Multiple sequence alignment - TraesCS5B01G125500

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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 TraesCS5B01G125500 chr5B 100.000 3374 0 0 1 3374 228272897 228269524 0.000000e+00 6231.0
1 TraesCS5B01G125500 chr5B 100.000 62 0 0 1517 1578 228271327 228271266 7.650000e-22 115.0
2 TraesCS5B01G125500 chr5B 100.000 62 0 0 1571 1632 228271381 228271320 7.650000e-22 115.0
3 TraesCS5B01G125500 chr5B 86.154 65 9 0 2916 2980 406604597 406604533 1.680000e-08 71.3
4 TraesCS5B01G125500 chrUn 91.047 1720 73 22 1571 3275 67924531 67926184 0.000000e+00 2248.0
5 TraesCS5B01G125500 chrUn 89.683 1638 91 28 1 1578 67922973 67924592 0.000000e+00 2017.0
6 TraesCS5B01G125500 chr5A 93.497 1138 35 12 1571 2697 278299939 278298830 0.000000e+00 1655.0
7 TraesCS5B01G125500 chr5A 90.255 903 45 22 703 1578 278300764 278299878 0.000000e+00 1140.0
8 TraesCS5B01G125500 chr5A 88.613 685 63 12 2702 3374 278298738 278298057 0.000000e+00 819.0
9 TraesCS5B01G125500 chr5A 88.587 368 36 6 3 366 278301516 278301151 3.090000e-120 442.0
10 TraesCS5B01G125500 chr5A 93.939 165 8 1 403 567 278301057 278300895 7.230000e-62 248.0
11 TraesCS5B01G125500 chr5A 85.714 77 11 0 2917 2993 105089241 105089165 7.760000e-12 82.4
12 TraesCS5B01G125500 chr1D 78.947 152 26 5 2827 2975 467315382 467315234 7.700000e-17 99.0
13 TraesCS5B01G125500 chr1D 95.833 48 2 0 604 651 41583180 41583133 1.000000e-10 78.7
14 TraesCS5B01G125500 chr5D 80.531 113 17 4 2896 3005 98247818 98247928 7.760000e-12 82.4
15 TraesCS5B01G125500 chr2B 79.167 120 23 2 2876 2994 77200772 77200890 7.760000e-12 82.4
16 TraesCS5B01G125500 chr2B 94.340 53 2 1 599 651 748078448 748078397 2.790000e-11 80.5
17 TraesCS5B01G125500 chr2B 86.441 59 4 3 2924 2980 41596247 41596191 1.010000e-05 62.1
18 TraesCS5B01G125500 chr3D 97.826 46 1 0 604 649 53484619 53484664 2.790000e-11 80.5
19 TraesCS5B01G125500 chr2D 95.918 49 2 0 604 652 532347281 532347233 2.790000e-11 80.5
20 TraesCS5B01G125500 chr7A 95.833 48 2 0 604 651 174213642 174213595 1.000000e-10 78.7
21 TraesCS5B01G125500 chr7D 95.833 48 1 1 601 648 53731169 53731215 3.610000e-10 76.8
22 TraesCS5B01G125500 chr3B 91.071 56 3 2 599 652 751943552 751943497 1.300000e-09 75.0
23 TraesCS5B01G125500 chr3B 87.500 56 5 2 2897 2951 475468989 475468935 2.810000e-06 63.9
24 TraesCS5B01G125500 chr3A 93.878 49 2 1 601 648 750397559 750397511 4.670000e-09 73.1
25 TraesCS5B01G125500 chr6D 77.273 132 14 10 2830 2949 277059195 277059068 2.810000e-06 63.9


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 TraesCS5B01G125500 chr5B 228269524 228272897 3373 True 2153.666667 6231 100.0000 1 3374 3 chr5B.!!$R2 3373
1 TraesCS5B01G125500 chrUn 67922973 67926184 3211 False 2132.500000 2248 90.3650 1 3275 2 chrUn.!!$F1 3274
2 TraesCS5B01G125500 chr5A 278298057 278301516 3459 True 860.800000 1655 90.9782 3 3374 5 chr5A.!!$R2 3371

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
567 667 0.380378 GCCAAAGTGCTGAAACGTGA 59.620 50.0 0.0 0.0 0.0 4.35 F
1574 1747 0.108615 AGGAGAATGACAAGTCGGCG 60.109 55.0 0.0 0.0 0.0 6.46 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1601 1774 0.041238 TGTCATTCTCCTCCTCCGGT 59.959 55.0 0.0 0.0 0.00 5.28 R
3077 3355 0.036164 TCACTTCGTGGGGTTCATGG 59.964 55.0 0.0 0.0 33.87 3.66 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
158 161 8.641499 TGAGTTTGTGTGAATTATTTTGGAAC 57.359 30.769 0.00 0.00 0.00 3.62
247 259 4.084287 AGTGGTTCACGTAGAAGGATACA 58.916 43.478 0.00 0.00 39.64 2.29
249 261 5.041940 GTGGTTCACGTAGAAGGATACATC 58.958 45.833 0.00 0.00 36.78 3.06
278 290 1.544759 GGACAACATGGGGTTTCGTCT 60.545 52.381 0.00 0.00 37.72 4.18
397 409 6.900568 GAACTAGGTTCTCATCTTGATGTG 57.099 41.667 10.01 8.12 39.23 3.21
398 410 5.350504 ACTAGGTTCTCATCTTGATGTGG 57.649 43.478 10.01 5.58 0.00 4.17
525 597 6.296489 CCCACTCTCCTATAAAACAGGAACTT 60.296 42.308 0.00 0.00 41.66 2.66
567 667 0.380378 GCCAAAGTGCTGAAACGTGA 59.620 50.000 0.00 0.00 0.00 4.35
575 675 5.836821 AGTGCTGAAACGTGAGATATCTA 57.163 39.130 4.89 0.00 0.00 1.98
601 701 9.692325 AAGCCAGATACATCTAATTTTCTCTTT 57.308 29.630 0.00 0.00 34.85 2.52
636 737 7.424227 AATTGTTTGAATTGCTTACCACATG 57.576 32.000 0.00 0.00 0.00 3.21
645 746 1.194547 GCTTACCACATGTGTCACGTG 59.805 52.381 23.79 21.25 40.80 4.49
649 750 1.872388 CCACATGTGTCACGTGGTTA 58.128 50.000 25.31 0.00 44.27 2.85
654 755 3.994392 ACATGTGTCACGTGGTTAATCTC 59.006 43.478 25.31 2.15 39.36 2.75
673 774 7.504924 AATCTCCTCTCAGATTAGTTACTCG 57.495 40.000 0.00 0.00 40.67 4.18
698 799 9.678941 CGATAAGTATGTTTAGTGCTGAAGATA 57.321 33.333 0.00 0.00 0.00 1.98
744 872 1.594397 CGTTGCATCGCACTCATGTAT 59.406 47.619 3.94 0.00 38.71 2.29
814 942 2.124736 CACATACCAGTGGCCCGG 60.125 66.667 9.78 0.00 35.88 5.73
874 1019 5.182487 TCAGTCTCTCTACTTACTCTGCAG 58.818 45.833 7.63 7.63 0.00 4.41
875 1020 4.941263 CAGTCTCTCTACTTACTCTGCAGT 59.059 45.833 14.67 0.00 36.55 4.40
877 1022 5.045869 AGTCTCTCTACTTACTCTGCAGTCT 60.046 44.000 14.67 2.22 33.62 3.24
879 1024 3.692101 TCTCTACTTACTCTGCAGTCTGC 59.308 47.826 18.32 18.32 45.29 4.26
959 1118 3.057174 TCTTCTTCTTCTTCTCTCCGCAC 60.057 47.826 0.00 0.00 0.00 5.34
960 1119 2.239400 TCTTCTTCTTCTCTCCGCACA 58.761 47.619 0.00 0.00 0.00 4.57
972 1131 1.134367 CTCCGCACATACTTCCTTCGA 59.866 52.381 0.00 0.00 0.00 3.71
979 1141 4.096682 GCACATACTTCCTTCGACTACTCT 59.903 45.833 0.00 0.00 0.00 3.24
982 1144 7.172875 GCACATACTTCCTTCGACTACTCTATA 59.827 40.741 0.00 0.00 0.00 1.31
985 1147 9.661563 CATACTTCCTTCGACTACTCTATATCT 57.338 37.037 0.00 0.00 0.00 1.98
987 1149 6.869913 ACTTCCTTCGACTACTCTATATCTCG 59.130 42.308 0.00 0.00 0.00 4.04
988 1150 5.170021 TCCTTCGACTACTCTATATCTCGC 58.830 45.833 0.00 0.00 0.00 5.03
989 1151 5.047164 TCCTTCGACTACTCTATATCTCGCT 60.047 44.000 0.00 0.00 0.00 4.93
990 1152 5.290158 CCTTCGACTACTCTATATCTCGCTC 59.710 48.000 0.00 0.00 0.00 5.03
991 1153 5.648178 TCGACTACTCTATATCTCGCTCT 57.352 43.478 0.00 0.00 0.00 4.09
992 1154 6.756299 TCGACTACTCTATATCTCGCTCTA 57.244 41.667 0.00 0.00 0.00 2.43
1032 1194 0.318275 GTCGATCGAGCTCATCCACC 60.318 60.000 20.09 0.00 0.00 4.61
1033 1195 0.466372 TCGATCGAGCTCATCCACCT 60.466 55.000 15.15 0.00 0.00 4.00
1034 1196 0.387202 CGATCGAGCTCATCCACCTT 59.613 55.000 15.40 0.00 0.00 3.50
1035 1197 1.601663 CGATCGAGCTCATCCACCTTC 60.602 57.143 15.40 0.00 0.00 3.46
1036 1198 1.410517 GATCGAGCTCATCCACCTTCA 59.589 52.381 15.40 0.00 0.00 3.02
1037 1199 1.489481 TCGAGCTCATCCACCTTCAT 58.511 50.000 15.40 0.00 0.00 2.57
1038 1200 1.410517 TCGAGCTCATCCACCTTCATC 59.589 52.381 15.40 0.00 0.00 2.92
1039 1201 1.411977 CGAGCTCATCCACCTTCATCT 59.588 52.381 15.40 0.00 0.00 2.90
1040 1202 2.625314 CGAGCTCATCCACCTTCATCTA 59.375 50.000 15.40 0.00 0.00 1.98
1041 1203 3.551863 CGAGCTCATCCACCTTCATCTAC 60.552 52.174 15.40 0.00 0.00 2.59
1042 1204 3.640967 GAGCTCATCCACCTTCATCTACT 59.359 47.826 9.40 0.00 0.00 2.57
1043 1205 3.640967 AGCTCATCCACCTTCATCTACTC 59.359 47.826 0.00 0.00 0.00 2.59
1057 1219 3.319137 TCTACTCTGCATTGTTCGCTT 57.681 42.857 0.00 0.00 0.00 4.68
1424 1597 3.371063 GCGTCCGAGGAGTGGTCA 61.371 66.667 0.00 0.00 0.00 4.02
1548 1721 1.226030 GACAACCGGCAGTACACCAC 61.226 60.000 0.00 0.00 0.00 4.16
1549 1722 1.964373 CAACCGGCAGTACACCACC 60.964 63.158 0.00 0.00 0.00 4.61
1550 1723 3.524648 AACCGGCAGTACACCACCG 62.525 63.158 0.00 8.41 45.21 4.94
1552 1725 3.687102 CGGCAGTACACCACCGGA 61.687 66.667 9.46 0.00 41.95 5.14
1553 1726 2.264794 GGCAGTACACCACCGGAG 59.735 66.667 9.46 0.00 0.00 4.63
1568 1741 2.593346 CGGAGGAGGAGAATGACAAG 57.407 55.000 0.00 0.00 0.00 3.16
1569 1742 1.827969 CGGAGGAGGAGAATGACAAGT 59.172 52.381 0.00 0.00 0.00 3.16
1570 1743 2.159170 CGGAGGAGGAGAATGACAAGTC 60.159 54.545 0.00 0.00 0.00 3.01
1571 1744 2.159170 GGAGGAGGAGAATGACAAGTCG 60.159 54.545 0.00 0.00 0.00 4.18
1572 1745 1.827969 AGGAGGAGAATGACAAGTCGG 59.172 52.381 0.00 0.00 0.00 4.79
1573 1746 1.646189 GAGGAGAATGACAAGTCGGC 58.354 55.000 0.00 0.00 0.00 5.54
1574 1747 0.108615 AGGAGAATGACAAGTCGGCG 60.109 55.000 0.00 0.00 0.00 6.46
1575 1748 1.084370 GGAGAATGACAAGTCGGCGG 61.084 60.000 7.21 0.00 0.00 6.13
1576 1749 1.696832 GAGAATGACAAGTCGGCGGC 61.697 60.000 1.71 1.71 0.00 6.53
1577 1750 3.083600 GAATGACAAGTCGGCGGCG 62.084 63.158 27.15 27.15 0.00 6.46
1595 1768 4.681978 GCCTCGACAACCGGCAGT 62.682 66.667 0.00 0.00 43.25 4.40
1596 1769 2.967397 CCTCGACAACCGGCAGTA 59.033 61.111 0.00 0.00 39.14 2.74
1597 1770 1.445582 CCTCGACAACCGGCAGTAC 60.446 63.158 0.00 0.00 39.14 2.73
1598 1771 1.287815 CTCGACAACCGGCAGTACA 59.712 57.895 0.00 0.00 39.14 2.90
1599 1772 1.007038 TCGACAACCGGCAGTACAC 60.007 57.895 0.00 0.00 39.14 2.90
1600 1773 2.025418 CGACAACCGGCAGTACACC 61.025 63.158 0.00 0.00 33.91 4.16
1601 1774 1.070105 GACAACCGGCAGTACACCA 59.930 57.895 0.00 0.00 0.00 4.17
1623 1796 1.827969 CGGAGGAGGAGAATGACAAGT 59.172 52.381 0.00 0.00 0.00 3.16
1756 1929 0.044702 TCCATGGAGGAGATGGTGGT 59.955 55.000 11.44 0.00 43.07 4.16
1838 2011 2.197324 GCCAAGAACCACCACCCA 59.803 61.111 0.00 0.00 0.00 4.51
1879 2052 4.504916 CCTGCTCGTCCGCCTCAG 62.505 72.222 0.00 0.00 0.00 3.35
1979 2152 0.446616 CGAGCAGCACGAGTACTACA 59.553 55.000 6.34 0.00 0.00 2.74
1994 2167 1.887198 ACTACAAGTAGCAGCACGAGT 59.113 47.619 7.14 0.00 36.66 4.18
2012 2185 0.179179 GTACGAGTACTGGTGGCGAC 60.179 60.000 19.61 6.83 33.45 5.19
2142 2315 1.546961 CAGTCGTGGGGAAGACTAGT 58.453 55.000 0.00 0.00 44.98 2.57
2175 2348 8.524487 ACTAATCATAGATTAGACCGACAATCC 58.476 37.037 25.41 0.00 35.97 3.01
2180 2356 1.717194 TTAGACCGACAATCCGCAAC 58.283 50.000 0.00 0.00 0.00 4.17
2226 2402 3.287222 CTTTTGGATTCCGGGCTAATCA 58.713 45.455 14.37 1.21 35.46 2.57
2227 2403 3.374042 TTTGGATTCCGGGCTAATCAA 57.626 42.857 14.37 2.57 35.46 2.57
2228 2404 2.638480 TGGATTCCGGGCTAATCAAG 57.362 50.000 14.37 0.00 35.46 3.02
2286 2463 0.321298 GGGAAGCAACCGAGCTGTTA 60.321 55.000 0.00 0.00 45.89 2.41
2330 2516 5.569059 GGTTCGTATGCACTTTTCTTGATTG 59.431 40.000 0.00 0.00 0.00 2.67
2350 2536 1.037579 ACGATCCCATGAGTCGCTGA 61.038 55.000 12.24 0.00 38.85 4.26
2356 2542 2.766263 TCCCATGAGTCGCTGAGTTAAT 59.234 45.455 0.00 0.00 0.00 1.40
2361 2547 6.093495 CCCATGAGTCGCTGAGTTAATAAAAA 59.907 38.462 0.00 0.00 0.00 1.94
2362 2548 7.182761 CCATGAGTCGCTGAGTTAATAAAAAG 58.817 38.462 0.00 0.00 0.00 2.27
2363 2549 7.064609 CCATGAGTCGCTGAGTTAATAAAAAGA 59.935 37.037 0.00 0.00 0.00 2.52
2541 2728 0.732880 CGACCACCATGACGAGTCAC 60.733 60.000 8.20 0.00 43.11 3.67
2694 2883 4.353777 ACTGGACCTCAGAGCAAGTATAA 58.646 43.478 0.00 0.00 46.18 0.98
2728 3004 2.641815 ACTGAGCTCCATGAAGACCTTT 59.358 45.455 12.15 0.00 0.00 3.11
2729 3005 3.840666 ACTGAGCTCCATGAAGACCTTTA 59.159 43.478 12.15 0.00 0.00 1.85
2775 3051 5.708948 TCAACACTTCAAACAAAAGTCTGG 58.291 37.500 0.00 0.00 34.79 3.86
2815 3092 0.233848 CGGACGCCTACAACAAACAC 59.766 55.000 0.00 0.00 0.00 3.32
2832 3109 5.410439 ACAAACACTGTATTTATCCACGGAC 59.590 40.000 0.00 0.00 36.10 4.79
2913 3190 6.827586 AGTGGAATTTAAGCAAACCGAATA 57.172 33.333 0.00 0.00 0.00 1.75
2968 3245 4.134563 ACCAGGCCGTATTCATTACATTC 58.865 43.478 0.00 0.00 0.00 2.67
2975 3252 6.192360 GCCGTATTCATTACATTCTTGACAC 58.808 40.000 0.00 0.00 0.00 3.67
3043 3320 4.496336 AGCGCCCATCCTCCAAGC 62.496 66.667 2.29 0.00 0.00 4.01
3050 3327 0.394899 CCATCCTCCAAGCCCTTGTC 60.395 60.000 7.21 0.00 38.85 3.18
3070 3347 2.032377 TCGTTTTCTTCCGTGTTCATGC 60.032 45.455 0.00 0.00 0.00 4.06
3126 3421 1.610554 GCCGGCAGGTAAGTGTAGGA 61.611 60.000 24.80 0.00 40.50 2.94
3127 3422 0.175073 CCGGCAGGTAAGTGTAGGAC 59.825 60.000 0.00 0.00 0.00 3.85
3128 3423 0.892755 CGGCAGGTAAGTGTAGGACA 59.107 55.000 0.00 0.00 0.00 4.02
3129 3424 1.480954 CGGCAGGTAAGTGTAGGACAT 59.519 52.381 0.00 0.00 0.00 3.06
3130 3425 2.691526 CGGCAGGTAAGTGTAGGACATA 59.308 50.000 0.00 0.00 0.00 2.29
3131 3426 3.243434 CGGCAGGTAAGTGTAGGACATAG 60.243 52.174 0.00 0.00 0.00 2.23
3132 3427 3.069729 GGCAGGTAAGTGTAGGACATAGG 59.930 52.174 0.00 0.00 0.00 2.57
3195 3490 0.541063 TGCCCAACTCCTACTCGTCA 60.541 55.000 0.00 0.00 0.00 4.35
3228 3523 1.002257 TGCGTCGTAGGTGGAGGTA 60.002 57.895 0.00 0.00 0.00 3.08
3232 3527 0.459078 GTCGTAGGTGGAGGTAAGGC 59.541 60.000 0.00 0.00 0.00 4.35
3235 3530 1.382146 TAGGTGGAGGTAAGGCCGG 60.382 63.158 0.00 0.00 43.70 6.13
3277 3572 2.879462 CGTCGAAGTACCAGCGCC 60.879 66.667 2.29 0.00 0.00 6.53
3280 3575 1.373748 TCGAAGTACCAGCGCCAAC 60.374 57.895 2.29 0.00 0.00 3.77
3302 3597 2.912025 CCCAGCTGGTGGCGTTTT 60.912 61.111 30.63 0.00 46.45 2.43
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
130 132 7.437862 TCCAAAATAATTCACACAAACTCAAGC 59.562 33.333 0.00 0.00 0.00 4.01
131 133 8.870160 TCCAAAATAATTCACACAAACTCAAG 57.130 30.769 0.00 0.00 0.00 3.02
132 134 9.092876 GTTCCAAAATAATTCACACAAACTCAA 57.907 29.630 0.00 0.00 0.00 3.02
183 186 2.481289 TCACCATAAACATGTCCGCA 57.519 45.000 0.00 0.00 0.00 5.69
213 225 2.944349 GTGAACCACTCACCGGTTTTAA 59.056 45.455 2.97 0.00 46.80 1.52
247 259 2.291800 CCATGTTGTCCTTTGGGGAGAT 60.292 50.000 0.00 0.00 46.10 2.75
249 261 1.549203 CCATGTTGTCCTTTGGGGAG 58.451 55.000 0.00 0.00 46.10 4.30
278 290 5.746245 GTGTAAAGCACATACAGCAAAACAA 59.254 36.000 0.00 0.00 46.91 2.83
388 400 1.695242 ACAACGGTACCCACATCAAGA 59.305 47.619 6.25 0.00 0.00 3.02
392 404 2.396590 ATCACAACGGTACCCACATC 57.603 50.000 6.25 0.00 0.00 3.06
395 407 2.619646 ACAAAATCACAACGGTACCCAC 59.380 45.455 6.25 0.00 0.00 4.61
396 408 2.933573 ACAAAATCACAACGGTACCCA 58.066 42.857 6.25 0.00 0.00 4.51
397 409 3.814283 TGTACAAAATCACAACGGTACCC 59.186 43.478 6.25 0.00 32.30 3.69
398 410 5.616488 ATGTACAAAATCACAACGGTACC 57.384 39.130 0.16 0.16 32.30 3.34
410 479 9.469097 TGTAAAGGTAATGGCTATGTACAAAAT 57.531 29.630 0.00 0.00 0.00 1.82
525 597 4.706035 ACCACTTGTATACGGTGAAAACA 58.294 39.130 22.27 0.00 33.32 2.83
575 675 9.692325 AAAGAGAAAATTAGATGTATCTGGCTT 57.308 29.630 4.67 0.00 37.76 4.35
614 715 5.752472 CACATGTGGTAAGCAATTCAAACAA 59.248 36.000 18.51 0.00 0.00 2.83
621 722 3.058293 CGTGACACATGTGGTAAGCAATT 60.058 43.478 28.64 5.13 34.19 2.32
636 737 3.056749 AGAGGAGATTAACCACGTGACAC 60.057 47.826 19.30 0.00 0.00 3.67
645 746 9.138596 AGTAACTAATCTGAGAGGAGATTAACC 57.861 37.037 0.00 0.00 41.99 2.85
649 750 7.284074 TCGAGTAACTAATCTGAGAGGAGATT 58.716 38.462 0.00 0.00 43.62 2.40
654 755 8.385898 ACTTATCGAGTAACTAATCTGAGAGG 57.614 38.462 0.00 0.00 36.65 3.69
698 799 7.256083 GCAAGATGCCTTTCCAAATCCTTATAT 60.256 37.037 0.00 0.00 37.42 0.86
700 801 5.163374 GCAAGATGCCTTTCCAAATCCTTAT 60.163 40.000 0.00 0.00 37.42 1.73
762 890 2.425312 GAGGATCGTCATGTCAGTGACT 59.575 50.000 23.29 7.08 44.89 3.41
778 906 1.992557 TGGGCCACTTTGTTAGAGGAT 59.007 47.619 0.00 0.00 36.79 3.24
814 942 1.335964 TGCTCTGCAGTCACGTAACTC 60.336 52.381 14.67 0.00 33.32 3.01
877 1022 3.576550 TGGACAGTACTATTCTGTGTGCA 59.423 43.478 0.00 0.00 44.68 4.57
879 1024 5.578336 CACATGGACAGTACTATTCTGTGTG 59.422 44.000 17.41 17.41 44.68 3.82
881 1026 5.724328 ACACATGGACAGTACTATTCTGTG 58.276 41.667 16.71 16.71 44.68 3.66
885 1030 6.535508 GGAAGAACACATGGACAGTACTATTC 59.464 42.308 0.00 0.00 0.00 1.75
959 1118 9.661563 AGATATAGAGTAGTCGAAGGAAGTATG 57.338 37.037 0.00 0.00 0.00 2.39
960 1119 9.880157 GAGATATAGAGTAGTCGAAGGAAGTAT 57.120 37.037 0.00 0.00 0.00 2.12
972 1131 6.703319 TGCTTAGAGCGAGATATAGAGTAGT 58.297 40.000 0.00 0.00 46.26 2.73
979 1141 3.191581 GTGCCTGCTTAGAGCGAGATATA 59.808 47.826 0.00 0.00 46.26 0.86
982 1144 0.103937 GTGCCTGCTTAGAGCGAGAT 59.896 55.000 0.00 0.00 46.26 2.75
985 1147 2.181777 CGTGCCTGCTTAGAGCGA 59.818 61.111 0.00 0.00 46.26 4.93
987 1149 3.198489 GCCGTGCCTGCTTAGAGC 61.198 66.667 0.00 0.00 42.82 4.09
988 1150 2.887568 CGCCGTGCCTGCTTAGAG 60.888 66.667 0.00 0.00 0.00 2.43
989 1151 4.451150 CCGCCGTGCCTGCTTAGA 62.451 66.667 0.00 0.00 0.00 2.10
990 1152 4.760047 ACCGCCGTGCCTGCTTAG 62.760 66.667 0.00 0.00 0.00 2.18
991 1153 4.752879 GACCGCCGTGCCTGCTTA 62.753 66.667 0.00 0.00 0.00 3.09
1032 1194 4.260132 GCGAACAATGCAGAGTAGATGAAG 60.260 45.833 0.00 0.00 0.00 3.02
1033 1195 3.618594 GCGAACAATGCAGAGTAGATGAA 59.381 43.478 0.00 0.00 0.00 2.57
1034 1196 3.118992 AGCGAACAATGCAGAGTAGATGA 60.119 43.478 0.00 0.00 33.85 2.92
1035 1197 3.193263 AGCGAACAATGCAGAGTAGATG 58.807 45.455 0.00 0.00 33.85 2.90
1036 1198 3.533606 AGCGAACAATGCAGAGTAGAT 57.466 42.857 0.00 0.00 33.85 1.98
1037 1199 3.319137 AAGCGAACAATGCAGAGTAGA 57.681 42.857 0.00 0.00 33.85 2.59
1038 1200 3.433274 TCAAAGCGAACAATGCAGAGTAG 59.567 43.478 0.00 0.00 33.85 2.57
1039 1201 3.398406 TCAAAGCGAACAATGCAGAGTA 58.602 40.909 0.00 0.00 33.85 2.59
1040 1202 2.221169 TCAAAGCGAACAATGCAGAGT 58.779 42.857 0.00 0.00 33.85 3.24
1041 1203 2.975410 TCAAAGCGAACAATGCAGAG 57.025 45.000 0.00 0.00 33.85 3.35
1042 1204 2.162208 GGATCAAAGCGAACAATGCAGA 59.838 45.455 0.00 0.00 33.85 4.26
1043 1205 2.523015 GGATCAAAGCGAACAATGCAG 58.477 47.619 0.00 0.00 33.85 4.41
1057 1219 2.368439 CTTTCTTGCCCATCGGATCAA 58.632 47.619 0.00 0.00 0.00 2.57
1424 1597 2.898738 CTGCGGATCACAGCCTCT 59.101 61.111 2.41 0.00 36.45 3.69
1548 1721 1.137872 CTTGTCATTCTCCTCCTCCGG 59.862 57.143 0.00 0.00 0.00 5.14
1549 1722 1.827969 ACTTGTCATTCTCCTCCTCCG 59.172 52.381 0.00 0.00 0.00 4.63
1550 1723 2.159170 CGACTTGTCATTCTCCTCCTCC 60.159 54.545 1.59 0.00 0.00 4.30
1551 1724 2.159170 CCGACTTGTCATTCTCCTCCTC 60.159 54.545 1.59 0.00 0.00 3.71
1552 1725 1.827969 CCGACTTGTCATTCTCCTCCT 59.172 52.381 1.59 0.00 0.00 3.69
1553 1726 1.740718 GCCGACTTGTCATTCTCCTCC 60.741 57.143 1.59 0.00 0.00 4.30
1554 1727 1.646189 GCCGACTTGTCATTCTCCTC 58.354 55.000 1.59 0.00 0.00 3.71
1555 1728 0.108615 CGCCGACTTGTCATTCTCCT 60.109 55.000 1.59 0.00 0.00 3.69
1556 1729 1.084370 CCGCCGACTTGTCATTCTCC 61.084 60.000 1.59 0.00 0.00 3.71
1557 1730 1.696832 GCCGCCGACTTGTCATTCTC 61.697 60.000 1.59 0.00 0.00 2.87
1558 1731 1.741770 GCCGCCGACTTGTCATTCT 60.742 57.895 1.59 0.00 0.00 2.40
1559 1732 2.785258 GCCGCCGACTTGTCATTC 59.215 61.111 1.59 0.00 0.00 2.67
1560 1733 3.118454 CGCCGCCGACTTGTCATT 61.118 61.111 1.59 0.00 36.29 2.57
1579 1752 1.445582 GTACTGCCGGTTGTCGAGG 60.446 63.158 1.90 0.00 42.43 4.63
1580 1753 1.007336 GTGTACTGCCGGTTGTCGAG 61.007 60.000 1.90 0.00 42.43 4.04
1581 1754 1.007038 GTGTACTGCCGGTTGTCGA 60.007 57.895 1.90 0.00 42.43 4.20
1582 1755 2.025418 GGTGTACTGCCGGTTGTCG 61.025 63.158 1.90 0.00 38.88 4.35
1583 1756 1.070105 TGGTGTACTGCCGGTTGTC 59.930 57.895 1.90 0.00 0.00 3.18
1584 1757 1.227734 GTGGTGTACTGCCGGTTGT 60.228 57.895 1.90 4.89 0.00 3.32
1585 1758 1.964373 GGTGGTGTACTGCCGGTTG 60.964 63.158 1.90 0.00 0.00 3.77
1586 1759 2.428622 GGTGGTGTACTGCCGGTT 59.571 61.111 1.90 0.00 0.00 4.44
1587 1760 3.998672 CGGTGGTGTACTGCCGGT 61.999 66.667 1.90 0.00 40.45 5.28
1589 1762 3.642778 CTCCGGTGGTGTACTGCCG 62.643 68.421 0.00 9.74 43.40 5.69
1590 1763 2.264794 CTCCGGTGGTGTACTGCC 59.735 66.667 0.00 0.00 34.15 4.85
1591 1764 2.227089 CTCCTCCGGTGGTGTACTGC 62.227 65.000 21.58 0.00 34.15 4.40
1592 1765 1.605058 CCTCCTCCGGTGGTGTACTG 61.605 65.000 21.58 3.65 32.24 2.74
1593 1766 1.305046 CCTCCTCCGGTGGTGTACT 60.305 63.158 21.58 0.00 32.24 2.73
1594 1767 1.304713 TCCTCCTCCGGTGGTGTAC 60.305 63.158 21.58 0.00 37.58 2.90
1595 1768 1.000019 CTCCTCCTCCGGTGGTGTA 60.000 63.158 21.58 6.10 37.58 2.90
1596 1769 2.283966 CTCCTCCTCCGGTGGTGT 60.284 66.667 21.58 0.00 37.58 4.16
1597 1770 0.978146 ATTCTCCTCCTCCGGTGGTG 60.978 60.000 21.58 18.66 37.58 4.17
1598 1771 0.978146 CATTCTCCTCCTCCGGTGGT 60.978 60.000 21.58 0.00 37.58 4.16
1599 1772 0.687757 TCATTCTCCTCCTCCGGTGG 60.688 60.000 16.75 16.75 37.67 4.61
1600 1773 0.461961 GTCATTCTCCTCCTCCGGTG 59.538 60.000 0.00 0.00 0.00 4.94
1601 1774 0.041238 TGTCATTCTCCTCCTCCGGT 59.959 55.000 0.00 0.00 0.00 5.28
1827 2000 1.374947 CGATGAGTGGGTGGTGGTT 59.625 57.895 0.00 0.00 0.00 3.67
1838 2011 1.153745 GAAGGCGCTGACGATGAGT 60.154 57.895 7.64 0.00 43.93 3.41
1979 2152 1.130749 CTCGTACTCGTGCTGCTACTT 59.869 52.381 0.00 0.00 38.33 2.24
1994 2167 1.638388 CGTCGCCACCAGTACTCGTA 61.638 60.000 0.00 0.00 0.00 3.43
2012 2185 1.796459 GTAGCACTAACAACCACACCG 59.204 52.381 0.00 0.00 0.00 4.94
2142 2315 7.117956 CGGTCTAATCTATGATTAGTCGAGTGA 59.882 40.741 23.27 0.00 34.68 3.41
2175 2348 2.223409 ACATGCATGCAGATTAGTTGCG 60.223 45.455 26.69 6.27 44.40 4.85
2180 2356 5.462068 CCAAAATCACATGCATGCAGATTAG 59.538 40.000 31.62 27.16 35.88 1.73
2226 2402 5.582689 AACTTGTTAGTTGCTTCTTGCTT 57.417 34.783 0.00 0.00 42.91 3.91
2227 2403 5.582689 AAACTTGTTAGTTGCTTCTTGCT 57.417 34.783 0.00 0.00 43.74 3.91
2228 2404 6.531594 AGAAAAACTTGTTAGTTGCTTCTTGC 59.468 34.615 0.00 0.00 43.74 4.01
2229 2405 8.466086 AAGAAAAACTTGTTAGTTGCTTCTTG 57.534 30.769 18.16 0.00 44.94 3.02
2230 2406 9.140286 GAAAGAAAAACTTGTTAGTTGCTTCTT 57.860 29.630 15.55 15.55 46.46 2.52
2231 2407 8.523658 AGAAAGAAAAACTTGTTAGTTGCTTCT 58.476 29.630 0.00 0.00 43.74 2.85
2232 2408 8.689251 AGAAAGAAAAACTTGTTAGTTGCTTC 57.311 30.769 0.00 0.00 43.74 3.86
2330 2516 0.596083 CAGCGACTCATGGGATCGTC 60.596 60.000 15.68 9.97 38.13 4.20
2356 2542 7.593644 GCTCGCTCCAAATTAAAGTTCTTTTTA 59.406 33.333 3.12 0.00 0.00 1.52
2361 2547 4.072131 TGCTCGCTCCAAATTAAAGTTCT 58.928 39.130 0.00 0.00 0.00 3.01
2362 2548 4.159120 GTGCTCGCTCCAAATTAAAGTTC 58.841 43.478 0.00 0.00 0.00 3.01
2363 2549 3.568007 TGTGCTCGCTCCAAATTAAAGTT 59.432 39.130 0.00 0.00 0.00 2.66
2412 2598 6.945519 GGTGTCATCGAGATCGACGAAACA 62.946 50.000 19.58 19.64 46.82 2.83
2557 2744 4.263209 ATCGCTCGCCTGCTCTCG 62.263 66.667 0.00 0.00 0.00 4.04
2558 2745 2.657944 CATCGCTCGCCTGCTCTC 60.658 66.667 0.00 0.00 0.00 3.20
2559 2746 4.887987 GCATCGCTCGCCTGCTCT 62.888 66.667 8.63 0.00 33.15 4.09
2560 2747 4.887987 AGCATCGCTCGCCTGCTC 62.888 66.667 11.48 0.00 42.35 4.26
2561 2748 4.887987 GAGCATCGCTCGCCTGCT 62.888 66.667 15.39 15.39 45.85 4.24
2580 2767 1.361668 CTCCCTGGTCGCATTGAACG 61.362 60.000 0.00 0.00 36.96 3.95
2694 2883 6.249911 TGGAGCTCAGTAGTACTGTACTAT 57.750 41.667 25.61 12.24 46.03 2.12
2705 2981 3.030291 AGGTCTTCATGGAGCTCAGTAG 58.970 50.000 17.19 8.05 39.48 2.57
2708 2984 3.347077 AAAGGTCTTCATGGAGCTCAG 57.653 47.619 17.19 3.67 42.29 3.35
2832 3109 2.591148 CGTATCACTGTCCGTAAACACG 59.409 50.000 0.00 0.00 0.00 4.49
2865 3142 9.284968 CTTAAAATGTATACAGATAGGGTTGGG 57.715 37.037 11.91 0.00 0.00 4.12
2900 3177 4.923281 GCATGAAAACTATTCGGTTTGCTT 59.077 37.500 0.00 0.00 39.08 3.91
2902 3179 4.233789 TGCATGAAAACTATTCGGTTTGC 58.766 39.130 0.00 0.00 39.08 3.68
2913 3190 2.890311 TCATCCGGTTTGCATGAAAACT 59.110 40.909 25.20 6.15 39.51 2.66
2998 3275 7.070821 ACGAATATTTGGACTATGTTAGGGTCT 59.929 37.037 7.61 0.00 0.00 3.85
3043 3320 1.263217 CACGGAAGAAAACGACAAGGG 59.737 52.381 0.00 0.00 0.00 3.95
3050 3327 2.307049 GCATGAACACGGAAGAAAACG 58.693 47.619 0.00 0.00 0.00 3.60
3077 3355 0.036164 TCACTTCGTGGGGTTCATGG 59.964 55.000 0.00 0.00 33.87 3.66
3104 3382 1.324740 TACACTTACCTGCCGGCGAT 61.325 55.000 23.90 12.29 0.00 4.58
3113 3391 5.202746 TGTCCTATGTCCTACACTTACCT 57.797 43.478 0.00 0.00 0.00 3.08
3126 3421 3.073062 GTGGGCTAATCCATGTCCTATGT 59.927 47.826 0.00 0.00 39.26 2.29
3127 3422 3.072915 TGTGGGCTAATCCATGTCCTATG 59.927 47.826 0.00 0.00 39.26 2.23
3128 3423 3.326521 TGTGGGCTAATCCATGTCCTAT 58.673 45.455 0.00 0.00 39.26 2.57
3129 3424 2.770447 TGTGGGCTAATCCATGTCCTA 58.230 47.619 0.00 0.00 39.26 2.94
3130 3425 1.595311 TGTGGGCTAATCCATGTCCT 58.405 50.000 0.00 0.00 39.26 3.85
3131 3426 2.233271 CATGTGGGCTAATCCATGTCC 58.767 52.381 0.00 0.00 39.26 4.02
3132 3427 2.233271 CCATGTGGGCTAATCCATGTC 58.767 52.381 0.00 0.00 39.26 3.06
3175 3470 0.824759 GACGAGTAGGAGTTGGGCAT 59.175 55.000 0.00 0.00 0.00 4.40
3195 3490 0.669077 ACGCACAAGTCTCGAACTCT 59.331 50.000 1.58 0.00 37.17 3.24
3200 3495 0.165295 CTACGACGCACAAGTCTCGA 59.835 55.000 0.00 0.00 38.90 4.04
3228 3523 3.797353 ACATCCATCGCCGGCCTT 61.797 61.111 23.46 5.17 0.00 4.35
3232 3527 2.588877 GTCCACATCCATCGCCGG 60.589 66.667 0.00 0.00 0.00 6.13
3235 3530 2.588877 CCCGTCCACATCCATCGC 60.589 66.667 0.00 0.00 0.00 4.58
3266 3561 2.048503 GTCGTTGGCGCTGGTACT 60.049 61.111 7.64 0.00 38.14 2.73
3277 3572 4.988598 ACCAGCTGGGCGTCGTTG 62.989 66.667 35.42 8.48 42.05 4.10
3346 3641 3.195591 CTATGAGGCCGCGCGTAGT 62.196 63.158 29.95 12.26 0.00 2.73


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

AutoCloner maintained by Alex Coulton.