Multiple sequence alignment - TraesCS1A01G255100

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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 TraesCS1A01G255100 chr1A 100.000 3063 0 0 629 3691 447004960 447008022 0.000000e+00 5657
1 TraesCS1A01G255100 chr1A 100.000 316 0 0 1 316 447004332 447004647 5.310000e-163 584
2 TraesCS1A01G255100 chr1B 91.231 3102 141 55 635 3691 466936115 466939130 0.000000e+00 4100
3 TraesCS1A01G255100 chr1B 82.534 292 24 15 4 284 466898609 466898884 7.970000e-57 231
4 TraesCS1A01G255100 chr1B 85.787 197 7 13 88 284 466935895 466936070 4.870000e-44 189
5 TraesCS1A01G255100 chr1B 78.189 243 26 11 630 870 466898947 466899164 2.990000e-26 130
6 TraesCS1A01G255100 chr1D 91.111 3105 131 62 630 3675 346662317 346665335 0.000000e+00 4071
7 TraesCS1A01G255100 chr1D 87.398 246 14 9 50 284 346662037 346662276 2.190000e-67 267


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 TraesCS1A01G255100 chr1A 447004332 447008022 3690 False 3120.5 5657 100.0000 1 3691 2 chr1A.!!$F1 3690
1 TraesCS1A01G255100 chr1B 466935895 466939130 3235 False 2144.5 4100 88.5090 88 3691 2 chr1B.!!$F2 3603
2 TraesCS1A01G255100 chr1D 346662037 346665335 3298 False 2169.0 4071 89.2545 50 3675 2 chr1D.!!$F1 3625

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
146 162 0.106217 GACCAGGAGAGGGAGAGAGG 60.106 65.0 0.00 0.0 0.0 3.69 F
874 907 0.321653 ATCCACCTCGCGCTTTTCTT 60.322 50.0 5.56 0.0 0.0 2.52 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1047 1085 0.030705 CCAGGGAGGAGGATGGAGAA 60.031 60.000 0.00 0.0 41.22 2.87 R
2851 2926 1.005805 CCAAGATGACATCCCCAACCA 59.994 52.381 11.92 0.0 0.00 3.67 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
19 20 1.910688 GTCCGTCTAAAAGAGAGCGG 58.089 55.000 0.00 0.00 44.02 5.52
20 21 0.172803 TCCGTCTAAAAGAGAGCGGC 59.827 55.000 0.00 0.00 43.16 6.53
21 22 0.806492 CCGTCTAAAAGAGAGCGGCC 60.806 60.000 0.00 0.00 39.96 6.13
22 23 0.108804 CGTCTAAAAGAGAGCGGCCA 60.109 55.000 2.24 0.00 33.72 5.36
23 24 1.671850 CGTCTAAAAGAGAGCGGCCAA 60.672 52.381 2.24 0.00 33.72 4.52
24 25 2.423577 GTCTAAAAGAGAGCGGCCAAA 58.576 47.619 2.24 0.00 33.72 3.28
25 26 2.812011 GTCTAAAAGAGAGCGGCCAAAA 59.188 45.455 2.24 0.00 33.72 2.44
26 27 3.252458 GTCTAAAAGAGAGCGGCCAAAAA 59.748 43.478 2.24 0.00 33.72 1.94
27 28 2.509052 AAAAGAGAGCGGCCAAAAAC 57.491 45.000 2.24 0.00 0.00 2.43
28 29 1.398692 AAAGAGAGCGGCCAAAAACA 58.601 45.000 2.24 0.00 0.00 2.83
29 30 1.398692 AAGAGAGCGGCCAAAAACAA 58.601 45.000 2.24 0.00 0.00 2.83
30 31 1.398692 AGAGAGCGGCCAAAAACAAA 58.601 45.000 2.24 0.00 0.00 2.83
31 32 1.338020 AGAGAGCGGCCAAAAACAAAG 59.662 47.619 2.24 0.00 0.00 2.77
32 33 0.389025 AGAGCGGCCAAAAACAAAGG 59.611 50.000 2.24 0.00 0.00 3.11
33 34 0.599991 GAGCGGCCAAAAACAAAGGG 60.600 55.000 2.24 0.00 0.00 3.95
34 35 1.045911 AGCGGCCAAAAACAAAGGGA 61.046 50.000 2.24 0.00 0.00 4.20
35 36 0.599991 GCGGCCAAAAACAAAGGGAG 60.600 55.000 2.24 0.00 0.00 4.30
36 37 1.036707 CGGCCAAAAACAAAGGGAGA 58.963 50.000 2.24 0.00 0.00 3.71
37 38 1.000274 CGGCCAAAAACAAAGGGAGAG 60.000 52.381 2.24 0.00 0.00 3.20
38 39 2.316108 GGCCAAAAACAAAGGGAGAGA 58.684 47.619 0.00 0.00 0.00 3.10
39 40 2.297315 GGCCAAAAACAAAGGGAGAGAG 59.703 50.000 0.00 0.00 0.00 3.20
40 41 3.222603 GCCAAAAACAAAGGGAGAGAGA 58.777 45.455 0.00 0.00 0.00 3.10
41 42 3.254411 GCCAAAAACAAAGGGAGAGAGAG 59.746 47.826 0.00 0.00 0.00 3.20
42 43 3.823304 CCAAAAACAAAGGGAGAGAGAGG 59.177 47.826 0.00 0.00 0.00 3.69
43 44 4.446311 CCAAAAACAAAGGGAGAGAGAGGA 60.446 45.833 0.00 0.00 0.00 3.71
44 45 4.632327 AAAACAAAGGGAGAGAGAGGAG 57.368 45.455 0.00 0.00 0.00 3.69
45 46 2.246091 ACAAAGGGAGAGAGAGGAGG 57.754 55.000 0.00 0.00 0.00 4.30
46 47 1.719378 ACAAAGGGAGAGAGAGGAGGA 59.281 52.381 0.00 0.00 0.00 3.71
47 48 2.292192 ACAAAGGGAGAGAGAGGAGGAG 60.292 54.545 0.00 0.00 0.00 3.69
48 49 1.994399 AAGGGAGAGAGAGGAGGAGA 58.006 55.000 0.00 0.00 0.00 3.71
55 56 3.954258 GAGAGAGAGGAGGAGAAAAGGAG 59.046 52.174 0.00 0.00 0.00 3.69
56 57 3.031013 GAGAGAGGAGGAGAAAAGGAGG 58.969 54.545 0.00 0.00 0.00 4.30
90 91 4.854924 CCACGCGCATCCATCCCA 62.855 66.667 5.73 0.00 0.00 4.37
107 112 0.733729 CCACGAAACCGTCCAAAACA 59.266 50.000 0.00 0.00 38.35 2.83
108 113 1.132643 CCACGAAACCGTCCAAAACAA 59.867 47.619 0.00 0.00 38.35 2.83
109 114 2.223618 CCACGAAACCGTCCAAAACAAT 60.224 45.455 0.00 0.00 38.35 2.71
138 154 2.938956 AACAAACAGACCAGGAGAGG 57.061 50.000 0.00 0.00 0.00 3.69
145 161 0.926293 AGACCAGGAGAGGGAGAGAG 59.074 60.000 0.00 0.00 0.00 3.20
146 162 0.106217 GACCAGGAGAGGGAGAGAGG 60.106 65.000 0.00 0.00 0.00 3.69
150 166 2.560841 CCAGGAGAGGGAGAGAGGAAAA 60.561 54.545 0.00 0.00 0.00 2.29
151 167 3.177228 CAGGAGAGGGAGAGAGGAAAAA 58.823 50.000 0.00 0.00 0.00 1.94
199 220 0.817229 CAGCTTAGCTAGGGGCAAGC 60.817 60.000 6.35 8.32 45.85 4.01
300 321 1.076438 CCCCCTCCCCTATTTCCATC 58.924 60.000 0.00 0.00 0.00 3.51
304 326 0.764890 CTCCCCTATTTCCATCGCCA 59.235 55.000 0.00 0.00 0.00 5.69
308 330 0.537371 CCTATTTCCATCGCCACCCC 60.537 60.000 0.00 0.00 0.00 4.95
667 689 3.349006 CACGCCACAGCTCACCAC 61.349 66.667 0.00 0.00 36.60 4.16
734 758 4.988598 CGCCCTCGCACCACTGTT 62.989 66.667 0.00 0.00 34.03 3.16
735 759 3.050275 GCCCTCGCACCACTGTTC 61.050 66.667 0.00 0.00 34.03 3.18
736 760 2.738521 CCCTCGCACCACTGTTCG 60.739 66.667 0.00 0.00 32.14 3.95
737 761 3.414700 CCTCGCACCACTGTTCGC 61.415 66.667 0.00 0.00 30.90 4.70
738 762 3.414700 CTCGCACCACTGTTCGCC 61.415 66.667 0.00 0.00 30.90 5.54
739 763 4.980805 TCGCACCACTGTTCGCCC 62.981 66.667 0.00 0.00 30.90 6.13
742 766 3.953775 CACCACTGTTCGCCCCCT 61.954 66.667 0.00 0.00 0.00 4.79
768 792 2.677979 GCTTGCCCGGTTTCTCGTC 61.678 63.158 0.00 0.00 0.00 4.20
769 793 2.356553 TTGCCCGGTTTCTCGTCG 60.357 61.111 0.00 0.00 0.00 5.12
771 795 4.736896 GCCCGGTTTCTCGTCGCT 62.737 66.667 0.00 0.00 0.00 4.93
772 796 2.506438 CCCGGTTTCTCGTCGCTC 60.506 66.667 0.00 0.00 0.00 5.03
773 797 2.874780 CCGGTTTCTCGTCGCTCG 60.875 66.667 0.00 0.00 41.41 5.03
774 798 2.175078 CGGTTTCTCGTCGCTCGA 59.825 61.111 2.98 2.98 46.83 4.04
803 836 1.002794 TAGGGAGGGGGATTCGGAGA 61.003 60.000 0.00 0.00 0.00 3.71
804 837 1.839296 GGGAGGGGGATTCGGAGAG 60.839 68.421 0.00 0.00 38.43 3.20
870 903 2.125106 GGATCCACCTCGCGCTTT 60.125 61.111 6.95 0.00 35.41 3.51
872 905 1.706287 GGATCCACCTCGCGCTTTTC 61.706 60.000 6.95 0.00 35.41 2.29
873 906 0.741221 GATCCACCTCGCGCTTTTCT 60.741 55.000 5.56 0.00 0.00 2.52
874 907 0.321653 ATCCACCTCGCGCTTTTCTT 60.322 50.000 5.56 0.00 0.00 2.52
875 908 1.207593 CCACCTCGCGCTTTTCTTG 59.792 57.895 5.56 0.00 0.00 3.02
877 910 2.176792 CCTCGCGCTTTTCTTGGC 59.823 61.111 5.56 0.00 0.00 4.52
922 955 1.880340 CGAGCGCCATCCTCTGTTC 60.880 63.158 2.29 0.00 0.00 3.18
926 959 2.190578 GCCATCCTCTGTTCCCCG 59.809 66.667 0.00 0.00 0.00 5.73
961 996 3.126225 GCCTGCAGCAGCTGAGAC 61.126 66.667 27.39 9.10 41.71 3.36
967 1002 3.768922 AGCAGCTGAGACCCGAGC 61.769 66.667 20.43 0.00 35.28 5.03
1063 1102 0.266152 TCCTTCTCCATCCTCCTCCC 59.734 60.000 0.00 0.00 0.00 4.30
1137 1176 3.470567 CGTCCTTGCGCTCGTGTC 61.471 66.667 9.73 0.00 0.00 3.67
1138 1177 3.112709 GTCCTTGCGCTCGTGTCC 61.113 66.667 9.73 0.00 0.00 4.02
1151 1190 1.280206 CGTGTCCGGGTTCTCGTTTC 61.280 60.000 0.00 0.00 0.00 2.78
1210 1249 1.268265 GATTTTCGATTTGTGCCGCC 58.732 50.000 0.00 0.00 0.00 6.13
1266 1320 2.368878 GAGAGGGGATTGGGGCCT 60.369 66.667 0.84 0.00 0.00 5.19
1391 1445 0.179121 CGGCCGATACTAACACAGCA 60.179 55.000 24.07 0.00 0.00 4.41
1392 1446 1.287425 GGCCGATACTAACACAGCAC 58.713 55.000 0.00 0.00 0.00 4.40
1393 1447 1.404986 GGCCGATACTAACACAGCACA 60.405 52.381 0.00 0.00 0.00 4.57
1394 1448 1.927174 GCCGATACTAACACAGCACAG 59.073 52.381 0.00 0.00 0.00 3.66
1395 1449 1.927174 CCGATACTAACACAGCACAGC 59.073 52.381 0.00 0.00 0.00 4.40
1424 1478 4.487948 ACAAGCAACAAATCATTCATCCG 58.512 39.130 0.00 0.00 0.00 4.18
1434 1488 0.800631 CATTCATCCGCATCCATCCG 59.199 55.000 0.00 0.00 0.00 4.18
1508 1574 4.719616 GCAAGACGCGACCGCAAC 62.720 66.667 15.93 7.36 42.06 4.17
1587 1653 1.771291 CCTTTCGTTTCGTTTCGTTGC 59.229 47.619 0.00 0.00 0.00 4.17
1593 1659 0.302288 TTTCGTTTCGTTGCGAGGTG 59.698 50.000 0.00 0.00 37.14 4.00
1599 1665 0.865111 TTCGTTGCGAGGTGTGATTG 59.135 50.000 0.00 0.00 37.14 2.67
1600 1666 0.948623 TCGTTGCGAGGTGTGATTGG 60.949 55.000 0.00 0.00 0.00 3.16
1601 1667 1.875963 GTTGCGAGGTGTGATTGGG 59.124 57.895 0.00 0.00 0.00 4.12
1602 1668 0.605319 GTTGCGAGGTGTGATTGGGA 60.605 55.000 0.00 0.00 0.00 4.37
1644 1713 1.598962 TCTCACTGTTGCTGCTGGC 60.599 57.895 0.00 0.00 42.22 4.85
1837 1906 1.517210 TTCGACCACGTCATCGACCA 61.517 55.000 17.75 4.61 46.41 4.02
1838 1907 1.800315 CGACCACGTCATCGACCAC 60.800 63.158 11.63 0.00 40.86 4.16
2507 2579 0.749649 AGAGCCTCATCATCGTGTCC 59.250 55.000 0.00 0.00 0.00 4.02
2631 2703 0.317160 CTACCTGCTGTCCAACACGA 59.683 55.000 0.00 0.00 0.00 4.35
2835 2910 2.885266 TCTCTTATACTACTGCTGCCGG 59.115 50.000 0.00 0.00 0.00 6.13
2836 2911 2.623889 CTCTTATACTACTGCTGCCGGT 59.376 50.000 1.90 0.00 0.00 5.28
2838 2913 0.387929 TATACTACTGCTGCCGGTGC 59.612 55.000 13.41 13.41 38.26 5.01
2968 3043 5.427378 TGATGATAAAACTCAATGGCTCGA 58.573 37.500 0.00 0.00 0.00 4.04
3043 3124 1.884075 CGGTCGGTGTGATCCTTGGA 61.884 60.000 0.00 0.00 0.00 3.53
3044 3125 0.323629 GGTCGGTGTGATCCTTGGAA 59.676 55.000 0.00 0.00 0.00 3.53
3048 3129 1.676014 CGGTGTGATCCTTGGAACTCC 60.676 57.143 0.00 0.00 0.00 3.85
3049 3130 1.676014 GGTGTGATCCTTGGAACTCCG 60.676 57.143 0.00 0.00 39.43 4.63
3050 3131 1.275291 GTGTGATCCTTGGAACTCCGA 59.725 52.381 0.00 0.00 39.43 4.55
3239 3328 4.375988 CGTTATGTGTACAGTGATCGATCG 59.624 45.833 20.03 9.36 0.00 3.69
3241 3330 4.837896 ATGTGTACAGTGATCGATCGAT 57.162 40.909 29.76 29.76 37.59 3.59
3302 3391 4.508124 AGTTTCTTTCTTGTGTCAGCTACG 59.492 41.667 0.00 0.00 0.00 3.51
3303 3392 3.026630 TCTTTCTTGTGTCAGCTACGG 57.973 47.619 0.00 0.00 0.00 4.02
3304 3393 2.069273 CTTTCTTGTGTCAGCTACGGG 58.931 52.381 0.00 0.00 0.00 5.28
3305 3394 1.045407 TTCTTGTGTCAGCTACGGGT 58.955 50.000 0.00 0.00 0.00 5.28
3306 3395 1.045407 TCTTGTGTCAGCTACGGGTT 58.955 50.000 0.00 0.00 0.00 4.11
3369 3468 5.159925 CAATCCGTGCATGTGAAAAATACA 58.840 37.500 4.96 0.00 0.00 2.29
3373 3472 3.913763 CGTGCATGTGAAAAATACACCTG 59.086 43.478 0.00 0.00 37.45 4.00
3411 3512 7.703755 TCTATCTATCTATCCTGTGTGGTGAT 58.296 38.462 0.00 0.00 37.07 3.06
3412 3513 6.602410 ATCTATCTATCCTGTGTGGTGATG 57.398 41.667 0.00 0.00 37.07 3.07
3413 3514 5.705400 TCTATCTATCCTGTGTGGTGATGA 58.295 41.667 0.00 0.00 37.07 2.92
3453 3554 4.784300 AGTCCAGACCAGTAGTAGTCTAGT 59.216 45.833 0.00 0.00 41.38 2.57
3454 3555 5.104817 AGTCCAGACCAGTAGTAGTCTAGTC 60.105 48.000 0.00 0.00 41.38 2.59
3455 3556 5.031495 TCCAGACCAGTAGTAGTCTAGTCT 58.969 45.833 0.00 0.00 41.38 3.24
3456 3557 6.098124 GTCCAGACCAGTAGTAGTCTAGTCTA 59.902 46.154 0.00 0.00 41.38 2.59
3457 3558 6.324512 TCCAGACCAGTAGTAGTCTAGTCTAG 59.675 46.154 0.00 0.00 41.38 2.43
3477 3578 7.177744 AGTCTAGGCTAGCAGTATAAATTCTCC 59.822 40.741 18.24 0.00 0.00 3.71
3512 3613 7.986085 TTTGTATCTTTCTCTCCTTTTCTGG 57.014 36.000 0.00 0.00 0.00 3.86
3526 3627 5.306937 TCCTTTTCTGGTTGATGTACTCTGA 59.693 40.000 0.00 0.00 0.00 3.27
3527 3628 6.013379 TCCTTTTCTGGTTGATGTACTCTGAT 60.013 38.462 0.00 0.00 0.00 2.90
3528 3629 6.314896 CCTTTTCTGGTTGATGTACTCTGATC 59.685 42.308 0.00 0.00 0.00 2.92
3529 3630 6.611613 TTTCTGGTTGATGTACTCTGATCT 57.388 37.500 0.00 0.00 0.00 2.75
3530 3631 5.588958 TCTGGTTGATGTACTCTGATCTG 57.411 43.478 0.00 0.00 0.00 2.90
3591 3692 0.433492 GTGCTGTAACGCGTGTACTG 59.567 55.000 14.98 19.99 0.00 2.74
3617 3718 1.133792 GGTTGATCCATCCATTCCGGT 60.134 52.381 0.00 0.00 34.18 5.28
3667 3771 6.485648 GTGAAGAATGTGGTACTGGTAAAAGT 59.514 38.462 0.00 0.00 0.00 2.66
3671 3775 8.147244 AGAATGTGGTACTGGTAAAAGTAGAT 57.853 34.615 0.00 0.00 33.35 1.98
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 1.910688 CCGCTCTCTTTTAGACGGAC 58.089 55.000 9.12 0.00 44.70 4.79
1 2 0.172803 GCCGCTCTCTTTTAGACGGA 59.827 55.000 15.42 0.00 44.70 4.69
5 6 2.851263 TTTGGCCGCTCTCTTTTAGA 57.149 45.000 0.00 0.00 0.00 2.10
6 7 3.004315 TGTTTTTGGCCGCTCTCTTTTAG 59.996 43.478 0.00 0.00 0.00 1.85
7 8 2.952978 TGTTTTTGGCCGCTCTCTTTTA 59.047 40.909 0.00 0.00 0.00 1.52
8 9 1.754226 TGTTTTTGGCCGCTCTCTTTT 59.246 42.857 0.00 0.00 0.00 2.27
9 10 1.398692 TGTTTTTGGCCGCTCTCTTT 58.601 45.000 0.00 0.00 0.00 2.52
10 11 1.398692 TTGTTTTTGGCCGCTCTCTT 58.601 45.000 0.00 0.00 0.00 2.85
11 12 1.338020 CTTTGTTTTTGGCCGCTCTCT 59.662 47.619 0.00 0.00 0.00 3.10
12 13 1.602920 CCTTTGTTTTTGGCCGCTCTC 60.603 52.381 0.00 0.00 0.00 3.20
13 14 0.389025 CCTTTGTTTTTGGCCGCTCT 59.611 50.000 0.00 0.00 0.00 4.09
14 15 0.599991 CCCTTTGTTTTTGGCCGCTC 60.600 55.000 0.00 0.00 0.00 5.03
15 16 1.045911 TCCCTTTGTTTTTGGCCGCT 61.046 50.000 0.00 0.00 0.00 5.52
16 17 0.599991 CTCCCTTTGTTTTTGGCCGC 60.600 55.000 0.00 0.00 0.00 6.53
17 18 1.000274 CTCTCCCTTTGTTTTTGGCCG 60.000 52.381 0.00 0.00 0.00 6.13
18 19 2.297315 CTCTCTCCCTTTGTTTTTGGCC 59.703 50.000 0.00 0.00 0.00 5.36
19 20 3.222603 TCTCTCTCCCTTTGTTTTTGGC 58.777 45.455 0.00 0.00 0.00 4.52
20 21 3.823304 CCTCTCTCTCCCTTTGTTTTTGG 59.177 47.826 0.00 0.00 0.00 3.28
21 22 4.718961 TCCTCTCTCTCCCTTTGTTTTTG 58.281 43.478 0.00 0.00 0.00 2.44
22 23 4.202514 CCTCCTCTCTCTCCCTTTGTTTTT 60.203 45.833 0.00 0.00 0.00 1.94
23 24 3.329225 CCTCCTCTCTCTCCCTTTGTTTT 59.671 47.826 0.00 0.00 0.00 2.43
24 25 2.909662 CCTCCTCTCTCTCCCTTTGTTT 59.090 50.000 0.00 0.00 0.00 2.83
25 26 2.112691 TCCTCCTCTCTCTCCCTTTGTT 59.887 50.000 0.00 0.00 0.00 2.83
26 27 1.719378 TCCTCCTCTCTCTCCCTTTGT 59.281 52.381 0.00 0.00 0.00 2.83
27 28 2.024464 TCTCCTCCTCTCTCTCCCTTTG 60.024 54.545 0.00 0.00 0.00 2.77
28 29 2.293246 TCTCCTCCTCTCTCTCCCTTT 58.707 52.381 0.00 0.00 0.00 3.11
29 30 1.994399 TCTCCTCCTCTCTCTCCCTT 58.006 55.000 0.00 0.00 0.00 3.95
30 31 1.994399 TTCTCCTCCTCTCTCTCCCT 58.006 55.000 0.00 0.00 0.00 4.20
31 32 2.838637 TTTCTCCTCCTCTCTCTCCC 57.161 55.000 0.00 0.00 0.00 4.30
32 33 3.031013 CCTTTTCTCCTCCTCTCTCTCC 58.969 54.545 0.00 0.00 0.00 3.71
33 34 3.954258 CTCCTTTTCTCCTCCTCTCTCTC 59.046 52.174 0.00 0.00 0.00 3.20
34 35 3.309848 CCTCCTTTTCTCCTCCTCTCTCT 60.310 52.174 0.00 0.00 0.00 3.10
35 36 3.031013 CCTCCTTTTCTCCTCCTCTCTC 58.969 54.545 0.00 0.00 0.00 3.20
36 37 2.385417 ACCTCCTTTTCTCCTCCTCTCT 59.615 50.000 0.00 0.00 0.00 3.10
37 38 2.764010 GACCTCCTTTTCTCCTCCTCTC 59.236 54.545 0.00 0.00 0.00 3.20
38 39 2.385417 AGACCTCCTTTTCTCCTCCTCT 59.615 50.000 0.00 0.00 0.00 3.69
39 40 2.764010 GAGACCTCCTTTTCTCCTCCTC 59.236 54.545 0.00 0.00 33.41 3.71
40 41 2.112691 TGAGACCTCCTTTTCTCCTCCT 59.887 50.000 0.00 0.00 37.99 3.69
41 42 2.541466 TGAGACCTCCTTTTCTCCTCC 58.459 52.381 0.00 0.00 37.99 4.30
42 43 4.835284 ATTGAGACCTCCTTTTCTCCTC 57.165 45.455 0.00 0.00 37.99 3.71
43 44 4.849235 AGAATTGAGACCTCCTTTTCTCCT 59.151 41.667 0.00 0.00 37.99 3.69
44 45 5.172687 AGAATTGAGACCTCCTTTTCTCC 57.827 43.478 0.00 0.00 37.99 3.71
45 46 5.799213 TGAGAATTGAGACCTCCTTTTCTC 58.201 41.667 17.49 17.49 37.80 2.87
46 47 5.545723 TCTGAGAATTGAGACCTCCTTTTCT 59.454 40.000 6.15 6.15 0.00 2.52
47 48 5.799213 TCTGAGAATTGAGACCTCCTTTTC 58.201 41.667 0.00 0.00 0.00 2.29
48 49 5.280419 CCTCTGAGAATTGAGACCTCCTTTT 60.280 44.000 6.17 0.00 32.44 2.27
55 56 1.556911 TGGCCTCTGAGAATTGAGACC 59.443 52.381 3.32 0.00 34.13 3.85
56 57 2.626840 GTGGCCTCTGAGAATTGAGAC 58.373 52.381 3.32 0.00 32.44 3.36
107 112 9.541143 CCTGGTCTGTTTGTTTTGTTTATTATT 57.459 29.630 0.00 0.00 0.00 1.40
108 113 8.919145 TCCTGGTCTGTTTGTTTTGTTTATTAT 58.081 29.630 0.00 0.00 0.00 1.28
109 114 8.294954 TCCTGGTCTGTTTGTTTTGTTTATTA 57.705 30.769 0.00 0.00 0.00 0.98
155 171 9.919416 TGCCATTGCCAATATAGTTATGTATAT 57.081 29.630 0.00 0.00 36.33 0.86
156 172 9.394767 CTGCCATTGCCAATATAGTTATGTATA 57.605 33.333 0.00 0.00 36.33 1.47
157 173 7.148018 GCTGCCATTGCCAATATAGTTATGTAT 60.148 37.037 0.00 0.00 36.33 2.29
158 174 6.150976 GCTGCCATTGCCAATATAGTTATGTA 59.849 38.462 0.00 0.00 36.33 2.29
159 175 5.047802 GCTGCCATTGCCAATATAGTTATGT 60.048 40.000 0.00 0.00 36.33 2.29
160 176 5.184479 AGCTGCCATTGCCAATATAGTTATG 59.816 40.000 0.00 0.00 36.33 1.90
176 192 2.061790 GCCCCTAGCTAAGCTGCCAT 62.062 60.000 0.00 0.00 40.10 4.40
177 193 2.746375 GCCCCTAGCTAAGCTGCCA 61.746 63.158 0.00 0.00 40.10 4.92
216 237 2.234187 CTCGAAAAGTAAAGCTTGCGC 58.766 47.619 0.00 0.00 37.52 6.09
223 244 0.446616 GGGCGGCTCGAAAAGTAAAG 59.553 55.000 9.56 0.00 0.00 1.85
285 306 0.764890 TGGCGATGGAAATAGGGGAG 59.235 55.000 0.00 0.00 0.00 4.30
628 650 2.366972 AGAGGGGGACGAATGGGG 60.367 66.667 0.00 0.00 0.00 4.96
629 651 2.911143 CAGAGGGGGACGAATGGG 59.089 66.667 0.00 0.00 0.00 4.00
630 652 1.915078 AAGCAGAGGGGGACGAATGG 61.915 60.000 0.00 0.00 0.00 3.16
631 653 0.462759 GAAGCAGAGGGGGACGAATG 60.463 60.000 0.00 0.00 0.00 2.67
632 654 0.909610 TGAAGCAGAGGGGGACGAAT 60.910 55.000 0.00 0.00 0.00 3.34
633 655 1.535444 TGAAGCAGAGGGGGACGAA 60.535 57.895 0.00 0.00 0.00 3.85
634 656 2.119611 TGAAGCAGAGGGGGACGA 59.880 61.111 0.00 0.00 0.00 4.20
635 657 2.266055 GTGAAGCAGAGGGGGACG 59.734 66.667 0.00 0.00 0.00 4.79
636 658 2.266055 CGTGAAGCAGAGGGGGAC 59.734 66.667 0.00 0.00 0.00 4.46
700 722 4.253257 GTACGAGGCTCGGCTCGG 62.253 72.222 36.81 22.23 45.59 4.63
782 806 1.236282 CCGAATCCCCCTCCCTAGT 59.764 63.158 0.00 0.00 0.00 2.57
905 938 1.522580 GGAACAGAGGATGGCGCTC 60.523 63.158 7.64 0.00 0.00 5.03
922 955 3.878667 GCAAGATCTCCCCCGGGG 61.879 72.222 34.65 34.65 46.11 5.73
967 1002 3.578272 CTCCTCTCGGTCTCGGCG 61.578 72.222 0.00 0.00 36.95 6.46
1047 1085 0.030705 CCAGGGAGGAGGATGGAGAA 60.031 60.000 0.00 0.00 41.22 2.87
1048 1086 1.231751 ACCAGGGAGGAGGATGGAGA 61.232 60.000 0.00 0.00 41.22 3.71
1050 1088 0.121197 AAACCAGGGAGGAGGATGGA 59.879 55.000 0.00 0.00 41.22 3.41
1051 1089 0.257039 CAAACCAGGGAGGAGGATGG 59.743 60.000 0.00 0.00 41.22 3.51
1053 1091 1.575447 GCCAAACCAGGGAGGAGGAT 61.575 60.000 0.00 0.00 41.22 3.24
1151 1190 2.751837 GGCAAGAAGAAGGCCCGG 60.752 66.667 0.00 0.00 41.90 5.73
1195 1234 3.059386 GGGGCGGCACAAATCGAA 61.059 61.111 12.47 0.00 0.00 3.71
1233 1285 1.213013 CTCCCACCGTCTCAACTCG 59.787 63.158 0.00 0.00 0.00 4.18
1322 1376 3.222603 CGAGAGGGGAATAAAATTGGGG 58.777 50.000 0.00 0.00 0.00 4.96
1391 1445 1.318576 GTTGCTTGTTGGGTAGCTGT 58.681 50.000 0.00 0.00 38.22 4.40
1392 1446 1.317613 TGTTGCTTGTTGGGTAGCTG 58.682 50.000 0.00 0.00 38.22 4.24
1393 1447 2.065899 TTGTTGCTTGTTGGGTAGCT 57.934 45.000 0.00 0.00 38.22 3.32
1394 1448 2.880963 TTTGTTGCTTGTTGGGTAGC 57.119 45.000 0.00 0.00 37.89 3.58
1395 1449 4.582701 TGATTTGTTGCTTGTTGGGTAG 57.417 40.909 0.00 0.00 0.00 3.18
1542 1608 7.255416 GGAATCCTCCTATTTCTTTGCTGATTC 60.255 40.741 0.00 0.00 38.88 2.52
1587 1653 0.321671 ACACTCCCAATCACACCTCG 59.678 55.000 0.00 0.00 0.00 4.63
1624 1691 0.533531 CCAGCAGCAACAGTGAGACA 60.534 55.000 0.00 0.00 0.00 3.41
1625 1692 1.849976 GCCAGCAGCAACAGTGAGAC 61.850 60.000 0.00 0.00 42.97 3.36
1644 1713 0.041839 GTCTGCACAGCACGACAAAG 60.042 55.000 13.07 0.00 37.00 2.77
1961 2033 4.241555 ATGATCACCGGGAGCGGC 62.242 66.667 6.32 0.00 33.60 6.53
2348 2420 4.546637 ACGAAGTACTTGCCGTCG 57.453 55.556 14.14 12.51 41.94 5.12
2507 2579 4.087892 CAGGTGAGGTCCAGCCCG 62.088 72.222 0.00 0.00 44.01 6.13
2567 2639 2.661866 ACCAGCTTCACGTCGTGC 60.662 61.111 20.56 9.27 32.98 5.34
2631 2703 1.275291 CATCACCTCGTGGTAGTGGTT 59.725 52.381 9.18 0.00 46.60 3.67
2838 2913 2.984155 AACCAGCAGCAGCAGCAG 60.984 61.111 12.92 3.65 45.49 4.24
2851 2926 1.005805 CCAAGATGACATCCCCAACCA 59.994 52.381 11.92 0.00 0.00 3.67
2852 2927 1.284785 TCCAAGATGACATCCCCAACC 59.715 52.381 11.92 0.00 0.00 3.77
2853 2928 2.648059 CTCCAAGATGACATCCCCAAC 58.352 52.381 11.92 0.00 0.00 3.77
2889 2964 0.749649 AGCCTAGAGATCACTTGCCG 59.250 55.000 0.00 0.00 0.00 5.69
2925 3000 0.109689 GAAGGACAGACGGACAGACG 60.110 60.000 0.00 0.00 40.31 4.18
3208 3297 6.144854 TCACTGTACACATAACGTTAGACAC 58.855 40.000 14.25 7.56 0.00 3.67
3239 3328 2.853731 AGACTCACCGTTGATCGATC 57.146 50.000 18.72 18.72 42.86 3.69
3241 3330 3.057019 CAAAAGACTCACCGTTGATCGA 58.943 45.455 0.00 0.00 42.86 3.59
3242 3331 2.800544 ACAAAAGACTCACCGTTGATCG 59.199 45.455 0.00 0.00 39.52 3.69
3244 3333 3.243068 GCAACAAAAGACTCACCGTTGAT 60.243 43.478 0.00 0.00 36.67 2.57
3245 3334 2.096819 GCAACAAAAGACTCACCGTTGA 59.903 45.455 0.00 0.00 36.67 3.18
3246 3335 2.097466 AGCAACAAAAGACTCACCGTTG 59.903 45.455 0.00 0.00 37.41 4.10
3247 3336 2.097466 CAGCAACAAAAGACTCACCGTT 59.903 45.455 0.00 0.00 0.00 4.44
3249 3338 1.670811 ACAGCAACAAAAGACTCACCG 59.329 47.619 0.00 0.00 0.00 4.94
3250 3339 3.128589 TCAACAGCAACAAAAGACTCACC 59.871 43.478 0.00 0.00 0.00 4.02
3253 3342 4.736793 CACATCAACAGCAACAAAAGACTC 59.263 41.667 0.00 0.00 0.00 3.36
3254 3343 4.440525 CCACATCAACAGCAACAAAAGACT 60.441 41.667 0.00 0.00 0.00 3.24
3302 3391 1.194218 CATCCAATCCAACCCAACCC 58.806 55.000 0.00 0.00 0.00 4.11
3303 3392 1.194218 CCATCCAATCCAACCCAACC 58.806 55.000 0.00 0.00 0.00 3.77
3304 3393 1.550072 CACCATCCAATCCAACCCAAC 59.450 52.381 0.00 0.00 0.00 3.77
3305 3394 1.935799 CACCATCCAATCCAACCCAA 58.064 50.000 0.00 0.00 0.00 4.12
3306 3395 0.614415 GCACCATCCAATCCAACCCA 60.614 55.000 0.00 0.00 0.00 4.51
3386 3485 7.091533 TCACCACACAGGATAGATAGATAGA 57.908 40.000 0.00 0.00 41.22 1.98
3387 3486 7.613411 TCATCACCACACAGGATAGATAGATAG 59.387 40.741 0.00 0.00 41.22 2.08
3411 3512 6.314917 TGGACTGGACTAGAAGCATATATCA 58.685 40.000 0.00 0.00 0.00 2.15
3412 3513 6.661377 TCTGGACTGGACTAGAAGCATATATC 59.339 42.308 0.00 0.00 0.00 1.63
3413 3514 6.435904 GTCTGGACTGGACTAGAAGCATATAT 59.564 42.308 0.00 0.00 0.00 0.86
3453 3554 7.242359 AGGAGAATTTATACTGCTAGCCTAGA 58.758 38.462 13.29 0.00 33.36 2.43
3454 3555 7.396055 AGAGGAGAATTTATACTGCTAGCCTAG 59.604 40.741 13.29 6.38 35.13 3.02
3455 3556 7.242359 AGAGGAGAATTTATACTGCTAGCCTA 58.758 38.462 13.29 1.67 35.13 3.93
3456 3557 6.081356 AGAGGAGAATTTATACTGCTAGCCT 58.919 40.000 13.29 0.00 35.13 4.58
3457 3558 6.353404 AGAGGAGAATTTATACTGCTAGCC 57.647 41.667 13.29 0.00 35.13 3.93
3527 3628 9.093458 ACATGTGTATACATAAGGATCATCAGA 57.907 33.333 9.18 0.00 45.53 3.27
3528 3629 9.716531 AACATGTGTATACATAAGGATCATCAG 57.283 33.333 9.18 0.00 45.53 2.90
3667 3771 4.335315 GGTTCGAAATGTTGGCATCATCTA 59.665 41.667 11.24 0.00 33.50 1.98


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

AutoCloner maintained by Alex Coulton.