Multiple sequence alignment - TraesCS7A01G085100

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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 TraesCS7A01G085100 chr7A 100.000 2195 0 0 1 2195 49234700 49232506 0.000000e+00 4054.0
1 TraesCS7A01G085100 chr7A 90.674 193 17 1 241 432 49270757 49270565 2.800000e-64 255.0
2 TraesCS7A01G085100 chr7A 78.780 410 43 24 61 451 49354352 49353968 3.640000e-58 235.0
3 TraesCS7A01G085100 chr4A 87.381 1680 87 53 565 2195 661302080 661300477 0.000000e+00 1812.0
4 TraesCS7A01G085100 chr4A 83.590 390 27 14 202 569 661302502 661302128 4.520000e-87 331.0
5 TraesCS7A01G085100 chr4A 85.780 218 25 4 243 459 661318590 661318378 2.190000e-55 226.0
6 TraesCS7A01G085100 chr4A 89.655 145 9 2 200 344 661313325 661313187 1.730000e-41 180.0
7 TraesCS7A01G085100 chr7D 88.354 1185 78 16 624 1785 46964920 46963773 0.000000e+00 1369.0
8 TraesCS7A01G085100 chr7D 91.143 350 21 5 1841 2189 46961518 46961178 1.190000e-127 466.0
9 TraesCS7A01G085100 chr7D 90.291 206 17 3 134 338 47113972 47113769 1.290000e-67 267.0
10 TraesCS7A01G085100 chr7D 85.714 238 18 7 40 270 46965672 46965444 1.010000e-58 237.0
11 TraesCS7A01G085100 chr7D 84.186 215 10 6 378 569 46965230 46965017 1.030000e-43 187.0
12 TraesCS7A01G085100 chr7D 86.705 173 9 6 375 536 47113693 47113524 1.730000e-41 180.0
13 TraesCS7A01G085100 chr7D 85.795 176 11 7 375 536 47056312 47056137 8.060000e-40 174.0
14 TraesCS7A01G085100 chr7D 92.593 108 4 3 235 340 46965415 46965310 3.770000e-33 152.0
15 TraesCS7A01G085100 chr7D 86.517 89 10 1 72 158 47081516 47081428 1.790000e-16 97.1
16 TraesCS7A01G085100 chr1A 96.809 94 3 0 241 334 552966527 552966434 8.110000e-35 158.0
17 TraesCS7A01G085100 chr1A 94.845 97 5 0 233 329 552905373 552905277 3.770000e-33 152.0
18 TraesCS7A01G085100 chr1D 93.137 102 7 0 234 335 461420076 461419975 1.360000e-32 150.0


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 TraesCS7A01G085100 chr7A 49232506 49234700 2194 True 4054.0 4054 100.0000 1 2195 1 chr7A.!!$R1 2194
1 TraesCS7A01G085100 chr4A 661300477 661302502 2025 True 1071.5 1812 85.4855 202 2195 2 chr4A.!!$R3 1993
2 TraesCS7A01G085100 chr7D 46961178 46965672 4494 True 482.2 1369 88.3980 40 2189 5 chr7D.!!$R3 2149

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
57 58 0.027716 CCTCGATCGATTGTCGTCGT 59.972 55.0 19.78 1.34 40.96 4.34 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1273 1520 0.390735 AAACTAGGACGCGCGGAATT 60.391 50.0 35.22 18.31 0.0 2.17 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
24 25 3.076278 CCATGGGCCGTGGCAATT 61.076 61.111 30.95 0.00 44.11 2.32
25 26 2.184836 CATGGGCCGTGGCAATTG 59.815 61.111 18.36 0.00 44.11 2.32
26 27 3.076278 ATGGGCCGTGGCAATTGG 61.076 61.111 13.76 0.00 44.11 3.16
30 31 3.310307 GCCGTGGCAATTGGGGTT 61.310 61.111 7.72 0.00 41.49 4.11
31 32 2.878089 GCCGTGGCAATTGGGGTTT 61.878 57.895 7.72 0.00 41.49 3.27
32 33 1.291906 CCGTGGCAATTGGGGTTTC 59.708 57.895 7.72 0.00 0.00 2.78
33 34 1.467678 CCGTGGCAATTGGGGTTTCA 61.468 55.000 7.72 0.00 0.00 2.69
34 35 0.038343 CGTGGCAATTGGGGTTTCAG 60.038 55.000 7.72 0.00 0.00 3.02
35 36 1.337118 GTGGCAATTGGGGTTTCAGA 58.663 50.000 7.72 0.00 0.00 3.27
36 37 1.000843 GTGGCAATTGGGGTTTCAGAC 59.999 52.381 7.72 0.00 0.00 3.51
37 38 1.337118 GGCAATTGGGGTTTCAGACA 58.663 50.000 7.72 0.00 0.00 3.41
38 39 1.000843 GGCAATTGGGGTTTCAGACAC 59.999 52.381 7.72 0.00 0.00 3.67
49 50 3.512680 GTTTCAGACACCTCGATCGATT 58.487 45.455 19.78 5.87 0.00 3.34
50 51 2.851805 TCAGACACCTCGATCGATTG 57.148 50.000 19.78 19.89 0.00 2.67
51 52 2.092323 TCAGACACCTCGATCGATTGT 58.908 47.619 24.80 24.80 0.00 2.71
57 58 0.027716 CCTCGATCGATTGTCGTCGT 59.972 55.000 19.78 1.34 40.96 4.34
70 71 9.397513 TCGATTGTCGTCGTTACGTAGTAAGTT 62.398 40.741 4.24 0.00 46.63 2.66
120 123 2.158959 CGTGGCTGCTACGTGCTAC 61.159 63.158 27.16 0.00 43.37 3.58
142 145 0.984829 CGTGACAGCGACATGTACAG 59.015 55.000 0.00 0.00 32.25 2.74
145 148 1.616374 TGACAGCGACATGTACAGGAA 59.384 47.619 15.54 0.00 32.25 3.36
146 149 2.233676 TGACAGCGACATGTACAGGAAT 59.766 45.455 15.54 0.00 32.25 3.01
198 201 0.590732 CGTCGCCCGTGATACAGTAC 60.591 60.000 0.00 0.00 0.00 2.73
227 235 8.333186 ACGTAGATTTTAGATATTTTTGACCGC 58.667 33.333 0.00 0.00 0.00 5.68
239 247 4.130281 GACCGCCGCGAAAACGAG 62.130 66.667 15.93 0.00 34.06 4.18
329 399 7.533426 ACTTACCACTATACTACAACGACTTG 58.467 38.462 0.00 0.00 0.00 3.16
331 401 4.159135 ACCACTATACTACAACGACTTGGG 59.841 45.833 0.00 0.00 0.00 4.12
340 410 1.135257 CAACGACTTGGGTGCAAAACA 60.135 47.619 0.00 0.00 0.00 2.83
341 411 1.398692 ACGACTTGGGTGCAAAACAT 58.601 45.000 0.00 0.00 0.00 2.71
342 412 2.577700 ACGACTTGGGTGCAAAACATA 58.422 42.857 0.00 0.00 0.00 2.29
344 414 3.190535 ACGACTTGGGTGCAAAACATATC 59.809 43.478 0.00 0.00 0.00 1.63
346 416 4.634004 CGACTTGGGTGCAAAACATATCTA 59.366 41.667 0.00 0.00 0.00 1.98
349 419 6.010219 ACTTGGGTGCAAAACATATCTAACT 58.990 36.000 0.00 0.00 0.00 2.24
351 421 5.321102 TGGGTGCAAAACATATCTAACTGT 58.679 37.500 0.00 0.00 0.00 3.55
352 422 5.772672 TGGGTGCAAAACATATCTAACTGTT 59.227 36.000 0.00 0.00 37.19 3.16
355 425 6.801862 GGTGCAAAACATATCTAACTGTTCAC 59.198 38.462 0.00 0.00 34.61 3.18
387 499 2.254546 TCATGCGAACCTGTCAGTTT 57.745 45.000 0.00 0.00 0.00 2.66
388 500 1.872952 TCATGCGAACCTGTCAGTTTG 59.127 47.619 0.00 0.00 34.71 2.93
433 550 0.035152 CACATCCAAGCTAGGTGGCA 60.035 55.000 0.00 0.00 35.99 4.92
465 589 2.365635 GCCTCTGGGTGGAGCCTA 60.366 66.667 0.00 0.00 37.43 3.93
466 590 2.736826 GCCTCTGGGTGGAGCCTAC 61.737 68.421 0.00 0.00 37.43 3.18
467 591 2.427245 CCTCTGGGTGGAGCCTACG 61.427 68.421 0.00 0.00 37.43 3.51
468 592 1.682684 CTCTGGGTGGAGCCTACGT 60.683 63.158 0.00 0.00 37.43 3.57
569 711 3.849951 CAGCTACGTCCGGGCCAT 61.850 66.667 4.39 0.00 0.00 4.40
570 712 3.849951 AGCTACGTCCGGGCCATG 61.850 66.667 4.39 0.00 0.00 3.66
571 713 4.157120 GCTACGTCCGGGCCATGT 62.157 66.667 4.39 0.00 0.00 3.21
575 776 1.044231 TACGTCCGGGCCATGTGTAT 61.044 55.000 4.39 0.00 0.00 2.29
613 824 2.652941 TAATTCCACGGTACCACGTC 57.347 50.000 13.54 0.00 46.75 4.34
614 825 0.388907 AATTCCACGGTACCACGTCG 60.389 55.000 13.54 0.00 46.75 5.12
615 826 2.824071 ATTCCACGGTACCACGTCGC 62.824 60.000 13.54 0.00 46.75 5.19
620 831 4.807039 GGTACCACGTCGCGCCAT 62.807 66.667 7.15 0.00 0.00 4.40
621 832 3.550992 GTACCACGTCGCGCCATG 61.551 66.667 0.00 0.00 0.00 3.66
754 968 4.760047 AACTAGCCACGGCCAGCG 62.760 66.667 2.24 0.00 43.17 5.18
809 1023 2.735134 GCTACGGAGTTGGTTAACACTG 59.265 50.000 8.10 1.38 37.78 3.66
961 1193 1.566211 CAAGGAGAAGCAGAGGAGGA 58.434 55.000 0.00 0.00 0.00 3.71
962 1194 1.481772 CAAGGAGAAGCAGAGGAGGAG 59.518 57.143 0.00 0.00 0.00 3.69
963 1195 0.032217 AGGAGAAGCAGAGGAGGAGG 60.032 60.000 0.00 0.00 0.00 4.30
964 1196 1.685355 GGAGAAGCAGAGGAGGAGGC 61.685 65.000 0.00 0.00 0.00 4.70
965 1197 2.015227 GAGAAGCAGAGGAGGAGGCG 62.015 65.000 0.00 0.00 0.00 5.52
966 1198 2.038007 AAGCAGAGGAGGAGGCGA 59.962 61.111 0.00 0.00 0.00 5.54
967 1199 1.608717 GAAGCAGAGGAGGAGGCGAA 61.609 60.000 0.00 0.00 0.00 4.70
968 1200 1.612395 AAGCAGAGGAGGAGGCGAAG 61.612 60.000 0.00 0.00 0.00 3.79
969 1201 3.087666 GCAGAGGAGGAGGCGAAGG 62.088 68.421 0.00 0.00 0.00 3.46
970 1202 2.042435 AGAGGAGGAGGCGAAGGG 60.042 66.667 0.00 0.00 0.00 3.95
971 1203 3.157949 GAGGAGGAGGCGAAGGGG 61.158 72.222 0.00 0.00 0.00 4.79
972 1204 3.680920 GAGGAGGAGGCGAAGGGGA 62.681 68.421 0.00 0.00 0.00 4.81
973 1205 2.687566 GGAGGAGGCGAAGGGGAA 60.688 66.667 0.00 0.00 0.00 3.97
974 1206 2.298661 GGAGGAGGCGAAGGGGAAA 61.299 63.158 0.00 0.00 0.00 3.13
975 1207 1.222113 GAGGAGGCGAAGGGGAAAG 59.778 63.158 0.00 0.00 0.00 2.62
976 1208 1.229529 AGGAGGCGAAGGGGAAAGA 60.230 57.895 0.00 0.00 0.00 2.52
977 1209 1.222113 GGAGGCGAAGGGGAAAGAG 59.778 63.158 0.00 0.00 0.00 2.85
978 1210 1.222113 GAGGCGAAGGGGAAAGAGG 59.778 63.158 0.00 0.00 0.00 3.69
979 1211 1.229529 AGGCGAAGGGGAAAGAGGA 60.230 57.895 0.00 0.00 0.00 3.71
980 1212 1.222113 GGCGAAGGGGAAAGAGGAG 59.778 63.158 0.00 0.00 0.00 3.69
981 1213 1.222113 GCGAAGGGGAAAGAGGAGG 59.778 63.158 0.00 0.00 0.00 4.30
982 1214 1.265454 GCGAAGGGGAAAGAGGAGGA 61.265 60.000 0.00 0.00 0.00 3.71
983 1215 0.827368 CGAAGGGGAAAGAGGAGGAG 59.173 60.000 0.00 0.00 0.00 3.69
984 1216 1.208706 GAAGGGGAAAGAGGAGGAGG 58.791 60.000 0.00 0.00 0.00 4.30
998 1239 1.144093 GAGGAGGAGGAGGAGATCGAA 59.856 57.143 0.00 0.00 0.00 3.71
1021 1262 1.153449 TTCGTATTGGAGCTGGGCG 60.153 57.895 0.00 0.00 0.00 6.13
1202 1443 1.455773 TCATCGCCTGATCGGTCCT 60.456 57.895 0.00 0.00 30.49 3.85
1207 1448 3.095347 GCCTGATCGGTCCTCCACC 62.095 68.421 0.00 0.00 42.69 4.61
1223 1470 2.411701 CCGATCCTTGCGTCGCTA 59.588 61.111 19.50 10.26 36.57 4.26
1230 1477 1.227089 CTTGCGTCGCTATGGCTCT 60.227 57.895 19.50 0.00 36.09 4.09
1237 1484 1.593750 CGCTATGGCTCTGCTCCAC 60.594 63.158 0.00 0.00 36.26 4.02
1239 1486 1.068753 CTATGGCTCTGCTCCACCG 59.931 63.158 0.00 0.00 36.26 4.94
1257 1504 1.931172 CCGTGTAATTAACCTCCTGCG 59.069 52.381 0.00 0.00 0.00 5.18
1258 1505 2.613691 CGTGTAATTAACCTCCTGCGT 58.386 47.619 0.00 0.00 0.00 5.24
1273 1520 3.070446 TCCTGCGTTTCTTCCTCTTGTAA 59.930 43.478 0.00 0.00 0.00 2.41
1278 1525 5.048991 TGCGTTTCTTCCTCTTGTAAATTCC 60.049 40.000 0.00 0.00 0.00 3.01
1343 1598 3.997021 GCTGTTCTTCAAGAAAGGATCGA 59.003 43.478 0.00 0.00 35.75 3.59
1364 1619 6.173339 TCGATGCTACCTCTTTTCTTTTGAT 58.827 36.000 0.00 0.00 0.00 2.57
1365 1620 6.655003 TCGATGCTACCTCTTTTCTTTTGATT 59.345 34.615 0.00 0.00 0.00 2.57
1366 1621 6.744537 CGATGCTACCTCTTTTCTTTTGATTG 59.255 38.462 0.00 0.00 0.00 2.67
1367 1622 7.361201 CGATGCTACCTCTTTTCTTTTGATTGA 60.361 37.037 0.00 0.00 0.00 2.57
1368 1623 7.206981 TGCTACCTCTTTTCTTTTGATTGAG 57.793 36.000 0.00 0.00 0.00 3.02
1369 1624 6.089476 GCTACCTCTTTTCTTTTGATTGAGC 58.911 40.000 0.00 0.00 0.00 4.26
1370 1625 6.072230 GCTACCTCTTTTCTTTTGATTGAGCT 60.072 38.462 0.00 0.00 0.00 4.09
1371 1626 6.721704 ACCTCTTTTCTTTTGATTGAGCTT 57.278 33.333 0.00 0.00 0.00 3.74
1372 1627 7.117285 ACCTCTTTTCTTTTGATTGAGCTTT 57.883 32.000 0.00 0.00 0.00 3.51
1373 1628 7.559486 ACCTCTTTTCTTTTGATTGAGCTTTT 58.441 30.769 0.00 0.00 0.00 2.27
1376 1631 9.090692 CTCTTTTCTTTTGATTGAGCTTTTGAA 57.909 29.630 0.00 0.00 0.00 2.69
1377 1632 8.872845 TCTTTTCTTTTGATTGAGCTTTTGAAC 58.127 29.630 0.00 0.00 0.00 3.18
1378 1633 8.545229 TTTTCTTTTGATTGAGCTTTTGAACA 57.455 26.923 0.00 0.00 0.00 3.18
1379 1634 7.760131 TTCTTTTGATTGAGCTTTTGAACAG 57.240 32.000 0.00 0.00 0.00 3.16
1383 1638 4.206375 TGATTGAGCTTTTGAACAGACCA 58.794 39.130 0.00 0.00 0.00 4.02
1398 1653 2.038295 CAGACCAGCTCTCTGTTTTCCT 59.962 50.000 9.10 0.00 38.66 3.36
1423 1678 7.645058 TTTTGATTTTGACTTCCTCTTCTGT 57.355 32.000 0.00 0.00 0.00 3.41
1424 1679 6.867662 TTGATTTTGACTTCCTCTTCTGTC 57.132 37.500 0.00 0.00 0.00 3.51
1436 1691 4.901849 TCCTCTTCTGTCTTTTCCTCTGAA 59.098 41.667 0.00 0.00 0.00 3.02
1446 1701 6.541278 TGTCTTTTCCTCTGAATATGCATCAG 59.459 38.462 0.19 5.88 44.53 2.90
1454 1709 3.818773 CTGAATATGCATCAGACATGCCA 59.181 43.478 9.76 0.00 45.74 4.92
1455 1710 4.403734 TGAATATGCATCAGACATGCCAT 58.596 39.130 0.19 1.60 43.94 4.40
1491 1746 2.289320 GGAGATGATCGATGAACAGGGG 60.289 54.545 0.54 0.00 0.00 4.79
1685 1940 1.226030 CCCGTTTCCTGTCGTTGTCC 61.226 60.000 0.00 0.00 0.00 4.02
1723 1981 5.446073 GCACGCCACTACTAAATTTCTTCTC 60.446 44.000 0.00 0.00 0.00 2.87
1775 2033 8.648557 TTACCTCTTGTTTCATGATAAGATCG 57.351 34.615 14.28 11.23 0.00 3.69
1793 2051 1.409790 TCGAACACGAACTTCCCAAGA 59.590 47.619 0.00 0.00 33.03 3.02
1794 2052 1.792949 CGAACACGAACTTCCCAAGAG 59.207 52.381 0.00 0.00 0.00 2.85
1795 2053 1.531578 GAACACGAACTTCCCAAGAGC 59.468 52.381 0.00 0.00 0.00 4.09
1796 2054 0.759346 ACACGAACTTCCCAAGAGCT 59.241 50.000 0.00 0.00 0.00 4.09
1797 2055 1.968493 ACACGAACTTCCCAAGAGCTA 59.032 47.619 0.00 0.00 0.00 3.32
1800 2058 2.897969 ACGAACTTCCCAAGAGCTAGAA 59.102 45.455 0.00 0.00 0.00 2.10
1802 2060 3.929610 CGAACTTCCCAAGAGCTAGAAAG 59.070 47.826 0.00 0.00 0.00 2.62
1803 2061 4.561734 CGAACTTCCCAAGAGCTAGAAAGT 60.562 45.833 0.00 0.00 0.00 2.66
1806 2064 5.088026 ACTTCCCAAGAGCTAGAAAGTACT 58.912 41.667 0.00 0.00 0.00 2.73
1917 4376 5.334105 CGTACATATGCTGGCTGGAATTTAC 60.334 44.000 1.58 0.00 0.00 2.01
1918 4377 4.796606 ACATATGCTGGCTGGAATTTACT 58.203 39.130 1.58 0.00 0.00 2.24
1919 4378 5.940617 ACATATGCTGGCTGGAATTTACTA 58.059 37.500 1.58 0.00 0.00 1.82
1966 4428 6.098409 TGAAAGGACTGGATACTGGATAAGTC 59.902 42.308 6.63 6.63 40.56 3.01
1996 4461 1.141657 AGGCATGGATAAGATGCACGT 59.858 47.619 0.00 0.00 46.77 4.49
2005 4470 5.356751 TGGATAAGATGCACGTTTTTGCTAT 59.643 36.000 0.00 0.00 43.41 2.97
2103 4568 7.860872 ACGTCTCCAAAATTTTGTCTAATTGTC 59.139 33.333 25.25 8.31 36.45 3.18
2165 4630 9.995957 TTTGGATTTATGTACATGAATACAACG 57.004 29.630 34.05 0.00 43.16 4.10
2190 4655 1.372872 GTGTTTGGTTGCCCGCATC 60.373 57.895 0.00 0.00 0.00 3.91
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
7 8 3.076278 AATTGCCACGGCCCATGG 61.076 61.111 15.25 15.25 41.09 3.66
8 9 2.184836 CAATTGCCACGGCCCATG 59.815 61.111 5.42 0.00 41.09 3.66
9 10 3.076278 CCAATTGCCACGGCCCAT 61.076 61.111 5.42 0.00 41.09 4.00
13 14 2.779951 GAAACCCCAATTGCCACGGC 62.780 60.000 0.00 0.00 42.35 5.68
14 15 1.291906 GAAACCCCAATTGCCACGG 59.708 57.895 0.00 0.00 0.00 4.94
15 16 0.038343 CTGAAACCCCAATTGCCACG 60.038 55.000 0.00 0.00 0.00 4.94
16 17 1.000843 GTCTGAAACCCCAATTGCCAC 59.999 52.381 0.00 0.00 0.00 5.01
17 18 1.337118 GTCTGAAACCCCAATTGCCA 58.663 50.000 0.00 0.00 0.00 4.92
18 19 1.000843 GTGTCTGAAACCCCAATTGCC 59.999 52.381 0.00 0.00 0.00 4.52
19 20 1.000843 GGTGTCTGAAACCCCAATTGC 59.999 52.381 5.65 0.00 0.00 3.56
20 21 2.558359 GAGGTGTCTGAAACCCCAATTG 59.442 50.000 13.48 0.00 38.57 2.32
21 22 2.814097 CGAGGTGTCTGAAACCCCAATT 60.814 50.000 13.48 0.00 38.57 2.32
22 23 1.271379 CGAGGTGTCTGAAACCCCAAT 60.271 52.381 13.48 0.00 38.57 3.16
23 24 0.107831 CGAGGTGTCTGAAACCCCAA 59.892 55.000 13.48 0.00 38.57 4.12
24 25 0.761323 TCGAGGTGTCTGAAACCCCA 60.761 55.000 13.48 0.00 38.57 4.96
25 26 0.613777 ATCGAGGTGTCTGAAACCCC 59.386 55.000 13.48 0.36 38.57 4.95
26 27 1.736032 CGATCGAGGTGTCTGAAACCC 60.736 57.143 10.26 4.62 38.57 4.11
27 28 1.201647 TCGATCGAGGTGTCTGAAACC 59.798 52.381 15.15 9.09 38.03 3.27
28 29 2.631418 TCGATCGAGGTGTCTGAAAC 57.369 50.000 15.15 0.00 0.00 2.78
29 30 3.056821 ACAATCGATCGAGGTGTCTGAAA 60.057 43.478 24.15 0.00 0.00 2.69
30 31 2.492088 ACAATCGATCGAGGTGTCTGAA 59.508 45.455 24.15 0.40 0.00 3.02
31 32 2.092323 ACAATCGATCGAGGTGTCTGA 58.908 47.619 24.15 1.09 0.00 3.27
32 33 2.455032 GACAATCGATCGAGGTGTCTG 58.545 52.381 34.98 22.70 38.75 3.51
33 34 1.064208 CGACAATCGATCGAGGTGTCT 59.936 52.381 36.47 20.68 43.74 3.41
34 35 1.202154 ACGACAATCGATCGAGGTGTC 60.202 52.381 33.80 33.80 43.74 3.67
35 36 0.809385 ACGACAATCGATCGAGGTGT 59.191 50.000 27.86 27.86 43.74 4.16
36 37 1.467875 GACGACAATCGATCGAGGTG 58.532 55.000 24.50 23.77 43.74 4.00
37 38 0.027716 CGACGACAATCGATCGAGGT 59.972 55.000 23.84 22.25 45.13 3.85
38 39 0.027716 ACGACGACAATCGATCGAGG 59.972 55.000 23.84 19.25 45.13 4.63
57 58 2.556189 TCGGCACCAACTTACTACGTAA 59.444 45.455 0.00 0.00 0.00 3.18
67 68 3.049674 CGCATGTCGGCACCAACT 61.050 61.111 0.00 0.00 33.78 3.16
120 123 2.174764 GTACATGTCGCTGTCACGTAG 58.825 52.381 0.00 0.00 0.00 3.51
128 131 3.780902 TGTATTCCTGTACATGTCGCTG 58.219 45.455 0.00 0.86 30.00 5.18
142 145 5.521544 GTCTGGACGAGTATCTTGTATTCC 58.478 45.833 0.00 0.00 0.00 3.01
182 185 0.171679 TGTGTACTGTATCACGGGCG 59.828 55.000 12.52 0.00 37.38 6.13
227 235 2.656192 TTTTCTTCTCGTTTTCGCGG 57.344 45.000 6.13 0.00 43.73 6.46
329 399 5.897377 ACAGTTAGATATGTTTTGCACCC 57.103 39.130 0.00 0.00 0.00 4.61
331 401 7.584987 AGTGAACAGTTAGATATGTTTTGCAC 58.415 34.615 0.00 0.00 39.66 4.57
349 419 8.093927 TCGCATGAATATGGATATAAGTGAACA 58.906 33.333 0.00 0.00 34.79 3.18
351 421 8.935844 GTTCGCATGAATATGGATATAAGTGAA 58.064 33.333 0.00 0.00 36.29 3.18
352 422 7.549134 GGTTCGCATGAATATGGATATAAGTGA 59.451 37.037 0.00 0.00 36.29 3.41
355 425 7.550551 ACAGGTTCGCATGAATATGGATATAAG 59.449 37.037 0.00 0.00 36.29 1.73
364 434 4.142609 ACTGACAGGTTCGCATGAATAT 57.857 40.909 7.51 0.00 36.29 1.28
366 436 2.479566 ACTGACAGGTTCGCATGAAT 57.520 45.000 7.51 0.00 36.29 2.57
387 499 2.425592 CTGCCGACCACTCAACCA 59.574 61.111 0.00 0.00 0.00 3.67
388 500 3.050275 GCTGCCGACCACTCAACC 61.050 66.667 0.00 0.00 0.00 3.77
458 582 0.745845 TCCTGTCGTACGTAGGCTCC 60.746 60.000 25.94 2.15 0.00 4.70
461 585 1.622232 GTTTCCTGTCGTACGTAGGC 58.378 55.000 25.94 14.74 0.00 3.93
464 588 2.594529 GACGTTTCCTGTCGTACGTA 57.405 50.000 16.05 5.01 46.02 3.57
486 621 2.835027 GGGTGTCCGATTTATGTCTCC 58.165 52.381 0.00 0.00 0.00 3.71
513 652 4.525996 TCCATGATGTAACATGTTCTGGG 58.474 43.478 15.85 8.44 44.00 4.45
544 683 0.523546 CGGACGTAGCTGCAGTACTG 60.524 60.000 18.93 18.93 0.00 2.74
545 684 1.654954 CCGGACGTAGCTGCAGTACT 61.655 60.000 16.64 7.36 0.00 2.73
569 711 5.272402 TCTCTCAAATCTGGAGGATACACA 58.728 41.667 0.00 0.00 41.41 3.72
570 712 5.860941 TCTCTCAAATCTGGAGGATACAC 57.139 43.478 0.00 0.00 41.41 2.90
571 713 8.553085 TTAATCTCTCAAATCTGGAGGATACA 57.447 34.615 0.00 0.00 41.41 2.29
575 776 7.127801 TGGAATTAATCTCTCAAATCTGGAGGA 59.872 37.037 0.00 0.00 33.18 3.71
615 826 3.164390 CTGTGATGCGAGCATGGCG 62.164 63.158 15.90 0.00 45.68 5.69
616 827 2.713770 CTGTGATGCGAGCATGGC 59.286 61.111 15.90 8.20 41.71 4.40
617 828 1.818363 AGCTGTGATGCGAGCATGG 60.818 57.895 15.90 4.30 37.70 3.66
618 829 1.352056 CAGCTGTGATGCGAGCATG 59.648 57.895 15.90 2.11 37.70 4.06
619 830 2.470362 GCAGCTGTGATGCGAGCAT 61.470 57.895 16.64 10.66 37.70 3.79
620 831 3.122971 GCAGCTGTGATGCGAGCA 61.123 61.111 16.64 0.00 37.70 4.26
754 968 4.675190 CCGATAGATTGATTGGCATGTC 57.325 45.455 0.00 0.00 39.76 3.06
767 981 3.442996 GGCTAATGCGCCGATAGAT 57.557 52.632 4.18 0.00 40.79 1.98
844 1065 2.620112 CCGCGATTGATGGATGGCC 61.620 63.158 8.23 0.00 0.00 5.36
961 1193 1.229529 TCCTCTTTCCCCTTCGCCT 60.230 57.895 0.00 0.00 0.00 5.52
962 1194 1.222113 CTCCTCTTTCCCCTTCGCC 59.778 63.158 0.00 0.00 0.00 5.54
963 1195 1.222113 CCTCCTCTTTCCCCTTCGC 59.778 63.158 0.00 0.00 0.00 4.70
964 1196 0.827368 CTCCTCCTCTTTCCCCTTCG 59.173 60.000 0.00 0.00 0.00 3.79
965 1197 1.208706 CCTCCTCCTCTTTCCCCTTC 58.791 60.000 0.00 0.00 0.00 3.46
966 1198 0.800239 TCCTCCTCCTCTTTCCCCTT 59.200 55.000 0.00 0.00 0.00 3.95
967 1199 0.341609 CTCCTCCTCCTCTTTCCCCT 59.658 60.000 0.00 0.00 0.00 4.79
968 1200 0.692756 CCTCCTCCTCCTCTTTCCCC 60.693 65.000 0.00 0.00 0.00 4.81
969 1201 0.340208 TCCTCCTCCTCCTCTTTCCC 59.660 60.000 0.00 0.00 0.00 3.97
970 1202 1.691163 CCTCCTCCTCCTCCTCTTTCC 60.691 61.905 0.00 0.00 0.00 3.13
971 1203 1.289530 TCCTCCTCCTCCTCCTCTTTC 59.710 57.143 0.00 0.00 0.00 2.62
972 1204 1.290732 CTCCTCCTCCTCCTCCTCTTT 59.709 57.143 0.00 0.00 0.00 2.52
973 1205 0.933700 CTCCTCCTCCTCCTCCTCTT 59.066 60.000 0.00 0.00 0.00 2.85
974 1206 0.047176 TCTCCTCCTCCTCCTCCTCT 59.953 60.000 0.00 0.00 0.00 3.69
975 1207 1.075536 GATCTCCTCCTCCTCCTCCTC 59.924 61.905 0.00 0.00 0.00 3.71
976 1208 1.158007 GATCTCCTCCTCCTCCTCCT 58.842 60.000 0.00 0.00 0.00 3.69
977 1209 0.251165 CGATCTCCTCCTCCTCCTCC 60.251 65.000 0.00 0.00 0.00 4.30
978 1210 0.768622 TCGATCTCCTCCTCCTCCTC 59.231 60.000 0.00 0.00 0.00 3.71
979 1211 1.144913 CTTCGATCTCCTCCTCCTCCT 59.855 57.143 0.00 0.00 0.00 3.69
980 1212 1.144093 TCTTCGATCTCCTCCTCCTCC 59.856 57.143 0.00 0.00 0.00 4.30
981 1213 2.649531 TCTTCGATCTCCTCCTCCTC 57.350 55.000 0.00 0.00 0.00 3.71
982 1214 2.176798 ACATCTTCGATCTCCTCCTCCT 59.823 50.000 0.00 0.00 0.00 3.69
983 1215 2.593026 ACATCTTCGATCTCCTCCTCC 58.407 52.381 0.00 0.00 0.00 4.30
984 1216 4.237349 GAACATCTTCGATCTCCTCCTC 57.763 50.000 0.00 0.00 0.00 3.71
998 1239 2.158900 CCCAGCTCCAATACGAACATCT 60.159 50.000 0.00 0.00 0.00 2.90
1006 1247 0.811616 CAGACGCCCAGCTCCAATAC 60.812 60.000 0.00 0.00 0.00 1.89
1202 1443 2.577059 GACGCAAGGATCGGTGGA 59.423 61.111 0.00 0.00 46.39 4.02
1207 1448 1.278172 CCATAGCGACGCAAGGATCG 61.278 60.000 23.70 2.65 46.39 3.69
1209 1450 1.595382 GCCATAGCGACGCAAGGAT 60.595 57.895 23.70 6.67 46.39 3.24
1210 1451 2.202878 GCCATAGCGACGCAAGGA 60.203 61.111 23.70 4.32 46.39 3.36
1212 1453 1.227089 AGAGCCATAGCGACGCAAG 60.227 57.895 23.70 10.78 46.67 4.01
1223 1470 3.005539 ACGGTGGAGCAGAGCCAT 61.006 61.111 0.00 0.00 37.81 4.40
1230 1477 2.303600 AGGTTAATTACACGGTGGAGCA 59.696 45.455 13.48 0.00 0.00 4.26
1237 1484 1.931172 CGCAGGAGGTTAATTACACGG 59.069 52.381 0.00 0.00 0.00 4.94
1239 1486 4.694037 AGAAACGCAGGAGGTTAATTACAC 59.306 41.667 0.00 0.00 0.00 2.90
1257 1504 5.391449 GCGGAATTTACAAGAGGAAGAAAC 58.609 41.667 0.00 0.00 0.00 2.78
1258 1505 4.153475 CGCGGAATTTACAAGAGGAAGAAA 59.847 41.667 0.00 0.00 0.00 2.52
1273 1520 0.390735 AAACTAGGACGCGCGGAATT 60.391 50.000 35.22 18.31 0.00 2.17
1343 1598 7.576477 GCTCAATCAAAAGAAAAGAGGTAGCAT 60.576 37.037 0.00 0.00 0.00 3.79
1364 1619 2.358898 GCTGGTCTGTTCAAAAGCTCAA 59.641 45.455 0.00 0.00 0.00 3.02
1365 1620 1.949525 GCTGGTCTGTTCAAAAGCTCA 59.050 47.619 0.00 0.00 0.00 4.26
1366 1621 2.225255 GAGCTGGTCTGTTCAAAAGCTC 59.775 50.000 6.71 6.71 46.80 4.09
1367 1622 2.158696 AGAGCTGGTCTGTTCAAAAGCT 60.159 45.455 8.83 0.00 43.38 3.74
1368 1623 2.225255 GAGAGCTGGTCTGTTCAAAAGC 59.775 50.000 14.96 0.00 34.71 3.51
1369 1624 3.497640 CAGAGAGCTGGTCTGTTCAAAAG 59.502 47.826 14.96 0.00 38.51 2.27
1370 1625 3.470709 CAGAGAGCTGGTCTGTTCAAAA 58.529 45.455 14.96 0.00 38.51 2.44
1371 1626 3.117491 CAGAGAGCTGGTCTGTTCAAA 57.883 47.619 14.96 0.00 38.51 2.69
1372 1627 2.827800 CAGAGAGCTGGTCTGTTCAA 57.172 50.000 14.96 0.00 38.51 2.69
1377 1632 2.038295 AGGAAAACAGAGAGCTGGTCTG 59.962 50.000 14.96 17.54 42.49 3.51
1378 1633 2.334023 AGGAAAACAGAGAGCTGGTCT 58.666 47.619 9.46 9.46 42.49 3.85
1379 1634 2.849294 AGGAAAACAGAGAGCTGGTC 57.151 50.000 0.00 0.00 42.49 4.02
1383 1638 6.721704 AATCAAAAAGGAAAACAGAGAGCT 57.278 33.333 0.00 0.00 0.00 4.09
1398 1653 8.066612 ACAGAAGAGGAAGTCAAAATCAAAAA 57.933 30.769 0.00 0.00 0.00 1.94
1423 1678 6.892485 TCTGATGCATATTCAGAGGAAAAGA 58.108 36.000 13.30 0.00 43.49 2.52
1436 1691 4.149598 ACAATGGCATGTCTGATGCATAT 58.850 39.130 0.00 0.45 46.21 1.78
1446 1701 3.149436 ACGCAATTACAATGGCATGTC 57.851 42.857 0.00 0.00 34.96 3.06
1447 1702 3.056962 TCAACGCAATTACAATGGCATGT 60.057 39.130 0.00 4.26 34.96 3.21
1454 1709 5.185454 TCATCTCCTCAACGCAATTACAAT 58.815 37.500 0.00 0.00 0.00 2.71
1455 1710 4.574892 TCATCTCCTCAACGCAATTACAA 58.425 39.130 0.00 0.00 0.00 2.41
1554 1809 8.986477 ATCCGAAAAGTAATGGATTTTCTTTG 57.014 30.769 8.31 0.00 41.24 2.77
1594 1849 1.810030 GTGACCCCGAATCTCGCAC 60.810 63.158 0.00 0.00 38.82 5.34
1685 1940 1.394917 GGCGTGCTTGATTGAGTGTAG 59.605 52.381 0.00 0.00 0.00 2.74
1723 1981 6.777213 ATACTTAGCTATCCGGTGAATAGG 57.223 41.667 0.00 0.00 0.00 2.57
1775 2033 1.531578 GCTCTTGGGAAGTTCGTGTTC 59.468 52.381 0.00 0.00 0.00 3.18
1837 2102 7.223387 GCAACGATGATGATGATATATACTGCA 59.777 37.037 0.00 0.00 0.00 4.41
1838 2103 7.223387 TGCAACGATGATGATGATATATACTGC 59.777 37.037 0.00 0.00 0.00 4.40
1839 2104 8.538039 GTGCAACGATGATGATGATATATACTG 58.462 37.037 0.00 0.00 0.00 2.74
1840 2105 8.253113 TGTGCAACGATGATGATGATATATACT 58.747 33.333 0.00 0.00 42.39 2.12
1841 2106 8.323854 GTGTGCAACGATGATGATGATATATAC 58.676 37.037 0.00 0.00 42.39 1.47
1842 2107 8.253113 AGTGTGCAACGATGATGATGATATATA 58.747 33.333 0.00 0.00 42.39 0.86
1843 2108 7.064253 CAGTGTGCAACGATGATGATGATATAT 59.936 37.037 0.00 0.00 42.39 0.86
1844 2109 6.366877 CAGTGTGCAACGATGATGATGATATA 59.633 38.462 0.00 0.00 42.39 0.86
1845 2110 5.178809 CAGTGTGCAACGATGATGATGATAT 59.821 40.000 0.00 0.00 42.39 1.63
1846 2111 4.508861 CAGTGTGCAACGATGATGATGATA 59.491 41.667 0.00 0.00 42.39 2.15
1847 2112 3.311596 CAGTGTGCAACGATGATGATGAT 59.688 43.478 0.00 0.00 42.39 2.45
1849 2114 2.674357 TCAGTGTGCAACGATGATGATG 59.326 45.455 0.00 0.00 42.39 3.07
1917 4376 8.258007 TCAGTGTGGATAACCTTTACATTCTAG 58.742 37.037 0.00 0.00 37.04 2.43
1918 4377 8.141298 TCAGTGTGGATAACCTTTACATTCTA 57.859 34.615 0.00 0.00 37.04 2.10
1919 4378 7.016153 TCAGTGTGGATAACCTTTACATTCT 57.984 36.000 0.00 0.00 37.04 2.40
2005 4470 3.567478 ATCTTGTCCACACGCGCGA 62.567 57.895 39.36 11.25 0.00 5.87
2039 4504 9.134734 GTTGTTCTCATGTACAAAAAGACAAAA 57.865 29.630 14.80 5.15 35.73 2.44
2074 4539 5.828299 AGACAAAATTTTGGAGACGTCAA 57.172 34.783 29.37 2.70 42.34 3.18
2120 4585 8.934507 ATCCAAATTTTGAAAAAGTCACGTAA 57.065 26.923 10.72 0.00 35.39 3.18
2164 4629 0.315869 GCAACCAAACACGTCAGTCG 60.316 55.000 0.00 0.00 46.00 4.18
2165 4630 0.028902 GGCAACCAAACACGTCAGTC 59.971 55.000 0.00 0.00 0.00 3.51


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

AutoCloner maintained by Alex Coulton.