Multiple sequence alignment - TraesCS5B01G565800

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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 TraesCS5B01G565800 chr5B 100.000 3359 0 0 1 3359 710501484 710504842 0.000000e+00 6204.0
1 TraesCS5B01G565800 chr5B 91.761 352 29 0 2954 3305 163293118 163292767 1.080000e-134 490.0
2 TraesCS5B01G565800 chr5B 88.515 357 37 3 2954 3307 642797949 642797594 2.390000e-116 429.0
3 TraesCS5B01G565800 chr5B 81.237 485 74 10 1001 1481 710499188 710498717 3.160000e-100 375.0
4 TraesCS5B01G565800 chr5B 91.525 59 5 0 3301 3359 163292741 163292683 7.720000e-12 82.4
5 TraesCS5B01G565800 chr5D 90.878 1776 113 24 772 2504 560189908 560191677 0.000000e+00 2337.0
6 TraesCS5B01G565800 chr5D 76.855 1361 279 24 1001 2340 560187499 560186154 0.000000e+00 736.0
7 TraesCS5B01G565800 chr5D 84.902 563 76 9 5 564 560189249 560189805 8.140000e-156 560.0
8 TraesCS5B01G565800 chr4A 92.315 1093 83 1 1413 2504 604642221 604641129 0.000000e+00 1552.0
9 TraesCS5B01G565800 chr4A 94.282 857 45 4 2506 3359 662095179 662096034 0.000000e+00 1308.0
10 TraesCS5B01G565800 chr4A 83.757 1336 186 19 1019 2340 5813225 5811907 0.000000e+00 1236.0
11 TraesCS5B01G565800 chr4A 78.151 1341 256 21 1019 2339 5816697 5815374 0.000000e+00 819.0
12 TraesCS5B01G565800 chr4A 76.867 1366 273 28 1001 2340 604659700 604661048 0.000000e+00 732.0
13 TraesCS5B01G565800 chr4A 90.598 468 37 5 952 1419 604648022 604647562 6.160000e-172 614.0
14 TraesCS5B01G565800 chr4A 87.972 424 45 6 274 693 604650625 604650204 2.330000e-136 496.0
15 TraesCS5B01G565800 chr4A 88.816 304 25 6 674 969 604648341 604648039 6.850000e-97 364.0
16 TraesCS5B01G565800 chr4D 83.517 1359 189 21 1001 2340 464238230 464239572 0.000000e+00 1236.0
17 TraesCS5B01G565800 chr4D 78.284 1340 258 18 1019 2340 464234941 464236265 0.000000e+00 832.0
18 TraesCS5B01G565800 chr4D 89.796 49 4 1 582 630 187247090 187247137 1.010000e-05 62.1
19 TraesCS5B01G565800 chr4B 83.621 1276 174 21 1079 2334 580526801 580528061 0.000000e+00 1166.0
20 TraesCS5B01G565800 chr4B 80.234 1113 185 21 1019 2112 580385066 580386162 0.000000e+00 804.0
21 TraesCS5B01G565800 chr2D 76.686 1557 296 38 828 2340 557479431 557477898 0.000000e+00 802.0
22 TraesCS5B01G565800 chr1A 91.379 406 35 0 2954 3359 24773908 24773503 1.050000e-154 556.0
23 TraesCS5B01G565800 chr1A 76.068 351 56 14 287 628 44709131 44708800 1.250000e-34 158.0
24 TraesCS5B01G565800 chr2A 89.901 406 41 0 2954 3359 58994671 58994266 1.070000e-144 523.0
25 TraesCS5B01G565800 chr6A 88.972 399 44 0 2954 3352 36084538 36084140 8.370000e-136 494.0
26 TraesCS5B01G565800 chr7B 87.192 406 40 1 2954 3359 446327110 446327503 5.110000e-123 451.0
27 TraesCS5B01G565800 chr7B 89.474 342 30 3 2510 2845 446326664 446327005 8.610000e-116 427.0
28 TraesCS5B01G565800 chr7B 85.667 300 28 1 2954 3253 602107331 602107615 5.450000e-78 302.0
29 TraesCS5B01G565800 chr7B 100.000 39 0 0 3321 3359 602107691 602107729 4.650000e-09 73.1
30 TraesCS5B01G565800 chr7A 79.762 252 35 10 2971 3207 263737518 263737768 5.760000e-38 169.0
31 TraesCS5B01G565800 chr3A 73.012 415 73 23 2505 2893 700754215 700754616 3.540000e-20 110.0
32 TraesCS5B01G565800 chr1B 87.879 66 7 1 1 66 423766835 423766771 3.590000e-10 76.8


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 TraesCS5B01G565800 chr5B 710501484 710504842 3358 False 6204.000000 6204 100.000000 1 3359 1 chr5B.!!$F1 3358
1 TraesCS5B01G565800 chr5D 560189249 560191677 2428 False 1448.500000 2337 87.890000 5 2504 2 chr5D.!!$F1 2499
2 TraesCS5B01G565800 chr5D 560186154 560187499 1345 True 736.000000 736 76.855000 1001 2340 1 chr5D.!!$R1 1339
3 TraesCS5B01G565800 chr4A 604641129 604642221 1092 True 1552.000000 1552 92.315000 1413 2504 1 chr4A.!!$R1 1091
4 TraesCS5B01G565800 chr4A 662095179 662096034 855 False 1308.000000 1308 94.282000 2506 3359 1 chr4A.!!$F2 853
5 TraesCS5B01G565800 chr4A 5811907 5816697 4790 True 1027.500000 1236 80.954000 1019 2340 2 chr4A.!!$R2 1321
6 TraesCS5B01G565800 chr4A 604659700 604661048 1348 False 732.000000 732 76.867000 1001 2340 1 chr4A.!!$F1 1339
7 TraesCS5B01G565800 chr4A 604647562 604650625 3063 True 491.333333 614 89.128667 274 1419 3 chr4A.!!$R3 1145
8 TraesCS5B01G565800 chr4D 464234941 464239572 4631 False 1034.000000 1236 80.900500 1001 2340 2 chr4D.!!$F2 1339
9 TraesCS5B01G565800 chr4B 580526801 580528061 1260 False 1166.000000 1166 83.621000 1079 2334 1 chr4B.!!$F2 1255
10 TraesCS5B01G565800 chr4B 580385066 580386162 1096 False 804.000000 804 80.234000 1019 2112 1 chr4B.!!$F1 1093
11 TraesCS5B01G565800 chr2D 557477898 557479431 1533 True 802.000000 802 76.686000 828 2340 1 chr2D.!!$R1 1512
12 TraesCS5B01G565800 chr7B 446326664 446327503 839 False 439.000000 451 88.333000 2510 3359 2 chr7B.!!$F1 849

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
151 152 0.035534 TGCCTAGGCGATGCTTTCAA 60.036 50.0 28.28 4.00 45.51 2.69 F
746 2634 0.248054 CAAATGTATGCGCGGACCAC 60.248 55.0 8.83 7.83 0.00 4.16 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1174 3161 0.252284 AGGTCGGAGATGAGTTGGGT 60.252 55.0 0.0 0.0 40.67 4.51 R
2504 8110 0.249398 TTTCTAGCTTCGTCCCTGCC 59.751 55.0 0.0 0.0 0.00 4.85 R

All possible primers

Listed here are all possible primers based on the multiple sequence alignment and SNPs generated previously. A lower penalty score indicates a better primer. If the AutoCloner primers did not work during PCR or sequencing, these could be used as alternatives.

Download all possible primers: (Forward) (Reverse)
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
62 63 8.291191 TGCAACATATTGTAATTTCTGATGGA 57.709 30.769 0.00 0.00 38.17 3.41
103 104 1.993956 ACACTACCATGGCAGCAAAA 58.006 45.000 13.04 0.00 0.00 2.44
104 105 2.528564 ACACTACCATGGCAGCAAAAT 58.471 42.857 13.04 0.00 0.00 1.82
105 106 2.899256 ACACTACCATGGCAGCAAAATT 59.101 40.909 13.04 0.00 0.00 1.82
107 108 3.194116 CACTACCATGGCAGCAAAATTCT 59.806 43.478 13.04 0.00 0.00 2.40
108 109 2.754946 ACCATGGCAGCAAAATTCTG 57.245 45.000 13.04 0.00 34.79 3.02
113 114 4.970392 CAGCAAAATTCTGCCGCA 57.030 50.000 0.00 0.00 43.73 5.69
114 115 2.733127 CAGCAAAATTCTGCCGCAG 58.267 52.632 14.62 14.62 43.73 5.18
115 116 1.080298 AGCAAAATTCTGCCGCAGC 60.080 52.632 15.98 2.85 43.73 5.25
116 117 1.080298 GCAAAATTCTGCCGCAGCT 60.080 52.632 15.98 2.48 40.80 4.24
117 118 1.349259 GCAAAATTCTGCCGCAGCTG 61.349 55.000 15.98 10.11 40.80 4.24
118 119 1.080298 AAAATTCTGCCGCAGCTGC 60.080 52.632 29.12 29.12 40.80 5.25
119 120 1.808531 AAAATTCTGCCGCAGCTGCA 61.809 50.000 36.03 17.81 42.21 4.41
120 121 1.601419 AAATTCTGCCGCAGCTGCAT 61.601 50.000 36.03 19.31 42.21 3.96
121 122 1.601419 AATTCTGCCGCAGCTGCATT 61.601 50.000 36.03 23.68 42.21 3.56
122 123 0.749091 ATTCTGCCGCAGCTGCATTA 60.749 50.000 36.03 20.40 42.21 1.90
124 125 0.749091 TCTGCCGCAGCTGCATTATT 60.749 50.000 36.03 0.00 42.21 1.40
128 129 2.165234 TGCCGCAGCTGCATTATTTTTA 59.835 40.909 36.03 10.17 42.21 1.52
133 134 6.186785 CCGCAGCTGCATTATTTTTAATTTG 58.813 36.000 36.03 14.83 42.21 2.32
140 141 7.518848 GCTGCATTATTTTTAATTTGCCTAGGC 60.519 37.037 27.71 27.71 42.35 3.93
141 142 6.478344 TGCATTATTTTTAATTTGCCTAGGCG 59.522 34.615 28.28 9.33 45.51 5.52
143 144 7.384932 GCATTATTTTTAATTTGCCTAGGCGAT 59.615 33.333 28.28 21.02 45.51 4.58
144 145 8.702438 CATTATTTTTAATTTGCCTAGGCGATG 58.298 33.333 28.28 13.06 45.51 3.84
151 152 0.035534 TGCCTAGGCGATGCTTTCAA 60.036 50.000 28.28 4.00 45.51 2.69
153 154 2.158827 TGCCTAGGCGATGCTTTCAATA 60.159 45.455 28.28 3.20 45.51 1.90
155 156 3.070018 CCTAGGCGATGCTTTCAATAGG 58.930 50.000 0.00 0.00 0.00 2.57
158 159 1.680338 GCGATGCTTTCAATAGGGGT 58.320 50.000 0.00 0.00 0.00 4.95
159 160 1.334869 GCGATGCTTTCAATAGGGGTG 59.665 52.381 0.00 0.00 0.00 4.61
160 161 2.643551 CGATGCTTTCAATAGGGGTGT 58.356 47.619 0.00 0.00 0.00 4.16
165 166 5.975693 TGCTTTCAATAGGGGTGTTTAAG 57.024 39.130 0.00 0.00 0.00 1.85
169 170 6.349363 GCTTTCAATAGGGGTGTTTAAGACAG 60.349 42.308 0.00 0.00 39.39 3.51
170 171 5.174037 TCAATAGGGGTGTTTAAGACAGG 57.826 43.478 0.00 0.00 39.39 4.00
178 179 1.133945 TGTTTAAGACAGGCAGCCACA 60.134 47.619 15.80 3.23 33.40 4.17
185 186 1.073025 CAGGCAGCCACAGGTACAA 59.927 57.895 15.80 0.00 0.00 2.41
194 195 2.160813 GCCACAGGTACAAACATTACCG 59.839 50.000 0.00 0.00 43.45 4.02
202 203 0.885196 CAAACATTACCGGTGGTGGG 59.115 55.000 19.93 4.63 36.19 4.61
204 205 2.070399 AACATTACCGGTGGTGGGCA 62.070 55.000 19.93 0.00 36.19 5.36
220 221 3.599584 CAGCATGCCCTCAACTGG 58.400 61.111 15.66 0.00 30.92 4.00
234 235 3.814625 TCAACTGGTGACATGTTAGCAA 58.185 40.909 21.03 5.98 41.51 3.91
240 241 5.992025 TGGTGACATGTTAGCAATGGCGA 62.992 47.826 18.89 0.00 39.91 5.54
248 249 4.301505 GCAATGGCGAGAGGTCAA 57.698 55.556 0.00 0.00 31.29 3.18
252 253 0.749454 AATGGCGAGAGGTCAATGGC 60.749 55.000 0.00 0.00 31.29 4.40
256 257 2.514824 GAGAGGTCAATGGCGGGC 60.515 66.667 0.00 0.00 0.00 6.13
353 356 7.232534 ACTTTCATTGTTAGTTTTCCATAGCCA 59.767 33.333 0.00 0.00 0.00 4.75
425 428 9.216117 GAGCCTAAAAGAATACAACAAAGACTA 57.784 33.333 0.00 0.00 0.00 2.59
436 439 9.816354 AATACAACAAAGACTAAAACAATTGCT 57.184 25.926 5.05 0.00 0.00 3.91
450 453 4.960329 ACAATTGCTTGCATTTTATTGCG 58.040 34.783 5.05 1.61 45.77 4.85
453 456 5.859521 ATTGCTTGCATTTTATTGCGAAA 57.140 30.435 0.00 0.00 45.77 3.46
461 464 8.486358 TTGCATTTTATTGCGAAATTTTGAAC 57.514 26.923 9.75 0.00 45.77 3.18
462 465 7.633621 TGCATTTTATTGCGAAATTTTGAACA 58.366 26.923 9.75 0.00 45.77 3.18
464 467 8.620641 GCATTTTATTGCGAAATTTTGAACAAG 58.379 29.630 9.75 0.00 32.06 3.16
472 475 5.634859 GCGAAATTTTGAACAAGTGATGGAT 59.365 36.000 9.75 0.00 0.00 3.41
475 478 8.853345 CGAAATTTTGAACAAGTGATGGATTAG 58.147 33.333 0.00 0.00 0.00 1.73
586 589 9.638300 GTTCTCGAAAATGCAAGTATAACTATG 57.362 33.333 0.00 0.00 0.00 2.23
600 603 9.892130 AAGTATAACTATGAATAATGCTAGCCC 57.108 33.333 13.29 0.00 0.00 5.19
601 604 9.046846 AGTATAACTATGAATAATGCTAGCCCA 57.953 33.333 13.29 0.00 0.00 5.36
609 612 2.902705 AATGCTAGCCCATGCAAATG 57.097 45.000 13.29 0.00 42.74 2.32
634 637 3.369052 CGGGTTGACAGCTAGTTATTCCA 60.369 47.826 0.00 0.00 0.00 3.53
636 639 4.395231 GGGTTGACAGCTAGTTATTCCAAC 59.605 45.833 0.00 0.00 32.28 3.77
746 2634 0.248054 CAAATGTATGCGCGGACCAC 60.248 55.000 8.83 7.83 0.00 4.16
747 2635 0.392461 AAATGTATGCGCGGACCACT 60.392 50.000 8.83 0.00 0.00 4.00
748 2636 0.462375 AATGTATGCGCGGACCACTA 59.538 50.000 8.83 0.00 0.00 2.74
752 2641 2.022240 TATGCGCGGACCACTATGCA 62.022 55.000 8.83 0.00 36.69 3.96
756 2645 1.089481 CGCGGACCACTATGCATTGT 61.089 55.000 3.54 6.15 0.00 2.71
760 2649 2.872245 CGGACCACTATGCATTGTTAGG 59.128 50.000 11.24 12.63 0.00 2.69
779 2668 1.585297 GTCCCTCCAACGAAAACGAA 58.415 50.000 0.00 0.00 0.00 3.85
910 2809 1.280998 TGCTTGGCTCCTTAACCTACC 59.719 52.381 0.00 0.00 0.00 3.18
950 2849 1.964223 CTACCTACCTCATGCACCGAT 59.036 52.381 0.00 0.00 0.00 4.18
957 2898 5.417894 CCTACCTCATGCACCGATAGTATAA 59.582 44.000 0.00 0.00 0.00 0.98
964 2905 7.312899 TCATGCACCGATAGTATAACATGTAG 58.687 38.462 0.00 0.00 36.08 2.74
996 2937 1.269778 CGTCTATCCATCCACGTGCAT 60.270 52.381 10.91 0.00 0.00 3.96
1036 3014 4.051167 TCCGGGTCCTAGACGCCA 62.051 66.667 0.00 0.00 41.49 5.69
1164 3151 2.762554 CCTCCACCACCACCACCAA 61.763 63.158 0.00 0.00 0.00 3.67
1171 3158 0.762418 CCACCACCACCAAGACACTA 59.238 55.000 0.00 0.00 0.00 2.74
1172 3159 1.542547 CCACCACCACCAAGACACTAC 60.543 57.143 0.00 0.00 0.00 2.73
1173 3160 1.416401 CACCACCACCAAGACACTACT 59.584 52.381 0.00 0.00 0.00 2.57
1174 3161 2.631062 CACCACCACCAAGACACTACTA 59.369 50.000 0.00 0.00 0.00 1.82
1179 3166 2.635915 CCACCAAGACACTACTACCCAA 59.364 50.000 0.00 0.00 0.00 4.12
1260 3247 4.838152 CATGTCCGCCTCACCCCG 62.838 72.222 0.00 0.00 0.00 5.73
1338 3328 1.226046 CACTGTCGCCGAGTACGAG 60.226 63.158 0.00 0.00 40.80 4.18
1350 3343 1.662629 GAGTACGAGACCGACATCGAA 59.337 52.381 2.09 0.00 41.40 3.71
1362 3364 0.620556 ACATCGAAGACCTTGCCCAT 59.379 50.000 0.00 0.00 42.51 4.00
1750 3769 2.747460 TCCTGCACGGCATCAAGC 60.747 61.111 0.00 0.00 38.13 4.01
1845 3864 5.412594 CAGTTTAATGTGGTCATGCTACTGT 59.587 40.000 0.00 0.00 34.86 3.55
1893 3918 7.476540 AACAAAAACAACCTACTTCCTCTTT 57.523 32.000 0.00 0.00 0.00 2.52
1896 3921 6.373186 AAAACAACCTACTTCCTCTTTTCG 57.627 37.500 0.00 0.00 0.00 3.46
1972 7576 0.679640 CCTTGGTCCGGCAATTGCTA 60.680 55.000 28.42 12.76 41.70 3.49
1998 7602 2.537560 CCATGACGAGATTGCGGCC 61.538 63.158 0.00 0.00 38.91 6.13
2055 7659 4.458829 TCCGACGCCCTCCAGGAT 62.459 66.667 0.00 0.00 38.24 3.24
2112 7716 0.321653 GTGTTGAGCGGGTGAAGGAT 60.322 55.000 0.00 0.00 0.00 3.24
2136 7740 3.617531 CGGTAAAATCTGGTGTGCTCTCT 60.618 47.826 0.00 0.00 0.00 3.10
2181 7785 3.810941 GTGTGTACAACCTCGATTTTGGA 59.189 43.478 0.00 0.00 0.00 3.53
2255 7859 4.767255 GGTGGAGGAGGCACGCAG 62.767 72.222 0.00 0.00 0.00 5.18
2348 7952 1.539712 CGATGCCATGCAAGAGCTAGA 60.540 52.381 0.00 0.00 43.62 2.43
2349 7953 2.780714 GATGCCATGCAAGAGCTAGAT 58.219 47.619 0.00 0.00 43.62 1.98
2578 8184 2.091541 GCCCAAACTATAGCAGTGCAA 58.908 47.619 19.20 0.94 37.63 4.08
2598 8204 6.230472 TGCAACACACATAATGTTAGAGAGT 58.770 36.000 0.00 0.00 40.64 3.24
2604 8210 6.757010 CACACATAATGTTAGAGAGTGGTACC 59.243 42.308 4.43 4.43 40.64 3.34
2708 8319 6.573434 TGTATAGCCACTTCTTGACATAGTG 58.427 40.000 0.00 0.00 39.13 2.74
2716 8327 7.308830 GCCACTTCTTGACATAGTGAGAAAATT 60.309 37.037 12.10 0.00 41.33 1.82
2747 8358 7.148967 GCAAACGGATGACTTCAAGAATTTTAC 60.149 37.037 0.00 0.00 0.00 2.01
2751 8362 6.524586 CGGATGACTTCAAGAATTTTACTTGC 59.475 38.462 0.00 0.00 42.76 4.01
2884 8496 7.970614 GGCTCACATTTTATAACTTTCCTTCTG 59.029 37.037 0.00 0.00 0.00 3.02
2916 8587 8.089625 TCCTCCTAATTGTACATGAATCAAGA 57.910 34.615 0.00 0.00 0.00 3.02
2919 8590 9.994432 CTCCTAATTGTACATGAATCAAGAAAC 57.006 33.333 0.00 0.00 0.00 2.78
3029 8702 3.777478 TCGGTAGCGAAATTTAGTCTGG 58.223 45.455 15.73 0.00 0.00 3.86
3056 8729 7.444487 AGACTAGATCTAATACACATGTGCGTA 59.556 37.037 25.68 11.98 35.15 4.42
3068 8741 4.388007 TGCGTAACGAGGCATACG 57.612 55.556 0.00 0.00 45.69 3.06
3079 8752 3.119101 ACGAGGCATACGTGAGAAGAATT 60.119 43.478 0.00 0.00 42.37 2.17
3170 8843 3.417275 ATTCGGCGGCTCGTCTCTG 62.417 63.158 7.21 0.00 0.00 3.35
3225 8898 0.630175 ATGGACATGGGGGATTGGGA 60.630 55.000 0.00 0.00 0.00 4.37
3238 8911 3.324846 GGGATTGGGAAATTAGGGATTGC 59.675 47.826 0.00 0.00 0.00 3.56
3269 8942 2.685388 CTGAGGCGAAGAGATGTAGACA 59.315 50.000 0.00 0.00 0.00 3.41
3285 8958 1.066929 AGACACACGCATACATCAGCA 60.067 47.619 0.00 0.00 0.00 4.41
3290 8963 4.576053 ACACACGCATACATCAGCATAAAT 59.424 37.500 0.00 0.00 0.00 1.40
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 8.677148 ATACCGATAAGAAATTGCAATACACT 57.323 30.769 13.39 9.46 0.00 3.55
1 2 8.556194 TGATACCGATAAGAAATTGCAATACAC 58.444 33.333 13.39 7.29 0.00 2.90
2 3 8.669946 TGATACCGATAAGAAATTGCAATACA 57.330 30.769 13.39 0.00 0.00 2.29
89 90 2.754946 CAGAATTTTGCTGCCATGGT 57.245 45.000 14.67 0.00 0.00 3.55
103 104 0.749091 TAATGCAGCTGCGGCAGAAT 60.749 50.000 32.72 20.44 45.68 2.40
104 105 0.749091 ATAATGCAGCTGCGGCAGAA 60.749 50.000 32.72 20.61 45.68 3.02
105 106 0.749091 AATAATGCAGCTGCGGCAGA 60.749 50.000 32.72 20.83 45.68 4.26
107 108 0.531657 AAAATAATGCAGCTGCGGCA 59.468 45.000 32.11 28.20 46.66 5.69
108 109 1.643880 AAAAATAATGCAGCTGCGGC 58.356 45.000 32.11 17.90 45.83 6.53
110 111 5.673717 GCAAATTAAAAATAATGCAGCTGCG 59.326 36.000 32.11 13.70 45.83 5.18
111 112 5.967088 GGCAAATTAAAAATAATGCAGCTGC 59.033 36.000 31.89 31.89 42.50 5.25
112 113 7.311364 AGGCAAATTAAAAATAATGCAGCTG 57.689 32.000 10.11 10.11 35.57 4.24
113 114 7.712205 CCTAGGCAAATTAAAAATAATGCAGCT 59.288 33.333 0.00 0.00 35.57 4.24
114 115 7.518848 GCCTAGGCAAATTAAAAATAATGCAGC 60.519 37.037 29.33 0.00 41.49 5.25
115 116 7.306749 CGCCTAGGCAAATTAAAAATAATGCAG 60.307 37.037 32.47 6.07 42.06 4.41
116 117 6.478344 CGCCTAGGCAAATTAAAAATAATGCA 59.522 34.615 32.47 0.00 42.06 3.96
117 118 6.699642 TCGCCTAGGCAAATTAAAAATAATGC 59.300 34.615 32.47 0.00 42.06 3.56
118 119 8.702438 CATCGCCTAGGCAAATTAAAAATAATG 58.298 33.333 32.47 10.87 42.06 1.90
119 120 7.384932 GCATCGCCTAGGCAAATTAAAAATAAT 59.615 33.333 32.47 4.53 42.06 1.28
120 121 6.699642 GCATCGCCTAGGCAAATTAAAAATAA 59.300 34.615 32.47 2.44 42.06 1.40
121 122 6.040391 AGCATCGCCTAGGCAAATTAAAAATA 59.960 34.615 32.47 3.82 42.06 1.40
122 123 5.049828 GCATCGCCTAGGCAAATTAAAAAT 58.950 37.500 32.47 8.78 42.06 1.82
124 125 3.699038 AGCATCGCCTAGGCAAATTAAAA 59.301 39.130 32.47 7.91 42.06 1.52
128 129 1.767759 AAGCATCGCCTAGGCAAATT 58.232 45.000 32.47 16.22 42.06 1.82
133 134 1.312815 ATTGAAAGCATCGCCTAGGC 58.687 50.000 24.75 24.75 34.24 3.93
140 141 2.643551 ACACCCCTATTGAAAGCATCG 58.356 47.619 0.00 0.00 0.00 3.84
141 142 6.377146 TCTTAAACACCCCTATTGAAAGCATC 59.623 38.462 0.00 0.00 0.00 3.91
143 144 5.475564 GTCTTAAACACCCCTATTGAAAGCA 59.524 40.000 0.00 0.00 0.00 3.91
144 145 5.475564 TGTCTTAAACACCCCTATTGAAAGC 59.524 40.000 0.00 0.00 31.20 3.51
151 152 2.916934 TGCCTGTCTTAAACACCCCTAT 59.083 45.455 0.00 0.00 33.24 2.57
153 154 1.073923 CTGCCTGTCTTAAACACCCCT 59.926 52.381 0.00 0.00 33.24 4.79
155 156 0.881796 GCTGCCTGTCTTAAACACCC 59.118 55.000 0.00 0.00 33.24 4.61
158 159 1.133945 TGTGGCTGCCTGTCTTAAACA 60.134 47.619 21.03 10.12 36.18 2.83
159 160 1.537202 CTGTGGCTGCCTGTCTTAAAC 59.463 52.381 21.03 7.40 0.00 2.01
160 161 1.545428 CCTGTGGCTGCCTGTCTTAAA 60.545 52.381 21.03 0.00 0.00 1.52
165 166 1.376037 GTACCTGTGGCTGCCTGTC 60.376 63.158 21.03 10.76 0.00 3.51
169 170 0.821711 TGTTTGTACCTGTGGCTGCC 60.822 55.000 12.87 12.87 0.00 4.85
170 171 1.247567 ATGTTTGTACCTGTGGCTGC 58.752 50.000 0.00 0.00 0.00 5.25
178 179 2.372837 ACCACCGGTAATGTTTGTACCT 59.627 45.455 6.87 0.00 39.16 3.08
185 186 1.303806 GCCCACCACCGGTAATGTT 60.304 57.895 6.87 0.00 32.11 2.71
202 203 2.707849 CCAGTTGAGGGCATGCTGC 61.708 63.158 18.92 7.80 44.08 5.25
204 205 1.303888 CACCAGTTGAGGGCATGCT 60.304 57.895 18.92 0.00 0.00 3.79
207 208 0.700564 ATGTCACCAGTTGAGGGCAT 59.299 50.000 0.00 0.00 33.71 4.40
217 218 2.159338 GCCATTGCTAACATGTCACCAG 60.159 50.000 0.00 0.00 33.53 4.00
220 221 1.737236 TCGCCATTGCTAACATGTCAC 59.263 47.619 0.00 0.00 34.43 3.67
234 235 1.153086 GCCATTGACCTCTCGCCAT 60.153 57.895 0.00 0.00 0.00 4.40
240 241 4.473520 CGCCCGCCATTGACCTCT 62.474 66.667 0.00 0.00 0.00 3.69
278 279 1.102978 ATTGACATAAACGGGCAGGC 58.897 50.000 0.00 0.00 0.00 4.85
350 353 6.509418 TGATGTGGTTACTTTCTAATTGGC 57.491 37.500 0.00 0.00 0.00 4.52
425 428 6.360148 CGCAATAAAATGCAAGCAATTGTTTT 59.640 30.769 4.61 11.83 46.76 2.43
429 432 5.205988 TCGCAATAAAATGCAAGCAATTG 57.794 34.783 0.00 0.00 46.76 2.32
431 434 5.859521 TTTCGCAATAAAATGCAAGCAAT 57.140 30.435 0.00 0.00 46.76 3.56
436 439 8.124823 TGTTCAAAATTTCGCAATAAAATGCAA 58.875 25.926 0.00 0.00 46.76 4.08
450 453 9.696917 ACTAATCCATCACTTGTTCAAAATTTC 57.303 29.630 0.00 0.00 0.00 2.17
503 506 9.791820 TCGAAATTCTTAATGTCACGTAATAGA 57.208 29.630 0.00 0.00 0.00 1.98
511 514 8.240883 AGTGTACTCGAAATTCTTAATGTCAC 57.759 34.615 0.00 0.00 0.00 3.67
512 515 8.827177 AAGTGTACTCGAAATTCTTAATGTCA 57.173 30.769 0.00 0.00 0.00 3.58
552 555 7.592938 ACTTGCATTTTCGAGAACATGAAATA 58.407 30.769 14.10 0.00 34.35 1.40
586 589 4.589216 TTTGCATGGGCTAGCATTATTC 57.411 40.909 18.24 2.63 40.94 1.75
609 612 0.602905 AACTAGCTGTCAACCCGTGC 60.603 55.000 0.00 0.00 0.00 5.34
634 637 7.934855 ATAGATTGTGATTTCTTGCTCTGTT 57.065 32.000 0.00 0.00 0.00 3.16
636 639 9.073368 CAAAATAGATTGTGATTTCTTGCTCTG 57.927 33.333 0.00 0.00 0.00 3.35
715 2603 6.183360 CGCGCATACATTTGTAATTCCAAAAA 60.183 34.615 8.75 0.00 37.81 1.94
724 2612 1.666700 GGTCCGCGCATACATTTGTAA 59.333 47.619 8.75 0.00 33.76 2.41
732 2620 1.557443 GCATAGTGGTCCGCGCATAC 61.557 60.000 8.75 4.08 0.00 2.39
746 2634 3.136443 TGGAGGGACCTAACAATGCATAG 59.864 47.826 0.00 0.00 39.86 2.23
747 2635 3.119319 TGGAGGGACCTAACAATGCATA 58.881 45.455 0.00 0.00 39.86 3.14
748 2636 1.922447 TGGAGGGACCTAACAATGCAT 59.078 47.619 0.00 0.00 39.86 3.96
752 2641 2.262637 TCGTTGGAGGGACCTAACAAT 58.737 47.619 10.08 0.00 39.86 2.71
756 2645 2.548493 CGTTTTCGTTGGAGGGACCTAA 60.548 50.000 0.00 0.00 37.80 2.69
760 2649 1.585297 TTCGTTTTCGTTGGAGGGAC 58.415 50.000 0.00 0.00 44.46 4.46
779 2668 0.329931 TTCAACGGCCATGTACCCAT 59.670 50.000 2.24 0.00 0.00 4.00
950 2849 6.994496 ACGTGCCTACTCTACATGTTATACTA 59.006 38.462 2.30 0.00 29.38 1.82
957 2898 1.400846 CGACGTGCCTACTCTACATGT 59.599 52.381 2.69 2.69 36.29 3.21
964 2905 1.263752 GGATAGACGACGTGCCTACTC 59.736 57.143 4.58 2.18 0.00 2.59
1077 3058 2.485814 GTCAAAGAATGTGAGTGGGAGC 59.514 50.000 0.00 0.00 28.95 4.70
1164 3151 4.936802 AGATGAGTTGGGTAGTAGTGTCT 58.063 43.478 0.00 0.00 0.00 3.41
1171 3158 2.100989 GTCGGAGATGAGTTGGGTAGT 58.899 52.381 0.00 0.00 40.67 2.73
1172 3159 1.409427 GGTCGGAGATGAGTTGGGTAG 59.591 57.143 0.00 0.00 40.67 3.18
1173 3160 1.006758 AGGTCGGAGATGAGTTGGGTA 59.993 52.381 0.00 0.00 40.67 3.69
1174 3161 0.252284 AGGTCGGAGATGAGTTGGGT 60.252 55.000 0.00 0.00 40.67 4.51
1179 3166 1.479709 CCTTGAGGTCGGAGATGAGT 58.520 55.000 0.00 0.00 40.67 3.41
1323 3313 2.393768 GGTCTCGTACTCGGCGACA 61.394 63.158 4.99 0.00 38.54 4.35
1338 3328 1.630148 CAAGGTCTTCGATGTCGGTC 58.370 55.000 2.25 0.00 40.29 4.79
1470 3472 2.842462 ACGGTGACACCCAGAGCA 60.842 61.111 19.11 0.00 33.75 4.26
1569 3574 4.402528 TCAATGACCGGTGGCGGG 62.403 66.667 14.63 0.00 0.00 6.13
1593 3598 3.461773 CTGGGGTCGGCGATGAGT 61.462 66.667 14.79 0.00 0.00 3.41
1657 3668 1.340657 CTGCTGCTCACGAACTCGAC 61.341 60.000 6.05 0.00 43.02 4.20
1845 3864 2.045561 TTTGTTCCTGTTTGGCTCGA 57.954 45.000 0.00 0.00 35.26 4.04
2035 7639 3.522731 CTGGAGGGCGTCGGAGAG 61.523 72.222 0.53 0.00 36.95 3.20
2055 7659 2.203938 GACCCCTCACCCACCTCA 60.204 66.667 0.00 0.00 0.00 3.86
2112 7716 0.878416 GCACACCAGATTTTACCGCA 59.122 50.000 0.00 0.00 0.00 5.69
2181 7785 1.256812 CCTTTGTTGGCTTCCCGAAT 58.743 50.000 0.00 0.00 0.00 3.34
2194 7798 0.463116 GACACCACGTCCACCTTTGT 60.463 55.000 0.00 0.00 38.85 2.83
2348 7952 6.995091 GGCTTTTCTCATCAACTATAGACCAT 59.005 38.462 6.78 0.00 0.00 3.55
2349 7953 6.349300 GGCTTTTCTCATCAACTATAGACCA 58.651 40.000 6.78 0.00 0.00 4.02
2491 8097 1.486310 TCCCTGCCAGTATGCTAGTTG 59.514 52.381 0.00 0.00 31.97 3.16
2497 8103 0.811616 CTTCGTCCCTGCCAGTATGC 60.812 60.000 0.00 0.00 31.97 3.14
2504 8110 0.249398 TTTCTAGCTTCGTCCCTGCC 59.751 55.000 0.00 0.00 0.00 4.85
2531 8137 0.321671 GCCAGAGCTTGACACCAGTA 59.678 55.000 0.00 0.00 35.50 2.74
2578 8184 6.360370 ACCACTCTCTAACATTATGTGTGT 57.640 37.500 0.00 0.00 41.14 3.72
2598 8204 2.623878 TGTTTTCGCTCTTGGTACCA 57.376 45.000 11.60 11.60 0.00 3.25
2604 8210 3.567530 TCATTGCATGTTTTCGCTCTTG 58.432 40.909 0.00 0.00 0.00 3.02
2654 8261 1.705337 GCGCGTGCTTGGTATGACAT 61.705 55.000 15.02 0.00 38.39 3.06
2708 8319 8.398665 AGTCATCCGTTTGCTTATAATTTTCTC 58.601 33.333 0.00 0.00 0.00 2.87
2716 8327 6.403049 TCTTGAAGTCATCCGTTTGCTTATA 58.597 36.000 0.00 0.00 0.00 0.98
2747 8358 9.065871 CGTAAATTATTTTCAGGAAGAAGCAAG 57.934 33.333 0.00 0.00 37.57 4.01
2838 8450 6.205853 TGAGCCGTGTGTCACTTTATATTTTT 59.794 34.615 4.27 0.00 31.34 1.94
2857 8469 6.436843 AGGAAAGTTATAAAATGTGAGCCG 57.563 37.500 0.00 0.00 0.00 5.52
2884 8496 5.099042 TGTACAATTAGGAGGAAAGCTCC 57.901 43.478 0.00 0.00 42.81 4.70
2899 8570 8.849168 TGTTCTGTTTCTTGATTCATGTACAAT 58.151 29.630 0.00 0.00 0.00 2.71
2969 8642 4.321718 TGCTGTTCTCTTCCTTGATTCAG 58.678 43.478 0.00 0.00 0.00 3.02
3029 8702 6.799441 CGCACATGTGTATTAGATCTAGTCTC 59.201 42.308 26.01 3.21 38.42 3.36
3056 8729 1.816835 TCTTCTCACGTATGCCTCGTT 59.183 47.619 0.00 0.00 39.55 3.85
3068 8741 5.526846 CCAAGCCTAGATCAATTCTTCTCAC 59.473 44.000 0.00 0.00 35.79 3.51
3079 8752 2.173356 CCAATCCACCAAGCCTAGATCA 59.827 50.000 0.00 0.00 0.00 2.92
3170 8843 0.598065 GGTGTCTGGTGGAATTGCAC 59.402 55.000 20.76 20.76 0.00 4.57
3201 8874 0.552848 ATCCCCCATGTCCATGTGAC 59.447 55.000 6.53 7.22 44.72 3.67
3211 8884 3.242011 CCTAATTTCCCAATCCCCCATG 58.758 50.000 0.00 0.00 0.00 3.66
3225 8898 2.749800 GCCTCCTCGCAATCCCTAATTT 60.750 50.000 0.00 0.00 0.00 1.82
3269 8942 4.815846 TCATTTATGCTGATGTATGCGTGT 59.184 37.500 0.00 0.00 0.00 4.49
3290 8963 7.518188 GGACTCATCCCTAATTCCTAATTTCA 58.482 38.462 0.00 0.00 39.39 2.69
3312 8985 3.039134 CACACGGCCCAAAAGGAC 58.961 61.111 0.00 0.00 42.38 3.85


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

AutoCloner maintained by Alex Coulton.