Multiple sequence alignment - TraesCS7A01G411700

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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 TraesCS7A01G411700 chr7A 100.000 3748 0 0 1 3748 602807415 602803668 0.000000e+00 6922.0
1 TraesCS7A01G411700 chr7A 81.855 248 31 9 3005 3239 297943014 297943260 2.950000e-46 196.0
2 TraesCS7A01G411700 chr7D 93.325 3056 146 25 719 3748 522504538 522501515 0.000000e+00 4460.0
3 TraesCS7A01G411700 chr7D 97.546 163 3 1 1 162 522510127 522509965 1.030000e-70 278.0
4 TraesCS7A01G411700 chr7D 92.414 145 11 0 212 356 522505395 522505251 1.360000e-49 207.0
5 TraesCS7A01G411700 chr7B 94.235 1301 52 9 781 2074 556458799 556457515 0.000000e+00 1965.0
6 TraesCS7A01G411700 chr7B 93.888 949 35 11 2067 3007 556457084 556456151 0.000000e+00 1410.0
7 TraesCS7A01G411700 chr7B 87.714 643 45 13 1 637 556459578 556458964 0.000000e+00 719.0
8 TraesCS7A01G411700 chr6B 88.173 947 96 10 1060 1995 11574700 11575641 0.000000e+00 1114.0
9 TraesCS7A01G411700 chr6B 86.615 650 78 3 2098 2747 11577456 11578096 0.000000e+00 710.0
10 TraesCS7A01G411700 chr6B 74.576 236 50 10 2101 2331 120803258 120803028 1.110000e-15 95.3
11 TraesCS7A01G411700 chr6B 72.766 235 56 8 2101 2331 10927324 10927554 5.190000e-09 73.1
12 TraesCS7A01G411700 chr6D 87.063 943 106 11 1060 1994 6319416 6320350 0.000000e+00 1051.0
13 TraesCS7A01G411700 chr6D 87.215 657 75 4 2091 2747 6320578 6321225 0.000000e+00 739.0
14 TraesCS7A01G411700 chr6D 84.756 656 91 4 2093 2748 6328274 6328920 0.000000e+00 649.0
15 TraesCS7A01G411700 chr6D 90.099 101 9 1 3144 3243 379334957 379334857 3.040000e-26 130.0
16 TraesCS7A01G411700 chr6D 74.262 237 49 11 2101 2331 50673040 50673270 5.160000e-14 89.8
17 TraesCS7A01G411700 chr6A 86.998 946 106 12 1060 1994 5861569 5862508 0.000000e+00 1050.0
18 TraesCS7A01G411700 chr1D 78.115 626 125 11 2118 2736 492534871 492534251 1.630000e-103 387.0
19 TraesCS7A01G411700 chr2B 75.108 695 153 18 1162 1846 792677572 792678256 1.310000e-79 307.0
20 TraesCS7A01G411700 chr5B 79.848 263 34 15 3005 3253 302843278 302843535 1.380000e-39 174.0
21 TraesCS7A01G411700 chr2A 84.058 138 12 7 3005 3133 583841337 583841201 1.410000e-24 124.0
22 TraesCS7A01G411700 chr3A 83.898 118 17 2 3127 3243 503556609 503556725 1.100000e-20 111.0
23 TraesCS7A01G411700 chr5D 83.186 113 18 1 3127 3238 452682312 452682424 6.620000e-18 102.0
24 TraesCS7A01G411700 chrUn 87.952 83 9 1 3011 3092 51484206 51484124 3.080000e-16 97.1
25 TraesCS7A01G411700 chr5A 88.571 70 8 0 3166 3235 601648653 601648722 6.670000e-13 86.1


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 TraesCS7A01G411700 chr7A 602803668 602807415 3747 True 6922.000000 6922 100.000000 1 3748 1 chr7A.!!$R1 3747
1 TraesCS7A01G411700 chr7D 522501515 522505395 3880 True 2333.500000 4460 92.869500 212 3748 2 chr7D.!!$R2 3536
2 TraesCS7A01G411700 chr7B 556456151 556459578 3427 True 1364.666667 1965 91.945667 1 3007 3 chr7B.!!$R1 3006
3 TraesCS7A01G411700 chr6B 11574700 11578096 3396 False 912.000000 1114 87.394000 1060 2747 2 chr6B.!!$F2 1687
4 TraesCS7A01G411700 chr6D 6319416 6321225 1809 False 895.000000 1051 87.139000 1060 2747 2 chr6D.!!$F3 1687
5 TraesCS7A01G411700 chr6D 6328274 6328920 646 False 649.000000 649 84.756000 2093 2748 1 chr6D.!!$F1 655
6 TraesCS7A01G411700 chr6A 5861569 5862508 939 False 1050.000000 1050 86.998000 1060 1994 1 chr6A.!!$F1 934
7 TraesCS7A01G411700 chr1D 492534251 492534871 620 True 387.000000 387 78.115000 2118 2736 1 chr1D.!!$R1 618
8 TraesCS7A01G411700 chr2B 792677572 792678256 684 False 307.000000 307 75.108000 1162 1846 1 chr2B.!!$F1 684

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
683 1095 0.250597 AACCTTTATATCGGCGGGGC 60.251 55.0 7.21 0.00 0.0 5.80 F
991 1419 0.251698 TCTTGAACCCCATGCATGCA 60.252 50.0 25.04 25.04 0.0 3.96 F
1017 1445 0.320771 ACATGAACACTCGAGCACCC 60.321 55.0 13.61 0.19 0.0 4.61 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2001 2449 1.081242 GTCACGGCCGACTACGAAA 60.081 57.895 35.90 4.23 42.66 3.46 R
2054 4236 2.126346 GGCACATTGAACGGCTGC 60.126 61.111 0.00 0.00 0.00 5.25 R
3007 5639 1.726791 CTGACGTGTGGCACTTATCAC 59.273 52.381 19.83 7.15 31.34 3.06 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
26 27 1.459592 CCGCTGAACTTACTTTCCACG 59.540 52.381 0.00 0.00 0.00 4.94
27 28 1.459592 CGCTGAACTTACTTTCCACGG 59.540 52.381 0.00 0.00 0.00 4.94
84 86 6.092944 TGCTTGGTAAAGTTGGTATGATAACG 59.907 38.462 0.00 0.00 35.69 3.18
91 93 9.148104 GTAAAGTTGGTATGATAACGAAGTCTT 57.852 33.333 0.00 0.00 45.00 3.01
98 100 7.919091 TGGTATGATAACGAAGTCTTGTATGAC 59.081 37.037 0.00 0.00 45.00 3.06
108 110 5.411831 AGTCTTGTATGACTGAATCTGCA 57.588 39.130 0.00 0.00 44.64 4.41
113 115 4.445453 TGTATGACTGAATCTGCATCACC 58.555 43.478 0.00 0.00 0.00 4.02
125 127 1.284491 TGCATCACCACCACCATACAT 59.716 47.619 0.00 0.00 0.00 2.29
162 164 2.125147 GCCCGTCATGCTGTGCTA 60.125 61.111 0.00 0.00 0.00 3.49
163 165 2.176273 GCCCGTCATGCTGTGCTAG 61.176 63.158 0.00 0.00 0.00 3.42
164 166 1.219124 CCCGTCATGCTGTGCTAGT 59.781 57.895 0.00 0.00 0.00 2.57
165 167 1.086067 CCCGTCATGCTGTGCTAGTG 61.086 60.000 0.00 0.00 0.00 2.74
166 168 0.390340 CCGTCATGCTGTGCTAGTGT 60.390 55.000 0.00 0.00 0.00 3.55
167 169 0.717784 CGTCATGCTGTGCTAGTGTG 59.282 55.000 0.00 0.00 0.00 3.82
168 170 0.445436 GTCATGCTGTGCTAGTGTGC 59.555 55.000 0.00 0.00 0.00 4.57
169 171 0.322648 TCATGCTGTGCTAGTGTGCT 59.677 50.000 0.00 0.00 0.00 4.40
173 175 1.673477 CTGTGCTAGTGTGCTGGGA 59.327 57.895 0.00 0.00 0.00 4.37
302 304 4.529769 AGAGTTCAGGAATCAGATGACACA 59.470 41.667 0.00 0.00 0.00 3.72
333 335 3.127376 TGCGTGAATGTCATCATTTCTGG 59.873 43.478 0.00 0.00 43.33 3.86
356 358 6.004574 GGTATTTAGAGAAAAGGCCTATGGG 58.995 44.000 5.16 0.00 0.00 4.00
395 560 1.953686 TCCAAAGCTTTTCCGGAGTTG 59.046 47.619 9.53 3.90 0.00 3.16
428 594 2.477245 AGAAAACAAAAGCCAGGGGTT 58.523 42.857 0.00 0.00 37.44 4.11
438 604 1.304134 CCAGGGGTTGCCTGGTAAC 60.304 63.158 18.04 18.04 46.92 2.50
439 605 1.304134 CAGGGGTTGCCTGGTAACC 60.304 63.158 31.48 31.48 45.32 2.85
446 614 4.159244 GGTTGCCTGGTAACCATATACA 57.841 45.455 33.37 0.72 45.37 2.29
454 622 6.824704 GCCTGGTAACCATATACAACTACAAA 59.175 38.462 0.00 0.00 30.82 2.83
481 660 5.010282 ACAATCAAGGATAAACCAGGTCAC 58.990 41.667 0.00 0.00 42.04 3.67
483 662 3.256704 TCAAGGATAAACCAGGTCACCT 58.743 45.455 0.00 0.00 42.04 4.00
505 684 5.163519 CCTTTTCTGATTGTTCCGCCATTAT 60.164 40.000 0.00 0.00 0.00 1.28
509 688 3.360867 TGATTGTTCCGCCATTATGGTT 58.639 40.909 13.28 0.00 40.46 3.67
510 689 3.380004 TGATTGTTCCGCCATTATGGTTC 59.620 43.478 13.28 0.00 40.46 3.62
512 691 3.011566 TGTTCCGCCATTATGGTTCAT 57.988 42.857 13.28 0.00 40.46 2.57
513 692 3.360867 TGTTCCGCCATTATGGTTCATT 58.639 40.909 13.28 0.00 40.46 2.57
514 693 4.527944 TGTTCCGCCATTATGGTTCATTA 58.472 39.130 13.28 0.00 40.46 1.90
515 694 4.950475 TGTTCCGCCATTATGGTTCATTAA 59.050 37.500 13.28 0.00 40.46 1.40
516 695 5.067153 TGTTCCGCCATTATGGTTCATTAAG 59.933 40.000 13.28 0.00 40.46 1.85
517 696 4.141287 TCCGCCATTATGGTTCATTAAGG 58.859 43.478 13.28 4.44 40.46 2.69
518 697 3.305335 CCGCCATTATGGTTCATTAAGGC 60.305 47.826 13.28 0.00 40.46 4.35
519 698 3.305335 CGCCATTATGGTTCATTAAGGCC 60.305 47.826 13.28 0.00 40.46 5.19
520 699 3.897505 GCCATTATGGTTCATTAAGGCCT 59.102 43.478 13.28 0.00 40.46 5.19
521 700 4.262164 GCCATTATGGTTCATTAAGGCCTG 60.262 45.833 5.69 0.00 40.46 4.85
526 705 2.171003 GGTTCATTAAGGCCTGTGCTT 58.829 47.619 5.69 0.00 37.74 3.91
554 736 5.872617 TGTACATAGTTCAAACTTGATCCCG 59.127 40.000 0.00 0.00 40.37 5.14
578 760 4.333649 TCTTGAATGTCATCATTTCTCGCC 59.666 41.667 0.00 0.00 43.33 5.54
582 764 5.999600 TGAATGTCATCATTTCTCGCCATAT 59.000 36.000 0.00 0.00 43.33 1.78
589 771 3.876914 TCATTTCTCGCCATATCACCAAC 59.123 43.478 0.00 0.00 0.00 3.77
629 974 1.999735 ACCACGCAGTTCATTCATACG 59.000 47.619 0.00 0.00 41.61 3.06
630 975 2.267426 CCACGCAGTTCATTCATACGA 58.733 47.619 0.00 0.00 41.61 3.43
679 1091 7.170320 ACATGTTTAGTAACCTTTATATCGGCG 59.830 37.037 0.00 0.00 33.15 6.46
681 1093 3.672767 AGTAACCTTTATATCGGCGGG 57.327 47.619 7.21 0.00 0.00 6.13
683 1095 0.250597 AACCTTTATATCGGCGGGGC 60.251 55.000 7.21 0.00 0.00 5.80
684 1096 1.740296 CCTTTATATCGGCGGGGCG 60.740 63.158 7.21 8.46 0.00 6.13
685 1097 1.740296 CTTTATATCGGCGGGGCGG 60.740 63.158 14.74 0.37 0.00 6.13
686 1098 2.162338 CTTTATATCGGCGGGGCGGA 62.162 60.000 14.74 6.41 41.73 5.54
687 1099 2.162338 TTTATATCGGCGGGGCGGAG 62.162 60.000 14.74 0.00 40.90 4.63
713 1125 1.756430 GGAGAGATTCCAAACAGGGC 58.244 55.000 0.00 0.00 46.01 5.19
714 1126 1.373570 GAGAGATTCCAAACAGGGCG 58.626 55.000 0.00 0.00 38.24 6.13
717 1129 2.505819 AGAGATTCCAAACAGGGCGTAT 59.494 45.455 0.00 0.00 38.24 3.06
739 1151 3.039452 TGCACATTCACCTGCACAT 57.961 47.368 0.00 0.00 38.49 3.21
747 1159 3.940209 TTCACCTGCACATTTTCCATC 57.060 42.857 0.00 0.00 0.00 3.51
758 1170 2.930826 TTTTCCATCCTCGCCCTATC 57.069 50.000 0.00 0.00 0.00 2.08
764 1176 0.613292 ATCCTCGCCCTATCATCGCT 60.613 55.000 0.00 0.00 0.00 4.93
770 1182 0.394565 GCCCTATCATCGCTTCCAGT 59.605 55.000 0.00 0.00 0.00 4.00
773 1185 2.288702 CCCTATCATCGCTTCCAGTGAG 60.289 54.545 0.00 0.00 38.24 3.51
775 1187 3.068732 CCTATCATCGCTTCCAGTGAGAA 59.931 47.826 0.00 0.00 38.24 2.87
779 1191 3.068732 TCATCGCTTCCAGTGAGAATAGG 59.931 47.826 0.00 0.00 38.24 2.57
785 1197 4.202172 GCTTCCAGTGAGAATAGGACTACC 60.202 50.000 0.00 0.00 0.00 3.18
822 1238 1.129811 CACTAAACCATCCGAAACGCC 59.870 52.381 0.00 0.00 0.00 5.68
933 1355 1.670087 GGATGAGACGTGTCACCTGTG 60.670 57.143 18.60 0.00 0.00 3.66
991 1419 0.251698 TCTTGAACCCCATGCATGCA 60.252 50.000 25.04 25.04 0.00 3.96
992 1420 0.828022 CTTGAACCCCATGCATGCAT 59.172 50.000 27.46 27.46 37.08 3.96
993 1421 1.208535 CTTGAACCCCATGCATGCATT 59.791 47.619 30.32 16.77 33.90 3.56
994 1422 0.537653 TGAACCCCATGCATGCATTG 59.462 50.000 30.32 25.67 33.90 2.82
1017 1445 0.320771 ACATGAACACTCGAGCACCC 60.321 55.000 13.61 0.19 0.00 4.61
1038 1466 2.850441 CAGTGCTTGCATATCGATCG 57.150 50.000 9.36 9.36 0.00 3.69
1039 1467 2.397549 CAGTGCTTGCATATCGATCGA 58.602 47.619 21.86 21.86 0.00 3.59
1617 2056 3.269347 GTGTGCACGACCAACGCT 61.269 61.111 13.13 0.00 46.94 5.07
1962 2410 1.730487 CGAGGAGGACAGGATCACG 59.270 63.158 0.00 0.00 0.00 4.35
2058 4240 1.734117 GCAAATCCACAACCGCAGC 60.734 57.895 0.00 0.00 0.00 5.25
2062 4244 3.842925 ATCCACAACCGCAGCCGTT 62.843 57.895 0.00 0.00 0.00 4.44
2086 4706 3.423539 TGTGCCTGATTAACTCTGCTT 57.576 42.857 0.00 0.00 0.00 3.91
2087 4707 3.076621 TGTGCCTGATTAACTCTGCTTG 58.923 45.455 0.00 0.00 0.00 4.01
2088 4708 2.086869 TGCCTGATTAACTCTGCTTGC 58.913 47.619 0.00 0.00 0.00 4.01
2089 4709 2.086869 GCCTGATTAACTCTGCTTGCA 58.913 47.619 0.00 0.00 0.00 4.08
2753 5376 5.219951 GGCGTACGAAATTGCATAAACAAAG 60.220 40.000 21.65 0.00 32.27 2.77
2841 5465 0.536233 TTGTTGTCGATGGGGGTGTG 60.536 55.000 0.00 0.00 0.00 3.82
2847 5471 3.010144 GATGGGGGTGTGCCTCAT 58.990 61.111 0.00 0.00 36.82 2.90
2851 5475 2.351276 GGGGTGTGCCTCATCGTT 59.649 61.111 0.00 0.00 34.61 3.85
2994 5626 3.930634 AAGAGAAGAAGGCAATGCAAC 57.069 42.857 7.79 0.00 0.00 4.17
3028 5660 1.337728 TGATAAGTGCCACACGTCAGG 60.338 52.381 0.00 0.00 39.64 3.86
3057 5689 1.089920 CTCCTGCCCTGACATTTTCG 58.910 55.000 0.00 0.00 0.00 3.46
3092 5724 1.203052 CACGCAAGGATGGCAAATTCT 59.797 47.619 0.00 0.00 46.39 2.40
3093 5725 1.203052 ACGCAAGGATGGCAAATTCTG 59.797 47.619 0.00 0.00 46.39 3.02
3106 5748 3.188460 GCAAATTCTGGCGAGTTTCTGTA 59.812 43.478 0.00 0.00 27.95 2.74
3133 5775 7.614124 AAATGAACTGAAGCACAAAAATTGT 57.386 28.000 0.00 0.00 46.75 2.71
3138 5780 5.904941 ACTGAAGCACAAAAATTGTCATGA 58.095 33.333 0.00 0.00 43.23 3.07
3139 5781 5.750067 ACTGAAGCACAAAAATTGTCATGAC 59.250 36.000 19.27 19.27 43.23 3.06
3142 5784 4.053295 AGCACAAAAATTGTCATGACTGC 58.947 39.130 25.55 22.02 43.23 4.40
3146 5788 4.810491 ACAAAAATTGTCATGACTGCCAAC 59.190 37.500 25.55 0.00 40.56 3.77
3165 5807 4.749245 AACTAAAGTTGTCATCCTTGCG 57.251 40.909 0.00 0.00 36.80 4.85
3170 5812 0.517316 GTTGTCATCCTTGCGTCACC 59.483 55.000 0.00 0.00 0.00 4.02
3178 5820 0.594796 CCTTGCGTCACCAAACTTGC 60.595 55.000 0.00 0.00 0.00 4.01
3196 5839 4.098807 ACTTGCCATAAAAACGTTTGGAGT 59.901 37.500 18.69 11.67 0.00 3.85
3217 5860 1.071299 TCATGTGCTCGTGCCACTT 59.929 52.632 7.05 1.55 38.71 3.16
3220 5863 1.509644 ATGTGCTCGTGCCACTTGTG 61.510 55.000 7.05 0.00 38.71 3.33
3349 5993 0.983467 AGGCCATTTCCCGCAAAAAT 59.017 45.000 5.01 0.00 0.00 1.82
3351 5995 2.771372 AGGCCATTTCCCGCAAAAATAT 59.229 40.909 5.01 0.00 0.00 1.28
3379 6023 8.686739 ATAGAAATAACCTAGGCCATGACTAT 57.313 34.615 9.30 9.12 0.00 2.12
3407 6051 9.784531 ATATGGCATTATAAGGACATATACAGC 57.215 33.333 28.61 3.52 46.31 4.40
3412 6056 8.446273 GCATTATAAGGACATATACAGCTGTTG 58.554 37.037 27.06 19.68 0.00 3.33
3413 6057 8.939929 CATTATAAGGACATATACAGCTGTTGG 58.060 37.037 27.06 14.22 0.00 3.77
3610 6254 6.704056 TCTTATTTCTCTTTCCTCCACCTT 57.296 37.500 0.00 0.00 0.00 3.50
3625 6269 5.304686 TCCACCTTCGCATTTATCCTATT 57.695 39.130 0.00 0.00 0.00 1.73
3631 6275 5.437289 TTCGCATTTATCCTATTTGGCAG 57.563 39.130 0.00 0.00 35.26 4.85
3633 6277 4.887071 TCGCATTTATCCTATTTGGCAGTT 59.113 37.500 0.00 0.00 35.26 3.16
3634 6278 6.058833 TCGCATTTATCCTATTTGGCAGTTA 58.941 36.000 0.00 0.00 35.26 2.24
3645 6289 9.303116 TCCTATTTGGCAGTTATAAGACAAAAA 57.697 29.630 9.16 0.00 45.05 1.94
3649 6293 8.810652 TTTGGCAGTTATAAGACAAAAACATC 57.189 30.769 3.81 0.00 39.63 3.06
3652 6296 6.523201 GGCAGTTATAAGACAAAAACATCGTG 59.477 38.462 0.00 0.00 0.00 4.35
3655 6299 7.750458 CAGTTATAAGACAAAAACATCGTGCAT 59.250 33.333 0.00 0.00 0.00 3.96
3657 6301 4.566545 AAGACAAAAACATCGTGCATGA 57.433 36.364 11.83 11.83 36.21 3.07
3668 6312 4.094887 ACATCGTGCATGACCTAACATTTC 59.905 41.667 11.65 0.00 36.21 2.17
3672 6316 1.676006 GCATGACCTAACATTTCCCCG 59.324 52.381 0.00 0.00 0.00 5.73
3682 6326 0.969917 CATTTCCCCGAATGCCACCA 60.970 55.000 0.00 0.00 31.00 4.17
3700 6344 0.390603 CATTCCTCGTTACGGTGCCA 60.391 55.000 4.53 0.00 0.00 4.92
3717 6361 1.946283 GCCAGTTGCTAGAAGGACACC 60.946 57.143 0.00 0.00 36.87 4.16
3739 6383 3.921119 TTTTGGTGATCATGCTCACAC 57.079 42.857 26.21 17.48 45.95 3.82
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
26 27 5.986135 GGCTAATGTCGATATGGATATGTCC 59.014 44.000 0.60 0.60 45.31 4.02
27 28 6.810911 AGGCTAATGTCGATATGGATATGTC 58.189 40.000 0.00 0.00 0.00 3.06
84 86 5.871524 TGCAGATTCAGTCATACAAGACTTC 59.128 40.000 0.00 0.00 46.26 3.01
91 93 4.080975 TGGTGATGCAGATTCAGTCATACA 60.081 41.667 0.00 0.00 0.00 2.29
98 100 1.741706 GTGGTGGTGATGCAGATTCAG 59.258 52.381 0.00 0.00 0.00 3.02
108 110 2.734755 CCATGTATGGTGGTGGTGAT 57.265 50.000 2.66 0.00 43.05 3.06
125 127 1.378762 GGTGAGGTAAGCAAGGCCA 59.621 57.895 5.01 0.00 0.00 5.36
136 138 2.607750 ATGACGGGCTGGTGAGGT 60.608 61.111 0.00 0.00 0.00 3.85
162 164 0.694771 ACACATCATCCCAGCACACT 59.305 50.000 0.00 0.00 0.00 3.55
163 165 2.401583 TACACATCATCCCAGCACAC 57.598 50.000 0.00 0.00 0.00 3.82
164 166 2.921821 CATACACATCATCCCAGCACA 58.078 47.619 0.00 0.00 0.00 4.57
165 167 1.605710 GCATACACATCATCCCAGCAC 59.394 52.381 0.00 0.00 0.00 4.40
166 168 1.491754 AGCATACACATCATCCCAGCA 59.508 47.619 0.00 0.00 0.00 4.41
167 169 2.149578 GAGCATACACATCATCCCAGC 58.850 52.381 0.00 0.00 0.00 4.85
168 170 3.766068 AGAGCATACACATCATCCCAG 57.234 47.619 0.00 0.00 0.00 4.45
169 171 5.830799 ATAAGAGCATACACATCATCCCA 57.169 39.130 0.00 0.00 0.00 4.37
226 228 7.093333 ACAAGGAAAGGAAACAAAAAGTGAGAT 60.093 33.333 0.00 0.00 0.00 2.75
227 229 6.210584 ACAAGGAAAGGAAACAAAAAGTGAGA 59.789 34.615 0.00 0.00 0.00 3.27
302 304 6.619744 TGATGACATTCACGCAAATGTTATT 58.380 32.000 16.66 7.42 46.99 1.40
356 358 2.620585 GGATGAAAAGCTGGACCATAGC 59.379 50.000 0.00 0.00 41.43 2.97
357 359 3.889815 TGGATGAAAAGCTGGACCATAG 58.110 45.455 0.00 0.00 0.00 2.23
358 360 4.314522 TTGGATGAAAAGCTGGACCATA 57.685 40.909 0.00 0.00 0.00 2.74
359 361 2.905415 TGGATGAAAAGCTGGACCAT 57.095 45.000 0.00 0.00 0.00 3.55
360 362 2.673775 TTGGATGAAAAGCTGGACCA 57.326 45.000 0.00 0.00 0.00 4.02
361 363 3.582714 CTTTGGATGAAAAGCTGGACC 57.417 47.619 0.00 0.00 30.84 4.46
395 560 7.042725 GGCTTTTGTTTTCTTTCAACTGTATCC 60.043 37.037 0.00 0.00 0.00 2.59
410 576 1.408127 GCAACCCCTGGCTTTTGTTTT 60.408 47.619 0.00 0.00 0.00 2.43
428 594 5.425862 TGTAGTTGTATATGGTTACCAGGCA 59.574 40.000 10.74 3.23 36.75 4.75
454 622 7.092444 TGACCTGGTTTATCCTTGATTGTAGAT 60.092 37.037 0.00 0.00 37.07 1.98
462 630 3.256704 AGGTGACCTGGTTTATCCTTGA 58.743 45.455 1.77 0.00 37.07 3.02
481 660 1.885887 TGGCGGAACAATCAGAAAAGG 59.114 47.619 0.00 0.00 0.00 3.11
483 662 5.394005 CCATAATGGCGGAACAATCAGAAAA 60.394 40.000 0.00 0.00 0.00 2.29
505 684 1.075374 AGCACAGGCCTTAATGAACCA 59.925 47.619 0.00 0.00 42.56 3.67
509 688 2.877097 TGAAGCACAGGCCTTAATGA 57.123 45.000 0.00 0.00 42.56 2.57
510 689 3.194116 ACAATGAAGCACAGGCCTTAATG 59.806 43.478 0.00 2.74 42.56 1.90
512 691 2.875296 ACAATGAAGCACAGGCCTTAA 58.125 42.857 0.00 0.00 42.56 1.85
513 692 2.584835 ACAATGAAGCACAGGCCTTA 57.415 45.000 0.00 0.00 42.56 2.69
514 693 2.162681 GTACAATGAAGCACAGGCCTT 58.837 47.619 0.00 0.00 42.56 4.35
515 694 1.073763 TGTACAATGAAGCACAGGCCT 59.926 47.619 0.00 0.00 42.56 5.19
516 695 1.533625 TGTACAATGAAGCACAGGCC 58.466 50.000 0.00 0.00 42.56 5.19
517 696 3.941483 ACTATGTACAATGAAGCACAGGC 59.059 43.478 0.00 0.00 41.61 4.85
518 697 5.643348 TGAACTATGTACAATGAAGCACAGG 59.357 40.000 0.00 0.00 0.00 4.00
519 698 6.726258 TGAACTATGTACAATGAAGCACAG 57.274 37.500 0.00 0.00 0.00 3.66
520 699 7.228507 AGTTTGAACTATGTACAATGAAGCACA 59.771 33.333 0.00 0.00 37.52 4.57
521 700 7.584987 AGTTTGAACTATGTACAATGAAGCAC 58.415 34.615 0.00 0.00 37.52 4.40
526 705 8.946085 GGATCAAGTTTGAACTATGTACAATGA 58.054 33.333 0.00 0.00 41.13 2.57
551 733 4.637534 AGAAATGATGACATTCAAGACGGG 59.362 41.667 0.00 0.00 44.67 5.28
554 736 5.261661 GCGAGAAATGATGACATTCAAGAC 58.738 41.667 0.00 0.00 44.67 3.01
589 771 6.976925 CGTGGTAAAATAGAGTACCTACCTTG 59.023 42.308 1.86 0.00 40.48 3.61
597 942 5.865552 TGAACTGCGTGGTAAAATAGAGTAC 59.134 40.000 0.00 0.00 0.00 2.73
599 944 4.890088 TGAACTGCGTGGTAAAATAGAGT 58.110 39.130 0.00 0.00 0.00 3.24
629 974 4.579340 TCCATCACTTGAGTATACTCCGTC 59.421 45.833 26.37 6.66 42.20 4.79
630 975 4.533815 TCCATCACTTGAGTATACTCCGT 58.466 43.478 26.37 20.43 42.20 4.69
639 1051 6.299141 ACTAAACATGTTCCATCACTTGAGT 58.701 36.000 12.39 0.00 0.00 3.41
684 1096 2.414840 GAATCTCTCCGCTCCGCTCC 62.415 65.000 0.00 0.00 0.00 4.70
685 1097 1.007849 GAATCTCTCCGCTCCGCTC 60.008 63.158 0.00 0.00 0.00 5.03
686 1098 2.494530 GGAATCTCTCCGCTCCGCT 61.495 63.158 0.00 0.00 33.37 5.52
687 1099 2.028337 GGAATCTCTCCGCTCCGC 59.972 66.667 0.00 0.00 33.37 5.54
694 1106 1.756430 GCCCTGTTTGGAATCTCTCC 58.244 55.000 0.00 0.00 45.64 3.71
695 1107 1.339151 ACGCCCTGTTTGGAATCTCTC 60.339 52.381 0.00 0.00 38.35 3.20
696 1108 0.693049 ACGCCCTGTTTGGAATCTCT 59.307 50.000 0.00 0.00 38.35 3.10
697 1109 2.396590 TACGCCCTGTTTGGAATCTC 57.603 50.000 0.00 0.00 38.35 2.75
698 1110 2.505819 AGATACGCCCTGTTTGGAATCT 59.494 45.455 0.00 0.00 38.35 2.40
699 1111 2.614057 CAGATACGCCCTGTTTGGAATC 59.386 50.000 0.00 0.00 38.35 2.52
700 1112 2.026262 ACAGATACGCCCTGTTTGGAAT 60.026 45.455 0.00 0.00 41.68 3.01
701 1113 1.349688 ACAGATACGCCCTGTTTGGAA 59.650 47.619 0.00 0.00 41.68 3.53
702 1114 0.981183 ACAGATACGCCCTGTTTGGA 59.019 50.000 0.00 0.00 41.68 3.53
703 1115 1.086696 CACAGATACGCCCTGTTTGG 58.913 55.000 2.69 0.00 42.44 3.28
704 1116 0.447801 GCACAGATACGCCCTGTTTG 59.552 55.000 2.69 0.00 42.44 2.93
705 1117 0.036164 TGCACAGATACGCCCTGTTT 59.964 50.000 2.69 0.00 42.44 2.83
706 1118 0.673644 GTGCACAGATACGCCCTGTT 60.674 55.000 13.17 0.00 42.44 3.16
707 1119 1.079127 GTGCACAGATACGCCCTGT 60.079 57.895 13.17 0.00 44.92 4.00
708 1120 0.462581 ATGTGCACAGATACGCCCTG 60.463 55.000 25.84 0.00 37.64 4.45
709 1121 0.253044 AATGTGCACAGATACGCCCT 59.747 50.000 25.84 1.33 0.00 5.19
710 1122 0.657840 GAATGTGCACAGATACGCCC 59.342 55.000 25.84 4.03 0.00 6.13
711 1123 1.062587 GTGAATGTGCACAGATACGCC 59.937 52.381 25.84 8.92 38.63 5.68
712 1124 1.062587 GGTGAATGTGCACAGATACGC 59.937 52.381 25.84 19.48 40.52 4.42
713 1125 2.349580 CAGGTGAATGTGCACAGATACG 59.650 50.000 25.84 6.39 40.52 3.06
714 1126 2.096496 GCAGGTGAATGTGCACAGATAC 59.904 50.000 25.84 20.69 40.52 2.24
717 1129 0.179023 TGCAGGTGAATGTGCACAGA 60.179 50.000 25.84 8.79 44.70 3.41
739 1151 2.123589 TGATAGGGCGAGGATGGAAAA 58.876 47.619 0.00 0.00 0.00 2.29
747 1159 0.389166 GAAGCGATGATAGGGCGAGG 60.389 60.000 0.00 0.00 0.00 4.63
758 1170 3.068732 TCCTATTCTCACTGGAAGCGATG 59.931 47.826 0.00 0.00 37.60 3.84
764 1176 3.952323 CGGTAGTCCTATTCTCACTGGAA 59.048 47.826 0.00 0.00 0.00 3.53
822 1238 1.727511 CGGTATGCCTGCCACCATTG 61.728 60.000 0.00 0.00 32.32 2.82
831 1247 0.966920 CCTACCTACCGGTATGCCTG 59.033 60.000 16.25 2.47 44.54 4.85
849 1265 1.499502 GTCTCTTGCAGCTTTCGCC 59.500 57.895 0.00 0.00 36.60 5.54
933 1355 1.336240 GGACATGACTGGCAAAACTGC 60.336 52.381 0.00 0.00 28.82 4.40
991 1419 3.310774 GCTCGAGTGTTCATGTATGCAAT 59.689 43.478 15.13 0.00 0.00 3.56
992 1420 2.672874 GCTCGAGTGTTCATGTATGCAA 59.327 45.455 15.13 0.00 0.00 4.08
993 1421 2.270923 GCTCGAGTGTTCATGTATGCA 58.729 47.619 15.13 0.00 0.00 3.96
994 1422 2.029728 GTGCTCGAGTGTTCATGTATGC 59.970 50.000 15.13 0.00 0.00 3.14
995 1423 2.604914 GGTGCTCGAGTGTTCATGTATG 59.395 50.000 15.13 0.00 0.00 2.39
1322 1756 4.821589 GGAGGAACTGCTCGGCCG 62.822 72.222 22.12 22.12 45.87 6.13
1776 2215 5.593285 AGTTTCTTCAACCTGGCAACAACA 61.593 41.667 0.00 0.00 39.22 3.33
1911 2356 1.808945 GACTTGTCTTCCTGCACCATG 59.191 52.381 0.00 0.00 0.00 3.66
1962 2410 2.737376 GCCTTGACGTCCGTGTCC 60.737 66.667 14.12 0.00 38.11 4.02
2001 2449 1.081242 GTCACGGCCGACTACGAAA 60.081 57.895 35.90 4.23 42.66 3.46
2054 4236 2.126346 GGCACATTGAACGGCTGC 60.126 61.111 0.00 0.00 0.00 5.25
2058 4240 3.440173 AGTTAATCAGGCACATTGAACGG 59.560 43.478 0.00 0.00 0.00 4.44
2062 4244 3.691118 GCAGAGTTAATCAGGCACATTGA 59.309 43.478 0.00 0.00 32.47 2.57
2881 5513 9.764363 TCCATGCTATATCTAAAAACAGTACAG 57.236 33.333 0.00 0.00 0.00 2.74
3007 5639 1.726791 CTGACGTGTGGCACTTATCAC 59.273 52.381 19.83 7.15 31.34 3.06
3035 5667 0.773644 AAATGTCAGGGCAGGAGTGT 59.226 50.000 0.00 0.00 0.00 3.55
3057 5689 2.076100 TGCGTGACTGGAATTGTCATC 58.924 47.619 0.94 0.00 44.74 2.92
3113 5755 6.476380 TCATGACAATTTTTGTGCTTCAGTTC 59.524 34.615 0.00 0.00 45.52 3.01
3146 5788 3.745975 TGACGCAAGGATGACAACTTTAG 59.254 43.478 0.00 0.00 46.39 1.85
3165 5807 4.208253 CGTTTTTATGGCAAGTTTGGTGAC 59.792 41.667 0.00 0.00 0.00 3.67
3170 5812 5.292101 TCCAAACGTTTTTATGGCAAGTTTG 59.708 36.000 11.66 10.16 43.54 2.93
3178 5820 5.583495 TGACAACTCCAAACGTTTTTATGG 58.417 37.500 11.66 10.69 0.00 2.74
3196 5839 1.227793 TGGCACGAGCACATGACAA 60.228 52.632 7.26 0.00 44.61 3.18
3217 5860 3.786553 AGGACCTGATAAGTACCACACA 58.213 45.455 0.00 0.00 0.00 3.72
3244 5888 9.573166 AGCATAACAATATACATGGTGTACATT 57.427 29.630 0.00 0.00 37.84 2.71
3247 5891 9.706691 AGTAGCATAACAATATACATGGTGTAC 57.293 33.333 0.00 0.00 35.42 2.90
3284 5928 9.581099 GAAAAGAAAACAAAGACTATTTGGTCA 57.419 29.630 5.43 0.00 38.57 4.02
3285 5929 9.803315 AGAAAAGAAAACAAAGACTATTTGGTC 57.197 29.630 5.43 0.00 36.56 4.02
3307 5951 9.638239 GCCTTCATTATTTCAACATACAAGAAA 57.362 29.630 0.00 0.00 35.92 2.52
3309 5953 7.395772 TGGCCTTCATTATTTCAACATACAAGA 59.604 33.333 3.32 0.00 0.00 3.02
3327 5971 0.829602 TTTGCGGGAAATGGCCTTCA 60.830 50.000 3.32 0.00 0.00 3.02
3351 5995 9.784376 AGTCATGGCCTAGGTTATTTCTATATA 57.216 33.333 11.31 0.00 0.00 0.86
3397 6041 7.753309 TTGTTTTACCAACAGCTGTATATGT 57.247 32.000 22.01 16.36 0.00 2.29
3405 6049 8.299570 CAAGATAAGATTGTTTTACCAACAGCT 58.700 33.333 0.00 0.00 0.00 4.24
3407 6051 9.831737 CTCAAGATAAGATTGTTTTACCAACAG 57.168 33.333 0.00 0.00 0.00 3.16
3412 6056 8.045176 ACTGCTCAAGATAAGATTGTTTTACC 57.955 34.615 0.00 0.00 0.00 2.85
3413 6057 9.899226 AAACTGCTCAAGATAAGATTGTTTTAC 57.101 29.630 0.00 0.00 0.00 2.01
3498 6142 9.933723 TTAGGAATAACTGGTTACTAGTTGAAC 57.066 33.333 21.53 12.58 38.70 3.18
3551 6195 8.510505 GGCTTGCCTTCTCTTAATTAATAGATG 58.489 37.037 12.55 13.72 0.00 2.90
3556 6200 5.770919 AGGGCTTGCCTTCTCTTAATTAAT 58.229 37.500 11.71 0.00 0.00 1.40
3583 6227 5.883115 GTGGAGGAAAGAGAAATAAGAAGGG 59.117 44.000 0.00 0.00 0.00 3.95
3584 6228 5.883115 GGTGGAGGAAAGAGAAATAAGAAGG 59.117 44.000 0.00 0.00 0.00 3.46
3610 6254 4.460263 ACTGCCAAATAGGATAAATGCGA 58.540 39.130 0.00 0.00 41.22 5.10
3625 6269 7.081349 CGATGTTTTTGTCTTATAACTGCCAA 58.919 34.615 0.00 0.00 0.00 4.52
3631 6275 7.748683 TCATGCACGATGTTTTTGTCTTATAAC 59.251 33.333 0.00 0.00 33.29 1.89
3633 6277 7.240674 GTCATGCACGATGTTTTTGTCTTATA 58.759 34.615 0.00 0.00 33.29 0.98
3634 6278 6.086222 GTCATGCACGATGTTTTTGTCTTAT 58.914 36.000 0.00 0.00 33.29 1.73
3640 6284 3.287312 AGGTCATGCACGATGTTTTTG 57.713 42.857 0.00 0.00 33.29 2.44
3645 6289 2.760634 TGTTAGGTCATGCACGATGT 57.239 45.000 0.00 0.00 33.29 3.06
3649 6293 2.097466 GGGAAATGTTAGGTCATGCACG 59.903 50.000 0.00 0.00 0.00 5.34
3652 6296 1.676006 CGGGGAAATGTTAGGTCATGC 59.324 52.381 0.00 0.00 0.00 4.06
3655 6299 3.616219 CATTCGGGGAAATGTTAGGTCA 58.384 45.455 0.00 0.00 32.97 4.02
3657 6301 2.375146 GCATTCGGGGAAATGTTAGGT 58.625 47.619 0.00 0.00 38.60 3.08
3668 6312 2.127232 GGAATGGTGGCATTCGGGG 61.127 63.158 0.00 0.00 41.23 5.73
3672 6316 1.463674 AACGAGGAATGGTGGCATTC 58.536 50.000 0.00 0.00 39.99 2.67
3682 6326 0.108329 CTGGCACCGTAACGAGGAAT 60.108 55.000 0.00 0.00 0.00 3.01
3688 6332 2.554272 GCAACTGGCACCGTAACG 59.446 61.111 0.00 0.00 43.97 3.18
3700 6344 4.439253 AAAAGGTGTCCTTCTAGCAACT 57.561 40.909 1.36 0.00 43.92 3.16
3728 6372 0.242555 TCTTACGCGTGTGAGCATGA 59.757 50.000 24.59 5.43 36.85 3.07


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

AutoCloner maintained by Alex Coulton.