Multiple sequence alignment - TraesCS3D01G141900

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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 TraesCS3D01G141900 chr3D 100.000 2985 0 0 1 2985 103872985 103875969 0.000000e+00 5513.0
1 TraesCS3D01G141900 chr3A 88.260 2896 201 49 170 2984 552318035 552315198 0.000000e+00 3336.0
2 TraesCS3D01G141900 chr3A 71.920 349 80 16 1625 1964 482936399 482936060 5.300000e-13 86.1
3 TraesCS3D01G141900 chr3A 77.686 121 20 6 1625 1741 482928149 482928032 1.920000e-07 67.6
4 TraesCS3D01G141900 chr3B 93.078 2066 76 19 203 2235 154484111 154486142 0.000000e+00 2961.0
5 TraesCS3D01G141900 chr3B 84.726 766 65 26 2235 2967 154486665 154487411 0.000000e+00 719.0
6 TraesCS3D01G141900 chr3B 95.833 96 3 1 13 108 154483991 154484085 1.430000e-33 154.0
7 TraesCS3D01G141900 chr1B 77.717 368 69 7 1149 1505 108093749 108093384 2.330000e-51 213.0
8 TraesCS3D01G141900 chr2B 72.500 360 73 24 1618 1964 796341861 796342207 3.170000e-15 93.5
9 TraesCS3D01G141900 chr2A 71.709 357 81 18 1618 1964 761541640 761541294 6.860000e-12 82.4
10 TraesCS3D01G141900 chr2D 72.761 268 57 14 1705 1964 637802801 637803060 3.190000e-10 76.8
11 TraesCS3D01G141900 chr2D 100.000 28 0 0 656 683 625536965 625536992 5.000000e-03 52.8


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 TraesCS3D01G141900 chr3D 103872985 103875969 2984 False 5513 5513 100.000000 1 2985 1 chr3D.!!$F1 2984
1 TraesCS3D01G141900 chr3A 552315198 552318035 2837 True 3336 3336 88.260000 170 2984 1 chr3A.!!$R3 2814
2 TraesCS3D01G141900 chr3B 154483991 154487411 3420 False 1278 2961 91.212333 13 2967 3 chr3B.!!$F1 2954

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
121 134 0.035317 TATATTGCTGCAGAGGCCGG 59.965 55.0 20.43 0.0 40.13 6.13 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1997 2042 0.525668 CCGATCGAGAAACGTGAGGG 60.526 60.0 18.66 0.0 43.13 4.3 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
41 42 5.597806 ACGTCTCAAACTAAGAATGTGTGA 58.402 37.500 0.00 0.00 31.60 3.58
73 74 6.814146 GTCAACTCTTAATACTTGAGGGACAG 59.186 42.308 0.00 0.00 36.82 3.51
103 116 0.111061 TAGAGCCGCCCCGAGTATTA 59.889 55.000 0.00 0.00 0.00 0.98
119 132 4.583871 AGTATTATATTGCTGCAGAGGCC 58.416 43.478 20.43 0.00 40.13 5.19
120 133 1.882912 TTATATTGCTGCAGAGGCCG 58.117 50.000 20.43 0.00 40.13 6.13
121 134 0.035317 TATATTGCTGCAGAGGCCGG 59.965 55.000 20.43 0.00 40.13 6.13
122 135 1.699054 ATATTGCTGCAGAGGCCGGA 61.699 55.000 20.43 0.00 40.13 5.14
123 136 1.699054 TATTGCTGCAGAGGCCGGAT 61.699 55.000 20.43 0.00 40.13 4.18
124 137 3.851470 TATTGCTGCAGAGGCCGGATG 62.851 57.143 20.43 0.00 40.13 3.51
125 138 4.479993 GCTGCAGAGGCCGGATGT 62.480 66.667 20.43 0.00 40.13 3.06
126 139 3.094062 GCTGCAGAGGCCGGATGTA 62.094 63.158 20.43 0.00 40.13 2.29
127 140 1.522092 CTGCAGAGGCCGGATGTAA 59.478 57.895 8.42 0.00 40.13 2.41
128 141 0.107456 CTGCAGAGGCCGGATGTAAT 59.893 55.000 8.42 0.00 40.13 1.89
129 142 0.106708 TGCAGAGGCCGGATGTAATC 59.893 55.000 5.05 0.00 40.57 1.75
130 143 0.946221 GCAGAGGCCGGATGTAATCG 60.946 60.000 5.05 0.00 46.86 3.34
131 144 0.673985 CAGAGGCCGGATGTAATCGA 59.326 55.000 5.05 0.00 46.86 3.59
132 145 1.273606 CAGAGGCCGGATGTAATCGAT 59.726 52.381 5.05 0.00 46.86 3.59
133 146 2.492088 CAGAGGCCGGATGTAATCGATA 59.508 50.000 5.05 0.00 46.86 2.92
134 147 2.755655 AGAGGCCGGATGTAATCGATAG 59.244 50.000 5.05 0.00 46.86 2.08
135 148 1.204941 AGGCCGGATGTAATCGATAGC 59.795 52.381 5.05 0.00 46.86 2.97
136 149 1.067142 GGCCGGATGTAATCGATAGCA 60.067 52.381 5.05 0.81 46.86 3.49
137 150 2.418746 GGCCGGATGTAATCGATAGCAT 60.419 50.000 5.05 12.58 46.86 3.79
138 151 2.860735 GCCGGATGTAATCGATAGCATC 59.139 50.000 23.21 23.21 46.86 3.91
139 152 3.429547 GCCGGATGTAATCGATAGCATCT 60.430 47.826 26.86 6.26 46.86 2.90
140 153 4.748892 CCGGATGTAATCGATAGCATCTT 58.251 43.478 26.86 6.32 46.86 2.40
141 154 4.800993 CCGGATGTAATCGATAGCATCTTC 59.199 45.833 26.86 17.32 46.86 2.87
142 155 5.402398 CGGATGTAATCGATAGCATCTTCA 58.598 41.667 26.86 7.78 46.86 3.02
143 156 5.287274 CGGATGTAATCGATAGCATCTTCAC 59.713 44.000 26.86 16.64 46.86 3.18
144 157 5.287274 GGATGTAATCGATAGCATCTTCACG 59.713 44.000 26.86 0.00 46.86 4.35
145 158 5.183014 TGTAATCGATAGCATCTTCACGT 57.817 39.130 0.00 0.00 0.00 4.49
146 159 6.308371 TGTAATCGATAGCATCTTCACGTA 57.692 37.500 0.00 0.00 0.00 3.57
147 160 6.909909 TGTAATCGATAGCATCTTCACGTAT 58.090 36.000 0.00 0.00 0.00 3.06
148 161 8.036273 TGTAATCGATAGCATCTTCACGTATA 57.964 34.615 0.00 0.00 0.00 1.47
149 162 8.674607 TGTAATCGATAGCATCTTCACGTATAT 58.325 33.333 0.00 0.00 0.00 0.86
150 163 7.977490 AATCGATAGCATCTTCACGTATATG 57.023 36.000 0.00 0.00 0.00 1.78
151 164 6.737254 TCGATAGCATCTTCACGTATATGA 57.263 37.500 0.00 0.00 0.00 2.15
152 165 7.141100 TCGATAGCATCTTCACGTATATGAA 57.859 36.000 0.00 0.00 37.08 2.57
153 166 7.762382 TCGATAGCATCTTCACGTATATGAAT 58.238 34.615 0.00 0.00 37.93 2.57
154 167 8.244113 TCGATAGCATCTTCACGTATATGAATT 58.756 33.333 0.00 0.00 37.93 2.17
155 168 9.503427 CGATAGCATCTTCACGTATATGAATTA 57.497 33.333 0.00 0.00 37.93 1.40
159 172 9.494271 AGCATCTTCACGTATATGAATTATTGT 57.506 29.630 0.00 0.00 37.93 2.71
214 227 1.408969 AAAGGTTGGCCGTGATTTGT 58.591 45.000 0.00 0.00 40.50 2.83
245 258 5.098893 GCACATATCTTCCACTCTATAGCG 58.901 45.833 0.00 0.00 0.00 4.26
275 288 1.135112 TGCTCGAATAGACACGCATGT 60.135 47.619 0.00 0.00 43.71 3.21
276 289 2.098443 TGCTCGAATAGACACGCATGTA 59.902 45.455 0.00 0.00 39.95 2.29
278 291 3.120286 GCTCGAATAGACACGCATGTATG 59.880 47.826 0.00 0.00 39.95 2.39
314 330 5.149977 GGAAAAAGAAGAGACGCATTCTTG 58.850 41.667 1.28 0.00 43.25 3.02
489 512 0.317479 ACCACAGCTCCACTTACGAC 59.683 55.000 0.00 0.00 0.00 4.34
522 545 6.939132 ATAGCTGAATCTTCTGGATTTGTG 57.061 37.500 0.00 0.00 43.90 3.33
545 568 1.337167 GCTCCACTTGCCAATTCAACC 60.337 52.381 0.00 0.00 0.00 3.77
546 569 1.273327 CTCCACTTGCCAATTCAACCC 59.727 52.381 0.00 0.00 0.00 4.11
629 652 0.250338 GGCCGTTTCTTGGTCAGACT 60.250 55.000 0.00 0.00 0.00 3.24
670 693 1.842052 ACGACCTCTTCCTCTTCCTC 58.158 55.000 0.00 0.00 0.00 3.71
671 694 1.356398 ACGACCTCTTCCTCTTCCTCT 59.644 52.381 0.00 0.00 0.00 3.69
672 695 2.225167 ACGACCTCTTCCTCTTCCTCTT 60.225 50.000 0.00 0.00 0.00 2.85
673 696 2.425668 CGACCTCTTCCTCTTCCTCTTC 59.574 54.545 0.00 0.00 0.00 2.87
674 697 2.764010 GACCTCTTCCTCTTCCTCTTCC 59.236 54.545 0.00 0.00 0.00 3.46
675 698 2.385417 ACCTCTTCCTCTTCCTCTTCCT 59.615 50.000 0.00 0.00 0.00 3.36
930 971 2.023181 CGCCATTGTCGCATTCCG 59.977 61.111 0.00 0.00 38.61 4.30
963 1004 1.535687 ACTCCACCGGTAAGGCAGT 60.536 57.895 6.87 8.38 46.52 4.40
1044 1089 1.303561 TCCAGCAATGGCACCTCAC 60.304 57.895 0.00 0.00 44.61 3.51
1074 1119 1.740296 CCGTTTCCTCATCGCCGTT 60.740 57.895 0.00 0.00 0.00 4.44
1380 1425 4.280494 CCGGACGGCCCATACTCG 62.280 72.222 0.00 0.00 34.14 4.18
1421 1466 2.588314 GATCAGCCCGCAGAGCAG 60.588 66.667 0.00 0.00 28.80 4.24
1437 1482 4.778415 AGCTACTGCGACGCCACG 62.778 66.667 18.69 8.33 45.42 4.94
1476 1521 2.375345 CCCCGGCAAGTCCTACCAT 61.375 63.158 0.00 0.00 0.00 3.55
1515 1560 9.872684 ATCCAAATCTCATGGTACTGATAAATT 57.127 29.630 0.00 0.00 39.09 1.82
1519 1564 7.639062 ATCTCATGGTACTGATAAATTCCCT 57.361 36.000 0.00 0.00 0.00 4.20
1563 1608 2.585247 GCGCCGGCTCGTTAGAAT 60.585 61.111 26.68 0.00 35.83 2.40
1570 1615 1.438651 GGCTCGTTAGAATGCACACA 58.561 50.000 0.00 0.00 0.00 3.72
1572 1617 2.030946 GGCTCGTTAGAATGCACACATC 59.969 50.000 0.00 0.00 34.62 3.06
1573 1618 2.932614 GCTCGTTAGAATGCACACATCT 59.067 45.455 0.00 0.00 34.62 2.90
1574 1619 3.242220 GCTCGTTAGAATGCACACATCTG 60.242 47.826 0.00 0.00 34.62 2.90
1575 1620 4.176271 CTCGTTAGAATGCACACATCTGA 58.824 43.478 0.00 0.00 34.62 3.27
1576 1621 3.926527 TCGTTAGAATGCACACATCTGAC 59.073 43.478 0.00 0.00 34.62 3.51
1577 1622 3.062639 CGTTAGAATGCACACATCTGACC 59.937 47.826 0.00 0.00 34.62 4.02
1578 1623 4.256920 GTTAGAATGCACACATCTGACCT 58.743 43.478 0.00 0.00 34.62 3.85
1579 1624 2.983229 AGAATGCACACATCTGACCTC 58.017 47.619 0.00 0.00 34.62 3.85
1580 1625 2.570752 AGAATGCACACATCTGACCTCT 59.429 45.455 0.00 0.00 34.62 3.69
1581 1626 2.398252 ATGCACACATCTGACCTCTG 57.602 50.000 0.00 0.00 0.00 3.35
1582 1627 1.341080 TGCACACATCTGACCTCTGA 58.659 50.000 0.00 0.00 0.00 3.27
1583 1628 1.274447 TGCACACATCTGACCTCTGAG 59.726 52.381 0.00 0.00 0.00 3.35
1584 1629 1.274728 GCACACATCTGACCTCTGAGT 59.725 52.381 3.66 0.00 0.00 3.41
1585 1630 2.673610 GCACACATCTGACCTCTGAGTC 60.674 54.545 3.66 2.55 37.28 3.36
1586 1631 2.824936 CACACATCTGACCTCTGAGTCT 59.175 50.000 3.66 0.00 37.66 3.24
1587 1632 2.824936 ACACATCTGACCTCTGAGTCTG 59.175 50.000 3.66 6.01 37.66 3.51
1588 1633 3.087781 CACATCTGACCTCTGAGTCTGA 58.912 50.000 3.66 10.50 45.22 3.27
1589 1634 3.088532 ACATCTGACCTCTGAGTCTGAC 58.911 50.000 14.20 0.00 44.34 3.51
1621 1666 0.749454 GCCGGCTGATGAACAGGAAT 60.749 55.000 22.15 0.00 45.82 3.01
1633 1678 4.710324 TGAACAGGAATTTCAACTACGGT 58.290 39.130 0.00 0.00 29.89 4.83
1784 1829 1.226888 GTGATGGTCGGCGAGTACC 60.227 63.158 11.20 9.95 36.24 3.34
1871 1916 3.414700 GTGGCCTCGAGTGCAACG 61.415 66.667 22.04 8.02 45.86 4.10
1997 2042 1.603456 GTACTAGCCCGAGGGAGTAC 58.397 60.000 18.51 18.51 37.96 2.73
2040 2085 0.324943 AAACCATAGCCTCACGTGCT 59.675 50.000 11.67 7.46 42.81 4.40
2041 2086 1.191535 AACCATAGCCTCACGTGCTA 58.808 50.000 11.67 9.75 44.78 3.49
2042 2087 0.460311 ACCATAGCCTCACGTGCTAC 59.540 55.000 11.67 1.75 43.59 3.58
2369 2962 1.072266 TAAAAGAGAGGGGCTTGCCA 58.928 50.000 14.04 0.00 0.00 4.92
2487 3080 4.179926 CTTGCAAGCTAGACACTAGACA 57.820 45.455 14.65 0.31 0.00 3.41
2506 3099 4.536090 AGACATAGGAAACAATGAGGGTCA 59.464 41.667 0.00 0.00 0.00 4.02
2542 3135 5.003692 TCTGAATGGAAGAAGACGATCAG 57.996 43.478 0.00 0.00 0.00 2.90
2640 3235 3.195396 TCAGATGATCATGTTGTGGTCGA 59.805 43.478 14.30 0.00 41.06 4.20
2657 3252 3.254657 GGTCGATCCTATTGTCTCTCCAG 59.745 52.174 0.00 0.00 0.00 3.86
2660 3255 3.885901 CGATCCTATTGTCTCTCCAGTGA 59.114 47.826 0.00 0.00 0.00 3.41
2665 3260 4.280677 CCTATTGTCTCTCCAGTGATCTCC 59.719 50.000 0.00 0.00 0.00 3.71
2666 3261 2.151502 TGTCTCTCCAGTGATCTCCC 57.848 55.000 0.00 0.00 0.00 4.30
2683 3297 9.125026 GTGATCTCCCAATTTATACACAAGATT 57.875 33.333 0.00 0.00 0.00 2.40
2688 3302 8.062065 TCCCAATTTATACACAAGATTGGTTC 57.938 34.615 11.24 0.00 43.20 3.62
2719 3349 6.601332 TGAATACAAGACCTTCTCCAAAGTT 58.399 36.000 0.00 0.00 0.00 2.66
2749 3379 0.388659 TGCAGCAAATCCCACACAAC 59.611 50.000 0.00 0.00 0.00 3.32
2757 3387 5.296531 AGCAAATCCCACACAACAAATTTTC 59.703 36.000 0.00 0.00 0.00 2.29
2763 3393 6.074648 TCCCACACAACAAATTTTCCTATCT 58.925 36.000 0.00 0.00 0.00 1.98
2798 3428 5.306678 TCCCTTGCACAAGTTTATGGAATTT 59.693 36.000 9.41 0.00 36.72 1.82
2799 3429 5.409214 CCCTTGCACAAGTTTATGGAATTTG 59.591 40.000 9.41 0.00 39.91 2.32
2824 3454 2.517638 TAGCCGGATTCCGCGAGA 60.518 61.111 19.80 0.00 46.86 4.04
2826 3456 2.345880 TAGCCGGATTCCGCGAGAAC 62.346 60.000 19.80 4.28 46.86 3.01
2830 3460 2.203029 GATTCCGCGAGAACCCCC 60.203 66.667 8.23 0.00 37.29 5.40
2906 3538 8.761575 AATATGTGGTCACAATTTTCATTGAC 57.238 30.769 7.92 0.00 45.41 3.18
2946 3578 0.387202 CGTCCTCTAGGCCATGTCTG 59.613 60.000 5.01 0.00 34.44 3.51
2958 3590 0.520404 CATGTCTGTTGAGCACCTGC 59.480 55.000 0.00 0.00 42.49 4.85
2973 3605 0.462759 CCTGCTCCCAAGTTCGGATC 60.463 60.000 0.00 0.00 0.00 3.36
2984 3616 0.902531 GTTCGGATCCTGTTCCTGGA 59.097 55.000 10.75 0.00 36.01 3.86
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
1 2 5.147330 AGACGTCCAATAGTGATGTTGAA 57.853 39.130 13.01 0.00 32.27 2.69
2 3 4.219725 TGAGACGTCCAATAGTGATGTTGA 59.780 41.667 13.01 0.00 32.27 3.18
3 4 4.494484 TGAGACGTCCAATAGTGATGTTG 58.506 43.478 13.01 0.00 32.27 3.33
4 5 4.801330 TGAGACGTCCAATAGTGATGTT 57.199 40.909 13.01 0.00 32.27 2.71
5 6 4.801330 TTGAGACGTCCAATAGTGATGT 57.199 40.909 13.01 0.00 34.74 3.06
6 7 5.171476 AGTTTGAGACGTCCAATAGTGATG 58.829 41.667 13.01 0.00 0.00 3.07
7 8 5.407407 AGTTTGAGACGTCCAATAGTGAT 57.593 39.130 13.01 0.00 0.00 3.06
8 9 4.866508 AGTTTGAGACGTCCAATAGTGA 57.133 40.909 13.01 0.00 0.00 3.41
9 10 6.387465 TCTTAGTTTGAGACGTCCAATAGTG 58.613 40.000 13.01 6.49 0.00 2.74
10 11 6.585695 TCTTAGTTTGAGACGTCCAATAGT 57.414 37.500 13.01 11.39 0.00 2.12
11 12 7.545965 ACATTCTTAGTTTGAGACGTCCAATAG 59.454 37.037 13.01 10.66 0.00 1.73
73 74 2.124529 GGCTCTACCTTGGGCTGC 60.125 66.667 0.00 0.00 34.51 5.25
103 116 1.228063 CCGGCCTCTGCAGCAATAT 60.228 57.895 9.47 0.00 40.13 1.28
119 132 5.287274 GTGAAGATGCTATCGATTACATCCG 59.713 44.000 25.14 0.00 39.79 4.18
120 133 5.287274 CGTGAAGATGCTATCGATTACATCC 59.713 44.000 25.14 16.64 39.79 3.51
121 134 5.859114 ACGTGAAGATGCTATCGATTACATC 59.141 40.000 23.01 23.01 39.35 3.06
122 135 5.773575 ACGTGAAGATGCTATCGATTACAT 58.226 37.500 1.71 7.94 0.00 2.29
123 136 5.183014 ACGTGAAGATGCTATCGATTACA 57.817 39.130 1.71 2.46 0.00 2.41
124 137 8.948946 CATATACGTGAAGATGCTATCGATTAC 58.051 37.037 1.71 0.00 0.00 1.89
125 138 8.889717 TCATATACGTGAAGATGCTATCGATTA 58.110 33.333 1.71 0.00 0.00 1.75
126 139 7.762382 TCATATACGTGAAGATGCTATCGATT 58.238 34.615 1.71 0.00 0.00 3.34
127 140 7.321745 TCATATACGTGAAGATGCTATCGAT 57.678 36.000 2.16 2.16 0.00 3.59
128 141 6.737254 TCATATACGTGAAGATGCTATCGA 57.263 37.500 0.00 0.00 0.00 3.59
129 142 7.977490 ATTCATATACGTGAAGATGCTATCG 57.023 36.000 0.00 0.00 41.05 2.92
133 146 9.494271 ACAATAATTCATATACGTGAAGATGCT 57.506 29.630 0.00 0.00 41.05 3.79
193 206 2.169561 ACAAATCACGGCCAACCTTTTT 59.830 40.909 2.24 0.00 0.00 1.94
194 207 1.760029 ACAAATCACGGCCAACCTTTT 59.240 42.857 2.24 0.00 0.00 2.27
201 214 4.312052 GCCTACAAATCACGGCCA 57.688 55.556 2.24 0.00 36.56 5.36
214 227 1.070134 GGAAGATATGTGCACGGCCTA 59.930 52.381 13.13 1.58 0.00 3.93
245 258 1.324736 CTATTCGAGCAAGCGTTGACC 59.675 52.381 2.51 0.00 0.00 4.02
314 330 1.664151 GACCGGTTAGTGCTGCAATAC 59.336 52.381 9.42 5.49 0.00 1.89
423 445 3.985019 TGGGAAATCATTGCAGCAATT 57.015 38.095 18.48 4.54 31.05 2.32
489 512 9.806203 CCAGAAGATTCAGCTATAGATTATGAG 57.194 37.037 3.21 0.00 0.00 2.90
522 545 2.436417 TGAATTGGCAAGTGGAGCTAC 58.564 47.619 4.31 0.00 0.00 3.58
545 568 1.440938 TTGCGTCCTGTTTGTTCCGG 61.441 55.000 0.00 0.00 0.00 5.14
546 569 0.591170 ATTGCGTCCTGTTTGTTCCG 59.409 50.000 0.00 0.00 0.00 4.30
629 652 4.961511 GCGACGGCACAGTGGTCA 62.962 66.667 1.84 0.00 39.62 4.02
670 693 6.656693 TGAATAAAGAAAGGAGCAAGAGGAAG 59.343 38.462 0.00 0.00 0.00 3.46
671 694 6.542821 TGAATAAAGAAAGGAGCAAGAGGAA 58.457 36.000 0.00 0.00 0.00 3.36
672 695 6.126863 TGAATAAAGAAAGGAGCAAGAGGA 57.873 37.500 0.00 0.00 0.00 3.71
673 696 5.163673 GCTGAATAAAGAAAGGAGCAAGAGG 60.164 44.000 0.00 0.00 0.00 3.69
674 697 5.163673 GGCTGAATAAAGAAAGGAGCAAGAG 60.164 44.000 0.00 0.00 0.00 2.85
675 698 4.702131 GGCTGAATAAAGAAAGGAGCAAGA 59.298 41.667 0.00 0.00 0.00 3.02
963 1004 2.544277 CGTTTTATATCCGCTCCACCGA 60.544 50.000 0.00 0.00 0.00 4.69
1052 1097 2.174319 GCGATGAGGAAACGGAGGC 61.174 63.158 0.00 0.00 0.00 4.70
1374 1419 3.031417 GCACAGGCCCCACGAGTAT 62.031 63.158 0.00 0.00 0.00 2.12
1380 1425 1.675641 CTTGTAGCACAGGCCCCAC 60.676 63.158 0.00 0.00 42.56 4.61
1437 1482 3.357079 CACGGCCACTGCTTGTCC 61.357 66.667 2.24 0.00 37.74 4.02
1515 1560 1.064003 TTTGCAGGTAAGCTCAGGGA 58.936 50.000 0.00 0.00 34.99 4.20
1519 1564 4.144297 AGTGAAATTTGCAGGTAAGCTCA 58.856 39.130 0.00 0.00 34.99 4.26
1557 1602 4.223700 AGAGGTCAGATGTGTGCATTCTAA 59.776 41.667 0.00 0.00 35.07 2.10
1563 1608 1.274447 CTCAGAGGTCAGATGTGTGCA 59.726 52.381 0.00 0.00 0.00 4.57
1570 1615 2.311542 AGGTCAGACTCAGAGGTCAGAT 59.688 50.000 1.53 0.00 38.57 2.90
1572 1617 2.091541 GAGGTCAGACTCAGAGGTCAG 58.908 57.143 1.53 0.00 38.57 3.51
1573 1618 1.707989 AGAGGTCAGACTCAGAGGTCA 59.292 52.381 1.53 0.00 39.97 4.02
1574 1619 2.091541 CAGAGGTCAGACTCAGAGGTC 58.908 57.143 1.53 0.00 39.97 3.85
1575 1620 1.707989 TCAGAGGTCAGACTCAGAGGT 59.292 52.381 1.53 0.00 39.97 3.85
1576 1621 2.091541 GTCAGAGGTCAGACTCAGAGG 58.908 57.143 1.53 0.00 39.97 3.69
1577 1622 2.091541 GGTCAGAGGTCAGACTCAGAG 58.908 57.143 0.00 0.00 39.97 3.35
1578 1623 1.707989 AGGTCAGAGGTCAGACTCAGA 59.292 52.381 0.00 0.00 39.97 3.27
1579 1624 2.091541 GAGGTCAGAGGTCAGACTCAG 58.908 57.143 0.00 0.00 39.97 3.35
1580 1625 1.707989 AGAGGTCAGAGGTCAGACTCA 59.292 52.381 0.00 0.00 39.97 3.41
1581 1626 2.091541 CAGAGGTCAGAGGTCAGACTC 58.908 57.143 0.00 0.00 37.77 3.36
1582 1627 1.272425 CCAGAGGTCAGAGGTCAGACT 60.272 57.143 0.00 0.00 33.55 3.24
1583 1628 1.181786 CCAGAGGTCAGAGGTCAGAC 58.818 60.000 0.00 0.00 0.00 3.51
1584 1629 0.613292 GCCAGAGGTCAGAGGTCAGA 60.613 60.000 0.00 0.00 0.00 3.27
1585 1630 1.612395 GGCCAGAGGTCAGAGGTCAG 61.612 65.000 0.00 0.00 0.00 3.51
1586 1631 1.610673 GGCCAGAGGTCAGAGGTCA 60.611 63.158 0.00 0.00 0.00 4.02
1587 1632 2.716017 CGGCCAGAGGTCAGAGGTC 61.716 68.421 2.24 0.00 0.00 3.85
1588 1633 2.681778 CGGCCAGAGGTCAGAGGT 60.682 66.667 2.24 0.00 0.00 3.85
1589 1634 3.465403 CCGGCCAGAGGTCAGAGG 61.465 72.222 2.24 0.00 0.00 3.69
1621 1666 1.373246 CGCCGGACCGTAGTTGAAA 60.373 57.895 13.94 0.00 0.00 2.69
1718 1763 0.605319 GGCGTCATCCAGAACCACAA 60.605 55.000 0.00 0.00 0.00 3.33
1997 2042 0.525668 CCGATCGAGAAACGTGAGGG 60.526 60.000 18.66 0.00 43.13 4.30
2143 2198 9.013229 TGCTTCAATTTCACTTGTTGATAGTAT 57.987 29.630 0.00 0.00 32.84 2.12
2328 2919 2.052782 AAAAGTCACTCCGCCTTGTT 57.947 45.000 0.00 0.00 0.00 2.83
2369 2962 1.002857 AGGGCCTCAGTTTATTGCCT 58.997 50.000 0.00 0.00 41.84 4.75
2381 2974 4.652822 TCTTTTTGTAAGAGAAGGGCCTC 58.347 43.478 6.46 0.00 0.00 4.70
2487 3080 4.236527 GGTGACCCTCATTGTTTCCTAT 57.763 45.455 0.00 0.00 0.00 2.57
2506 3099 0.112606 TTCAGAGACTCTCCGTGGGT 59.887 55.000 0.69 0.00 0.00 4.51
2558 3151 1.406069 CCTTGAGACGGGACAATGAGG 60.406 57.143 0.00 0.00 0.00 3.86
2583 3178 1.661460 GCAAAGTGTCAAGCTCTTCGC 60.661 52.381 0.00 0.00 39.57 4.70
2619 3214 3.524541 TCGACCACAACATGATCATCTG 58.475 45.455 4.86 8.87 0.00 2.90
2640 3235 5.714863 AGATCACTGGAGAGACAATAGGAT 58.285 41.667 0.00 0.00 0.00 3.24
2657 3252 8.682936 ATCTTGTGTATAAATTGGGAGATCAC 57.317 34.615 0.00 0.00 0.00 3.06
2660 3255 8.061304 ACCAATCTTGTGTATAAATTGGGAGAT 58.939 33.333 14.85 0.00 46.88 2.75
2666 3261 9.225201 CATCGAACCAATCTTGTGTATAAATTG 57.775 33.333 0.00 0.00 0.00 2.32
2683 3297 4.944962 CTTGTATTCAAGCATCGAACCA 57.055 40.909 0.00 0.00 43.34 3.67
2734 3364 5.497635 AAAATTTGTTGTGTGGGATTTGC 57.502 34.783 0.00 0.00 0.00 3.68
2799 3429 1.101635 GGAATCCGGCTAGGTTTGCC 61.102 60.000 0.00 0.00 46.42 4.52
2826 3456 0.698238 TGATCTGAAACACCAGGGGG 59.302 55.000 0.00 0.00 41.29 5.40
2830 3460 3.070018 GGAGTGTGATCTGAAACACCAG 58.930 50.000 18.08 0.00 46.32 4.00
2906 3538 1.136695 ACACTTGCATTTGGTGTGGTG 59.863 47.619 12.25 0.00 41.75 4.17
2958 3590 0.905357 ACAGGATCCGAACTTGGGAG 59.095 55.000 5.98 0.00 36.91 4.30
2963 3595 1.279271 CCAGGAACAGGATCCGAACTT 59.721 52.381 5.98 0.00 44.60 2.66


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

AutoCloner maintained by Alex Coulton.