Multiple sequence alignment - TraesCS5D01G212600

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 TraesCS5D01G212600 chr5D 100.000 5396 0 0 748 6143 321894743 321900138 0.000000e+00 9965
1 TraesCS5D01G212600 chr5D 86.355 1627 159 28 753 2336 321884361 321885967 0.000000e+00 1716
2 TraesCS5D01G212600 chr5D 100.000 501 0 0 1 501 321893996 321894496 0.000000e+00 926
3 TraesCS5D01G212600 chr5D 83.427 1068 93 38 4624 5629 321888366 321889411 0.000000e+00 915
4 TraesCS5D01G212600 chr5D 82.455 1100 121 31 3276 4333 321887075 321888144 0.000000e+00 896
5 TraesCS5D01G212600 chr5D 82.632 950 99 20 2528 3462 321886009 321886907 0.000000e+00 780
6 TraesCS5D01G212600 chr5D 89.835 364 34 3 1 362 214288508 214288146 1.210000e-126 464
7 TraesCS5D01G212600 chr5D 87.845 362 41 3 2 361 193199101 193199461 7.360000e-114 422
8 TraesCS5D01G212600 chr5D 94.805 154 8 0 2334 2487 430524560 430524713 2.210000e-59 241
9 TraesCS5D01G212600 chr5A 94.663 2698 117 14 748 3433 417038797 417041479 0.000000e+00 4159
10 TraesCS5D01G212600 chr5A 86.790 1620 155 31 753 2336 417024971 417026567 0.000000e+00 1751
11 TraesCS5D01G212600 chr5A 94.449 1099 49 2 3237 4323 417041508 417042606 0.000000e+00 1681
12 TraesCS5D01G212600 chr5A 87.543 875 84 17 4357 5227 417042604 417043457 0.000000e+00 989
13 TraesCS5D01G212600 chr5A 84.295 1057 92 32 4624 5624 417028838 417029876 0.000000e+00 965
14 TraesCS5D01G212600 chr5A 82.524 1133 127 36 3237 4327 417027510 417028613 0.000000e+00 929
15 TraesCS5D01G212600 chr5A 84.274 744 87 12 2734 3462 417026782 417027510 0.000000e+00 699
16 TraesCS5D01G212600 chr5A 94.335 406 21 2 97 501 417038363 417038767 6.760000e-174 621
17 TraesCS5D01G212600 chr5A 85.033 608 51 19 5567 6143 417044080 417044678 3.190000e-162 582
18 TraesCS5D01G212600 chr5A 87.912 364 40 4 1 361 248821125 248820763 5.690000e-115 425
19 TraesCS5D01G212600 chr5A 93.805 226 14 0 3237 3462 417041358 417041583 2.120000e-89 340
20 TraesCS5D01G212600 chr5A 94.118 153 9 0 2334 2486 17305664 17305816 3.700000e-57 233
21 TraesCS5D01G212600 chr5A 94.118 153 9 0 2334 2486 17325124 17325276 3.700000e-57 233
22 TraesCS5D01G212600 chr5A 79.355 310 31 15 5268 5544 417043452 417043761 2.920000e-43 187
23 TraesCS5D01G212600 chr5B 90.336 2949 171 50 3237 6143 373040376 373043252 0.000000e+00 3762
24 TraesCS5D01G212600 chr5B 95.097 1591 72 5 748 2336 373037958 373039544 0.000000e+00 2501
25 TraesCS5D01G212600 chr5B 86.230 1634 157 30 748 2336 372862265 372863875 0.000000e+00 1709
26 TraesCS5D01G212600 chr5B 91.992 949 64 6 2486 3433 373039552 373040489 0.000000e+00 1321
27 TraesCS5D01G212600 chr5B 83.779 1085 120 33 3278 4326 372865244 372866308 0.000000e+00 977
28 TraesCS5D01G212600 chr5B 83.298 934 110 19 2520 3437 372863909 372864812 0.000000e+00 819
29 TraesCS5D01G212600 chr5B 84.270 712 75 17 4496 5182 372866376 372867075 0.000000e+00 660
30 TraesCS5D01G212600 chr5B 90.354 508 38 5 1 498 373037441 373037947 0.000000e+00 656
31 TraesCS5D01G212600 chr5B 84.950 299 25 7 5165 5443 372867242 372867540 1.010000e-72 285
32 TraesCS5D01G212600 chr3B 90.838 2041 110 33 4128 6143 585726718 585728706 0.000000e+00 2662
33 TraesCS5D01G212600 chr3B 93.785 1593 92 7 748 2336 585720173 585721762 0.000000e+00 2386
34 TraesCS5D01G212600 chr3B 92.562 968 56 5 2479 3433 585721763 585722727 0.000000e+00 1375
35 TraesCS5D01G212600 chr3B 93.627 612 33 2 3237 3842 585722600 585723211 0.000000e+00 909
36 TraesCS5D01G212600 chr3B 93.103 232 6 3 3907 4131 585725382 585725610 1.280000e-86 331
37 TraesCS5D01G212600 chr3B 88.356 146 11 2 3316 3455 585722523 585722668 2.940000e-38 171
38 TraesCS5D01G212600 chr2D 85.540 1805 201 35 3423 5197 43651330 43653104 0.000000e+00 1832
39 TraesCS5D01G212600 chr2D 86.520 1595 162 25 748 2332 43837135 43835584 0.000000e+00 1705
40 TraesCS5D01G212600 chr2D 85.045 1685 208 23 3538 5200 43834420 43832758 0.000000e+00 1676
41 TraesCS5D01G212600 chr2D 87.193 976 103 7 2486 3454 43650227 43651187 0.000000e+00 1090
42 TraesCS5D01G212600 chr2D 86.401 978 108 9 2486 3455 43835572 43834612 0.000000e+00 1046
43 TraesCS5D01G212600 chr2D 84.304 790 88 16 1017 1800 43648974 43649733 0.000000e+00 739
44 TraesCS5D01G212600 chr2D 89.759 498 44 5 1844 2338 43649728 43650221 1.120000e-176 630
45 TraesCS5D01G212600 chr2D 87.029 239 27 4 748 984 43648740 43648976 3.650000e-67 267
46 TraesCS5D01G212600 chr2A 84.739 1802 219 33 3423 5194 46074197 46075972 0.000000e+00 1753
47 TraesCS5D01G212600 chr2A 85.759 1601 175 24 748 2338 46071539 46073096 0.000000e+00 1644
48 TraesCS5D01G212600 chr2A 86.168 976 111 9 2486 3454 46073102 46074060 0.000000e+00 1033
49 TraesCS5D01G212600 chr2A 94.702 151 7 1 2334 2484 13356083 13356232 3.700000e-57 233
50 TraesCS5D01G212600 chr2A 93.377 151 9 1 2334 2484 13330110 13330259 8.010000e-54 222
51 TraesCS5D01G212600 chr2B 88.204 373 30 5 1 361 232497737 232498107 3.400000e-117 433
52 TraesCS5D01G212600 chr2B 86.740 362 46 2 1 361 232517649 232518009 9.590000e-108 401
53 TraesCS5D01G212600 chr6D 88.187 364 30 8 1 361 106985878 106986231 7.360000e-114 422
54 TraesCS5D01G212600 chr6A 86.667 360 43 5 5 361 359675394 359675751 1.600000e-105 394
55 TraesCS5D01G212600 chr7D 94.805 154 8 0 2334 2487 633740549 633740702 2.210000e-59 241
56 TraesCS5D01G212600 chr4B 94.118 153 8 1 2334 2486 6958642 6958793 1.330000e-56 231
57 TraesCS5D01G212600 chr1A 92.857 154 11 0 2334 2487 564081836 564081989 2.230000e-54 224


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 TraesCS5D01G212600 chr5D 321893996 321900138 6142 False 5445.500000 9965 100.000000 1 6143 2 chr5D.!!$F4 6142
1 TraesCS5D01G212600 chr5D 321884361 321889411 5050 False 1076.750000 1716 83.717250 753 5629 4 chr5D.!!$F3 4876
2 TraesCS5D01G212600 chr5A 417038363 417044678 6315 False 1222.714286 4159 89.883286 97 6143 7 chr5A.!!$F4 6046
3 TraesCS5D01G212600 chr5A 417024971 417029876 4905 False 1086.000000 1751 84.470750 753 5624 4 chr5A.!!$F3 4871
4 TraesCS5D01G212600 chr5B 373037441 373043252 5811 False 2060.000000 3762 91.944750 1 6143 4 chr5B.!!$F2 6142
5 TraesCS5D01G212600 chr5B 372862265 372867540 5275 False 890.000000 1709 84.505400 748 5443 5 chr5B.!!$F1 4695
6 TraesCS5D01G212600 chr3B 585720173 585728706 8533 False 1305.666667 2662 92.045167 748 6143 6 chr3B.!!$F1 5395
7 TraesCS5D01G212600 chr2D 43832758 43837135 4377 True 1475.666667 1705 85.988667 748 5200 3 chr2D.!!$R1 4452
8 TraesCS5D01G212600 chr2D 43648740 43653104 4364 False 911.600000 1832 86.765000 748 5197 5 chr2D.!!$F1 4449
9 TraesCS5D01G212600 chr2A 46071539 46075972 4433 False 1476.666667 1753 85.555333 748 5194 3 chr2A.!!$F3 4446

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
90 100 0.606401 CCACGCCCTGATGTCTTGTT 60.606 55.0 0.00 0.00 0.00 2.83 F
1237 1270 0.676184 GATCATGCTAGAGGACGGCA 59.324 55.0 0.00 0.00 40.32 5.69 F
2666 2746 0.397957 ACGGCCCCCTTGTTTTCTTT 60.398 50.0 0.00 0.00 0.00 2.52 F
3829 4840 0.519175 GCGTGTGTTGACGATGATGC 60.519 55.0 0.00 0.00 42.10 3.91 F
4376 8678 0.178921 AGGGTGGTGAGAGCTCTTCA 60.179 55.0 19.36 14.14 0.00 3.02 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1351 1384 0.038251 TGCAAGTCCGCTGAGTACAG 60.038 55.000 0.00 0.0 45.91 2.74 R
2975 3062 1.774254 AGTGTTGTGGATTCAGGACCA 59.226 47.619 0.00 0.0 0.00 4.02 R
4355 8657 0.689623 AAGAGCTCTCACCACCCTTG 59.310 55.000 18.55 0.0 0.00 3.61 R
4884 9243 0.747255 ATCACCTCCGATTCGTCCAG 59.253 55.000 5.20 0.0 0.00 3.86 R
5707 10720 1.068474 CAGTTCACCTTTACGCCTCG 58.932 55.000 0.00 0.0 0.00 4.63 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
34 35 2.680913 CGAAGAAGGGCAGCAACCG 61.681 63.158 0.00 0.00 0.00 4.44
90 100 0.606401 CCACGCCCTGATGTCTTGTT 60.606 55.000 0.00 0.00 0.00 2.83
126 136 2.035832 CCTTTTGCGTTGATTCCACCTT 59.964 45.455 0.00 0.00 0.00 3.50
139 150 4.870123 TTCCACCTTCCAAAATCACATG 57.130 40.909 0.00 0.00 0.00 3.21
159 170 7.228507 TCACATGTATTCCAAAATAATCCTCCG 59.771 37.037 0.00 0.00 0.00 4.63
205 216 6.992123 ACTTCGTTTGATATGGATATTCTGCA 59.008 34.615 0.00 0.00 0.00 4.41
493 504 2.543861 CCTTCGGTCGATGTATCAGTGG 60.544 54.545 0.00 0.00 0.00 4.00
986 1007 1.938585 AGACCCCATCTCTCGAACAA 58.061 50.000 0.00 0.00 28.16 2.83
1188 1218 2.417719 GAGGGTAATGCTAAGATGGCG 58.582 52.381 0.00 0.00 0.00 5.69
1222 1255 1.314867 GGGTGGGAGGAGGAGATCA 59.685 63.158 0.00 0.00 0.00 2.92
1227 1260 1.505098 TGGGAGGAGGAGATCATGCTA 59.495 52.381 0.00 0.00 29.85 3.49
1237 1270 0.676184 GATCATGCTAGAGGACGGCA 59.324 55.000 0.00 0.00 40.32 5.69
1546 1585 4.853468 TTTCATGCCCTAGTGGTGAATA 57.147 40.909 0.00 0.00 36.04 1.75
1601 1641 2.647875 CGGATCAGGCCGCTAGAG 59.352 66.667 0.00 0.00 45.38 2.43
1647 1689 6.992063 ACTGATATGAATGTTTGGTCAGTC 57.008 37.500 0.00 0.00 40.33 3.51
2409 2486 7.332557 TGGTATTCTTGTTAATGATGTACCGT 58.667 34.615 0.00 0.00 33.50 4.83
2410 2487 7.493320 TGGTATTCTTGTTAATGATGTACCGTC 59.507 37.037 0.00 0.00 33.50 4.79
2431 2508 5.278266 CGTCCTGTGTGGTGAATTTTGTATT 60.278 40.000 0.00 0.00 37.07 1.89
2637 2717 4.469945 AGAGGGAATGAGAATTTCGGTACA 59.530 41.667 0.00 0.00 0.00 2.90
2666 2746 0.397957 ACGGCCCCCTTGTTTTCTTT 60.398 50.000 0.00 0.00 0.00 2.52
2975 3062 4.918360 TGTGGAGGGGGTGGCAGT 62.918 66.667 0.00 0.00 0.00 4.40
3117 3207 2.030185 GCAGCTCCATGGATATGCAAAG 60.030 50.000 31.66 19.71 36.28 2.77
3164 3254 2.045634 ATCCTCGTCGACGGTGGA 60.046 61.111 36.16 36.16 42.63 4.02
3454 4441 1.697394 ATGCCCCCTCCATGTAGCA 60.697 57.895 0.00 0.00 34.28 3.49
3455 4442 1.070127 ATGCCCCCTCCATGTAGCAT 61.070 55.000 0.00 0.00 34.94 3.79
3473 4460 1.065636 CATGACTCCACAGAGCACCAT 60.066 52.381 0.00 0.00 44.65 3.55
3728 4724 5.104318 GGAGGGAGAAAGATAACAAGGTCAT 60.104 44.000 0.00 0.00 0.00 3.06
3812 4820 3.131223 TCTTCTTTCTCTGGTATCCTGCG 59.869 47.826 0.00 0.00 0.00 5.18
3829 4840 0.519175 GCGTGTGTTGACGATGATGC 60.519 55.000 0.00 0.00 42.10 3.91
3958 7104 1.705002 CCCACACCTCCCAAGACACA 61.705 60.000 0.00 0.00 0.00 3.72
3999 7145 2.509336 GCTGTCGGGGTCATCGTG 60.509 66.667 0.00 0.00 0.00 4.35
4376 8678 0.178921 AGGGTGGTGAGAGCTCTTCA 60.179 55.000 19.36 14.14 0.00 3.02
4638 8991 2.281345 CGGAGGGAGATGGCATGC 60.281 66.667 9.90 9.90 0.00 4.06
4639 8992 2.815945 CGGAGGGAGATGGCATGCT 61.816 63.158 18.92 1.44 0.00 3.79
4669 9022 1.749638 GCTCAGCTGATGCCAAGCT 60.750 57.895 18.63 0.00 41.31 3.74
4731 9084 2.982744 GAACGCAAGGGCAAGGCTC 61.983 63.158 0.00 0.00 46.39 4.70
4746 9099 1.003580 AGGCTCGAAAATCTTCTGGCA 59.996 47.619 0.00 0.00 33.64 4.92
4770 9123 2.266279 AGAAAATGGGGTCTTCGGAGA 58.734 47.619 0.00 0.00 0.00 3.71
4781 9137 2.590391 CTTCGGAGAGCAGCAGCCAT 62.590 60.000 0.00 0.00 43.56 4.40
4884 9243 3.453070 GAGGCTCCTGTCATCGCCC 62.453 68.421 2.15 0.00 43.48 6.13
4946 9305 1.350351 AGCTGGTGGCAGGATATGATC 59.650 52.381 0.00 0.00 44.79 2.92
5076 9486 4.095483 AGTTGTCTGTGCTTTCTGAACTTG 59.905 41.667 0.00 0.00 0.00 3.16
5098 9508 6.737254 TGAAATAAAAGGAGACATTCGTCC 57.263 37.500 0.00 0.00 43.73 4.79
5200 9817 7.343357 TGTTTTTCTTCTTCTTCCTGGAGTAA 58.657 34.615 0.00 0.00 0.00 2.24
5209 9826 0.323629 TCCTGGAGTAAACCAAGCGG 59.676 55.000 0.00 0.00 39.59 5.52
5307 9935 1.978454 GGAATCTGATCCTGCCCAAG 58.022 55.000 0.00 0.00 36.50 3.61
5334 9962 1.284982 CGGGTTGTGAGCAGTTCTCG 61.285 60.000 0.00 0.00 44.86 4.04
5415 10079 1.228245 TCCTGGTGAAACTGGCAGC 60.228 57.895 15.89 0.00 36.74 5.25
5474 10156 1.026182 TTCCACCATCATCAGCGCAC 61.026 55.000 11.47 0.00 0.00 5.34
5475 10157 1.746239 CCACCATCATCAGCGCACA 60.746 57.895 11.47 0.00 0.00 4.57
5517 10206 5.340803 TGTAAAGATGAACTCGGATTCTCG 58.659 41.667 2.03 0.00 0.00 4.04
5530 10219 2.449031 ATTCTCGGCGCACACAAGGA 62.449 55.000 10.83 0.00 0.00 3.36
5552 10248 4.564782 TGGAAGAGTCAAGATTGATGCT 57.435 40.909 0.00 0.00 39.73 3.79
5562 10258 9.495754 GAGTCAAGATTGATGCTATGTAAAAAC 57.504 33.333 0.00 0.00 39.73 2.43
5814 10831 2.712057 ATGCAGAACTTTTTGCCTCG 57.288 45.000 2.33 0.00 39.54 4.63
5844 10862 9.694137 AACTTATAAAATAGATACCGAGAGCAC 57.306 33.333 0.00 0.00 0.00 4.40
5882 10901 4.818546 CCAGCAACTGATAAAGATCCGAAT 59.181 41.667 0.00 0.00 32.44 3.34
6026 11049 2.224793 ACTTTCTGCACCTAAGGTTCCC 60.225 50.000 0.00 0.00 31.02 3.97
6075 11098 0.901580 ACCCGAAGCTTTCTCCGGTA 60.902 55.000 19.42 0.00 40.30 4.02
6115 11140 4.847444 GCCGAGGAAGAGCAGCCC 62.847 72.222 0.00 0.00 0.00 5.19
6116 11141 3.080121 CCGAGGAAGAGCAGCCCT 61.080 66.667 0.00 0.00 0.00 5.19
6117 11142 2.498726 CGAGGAAGAGCAGCCCTC 59.501 66.667 5.55 5.55 42.24 4.30
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
73 83 0.606401 CCAACAAGACATCAGGGCGT 60.606 55.000 0.00 0.00 0.00 5.68
81 91 1.703411 CCACAACCCCAACAAGACAT 58.297 50.000 0.00 0.00 0.00 3.06
90 100 4.938756 AGGAGGCCCACAACCCCA 62.939 66.667 0.00 0.00 33.88 4.96
159 170 8.311120 CGAAGTCCAAATGCGATAAAAATTTAC 58.689 33.333 0.00 0.00 0.00 2.01
230 241 1.073025 CAGTGCCCAGTGCCAGTTA 59.927 57.895 0.00 0.00 40.16 2.24
409 420 7.165977 GCTTATAAAAAGTAATGAAAGGAGCGC 59.834 37.037 0.00 0.00 0.00 5.92
760 771 1.113788 ATCCATGGTGAAAATGGCGG 58.886 50.000 12.58 0.00 43.70 6.13
852 865 1.351350 AGGAAGTGGCAGTTTAGTCCC 59.649 52.381 9.30 5.36 0.00 4.46
1188 1218 3.391382 CCGACCCACTCCCTCACC 61.391 72.222 0.00 0.00 0.00 4.02
1222 1255 1.141881 CGTTGCCGTCCTCTAGCAT 59.858 57.895 0.00 0.00 36.20 3.79
1237 1270 2.357517 CTTGTGCTCCTCGCCGTT 60.358 61.111 0.00 0.00 38.05 4.44
1351 1384 0.038251 TGCAAGTCCGCTGAGTACAG 60.038 55.000 0.00 0.00 45.91 2.74
1399 1432 2.600769 AGACGCCGACCCAGACTT 60.601 61.111 0.00 0.00 0.00 3.01
1601 1641 4.391830 TCGTTAGAGATGCATGGTGAAAAC 59.608 41.667 2.46 0.13 0.00 2.43
1647 1689 6.461110 TCGAGATGTAAACCCCTACTAAAG 57.539 41.667 0.00 0.00 0.00 1.85
2135 2199 8.154649 ACACAAGAGGAAACACATAAGTTAAG 57.845 34.615 0.00 0.00 0.00 1.85
2378 2455 9.113838 ACATCATTAACAAGAATACCATCAGAC 57.886 33.333 0.00 0.00 0.00 3.51
2389 2466 5.872617 CAGGACGGTACATCATTAACAAGAA 59.127 40.000 0.00 0.00 0.00 2.52
2409 2486 5.830457 TCAATACAAAATTCACCACACAGGA 59.170 36.000 0.00 0.00 41.22 3.86
2410 2487 6.083098 TCAATACAAAATTCACCACACAGG 57.917 37.500 0.00 0.00 45.67 4.00
2431 2508 3.051327 TCGCGAAACTTACAATCGTTCA 58.949 40.909 6.20 0.00 38.75 3.18
2448 2525 6.133392 CACCTTACATTAATTAACCATCGCG 58.867 40.000 0.00 0.00 0.00 5.87
2637 2717 2.189521 GGGGCCGTCGATGAACAT 59.810 61.111 6.11 0.00 0.00 2.71
2666 2746 3.002451 CCGTCCGTATGTGAAAACAAACA 59.998 43.478 0.00 0.00 0.00 2.83
2975 3062 1.774254 AGTGTTGTGGATTCAGGACCA 59.226 47.619 0.00 0.00 0.00 4.02
3105 3195 3.870538 ATCTCCTGCTTTGCATATCCA 57.129 42.857 0.00 0.00 38.13 3.41
3117 3207 7.475840 CAACAATTTCCTTTACTATCTCCTGC 58.524 38.462 0.00 0.00 0.00 4.85
3280 3451 2.832201 GCATGCAGGGGGCTTCTC 60.832 66.667 14.21 0.00 45.15 2.87
3454 4441 1.209019 GATGGTGCTCTGTGGAGTCAT 59.791 52.381 0.00 0.00 41.38 3.06
3455 4442 0.610174 GATGGTGCTCTGTGGAGTCA 59.390 55.000 0.00 0.00 41.38 3.41
3473 4460 3.208594 CTTTCGATGATCTGGCCATTGA 58.791 45.455 5.51 0.00 33.78 2.57
3812 4820 1.800586 ACAGCATCATCGTCAACACAC 59.199 47.619 0.00 0.00 0.00 3.82
3891 7037 1.352622 TGCCCAAGTGGTCAGGTTCT 61.353 55.000 0.00 0.00 36.04 3.01
3958 7104 1.746220 CGGAGACTCGATCTTCCTGTT 59.254 52.381 0.00 0.00 38.00 3.16
4355 8657 0.689623 AAGAGCTCTCACCACCCTTG 59.310 55.000 18.55 0.00 0.00 3.61
4376 8678 4.077822 CCATCTTCTGAGCCTTCTGTTTT 58.922 43.478 0.00 0.00 0.00 2.43
4669 9022 1.195442 TGTAGGATCAACCCGGCACA 61.195 55.000 0.00 0.00 40.05 4.57
4731 9084 4.488126 TCTTTGTGCCAGAAGATTTTCG 57.512 40.909 0.00 0.00 38.38 3.46
4746 9099 2.890945 CCGAAGACCCCATTTTCTTTGT 59.109 45.455 0.00 0.00 33.06 2.83
4781 9137 3.640407 GAGCCACTGGTGCCTCCA 61.640 66.667 0.88 0.00 45.01 3.86
4845 9204 1.949525 GCCATTGGTCACGCATATCTT 59.050 47.619 4.26 0.00 0.00 2.40
4884 9243 0.747255 ATCACCTCCGATTCGTCCAG 59.253 55.000 5.20 0.00 0.00 3.86
4946 9305 1.882623 GGAAAGTTGAGGCCAGACTTG 59.117 52.381 16.15 0.00 34.13 3.16
5051 9423 5.053145 AGTTCAGAAAGCACAGACAACTAG 58.947 41.667 0.00 0.00 0.00 2.57
5053 9425 3.878778 AGTTCAGAAAGCACAGACAACT 58.121 40.909 0.00 0.00 0.00 3.16
5076 9486 6.986904 AGGACGAATGTCTCCTTTTATTTC 57.013 37.500 0.00 0.00 44.83 2.17
5098 9508 5.047802 ACCAAACATGAGGAGCAAAACATAG 60.048 40.000 0.00 0.00 0.00 2.23
5182 9799 5.228945 TGGTTTACTCCAGGAAGAAGAAG 57.771 43.478 0.00 0.00 33.19 2.85
5209 9826 4.383173 TGGATGCATGATGATACACAGAC 58.617 43.478 2.46 0.00 0.00 3.51
5210 9827 4.693042 TGGATGCATGATGATACACAGA 57.307 40.909 2.46 0.00 0.00 3.41
5211 9828 5.278315 CCTTTGGATGCATGATGATACACAG 60.278 44.000 2.46 0.00 0.00 3.66
5212 9829 4.581409 CCTTTGGATGCATGATGATACACA 59.419 41.667 2.46 0.00 0.00 3.72
5307 9935 3.332493 CTCACAACCCGCTGCATGC 62.332 63.158 11.82 11.82 38.57 4.06
5313 9941 1.598130 GAACTGCTCACAACCCGCT 60.598 57.895 0.00 0.00 0.00 5.52
5415 10079 2.126228 TAGCCGGCGAGTTTGACG 60.126 61.111 23.20 0.00 41.03 4.35
5517 10206 1.926511 CTTCCATCCTTGTGTGCGCC 61.927 60.000 4.18 0.00 0.00 6.53
5530 10219 5.113446 AGCATCAATCTTGACTCTTCCAT 57.887 39.130 0.00 0.00 40.49 3.41
5552 10248 5.998981 TCCGAGCTTTTCTGGTTTTTACATA 59.001 36.000 0.00 0.00 0.00 2.29
5562 10258 4.034510 GTGAACATATCCGAGCTTTTCTGG 59.965 45.833 0.00 0.00 0.00 3.86
5707 10720 1.068474 CAGTTCACCTTTACGCCTCG 58.932 55.000 0.00 0.00 0.00 4.63
5814 10831 9.485206 TCTCGGTATCTATTTTATAAGTTTGGC 57.515 33.333 0.00 0.00 0.00 4.52
5844 10862 2.840974 CTGGTAGGACCTGCAAACG 58.159 57.895 12.04 0.00 39.58 3.60
5882 10901 6.599244 CCAGATTGTTCCTTTGCTATCTGTTA 59.401 38.462 0.00 0.00 40.63 2.41
5932 10951 3.733960 CTCGTGGGCTCGACGTGA 61.734 66.667 0.00 0.00 38.04 4.35
5951 10974 2.717809 GCCACTCGCTTCGTCGTTC 61.718 63.158 0.00 0.00 0.00 3.95
5957 10980 1.083489 TTTTATGGCCACTCGCTTCG 58.917 50.000 8.16 0.00 37.74 3.79
6026 11049 1.335324 CCAAAGTTGCGAGGAAAGCAG 60.335 52.381 0.00 0.00 46.01 4.24
6115 11140 2.099921 CCTGTAGTCCATGAAGACGGAG 59.900 54.545 0.00 0.00 41.83 4.63
6116 11141 2.100197 CCTGTAGTCCATGAAGACGGA 58.900 52.381 0.00 0.00 41.83 4.69
6117 11142 1.137086 CCCTGTAGTCCATGAAGACGG 59.863 57.143 0.00 0.00 41.83 4.79


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

AutoCloner maintained by Alex Coulton.