Multiple sequence alignment - TraesCS5B01G140000

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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 TraesCS5B01G140000 chr5B 100.000 5205 0 0 1 5205 264291770 264286566 0.000000e+00 9612.0
1 TraesCS5B01G140000 chr5B 86.466 266 33 3 3062 3325 527760361 527760625 6.590000e-74 289.0
2 TraesCS5B01G140000 chr5B 80.556 288 43 11 4677 4952 582329118 582328832 5.280000e-50 209.0
3 TraesCS5B01G140000 chr5D 96.284 2341 55 9 599 2914 239273016 239275349 0.000000e+00 3812.0
4 TraesCS5B01G140000 chr5D 97.672 1074 23 2 3266 4337 239275745 239276818 0.000000e+00 1844.0
5 TraesCS5B01G140000 chr5D 89.899 594 59 1 9 602 239271970 239272562 0.000000e+00 763.0
6 TraesCS5B01G140000 chr5D 96.466 283 10 0 2916 3198 239275467 239275749 7.890000e-128 468.0
7 TraesCS5B01G140000 chr5D 89.045 356 17 13 4335 4678 239276849 239277194 6.230000e-114 422.0
8 TraesCS5B01G140000 chr5D 94.340 265 13 1 4941 5205 239277193 239277455 6.280000e-109 405.0
9 TraesCS5B01G140000 chr5D 85.766 274 36 2 4673 4944 57849794 57850066 2.370000e-73 287.0
10 TraesCS5B01G140000 chr5D 84.091 264 36 5 3062 3322 327480331 327480591 3.110000e-62 250.0
11 TraesCS5B01G140000 chr5D 85.526 228 29 3 3108 3334 434580203 434580427 8.710000e-58 235.0
12 TraesCS5B01G140000 chr5D 85.294 204 26 4 395 596 445193666 445193867 1.900000e-49 207.0
13 TraesCS5B01G140000 chr5D 80.228 263 47 5 3062 3322 482341268 482341527 5.320000e-45 193.0
14 TraesCS5B01G140000 chr5D 76.000 275 55 9 264 530 384698037 384698308 1.180000e-26 132.0
15 TraesCS5B01G140000 chr5A 95.222 1779 54 14 2916 4678 314670304 314668541 0.000000e+00 2785.0
16 TraesCS5B01G140000 chr5A 96.492 1397 36 7 1524 2916 314671807 314670420 0.000000e+00 2296.0
17 TraesCS5B01G140000 chr5A 90.667 600 52 4 1 599 314742545 314741949 0.000000e+00 795.0
18 TraesCS5B01G140000 chr5A 93.882 425 16 5 1112 1527 314672270 314671847 2.640000e-177 632.0
19 TraesCS5B01G140000 chr5A 92.677 437 26 4 653 1087 314672682 314672250 4.430000e-175 625.0
20 TraesCS5B01G140000 chr5A 84.017 463 74 0 11 473 477582873 477582411 3.700000e-121 446.0
21 TraesCS5B01G140000 chr5A 93.609 266 9 6 4941 5205 314668542 314668284 1.760000e-104 390.0
22 TraesCS5B01G140000 chr5A 81.726 394 64 7 207 596 562503125 562503514 6.500000e-84 322.0
23 TraesCS5B01G140000 chrUn 100.000 407 0 0 3299 3705 477999196 477999602 0.000000e+00 752.0
24 TraesCS5B01G140000 chrUn 79.924 264 48 5 3062 3322 329026401 329026662 6.880000e-44 189.0
25 TraesCS5B01G140000 chrUn 86.875 160 21 0 3163 3322 93373532 93373691 4.140000e-41 180.0
26 TraesCS5B01G140000 chrUn 80.000 260 36 9 3068 3324 16908590 16908344 1.490000e-40 178.0
27 TraesCS5B01G140000 chrUn 81.166 223 31 8 3062 3283 22157566 22157778 8.960000e-38 169.0
28 TraesCS5B01G140000 chr7D 84.757 597 89 2 4 599 497044461 497043866 9.650000e-167 597.0
29 TraesCS5B01G140000 chr7D 77.052 597 132 5 5 599 12913826 12913233 6.460000e-89 339.0
30 TraesCS5B01G140000 chr7D 88.213 263 27 4 3062 3322 199606876 199607136 1.410000e-80 311.0
31 TraesCS5B01G140000 chr7D 87.218 266 30 4 3062 3325 485106720 485106457 3.050000e-77 300.0
32 TraesCS5B01G140000 chr7D 83.051 177 24 3 1199 1375 623646394 623646224 6.980000e-34 156.0
33 TraesCS5B01G140000 chr7D 81.068 206 27 9 1158 1362 143976646 143976840 2.510000e-33 154.0
34 TraesCS5B01G140000 chr7D 90.741 54 5 0 1191 1244 421642699 421642752 7.230000e-09 73.1
35 TraesCS5B01G140000 chr7A 83.811 593 96 0 4 596 20689609 20690201 9.780000e-157 564.0
36 TraesCS5B01G140000 chr7A 83.813 278 34 9 3062 3332 7764667 7764394 2.410000e-63 254.0
37 TraesCS5B01G140000 chr7B 83.838 594 93 3 4 596 572029907 572030498 3.520000e-156 562.0
38 TraesCS5B01G140000 chr7B 87.218 266 32 2 3058 3323 157803239 157802976 8.470000e-78 302.0
39 TraesCS5B01G140000 chr7B 87.356 261 33 0 3062 3322 540063459 540063199 3.050000e-77 300.0
40 TraesCS5B01G140000 chr7B 86.716 271 31 4 4676 4942 586328560 586328829 3.940000e-76 296.0
41 TraesCS5B01G140000 chr7B 88.085 235 27 1 3092 3326 107645342 107645109 1.430000e-70 278.0
42 TraesCS5B01G140000 chr7B 85.824 261 35 1 3064 3322 535826501 535826761 5.130000e-70 276.0
43 TraesCS5B01G140000 chr7B 80.097 206 31 7 1158 1362 107821166 107820970 1.510000e-30 145.0
44 TraesCS5B01G140000 chr4B 79.264 598 117 6 2 596 567438493 567437900 1.350000e-110 411.0
45 TraesCS5B01G140000 chr4B 79.623 584 106 12 18 595 467456692 467457268 1.740000e-109 407.0
46 TraesCS5B01G140000 chr4B 84.030 263 36 4 3062 3324 240192941 240193197 1.120000e-61 248.0
47 TraesCS5B01G140000 chr4B 79.245 159 23 8 1205 1357 487664250 487664096 9.220000e-18 102.0
48 TraesCS5B01G140000 chr1D 78.167 600 119 12 5 599 245971230 245970638 6.370000e-99 372.0
49 TraesCS5B01G140000 chr1D 85.932 263 29 8 3065 3324 431805280 431805023 1.850000e-69 274.0
50 TraesCS5B01G140000 chr1D 84.109 258 37 3 3055 3310 470222416 470222671 4.030000e-61 246.0
51 TraesCS5B01G140000 chr1D 81.343 268 44 6 3062 3326 374265244 374265508 4.080000e-51 213.0
52 TraesCS5B01G140000 chr1D 84.762 210 26 4 3062 3270 7582572 7582776 6.830000e-49 206.0
53 TraesCS5B01G140000 chr1D 87.500 128 16 0 3184 3311 398368483 398368610 1.170000e-31 148.0
54 TraesCS5B01G140000 chr1D 78.469 209 36 8 3060 3265 30621435 30621637 1.520000e-25 128.0
55 TraesCS5B01G140000 chr1D 81.818 154 22 3 3062 3215 398867799 398867652 1.970000e-24 124.0
56 TraesCS5B01G140000 chr1D 85.217 115 15 1 3060 3174 30593060 30593172 3.290000e-22 117.0
57 TraesCS5B01G140000 chr1D 79.503 161 30 2 3099 3259 426167675 426167518 1.530000e-20 111.0
58 TraesCS5B01G140000 chr1D 91.549 71 6 0 3248 3318 367685419 367685489 1.190000e-16 99.0
59 TraesCS5B01G140000 chr1D 74.222 225 50 6 3098 3320 388622205 388621987 2.580000e-13 87.9
60 TraesCS5B01G140000 chr1D 88.889 54 6 0 1191 1244 231215344 231215397 3.360000e-07 67.6
61 TraesCS5B01G140000 chr1D 88.889 54 6 0 1191 1244 377722355 377722302 3.360000e-07 67.6
62 TraesCS5B01G140000 chr3B 87.681 276 29 4 4677 4949 694098826 694099099 3.030000e-82 316.0
63 TraesCS5B01G140000 chr3B 79.279 222 33 10 1163 1379 550318830 550318617 5.430000e-30 143.0
64 TraesCS5B01G140000 chr3D 87.132 272 33 2 4676 4945 168186563 168186292 1.820000e-79 307.0
65 TraesCS5B01G140000 chr3D 81.081 259 43 6 3064 3319 134818551 134818806 8.840000e-48 202.0
66 TraesCS5B01G140000 chr3D 78.733 221 35 9 1163 1379 422477273 422477061 2.530000e-28 137.0
67 TraesCS5B01G140000 chr2A 86.466 266 31 2 3062 3323 194713400 194713136 2.370000e-73 287.0
68 TraesCS5B01G140000 chr1A 90.278 216 17 3 4681 4894 74605640 74605853 3.970000e-71 279.0
69 TraesCS5B01G140000 chr1A 84.586 266 30 8 3063 3323 52241319 52241578 2.410000e-63 254.0
70 TraesCS5B01G140000 chr1B 85.091 275 34 4 4677 4945 643121394 643121121 1.850000e-69 274.0
71 TraesCS5B01G140000 chr1B 81.579 266 42 6 4682 4942 405185953 405185690 4.080000e-51 213.0
72 TraesCS5B01G140000 chr2D 84.733 262 36 3 3062 3322 608922192 608922450 5.170000e-65 259.0
73 TraesCS5B01G140000 chr2D 84.291 261 40 1 3055 3315 547952799 547952540 2.410000e-63 254.0
74 TraesCS5B01G140000 chr6B 85.657 251 27 5 4677 4922 90146915 90146669 6.690000e-64 255.0
75 TraesCS5B01G140000 chr4D 80.784 255 42 4 3062 3311 416861620 416861872 5.320000e-45 193.0
76 TraesCS5B01G140000 chr4D 83.226 155 24 2 3062 3216 66517061 66516909 1.950000e-29 141.0
77 TraesCS5B01G140000 chr4D 79.114 158 32 1 345 501 462832278 462832435 1.980000e-19 108.0
78 TraesCS5B01G140000 chr4D 83.077 65 11 0 1215 1279 421330643 421330707 5.630000e-05 60.2
79 TraesCS5B01G140000 chr6D 76.580 269 58 5 3058 3324 450529267 450529002 5.430000e-30 143.0
80 TraesCS5B01G140000 chr6D 88.462 78 9 0 3060 3137 346840882 346840805 1.540000e-15 95.3
81 TraesCS5B01G140000 chr6D 82.796 93 14 2 3231 3322 353211720 353211629 1.200000e-11 82.4
82 TraesCS5B01G140000 chr6D 75.735 136 28 4 3194 3327 337847300 337847432 4.350000e-06 63.9
83 TraesCS5B01G140000 chr2B 83.186 113 16 2 1156 1265 800861864 800861752 3.320000e-17 100.0
84 TraesCS5B01G140000 chr6A 86.667 60 8 0 1191 1250 169184671 169184612 3.360000e-07 67.6
85 TraesCS5B01G140000 chr6A 86.667 60 8 0 1191 1250 421524878 421524937 3.360000e-07 67.6
86 TraesCS5B01G140000 chr6A 86.667 60 8 0 1191 1250 568045082 568045141 3.360000e-07 67.6
87 TraesCS5B01G140000 chr6A 84.848 66 9 1 1201 1265 42120719 42120654 1.210000e-06 65.8
88 TraesCS5B01G140000 chr6A 85.000 60 9 0 1191 1250 13387307 13387366 1.570000e-05 62.1


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 TraesCS5B01G140000 chr5B 264286566 264291770 5204 True 9612.000000 9612 100.0000 1 5205 1 chr5B.!!$R1 5204
1 TraesCS5B01G140000 chr5D 239271970 239277455 5485 False 1285.666667 3812 93.9510 9 5205 6 chr5D.!!$F7 5196
2 TraesCS5B01G140000 chr5A 314668284 314672682 4398 True 1345.600000 2785 94.3764 653 5205 5 chr5A.!!$R3 4552
3 TraesCS5B01G140000 chr5A 314741949 314742545 596 True 795.000000 795 90.6670 1 599 1 chr5A.!!$R1 598
4 TraesCS5B01G140000 chr7D 497043866 497044461 595 True 597.000000 597 84.7570 4 599 1 chr7D.!!$R3 595
5 TraesCS5B01G140000 chr7D 12913233 12913826 593 True 339.000000 339 77.0520 5 599 1 chr7D.!!$R1 594
6 TraesCS5B01G140000 chr7A 20689609 20690201 592 False 564.000000 564 83.8110 4 596 1 chr7A.!!$F1 592
7 TraesCS5B01G140000 chr7B 572029907 572030498 591 False 562.000000 562 83.8380 4 596 1 chr7B.!!$F2 592
8 TraesCS5B01G140000 chr4B 567437900 567438493 593 True 411.000000 411 79.2640 2 596 1 chr4B.!!$R2 594
9 TraesCS5B01G140000 chr4B 467456692 467457268 576 False 407.000000 407 79.6230 18 595 1 chr4B.!!$F2 577
10 TraesCS5B01G140000 chr1D 245970638 245971230 592 True 372.000000 372 78.1670 5 599 1 chr1D.!!$R1 594

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
669 1137 1.058129 CTGATTTTTGCAATCACGCGC 59.942 47.619 5.73 0.0 33.51 6.86 F
1571 2093 1.338579 GGACTTCTCTGGAGGCAAGTG 60.339 57.143 8.69 0.0 29.14 3.16 F
1673 2196 1.535462 GTTCCCAGATGTTGTGTTCGG 59.465 52.381 0.00 0.0 0.00 4.30 F
2029 2558 3.753272 GGAATGCTGCACTTTTCTACTCA 59.247 43.478 3.57 0.0 0.00 3.41 F
2984 3646 2.954020 ATGCGCGTATGTCAGGACCG 62.954 60.000 9.48 0.0 0.00 4.79 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1663 2186 1.268539 CCAGCAGAAACCGAACACAAC 60.269 52.381 0.00 0.0 0.0 3.32 R
2931 3593 2.224161 GCTGGCGGATGAGATAAGAAGT 60.224 50.000 0.00 0.0 0.0 3.01 R
2984 3646 2.732412 TCACTGCTAAGCTCTGACAC 57.268 50.000 0.00 0.0 0.0 3.67 R
4022 4689 1.629043 GGTATATCGTGCCCCTGAGA 58.371 55.000 0.00 0.0 0.0 3.27 R
4770 5485 0.527113 TCGGAATTACTTGTCGCGGA 59.473 50.000 6.13 0.0 0.0 5.54 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
135 140 3.717294 GGCCACCGTCACATCCCT 61.717 66.667 0.00 0.00 0.00 4.20
178 183 2.204059 ACAGCCTTGCCCTCCTCT 60.204 61.111 0.00 0.00 0.00 3.69
279 284 1.931635 AGGCTCGACTTCCTCTTCTT 58.068 50.000 0.00 0.00 0.00 2.52
313 318 2.830370 GGCTTGGGATTGCTCGGG 60.830 66.667 0.00 0.00 0.00 5.14
326 331 1.821332 CTCGGGATTTGGCCAGAGC 60.821 63.158 5.11 3.55 41.98 4.09
364 369 1.600638 CTGGCAGCAGAGACATCCA 59.399 57.895 0.00 0.00 0.00 3.41
372 377 1.340405 GCAGAGACATCCATGGGTGTT 60.340 52.381 31.01 20.13 0.00 3.32
376 381 3.157087 GAGACATCCATGGGTGTTGTTT 58.843 45.455 31.01 16.96 0.00 2.83
433 439 1.333636 CCTCTTCGAGCATCAGGGGT 61.334 60.000 0.00 0.00 33.17 4.95
493 504 5.279384 GTGTCTTAGTGTCGTTCTTCTTCA 58.721 41.667 0.00 0.00 0.00 3.02
522 533 3.435566 GATGTCTTGTATTCTCGCGACA 58.564 45.455 3.71 0.00 36.06 4.35
537 548 1.517257 GACATCCTCGGTGCTGTCG 60.517 63.158 0.00 0.00 0.00 4.35
558 569 3.251571 GTTGGAGATGTTGGTCGTCTAC 58.748 50.000 0.00 0.00 41.88 2.59
577 588 5.124936 GTCTACTTGTTGGTTGGACTGTTTT 59.875 40.000 0.00 0.00 0.00 2.43
590 601 1.156736 CTGTTTTTCTGGTCGGCGAT 58.843 50.000 14.79 0.00 0.00 4.58
615 1083 4.006357 GGTGGGTCCAACGCGGTA 62.006 66.667 12.47 0.00 33.25 4.02
630 1098 3.679980 ACGCGGTAGATGATTTATGCATC 59.320 43.478 12.47 0.00 41.85 3.91
638 1106 8.721478 GGTAGATGATTTATGCATCATAACGTT 58.279 33.333 0.19 5.88 42.85 3.99
669 1137 1.058129 CTGATTTTTGCAATCACGCGC 59.942 47.619 5.73 0.00 33.51 6.86
685 1153 1.518572 CGCGTCAGGCTCCGTAATT 60.519 57.895 0.00 0.00 40.44 1.40
747 1215 3.077359 GCTCCATAAATTCCAGGGATCG 58.923 50.000 0.00 0.00 0.00 3.69
1036 1506 2.720758 CGAGTGAGCAAACTCCGCG 61.721 63.158 0.00 0.00 43.09 6.46
1216 1690 6.969993 TTGTCCTAAGGCAAACTTGTTTAT 57.030 33.333 0.00 0.00 40.37 1.40
1355 1830 8.057536 TCTTACCACATTTTTGTACAGTGTTT 57.942 30.769 0.00 1.80 0.00 2.83
1456 1935 9.705290 AAAAATGTGACTACAGAAAACAACTTT 57.295 25.926 0.00 0.00 40.79 2.66
1571 2093 1.338579 GGACTTCTCTGGAGGCAAGTG 60.339 57.143 8.69 0.00 29.14 3.16
1663 2186 9.372369 CTTTTCTTAACTACTAGTTCCCAGATG 57.628 37.037 0.00 0.00 39.51 2.90
1673 2196 1.535462 GTTCCCAGATGTTGTGTTCGG 59.465 52.381 0.00 0.00 0.00 4.30
1784 2307 5.589050 GGTGGTGAATTAATCTGGTAGGTTC 59.411 44.000 0.00 0.00 0.00 3.62
1924 2447 7.803189 AGCAATTTAGTTTCTTGACACATAACG 59.197 33.333 0.00 0.00 0.00 3.18
2029 2558 3.753272 GGAATGCTGCACTTTTCTACTCA 59.247 43.478 3.57 0.00 0.00 3.41
2379 2925 4.696877 TGGTGAAAGATCTATGTGCACAAG 59.303 41.667 25.72 20.73 0.00 3.16
2444 2990 9.962783 CACTAGGGGTATACGATATATTTTAGC 57.037 37.037 0.00 0.00 0.00 3.09
2481 3027 8.833231 TTGCACTTCTATTTATGTATAGGAGC 57.167 34.615 0.00 0.00 37.27 4.70
2760 3306 9.674824 CATCTCAAGATGCCTTTTTCATTATAC 57.325 33.333 7.05 0.00 44.44 1.47
2857 3403 8.672815 TGCATGTATAAGAAATTTTGACGATCA 58.327 29.630 0.00 0.00 0.00 2.92
2874 3420 6.039605 TGACGATCATGCCAAATCAAACATAT 59.960 34.615 0.00 0.00 0.00 1.78
2875 3421 7.228308 TGACGATCATGCCAAATCAAACATATA 59.772 33.333 0.00 0.00 0.00 0.86
2876 3422 8.114331 ACGATCATGCCAAATCAAACATATAT 57.886 30.769 0.00 0.00 0.00 0.86
2931 3593 6.127451 TGTCAAATCTGAGCTCGGTCTTATAA 60.127 38.462 21.88 1.17 30.14 0.98
2984 3646 2.954020 ATGCGCGTATGTCAGGACCG 62.954 60.000 9.48 0.00 0.00 4.79
3090 3752 6.258160 CCTCCATTTTTATTTACTCTGCGTG 58.742 40.000 0.00 0.00 0.00 5.34
3297 3960 9.456147 TTTTACTTAGGTCAAAGCTAATATGCA 57.544 29.630 0.00 0.00 37.52 3.96
3946 4613 5.611128 AGCATGAGATTCAAGAAGAGCTA 57.389 39.130 0.00 0.00 0.00 3.32
4022 4689 2.928334 CAGAAAGGCATAGAGGTGCAT 58.072 47.619 0.00 0.00 46.81 3.96
4097 4764 1.476471 GCAATCCATCTCAGTCCCCTG 60.476 57.143 0.00 0.00 40.25 4.45
4141 4808 3.788672 GGTGAAGCCCATCGATTCT 57.211 52.632 0.00 0.00 0.00 2.40
4144 4811 2.356069 GGTGAAGCCCATCGATTCTTTC 59.644 50.000 0.00 0.00 0.00 2.62
4167 4834 2.250939 CGAAGCACTTGTTCCCGCA 61.251 57.895 0.00 0.00 0.00 5.69
4329 4998 7.653647 TGTTATGTAGCCCTTTGTTAAGTTTG 58.346 34.615 0.00 0.00 0.00 2.93
4360 5062 9.174166 GTATGTCATTTCCACTATTTAGTTGGT 57.826 33.333 0.00 0.00 33.46 3.67
4379 5088 8.492673 AGTTGGTACTGTATAACATGACAATG 57.507 34.615 0.00 0.00 34.93 2.82
4396 5105 3.611986 ACAATGCGCCAAATAAACATTCG 59.388 39.130 4.18 0.00 0.00 3.34
4539 5248 4.142578 TGTTGCAAGAACGTTGCTTCTAAA 60.143 37.500 5.00 1.18 45.13 1.85
4574 5283 8.833231 TTTGTTTTTGTTTTTACCACAGATGA 57.167 26.923 0.00 0.00 0.00 2.92
4575 5284 7.820044 TGTTTTTGTTTTTACCACAGATGAC 57.180 32.000 0.00 0.00 0.00 3.06
4576 5285 7.378966 TGTTTTTGTTTTTACCACAGATGACA 58.621 30.769 0.00 0.00 0.00 3.58
4616 5325 9.354673 TGAAAAGTTAAGATTCTTCCATCAAGT 57.645 29.630 1.27 0.00 33.27 3.16
4678 5393 5.578336 GGAATTTCCAAATCAAGCAAGCTAC 59.422 40.000 10.67 0.00 36.28 3.58
4679 5394 5.990120 ATTTCCAAATCAAGCAAGCTACT 57.010 34.783 0.00 0.00 0.00 2.57
4680 5395 5.789643 TTTCCAAATCAAGCAAGCTACTT 57.210 34.783 0.00 0.00 0.00 2.24
4681 5396 5.376854 TTCCAAATCAAGCAAGCTACTTC 57.623 39.130 0.00 0.00 0.00 3.01
4682 5397 3.758554 TCCAAATCAAGCAAGCTACTTCC 59.241 43.478 0.00 0.00 0.00 3.46
4683 5398 3.760684 CCAAATCAAGCAAGCTACTTCCT 59.239 43.478 0.00 0.00 0.00 3.36
4684 5399 4.142513 CCAAATCAAGCAAGCTACTTCCTC 60.143 45.833 0.00 0.00 0.00 3.71
4685 5400 2.770164 TCAAGCAAGCTACTTCCTCC 57.230 50.000 0.00 0.00 0.00 4.30
4686 5401 1.066858 TCAAGCAAGCTACTTCCTCCG 60.067 52.381 0.00 0.00 0.00 4.63
4687 5402 0.977395 AAGCAAGCTACTTCCTCCGT 59.023 50.000 0.00 0.00 0.00 4.69
4688 5403 0.977395 AGCAAGCTACTTCCTCCGTT 59.023 50.000 0.00 0.00 0.00 4.44
4689 5404 1.066787 AGCAAGCTACTTCCTCCGTTC 60.067 52.381 0.00 0.00 0.00 3.95
4690 5405 2.007547 GCAAGCTACTTCCTCCGTTCC 61.008 57.143 0.00 0.00 0.00 3.62
4691 5406 1.550976 CAAGCTACTTCCTCCGTTCCT 59.449 52.381 0.00 0.00 0.00 3.36
4692 5407 2.758979 CAAGCTACTTCCTCCGTTCCTA 59.241 50.000 0.00 0.00 0.00 2.94
4693 5408 3.097342 AGCTACTTCCTCCGTTCCTAA 57.903 47.619 0.00 0.00 0.00 2.69
4694 5409 3.438183 AGCTACTTCCTCCGTTCCTAAA 58.562 45.455 0.00 0.00 0.00 1.85
4695 5410 4.031611 AGCTACTTCCTCCGTTCCTAAAT 58.968 43.478 0.00 0.00 0.00 1.40
4696 5411 5.206587 AGCTACTTCCTCCGTTCCTAAATA 58.793 41.667 0.00 0.00 0.00 1.40
4697 5412 5.068855 AGCTACTTCCTCCGTTCCTAAATAC 59.931 44.000 0.00 0.00 0.00 1.89
4698 5413 5.068855 GCTACTTCCTCCGTTCCTAAATACT 59.931 44.000 0.00 0.00 0.00 2.12
4699 5414 5.595257 ACTTCCTCCGTTCCTAAATACTC 57.405 43.478 0.00 0.00 0.00 2.59
4700 5415 4.405036 ACTTCCTCCGTTCCTAAATACTCC 59.595 45.833 0.00 0.00 0.00 3.85
4701 5416 3.303049 TCCTCCGTTCCTAAATACTCCC 58.697 50.000 0.00 0.00 0.00 4.30
4702 5417 3.052338 TCCTCCGTTCCTAAATACTCCCT 60.052 47.826 0.00 0.00 0.00 4.20
4703 5418 3.321396 CCTCCGTTCCTAAATACTCCCTC 59.679 52.174 0.00 0.00 0.00 4.30
4704 5419 3.303049 TCCGTTCCTAAATACTCCCTCC 58.697 50.000 0.00 0.00 0.00 4.30
4705 5420 2.035576 CCGTTCCTAAATACTCCCTCCG 59.964 54.545 0.00 0.00 0.00 4.63
4706 5421 2.692041 CGTTCCTAAATACTCCCTCCGT 59.308 50.000 0.00 0.00 0.00 4.69
4707 5422 3.131755 CGTTCCTAAATACTCCCTCCGTT 59.868 47.826 0.00 0.00 0.00 4.44
4708 5423 4.691175 GTTCCTAAATACTCCCTCCGTTC 58.309 47.826 0.00 0.00 0.00 3.95
4709 5424 2.954318 TCCTAAATACTCCCTCCGTTCG 59.046 50.000 0.00 0.00 0.00 3.95
4710 5425 2.035576 CCTAAATACTCCCTCCGTTCGG 59.964 54.545 4.74 4.74 0.00 4.30
4711 5426 1.856629 AAATACTCCCTCCGTTCGGA 58.143 50.000 13.34 13.34 0.00 4.55
4712 5427 1.856629 AATACTCCCTCCGTTCGGAA 58.143 50.000 14.79 0.00 33.41 4.30
4713 5428 2.083628 ATACTCCCTCCGTTCGGAAT 57.916 50.000 14.79 2.14 33.41 3.01
4714 5429 1.856629 TACTCCCTCCGTTCGGAATT 58.143 50.000 14.79 0.00 33.41 2.17
4715 5430 1.856629 ACTCCCTCCGTTCGGAATTA 58.143 50.000 14.79 2.82 33.41 1.40
4716 5431 1.479730 ACTCCCTCCGTTCGGAATTAC 59.520 52.381 14.79 0.00 33.41 1.89
4717 5432 1.755380 CTCCCTCCGTTCGGAATTACT 59.245 52.381 14.79 0.00 33.41 2.24
4718 5433 1.753073 TCCCTCCGTTCGGAATTACTC 59.247 52.381 14.79 0.00 33.41 2.59
4719 5434 1.535437 CCCTCCGTTCGGAATTACTCG 60.535 57.143 14.79 1.97 33.41 4.18
4720 5435 1.133790 CCTCCGTTCGGAATTACTCGT 59.866 52.381 14.79 0.00 33.41 4.18
4721 5436 2.448219 CTCCGTTCGGAATTACTCGTC 58.552 52.381 14.79 0.00 33.41 4.20
4722 5437 2.086869 TCCGTTCGGAATTACTCGTCT 58.913 47.619 11.66 0.00 0.00 4.18
4723 5438 2.096496 TCCGTTCGGAATTACTCGTCTC 59.904 50.000 11.66 0.00 0.00 3.36
4724 5439 2.099621 CGTTCGGAATTACTCGTCTCG 58.900 52.381 0.00 0.00 0.00 4.04
4725 5440 2.448219 GTTCGGAATTACTCGTCTCGG 58.552 52.381 0.00 0.00 0.00 4.63
4726 5441 2.028420 TCGGAATTACTCGTCTCGGA 57.972 50.000 0.00 0.00 0.00 4.55
4727 5442 2.358957 TCGGAATTACTCGTCTCGGAA 58.641 47.619 0.00 0.00 0.00 4.30
4728 5443 2.749076 TCGGAATTACTCGTCTCGGAAA 59.251 45.455 0.00 0.00 0.00 3.13
4729 5444 2.850647 CGGAATTACTCGTCTCGGAAAC 59.149 50.000 0.00 0.00 0.00 2.78
4730 5445 3.185330 GGAATTACTCGTCTCGGAAACC 58.815 50.000 0.00 0.00 0.00 3.27
4749 5464 8.937634 GGAAACCGATGTATCTAGAACTAAAA 57.062 34.615 0.00 0.00 0.00 1.52
4750 5465 9.543783 GGAAACCGATGTATCTAGAACTAAAAT 57.456 33.333 0.00 0.00 0.00 1.82
4753 5468 9.674824 AACCGATGTATCTAGAACTAAAATACG 57.325 33.333 0.00 0.00 0.00 3.06
4754 5469 8.844244 ACCGATGTATCTAGAACTAAAATACGT 58.156 33.333 0.00 0.00 0.00 3.57
4755 5470 9.327529 CCGATGTATCTAGAACTAAAATACGTC 57.672 37.037 0.00 16.33 36.31 4.34
4772 5487 9.490379 AAAATACGTCTAGATACATCCATTTCC 57.510 33.333 0.00 0.00 0.00 3.13
4773 5488 5.122512 ACGTCTAGATACATCCATTTCCG 57.877 43.478 0.00 0.00 0.00 4.30
4774 5489 3.921021 CGTCTAGATACATCCATTTCCGC 59.079 47.826 0.00 0.00 0.00 5.54
4775 5490 3.921021 GTCTAGATACATCCATTTCCGCG 59.079 47.826 0.00 0.00 0.00 6.46
4776 5491 3.824443 TCTAGATACATCCATTTCCGCGA 59.176 43.478 8.23 0.00 0.00 5.87
4777 5492 2.755650 AGATACATCCATTTCCGCGAC 58.244 47.619 8.23 0.00 0.00 5.19
4778 5493 2.102420 AGATACATCCATTTCCGCGACA 59.898 45.455 8.23 0.00 0.00 4.35
4779 5494 2.388310 TACATCCATTTCCGCGACAA 57.612 45.000 8.23 0.00 0.00 3.18
4780 5495 1.086696 ACATCCATTTCCGCGACAAG 58.913 50.000 8.23 0.00 0.00 3.16
4781 5496 1.086696 CATCCATTTCCGCGACAAGT 58.913 50.000 8.23 0.00 0.00 3.16
4782 5497 2.276201 CATCCATTTCCGCGACAAGTA 58.724 47.619 8.23 0.00 0.00 2.24
4783 5498 2.459060 TCCATTTCCGCGACAAGTAA 57.541 45.000 8.23 0.00 0.00 2.24
4784 5499 2.980568 TCCATTTCCGCGACAAGTAAT 58.019 42.857 8.23 0.00 0.00 1.89
4785 5500 3.340034 TCCATTTCCGCGACAAGTAATT 58.660 40.909 8.23 0.00 0.00 1.40
4786 5501 3.372822 TCCATTTCCGCGACAAGTAATTC 59.627 43.478 8.23 0.00 0.00 2.17
4787 5502 3.486875 CCATTTCCGCGACAAGTAATTCC 60.487 47.826 8.23 0.00 0.00 3.01
4788 5503 1.352114 TTCCGCGACAAGTAATTCCG 58.648 50.000 8.23 0.00 0.00 4.30
4789 5504 0.527113 TCCGCGACAAGTAATTCCGA 59.473 50.000 8.23 0.00 0.00 4.55
4790 5505 1.067706 TCCGCGACAAGTAATTCCGAA 60.068 47.619 8.23 0.00 0.00 4.30
4791 5506 1.931172 CCGCGACAAGTAATTCCGAAT 59.069 47.619 8.23 0.00 0.00 3.34
4792 5507 2.285602 CCGCGACAAGTAATTCCGAATG 60.286 50.000 8.23 0.00 0.00 2.67
4793 5508 2.285602 CGCGACAAGTAATTCCGAATGG 60.286 50.000 0.00 0.00 0.00 3.16
4794 5509 2.933906 GCGACAAGTAATTCCGAATGGA 59.066 45.455 0.00 0.00 44.61 3.41
4806 5521 4.194678 TCCGAATGGAGGGAGTATAAGT 57.805 45.455 0.00 0.00 40.17 2.24
4807 5522 4.150359 TCCGAATGGAGGGAGTATAAGTC 58.850 47.826 0.00 0.00 40.17 3.01
4808 5523 4.140994 TCCGAATGGAGGGAGTATAAGTCT 60.141 45.833 0.00 0.00 40.17 3.24
4809 5524 4.589374 CCGAATGGAGGGAGTATAAGTCTT 59.411 45.833 0.00 0.00 37.49 3.01
4810 5525 5.070580 CCGAATGGAGGGAGTATAAGTCTTT 59.929 44.000 0.00 0.00 37.49 2.52
4811 5526 5.986135 CGAATGGAGGGAGTATAAGTCTTTG 59.014 44.000 0.00 0.00 0.00 2.77
4812 5527 6.407074 CGAATGGAGGGAGTATAAGTCTTTGT 60.407 42.308 0.00 0.00 0.00 2.83
4813 5528 7.201884 CGAATGGAGGGAGTATAAGTCTTTGTA 60.202 40.741 0.00 0.00 0.00 2.41
4814 5529 7.604657 ATGGAGGGAGTATAAGTCTTTGTAG 57.395 40.000 0.00 0.00 0.00 2.74
4815 5530 6.738635 TGGAGGGAGTATAAGTCTTTGTAGA 58.261 40.000 0.00 0.00 0.00 2.59
4816 5531 6.834451 TGGAGGGAGTATAAGTCTTTGTAGAG 59.166 42.308 0.00 0.00 0.00 2.43
4817 5532 7.061688 GGAGGGAGTATAAGTCTTTGTAGAGA 58.938 42.308 0.00 0.00 0.00 3.10
4818 5533 7.726738 GGAGGGAGTATAAGTCTTTGTAGAGAT 59.273 40.741 0.00 0.00 0.00 2.75
4819 5534 9.138596 GAGGGAGTATAAGTCTTTGTAGAGATT 57.861 37.037 0.00 0.00 0.00 2.40
4820 5535 9.138596 AGGGAGTATAAGTCTTTGTAGAGATTC 57.861 37.037 0.00 0.00 0.00 2.52
4821 5536 8.361889 GGGAGTATAAGTCTTTGTAGAGATTCC 58.638 40.741 0.00 0.00 0.00 3.01
4822 5537 8.915036 GGAGTATAAGTCTTTGTAGAGATTCCA 58.085 37.037 0.00 0.00 0.00 3.53
4830 5545 9.606631 AGTCTTTGTAGAGATTCCAATATGAAC 57.393 33.333 0.00 0.00 0.00 3.18
4831 5546 9.606631 GTCTTTGTAGAGATTCCAATATGAACT 57.393 33.333 0.00 0.00 0.00 3.01
4839 5554 8.307483 AGAGATTCCAATATGAACTACATACGG 58.693 37.037 0.00 0.00 43.12 4.02
4840 5555 8.190326 AGATTCCAATATGAACTACATACGGA 57.810 34.615 0.00 0.00 43.12 4.69
4841 5556 8.816894 AGATTCCAATATGAACTACATACGGAT 58.183 33.333 0.00 0.00 43.12 4.18
4842 5557 8.777865 ATTCCAATATGAACTACATACGGATG 57.222 34.615 5.94 5.94 43.12 3.51
4844 5559 8.411991 TCCAATATGAACTACATACGGATGTA 57.588 34.615 19.32 19.32 44.77 2.29
4845 5560 9.031537 TCCAATATGAACTACATACGGATGTAT 57.968 33.333 20.64 7.28 45.42 2.29
4851 5566 8.570068 TGAACTACATACGGATGTATATAGCA 57.430 34.615 20.64 11.67 45.42 3.49
4852 5567 9.185680 TGAACTACATACGGATGTATATAGCAT 57.814 33.333 20.64 4.15 45.42 3.79
4855 5570 9.848710 ACTACATACGGATGTATATAGCATAGT 57.151 33.333 20.64 10.71 45.42 2.12
4862 5577 9.463902 ACGGATGTATATAGCATAGTTTAGAGT 57.536 33.333 0.00 0.00 0.00 3.24
4863 5578 9.723447 CGGATGTATATAGCATAGTTTAGAGTG 57.277 37.037 0.00 0.00 0.00 3.51
4881 5596 4.992381 AGTGTAGATTCACTCGTTTTGC 57.008 40.909 0.00 0.00 44.07 3.68
4882 5597 4.632153 AGTGTAGATTCACTCGTTTTGCT 58.368 39.130 0.00 0.00 44.07 3.91
4883 5598 4.686554 AGTGTAGATTCACTCGTTTTGCTC 59.313 41.667 0.00 0.00 44.07 4.26
4884 5599 3.994392 TGTAGATTCACTCGTTTTGCTCC 59.006 43.478 0.00 0.00 0.00 4.70
4885 5600 2.069273 AGATTCACTCGTTTTGCTCCG 58.931 47.619 0.00 0.00 0.00 4.63
4886 5601 1.798813 GATTCACTCGTTTTGCTCCGT 59.201 47.619 0.00 0.00 0.00 4.69
4887 5602 2.512485 TTCACTCGTTTTGCTCCGTA 57.488 45.000 0.00 0.00 0.00 4.02
4888 5603 2.736144 TCACTCGTTTTGCTCCGTAT 57.264 45.000 0.00 0.00 0.00 3.06
4889 5604 2.333926 TCACTCGTTTTGCTCCGTATG 58.666 47.619 0.00 0.00 0.00 2.39
4890 5605 2.066262 CACTCGTTTTGCTCCGTATGT 58.934 47.619 0.00 0.00 0.00 2.29
4891 5606 3.057386 TCACTCGTTTTGCTCCGTATGTA 60.057 43.478 0.00 0.00 0.00 2.29
4892 5607 3.303495 CACTCGTTTTGCTCCGTATGTAG 59.697 47.826 0.00 0.00 0.00 2.74
4893 5608 3.057033 ACTCGTTTTGCTCCGTATGTAGT 60.057 43.478 0.00 0.00 0.00 2.73
4894 5609 3.504863 TCGTTTTGCTCCGTATGTAGTC 58.495 45.455 0.00 0.00 0.00 2.59
4895 5610 2.601763 CGTTTTGCTCCGTATGTAGTCC 59.398 50.000 0.00 0.00 0.00 3.85
4896 5611 3.592059 GTTTTGCTCCGTATGTAGTCCA 58.408 45.455 0.00 0.00 0.00 4.02
4897 5612 4.189231 GTTTTGCTCCGTATGTAGTCCAT 58.811 43.478 0.00 0.00 37.58 3.41
4898 5613 5.353938 GTTTTGCTCCGTATGTAGTCCATA 58.646 41.667 0.00 0.00 34.86 2.74
4899 5614 5.801531 TTTGCTCCGTATGTAGTCCATAT 57.198 39.130 0.00 0.00 38.29 1.78
4900 5615 5.801531 TTGCTCCGTATGTAGTCCATATT 57.198 39.130 0.00 0.00 38.29 1.28
4901 5616 5.134202 TGCTCCGTATGTAGTCCATATTG 57.866 43.478 0.00 0.00 38.29 1.90
4902 5617 4.021456 TGCTCCGTATGTAGTCCATATTGG 60.021 45.833 0.00 0.00 38.29 3.16
4903 5618 4.219944 GCTCCGTATGTAGTCCATATTGGA 59.780 45.833 0.00 0.00 45.98 3.53
4918 5633 7.872138 TCCATATTGGAATCACTAAAAGGACT 58.128 34.615 0.00 0.00 45.00 3.85
4919 5634 8.336235 TCCATATTGGAATCACTAAAAGGACTT 58.664 33.333 0.00 0.00 45.00 3.01
4920 5635 9.627123 CCATATTGGAATCACTAAAAGGACTTA 57.373 33.333 0.00 0.00 40.96 2.24
4933 5648 9.828039 ACTAAAAGGACTTATATTTAGGAACGG 57.172 33.333 8.47 0.00 38.86 4.44
4935 5650 8.959705 AAAAGGACTTATATTTAGGAACGGAG 57.040 34.615 0.00 0.00 0.00 4.63
4936 5651 6.667558 AGGACTTATATTTAGGAACGGAGG 57.332 41.667 0.00 0.00 0.00 4.30
4937 5652 5.543020 AGGACTTATATTTAGGAACGGAGGG 59.457 44.000 0.00 0.00 0.00 4.30
4938 5653 5.541484 GGACTTATATTTAGGAACGGAGGGA 59.459 44.000 0.00 0.00 0.00 4.20
4939 5654 6.295180 GGACTTATATTTAGGAACGGAGGGAG 60.295 46.154 0.00 0.00 0.00 4.30
4940 5655 6.141790 ACTTATATTTAGGAACGGAGGGAGT 58.858 40.000 0.00 0.00 0.00 3.85
4941 5656 7.300658 ACTTATATTTAGGAACGGAGGGAGTA 58.699 38.462 0.00 0.00 0.00 2.59
4955 5670 6.491403 ACGGAGGGAGTATATTGTAATACGTT 59.509 38.462 0.00 0.00 37.41 3.99
5007 5722 7.181125 AGAGGGAGTAATATATTGGGATCACAC 59.819 40.741 8.28 1.60 0.00 3.82
5008 5723 6.070767 AGGGAGTAATATATTGGGATCACACG 60.071 42.308 8.28 0.00 0.00 4.49
5012 5727 7.907389 AGTAATATATTGGGATCACACGATGT 58.093 34.615 8.28 0.00 29.66 3.06
5033 5748 8.353684 CGATGTGACTTCTATAGGAACAAGTAT 58.646 37.037 0.00 0.00 30.23 2.12
5093 5808 9.630098 AAATACATGAATGAAACTTGTAAGCTG 57.370 29.630 0.00 0.00 0.00 4.24
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
135 140 0.960364 GGGCGGAATGAGAAGCAACA 60.960 55.000 0.00 0.00 0.00 3.33
178 183 1.373748 GCCGGACGTGTGAGCTTTA 60.374 57.895 5.05 0.00 0.00 1.85
279 284 1.909141 GCCGTCAGAGAACGAGTCGA 61.909 60.000 21.50 0.00 45.37 4.20
313 318 2.481903 GATTTCGCTCTGGCCAAATC 57.518 50.000 7.01 8.43 44.17 2.17
326 331 2.838386 CACAAGATGCAGGGATTTCG 57.162 50.000 0.00 0.00 0.00 3.46
364 369 2.965147 CCAAGAAGGAAACAACACCCAT 59.035 45.455 0.00 0.00 41.22 4.00
376 381 2.665000 CAGCGCCTCCAAGAAGGA 59.335 61.111 2.29 0.00 46.75 3.36
433 439 5.271598 TCCGGAATACCAAACCTAGAGTTA 58.728 41.667 0.00 0.00 37.88 2.24
493 504 5.028549 AGAATACAAGACATCGCCTTCAT 57.971 39.130 0.00 0.00 0.00 2.57
502 513 3.503827 TGTCGCGAGAATACAAGACAT 57.496 42.857 10.24 0.00 45.01 3.06
522 533 1.079819 CAACGACAGCACCGAGGAT 60.080 57.895 0.00 0.00 0.00 3.24
537 548 2.457366 AGACGACCAACATCTCCAAC 57.543 50.000 0.00 0.00 0.00 3.77
558 569 4.864247 CAGAAAAACAGTCCAACCAACAAG 59.136 41.667 0.00 0.00 0.00 3.16
577 588 2.739913 CAACTAAAATCGCCGACCAGAA 59.260 45.455 0.00 0.00 0.00 3.02
612 1080 8.256611 ACGTTATGATGCATAAATCATCTACC 57.743 34.615 0.00 0.00 42.38 3.18
630 1098 5.651172 TCAGATTCGGCATAAACGTTATG 57.349 39.130 0.00 7.25 0.00 1.90
638 1106 5.321959 TGCAAAAATCAGATTCGGCATAA 57.678 34.783 10.63 0.00 0.00 1.90
669 1137 1.722011 AACAATTACGGAGCCTGACG 58.278 50.000 0.00 0.00 0.00 4.35
685 1153 2.118313 TCAGACTCGGATCGGTAACA 57.882 50.000 0.00 0.00 0.00 2.41
747 1215 1.712018 GCCGAAACCGCCATAAGGAC 61.712 60.000 0.00 0.00 36.89 3.85
878 1348 0.621571 CAATCTCCCTCCCACCCTCA 60.622 60.000 0.00 0.00 0.00 3.86
921 1391 8.541899 TTAGTTTTTCTTAGGGTTCCAAACAT 57.458 30.769 0.00 0.00 0.00 2.71
999 1469 1.808512 CGCACCTTTATCACGGCCATA 60.809 52.381 2.24 0.00 0.00 2.74
1036 1506 2.147150 GTCCTCAACACTCTTTGCCTC 58.853 52.381 0.00 0.00 0.00 4.70
1376 1851 8.419076 TCAAATTAACCAAGTTCAAAAAGAGC 57.581 30.769 0.00 0.00 0.00 4.09
1571 2093 9.912634 TCAACTGAATCAAGAAAATGGTTAATC 57.087 29.630 0.00 0.00 0.00 1.75
1650 2173 3.679980 CGAACACAACATCTGGGAACTAG 59.320 47.826 0.00 0.00 30.48 2.57
1651 2174 3.556213 CCGAACACAACATCTGGGAACTA 60.556 47.826 0.00 0.00 30.48 2.24
1652 2175 2.494059 CGAACACAACATCTGGGAACT 58.506 47.619 0.00 0.00 30.48 3.01
1663 2186 1.268539 CCAGCAGAAACCGAACACAAC 60.269 52.381 0.00 0.00 0.00 3.32
1673 2196 3.685272 GGCTTAAGTAGACCAGCAGAAAC 59.315 47.826 4.02 0.00 33.64 2.78
1784 2307 4.728882 GCCGCTGAAACTTGATTGTAGATG 60.729 45.833 0.00 0.00 0.00 2.90
1924 2447 5.160641 CAACATTACACAACCAATACCTGC 58.839 41.667 0.00 0.00 0.00 4.85
1966 2492 5.382618 AGAAACATGGAATCTGTTGCTTC 57.617 39.130 0.00 0.00 39.04 3.86
2029 2558 7.300556 ACTATCATGTGAATGTCAGCTATCT 57.699 36.000 0.00 0.00 0.00 1.98
2444 2990 7.406799 AATAGAAGTGCAAAATGAAAAACGG 57.593 32.000 0.00 0.00 0.00 4.44
2642 3188 9.136323 ACAAAGAAAGGAAGTATCAATGAAAGT 57.864 29.630 0.00 0.00 0.00 2.66
2650 3196 9.567776 TGACATAAACAAAGAAAGGAAGTATCA 57.432 29.630 0.00 0.00 0.00 2.15
2658 3204 8.383318 TCTCTTCTGACATAAACAAAGAAAGG 57.617 34.615 0.00 0.00 0.00 3.11
2661 3207 9.559732 TTCATCTCTTCTGACATAAACAAAGAA 57.440 29.630 0.00 0.00 0.00 2.52
2874 3420 4.358214 TGGATGCGAGGGGATATGTAATA 58.642 43.478 0.00 0.00 0.00 0.98
2875 3421 3.181329 TGGATGCGAGGGGATATGTAAT 58.819 45.455 0.00 0.00 0.00 1.89
2876 3422 2.615391 TGGATGCGAGGGGATATGTAA 58.385 47.619 0.00 0.00 0.00 2.41
2931 3593 2.224161 GCTGGCGGATGAGATAAGAAGT 60.224 50.000 0.00 0.00 0.00 3.01
2984 3646 2.732412 TCACTGCTAAGCTCTGACAC 57.268 50.000 0.00 0.00 0.00 3.67
3090 3752 6.305693 AGTTTGACTTGAGACAATGCTAAC 57.694 37.500 0.00 0.00 30.67 2.34
3149 3811 7.920682 GGTATTGATTTGGTATTGTGGATGTTC 59.079 37.037 0.00 0.00 0.00 3.18
4022 4689 1.629043 GGTATATCGTGCCCCTGAGA 58.371 55.000 0.00 0.00 0.00 3.27
4097 4764 3.435186 GCCTGTTTCTGCCGGCTC 61.435 66.667 29.70 12.94 39.42 4.70
4167 4834 2.285969 AGGAGCCTGGCTGTGGAT 60.286 61.111 28.82 0.00 39.88 3.41
4354 5056 7.065803 GCATTGTCATGTTATACAGTACCAACT 59.934 37.037 7.91 0.00 32.15 3.16
4360 5062 4.509970 GGCGCATTGTCATGTTATACAGTA 59.490 41.667 10.83 0.00 32.28 2.74
4403 5112 5.187967 CAGGATATATAGAGCGGGTTTCCTT 59.812 44.000 0.00 0.00 0.00 3.36
4539 5248 9.995957 GTAAAAACAAAAACAAATGCCAAGTAT 57.004 25.926 0.00 0.00 0.00 2.12
4576 5285 9.868277 TCTTAACTTTTCATTCAACACAAATGT 57.132 25.926 0.00 0.00 42.46 2.71
4628 5337 5.696724 GCTACGAATGCATAATGTCTTAGGT 59.303 40.000 0.00 0.00 0.00 3.08
4629 5338 5.164051 CGCTACGAATGCATAATGTCTTAGG 60.164 44.000 0.00 0.00 0.00 2.69
4630 5339 5.164051 CCGCTACGAATGCATAATGTCTTAG 60.164 44.000 0.00 2.51 0.00 2.18
4640 5354 1.967319 AATTCCCGCTACGAATGCAT 58.033 45.000 0.00 0.00 30.39 3.96
4678 5393 4.202233 GGGAGTATTTAGGAACGGAGGAAG 60.202 50.000 0.00 0.00 0.00 3.46
4679 5394 3.708121 GGGAGTATTTAGGAACGGAGGAA 59.292 47.826 0.00 0.00 0.00 3.36
4680 5395 3.052338 AGGGAGTATTTAGGAACGGAGGA 60.052 47.826 0.00 0.00 0.00 3.71
4681 5396 3.306613 AGGGAGTATTTAGGAACGGAGG 58.693 50.000 0.00 0.00 0.00 4.30
4682 5397 3.321396 GGAGGGAGTATTTAGGAACGGAG 59.679 52.174 0.00 0.00 0.00 4.63
4683 5398 3.303049 GGAGGGAGTATTTAGGAACGGA 58.697 50.000 0.00 0.00 0.00 4.69
4684 5399 2.035576 CGGAGGGAGTATTTAGGAACGG 59.964 54.545 0.00 0.00 0.00 4.44
4685 5400 2.692041 ACGGAGGGAGTATTTAGGAACG 59.308 50.000 0.00 0.00 0.00 3.95
4686 5401 4.691175 GAACGGAGGGAGTATTTAGGAAC 58.309 47.826 0.00 0.00 0.00 3.62
4687 5402 3.382546 CGAACGGAGGGAGTATTTAGGAA 59.617 47.826 0.00 0.00 0.00 3.36
4688 5403 2.954318 CGAACGGAGGGAGTATTTAGGA 59.046 50.000 0.00 0.00 0.00 2.94
4689 5404 2.035576 CCGAACGGAGGGAGTATTTAGG 59.964 54.545 7.53 0.00 37.50 2.69
4690 5405 2.954318 TCCGAACGGAGGGAGTATTTAG 59.046 50.000 12.04 0.00 39.76 1.85
4691 5406 3.017048 TCCGAACGGAGGGAGTATTTA 57.983 47.619 12.04 0.00 39.76 1.40
4692 5407 1.856629 TCCGAACGGAGGGAGTATTT 58.143 50.000 12.04 0.00 39.76 1.40
4693 5408 1.856629 TTCCGAACGGAGGGAGTATT 58.143 50.000 15.34 0.00 46.06 1.89
4694 5409 2.083628 ATTCCGAACGGAGGGAGTAT 57.916 50.000 15.34 3.38 46.06 2.12
4695 5410 1.856629 AATTCCGAACGGAGGGAGTA 58.143 50.000 15.34 1.05 46.06 2.59
4696 5411 1.479730 GTAATTCCGAACGGAGGGAGT 59.520 52.381 15.34 4.12 46.06 3.85
4697 5412 1.755380 AGTAATTCCGAACGGAGGGAG 59.245 52.381 15.34 0.00 46.06 4.30
4698 5413 1.753073 GAGTAATTCCGAACGGAGGGA 59.247 52.381 15.34 2.49 46.06 4.20
4699 5414 1.535437 CGAGTAATTCCGAACGGAGGG 60.535 57.143 15.34 0.00 46.06 4.30
4700 5415 1.133790 ACGAGTAATTCCGAACGGAGG 59.866 52.381 15.34 4.28 46.06 4.30
4701 5416 2.097142 AGACGAGTAATTCCGAACGGAG 59.903 50.000 15.34 5.60 46.06 4.63
4702 5417 2.086869 AGACGAGTAATTCCGAACGGA 58.913 47.619 12.04 12.04 43.52 4.69
4703 5418 2.448219 GAGACGAGTAATTCCGAACGG 58.552 52.381 6.94 6.94 0.00 4.44
4704 5419 2.099621 CGAGACGAGTAATTCCGAACG 58.900 52.381 0.00 0.00 0.00 3.95
4705 5420 2.096496 TCCGAGACGAGTAATTCCGAAC 59.904 50.000 0.00 0.00 0.00 3.95
4706 5421 2.358957 TCCGAGACGAGTAATTCCGAA 58.641 47.619 0.00 0.00 0.00 4.30
4707 5422 2.028420 TCCGAGACGAGTAATTCCGA 57.972 50.000 0.00 0.00 0.00 4.55
4708 5423 2.838386 TTCCGAGACGAGTAATTCCG 57.162 50.000 0.00 0.00 0.00 4.30
4709 5424 3.185330 GGTTTCCGAGACGAGTAATTCC 58.815 50.000 0.00 0.00 0.00 3.01
4724 5439 8.937634 TTTTAGTTCTAGATACATCGGTTTCC 57.062 34.615 0.00 0.00 0.00 3.13
4727 5442 9.674824 CGTATTTTAGTTCTAGATACATCGGTT 57.325 33.333 0.00 0.00 0.00 4.44
4728 5443 8.844244 ACGTATTTTAGTTCTAGATACATCGGT 58.156 33.333 0.00 0.00 0.00 4.69
4729 5444 9.327529 GACGTATTTTAGTTCTAGATACATCGG 57.672 37.037 0.00 0.00 0.00 4.18
4746 5461 9.490379 GGAAATGGATGTATCTAGACGTATTTT 57.510 33.333 0.00 0.00 0.00 1.82
4747 5462 7.813148 CGGAAATGGATGTATCTAGACGTATTT 59.187 37.037 0.00 0.00 0.00 1.40
4748 5463 7.313646 CGGAAATGGATGTATCTAGACGTATT 58.686 38.462 0.00 0.00 0.00 1.89
4749 5464 6.625300 GCGGAAATGGATGTATCTAGACGTAT 60.625 42.308 0.00 0.00 0.00 3.06
4750 5465 5.335426 GCGGAAATGGATGTATCTAGACGTA 60.335 44.000 0.00 0.00 0.00 3.57
4751 5466 4.558898 GCGGAAATGGATGTATCTAGACGT 60.559 45.833 0.00 0.00 0.00 4.34
4752 5467 3.921021 GCGGAAATGGATGTATCTAGACG 59.079 47.826 0.00 0.00 0.00 4.18
4753 5468 3.921021 CGCGGAAATGGATGTATCTAGAC 59.079 47.826 0.00 0.00 0.00 2.59
4754 5469 3.824443 TCGCGGAAATGGATGTATCTAGA 59.176 43.478 6.13 0.00 0.00 2.43
4755 5470 3.921021 GTCGCGGAAATGGATGTATCTAG 59.079 47.826 6.13 0.00 0.00 2.43
4756 5471 3.319689 TGTCGCGGAAATGGATGTATCTA 59.680 43.478 6.13 0.00 0.00 1.98
4757 5472 2.102420 TGTCGCGGAAATGGATGTATCT 59.898 45.455 6.13 0.00 0.00 1.98
4758 5473 2.479837 TGTCGCGGAAATGGATGTATC 58.520 47.619 6.13 0.00 0.00 2.24
4759 5474 2.613026 TGTCGCGGAAATGGATGTAT 57.387 45.000 6.13 0.00 0.00 2.29
4760 5475 2.276201 CTTGTCGCGGAAATGGATGTA 58.724 47.619 6.13 0.00 0.00 2.29
4761 5476 1.086696 CTTGTCGCGGAAATGGATGT 58.913 50.000 6.13 0.00 0.00 3.06
4762 5477 1.086696 ACTTGTCGCGGAAATGGATG 58.913 50.000 6.13 0.00 0.00 3.51
4763 5478 2.684001 TACTTGTCGCGGAAATGGAT 57.316 45.000 6.13 0.00 0.00 3.41
4764 5479 2.459060 TTACTTGTCGCGGAAATGGA 57.541 45.000 6.13 0.00 0.00 3.41
4765 5480 3.486875 GGAATTACTTGTCGCGGAAATGG 60.487 47.826 6.13 0.00 0.00 3.16
4766 5481 3.680789 GGAATTACTTGTCGCGGAAATG 58.319 45.455 6.13 0.00 0.00 2.32
4767 5482 2.350498 CGGAATTACTTGTCGCGGAAAT 59.650 45.455 6.13 0.00 0.00 2.17
4768 5483 1.727880 CGGAATTACTTGTCGCGGAAA 59.272 47.619 6.13 0.00 0.00 3.13
4769 5484 1.067706 TCGGAATTACTTGTCGCGGAA 60.068 47.619 6.13 0.00 0.00 4.30
4770 5485 0.527113 TCGGAATTACTTGTCGCGGA 59.473 50.000 6.13 0.00 0.00 5.54
4771 5486 1.352114 TTCGGAATTACTTGTCGCGG 58.648 50.000 6.13 0.00 0.00 6.46
4772 5487 2.285602 CCATTCGGAATTACTTGTCGCG 60.286 50.000 0.00 0.00 0.00 5.87
4773 5488 2.933906 TCCATTCGGAATTACTTGTCGC 59.066 45.455 0.00 0.00 38.83 5.19
4774 5489 3.555956 CCTCCATTCGGAATTACTTGTCG 59.444 47.826 0.00 0.00 42.21 4.35
4775 5490 3.877508 CCCTCCATTCGGAATTACTTGTC 59.122 47.826 0.00 0.00 42.21 3.18
4776 5491 3.521937 TCCCTCCATTCGGAATTACTTGT 59.478 43.478 0.00 0.00 42.21 3.16
4777 5492 4.130118 CTCCCTCCATTCGGAATTACTTG 58.870 47.826 0.00 0.00 42.21 3.16
4778 5493 3.780850 ACTCCCTCCATTCGGAATTACTT 59.219 43.478 0.00 0.00 42.21 2.24
4779 5494 3.385115 ACTCCCTCCATTCGGAATTACT 58.615 45.455 0.00 0.00 42.21 2.24
4780 5495 3.840124 ACTCCCTCCATTCGGAATTAC 57.160 47.619 0.00 0.00 42.21 1.89
4781 5496 6.785963 ACTTATACTCCCTCCATTCGGAATTA 59.214 38.462 0.00 0.00 42.21 1.40
4782 5497 5.607171 ACTTATACTCCCTCCATTCGGAATT 59.393 40.000 0.00 0.00 42.21 2.17
4783 5498 5.155905 ACTTATACTCCCTCCATTCGGAAT 58.844 41.667 0.00 0.00 42.21 3.01
4784 5499 4.553678 ACTTATACTCCCTCCATTCGGAA 58.446 43.478 0.00 0.00 42.21 4.30
4785 5500 4.140994 AGACTTATACTCCCTCCATTCGGA 60.141 45.833 0.00 0.00 39.79 4.55
4786 5501 4.153411 AGACTTATACTCCCTCCATTCGG 58.847 47.826 0.00 0.00 0.00 4.30
4787 5502 5.793030 AAGACTTATACTCCCTCCATTCG 57.207 43.478 0.00 0.00 0.00 3.34
4788 5503 6.890293 ACAAAGACTTATACTCCCTCCATTC 58.110 40.000 0.00 0.00 0.00 2.67
4789 5504 6.893020 ACAAAGACTTATACTCCCTCCATT 57.107 37.500 0.00 0.00 0.00 3.16
4790 5505 7.363031 TCTACAAAGACTTATACTCCCTCCAT 58.637 38.462 0.00 0.00 0.00 3.41
4791 5506 6.738635 TCTACAAAGACTTATACTCCCTCCA 58.261 40.000 0.00 0.00 0.00 3.86
4792 5507 7.061688 TCTCTACAAAGACTTATACTCCCTCC 58.938 42.308 0.00 0.00 0.00 4.30
4793 5508 8.700439 ATCTCTACAAAGACTTATACTCCCTC 57.300 38.462 0.00 0.00 0.00 4.30
4794 5509 9.138596 GAATCTCTACAAAGACTTATACTCCCT 57.861 37.037 0.00 0.00 0.00 4.20
4795 5510 8.361889 GGAATCTCTACAAAGACTTATACTCCC 58.638 40.741 0.00 0.00 0.00 4.30
4796 5511 8.915036 TGGAATCTCTACAAAGACTTATACTCC 58.085 37.037 0.00 0.00 0.00 3.85
4804 5519 9.606631 GTTCATATTGGAATCTCTACAAAGACT 57.393 33.333 0.00 0.00 0.00 3.24
4805 5520 9.606631 AGTTCATATTGGAATCTCTACAAAGAC 57.393 33.333 0.00 0.00 0.00 3.01
4813 5528 8.307483 CCGTATGTAGTTCATATTGGAATCTCT 58.693 37.037 5.56 0.00 40.54 3.10
4814 5529 8.304596 TCCGTATGTAGTTCATATTGGAATCTC 58.695 37.037 9.72 0.00 40.31 2.75
4815 5530 8.190326 TCCGTATGTAGTTCATATTGGAATCT 57.810 34.615 9.72 0.00 40.31 2.40
4816 5531 8.873830 CATCCGTATGTAGTTCATATTGGAATC 58.126 37.037 13.81 0.00 43.20 2.52
4817 5532 8.375506 ACATCCGTATGTAGTTCATATTGGAAT 58.624 33.333 13.81 6.58 44.66 3.01
4818 5533 7.732025 ACATCCGTATGTAGTTCATATTGGAA 58.268 34.615 13.81 3.55 44.66 3.53
4819 5534 7.297936 ACATCCGTATGTAGTTCATATTGGA 57.702 36.000 12.80 12.80 44.66 3.53
4836 5551 9.463902 ACTCTAAACTATGCTATATACATCCGT 57.536 33.333 2.36 0.00 0.00 4.69
4837 5552 9.723447 CACTCTAAACTATGCTATATACATCCG 57.277 37.037 2.36 0.00 0.00 4.18
4847 5562 9.409918 AGTGAATCTACACTCTAAACTATGCTA 57.590 33.333 0.00 0.00 46.36 3.49
4848 5563 8.299990 AGTGAATCTACACTCTAAACTATGCT 57.700 34.615 0.00 0.00 46.36 3.79
4861 5576 4.143094 GGAGCAAAACGAGTGAATCTACAC 60.143 45.833 0.00 0.00 40.60 2.90
4862 5577 3.994392 GGAGCAAAACGAGTGAATCTACA 59.006 43.478 0.00 0.00 0.00 2.74
4863 5578 3.060895 CGGAGCAAAACGAGTGAATCTAC 59.939 47.826 0.00 0.00 0.00 2.59
4864 5579 3.250744 CGGAGCAAAACGAGTGAATCTA 58.749 45.455 0.00 0.00 0.00 1.98
4865 5580 2.069273 CGGAGCAAAACGAGTGAATCT 58.931 47.619 0.00 0.00 0.00 2.40
4866 5581 1.798813 ACGGAGCAAAACGAGTGAATC 59.201 47.619 0.00 0.00 0.00 2.52
4867 5582 1.878953 ACGGAGCAAAACGAGTGAAT 58.121 45.000 0.00 0.00 0.00 2.57
4868 5583 2.512485 TACGGAGCAAAACGAGTGAA 57.488 45.000 0.00 0.00 0.00 3.18
4869 5584 2.288579 ACATACGGAGCAAAACGAGTGA 60.289 45.455 0.00 0.00 0.00 3.41
4870 5585 2.066262 ACATACGGAGCAAAACGAGTG 58.934 47.619 0.00 0.00 0.00 3.51
4871 5586 2.450609 ACATACGGAGCAAAACGAGT 57.549 45.000 0.00 0.00 0.00 4.18
4872 5587 3.508762 ACTACATACGGAGCAAAACGAG 58.491 45.455 0.00 0.00 0.00 4.18
4873 5588 3.504863 GACTACATACGGAGCAAAACGA 58.495 45.455 0.00 0.00 0.00 3.85
4874 5589 2.601763 GGACTACATACGGAGCAAAACG 59.398 50.000 0.00 0.00 0.00 3.60
4875 5590 3.592059 TGGACTACATACGGAGCAAAAC 58.408 45.455 0.00 0.00 0.00 2.43
4876 5591 3.965379 TGGACTACATACGGAGCAAAA 57.035 42.857 0.00 0.00 0.00 2.44
4877 5592 5.801531 ATATGGACTACATACGGAGCAAA 57.198 39.130 0.00 0.00 44.41 3.68
4878 5593 5.510690 CCAATATGGACTACATACGGAGCAA 60.511 44.000 0.00 0.00 44.41 3.91
4879 5594 4.021456 CCAATATGGACTACATACGGAGCA 60.021 45.833 0.00 0.00 44.41 4.26
4880 5595 4.219944 TCCAATATGGACTACATACGGAGC 59.780 45.833 0.00 0.00 42.67 4.70
4881 5596 5.977489 TCCAATATGGACTACATACGGAG 57.023 43.478 0.00 0.00 42.67 4.63
4893 5608 7.872138 AGTCCTTTTAGTGATTCCAATATGGA 58.128 34.615 0.00 0.00 46.61 3.41
4894 5609 8.525290 AAGTCCTTTTAGTGATTCCAATATGG 57.475 34.615 0.00 0.00 39.43 2.74
4907 5622 9.828039 CCGTTCCTAAATATAAGTCCTTTTAGT 57.172 33.333 0.00 0.00 32.35 2.24
4910 5625 7.991460 CCTCCGTTCCTAAATATAAGTCCTTTT 59.009 37.037 0.00 0.00 0.00 2.27
4911 5626 7.419865 CCCTCCGTTCCTAAATATAAGTCCTTT 60.420 40.741 0.00 0.00 0.00 3.11
4912 5627 6.042897 CCCTCCGTTCCTAAATATAAGTCCTT 59.957 42.308 0.00 0.00 0.00 3.36
4913 5628 5.543020 CCCTCCGTTCCTAAATATAAGTCCT 59.457 44.000 0.00 0.00 0.00 3.85
4914 5629 5.541484 TCCCTCCGTTCCTAAATATAAGTCC 59.459 44.000 0.00 0.00 0.00 3.85
4915 5630 6.267242 ACTCCCTCCGTTCCTAAATATAAGTC 59.733 42.308 0.00 0.00 0.00 3.01
4916 5631 6.141790 ACTCCCTCCGTTCCTAAATATAAGT 58.858 40.000 0.00 0.00 0.00 2.24
4917 5632 6.667558 ACTCCCTCCGTTCCTAAATATAAG 57.332 41.667 0.00 0.00 0.00 1.73
4920 5635 8.759782 CAATATACTCCCTCCGTTCCTAAATAT 58.240 37.037 0.00 0.00 0.00 1.28
4921 5636 7.731688 ACAATATACTCCCTCCGTTCCTAAATA 59.268 37.037 0.00 0.00 0.00 1.40
4922 5637 6.557633 ACAATATACTCCCTCCGTTCCTAAAT 59.442 38.462 0.00 0.00 0.00 1.40
4923 5638 5.901276 ACAATATACTCCCTCCGTTCCTAAA 59.099 40.000 0.00 0.00 0.00 1.85
4924 5639 5.461327 ACAATATACTCCCTCCGTTCCTAA 58.539 41.667 0.00 0.00 0.00 2.69
4925 5640 5.070823 ACAATATACTCCCTCCGTTCCTA 57.929 43.478 0.00 0.00 0.00 2.94
4926 5641 3.924922 ACAATATACTCCCTCCGTTCCT 58.075 45.455 0.00 0.00 0.00 3.36
4927 5642 5.796424 TTACAATATACTCCCTCCGTTCC 57.204 43.478 0.00 0.00 0.00 3.62
4928 5643 7.025963 CGTATTACAATATACTCCCTCCGTTC 58.974 42.308 0.00 0.00 0.00 3.95
4929 5644 6.491403 ACGTATTACAATATACTCCCTCCGTT 59.509 38.462 0.00 0.00 0.00 4.44
4930 5645 6.006449 ACGTATTACAATATACTCCCTCCGT 58.994 40.000 0.00 0.00 0.00 4.69
4931 5646 6.506500 ACGTATTACAATATACTCCCTCCG 57.493 41.667 0.00 0.00 0.00 4.63
4932 5647 8.120140 AGAACGTATTACAATATACTCCCTCC 57.880 38.462 0.00 0.00 0.00 4.30
4933 5648 8.790718 TGAGAACGTATTACAATATACTCCCTC 58.209 37.037 0.00 0.00 0.00 4.30
4934 5649 8.701908 TGAGAACGTATTACAATATACTCCCT 57.298 34.615 0.00 0.00 0.00 4.20
4935 5650 9.754382 TTTGAGAACGTATTACAATATACTCCC 57.246 33.333 0.00 0.00 0.00 4.30
5007 5722 6.565234 ACTTGTTCCTATAGAAGTCACATCG 58.435 40.000 0.00 0.00 34.29 3.84
5039 5754 8.748412 CCCTTTATGTTTTGAGTTGGATTCATA 58.252 33.333 0.00 0.00 0.00 2.15
5093 5808 4.915085 CGGTTTAACCAATCACATTGTGAC 59.085 41.667 21.19 6.32 41.12 3.67


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

AutoCloner maintained by Alex Coulton.