Multiple sequence alignment - TraesCS4D01G308200

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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 TraesCS4D01G308200 chr4D 100.000 5234 0 0 1 5234 476307419 476302186 0.000000e+00 9666
1 TraesCS4D01G308200 chr4A 93.992 4311 152 45 428 4669 683488955 683484683 0.000000e+00 6427
2 TraesCS4D01G308200 chr4A 90.504 337 26 3 4900 5232 683484427 683484093 1.730000e-119 440
3 TraesCS4D01G308200 chr4A 91.111 225 14 2 253 472 683489162 683488939 3.060000e-77 300
4 TraesCS4D01G308200 chr4A 89.767 215 13 5 4671 4878 683484633 683484421 3.110000e-67 267
5 TraesCS4D01G308200 chr4A 87.903 124 13 2 1 123 683489410 683489288 1.520000e-30 145
6 TraesCS4D01G308200 chr4B 92.732 4114 173 46 1157 5232 600657854 600653829 0.000000e+00 5825
7 TraesCS4D01G308200 chr4B 87.058 904 59 24 250 1129 600659065 600658196 0.000000e+00 968
8 TraesCS4D01G308200 chr2D 79.735 2339 335 94 1963 4238 367504813 367502551 0.000000e+00 1565
9 TraesCS4D01G308200 chr2D 93.939 231 14 0 1249 1479 367505464 367505234 3.000000e-92 350
10 TraesCS4D01G308200 chr2D 81.716 268 47 2 2859 3125 367921944 367922210 6.820000e-54 222
11 TraesCS4D01G308200 chr2D 78.696 230 47 2 4014 4242 367923050 367923278 9.080000e-33 152
12 TraesCS4D01G308200 chr2A 83.166 1396 181 30 2859 4238 497653850 497652493 0.000000e+00 1227
13 TraesCS4D01G308200 chr2A 76.831 833 136 41 1963 2763 497654768 497653961 2.920000e-112 416
14 TraesCS4D01G308200 chr2A 92.672 232 17 0 1249 1480 497655429 497655198 8.400000e-88 335
15 TraesCS4D01G308200 chr2A 81.343 268 48 2 2859 3125 498042668 498042934 3.170000e-52 217
16 TraesCS4D01G308200 chr2A 88.356 146 11 2 121 260 31956688 31956543 2.510000e-38 171
17 TraesCS4D01G308200 chr2A 77.391 230 50 2 4014 4242 498043774 498044002 9.140000e-28 135
18 TraesCS4D01G308200 chr2B 85.181 992 121 17 2859 3843 436239392 436238420 0.000000e+00 994
19 TraesCS4D01G308200 chr2B 77.167 819 131 39 1963 2763 436240278 436239498 4.840000e-115 425
20 TraesCS4D01G308200 chr2B 94.068 236 14 0 1249 1484 436240940 436240705 4.980000e-95 359
21 TraesCS4D01G308200 chr2B 85.443 316 34 5 3932 4238 436238364 436238052 8.460000e-83 318
22 TraesCS4D01G308200 chr2B 81.716 268 47 2 2859 3125 436960280 436960546 6.820000e-54 222
23 TraesCS4D01G308200 chr2B 77.826 230 49 2 4014 4242 436961386 436961614 1.970000e-29 141
24 TraesCS4D01G308200 chr6A 81.116 233 41 1 1249 1478 33542559 33542327 3.220000e-42 183
25 TraesCS4D01G308200 chr7B 90.141 142 8 2 121 256 112000851 112000710 4.160000e-41 180
26 TraesCS4D01G308200 chr6B 90.580 138 7 3 121 253 369003555 369003691 1.500000e-40 178
27 TraesCS4D01G308200 chr3B 95.495 111 5 0 122 232 612364619 612364729 1.500000e-40 178
28 TraesCS4D01G308200 chr7D 90.000 140 9 2 121 255 419122427 419122288 5.390000e-40 176
29 TraesCS4D01G308200 chr7D 88.966 145 10 2 121 259 50710381 50710237 1.940000e-39 174
30 TraesCS4D01G308200 chr5D 89.928 139 8 2 121 253 424047279 424047141 1.940000e-39 174
31 TraesCS4D01G308200 chr5D 86.709 158 14 3 121 271 331405022 331404865 9.010000e-38 169
32 TraesCS4D01G308200 chr5B 89.437 142 9 3 121 256 588950786 588950645 1.940000e-39 174


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 TraesCS4D01G308200 chr4D 476302186 476307419 5233 True 9666.000000 9666 100.00000 1 5234 1 chr4D.!!$R1 5233
1 TraesCS4D01G308200 chr4A 683484093 683489410 5317 True 1515.800000 6427 90.65540 1 5232 5 chr4A.!!$R1 5231
2 TraesCS4D01G308200 chr4B 600653829 600659065 5236 True 3396.500000 5825 89.89500 250 5232 2 chr4B.!!$R1 4982
3 TraesCS4D01G308200 chr2D 367502551 367505464 2913 True 957.500000 1565 86.83700 1249 4238 2 chr2D.!!$R1 2989
4 TraesCS4D01G308200 chr2A 497652493 497655429 2936 True 659.333333 1227 84.22300 1249 4238 3 chr2A.!!$R2 2989
5 TraesCS4D01G308200 chr2B 436238052 436240940 2888 True 524.000000 994 85.46475 1249 4238 4 chr2B.!!$R1 2989

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
620 661 0.456653 AACAATCTCGGCAATTGCGC 60.457 50.0 23.48 15.26 43.26 6.09 F
1612 2014 0.724785 GCACGTTTGCGCTTTACTCC 60.725 55.0 9.73 0.00 39.50 3.85 F
2267 2710 0.319211 CGGCTTGTACAACCTCGTCA 60.319 55.0 18.78 0.00 0.00 4.35 F
3789 4300 0.853530 AGGAGCCCAAGGAGTTTGTT 59.146 50.0 0.00 0.00 34.87 2.83 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2212 2655 0.320374 GGAACCACACCGAGATGACA 59.680 55.000 0.00 0.00 0.00 3.58 R
3543 4054 1.307084 GTAGAGGAGGCCAACCCCT 60.307 63.158 5.01 6.91 38.81 4.79 R
4014 4537 2.015456 TCAGTTGCTTCTCCTCCTCA 57.985 50.000 0.00 0.00 0.00 3.86 R
5166 5772 0.401979 CTGATCCCCCACCCCACTAT 60.402 60.000 0.00 0.00 0.00 2.12 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
22 23 2.615618 GCGCATGCGTTCGAGTAG 59.384 61.111 37.54 10.41 42.09 2.57
36 37 5.454554 CGTTCGAGTAGGTAACATGTGTATG 59.545 44.000 0.00 0.00 40.24 2.39
40 41 5.971792 CGAGTAGGTAACATGTGTATGTGAG 59.028 44.000 0.00 0.00 46.54 3.51
44 45 3.682858 GGTAACATGTGTATGTGAGCGTT 59.317 43.478 0.00 0.00 46.54 4.84
46 47 3.811722 ACATGTGTATGTGAGCGTTTG 57.188 42.857 0.00 0.00 45.54 2.93
55 56 3.666883 TGTGAGCGTTTGTGTTTGTAG 57.333 42.857 0.00 0.00 0.00 2.74
109 111 7.483307 TCTAAACCAAGTATATCACACCGTAC 58.517 38.462 0.00 0.00 0.00 3.67
123 125 2.047560 GTACGTGCTCCCGCCTTT 60.048 61.111 0.00 0.00 34.43 3.11
125 127 2.280552 TACGTGCTCCCGCCTTTCT 61.281 57.895 0.00 0.00 34.43 2.52
126 128 0.966875 TACGTGCTCCCGCCTTTCTA 60.967 55.000 0.00 0.00 34.43 2.10
127 129 1.519455 CGTGCTCCCGCCTTTCTAG 60.519 63.158 0.00 0.00 34.43 2.43
130 132 0.981183 TGCTCCCGCCTTTCTAGAAA 59.019 50.000 16.85 16.85 34.43 2.52
132 134 2.026262 TGCTCCCGCCTTTCTAGAAATT 60.026 45.455 18.02 0.00 34.43 1.82
134 136 3.444034 GCTCCCGCCTTTCTAGAAATTTT 59.556 43.478 18.02 0.00 0.00 1.82
136 138 5.124936 GCTCCCGCCTTTCTAGAAATTTTAA 59.875 40.000 18.02 2.96 0.00 1.52
138 140 6.005198 TCCCGCCTTTCTAGAAATTTTAACA 58.995 36.000 18.02 0.00 0.00 2.41
140 142 6.806739 CCCGCCTTTCTAGAAATTTTAACAAG 59.193 38.462 18.02 3.46 0.00 3.16
141 143 7.368059 CCGCCTTTCTAGAAATTTTAACAAGT 58.632 34.615 18.02 0.00 0.00 3.16
142 144 7.326063 CCGCCTTTCTAGAAATTTTAACAAGTG 59.674 37.037 18.02 2.53 0.00 3.16
143 145 8.073768 CGCCTTTCTAGAAATTTTAACAAGTGA 58.926 33.333 18.02 0.00 0.00 3.41
144 146 9.181805 GCCTTTCTAGAAATTTTAACAAGTGAC 57.818 33.333 18.02 0.00 0.00 3.67
153 155 9.537848 GAAATTTTAACAAGTGACTACATACGG 57.462 33.333 0.00 0.00 0.00 4.02
154 156 8.836268 AATTTTAACAAGTGACTACATACGGA 57.164 30.769 0.00 0.00 0.00 4.69
155 157 7.878477 TTTTAACAAGTGACTACATACGGAG 57.122 36.000 0.00 0.00 0.00 4.63
156 158 3.505464 ACAAGTGACTACATACGGAGC 57.495 47.619 0.00 0.00 0.00 4.70
157 159 2.823747 ACAAGTGACTACATACGGAGCA 59.176 45.455 0.00 0.00 0.00 4.26
160 162 4.530710 AGTGACTACATACGGAGCAAAA 57.469 40.909 0.00 0.00 0.00 2.44
162 164 6.216801 AGTGACTACATACGGAGCAAAATA 57.783 37.500 0.00 0.00 0.00 1.40
164 166 6.757010 AGTGACTACATACGGAGCAAAATAAG 59.243 38.462 0.00 0.00 0.00 1.73
165 167 6.534079 GTGACTACATACGGAGCAAAATAAGT 59.466 38.462 0.00 0.00 0.00 2.24
166 168 6.533723 TGACTACATACGGAGCAAAATAAGTG 59.466 38.462 0.00 0.00 0.00 3.16
167 169 6.636705 ACTACATACGGAGCAAAATAAGTGA 58.363 36.000 0.00 0.00 0.00 3.41
168 170 7.101054 ACTACATACGGAGCAAAATAAGTGAA 58.899 34.615 0.00 0.00 0.00 3.18
169 171 7.769044 ACTACATACGGAGCAAAATAAGTGAAT 59.231 33.333 0.00 0.00 0.00 2.57
170 172 7.016361 ACATACGGAGCAAAATAAGTGAATC 57.984 36.000 0.00 0.00 0.00 2.52
171 173 6.823689 ACATACGGAGCAAAATAAGTGAATCT 59.176 34.615 0.00 0.00 0.00 2.40
172 174 7.985184 ACATACGGAGCAAAATAAGTGAATCTA 59.015 33.333 0.00 0.00 0.00 1.98
174 176 6.170506 ACGGAGCAAAATAAGTGAATCTACA 58.829 36.000 0.00 0.00 0.00 2.74
175 177 6.092259 ACGGAGCAAAATAAGTGAATCTACAC 59.908 38.462 0.00 0.00 40.60 2.90
213 215 9.524496 TCTATATACATCCGTATGTGGTAGTTT 57.476 33.333 3.56 0.00 45.99 2.66
218 220 7.548196 ACATCCGTATGTGGTAGTTTATTTG 57.452 36.000 0.00 0.00 44.79 2.32
219 221 7.332557 ACATCCGTATGTGGTAGTTTATTTGA 58.667 34.615 0.00 0.00 44.79 2.69
220 222 7.825270 ACATCCGTATGTGGTAGTTTATTTGAA 59.175 33.333 0.00 0.00 44.79 2.69
222 224 8.795842 TCCGTATGTGGTAGTTTATTTGAAAT 57.204 30.769 0.00 0.00 0.00 2.17
223 225 8.885722 TCCGTATGTGGTAGTTTATTTGAAATC 58.114 33.333 0.00 0.00 0.00 2.17
225 227 9.916397 CGTATGTGGTAGTTTATTTGAAATCTC 57.084 33.333 0.00 0.00 0.00 2.75
283 285 5.221362 ACCCTTTTTCCCGATAGTGTTTTTG 60.221 40.000 0.00 0.00 0.00 2.44
307 309 4.289238 TCGACTTATAAAACAAGCCCCA 57.711 40.909 0.00 0.00 0.00 4.96
386 394 5.818857 ACATGTACAAGTAAAGGTGAAACGT 59.181 36.000 1.03 0.00 38.12 3.99
481 518 3.625764 GCATTATTTGTCGCCTACTCCAA 59.374 43.478 0.00 0.00 0.00 3.53
483 520 5.569413 CATTATTTGTCGCCTACTCCAAAC 58.431 41.667 0.00 0.00 30.37 2.93
493 530 2.611224 CCTACTCCAAACGTACACACCC 60.611 54.545 0.00 0.00 0.00 4.61
521 561 1.972795 TCGGCAAGTAACCTACCTTGT 59.027 47.619 0.00 0.00 0.00 3.16
534 574 6.287589 ACCTACCTTGTAGAAGATCAGTTG 57.712 41.667 0.19 0.00 0.00 3.16
615 656 2.161609 GGACGAAAACAATCTCGGCAAT 59.838 45.455 0.00 0.00 45.15 3.56
616 657 3.365969 GGACGAAAACAATCTCGGCAATT 60.366 43.478 0.00 0.00 45.15 2.32
619 660 1.981254 AAACAATCTCGGCAATTGCG 58.019 45.000 23.48 18.08 43.26 4.85
620 661 0.456653 AACAATCTCGGCAATTGCGC 60.457 50.000 23.48 15.26 43.26 6.09
621 662 1.935917 CAATCTCGGCAATTGCGCG 60.936 57.895 25.74 25.74 43.26 6.86
622 663 3.739782 AATCTCGGCAATTGCGCGC 62.740 57.895 27.26 27.26 43.26 6.86
690 736 6.090628 TGGCAGCATTCGTTTGAATATTTTTC 59.909 34.615 0.00 0.00 42.94 2.29
743 789 4.006319 ACTTTTAAGTGCTCATGAGGCTC 58.994 43.478 23.89 15.65 37.98 4.70
878 929 2.877168 CCTCATGTGCTAGCTCAAATCC 59.123 50.000 22.16 0.00 0.00 3.01
896 947 2.546778 TCCGCACCGCTCTATTTAAAG 58.453 47.619 0.00 0.00 0.00 1.85
955 1014 1.449070 CAGCTGCAGATCTTCGCCA 60.449 57.895 20.43 0.00 0.00 5.69
1099 1167 1.951209 TGCAGAGAAGGTGTCCCATA 58.049 50.000 0.00 0.00 0.00 2.74
1129 1197 1.636148 TGGCTCCCGGGTATGTATAC 58.364 55.000 22.86 4.14 0.00 1.47
1150 1221 2.985847 GTGTGCTCCCCCTGCAAC 60.986 66.667 0.00 0.00 42.41 4.17
1153 1224 4.020617 TGCTCCCCCTGCAACTCG 62.021 66.667 0.00 0.00 37.51 4.18
1154 1225 3.706373 GCTCCCCCTGCAACTCGA 61.706 66.667 0.00 0.00 0.00 4.04
1155 1226 3.036429 GCTCCCCCTGCAACTCGAT 62.036 63.158 0.00 0.00 0.00 3.59
1161 1543 1.293924 CCCTGCAACTCGATGATCAC 58.706 55.000 0.00 0.00 0.00 3.06
1192 1574 1.765904 TGCATTTATCTGACGGGGCTA 59.234 47.619 0.00 0.00 0.00 3.93
1215 1597 3.628487 GCAGTGAGTAGAGTACCCTACTG 59.372 52.174 20.54 10.63 46.66 2.74
1238 1620 2.739849 TTCCTTTGGGCGACGCATGA 62.740 55.000 23.09 2.96 0.00 3.07
1239 1621 2.480555 CTTTGGGCGACGCATGAC 59.519 61.111 23.09 9.03 0.00 3.06
1421 1805 5.186603 GCTCATCATCTACACCCTCATCATA 59.813 44.000 0.00 0.00 0.00 2.15
1488 1886 5.839621 ACAACGGAGATGGTATGTATACAC 58.160 41.667 7.96 0.00 33.36 2.90
1558 1956 2.223900 GGATTGCTTAAGCTGGATTGCC 60.224 50.000 26.90 14.50 42.66 4.52
1566 1964 2.707849 GCTGGATTGCCCACTGCTG 61.708 63.158 0.00 0.00 40.82 4.41
1612 2014 0.724785 GCACGTTTGCGCTTTACTCC 60.725 55.000 9.73 0.00 39.50 3.85
1854 2256 7.361127 GCAATCTCTGGTAATCAATCAATCAG 58.639 38.462 0.00 0.00 0.00 2.90
1855 2257 7.228108 GCAATCTCTGGTAATCAATCAATCAGA 59.772 37.037 0.00 0.00 0.00 3.27
1856 2258 9.286170 CAATCTCTGGTAATCAATCAATCAGAT 57.714 33.333 0.00 0.00 39.09 2.90
1896 2298 8.193250 TCAAAGAGTCAACGCCTATTAATTAC 57.807 34.615 0.00 0.00 0.00 1.89
2000 2428 3.072915 TGAGTGGGATCAGAGAAAAAGCA 59.927 43.478 0.00 0.00 0.00 3.91
2056 2488 8.773216 AGGAAGGATTAGTAGCTAAGATGTTTT 58.227 33.333 0.00 0.00 29.02 2.43
2112 2555 2.676471 ACGGCCTTCCATGGTTGC 60.676 61.111 12.58 12.53 0.00 4.17
2212 2655 1.374252 CGGCTACACGTTTGCTCCT 60.374 57.895 0.00 0.00 0.00 3.69
2251 2694 2.555565 TTTTCATTGCGGGCATCGGC 62.556 55.000 0.00 0.00 39.69 5.54
2267 2710 0.319211 CGGCTTGTACAACCTCGTCA 60.319 55.000 18.78 0.00 0.00 4.35
2559 3020 2.162408 GGCTGTTCAGGTACTTCATTGC 59.838 50.000 1.97 0.00 34.60 3.56
2570 3031 7.119699 TCAGGTACTTCATTGCTTCTTTACATG 59.880 37.037 0.00 0.00 34.60 3.21
2602 3065 6.554334 TTTTGGAAGTCAACTATCTTTCCG 57.446 37.500 0.00 0.00 34.67 4.30
3098 3609 1.227823 CGCCTTCAGAACCACCACA 60.228 57.895 0.00 0.00 0.00 4.17
3134 3645 4.625564 GCTTATGGTAAGTTGGTAGCCACT 60.626 45.833 0.00 0.00 30.78 4.00
3140 3651 1.920610 AGTTGGTAGCCACTACTCGT 58.079 50.000 0.00 0.00 37.16 4.18
3192 3703 2.364970 CAACAGCCTGATGGGTCAAAAA 59.635 45.455 0.00 0.00 43.07 1.94
3196 3707 2.568509 AGCCTGATGGGTCAAAAATTGG 59.431 45.455 0.00 0.00 40.58 3.16
3204 3715 6.440010 TGATGGGTCAAAAATTGGTGTGATAT 59.560 34.615 0.00 0.00 0.00 1.63
3346 3857 2.094182 GTCGTGTTTGGCTCCATAGAGA 60.094 50.000 0.00 0.00 43.39 3.10
3789 4300 0.853530 AGGAGCCCAAGGAGTTTGTT 59.146 50.000 0.00 0.00 34.87 2.83
4014 4537 1.052124 TCCACTCCAACCGGACAGTT 61.052 55.000 9.46 0.00 35.91 3.16
4251 4774 1.834188 AGTGATTTTACCCCAAGCGG 58.166 50.000 0.00 0.00 0.00 5.52
4308 4834 3.719268 TGTGATTCTGGCTGTATGGTT 57.281 42.857 0.00 0.00 0.00 3.67
4326 4852 3.136809 TGGTTGTACTACTTTGAAGGGCA 59.863 43.478 7.38 0.00 0.00 5.36
4346 4872 3.753272 GCAAAGAGGATATGTGTGTGTGT 59.247 43.478 0.00 0.00 0.00 3.72
4347 4873 4.378770 GCAAAGAGGATATGTGTGTGTGTG 60.379 45.833 0.00 0.00 0.00 3.82
4436 4962 3.858238 GTGTACCGTTATCTGAGCTGAAC 59.142 47.826 0.00 0.00 0.00 3.18
4525 5064 5.357878 TGTCATAAGCAAGGTTCATGATTCC 59.642 40.000 0.00 2.61 0.00 3.01
4534 5073 5.728637 AGGTTCATGATTCCTTTTTGACC 57.271 39.130 12.43 6.07 0.00 4.02
4555 5094 1.003839 TCGGAATGCAGTGGTGGAC 60.004 57.895 0.00 0.00 0.00 4.02
4556 5095 1.003355 CGGAATGCAGTGGTGGACT 60.003 57.895 0.00 0.00 34.02 3.85
4577 5116 5.717119 ACTCAGGATTTTCAACATGAATGC 58.283 37.500 0.00 0.00 36.11 3.56
4722 5312 4.396166 AGTTACATCGCAAAATCAAGGAGG 59.604 41.667 0.00 0.00 0.00 4.30
4757 5348 9.163899 GTTAACTCTACAATCCCCTTTTAGAAG 57.836 37.037 0.00 0.00 0.00 2.85
4852 5450 2.031245 TGGAAGCACGCACAAATTGTAG 60.031 45.455 0.00 0.00 0.00 2.74
4881 5479 2.847327 TTCACCTTGCTCCTTCTCTG 57.153 50.000 0.00 0.00 0.00 3.35
4955 5553 5.437289 AAATGTTGCTGAAACTCGATTGA 57.563 34.783 0.00 0.00 39.70 2.57
4968 5570 5.153950 ACTCGATTGACTTTTAGAAGCCT 57.846 39.130 0.00 0.00 36.29 4.58
4969 5571 6.282199 ACTCGATTGACTTTTAGAAGCCTA 57.718 37.500 0.00 0.00 36.29 3.93
4988 5590 4.240888 CCTATACGGCAGACAGATCAATG 58.759 47.826 0.00 0.00 0.00 2.82
5015 5617 1.270893 GGTCACCCTCTGTTCTTGGTC 60.271 57.143 0.00 0.00 0.00 4.02
5019 5621 0.905357 CCCTCTGTTCTTGGTCGGAT 59.095 55.000 0.00 0.00 0.00 4.18
5059 5664 8.527567 AGAAGAAGAAGATTAGAAAACTCACG 57.472 34.615 0.00 0.00 0.00 4.35
5166 5772 2.741092 GGCCGTGGTGACAGAGAA 59.259 61.111 0.00 0.00 44.46 2.87
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
7 8 1.587034 GTTACCTACTCGAACGCATGC 59.413 52.381 7.91 7.91 0.00 4.06
12 13 3.829948 ACACATGTTACCTACTCGAACG 58.170 45.455 0.00 0.00 0.00 3.95
17 18 5.749109 GCTCACATACACATGTTACCTACTC 59.251 44.000 0.00 0.00 42.98 2.59
22 23 3.259064 ACGCTCACATACACATGTTACC 58.741 45.455 0.00 0.00 42.98 2.85
36 37 2.031683 AGCTACAAACACAAACGCTCAC 59.968 45.455 0.00 0.00 0.00 3.51
40 41 4.833469 AAAAAGCTACAAACACAAACGC 57.167 36.364 0.00 0.00 0.00 4.84
65 66 7.445707 GGTTTAGATTTCCTTCTGAAGTGACTT 59.554 37.037 15.72 0.00 33.63 3.01
67 68 6.710744 TGGTTTAGATTTCCTTCTGAAGTGAC 59.289 38.462 15.72 3.65 33.63 3.67
117 119 8.073768 TCACTTGTTAAAATTTCTAGAAAGGCG 58.926 33.333 21.75 6.55 33.32 5.52
127 129 9.537848 CCGTATGTAGTCACTTGTTAAAATTTC 57.462 33.333 0.00 0.00 0.00 2.17
130 132 7.064253 GCTCCGTATGTAGTCACTTGTTAAAAT 59.936 37.037 0.00 0.00 0.00 1.82
132 134 5.865552 GCTCCGTATGTAGTCACTTGTTAAA 59.134 40.000 0.00 0.00 0.00 1.52
134 136 4.460034 TGCTCCGTATGTAGTCACTTGTTA 59.540 41.667 0.00 0.00 0.00 2.41
136 138 2.823747 TGCTCCGTATGTAGTCACTTGT 59.176 45.455 0.00 0.00 0.00 3.16
138 140 4.530710 TTTGCTCCGTATGTAGTCACTT 57.469 40.909 0.00 0.00 0.00 3.16
140 142 6.534079 ACTTATTTTGCTCCGTATGTAGTCAC 59.466 38.462 0.00 0.00 0.00 3.67
141 143 6.533723 CACTTATTTTGCTCCGTATGTAGTCA 59.466 38.462 0.00 0.00 0.00 3.41
142 144 6.755141 TCACTTATTTTGCTCCGTATGTAGTC 59.245 38.462 0.00 0.00 0.00 2.59
143 145 6.636705 TCACTTATTTTGCTCCGTATGTAGT 58.363 36.000 0.00 0.00 0.00 2.73
144 146 7.534085 TTCACTTATTTTGCTCCGTATGTAG 57.466 36.000 0.00 0.00 0.00 2.74
145 147 7.985184 AGATTCACTTATTTTGCTCCGTATGTA 59.015 33.333 0.00 0.00 0.00 2.29
146 148 6.823689 AGATTCACTTATTTTGCTCCGTATGT 59.176 34.615 0.00 0.00 0.00 2.29
147 149 7.251704 AGATTCACTTATTTTGCTCCGTATG 57.748 36.000 0.00 0.00 0.00 2.39
149 151 7.277098 GTGTAGATTCACTTATTTTGCTCCGTA 59.723 37.037 0.00 0.00 35.68 4.02
150 152 6.092259 GTGTAGATTCACTTATTTTGCTCCGT 59.908 38.462 0.00 0.00 35.68 4.69
152 154 7.550906 AGAGTGTAGATTCACTTATTTTGCTCC 59.449 37.037 0.98 0.00 46.81 4.70
153 155 8.485976 AGAGTGTAGATTCACTTATTTTGCTC 57.514 34.615 0.98 0.00 46.81 4.26
154 156 9.944376 TTAGAGTGTAGATTCACTTATTTTGCT 57.056 29.630 0.98 0.00 46.81 3.91
187 189 9.524496 AAACTACCACATACGGATGTATATAGA 57.476 33.333 22.62 5.04 44.82 1.98
192 194 9.268268 CAAATAAACTACCACATACGGATGTAT 57.732 33.333 14.23 7.46 44.82 2.29
193 195 8.476447 TCAAATAAACTACCACATACGGATGTA 58.524 33.333 14.23 0.00 44.82 2.29
195 197 7.780008 TCAAATAAACTACCACATACGGATG 57.220 36.000 5.94 5.94 39.16 3.51
197 199 8.795842 ATTTCAAATAAACTACCACATACGGA 57.204 30.769 0.00 0.00 0.00 4.69
198 200 8.889717 AGATTTCAAATAAACTACCACATACGG 58.110 33.333 0.00 0.00 0.00 4.02
235 237 9.822185 GGTAAAATATACTCCCTTCGTTTCTAA 57.178 33.333 0.00 0.00 0.00 2.10
236 238 8.424133 GGGTAAAATATACTCCCTTCGTTTCTA 58.576 37.037 0.00 0.00 35.63 2.10
237 239 7.126879 AGGGTAAAATATACTCCCTTCGTTTCT 59.873 37.037 0.00 0.00 45.19 2.52
238 240 7.278135 AGGGTAAAATATACTCCCTTCGTTTC 58.722 38.462 0.00 0.00 45.19 2.78
239 241 7.204243 AGGGTAAAATATACTCCCTTCGTTT 57.796 36.000 0.00 0.00 45.19 3.60
246 248 6.263842 CGGGAAAAAGGGTAAAATATACTCCC 59.736 42.308 0.00 0.00 38.50 4.30
247 249 7.056006 TCGGGAAAAAGGGTAAAATATACTCC 58.944 38.462 0.00 0.00 0.00 3.85
248 250 8.687292 ATCGGGAAAAAGGGTAAAATATACTC 57.313 34.615 0.00 0.00 0.00 2.59
268 270 5.107133 AGTCGATACAAAAACACTATCGGG 58.893 41.667 6.49 0.00 39.69 5.14
283 285 5.818857 TGGGGCTTGTTTTATAAGTCGATAC 59.181 40.000 0.00 0.00 30.68 2.24
307 309 3.895232 ATTCACTGCTCGTATGACCTT 57.105 42.857 0.00 0.00 0.00 3.50
386 394 0.035915 TCCGGATCGTTTTGGCATCA 60.036 50.000 0.00 0.00 0.00 3.07
481 518 3.656559 GATGTACTTGGGTGTGTACGTT 58.343 45.455 0.00 0.00 41.16 3.99
483 520 2.256174 CGATGTACTTGGGTGTGTACG 58.744 52.381 0.00 0.00 41.16 3.67
493 530 3.596214 AGGTTACTTGCCGATGTACTTG 58.404 45.455 0.00 0.00 0.00 3.16
534 574 9.241317 CATTGGTGCTATTTTAATCAGATCAAC 57.759 33.333 0.00 0.00 0.00 3.18
564 605 8.655935 ACATTTTCCTCAGATAAACAAATCCT 57.344 30.769 0.00 0.00 0.00 3.24
587 628 4.084066 CGAGATTGTTTTCGTCCATTGACA 60.084 41.667 0.00 0.00 41.85 3.58
599 640 2.327568 CGCAATTGCCGAGATTGTTTT 58.672 42.857 24.24 0.00 36.96 2.43
626 667 1.401905 GTTAGCAAATGAAGCCTCGGG 59.598 52.381 0.00 0.00 0.00 5.14
634 675 6.429692 TCGAAGAAGATTGGTTAGCAAATGAA 59.570 34.615 0.00 0.00 0.00 2.57
743 789 9.683069 GGTGATAATTGGTGCTATTTTAATCAG 57.317 33.333 0.00 0.00 0.00 2.90
802 848 2.357517 GAGGTGGCACTGACCGTG 60.358 66.667 18.45 0.00 46.58 4.94
878 929 3.544244 GCTTCTTTAAATAGAGCGGTGCG 60.544 47.826 0.00 0.00 0.00 5.34
896 947 0.988063 AGGAAGAAGGTGAGGGCTTC 59.012 55.000 0.00 0.00 36.81 3.86
947 1006 1.601419 CTCCGGGTTAGTGGCGAAGA 61.601 60.000 0.00 0.00 0.00 2.87
955 1014 1.823610 GCAGTTCTACTCCGGGTTAGT 59.176 52.381 0.00 0.00 0.00 2.24
1028 1096 4.363990 CAGGCGCTGTCTCCGTGT 62.364 66.667 7.64 0.00 0.00 4.49
1071 1139 0.329261 CCTTCTCTGCATCACCCCAA 59.671 55.000 0.00 0.00 0.00 4.12
1099 1167 2.440599 GGAGCCATGGTGGTTGGT 59.559 61.111 14.67 0.00 40.46 3.67
1129 1197 2.044650 CAGGGGGAGCACACATGG 60.045 66.667 0.00 0.00 0.00 3.66
1137 1205 3.036429 ATCGAGTTGCAGGGGGAGC 62.036 63.158 0.00 0.00 0.00 4.70
1140 1211 0.533755 GATCATCGAGTTGCAGGGGG 60.534 60.000 0.00 0.00 0.00 5.40
1150 1221 2.862536 AGCAATTGACGTGATCATCGAG 59.137 45.455 19.74 6.76 37.11 4.04
1153 1224 3.103738 GCAAGCAATTGACGTGATCATC 58.896 45.455 10.34 0.00 37.11 2.92
1154 1225 2.488937 TGCAAGCAATTGACGTGATCAT 59.511 40.909 10.34 0.00 37.11 2.45
1155 1226 1.878734 TGCAAGCAATTGACGTGATCA 59.121 42.857 10.34 0.00 34.65 2.92
1161 1543 5.228635 GTCAGATAAATGCAAGCAATTGACG 59.771 40.000 10.34 0.00 0.00 4.35
1192 1574 3.524380 AGTAGGGTACTCTACTCACTGCT 59.476 47.826 26.76 6.21 44.62 4.24
1215 1597 1.866925 CGTCGCCCAAAGGAAGTTC 59.133 57.895 0.00 0.00 33.47 3.01
1238 1620 5.105023 CCAGCTCACCTGCATATATATCAGT 60.105 44.000 15.25 1.68 40.36 3.41
1239 1621 5.358090 CCAGCTCACCTGCATATATATCAG 58.642 45.833 11.96 11.96 40.36 2.90
1421 1805 3.451178 AGACGTACTTGAGCATGGGTATT 59.549 43.478 0.00 0.00 0.00 1.89
1558 1956 1.954528 CCAGCAAGAACAGCAGTGG 59.045 57.895 0.00 0.00 0.00 4.00
1566 1964 2.195922 CAAACAACAGCCAGCAAGAAC 58.804 47.619 0.00 0.00 0.00 3.01
1612 2014 2.078849 TTGCATACCGCGATATCAGG 57.921 50.000 8.23 11.49 46.97 3.86
2000 2428 3.073062 ACATACTTTGAGTGAGGCTTGGT 59.927 43.478 0.00 0.00 0.00 3.67
2009 2437 5.869344 TCCTTCGATTCACATACTTTGAGTG 59.131 40.000 0.00 0.00 34.67 3.51
2056 2488 8.561536 TGGACTGATGGGTAAAGAATATAAGA 57.438 34.615 0.00 0.00 0.00 2.10
2065 2497 3.941483 GTGTGATGGACTGATGGGTAAAG 59.059 47.826 0.00 0.00 0.00 1.85
2112 2555 2.480224 CACCACTTGTGCTGTTCAAG 57.520 50.000 10.61 10.61 45.15 3.02
2212 2655 0.320374 GGAACCACACCGAGATGACA 59.680 55.000 0.00 0.00 0.00 3.58
2251 2694 4.929211 TCATGAATGACGAGGTTGTACAAG 59.071 41.667 8.98 0.00 0.00 3.16
2267 2710 3.490933 CGTAGGACACCGACATCATGAAT 60.491 47.826 0.00 0.00 0.00 2.57
2458 2902 8.890718 AGTGAATTCATCATGTCAGATTAACTG 58.109 33.333 12.12 0.00 43.02 3.16
2602 3065 4.392138 GGTTCTGTTATGACTTGTGGCTAC 59.608 45.833 0.00 0.00 0.00 3.58
3134 3645 7.899178 AACACAAATCATTGATGTACGAGTA 57.101 32.000 0.00 0.00 38.94 2.59
3192 3703 6.318648 GTCACCAACATACATATCACACCAAT 59.681 38.462 0.00 0.00 0.00 3.16
3196 3707 5.232202 CGAGTCACCAACATACATATCACAC 59.768 44.000 0.00 0.00 0.00 3.82
3204 3715 1.337728 CCTGCGAGTCACCAACATACA 60.338 52.381 0.00 0.00 0.00 2.29
3346 3857 6.619464 ACAGTATGGAAGAGAGGTAGATCAT 58.381 40.000 0.00 0.00 43.62 2.45
3543 4054 1.307084 GTAGAGGAGGCCAACCCCT 60.307 63.158 5.01 6.91 38.81 4.79
4014 4537 2.015456 TCAGTTGCTTCTCCTCCTCA 57.985 50.000 0.00 0.00 0.00 3.86
4251 4774 2.054363 CATCCTCGATCATACGCACAC 58.946 52.381 0.00 0.00 0.00 3.82
4326 4852 3.753272 GCACACACACACATATCCTCTTT 59.247 43.478 0.00 0.00 0.00 2.52
4368 4894 4.881920 AGAAAACCATCAAATCCAAACCG 58.118 39.130 0.00 0.00 0.00 4.44
4457 4984 8.334263 TGAAGTTGTACTTGCAATATCATCAA 57.666 30.769 0.00 0.00 38.80 2.57
4458 4985 7.920160 TGAAGTTGTACTTGCAATATCATCA 57.080 32.000 0.00 0.00 38.80 3.07
4525 5064 1.401018 GCATTCCGACCGGTCAAAAAG 60.401 52.381 32.80 22.14 36.47 2.27
4534 5073 2.047274 ACCACTGCATTCCGACCG 60.047 61.111 0.00 0.00 0.00 4.79
4555 5094 4.796830 CGCATTCATGTTGAAAATCCTGAG 59.203 41.667 0.00 0.00 40.12 3.35
4556 5095 4.380761 CCGCATTCATGTTGAAAATCCTGA 60.381 41.667 0.00 0.00 40.12 3.86
4722 5312 7.065923 GGGGATTGTAGAGTTAACTTGTGATTC 59.934 40.741 10.02 4.12 0.00 2.52
4757 5348 4.313020 AGATGATGCCATTATTCCCCTC 57.687 45.455 0.00 0.00 32.09 4.30
4852 5450 4.082026 AGGAGCAAGGTGAAATTTATGCAC 60.082 41.667 12.11 7.30 36.30 4.57
4881 5479 4.284550 TGGCTCCCAGTGGGCAAC 62.285 66.667 24.75 15.32 43.94 4.17
4897 5495 1.324005 GGTCGAGGGAGGAAGGAGTG 61.324 65.000 0.00 0.00 0.00 3.51
4930 5528 4.223320 TCGAGTTTCAGCAACATTTTCC 57.777 40.909 0.00 0.00 37.93 3.13
4936 5534 3.466836 AGTCAATCGAGTTTCAGCAACA 58.533 40.909 0.00 0.00 37.93 3.33
4968 5570 3.895041 TCCATTGATCTGTCTGCCGTATA 59.105 43.478 0.00 0.00 0.00 1.47
4969 5571 2.700371 TCCATTGATCTGTCTGCCGTAT 59.300 45.455 0.00 0.00 0.00 3.06
5015 5617 8.718102 TTCTTCTAGGTTTCTGAATTTATCCG 57.282 34.615 0.00 0.00 0.00 4.18
5166 5772 0.401979 CTGATCCCCCACCCCACTAT 60.402 60.000 0.00 0.00 0.00 2.12


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

AutoCloner maintained by Alex Coulton.