Multiple sequence alignment - TraesCS7A01G390200

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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 TraesCS7A01G390200 chr7A 100.000 6915 0 0 1 6915 566526802 566533716 0.000000e+00 12770
1 TraesCS7A01G390200 chr7A 85.638 1128 79 38 104 1217 566279795 566280853 0.000000e+00 1109
2 TraesCS7A01G390200 chr7A 85.638 1128 79 40 104 1217 566303594 566304652 0.000000e+00 1109
3 TraesCS7A01G390200 chr7A 85.638 1128 79 40 104 1217 566327197 566328255 0.000000e+00 1109
4 TraesCS7A01G390200 chr7A 85.550 1128 80 38 104 1217 566263131 566264189 0.000000e+00 1103
5 TraesCS7A01G390200 chr7A 85.474 1129 80 39 104 1217 566292091 566293150 0.000000e+00 1099
6 TraesCS7A01G390200 chr7A 84.740 1114 78 40 104 1204 566339467 566340501 0.000000e+00 1031
7 TraesCS7A01G390200 chr7A 84.725 1054 78 38 104 1143 566315419 566316403 0.000000e+00 977
8 TraesCS7A01G390200 chr7A 99.240 263 2 0 3074 3336 679063945 679064207 6.280000e-130 475
9 TraesCS7A01G390200 chr7A 97.736 265 5 1 3072 3335 80195818 80195554 8.180000e-124 455
10 TraesCS7A01G390200 chr7A 96.269 134 5 0 1 134 566357261 566357394 3.250000e-53 220
11 TraesCS7A01G390200 chr7D 94.196 3084 105 25 1 3074 500614409 500617428 0.000000e+00 4636
12 TraesCS7A01G390200 chr7D 95.818 1626 50 8 3335 4944 500617430 500619053 0.000000e+00 2610
13 TraesCS7A01G390200 chr7D 96.856 1304 26 7 5145 6436 500619673 500620973 0.000000e+00 2167
14 TraesCS7A01G390200 chr7D 91.244 651 30 12 570 1217 500251213 500251839 0.000000e+00 861
15 TraesCS7A01G390200 chr7D 96.200 421 6 2 6496 6915 500620976 500621387 0.000000e+00 680
16 TraesCS7A01G390200 chr7D 87.413 286 28 7 4581 4862 517004039 517003758 8.650000e-84 322
17 TraesCS7A01G390200 chr7D 94.608 204 10 1 4943 5146 500619312 500619514 1.450000e-81 315
18 TraesCS7A01G390200 chr7B 93.712 1829 56 19 3335 5146 528750054 528751840 0.000000e+00 2686
19 TraesCS7A01G390200 chr7B 96.357 1400 48 3 568 1965 528747442 528748840 0.000000e+00 2300
20 TraesCS7A01G390200 chr7B 94.665 1462 67 7 5145 6597 528752001 528753460 0.000000e+00 2257
21 TraesCS7A01G390200 chr7B 93.214 1120 38 7 1960 3074 528748966 528750052 0.000000e+00 1613
22 TraesCS7A01G390200 chr7B 90.199 806 55 14 5220 6016 663047761 663046971 0.000000e+00 1029
23 TraesCS7A01G390200 chr7B 93.657 268 7 6 6654 6912 528754396 528754662 6.500000e-105 392
24 TraesCS7A01G390200 chr7B 87.814 279 11 5 940 1217 528726991 528727247 8.710000e-79 305
25 TraesCS7A01G390200 chr7B 83.384 331 34 12 1 327 528746788 528747101 3.160000e-73 287
26 TraesCS7A01G390200 chr7B 82.540 315 39 8 6056 6368 663046970 663046670 5.320000e-66 263
27 TraesCS7A01G390200 chr6B 89.234 1096 91 9 4943 6016 45803951 45802861 0.000000e+00 1345
28 TraesCS7A01G390200 chr6B 88.352 807 75 11 5220 6016 44391099 44391896 0.000000e+00 952
29 TraesCS7A01G390200 chr6B 87.940 796 74 9 5227 6016 44497814 44497035 0.000000e+00 918
30 TraesCS7A01G390200 chr6B 88.073 654 65 8 5227 5873 44795150 44794503 0.000000e+00 763
31 TraesCS7A01G390200 chr6B 88.618 369 39 2 4207 4572 45804473 45804105 4.920000e-121 446
32 TraesCS7A01G390200 chr6B 93.411 258 11 4 3909 4166 45804720 45804469 1.820000e-100 377
33 TraesCS7A01G390200 chr6B 86.262 313 27 10 6056 6368 45802860 45802564 6.690000e-85 326
34 TraesCS7A01G390200 chr6B 85.443 316 30 8 6056 6369 44497034 44496733 1.450000e-81 315
35 TraesCS7A01G390200 chr6B 83.492 315 33 10 6056 6368 44391897 44392194 6.830000e-70 276
36 TraesCS7A01G390200 chr2B 88.287 1016 94 7 5021 6016 83408395 83409405 0.000000e+00 1194
37 TraesCS7A01G390200 chr2B 88.543 803 77 9 5220 6016 195644154 195644947 0.000000e+00 959
38 TraesCS7A01G390200 chr2B 92.248 258 13 4 3909 4166 83407214 83407464 6.590000e-95 359
39 TraesCS7A01G390200 chr2B 87.413 286 27 8 4581 4862 1978464 1978744 3.110000e-83 320
40 TraesCS7A01G390200 chr2B 87.645 259 30 1 4207 4463 83407460 83407718 4.050000e-77 300
41 TraesCS7A01G390200 chr2B 84.790 309 31 9 6056 6362 195644948 195645242 5.240000e-76 296
42 TraesCS7A01G390200 chr6A 97.398 269 6 1 3069 3336 586802514 586802246 2.270000e-124 457
43 TraesCS7A01G390200 chr6A 96.667 270 8 1 3074 3342 169184442 169184711 1.370000e-121 448
44 TraesCS7A01G390200 chr5A 97.048 271 8 0 3068 3338 385384143 385383873 2.270000e-124 457
45 TraesCS7A01G390200 chr5A 98.099 263 3 1 3075 3335 598682815 598683077 2.270000e-124 457
46 TraesCS7A01G390200 chr5A 97.368 266 4 2 3075 3339 556734461 556734724 3.800000e-122 449
47 TraesCS7A01G390200 chr2A 97.736 265 4 2 3072 3335 746759126 746759389 8.180000e-124 455
48 TraesCS7A01G390200 chr4A 98.069 259 5 0 3077 3335 96473532 96473274 1.060000e-122 451
49 TraesCS7A01G390200 chr3D 88.850 287 27 5 4581 4863 369413424 369413709 1.430000e-91 348
50 TraesCS7A01G390200 chr3D 87.063 286 30 7 4581 4862 46555755 46556037 4.030000e-82 316
51 TraesCS7A01G390200 chr5D 87.762 286 30 5 4581 4862 521720861 521721145 5.170000e-86 329
52 TraesCS7A01G390200 chr3A 86.942 291 27 7 4581 4863 490622604 490622891 4.030000e-82 316
53 TraesCS7A01G390200 chr4D 87.063 286 26 10 4581 4862 319249185 319248907 5.210000e-81 313


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 TraesCS7A01G390200 chr7A 566526802 566533716 6914 False 12770.000000 12770 100.000000 1 6915 1 chr7A.!!$F9 6914
1 TraesCS7A01G390200 chr7A 566279795 566280853 1058 False 1109.000000 1109 85.638000 104 1217 1 chr7A.!!$F2 1113
2 TraesCS7A01G390200 chr7A 566303594 566304652 1058 False 1109.000000 1109 85.638000 104 1217 1 chr7A.!!$F4 1113
3 TraesCS7A01G390200 chr7A 566327197 566328255 1058 False 1109.000000 1109 85.638000 104 1217 1 chr7A.!!$F6 1113
4 TraesCS7A01G390200 chr7A 566263131 566264189 1058 False 1103.000000 1103 85.550000 104 1217 1 chr7A.!!$F1 1113
5 TraesCS7A01G390200 chr7A 566292091 566293150 1059 False 1099.000000 1099 85.474000 104 1217 1 chr7A.!!$F3 1113
6 TraesCS7A01G390200 chr7A 566339467 566340501 1034 False 1031.000000 1031 84.740000 104 1204 1 chr7A.!!$F7 1100
7 TraesCS7A01G390200 chr7A 566315419 566316403 984 False 977.000000 977 84.725000 104 1143 1 chr7A.!!$F5 1039
8 TraesCS7A01G390200 chr7D 500614409 500621387 6978 False 2081.600000 4636 95.535600 1 6915 5 chr7D.!!$F2 6914
9 TraesCS7A01G390200 chr7D 500251213 500251839 626 False 861.000000 861 91.244000 570 1217 1 chr7D.!!$F1 647
10 TraesCS7A01G390200 chr7B 528746788 528754662 7874 False 1589.166667 2686 92.498167 1 6912 6 chr7B.!!$F2 6911
11 TraesCS7A01G390200 chr7B 663046670 663047761 1091 True 646.000000 1029 86.369500 5220 6368 2 chr7B.!!$R1 1148
12 TraesCS7A01G390200 chr6B 44794503 44795150 647 True 763.000000 763 88.073000 5227 5873 1 chr6B.!!$R1 646
13 TraesCS7A01G390200 chr6B 45802564 45804720 2156 True 623.500000 1345 89.381250 3909 6368 4 chr6B.!!$R3 2459
14 TraesCS7A01G390200 chr6B 44496733 44497814 1081 True 616.500000 918 86.691500 5227 6369 2 chr6B.!!$R2 1142
15 TraesCS7A01G390200 chr6B 44391099 44392194 1095 False 614.000000 952 85.922000 5220 6368 2 chr6B.!!$F1 1148
16 TraesCS7A01G390200 chr2B 195644154 195645242 1088 False 627.500000 959 86.666500 5220 6362 2 chr2B.!!$F3 1142
17 TraesCS7A01G390200 chr2B 83407214 83409405 2191 False 617.666667 1194 89.393333 3909 6016 3 chr2B.!!$F2 2107

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
933 1221 0.601841 GACGCGGTCAAAAGGGAGAA 60.602 55.000 12.47 0.0 32.09 2.87 F
1634 1922 0.878086 GCTAGATCGCAGAGGCAACC 60.878 60.000 0.00 0.0 43.63 3.77 F
3047 3486 1.133025 CAGGCATGGATCGTGGTTTTC 59.867 52.381 0.00 0.0 0.00 2.29 F
4309 4756 0.184692 TTGGCAGTGGTCCATTCACA 59.815 50.000 0.00 0.0 37.58 3.58 F
4703 5515 1.000060 GAGCCAAGTGCATGCAGAAAA 60.000 47.619 23.41 0.0 44.83 2.29 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1880 2169 0.874390 GGCGCTCACACAGATTTCAA 59.126 50.0 7.64 0.0 0.00 2.69 R
3514 3956 1.428869 AGAAGTGACCAAGTCAGGCT 58.571 50.0 0.00 0.0 43.57 4.58 R
4630 5441 0.249447 GTGGCTTGCACTTCCCAAAC 60.249 55.0 0.00 0.0 0.00 2.93 R
5783 7209 0.550914 TCTCCTGGCCTTGTTGTGTT 59.449 50.0 3.32 0.0 0.00 3.32 R
6162 7605 1.635663 GAAACGTGATGCAGACCGGG 61.636 60.0 6.32 0.0 0.00 5.73 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
168 170 1.264020 CACATGATAAATCACCGCCGG 59.736 52.381 0.00 0.00 40.03 6.13
201 203 5.667466 ACCATCATGCAGAAATTTGATTCC 58.333 37.500 0.00 0.00 0.00 3.01
203 205 6.126883 ACCATCATGCAGAAATTTGATTCCAT 60.127 34.615 0.00 0.00 0.00 3.41
345 365 1.134310 TGCATGTCTAGGGCACATCTG 60.134 52.381 0.00 0.00 31.83 2.90
365 385 8.037382 CATCTGGATGTGCCTTAGTTATTATG 57.963 38.462 2.69 0.00 37.63 1.90
371 391 7.148340 GGATGTGCCTTAGTTATTATGCATCTC 60.148 40.741 0.19 0.00 32.28 2.75
398 418 9.918630 AATGACTCAATCAAACATAAAAAGGAG 57.081 29.630 0.00 0.00 41.93 3.69
401 422 9.965824 GACTCAATCAAACATAAAAAGGAGAAA 57.034 29.630 0.00 0.00 0.00 2.52
481 502 6.000246 TGTTCAATATCAGGGCACATCTAA 58.000 37.500 0.00 0.00 0.00 2.10
631 917 1.145571 TGTTCTTGGGTAACAGGCCT 58.854 50.000 0.00 0.00 39.74 5.19
697 983 2.173519 CCACAAATGAGCTTGGGTGAT 58.826 47.619 0.00 0.00 0.00 3.06
721 1007 2.997952 TAACGCGACAAAGCCCAGCA 62.998 55.000 15.93 0.00 0.00 4.41
726 1012 0.734889 CGACAAAGCCCAGCAATAGG 59.265 55.000 0.00 0.00 0.00 2.57
750 1036 5.416013 GGTTGCTAGAGCTGTCCTTTTATTT 59.584 40.000 2.72 0.00 42.66 1.40
933 1221 0.601841 GACGCGGTCAAAAGGGAGAA 60.602 55.000 12.47 0.00 32.09 2.87
1634 1922 0.878086 GCTAGATCGCAGAGGCAACC 60.878 60.000 0.00 0.00 43.63 3.77
1643 1931 2.446435 GCAGAGGCAACCCATTTCTAA 58.554 47.619 0.00 0.00 40.72 2.10
1650 1938 4.040339 AGGCAACCCATTTCTAAGGTTTTG 59.960 41.667 0.00 0.00 41.97 2.44
1666 1954 3.425094 GGTTTTGGGTTGCGTTGTTTTTC 60.425 43.478 0.00 0.00 0.00 2.29
1729 2017 1.522668 CGCTGGATTTGTGGTGAGAA 58.477 50.000 0.00 0.00 0.00 2.87
1841 2130 5.636837 TCGGTTCTGCTAACATTATTTTGC 58.363 37.500 5.14 0.00 0.00 3.68
1946 2235 9.220767 GAGTTAAATGTTGTTCTTCTAGACCAT 57.779 33.333 0.00 0.00 0.00 3.55
2042 2463 4.506654 GCATAGAGTACGGGTTTGTGTATG 59.493 45.833 0.00 0.00 0.00 2.39
2064 2485 6.449635 TGTTGATATGGCATTACTGGTTTC 57.550 37.500 4.78 0.00 0.00 2.78
2065 2486 5.948758 TGTTGATATGGCATTACTGGTTTCA 59.051 36.000 4.78 0.00 0.00 2.69
2103 2524 5.177696 GCGTTTCTCTAGACTTGTGATTTGT 59.822 40.000 0.00 0.00 0.00 2.83
2118 2539 5.970612 TGTGATTTGTGTTCGAAGTTCAATG 59.029 36.000 0.00 0.00 0.00 2.82
2146 2567 6.019156 TGGCGACAAAGCTCTTTAAAATTTTG 60.019 34.615 13.76 0.00 37.44 2.44
2213 2634 8.268850 AGTATTGTGTGTGGATCAATTTAGTC 57.731 34.615 0.00 0.00 34.35 2.59
2248 2669 6.036577 CCAGCATTTGGGTATTTTAGTTGT 57.963 37.500 0.00 0.00 43.75 3.32
2429 2850 3.447944 GCTAGGCTACTTTCCAGTACTGT 59.552 47.826 21.18 5.19 34.06 3.55
2523 2945 9.579932 GGAAATCATAAGATGGGAGTTAGAAAT 57.420 33.333 0.00 0.00 33.90 2.17
2538 2960 7.093945 GGAGTTAGAAATGATTGCCCTGTTTTA 60.094 37.037 0.00 0.00 0.00 1.52
2612 3034 1.630369 TCAGCTAGTTGGCAAGGATGT 59.370 47.619 0.00 0.00 34.17 3.06
2613 3035 1.741706 CAGCTAGTTGGCAAGGATGTG 59.258 52.381 0.00 0.00 34.17 3.21
2614 3036 1.630369 AGCTAGTTGGCAAGGATGTGA 59.370 47.619 0.00 0.00 34.17 3.58
2615 3037 2.012673 GCTAGTTGGCAAGGATGTGAG 58.987 52.381 0.00 0.00 0.00 3.51
2616 3038 2.355108 GCTAGTTGGCAAGGATGTGAGA 60.355 50.000 0.00 0.00 0.00 3.27
2617 3039 2.957402 AGTTGGCAAGGATGTGAGAA 57.043 45.000 0.00 0.00 0.00 2.87
2618 3040 3.446442 AGTTGGCAAGGATGTGAGAAT 57.554 42.857 0.00 0.00 0.00 2.40
2619 3041 4.574674 AGTTGGCAAGGATGTGAGAATA 57.425 40.909 0.00 0.00 0.00 1.75
2620 3042 5.121380 AGTTGGCAAGGATGTGAGAATAT 57.879 39.130 0.00 0.00 0.00 1.28
2621 3043 4.885907 AGTTGGCAAGGATGTGAGAATATG 59.114 41.667 0.00 0.00 0.00 1.78
2741 3173 3.067601 GGGTTTTGGTTAGGCATAATCCG 59.932 47.826 0.00 0.00 0.00 4.18
2755 3187 5.581605 GCATAATCCGTATGGCCATAATTG 58.418 41.667 27.04 18.36 40.15 2.32
2756 3188 5.356751 GCATAATCCGTATGGCCATAATTGA 59.643 40.000 27.04 21.48 40.15 2.57
2881 3313 1.668826 ACCAGGTTGATTCCAGGCTA 58.331 50.000 0.00 0.00 37.62 3.93
2888 3320 5.888161 CAGGTTGATTCCAGGCTAGTTAATT 59.112 40.000 0.00 0.00 0.00 1.40
2896 3328 6.824958 TCCAGGCTAGTTAATTCTGGTAAT 57.175 37.500 0.00 0.00 43.83 1.89
2958 3390 5.299279 ACACCTTCGATTTCACATGTTCTTT 59.701 36.000 0.00 0.00 0.00 2.52
2961 3393 6.183360 ACCTTCGATTTCACATGTTCTTTTGT 60.183 34.615 0.00 0.00 0.00 2.83
2962 3394 7.012894 ACCTTCGATTTCACATGTTCTTTTGTA 59.987 33.333 0.00 0.00 0.00 2.41
2963 3395 7.323656 CCTTCGATTTCACATGTTCTTTTGTAC 59.676 37.037 0.00 0.00 0.00 2.90
2964 3396 7.252965 TCGATTTCACATGTTCTTTTGTACA 57.747 32.000 0.00 0.00 34.32 2.90
2965 3397 7.351981 TCGATTTCACATGTTCTTTTGTACAG 58.648 34.615 0.00 0.00 33.35 2.74
2966 3398 7.011950 TCGATTTCACATGTTCTTTTGTACAGT 59.988 33.333 0.00 0.00 33.35 3.55
2967 3399 8.279800 CGATTTCACATGTTCTTTTGTACAGTA 58.720 33.333 0.00 0.00 33.35 2.74
3047 3486 1.133025 CAGGCATGGATCGTGGTTTTC 59.867 52.381 0.00 0.00 0.00 2.29
3074 3516 6.237901 TGCTCTTTTGTGGTGATTAGTATGT 58.762 36.000 0.00 0.00 0.00 2.29
3075 3517 7.390823 TGCTCTTTTGTGGTGATTAGTATGTA 58.609 34.615 0.00 0.00 0.00 2.29
3076 3518 7.333423 TGCTCTTTTGTGGTGATTAGTATGTAC 59.667 37.037 0.00 0.00 0.00 2.90
3077 3519 7.549488 GCTCTTTTGTGGTGATTAGTATGTACT 59.451 37.037 0.00 0.00 40.24 2.73
3078 3520 8.997621 TCTTTTGTGGTGATTAGTATGTACTC 57.002 34.615 0.00 0.00 37.73 2.59
3079 3521 8.038944 TCTTTTGTGGTGATTAGTATGTACTCC 58.961 37.037 0.00 0.00 37.73 3.85
3080 3522 5.864418 TGTGGTGATTAGTATGTACTCCC 57.136 43.478 0.00 0.00 37.73 4.30
3081 3523 5.525484 TGTGGTGATTAGTATGTACTCCCT 58.475 41.667 0.00 0.00 37.73 4.20
3082 3524 5.597182 TGTGGTGATTAGTATGTACTCCCTC 59.403 44.000 0.00 0.00 37.73 4.30
3083 3525 5.010820 GTGGTGATTAGTATGTACTCCCTCC 59.989 48.000 0.00 0.00 37.73 4.30
3084 3526 4.217983 GGTGATTAGTATGTACTCCCTCCG 59.782 50.000 0.00 0.00 37.73 4.63
3085 3527 4.826183 GTGATTAGTATGTACTCCCTCCGT 59.174 45.833 0.00 0.00 37.73 4.69
3086 3528 5.301298 GTGATTAGTATGTACTCCCTCCGTT 59.699 44.000 0.00 0.00 37.73 4.44
3087 3529 5.895534 TGATTAGTATGTACTCCCTCCGTTT 59.104 40.000 0.00 0.00 37.73 3.60
3088 3530 6.381994 TGATTAGTATGTACTCCCTCCGTTTT 59.618 38.462 0.00 0.00 37.73 2.43
3089 3531 6.610075 TTAGTATGTACTCCCTCCGTTTTT 57.390 37.500 0.00 0.00 37.73 1.94
3090 3532 7.716799 TTAGTATGTACTCCCTCCGTTTTTA 57.283 36.000 0.00 0.00 37.73 1.52
3091 3533 6.803366 AGTATGTACTCCCTCCGTTTTTAT 57.197 37.500 0.00 0.00 0.00 1.40
3092 3534 7.191593 AGTATGTACTCCCTCCGTTTTTATT 57.808 36.000 0.00 0.00 0.00 1.40
3093 3535 7.627311 AGTATGTACTCCCTCCGTTTTTATTT 58.373 34.615 0.00 0.00 0.00 1.40
3094 3536 8.761689 AGTATGTACTCCCTCCGTTTTTATTTA 58.238 33.333 0.00 0.00 0.00 1.40
3095 3537 9.038803 GTATGTACTCCCTCCGTTTTTATTTAG 57.961 37.037 0.00 0.00 0.00 1.85
3096 3538 7.008021 TGTACTCCCTCCGTTTTTATTTAGT 57.992 36.000 0.00 0.00 0.00 2.24
3097 3539 7.099120 TGTACTCCCTCCGTTTTTATTTAGTC 58.901 38.462 0.00 0.00 0.00 2.59
3098 3540 6.370186 ACTCCCTCCGTTTTTATTTAGTCT 57.630 37.500 0.00 0.00 0.00 3.24
3099 3541 6.171213 ACTCCCTCCGTTTTTATTTAGTCTG 58.829 40.000 0.00 0.00 0.00 3.51
3100 3542 4.939439 TCCCTCCGTTTTTATTTAGTCTGC 59.061 41.667 0.00 0.00 0.00 4.26
3101 3543 4.698304 CCCTCCGTTTTTATTTAGTCTGCA 59.302 41.667 0.00 0.00 0.00 4.41
3102 3544 5.357032 CCCTCCGTTTTTATTTAGTCTGCAT 59.643 40.000 0.00 0.00 0.00 3.96
3103 3545 6.540914 CCCTCCGTTTTTATTTAGTCTGCATA 59.459 38.462 0.00 0.00 0.00 3.14
3104 3546 7.228706 CCCTCCGTTTTTATTTAGTCTGCATAT 59.771 37.037 0.00 0.00 0.00 1.78
3105 3547 8.621286 CCTCCGTTTTTATTTAGTCTGCATATT 58.379 33.333 0.00 0.00 0.00 1.28
3108 3550 9.382244 CCGTTTTTATTTAGTCTGCATATTAGC 57.618 33.333 0.00 0.00 0.00 3.09
3114 3556 9.627123 TTATTTAGTCTGCATATTAGCTTTGGT 57.373 29.630 0.00 0.00 34.99 3.67
3115 3557 7.553881 TTTAGTCTGCATATTAGCTTTGGTC 57.446 36.000 0.00 0.00 34.99 4.02
3116 3558 5.102953 AGTCTGCATATTAGCTTTGGTCA 57.897 39.130 0.00 0.00 34.99 4.02
3117 3559 5.500234 AGTCTGCATATTAGCTTTGGTCAA 58.500 37.500 0.00 0.00 34.99 3.18
3118 3560 5.945784 AGTCTGCATATTAGCTTTGGTCAAA 59.054 36.000 0.00 0.00 34.99 2.69
3140 3582 7.812309 AAAGTCAAGCTTTGTAAGTTTTGAC 57.188 32.000 19.57 19.57 45.00 3.18
3144 3586 8.548433 GTCAAGCTTTGTAAGTTTTGACTAAG 57.452 34.615 19.73 5.96 43.65 2.18
3145 3587 8.182227 GTCAAGCTTTGTAAGTTTTGACTAAGT 58.818 33.333 19.73 0.00 43.65 2.24
3146 3588 8.736244 TCAAGCTTTGTAAGTTTTGACTAAGTT 58.264 29.630 0.00 0.00 32.90 2.66
3147 3589 9.353999 CAAGCTTTGTAAGTTTTGACTAAGTTT 57.646 29.630 0.00 0.00 34.21 2.66
3279 3721 8.865590 TTTCTATAAACTTGGTCAAACTTTGC 57.134 30.769 0.00 0.00 0.00 3.68
3280 3722 7.575414 TCTATAAACTTGGTCAAACTTTGCA 57.425 32.000 0.00 0.00 0.00 4.08
3281 3723 8.001881 TCTATAAACTTGGTCAAACTTTGCAA 57.998 30.769 0.00 0.00 0.00 4.08
3282 3724 8.470805 TCTATAAACTTGGTCAAACTTTGCAAA 58.529 29.630 12.14 12.14 0.00 3.68
3283 3725 5.861222 AAACTTGGTCAAACTTTGCAAAG 57.139 34.783 32.53 32.53 41.73 2.77
3294 3736 3.769536 ACTTTGCAAAGTTTGACTTCGG 58.230 40.909 33.85 11.40 46.52 4.30
3295 3737 3.192633 ACTTTGCAAAGTTTGACTTCGGT 59.807 39.130 33.85 12.02 46.52 4.69
3296 3738 3.414549 TTGCAAAGTTTGACTTCGGTC 57.585 42.857 19.82 0.00 37.47 4.79
3309 3751 5.405331 GACTTCGGTCAAACCTAATATGC 57.595 43.478 0.00 0.00 43.91 3.14
3310 3752 4.839121 ACTTCGGTCAAACCTAATATGCA 58.161 39.130 0.00 0.00 35.66 3.96
3311 3753 4.876107 ACTTCGGTCAAACCTAATATGCAG 59.124 41.667 0.00 0.00 35.66 4.41
3312 3754 4.746535 TCGGTCAAACCTAATATGCAGA 57.253 40.909 0.00 0.00 35.66 4.26
3313 3755 4.439057 TCGGTCAAACCTAATATGCAGAC 58.561 43.478 0.00 0.00 35.66 3.51
3314 3756 4.161565 TCGGTCAAACCTAATATGCAGACT 59.838 41.667 0.00 0.00 35.66 3.24
3315 3757 5.361571 TCGGTCAAACCTAATATGCAGACTA 59.638 40.000 0.00 0.00 35.66 2.59
3316 3758 6.046593 CGGTCAAACCTAATATGCAGACTAA 58.953 40.000 0.00 0.00 35.66 2.24
3317 3759 6.537301 CGGTCAAACCTAATATGCAGACTAAA 59.463 38.462 0.00 0.00 35.66 1.85
3318 3760 7.226720 CGGTCAAACCTAATATGCAGACTAAAT 59.773 37.037 0.00 0.00 35.66 1.40
3319 3761 9.555727 GGTCAAACCTAATATGCAGACTAAATA 57.444 33.333 0.00 0.00 34.73 1.40
3330 3772 6.817765 TGCAGACTAAATAAAAACAGAGGG 57.182 37.500 0.00 0.00 0.00 4.30
3331 3773 6.539173 TGCAGACTAAATAAAAACAGAGGGA 58.461 36.000 0.00 0.00 0.00 4.20
3332 3774 6.655003 TGCAGACTAAATAAAAACAGAGGGAG 59.345 38.462 0.00 0.00 0.00 4.30
3333 3775 6.655425 GCAGACTAAATAAAAACAGAGGGAGT 59.345 38.462 0.00 0.00 0.00 3.85
3383 3825 7.686434 ACCTACAGAAAACTTAGGCAAGAATA 58.314 34.615 4.13 0.00 36.57 1.75
3501 3943 7.959658 ATGGAAAATGTGATTACATGGAGAA 57.040 32.000 3.56 0.00 46.54 2.87
3897 4341 0.405585 TTCAAGGAGCTTTCCTGGGG 59.594 55.000 0.00 0.00 40.59 4.96
4058 4503 6.437162 AGCATGCATCCTTTTTAGAGGTAAAA 59.563 34.615 21.98 0.00 36.52 1.52
4219 4664 7.012421 GTGATAGTTCTGTCTTGAACCTTTTGT 59.988 37.037 4.08 0.00 45.25 2.83
4224 4669 4.094294 TCTGTCTTGAACCTTTTGTCGTTG 59.906 41.667 0.00 0.00 0.00 4.10
4297 4744 3.776969 TCATAAGGATCTGAGTTGGCAGT 59.223 43.478 0.00 0.00 37.20 4.40
4309 4756 0.184692 TTGGCAGTGGTCCATTCACA 59.815 50.000 0.00 0.00 37.58 3.58
4315 4762 3.005554 CAGTGGTCCATTCACAGCTTAG 58.994 50.000 0.00 0.00 37.58 2.18
4322 4769 5.938125 GGTCCATTCACAGCTTAGAAGTTAA 59.062 40.000 4.17 0.00 0.00 2.01
4377 4824 6.604171 TGGAGGATGTACATATGCTTGATTT 58.396 36.000 8.71 0.00 0.00 2.17
4394 4841 9.979578 TGCTTGATTTGACTAATGTATGTTTTT 57.020 25.926 0.00 0.00 0.00 1.94
4476 4923 8.232913 ACAACCGACAATATATAGCCAAAAAT 57.767 30.769 0.00 0.00 0.00 1.82
4534 5334 8.641498 AATTGAAATAATGTCTGAGTGACCTT 57.359 30.769 0.00 0.00 44.75 3.50
4563 5363 7.858382 TCCATGTTGTTAGACGTAATGTTTTTG 59.142 33.333 0.00 0.00 0.00 2.44
4578 5378 3.117663 TGTTTTTGAGCTGGTACTCCCTT 60.118 43.478 0.00 0.00 35.72 3.95
4622 5433 3.833070 AGGACAGATTACGGAGTGAAGTT 59.167 43.478 0.00 0.00 45.73 2.66
4703 5515 1.000060 GAGCCAAGTGCATGCAGAAAA 60.000 47.619 23.41 0.00 44.83 2.29
4745 5557 6.704493 TGAATGTTATAGGTCTTGATTACCGC 59.296 38.462 0.00 0.00 42.15 5.68
4829 5642 8.783833 TCTTTTGTGGACAAATTTTGAATGAA 57.216 26.923 15.81 0.00 44.30 2.57
4949 6022 7.626999 TGGTCCCAGTTAATACATATAAGCT 57.373 36.000 0.00 0.00 0.00 3.74
4952 6025 9.032624 GGTCCCAGTTAATACATATAAGCTAGA 57.967 37.037 0.00 0.00 0.00 2.43
5047 6121 8.600625 TGTTTCGTAGCAAGTTATCATTGTATC 58.399 33.333 0.00 0.00 0.00 2.24
5119 6193 4.584874 TCTTGATGAAATACGCAAAGGGA 58.415 39.130 0.00 0.00 0.00 4.20
5292 6711 6.654582 TGTCACATGTTGCTTGTTATATCTGT 59.345 34.615 0.00 0.00 0.00 3.41
5502 6926 3.651803 TGTTTCTTAAATGGTTGCCGG 57.348 42.857 0.00 0.00 0.00 6.13
5620 7044 1.273886 GCTCCTTCGGATATCACTCCC 59.726 57.143 4.83 0.00 31.04 4.30
5783 7209 2.046411 ACGTGCGGGCATTCATCA 60.046 55.556 0.00 0.00 0.00 3.07
5925 7357 4.709397 CCAGAGAGTCTAATCTCAACAGGT 59.291 45.833 9.81 0.00 46.81 4.00
6022 7459 3.876320 CTGAGCTCTCTTGGATTTTAGCC 59.124 47.826 16.19 0.00 0.00 3.93
6073 7510 0.974383 CGCCCCTCGGGTATTAAGAT 59.026 55.000 0.55 0.00 46.51 2.40
6162 7605 0.318445 CTTGCACTTGTGCTTCCTGC 60.318 55.000 23.53 0.00 43.25 4.85
6377 7822 1.016653 GCAGCGTCTCTTTCTGACCC 61.017 60.000 0.00 0.00 0.00 4.46
6466 7912 0.250124 ACATTTTCCTGTCACGGCGA 60.250 50.000 16.62 0.00 0.00 5.54
6490 7936 4.095410 TCACTTTTCTGTGCAAGTGTTG 57.905 40.909 12.42 0.00 46.76 3.33
6494 7940 0.395586 TTCTGTGCAAGTGTTGGCCT 60.396 50.000 3.32 0.00 0.00 5.19
6588 8034 8.860780 AAGAATTGCTTTTCACTTCTATCTCT 57.139 30.769 0.00 0.00 41.89 3.10
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
67 69 0.868406 CTTGTTTGACCTCCACGCTC 59.132 55.000 0.00 0.00 0.00 5.03
168 170 6.455360 TTCTGCATGATGGTTTTCTTATCC 57.545 37.500 0.00 0.00 0.00 2.59
219 221 6.001460 CCCCGGCAAGATAAATATCAACTTA 58.999 40.000 0.00 0.00 35.17 2.24
303 310 7.784037 TGCAAAAGCATGGACTTTCAATATAT 58.216 30.769 0.00 0.00 38.92 0.86
322 329 2.284754 TGTGCCCTAGACATGCAAAA 57.715 45.000 0.00 0.00 36.65 2.44
345 365 6.656693 AGATGCATAATAACTAAGGCACATCC 59.343 38.462 0.00 0.00 33.67 3.51
363 383 6.152154 TGTTTGATTGAGTCATTGAGATGCAT 59.848 34.615 0.00 0.00 36.54 3.96
365 385 5.946298 TGTTTGATTGAGTCATTGAGATGC 58.054 37.500 0.00 0.00 36.54 3.91
371 391 9.695526 TCCTTTTTATGTTTGATTGAGTCATTG 57.304 29.630 0.00 0.00 36.54 2.82
403 424 6.935167 AGAATCATGCGGGTATTTTCTTTTT 58.065 32.000 0.00 0.00 0.00 1.94
404 425 6.405842 GGAGAATCATGCGGGTATTTTCTTTT 60.406 38.462 0.00 0.00 36.25 2.27
405 426 5.067805 GGAGAATCATGCGGGTATTTTCTTT 59.932 40.000 0.00 0.00 36.25 2.52
406 427 4.580580 GGAGAATCATGCGGGTATTTTCTT 59.419 41.667 0.00 0.00 36.25 2.52
407 428 4.137543 GGAGAATCATGCGGGTATTTTCT 58.862 43.478 0.00 0.00 36.25 2.52
408 429 3.882888 TGGAGAATCATGCGGGTATTTTC 59.117 43.478 0.00 0.00 36.25 2.29
559 842 9.278978 TGCACTAACTTTTTAATATCTGTGACA 57.721 29.630 0.00 0.00 0.00 3.58
560 843 9.543018 GTGCACTAACTTTTTAATATCTGTGAC 57.457 33.333 10.32 0.00 0.00 3.67
561 844 9.278978 TGTGCACTAACTTTTTAATATCTGTGA 57.721 29.630 19.41 0.00 0.00 3.58
562 845 9.546909 CTGTGCACTAACTTTTTAATATCTGTG 57.453 33.333 19.41 0.00 0.00 3.66
563 846 9.502091 TCTGTGCACTAACTTTTTAATATCTGT 57.498 29.630 19.41 0.00 0.00 3.41
592 875 1.923356 TTTGTGGGGGAGCAAGAATC 58.077 50.000 0.00 0.00 0.00 2.52
593 876 2.181975 CATTTGTGGGGGAGCAAGAAT 58.818 47.619 0.00 0.00 0.00 2.40
697 983 2.745728 GCTTTGTCGCGTTAGCCTA 58.254 52.632 5.77 0.00 41.18 3.93
721 1007 2.436173 GGACAGCTCTAGCAACCCTATT 59.564 50.000 4.54 0.00 45.16 1.73
726 1012 2.481289 AAAGGACAGCTCTAGCAACC 57.519 50.000 4.54 4.61 45.16 3.77
732 1018 5.175859 CACCGAAATAAAAGGACAGCTCTA 58.824 41.667 0.00 0.00 0.00 2.43
750 1036 4.500205 CCCTATTTAGTTCGCATACACCGA 60.500 45.833 0.00 0.00 0.00 4.69
933 1221 0.667792 GCCTTCTCGTCTCGTTTGCT 60.668 55.000 0.00 0.00 0.00 3.91
1589 1877 2.728690 TGAAGCAAGCATCGCAAAAT 57.271 40.000 0.00 0.00 0.00 1.82
1634 1922 4.314961 GCAACCCAAAACCTTAGAAATGG 58.685 43.478 0.00 0.00 0.00 3.16
1643 1931 0.899019 AACAACGCAACCCAAAACCT 59.101 45.000 0.00 0.00 0.00 3.50
1666 1954 2.358898 CCCTGGATCACAAAATTAGGCG 59.641 50.000 0.00 0.00 0.00 5.52
1729 2017 4.796038 TTAGCACGTTTAGTTAGCTCCT 57.204 40.909 0.00 0.00 34.47 3.69
1880 2169 0.874390 GGCGCTCACACAGATTTCAA 59.126 50.000 7.64 0.00 0.00 2.69
1883 2172 1.317613 TTTGGCGCTCACACAGATTT 58.682 45.000 7.64 0.00 0.00 2.17
1946 2235 5.955959 TGTGGCTACTAAGGAACAGATAAGA 59.044 40.000 0.64 0.00 0.00 2.10
2042 2463 6.095440 ACTGAAACCAGTAATGCCATATCAAC 59.905 38.462 0.00 0.00 42.66 3.18
2064 2485 3.560068 AGAAACGCTACCTTGACAAACTG 59.440 43.478 0.00 0.00 0.00 3.16
2065 2486 3.805207 AGAAACGCTACCTTGACAAACT 58.195 40.909 0.00 0.00 0.00 2.66
2103 2524 2.548057 GCCAGTCATTGAACTTCGAACA 59.452 45.455 0.00 0.00 0.00 3.18
2118 2539 1.230324 AAAGAGCTTTGTCGCCAGTC 58.770 50.000 0.00 0.00 0.00 3.51
2190 2611 6.315144 CCGACTAAATTGATCCACACACAATA 59.685 38.462 0.00 0.00 34.48 1.90
2343 2764 6.553953 TGTCCATGGTGCTAACTAAGATTA 57.446 37.500 12.58 0.00 0.00 1.75
2351 2772 4.584327 ACTTTTTGTCCATGGTGCTAAC 57.416 40.909 12.58 2.23 0.00 2.34
2429 2850 5.925506 TCATATTACGGAGAACCAGTTCA 57.074 39.130 12.76 0.00 41.84 3.18
2476 2897 9.893305 ATTTCCTTCTTAATTACACAAACTTCG 57.107 29.630 0.00 0.00 0.00 3.79
2504 2925 7.449704 GGCAATCATTTCTAACTCCCATCTTAT 59.550 37.037 0.00 0.00 0.00 1.73
2508 2929 4.279420 GGGCAATCATTTCTAACTCCCATC 59.721 45.833 0.00 0.00 0.00 3.51
2612 3034 3.885901 ACTAGAGCTCACGCATATTCTCA 59.114 43.478 17.77 0.00 39.10 3.27
2613 3035 4.497473 ACTAGAGCTCACGCATATTCTC 57.503 45.455 17.77 0.00 39.10 2.87
2614 3036 6.582677 ATTACTAGAGCTCACGCATATTCT 57.417 37.500 17.77 0.00 39.10 2.40
2615 3037 6.090088 CCAATTACTAGAGCTCACGCATATTC 59.910 42.308 17.77 0.00 39.10 1.75
2616 3038 5.928839 CCAATTACTAGAGCTCACGCATATT 59.071 40.000 17.77 5.43 39.10 1.28
2617 3039 5.011125 ACCAATTACTAGAGCTCACGCATAT 59.989 40.000 17.77 0.00 39.10 1.78
2618 3040 4.341235 ACCAATTACTAGAGCTCACGCATA 59.659 41.667 17.77 0.00 39.10 3.14
2619 3041 3.133003 ACCAATTACTAGAGCTCACGCAT 59.867 43.478 17.77 0.00 39.10 4.73
2620 3042 2.496070 ACCAATTACTAGAGCTCACGCA 59.504 45.455 17.77 0.00 39.10 5.24
2621 3043 3.166489 ACCAATTACTAGAGCTCACGC 57.834 47.619 17.77 0.00 0.00 5.34
2687 3119 5.982890 AACCCAAATCTAGTTGAACATGG 57.017 39.130 0.00 0.00 0.00 3.66
2741 3173 9.463443 GATAAAACACTTCAATTATGGCCATAC 57.537 33.333 25.39 3.73 0.00 2.39
3047 3486 1.915141 ATCACCACAAAAGAGCAGGG 58.085 50.000 0.00 0.00 0.00 4.45
3074 3516 7.325694 CAGACTAAATAAAAACGGAGGGAGTA 58.674 38.462 0.00 0.00 0.00 2.59
3075 3517 6.171213 CAGACTAAATAAAAACGGAGGGAGT 58.829 40.000 0.00 0.00 0.00 3.85
3076 3518 5.064834 GCAGACTAAATAAAAACGGAGGGAG 59.935 44.000 0.00 0.00 0.00 4.30
3077 3519 4.939439 GCAGACTAAATAAAAACGGAGGGA 59.061 41.667 0.00 0.00 0.00 4.20
3078 3520 4.698304 TGCAGACTAAATAAAAACGGAGGG 59.302 41.667 0.00 0.00 0.00 4.30
3079 3521 5.873179 TGCAGACTAAATAAAAACGGAGG 57.127 39.130 0.00 0.00 0.00 4.30
3082 3524 9.382244 GCTAATATGCAGACTAAATAAAAACGG 57.618 33.333 0.00 0.00 0.00 4.44
3088 3530 9.627123 ACCAAAGCTAATATGCAGACTAAATAA 57.373 29.630 0.00 0.00 34.99 1.40
3089 3531 9.273016 GACCAAAGCTAATATGCAGACTAAATA 57.727 33.333 0.00 0.00 34.99 1.40
3090 3532 7.775093 TGACCAAAGCTAATATGCAGACTAAAT 59.225 33.333 0.00 0.00 34.99 1.40
3091 3533 7.109501 TGACCAAAGCTAATATGCAGACTAAA 58.890 34.615 0.00 0.00 34.99 1.85
3092 3534 6.649155 TGACCAAAGCTAATATGCAGACTAA 58.351 36.000 0.00 0.00 34.99 2.24
3093 3535 6.233905 TGACCAAAGCTAATATGCAGACTA 57.766 37.500 0.00 0.00 34.99 2.59
3094 3536 5.102953 TGACCAAAGCTAATATGCAGACT 57.897 39.130 0.00 0.00 34.99 3.24
3095 3537 5.818136 TTGACCAAAGCTAATATGCAGAC 57.182 39.130 0.00 0.00 34.99 3.51
3096 3538 6.441093 CTTTGACCAAAGCTAATATGCAGA 57.559 37.500 9.25 0.00 40.94 4.26
3119 3561 8.182227 ACTTAGTCAAAACTTACAAAGCTTGAC 58.818 33.333 18.45 18.45 45.61 3.18
3120 3562 8.276252 ACTTAGTCAAAACTTACAAAGCTTGA 57.724 30.769 0.00 0.00 36.92 3.02
3121 3563 8.911247 AACTTAGTCAAAACTTACAAAGCTTG 57.089 30.769 0.00 0.00 36.92 4.01
3253 3695 9.308318 GCAAAGTTTGACCAAGTTTATAGAAAA 57.692 29.630 19.82 0.00 36.07 2.29
3254 3696 8.470805 TGCAAAGTTTGACCAAGTTTATAGAAA 58.529 29.630 19.82 0.00 36.07 2.52
3255 3697 8.001881 TGCAAAGTTTGACCAAGTTTATAGAA 57.998 30.769 19.82 0.00 36.07 2.10
3256 3698 7.575414 TGCAAAGTTTGACCAAGTTTATAGA 57.425 32.000 19.82 0.00 36.07 1.98
3257 3699 8.641499 TTTGCAAAGTTTGACCAAGTTTATAG 57.359 30.769 19.82 0.00 36.07 1.31
3258 3700 8.254508 ACTTTGCAAAGTTTGACCAAGTTTATA 58.745 29.630 33.85 0.00 46.52 0.98
3259 3701 7.102993 ACTTTGCAAAGTTTGACCAAGTTTAT 58.897 30.769 33.85 10.04 46.52 1.40
3260 3702 6.459923 ACTTTGCAAAGTTTGACCAAGTTTA 58.540 32.000 33.85 0.00 46.52 2.01
3261 3703 5.304778 ACTTTGCAAAGTTTGACCAAGTTT 58.695 33.333 33.85 11.08 46.52 2.66
3262 3704 4.893608 ACTTTGCAAAGTTTGACCAAGTT 58.106 34.783 33.85 11.27 46.52 2.66
3263 3705 4.535526 ACTTTGCAAAGTTTGACCAAGT 57.464 36.364 33.85 17.53 46.52 3.16
3272 3714 6.128842 GACCGAAGTCAAACTTTGCAAAGTT 61.129 40.000 39.24 39.24 45.31 2.66
3273 3715 4.674362 GACCGAAGTCAAACTTTGCAAAGT 60.674 41.667 33.85 33.85 45.47 2.66
3274 3716 3.769536 ACCGAAGTCAAACTTTGCAAAG 58.230 40.909 32.53 32.53 38.80 2.77
3275 3717 3.765026 GACCGAAGTCAAACTTTGCAAA 58.235 40.909 12.14 12.14 38.80 3.68
3276 3718 3.414549 GACCGAAGTCAAACTTTGCAA 57.585 42.857 0.00 0.00 38.80 4.08
3287 3729 4.873827 TGCATATTAGGTTTGACCGAAGTC 59.126 41.667 0.00 0.00 44.90 3.01
3288 3730 4.839121 TGCATATTAGGTTTGACCGAAGT 58.161 39.130 0.00 0.00 44.90 3.01
3289 3731 5.006746 GTCTGCATATTAGGTTTGACCGAAG 59.993 44.000 0.00 0.00 44.90 3.79
3290 3732 4.873827 GTCTGCATATTAGGTTTGACCGAA 59.126 41.667 0.00 0.00 44.90 4.30
3291 3733 4.161565 AGTCTGCATATTAGGTTTGACCGA 59.838 41.667 0.00 0.00 44.90 4.69
3292 3734 4.442706 AGTCTGCATATTAGGTTTGACCG 58.557 43.478 0.00 0.00 44.90 4.79
3293 3735 7.859325 TTTAGTCTGCATATTAGGTTTGACC 57.141 36.000 0.00 0.00 38.99 4.02
3304 3746 9.125026 CCCTCTGTTTTTATTTAGTCTGCATAT 57.875 33.333 0.00 0.00 0.00 1.78
3305 3747 8.325787 TCCCTCTGTTTTTATTTAGTCTGCATA 58.674 33.333 0.00 0.00 0.00 3.14
3306 3748 7.175104 TCCCTCTGTTTTTATTTAGTCTGCAT 58.825 34.615 0.00 0.00 0.00 3.96
3307 3749 6.539173 TCCCTCTGTTTTTATTTAGTCTGCA 58.461 36.000 0.00 0.00 0.00 4.41
3308 3750 6.655425 ACTCCCTCTGTTTTTATTTAGTCTGC 59.345 38.462 0.00 0.00 0.00 4.26
3309 3751 9.892130 ATACTCCCTCTGTTTTTATTTAGTCTG 57.108 33.333 0.00 0.00 0.00 3.51
3319 3761 9.892130 CTAGAATGTAATACTCCCTCTGTTTTT 57.108 33.333 0.00 0.00 0.00 1.94
3320 3762 8.487028 CCTAGAATGTAATACTCCCTCTGTTTT 58.513 37.037 0.00 0.00 0.00 2.43
3321 3763 7.419172 GCCTAGAATGTAATACTCCCTCTGTTT 60.419 40.741 0.00 0.00 0.00 2.83
3322 3764 6.042208 GCCTAGAATGTAATACTCCCTCTGTT 59.958 42.308 0.00 0.00 0.00 3.16
3323 3765 5.540719 GCCTAGAATGTAATACTCCCTCTGT 59.459 44.000 0.00 0.00 0.00 3.41
3324 3766 5.777732 AGCCTAGAATGTAATACTCCCTCTG 59.222 44.000 0.00 0.00 0.00 3.35
3325 3767 5.971493 AGCCTAGAATGTAATACTCCCTCT 58.029 41.667 0.00 0.00 0.00 3.69
3326 3768 6.673839 AAGCCTAGAATGTAATACTCCCTC 57.326 41.667 0.00 0.00 0.00 4.30
3327 3769 8.743636 ATAAAGCCTAGAATGTAATACTCCCT 57.256 34.615 0.00 0.00 0.00 4.20
3328 3770 8.041919 GGATAAAGCCTAGAATGTAATACTCCC 58.958 40.741 0.00 0.00 0.00 4.30
3329 3771 8.041919 GGGATAAAGCCTAGAATGTAATACTCC 58.958 40.741 0.00 0.00 0.00 3.85
3330 3772 8.594550 TGGGATAAAGCCTAGAATGTAATACTC 58.405 37.037 0.00 0.00 0.00 2.59
3331 3773 8.506196 TGGGATAAAGCCTAGAATGTAATACT 57.494 34.615 0.00 0.00 0.00 2.12
3332 3774 9.569122 TTTGGGATAAAGCCTAGAATGTAATAC 57.431 33.333 0.00 0.00 0.00 1.89
3333 3775 9.569122 GTTTGGGATAAAGCCTAGAATGTAATA 57.431 33.333 0.00 0.00 0.00 0.98
3383 3825 5.536497 AGATTTTTAAGGGTCCTGGATGT 57.464 39.130 0.00 0.00 0.00 3.06
3501 3943 8.823220 ACCAAGTCAGGCTAATTTAAATATGT 57.177 30.769 0.01 0.00 0.00 2.29
3514 3956 1.428869 AGAAGTGACCAAGTCAGGCT 58.571 50.000 0.00 0.00 43.57 4.58
3742 4186 9.478019 CGCTGAACAAAGTAATATGAAAGTTAG 57.522 33.333 0.00 0.00 0.00 2.34
3897 4341 3.193691 TCACCTGTTAGAAGTCTGCTAGC 59.806 47.826 8.10 8.10 0.00 3.42
4058 4503 3.562973 CAGTTGCACACATCAGAGTTCTT 59.437 43.478 0.00 0.00 0.00 2.52
4109 4554 8.613060 AAAGCATATATCAATTCACGAGACAT 57.387 30.769 0.00 0.00 0.00 3.06
4219 4664 3.878699 ACATAATCATCAGCATGCAACGA 59.121 39.130 21.98 13.57 34.76 3.85
4224 4669 3.243267 TGCACACATAATCATCAGCATGC 60.243 43.478 10.51 10.51 34.76 4.06
4281 4728 0.326264 ACCACTGCCAACTCAGATCC 59.674 55.000 0.00 0.00 37.51 3.36
4297 4744 3.327757 ACTTCTAAGCTGTGAATGGACCA 59.672 43.478 0.00 0.00 0.00 4.02
4309 4756 7.988028 GTGGTGATTCCTATTAACTTCTAAGCT 59.012 37.037 0.00 0.00 37.07 3.74
4315 4762 6.415573 ACCTGTGGTGATTCCTATTAACTTC 58.584 40.000 0.00 0.00 32.98 3.01
4445 4892 9.175312 TGGCTATATATTGTCGGTTGTTTAAAA 57.825 29.630 0.00 0.00 0.00 1.52
4534 5334 7.499321 ACATTACGTCTAACAACATGGAAAA 57.501 32.000 0.00 0.00 0.00 2.29
4563 5363 1.205893 CACTGAAGGGAGTACCAGCTC 59.794 57.143 0.00 0.00 43.89 4.09
4628 5439 0.681175 GGCTTGCACTTCCCAAACAT 59.319 50.000 0.00 0.00 0.00 2.71
4629 5440 0.685785 TGGCTTGCACTTCCCAAACA 60.686 50.000 0.00 0.00 0.00 2.83
4630 5441 0.249447 GTGGCTTGCACTTCCCAAAC 60.249 55.000 0.00 0.00 0.00 2.93
4631 5442 1.398958 GGTGGCTTGCACTTCCCAAA 61.399 55.000 0.00 0.00 0.00 3.28
4829 5642 5.121142 CCGTCCACGAATAAGTGTACATTTT 59.879 40.000 9.05 5.01 43.02 1.82
4852 5665 6.948589 AGTTAGTTTCTTGAATACTCCCTCC 58.051 40.000 0.00 0.00 0.00 4.30
4949 6022 7.490657 AACCACTAACACATCCATAACTCTA 57.509 36.000 0.00 0.00 0.00 2.43
4952 6025 6.650120 CCTAACCACTAACACATCCATAACT 58.350 40.000 0.00 0.00 0.00 2.24
5006 6080 5.924475 ACGAAACAAGTTATTGGACAGAG 57.076 39.130 0.00 0.00 40.97 3.35
5047 6121 0.457853 TTACTCGGCAAGCTACTGCG 60.458 55.000 4.36 0.97 43.60 5.18
5255 6672 7.365741 AGCAACATGTGACAGAATAAAAGAAG 58.634 34.615 0.00 0.00 0.00 2.85
5292 6711 4.695396 ACTTGCATTCAATTCAGCACAAA 58.305 34.783 0.00 0.00 36.62 2.83
5332 6751 7.170965 TGCTCTAGAGGAACAGAAAAATCAAT 58.829 34.615 21.23 0.00 0.00 2.57
5347 6767 4.583907 TCAGACTTCATGATGCTCTAGAGG 59.416 45.833 21.23 3.60 0.00 3.69
5502 6926 3.926527 TCAGGTATCGATGATTATTGCGC 59.073 43.478 8.54 0.00 0.00 6.09
5620 7044 3.260483 CTAGAAGCAGCAGCCGCG 61.260 66.667 0.00 0.00 45.49 6.46
5783 7209 0.550914 TCTCCTGGCCTTGTTGTGTT 59.449 50.000 3.32 0.00 0.00 3.32
6073 7510 4.094294 CCAGATCTCGCCGATTTTTACAAA 59.906 41.667 0.00 0.00 30.84 2.83
6162 7605 1.635663 GAAACGTGATGCAGACCGGG 61.636 60.000 6.32 0.00 0.00 5.73
6377 7822 7.979444 TCTTGTAATAACTCTTGAAACCCTG 57.021 36.000 0.00 0.00 0.00 4.45
6406 7852 4.760047 CGTGTTCAGAGGCCGGGG 62.760 72.222 2.18 0.00 0.00 5.73
6466 7912 3.004752 ACTTGCACAGAAAAGTGAGGT 57.995 42.857 0.00 0.00 42.05 3.85
6494 7940 3.133464 GCCAGCGTTGCCAGCATA 61.133 61.111 0.00 0.00 37.01 3.14
6506 7952 3.730061 CGAACAAGAAATGATGAGCCAGC 60.730 47.826 0.00 0.00 0.00 4.85
6588 8034 4.160439 ACTCGATTGGCTCAGTTCAGATAA 59.840 41.667 0.00 0.00 0.00 1.75
6865 9208 2.788640 AATGGCCATGCATGCGACC 61.789 57.895 21.63 20.29 0.00 4.79
6866 9209 1.590525 CAATGGCCATGCATGCGAC 60.591 57.895 21.63 16.57 0.00 5.19
6867 9210 2.787567 CCAATGGCCATGCATGCGA 61.788 57.895 21.63 13.81 0.00 5.10
6868 9211 2.279851 CCAATGGCCATGCATGCG 60.280 61.111 21.63 15.04 0.00 4.73
6869 9212 2.590575 GCCAATGGCCATGCATGC 60.591 61.111 21.63 15.56 44.06 4.06


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

AutoCloner maintained by Alex Coulton.