Multiple sequence alignment - TraesCS3A01G354800

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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 TraesCS3A01G354800 chr3A 100.000 5472 0 0 1 5472 602690711 602685240 0.000000e+00 10105.0
1 TraesCS3A01G354800 chr3D 93.181 3109 135 29 27 3095 460423261 460420190 0.000000e+00 4495.0
2 TraesCS3A01G354800 chr3D 96.667 2130 47 11 3168 5287 460420100 460417985 0.000000e+00 3518.0
3 TraesCS3A01G354800 chr3D 98.137 161 3 0 5312 5472 460417846 460417686 1.160000e-71 281.0
4 TraesCS3A01G354800 chr3D 93.182 44 3 0 3097 3140 558222065 558222108 1.270000e-06 65.8
5 TraesCS3A01G354800 chr3B 93.828 2900 111 35 2469 5315 610499747 610496863 0.000000e+00 4301.0
6 TraesCS3A01G354800 chr3B 89.960 2251 133 33 259 2470 610502057 610499861 0.000000e+00 2819.0
7 TraesCS3A01G354800 chr3B 92.903 155 11 0 5318 5472 610496777 610496623 5.520000e-55 226.0
8 TraesCS3A01G354800 chr3B 83.529 85 9 2 3060 3139 111851134 111851050 2.110000e-09 75.0
9 TraesCS3A01G354800 chrUn 98.492 398 6 0 4032 4429 478989335 478989732 0.000000e+00 702.0
10 TraesCS3A01G354800 chr7A 79.826 917 127 29 1449 2335 269092832 269091944 2.800000e-172 616.0
11 TraesCS3A01G354800 chr7A 97.561 41 1 0 3098 3138 290618212 290618252 2.730000e-08 71.3
12 TraesCS3A01G354800 chr4A 79.599 897 127 27 1464 2330 353126188 353125318 4.720000e-165 592.0
13 TraesCS3A01G354800 chr1B 87.838 74 7 1 3068 3141 48971088 48971159 9.770000e-13 86.1
14 TraesCS3A01G354800 chr1B 97.619 42 1 0 3099 3140 282135824 282135783 7.600000e-09 73.1
15 TraesCS3A01G354800 chr6D 100.000 44 0 0 3098 3141 27509779 27509736 1.260000e-11 82.4
16 TraesCS3A01G354800 chr6D 97.561 41 1 0 3101 3141 413078285 413078325 2.730000e-08 71.3
17 TraesCS3A01G354800 chr2B 97.674 43 1 0 3099 3141 148242234 148242192 2.110000e-09 75.0
18 TraesCS3A01G354800 chr1D 97.619 42 1 0 3100 3141 184473417 184473458 7.600000e-09 73.1


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 TraesCS3A01G354800 chr3A 602685240 602690711 5471 True 10105.000000 10105 100.000000 1 5472 1 chr3A.!!$R1 5471
1 TraesCS3A01G354800 chr3D 460417686 460423261 5575 True 2764.666667 4495 95.995000 27 5472 3 chr3D.!!$R1 5445
2 TraesCS3A01G354800 chr3B 610496623 610502057 5434 True 2448.666667 4301 92.230333 259 5472 3 chr3B.!!$R2 5213
3 TraesCS3A01G354800 chr7A 269091944 269092832 888 True 616.000000 616 79.826000 1449 2335 1 chr7A.!!$R1 886
4 TraesCS3A01G354800 chr4A 353125318 353126188 870 True 592.000000 592 79.599000 1464 2330 1 chr4A.!!$R1 866

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
38 39 0.032952 AGACGAGCGGCTTTGTACAA 59.967 50.000 2.97 3.59 0.00 2.41 F
394 401 0.037697 CAACGAACATCCCACGGAGA 60.038 55.000 0.00 0.00 34.05 3.71 F
597 612 0.096976 CGAAACGTGCCCAATGCTAG 59.903 55.000 0.00 0.00 42.00 3.42 F
605 620 0.107654 GCCCAATGCTAGTCGGTCTT 60.108 55.000 0.00 0.00 36.87 3.01 F
610 625 0.456221 ATGCTAGTCGGTCTTCGTGG 59.544 55.000 0.00 0.00 40.32 4.94 F
1094 1155 0.737715 TTGTTTGTTTGGCACCGCAC 60.738 50.000 0.00 0.00 0.00 5.34 F
1120 1188 0.853586 AATTGGGGTTCCTAGGGCCA 60.854 55.000 20.13 5.34 0.00 5.36 F
1610 1678 1.884579 CACCTCTTTGCTGCAGATTGT 59.115 47.619 20.43 0.63 0.00 2.71 F
3111 3382 2.094649 GTCGCCTTTGTACTAGAGCTGT 60.095 50.000 0.00 0.00 0.00 4.40 F
4063 4340 0.798776 CGATTGTTGTCCAGACTGCC 59.201 55.000 0.00 0.00 0.00 4.85 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1522 1590 0.248289 CGTCATACCCCGACCTGTTT 59.752 55.000 0.00 0.00 0.00 2.83 R
2097 2187 2.490115 CCAGTTTACCCAATTAGCGCAA 59.510 45.455 11.47 1.85 0.00 4.85 R
2244 2343 2.606308 GCAGAACACATCAAAGGCACAG 60.606 50.000 0.00 0.00 0.00 3.66 R
2291 2391 5.426689 AGAAAGTGATGGCTGATAGTTCA 57.573 39.130 0.00 0.00 0.00 3.18 R
2779 3002 2.875933 CAGTGCCGTTTGACCTTTCTTA 59.124 45.455 0.00 0.00 0.00 2.10 R
2878 3101 2.794350 GGCAGTGTTTCCATTTTTGTCG 59.206 45.455 0.00 0.00 0.00 4.35 R
3111 3382 4.887071 CCCTCCGATCCAAATTAATTGTCA 59.113 41.667 0.39 0.00 37.32 3.58 R
3613 3887 3.691609 GCAGGAAATAGGAAACAGTGAGG 59.308 47.826 0.00 0.00 0.00 3.86 R
4393 4670 0.390998 AGCTTGAGCCGCTTCTTCTC 60.391 55.000 0.00 0.00 43.38 2.87 R
5196 5492 1.734388 AAAACCAACGGAGCCTGCAC 61.734 55.000 0.00 0.00 0.00 4.57 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
24 25 4.842292 GCATCATCTGCCAGACGA 57.158 55.556 0.00 0.00 45.66 4.20
25 26 2.602738 GCATCATCTGCCAGACGAG 58.397 57.895 0.00 0.00 45.66 4.18
26 27 1.497223 GCATCATCTGCCAGACGAGC 61.497 60.000 0.00 0.00 45.66 5.03
27 28 1.067084 ATCATCTGCCAGACGAGCG 59.933 57.895 0.00 0.00 0.00 5.03
28 29 2.360949 ATCATCTGCCAGACGAGCGG 62.361 60.000 0.00 0.00 38.00 5.52
33 34 3.793144 GCCAGACGAGCGGCTTTG 61.793 66.667 2.97 2.46 45.29 2.77
38 39 0.032952 AGACGAGCGGCTTTGTACAA 59.967 50.000 2.97 3.59 0.00 2.41
61 62 1.133606 ACGACAAGGTGGGTGGAAAAT 60.134 47.619 0.00 0.00 0.00 1.82
63 64 1.618343 GACAAGGTGGGTGGAAAATGG 59.382 52.381 0.00 0.00 0.00 3.16
83 85 4.148825 AGACGGGCAGCGGCTAAG 62.149 66.667 9.17 3.07 40.87 2.18
121 123 2.355513 GGCCTTTCTCATCTGAGCAGAA 60.356 50.000 4.06 0.00 41.36 3.02
135 137 6.104665 TCTGAGCAGAAAATCATCTACACTG 58.895 40.000 0.00 0.00 33.91 3.66
195 198 1.154093 GTGATCCGACGCTCGTTCA 60.154 57.895 0.00 6.48 38.40 3.18
214 217 2.093500 TCACAAGCCGTAGCATCAAGAT 60.093 45.455 0.00 0.00 43.56 2.40
215 218 2.679837 CACAAGCCGTAGCATCAAGATT 59.320 45.455 0.00 0.00 43.56 2.40
216 219 2.939103 ACAAGCCGTAGCATCAAGATTC 59.061 45.455 0.00 0.00 43.56 2.52
217 220 2.938451 CAAGCCGTAGCATCAAGATTCA 59.062 45.455 0.00 0.00 43.56 2.57
218 221 3.266510 AGCCGTAGCATCAAGATTCAA 57.733 42.857 0.00 0.00 43.56 2.69
219 222 3.201290 AGCCGTAGCATCAAGATTCAAG 58.799 45.455 0.00 0.00 43.56 3.02
220 223 3.118629 AGCCGTAGCATCAAGATTCAAGA 60.119 43.478 0.00 0.00 43.56 3.02
221 224 3.001736 GCCGTAGCATCAAGATTCAAGAC 59.998 47.826 0.00 0.00 39.53 3.01
222 225 3.557595 CCGTAGCATCAAGATTCAAGACC 59.442 47.826 0.00 0.00 0.00 3.85
223 226 4.183865 CGTAGCATCAAGATTCAAGACCA 58.816 43.478 0.00 0.00 0.00 4.02
224 227 4.033358 CGTAGCATCAAGATTCAAGACCAC 59.967 45.833 0.00 0.00 0.00 4.16
225 228 4.298103 AGCATCAAGATTCAAGACCACT 57.702 40.909 0.00 0.00 0.00 4.00
274 277 6.434596 TGTTTCGTTGTCATGTGGAAAATAG 58.565 36.000 0.00 0.00 0.00 1.73
341 348 0.974383 TTCTTCTCGTCCACCTTCCC 59.026 55.000 0.00 0.00 0.00 3.97
392 399 0.320073 GACAACGAACATCCCACGGA 60.320 55.000 0.00 0.00 35.55 4.69
393 400 0.320421 ACAACGAACATCCCACGGAG 60.320 55.000 0.00 0.00 34.05 4.63
394 401 0.037697 CAACGAACATCCCACGGAGA 60.038 55.000 0.00 0.00 34.05 3.71
427 441 2.690778 AAAAGCGTGCGCATCCTCC 61.691 57.895 15.91 0.00 44.88 4.30
476 490 0.385974 GCACACGCTAAAAGCCACTG 60.386 55.000 0.00 0.00 38.18 3.66
514 528 1.442857 CTGTCAGTGACTCCGTCGC 60.443 63.158 23.29 0.00 42.60 5.19
558 572 2.372264 CACACCATCCCCAATCAGAAG 58.628 52.381 0.00 0.00 0.00 2.85
561 575 3.019564 CACCATCCCCAATCAGAAGTTC 58.980 50.000 0.00 0.00 0.00 3.01
562 576 2.922283 ACCATCCCCAATCAGAAGTTCT 59.078 45.455 0.00 0.00 0.00 3.01
597 612 0.096976 CGAAACGTGCCCAATGCTAG 59.903 55.000 0.00 0.00 42.00 3.42
605 620 0.107654 GCCCAATGCTAGTCGGTCTT 60.108 55.000 0.00 0.00 36.87 3.01
606 621 1.941325 CCCAATGCTAGTCGGTCTTC 58.059 55.000 0.00 0.00 0.00 2.87
610 625 0.456221 ATGCTAGTCGGTCTTCGTGG 59.544 55.000 0.00 0.00 40.32 4.94
644 659 0.919289 TTCCCCACTCCCATTCTCCC 60.919 60.000 0.00 0.00 0.00 4.30
667 682 2.806856 CTCTTGGACTCATGCGCGC 61.807 63.158 27.26 27.26 0.00 6.86
770 795 2.203422 CCCACCACGGCTTTTCCA 60.203 61.111 0.00 0.00 34.01 3.53
771 796 2.268076 CCCACCACGGCTTTTCCAG 61.268 63.158 0.00 0.00 34.01 3.86
812 837 4.323477 CTCGGCCGAACCCCAACA 62.323 66.667 30.53 2.79 33.26 3.33
871 896 2.963371 GAGTCGTTGCCGTCTCCT 59.037 61.111 0.00 0.00 41.44 3.69
872 897 1.153997 GAGTCGTTGCCGTCTCCTC 60.154 63.158 0.00 0.00 41.44 3.71
873 898 2.126031 GTCGTTGCCGTCTCCTCC 60.126 66.667 0.00 0.00 35.01 4.30
874 899 2.282958 TCGTTGCCGTCTCCTCCT 60.283 61.111 0.00 0.00 35.01 3.69
875 900 2.182030 CGTTGCCGTCTCCTCCTC 59.818 66.667 0.00 0.00 0.00 3.71
1094 1155 0.737715 TTGTTTGTTTGGCACCGCAC 60.738 50.000 0.00 0.00 0.00 5.34
1120 1188 0.853586 AATTGGGGTTCCTAGGGCCA 60.854 55.000 20.13 5.34 0.00 5.36
1152 1220 6.163476 TCGCTGTACTGTACTGATTTGATTT 58.837 36.000 23.64 0.00 0.00 2.17
1154 1222 6.546395 GCTGTACTGTACTGATTTGATTTGG 58.454 40.000 23.64 0.97 0.00 3.28
1155 1223 6.494893 TGTACTGTACTGATTTGATTTGGC 57.505 37.500 17.98 0.00 0.00 4.52
1156 1224 5.414454 TGTACTGTACTGATTTGATTTGGCC 59.586 40.000 17.98 0.00 0.00 5.36
1588 1656 2.422519 GCATCATGGTGAGGTTCCATCT 60.423 50.000 11.02 0.00 42.92 2.90
1590 1658 3.634397 TCATGGTGAGGTTCCATCTTC 57.366 47.619 0.00 0.00 42.92 2.87
1610 1678 1.884579 CACCTCTTTGCTGCAGATTGT 59.115 47.619 20.43 0.63 0.00 2.71
1703 1786 2.546778 TGGTACTAGCGCTATGTTTGC 58.453 47.619 19.19 6.33 0.00 3.68
1719 1802 7.659390 GCTATGTTTGCTCCAGTATCTAGAAAT 59.341 37.037 0.00 0.00 0.00 2.17
1720 1803 7.798596 ATGTTTGCTCCAGTATCTAGAAATG 57.201 36.000 0.00 0.00 0.00 2.32
1742 1825 4.035792 TGTGTGTGCAAAAGTGTATGTACC 59.964 41.667 0.00 0.00 32.06 3.34
1757 1840 8.467598 AGTGTATGTACCAGTATAGTTGTGAAG 58.532 37.037 0.00 0.00 0.00 3.02
1790 1874 3.685058 GCTTGGTATAGCTTCTTTTGCG 58.315 45.455 3.20 0.00 38.15 4.85
1853 1939 5.582269 ACACACATAGCATAGCACTAACTTG 59.418 40.000 0.00 0.00 0.00 3.16
1880 1968 4.098349 TGAGTCAGATATTTTGCATTGCCC 59.902 41.667 6.12 0.00 0.00 5.36
1888 1978 4.670896 ATTTTGCATTGCCCCATACTAC 57.329 40.909 6.12 0.00 0.00 2.73
1982 2072 3.937706 CTGTAGAGGTCTTTGCTGATTGG 59.062 47.826 0.00 0.00 0.00 3.16
1994 2084 7.225341 GTCTTTGCTGATTGGTTTCTTCATTTT 59.775 33.333 0.00 0.00 0.00 1.82
1995 2085 7.439056 TCTTTGCTGATTGGTTTCTTCATTTTC 59.561 33.333 0.00 0.00 0.00 2.29
1996 2086 6.409524 TGCTGATTGGTTTCTTCATTTTCT 57.590 33.333 0.00 0.00 0.00 2.52
2061 2151 2.843701 CTTCTGACCTCAGTGCAAGTT 58.156 47.619 2.25 0.00 44.12 2.66
2078 2168 8.850156 AGTGCAAGTTTGTTTATAAGAGATTGT 58.150 29.630 0.00 0.00 0.00 2.71
2097 2187 6.488006 AGATTGTGCTGTTACACTTCAAAGAT 59.512 34.615 0.00 0.00 41.30 2.40
2188 2279 6.263842 TGATTGGTGCTTGATCTGGATATTTC 59.736 38.462 0.00 0.00 0.00 2.17
2291 2391 3.053395 TCCTGGATAGCTTGCTTCCAATT 60.053 43.478 19.20 0.00 38.99 2.32
2296 2396 4.400567 GGATAGCTTGCTTCCAATTGAACT 59.599 41.667 7.12 0.00 0.00 3.01
2298 2398 6.264067 GGATAGCTTGCTTCCAATTGAACTAT 59.736 38.462 7.12 3.58 0.00 2.12
2396 2496 7.092444 TGGGGTAATCAGTACTTCATTTGATCT 60.092 37.037 0.00 0.00 32.80 2.75
2490 2712 9.520204 CCATTAGTTATGTAGGAAGCAATTTTG 57.480 33.333 0.00 0.00 31.99 2.44
2779 3002 3.620374 CACAGCTAGCAAGACGAAATGAT 59.380 43.478 18.83 0.00 0.00 2.45
2848 3071 5.368145 TGTGATGTTCTTAGAGCACTTGTT 58.632 37.500 0.00 0.00 0.00 2.83
3076 3302 4.624913 TGATCAATCAACTACTCCCTCCT 58.375 43.478 0.00 0.00 33.08 3.69
3111 3382 2.094649 GTCGCCTTTGTACTAGAGCTGT 60.095 50.000 0.00 0.00 0.00 4.40
3116 3387 4.799586 GCCTTTGTACTAGAGCTGTGACAA 60.800 45.833 0.00 0.00 0.00 3.18
3128 3399 7.093322 AGAGCTGTGACAATTAATTTGGATC 57.907 36.000 0.00 0.00 39.80 3.36
3141 3412 3.838244 TTTGGATCGGAGGGAGTATTG 57.162 47.619 0.00 0.00 0.00 1.90
3201 3472 5.294306 TGAATCAAATCAGCGATGTACTTCC 59.706 40.000 0.00 0.00 0.00 3.46
3206 3477 5.490139 AATCAGCGATGTACTTCCATTTG 57.510 39.130 0.00 0.00 0.00 2.32
3212 3483 5.295292 AGCGATGTACTTCCATTTGATCTTG 59.705 40.000 3.35 0.00 0.00 3.02
3294 3565 6.286758 TCCAAGCAAATGCATTAGAAACAAA 58.713 32.000 13.39 0.00 45.16 2.83
3296 3567 7.118101 TCCAAGCAAATGCATTAGAAACAAATC 59.882 33.333 13.39 0.00 45.16 2.17
3350 3623 7.801716 TGCGATGTAAATAATTTCTTAGGCT 57.198 32.000 0.00 0.00 0.00 4.58
3551 3824 9.309516 TCACTCGTCTATTACATGTTTTTATCC 57.690 33.333 2.30 0.00 0.00 2.59
3613 3887 5.235831 GTGGACTTACCGTTCTTAATATGGC 59.764 44.000 0.00 0.00 42.61 4.40
3631 3908 3.686016 TGGCCTCACTGTTTCCTATTTC 58.314 45.455 3.32 0.00 0.00 2.17
3988 4265 2.127251 GTTGCTGTGCTTTTTGCTACC 58.873 47.619 0.00 0.00 43.37 3.18
4030 4307 3.074412 CACTGTACCTGGTGGAAATGAC 58.926 50.000 10.23 0.00 37.04 3.06
4063 4340 0.798776 CGATTGTTGTCCAGACTGCC 59.201 55.000 0.00 0.00 0.00 4.85
4150 4427 4.447138 TCAAATAACAGTTGTCAGGGGT 57.553 40.909 0.00 0.00 0.00 4.95
4156 4433 1.283613 ACAGTTGTCAGGGGTGAAACA 59.716 47.619 0.00 0.00 39.98 2.83
4162 4439 1.954382 GTCAGGGGTGAAACAAAGTCC 59.046 52.381 0.00 0.00 39.98 3.85
4541 4818 6.823182 TGTACATGCTTAATCAAGTGTATGCT 59.177 34.615 0.00 0.00 30.41 3.79
4679 4956 8.006298 ACAATTCCTTTCTGTAATGACAAACA 57.994 30.769 0.00 0.00 34.35 2.83
4770 5047 4.094294 TGTTGTACAAGTCAGTTGCACTTC 59.906 41.667 8.98 0.00 40.15 3.01
4931 5208 5.790593 TCTACTTGTAACCTGTCATCAACC 58.209 41.667 0.00 0.00 0.00 3.77
4935 5212 1.463444 GTAACCTGTCATCAACCGCAC 59.537 52.381 0.00 0.00 0.00 5.34
5048 5325 0.873743 GCGACTGCAGGCTCTGATAC 60.874 60.000 19.55 0.00 42.15 2.24
5116 5393 8.844244 GCTGATTTTGTATGGACTTCTTATGAT 58.156 33.333 0.00 0.00 0.00 2.45
5189 5485 9.574516 AACTATTAAACCTTTCTCAATGTGACT 57.425 29.630 0.00 0.00 0.00 3.41
5190 5486 9.003658 ACTATTAAACCTTTCTCAATGTGACTG 57.996 33.333 0.00 0.00 0.00 3.51
5191 5487 4.574599 AAACCTTTCTCAATGTGACTGC 57.425 40.909 0.00 0.00 0.00 4.40
5192 5488 3.213206 ACCTTTCTCAATGTGACTGCA 57.787 42.857 0.00 0.00 0.00 4.41
5193 5489 3.144506 ACCTTTCTCAATGTGACTGCAG 58.855 45.455 13.48 13.48 0.00 4.41
5194 5490 2.486982 CCTTTCTCAATGTGACTGCAGG 59.513 50.000 19.93 0.00 0.00 4.85
5195 5491 3.405831 CTTTCTCAATGTGACTGCAGGA 58.594 45.455 19.93 0.29 0.00 3.86
5196 5492 2.756840 TCTCAATGTGACTGCAGGAG 57.243 50.000 19.93 12.67 0.00 3.69
5227 5523 4.511082 TCCGTTGGTTTTAGTTCCTTTACG 59.489 41.667 0.00 0.00 0.00 3.18
5229 5525 4.539870 GTTGGTTTTAGTTCCTTTACGGC 58.460 43.478 0.00 0.00 0.00 5.68
5267 5571 5.757886 TGCTGATTCTTTTGGACTTAAACG 58.242 37.500 0.00 0.00 0.00 3.60
5335 5765 7.215719 AGTAACAATTTAAACCTTCCTCAGC 57.784 36.000 0.00 0.00 0.00 4.26
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
8 9 1.213733 CGCTCGTCTGGCAGATGATG 61.214 60.000 33.15 26.61 39.34 3.07
9 10 1.067084 CGCTCGTCTGGCAGATGAT 59.933 57.895 33.15 0.00 39.34 2.45
10 11 2.491621 CGCTCGTCTGGCAGATGA 59.508 61.111 31.52 31.52 37.89 2.92
11 12 2.584418 CCGCTCGTCTGGCAGATG 60.584 66.667 27.16 27.16 32.57 2.90
17 18 1.080093 TACAAAGCCGCTCGTCTGG 60.080 57.895 0.00 0.00 0.00 3.86
18 19 0.666274 TGTACAAAGCCGCTCGTCTG 60.666 55.000 0.00 0.00 0.00 3.51
19 20 0.032952 TTGTACAAAGCCGCTCGTCT 59.967 50.000 5.64 0.00 0.00 4.18
20 21 0.163146 GTTGTACAAAGCCGCTCGTC 59.837 55.000 10.51 0.00 0.00 4.20
21 22 0.531090 TGTTGTACAAAGCCGCTCGT 60.531 50.000 10.51 0.00 0.00 4.18
22 23 0.584396 TTGTTGTACAAAGCCGCTCG 59.416 50.000 10.51 0.00 34.76 5.03
23 24 1.659211 CGTTGTTGTACAAAGCCGCTC 60.659 52.381 10.51 0.00 40.15 5.03
24 25 0.306533 CGTTGTTGTACAAAGCCGCT 59.693 50.000 10.51 0.00 40.15 5.52
25 26 0.305313 TCGTTGTTGTACAAAGCCGC 59.695 50.000 10.51 0.00 40.15 6.53
26 27 1.328069 TGTCGTTGTTGTACAAAGCCG 59.672 47.619 10.51 12.10 40.15 5.52
27 28 3.359654 CTTGTCGTTGTTGTACAAAGCC 58.640 45.455 10.51 0.00 40.15 4.35
28 29 3.181504 ACCTTGTCGTTGTTGTACAAAGC 60.182 43.478 10.51 0.00 40.15 3.51
29 30 4.339429 CACCTTGTCGTTGTTGTACAAAG 58.661 43.478 10.51 1.22 40.15 2.77
30 31 3.127203 CCACCTTGTCGTTGTTGTACAAA 59.873 43.478 10.51 0.00 40.15 2.83
31 32 2.678836 CCACCTTGTCGTTGTTGTACAA 59.321 45.455 3.59 3.59 35.42 2.41
32 33 2.281517 CCACCTTGTCGTTGTTGTACA 58.718 47.619 0.00 0.00 0.00 2.90
33 34 1.600485 CCCACCTTGTCGTTGTTGTAC 59.400 52.381 0.00 0.00 0.00 2.90
38 39 1.153046 CCACCCACCTTGTCGTTGT 60.153 57.895 0.00 0.00 0.00 3.32
103 105 6.738832 TGATTTTCTGCTCAGATGAGAAAG 57.261 37.500 13.98 9.74 44.74 2.62
173 175 1.028330 ACGAGCGTCGGATCACCTTA 61.028 55.000 11.13 0.00 45.59 2.69
180 183 0.732880 CTTGTGAACGAGCGTCGGAT 60.733 55.000 11.13 1.37 45.59 4.18
195 198 2.698855 ATCTTGATGCTACGGCTTGT 57.301 45.000 0.00 0.00 39.59 3.16
221 224 3.275999 CGTAATAAAAGGGACCCAGTGG 58.724 50.000 14.60 0.63 37.80 4.00
222 225 3.275999 CCGTAATAAAAGGGACCCAGTG 58.724 50.000 14.60 0.00 0.00 3.66
223 226 3.639672 CCGTAATAAAAGGGACCCAGT 57.360 47.619 14.60 0.00 0.00 4.00
241 244 0.099791 ACAACGAAACAAAGTGCCCG 59.900 50.000 0.00 0.00 0.00 6.13
274 277 1.002624 TGGCAGGTCCCGTCATTTC 60.003 57.895 0.00 0.00 0.00 2.17
341 348 3.494048 GCTGGTGACATGGAAGGAGATAG 60.494 52.174 0.00 0.00 41.51 2.08
427 441 3.357079 GGACTGTGGCACTTGCGG 61.357 66.667 19.83 0.00 43.26 5.69
476 490 2.745492 GGGCTGTGCTGCTCTGTC 60.745 66.667 0.00 2.72 0.00 3.51
514 528 0.035458 GATGGGCGAGGATTAGTGGG 59.965 60.000 0.00 0.00 0.00 4.61
558 572 7.097570 CGTTTCGTTTTTGTATTCTGTCAGAAC 60.098 37.037 17.49 7.53 37.00 3.01
561 575 6.138546 CACGTTTCGTTTTTGTATTCTGTCAG 59.861 38.462 0.00 0.00 38.32 3.51
562 576 5.960683 CACGTTTCGTTTTTGTATTCTGTCA 59.039 36.000 0.00 0.00 38.32 3.58
564 578 4.731480 GCACGTTTCGTTTTTGTATTCTGT 59.269 37.500 0.00 0.00 38.32 3.41
597 612 3.031660 GTCATCCACGAAGACCGAC 57.968 57.895 0.00 0.00 41.76 4.79
610 625 0.802607 GGGAAGACTCGTGCGTCATC 60.803 60.000 0.00 0.00 36.38 2.92
678 693 4.785453 GCTTCCCTCTGCGTGGGG 62.785 72.222 13.33 8.23 44.67 4.96
679 694 3.710722 AGCTTCCCTCTGCGTGGG 61.711 66.667 8.75 8.75 45.90 4.61
714 729 1.301401 GAAGCGGTGCAGTGGTACA 60.301 57.895 0.00 0.00 0.00 2.90
812 837 1.903183 CGGAGAGAGAGGGAGGTTTTT 59.097 52.381 0.00 0.00 0.00 1.94
870 895 2.760385 GTGGGGGAGGACGAGGAG 60.760 72.222 0.00 0.00 0.00 3.69
871 896 4.393778 GGTGGGGGAGGACGAGGA 62.394 72.222 0.00 0.00 0.00 3.71
1094 1155 2.112815 GGAACCCCAATTCCGCTCG 61.113 63.158 0.00 0.00 38.95 5.03
1152 1220 2.427245 CCCAAACACCAAACGGCCA 61.427 57.895 2.24 0.00 0.00 5.36
1154 1222 2.279851 GCCCAAACACCAAACGGC 60.280 61.111 0.00 0.00 0.00 5.68
1155 1223 2.026879 CGCCCAAACACCAAACGG 59.973 61.111 0.00 0.00 0.00 4.44
1156 1224 2.656973 GCGCCCAAACACCAAACG 60.657 61.111 0.00 0.00 0.00 3.60
1203 1271 1.375523 ACCGACATCGCCTTTCCAC 60.376 57.895 0.00 0.00 38.18 4.02
1204 1272 1.375396 CACCGACATCGCCTTTCCA 60.375 57.895 0.00 0.00 38.18 3.53
1205 1273 1.359459 GACACCGACATCGCCTTTCC 61.359 60.000 0.00 0.00 38.18 3.13
1206 1274 1.683790 CGACACCGACATCGCCTTTC 61.684 60.000 0.00 0.00 38.22 2.62
1207 1275 1.736645 CGACACCGACATCGCCTTT 60.737 57.895 0.00 0.00 38.22 3.11
1522 1590 0.248289 CGTCATACCCCGACCTGTTT 59.752 55.000 0.00 0.00 0.00 2.83
1610 1678 3.433031 CCGCAATTTACCAGAGGGATACA 60.433 47.826 0.00 0.00 38.05 2.29
1703 1786 5.521735 GCACACACATTTCTAGATACTGGAG 59.478 44.000 0.00 0.00 0.00 3.86
1719 1802 4.035792 GGTACATACACTTTTGCACACACA 59.964 41.667 0.00 0.00 0.00 3.72
1720 1803 4.035792 TGGTACATACACTTTTGCACACAC 59.964 41.667 0.00 0.00 0.00 3.82
1742 1825 6.530181 TCGTATTGCACTTCACAACTATACTG 59.470 38.462 0.00 0.00 0.00 2.74
1757 1840 4.318831 GCTATACCAAGCTTCGTATTGCAC 60.319 45.833 30.30 13.22 40.85 4.57
1790 1874 2.507407 TCCCCAAACAGCAGGTAATC 57.493 50.000 0.00 0.00 0.00 1.75
1853 1939 6.909357 GCAATGCAAAATATCTGACTCACTAC 59.091 38.462 0.00 0.00 0.00 2.73
1996 2086 9.793259 CACCTAATAGGCTAATATTCCTTTGAA 57.207 33.333 6.17 0.00 39.63 2.69
2061 2151 9.278978 TGTAACAGCACAATCTCTTATAAACAA 57.721 29.630 0.00 0.00 0.00 2.83
2078 2168 4.554526 CGCAATCTTTGAAGTGTAACAGCA 60.555 41.667 0.00 0.00 41.43 4.41
2097 2187 2.490115 CCAGTTTACCCAATTAGCGCAA 59.510 45.455 11.47 1.85 0.00 4.85
2161 2252 3.548770 TCCAGATCAAGCACCAATCATC 58.451 45.455 0.00 0.00 0.00 2.92
2206 2305 7.807977 ATCTACAATTATAGGTGTTTGCAGG 57.192 36.000 0.00 0.00 0.00 4.85
2244 2343 2.606308 GCAGAACACATCAAAGGCACAG 60.606 50.000 0.00 0.00 0.00 3.66
2291 2391 5.426689 AGAAAGTGATGGCTGATAGTTCA 57.573 39.130 0.00 0.00 0.00 3.18
2779 3002 2.875933 CAGTGCCGTTTGACCTTTCTTA 59.124 45.455 0.00 0.00 0.00 2.10
2878 3101 2.794350 GGCAGTGTTTCCATTTTTGTCG 59.206 45.455 0.00 0.00 0.00 4.35
2958 3181 8.521176 GGTATACGGTAATCATATAGGCTATGG 58.479 40.741 17.24 9.18 0.00 2.74
3076 3302 7.164230 ACAAAGGCGACAAATAATTTGGATA 57.836 32.000 0.00 0.00 44.81 2.59
3111 3382 4.887071 CCCTCCGATCCAAATTAATTGTCA 59.113 41.667 0.39 0.00 37.32 3.58
3116 3387 6.704056 ATACTCCCTCCGATCCAAATTAAT 57.296 37.500 0.00 0.00 0.00 1.40
3128 3399 5.793030 AGAGATAAACAATACTCCCTCCG 57.207 43.478 0.00 0.00 0.00 4.63
3294 3565 9.491675 CACAATCTTATCAGCTTAGAGAATGAT 57.508 33.333 7.73 0.00 36.42 2.45
3296 3567 8.659925 ACACAATCTTATCAGCTTAGAGAATG 57.340 34.615 0.00 0.00 0.00 2.67
3578 3851 6.549912 ACGGTAAGTCCACAATAAGTTTTC 57.450 37.500 0.00 0.00 35.57 2.29
3587 3861 6.819649 CCATATTAAGAACGGTAAGTCCACAA 59.180 38.462 0.00 0.00 35.57 3.33
3613 3887 3.691609 GCAGGAAATAGGAAACAGTGAGG 59.308 47.826 0.00 0.00 0.00 3.86
3631 3908 6.749118 GCAAAAGAACAATAACTATCTGCAGG 59.251 38.462 15.13 0.00 0.00 4.85
4030 4307 3.641648 AACAATCGCAACTCCATTGTTG 58.358 40.909 8.15 3.34 45.00 3.33
4150 4427 1.942677 TTCGCTCGGACTTTGTTTCA 58.057 45.000 0.00 0.00 0.00 2.69
4156 4433 1.226746 CAACCTTTCGCTCGGACTTT 58.773 50.000 0.00 0.00 0.00 2.66
4162 4439 0.512952 CCTCAACAACCTTTCGCTCG 59.487 55.000 0.00 0.00 0.00 5.03
4294 4571 5.222048 ACCAGTCATTGTAACACCACCTATT 60.222 40.000 0.00 0.00 0.00 1.73
4393 4670 0.390998 AGCTTGAGCCGCTTCTTCTC 60.391 55.000 0.00 0.00 43.38 2.87
4477 4754 2.054799 AGGCTGAGTTCAAACACCCTA 58.945 47.619 0.00 0.00 0.00 3.53
4541 4818 4.590918 TCAAACACCCTGTGTCTTACAAA 58.409 39.130 0.00 0.00 46.79 2.83
4679 4956 3.566351 GCCTCCCTTTTAGGTATGCATT 58.434 45.455 3.54 0.00 36.43 3.56
4708 4985 3.603532 TCTTCAACTGCATGAGCCTTAG 58.396 45.455 0.00 0.00 41.13 2.18
4931 5208 4.604843 AGTCATGAAATGTATGTGTGCG 57.395 40.909 0.00 0.00 46.80 5.34
4935 5212 9.708222 GCTTACTTAAGTCATGAAATGTATGTG 57.292 33.333 12.39 0.00 38.44 3.21
5048 5325 7.277539 TGCTTGATTGTGTAAAGGAACAAAAAG 59.722 33.333 0.00 0.00 39.57 2.27
5194 5490 2.743928 CCAACGGAGCCTGCACTC 60.744 66.667 0.00 0.00 35.86 3.51
5195 5491 2.624674 AAACCAACGGAGCCTGCACT 62.625 55.000 0.00 0.00 0.00 4.40
5196 5492 1.734388 AAAACCAACGGAGCCTGCAC 61.734 55.000 0.00 0.00 0.00 4.57
5335 5765 5.106555 ACAAGATCAACAAATTACCGCTCAG 60.107 40.000 0.00 0.00 0.00 3.35


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

AutoCloner maintained by Alex Coulton.