Multiple sequence alignment - TraesCS3D01G538500

Loading Multiple Alignment...

Download Multiple Sequence Alignment: (Fasta) (Clustal)


BLAST Results


Shown here are the results of a BLAST search against the genome using the input sequence. The pipeline uses this to extract flanking regions for cloning. If the result of the multiple sequence alignment is not as expected, these results could be used for further investigation.

qseqid sseqid percentage.identical alignment.length no.mismatch no.gap.openings qstart qend sstart send evalue bitscore
0 TraesCS3D01G538500 chr3D 100.000 5341 0 0 1 5341 611167474 611162134 0.000000e+00 9864.0
1 TraesCS3D01G538500 chr3D 79.142 1376 228 43 3004 4338 611253148 611251791 0.000000e+00 896.0
2 TraesCS3D01G538500 chr3D 77.434 904 173 24 3437 4321 611297369 611298260 1.330000e-140 510.0
3 TraesCS3D01G538500 chr3D 74.194 1147 211 48 2287 3391 611296112 611297215 3.000000e-107 399.0
4 TraesCS3D01G538500 chr3D 80.399 301 50 6 2625 2917 611253484 611253185 2.500000e-53 220.0
5 TraesCS3D01G538500 chr3D 72.925 735 144 43 3402 4130 611217212 611216527 2.520000e-48 204.0
6 TraesCS3D01G538500 chr3D 83.871 124 15 5 2350 2470 611218374 611218253 4.370000e-21 113.0
7 TraesCS3D01G538500 chr3B 94.151 1966 90 11 3398 5341 828918458 828916496 0.000000e+00 2970.0
8 TraesCS3D01G538500 chr3B 93.206 1413 78 12 1997 3395 828920043 828918635 0.000000e+00 2061.0
9 TraesCS3D01G538500 chr3B 84.033 1691 156 49 346 1949 828921714 828920051 0.000000e+00 1522.0
10 TraesCS3D01G538500 chr3B 80.277 938 152 27 3431 4350 829014093 829013171 0.000000e+00 676.0
11 TraesCS3D01G538500 chr3B 81.570 586 56 23 345 892 828924693 828924122 2.280000e-118 436.0
12 TraesCS3D01G538500 chr3B 75.295 931 180 38 3412 4321 829039310 829040211 3.000000e-107 399.0
13 TraesCS3D01G538500 chr3B 81.870 353 48 13 2967 3305 829008149 829007799 3.150000e-72 283.0
14 TraesCS3D01G538500 chr3B 82.390 318 50 4 3006 3322 829014557 829014245 6.820000e-69 272.0
15 TraesCS3D01G538500 chr3B 78.100 379 53 16 3014 3364 829038779 829039155 4.190000e-51 213.0
16 TraesCS3D01G538500 chr3B 93.893 131 6 2 209 337 828921915 828921785 4.220000e-46 196.0
17 TraesCS3D01G538500 chr3B 93.846 130 6 2 209 337 828924893 828924765 1.520000e-45 195.0
18 TraesCS3D01G538500 chr3B 72.456 737 149 34 3592 4325 829007474 829006789 2.540000e-43 187.0
19 TraesCS3D01G538500 chr3B 94.231 104 4 2 130 233 256530602 256530501 1.990000e-34 158.0
20 TraesCS3D01G538500 chr3B 91.892 111 7 2 120 229 550799505 550799614 2.580000e-33 154.0
21 TraesCS3D01G538500 chr3B 93.617 94 6 0 14 107 828922438 828922345 2.010000e-29 141.0
22 TraesCS3D01G538500 chr3B 81.208 149 22 6 2326 2470 829008775 829008629 1.220000e-21 115.0
23 TraesCS3D01G538500 chr3B 81.600 125 21 2 1143 1266 828999189 828999066 9.460000e-18 102.0
24 TraesCS3D01G538500 chr3A 96.371 1736 47 9 3394 5118 746088256 746086526 0.000000e+00 2843.0
25 TraesCS3D01G538500 chr3A 89.919 1855 126 31 1568 3395 746090172 746088352 0.000000e+00 2333.0
26 TraesCS3D01G538500 chr3A 90.728 852 58 10 672 1517 746091096 746090260 0.000000e+00 1116.0
27 TraesCS3D01G538500 chr3A 95.278 593 20 5 336 922 746095093 746094503 0.000000e+00 933.0
28 TraesCS3D01G538500 chr3A 76.829 902 173 32 3437 4321 746188104 746188986 4.840000e-130 475.0
29 TraesCS3D01G538500 chr3A 96.903 226 7 0 5116 5341 746086413 746086188 3.900000e-101 379.0
30 TraesCS3D01G538500 chr3A 72.270 934 172 64 3431 4352 746168711 746167853 5.420000e-50 209.0
31 TraesCS3D01G538500 chr3A 95.902 122 4 1 217 337 746095284 746095163 4.220000e-46 196.0
32 TraesCS3D01G538500 chr3A 85.083 181 27 0 3014 3194 746187562 746187742 9.130000e-43 185.0
33 TraesCS3D01G538500 chr3A 83.505 194 32 0 1037 1230 746186144 746186337 1.180000e-41 182.0
34 TraesCS3D01G538500 chr3A 79.121 182 32 6 5003 5180 437617267 437617446 2.610000e-23 121.0
35 TraesCS3D01G538500 chr3A 80.822 146 26 2 2326 2470 746169911 746169767 4.370000e-21 113.0
36 TraesCS3D01G538500 chr3A 93.333 45 3 0 4344 4388 616476015 616476059 3.450000e-07 67.6
37 TraesCS3D01G538500 chr1B 77.215 316 65 4 2614 2927 6566068 6566378 1.530000e-40 178.0
38 TraesCS3D01G538500 chr1B 80.137 146 25 4 2327 2469 6565757 6565901 7.320000e-19 106.0
39 TraesCS3D01G538500 chr1B 87.013 77 8 2 2614 2689 620705499 620705424 9.530000e-13 86.1
40 TraesCS3D01G538500 chr6B 96.970 99 2 1 132 229 646734 646636 1.190000e-36 165.0
41 TraesCS3D01G538500 chr6B 87.013 77 8 2 2614 2689 94092952 94093027 9.530000e-13 86.1
42 TraesCS3D01G538500 chrUn 96.939 98 2 1 122 218 325927170 325927267 4.280000e-36 163.0
43 TraesCS3D01G538500 chr6D 96.040 101 2 2 123 221 464673600 464673700 4.280000e-36 163.0
44 TraesCS3D01G538500 chr6D 74.608 319 55 21 5009 5313 367372553 367372859 3.380000e-22 117.0
45 TraesCS3D01G538500 chr6D 87.013 77 8 2 2614 2689 225592372 225592297 9.530000e-13 86.1
46 TraesCS3D01G538500 chr6D 100.000 28 0 0 4404 4431 82960962 82960989 1.000000e-02 52.8
47 TraesCS3D01G538500 chr1A 96.939 98 2 1 122 218 272648126 272648029 4.280000e-36 163.0
48 TraesCS3D01G538500 chr1A 93.519 108 5 2 124 230 543063458 543063564 5.540000e-35 159.0
49 TraesCS3D01G538500 chr1A 75.000 144 30 5 4985 5123 498044310 498044168 1.610000e-05 62.1
50 TraesCS3D01G538500 chr5D 96.000 100 3 1 126 225 401281327 401281229 1.540000e-35 161.0
51 TraesCS3D01G538500 chr5D 88.235 68 5 3 272 337 355051835 355051769 1.590000e-10 78.7
52 TraesCS3D01G538500 chr5D 97.500 40 1 0 4350 4389 47527594 47527555 9.600000e-08 69.4
53 TraesCS3D01G538500 chr2B 93.396 106 6 1 113 218 36422934 36423038 7.160000e-34 156.0
54 TraesCS3D01G538500 chr2B 81.250 112 17 4 5061 5170 543333190 543333081 2.650000e-13 87.9
55 TraesCS3D01G538500 chr7D 75.358 349 64 19 4976 5311 432431802 432431463 1.200000e-31 148.0
56 TraesCS3D01G538500 chr7D 87.013 77 8 2 2614 2689 351624210 351624135 9.530000e-13 86.1
57 TraesCS3D01G538500 chr2D 83.594 128 14 6 5001 5122 442455725 442455851 4.370000e-21 113.0
58 TraesCS3D01G538500 chr2D 87.013 77 8 2 2614 2689 75409054 75408979 9.530000e-13 86.1
59 TraesCS3D01G538500 chr2D 94.737 38 2 0 4389 4426 543168454 543168491 5.780000e-05 60.2
60 TraesCS3D01G538500 chr2A 76.699 206 40 6 4976 5175 733848812 733848609 2.030000e-19 108.0
61 TraesCS3D01G538500 chr2A 76.471 187 31 13 4990 5170 731380904 731381083 7.370000e-14 89.8
62 TraesCS3D01G538500 chr7A 80.451 133 20 5 5036 5164 685502720 685502850 4.400000e-16 97.1
63 TraesCS3D01G538500 chr7A 80.451 133 20 5 5036 5164 685540283 685540413 4.400000e-16 97.1
64 TraesCS3D01G538500 chr7A 86.486 74 10 0 4349 4422 229207106 229207033 1.230000e-11 82.4
65 TraesCS3D01G538500 chr7A 97.436 39 1 0 4350 4388 561581036 561580998 3.450000e-07 67.6
66 TraesCS3D01G538500 chr4A 85.393 89 8 1 4347 4430 67170173 67170261 2.650000e-13 87.9
67 TraesCS3D01G538500 chr1D 87.013 77 7 1 4357 4430 347200779 347200855 3.430000e-12 84.2
68 TraesCS3D01G538500 chr6A 88.060 67 7 1 272 337 582504540 582504474 1.590000e-10 78.7
69 TraesCS3D01G538500 chr4D 88.235 68 5 3 272 337 19455568 19455634 1.590000e-10 78.7
70 TraesCS3D01G538500 chr4B 97.619 42 1 0 37 78 130216140 130216099 7.420000e-09 73.1
71 TraesCS3D01G538500 chr5A 97.561 41 1 0 4348 4388 598666728 598666768 2.670000e-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 TraesCS3D01G538500 chr3D 611162134 611167474 5340 True 9864.000000 9864 100.000000 1 5341 1 chr3D.!!$R1 5340
1 TraesCS3D01G538500 chr3D 611251791 611253484 1693 True 558.000000 896 79.770500 2625 4338 2 chr3D.!!$R3 1713
2 TraesCS3D01G538500 chr3D 611296112 611298260 2148 False 454.500000 510 75.814000 2287 4321 2 chr3D.!!$F1 2034
3 TraesCS3D01G538500 chr3B 828916496 828924893 8397 True 1074.428571 2970 90.616571 14 5341 7 chr3B.!!$R3 5327
4 TraesCS3D01G538500 chr3B 829013171 829014557 1386 True 474.000000 676 81.333500 3006 4350 2 chr3B.!!$R5 1344
5 TraesCS3D01G538500 chr3B 829038779 829040211 1432 False 306.000000 399 76.697500 3014 4321 2 chr3B.!!$F2 1307
6 TraesCS3D01G538500 chr3A 746086188 746095284 9096 True 1300.000000 2843 94.183500 217 5341 6 chr3A.!!$R1 5124
7 TraesCS3D01G538500 chr3A 746186144 746188986 2842 False 280.666667 475 81.805667 1037 4321 3 chr3A.!!$F3 3284

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
101 2544 0.763035 ACCACTGCCGGTAGTTCTTT 59.237 50.000 23.75 4.38 37.57 2.52 F
1319 7995 1.068610 TCGCACAAATTAGCAAGCACC 60.069 47.619 0.00 0.00 0.00 5.01 F
1712 8441 0.034574 ATGGGTATCGGCTTGTTGCA 60.035 50.000 0.00 0.00 45.15 4.08 F
1807 8537 0.166814 GATGACAGCTTCAACGGTGC 59.833 55.000 0.00 0.00 37.92 5.01 F
3121 10121 0.310854 GGTTTCCACAGCAGGTTTCG 59.689 55.000 0.00 0.00 0.00 3.46 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1357 8033 0.030908 CGATGCCTACGAGAAGGACC 59.969 60.000 7.29 0.00 39.15 4.46 R
3299 10327 0.884704 GTCTCAAGCAAGCCCGACAA 60.885 55.000 0.00 0.00 0.00 3.18 R
3665 10887 6.545666 TGAAAAATACCTGCCATGAATCGTAT 59.454 34.615 0.00 0.00 0.00 3.06 R
3975 11206 6.505044 TGATCATTGTGTTCCTGATTTCTG 57.495 37.500 0.00 0.00 30.00 3.02 R
4915 12193 0.752376 GAGGTACGTAGAGGCTGGCT 60.752 60.000 2.24 2.24 0.00 4.75 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
58 2501 1.074775 GAAGGTCACATGGCCACCA 59.925 57.895 8.16 0.00 43.78 4.17
91 2534 4.704833 CCACCCTGACCACTGCCG 62.705 72.222 0.00 0.00 0.00 5.69
101 2544 0.763035 ACCACTGCCGGTAGTTCTTT 59.237 50.000 23.75 4.38 37.57 2.52
102 2545 1.972795 ACCACTGCCGGTAGTTCTTTA 59.027 47.619 23.75 0.00 37.57 1.85
115 2970 7.176340 CCGGTAGTTCTTTAGGCATATAGTAGT 59.824 40.741 0.00 0.00 0.00 2.73
149 3004 8.544687 AAAATATAGTACTCCCTCCGTAAACT 57.455 34.615 0.00 0.00 0.00 2.66
150 3005 9.646522 AAAATATAGTACTCCCTCCGTAAACTA 57.353 33.333 0.00 0.00 0.00 2.24
151 3006 9.646522 AAATATAGTACTCCCTCCGTAAACTAA 57.353 33.333 0.00 0.00 0.00 2.24
152 3007 9.819754 AATATAGTACTCCCTCCGTAAACTAAT 57.180 33.333 0.00 0.00 0.00 1.73
157 3012 9.294614 AGTACTCCCTCCGTAAACTAATATAAG 57.705 37.037 0.00 0.00 0.00 1.73
158 3013 9.289782 GTACTCCCTCCGTAAACTAATATAAGA 57.710 37.037 0.00 0.00 0.00 2.10
159 3014 8.406730 ACTCCCTCCGTAAACTAATATAAGAG 57.593 38.462 0.00 0.00 0.00 2.85
160 3015 7.039853 ACTCCCTCCGTAAACTAATATAAGAGC 60.040 40.741 0.00 0.00 0.00 4.09
161 3016 6.072286 TCCCTCCGTAAACTAATATAAGAGCG 60.072 42.308 0.00 0.00 0.00 5.03
162 3017 6.294397 CCCTCCGTAAACTAATATAAGAGCGT 60.294 42.308 0.00 0.00 0.00 5.07
163 3018 7.144000 CCTCCGTAAACTAATATAAGAGCGTT 58.856 38.462 0.00 0.00 0.00 4.84
164 3019 7.650903 CCTCCGTAAACTAATATAAGAGCGTTT 59.349 37.037 0.00 0.00 0.00 3.60
165 3020 9.669353 CTCCGTAAACTAATATAAGAGCGTTTA 57.331 33.333 0.00 0.00 0.00 2.01
166 3021 9.669353 TCCGTAAACTAATATAAGAGCGTTTAG 57.331 33.333 0.00 0.00 30.36 1.85
167 3022 9.669353 CCGTAAACTAATATAAGAGCGTTTAGA 57.331 33.333 0.00 0.00 30.36 2.10
212 3067 9.530633 AAACGCTCTTATATTAGTTTACAGAGG 57.469 33.333 0.00 0.00 31.14 3.69
213 3068 8.461249 ACGCTCTTATATTAGTTTACAGAGGA 57.539 34.615 0.00 0.00 0.00 3.71
214 3069 8.910944 ACGCTCTTATATTAGTTTACAGAGGAA 58.089 33.333 0.00 0.00 0.00 3.36
523 3449 2.124778 GGAGGCAGGAGCAGCTTC 60.125 66.667 0.00 0.00 44.61 3.86
641 3582 9.114952 GGACCTGATTATTTTTCCTTCTCTTAG 57.885 37.037 0.00 0.00 0.00 2.18
646 3587 9.720769 TGATTATTTTTCCTTCTCTTAGTTCGT 57.279 29.630 0.00 0.00 0.00 3.85
656 3597 3.265221 TCTCTTAGTTCGTGGTCCTCCTA 59.735 47.826 0.00 0.00 34.23 2.94
657 3598 4.015084 CTCTTAGTTCGTGGTCCTCCTAA 58.985 47.826 0.00 0.00 34.23 2.69
658 3599 4.410099 TCTTAGTTCGTGGTCCTCCTAAA 58.590 43.478 0.00 0.00 34.23 1.85
660 3601 3.679824 AGTTCGTGGTCCTCCTAAAAG 57.320 47.619 0.00 0.00 34.23 2.27
667 6675 4.502604 CGTGGTCCTCCTAAAAGACAAAGA 60.503 45.833 0.00 0.00 31.99 2.52
723 7327 7.097192 GTGAACTGTATTGTATCTCTGGTTCA 58.903 38.462 0.00 0.00 38.34 3.18
840 7457 4.569966 GTCCAACTGCTCACTGATTGATAG 59.430 45.833 0.00 0.00 32.17 2.08
934 7552 1.274167 AGAAAATGACGTACCAGCGGA 59.726 47.619 0.00 0.00 35.98 5.54
997 7618 2.294074 ACCGTGCAGCTTAACAAGAAA 58.706 42.857 0.00 0.00 0.00 2.52
1146 7767 1.986882 CACAGGAAAAGGGAGCAGTT 58.013 50.000 0.00 0.00 0.00 3.16
1281 7957 6.819284 TCACCCGTTAATTTTCCTATATCGT 58.181 36.000 0.00 0.00 0.00 3.73
1283 7959 6.702723 CACCCGTTAATTTTCCTATATCGTCA 59.297 38.462 0.00 0.00 0.00 4.35
1286 7962 7.817962 CCCGTTAATTTTCCTATATCGTCATCT 59.182 37.037 0.00 0.00 0.00 2.90
1318 7994 2.095768 TCTCGCACAAATTAGCAAGCAC 60.096 45.455 0.00 0.00 0.00 4.40
1319 7995 1.068610 TCGCACAAATTAGCAAGCACC 60.069 47.619 0.00 0.00 0.00 5.01
1320 7996 1.335780 CGCACAAATTAGCAAGCACCA 60.336 47.619 0.00 0.00 0.00 4.17
1321 7997 2.753296 GCACAAATTAGCAAGCACCAA 58.247 42.857 0.00 0.00 0.00 3.67
1322 7998 2.733026 GCACAAATTAGCAAGCACCAAG 59.267 45.455 0.00 0.00 0.00 3.61
1323 7999 2.733026 CACAAATTAGCAAGCACCAAGC 59.267 45.455 0.00 0.00 46.19 4.01
1337 8013 4.485163 GCACCAAGCAGTAAAATAACAGG 58.515 43.478 0.00 0.00 44.79 4.00
1338 8014 4.618227 GCACCAAGCAGTAAAATAACAGGG 60.618 45.833 0.00 0.00 44.79 4.45
1357 8033 3.512680 GGGACAAAGATCTAGTGTCACG 58.487 50.000 27.87 4.65 42.81 4.35
1416 8102 2.046314 GGGTTCTGCCGCTGCTTA 60.046 61.111 0.70 0.00 38.71 3.09
1417 8103 2.399356 GGGTTCTGCCGCTGCTTAC 61.399 63.158 0.70 0.00 38.71 2.34
1418 8104 1.376037 GGTTCTGCCGCTGCTTACT 60.376 57.895 0.70 0.00 38.71 2.24
1419 8105 1.639298 GGTTCTGCCGCTGCTTACTG 61.639 60.000 0.70 0.00 38.71 2.74
1420 8106 2.034879 TTCTGCCGCTGCTTACTGC 61.035 57.895 0.70 0.00 43.25 4.40
1457 8143 4.408821 CCCTAGGCCGCTGTTGCA 62.409 66.667 2.05 0.00 39.64 4.08
1467 8153 0.167470 CGCTGTTGCATGGTCTCTTG 59.833 55.000 0.00 0.00 39.64 3.02
1470 8156 2.035066 GCTGTTGCATGGTCTCTTGTTT 59.965 45.455 0.00 0.00 39.41 2.83
1480 8166 4.211125 TGGTCTCTTGTTTGGCAATGTTA 58.789 39.130 0.00 0.00 36.36 2.41
1482 8168 4.982295 GGTCTCTTGTTTGGCAATGTTAAC 59.018 41.667 0.00 0.00 36.36 2.01
1492 8178 2.224784 GGCAATGTTAACGGTTTCGAGT 59.775 45.455 0.00 0.00 40.11 4.18
1493 8179 3.304190 GGCAATGTTAACGGTTTCGAGTT 60.304 43.478 0.00 0.00 40.11 3.01
1505 8191 2.234300 TTCGAGTTGAGTTGGGTCAC 57.766 50.000 0.00 0.00 0.00 3.67
1506 8192 1.116308 TCGAGTTGAGTTGGGTCACA 58.884 50.000 0.00 0.00 0.00 3.58
1517 8203 1.152756 GGGTCACAGCTGGGTTTGT 60.153 57.895 17.28 0.00 0.00 2.83
1519 8205 1.111277 GGTCACAGCTGGGTTTGTTT 58.889 50.000 17.28 0.00 0.00 2.83
1520 8206 1.067060 GGTCACAGCTGGGTTTGTTTC 59.933 52.381 17.28 1.79 0.00 2.78
1522 8208 2.427095 GTCACAGCTGGGTTTGTTTCTT 59.573 45.455 17.28 0.00 0.00 2.52
1523 8209 2.687935 TCACAGCTGGGTTTGTTTCTTC 59.312 45.455 17.28 0.00 0.00 2.87
1530 8234 2.091885 TGGGTTTGTTTCTTCCAGAGCT 60.092 45.455 0.00 0.00 0.00 4.09
1534 8238 3.864789 TTGTTTCTTCCAGAGCTCCTT 57.135 42.857 10.93 0.00 0.00 3.36
1535 8239 3.131709 TGTTTCTTCCAGAGCTCCTTG 57.868 47.619 10.93 2.65 0.00 3.61
1540 8244 1.758440 TTCCAGAGCTCCTTGTGCGT 61.758 55.000 10.93 0.00 35.28 5.24
1566 8270 2.032808 GTGTCTTCGTGAAGTCAAAGCC 60.033 50.000 10.36 0.00 37.98 4.35
1571 8297 1.148310 CGTGAAGTCAAAGCCGACAT 58.852 50.000 1.86 0.00 38.43 3.06
1582 8308 0.977627 AGCCGACATGAGATGGGTGA 60.978 55.000 0.00 0.00 33.60 4.02
1590 8316 0.541392 TGAGATGGGTGATCGGTTGG 59.459 55.000 0.00 0.00 36.04 3.77
1645 8372 3.742369 CCATGCAATGTTCTTTGTTGGAC 59.258 43.478 0.00 0.00 44.81 4.02
1664 8391 3.644884 ACTTGTCTAGTCACCGACTTG 57.355 47.619 1.36 0.58 40.28 3.16
1666 8393 3.243434 ACTTGTCTAGTCACCGACTTGTG 60.243 47.826 1.36 0.00 40.28 3.33
1699 8426 2.915079 CATGGGACGGCATGGGTA 59.085 61.111 0.00 0.00 0.00 3.69
1705 8432 3.161450 ACGGCATGGGTATCGGCT 61.161 61.111 0.00 0.00 0.00 5.52
1712 8441 0.034574 ATGGGTATCGGCTTGTTGCA 60.035 50.000 0.00 0.00 45.15 4.08
1713 8442 0.676466 TGGGTATCGGCTTGTTGCAG 60.676 55.000 0.00 0.00 45.15 4.41
1718 8447 0.250467 ATCGGCTTGTTGCAGTGAGT 60.250 50.000 0.00 0.00 45.15 3.41
1719 8448 1.159713 TCGGCTTGTTGCAGTGAGTG 61.160 55.000 0.00 0.00 45.15 3.51
1723 8452 2.035066 GGCTTGTTGCAGTGAGTGATTT 59.965 45.455 0.00 0.00 45.15 2.17
1734 8463 2.948979 GTGAGTGATTTGTTGGTGGTCA 59.051 45.455 0.00 0.00 0.00 4.02
1752 8482 1.482182 TCATCATGGTGAAGTCGGAGG 59.518 52.381 6.09 0.00 0.00 4.30
1754 8484 1.191489 TCATGGTGAAGTCGGAGGCA 61.191 55.000 0.00 0.00 0.00 4.75
1766 8496 3.567797 GAGGCATTGGCTCGCGAC 61.568 66.667 22.55 1.87 44.75 5.19
1795 8525 3.256558 TGACGATGAAGCTTGATGACAG 58.743 45.455 2.10 0.00 0.00 3.51
1802 8532 3.911661 AAGCTTGATGACAGCTTCAAC 57.088 42.857 0.00 2.14 44.46 3.18
1807 8537 0.166814 GATGACAGCTTCAACGGTGC 59.833 55.000 0.00 0.00 37.92 5.01
1819 8549 3.135994 TCAACGGTGCTTTTCTCCTAAC 58.864 45.455 0.00 0.00 0.00 2.34
1820 8550 2.875933 CAACGGTGCTTTTCTCCTAACA 59.124 45.455 0.00 0.00 0.00 2.41
1822 8552 1.464997 CGGTGCTTTTCTCCTAACAGC 59.535 52.381 0.00 0.00 0.00 4.40
1839 8579 0.459899 AGCTGTGTGTCTTCGTGTGA 59.540 50.000 0.00 0.00 0.00 3.58
1850 8590 0.601558 TTCGTGTGAGTAGCCAGGTC 59.398 55.000 0.00 0.00 0.00 3.85
1875 8615 2.806244 CGGTGTTGCCCTATGTTATAGC 59.194 50.000 0.00 0.00 0.00 2.97
1876 8616 3.494398 CGGTGTTGCCCTATGTTATAGCT 60.494 47.826 0.00 0.00 0.00 3.32
1877 8617 4.262292 CGGTGTTGCCCTATGTTATAGCTA 60.262 45.833 0.00 0.00 0.00 3.32
1879 8619 5.221661 GGTGTTGCCCTATGTTATAGCTAGT 60.222 44.000 0.00 0.00 0.00 2.57
1880 8620 5.696724 GTGTTGCCCTATGTTATAGCTAGTG 59.303 44.000 0.00 0.00 0.00 2.74
1882 8622 3.838317 TGCCCTATGTTATAGCTAGTGGG 59.162 47.826 0.00 4.16 35.47 4.61
1883 8623 3.197983 GCCCTATGTTATAGCTAGTGGGG 59.802 52.174 0.00 4.98 33.15 4.96
1884 8624 4.426704 CCCTATGTTATAGCTAGTGGGGT 58.573 47.826 0.00 0.00 0.00 4.95
1885 8625 4.223032 CCCTATGTTATAGCTAGTGGGGTG 59.777 50.000 0.00 0.00 0.00 4.61
1887 8627 3.124856 TGTTATAGCTAGTGGGGTGGT 57.875 47.619 0.00 0.00 0.00 4.16
1888 8628 2.769663 TGTTATAGCTAGTGGGGTGGTG 59.230 50.000 0.00 0.00 0.00 4.17
1890 8630 2.496679 ATAGCTAGTGGGGTGGTGAT 57.503 50.000 0.00 0.00 0.00 3.06
1891 8631 3.630625 ATAGCTAGTGGGGTGGTGATA 57.369 47.619 0.00 0.00 0.00 2.15
1892 8632 2.263895 AGCTAGTGGGGTGGTGATAA 57.736 50.000 0.00 0.00 0.00 1.75
1908 8648 4.935205 GGTGATAATTTTGCTTGGTTTCCC 59.065 41.667 0.00 0.00 0.00 3.97
1918 8658 6.926630 TTGCTTGGTTTCCCACTAATTAAT 57.073 33.333 0.00 0.00 41.67 1.40
1921 8661 6.268847 TGCTTGGTTTCCCACTAATTAATTGT 59.731 34.615 11.05 4.48 41.67 2.71
1923 8663 6.031751 TGGTTTCCCACTAATTAATTGTGC 57.968 37.500 11.05 4.58 35.17 4.57
1925 8665 6.099341 GGTTTCCCACTAATTAATTGTGCAG 58.901 40.000 11.05 2.78 0.00 4.41
2125 8870 6.071952 CCACACAAGTTAATTAGCCACTTCAT 60.072 38.462 0.00 0.00 0.00 2.57
2128 8873 5.354234 ACAAGTTAATTAGCCACTTCATCCG 59.646 40.000 0.00 0.00 0.00 4.18
2134 8879 0.883833 AGCCACTTCATCCGCAAAAG 59.116 50.000 0.00 0.00 0.00 2.27
2137 8882 2.288152 GCCACTTCATCCGCAAAAGAAA 60.288 45.455 0.00 0.00 0.00 2.52
2138 8883 3.614870 GCCACTTCATCCGCAAAAGAAAT 60.615 43.478 0.00 0.00 0.00 2.17
2139 8884 4.380444 GCCACTTCATCCGCAAAAGAAATA 60.380 41.667 0.00 0.00 0.00 1.40
2140 8885 5.335127 CCACTTCATCCGCAAAAGAAATAG 58.665 41.667 0.00 0.00 0.00 1.73
2141 8886 4.795278 CACTTCATCCGCAAAAGAAATAGC 59.205 41.667 0.00 0.00 0.00 2.97
2142 8887 4.142381 ACTTCATCCGCAAAAGAAATAGCC 60.142 41.667 0.00 0.00 0.00 3.93
2143 8888 3.351740 TCATCCGCAAAAGAAATAGCCA 58.648 40.909 0.00 0.00 0.00 4.75
2144 8889 3.378112 TCATCCGCAAAAGAAATAGCCAG 59.622 43.478 0.00 0.00 0.00 4.85
2247 8992 3.866883 ACTCCCAAATTATGTTTGGCG 57.133 42.857 15.38 11.77 45.70 5.69
2341 9295 4.967084 TTAGCAAGTGGACTCAAGGTAA 57.033 40.909 0.00 0.00 0.00 2.85
2480 9434 5.680619 ACTTCATGAAACCACTACAGTTCA 58.319 37.500 9.88 0.00 0.00 3.18
2491 9445 1.195442 TACAGTTCACCGGCCATGGA 61.195 55.000 18.40 0.00 0.00 3.41
2506 9460 4.322953 GGCCATGGAATTTTTGACAGTGAT 60.323 41.667 18.40 0.00 0.00 3.06
2547 9501 2.768253 TACTGGTGCTTCACATCCAG 57.232 50.000 8.28 8.28 45.53 3.86
2550 9504 1.002888 CTGGTGCTTCACATCCAGTCT 59.997 52.381 0.00 0.00 40.16 3.24
2560 9514 3.565902 TCACATCCAGTCTACTCGCTATG 59.434 47.826 0.00 0.00 0.00 2.23
2562 9516 3.954904 ACATCCAGTCTACTCGCTATGTT 59.045 43.478 0.00 0.00 0.00 2.71
2605 9569 3.921021 TGTTTGTTTGTTTGCGTAAGTGG 59.079 39.130 0.00 0.00 41.68 4.00
2910 9887 1.745087 CAATGCCACACAGGTCATACC 59.255 52.381 0.00 0.00 40.61 2.73
3121 10121 0.310854 GGTTTCCACAGCAGGTTTCG 59.689 55.000 0.00 0.00 0.00 3.46
3195 10197 9.722056 CTGAAAATAAATGTAATCCACTAGCAC 57.278 33.333 0.00 0.00 0.00 4.40
3299 10327 3.240302 AGTTGTACAGCTCCAGGTTAGT 58.760 45.455 6.38 0.00 0.00 2.24
3365 10395 0.322546 AAACCTGCCGGTCATCTTCC 60.323 55.000 1.90 0.00 44.73 3.46
3396 10615 1.940613 GCACTTTCTCTGAAACGTGGT 59.059 47.619 16.35 0.00 0.00 4.16
3434 10656 6.811954 TGGTAATTTTTCTCGCCTTCTTTTT 58.188 32.000 0.00 0.00 0.00 1.94
3479 10701 1.745087 CAAGTGTTGCACAAGGACTGT 59.255 47.619 2.01 0.00 39.56 3.55
3644 10866 1.558167 TTAAGAGCATCCGCACCCCA 61.558 55.000 0.00 0.00 42.27 4.96
3665 10887 5.183713 CCCAATGTTTATTCTCAACTCTGCA 59.816 40.000 0.00 0.00 0.00 4.41
4633 11899 8.236586 GGAAATTTTCCCAAAAAGATGCATTAC 58.763 33.333 16.06 0.00 44.30 1.89
4837 12106 7.654116 TGAGTGACATGTAAAACGACATTTAGA 59.346 33.333 0.00 0.00 37.99 2.10
5127 12526 7.936496 TCCTGCTTTGTTGTATTGATTATGA 57.064 32.000 0.00 0.00 0.00 2.15
5218 12617 4.102681 GGCACCCCGGCTTATATAGATATT 59.897 45.833 0.00 0.00 37.17 1.28
5219 12618 5.397559 GGCACCCCGGCTTATATAGATATTT 60.398 44.000 0.00 0.00 37.17 1.40
5311 12710 1.003118 TGGAGTATGCGCCAAGTCTTT 59.997 47.619 4.18 0.00 41.62 2.52
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
9 10 2.260434 CATGGTGGCTGCAACTGC 59.740 61.111 7.18 0.00 42.50 4.40
10 11 1.604308 TCCATGGTGGCTGCAACTG 60.604 57.895 12.58 0.00 37.47 3.16
11 12 1.604593 GTCCATGGTGGCTGCAACT 60.605 57.895 12.58 0.00 37.47 3.16
12 13 2.639327 GGTCCATGGTGGCTGCAAC 61.639 63.158 12.58 0.00 37.47 4.17
14 15 4.365111 GGGTCCATGGTGGCTGCA 62.365 66.667 12.58 0.00 37.47 4.41
16 17 3.660571 TGGGGTCCATGGTGGCTG 61.661 66.667 12.58 0.00 37.47 4.85
79 2522 0.389948 GAACTACCGGCAGTGGTCAG 60.390 60.000 8.45 0.00 39.66 3.51
85 2528 1.066358 GCCTAAAGAACTACCGGCAGT 60.066 52.381 0.00 0.00 37.48 4.40
91 2534 9.911138 GAACTACTATATGCCTAAAGAACTACC 57.089 37.037 0.00 0.00 0.00 3.18
125 2980 9.646522 TTAGTTTACGGAGGGAGTACTATATTT 57.353 33.333 0.00 0.00 0.00 1.40
132 2987 9.289782 TCTTATATTAGTTTACGGAGGGAGTAC 57.710 37.037 0.00 0.00 0.00 2.73
133 2988 9.512588 CTCTTATATTAGTTTACGGAGGGAGTA 57.487 37.037 0.00 0.00 0.00 2.59
134 2989 7.039853 GCTCTTATATTAGTTTACGGAGGGAGT 60.040 40.741 0.00 0.00 0.00 3.85
135 2990 7.314393 GCTCTTATATTAGTTTACGGAGGGAG 58.686 42.308 0.00 0.00 0.00 4.30
136 2991 6.072286 CGCTCTTATATTAGTTTACGGAGGGA 60.072 42.308 0.00 0.00 34.63 4.20
137 2992 6.091437 CGCTCTTATATTAGTTTACGGAGGG 58.909 44.000 0.00 0.00 0.00 4.30
138 2993 6.675987 ACGCTCTTATATTAGTTTACGGAGG 58.324 40.000 0.00 0.00 0.00 4.30
139 2994 8.571461 AAACGCTCTTATATTAGTTTACGGAG 57.429 34.615 0.00 0.00 31.14 4.63
140 2995 9.669353 CTAAACGCTCTTATATTAGTTTACGGA 57.331 33.333 0.00 0.00 34.29 4.69
141 2996 9.669353 TCTAAACGCTCTTATATTAGTTTACGG 57.331 33.333 0.00 0.00 34.29 4.02
186 3041 9.530633 CCTCTGTAAACTAATATAAGAGCGTTT 57.469 33.333 0.00 0.00 0.00 3.60
187 3042 8.910944 TCCTCTGTAAACTAATATAAGAGCGTT 58.089 33.333 0.00 0.00 0.00 4.84
188 3043 8.461249 TCCTCTGTAAACTAATATAAGAGCGT 57.539 34.615 0.00 0.00 0.00 5.07
189 3044 9.400638 CTTCCTCTGTAAACTAATATAAGAGCG 57.599 37.037 0.00 0.00 0.00 5.03
205 3060 9.653287 CATCACTTAACAAATACTTCCTCTGTA 57.347 33.333 0.00 0.00 0.00 2.74
206 3061 8.157476 ACATCACTTAACAAATACTTCCTCTGT 58.843 33.333 0.00 0.00 0.00 3.41
207 3062 8.553459 ACATCACTTAACAAATACTTCCTCTG 57.447 34.615 0.00 0.00 0.00 3.35
208 3063 8.598041 AGACATCACTTAACAAATACTTCCTCT 58.402 33.333 0.00 0.00 0.00 3.69
209 3064 8.779354 AGACATCACTTAACAAATACTTCCTC 57.221 34.615 0.00 0.00 0.00 3.71
290 3147 2.817258 CCCGTGCCAAACTCTAAAATGA 59.183 45.455 0.00 0.00 0.00 2.57
364 3290 1.545706 AACTCACCTCTTCTCCCGGC 61.546 60.000 0.00 0.00 0.00 6.13
366 3292 0.247736 CCAACTCACCTCTTCTCCCG 59.752 60.000 0.00 0.00 0.00 5.14
620 3561 9.720769 ACGAACTAAGAGAAGGAAAAATAATCA 57.279 29.630 0.00 0.00 0.00 2.57
641 3582 3.243975 TGTCTTTTAGGAGGACCACGAAC 60.244 47.826 0.00 0.00 38.94 3.95
644 3585 3.396260 TTGTCTTTTAGGAGGACCACG 57.604 47.619 0.00 0.00 38.94 4.94
646 3587 4.905456 TCTCTTTGTCTTTTAGGAGGACCA 59.095 41.667 0.00 0.00 38.94 4.02
660 3601 9.458374 GCAGAATTATAGACTAGTCTCTTTGTC 57.542 37.037 28.42 19.62 40.93 3.18
667 6675 7.782644 AGTTCCAGCAGAATTATAGACTAGTCT 59.217 37.037 27.72 27.72 39.09 3.24
723 7327 4.158394 GGATCCACACACTGCATTAAACAT 59.842 41.667 6.95 0.00 0.00 2.71
777 7392 1.302511 AATGTGCCAGTCGGGTGTC 60.303 57.895 0.00 0.00 39.65 3.67
840 7457 0.744771 GGAGGCCGGTCAAGATCAAC 60.745 60.000 9.71 0.00 0.00 3.18
934 7552 7.304497 TCTTGCTTAAGTAGAAGAAGAAGGT 57.696 36.000 4.02 0.00 0.00 3.50
997 7618 1.312371 ACGTTGCTTGGCGCCATATT 61.312 50.000 33.25 7.70 38.05 1.28
1146 7767 3.961414 GGGGTCCCGTCCAAGCAA 61.961 66.667 0.48 0.00 0.00 3.91
1318 7994 4.764823 TGTCCCTGTTATTTTACTGCTTGG 59.235 41.667 0.00 0.00 0.00 3.61
1319 7995 5.957842 TGTCCCTGTTATTTTACTGCTTG 57.042 39.130 0.00 0.00 0.00 4.01
1320 7996 6.775629 TCTTTGTCCCTGTTATTTTACTGCTT 59.224 34.615 0.00 0.00 0.00 3.91
1321 7997 6.303839 TCTTTGTCCCTGTTATTTTACTGCT 58.696 36.000 0.00 0.00 0.00 4.24
1322 7998 6.569179 TCTTTGTCCCTGTTATTTTACTGC 57.431 37.500 0.00 0.00 0.00 4.40
1323 7999 8.567285 AGATCTTTGTCCCTGTTATTTTACTG 57.433 34.615 0.00 0.00 0.00 2.74
1324 8000 9.892130 CTAGATCTTTGTCCCTGTTATTTTACT 57.108 33.333 0.00 0.00 0.00 2.24
1331 8007 5.778241 TGACACTAGATCTTTGTCCCTGTTA 59.222 40.000 24.15 9.94 39.16 2.41
1337 8013 3.056749 ACCGTGACACTAGATCTTTGTCC 60.057 47.826 24.15 17.48 39.16 4.02
1338 8014 4.167268 GACCGTGACACTAGATCTTTGTC 58.833 47.826 21.95 21.95 40.14 3.18
1357 8033 0.030908 CGATGCCTACGAGAAGGACC 59.969 60.000 7.29 0.00 39.15 4.46
1409 8095 2.182842 CATCCCCGCAGTAAGCAGC 61.183 63.158 0.00 0.00 46.13 5.25
1416 8102 4.047125 CCCCAACATCCCCGCAGT 62.047 66.667 0.00 0.00 0.00 4.40
1417 8103 4.047125 ACCCCAACATCCCCGCAG 62.047 66.667 0.00 0.00 0.00 5.18
1418 8104 4.358841 CACCCCAACATCCCCGCA 62.359 66.667 0.00 0.00 0.00 5.69
1447 8133 0.957395 AAGAGACCATGCAACAGCGG 60.957 55.000 0.00 0.00 0.00 5.52
1449 8135 1.242076 ACAAGAGACCATGCAACAGC 58.758 50.000 0.00 0.00 0.00 4.40
1450 8136 3.551454 CCAAACAAGAGACCATGCAACAG 60.551 47.826 0.00 0.00 0.00 3.16
1454 8140 0.961019 GCCAAACAAGAGACCATGCA 59.039 50.000 0.00 0.00 0.00 3.96
1457 8143 3.233507 ACATTGCCAAACAAGAGACCAT 58.766 40.909 0.00 0.00 42.87 3.55
1467 8153 3.180782 CGAAACCGTTAACATTGCCAAAC 59.819 43.478 6.39 0.00 0.00 2.93
1470 8156 2.219458 TCGAAACCGTTAACATTGCCA 58.781 42.857 6.39 0.00 0.00 4.92
1480 8166 1.937899 CCAACTCAACTCGAAACCGTT 59.062 47.619 0.00 0.00 0.00 4.44
1482 8168 0.865769 CCCAACTCAACTCGAAACCG 59.134 55.000 0.00 0.00 0.00 4.44
1492 8178 0.179020 CCAGCTGTGACCCAACTCAA 60.179 55.000 13.81 0.00 0.00 3.02
1493 8179 1.451504 CCAGCTGTGACCCAACTCA 59.548 57.895 13.81 0.00 0.00 3.41
1505 8191 2.031120 TGGAAGAAACAAACCCAGCTG 58.969 47.619 6.78 6.78 0.00 4.24
1506 8192 2.091885 TCTGGAAGAAACAAACCCAGCT 60.092 45.455 0.00 0.00 42.31 4.24
1517 8203 2.811873 GCACAAGGAGCTCTGGAAGAAA 60.812 50.000 14.64 0.00 46.34 2.52
1519 8205 0.322975 GCACAAGGAGCTCTGGAAGA 59.677 55.000 14.64 0.00 43.69 2.87
1520 8206 1.018226 CGCACAAGGAGCTCTGGAAG 61.018 60.000 14.64 2.76 0.00 3.46
1522 8208 2.159819 GACGCACAAGGAGCTCTGGA 62.160 60.000 14.64 0.00 0.00 3.86
1523 8209 1.739562 GACGCACAAGGAGCTCTGG 60.740 63.158 14.64 5.99 0.00 3.86
1540 8244 0.742505 ACTTCACGAAGACACGGTGA 59.257 50.000 16.29 0.00 40.79 4.02
1566 8270 1.603931 CCGATCACCCATCTCATGTCG 60.604 57.143 0.00 0.00 0.00 4.35
1571 8297 0.541392 CCAACCGATCACCCATCTCA 59.459 55.000 0.00 0.00 0.00 3.27
1590 8316 2.821366 CTGCACGGATGGCCTCAC 60.821 66.667 3.32 0.00 0.00 3.51
1622 8349 3.640498 TCCAACAAAGAACATTGCATGGA 59.360 39.130 11.18 11.18 42.55 3.41
1625 8352 4.942761 AGTCCAACAAAGAACATTGCAT 57.057 36.364 0.00 0.00 33.52 3.96
1645 8372 3.243434 ACACAAGTCGGTGACTAGACAAG 60.243 47.826 12.47 7.71 42.59 3.16
1662 8389 1.804151 GCCAAGCAATCGACTACACAA 59.196 47.619 0.00 0.00 0.00 3.33
1664 8391 1.438651 TGCCAAGCAATCGACTACAC 58.561 50.000 0.00 0.00 34.76 2.90
1666 8393 1.331756 CCATGCCAAGCAATCGACTAC 59.668 52.381 0.00 0.00 43.62 2.73
1699 8426 0.250467 ACTCACTGCAACAAGCCGAT 60.250 50.000 0.00 0.00 44.83 4.18
1705 8432 4.422840 CAACAAATCACTCACTGCAACAA 58.577 39.130 0.00 0.00 0.00 2.83
1712 8441 3.214328 GACCACCAACAAATCACTCACT 58.786 45.455 0.00 0.00 0.00 3.41
1713 8442 2.948979 TGACCACCAACAAATCACTCAC 59.051 45.455 0.00 0.00 0.00 3.51
1718 8447 3.510753 CCATGATGACCACCAACAAATCA 59.489 43.478 0.00 0.00 31.17 2.57
1719 8448 3.511146 ACCATGATGACCACCAACAAATC 59.489 43.478 0.00 0.00 31.17 2.17
1723 8452 1.423161 TCACCATGATGACCACCAACA 59.577 47.619 0.00 0.00 31.96 3.33
1734 8463 0.179000 GCCTCCGACTTCACCATGAT 59.821 55.000 0.00 0.00 0.00 2.45
1754 8484 3.760035 ACTCCGTCGCGAGCCAAT 61.760 61.111 10.24 0.00 32.79 3.16
1766 8496 1.202348 AGCTTCATCGTCATCACTCCG 60.202 52.381 0.00 0.00 0.00 4.63
1772 8502 3.867493 TGTCATCAAGCTTCATCGTCATC 59.133 43.478 0.00 0.00 0.00 2.92
1776 8506 2.005451 GCTGTCATCAAGCTTCATCGT 58.995 47.619 0.00 0.00 0.00 3.73
1783 8513 1.802960 CGTTGAAGCTGTCATCAAGCT 59.197 47.619 0.00 0.00 41.08 3.74
1795 8525 1.335051 GGAGAAAAGCACCGTTGAAGC 60.335 52.381 0.00 0.00 0.00 3.86
1801 8531 2.767505 CTGTTAGGAGAAAAGCACCGT 58.232 47.619 0.00 0.00 31.80 4.83
1802 8532 1.464997 GCTGTTAGGAGAAAAGCACCG 59.535 52.381 0.00 0.00 34.01 4.94
1807 8537 4.130118 ACACACAGCTGTTAGGAGAAAAG 58.870 43.478 18.94 4.14 0.00 2.27
1819 8549 0.578683 CACACGAAGACACACAGCTG 59.421 55.000 13.48 13.48 0.00 4.24
1820 8550 0.459899 TCACACGAAGACACACAGCT 59.540 50.000 0.00 0.00 0.00 4.24
1822 8552 2.209838 ACTCACACGAAGACACACAG 57.790 50.000 0.00 0.00 0.00 3.66
1864 8604 4.838986 ACCACCCCACTAGCTATAACATAG 59.161 45.833 0.00 0.00 0.00 2.23
1866 8606 3.391296 CACCACCCCACTAGCTATAACAT 59.609 47.826 0.00 0.00 0.00 2.71
1875 8615 4.097892 GCAAAATTATCACCACCCCACTAG 59.902 45.833 0.00 0.00 0.00 2.57
1876 8616 4.020543 GCAAAATTATCACCACCCCACTA 58.979 43.478 0.00 0.00 0.00 2.74
1877 8617 2.831526 GCAAAATTATCACCACCCCACT 59.168 45.455 0.00 0.00 0.00 4.00
1879 8619 3.182887 AGCAAAATTATCACCACCCCA 57.817 42.857 0.00 0.00 0.00 4.96
1880 8620 3.369366 CCAAGCAAAATTATCACCACCCC 60.369 47.826 0.00 0.00 0.00 4.95
1882 8622 4.535526 ACCAAGCAAAATTATCACCACC 57.464 40.909 0.00 0.00 0.00 4.61
1883 8623 5.408299 GGAAACCAAGCAAAATTATCACCAC 59.592 40.000 0.00 0.00 0.00 4.16
1884 8624 5.546526 GGAAACCAAGCAAAATTATCACCA 58.453 37.500 0.00 0.00 0.00 4.17
1908 8648 7.545362 AGTAGAGCTGCACAATTAATTAGTG 57.455 36.000 18.56 18.56 36.39 2.74
1918 8658 8.792830 AATTAATAAGAAGTAGAGCTGCACAA 57.207 30.769 1.02 0.00 0.00 3.33
1921 8661 9.031360 CGTTAATTAATAAGAAGTAGAGCTGCA 57.969 33.333 1.02 0.00 0.00 4.41
1946 8686 5.295950 AGGCAAAATCTCTACATCATCTCG 58.704 41.667 0.00 0.00 0.00 4.04
1958 8698 5.108385 TCTCAAAACGAAGGCAAAATCTC 57.892 39.130 0.00 0.00 0.00 2.75
1992 8732 5.895636 AAATTTTGTGCCGAGACATGATA 57.104 34.783 0.00 0.00 0.00 2.15
1994 8734 4.037327 TGAAAATTTTGTGCCGAGACATGA 59.963 37.500 8.47 0.00 0.00 3.07
1995 8735 4.297510 TGAAAATTTTGTGCCGAGACATG 58.702 39.130 8.47 0.00 0.00 3.21
2125 8870 1.472480 GCTGGCTATTTCTTTTGCGGA 59.528 47.619 0.00 0.00 0.00 5.54
2128 8873 3.317603 TTGGCTGGCTATTTCTTTTGC 57.682 42.857 2.00 0.00 0.00 3.68
2218 8963 5.193679 ACATAATTTGGGAGTTAGGTCTGC 58.806 41.667 0.00 0.00 0.00 4.26
2247 8992 4.120331 GGGCGGCATGTGCTTGAC 62.120 66.667 12.47 0.25 41.70 3.18
2410 9364 2.766313 CGACCAGAACAATCCTTGACA 58.234 47.619 0.00 0.00 0.00 3.58
2411 9365 1.464997 GCGACCAGAACAATCCTTGAC 59.535 52.381 0.00 0.00 0.00 3.18
2480 9434 1.275010 GTCAAAAATTCCATGGCCGGT 59.725 47.619 6.96 0.00 0.00 5.28
2566 9520 8.638565 CAAACAAACAAACAAACAAACAAACAA 58.361 25.926 0.00 0.00 0.00 2.83
2568 9522 8.162906 ACAAACAAACAAACAAACAAACAAAC 57.837 26.923 0.00 0.00 0.00 2.93
2569 9523 8.742554 AACAAACAAACAAACAAACAAACAAA 57.257 23.077 0.00 0.00 0.00 2.83
2570 9524 8.638565 CAAACAAACAAACAAACAAACAAACAA 58.361 25.926 0.00 0.00 0.00 2.83
2571 9525 7.201350 GCAAACAAACAAACAAACAAACAAACA 60.201 29.630 0.00 0.00 0.00 2.83
2572 9526 7.107380 GCAAACAAACAAACAAACAAACAAAC 58.893 30.769 0.00 0.00 0.00 2.93
2576 9530 4.964555 ACGCAAACAAACAAACAAACAAAC 59.035 33.333 0.00 0.00 0.00 2.93
2580 9534 5.781233 CACTTACGCAAACAAACAAACAAAC 59.219 36.000 0.00 0.00 0.00 2.93
2605 9569 6.879458 AGGACATATCAAACAGGTTACAGAAC 59.121 38.462 0.00 0.00 34.56 3.01
2910 9887 6.255887 GGTATTCTGTGAACTCGGTAAATGAG 59.744 42.308 0.00 0.00 39.40 2.90
3121 10121 1.926510 GCATCCGCAAAGCATTTAACC 59.073 47.619 0.00 0.00 35.03 2.85
3195 10197 8.064336 AGTGGTACTTTAGTTCAGGTATACAG 57.936 38.462 5.01 0.00 0.00 2.74
3284 10312 1.000955 CGACAACTAACCTGGAGCTGT 59.999 52.381 0.00 0.00 0.00 4.40
3299 10327 0.884704 GTCTCAAGCAAGCCCGACAA 60.885 55.000 0.00 0.00 0.00 3.18
3644 10866 7.549134 TCGTATGCAGAGTTGAGAATAAACATT 59.451 33.333 0.00 0.00 0.00 2.71
3665 10887 6.545666 TGAAAAATACCTGCCATGAATCGTAT 59.454 34.615 0.00 0.00 0.00 3.06
3975 11206 6.505044 TGATCATTGTGTTCCTGATTTCTG 57.495 37.500 0.00 0.00 30.00 3.02
4633 11899 7.393551 AGCAACATTTGACGAATTAACAAAG 57.606 32.000 0.00 0.00 37.04 2.77
4837 12106 3.004210 TGCGTTCATGCTTACAAACATGT 59.996 39.130 0.00 0.00 43.34 3.21
4915 12193 0.752376 GAGGTACGTAGAGGCTGGCT 60.752 60.000 2.24 2.24 0.00 4.75
5045 12326 2.486013 GGTAAACCTCGTCCCTTGTGTT 60.486 50.000 0.00 0.00 0.00 3.32
5046 12327 1.071228 GGTAAACCTCGTCCCTTGTGT 59.929 52.381 0.00 0.00 0.00 3.72
5047 12328 1.346722 AGGTAAACCTCGTCCCTTGTG 59.653 52.381 0.00 0.00 44.77 3.33
5048 12329 1.725803 AGGTAAACCTCGTCCCTTGT 58.274 50.000 0.00 0.00 44.77 3.16
5049 12330 2.167900 CCTAGGTAAACCTCGTCCCTTG 59.832 54.545 4.57 0.00 44.77 3.61
5050 12331 2.225470 ACCTAGGTAAACCTCGTCCCTT 60.225 50.000 14.41 0.00 44.77 3.95
5052 12333 1.753649 GACCTAGGTAAACCTCGTCCC 59.246 57.143 16.29 0.00 44.77 4.46
5127 12526 8.948401 AGATCACCTATACTCTGTACATCATT 57.052 34.615 0.00 0.00 0.00 2.57
5157 12556 6.183360 GGCAGATTCATTCACATTTGATCTCA 60.183 38.462 0.00 0.00 0.00 3.27
5218 12617 2.376181 GTGTAAACCTTAGGGACCCCAA 59.624 50.000 7.00 0.00 38.92 4.12
5219 12618 1.987368 GTGTAAACCTTAGGGACCCCA 59.013 52.381 7.00 0.00 38.92 4.96
5311 12710 2.439507 AGCTTCAAGAAGGAAGGACACA 59.560 45.455 11.44 0.00 43.54 3.72


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

AutoCloner maintained by Alex Coulton.