Multiple sequence alignment - TraesCS3B01G333600

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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 TraesCS3B01G333600 chr3B 100.000 5546 0 0 1 5546 540200229 540205774 0.000000e+00 10242.0
1 TraesCS3B01G333600 chr3B 100.000 1641 0 0 5786 7426 540206014 540207654 0.000000e+00 3031.0
2 TraesCS3B01G333600 chr3B 100.000 28 0 0 5828 5855 136479630 136479657 1.300000e-02 52.8
3 TraesCS3B01G333600 chr3D 97.570 2922 34 15 2611 5526 414368788 414371678 0.000000e+00 4968.0
4 TraesCS3B01G333600 chr3D 95.697 2115 55 11 512 2613 414366616 414368707 0.000000e+00 3369.0
5 TraesCS3B01G333600 chr3D 94.329 1587 52 21 5787 7356 414372028 414373593 0.000000e+00 2398.0
6 TraesCS3B01G333600 chr3A 93.096 1941 96 17 3136 5070 536637916 536636008 0.000000e+00 2808.0
7 TraesCS3B01G333600 chr3A 89.310 1637 100 23 1495 3114 536639483 536637905 0.000000e+00 1984.0
8 TraesCS3B01G333600 chr3A 90.999 1111 75 14 6112 7213 536635229 536634135 0.000000e+00 1474.0
9 TraesCS3B01G333600 chr3A 93.092 941 50 12 512 1445 536640414 536639482 0.000000e+00 1363.0
10 TraesCS3B01G333600 chr3A 89.251 521 42 10 1 512 442288818 442289333 2.260000e-179 640.0
11 TraesCS3B01G333600 chr3A 92.517 441 31 2 5107 5546 536636005 536635566 1.360000e-176 630.0
12 TraesCS3B01G333600 chr3A 93.846 195 8 4 1410 1601 419540288 419540095 2.620000e-74 291.0
13 TraesCS3B01G333600 chr3A 93.367 196 10 3 1401 1594 642038743 642038937 3.390000e-73 287.0
14 TraesCS3B01G333600 chr3A 87.719 228 11 10 7215 7426 536634056 536633830 4.450000e-62 250.0
15 TraesCS3B01G333600 chr3A 91.818 110 7 2 5859 5967 536635544 536635436 1.290000e-32 152.0
16 TraesCS3B01G333600 chr3A 90.000 70 7 0 5786 5855 102680760 102680829 2.850000e-14 91.6
17 TraesCS3B01G333600 chr5B 92.577 485 30 5 1 482 536922643 536922162 0.000000e+00 691.0
18 TraesCS3B01G333600 chr5B 91.051 514 43 3 1 513 669163630 669164141 0.000000e+00 691.0
19 TraesCS3B01G333600 chr5B 93.782 193 10 2 1404 1595 631795000 631794809 9.430000e-74 289.0
20 TraesCS3B01G333600 chr7B 90.541 518 43 5 1 515 670032277 670032791 0.000000e+00 680.0
21 TraesCS3B01G333600 chr7B 89.942 517 45 5 1 515 670049394 670049905 0.000000e+00 660.0
22 TraesCS3B01G333600 chr7B 89.749 517 49 3 1 515 79072983 79072469 0.000000e+00 658.0
23 TraesCS3B01G333600 chr6B 90.385 520 36 11 1 516 55438743 55438234 0.000000e+00 671.0
24 TraesCS3B01G333600 chr4A 87.356 522 60 6 1 520 648317066 648317583 1.780000e-165 593.0
25 TraesCS3B01G333600 chr7A 87.597 516 46 14 1 513 306350979 306351479 3.860000e-162 582.0
26 TraesCS3B01G333600 chr5A 95.187 187 7 2 1409 1594 13889429 13889614 2.030000e-75 294.0
27 TraesCS3B01G333600 chr4B 94.271 192 7 4 1409 1597 295687857 295687667 2.620000e-74 291.0
28 TraesCS3B01G333600 chr4B 93.401 197 8 4 1407 1599 455621635 455621440 3.390000e-73 287.0
29 TraesCS3B01G333600 chr6A 94.211 190 9 2 1406 1594 101870131 101869943 9.430000e-74 289.0
30 TraesCS3B01G333600 chr2A 93.814 194 9 3 1403 1595 286445860 286446051 9.430000e-74 289.0
31 TraesCS3B01G333600 chr1D 97.297 37 0 1 5822 5858 433281517 433281482 2.240000e-05 62.1
32 TraesCS3B01G333600 chr1B 100.000 31 0 0 5828 5858 585312951 585312921 2.890000e-04 58.4


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 TraesCS3B01G333600 chr3B 540200229 540207654 7425 False 6636.500000 10242 100.000000 1 7426 2 chr3B.!!$F2 7425
1 TraesCS3B01G333600 chr3D 414366616 414373593 6977 False 3578.333333 4968 95.865333 512 7356 3 chr3D.!!$F1 6844
2 TraesCS3B01G333600 chr3A 536633830 536640414 6584 True 1237.285714 2808 91.221571 512 7426 7 chr3A.!!$R2 6914
3 TraesCS3B01G333600 chr3A 442288818 442289333 515 False 640.000000 640 89.251000 1 512 1 chr3A.!!$F2 511
4 TraesCS3B01G333600 chr5B 669163630 669164141 511 False 691.000000 691 91.051000 1 513 1 chr5B.!!$F1 512
5 TraesCS3B01G333600 chr7B 670032277 670032791 514 False 680.000000 680 90.541000 1 515 1 chr7B.!!$F1 514
6 TraesCS3B01G333600 chr7B 670049394 670049905 511 False 660.000000 660 89.942000 1 515 1 chr7B.!!$F2 514
7 TraesCS3B01G333600 chr7B 79072469 79072983 514 True 658.000000 658 89.749000 1 515 1 chr7B.!!$R1 514
8 TraesCS3B01G333600 chr6B 55438234 55438743 509 True 671.000000 671 90.385000 1 516 1 chr6B.!!$R1 515
9 TraesCS3B01G333600 chr4A 648317066 648317583 517 False 593.000000 593 87.356000 1 520 1 chr4A.!!$F1 519
10 TraesCS3B01G333600 chr7A 306350979 306351479 500 False 582.000000 582 87.597000 1 513 1 chr7A.!!$F1 512

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
775 800 0.036388 CGGAGTGCAGTACCATTGGT 60.036 55.000 13.94 13.94 40.16 3.67 F
1458 1487 0.038599 TGCTGCCTTGTGACCATGAT 59.961 50.000 0.00 0.00 0.00 2.45 F
1637 1666 0.036388 TCTGTGGTCAAGGGAATCGC 60.036 55.000 0.00 0.00 0.00 4.58 F
1841 1870 0.881118 TGCCATGCCGAGAGTTTTTC 59.119 50.000 0.00 0.00 0.00 2.29 F
2215 2253 1.621317 GGAGGAGGGCAGCTAGATTAC 59.379 57.143 0.00 0.00 0.00 1.89 F
2378 2416 4.211125 TGAACAACAGGTGGCATCTTTTA 58.789 39.130 0.00 0.00 0.00 1.52 F
3972 4104 5.241728 CCGTGATCACATTATCCTCTCTACA 59.758 44.000 24.93 0.00 0.00 2.74 F
5949 6173 2.159128 ACATCTGCATCAGGAACTCTCG 60.159 50.000 0.00 0.00 34.60 4.04 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1637 1666 0.889186 ACCTAACAAAGCACTGCCGG 60.889 55.000 0.00 0.0 0.00 6.13 R
2378 2416 8.110860 ACGTCCACAGAAAATCATTTAAAGAT 57.889 30.769 0.00 0.0 0.00 2.40 R
3507 3637 2.162208 TCTTGGAAATCATGCACGAAGC 59.838 45.455 0.00 0.0 45.96 3.86 R
4072 4205 9.686683 ATTACAACACCTATGAGCTTTCTAAAT 57.313 29.630 0.00 0.0 0.00 1.40 R
4127 4260 0.476771 GTTGGTGGGAACTGGAAGGA 59.523 55.000 0.00 0.0 39.30 3.36 R
4333 4466 5.899120 ATATGCCATCAGATTGCATCTTC 57.101 39.130 22.14 0.0 44.15 2.87 R
5951 6175 0.105194 TGAGGACCAGGAGGACACAA 60.105 55.000 0.00 0.0 38.69 3.33 R
7156 7482 0.032952 AGCTGACGTTACCGCTGAAA 59.967 50.000 0.00 0.0 37.70 2.69 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
25 26 5.516696 CGACGAACTCATCTACAATGTTCAT 59.483 40.000 0.00 0.00 37.46 2.57
165 166 2.649034 GCTGTTCCTCGGACGACA 59.351 61.111 0.00 0.00 0.00 4.35
202 203 2.210711 CGGGACTAGGAGGGGATGC 61.211 68.421 0.00 0.00 0.00 3.91
203 204 1.074471 GGGACTAGGAGGGGATGCA 60.074 63.158 0.00 0.00 0.00 3.96
369 386 2.018727 ATACACCACGCGCGGGATAA 62.019 55.000 37.25 16.52 0.00 1.75
472 489 3.242059 GCGCGCTAAAACGGACTAATTTA 60.242 43.478 26.67 0.00 0.00 1.40
477 494 4.330894 GCTAAAACGGACTAATTTACGGCT 59.669 41.667 0.00 0.00 0.00 5.52
520 537 3.273434 GTTGGAGATGCTCTAATGCACA 58.727 45.455 0.00 0.00 46.33 4.57
603 628 3.857854 GCACGGCTCACATCGCTG 61.858 66.667 0.00 0.00 39.62 5.18
616 641 1.663379 ATCGCTGTCCAACGATCGGA 61.663 55.000 20.98 4.08 45.35 4.55
736 761 3.864789 TCATCCCAAAGAGCTTATCCC 57.135 47.619 0.00 0.00 0.00 3.85
768 793 0.039798 TCAACGTCGGAGTGCAGTAC 60.040 55.000 0.00 0.00 0.00 2.73
770 795 1.457823 AACGTCGGAGTGCAGTACCA 61.458 55.000 0.00 0.00 0.00 3.25
771 796 1.248785 ACGTCGGAGTGCAGTACCAT 61.249 55.000 0.00 0.00 0.00 3.55
775 800 0.036388 CGGAGTGCAGTACCATTGGT 60.036 55.000 13.94 13.94 40.16 3.67
776 801 1.453155 GGAGTGCAGTACCATTGGTG 58.547 55.000 18.83 2.96 36.19 4.17
974 1001 0.539986 GCCTCCCACTGTTATCGGAA 59.460 55.000 0.00 0.00 0.00 4.30
975 1002 1.742750 GCCTCCCACTGTTATCGGAAC 60.743 57.143 0.00 0.00 0.00 3.62
979 1006 0.390603 CCACTGTTATCGGAACCGCA 60.391 55.000 8.48 0.12 39.59 5.69
1033 1060 3.162154 GTAAGCTCCCCTCCCCCG 61.162 72.222 0.00 0.00 0.00 5.73
1181 1209 2.285083 CGGTTGAGCGATAAATTGGGA 58.715 47.619 0.00 0.00 0.00 4.37
1193 1221 1.923356 AATTGGGAAGTGGCGATGTT 58.077 45.000 0.00 0.00 0.00 2.71
1398 1427 3.678056 TTCTGCACTGTTAGTGGTAGG 57.322 47.619 10.62 0.00 46.01 3.18
1413 1442 1.831736 GGTAGGCTGCTAGTTGGAAGA 59.168 52.381 1.79 0.00 0.00 2.87
1458 1487 0.038599 TGCTGCCTTGTGACCATGAT 59.961 50.000 0.00 0.00 0.00 2.45
1469 1498 3.057969 TGACCATGATGTCACAGGTTC 57.942 47.619 9.50 5.35 40.22 3.62
1514 1543 1.838112 CAATGTAGGGAAAGGCTGCA 58.162 50.000 0.50 0.00 0.00 4.41
1548 1577 4.257810 TGGTCGGACCCTTCCCCA 62.258 66.667 23.81 0.69 38.99 4.96
1563 1592 2.113774 CCAGACCCTGTGCAAGCA 59.886 61.111 0.00 0.00 0.00 3.91
1637 1666 0.036388 TCTGTGGTCAAGGGAATCGC 60.036 55.000 0.00 0.00 0.00 4.58
1641 1670 3.202706 GTCAAGGGAATCGCCGGC 61.203 66.667 19.07 19.07 37.63 6.13
1740 1769 1.877680 GCTTGGTTGGGCAAATTGGAC 60.878 52.381 0.00 0.00 0.00 4.02
1825 1854 4.142609 TCCTCAGTTGATATGTTCTGCC 57.857 45.455 0.00 0.00 0.00 4.85
1841 1870 0.881118 TGCCATGCCGAGAGTTTTTC 59.119 50.000 0.00 0.00 0.00 2.29
1942 1971 3.436470 GGGAAGCCCTGGCATTATCTTTA 60.436 47.826 11.38 0.00 44.88 1.85
2012 2041 5.675970 ACAAACTCGATTGTGTGAATTACG 58.324 37.500 3.65 0.00 41.78 3.18
2013 2042 5.464057 ACAAACTCGATTGTGTGAATTACGA 59.536 36.000 3.65 0.00 41.78 3.43
2014 2043 5.763444 AACTCGATTGTGTGAATTACGAG 57.237 39.130 0.00 0.00 46.80 4.18
2016 2045 5.763444 CTCGATTGTGTGAATTACGAGTT 57.237 39.130 0.00 0.00 40.11 3.01
2017 2046 6.153212 CTCGATTGTGTGAATTACGAGTTT 57.847 37.500 0.00 0.00 40.11 2.66
2018 2047 7.273188 CTCGATTGTGTGAATTACGAGTTTA 57.727 36.000 0.00 0.00 40.11 2.01
2215 2253 1.621317 GGAGGAGGGCAGCTAGATTAC 59.379 57.143 0.00 0.00 0.00 1.89
2249 2287 5.621329 CGGTCGCATATATCATGGTTACTCA 60.621 44.000 0.00 0.00 0.00 3.41
2342 2380 7.912250 CACTTATGCTAACTCATTTCCAATCAC 59.088 37.037 0.00 0.00 0.00 3.06
2378 2416 4.211125 TGAACAACAGGTGGCATCTTTTA 58.789 39.130 0.00 0.00 0.00 1.52
3146 3276 8.421002 ACAACAAAGCCTTTAATGTTAACAGAT 58.579 29.630 14.65 8.07 34.45 2.90
3147 3277 9.260002 CAACAAAGCCTTTAATGTTAACAGATT 57.740 29.630 14.65 7.04 34.45 2.40
3148 3278 9.830975 AACAAAGCCTTTAATGTTAACAGATTT 57.169 25.926 14.65 7.46 34.45 2.17
3507 3637 7.012327 TGACTCAAATTTAGGAAGTTGACACTG 59.988 37.037 0.00 0.00 42.80 3.66
3972 4104 5.241728 CCGTGATCACATTATCCTCTCTACA 59.758 44.000 24.93 0.00 0.00 2.74
4072 4205 7.570132 TCAATTCGGAGGGATTCTTATGTTTA 58.430 34.615 0.00 0.00 0.00 2.01
4127 4260 7.963532 TGACTAGTTCTCTGTTCAATAACCTT 58.036 34.615 0.00 0.00 34.49 3.50
4333 4466 9.823647 ACTAACAGAATACATGAACTAATCTGG 57.176 33.333 0.00 0.00 37.67 3.86
4459 4592 2.290514 TGCCTTAGATGCAAGCAGAACT 60.291 45.455 0.00 3.07 35.40 3.01
4759 4892 4.746611 AGCTGTACAATTCAAAAGCTTTGC 59.253 37.500 13.54 7.03 37.74 3.68
5412 5545 8.738199 TTACAATCGTCTAGAGTTACAGTTTG 57.262 34.615 0.00 0.00 0.00 2.93
5508 5642 3.381272 TGCCTTTTTGGTCACTCTGAAAG 59.619 43.478 0.00 0.00 38.35 2.62
5532 5666 7.177878 AGTATGAATCACCAGAAGAACCAATT 58.822 34.615 0.00 0.00 0.00 2.32
5852 6075 6.912951 TCTTATATTTTAGGACGGAGGGAG 57.087 41.667 0.00 0.00 0.00 4.30
5949 6173 2.159128 ACATCTGCATCAGGAACTCTCG 60.159 50.000 0.00 0.00 34.60 4.04
5951 6175 0.534412 CTGCATCAGGAACTCTCGGT 59.466 55.000 0.00 0.00 34.60 4.69
5983 6207 1.180029 GTCCTCACCTTGCAATGCAT 58.820 50.000 9.39 0.00 38.76 3.96
6134 6450 7.441836 ACTACATGTCAACTACAACTTGATGA 58.558 34.615 0.00 0.00 42.70 2.92
6145 6465 7.959175 ACTACAACTTGATGACAGGTAGTTTA 58.041 34.615 0.00 0.00 37.31 2.01
6169 6489 1.535028 CTGGACGCATGTTAAACTGCA 59.465 47.619 10.20 0.00 38.30 4.41
6170 6490 2.158559 TGGACGCATGTTAAACTGCAT 58.841 42.857 10.20 0.00 38.30 3.96
6399 6719 4.201960 GCCTCCTAGTAAAAATTGCTCAGC 60.202 45.833 0.00 0.00 0.00 4.26
6506 6826 3.469008 TGAGTTGACATTTGACGACCT 57.531 42.857 0.00 0.00 0.00 3.85
6728 7048 3.593442 TCAACAATCTCCCAAGTTGGT 57.407 42.857 20.54 0.00 41.14 3.67
6732 7052 1.270550 CAATCTCCCAAGTTGGTGTGC 59.729 52.381 20.54 0.00 35.17 4.57
6735 7055 1.227823 TCCCAAGTTGGTGTGCTCG 60.228 57.895 20.54 3.55 35.17 5.03
6736 7056 2.639286 CCAAGTTGGTGTGCTCGC 59.361 61.111 14.21 0.00 31.35 5.03
6739 7059 0.311790 CAAGTTGGTGTGCTCGCATT 59.688 50.000 1.32 0.00 0.00 3.56
6740 7060 1.535028 CAAGTTGGTGTGCTCGCATTA 59.465 47.619 1.32 0.00 0.00 1.90
6741 7061 2.113860 AGTTGGTGTGCTCGCATTAT 57.886 45.000 1.32 0.00 0.00 1.28
6742 7062 1.739466 AGTTGGTGTGCTCGCATTATG 59.261 47.619 1.32 0.00 0.00 1.90
6744 7064 2.675844 GTTGGTGTGCTCGCATTATGTA 59.324 45.455 1.32 0.00 0.00 2.29
6747 7067 4.893608 TGGTGTGCTCGCATTATGTATAT 58.106 39.130 1.32 0.00 0.00 0.86
6776 7096 5.405269 GGAATTGGTGTTGAAATGCAGTTAC 59.595 40.000 0.00 0.00 0.00 2.50
6777 7097 5.789643 ATTGGTGTTGAAATGCAGTTACT 57.210 34.783 0.00 0.00 0.00 2.24
6782 7102 7.199766 TGGTGTTGAAATGCAGTTACTAAAAG 58.800 34.615 0.00 0.00 0.00 2.27
6784 7104 7.704899 GGTGTTGAAATGCAGTTACTAAAAGTT 59.295 33.333 0.00 0.00 0.00 2.66
6785 7105 9.724839 GTGTTGAAATGCAGTTACTAAAAGTTA 57.275 29.630 0.00 0.00 0.00 2.24
6797 7117 8.610035 AGTTACTAAAAGTTAAGTGTTGACAGC 58.390 33.333 0.00 0.00 0.00 4.40
6862 7182 3.139077 GTGCCTTGTTGTAACTAGCTGT 58.861 45.455 0.00 0.00 31.71 4.40
6915 7235 1.585002 CGTGTGTTTGTTGGTGGCG 60.585 57.895 0.00 0.00 0.00 5.69
6916 7236 1.876263 GTGTGTTTGTTGGTGGCGC 60.876 57.895 0.00 0.00 0.00 6.53
6965 7285 1.897802 TGTAAGGAACCGGTCTTCTCC 59.102 52.381 8.04 11.88 0.00 3.71
6982 7302 3.122480 TCTCCTGGCTTTTGGATGGATA 58.878 45.455 0.00 0.00 0.00 2.59
7002 7322 5.532779 GGATATTTCCCTCACCAATCTCAAC 59.467 44.000 0.00 0.00 35.84 3.18
7161 7487 3.726517 CACCACCGCGCCTTTCAG 61.727 66.667 0.00 0.00 0.00 3.02
7182 7509 2.281140 GGTAACGTCAGCTCTTCTCC 57.719 55.000 0.00 0.00 0.00 3.71
7190 7517 0.175302 CAGCTCTTCTCCGTGCTCAT 59.825 55.000 0.00 0.00 31.96 2.90
7229 7633 5.050431 GCTAAGTACGAGTAGTAGTAGTGGC 60.050 48.000 1.33 4.34 37.98 5.01
7238 7648 5.679601 AGTAGTAGTAGTGGCAGTAGGTAC 58.320 45.833 1.37 7.82 0.00 3.34
7361 7771 4.749310 CGGCTGAGCTGCGTCCTT 62.749 66.667 3.72 0.00 0.00 3.36
7362 7772 2.359230 GGCTGAGCTGCGTCCTTT 60.359 61.111 3.72 0.00 0.00 3.11
7364 7774 1.963338 GCTGAGCTGCGTCCTTTGT 60.963 57.895 0.00 0.00 0.00 2.83
7367 7777 0.391228 TGAGCTGCGTCCTTTGTGTA 59.609 50.000 0.00 0.00 0.00 2.90
7371 7793 2.290641 AGCTGCGTCCTTTGTGTAAAAG 59.709 45.455 0.00 0.00 0.00 2.27
7378 7800 3.066760 GTCCTTTGTGTAAAAGCTGCACT 59.933 43.478 1.02 0.00 40.98 4.40
7389 7811 1.835494 AGCTGCACTGCTCATCAAAT 58.165 45.000 1.02 0.00 39.34 2.32
7393 7815 3.428999 GCTGCACTGCTCATCAAATCAAT 60.429 43.478 1.98 0.00 0.00 2.57
7394 7816 4.104696 TGCACTGCTCATCAAATCAATG 57.895 40.909 1.98 0.00 0.00 2.82
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
421 438 4.675029 CGGGTCGCTTCAACGGGT 62.675 66.667 0.00 0.00 0.00 5.28
603 628 3.667261 CGTATAACATCCGATCGTTGGAC 59.333 47.826 15.09 7.75 38.60 4.02
736 761 1.856597 GACGTTGACGGAATATTCGGG 59.143 52.381 22.54 13.71 44.95 5.14
761 786 0.251121 CACCCACCAATGGTACTGCA 60.251 55.000 3.85 0.00 45.66 4.41
768 793 4.312443 GACGTATATACACCCACCAATGG 58.688 47.826 13.22 0.00 46.81 3.16
770 795 3.325716 GGGACGTATATACACCCACCAAT 59.674 47.826 26.87 0.88 40.12 3.16
771 796 2.699846 GGGACGTATATACACCCACCAA 59.300 50.000 26.87 0.00 40.12 3.67
1005 1032 1.677637 GGAGCTTACAGAGGGACGGG 61.678 65.000 0.00 0.00 0.00 5.28
1033 1060 0.466124 AAGGCCAGCTAATCGGAGAC 59.534 55.000 5.01 0.00 42.51 3.36
1176 1204 0.109532 TGAACATCGCCACTTCCCAA 59.890 50.000 0.00 0.00 0.00 4.12
1181 1209 1.073025 TGCCTGAACATCGCCACTT 59.927 52.632 0.00 0.00 0.00 3.16
1193 1221 0.684535 TCACCTCAATTCGTGCCTGA 59.315 50.000 0.00 0.00 0.00 3.86
1398 1427 1.742071 GCTCCTCTTCCAACTAGCAGC 60.742 57.143 0.00 0.00 0.00 5.25
1413 1442 4.711949 CACTGCGCCAAGGCTCCT 62.712 66.667 4.18 0.00 39.32 3.69
1458 1487 2.620251 CAGGACTTGAACCTGTGACA 57.380 50.000 0.00 0.00 46.71 3.58
1466 1495 1.609072 GGCTGTTTCCAGGACTTGAAC 59.391 52.381 0.00 0.00 39.22 3.18
1468 1497 1.072331 GAGGCTGTTTCCAGGACTTGA 59.928 52.381 0.00 0.00 39.22 3.02
1469 1498 1.072965 AGAGGCTGTTTCCAGGACTTG 59.927 52.381 0.00 0.00 39.22 3.16
1563 1592 1.910722 CCCAGTGCATGTAGCTCCT 59.089 57.895 0.00 0.00 45.94 3.69
1637 1666 0.889186 ACCTAACAAAGCACTGCCGG 60.889 55.000 0.00 0.00 0.00 6.13
1641 1670 3.648339 AATGCACCTAACAAAGCACTG 57.352 42.857 0.00 0.00 40.14 3.66
1740 1769 4.384056 CAGTCTAAATATGAGCACCCTGG 58.616 47.826 0.00 0.00 0.00 4.45
1825 1854 4.667668 CGAAGAAGAAAAACTCTCGGCATG 60.668 45.833 0.00 0.00 31.02 4.06
1841 1870 2.475187 CGGCATGAAAGAAGCGAAGAAG 60.475 50.000 0.00 0.00 0.00 2.85
2215 2253 2.004583 TATGCGACCGGACAAGAAAG 57.995 50.000 9.46 0.00 0.00 2.62
2378 2416 8.110860 ACGTCCACAGAAAATCATTTAAAGAT 57.889 30.769 0.00 0.00 0.00 2.40
3034 3161 9.357652 GAATTGAGTTTTCTAGCATTTGCAATA 57.642 29.630 0.00 0.00 45.16 1.90
3507 3637 2.162208 TCTTGGAAATCATGCACGAAGC 59.838 45.455 0.00 0.00 45.96 3.86
4072 4205 9.686683 ATTACAACACCTATGAGCTTTCTAAAT 57.313 29.630 0.00 0.00 0.00 1.40
4127 4260 0.476771 GTTGGTGGGAACTGGAAGGA 59.523 55.000 0.00 0.00 39.30 3.36
4333 4466 5.899120 ATATGCCATCAGATTGCATCTTC 57.101 39.130 22.14 0.00 44.15 2.87
4607 4740 8.962884 ATAACCATTTTCATAGCAAATTTCCC 57.037 30.769 0.00 0.00 0.00 3.97
4759 4892 7.441157 TCCGCCTAAGATTGTACTGAATAAATG 59.559 37.037 0.00 0.00 0.00 2.32
5394 5527 4.148348 GTGTGCAAACTGTAACTCTAGACG 59.852 45.833 0.00 0.00 0.00 4.18
5508 5642 7.396540 AATTGGTTCTTCTGGTGATTCATAC 57.603 36.000 0.00 0.00 0.00 2.39
5826 6049 7.014449 TCCCTCCGTCCTAAAATATAAGATGA 58.986 38.462 0.00 0.00 0.00 2.92
5949 6173 1.128188 AGGACCAGGAGGACACAACC 61.128 60.000 0.00 0.00 38.69 3.77
5951 6175 0.105194 TGAGGACCAGGAGGACACAA 60.105 55.000 0.00 0.00 38.69 3.33
5983 6207 3.009723 GAGAGCATTCGTCCCAAATCAA 58.990 45.455 0.00 0.00 0.00 2.57
6072 6302 6.547141 CCATTGGGATCATTTAAAGCAGAGTA 59.453 38.462 0.00 0.00 35.59 2.59
6145 6465 3.938963 CAGTTTAACATGCGTCCAGGTAT 59.061 43.478 0.00 0.00 34.41 2.73
6169 6489 4.156455 ACCTGCAGAAACGATGGAATAT 57.844 40.909 17.39 0.00 0.00 1.28
6170 6490 3.627395 ACCTGCAGAAACGATGGAATA 57.373 42.857 17.39 0.00 0.00 1.75
6321 6641 8.157476 AGATTTCAGTTCTTGGTACTTGTGTAT 58.843 33.333 0.00 0.00 0.00 2.29
6373 6693 3.696548 AGCAATTTTTACTAGGAGGCTGC 59.303 43.478 0.00 0.00 0.00 5.25
6399 6719 1.278172 CCTTCGTATGCCGCGATCAG 61.278 60.000 8.23 0.00 38.21 2.90
6529 6849 5.796350 AACAGCGTAAACCAACATCTATC 57.204 39.130 0.00 0.00 0.00 2.08
6662 6982 9.632638 AGCTATACATCAACCATTACATTTTCT 57.367 29.630 0.00 0.00 0.00 2.52
6728 7048 6.589907 CCACTTATATACATAATGCGAGCACA 59.410 38.462 0.00 0.00 0.00 4.57
6740 7060 9.693739 TTCAACACCAATTCCACTTATATACAT 57.306 29.630 0.00 0.00 0.00 2.29
6741 7061 9.521841 TTTCAACACCAATTCCACTTATATACA 57.478 29.630 0.00 0.00 0.00 2.29
6744 7064 7.981225 GCATTTCAACACCAATTCCACTTATAT 59.019 33.333 0.00 0.00 0.00 0.86
6747 7067 5.069648 TGCATTTCAACACCAATTCCACTTA 59.930 36.000 0.00 0.00 0.00 2.24
6776 7096 7.126398 GTCAGCTGTCAACACTTAACTTTTAG 58.874 38.462 14.67 0.00 0.00 1.85
6777 7097 6.037830 GGTCAGCTGTCAACACTTAACTTTTA 59.962 38.462 14.67 0.00 0.00 1.52
6782 7102 3.248602 CAGGTCAGCTGTCAACACTTAAC 59.751 47.826 14.67 0.00 0.00 2.01
6784 7104 2.434336 ACAGGTCAGCTGTCAACACTTA 59.566 45.455 14.67 0.00 0.00 2.24
6785 7105 1.210478 ACAGGTCAGCTGTCAACACTT 59.790 47.619 14.67 0.00 0.00 3.16
6846 7166 4.682778 AGTGGACAGCTAGTTACAACAA 57.317 40.909 0.00 0.00 0.00 2.83
6862 7182 1.300963 GGCTGCCAGATCAAGTGGA 59.699 57.895 15.17 0.00 37.23 4.02
6915 7235 4.778143 ATTGACAGGGACCGCGGC 62.778 66.667 28.58 18.35 0.00 6.53
6916 7236 2.046314 AATTGACAGGGACCGCGG 60.046 61.111 26.86 26.86 0.00 6.46
6965 7285 5.205759 GGAAATATCCATCCAAAAGCCAG 57.794 43.478 0.00 0.00 45.79 4.85
6982 7302 3.347216 CGTTGAGATTGGTGAGGGAAAT 58.653 45.455 0.00 0.00 0.00 2.17
7002 7322 1.070445 CAGCTTATCCTCCCCTGCG 59.930 63.158 0.00 0.00 0.00 5.18
7156 7482 0.032952 AGCTGACGTTACCGCTGAAA 59.967 50.000 0.00 0.00 37.70 2.69
7157 7483 0.388134 GAGCTGACGTTACCGCTGAA 60.388 55.000 0.00 0.00 37.70 3.02
7161 7487 0.109226 AGAAGAGCTGACGTTACCGC 60.109 55.000 0.00 0.00 37.70 5.68
7170 7496 0.895559 TGAGCACGGAGAAGAGCTGA 60.896 55.000 0.00 0.00 37.48 4.26
7213 7540 3.808726 CCTACTGCCACTACTACTACTCG 59.191 52.174 0.00 0.00 0.00 4.18
7238 7648 6.194463 CACGGCAAAGAATAACATCACATAG 58.806 40.000 0.00 0.00 0.00 2.23
7356 7766 3.066760 AGTGCAGCTTTTACACAAAGGAC 59.933 43.478 8.23 0.00 36.76 3.85
7357 7767 3.066621 CAGTGCAGCTTTTACACAAAGGA 59.933 43.478 8.23 0.00 36.76 3.36
7358 7768 3.374745 CAGTGCAGCTTTTACACAAAGG 58.625 45.455 8.23 0.00 36.76 3.11
7359 7769 2.791004 GCAGTGCAGCTTTTACACAAAG 59.209 45.455 11.09 0.00 36.76 2.77
7360 7770 2.426738 AGCAGTGCAGCTTTTACACAAA 59.573 40.909 19.20 0.00 43.70 2.83
7361 7771 2.023673 AGCAGTGCAGCTTTTACACAA 58.976 42.857 19.20 0.00 43.70 3.33
7362 7772 1.603802 GAGCAGTGCAGCTTTTACACA 59.396 47.619 19.20 0.00 46.75 3.72
7364 7774 1.965935 TGAGCAGTGCAGCTTTTACA 58.034 45.000 19.20 1.50 46.75 2.41
7367 7777 1.612676 TGATGAGCAGTGCAGCTTTT 58.387 45.000 19.20 0.00 46.75 2.27
7371 7793 1.471287 TGATTTGATGAGCAGTGCAGC 59.529 47.619 19.20 9.51 0.00 5.25
7378 7800 7.814107 GGTTTTCTTACATTGATTTGATGAGCA 59.186 33.333 0.00 0.00 0.00 4.26


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

AutoCloner maintained by Alex Coulton.