAAAGAGCATGTG 57.632 39.130 0.00 0.00 42.69 3.21 R
3973 5371 0.031721 AGAAGAAGTCGTTCGCCGTT 59.968 50.000 0.00 0.00 37.79 4.44 R
4249 5647 0.106819 ATACGTCGCCCTCCACTAGT 60.107 55.000 0.00 0.00 0.00 2.57 R
4996 6423 0.174162 GTTTGGTGATCATGGCTGCC 59.826 55.000 12.87 12.87 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
26 27 9.983024 ATAACATCTACATGTAGGTATAGAGCT 57.017 33.333 28.33 7.19 42.89 4.09
40 41 7.920160 GGTATAGAGCTACCTACGATTTAGT 57.080 40.000 0.00 0.00 38.51 2.24
41 42 7.973601 GGTATAGAGCTACCTACGATTTAGTC 58.026 42.308 0.00 0.00 38.51 2.59
42 43 7.065683 GGTATAGAGCTACCTACGATTTAGTCC 59.934 44.444 0.00 0.00 38.51 3.85
43 44 4.789807 AGAGCTACCTACGATTTAGTCCA 58.210 43.478 0.00 0.00 0.00 4.02
44 45 5.386924 AGAGCTACCTACGATTTAGTCCAT 58.613 41.667 0.00 0.00 0.00 3.41
45 46 6.540995 AGAGCTACCTACGATTTAGTCCATA 58.459 40.000 0.00 0.00 0.00 2.74
46 47 7.176490 AGAGCTACCTACGATTTAGTCCATAT 58.824 38.462 0.00 0.00 0.00 1.78
47 48 7.337436 AGAGCTACCTACGATTTAGTCCATATC 59.663 40.741 0.00 0.00 0.00 1.63
48 49 7.176490 AGCTACCTACGATTTAGTCCATATCT 58.824 38.462 0.00 0.00 0.00 1.98
49 50 7.337436 AGCTACCTACGATTTAGTCCATATCTC 59.663 40.741 0.00 0.00 0.00 2.75
50 51 7.120873 GCTACCTACGATTTAGTCCATATCTCA 59.879 40.741 0.00 0.00 0.00 3.27
51 52 7.834881 ACCTACGATTTAGTCCATATCTCAA 57.165 36.000 0.00 0.00 0.00 3.02
52 53 8.423906 ACCTACGATTTAGTCCATATCTCAAT 57.576 34.615 0.00 0.00 0.00 2.57
53 54 8.307483 ACCTACGATTTAGTCCATATCTCAATG 58.693 37.037 0.00 0.00 0.00 2.82
54 55 7.276658 CCTACGATTTAGTCCATATCTCAATGC 59.723 40.741 0.00 0.00 0.00 3.56
55 56 6.524734 ACGATTTAGTCCATATCTCAATGCA 58.475 36.000 0.00 0.00 0.00 3.96
56 57 7.164122 ACGATTTAGTCCATATCTCAATGCAT 58.836 34.615 0.00 0.00 0.00 3.96
57 58 7.332926 ACGATTTAGTCCATATCTCAATGCATC 59.667 37.037 0.00 0.00 0.00 3.91
58 59 7.332678 CGATTTAGTCCATATCTCAATGCATCA 59.667 37.037 0.00 0.00 0.00 3.07
59 60 7.734924 TTTAGTCCATATCTCAATGCATCAC 57.265 36.000 0.00 0.00 0.00 3.06
60 61 5.563876 AGTCCATATCTCAATGCATCACT 57.436 39.130 0.00 0.00 0.00 3.41
61 62 6.676990 AGTCCATATCTCAATGCATCACTA 57.323 37.500 0.00 0.00 0.00 2.74
62 63 6.462500 AGTCCATATCTCAATGCATCACTAC 58.538 40.000 0.00 0.00 0.00 2.73
63 64 5.347093 GTCCATATCTCAATGCATCACTACG 59.653 44.000 0.00 0.00 0.00 3.51
64 65 5.011023 TCCATATCTCAATGCATCACTACGT 59.989 40.000 0.00 0.00 0.00 3.57
65 66 5.698089 CCATATCTCAATGCATCACTACGTT 59.302 40.000 0.00 0.00 0.00 3.99
66 67 6.203530 CCATATCTCAATGCATCACTACGTTT 59.796 38.462 0.00 0.00 0.00 3.60
67 68 4.926860 TCTCAATGCATCACTACGTTTG 57.073 40.909 0.00 0.00 0.00 2.93
68 69 4.314961 TCTCAATGCATCACTACGTTTGT 58.685 39.130 0.00 0.00 0.00 2.83
69 70 4.754618 TCTCAATGCATCACTACGTTTGTT 59.245 37.500 0.00 0.00 0.00 2.83
70 71 5.029650 TCAATGCATCACTACGTTTGTTC 57.970 39.130 0.00 0.00 0.00 3.18
71 72 3.722555 ATGCATCACTACGTTTGTTCG 57.277 42.857 0.00 0.00 0.00 3.95
72 73 2.745102 TGCATCACTACGTTTGTTCGA 58.255 42.857 0.00 0.00 34.70 3.71
73 74 3.124560 TGCATCACTACGTTTGTTCGAA 58.875 40.909 0.00 0.00 34.70 3.71
74 75 3.183574 TGCATCACTACGTTTGTTCGAAG 59.816 43.478 0.00 0.00 34.70 3.79
75 76 3.427528 GCATCACTACGTTTGTTCGAAGA 59.572 43.478 0.00 0.00 34.70 2.87
76 77 4.433022 GCATCACTACGTTTGTTCGAAGAG 60.433 45.833 0.00 0.00 38.43 2.85
77 78 3.047796 TCACTACGTTTGTTCGAAGAGC 58.952 45.455 0.00 0.00 38.43 4.09
117 118 6.183347 AGGAAATCAAAAGGACCATGACTAG 58.817 40.000 0.00 0.00 0.00 2.57
190 191 5.816258 AGTAGAATCAACATCAGTGCATCAG 59.184 40.000 0.00 0.00 0.00 2.90
201 202 2.100418 CAGTGCATCAGCTAGCTAGTCA 59.900 50.000 18.86 10.24 42.74 3.41
222 224 3.785859 GCAGATCCGGTGGGCAGA 61.786 66.667 0.00 0.00 0.00 4.26
225 227 0.816825 CAGATCCGGTGGGCAGAATG 60.817 60.000 0.00 0.00 40.87 2.67
237 239 5.105392 GGTGGGCAGAATGTTTTTATGATGA 60.105 40.000 0.00 0.00 39.31 2.92
239 241 5.036737 GGGCAGAATGTTTTTATGATGACG 58.963 41.667 0.00 0.00 39.31 4.35
261 263 3.256631 GTCTACCCAGTTGGAGTTTACGA 59.743 47.826 0.00 0.00 37.39 3.43
266 268 3.408634 CCAGTTGGAGTTTACGACCAAT 58.591 45.455 14.06 5.26 43.89 3.16
267 269 3.818773 CCAGTTGGAGTTTACGACCAATT 59.181 43.478 14.06 9.50 43.89 2.32
268 270 4.277423 CCAGTTGGAGTTTACGACCAATTT 59.723 41.667 14.06 6.82 43.89 1.82
330 332 2.774809 GGACCTCCTTCATCTTAGGCTT 59.225 50.000 0.00 0.00 32.59 4.35
372 374 9.477484 TTTCTGTAGAAAGTTGTCACTCTATTC 57.523 33.333 3.05 0.00 38.94 1.75
404 406 7.334858 TGCAGTTGTATCAACTCCATATAACA 58.665 34.615 11.47 0.40 32.84 2.41
476 479 2.174319 GCGCCAGCAACTAGTAGCC 61.174 63.158 0.00 0.00 44.35 3.93
510 513 0.878523 CACGACCTCAAGGCGTTCAA 60.879 55.000 13.40 0.00 42.72 2.69
594 611 4.633565 TGCTGCAAACTAAAACCCAAAAAG 59.366 37.500 0.00 0.00 0.00 2.27
615 632 5.904362 AGGAACCATTATCTTTGTCAAGC 57.096 39.130 0.00 0.00 0.00 4.01
687 706 2.633967 ACGTGGTCACCCTGTATAAACA 59.366 45.455 0.00 0.00 0.00 2.83
1045 1078 0.401738 ACTGCTTGCTGTGGTGGTAT 59.598 50.000 4.40 0.00 0.00 2.73
1143 1367 9.765795 GATATAATGAACCCTGGTATATACTGC 57.234 37.037 12.54 0.00 0.00 4.40
1357 1714 3.367498 GGCACCTAGGTCTCAATATAGCG 60.367 52.174 12.84 0.00 0.00 4.26
1412 1769 9.642327 TTCATGACATATTGACTTTCCAAATTG 57.358 29.630 0.00 0.00 0.00 2.32
1458 1815 2.489329 ACGGTCAATGATTGCTTTCCAG 59.511 45.455 0.00 1.29 0.00 3.86
1459 1816 2.159338 CGGTCAATGATTGCTTTCCAGG 60.159 50.000 0.00 0.00 0.00 4.45
1467 1824 7.818930 TCAATGATTGCTTTCCAGGAAATTAAC 59.181 33.333 15.38 6.31 33.45 2.01
1483 1840 9.762381 AGGAAATTAACATATTACTGGTTTCCA 57.238 29.630 13.54 0.00 42.64 3.53
1512 1871 6.007703 TGATTATTTTCGAGACAAAAGGGGT 58.992 36.000 0.00 0.00 0.00 4.95
1513 1872 7.169591 TGATTATTTTCGAGACAAAAGGGGTA 58.830 34.615 0.00 0.00 0.00 3.69
1514 1873 7.832187 TGATTATTTTCGAGACAAAAGGGGTAT 59.168 33.333 0.00 0.00 0.00 2.73
1515 1874 5.897377 ATTTTCGAGACAAAAGGGGTATG 57.103 39.130 0.00 0.00 0.00 2.39
1516 1875 4.360951 TTTCGAGACAAAAGGGGTATGT 57.639 40.909 0.00 0.00 0.00 2.29
1517 1876 5.486735 TTTCGAGACAAAAGGGGTATGTA 57.513 39.130 0.00 0.00 0.00 2.29
1522 1881 8.118976 TCGAGACAAAAGGGGTATGTATATAG 57.881 38.462 0.00 0.00 0.00 1.31
1565 1925 9.234384 GGTATCGGATATGACAAATAATACGAG 57.766 37.037 0.29 0.00 0.00 4.18
1579 1939 8.786898 CAAATAATACGAGACATCATCCCAAAT 58.213 33.333 0.00 0.00 0.00 2.32
1588 1948 7.226523 CGAGACATCATCCCAAATGTTTGTATA 59.773 37.037 4.92 0.00 36.28 1.47
1666 2033 9.333724 TCTAGTATTTCTTTAAATTAAGGCCGG 57.666 33.333 0.00 0.00 36.67 6.13
1667 2034 7.342769 AGTATTTCTTTAAATTAAGGCCGGG 57.657 36.000 2.18 0.00 36.67 5.73
1677 2044 0.475044 TAAGGCCGGGTCACACTTTT 59.525 50.000 2.18 0.00 0.00 2.27
1681 2048 0.236449 GCCGGGTCACACTTTTAACG 59.764 55.000 2.18 0.00 0.00 3.18
1682 2049 0.869730 CCGGGTCACACTTTTAACGG 59.130 55.000 0.00 0.00 0.00 4.44
1735 2102 7.280652 GGGTCACACTTTTAACGGCTAATATTA 59.719 37.037 0.00 0.00 0.00 0.98
2168 3004 9.694520 CTAATGAGTGAAATAAACGAATCAGTG 57.305 33.333 0.00 0.00 0.00 3.66
2186 3022 7.678947 ATCAGTGCATACCTAATCTAATTGC 57.321 36.000 0.00 0.00 0.00 3.56
2187 3023 6.830912 TCAGTGCATACCTAATCTAATTGCT 58.169 36.000 0.00 0.00 0.00 3.91
2191 3027 8.378565 AGTGCATACCTAATCTAATTGCTACAT 58.621 33.333 0.00 0.00 0.00 2.29
2192 3028 9.653287 GTGCATACCTAATCTAATTGCTACATA 57.347 33.333 0.00 0.00 0.00 2.29
2193 3029 9.653287 TGCATACCTAATCTAATTGCTACATAC 57.347 33.333 0.00 0.00 0.00 2.39
2194 3030 9.877178 GCATACCTAATCTAATTGCTACATACT 57.123 33.333 0.00 0.00 0.00 2.12
2197 3033 7.908453 ACCTAATCTAATTGCTACATACTCCC 58.092 38.462 0.00 0.00 0.00 4.30
2198 3034 7.735321 ACCTAATCTAATTGCTACATACTCCCT 59.265 37.037 0.00 0.00 0.00 4.20
2199 3035 8.254508 CCTAATCTAATTGCTACATACTCCCTC 58.745 40.741 0.00 0.00 0.00 4.30
2200 3036 6.613153 ATCTAATTGCTACATACTCCCTCC 57.387 41.667 0.00 0.00 0.00 4.30
2201 3037 3.753294 AATTGCTACATACTCCCTCCG 57.247 47.619 0.00 0.00 0.00 4.63
2202 3038 2.154567 TTGCTACATACTCCCTCCGT 57.845 50.000 0.00 0.00 0.00 4.69
2203 3039 2.154567 TGCTACATACTCCCTCCGTT 57.845 50.000 0.00 0.00 0.00 4.44
2204 3040 2.029623 TGCTACATACTCCCTCCGTTC 58.970 52.381 0.00 0.00 0.00 3.95
2205 3041 1.340568 GCTACATACTCCCTCCGTTCC 59.659 57.143 0.00 0.00 0.00 3.62
2206 3042 2.946785 CTACATACTCCCTCCGTTCCT 58.053 52.381 0.00 0.00 0.00 3.36
2207 3043 3.749954 GCTACATACTCCCTCCGTTCCTA 60.750 52.174 0.00 0.00 0.00 2.94
2208 3044 3.393426 ACATACTCCCTCCGTTCCTAA 57.607 47.619 0.00 0.00 0.00 2.69
2209 3045 3.716431 ACATACTCCCTCCGTTCCTAAA 58.284 45.455 0.00 0.00 0.00 1.85
2210 3046 4.296056 ACATACTCCCTCCGTTCCTAAAT 58.704 43.478 0.00 0.00 0.00 1.40
2211 3047 5.461327 ACATACTCCCTCCGTTCCTAAATA 58.539 41.667 0.00 0.00 0.00 1.40
2212 3048 6.082707 ACATACTCCCTCCGTTCCTAAATAT 58.917 40.000 0.00 0.00 0.00 1.28
2213 3049 7.243824 ACATACTCCCTCCGTTCCTAAATATA 58.756 38.462 0.00 0.00 0.00 0.86
2214 3050 7.731688 ACATACTCCCTCCGTTCCTAAATATAA 59.268 37.037 0.00 0.00 0.00 0.98
2215 3051 6.667558 ACTCCCTCCGTTCCTAAATATAAG 57.332 41.667 0.00 0.00 0.00 1.73
2216 3052 5.543020 ACTCCCTCCGTTCCTAAATATAAGG 59.457 44.000 0.00 0.00 35.26 2.69
2217 3053 5.470501 TCCCTCCGTTCCTAAATATAAGGT 58.529 41.667 4.41 0.00 35.48 3.50
2218 3054 5.306160 TCCCTCCGTTCCTAAATATAAGGTG 59.694 44.000 4.41 0.00 35.48 4.00
2219 3055 5.071384 CCCTCCGTTCCTAAATATAAGGTGT 59.929 44.000 4.41 0.00 35.48 4.16
2220 3056 6.268387 CCCTCCGTTCCTAAATATAAGGTGTA 59.732 42.308 4.41 0.00 35.48 2.90
2221 3057 7.038516 CCCTCCGTTCCTAAATATAAGGTGTAT 60.039 40.741 4.41 0.00 35.48 2.29
2222 3058 8.373220 CCTCCGTTCCTAAATATAAGGTGTATT 58.627 37.037 4.41 0.00 35.48 1.89
2259 3095 7.907214 AGTCAACTATTGTCTATGTTTGACC 57.093 36.000 13.94 3.78 38.67 4.02
2260 3096 7.450074 AGTCAACTATTGTCTATGTTTGACCA 58.550 34.615 13.94 0.00 38.67 4.02
2261 3097 8.103305 AGTCAACTATTGTCTATGTTTGACCAT 58.897 33.333 13.94 0.00 38.67 3.55
2262 3098 8.391106 GTCAACTATTGTCTATGTTTGACCATC 58.609 37.037 0.00 0.00 35.41 3.51
2263 3099 8.321353 TCAACTATTGTCTATGTTTGACCATCT 58.679 33.333 0.00 0.00 33.83 2.90
2264 3100 8.950210 CAACTATTGTCTATGTTTGACCATCTT 58.050 33.333 0.00 0.00 33.83 2.40
2265 3101 9.520515 AACTATTGTCTATGTTTGACCATCTTT 57.479 29.630 0.00 0.00 33.83 2.52
2270 3106 8.662781 TGTCTATGTTTGACCATCTTTATAGC 57.337 34.615 0.00 0.00 33.83 2.97
2271 3107 8.264347 TGTCTATGTTTGACCATCTTTATAGCA 58.736 33.333 0.00 0.00 33.83 3.49
2272 3108 9.109393 GTCTATGTTTGACCATCTTTATAGCAA 57.891 33.333 0.00 0.00 0.00 3.91
2273 3109 9.679661 TCTATGTTTGACCATCTTTATAGCAAA 57.320 29.630 0.00 0.00 0.00 3.68
2351 3187 9.358406 TGATGAACCTAATGATAATGATTTGCT 57.642 29.630 0.00 0.00 0.00 3.91
2398 3234 9.706691 TGTCTATAAACTTGGTCAAACTTAGAG 57.293 33.333 0.00 0.00 0.00 2.43
2443 3279 9.760077 AAATAGTACACCTTATATTGAGGAACG 57.240 33.333 10.81 0.00 37.72 3.95
2444 3280 6.158023 AGTACACCTTATATTGAGGAACGG 57.842 41.667 10.81 0.00 37.72 4.44
2445 3281 5.895534 AGTACACCTTATATTGAGGAACGGA 59.104 40.000 10.81 0.00 37.72 4.69
2446 3282 5.277857 ACACCTTATATTGAGGAACGGAG 57.722 43.478 10.81 0.00 37.72 4.63
2447 3283 4.101119 ACACCTTATATTGAGGAACGGAGG 59.899 45.833 10.81 0.00 37.72 4.30
2448 3284 3.646637 ACCTTATATTGAGGAACGGAGGG 59.353 47.826 10.81 0.00 37.72 4.30
2449 3285 3.901844 CCTTATATTGAGGAACGGAGGGA 59.098 47.826 0.00 0.00 36.33 4.20
2450 3286 4.021016 CCTTATATTGAGGAACGGAGGGAG 60.021 50.000 0.00 0.00 36.33 4.30
2677 3609 7.715249 TCCTTCTAAAGATATGTTACCATGCAC 59.285 37.037 0.00 0.00 32.29 4.57
2680 3612 3.838244 AGATATGTTACCATGCACGGT 57.162 42.857 10.40 10.40 43.46 4.83
2921 3853 9.881773 ATTTATGATACACCAGTTTTATGGGAT 57.118 29.630 0.00 0.00 45.25 3.85
2942 3874 2.660189 ATTTTGATTTGAGCAGCCCG 57.340 45.000 0.00 0.00 0.00 6.13
2955 3887 1.268539 GCAGCCCGGTATTTTTCATCG 60.269 52.381 0.00 0.00 0.00 3.84
2960 3892 2.943033 CCCGGTATTTTTCATCGAGCTT 59.057 45.455 0.00 0.00 0.00 3.74
2966 3898 6.846283 CGGTATTTTTCATCGAGCTTGTAATC 59.154 38.462 0.00 0.00 0.00 1.75
2968 3900 8.398665 GGTATTTTTCATCGAGCTTGTAATCTT 58.601 33.333 0.00 0.00 0.00 2.40
2969 3901 9.774742 GTATTTTTCATCGAGCTTGTAATCTTT 57.225 29.630 0.00 0.00 0.00 2.52
2996 3928 8.574251 TTTTAGCAAAATCCAGCTAGTAATCA 57.426 30.769 0.00 0.00 43.50 2.57
3018 3950 3.720949 GCAGAAATAATGCATGCCTCA 57.279 42.857 16.68 0.00 43.31 3.86
3032 3964 7.822161 TGCATGCCTCAACTAATTATACATT 57.178 32.000 16.68 0.00 0.00 2.71
3037 3969 7.224297 TGCCTCAACTAATTATACATTCCCTC 58.776 38.462 0.00 0.00 0.00 4.30
3113 4045 2.987413 TTGTTGACGCAGGCAAATAG 57.013 45.000 0.00 0.00 0.00 1.73
3127 4366 7.260603 GCAGGCAAATAGTTCATAATCAGTTT 58.739 34.615 0.00 0.00 0.00 2.66
3212 4451 4.156455 TCCAATGGTCCTAGAGAAATGC 57.844 45.455 0.00 0.00 0.00 3.56
3241 4480 5.461317 CCCTCCCCTAATGTCTCCTATACTT 60.461 48.000 0.00 0.00 0.00 2.24
3264 4503 9.953565 ACTTATACATTTTGCCTCTTAAGTACA 57.046 29.630 1.63 0.00 29.47 2.90
3311 4550 6.659745 TGAGTACTCCTGCTTTTTACACTA 57.340 37.500 20.11 0.00 0.00 2.74
3440 4687 6.182039 TCTTAATTTGCTCTGGAATTGTCG 57.818 37.500 0.00 0.00 0.00 4.35
3446 4693 2.290260 TGCTCTGGAATTGTCGGACATT 60.290 45.455 12.26 5.65 0.00 2.71
3453 4700 4.226761 GGAATTGTCGGACATTGTTTCAC 58.773 43.478 12.26 4.69 0.00 3.18
3464 4711 6.640499 CGGACATTGTTTCACATTTAACATGT 59.360 34.615 0.00 0.00 34.52 3.21
3499 4746 8.962884 ATCGATATATGCAGGCATAAACAATA 57.037 30.769 17.01 7.03 41.53 1.90
3555 4806 9.914131 TGACATATACTACTCATCAAATAGCAC 57.086 33.333 0.00 0.00 0.00 4.40
3563 4814 5.869350 ACTCATCAAATAGCACGTAAAAGC 58.131 37.500 0.00 0.00 0.00 3.51
3684 4945 7.858052 CTTGGACATCAAGTGAACAATTTAC 57.142 36.000 0.00 0.00 45.81 2.01
3973 5371 4.455533 GTGTGCAAGAACATGAAGATGGTA 59.544 41.667 0.00 0.00 33.39 3.25
4267 5665 0.322816 AACTAGTGGAGGGCGACGTA 60.323 55.000 0.00 0.00 0.00 3.57
4660 6065 5.163953 CCACGCGCTTATCCTAATGAATAAG 60.164 44.000 5.73 0.00 0.00 1.73
4664 6069 7.817962 ACGCGCTTATCCTAATGAATAAGTTAT 59.182 33.333 5.73 0.00 0.00 1.89
4665 6070 9.297586 CGCGCTTATCCTAATGAATAAGTTATA 57.702 33.333 5.56 0.00 0.00 0.98
4697 6102 8.356533 AGTAAACAAAGAAAACATGCATCAAG 57.643 30.769 0.00 0.00 0.00 3.02
4795 6214 2.142319 GGATCGAGGAGGAGTACGTAC 58.858 57.143 18.10 18.10 0.00 3.67
4796 6215 1.791785 GATCGAGGAGGAGTACGTACG 59.208 57.143 19.49 15.01 0.00 3.67
4929 6350 7.014230 TCCAAGGTCTAATTCCTGTTTTCTTTG 59.986 37.037 0.00 0.00 35.27 2.77
4985 6408 2.515290 CCTCTGCGCATCATGGCA 60.515 61.111 12.24 0.00 37.63 4.92
4996 6423 2.067013 CATCATGGCATCGACTAGCAG 58.933 52.381 0.00 0.00 0.00 4.24
5021 6448 3.194116 AGCCATGATCACCAAACACAATC 59.806 43.478 0.00 0.00 0.00 2.67
5229 7570 1.668101 GGTCTCACGGCTCTACCTGG 61.668 65.000 0.00 0.00 35.61 4.45
5369 7713 1.443407 CGTACCCATCCTGCTCCAG 59.557 63.158 0.00 0.00 0.00 3.86
5444 7788 6.370453 TGTTGTAGCTGTATCCTATACCTGA 58.630 40.000 0.00 0.00 0.00 3.86
5470 7814 2.279517 GCGCCACCTCATACTCCG 60.280 66.667 0.00 0.00 0.00 4.63
5477 7821 4.647615 CTCATACTCCGGCGGCGG 62.648 72.222 41.57 41.57 0.00 6.13
5513 7866 4.944619 TGTACTCATCATCCCAGATGTC 57.055 45.455 4.60 0.00 44.46 3.06
5589 7942 3.060000 TGCTGCTGCATCTGTGGC 61.060 61.111 14.93 2.16 45.31 5.01
5601 7954 1.920325 CTGTGGCCTCTTCCTGGGA 60.920 63.158 3.32 0.00 0.00 4.37
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 9.983024 AGCTCTATACCTACATGTAGATGTTAT 57.017 33.333 30.41 21.12 40.05 1.89
2 3 9.233649 GTAGCTCTATACCTACATGTAGATGTT 57.766 37.037 30.41 15.78 40.05 2.71
3 4 7.830201 GGTAGCTCTATACCTACATGTAGATGT 59.170 40.741 30.41 22.53 41.78 3.06
4 5 8.215926 GGTAGCTCTATACCTACATGTAGATG 57.784 42.308 30.41 18.48 41.78 2.90
16 17 7.065683 GGACTAAATCGTAGGTAGCTCTATACC 59.934 44.444 0.00 0.00 44.81 2.73
17 18 7.605691 TGGACTAAATCGTAGGTAGCTCTATAC 59.394 40.741 0.00 0.00 0.00 1.47
18 19 7.683578 TGGACTAAATCGTAGGTAGCTCTATA 58.316 38.462 0.00 0.00 0.00 1.31
19 20 6.540995 TGGACTAAATCGTAGGTAGCTCTAT 58.459 40.000 0.00 0.00 0.00 1.98
20 21 5.933617 TGGACTAAATCGTAGGTAGCTCTA 58.066 41.667 0.00 0.00 0.00 2.43
21 22 4.789807 TGGACTAAATCGTAGGTAGCTCT 58.210 43.478 0.00 0.00 0.00 4.09
22 23 5.708877 ATGGACTAAATCGTAGGTAGCTC 57.291 43.478 0.00 0.00 0.00 4.09
23 24 7.176490 AGATATGGACTAAATCGTAGGTAGCT 58.824 38.462 0.00 0.00 0.00 3.32
24 25 7.120873 TGAGATATGGACTAAATCGTAGGTAGC 59.879 40.741 0.00 0.00 0.00 3.58
25 26 8.563123 TGAGATATGGACTAAATCGTAGGTAG 57.437 38.462 0.00 0.00 0.00 3.18
26 27 8.929260 TTGAGATATGGACTAAATCGTAGGTA 57.071 34.615 0.00 0.00 0.00 3.08
27 28 7.834881 TTGAGATATGGACTAAATCGTAGGT 57.165 36.000 0.00 0.00 0.00 3.08
28 29 7.276658 GCATTGAGATATGGACTAAATCGTAGG 59.723 40.741 0.00 0.00 0.00 3.18
29 30 7.814587 TGCATTGAGATATGGACTAAATCGTAG 59.185 37.037 0.00 0.00 0.00 3.51
30 31 7.666623 TGCATTGAGATATGGACTAAATCGTA 58.333 34.615 0.00 0.00 0.00 3.43
31 32 6.524734 TGCATTGAGATATGGACTAAATCGT 58.475 36.000 0.00 0.00 0.00 3.73
32 33 7.332678 TGATGCATTGAGATATGGACTAAATCG 59.667 37.037 0.00 0.00 0.00 3.34
33 34 8.449397 GTGATGCATTGAGATATGGACTAAATC 58.551 37.037 0.00 0.00 0.00 2.17
34 35 8.162085 AGTGATGCATTGAGATATGGACTAAAT 58.838 33.333 0.00 0.00 0.00 1.40
35 36 7.512130 AGTGATGCATTGAGATATGGACTAAA 58.488 34.615 0.00 0.00 0.00 1.85
36 37 7.071069 AGTGATGCATTGAGATATGGACTAA 57.929 36.000 0.00 0.00 0.00 2.24
37 38 6.676990 AGTGATGCATTGAGATATGGACTA 57.323 37.500 0.00 0.00 0.00 2.59
38 39 5.563876 AGTGATGCATTGAGATATGGACT 57.436 39.130 0.00 0.00 0.00 3.85
39 40 5.347093 CGTAGTGATGCATTGAGATATGGAC 59.653 44.000 0.00 0.00 0.00 4.02
40 41 5.011023 ACGTAGTGATGCATTGAGATATGGA 59.989 40.000 0.00 0.00 42.51 3.41
41 42 5.233225 ACGTAGTGATGCATTGAGATATGG 58.767 41.667 0.00 0.00 42.51 2.74
42 43 6.775939 AACGTAGTGATGCATTGAGATATG 57.224 37.500 0.00 0.00 45.00 1.78
43 44 6.763135 ACAAACGTAGTGATGCATTGAGATAT 59.237 34.615 0.00 0.00 45.00 1.63
44 45 6.106003 ACAAACGTAGTGATGCATTGAGATA 58.894 36.000 0.00 0.00 45.00 1.98
45 46 4.937620 ACAAACGTAGTGATGCATTGAGAT 59.062 37.500 0.00 0.00 45.00 2.75
46 47 4.314961 ACAAACGTAGTGATGCATTGAGA 58.685 39.130 0.00 0.00 45.00 3.27
47 48 4.668576 ACAAACGTAGTGATGCATTGAG 57.331 40.909 0.00 0.00 45.00 3.02
48 49 4.376920 CGAACAAACGTAGTGATGCATTGA 60.377 41.667 0.00 0.00 45.00 2.57
49 50 3.840209 CGAACAAACGTAGTGATGCATTG 59.160 43.478 0.00 0.00 45.00 2.82
50 51 3.743911 TCGAACAAACGTAGTGATGCATT 59.256 39.130 0.00 0.00 45.00 3.56
51 52 3.322369 TCGAACAAACGTAGTGATGCAT 58.678 40.909 0.00 0.00 45.00 3.96
52 53 2.745102 TCGAACAAACGTAGTGATGCA 58.255 42.857 6.19 0.00 45.00 3.96
53 54 3.427528 TCTTCGAACAAACGTAGTGATGC 59.572 43.478 6.19 0.00 45.00 3.91
54 55 4.433022 GCTCTTCGAACAAACGTAGTGATG 60.433 45.833 6.19 0.00 45.00 3.07
55 56 3.673809 GCTCTTCGAACAAACGTAGTGAT 59.326 43.478 6.19 0.00 45.00 3.06
56 57 3.047796 GCTCTTCGAACAAACGTAGTGA 58.952 45.455 6.19 0.00 45.00 3.41
57 58 2.792674 TGCTCTTCGAACAAACGTAGTG 59.207 45.455 0.00 0.00 45.00 2.74
59 60 3.050619 ACTGCTCTTCGAACAAACGTAG 58.949 45.455 0.00 0.00 33.32 3.51
60 61 3.088194 ACTGCTCTTCGAACAAACGTA 57.912 42.857 0.00 0.00 34.70 3.57
61 62 1.935933 ACTGCTCTTCGAACAAACGT 58.064 45.000 0.00 0.00 34.70 3.99
62 63 3.319238 AAACTGCTCTTCGAACAAACG 57.681 42.857 0.00 0.00 0.00 3.60
63 64 4.658071 TCAAAACTGCTCTTCGAACAAAC 58.342 39.130 0.00 0.00 0.00 2.93
64 65 4.955925 TCAAAACTGCTCTTCGAACAAA 57.044 36.364 0.00 0.00 0.00 2.83
65 66 5.065859 TCAATCAAAACTGCTCTTCGAACAA 59.934 36.000 0.00 0.00 0.00 2.83
66 67 4.574421 TCAATCAAAACTGCTCTTCGAACA 59.426 37.500 0.00 0.00 0.00 3.18
67 68 5.095691 TCAATCAAAACTGCTCTTCGAAC 57.904 39.130 0.00 0.00 0.00 3.95
68 69 5.469760 TCATCAATCAAAACTGCTCTTCGAA 59.530 36.000 0.00 0.00 0.00 3.71
69 70 4.996758 TCATCAATCAAAACTGCTCTTCGA 59.003 37.500 0.00 0.00 0.00 3.71
70 71 5.287170 TCATCAATCAAAACTGCTCTTCG 57.713 39.130 0.00 0.00 0.00 3.79
71 72 6.072286 TCCTTCATCAATCAAAACTGCTCTTC 60.072 38.462 0.00 0.00 0.00 2.87
72 73 5.771666 TCCTTCATCAATCAAAACTGCTCTT 59.228 36.000 0.00 0.00 0.00 2.85
73 74 5.319453 TCCTTCATCAATCAAAACTGCTCT 58.681 37.500 0.00 0.00 0.00 4.09
74 75 5.633830 TCCTTCATCAATCAAAACTGCTC 57.366 39.130 0.00 0.00 0.00 4.26
75 76 6.409524 TTTCCTTCATCAATCAAAACTGCT 57.590 33.333 0.00 0.00 0.00 4.24
76 77 6.869913 TGATTTCCTTCATCAATCAAAACTGC 59.130 34.615 0.00 0.00 34.66 4.40
77 78 8.821147 TTGATTTCCTTCATCAATCAAAACTG 57.179 30.769 4.46 0.00 41.67 3.16
117 118 0.179108 GGACTACTGGACGACCATGC 60.179 60.000 7.16 0.00 45.87 4.06
130 131 3.397849 AGTTTCTTTGGTCCGGACTAC 57.602 47.619 32.52 18.41 0.00 2.73
190 191 3.367292 GGATCTGCAGATGACTAGCTAGC 60.367 52.174 33.33 14.23 34.37 3.42
201 202 3.112205 GCCCACCGGATCTGCAGAT 62.112 63.158 29.09 29.09 37.51 2.90
222 224 6.882140 TGGGTAGACGTCATCATAAAAACATT 59.118 34.615 19.50 0.00 0.00 2.71
225 227 5.873164 ACTGGGTAGACGTCATCATAAAAAC 59.127 40.000 19.50 1.49 0.00 2.43
237 239 1.713297 AACTCCAACTGGGTAGACGT 58.287 50.000 0.00 0.00 38.11 4.34
239 241 3.256631 TCGTAAACTCCAACTGGGTAGAC 59.743 47.826 0.00 0.00 38.11 2.59
266 268 9.734620 CGCTATCAATGATGGAAGAAAATAAAA 57.265 29.630 10.89 0.00 0.00 1.52
267 269 8.352201 CCGCTATCAATGATGGAAGAAAATAAA 58.648 33.333 10.89 0.00 0.00 1.40
268 270 7.502226 ACCGCTATCAATGATGGAAGAAAATAA 59.498 33.333 10.89 0.00 0.00 1.40
359 361 3.618594 GCAATGAGCGAATAGAGTGACAA 59.381 43.478 0.00 0.00 0.00 3.18
594 611 5.649831 AGAGCTTGACAAAGATAATGGTTCC 59.350 40.000 0.00 0.00 35.19 3.62
687 706 2.092103 TCACAGCCCCACTAACTGTTTT 60.092 45.455 0.00 0.00 42.59 2.43
766 793 8.742777 ACTAATATCACCGTGTAGTTTGAGTAA 58.257 33.333 0.00 0.00 0.00 2.24
1045 1078 1.900351 CCGGAGAGCAGACCATGAA 59.100 57.895 0.00 0.00 0.00 2.57
1357 1714 7.545362 ACATCATGCACTACAAATAAGACTC 57.455 36.000 0.00 0.00 0.00 3.36
1397 1754 5.240891 TGCAAACACAATTTGGAAAGTCAA 58.759 33.333 0.78 0.00 0.00 3.18
1412 1769 2.813061 AGTTGAAGTGCATGCAAACAC 58.187 42.857 26.50 17.66 37.05 3.32
1650 2017 3.759618 TGTGACCCGGCCTTAATTTAAAG 59.240 43.478 0.00 0.00 0.00 1.85
1653 2020 2.306512 AGTGTGACCCGGCCTTAATTTA 59.693 45.455 0.00 0.00 0.00 1.40
1657 2024 0.475044 AAAGTGTGACCCGGCCTTAA 59.525 50.000 0.00 0.00 0.00 1.85
1658 2025 0.475044 AAAAGTGTGACCCGGCCTTA 59.525 50.000 0.00 0.00 0.00 2.69
1659 2026 0.475044 TAAAAGTGTGACCCGGCCTT 59.525 50.000 0.00 0.00 0.00 4.35
1660 2027 0.475044 TTAAAAGTGTGACCCGGCCT 59.525 50.000 0.00 0.00 0.00 5.19
1661 2028 0.594602 GTTAAAAGTGTGACCCGGCC 59.405 55.000 0.00 0.00 0.00 6.13
1662 2029 0.236449 CGTTAAAAGTGTGACCCGGC 59.764 55.000 0.00 0.00 0.00 6.13
1663 2030 0.869730 CCGTTAAAAGTGTGACCCGG 59.130 55.000 0.00 0.00 0.00 5.73
1664 2031 0.236449 GCCGTTAAAAGTGTGACCCG 59.764 55.000 0.00 0.00 0.00 5.28
1665 2032 1.601166 AGCCGTTAAAAGTGTGACCC 58.399 50.000 0.00 0.00 0.00 4.46
1666 2033 6.673154 ATATTAGCCGTTAAAAGTGTGACC 57.327 37.500 0.00 0.00 0.00 4.02
1667 2034 8.876790 AGTAATATTAGCCGTTAAAAGTGTGAC 58.123 33.333 0.00 0.00 0.00 3.67
1940 2310 6.929049 TCATCGTATTTCCATACCTTGACATC 59.071 38.462 0.00 0.00 32.79 3.06
2142 2971 9.694520 CACTGATTCGTTTATTTCACTCATTAG 57.305 33.333 0.00 0.00 0.00 1.73
2165 3001 7.735917 TGTAGCAATTAGATTAGGTATGCACT 58.264 34.615 0.00 0.00 34.89 4.40
2166 3002 7.962964 TGTAGCAATTAGATTAGGTATGCAC 57.037 36.000 0.00 0.00 34.89 4.57
2168 3004 9.877178 AGTATGTAGCAATTAGATTAGGTATGC 57.123 33.333 0.00 0.00 0.00 3.14
2186 3022 2.946785 AGGAACGGAGGGAGTATGTAG 58.053 52.381 0.00 0.00 0.00 2.74
2187 3023 4.524802 TTAGGAACGGAGGGAGTATGTA 57.475 45.455 0.00 0.00 0.00 2.29
2191 3027 6.723052 CCTTATATTTAGGAACGGAGGGAGTA 59.277 42.308 0.00 0.00 34.56 2.59
2192 3028 5.543020 CCTTATATTTAGGAACGGAGGGAGT 59.457 44.000 0.00 0.00 34.56 3.85
2193 3029 5.543020 ACCTTATATTTAGGAACGGAGGGAG 59.457 44.000 9.82 0.00 36.58 4.30
2194 3030 5.306160 CACCTTATATTTAGGAACGGAGGGA 59.694 44.000 9.82 0.00 36.58 4.20
2195 3031 5.071384 ACACCTTATATTTAGGAACGGAGGG 59.929 44.000 9.82 0.00 36.58 4.30
2196 3032 6.170846 ACACCTTATATTTAGGAACGGAGG 57.829 41.667 9.82 0.00 36.58 4.30
2233 3069 8.784043 GGTCAAACATAGACAATAGTTGACTTT 58.216 33.333 11.96 0.00 38.92 2.66
2234 3070 7.936847 TGGTCAAACATAGACAATAGTTGACTT 59.063 33.333 11.96 0.00 38.92 3.01
2235 3071 7.450074 TGGTCAAACATAGACAATAGTTGACT 58.550 34.615 11.96 0.00 38.92 3.41
2236 3072 7.667043 TGGTCAAACATAGACAATAGTTGAC 57.333 36.000 0.00 0.00 38.57 3.18
2237 3073 8.321353 AGATGGTCAAACATAGACAATAGTTGA 58.679 33.333 0.00 0.00 37.74 3.18
2238 3074 8.498054 AGATGGTCAAACATAGACAATAGTTG 57.502 34.615 0.00 0.00 37.74 3.16
2239 3075 9.520515 AAAGATGGTCAAACATAGACAATAGTT 57.479 29.630 0.00 0.00 37.74 2.24
2244 3080 9.109393 GCTATAAAGATGGTCAAACATAGACAA 57.891 33.333 0.00 0.00 37.74 3.18
2245 3081 8.264347 TGCTATAAAGATGGTCAAACATAGACA 58.736 33.333 0.00 0.00 37.74 3.41
2246 3082 8.662781 TGCTATAAAGATGGTCAAACATAGAC 57.337 34.615 0.00 0.00 35.29 2.59
2247 3083 9.679661 TTTGCTATAAAGATGGTCAAACATAGA 57.320 29.630 0.00 0.00 0.00 1.98
2325 3161 9.358406 AGCAAATCATTATCATTAGGTTCATCA 57.642 29.630 0.00 0.00 0.00 3.07
2372 3208 9.706691 CTCTAAGTTTGACCAAGTTTATAGACA 57.293 33.333 0.00 0.00 30.16 3.41
2417 3253 9.760077 CGTTCCTCAATATAAGGTGTACTATTT 57.240 33.333 0.00 0.00 35.29 1.40
2418 3254 8.365647 CCGTTCCTCAATATAAGGTGTACTATT 58.634 37.037 0.00 0.00 35.29 1.73
2419 3255 7.727186 TCCGTTCCTCAATATAAGGTGTACTAT 59.273 37.037 0.00 0.00 35.29 2.12
2420 3256 7.062322 TCCGTTCCTCAATATAAGGTGTACTA 58.938 38.462 0.00 0.00 35.29 1.82
2421 3257 5.895534 TCCGTTCCTCAATATAAGGTGTACT 59.104 40.000 0.00 0.00 35.29 2.73
2422 3258 6.152932 TCCGTTCCTCAATATAAGGTGTAC 57.847 41.667 4.45 0.00 35.29 2.90
2423 3259 5.303589 CCTCCGTTCCTCAATATAAGGTGTA 59.696 44.000 4.45 0.00 35.29 2.90
2424 3260 4.101119 CCTCCGTTCCTCAATATAAGGTGT 59.899 45.833 4.45 0.00 35.29 4.16
2425 3261 4.503296 CCCTCCGTTCCTCAATATAAGGTG 60.503 50.000 4.45 0.00 35.29 4.00
2426 3262 3.646637 CCCTCCGTTCCTCAATATAAGGT 59.353 47.826 4.45 0.00 35.29 3.50
2427 3263 3.901844 TCCCTCCGTTCCTCAATATAAGG 59.098 47.826 0.00 0.00 35.05 2.69
2428 3264 4.589374 ACTCCCTCCGTTCCTCAATATAAG 59.411 45.833 0.00 0.00 0.00 1.73
2429 3265 4.553678 ACTCCCTCCGTTCCTCAATATAA 58.446 43.478 0.00 0.00 0.00 0.98
2430 3266 4.194678 ACTCCCTCCGTTCCTCAATATA 57.805 45.455 0.00 0.00 0.00 0.86
2431 3267 3.047695 ACTCCCTCCGTTCCTCAATAT 57.952 47.619 0.00 0.00 0.00 1.28
2432 3268 2.544844 ACTCCCTCCGTTCCTCAATA 57.455 50.000 0.00 0.00 0.00 1.90
2433 3269 2.108970 GTACTCCCTCCGTTCCTCAAT 58.891 52.381 0.00 0.00 0.00 2.57
2434 3270 1.076677 AGTACTCCCTCCGTTCCTCAA 59.923 52.381 0.00 0.00 0.00 3.02
2435 3271 0.702902 AGTACTCCCTCCGTTCCTCA 59.297 55.000 0.00 0.00 0.00 3.86
2436 3272 2.725221 TAGTACTCCCTCCGTTCCTC 57.275 55.000 0.00 0.00 0.00 3.71
2437 3273 3.463048 TTTAGTACTCCCTCCGTTCCT 57.537 47.619 0.00 0.00 0.00 3.36
2438 3274 6.267242 AGAATATTTAGTACTCCCTCCGTTCC 59.733 42.308 0.00 0.00 0.00 3.62
2439 3275 7.146648 CAGAATATTTAGTACTCCCTCCGTTC 58.853 42.308 0.00 0.00 0.00 3.95
2440 3276 6.041751 CCAGAATATTTAGTACTCCCTCCGTT 59.958 42.308 0.00 0.00 0.00 4.44
2441 3277 5.539193 CCAGAATATTTAGTACTCCCTCCGT 59.461 44.000 0.00 0.00 0.00 4.69
2442 3278 5.047235 CCCAGAATATTTAGTACTCCCTCCG 60.047 48.000 0.00 0.00 0.00 4.63
2443 3279 5.845065 ACCCAGAATATTTAGTACTCCCTCC 59.155 44.000 0.00 0.00 0.00 4.30
2444 3280 6.997942 ACCCAGAATATTTAGTACTCCCTC 57.002 41.667 0.00 0.00 0.00 4.30
2493 3425 8.642020 CGTATATACCCAGAAAATTTAGTACGC 58.358 37.037 7.30 0.00 0.00 4.42
2895 3827 9.881773 ATCCCATAAAACTGGTGTATCATAAAT 57.118 29.630 0.00 0.00 34.23 1.40
2921 3853 3.119173 CCGGGCTGCTCAAATCAAAATTA 60.119 43.478 0.00 0.00 0.00 1.40
2937 3869 2.561569 CTCGATGAAAAATACCGGGCT 58.438 47.619 6.32 0.00 0.00 5.19
2942 3874 7.920738 AGATTACAAGCTCGATGAAAAATACC 58.079 34.615 0.00 0.00 0.00 2.73
3011 3943 7.759607 AGGGAATGTATAATTAGTTGAGGCAT 58.240 34.615 0.00 0.00 0.00 4.40
3012 3944 7.147391 TGAGGGAATGTATAATTAGTTGAGGCA 60.147 37.037 0.00 0.00 0.00 4.75
3013 3945 7.224297 TGAGGGAATGTATAATTAGTTGAGGC 58.776 38.462 0.00 0.00 0.00 4.70
3014 3946 9.627123 TTTGAGGGAATGTATAATTAGTTGAGG 57.373 33.333 0.00 0.00 0.00 3.86
3113 4045 5.048083 TGGCAACTCCAAACTGATTATGAAC 60.048 40.000 0.00 0.00 43.21 3.18
3212 4451 4.046103 AGGAGACATTAGGGGAGGGTATAG 59.954 50.000 0.00 0.00 0.00 1.31
3241 4480 9.817809 CTCTGTACTTAAGAGGCAAAATGTATA 57.182 33.333 10.09 0.00 38.00 1.47
3283 4522 6.650807 TGTAAAAAGCAGGAGTACTCAATGAG 59.349 38.462 23.91 8.98 35.52 2.90
3288 4527 5.546621 AGTGTAAAAAGCAGGAGTACTCA 57.453 39.130 23.91 0.00 0.00 3.41
3296 4535 7.595130 GGAGAAAACAATAGTGTAAAAAGCAGG 59.405 37.037 0.00 0.00 36.80 4.85
3329 4568 5.106515 GCTCTCTTCGCCTTTTTGTTAAGAT 60.107 40.000 0.00 0.00 0.00 2.40
3330 4569 4.213482 GCTCTCTTCGCCTTTTTGTTAAGA 59.787 41.667 0.00 0.00 0.00 2.10
3331 4570 4.214332 AGCTCTCTTCGCCTTTTTGTTAAG 59.786 41.667 0.00 0.00 0.00 1.85
3332 4571 4.024048 CAGCTCTCTTCGCCTTTTTGTTAA 60.024 41.667 0.00 0.00 0.00 2.01
3333 4572 3.498397 CAGCTCTCTTCGCCTTTTTGTTA 59.502 43.478 0.00 0.00 0.00 2.41
3334 4573 2.291741 CAGCTCTCTTCGCCTTTTTGTT 59.708 45.455 0.00 0.00 0.00 2.83
3335 4574 1.876156 CAGCTCTCTTCGCCTTTTTGT 59.124 47.619 0.00 0.00 0.00 2.83
3464 4711 7.084486 GCCTGCATATATCGATCATCGTATAA 58.916 38.462 7.00 0.00 41.35 0.98
3563 4814 5.368256 AGAAAGCTACAAAAGAGCATGTG 57.632 39.130 0.00 0.00 42.69 3.21
3683 4944 6.365970 AACTGATAGACACATGGAGAAAGT 57.634 37.500 0.00 0.00 0.00 2.66
3684 4945 7.776107 TCTAACTGATAGACACATGGAGAAAG 58.224 38.462 0.00 0.00 35.68 2.62
3826 5095 9.479549 TGATATATGTCTGGCATTCTAGATGTA 57.520 33.333 0.00 0.00 38.94 2.29
3839 5108 9.860898 TGACGAATTCTAATGATATATGTCTGG 57.139 33.333 3.52 0.00 0.00 3.86
3900 5297 3.699038 ACACAGTTGCACACCAAAGTTAT 59.301 39.130 0.00 0.00 34.68 1.89
3973 5371 0.031721 AGAAGAAGTCGTTCGCCGTT 59.968 50.000 0.00 0.00 37.79 4.44
4249 5647 0.106819 ATACGTCGCCCTCCACTAGT 60.107 55.000 0.00 0.00 0.00 2.57
4289 5687 1.947456 GTTGTTCACCTGGAAGTGGAC 59.053 52.381 0.00 0.00 45.12 4.02
4633 6031 2.433868 TTAGGATAAGCGCGTGGATC 57.566 50.000 8.43 7.82 0.00 3.36
4665 6070 9.083080 GCATGTTTTCTTTGTTTACTTGTACTT 57.917 29.630 0.00 0.00 0.00 2.24
4721 6140 6.674694 ACTAGTAACTACACCACATCGTAG 57.325 41.667 0.00 0.00 40.77 3.51
4795 6214 2.024305 CGGGAGCTAGCACGTACG 59.976 66.667 18.83 15.01 0.00 3.67
4796 6215 2.412112 CCGGGAGCTAGCACGTAC 59.588 66.667 18.83 3.89 0.00 3.67
4815 6236 3.367703 CCACCGTTTATTCTACACGACCT 60.368 47.826 0.00 0.00 35.93 3.85
4869 6290 9.880157 ATTTCATATTGAAGTTTAGCAGCATTT 57.120 25.926 0.00 0.00 37.70 2.32
4911 6332 5.467035 TGGCCAAAGAAAACAGGAATTAG 57.533 39.130 0.61 0.00 0.00 1.73
4929 6350 5.391312 ACAAGATTAAAACACAGATGGCC 57.609 39.130 0.00 0.00 0.00 5.36
4985 6408 1.406065 ATGGCTGCCTGCTAGTCGAT 61.406 55.000 21.03 0.00 42.39 3.59
4996 6423 0.174162 GTTTGGTGATCATGGCTGCC 59.826 55.000 12.87 12.87 0.00 4.85
5021 6448 4.217118 AGGTCTGTTTTGCTATCTGCTTTG 59.783 41.667 0.00 0.00 43.37 2.77
5391 7735 4.181010 CAGCCGGCCACCAGCTAT 62.181 66.667 26.15 0.00 43.05 2.97
5444 7788 3.570212 AGGTGGCGCCTCCTGTTT 61.570 61.111 41.49 23.04 46.96 2.83
5479 7823 3.649986 GTACATGCCGATGCCGCC 61.650 66.667 0.00 0.00 36.33 6.13
5513 7866 6.863645 CGACTATGACTACAATGGTATCCAAG 59.136 42.308 0.00 0.00 36.95 3.61
5589 7942 1.296715 CGGTTGTCCCAGGAAGAGG 59.703 63.158 0.00 0.00 0.00 3.69


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

AutoCloner maintained by Alex Coulton.