Multiple sequence alignment - TraesCS4B01G134800

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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 TraesCS4B01G134800 chr4B 100.000 2951 0 0 1 2951 175560154 175563104 0.000000e+00 5450.0
1 TraesCS4B01G134800 chr4A 93.773 1606 57 15 385 1968 462205676 462204092 0.000000e+00 2372.0
2 TraesCS4B01G134800 chr4A 94.995 959 36 3 1993 2951 462204034 462203088 0.000000e+00 1495.0
3 TraesCS4B01G134800 chr4A 90.805 870 28 13 1993 2858 611199676 611200497 0.000000e+00 1116.0
4 TraesCS4B01G134800 chr4A 93.275 342 19 2 1627 1968 611199281 611199618 4.390000e-138 501.0
5 TraesCS4B01G134800 chr4A 90.571 350 29 3 32 380 462206286 462205940 7.450000e-126 460.0
6 TraesCS4B01G134800 chr4A 91.026 78 7 0 1512 1589 27665579 27665656 4.020000e-19 106.0
7 TraesCS4B01G134800 chr4D 93.384 1451 49 20 555 1968 115120955 115122395 0.000000e+00 2104.0
8 TraesCS4B01G134800 chr4D 95.946 518 20 1 2435 2951 115123434 115123951 0.000000e+00 839.0
9 TraesCS4B01G134800 chr4D 88.941 642 39 16 2226 2858 447980075 447980693 0.000000e+00 763.0
10 TraesCS4B01G134800 chr4D 91.974 461 21 4 1993 2448 115122453 115122902 1.490000e-177 632.0
11 TraesCS4B01G134800 chr4D 95.614 342 15 0 1627 1968 447979498 447979839 1.550000e-152 549.0
12 TraesCS4B01G134800 chr4D 88.428 458 33 12 2 459 115068002 115068439 4.330000e-148 534.0
13 TraesCS4B01G134800 chr4D 91.060 302 7 4 1993 2294 447979897 447980178 9.920000e-105 390.0
14 TraesCS4B01G134800 chr3D 90.031 953 44 7 1993 2944 554392136 554393038 0.000000e+00 1186.0
15 TraesCS4B01G134800 chr3D 89.074 421 24 13 1559 1968 554391669 554392078 1.220000e-138 503.0
16 TraesCS4B01G134800 chr2B 91.475 868 26 11 1993 2858 654362431 654361610 0.000000e+00 1149.0
17 TraesCS4B01G134800 chr2B 95.906 342 14 0 1627 1968 654362830 654362489 3.320000e-154 555.0
18 TraesCS4B01G134800 chr2B 90.741 54 5 0 1366 1419 66199483 66199430 4.080000e-09 73.1
19 TraesCS4B01G134800 chr7B 90.679 869 29 16 1993 2858 686929505 686930324 0.000000e+00 1109.0
20 TraesCS4B01G134800 chr7B 92.152 446 22 2 1993 2438 109172202 109171770 4.180000e-173 617.0
21 TraesCS4B01G134800 chr7B 95.614 342 15 0 1627 1968 686929106 686929447 1.550000e-152 549.0
22 TraesCS4B01G134800 chr7B 91.975 324 18 6 2623 2944 109180132 109180449 5.800000e-122 448.0
23 TraesCS4B01G134800 chr7A 90.207 868 30 14 1993 2858 284784814 284785628 0.000000e+00 1081.0
24 TraesCS4B01G134800 chr5B 90.115 870 33 13 1993 2858 614981278 614980458 0.000000e+00 1081.0
25 TraesCS4B01G134800 chr5B 94.152 342 19 1 1627 1968 614981676 614981336 1.210000e-143 520.0
26 TraesCS4B01G134800 chr6D 87.903 868 26 16 1993 2858 163353177 163353967 0.000000e+00 948.0
27 TraesCS4B01G134800 chr6D 91.529 425 21 7 1559 1968 163352695 163353119 3.300000e-159 571.0
28 TraesCS4B01G134800 chr2A 91.500 600 24 14 2274 2871 711071160 711071734 0.000000e+00 800.0
29 TraesCS4B01G134800 chr2A 94.444 342 16 1 1627 1968 711070410 711070748 9.370000e-145 523.0
30 TraesCS4B01G134800 chr2A 90.106 283 7 5 1993 2275 711070806 711071067 6.050000e-92 348.0


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 TraesCS4B01G134800 chr4B 175560154 175563104 2950 False 5450.000000 5450 100.000000 1 2951 1 chr4B.!!$F1 2950
1 TraesCS4B01G134800 chr4A 462203088 462206286 3198 True 1442.333333 2372 93.113000 32 2951 3 chr4A.!!$R1 2919
2 TraesCS4B01G134800 chr4A 611199281 611200497 1216 False 808.500000 1116 92.040000 1627 2858 2 chr4A.!!$F2 1231
3 TraesCS4B01G134800 chr4D 115120955 115123951 2996 False 1191.666667 2104 93.768000 555 2951 3 chr4D.!!$F2 2396
4 TraesCS4B01G134800 chr4D 447979498 447980693 1195 False 567.333333 763 91.871667 1627 2858 3 chr4D.!!$F3 1231
5 TraesCS4B01G134800 chr3D 554391669 554393038 1369 False 844.500000 1186 89.552500 1559 2944 2 chr3D.!!$F1 1385
6 TraesCS4B01G134800 chr2B 654361610 654362830 1220 True 852.000000 1149 93.690500 1627 2858 2 chr2B.!!$R2 1231
7 TraesCS4B01G134800 chr7B 686929106 686930324 1218 False 829.000000 1109 93.146500 1627 2858 2 chr7B.!!$F2 1231
8 TraesCS4B01G134800 chr7A 284784814 284785628 814 False 1081.000000 1081 90.207000 1993 2858 1 chr7A.!!$F1 865
9 TraesCS4B01G134800 chr5B 614980458 614981676 1218 True 800.500000 1081 92.133500 1627 2858 2 chr5B.!!$R1 1231
10 TraesCS4B01G134800 chr6D 163352695 163353967 1272 False 759.500000 948 89.716000 1559 2858 2 chr6D.!!$F1 1299
11 TraesCS4B01G134800 chr2A 711070410 711071734 1324 False 557.000000 800 92.016667 1627 2871 3 chr2A.!!$F1 1244

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
207 208 0.030638 CGACAAGGGTGCCAACAAAG 59.969 55.000 0.00 0.00 0.00 2.77 F
446 706 0.108898 CCTGTTGCAGTCTCTCGAGG 60.109 60.000 13.56 3.44 0.00 4.63 F
759 1032 1.303074 TCGTCTACTCGGCCAGTGT 60.303 57.895 15.55 11.37 36.43 3.55 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1173 1464 0.179078 GATGCAGAGGAGAGCTGTGG 60.179 60.000 0.00 0.0 35.81 4.17 R
1334 1625 2.261671 CGGTGAGGTCCCAGAACG 59.738 66.667 0.00 0.0 0.00 3.95 R
2051 2410 2.600420 CACTACACACTCACATCGATGC 59.400 50.000 25.11 0.0 0.00 3.91 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
27 28 4.537260 CCCTGATGGCCCAAACAA 57.463 55.556 0.00 0.00 0.00 2.83
28 29 2.995480 CCCTGATGGCCCAAACAAT 58.005 52.632 0.00 0.00 0.00 2.71
29 30 1.278537 CCCTGATGGCCCAAACAATT 58.721 50.000 0.00 0.00 0.00 2.32
30 31 1.065998 CCCTGATGGCCCAAACAATTG 60.066 52.381 3.24 3.24 36.25 2.32
46 47 8.334632 CCAAACAATTGACTTACACCAAATTTC 58.665 33.333 13.59 0.00 38.94 2.17
51 52 9.919348 CAATTGACTTACACCAAATTTCTTTTG 57.081 29.630 0.00 0.00 43.64 2.44
55 56 8.188139 TGACTTACACCAAATTTCTTTTGAGAC 58.812 33.333 0.00 0.00 46.36 3.36
66 67 8.782533 AATTTCTTTTGAGACGACATACAAAC 57.217 30.769 0.00 0.00 33.09 2.93
74 75 1.871039 ACGACATACAAACTGCCACAC 59.129 47.619 0.00 0.00 0.00 3.82
79 80 1.975660 TACAAACTGCCACACCCTTC 58.024 50.000 0.00 0.00 0.00 3.46
83 84 1.692411 AACTGCCACACCCTTCTTTC 58.308 50.000 0.00 0.00 0.00 2.62
85 86 0.895559 CTGCCACACCCTTCTTTCCC 60.896 60.000 0.00 0.00 0.00 3.97
87 88 2.081585 GCCACACCCTTCTTTCCCCT 62.082 60.000 0.00 0.00 0.00 4.79
88 89 0.251341 CCACACCCTTCTTTCCCCTG 60.251 60.000 0.00 0.00 0.00 4.45
104 105 2.224769 CCCCTGGAACTAGAACAAAGCA 60.225 50.000 0.00 0.00 0.00 3.91
105 106 3.562176 CCCCTGGAACTAGAACAAAGCAT 60.562 47.826 0.00 0.00 0.00 3.79
118 119 5.893255 AGAACAAAGCATATGCCAGGATTTA 59.107 36.000 23.96 0.00 43.38 1.40
127 128 7.039923 AGCATATGCCAGGATTTAGAATTTGAG 60.040 37.037 23.96 0.00 43.38 3.02
129 130 6.705863 ATGCCAGGATTTAGAATTTGAGAC 57.294 37.500 0.00 0.00 0.00 3.36
142 143 7.251321 AGAATTTGAGACTAGTTGTGATCCT 57.749 36.000 0.00 0.00 0.00 3.24
156 157 3.448686 GTGATCCTCACGGACTATTGTG 58.551 50.000 0.00 0.00 43.51 3.33
162 163 3.306780 CCTCACGGACTATTGTGTTTCCT 60.307 47.826 0.00 0.00 37.38 3.36
163 164 4.315803 CTCACGGACTATTGTGTTTCCTT 58.684 43.478 0.00 0.00 37.38 3.36
188 189 3.056250 TGATCTTGTGAAGTGGAGAGCTC 60.056 47.826 5.27 5.27 0.00 4.09
196 197 1.216710 GTGGAGAGCTCGACAAGGG 59.783 63.158 13.75 0.00 38.07 3.95
207 208 0.030638 CGACAAGGGTGCCAACAAAG 59.969 55.000 0.00 0.00 0.00 2.77
222 223 4.558470 CCAACAAAGTAGCATTATGTTGCG 59.442 41.667 10.55 2.50 45.80 4.85
325 326 0.909610 AAACGCTCCCTCCCTGATCA 60.910 55.000 0.00 0.00 0.00 2.92
347 348 9.171877 GATCAAGAATCACCTTCAAAGAGTAAT 57.828 33.333 0.00 0.00 36.24 1.89
349 350 6.749923 AGAATCACCTTCAAAGAGTAATGC 57.250 37.500 0.00 0.00 36.24 3.56
357 358 7.714377 CACCTTCAAAGAGTAATGCTAGATGAT 59.286 37.037 0.00 0.00 0.00 2.45
380 381 1.783711 GATGAGAATAGCACGCACTCG 59.216 52.381 0.00 0.00 42.43 4.18
381 382 0.808755 TGAGAATAGCACGCACTCGA 59.191 50.000 0.00 0.00 39.41 4.04
382 383 1.192793 GAGAATAGCACGCACTCGAC 58.807 55.000 0.00 0.00 39.41 4.20
383 384 0.526211 AGAATAGCACGCACTCGACA 59.474 50.000 0.00 0.00 39.41 4.35
398 658 1.599518 GACACCGTTGGCACCATCA 60.600 57.895 0.00 0.00 0.00 3.07
401 661 0.959867 CACCGTTGGCACCATCATGA 60.960 55.000 0.00 0.00 0.00 3.07
415 675 3.305676 CCATCATGATCGTAGGACTCACC 60.306 52.174 4.86 0.00 39.35 4.02
446 706 0.108898 CCTGTTGCAGTCTCTCGAGG 60.109 60.000 13.56 3.44 0.00 4.63
447 707 0.108898 CTGTTGCAGTCTCTCGAGGG 60.109 60.000 13.56 9.92 0.00 4.30
459 719 2.509336 CGAGGGCCAACGTGCTAG 60.509 66.667 6.18 0.00 0.00 3.42
502 762 2.901839 TGGACCAAGTTCCACCTACTAC 59.098 50.000 0.00 0.00 41.00 2.73
503 763 3.171528 GGACCAAGTTCCACCTACTACT 58.828 50.000 0.00 0.00 35.49 2.57
504 764 4.202706 TGGACCAAGTTCCACCTACTACTA 60.203 45.833 0.00 0.00 41.00 1.82
505 765 4.401837 GGACCAAGTTCCACCTACTACTAG 59.598 50.000 0.00 0.00 35.49 2.57
506 766 5.008165 ACCAAGTTCCACCTACTACTAGT 57.992 43.478 0.00 0.00 0.00 2.57
507 767 5.015515 ACCAAGTTCCACCTACTACTAGTC 58.984 45.833 0.00 0.00 0.00 2.59
547 807 6.459710 CCCAACTTTAAGAACAAAGTCAGGTC 60.460 42.308 0.00 0.00 45.68 3.85
548 808 6.094881 CCAACTTTAAGAACAAAGTCAGGTCA 59.905 38.462 0.00 0.00 45.68 4.02
549 809 6.927294 ACTTTAAGAACAAAGTCAGGTCAG 57.073 37.500 0.00 0.00 43.59 3.51
550 810 5.823045 ACTTTAAGAACAAAGTCAGGTCAGG 59.177 40.000 0.00 0.00 43.59 3.86
551 811 3.933861 AAGAACAAAGTCAGGTCAGGT 57.066 42.857 0.00 0.00 0.00 4.00
552 812 3.477210 AGAACAAAGTCAGGTCAGGTC 57.523 47.619 0.00 0.00 0.00 3.85
599 862 7.822822 TCTTTTCTTCTCCTTTTCTATTACCGG 59.177 37.037 0.00 0.00 0.00 5.28
613 882 2.483014 TACCGGGAGTTTTGACCATG 57.517 50.000 6.32 0.00 0.00 3.66
759 1032 1.303074 TCGTCTACTCGGCCAGTGT 60.303 57.895 15.55 11.37 36.43 3.55
994 1285 3.441922 TCTTCTTGACACCTCAGATCTCG 59.558 47.826 0.00 0.00 0.00 4.04
1186 1477 4.154347 CCGGCCACAGCTCTCCTC 62.154 72.222 2.24 0.00 39.73 3.71
1187 1478 3.073735 CGGCCACAGCTCTCCTCT 61.074 66.667 2.24 0.00 39.73 3.69
1620 1911 1.945394 GATCACGAGGTAAGCGTAGGA 59.055 52.381 0.00 0.00 40.44 2.94
1869 2175 0.989212 TAGAGGAGGAGGAGGTCGCT 60.989 60.000 0.00 0.00 0.00 4.93
1968 2277 7.164122 CCCATTGATCATACATGTAGCTACTT 58.836 38.462 23.84 15.44 0.00 2.24
1969 2278 7.332926 CCCATTGATCATACATGTAGCTACTTC 59.667 40.741 23.84 5.60 0.00 3.01
1970 2279 7.332926 CCATTGATCATACATGTAGCTACTTCC 59.667 40.741 23.84 0.00 0.00 3.46
1971 2280 6.013842 TGATCATACATGTAGCTACTTCCG 57.986 41.667 23.84 12.01 0.00 4.30
1972 2281 5.535030 TGATCATACATGTAGCTACTTCCGT 59.465 40.000 23.84 16.48 0.00 4.69
1973 2282 6.713450 TGATCATACATGTAGCTACTTCCGTA 59.287 38.462 23.84 17.85 0.00 4.02
1974 2283 6.555812 TCATACATGTAGCTACTTCCGTAG 57.444 41.667 23.84 8.61 44.77 3.51
1975 2284 6.060136 TCATACATGTAGCTACTTCCGTAGT 58.940 40.000 23.84 13.42 44.02 2.73
1976 2285 6.544931 TCATACATGTAGCTACTTCCGTAGTT 59.455 38.462 23.84 4.69 44.02 2.24
2009 2360 2.167487 AGAAGAAGTCGAAGGGATCAGC 59.833 50.000 0.00 0.00 0.00 4.26
2051 2410 8.611654 TGATCATGAACATAACAGGTGATATG 57.388 34.615 0.00 5.87 36.99 1.78
2055 2414 6.866010 TGAACATAACAGGTGATATGCATC 57.134 37.500 0.19 0.00 35.12 3.91
2157 2531 5.163703 TGTGTGCAAGTACAGTTAACAAAGG 60.164 40.000 8.61 0.00 0.00 3.11
2165 2539 5.883673 AGTACAGTTAACAAAGGACAGCAAA 59.116 36.000 8.61 0.00 0.00 3.68
2166 2540 5.652994 ACAGTTAACAAAGGACAGCAAAA 57.347 34.783 8.61 0.00 0.00 2.44
2167 2541 6.031751 ACAGTTAACAAAGGACAGCAAAAA 57.968 33.333 8.61 0.00 0.00 1.94
2235 2614 9.774742 GTTGAATGGTGAAATCATACTTTAGAC 57.225 33.333 0.00 0.00 0.00 2.59
2257 2636 4.823989 ACCCTTCTGTGTTGAAAGATGAAG 59.176 41.667 0.00 0.00 0.00 3.02
2294 2767 5.248248 TCCTTCTGTGTTGAATGATGAGGTA 59.752 40.000 0.00 0.00 0.00 3.08
2310 2784 3.469771 TGAGGTAGTGTAGATATGGGGGT 59.530 47.826 0.00 0.00 0.00 4.95
2805 3829 4.637276 TGTAACATATAACGGCCATCCTG 58.363 43.478 2.24 0.00 0.00 3.86
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
10 11 1.065998 CAATTGTTTGGGCCATCAGGG 60.066 52.381 7.26 0.33 40.85 4.45
11 12 1.901159 TCAATTGTTTGGGCCATCAGG 59.099 47.619 7.26 4.46 33.44 3.86
12 13 2.564062 AGTCAATTGTTTGGGCCATCAG 59.436 45.455 7.26 0.00 33.44 2.90
13 14 2.607499 AGTCAATTGTTTGGGCCATCA 58.393 42.857 7.26 7.51 33.44 3.07
14 15 3.683365 AAGTCAATTGTTTGGGCCATC 57.317 42.857 7.26 4.48 33.44 3.51
15 16 3.900601 TGTAAGTCAATTGTTTGGGCCAT 59.099 39.130 7.26 0.00 33.44 4.40
16 17 3.068873 GTGTAAGTCAATTGTTTGGGCCA 59.931 43.478 0.00 0.00 33.44 5.36
17 18 3.554129 GGTGTAAGTCAATTGTTTGGGCC 60.554 47.826 5.13 0.00 33.44 5.80
18 19 3.068873 TGGTGTAAGTCAATTGTTTGGGC 59.931 43.478 5.13 0.00 33.44 5.36
19 20 4.927978 TGGTGTAAGTCAATTGTTTGGG 57.072 40.909 5.13 0.00 33.44 4.12
20 21 7.784633 AATTTGGTGTAAGTCAATTGTTTGG 57.215 32.000 5.13 0.00 33.44 3.28
21 22 9.097257 AGAAATTTGGTGTAAGTCAATTGTTTG 57.903 29.630 5.13 0.00 0.00 2.93
22 23 9.665719 AAGAAATTTGGTGTAAGTCAATTGTTT 57.334 25.926 5.13 4.46 0.00 2.83
23 24 9.665719 AAAGAAATTTGGTGTAAGTCAATTGTT 57.334 25.926 5.13 0.00 0.00 2.83
24 25 9.665719 AAAAGAAATTTGGTGTAAGTCAATTGT 57.334 25.926 5.13 0.00 0.00 2.71
25 26 9.919348 CAAAAGAAATTTGGTGTAAGTCAATTG 57.081 29.630 0.00 0.00 43.85 2.32
26 27 9.883142 TCAAAAGAAATTTGGTGTAAGTCAATT 57.117 25.926 0.00 0.00 46.85 2.32
27 28 9.533253 CTCAAAAGAAATTTGGTGTAAGTCAAT 57.467 29.630 0.00 0.00 46.85 2.57
28 29 8.744652 TCTCAAAAGAAATTTGGTGTAAGTCAA 58.255 29.630 0.00 0.00 46.85 3.18
29 30 8.188139 GTCTCAAAAGAAATTTGGTGTAAGTCA 58.812 33.333 0.00 0.00 46.85 3.41
30 31 7.376072 CGTCTCAAAAGAAATTTGGTGTAAGTC 59.624 37.037 0.00 0.00 46.85 3.01
46 47 5.140177 GCAGTTTGTATGTCGTCTCAAAAG 58.860 41.667 0.00 0.00 32.81 2.27
51 52 2.412089 GTGGCAGTTTGTATGTCGTCTC 59.588 50.000 0.00 0.00 0.00 3.36
55 56 1.196808 GGTGTGGCAGTTTGTATGTCG 59.803 52.381 0.00 0.00 0.00 4.35
66 67 0.895559 GGGAAAGAAGGGTGTGGCAG 60.896 60.000 0.00 0.00 0.00 4.85
74 75 1.076438 AGTTCCAGGGGAAAGAAGGG 58.924 55.000 0.00 0.00 43.86 3.95
79 80 4.367039 TTGTTCTAGTTCCAGGGGAAAG 57.633 45.455 0.00 0.00 43.86 2.62
83 84 2.224769 TGCTTTGTTCTAGTTCCAGGGG 60.225 50.000 0.00 0.00 0.00 4.79
85 86 5.220931 GCATATGCTTTGTTCTAGTTCCAGG 60.221 44.000 20.64 0.00 38.21 4.45
87 88 4.640201 GGCATATGCTTTGTTCTAGTTCCA 59.360 41.667 26.12 0.00 41.70 3.53
88 89 4.640201 TGGCATATGCTTTGTTCTAGTTCC 59.360 41.667 26.12 5.84 41.70 3.62
104 105 8.223330 AGTCTCAAATTCTAAATCCTGGCATAT 58.777 33.333 0.00 0.00 0.00 1.78
105 106 7.577303 AGTCTCAAATTCTAAATCCTGGCATA 58.423 34.615 0.00 0.00 0.00 3.14
118 119 7.038729 TGAGGATCACAACTAGTCTCAAATTCT 60.039 37.037 0.00 0.00 42.56 2.40
142 143 4.062293 CAAGGAAACACAATAGTCCGTGA 58.938 43.478 0.00 0.00 40.73 4.35
145 146 3.188460 CACCAAGGAAACACAATAGTCCG 59.812 47.826 0.00 0.00 35.19 4.79
147 148 5.940470 AGATCACCAAGGAAACACAATAGTC 59.060 40.000 0.00 0.00 0.00 2.59
153 154 3.631686 CACAAGATCACCAAGGAAACACA 59.368 43.478 0.00 0.00 0.00 3.72
156 157 4.580580 ACTTCACAAGATCACCAAGGAAAC 59.419 41.667 0.00 0.00 0.00 2.78
162 163 3.390967 TCTCCACTTCACAAGATCACCAA 59.609 43.478 0.00 0.00 0.00 3.67
163 164 2.972021 TCTCCACTTCACAAGATCACCA 59.028 45.455 0.00 0.00 0.00 4.17
188 189 0.030638 CTTTGTTGGCACCCTTGTCG 59.969 55.000 0.00 0.00 0.00 4.35
196 197 5.059404 ACATAATGCTACTTTGTTGGCAC 57.941 39.130 0.00 0.00 37.52 5.01
207 208 4.616181 AAGGTTCGCAACATAATGCTAC 57.384 40.909 0.00 0.00 44.21 3.58
222 223 5.124617 CCTTTTGAGGAGCTCATAAAGGTTC 59.875 44.000 24.85 4.66 43.52 3.62
251 252 0.383949 TTTCTTGCGAGTTTGTGGGC 59.616 50.000 0.00 0.00 0.00 5.36
274 275 4.409718 TTTTTGCCCCTTTTAGGTTGTC 57.590 40.909 0.00 0.00 31.93 3.18
278 279 4.904853 TGAAGATTTTTGCCCCTTTTAGGT 59.095 37.500 0.00 0.00 31.93 3.08
325 326 6.944862 AGCATTACTCTTTGAAGGTGATTCTT 59.055 34.615 0.00 0.00 38.83 2.52
347 348 5.163571 GCTATTCTCATCCGATCATCTAGCA 60.164 44.000 0.00 0.00 0.00 3.49
349 350 6.264832 GTGCTATTCTCATCCGATCATCTAG 58.735 44.000 0.00 0.00 0.00 2.43
357 358 0.744281 TGCGTGCTATTCTCATCCGA 59.256 50.000 0.00 0.00 0.00 4.55
380 381 0.960364 ATGATGGTGCCAACGGTGTC 60.960 55.000 0.00 0.00 0.00 3.67
381 382 1.074775 ATGATGGTGCCAACGGTGT 59.925 52.632 0.00 0.00 0.00 4.16
382 383 0.959867 TCATGATGGTGCCAACGGTG 60.960 55.000 0.00 0.00 0.00 4.94
383 384 0.034186 ATCATGATGGTGCCAACGGT 60.034 50.000 7.59 0.00 0.00 4.83
398 658 1.319541 CCGGTGAGTCCTACGATCAT 58.680 55.000 0.00 0.00 0.00 2.45
401 661 0.968901 TTGCCGGTGAGTCCTACGAT 60.969 55.000 1.90 0.00 0.00 3.73
432 692 3.071206 GGCCCTCGAGAGACTGCA 61.071 66.667 15.71 0.00 34.24 4.41
433 693 2.650116 TTGGCCCTCGAGAGACTGC 61.650 63.158 15.71 8.06 35.39 4.40
436 696 2.182030 CGTTGGCCCTCGAGAGAC 59.818 66.667 15.71 2.30 35.39 3.36
446 706 0.245539 TCACTACTAGCACGTTGGCC 59.754 55.000 0.00 0.00 0.00 5.36
447 707 1.993370 CTTCACTACTAGCACGTTGGC 59.007 52.381 0.00 0.00 0.00 4.52
459 719 3.826729 ACTTGGGATTTTGCCTTCACTAC 59.173 43.478 0.00 0.00 0.00 2.73
502 762 1.519719 GAGCACCCCAGCTGACTAG 59.480 63.158 17.39 3.45 46.75 2.57
503 763 2.351244 CGAGCACCCCAGCTGACTA 61.351 63.158 17.39 0.00 46.75 2.59
504 764 3.699894 CGAGCACCCCAGCTGACT 61.700 66.667 17.39 4.01 46.75 3.41
541 801 1.550524 CGAGGAAATGACCTGACCTGA 59.449 52.381 0.00 0.00 40.73 3.86
547 807 0.745845 CTGCCCGAGGAAATGACCTG 60.746 60.000 0.00 0.00 40.73 4.00
548 808 1.201429 ACTGCCCGAGGAAATGACCT 61.201 55.000 0.00 0.00 43.64 3.85
549 809 0.744771 GACTGCCCGAGGAAATGACC 60.745 60.000 0.00 0.00 0.00 4.02
550 810 0.250513 AGACTGCCCGAGGAAATGAC 59.749 55.000 0.00 0.00 0.00 3.06
551 811 1.480954 GTAGACTGCCCGAGGAAATGA 59.519 52.381 0.00 0.00 0.00 2.57
552 812 1.482593 AGTAGACTGCCCGAGGAAATG 59.517 52.381 0.00 0.00 0.00 2.32
599 862 4.280677 TGACATTTCCATGGTCAAAACTCC 59.719 41.667 12.58 0.00 34.27 3.85
660 932 1.074775 ATTTTCTGCCCGTGCTCCA 59.925 52.632 0.00 0.00 38.71 3.86
670 942 0.383231 CCATCCGAGCCATTTTCTGC 59.617 55.000 0.00 0.00 0.00 4.26
711 983 4.216257 GTGCCAAGTCATCTGAAAAGCTAA 59.784 41.667 0.00 0.00 0.00 3.09
946 1234 3.256960 GGAGGAGGTGGTGGCCAA 61.257 66.667 7.24 0.00 34.18 4.52
994 1285 0.727398 GAGGCGCTGACCATTGTAAC 59.273 55.000 7.64 0.00 0.00 2.50
1173 1464 0.179078 GATGCAGAGGAGAGCTGTGG 60.179 60.000 0.00 0.00 35.81 4.17
1176 1467 0.531090 GCAGATGCAGAGGAGAGCTG 60.531 60.000 0.00 0.00 41.59 4.24
1182 1473 3.079478 AGCCGCAGATGCAGAGGA 61.079 61.111 5.55 0.00 42.21 3.71
1185 1476 2.125391 GTGAGCCGCAGATGCAGA 60.125 61.111 5.55 0.00 42.21 4.26
1186 1477 3.200593 GGTGAGCCGCAGATGCAG 61.201 66.667 5.55 0.00 42.21 4.41
1187 1478 3.709633 AGGTGAGCCGCAGATGCA 61.710 61.111 5.55 0.00 42.21 3.96
1334 1625 2.261671 CGGTGAGGTCCCAGAACG 59.738 66.667 0.00 0.00 0.00 3.95
1491 1782 4.103103 GTCAAAGCCGCCGCCTTC 62.103 66.667 0.00 0.00 34.57 3.46
1752 2058 2.986290 CCGTGCAGGTCCCACATA 59.014 61.111 5.57 0.00 32.85 2.29
1968 2277 5.414789 TCTCATTTGAATGGAACTACGGA 57.585 39.130 4.05 0.00 37.03 4.69
1969 2278 5.874810 TCTTCTCATTTGAATGGAACTACGG 59.125 40.000 4.05 0.00 37.03 4.02
1970 2279 6.968131 TCTTCTCATTTGAATGGAACTACG 57.032 37.500 4.05 0.00 37.03 3.51
1971 2280 8.329203 ACTTCTTCTCATTTGAATGGAACTAC 57.671 34.615 4.05 0.00 37.03 2.73
1972 2281 7.331934 CGACTTCTTCTCATTTGAATGGAACTA 59.668 37.037 4.05 0.00 37.03 2.24
1973 2282 6.148480 CGACTTCTTCTCATTTGAATGGAACT 59.852 38.462 4.05 0.00 37.03 3.01
1974 2283 6.147821 TCGACTTCTTCTCATTTGAATGGAAC 59.852 38.462 4.05 0.00 37.03 3.62
1975 2284 6.230472 TCGACTTCTTCTCATTTGAATGGAA 58.770 36.000 4.05 5.90 37.03 3.53
1976 2285 5.793817 TCGACTTCTTCTCATTTGAATGGA 58.206 37.500 4.05 0.00 37.03 3.41
2009 2360 7.085746 TCATGATCATGTTGCTTGTAAACTTG 58.914 34.615 30.01 5.26 39.72 3.16
2051 2410 2.600420 CACTACACACTCACATCGATGC 59.400 50.000 25.11 0.00 0.00 3.91
2055 2414 3.759418 CCTACACTACACACTCACATCG 58.241 50.000 0.00 0.00 0.00 3.84
2235 2614 4.823989 ACTTCATCTTTCAACACAGAAGGG 59.176 41.667 0.00 0.00 36.29 3.95
2257 2636 5.552178 ACACAGAAGGATCCAAAGTAAGAC 58.448 41.667 15.82 0.00 0.00 3.01
2294 2767 5.727630 ACTATTGACCCCCATATCTACACT 58.272 41.667 0.00 0.00 0.00 3.55
2555 3579 5.163652 TGTCTAGTGAAGTATCATGTGTCCG 60.164 44.000 0.00 0.00 38.01 4.79
2567 3591 4.616143 CGCACAGTGTATGTCTAGTGAAGT 60.616 45.833 1.61 0.00 41.41 3.01
2805 3829 4.619973 TCAGAAACATTTTCATGTGTGCC 58.380 39.130 1.72 0.00 43.34 5.01


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

AutoCloner maintained by Alex Coulton.