Multiple sequence alignment - TraesCS5B01G089500

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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 TraesCS5B01G089500 chr5B 100.000 2558 0 0 1 2558 115320830 115318273 0.000000e+00 4724
1 TraesCS5B01G089500 chr5B 93.006 529 36 1 1 529 442744826 442745353 0.000000e+00 771
2 TraesCS5B01G089500 chr5B 92.844 531 37 1 1 531 631783912 631783383 0.000000e+00 769
3 TraesCS5B01G089500 chr5B 92.952 525 37 0 1 525 508125300 508125824 0.000000e+00 765
4 TraesCS5B01G089500 chr5B 84.360 211 21 8 1158 1362 115319631 115319427 2.010000e-46 196
5 TraesCS5B01G089500 chr5B 84.360 211 21 8 1200 1404 115319673 115319469 2.010000e-46 196
6 TraesCS5B01G089500 chr5A 90.278 864 54 14 533 1386 109344924 109344081 0.000000e+00 1103
7 TraesCS5B01G089500 chr5A 92.661 763 28 9 1818 2558 109343734 109342978 0.000000e+00 1074
8 TraesCS5B01G089500 chr5A 91.409 582 36 6 1200 1781 109344303 109343736 0.000000e+00 785
9 TraesCS5B01G089500 chr5A 84.021 194 24 3 1211 1404 109344339 109344153 2.020000e-41 180
10 TraesCS5B01G089500 chr5D 89.503 886 53 13 1245 2097 105350150 105349272 0.000000e+00 1085
11 TraesCS5B01G089500 chr5D 90.060 835 45 15 535 1362 105350788 105349985 0.000000e+00 1048
12 TraesCS5B01G089500 chr5D 93.231 458 15 7 2116 2558 105349287 105348831 0.000000e+00 660
13 TraesCS5B01G089500 chr2D 93.536 526 33 1 1 526 623305596 623306120 0.000000e+00 782
14 TraesCS5B01G089500 chr3A 93.333 525 35 0 1 525 65351710 65351186 0.000000e+00 776
15 TraesCS5B01G089500 chr2B 93.499 523 33 1 1 522 801147369 801146847 0.000000e+00 776
16 TraesCS5B01G089500 chr2B 92.697 534 35 4 1 533 508413074 508412544 0.000000e+00 767
17 TraesCS5B01G089500 chr6B 92.939 524 36 1 1 523 445849841 445849318 0.000000e+00 761
18 TraesCS5B01G089500 chr7B 92.762 525 38 0 1 525 89970697 89971221 0.000000e+00 760


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 TraesCS5B01G089500 chr5B 115318273 115320830 2557 True 1705.333333 4724 89.573333 1 2558 3 chr5B.!!$R2 2557
1 TraesCS5B01G089500 chr5B 442744826 442745353 527 False 771.000000 771 93.006000 1 529 1 chr5B.!!$F1 528
2 TraesCS5B01G089500 chr5B 631783383 631783912 529 True 769.000000 769 92.844000 1 531 1 chr5B.!!$R1 530
3 TraesCS5B01G089500 chr5B 508125300 508125824 524 False 765.000000 765 92.952000 1 525 1 chr5B.!!$F2 524
4 TraesCS5B01G089500 chr5A 109342978 109344924 1946 True 785.500000 1103 89.592250 533 2558 4 chr5A.!!$R1 2025
5 TraesCS5B01G089500 chr5D 105348831 105350788 1957 True 931.000000 1085 90.931333 535 2558 3 chr5D.!!$R1 2023
6 TraesCS5B01G089500 chr2D 623305596 623306120 524 False 782.000000 782 93.536000 1 526 1 chr2D.!!$F1 525
7 TraesCS5B01G089500 chr3A 65351186 65351710 524 True 776.000000 776 93.333000 1 525 1 chr3A.!!$R1 524
8 TraesCS5B01G089500 chr2B 801146847 801147369 522 True 776.000000 776 93.499000 1 522 1 chr2B.!!$R2 521
9 TraesCS5B01G089500 chr2B 508412544 508413074 530 True 767.000000 767 92.697000 1 533 1 chr2B.!!$R1 532
10 TraesCS5B01G089500 chr6B 445849318 445849841 523 True 761.000000 761 92.939000 1 523 1 chr6B.!!$R1 522
11 TraesCS5B01G089500 chr7B 89970697 89971221 524 False 760.000000 760 92.762000 1 525 1 chr7B.!!$F1 524

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
526 530 0.323451 GGGGTGGAGTTGGCCTTAAG 60.323 60.0 3.32 0.0 0.0 1.85 F
1329 1350 0.106217 AACCTGACCCAACACCCAAG 60.106 55.0 0.00 0.0 0.0 3.61 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1547 1568 0.178944 TCCCTCCCGTCAGTTGAAGA 60.179 55.0 0.0 0.0 0.0 2.87 R
2308 2356 0.178975 AAAATGTGGGAAGTGGCCGA 60.179 50.0 0.0 0.0 0.0 5.54 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
174 175 1.238439 AATGACTTGGTTGAGCACGG 58.762 50.000 0.00 0.00 0.00 4.94
203 204 5.482163 TCATATTGGCAACCGATAGATGA 57.518 39.130 0.00 0.00 33.81 2.92
295 298 9.072294 CAATTTCGATTGGGTTGTAAAACTATC 57.928 33.333 0.00 0.00 30.93 2.08
445 449 4.954118 AGGACAGGCCCGGACACA 62.954 66.667 0.73 0.00 37.37 3.72
449 453 4.263572 CAGGCCCGGACACAACCA 62.264 66.667 0.73 0.00 0.00 3.67
456 460 1.667830 CGGACACAACCACATCGCT 60.668 57.895 0.00 0.00 0.00 4.93
480 484 2.200373 CCAAAGGGACAGAATTCGGT 57.800 50.000 11.21 11.21 35.59 4.69
508 512 2.505498 CGTCCGTTTGAGATCGCGG 61.505 63.158 6.13 8.60 44.95 6.46
526 530 0.323451 GGGGTGGAGTTGGCCTTAAG 60.323 60.000 3.32 0.00 0.00 1.85
527 531 0.696501 GGGTGGAGTTGGCCTTAAGA 59.303 55.000 3.32 0.00 0.00 2.10
528 532 1.340114 GGGTGGAGTTGGCCTTAAGAG 60.340 57.143 3.32 0.00 0.00 2.85
529 533 1.454201 GTGGAGTTGGCCTTAAGAGC 58.546 55.000 3.32 5.73 0.00 4.09
530 534 1.064003 TGGAGTTGGCCTTAAGAGCA 58.936 50.000 3.32 0.00 0.00 4.26
531 535 1.635487 TGGAGTTGGCCTTAAGAGCAT 59.365 47.619 3.32 0.00 0.00 3.79
539 543 3.202097 GGCCTTAAGAGCATTGTCTCTC 58.798 50.000 3.36 0.00 42.25 3.20
540 544 3.202097 GCCTTAAGAGCATTGTCTCTCC 58.798 50.000 3.36 0.00 42.25 3.71
543 547 2.663826 AAGAGCATTGTCTCTCCGAC 57.336 50.000 9.91 0.00 42.25 4.79
565 569 3.120477 CGGATCGAGTAATCGAGAAGGAG 60.120 52.174 20.65 5.36 45.70 3.69
589 593 3.740590 CGTAGCAAAAGCAGAGACAATG 58.259 45.455 0.00 0.00 0.00 2.82
610 614 1.273886 GAAGAAGACGAAGGTGGAGCT 59.726 52.381 0.00 0.00 0.00 4.09
684 689 2.093128 GGGGTCCTAGATCTCGCAAAAA 60.093 50.000 0.00 0.00 0.00 1.94
685 690 3.433740 GGGGTCCTAGATCTCGCAAAAAT 60.434 47.826 0.00 0.00 0.00 1.82
904 910 5.125257 GTCGGGCCTATAAATCCTCTACTAC 59.875 48.000 0.84 0.00 0.00 2.73
905 911 4.096081 CGGGCCTATAAATCCTCTACTACG 59.904 50.000 0.84 0.00 0.00 3.51
912 918 1.595466 ATCCTCTACTACGTCTGCCG 58.405 55.000 0.00 0.00 44.03 5.69
940 946 2.932663 ACAGCCAAGTGTGATTCCG 58.067 52.632 0.00 0.00 0.00 4.30
941 947 0.606401 ACAGCCAAGTGTGATTCCGG 60.606 55.000 0.00 0.00 0.00 5.14
943 949 0.606401 AGCCAAGTGTGATTCCGGTG 60.606 55.000 0.00 0.00 0.00 4.94
944 950 0.605319 GCCAAGTGTGATTCCGGTGA 60.605 55.000 0.00 0.00 0.00 4.02
945 951 1.156736 CCAAGTGTGATTCCGGTGAC 58.843 55.000 0.00 0.00 0.00 3.67
946 952 1.542328 CCAAGTGTGATTCCGGTGACA 60.542 52.381 0.00 0.00 0.00 3.58
947 953 1.531149 CAAGTGTGATTCCGGTGACAC 59.469 52.381 15.56 15.56 39.22 3.67
948 954 0.756294 AGTGTGATTCCGGTGACACA 59.244 50.000 21.48 20.63 40.99 3.72
949 955 3.299050 TGTGATTCCGGTGACACAC 57.701 52.632 19.72 15.30 38.14 3.82
963 969 2.159099 TGACACACACAAGGAGAGTGAC 60.159 50.000 0.00 0.00 40.74 3.67
974 980 1.252175 GAGAGTGACCTGAGTGAGCA 58.748 55.000 0.00 0.00 0.00 4.26
976 982 0.389687 GAGTGACCTGAGTGAGCAGC 60.390 60.000 0.00 0.00 34.56 5.25
977 983 0.831288 AGTGACCTGAGTGAGCAGCT 60.831 55.000 0.00 0.00 34.56 4.24
1011 1020 2.125512 GCGACGATGAGGGCAACT 60.126 61.111 0.00 0.00 0.00 3.16
1116 1125 3.555324 GAGCCCAGCCTAGAGCCC 61.555 72.222 0.00 0.00 45.47 5.19
1170 1179 0.736325 CGCAGACCGACCCTAAACTG 60.736 60.000 0.00 0.00 40.02 3.16
1191 1200 3.057337 CCGAAACCTGACCCGACT 58.943 61.111 0.00 0.00 0.00 4.18
1212 1221 0.906775 CCAAGCCCGACCCTAAACTA 59.093 55.000 0.00 0.00 0.00 2.24
1227 1236 1.975660 AACTAGCGCCAAAACCTGAA 58.024 45.000 2.29 0.00 0.00 3.02
1237 1258 3.530535 CCAAAACCTGAACCAAAACCAG 58.469 45.455 0.00 0.00 0.00 4.00
1238 1259 3.196685 CCAAAACCTGAACCAAAACCAGA 59.803 43.478 0.00 0.00 0.00 3.86
1239 1260 4.180817 CAAAACCTGAACCAAAACCAGAC 58.819 43.478 0.00 0.00 0.00 3.51
1240 1261 2.067365 ACCTGAACCAAAACCAGACC 57.933 50.000 0.00 0.00 0.00 3.85
1241 1262 1.328279 CCTGAACCAAAACCAGACCC 58.672 55.000 0.00 0.00 0.00 4.46
1242 1263 1.410932 CCTGAACCAAAACCAGACCCA 60.411 52.381 0.00 0.00 0.00 4.51
1243 1264 1.681264 CTGAACCAAAACCAGACCCAC 59.319 52.381 0.00 0.00 0.00 4.61
1244 1265 1.006043 TGAACCAAAACCAGACCCACA 59.994 47.619 0.00 0.00 0.00 4.17
1245 1266 1.681264 GAACCAAAACCAGACCCACAG 59.319 52.381 0.00 0.00 0.00 3.66
1246 1267 0.755327 ACCAAAACCAGACCCACAGC 60.755 55.000 0.00 0.00 0.00 4.40
1247 1268 1.463553 CCAAAACCAGACCCACAGCC 61.464 60.000 0.00 0.00 0.00 4.85
1248 1269 1.152546 AAAACCAGACCCACAGCCC 60.153 57.895 0.00 0.00 0.00 5.19
1321 1342 2.281208 CGCCGAAACCTGACCCAA 60.281 61.111 0.00 0.00 0.00 4.12
1322 1343 2.613506 CGCCGAAACCTGACCCAAC 61.614 63.158 0.00 0.00 0.00 3.77
1323 1344 1.527380 GCCGAAACCTGACCCAACA 60.527 57.895 0.00 0.00 0.00 3.33
1324 1345 1.792118 GCCGAAACCTGACCCAACAC 61.792 60.000 0.00 0.00 0.00 3.32
1325 1346 1.170290 CCGAAACCTGACCCAACACC 61.170 60.000 0.00 0.00 0.00 4.16
1326 1347 1.170290 CGAAACCTGACCCAACACCC 61.170 60.000 0.00 0.00 0.00 4.61
1327 1348 0.106419 GAAACCTGACCCAACACCCA 60.106 55.000 0.00 0.00 0.00 4.51
1328 1349 0.336737 AAACCTGACCCAACACCCAA 59.663 50.000 0.00 0.00 0.00 4.12
1329 1350 0.106217 AACCTGACCCAACACCCAAG 60.106 55.000 0.00 0.00 0.00 3.61
1330 1351 1.903404 CCTGACCCAACACCCAAGC 60.903 63.158 0.00 0.00 0.00 4.01
1331 1352 1.903404 CTGACCCAACACCCAAGCC 60.903 63.158 0.00 0.00 0.00 4.35
1332 1353 2.600470 GACCCAACACCCAAGCCC 60.600 66.667 0.00 0.00 0.00 5.19
1333 1354 4.596585 ACCCAACACCCAAGCCCG 62.597 66.667 0.00 0.00 0.00 6.13
1334 1355 4.278513 CCCAACACCCAAGCCCGA 62.279 66.667 0.00 0.00 0.00 5.14
1335 1356 2.983592 CCAACACCCAAGCCCGAC 60.984 66.667 0.00 0.00 0.00 4.79
1336 1357 2.983592 CAACACCCAAGCCCGACC 60.984 66.667 0.00 0.00 0.00 4.79
1337 1358 4.280019 AACACCCAAGCCCGACCC 62.280 66.667 0.00 0.00 0.00 4.46
1339 1360 3.006728 CACCCAAGCCCGACCCTA 61.007 66.667 0.00 0.00 0.00 3.53
1340 1361 2.204029 ACCCAAGCCCGACCCTAA 60.204 61.111 0.00 0.00 0.00 2.69
1341 1362 1.848895 ACCCAAGCCCGACCCTAAA 60.849 57.895 0.00 0.00 0.00 1.85
1342 1363 1.378119 CCCAAGCCCGACCCTAAAC 60.378 63.158 0.00 0.00 0.00 2.01
1343 1364 1.378119 CCAAGCCCGACCCTAAACC 60.378 63.158 0.00 0.00 0.00 3.27
1344 1365 1.743995 CAAGCCCGACCCTAAACCG 60.744 63.158 0.00 0.00 0.00 4.44
1345 1366 2.963101 AAGCCCGACCCTAAACCGG 61.963 63.158 0.00 0.00 42.64 5.28
1347 1368 4.825252 CCCGACCCTAAACCGGCG 62.825 72.222 0.00 0.00 41.74 6.46
1518 1539 4.700365 CAGTCGTCGTCGCAGCCA 62.700 66.667 0.00 0.00 36.96 4.75
1658 1679 3.021695 TGTCTCCGGTGATGGTTAGTAG 58.978 50.000 9.83 0.00 0.00 2.57
1659 1680 3.022406 GTCTCCGGTGATGGTTAGTAGT 58.978 50.000 9.83 0.00 0.00 2.73
1664 1685 4.340097 TCCGGTGATGGTTAGTAGTATGTG 59.660 45.833 0.00 0.00 0.00 3.21
1679 1700 0.968405 ATGTGTTGCATGTGTTCCCC 59.032 50.000 0.00 0.00 36.26 4.81
1694 1715 3.066190 CCCCCGTCTCTGCACGTA 61.066 66.667 0.00 0.00 38.14 3.57
1695 1716 2.181021 CCCCGTCTCTGCACGTAC 59.819 66.667 0.00 0.00 38.14 3.67
1700 1721 0.454620 CGTCTCTGCACGTACTGTCC 60.455 60.000 0.00 0.00 34.95 4.02
1726 1747 1.795768 TGTTCGTGTGAGCCATCTTC 58.204 50.000 0.00 0.00 0.00 2.87
1777 1811 6.140303 CCATGAATAAACAGAGGAACATGG 57.860 41.667 0.00 0.00 44.29 3.66
1781 1815 6.720309 TGAATAAACAGAGGAACATGGATCA 58.280 36.000 0.00 0.00 0.00 2.92
1806 1840 5.641636 TGCATGTATCTCAACGTACATTTGT 59.358 36.000 0.00 0.00 38.98 2.83
1886 1920 8.680903 ACTCCTTTAATTTCATCTATGTTGCAG 58.319 33.333 0.00 0.00 0.00 4.41
1946 1987 6.546034 AGTGTTCCATAATATTTGTGGCTACC 59.454 38.462 12.44 8.46 41.26 3.18
2001 2049 6.554334 TTCAGAACTTAATTCCTCAAACGG 57.446 37.500 0.00 0.00 38.16 4.44
2044 2092 5.881923 ACCCACAGTTTCAGTTAGAACTA 57.118 39.130 0.00 0.00 37.08 2.24
2045 2093 6.243216 ACCCACAGTTTCAGTTAGAACTAA 57.757 37.500 0.00 0.00 37.08 2.24
2046 2094 6.289064 ACCCACAGTTTCAGTTAGAACTAAG 58.711 40.000 0.00 0.00 37.08 2.18
2064 2112 2.200092 GGGCCTGTTTGGTTGGGA 59.800 61.111 0.84 0.00 38.35 4.37
2173 2221 8.379331 GGAAAGGCAGAGAAAGATATAGGTTAT 58.621 37.037 0.00 0.00 0.00 1.89
2180 2228 8.097662 CAGAGAAAGATATAGGTTATCCCAACC 58.902 40.741 0.00 0.00 40.58 3.77
2193 2241 6.294508 GGTTATCCCAACCCAAAATATCATCG 60.295 42.308 0.00 0.00 34.26 3.84
2274 2322 5.290493 TCCTGTAACAAGACACAGTCATT 57.710 39.130 0.00 0.00 40.47 2.57
2290 2338 4.095483 CAGTCATTGGCAATAACAGGAGAC 59.905 45.833 15.63 14.50 0.00 3.36
2308 2356 3.823304 GAGACTGAAAAGTGGCAGGAAAT 59.177 43.478 0.00 0.00 36.47 2.17
2310 2358 2.554032 ACTGAAAAGTGGCAGGAAATCG 59.446 45.455 0.00 0.00 36.47 3.34
2311 2359 1.885887 TGAAAAGTGGCAGGAAATCGG 59.114 47.619 0.00 0.00 0.00 4.18
2312 2360 0.603065 AAAAGTGGCAGGAAATCGGC 59.397 50.000 0.00 0.00 35.80 5.54
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
92 93 4.136796 TGGAACTGGACAAACTGATCAAG 58.863 43.478 0.00 0.00 0.00 3.02
149 150 5.108517 GTGCTCAACCAAGTCATTTTGAAA 58.891 37.500 0.00 0.00 0.00 2.69
174 175 1.963515 GGTTGCCAATATGATCCCACC 59.036 52.381 0.00 0.00 0.00 4.61
313 316 7.656707 AAACAAGTTTGCATGTCCAAATATC 57.343 32.000 0.00 0.00 37.09 1.63
422 426 3.866582 CGGGCCTGTCCTGGGATC 61.867 72.222 2.29 0.00 37.58 3.36
445 449 0.981183 TTGGGTAGAGCGATGTGGTT 59.019 50.000 0.00 0.00 0.00 3.67
449 453 0.541863 CCCTTTGGGTAGAGCGATGT 59.458 55.000 0.00 0.00 38.25 3.06
456 460 3.055385 CGAATTCTGTCCCTTTGGGTAGA 60.055 47.826 3.52 5.58 44.74 2.59
476 480 2.049802 GACGTCCGCTTTGACCGA 60.050 61.111 3.51 0.00 31.35 4.69
508 512 0.696501 TCTTAAGGCCAACTCCACCC 59.303 55.000 5.01 0.00 0.00 4.61
554 558 1.649815 CTACGCGCTCCTTCTCGAT 59.350 57.895 5.73 0.00 0.00 3.59
589 593 1.673329 GCTCCACCTTCGTCTTCTTCC 60.673 57.143 0.00 0.00 0.00 3.46
610 614 4.344865 GCAAAGAGCCGGTCCCCA 62.345 66.667 1.90 0.00 37.23 4.96
881 887 4.399483 AGTAGAGGATTTATAGGCCCGA 57.601 45.455 0.00 0.00 0.00 5.14
905 911 2.280119 TGTGAGTGTGCGGCAGAC 60.280 61.111 21.33 21.33 0.00 3.51
912 918 1.097547 ACTTGGCTGTGTGAGTGTGC 61.098 55.000 0.00 0.00 0.00 4.57
936 942 0.462937 CCTTGTGTGTGTCACCGGAA 60.463 55.000 9.46 0.00 45.61 4.30
937 943 1.145156 CCTTGTGTGTGTCACCGGA 59.855 57.895 9.46 0.00 45.61 5.14
939 945 0.104120 TCTCCTTGTGTGTGTCACCG 59.896 55.000 0.00 0.00 45.61 4.94
940 946 1.139058 ACTCTCCTTGTGTGTGTCACC 59.861 52.381 0.00 0.00 45.61 4.02
941 947 2.159099 TCACTCTCCTTGTGTGTGTCAC 60.159 50.000 0.00 0.00 46.31 3.67
943 949 2.474816 GTCACTCTCCTTGTGTGTGTC 58.525 52.381 0.00 0.00 40.09 3.67
944 950 1.139058 GGTCACTCTCCTTGTGTGTGT 59.861 52.381 0.00 0.00 40.09 3.72
945 951 1.414181 AGGTCACTCTCCTTGTGTGTG 59.586 52.381 0.00 0.00 40.09 3.82
946 952 1.414181 CAGGTCACTCTCCTTGTGTGT 59.586 52.381 0.00 0.00 40.09 3.72
947 953 1.688735 TCAGGTCACTCTCCTTGTGTG 59.311 52.381 0.00 0.00 40.41 3.82
948 954 1.967066 CTCAGGTCACTCTCCTTGTGT 59.033 52.381 0.00 0.00 36.83 3.72
949 955 1.967066 ACTCAGGTCACTCTCCTTGTG 59.033 52.381 0.00 0.00 36.82 3.33
954 960 0.530288 GCTCACTCAGGTCACTCTCC 59.470 60.000 0.00 0.00 0.00 3.71
956 962 1.255882 CTGCTCACTCAGGTCACTCT 58.744 55.000 0.00 0.00 0.00 3.24
957 963 0.389687 GCTGCTCACTCAGGTCACTC 60.390 60.000 0.00 0.00 34.74 3.51
963 969 4.831698 GCTAGCTGCTCACTCAGG 57.168 61.111 4.91 0.00 38.95 3.86
976 982 1.361993 CCGCTCACTGGCTAGCTAG 59.638 63.158 25.03 25.03 36.56 3.42
977 983 3.526430 CCGCTCACTGGCTAGCTA 58.474 61.111 15.72 7.83 36.56 3.32
985 994 3.250323 CATCGTCGCCGCTCACTG 61.250 66.667 0.00 0.00 0.00 3.66
1009 1018 2.358003 GCACAGCGAGAAGGCAGT 60.358 61.111 0.00 0.00 32.43 4.40
1011 1020 1.962822 CAAGCACAGCGAGAAGGCA 60.963 57.895 0.00 0.00 34.64 4.75
1095 1104 1.071128 CTCTAGGCTGGGCTCATGC 59.929 63.158 0.00 0.00 38.76 4.06
1191 1200 1.539372 TTTAGGGTCGGGCTTGGGA 60.539 57.895 0.00 0.00 0.00 4.37
1212 1221 1.040339 TTGGTTCAGGTTTTGGCGCT 61.040 50.000 7.64 0.00 0.00 5.92
1227 1236 0.755327 GCTGTGGGTCTGGTTTTGGT 60.755 55.000 0.00 0.00 0.00 3.67
1239 1260 3.801068 TTTTGGGTCGGGCTGTGGG 62.801 63.158 0.00 0.00 0.00 4.61
1240 1261 2.203422 TTTTGGGTCGGGCTGTGG 60.203 61.111 0.00 0.00 0.00 4.17
1241 1262 2.561037 GGTTTTGGGTCGGGCTGTG 61.561 63.158 0.00 0.00 0.00 3.66
1242 1263 2.203437 GGTTTTGGGTCGGGCTGT 60.203 61.111 0.00 0.00 0.00 4.40
1243 1264 3.361977 CGGTTTTGGGTCGGGCTG 61.362 66.667 0.00 0.00 0.00 4.85
1244 1265 4.653888 CCGGTTTTGGGTCGGGCT 62.654 66.667 0.00 0.00 40.07 5.19
1248 1269 3.666253 GGCACCGGTTTTGGGTCG 61.666 66.667 2.97 0.00 34.97 4.79
1308 1329 0.106419 TGGGTGTTGGGTCAGGTTTC 60.106 55.000 0.00 0.00 0.00 2.78
1309 1330 0.336737 TTGGGTGTTGGGTCAGGTTT 59.663 50.000 0.00 0.00 0.00 3.27
1310 1331 0.106217 CTTGGGTGTTGGGTCAGGTT 60.106 55.000 0.00 0.00 0.00 3.50
1311 1332 1.536676 CTTGGGTGTTGGGTCAGGT 59.463 57.895 0.00 0.00 0.00 4.00
1312 1333 1.903404 GCTTGGGTGTTGGGTCAGG 60.903 63.158 0.00 0.00 0.00 3.86
1313 1334 1.903404 GGCTTGGGTGTTGGGTCAG 60.903 63.158 0.00 0.00 0.00 3.51
1314 1335 2.197324 GGCTTGGGTGTTGGGTCA 59.803 61.111 0.00 0.00 0.00 4.02
1315 1336 2.600470 GGGCTTGGGTGTTGGGTC 60.600 66.667 0.00 0.00 0.00 4.46
1316 1337 4.596585 CGGGCTTGGGTGTTGGGT 62.597 66.667 0.00 0.00 0.00 4.51
1317 1338 4.278513 TCGGGCTTGGGTGTTGGG 62.279 66.667 0.00 0.00 0.00 4.12
1318 1339 2.983592 GTCGGGCTTGGGTGTTGG 60.984 66.667 0.00 0.00 0.00 3.77
1319 1340 2.983592 GGTCGGGCTTGGGTGTTG 60.984 66.667 0.00 0.00 0.00 3.33
1320 1341 4.280019 GGGTCGGGCTTGGGTGTT 62.280 66.667 0.00 0.00 0.00 3.32
1321 1342 3.857521 TAGGGTCGGGCTTGGGTGT 62.858 63.158 0.00 0.00 0.00 4.16
1322 1343 2.132089 TTTAGGGTCGGGCTTGGGTG 62.132 60.000 0.00 0.00 0.00 4.61
1323 1344 1.848895 TTTAGGGTCGGGCTTGGGT 60.849 57.895 0.00 0.00 0.00 4.51
1324 1345 1.378119 GTTTAGGGTCGGGCTTGGG 60.378 63.158 0.00 0.00 0.00 4.12
1325 1346 1.378119 GGTTTAGGGTCGGGCTTGG 60.378 63.158 0.00 0.00 0.00 3.61
1326 1347 1.743995 CGGTTTAGGGTCGGGCTTG 60.744 63.158 0.00 0.00 0.00 4.01
1327 1348 2.666812 CGGTTTAGGGTCGGGCTT 59.333 61.111 0.00 0.00 0.00 4.35
1328 1349 3.396570 CCGGTTTAGGGTCGGGCT 61.397 66.667 0.00 0.00 40.07 5.19
1330 1351 4.825252 CGCCGGTTTAGGGTCGGG 62.825 72.222 1.90 0.00 43.55 5.14
1335 1356 4.763646 TTCGGCGCCGGTTTAGGG 62.764 66.667 44.95 18.23 40.25 3.53
1336 1357 2.743149 TTTCGGCGCCGGTTTAGG 60.743 61.111 44.95 19.03 40.25 2.69
1337 1358 2.477396 GTTTCGGCGCCGGTTTAG 59.523 61.111 44.95 19.83 40.25 1.85
1338 1359 3.049074 GGTTTCGGCGCCGGTTTA 61.049 61.111 44.95 26.43 40.25 2.01
1339 1360 4.941309 AGGTTTCGGCGCCGGTTT 62.941 61.111 44.95 24.75 40.25 3.27
1346 1367 2.742372 CTGGGTCAGGTTTCGGCG 60.742 66.667 0.00 0.00 0.00 6.46
1347 1368 3.056328 GCTGGGTCAGGTTTCGGC 61.056 66.667 0.00 0.00 31.21 5.54
1348 1369 1.966451 GTGCTGGGTCAGGTTTCGG 60.966 63.158 0.00 0.00 31.21 4.30
1349 1370 1.966451 GGTGCTGGGTCAGGTTTCG 60.966 63.158 0.00 0.00 31.21 3.46
1416 1437 2.361737 GGCTTGGGGTCAGGCTTC 60.362 66.667 0.87 0.00 44.26 3.86
1518 1539 3.660111 GAACGTGGCGGCTGCTTT 61.660 61.111 18.85 5.71 42.25 3.51
1547 1568 0.178944 TCCCTCCCGTCAGTTGAAGA 60.179 55.000 0.00 0.00 0.00 2.87
1621 1642 4.082787 CGGAGACAAATTAAGCACCAACAT 60.083 41.667 0.00 0.00 0.00 2.71
1658 1679 2.094752 GGGGAACACATGCAACACATAC 60.095 50.000 0.00 0.00 36.64 2.39
1659 1680 2.166829 GGGGAACACATGCAACACATA 58.833 47.619 0.00 0.00 36.64 2.29
1679 1700 1.154016 CAGTACGTGCAGAGACGGG 60.154 63.158 6.38 0.00 43.84 5.28
1700 1721 0.307760 GCTCACACGAACAAACTGGG 59.692 55.000 0.00 0.00 0.00 4.45
1726 1747 1.298413 CGGGAGATACACTGACGCG 60.298 63.158 3.53 3.53 0.00 6.01
1777 1811 5.691754 TGTACGTTGAGATACATGCATGATC 59.308 40.000 32.75 26.01 0.00 2.92
1781 1815 6.316140 ACAAATGTACGTTGAGATACATGCAT 59.684 34.615 14.20 0.00 40.36 3.96
1793 1827 7.372396 GTGAAGTACTGAAACAAATGTACGTTG 59.628 37.037 0.00 4.37 39.87 4.10
1806 1840 7.556275 ACCAGAAAATCAAGTGAAGTACTGAAA 59.444 33.333 0.00 0.00 40.26 2.69
1878 1912 4.584325 AGGAACACAATAACACTGCAACAT 59.416 37.500 0.00 0.00 0.00 2.71
1886 1920 6.801862 GCATAGTTGAAGGAACACAATAACAC 59.198 38.462 0.00 0.00 36.98 3.32
1946 1987 1.322538 CCCTGCCTTTCCATTTCCCG 61.323 60.000 0.00 0.00 0.00 5.14
2025 2073 5.701290 CCCCTTAGTTCTAACTGAAACTGTG 59.299 44.000 5.62 0.00 40.07 3.66
2044 2092 1.459348 CCAACCAAACAGGCCCCTT 60.459 57.895 0.00 0.00 43.14 3.95
2045 2093 2.201210 CCAACCAAACAGGCCCCT 59.799 61.111 0.00 0.00 43.14 4.79
2046 2094 2.922503 CCCAACCAAACAGGCCCC 60.923 66.667 0.00 0.00 43.14 5.80
2064 2112 2.343484 TCTGACTGACCCGATATCGT 57.657 50.000 22.81 6.15 37.74 3.73
2111 2159 7.678837 TGATCCACCTGCAAAATAATCTTTTT 58.321 30.769 0.00 0.00 0.00 1.94
2112 2160 7.243604 TGATCCACCTGCAAAATAATCTTTT 57.756 32.000 0.00 0.00 0.00 2.27
2113 2161 6.855763 TGATCCACCTGCAAAATAATCTTT 57.144 33.333 0.00 0.00 0.00 2.52
2118 2166 4.402155 GGTCATGATCCACCTGCAAAATAA 59.598 41.667 0.00 0.00 0.00 1.40
2173 2221 2.955660 GCGATGATATTTTGGGTTGGGA 59.044 45.455 0.00 0.00 0.00 4.37
2180 2228 7.488792 TCATTCAAACAAGCGATGATATTTTGG 59.511 33.333 0.00 0.00 0.00 3.28
2193 2241 4.512571 AGGCAACATTTCATTCAAACAAGC 59.487 37.500 0.00 0.00 41.41 4.01
2274 2322 4.365514 TTTCAGTCTCCTGTTATTGCCA 57.634 40.909 0.00 0.00 39.82 4.92
2290 2338 2.095059 CCGATTTCCTGCCACTTTTCAG 60.095 50.000 0.00 0.00 0.00 3.02
2308 2356 0.178975 AAAATGTGGGAAGTGGCCGA 60.179 50.000 0.00 0.00 0.00 5.54
2310 2358 0.320683 GCAAAATGTGGGAAGTGGCC 60.321 55.000 0.00 0.00 0.00 5.36
2311 2359 0.320683 GGCAAAATGTGGGAAGTGGC 60.321 55.000 0.00 0.00 0.00 5.01
2312 2360 1.001181 CAGGCAAAATGTGGGAAGTGG 59.999 52.381 0.00 0.00 0.00 4.00


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

AutoCloner maintained by Alex Coulton.