Multiple sequence alignment - TraesCS5A01G547900

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 TraesCS5A01G547900 chr5A 100.000 4571 0 0 1 4571 702142043 702137473 0.000000e+00 8442.0
1 TraesCS5A01G547900 chr5A 97.561 41 1 0 3412 3452 702138672 702138632 2.280000e-08 71.3
2 TraesCS5A01G547900 chr4D 93.241 3388 171 22 1 3346 505993123 505989752 0.000000e+00 4935.0
3 TraesCS5A01G547900 chr4D 88.828 546 16 7 3738 4283 505989615 505989115 3.000000e-176 628.0
4 TraesCS5A01G547900 chr4D 95.533 291 13 0 4281 4571 505989063 505988773 2.490000e-127 466.0
5 TraesCS5A01G547900 chr4D 89.394 132 14 0 3412 3543 505989743 505989612 2.830000e-37 167.0
6 TraesCS5A01G547900 chr4B 88.850 3453 322 23 1 3402 661684377 661680937 0.000000e+00 4185.0
7 TraesCS5A01G547900 chr4B 89.680 2684 250 16 1 2663 661492475 661495152 0.000000e+00 3397.0
8 TraesCS5A01G547900 chr4B 91.710 1146 57 12 3412 4542 661495932 661497054 0.000000e+00 1555.0
9 TraesCS5A01G547900 chr4B 91.366 1135 60 14 3415 4542 661680964 661679861 0.000000e+00 1519.0
10 TraesCS5A01G547900 chr4B 94.063 758 41 2 2659 3412 661495215 661495972 0.000000e+00 1147.0
11 TraesCS5A01G547900 chrUn 77.257 1473 239 58 1948 3363 88950048 88951481 0.000000e+00 776.0
12 TraesCS5A01G547900 chrUn 77.273 1474 237 61 1948 3363 269543349 269541916 0.000000e+00 776.0
13 TraesCS5A01G547900 chrUn 77.174 1472 242 59 1948 3363 88958397 88959830 0.000000e+00 771.0
14 TraesCS5A01G547900 chrUn 80.504 754 113 22 3421 4162 88953443 88954174 8.650000e-152 547.0
15 TraesCS5A01G547900 chrUn 80.504 754 113 22 3421 4162 269539954 269539223 8.650000e-152 547.0
16 TraesCS5A01G547900 chrUn 80.461 737 109 23 3438 4162 88961853 88962566 8.710000e-147 531.0
17 TraesCS5A01G547900 chr1B 85.211 568 56 17 3700 4262 89697421 89696877 3.990000e-155 558.0
18 TraesCS5A01G547900 chr1B 86.381 257 32 3 4317 4571 89696854 89696599 1.250000e-70 278.0
19 TraesCS5A01G547900 chr7B 82.651 611 89 8 2802 3406 746223777 746224376 4.050000e-145 525.0
20 TraesCS5A01G547900 chr7B 83.363 565 87 6 2847 3406 744679414 744678852 2.440000e-142 516.0
21 TraesCS5A01G547900 chr7B 80.723 332 43 15 3833 4158 744678557 744678241 5.910000e-59 239.0
22 TraesCS5A01G547900 chr7B 80.180 333 45 14 3833 4159 746224671 746224988 3.560000e-56 230.0
23 TraesCS5A01G547900 chr7D 82.250 569 94 7 2844 3406 632498658 632498091 6.880000e-133 484.0
24 TraesCS5A01G547900 chr7A 82.222 180 30 2 4367 4544 735053594 735053415 2.200000e-33 154.0


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 TraesCS5A01G547900 chr5A 702137473 702142043 4570 True 4256.65 8442 98.780500 1 4571 2 chr5A.!!$R1 4570
1 TraesCS5A01G547900 chr4D 505988773 505993123 4350 True 1549.00 4935 91.749000 1 4571 4 chr4D.!!$R1 4570
2 TraesCS5A01G547900 chr4B 661679861 661684377 4516 True 2852.00 4185 90.108000 1 4542 2 chr4B.!!$R1 4541
3 TraesCS5A01G547900 chr4B 661492475 661497054 4579 False 2033.00 3397 91.817667 1 4542 3 chr4B.!!$F1 4541
4 TraesCS5A01G547900 chrUn 88950048 88954174 4126 False 661.50 776 78.880500 1948 4162 2 chrUn.!!$F1 2214
5 TraesCS5A01G547900 chrUn 269539223 269543349 4126 True 661.50 776 78.888500 1948 4162 2 chrUn.!!$R1 2214
6 TraesCS5A01G547900 chrUn 88958397 88962566 4169 False 651.00 771 78.817500 1948 4162 2 chrUn.!!$F2 2214
7 TraesCS5A01G547900 chr1B 89696599 89697421 822 True 418.00 558 85.796000 3700 4571 2 chr1B.!!$R1 871
8 TraesCS5A01G547900 chr7B 744678241 744679414 1173 True 377.50 516 82.043000 2847 4158 2 chr7B.!!$R1 1311
9 TraesCS5A01G547900 chr7B 746223777 746224988 1211 False 377.50 525 81.415500 2802 4159 2 chr7B.!!$F1 1357
10 TraesCS5A01G547900 chr7D 632498091 632498658 567 True 484.00 484 82.250000 2844 3406 1 chr7D.!!$R1 562

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
136 147 0.251341 AGATGCAAGGGGTGTTCCAC 60.251 55.0 0.0 0.0 37.22 4.02 F
1242 1266 0.101040 CAATACCGTCGTTCCGCCTA 59.899 55.0 0.0 0.0 0.00 3.93 F
1578 1602 0.105039 CCGGCTCTAGGCTCGATTTT 59.895 55.0 0.0 0.0 41.46 1.82 F
1818 1842 0.179067 TCTTTGCGAACCTCCACGTT 60.179 50.0 0.0 0.0 0.00 3.99 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1487 1511 0.096976 GGCGTCGTGTTCATTCATGG 59.903 55.000 0.0 0.0 0.0 3.66 R
2442 2483 1.066143 TGTTCGGCCTTGATCCTCTTC 60.066 52.381 0.0 0.0 0.0 2.87 R
3528 5636 0.902531 TCCCCTTGAACGAGATCACC 59.097 55.000 0.0 0.0 0.0 4.02 R
3593 5701 1.402259 ACTCTATGAAGCGAGGACACG 59.598 52.381 0.0 0.0 0.0 4.49 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
54 64 4.116961 CCTCAAAACCGAGATAACGCATA 58.883 43.478 0.00 0.00 34.79 3.14
99 109 6.465751 CCTTAGGCCCACAATTCATAGACATA 60.466 42.308 0.00 0.00 0.00 2.29
112 122 6.402981 TCATAGACATAGGTGGCCTCTATA 57.597 41.667 15.52 5.98 34.61 1.31
128 139 4.163078 CCTCTATACCATAGATGCAAGGGG 59.837 50.000 0.00 0.00 0.00 4.79
129 140 4.763355 TCTATACCATAGATGCAAGGGGT 58.237 43.478 0.00 0.00 0.00 4.95
135 146 1.367346 TAGATGCAAGGGGTGTTCCA 58.633 50.000 0.00 0.00 37.22 3.53
136 147 0.251341 AGATGCAAGGGGTGTTCCAC 60.251 55.000 0.00 0.00 37.22 4.02
143 155 2.067365 AGGGGTGTTCCACTTTTCAC 57.933 50.000 0.00 0.00 46.91 3.18
146 158 2.764010 GGGGTGTTCCACTTTTCACTTT 59.236 45.455 0.00 0.00 37.22 2.66
149 161 4.629634 GGGTGTTCCACTTTTCACTTTTTG 59.370 41.667 0.00 0.00 34.40 2.44
150 162 4.092821 GGTGTTCCACTTTTCACTTTTTGC 59.907 41.667 0.00 0.00 34.40 3.68
151 163 4.688413 GTGTTCCACTTTTCACTTTTTGCA 59.312 37.500 0.00 0.00 0.00 4.08
152 164 4.688413 TGTTCCACTTTTCACTTTTTGCAC 59.312 37.500 0.00 0.00 0.00 4.57
154 166 3.057174 TCCACTTTTCACTTTTTGCACGT 60.057 39.130 0.00 0.00 0.00 4.49
155 167 4.156190 TCCACTTTTCACTTTTTGCACGTA 59.844 37.500 0.00 0.00 0.00 3.57
156 168 4.499040 CCACTTTTCACTTTTTGCACGTAG 59.501 41.667 0.00 0.00 0.00 3.51
158 170 5.971202 CACTTTTCACTTTTTGCACGTAGAT 59.029 36.000 0.00 0.00 0.00 1.98
159 171 6.140737 CACTTTTCACTTTTTGCACGTAGATC 59.859 38.462 0.00 0.00 0.00 2.75
160 172 4.383774 TTCACTTTTTGCACGTAGATCG 57.616 40.909 0.00 0.00 46.00 3.69
161 173 3.644823 TCACTTTTTGCACGTAGATCGA 58.355 40.909 0.00 0.00 42.86 3.59
162 174 4.242475 TCACTTTTTGCACGTAGATCGAT 58.758 39.130 0.00 0.00 42.86 3.59
174 194 0.977627 AGATCGATGACAGGGTGGCA 60.978 55.000 0.54 0.00 41.29 4.92
221 241 1.555075 GGTGTCTACAGATGCAAGGGA 59.445 52.381 0.00 0.00 0.00 4.20
232 252 3.766051 AGATGCAAGGGATGTTCCTTTTC 59.234 43.478 0.00 0.00 44.14 2.29
241 261 2.094100 TGTTCCTTTTCCCCATGCAA 57.906 45.000 0.00 0.00 0.00 4.08
336 357 8.554528 TCGGATAAGTTAGAACATTACTACTCG 58.445 37.037 0.00 0.00 0.00 4.18
447 468 5.572511 TCAAATGCGACAAAAATACATCTGC 59.427 36.000 0.00 0.00 0.00 4.26
476 497 3.995048 TGTATAGCACTCGTCCTCTATCG 59.005 47.826 0.00 0.00 0.00 2.92
499 520 4.694760 TGTTGCCTGATGTAGATAGCAT 57.305 40.909 0.00 0.00 0.00 3.79
528 549 3.181480 CCTGTCACCCGTCAAATTTTGTT 60.181 43.478 8.89 0.00 0.00 2.83
593 614 8.607459 CCTCAGAACAAATACATTATCTGTCAC 58.393 37.037 0.00 0.00 39.39 3.67
594 615 9.376075 CTCAGAACAAATACATTATCTGTCACT 57.624 33.333 0.00 0.00 39.39 3.41
682 703 1.580845 AATTGTCTGCAGTGCGCTCC 61.581 55.000 14.67 0.00 43.06 4.70
702 723 5.619533 GCTCCGAGTTCTATATAAACGGGAG 60.620 48.000 23.91 23.91 45.25 4.30
823 844 7.931948 CACCTTGAAGTAGGTTATAGGGTAATG 59.068 40.741 0.00 0.00 46.39 1.90
842 863 0.315251 GGAAGCAAGAAAGCCACCAC 59.685 55.000 0.00 0.00 34.23 4.16
905 926 6.353082 CCAACTCCAACTATAGTCAAATCCCT 60.353 42.308 5.70 0.00 0.00 4.20
908 929 6.040616 ACTCCAACTATAGTCAAATCCCTACG 59.959 42.308 5.70 0.00 0.00 3.51
931 955 5.130705 ACTCTTCTTCCACCCTTTCTTTT 57.869 39.130 0.00 0.00 0.00 2.27
933 957 4.134563 TCTTCTTCCACCCTTTCTTTTCG 58.865 43.478 0.00 0.00 0.00 3.46
1050 1074 0.901827 TCTCTGGCGAAACCTATGCA 59.098 50.000 0.00 0.00 40.22 3.96
1071 1095 2.105128 GCTGTCTCATCGGACCCG 59.895 66.667 1.31 1.31 41.35 5.28
1078 1102 2.760799 CATCGGACCCGGTACCCA 60.761 66.667 6.25 0.00 40.25 4.51
1079 1103 2.039299 ATCGGACCCGGTACCCAA 59.961 61.111 6.25 0.00 40.25 4.12
1095 1119 1.372582 CCAACGACATCCATGGACAG 58.627 55.000 18.99 15.50 34.82 3.51
1107 1131 3.260884 TCCATGGACAGTCCTTCAAGTAC 59.739 47.826 20.82 0.00 37.46 2.73
1118 1142 3.259876 TCCTTCAAGTACGTGCCAATAGT 59.740 43.478 3.67 0.00 0.00 2.12
1150 1174 3.433031 CGACAAGTCCCCAATGGCTAATA 60.433 47.826 0.00 0.00 0.00 0.98
1176 1200 5.473504 GCTCTCATCAAAAACACCCTTCTTA 59.526 40.000 0.00 0.00 0.00 2.10
1242 1266 0.101040 CAATACCGTCGTTCCGCCTA 59.899 55.000 0.00 0.00 0.00 3.93
1260 1284 5.452776 CCGCCTACTTAATGAGTTGATGGTA 60.453 44.000 0.00 0.00 39.86 3.25
1281 1305 0.800631 CGCAATCATCTGTGTGCACT 59.199 50.000 19.41 0.00 36.80 4.40
1459 1483 2.821437 TCTCATCGTCCTCCTCCTTTT 58.179 47.619 0.00 0.00 0.00 2.27
1487 1511 1.676014 CCGGGACAGTGTTTCTCATCC 60.676 57.143 0.00 0.00 0.00 3.51
1492 1516 3.307691 GGACAGTGTTTCTCATCCCATGA 60.308 47.826 0.00 0.00 37.76 3.07
1493 1517 4.326826 GACAGTGTTTCTCATCCCATGAA 58.673 43.478 0.00 0.00 39.11 2.57
1502 1526 3.197549 TCTCATCCCATGAATGAACACGA 59.802 43.478 10.68 4.02 39.11 4.35
1578 1602 0.105039 CCGGCTCTAGGCTCGATTTT 59.895 55.000 0.00 0.00 41.46 1.82
1641 1665 7.092444 ACTGAGGTGTCAAATATGGATTCCTTA 60.092 37.037 3.95 2.40 30.14 2.69
1644 1668 5.241728 GGTGTCAAATATGGATTCCTTAGGC 59.758 44.000 3.95 0.00 0.00 3.93
1668 1692 4.451150 GATCACCGCTCGCCACCA 62.451 66.667 0.00 0.00 0.00 4.17
1701 1725 3.664888 TGGGCTCAAGGCATGGCT 61.665 61.111 17.44 17.44 44.01 4.75
1738 1762 1.979693 GTGGCGGTCTCAGAGGAGT 60.980 63.158 0.00 0.00 42.05 3.85
1764 1788 1.271488 TGGGTGTTCGTGGGGATTTAC 60.271 52.381 0.00 0.00 0.00 2.01
1774 1798 0.812811 GGGGATTTACGACGGCTTCC 60.813 60.000 0.00 0.00 0.00 3.46
1782 1806 3.069318 GACGGCTTCCTCGGTCCT 61.069 66.667 0.00 0.00 32.29 3.85
1818 1842 0.179067 TCTTTGCGAACCTCCACGTT 60.179 50.000 0.00 0.00 0.00 3.99
1875 1899 1.855295 ACATCCAATGCAATGAGCCA 58.145 45.000 2.50 0.00 44.83 4.75
1901 1925 9.918630 AACAACCAATTCTGATAATCTCTTTTG 57.081 29.630 0.00 0.00 0.00 2.44
2295 2320 1.350351 AGATCATGGATGGCCTACAGC 59.650 52.381 3.32 0.00 42.60 4.40
2442 2483 1.866015 TCTGGGTGATACAGGAGGTG 58.134 55.000 0.00 0.00 36.62 4.00
2465 2506 2.771943 AGAGGATCAAGGCCGAACATAA 59.228 45.455 0.00 0.00 37.82 1.90
2539 2583 2.911143 CATTCGGGGCTGGCTACT 59.089 61.111 0.00 0.00 0.00 2.57
2719 2831 4.202295 TGCTATCAGTCTAGCATTCAAGGG 60.202 45.833 1.81 0.00 46.92 3.95
2761 2873 7.283127 TCCAGTTAATTCCATGAGATAAGTTGC 59.717 37.037 0.00 0.00 0.00 4.17
2792 2904 4.020543 TGCGTAGGCCCTTTAATTCATTT 58.979 39.130 0.00 0.00 38.85 2.32
2878 2992 9.185192 GTTGATGAAGAACCTAAAAATTGTGAG 57.815 33.333 0.00 0.00 0.00 3.51
2893 3007 6.389830 AATTGTGAGTGTGACTTGCAATTA 57.610 33.333 0.00 0.00 39.10 1.40
3015 3132 3.754850 TCCTGAAATGTCAATCTGCACAG 59.245 43.478 0.00 0.00 31.88 3.66
3029 3146 4.835678 TCTGCACAGCTGATAATTCAAGA 58.164 39.130 23.35 8.39 31.90 3.02
3146 3264 1.073722 CCATCACTGCACCACCACT 59.926 57.895 0.00 0.00 0.00 4.00
3231 5335 1.815003 CAAAGAGGTGGTTGATGAGGC 59.185 52.381 0.00 0.00 0.00 4.70
3363 5469 1.532316 AACACAAGCCTGCCTGCAT 60.532 52.632 0.00 0.00 0.00 3.96
3368 5474 0.889994 CAAGCCTGCCTGCATAAACA 59.110 50.000 0.00 0.00 0.00 2.83
3369 5475 0.890683 AAGCCTGCCTGCATAAACAC 59.109 50.000 0.00 0.00 0.00 3.32
3399 5507 9.619316 TTTTGAAATTGTTCGTACCTTCATATG 57.381 29.630 0.00 0.00 36.46 1.78
3400 5508 6.781138 TGAAATTGTTCGTACCTTCATATGC 58.219 36.000 0.00 0.00 36.46 3.14
3401 5509 5.751243 AATTGTTCGTACCTTCATATGCC 57.249 39.130 0.00 0.00 0.00 4.40
3402 5510 4.481368 TTGTTCGTACCTTCATATGCCT 57.519 40.909 0.00 0.00 0.00 4.75
3403 5511 5.601583 TTGTTCGTACCTTCATATGCCTA 57.398 39.130 0.00 0.00 0.00 3.93
3404 5512 5.801531 TGTTCGTACCTTCATATGCCTAT 57.198 39.130 0.00 0.00 0.00 2.57
3405 5513 6.169557 TGTTCGTACCTTCATATGCCTATT 57.830 37.500 0.00 0.00 0.00 1.73
3406 5514 5.989168 TGTTCGTACCTTCATATGCCTATTG 59.011 40.000 0.00 0.00 0.00 1.90
3407 5515 5.801531 TCGTACCTTCATATGCCTATTGT 57.198 39.130 0.00 0.00 0.00 2.71
3408 5516 6.169557 TCGTACCTTCATATGCCTATTGTT 57.830 37.500 0.00 0.00 0.00 2.83
3409 5517 6.588204 TCGTACCTTCATATGCCTATTGTTT 58.412 36.000 0.00 0.00 0.00 2.83
3410 5518 7.051623 TCGTACCTTCATATGCCTATTGTTTT 58.948 34.615 0.00 0.00 0.00 2.43
3411 5519 7.554835 TCGTACCTTCATATGCCTATTGTTTTT 59.445 33.333 0.00 0.00 0.00 1.94
3480 5588 3.265791 GGACTACCATGAACTGCTCAAG 58.734 50.000 0.00 0.00 37.67 3.02
3517 5625 7.147724 ACGAAAGGAGAAAGTACCATGATGATA 60.148 37.037 0.00 0.00 0.00 2.15
3528 5636 8.843885 AGTACCATGATGATATTTCTGTCATG 57.156 34.615 17.08 17.08 40.92 3.07
3553 5661 0.179000 CTCGTTCAAGGGGAGGATGG 59.821 60.000 0.00 0.00 0.00 3.51
3586 5694 2.752903 GTTTAGGCATAGTGTTGGTGGG 59.247 50.000 0.00 0.00 0.00 4.61
3593 5701 0.254747 TAGTGTTGGTGGGGCATAGC 59.745 55.000 0.00 0.00 0.00 2.97
3723 5838 2.766313 TGGTGACATCGGAAAGACAAG 58.234 47.619 0.00 0.00 33.40 3.16
3905 6025 0.684153 ATCAGGTTTCCCGGCAATGG 60.684 55.000 0.00 0.00 35.12 3.16
3915 6035 1.142060 CCCGGCAATGGTGGTTATAGA 59.858 52.381 0.00 0.00 0.00 1.98
3928 6051 5.013079 GGTGGTTATAGATGATGGTGATGGA 59.987 44.000 0.00 0.00 0.00 3.41
3934 6057 8.778358 GTTATAGATGATGGTGATGGAAAGAAC 58.222 37.037 0.00 0.00 0.00 3.01
3935 6058 5.183530 AGATGATGGTGATGGAAAGAACA 57.816 39.130 0.00 0.00 0.00 3.18
3938 6061 2.584835 TGGTGATGGAAAGAACAGGG 57.415 50.000 0.00 0.00 0.00 4.45
3939 6062 1.075374 TGGTGATGGAAAGAACAGGGG 59.925 52.381 0.00 0.00 0.00 4.79
3942 6065 3.496331 GTGATGGAAAGAACAGGGGAAA 58.504 45.455 0.00 0.00 0.00 3.13
3943 6066 3.255888 GTGATGGAAAGAACAGGGGAAAC 59.744 47.826 0.00 0.00 0.00 2.78
3945 6068 2.944129 TGGAAAGAACAGGGGAAACTG 58.056 47.619 0.00 0.00 44.03 3.16
4029 6154 7.671819 TGCTATATTCCAGTACTAGAAGCTGAT 59.328 37.037 9.60 3.70 32.39 2.90
4076 6201 6.636562 TTTACCCAATTAAAACTTCTCGCA 57.363 33.333 0.00 0.00 0.00 5.10
4175 6305 6.932356 AGACTATGCATACTGATTTTGGTG 57.068 37.500 1.16 0.00 0.00 4.17
4200 6331 6.405842 GGGGAGAAACATAGCCTAAACATTTG 60.406 42.308 0.00 0.00 0.00 2.32
4284 6477 7.179160 TGGTCCTATGACTCATATTCATGTAGG 59.821 40.741 0.00 0.00 41.47 3.18
4339 6534 3.135530 AGTTGGCCATATCCAGAAGTCTC 59.864 47.826 6.09 0.00 37.44 3.36
4547 6745 2.101783 CTGCAACCTCATTAATGGCCA 58.898 47.619 8.56 8.56 0.00 5.36
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
29 32 4.142116 TGCGTTATCTCGGTTTTGAGGATA 60.142 41.667 0.00 0.00 36.61 2.59
99 109 4.357325 CATCTATGGTATAGAGGCCACCT 58.643 47.826 5.01 3.86 37.62 4.00
112 122 1.298953 ACACCCCTTGCATCTATGGT 58.701 50.000 0.00 0.00 0.00 3.55
129 140 4.688413 GTGCAAAAAGTGAAAAGTGGAACA 59.312 37.500 0.00 0.00 41.43 3.18
135 146 5.554822 TCTACGTGCAAAAAGTGAAAAGT 57.445 34.783 0.00 0.00 0.00 2.66
136 147 5.336990 CGATCTACGTGCAAAAAGTGAAAAG 59.663 40.000 0.00 0.00 37.22 2.27
143 155 4.091365 TGTCATCGATCTACGTGCAAAAAG 59.909 41.667 0.00 0.00 43.13 2.27
146 158 3.179048 CTGTCATCGATCTACGTGCAAA 58.821 45.455 0.00 0.00 43.13 3.68
149 161 1.600663 CCCTGTCATCGATCTACGTGC 60.601 57.143 0.00 0.00 43.13 5.34
150 162 1.676529 ACCCTGTCATCGATCTACGTG 59.323 52.381 0.00 0.00 43.13 4.49
151 163 1.676529 CACCCTGTCATCGATCTACGT 59.323 52.381 0.00 0.00 43.13 3.57
152 164 1.001268 CCACCCTGTCATCGATCTACG 60.001 57.143 0.00 0.00 44.09 3.51
154 166 1.040646 GCCACCCTGTCATCGATCTA 58.959 55.000 0.00 0.00 0.00 1.98
155 167 0.977627 TGCCACCCTGTCATCGATCT 60.978 55.000 0.00 0.00 0.00 2.75
156 168 0.811616 GTGCCACCCTGTCATCGATC 60.812 60.000 0.00 0.00 0.00 3.69
158 170 1.913262 AGTGCCACCCTGTCATCGA 60.913 57.895 0.00 0.00 0.00 3.59
159 171 1.742880 CAGTGCCACCCTGTCATCG 60.743 63.158 0.00 0.00 0.00 3.84
160 172 2.042831 GCAGTGCCACCCTGTCATC 61.043 63.158 2.85 0.00 32.41 2.92
161 173 2.034687 GCAGTGCCACCCTGTCAT 59.965 61.111 2.85 0.00 32.41 3.06
193 213 3.668447 CATCTGTAGACACCAAGTTGCT 58.332 45.455 0.00 0.00 0.00 3.91
221 241 2.323999 TGCATGGGGAAAAGGAACAT 57.676 45.000 0.00 0.00 0.00 2.71
232 252 2.334946 CGTGTGACCTTGCATGGGG 61.335 63.158 21.67 10.90 0.00 4.96
235 255 1.511850 TTCTCGTGTGACCTTGCATG 58.488 50.000 0.00 0.00 0.00 4.06
241 261 4.543590 AGATTCAATTCTCGTGTGACCT 57.456 40.909 0.00 0.00 0.00 3.85
476 497 4.635223 TGCTATCTACATCAGGCAACATC 58.365 43.478 0.00 0.00 41.41 3.06
528 549 1.079127 GCCGAGGAACTTGCTAGCA 60.079 57.895 14.93 14.93 41.55 3.49
593 614 6.024049 GCGGTTTGATTTCTTGAAGATACAG 58.976 40.000 0.00 0.00 0.00 2.74
594 615 5.705441 AGCGGTTTGATTTCTTGAAGATACA 59.295 36.000 0.00 0.00 0.00 2.29
682 703 5.240183 TCACCTCCCGTTTATATAGAACTCG 59.760 44.000 6.36 0.43 0.00 4.18
702 723 3.181472 GGATGAATTGAAATGGCCTCACC 60.181 47.826 3.32 0.00 39.84 4.02
823 844 0.315251 GTGGTGGCTTTCTTGCTTCC 59.685 55.000 0.00 0.00 0.00 3.46
842 863 4.578105 GGCAATCCTTCCTTAGAGTGAATG 59.422 45.833 0.00 0.00 29.81 2.67
905 926 2.599408 AGGGTGGAAGAAGAGTCGTA 57.401 50.000 0.00 0.00 0.00 3.43
908 929 4.359434 AAGAAAGGGTGGAAGAAGAGTC 57.641 45.455 0.00 0.00 0.00 3.36
931 955 5.395324 GGGATGGATGAGTAGAAGTTTTCGA 60.395 44.000 0.00 0.00 34.02 3.71
933 957 5.104318 AGGGGATGGATGAGTAGAAGTTTTC 60.104 44.000 0.00 0.00 0.00 2.29
1050 1074 2.362503 TCCGATGAGACAGCCGGT 60.363 61.111 1.90 0.00 42.34 5.28
1078 1102 1.066143 GGACTGTCCATGGATGTCGTT 60.066 52.381 28.71 11.12 36.28 3.85
1079 1103 0.537188 GGACTGTCCATGGATGTCGT 59.463 55.000 28.71 19.66 36.28 4.34
1095 1119 1.873698 TTGGCACGTACTTGAAGGAC 58.126 50.000 3.09 0.00 0.00 3.85
1107 1131 2.514013 GGCGACGACTATTGGCACG 61.514 63.158 0.00 0.00 0.00 5.34
1150 1174 3.771216 AGGGTGTTTTTGATGAGAGCAT 58.229 40.909 0.00 0.00 37.47 3.79
1176 1200 0.468226 TGGCCGCTCCGAATAAAGAT 59.532 50.000 0.00 0.00 37.80 2.40
1242 1266 4.189231 GCGGTACCATCAACTCATTAAGT 58.811 43.478 13.54 0.00 41.10 2.24
1260 1284 0.606130 TGCACACAGATGATTGCGGT 60.606 50.000 0.00 0.00 37.82 5.68
1459 1483 1.416243 ACACTGTCCCGGTGACTAAA 58.584 50.000 19.61 3.86 42.79 1.85
1487 1511 0.096976 GGCGTCGTGTTCATTCATGG 59.903 55.000 0.00 0.00 0.00 3.66
1492 1516 1.651987 CCTATGGCGTCGTGTTCATT 58.348 50.000 0.00 0.00 0.00 2.57
1493 1517 0.810031 GCCTATGGCGTCGTGTTCAT 60.810 55.000 0.00 0.00 39.62 2.57
1536 1560 4.619160 GCTGTGGCTAAGGATTTTTCAAGG 60.619 45.833 0.00 0.00 35.22 3.61
1539 1563 2.825532 GGCTGTGGCTAAGGATTTTTCA 59.174 45.455 0.00 0.00 38.73 2.69
1566 1590 2.235155 TGGCACACTAAAATCGAGCCTA 59.765 45.455 7.87 0.00 41.12 3.93
1668 1692 1.518056 CCCACTGCACATTGTCGCTT 61.518 55.000 10.93 0.00 0.00 4.68
1674 1698 0.242825 CTTGAGCCCACTGCACATTG 59.757 55.000 0.00 0.00 44.83 2.82
1713 1737 2.266055 GAGACCGCCACCTGGAAG 59.734 66.667 0.00 0.00 37.39 3.46
1738 1762 2.190843 CACGAACACCCACCCACA 59.809 61.111 0.00 0.00 0.00 4.17
1764 1788 4.493747 GGACCGAGGAAGCCGTCG 62.494 72.222 0.00 0.00 46.61 5.12
1774 1798 2.105128 GGTCGCATCAGGACCGAG 59.895 66.667 0.00 0.00 44.04 4.63
1782 1806 0.393944 AGAGGTAGTCGGTCGCATCA 60.394 55.000 0.00 0.00 0.00 3.07
1825 1849 3.494850 CACCCTTGAGTGTGTGGTT 57.505 52.632 0.00 0.00 32.89 3.67
1863 1887 1.340088 TGGTTGTTGGCTCATTGCAT 58.660 45.000 0.00 0.00 45.15 3.96
1875 1899 9.918630 CAAAAGAGATTATCAGAATTGGTTGTT 57.081 29.630 0.00 0.00 0.00 2.83
1916 1940 3.278574 CGTTCAAATTCTGGGCTATGGA 58.721 45.455 0.00 0.00 0.00 3.41
1917 1941 3.016736 ACGTTCAAATTCTGGGCTATGG 58.983 45.455 0.00 0.00 0.00 2.74
2039 2063 3.071206 TCTCCCTCAGCGCCTGAC 61.071 66.667 2.29 0.00 35.39 3.51
2096 2121 1.682849 CCCAATCTCCGGGTTGTCA 59.317 57.895 0.00 0.00 39.05 3.58
2211 2236 5.385198 GAGGATGTTATTAAGATTGGGCCA 58.615 41.667 0.00 0.00 0.00 5.36
2212 2237 4.455877 CGAGGATGTTATTAAGATTGGGCC 59.544 45.833 0.00 0.00 0.00 5.80
2442 2483 1.066143 TGTTCGGCCTTGATCCTCTTC 60.066 52.381 0.00 0.00 0.00 2.87
2598 2643 2.086869 CAATGGTCGGAGATGTGCTTT 58.913 47.619 0.00 0.00 40.67 3.51
2719 2831 3.996480 ACTGGAAACACAGACTTCTAGC 58.004 45.455 0.00 0.00 40.97 3.42
2761 2873 1.227380 GGCCTACGCATGAGGTGAG 60.227 63.158 0.00 0.00 36.37 3.51
2809 2921 6.992063 ATTGTTGAGCTAATGTTGGACTAG 57.008 37.500 0.00 0.00 0.00 2.57
2842 2956 1.402613 TCTTCATCAACATGCATGGCG 59.597 47.619 29.41 19.53 0.00 5.69
3015 3132 6.804770 ATGAGCATCTCTTGAATTATCAGC 57.195 37.500 0.00 0.00 34.21 4.26
3146 3264 2.036217 ACTTGTCGTTTGGACCGATACA 59.964 45.455 0.00 0.00 45.46 2.29
3328 5433 4.323417 TGTGTTGTGCAAAGTATAGAGGG 58.677 43.478 0.00 0.00 0.00 4.30
3413 5521 9.619316 CATATGAAGGTACGAACAATTTCAAAA 57.381 29.630 0.00 0.00 30.74 2.44
3414 5522 7.753132 GCATATGAAGGTACGAACAATTTCAAA 59.247 33.333 6.97 0.00 30.74 2.69
3415 5523 7.247728 GCATATGAAGGTACGAACAATTTCAA 58.752 34.615 6.97 0.00 30.74 2.69
3416 5524 6.183360 GGCATATGAAGGTACGAACAATTTCA 60.183 38.462 6.97 0.00 0.00 2.69
3417 5525 6.038271 AGGCATATGAAGGTACGAACAATTTC 59.962 38.462 6.97 0.00 0.00 2.17
3418 5526 5.885912 AGGCATATGAAGGTACGAACAATTT 59.114 36.000 6.97 0.00 0.00 1.82
3419 5527 5.437060 AGGCATATGAAGGTACGAACAATT 58.563 37.500 6.97 0.00 0.00 2.32
3420 5528 5.036117 AGGCATATGAAGGTACGAACAAT 57.964 39.130 6.97 0.00 0.00 2.71
3421 5529 4.481368 AGGCATATGAAGGTACGAACAA 57.519 40.909 6.97 0.00 0.00 2.83
3422 5530 5.801531 ATAGGCATATGAAGGTACGAACA 57.198 39.130 6.97 0.00 0.00 3.18
3423 5531 6.220930 TCAATAGGCATATGAAGGTACGAAC 58.779 40.000 6.97 0.00 0.00 3.95
3424 5532 6.413783 TCAATAGGCATATGAAGGTACGAA 57.586 37.500 6.97 0.00 0.00 3.85
3425 5533 6.605471 ATCAATAGGCATATGAAGGTACGA 57.395 37.500 6.97 0.00 0.00 3.43
3426 5534 7.672983 AAATCAATAGGCATATGAAGGTACG 57.327 36.000 6.97 0.00 0.00 3.67
3427 5535 9.066892 TGAAAATCAATAGGCATATGAAGGTAC 57.933 33.333 6.97 0.00 0.00 3.34
3428 5536 9.288576 CTGAAAATCAATAGGCATATGAAGGTA 57.711 33.333 6.97 0.00 0.00 3.08
3429 5537 7.232127 CCTGAAAATCAATAGGCATATGAAGGT 59.768 37.037 6.97 0.00 0.00 3.50
3430 5538 7.232127 ACCTGAAAATCAATAGGCATATGAAGG 59.768 37.037 6.97 0.00 33.57 3.46
3431 5539 8.174733 ACCTGAAAATCAATAGGCATATGAAG 57.825 34.615 6.97 0.00 33.57 3.02
3432 5540 9.812347 ATACCTGAAAATCAATAGGCATATGAA 57.188 29.630 6.97 0.00 33.57 2.57
3433 5541 9.234827 CATACCTGAAAATCAATAGGCATATGA 57.765 33.333 6.97 0.00 33.57 2.15
3434 5542 8.464404 CCATACCTGAAAATCAATAGGCATATG 58.536 37.037 0.00 0.00 33.57 1.78
3435 5543 8.393259 TCCATACCTGAAAATCAATAGGCATAT 58.607 33.333 0.00 0.00 33.57 1.78
3436 5544 7.665559 GTCCATACCTGAAAATCAATAGGCATA 59.334 37.037 0.00 0.00 33.57 3.14
3480 5588 4.873746 TCTCCTTTCGTCATGGGATATC 57.126 45.455 0.00 0.00 0.00 1.63
3517 5625 4.478206 ACGAGATCACCATGACAGAAAT 57.522 40.909 0.00 0.00 0.00 2.17
3528 5636 0.902531 TCCCCTTGAACGAGATCACC 59.097 55.000 0.00 0.00 0.00 4.02
3593 5701 1.402259 ACTCTATGAAGCGAGGACACG 59.598 52.381 0.00 0.00 0.00 4.49
3643 5757 9.498176 GGTCTTTATTAACTCTGAAACACCTTA 57.502 33.333 0.00 0.00 0.00 2.69
3723 5838 1.423395 CTTTGACAGTCCTGCTCGTC 58.577 55.000 0.00 0.00 0.00 4.20
3772 5888 6.653989 TCTCAAGAGAAGGAAAACAAAGACT 58.346 36.000 0.00 0.00 33.91 3.24
3905 6025 6.114187 TCCATCACCATCATCTATAACCAC 57.886 41.667 0.00 0.00 0.00 4.16
3915 6035 4.275810 CCTGTTCTTTCCATCACCATCAT 58.724 43.478 0.00 0.00 0.00 2.45
3928 6051 9.462606 CTTATTATACAGTTTCCCCTGTTCTTT 57.537 33.333 0.00 0.00 42.99 2.52
3934 6057 6.591935 TGAGCTTATTATACAGTTTCCCCTG 58.408 40.000 0.00 0.00 38.45 4.45
3935 6058 6.824958 TGAGCTTATTATACAGTTTCCCCT 57.175 37.500 0.00 0.00 0.00 4.79
4029 6154 3.129502 GGCGCAGAGAAGCATGCA 61.130 61.111 21.98 0.00 42.68 3.96
4175 6305 4.230745 TGTTTAGGCTATGTTTCTCCCC 57.769 45.455 0.00 0.00 0.00 4.81


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

AutoCloner maintained by Alex Coulton.