Multiple sequence alignment - TraesCS6B01G067200

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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 TraesCS6B01G067200 chr6B 100.000 3116 0 0 1 3116 45541221 45544336 0.000000e+00 5755.0
1 TraesCS6B01G067200 chr6B 75.393 191 39 6 397 582 619518599 619518786 5.540000e-13 86.1
2 TraesCS6B01G067200 chrUn 91.483 2313 128 23 709 3002 94997731 94999993 0.000000e+00 3116.0
3 TraesCS6B01G067200 chrUn 85.673 691 58 10 1 674 94997066 94997732 0.000000e+00 689.0
4 TraesCS6B01G067200 chr6A 88.908 1731 110 32 738 2438 26529152 26530830 0.000000e+00 2058.0
5 TraesCS6B01G067200 chr6A 90.154 325 21 7 2565 2885 26531386 26531703 2.240000e-111 412.0
6 TraesCS6B01G067200 chr6A 82.773 238 28 10 2882 3116 26532469 26532696 1.900000e-47 200.0
7 TraesCS6B01G067200 chr2D 84.946 93 8 4 3024 3116 286669740 286669654 4.280000e-14 89.8
8 TraesCS6B01G067200 chr4D 76.571 175 31 6 431 598 379553052 379552881 1.540000e-13 87.9
9 TraesCS6B01G067200 chr7D 73.684 190 47 3 401 589 580762906 580763093 1.550000e-08 71.3
10 TraesCS6B01G067200 chr5B 79.412 102 20 1 438 539 571611153 571611053 1.550000e-08 71.3
11 TraesCS6B01G067200 chr2B 97.368 38 1 0 3079 3116 3664381 3664344 7.210000e-07 65.8
12 TraesCS6B01G067200 chr2B 97.368 38 1 0 3079 3116 3681737 3681774 7.210000e-07 65.8
13 TraesCS6B01G067200 chr2B 97.368 38 1 0 3079 3116 3692250 3692213 7.210000e-07 65.8


These results show the homologous regions that are presented in the multiple sequence alignment. HSPs from the BLAST search that are within 2000 bases of each other have been grouped together. Homologous regions that are purely upstream or downstream may be removed if they don't overlap both primers.

query scaffold start end length rev.comp avg.bitscore max.bitscore avg.percent.identical query.start query.end num_hsp groupid homo_length
0 TraesCS6B01G067200 chr6B 45541221 45544336 3115 False 5755.0 5755 100.000000 1 3116 1 chr6B.!!$F1 3115
1 TraesCS6B01G067200 chrUn 94997066 94999993 2927 False 1902.5 3116 88.578000 1 3002 2 chrUn.!!$F1 3001
2 TraesCS6B01G067200 chr6A 26529152 26532696 3544 False 890.0 2058 87.278333 738 3116 3 chr6A.!!$F1 2378

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
597 606 0.039437 GTGCCGACTCACTCTTTCGA 60.039 55.0 0.0 0.0 34.62 3.71 F
2004 2048 0.174845 CGTGGGAAGCGTTGGAGATA 59.825 55.0 0.0 0.0 0.00 1.98 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2100 2144 0.179225 CAGTTCAACGCGGGATTTCG 60.179 55.0 12.47 0.0 0.0 3.46 R
2904 4170 0.034337 GGACAAACACGACAGGGCTA 59.966 55.0 0.00 0.0 0.0 3.93 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
37 38 4.766891 ACTATACATTGTTGCAGCCTTTGT 59.233 37.500 0.00 1.95 0.00 2.83
81 82 2.260154 TGAAGGTACGACGTCGCCA 61.260 57.895 35.92 22.22 44.43 5.69
84 85 2.467946 AAGGTACGACGTCGCCACTG 62.468 60.000 35.92 11.11 44.43 3.66
85 86 2.557805 GTACGACGTCGCCACTGA 59.442 61.111 35.92 12.89 44.43 3.41
86 87 1.081906 GTACGACGTCGCCACTGAA 60.082 57.895 35.92 11.30 44.43 3.02
118 120 4.294523 GGCACGATGCTGTAACCA 57.705 55.556 9.31 0.00 44.28 3.67
125 127 0.529773 GATGCTGTAACCATCGCCGA 60.530 55.000 0.00 0.00 30.88 5.54
150 152 0.745486 CTGGAACCAGCGATGCATGA 60.745 55.000 2.46 0.00 37.24 3.07
151 153 0.322366 TGGAACCAGCGATGCATGAA 60.322 50.000 2.46 0.00 0.00 2.57
152 154 0.379669 GGAACCAGCGATGCATGAAG 59.620 55.000 2.46 0.00 0.00 3.02
153 155 1.089920 GAACCAGCGATGCATGAAGT 58.910 50.000 2.46 0.00 0.00 3.01
154 156 1.470098 GAACCAGCGATGCATGAAGTT 59.530 47.619 2.46 0.00 0.00 2.66
155 157 0.806868 ACCAGCGATGCATGAAGTTG 59.193 50.000 2.46 3.58 0.00 3.16
156 158 0.524816 CCAGCGATGCATGAAGTTGC 60.525 55.000 2.46 0.00 43.07 4.17
157 159 0.450583 CAGCGATGCATGAAGTTGCT 59.549 50.000 2.46 0.00 43.18 3.91
158 160 1.667212 CAGCGATGCATGAAGTTGCTA 59.333 47.619 2.46 0.00 43.18 3.49
159 161 2.289820 CAGCGATGCATGAAGTTGCTAT 59.710 45.455 2.46 0.00 43.18 2.97
160 162 2.289820 AGCGATGCATGAAGTTGCTATG 59.710 45.455 2.46 0.00 43.18 2.23
161 163 2.603892 GCGATGCATGAAGTTGCTATGG 60.604 50.000 2.46 0.00 43.18 2.74
162 164 2.603892 CGATGCATGAAGTTGCTATGGC 60.604 50.000 2.46 0.00 43.18 4.40
262 265 3.932580 CTACTGCTCCGCCACGCAA 62.933 63.158 0.00 0.00 35.46 4.85
278 281 1.737029 CGCAAGTCGATCCATGTGACT 60.737 52.381 0.00 0.00 44.46 3.41
336 339 2.139917 CCACTTCGTCGACCATTTTCA 58.860 47.619 10.58 0.00 0.00 2.69
347 350 4.048504 CGACCATTTTCAAAACTTGTCCC 58.951 43.478 0.00 0.00 0.00 4.46
354 357 0.316689 CAAAACTTGTCCCGCACGAC 60.317 55.000 0.00 0.00 0.00 4.34
362 365 1.595929 TCCCGCACGACAGAAAACC 60.596 57.895 0.00 0.00 0.00 3.27
363 366 1.890041 CCCGCACGACAGAAAACCA 60.890 57.895 0.00 0.00 0.00 3.67
364 367 1.440938 CCCGCACGACAGAAAACCAA 61.441 55.000 0.00 0.00 0.00 3.67
403 406 2.289444 ACGTTGGTCACTACTTGGATGG 60.289 50.000 0.00 0.00 0.00 3.51
411 414 4.710375 GTCACTACTTGGATGGTTAGGAGA 59.290 45.833 0.00 0.00 0.00 3.71
412 415 5.187186 GTCACTACTTGGATGGTTAGGAGAA 59.813 44.000 0.00 0.00 0.00 2.87
418 421 2.027192 TGGATGGTTAGGAGAACAGTGC 60.027 50.000 0.00 0.00 0.00 4.40
425 428 4.647399 GGTTAGGAGAACAGTGCTATCTCT 59.353 45.833 16.32 8.59 39.59 3.10
450 453 3.679824 AACGAGGGTTCAAGTTCTAGG 57.320 47.619 0.00 0.00 0.00 3.02
469 472 1.997606 GGCTTGACATTTGATGCTTGC 59.002 47.619 0.00 0.00 0.00 4.01
487 490 9.698617 GATGCTTGCATTTTTCTGAATTTATTC 57.301 29.630 9.59 0.00 37.31 1.75
499 502 4.004314 TGAATTTATTCCACGCCTTTCGA 58.996 39.130 0.32 0.00 37.53 3.71
504 507 0.527113 TTCCACGCCTTTCGACGATA 59.473 50.000 0.00 0.00 41.67 2.92
527 536 1.760613 TGTTCAGTGGGAAGAGACGTT 59.239 47.619 0.00 0.00 35.82 3.99
528 537 2.169769 TGTTCAGTGGGAAGAGACGTTT 59.830 45.455 0.00 0.00 35.82 3.60
530 539 2.036387 TCAGTGGGAAGAGACGTTTCA 58.964 47.619 8.98 0.00 0.00 2.69
554 563 8.758829 TCAGTTGACTACAAAGACATATATGGT 58.241 33.333 16.96 7.15 37.77 3.55
584 593 3.119065 TCGGTCTTAACATAATGTGCCGA 60.119 43.478 0.00 0.00 42.58 5.54
586 595 4.189231 GGTCTTAACATAATGTGCCGACT 58.811 43.478 0.00 0.00 0.00 4.18
587 596 4.270325 GGTCTTAACATAATGTGCCGACTC 59.730 45.833 0.00 0.00 0.00 3.36
589 598 4.868171 TCTTAACATAATGTGCCGACTCAC 59.132 41.667 0.00 0.00 37.48 3.51
593 602 3.055819 ACATAATGTGCCGACTCACTCTT 60.056 43.478 0.00 0.00 37.81 2.85
597 606 0.039437 GTGCCGACTCACTCTTTCGA 60.039 55.000 0.00 0.00 34.62 3.71
624 642 8.230486 GTGTAGAACATGTGTTTTCTTATCAGG 58.770 37.037 0.00 0.00 38.56 3.86
625 643 6.824305 AGAACATGTGTTTTCTTATCAGGG 57.176 37.500 0.00 0.00 38.56 4.45
631 649 4.935205 TGTGTTTTCTTATCAGGGTCATCG 59.065 41.667 0.00 0.00 0.00 3.84
632 650 4.332819 GTGTTTTCTTATCAGGGTCATCGG 59.667 45.833 0.00 0.00 0.00 4.18
644 662 2.095263 GGGTCATCGGTGTGTTGAAATG 60.095 50.000 0.00 0.00 0.00 2.32
670 688 2.677542 TACTACAGGCCATCGATCCT 57.322 50.000 5.01 0.00 0.00 3.24
675 693 2.620251 CAGGCCATCGATCCTGTAAA 57.380 50.000 20.11 0.00 43.66 2.01
676 694 3.131709 CAGGCCATCGATCCTGTAAAT 57.868 47.619 20.11 0.00 43.66 1.40
677 695 4.271696 CAGGCCATCGATCCTGTAAATA 57.728 45.455 20.11 0.00 43.66 1.40
679 697 3.003480 GGCCATCGATCCTGTAAATAGC 58.997 50.000 0.00 0.00 0.00 2.97
680 698 2.668457 GCCATCGATCCTGTAAATAGCG 59.332 50.000 0.00 0.00 0.00 4.26
681 699 3.614150 GCCATCGATCCTGTAAATAGCGA 60.614 47.826 0.00 0.00 0.00 4.93
682 700 4.748892 CCATCGATCCTGTAAATAGCGAT 58.251 43.478 0.00 0.00 37.47 4.58
683 701 4.800993 CCATCGATCCTGTAAATAGCGATC 59.199 45.833 0.00 0.00 35.16 3.69
687 705 5.940603 GATCCTGTAAATAGCGATCGATG 57.059 43.478 21.57 0.00 0.00 3.84
688 706 4.174411 TCCTGTAAATAGCGATCGATGG 57.826 45.455 21.57 8.40 0.00 3.51
689 707 3.572682 TCCTGTAAATAGCGATCGATGGT 59.427 43.478 21.57 2.89 0.00 3.55
690 708 3.921021 CCTGTAAATAGCGATCGATGGTC 59.079 47.826 21.57 0.00 0.00 4.02
691 709 3.561503 TGTAAATAGCGATCGATGGTCG 58.438 45.455 21.57 1.78 42.10 4.79
703 721 2.725641 TGGTCGACCAGTGACGTG 59.274 61.111 33.23 0.00 42.01 4.49
704 722 2.122797 TGGTCGACCAGTGACGTGT 61.123 57.895 33.23 0.00 42.01 4.49
705 723 0.818852 TGGTCGACCAGTGACGTGTA 60.819 55.000 33.23 6.51 42.01 2.90
706 724 0.386478 GGTCGACCAGTGACGTGTAC 60.386 60.000 29.75 0.00 37.22 2.90
707 725 0.308684 GTCGACCAGTGACGTGTACA 59.691 55.000 3.51 0.00 0.00 2.90
708 726 1.068748 GTCGACCAGTGACGTGTACAT 60.069 52.381 3.51 0.00 0.00 2.29
709 727 2.160219 GTCGACCAGTGACGTGTACATA 59.840 50.000 3.51 0.00 0.00 2.29
710 728 2.160219 TCGACCAGTGACGTGTACATAC 59.840 50.000 0.00 0.00 0.00 2.39
711 729 2.161012 CGACCAGTGACGTGTACATACT 59.839 50.000 0.00 0.00 0.00 2.12
712 730 3.371898 CGACCAGTGACGTGTACATACTA 59.628 47.826 0.00 0.00 0.00 1.82
713 731 4.656041 GACCAGTGACGTGTACATACTAC 58.344 47.826 0.00 0.00 0.00 2.73
714 732 3.125829 ACCAGTGACGTGTACATACTACG 59.874 47.826 0.00 0.00 42.98 3.51
717 735 5.384787 CAGTGACGTGTACATACTACGAAA 58.615 41.667 9.49 0.00 40.01 3.46
723 741 4.795278 CGTGTACATACTACGAAAGGGAAC 59.205 45.833 0.00 0.00 40.01 3.62
726 744 6.646240 GTGTACATACTACGAAAGGGAACAAA 59.354 38.462 0.00 0.00 0.00 2.83
729 747 7.141100 ACATACTACGAAAGGGAACAAAATG 57.859 36.000 0.00 0.00 0.00 2.32
746 767 7.623268 ACAAAATGCTACTCGAAATGTTTTC 57.377 32.000 0.00 0.00 0.00 2.29
757 778 4.036262 TCGAAATGTTTTCCTTGTGACCAG 59.964 41.667 0.00 0.00 0.00 4.00
787 808 7.555965 TCTCCAGAAAATCAATCGAGATGTAA 58.444 34.615 0.00 0.00 0.00 2.41
808 829 1.599797 ACCGCGCCTGCTTTTTACT 60.600 52.632 0.00 0.00 39.65 2.24
811 832 1.212751 GCGCCTGCTTTTTACTGGG 59.787 57.895 0.00 0.00 38.39 4.45
840 861 2.747855 CCACAAGAAGCTCCGGGC 60.748 66.667 0.00 3.80 42.19 6.13
885 914 4.441695 TCTCCGGCTGCAGCTTCG 62.442 66.667 35.82 29.84 41.70 3.79
1073 1102 1.533753 CAAAGCCTCCCAAGCCCAA 60.534 57.895 0.00 0.00 0.00 4.12
1079 1108 3.516512 TCCCAAGCCCAAGCCCAA 61.517 61.111 0.00 0.00 41.25 4.12
1305 1340 4.773117 GTCCTCGCCGTGTCCGTC 62.773 72.222 0.00 0.00 0.00 4.79
1497 1538 1.512230 GTACATACGCACCGTGGGA 59.488 57.895 21.38 6.42 41.39 4.37
1920 1961 2.675772 GACGTCTCCCCACGACCT 60.676 66.667 8.70 0.00 42.69 3.85
1926 1967 4.316823 TCCCCACGACCTCTGGCT 62.317 66.667 0.00 0.00 0.00 4.75
1960 2004 1.162085 GAGGGGGAGATGGGCCTAT 59.838 63.158 0.00 0.00 0.00 2.57
1989 2033 0.924090 GTAGAGCGCTGAAATCGTGG 59.076 55.000 18.48 0.00 0.00 4.94
2004 2048 0.174845 CGTGGGAAGCGTTGGAGATA 59.825 55.000 0.00 0.00 0.00 1.98
2015 2059 3.285215 GGAGATAGCCGGCGTCGA 61.285 66.667 23.20 8.45 39.00 4.20
2103 2147 3.115892 GGCATCAACGCCGACGAA 61.116 61.111 0.00 0.00 43.52 3.85
2108 2152 1.087771 ATCAACGCCGACGAAATCCC 61.088 55.000 0.00 0.00 43.93 3.85
2109 2153 2.812178 AACGCCGACGAAATCCCG 60.812 61.111 0.00 0.00 43.93 5.14
2138 2182 2.632541 GATCGATGCTGCTGCTGC 59.367 61.111 22.51 22.51 40.48 5.25
2139 2183 1.888172 GATCGATGCTGCTGCTGCT 60.888 57.895 27.67 15.76 40.48 4.24
2140 2184 2.107151 GATCGATGCTGCTGCTGCTG 62.107 60.000 27.67 16.73 40.48 4.41
2147 2191 4.274008 TGCTGCTGCTGCTTGGGA 62.274 61.111 27.67 8.50 40.48 4.37
2244 2288 0.250901 ACGCAAAAGATGTGCTCCCT 60.251 50.000 0.00 0.00 43.55 4.20
2246 2290 1.667724 CGCAAAAGATGTGCTCCCTAG 59.332 52.381 0.00 0.00 39.95 3.02
2335 2380 8.554528 CATGTTCATCTTCTGGTTCATATACAC 58.445 37.037 0.00 0.00 0.00 2.90
2345 2392 6.755141 TCTGGTTCATATACACGAGCTTAAAC 59.245 38.462 0.00 0.00 0.00 2.01
2396 2446 5.327891 GCTCATCGATTTCAGGTTTCTTTC 58.672 41.667 0.00 0.00 0.00 2.62
2401 2451 6.875948 TCGATTTCAGGTTTCTTTCAATCA 57.124 33.333 0.00 0.00 0.00 2.57
2410 2460 8.054572 TCAGGTTTCTTTCAATCATCCATGATA 58.945 33.333 2.41 0.00 46.22 2.15
2452 2788 4.464244 TGGCCAATTTACGATCCATTTCAA 59.536 37.500 0.61 0.00 0.00 2.69
2453 2789 5.128499 TGGCCAATTTACGATCCATTTCAAT 59.872 36.000 0.61 0.00 0.00 2.57
2454 2790 6.048509 GGCCAATTTACGATCCATTTCAATT 58.951 36.000 0.00 0.00 0.00 2.32
2455 2791 6.538381 GGCCAATTTACGATCCATTTCAATTT 59.462 34.615 0.00 0.00 0.00 1.82
2456 2792 7.065683 GGCCAATTTACGATCCATTTCAATTTT 59.934 33.333 0.00 0.00 0.00 1.82
2457 2793 8.116136 GCCAATTTACGATCCATTTCAATTTTC 58.884 33.333 0.00 0.00 0.00 2.29
2458 2794 9.149225 CCAATTTACGATCCATTTCAATTTTCA 57.851 29.630 0.00 0.00 0.00 2.69
2494 2830 2.034124 GGGGATGGTGATGTGGAATTG 58.966 52.381 0.00 0.00 0.00 2.32
2557 2893 2.021355 ATCCTCTGCGCTCAAAAGAG 57.979 50.000 9.73 11.93 37.73 2.85
2564 2900 4.659002 GCTCAAAAGAGCGCATCG 57.341 55.556 11.47 0.00 38.52 3.84
2631 3124 7.361885 CCTGAATCAGAATTCTCAAGGAAGTTG 60.362 40.741 12.53 0.00 41.63 3.16
2754 3250 2.438434 GGTGGGCAGTCAATCCCG 60.438 66.667 0.00 0.00 45.60 5.14
2802 3298 6.532657 GTGCATCATTTATTTGTCCCAAGAAG 59.467 38.462 0.00 0.00 0.00 2.85
2826 3322 5.300969 TGCTGCTGTTCATTAAATGAGAC 57.699 39.130 0.00 0.00 40.94 3.36
2871 3367 5.843673 TCTGATGAGACATGGAGTAGAAC 57.156 43.478 0.00 0.00 0.00 3.01
2881 3377 1.336887 TGGAGTAGAACGCAAGCACTC 60.337 52.381 2.01 2.01 45.62 3.51
2889 3385 1.140589 CGCAAGCACTCGAGGAGAT 59.859 57.895 18.41 4.58 33.32 2.75
2904 4170 5.104776 TCGAGGAGATTGGACAAGATCATTT 60.105 40.000 0.00 0.00 0.00 2.32
2908 4174 5.240403 GGAGATTGGACAAGATCATTTAGCC 59.760 44.000 0.00 0.00 0.00 3.93
2924 4190 1.525077 GCCCTGTCGTGTTTGTCCA 60.525 57.895 0.00 0.00 0.00 4.02
2966 4232 3.460103 GGAAAGAAGTCCGTGTTACACA 58.540 45.455 16.09 0.00 33.40 3.72
2972 4238 0.505655 GTCCGTGTTACACAACGAGC 59.494 55.000 16.09 0.00 37.48 5.03
2975 4241 1.205657 CGTGTTACACAACGAGCAGT 58.794 50.000 16.09 0.00 37.48 4.40
3003 4269 2.203126 GGGCGAGCTCCATGGAAG 60.203 66.667 17.00 11.06 0.00 3.46
3004 4270 2.899339 GGCGAGCTCCATGGAAGC 60.899 66.667 17.00 19.89 0.00 3.86
3009 4275 1.134401 CGAGCTCCATGGAAGCCTTTA 60.134 52.381 24.08 0.00 0.00 1.85
3010 4276 2.486191 CGAGCTCCATGGAAGCCTTTAT 60.486 50.000 24.08 11.56 0.00 1.40
3011 4277 3.560105 GAGCTCCATGGAAGCCTTTATT 58.440 45.455 24.08 11.01 0.00 1.40
3012 4278 3.956848 GAGCTCCATGGAAGCCTTTATTT 59.043 43.478 24.08 10.47 0.00 1.40
3013 4279 4.356436 AGCTCCATGGAAGCCTTTATTTT 58.644 39.130 24.08 7.97 0.00 1.82
3014 4280 4.161001 AGCTCCATGGAAGCCTTTATTTTG 59.839 41.667 24.08 8.11 0.00 2.44
3017 4283 6.678568 TCCATGGAAGCCTTTATTTTGAAA 57.321 33.333 13.46 0.00 0.00 2.69
3018 4284 7.256494 TCCATGGAAGCCTTTATTTTGAAAT 57.744 32.000 13.46 0.00 0.00 2.17
3019 4285 7.688343 TCCATGGAAGCCTTTATTTTGAAATT 58.312 30.769 13.46 0.00 0.00 1.82
3020 4286 8.162746 TCCATGGAAGCCTTTATTTTGAAATTT 58.837 29.630 13.46 0.00 0.00 1.82
3021 4287 8.795513 CCATGGAAGCCTTTATTTTGAAATTTT 58.204 29.630 5.56 0.00 0.00 1.82
3073 4339 3.784338 TCGGAAGAAAAAGTACACGTGT 58.216 40.909 26.52 26.52 37.03 4.49
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
12 13 4.494091 AGGCTGCAACAATGTATAGTCT 57.506 40.909 0.50 0.00 0.00 3.24
37 38 2.027561 CCACTGGTTCCTACATTTCCGA 60.028 50.000 0.00 0.00 0.00 4.55
113 115 1.517694 GCGTCTTCGGCGATGGTTA 60.518 57.895 20.67 0.30 37.56 2.85
118 120 3.001902 TTCCAGCGTCTTCGGCGAT 62.002 57.895 11.76 0.00 37.56 4.58
155 157 3.788797 GCAACTTACGTCATTGCCATAGC 60.789 47.826 16.46 0.00 42.32 2.97
156 158 3.544048 CGCAACTTACGTCATTGCCATAG 60.544 47.826 19.66 7.34 44.71 2.23
157 159 2.350192 CGCAACTTACGTCATTGCCATA 59.650 45.455 19.66 0.00 44.71 2.74
158 160 1.130373 CGCAACTTACGTCATTGCCAT 59.870 47.619 19.66 0.00 44.71 4.40
159 161 0.515127 CGCAACTTACGTCATTGCCA 59.485 50.000 19.66 0.00 44.71 4.92
160 162 0.179200 CCGCAACTTACGTCATTGCC 60.179 55.000 19.66 7.70 44.71 4.52
161 163 0.793104 GCCGCAACTTACGTCATTGC 60.793 55.000 17.05 17.05 44.21 3.56
162 164 0.518355 CGCCGCAACTTACGTCATTG 60.518 55.000 0.00 0.00 0.00 2.82
163 165 1.632046 CCGCCGCAACTTACGTCATT 61.632 55.000 0.00 0.00 0.00 2.57
164 166 2.098233 CCGCCGCAACTTACGTCAT 61.098 57.895 0.00 0.00 0.00 3.06
165 167 2.735478 CCGCCGCAACTTACGTCA 60.735 61.111 0.00 0.00 0.00 4.35
166 168 4.143363 GCCGCCGCAACTTACGTC 62.143 66.667 0.00 0.00 34.03 4.34
262 265 2.093973 GGAACAGTCACATGGATCGACT 60.094 50.000 0.00 0.50 40.60 4.18
266 269 2.386661 ACGGAACAGTCACATGGATC 57.613 50.000 0.00 0.00 0.00 3.36
278 281 0.813184 GATCGGTCACCTACGGAACA 59.187 55.000 0.00 0.00 40.41 3.18
336 339 0.745128 TGTCGTGCGGGACAAGTTTT 60.745 50.000 7.14 0.00 43.55 2.43
347 350 0.653323 CGTTGGTTTTCTGTCGTGCG 60.653 55.000 0.00 0.00 0.00 5.34
354 357 2.478879 GGTGTTCACCGTTGGTTTTCTG 60.479 50.000 6.22 0.00 31.02 3.02
362 365 0.591170 GACCATGGTGTTCACCGTTG 59.409 55.000 25.52 12.55 0.00 4.10
363 366 0.181587 TGACCATGGTGTTCACCGTT 59.818 50.000 25.52 1.48 0.00 4.44
364 367 0.534203 GTGACCATGGTGTTCACCGT 60.534 55.000 25.52 13.27 0.00 4.83
380 383 2.033372 TCCAAGTAGTGACCAACGTGA 58.967 47.619 0.00 0.00 0.00 4.35
403 406 5.845391 AGAGATAGCACTGTTCTCCTAAC 57.155 43.478 4.12 0.00 37.24 2.34
411 414 3.487711 CGTTCGCTAGAGATAGCACTGTT 60.488 47.826 7.92 0.00 42.95 3.16
412 415 2.032302 CGTTCGCTAGAGATAGCACTGT 59.968 50.000 7.92 0.00 42.95 3.55
418 421 2.496111 ACCCTCGTTCGCTAGAGATAG 58.504 52.381 0.00 0.00 36.65 2.08
432 435 1.550976 AGCCTAGAACTTGAACCCTCG 59.449 52.381 0.00 0.00 0.00 4.63
433 436 3.339141 CAAGCCTAGAACTTGAACCCTC 58.661 50.000 16.32 0.00 45.99 4.30
443 446 4.397417 AGCATCAAATGTCAAGCCTAGAAC 59.603 41.667 0.00 0.00 0.00 3.01
450 453 2.679450 TGCAAGCATCAAATGTCAAGC 58.321 42.857 0.00 0.00 0.00 4.01
469 472 6.813152 AGGCGTGGAATAAATTCAGAAAAATG 59.187 34.615 5.15 0.00 38.53 2.32
499 502 3.513912 TCTTCCCACTGAACACATATCGT 59.486 43.478 0.00 0.00 0.00 3.73
504 507 2.289072 CGTCTCTTCCCACTGAACACAT 60.289 50.000 0.00 0.00 0.00 3.21
527 536 9.599866 CCATATATGTCTTTGTAGTCAACTGAA 57.400 33.333 11.73 0.00 32.93 3.02
528 537 8.758829 ACCATATATGTCTTTGTAGTCAACTGA 58.241 33.333 11.73 0.00 32.93 3.41
554 563 8.714179 CACATTATGTTAAGACCGACAAAGTTA 58.286 33.333 0.00 0.00 0.00 2.24
555 564 7.581476 CACATTATGTTAAGACCGACAAAGTT 58.419 34.615 0.00 0.00 0.00 2.66
557 566 6.021596 GCACATTATGTTAAGACCGACAAAG 58.978 40.000 0.00 0.00 0.00 2.77
561 570 3.000925 CGGCACATTATGTTAAGACCGAC 59.999 47.826 12.22 0.00 40.49 4.79
593 602 6.046593 AGAAAACACATGTTCTACACTCGAA 58.953 36.000 0.00 0.00 37.25 3.71
597 606 8.902540 TGATAAGAAAACACATGTTCTACACT 57.097 30.769 0.00 0.00 37.25 3.55
601 618 7.458397 ACCCTGATAAGAAAACACATGTTCTA 58.542 34.615 0.00 0.00 37.25 2.10
608 625 4.935205 CGATGACCCTGATAAGAAAACACA 59.065 41.667 0.00 0.00 0.00 3.72
624 642 2.811431 TCATTTCAACACACCGATGACC 59.189 45.455 0.00 0.00 0.00 4.02
625 643 3.667960 GCTCATTTCAACACACCGATGAC 60.668 47.826 0.00 0.00 0.00 3.06
631 649 3.733443 AAAGGCTCATTTCAACACACC 57.267 42.857 0.00 0.00 0.00 4.16
632 650 5.438761 AGTAAAGGCTCATTTCAACACAC 57.561 39.130 0.00 0.00 0.00 3.82
670 688 3.251487 TCGACCATCGATCGCTATTTACA 59.749 43.478 11.09 0.00 44.82 2.41
683 701 1.514228 CGTCACTGGTCGACCATCG 60.514 63.158 36.21 29.34 46.46 3.84
684 702 0.732880 CACGTCACTGGTCGACCATC 60.733 60.000 36.21 23.52 46.46 3.51
685 703 1.289066 CACGTCACTGGTCGACCAT 59.711 57.895 36.21 22.96 46.46 3.55
686 704 0.818852 TACACGTCACTGGTCGACCA 60.819 55.000 34.13 34.13 45.30 4.02
687 705 0.386478 GTACACGTCACTGGTCGACC 60.386 60.000 28.17 28.17 0.00 4.79
688 706 0.308684 TGTACACGTCACTGGTCGAC 59.691 55.000 7.13 7.13 0.00 4.20
689 707 1.241165 ATGTACACGTCACTGGTCGA 58.759 50.000 0.00 0.00 0.00 4.20
690 708 2.161012 AGTATGTACACGTCACTGGTCG 59.839 50.000 0.00 0.00 0.00 4.79
691 709 3.844577 AGTATGTACACGTCACTGGTC 57.155 47.619 0.00 0.00 0.00 4.02
692 710 3.125829 CGTAGTATGTACACGTCACTGGT 59.874 47.826 0.00 0.00 0.00 4.00
693 711 3.371898 TCGTAGTATGTACACGTCACTGG 59.628 47.826 0.00 0.00 34.63 4.00
694 712 4.588805 TCGTAGTATGTACACGTCACTG 57.411 45.455 0.00 0.00 34.63 3.66
695 713 5.391310 CCTTTCGTAGTATGTACACGTCACT 60.391 44.000 0.00 2.13 34.63 3.41
696 714 4.790140 CCTTTCGTAGTATGTACACGTCAC 59.210 45.833 0.00 0.00 34.63 3.67
697 715 4.142622 CCCTTTCGTAGTATGTACACGTCA 60.143 45.833 0.00 0.00 34.63 4.35
698 716 4.094887 TCCCTTTCGTAGTATGTACACGTC 59.905 45.833 0.00 0.00 34.63 4.34
699 717 4.009675 TCCCTTTCGTAGTATGTACACGT 58.990 43.478 0.00 0.00 34.63 4.49
700 718 4.621068 TCCCTTTCGTAGTATGTACACG 57.379 45.455 0.00 0.00 34.45 4.49
701 719 5.713025 TGTTCCCTTTCGTAGTATGTACAC 58.287 41.667 0.00 0.00 0.00 2.90
702 720 5.981088 TGTTCCCTTTCGTAGTATGTACA 57.019 39.130 0.00 0.00 0.00 2.90
703 721 7.656707 TTTTGTTCCCTTTCGTAGTATGTAC 57.343 36.000 0.00 0.00 0.00 2.90
704 722 7.148373 GCATTTTGTTCCCTTTCGTAGTATGTA 60.148 37.037 0.00 0.00 0.00 2.29
705 723 6.349033 GCATTTTGTTCCCTTTCGTAGTATGT 60.349 38.462 0.00 0.00 0.00 2.29
706 724 6.027749 GCATTTTGTTCCCTTTCGTAGTATG 58.972 40.000 0.00 0.00 0.00 2.39
707 725 5.944007 AGCATTTTGTTCCCTTTCGTAGTAT 59.056 36.000 0.00 0.00 0.00 2.12
708 726 5.310451 AGCATTTTGTTCCCTTTCGTAGTA 58.690 37.500 0.00 0.00 0.00 1.82
709 727 4.142038 AGCATTTTGTTCCCTTTCGTAGT 58.858 39.130 0.00 0.00 0.00 2.73
710 728 4.766404 AGCATTTTGTTCCCTTTCGTAG 57.234 40.909 0.00 0.00 0.00 3.51
711 729 5.310451 AGTAGCATTTTGTTCCCTTTCGTA 58.690 37.500 0.00 0.00 0.00 3.43
712 730 4.142038 AGTAGCATTTTGTTCCCTTTCGT 58.858 39.130 0.00 0.00 0.00 3.85
713 731 4.669197 CGAGTAGCATTTTGTTCCCTTTCG 60.669 45.833 0.00 0.00 0.00 3.46
714 732 4.454504 TCGAGTAGCATTTTGTTCCCTTTC 59.545 41.667 0.00 0.00 0.00 2.62
717 735 3.695830 TCGAGTAGCATTTTGTTCCCT 57.304 42.857 0.00 0.00 0.00 4.20
723 741 6.863126 AGGAAAACATTTCGAGTAGCATTTTG 59.137 34.615 0.00 0.00 0.00 2.44
726 744 6.016276 ACAAGGAAAACATTTCGAGTAGCATT 60.016 34.615 0.00 0.00 0.00 3.56
729 747 5.049680 TCACAAGGAAAACATTTCGAGTAGC 60.050 40.000 0.00 0.00 0.00 3.58
746 767 1.363744 GAGATTCGCTGGTCACAAGG 58.636 55.000 0.00 0.00 0.00 3.61
757 778 4.271049 TCGATTGATTTTCTGGAGATTCGC 59.729 41.667 0.00 0.00 0.00 4.70
787 808 1.448922 TAAAAAGCAGGCGCGGTGTT 61.449 50.000 8.83 0.00 45.49 3.32
840 861 1.130613 GCGCGACAAGTAGCAAGTG 59.869 57.895 12.10 0.00 0.00 3.16
1056 1085 1.228988 CTTGGGCTTGGGAGGCTTT 60.229 57.895 0.00 0.00 46.98 3.51
1079 1108 3.483869 GCTTCATCCTCCCCGGCT 61.484 66.667 0.00 0.00 0.00 5.52
1085 1114 2.110006 GCTCCGGCTTCATCCTCC 59.890 66.667 0.00 0.00 35.22 4.30
1119 1154 4.368543 AACGGGAAGACGGCGTCC 62.369 66.667 34.04 21.11 41.35 4.79
1242 1277 2.520741 GGGAGGCGAGAGGAGGAG 60.521 72.222 0.00 0.00 0.00 3.69
1243 1278 4.144727 GGGGAGGCGAGAGGAGGA 62.145 72.222 0.00 0.00 0.00 3.71
1305 1340 2.115911 CAGGACGAGGAGGAGGACG 61.116 68.421 0.00 0.00 0.00 4.79
1873 1914 4.899239 CCTCGGGAGCGCCATCAC 62.899 72.222 9.31 0.00 35.15 3.06
1913 1954 1.009389 GTTCGAAGCCAGAGGTCGTG 61.009 60.000 0.00 0.00 0.00 4.35
1920 1961 1.664649 CGCACTGTTCGAAGCCAGA 60.665 57.895 19.35 0.00 32.06 3.86
1960 2004 1.332065 CAGCGCTCTACTGATCTTCGA 59.668 52.381 7.13 0.00 37.32 3.71
1989 2033 0.876342 CGGCTATCTCCAACGCTTCC 60.876 60.000 0.00 0.00 0.00 3.46
2015 2059 2.284699 AAGCCGACCTGCCTACCT 60.285 61.111 0.00 0.00 0.00 3.08
2100 2144 0.179225 CAGTTCAACGCGGGATTTCG 60.179 55.000 12.47 0.00 0.00 3.46
2103 2147 3.263941 GCAGTTCAACGCGGGATT 58.736 55.556 12.47 0.00 0.00 3.01
2109 2153 0.314578 CATCGATCGCAGTTCAACGC 60.315 55.000 11.09 0.00 0.00 4.84
2138 2182 3.555586 CCAAAAACTTCCATCCCAAGCAG 60.556 47.826 0.00 0.00 0.00 4.24
2139 2183 2.368221 CCAAAAACTTCCATCCCAAGCA 59.632 45.455 0.00 0.00 0.00 3.91
2140 2184 2.632512 TCCAAAAACTTCCATCCCAAGC 59.367 45.455 0.00 0.00 0.00 4.01
2141 2185 3.897505 ACTCCAAAAACTTCCATCCCAAG 59.102 43.478 0.00 0.00 0.00 3.61
2142 2186 3.640967 CACTCCAAAAACTTCCATCCCAA 59.359 43.478 0.00 0.00 0.00 4.12
2143 2187 3.117322 TCACTCCAAAAACTTCCATCCCA 60.117 43.478 0.00 0.00 0.00 4.37
2144 2188 3.496331 TCACTCCAAAAACTTCCATCCC 58.504 45.455 0.00 0.00 0.00 3.85
2147 2191 4.202151 GCTGTTCACTCCAAAAACTTCCAT 60.202 41.667 0.00 0.00 0.00 3.41
2285 2329 6.587608 TGCGCTTATGATGTTCATATCTACTG 59.412 38.462 9.73 0.00 38.94 2.74
2372 2419 2.932614 AGAAACCTGAAATCGATGAGCG 59.067 45.455 0.00 0.00 42.69 5.03
2387 2437 7.917505 GTGTATCATGGATGATTGAAAGAAACC 59.082 37.037 7.42 0.00 44.70 3.27
2410 2460 9.683870 ATTGGCCAAAAATTTGAATATATGTGT 57.316 25.926 24.71 0.00 40.55 3.72
2424 2474 5.413309 TGGATCGTAAATTGGCCAAAAAT 57.587 34.783 24.71 13.97 0.00 1.82
2439 2775 6.095432 TGGTTGAAAATTGAAATGGATCGT 57.905 33.333 0.00 0.00 0.00 3.73
2457 2793 1.654220 CCACGCCTCAACTTGGTTG 59.346 57.895 4.25 4.25 43.99 3.77
2458 2794 1.528309 CCCACGCCTCAACTTGGTT 60.528 57.895 0.00 0.00 0.00 3.67
2469 2805 2.516930 CATCACCATCCCCACGCC 60.517 66.667 0.00 0.00 0.00 5.68
2494 2830 6.323225 AGTTCATTTCAGATTGGAATGGGATC 59.677 38.462 9.55 0.00 0.00 3.36
2499 2835 6.519679 TCCAGTTCATTTCAGATTGGAATG 57.480 37.500 4.09 4.09 32.21 2.67
2500 2836 6.323225 GGATCCAGTTCATTTCAGATTGGAAT 59.677 38.462 6.95 0.00 36.13 3.01
2557 2893 2.732366 TCTGAATCTAAGTCGATGCGC 58.268 47.619 0.00 0.00 0.00 6.09
2564 2900 7.865707 TGTGCTTTCTTTTCTGAATCTAAGTC 58.134 34.615 0.00 0.00 0.00 3.01
2754 3250 3.084039 TCTGCATTTTGATGAGGTGACC 58.916 45.455 0.00 0.00 0.00 4.02
2802 3298 4.100707 TCATTTAATGAACAGCAGCAGC 57.899 40.909 5.03 0.00 36.11 5.25
2871 3367 0.459237 AATCTCCTCGAGTGCTTGCG 60.459 55.000 12.31 0.00 0.00 4.85
2881 3377 3.808466 TGATCTTGTCCAATCTCCTCG 57.192 47.619 0.00 0.00 0.00 4.63
2889 3385 4.263905 ACAGGGCTAAATGATCTTGTCCAA 60.264 41.667 0.00 0.00 0.00 3.53
2904 4170 0.034337 GGACAAACACGACAGGGCTA 59.966 55.000 0.00 0.00 0.00 3.93
2908 4174 0.462937 TGGTGGACAAACACGACAGG 60.463 55.000 0.00 0.00 42.23 4.00
2924 4190 1.545651 GCAAGAAACAGCCTACCTGGT 60.546 52.381 4.05 4.05 45.52 4.00
2959 4225 0.934496 TGCACTGCTCGTTGTGTAAC 59.066 50.000 1.98 0.00 36.63 2.50
2965 4231 1.001487 TCCAAAATGCACTGCTCGTTG 60.001 47.619 1.98 3.79 0.00 4.10
2966 4232 1.267806 CTCCAAAATGCACTGCTCGTT 59.732 47.619 1.98 0.00 0.00 3.85
2972 4238 1.213537 CGCCCTCCAAAATGCACTG 59.786 57.895 0.00 0.00 0.00 3.66
2975 4241 2.342650 GCTCGCCCTCCAAAATGCA 61.343 57.895 0.00 0.00 0.00 3.96
3046 4312 7.219344 CACGTGTACTTTTTCTTCCGAATTTTT 59.781 33.333 7.58 0.00 0.00 1.94
3050 4316 4.812626 ACACGTGTACTTTTTCTTCCGAAT 59.187 37.500 21.98 0.00 0.00 3.34
3054 4320 6.535274 ACATACACGTGTACTTTTTCTTCC 57.465 37.500 29.54 0.00 32.72 3.46
3058 4324 7.642071 TCCTTACATACACGTGTACTTTTTC 57.358 36.000 29.54 0.00 34.50 2.29
3062 4328 6.276832 ACATCCTTACATACACGTGTACTT 57.723 37.500 29.54 20.70 34.50 2.24
3063 4329 5.909621 ACATCCTTACATACACGTGTACT 57.090 39.130 29.54 19.43 34.50 2.73
3064 4330 7.703621 ACATTACATCCTTACATACACGTGTAC 59.296 37.037 29.54 0.00 34.50 2.90
3065 4331 7.774134 ACATTACATCCTTACATACACGTGTA 58.226 34.615 29.15 29.15 33.62 2.90
3071 4337 9.581099 CGCATATACATTACATCCTTACATACA 57.419 33.333 0.00 0.00 0.00 2.29
3072 4338 9.582431 ACGCATATACATTACATCCTTACATAC 57.418 33.333 0.00 0.00 0.00 2.39
3073 4339 9.581099 CACGCATATACATTACATCCTTACATA 57.419 33.333 0.00 0.00 0.00 2.29


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

AutoCloner maintained by Alex Coulton.