Multiple sequence alignment - TraesCS6A01G319500

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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 TraesCS6A01G319500 chr6A 100.000 2836 0 0 1 2836 554854524 554857359 0.000000e+00 5238.0
1 TraesCS6A01G319500 chr6A 80.750 587 87 15 1069 1633 555088983 555089565 4.340000e-118 435.0
2 TraesCS6A01G319500 chr6A 94.872 39 2 0 1992 2030 158921701 158921739 8.480000e-06 62.1
3 TraesCS6A01G319500 chr6B 90.397 1864 140 28 754 2610 615275163 615276994 0.000000e+00 2414.0
4 TraesCS6A01G319500 chr6B 88.615 1256 89 33 754 1992 615230023 615231241 0.000000e+00 1478.0
5 TraesCS6A01G319500 chr6B 89.167 1117 65 25 749 1837 615166758 615167846 0.000000e+00 1341.0
6 TraesCS6A01G319500 chr6B 92.893 605 34 6 111 708 615166160 615166762 0.000000e+00 870.0
7 TraesCS6A01G319500 chr6B 81.678 584 78 13 1069 1633 615605438 615606011 2.570000e-125 459.0
8 TraesCS6A01G319500 chr6B 83.721 344 44 8 115 450 615228804 615229143 5.900000e-82 315.0
9 TraesCS6A01G319500 chr6B 93.056 144 10 0 2693 2836 615277282 615277425 7.960000e-51 211.0
10 TraesCS6A01G319500 chr6D 91.242 1039 61 17 754 1778 409583870 409584892 0.000000e+00 1387.0
11 TraesCS6A01G319500 chr6D 88.945 986 58 24 750 1708 409515987 409516948 0.000000e+00 1170.0
12 TraesCS6A01G319500 chr6D 90.517 580 45 8 131 705 409515410 409515984 0.000000e+00 758.0
13 TraesCS6A01G319500 chr6D 81.919 542 64 20 1069 1584 409655215 409655748 7.260000e-116 427.0
14 TraesCS6A01G319500 chr6D 80.000 525 64 28 115 606 409582659 409583175 1.620000e-92 350.0
15 TraesCS6A01G319500 chr6D 89.623 106 11 0 1 106 409515209 409515314 4.930000e-28 135.0
16 TraesCS6A01G319500 chr4A 93.061 245 17 0 2038 2282 67507175 67506931 2.690000e-95 359.0
17 TraesCS6A01G319500 chr7A 92.276 246 19 0 2037 2282 4909536 4909781 1.620000e-92 350.0
18 TraesCS6A01G319500 chr5A 91.870 246 20 0 2037 2282 19817842 19818087 7.520000e-91 344.0
19 TraesCS6A01G319500 chr5A 91.743 109 9 0 2174 2282 667829077 667828969 4.890000e-33 152.0
20 TraesCS6A01G319500 chr2D 91.463 246 21 0 2037 2282 306148706 306148951 3.500000e-89 339.0
21 TraesCS6A01G319500 chr2A 90.574 244 23 0 2039 2282 444298750 444298993 9.800000e-85 324.0
22 TraesCS6A01G319500 chr5D 90.303 165 16 0 1406 1570 353795673 353795837 1.710000e-52 217.0
23 TraesCS6A01G319500 chrUn 95.238 42 1 1 713 753 336469341 336469382 6.560000e-07 65.8
24 TraesCS6A01G319500 chrUn 92.857 42 2 1 713 753 397152016 397152057 3.050000e-05 60.2
25 TraesCS6A01G319500 chr5B 97.368 38 0 1 716 752 624117881 624117844 2.360000e-06 63.9
26 TraesCS6A01G319500 chr5B 97.368 38 0 1 716 752 627709689 627709652 2.360000e-06 63.9
27 TraesCS6A01G319500 chr4B 93.182 44 2 1 710 752 277318057 277318100 2.360000e-06 63.9
28 TraesCS6A01G319500 chr4B 90.909 44 3 1 710 752 97493260 97493303 1.100000e-04 58.4
29 TraesCS6A01G319500 chr3D 91.489 47 2 2 712 757 7259738 7259783 2.360000e-06 63.9
30 TraesCS6A01G319500 chr1B 97.297 37 1 0 716 752 484800940 484800904 2.360000e-06 63.9
31 TraesCS6A01G319500 chr1B 93.023 43 2 1 712 753 229996041 229996083 8.480000e-06 62.1


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 TraesCS6A01G319500 chr6A 554854524 554857359 2835 False 5238.000000 5238 100.0000 1 2836 1 chr6A.!!$F2 2835
1 TraesCS6A01G319500 chr6A 555088983 555089565 582 False 435.000000 435 80.7500 1069 1633 1 chr6A.!!$F3 564
2 TraesCS6A01G319500 chr6B 615275163 615277425 2262 False 1312.500000 2414 91.7265 754 2836 2 chr6B.!!$F4 2082
3 TraesCS6A01G319500 chr6B 615166160 615167846 1686 False 1105.500000 1341 91.0300 111 1837 2 chr6B.!!$F2 1726
4 TraesCS6A01G319500 chr6B 615228804 615231241 2437 False 896.500000 1478 86.1680 115 1992 2 chr6B.!!$F3 1877
5 TraesCS6A01G319500 chr6B 615605438 615606011 573 False 459.000000 459 81.6780 1069 1633 1 chr6B.!!$F1 564
6 TraesCS6A01G319500 chr6D 409582659 409584892 2233 False 868.500000 1387 85.6210 115 1778 2 chr6D.!!$F3 1663
7 TraesCS6A01G319500 chr6D 409515209 409516948 1739 False 687.666667 1170 89.6950 1 1708 3 chr6D.!!$F2 1707
8 TraesCS6A01G319500 chr6D 409655215 409655748 533 False 427.000000 427 81.9190 1069 1584 1 chr6D.!!$F1 515

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
990 2056 0.0297 GTACCGCACCACCAAACAAC 59.97 55.0 0.0 0.0 0.0 3.32 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2615 3751 0.175531 GCGGAAATTGGGGTGGATTG 59.824 55.0 0.0 0.0 0.0 2.67 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
47 48 6.699204 CCATAAAACACACAACATTTGCTACA 59.301 34.615 0.00 0.00 0.00 2.74
64 65 4.202461 TGCTACATTTCCAACCACTTCTCT 60.202 41.667 0.00 0.00 0.00 3.10
65 66 5.012664 TGCTACATTTCCAACCACTTCTCTA 59.987 40.000 0.00 0.00 0.00 2.43
70 71 6.605594 ACATTTCCAACCACTTCTCTACAAAA 59.394 34.615 0.00 0.00 0.00 2.44
74 75 8.561738 TTCCAACCACTTCTCTACAAAATATC 57.438 34.615 0.00 0.00 0.00 1.63
75 76 7.110155 TCCAACCACTTCTCTACAAAATATCC 58.890 38.462 0.00 0.00 0.00 2.59
82 83 8.265055 CACTTCTCTACAAAATATCCCTGGTTA 58.735 37.037 0.00 0.00 0.00 2.85
101 102 8.477256 CCTGGTTAAAATGATTTATGTGACCAT 58.523 33.333 5.52 0.00 37.46 3.55
209 287 7.038658 AGCTTAAGGGCACATTTTTATTAACCA 60.039 33.333 4.29 0.00 34.17 3.67
220 298 7.291416 ACATTTTTATTAACCAGACCAAACCCT 59.709 33.333 0.00 0.00 0.00 4.34
270 348 1.282382 CGAAGGAGGGGAGGGTAAAA 58.718 55.000 0.00 0.00 0.00 1.52
305 383 1.414181 GGAGCATTAGCAGCAGACCTA 59.586 52.381 0.00 0.00 45.49 3.08
396 475 4.646945 TGAAAAAGTGCTACAAATCCACCA 59.353 37.500 0.00 0.00 0.00 4.17
414 493 3.851403 CACCAAACAAAACGACAGACAAG 59.149 43.478 0.00 0.00 0.00 3.16
439 518 2.664424 CGACATTGTTTAAGGGCACACG 60.664 50.000 0.00 0.00 0.00 4.49
619 992 9.688091 TGGTAAAATAGCAGTATACAATTGGAA 57.312 29.630 10.83 0.00 0.00 3.53
664 1699 9.935241 AAGATTGATATGTGCTAAGGTATACAG 57.065 33.333 5.01 0.00 0.00 2.74
682 1717 8.957466 GGTATACAGTTTGGCTTTAGAAGATTT 58.043 33.333 5.01 0.00 0.00 2.17
708 1743 6.574350 CCAAAAGTCTGATAGTACCAGTAGG 58.426 44.000 0.00 0.00 42.21 3.18
709 1744 5.855740 AAAGTCTGATAGTACCAGTAGGC 57.144 43.478 0.00 0.00 39.06 3.93
710 1745 4.521536 AGTCTGATAGTACCAGTAGGCA 57.478 45.455 0.00 0.00 39.06 4.75
711 1746 4.465886 AGTCTGATAGTACCAGTAGGCAG 58.534 47.826 0.00 0.00 39.06 4.85
712 1747 4.079672 AGTCTGATAGTACCAGTAGGCAGT 60.080 45.833 0.00 0.00 39.06 4.40
713 1748 5.132312 AGTCTGATAGTACCAGTAGGCAGTA 59.868 44.000 0.00 0.00 39.06 2.74
714 1749 5.239087 GTCTGATAGTACCAGTAGGCAGTAC 59.761 48.000 0.00 0.00 39.06 2.73
715 1750 5.132312 TCTGATAGTACCAGTAGGCAGTACT 59.868 44.000 7.18 7.18 46.34 2.73
724 1759 4.522722 AGTAGGCAGTACTGTCAAGAAC 57.477 45.455 28.22 18.96 40.76 3.01
725 1760 2.440539 AGGCAGTACTGTCAAGAACG 57.559 50.000 28.22 0.00 37.73 3.95
726 1761 1.687123 AGGCAGTACTGTCAAGAACGT 59.313 47.619 28.22 3.71 37.73 3.99
727 1762 2.102588 AGGCAGTACTGTCAAGAACGTT 59.897 45.455 28.22 0.00 37.73 3.99
728 1763 2.475487 GGCAGTACTGTCAAGAACGTTC 59.525 50.000 22.46 20.71 34.82 3.95
729 1764 3.381949 GCAGTACTGTCAAGAACGTTCT 58.618 45.455 24.93 24.93 39.74 3.01
731 1766 4.980434 GCAGTACTGTCAAGAACGTTCTTA 59.020 41.667 35.97 23.16 45.23 2.10
732 1767 5.634020 GCAGTACTGTCAAGAACGTTCTTAT 59.366 40.000 35.97 22.78 45.23 1.73
733 1768 6.805271 GCAGTACTGTCAAGAACGTTCTTATA 59.195 38.462 35.97 25.93 45.23 0.98
734 1769 7.488471 GCAGTACTGTCAAGAACGTTCTTATAT 59.512 37.037 35.97 23.35 45.23 0.86
735 1770 9.355215 CAGTACTGTCAAGAACGTTCTTATATT 57.645 33.333 35.97 23.10 45.23 1.28
739 1774 9.314321 ACTGTCAAGAACGTTCTTATATTATGG 57.686 33.333 35.97 23.38 45.23 2.74
740 1775 8.657074 TGTCAAGAACGTTCTTATATTATGGG 57.343 34.615 35.97 22.77 45.23 4.00
741 1776 8.479689 TGTCAAGAACGTTCTTATATTATGGGA 58.520 33.333 35.97 24.34 45.23 4.37
742 1777 8.762426 GTCAAGAACGTTCTTATATTATGGGAC 58.238 37.037 35.97 29.18 45.23 4.46
743 1778 8.479689 TCAAGAACGTTCTTATATTATGGGACA 58.520 33.333 35.97 10.22 45.23 4.02
744 1779 8.765219 CAAGAACGTTCTTATATTATGGGACAG 58.235 37.037 35.97 18.59 44.16 3.51
745 1780 7.442656 AGAACGTTCTTATATTATGGGACAGG 58.557 38.462 24.93 0.00 36.15 4.00
746 1781 7.472945 AGAACGTTCTTATATTATGGGACAGGG 60.473 40.741 24.93 0.00 36.15 4.45
927 1968 2.339418 ACGTGATCGCCGTTTCAAATA 58.661 42.857 0.00 0.00 41.18 1.40
933 1974 0.850391 CGCCGTTTCAAATACGCGTC 60.850 55.000 18.63 0.00 37.67 5.19
946 2004 3.838795 GCGTCGACATGCACGTCC 61.839 66.667 17.16 0.00 38.32 4.79
948 2006 1.135939 CGTCGACATGCACGTCCTA 59.864 57.895 17.16 0.00 31.91 2.94
988 2054 4.144418 GTACCGCACCACCAAACA 57.856 55.556 0.00 0.00 0.00 2.83
989 2055 2.406205 GTACCGCACCACCAAACAA 58.594 52.632 0.00 0.00 0.00 2.83
990 2056 0.029700 GTACCGCACCACCAAACAAC 59.970 55.000 0.00 0.00 0.00 3.32
991 2057 1.102222 TACCGCACCACCAAACAACC 61.102 55.000 0.00 0.00 0.00 3.77
992 2058 2.124693 CCGCACCACCAAACAACCT 61.125 57.895 0.00 0.00 0.00 3.50
993 2059 1.358759 CGCACCACCAAACAACCTC 59.641 57.895 0.00 0.00 0.00 3.85
994 2060 1.380403 CGCACCACCAAACAACCTCA 61.380 55.000 0.00 0.00 0.00 3.86
999 2065 2.232696 ACCACCAAACAACCTCAAACAC 59.767 45.455 0.00 0.00 0.00 3.32
1002 2068 2.495669 ACCAAACAACCTCAAACACCAG 59.504 45.455 0.00 0.00 0.00 4.00
1003 2069 2.495669 CCAAACAACCTCAAACACCAGT 59.504 45.455 0.00 0.00 0.00 4.00
1008 2074 0.916086 ACCTCAAACACCAGTCACCA 59.084 50.000 0.00 0.00 0.00 4.17
1029 2120 1.000163 GAGCACGAGAACTCAACTCCA 60.000 52.381 0.00 0.00 32.98 3.86
1057 2148 2.635915 TCCGAGGAGAGGCAAAACTTTA 59.364 45.455 0.00 0.00 0.00 1.85
1065 2156 1.127951 AGGCAAAACTTTATCGCGACG 59.872 47.619 12.93 2.59 0.00 5.12
1149 2243 1.000612 GGACTCCCTCTTCCTCCGT 59.999 63.158 0.00 0.00 0.00 4.69
1402 2520 2.815647 GGAGCCGGAGCAAGTTCG 60.816 66.667 5.05 0.00 43.56 3.95
1621 2748 5.471456 GCTTCTGTTTCTGATTCTTCTTGGA 59.529 40.000 0.00 0.00 0.00 3.53
1664 2791 4.500116 GGGCAGTCCTCGCGAGAC 62.500 72.222 36.59 28.49 35.39 3.36
1687 2814 1.532007 GCGGGTAAAAATGTGTCGTCA 59.468 47.619 0.00 0.00 0.00 4.35
1806 2940 8.761575 TCATTAGCATTTTTGAAAGGATGTTC 57.238 30.769 5.62 0.00 0.00 3.18
1842 2976 3.824028 TATTCGTCGGTGAGCATGGCC 62.824 57.143 0.00 0.00 0.00 5.36
1945 3079 6.241645 CAACTCCCTCTTCTTCAGGTTATTT 58.758 40.000 0.00 0.00 0.00 1.40
1947 3081 7.569599 ACTCCCTCTTCTTCAGGTTATTTAA 57.430 36.000 0.00 0.00 0.00 1.52
1951 3085 9.822727 TCCCTCTTCTTCAGGTTATTTAATTTT 57.177 29.630 0.00 0.00 0.00 1.82
1957 3091 6.378848 TCTTCAGGTTATTTAATTTTCCCGGG 59.621 38.462 16.85 16.85 0.00 5.73
1959 3093 6.017830 TCAGGTTATTTAATTTTCCCGGGTT 58.982 36.000 22.86 10.14 0.00 4.11
1960 3094 7.180663 TCAGGTTATTTAATTTTCCCGGGTTA 58.819 34.615 22.86 8.96 0.00 2.85
1961 3095 7.673082 TCAGGTTATTTAATTTTCCCGGGTTAA 59.327 33.333 22.86 14.98 0.00 2.01
1962 3096 7.760794 CAGGTTATTTAATTTTCCCGGGTTAAC 59.239 37.037 22.86 13.79 0.00 2.01
1963 3097 7.675195 AGGTTATTTAATTTTCCCGGGTTAACT 59.325 33.333 22.86 13.92 0.00 2.24
1965 3099 9.709495 GTTATTTAATTTTCCCGGGTTAACTTT 57.291 29.630 22.86 13.71 0.00 2.66
1998 3132 7.180229 TCTGACAATTTTCATGAGTACTCCCTA 59.820 37.037 20.11 1.91 0.00 3.53
2001 3135 7.861629 ACAATTTTCATGAGTACTCCCTATGA 58.138 34.615 20.11 18.02 0.00 2.15
2049 3183 8.662781 ATTAGTACATATCGATGCAACACTTT 57.337 30.769 8.54 0.00 36.43 2.66
2050 3184 6.985188 AGTACATATCGATGCAACACTTTT 57.015 33.333 8.54 0.00 36.43 2.27
2059 3193 6.148948 TCGATGCAACACTTTTCATTTTAGG 58.851 36.000 0.00 0.00 0.00 2.69
2061 3195 4.047822 TGCAACACTTTTCATTTTAGGCG 58.952 39.130 0.00 0.00 0.00 5.52
2062 3196 3.428534 GCAACACTTTTCATTTTAGGCGG 59.571 43.478 0.00 0.00 0.00 6.13
2077 3211 4.079446 CGGAGCTTGCTTTGGGAA 57.921 55.556 0.00 0.00 0.00 3.97
2125 3259 5.892348 ACAATGTCCCCTTGAAGAATACTT 58.108 37.500 0.00 0.00 39.24 2.24
2150 3284 5.618640 GCTCTTTAACTCGGAGTCGTAGAAA 60.619 44.000 11.71 6.55 39.69 2.52
2158 3292 3.681897 TCGGAGTCGTAGAAACTAGTGTC 59.318 47.826 4.74 4.74 39.69 3.67
2180 3314 0.304705 CTTGCTTGCTCGAAACGTGT 59.695 50.000 0.00 0.00 0.00 4.49
2199 3333 4.130118 GTGTTTGAGGAGTGATGTGTCTT 58.870 43.478 0.00 0.00 0.00 3.01
2236 3370 2.154798 CTTCGGAGAGCGACCACCAA 62.155 60.000 0.00 0.00 38.43 3.67
2238 3372 2.636412 CGGAGAGCGACCACCAAGA 61.636 63.158 0.00 0.00 0.00 3.02
2262 3396 3.614150 GCATCTTGAAGTGGAGTACGACA 60.614 47.826 0.00 0.00 0.00 4.35
2269 3403 4.823442 TGAAGTGGAGTACGACAACTTCTA 59.177 41.667 27.19 18.18 34.81 2.10
2275 3409 4.398673 GGAGTACGACAACTTCTACTCCAT 59.601 45.833 15.84 0.00 44.59 3.41
2283 3417 4.156922 ACAACTTCTACTCCATGAGAGACG 59.843 45.833 15.51 7.69 46.50 4.18
2321 3455 0.459585 TATGAGCGGACTCGTTTGGC 60.460 55.000 0.00 0.00 46.69 4.52
2336 3470 0.961019 TTGGCCATTCAACTCACAGC 59.039 50.000 6.09 0.00 0.00 4.40
2342 3476 3.877559 CCATTCAACTCACAGCCAGATA 58.122 45.455 0.00 0.00 0.00 1.98
2347 3481 7.230108 CCATTCAACTCACAGCCAGATAATATT 59.770 37.037 0.00 0.00 0.00 1.28
2349 3483 6.888105 TCAACTCACAGCCAGATAATATTGA 58.112 36.000 0.00 0.00 0.00 2.57
2359 3493 7.502226 CAGCCAGATAATATTGAAACCTTGGTA 59.498 37.037 0.00 0.00 0.00 3.25
2427 3561 5.013568 TCTCGTTCCAAAGTTTAGACACA 57.986 39.130 0.00 0.00 0.00 3.72
2431 3565 2.489971 TCCAAAGTTTAGACACAGCCG 58.510 47.619 0.00 0.00 0.00 5.52
2432 3566 1.069227 CCAAAGTTTAGACACAGCCGC 60.069 52.381 0.00 0.00 0.00 6.53
2438 3572 1.164411 TTAGACACAGCCGCCAAATG 58.836 50.000 0.00 0.00 0.00 2.32
2460 3594 0.537143 TCGAAGCACAGGCAAACCAT 60.537 50.000 0.00 0.00 44.61 3.55
2523 3659 1.378514 CCCAACCACCCATTCTCCG 60.379 63.158 0.00 0.00 0.00 4.63
2560 3696 2.040009 ATGACCCGCCACCTATTCCG 62.040 60.000 0.00 0.00 0.00 4.30
2643 3779 1.322538 CCAATTTCCGCCTCCCCTTG 61.323 60.000 0.00 0.00 0.00 3.61
2644 3780 1.682344 AATTTCCGCCTCCCCTTGC 60.682 57.895 0.00 0.00 0.00 4.01
2706 4063 2.438434 CCATCACCGCCCAACTCC 60.438 66.667 0.00 0.00 0.00 3.85
2746 4103 0.676184 TATGGCTTGGTTTTGCGCAA 59.324 45.000 21.02 21.02 0.00 4.85
2787 4144 6.596497 GGATTCCGGTAACAAACTTCTTATCA 59.404 38.462 0.00 0.00 0.00 2.15
2793 4150 7.386848 CCGGTAACAAACTTCTTATCAAGAGAA 59.613 37.037 0.00 0.00 39.03 2.87
2822 4179 3.639561 TGTGTGAGGCTACTGAGTTGTTA 59.360 43.478 0.00 0.00 0.00 2.41
2826 4183 5.700832 TGTGAGGCTACTGAGTTGTTATTTG 59.299 40.000 0.00 0.00 0.00 2.32
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
14 15 3.482436 TGTGTGTTTTATGGACCAGACC 58.518 45.455 0.00 0.00 0.00 3.85
47 48 7.839680 ATTTTGTAGAGAAGTGGTTGGAAAT 57.160 32.000 0.00 0.00 0.00 2.17
74 75 7.093552 TGGTCACATAAATCATTTTAACCAGGG 60.094 37.037 0.00 0.00 31.33 4.45
75 76 7.835822 TGGTCACATAAATCATTTTAACCAGG 58.164 34.615 0.00 0.00 31.33 4.45
92 93 6.112734 TCATTTCGCTAGTTAATGGTCACAT 58.887 36.000 11.23 0.00 39.54 3.21
93 94 5.483811 TCATTTCGCTAGTTAATGGTCACA 58.516 37.500 11.23 0.00 31.74 3.58
101 102 8.201464 TGATGGTATCTTCATTTCGCTAGTTAA 58.799 33.333 0.00 0.00 0.00 2.01
106 107 4.991056 GCTGATGGTATCTTCATTTCGCTA 59.009 41.667 0.00 0.00 0.00 4.26
108 109 3.561310 TGCTGATGGTATCTTCATTTCGC 59.439 43.478 0.00 0.00 0.00 4.70
109 110 4.571984 TGTGCTGATGGTATCTTCATTTCG 59.428 41.667 0.00 0.00 0.00 3.46
209 287 8.442374 TGTATTTTCTTTAGTAGGGTTTGGTCT 58.558 33.333 0.00 0.00 0.00 3.85
241 319 2.781757 TCCCCTCCTTCGTATCTCTGTA 59.218 50.000 0.00 0.00 0.00 2.74
270 348 1.071471 CTCCAACTTGCCTCCGTGT 59.929 57.895 0.00 0.00 0.00 4.49
396 475 4.260620 CGATCCTTGTCTGTCGTTTTGTTT 60.261 41.667 0.00 0.00 0.00 2.83
414 493 3.013921 TGCCCTTAAACAATGTCGATCC 58.986 45.455 0.00 0.00 0.00 3.36
651 1028 7.046033 TCTAAAGCCAAACTGTATACCTTAGC 58.954 38.462 0.00 0.00 0.00 3.09
656 1033 8.507524 AATCTTCTAAAGCCAAACTGTATACC 57.492 34.615 0.00 0.00 0.00 2.73
682 1717 4.286032 ACTGGTACTATCAGACTTTTGGCA 59.714 41.667 3.17 0.00 36.22 4.92
708 1743 3.381949 AGAACGTTCTTGACAGTACTGC 58.618 45.455 24.93 15.35 32.55 4.40
709 1744 8.912787 ATATAAGAACGTTCTTGACAGTACTG 57.087 34.615 40.39 21.44 46.34 2.74
713 1748 9.314321 CCATAATATAAGAACGTTCTTGACAGT 57.686 33.333 40.39 28.47 46.34 3.55
714 1749 8.765219 CCCATAATATAAGAACGTTCTTGACAG 58.235 37.037 40.39 25.99 46.34 3.51
715 1750 8.479689 TCCCATAATATAAGAACGTTCTTGACA 58.520 33.333 40.39 28.56 46.34 3.58
716 1751 8.762426 GTCCCATAATATAAGAACGTTCTTGAC 58.238 37.037 40.39 31.50 46.34 3.18
717 1752 8.479689 TGTCCCATAATATAAGAACGTTCTTGA 58.520 33.333 40.39 31.02 46.34 3.02
718 1753 8.657074 TGTCCCATAATATAAGAACGTTCTTG 57.343 34.615 40.39 27.49 46.34 3.02
720 1755 7.442656 CCTGTCCCATAATATAAGAACGTTCT 58.557 38.462 24.93 24.93 39.74 3.01
721 1756 6.649557 CCCTGTCCCATAATATAAGAACGTTC 59.350 42.308 20.71 20.71 0.00 3.95
722 1757 6.465321 CCCCTGTCCCATAATATAAGAACGTT 60.465 42.308 0.00 0.00 0.00 3.99
723 1758 5.012768 CCCCTGTCCCATAATATAAGAACGT 59.987 44.000 0.00 0.00 0.00 3.99
724 1759 5.247564 TCCCCTGTCCCATAATATAAGAACG 59.752 44.000 0.00 0.00 0.00 3.95
725 1760 6.272558 ACTCCCCTGTCCCATAATATAAGAAC 59.727 42.308 0.00 0.00 0.00 3.01
726 1761 6.399013 ACTCCCCTGTCCCATAATATAAGAA 58.601 40.000 0.00 0.00 0.00 2.52
727 1762 5.989717 ACTCCCCTGTCCCATAATATAAGA 58.010 41.667 0.00 0.00 0.00 2.10
728 1763 6.960542 ACTACTCCCCTGTCCCATAATATAAG 59.039 42.308 0.00 0.00 0.00 1.73
729 1764 6.882155 ACTACTCCCCTGTCCCATAATATAA 58.118 40.000 0.00 0.00 0.00 0.98
730 1765 6.494429 ACTACTCCCCTGTCCCATAATATA 57.506 41.667 0.00 0.00 0.00 0.86
731 1766 5.370623 ACTACTCCCCTGTCCCATAATAT 57.629 43.478 0.00 0.00 0.00 1.28
732 1767 4.845530 ACTACTCCCCTGTCCCATAATA 57.154 45.455 0.00 0.00 0.00 0.98
733 1768 3.726837 ACTACTCCCCTGTCCCATAAT 57.273 47.619 0.00 0.00 0.00 1.28
734 1769 4.845530 ATACTACTCCCCTGTCCCATAA 57.154 45.455 0.00 0.00 0.00 1.90
735 1770 4.671207 TGTATACTACTCCCCTGTCCCATA 59.329 45.833 4.17 0.00 0.00 2.74
736 1771 3.469771 TGTATACTACTCCCCTGTCCCAT 59.530 47.826 4.17 0.00 0.00 4.00
737 1772 2.860679 TGTATACTACTCCCCTGTCCCA 59.139 50.000 4.17 0.00 0.00 4.37
738 1773 3.607490 TGTATACTACTCCCCTGTCCC 57.393 52.381 4.17 0.00 0.00 4.46
739 1774 6.099269 TCAAATTGTATACTACTCCCCTGTCC 59.901 42.308 4.17 0.00 0.00 4.02
740 1775 7.120923 TCAAATTGTATACTACTCCCCTGTC 57.879 40.000 4.17 0.00 0.00 3.51
741 1776 7.691993 ATCAAATTGTATACTACTCCCCTGT 57.308 36.000 4.17 0.00 0.00 4.00
742 1777 8.871125 ACTATCAAATTGTATACTACTCCCCTG 58.129 37.037 4.17 0.00 0.00 4.45
745 1780 9.837525 CGTACTATCAAATTGTATACTACTCCC 57.162 37.037 4.17 0.00 0.00 4.30
843 1884 1.075374 TGGGTTGATTAGGCACTGCTT 59.925 47.619 0.00 0.00 41.52 3.91
844 1885 0.698238 TGGGTTGATTAGGCACTGCT 59.302 50.000 0.00 0.00 41.52 4.24
845 1886 1.406539 CATGGGTTGATTAGGCACTGC 59.593 52.381 0.00 0.00 41.52 4.40
846 1887 1.406539 GCATGGGTTGATTAGGCACTG 59.593 52.381 0.00 0.00 41.52 3.66
933 1974 0.867753 GCTCTAGGACGTGCATGTCG 60.868 60.000 28.11 17.14 39.83 4.35
982 2048 2.495669 ACTGGTGTTTGAGGTTGTTTGG 59.504 45.455 0.00 0.00 0.00 3.28
983 2049 3.192422 TGACTGGTGTTTGAGGTTGTTTG 59.808 43.478 0.00 0.00 0.00 2.93
984 2050 3.192633 GTGACTGGTGTTTGAGGTTGTTT 59.807 43.478 0.00 0.00 0.00 2.83
985 2051 2.752903 GTGACTGGTGTTTGAGGTTGTT 59.247 45.455 0.00 0.00 0.00 2.83
986 2052 2.365582 GTGACTGGTGTTTGAGGTTGT 58.634 47.619 0.00 0.00 0.00 3.32
987 2053 1.676006 GGTGACTGGTGTTTGAGGTTG 59.324 52.381 0.00 0.00 0.00 3.77
988 2054 1.283613 TGGTGACTGGTGTTTGAGGTT 59.716 47.619 0.00 0.00 0.00 3.50
989 2055 0.916086 TGGTGACTGGTGTTTGAGGT 59.084 50.000 0.00 0.00 0.00 3.85
990 2056 1.140852 TCTGGTGACTGGTGTTTGAGG 59.859 52.381 0.00 0.00 0.00 3.86
991 2057 2.487934 CTCTGGTGACTGGTGTTTGAG 58.512 52.381 0.00 0.00 0.00 3.02
992 2058 1.475034 GCTCTGGTGACTGGTGTTTGA 60.475 52.381 0.00 0.00 0.00 2.69
993 2059 0.947244 GCTCTGGTGACTGGTGTTTG 59.053 55.000 0.00 0.00 0.00 2.93
994 2060 0.546122 TGCTCTGGTGACTGGTGTTT 59.454 50.000 0.00 0.00 0.00 2.83
999 2065 1.080230 CTCGTGCTCTGGTGACTGG 60.080 63.158 0.00 0.00 0.00 4.00
1002 2068 0.315568 AGTTCTCGTGCTCTGGTGAC 59.684 55.000 0.00 0.00 0.00 3.67
1003 2069 0.598562 GAGTTCTCGTGCTCTGGTGA 59.401 55.000 0.00 0.00 0.00 4.02
1008 2074 1.271102 GGAGTTGAGTTCTCGTGCTCT 59.729 52.381 13.27 0.00 33.26 4.09
1046 2137 1.520368 CGTCGCGATAAAGTTTTGCC 58.480 50.000 14.06 0.00 0.00 4.52
1149 2243 1.271856 TTACAACGGAGATGAGGGCA 58.728 50.000 0.00 0.00 33.32 5.36
1319 2437 4.821589 CGGAGCACTCTTCGCCCC 62.822 72.222 0.00 0.00 34.09 5.80
1471 2589 2.743928 GAAGGTGCCGAGCCACTG 60.744 66.667 0.00 0.00 36.03 3.66
1673 2800 1.305201 AGCCGTGACGACACATTTTT 58.695 45.000 17.71 0.00 46.20 1.94
1687 2814 1.915228 TACCTAGTCCGGTAGCCGT 59.085 57.895 0.00 0.00 46.80 5.68
1699 2830 2.158943 CCTCGCCCCTTTTTCTACCTAG 60.159 54.545 0.00 0.00 0.00 3.02
1709 2840 3.721706 CTGCTCCCTCGCCCCTTT 61.722 66.667 0.00 0.00 0.00 3.11
1712 2843 4.168291 CTTCTGCTCCCTCGCCCC 62.168 72.222 0.00 0.00 0.00 5.80
1713 2844 2.376228 GATCTTCTGCTCCCTCGCCC 62.376 65.000 0.00 0.00 0.00 6.13
1786 2920 9.783081 ATTAAAGAACATCCTTTCAAAAATGCT 57.217 25.926 0.00 0.00 37.52 3.79
1833 2967 0.462759 GACTACAGGTGGCCATGCTC 60.463 60.000 9.72 0.00 0.00 4.26
1865 2999 0.884704 GCACGTCCTCTGCCTTTGAA 60.885 55.000 0.00 0.00 0.00 2.69
1866 3000 1.301716 GCACGTCCTCTGCCTTTGA 60.302 57.895 0.00 0.00 0.00 2.69
1872 3006 0.944386 TTTTGAAGCACGTCCTCTGC 59.056 50.000 0.00 0.00 34.63 4.26
1878 3012 1.792367 GGGCAAATTTTGAAGCACGTC 59.208 47.619 13.26 0.00 0.00 4.34
2026 3160 7.762159 TGAAAAGTGTTGCATCGATATGTACTA 59.238 33.333 0.00 0.00 35.38 1.82
2028 3162 6.771076 TGAAAAGTGTTGCATCGATATGTAC 58.229 36.000 0.00 0.00 35.38 2.90
2049 3183 1.472480 GCAAGCTCCGCCTAAAATGAA 59.528 47.619 0.00 0.00 0.00 2.57
2050 3184 1.094785 GCAAGCTCCGCCTAAAATGA 58.905 50.000 0.00 0.00 0.00 2.57
2059 3193 1.598701 ATTCCCAAAGCAAGCTCCGC 61.599 55.000 0.00 0.00 0.00 5.54
2061 3195 1.067354 CACATTCCCAAAGCAAGCTCC 60.067 52.381 0.00 0.00 0.00 4.70
2062 3196 1.067354 CCACATTCCCAAAGCAAGCTC 60.067 52.381 0.00 0.00 0.00 4.09
2077 3211 5.346101 CCCGAAAAGGTTGTGTATCCACAT 61.346 45.833 0.00 0.00 43.46 3.21
2089 3223 2.235891 GACATTGTCCCCGAAAAGGTT 58.764 47.619 5.44 0.00 38.74 3.50
2125 3259 1.884579 ACGACTCCGAGTTAAAGAGCA 59.115 47.619 1.71 0.00 39.50 4.26
2150 3284 1.341531 AGCAAGCAAGACGACACTAGT 59.658 47.619 0.00 0.00 0.00 2.57
2158 3292 0.449507 CGTTTCGAGCAAGCAAGACG 60.450 55.000 0.00 0.00 0.00 4.18
2180 3314 4.422073 ACAAGACACATCACTCCTCAAA 57.578 40.909 0.00 0.00 0.00 2.69
2199 3333 1.790755 AGCAACGTCGCTTGAATACA 58.209 45.000 0.00 0.00 39.99 2.29
2221 3355 0.390472 CTTCTTGGTGGTCGCTCTCC 60.390 60.000 0.00 0.00 0.00 3.71
2236 3370 4.619394 CGTACTCCACTTCAAGATGCTTCT 60.619 45.833 0.00 0.00 0.00 2.85
2238 3372 3.258372 TCGTACTCCACTTCAAGATGCTT 59.742 43.478 0.00 0.00 0.00 3.91
2247 3381 4.240175 AGAAGTTGTCGTACTCCACTTC 57.760 45.455 16.56 16.56 34.17 3.01
2262 3396 4.337145 ACGTCTCTCATGGAGTAGAAGTT 58.663 43.478 9.98 0.00 42.40 2.66
2269 3403 4.505918 CCCTCTATACGTCTCTCATGGAGT 60.506 50.000 0.00 0.00 42.40 3.85
2275 3409 5.366186 AGTTACTCCCTCTATACGTCTCTCA 59.634 44.000 0.00 0.00 0.00 3.27
2283 3417 8.614346 CGCTCATATAAGTTACTCCCTCTATAC 58.386 40.741 0.00 0.00 0.00 1.47
2321 3455 2.189594 TCTGGCTGTGAGTTGAATGG 57.810 50.000 0.00 0.00 0.00 3.16
2336 3470 8.980481 ACTACCAAGGTTTCAATATTATCTGG 57.020 34.615 0.00 0.00 0.00 3.86
2342 3476 8.927675 TTGTGTACTACCAAGGTTTCAATATT 57.072 30.769 0.00 0.00 0.00 1.28
2347 3481 6.597562 AGAATTGTGTACTACCAAGGTTTCA 58.402 36.000 0.00 0.00 0.00 2.69
2349 3483 9.662947 GTATAGAATTGTGTACTACCAAGGTTT 57.337 33.333 0.00 0.00 0.00 3.27
2359 3493 9.263538 CTAGAGTCGAGTATAGAATTGTGTACT 57.736 37.037 15.39 11.15 0.00 2.73
2394 3528 2.735151 TGGAACGAGAGATGCTAAGGA 58.265 47.619 0.00 0.00 0.00 3.36
2412 3546 1.069227 GCGGCTGTGTCTAAACTTTGG 60.069 52.381 0.00 0.00 0.00 3.28
2427 3561 0.240945 CTTCGAAACATTTGGCGGCT 59.759 50.000 11.43 0.00 0.00 5.52
2431 3565 2.053627 CTGTGCTTCGAAACATTTGGC 58.946 47.619 4.30 0.32 0.00 4.52
2432 3566 2.664916 CCTGTGCTTCGAAACATTTGG 58.335 47.619 4.30 4.16 0.00 3.28
2438 3572 1.477105 GTTTGCCTGTGCTTCGAAAC 58.523 50.000 0.00 0.00 38.71 2.78
2495 3631 1.229076 GTGGTTGGGGTTCCTGTGT 59.771 57.895 0.00 0.00 0.00 3.72
2611 3747 1.264045 AAATTGGGGTGGATTGGCCG 61.264 55.000 0.00 0.00 40.66 6.13
2612 3748 0.541392 GAAATTGGGGTGGATTGGCC 59.459 55.000 0.00 0.00 37.10 5.36
2613 3749 0.541392 GGAAATTGGGGTGGATTGGC 59.459 55.000 0.00 0.00 0.00 4.52
2614 3750 0.823460 CGGAAATTGGGGTGGATTGG 59.177 55.000 0.00 0.00 0.00 3.16
2615 3751 0.175531 GCGGAAATTGGGGTGGATTG 59.824 55.000 0.00 0.00 0.00 2.67
2616 3752 0.975556 GGCGGAAATTGGGGTGGATT 60.976 55.000 0.00 0.00 0.00 3.01
2617 3753 1.381191 GGCGGAAATTGGGGTGGAT 60.381 57.895 0.00 0.00 0.00 3.41
2618 3754 2.036572 GGCGGAAATTGGGGTGGA 59.963 61.111 0.00 0.00 0.00 4.02
2627 3763 2.043953 GCAAGGGGAGGCGGAAAT 60.044 61.111 0.00 0.00 0.00 2.17
2676 3812 3.530260 GATGGTGGCGGCAATGGG 61.530 66.667 15.50 0.00 0.00 4.00
2677 3813 2.755064 TGATGGTGGCGGCAATGG 60.755 61.111 15.50 0.00 0.00 3.16
2678 3814 2.491152 GTGATGGTGGCGGCAATG 59.509 61.111 15.50 0.00 0.00 2.82
2679 3815 2.755469 GGTGATGGTGGCGGCAAT 60.755 61.111 15.50 4.06 0.00 3.56
2686 3822 3.061848 GTTGGGCGGTGATGGTGG 61.062 66.667 0.00 0.00 0.00 4.61
2687 3823 2.034066 AGTTGGGCGGTGATGGTG 59.966 61.111 0.00 0.00 0.00 4.17
2688 3824 2.351276 GAGTTGGGCGGTGATGGT 59.649 61.111 0.00 0.00 0.00 3.55
2689 3825 2.438434 GGAGTTGGGCGGTGATGG 60.438 66.667 0.00 0.00 0.00 3.51
2690 3826 1.746615 CTGGAGTTGGGCGGTGATG 60.747 63.158 0.00 0.00 0.00 3.07
2691 3827 2.671070 CTGGAGTTGGGCGGTGAT 59.329 61.111 0.00 0.00 0.00 3.06
2733 4090 4.100981 GCAGTTGCGCAAAACCAA 57.899 50.000 26.87 0.00 0.00 3.67
2746 4103 2.568623 ATCCAAAAGGTCGAAGCAGT 57.431 45.000 0.00 0.00 0.00 4.40
2787 4144 3.823304 GCCTCACACAAAGGAATTCTCTT 59.177 43.478 5.23 4.52 35.83 2.85
2793 4150 3.327757 TCAGTAGCCTCACACAAAGGAAT 59.672 43.478 0.00 0.00 35.83 3.01


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

AutoCloner maintained by Alex Coulton.