Multiple sequence alignment - TraesCS7B01G233500

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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 TraesCS7B01G233500 chr7B 100.000 4553 0 0 1 4553 437362359 437366911 0.000000e+00 8408.0
1 TraesCS7B01G233500 chr7B 89.041 73 8 0 1 73 730231193 730231121 1.740000e-14 91.6
2 TraesCS7B01G233500 chr7A 89.654 4021 217 107 656 4534 511950754 511946791 0.000000e+00 4937.0
3 TraesCS7B01G233500 chr7A 84.694 392 23 12 255 619 511951287 511950906 1.560000e-94 357.0
4 TraesCS7B01G233500 chr7D 94.294 3032 82 39 105 3092 421166162 421169146 0.000000e+00 4556.0
5 TraesCS7B01G233500 chr7D 94.589 1497 29 16 3078 4552 421169161 421170627 0.000000e+00 2268.0
6 TraesCS7B01G233500 chr7D 87.179 78 10 0 1 78 121687686 121687763 6.270000e-14 89.8
7 TraesCS7B01G233500 chr6A 78.457 311 47 16 1929 2226 558981578 558981881 7.780000e-43 185.0
8 TraesCS7B01G233500 chr6D 77.389 314 45 21 1929 2226 414000946 414001249 3.640000e-36 163.0
9 TraesCS7B01G233500 chr6D 94.521 73 4 0 1 73 263436504 263436576 3.720000e-21 113.0
10 TraesCS7B01G233500 chr6B 76.074 326 55 19 1929 2240 623740562 623740878 1.020000e-31 148.0
11 TraesCS7B01G233500 chr3A 78.448 232 42 5 2017 2244 623777532 623777759 1.320000e-30 145.0
12 TraesCS7B01G233500 chr5D 95.833 72 3 0 1 72 488891203 488891132 2.880000e-22 117.0
13 TraesCS7B01G233500 chr1A 94.203 69 4 0 5 73 543653701 543653769 6.230000e-19 106.0
14 TraesCS7B01G233500 chr4D 91.892 74 6 0 1 74 101499025 101499098 2.240000e-18 104.0
15 TraesCS7B01G233500 chr4A 89.189 74 8 0 1 74 11649755 11649828 4.850000e-15 93.5
16 TraesCS7B01G233500 chr3B 91.176 68 6 0 1 68 758367142 758367209 4.850000e-15 93.5
17 TraesCS7B01G233500 chr2B 87.838 74 9 0 1 74 280500577 280500650 2.260000e-13 87.9
18 TraesCS7B01G233500 chr1D 91.071 56 5 0 443 498 21449044 21449099 4.880000e-10 76.8


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 TraesCS7B01G233500 chr7B 437362359 437366911 4552 False 8408 8408 100.0000 1 4553 1 chr7B.!!$F1 4552
1 TraesCS7B01G233500 chr7A 511946791 511951287 4496 True 2647 4937 87.1740 255 4534 2 chr7A.!!$R1 4279
2 TraesCS7B01G233500 chr7D 421166162 421170627 4465 False 3412 4556 94.4415 105 4552 2 chr7D.!!$F2 4447

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
35 36 0.179073 CCTGGTGGGCTCAAGATACG 60.179 60.0 0.00 0.0 0.00 3.06 F
1313 1503 0.108992 GCATCTACGACGTCAACCCA 60.109 55.0 17.16 0.0 0.00 4.51 F
2574 2781 0.112995 TCCAAGCTGGACTTTGCCAT 59.887 50.0 0.00 0.0 42.67 4.40 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1931 2133 0.390340 ACAGCATGCTCGTGTACTGG 60.390 55.0 19.68 5.73 42.53 4.00 R
2991 3233 0.456995 CTTTCCTCCGAGACACGAGC 60.457 60.0 0.00 0.00 45.77 5.03 R
3857 4196 0.725117 GCCTTGCGGTGTGTATGTAC 59.275 55.0 0.00 0.00 0.00 2.90 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
17 18 4.081050 GCACCAGGACTTGAACCC 57.919 61.111 0.00 0.00 0.00 4.11
18 19 1.456287 GCACCAGGACTTGAACCCT 59.544 57.895 0.00 0.00 0.00 4.34
22 23 3.329300 CAGGACTTGAACCCTGGTG 57.671 57.895 0.00 0.00 44.68 4.17
23 24 0.250901 CAGGACTTGAACCCTGGTGG 60.251 60.000 0.00 0.00 44.68 4.61
34 35 3.788672 CCTGGTGGGCTCAAGATAC 57.211 57.895 0.00 0.00 0.00 2.24
35 36 0.179073 CCTGGTGGGCTCAAGATACG 60.179 60.000 0.00 0.00 0.00 3.06
36 37 0.824109 CTGGTGGGCTCAAGATACGA 59.176 55.000 0.00 0.00 0.00 3.43
37 38 0.535335 TGGTGGGCTCAAGATACGAC 59.465 55.000 0.00 0.00 0.00 4.34
38 39 0.824759 GGTGGGCTCAAGATACGACT 59.175 55.000 0.00 0.00 0.00 4.18
39 40 1.471676 GGTGGGCTCAAGATACGACTG 60.472 57.143 0.00 0.00 0.00 3.51
40 41 1.204941 GTGGGCTCAAGATACGACTGT 59.795 52.381 0.00 0.00 0.00 3.55
41 42 1.476891 TGGGCTCAAGATACGACTGTC 59.523 52.381 0.00 0.00 0.00 3.51
42 43 1.202428 GGGCTCAAGATACGACTGTCC 60.202 57.143 1.55 0.00 0.00 4.02
43 44 1.202428 GGCTCAAGATACGACTGTCCC 60.202 57.143 1.55 0.00 0.00 4.46
44 45 1.751924 GCTCAAGATACGACTGTCCCT 59.248 52.381 1.55 0.00 0.00 4.20
45 46 2.223618 GCTCAAGATACGACTGTCCCTC 60.224 54.545 1.55 0.00 0.00 4.30
46 47 3.283751 CTCAAGATACGACTGTCCCTCT 58.716 50.000 1.55 0.00 0.00 3.69
47 48 4.452825 CTCAAGATACGACTGTCCCTCTA 58.547 47.826 1.55 0.00 0.00 2.43
48 49 4.851843 TCAAGATACGACTGTCCCTCTAA 58.148 43.478 1.55 0.00 0.00 2.10
49 50 4.639310 TCAAGATACGACTGTCCCTCTAAC 59.361 45.833 1.55 0.00 0.00 2.34
50 51 3.553904 AGATACGACTGTCCCTCTAACC 58.446 50.000 1.55 0.00 0.00 2.85
51 52 2.885135 TACGACTGTCCCTCTAACCA 57.115 50.000 1.55 0.00 0.00 3.67
52 53 2.233305 ACGACTGTCCCTCTAACCAT 57.767 50.000 1.55 0.00 0.00 3.55
53 54 3.377253 ACGACTGTCCCTCTAACCATA 57.623 47.619 1.55 0.00 0.00 2.74
54 55 3.022406 ACGACTGTCCCTCTAACCATAC 58.978 50.000 1.55 0.00 0.00 2.39
55 56 3.021695 CGACTGTCCCTCTAACCATACA 58.978 50.000 1.55 0.00 0.00 2.29
56 57 3.446161 CGACTGTCCCTCTAACCATACAA 59.554 47.826 1.55 0.00 0.00 2.41
57 58 4.677250 CGACTGTCCCTCTAACCATACAAC 60.677 50.000 1.55 0.00 0.00 3.32
58 59 3.518303 ACTGTCCCTCTAACCATACAACC 59.482 47.826 0.00 0.00 0.00 3.77
59 60 3.517901 CTGTCCCTCTAACCATACAACCA 59.482 47.826 0.00 0.00 0.00 3.67
60 61 3.262405 TGTCCCTCTAACCATACAACCAC 59.738 47.826 0.00 0.00 0.00 4.16
61 62 3.262405 GTCCCTCTAACCATACAACCACA 59.738 47.826 0.00 0.00 0.00 4.17
62 63 3.517901 TCCCTCTAACCATACAACCACAG 59.482 47.826 0.00 0.00 0.00 3.66
63 64 3.370527 CCCTCTAACCATACAACCACAGG 60.371 52.174 0.00 0.00 0.00 4.00
64 65 3.263425 CCTCTAACCATACAACCACAGGT 59.737 47.826 0.00 0.00 37.65 4.00
74 75 3.834726 CCACAGGTTGGTTCGCAA 58.165 55.556 0.00 0.00 41.10 4.85
75 76 2.111162 CCACAGGTTGGTTCGCAAA 58.889 52.632 0.00 0.00 41.10 3.68
76 77 0.457851 CCACAGGTTGGTTCGCAAAA 59.542 50.000 0.00 0.00 41.10 2.44
77 78 1.555477 CACAGGTTGGTTCGCAAAAC 58.445 50.000 0.00 0.00 0.00 2.43
78 79 0.458260 ACAGGTTGGTTCGCAAAACC 59.542 50.000 10.39 10.39 43.08 3.27
86 87 4.657436 TGGTTCGCAAAACCAAAATAGT 57.343 36.364 16.24 0.00 46.44 2.12
87 88 5.012328 TGGTTCGCAAAACCAAAATAGTT 57.988 34.783 16.24 0.00 46.44 2.24
88 89 4.806247 TGGTTCGCAAAACCAAAATAGTTG 59.194 37.500 16.24 0.00 46.44 3.16
89 90 4.210328 GGTTCGCAAAACCAAAATAGTTGG 59.790 41.667 12.05 3.55 44.91 3.77
90 91 4.920640 TCGCAAAACCAAAATAGTTGGA 57.079 36.364 11.96 0.00 42.06 3.53
91 92 4.865776 TCGCAAAACCAAAATAGTTGGAG 58.134 39.130 11.96 0.88 42.06 3.86
92 93 3.428534 CGCAAAACCAAAATAGTTGGAGC 59.571 43.478 11.96 8.69 42.06 4.70
93 94 3.745975 GCAAAACCAAAATAGTTGGAGCC 59.254 43.478 11.96 0.00 42.06 4.70
94 95 4.742138 GCAAAACCAAAATAGTTGGAGCCA 60.742 41.667 11.96 0.00 42.06 4.75
95 96 4.600692 AAACCAAAATAGTTGGAGCCAC 57.399 40.909 11.96 0.00 42.06 5.01
96 97 3.525800 ACCAAAATAGTTGGAGCCACT 57.474 42.857 11.96 0.00 42.06 4.00
97 98 4.650972 ACCAAAATAGTTGGAGCCACTA 57.349 40.909 11.96 0.00 42.06 2.74
98 99 4.589908 ACCAAAATAGTTGGAGCCACTAG 58.410 43.478 11.96 0.00 42.06 2.57
99 100 4.288626 ACCAAAATAGTTGGAGCCACTAGA 59.711 41.667 11.96 0.00 42.06 2.43
100 101 5.044846 ACCAAAATAGTTGGAGCCACTAGAT 60.045 40.000 11.96 0.00 42.06 1.98
101 102 5.888161 CCAAAATAGTTGGAGCCACTAGATT 59.112 40.000 0.00 0.00 42.06 2.40
102 103 6.038714 CCAAAATAGTTGGAGCCACTAGATTC 59.961 42.308 0.00 0.00 42.06 2.52
103 104 2.969628 AGTTGGAGCCACTAGATTCG 57.030 50.000 0.00 0.00 0.00 3.34
106 107 2.145397 TGGAGCCACTAGATTCGAGT 57.855 50.000 0.00 0.00 0.00 4.18
400 420 6.154534 TCCATGTATGCATATGGAGTAGTACC 59.845 42.308 22.19 2.12 44.84 3.34
401 421 6.155221 CCATGTATGCATATGGAGTAGTACCT 59.845 42.308 19.84 0.00 44.19 3.08
402 422 7.342026 CCATGTATGCATATGGAGTAGTACCTA 59.658 40.741 19.84 0.00 44.19 3.08
403 423 8.749354 CATGTATGCATATGGAGTAGTACCTAA 58.251 37.037 10.16 0.00 33.30 2.69
419 439 4.307032 ACCTAACTAACTACCTCGGACA 57.693 45.455 0.00 0.00 0.00 4.02
505 525 1.134699 CCATCGGCTGACAGCTTTCTA 60.135 52.381 25.92 8.50 41.99 2.10
528 548 1.605058 GCCCAGGCTCGACTACTCAA 61.605 60.000 0.08 0.00 38.26 3.02
548 570 1.375908 TCGGCATGAACTGTGCTCC 60.376 57.895 0.00 0.00 42.16 4.70
561 583 0.948678 GTGCTCCGCCAACAAGTTTA 59.051 50.000 0.00 0.00 0.00 2.01
563 585 1.335496 TGCTCCGCCAACAAGTTTAAC 59.665 47.619 0.00 0.00 0.00 2.01
571 593 3.118555 GCCAACAAGTTTAACCCAAACCT 60.119 43.478 0.00 0.00 46.55 3.50
623 651 4.452733 GCACGAGGGAAGGGACGG 62.453 72.222 0.00 0.00 0.00 4.79
628 656 4.377760 AGGGAAGGGACGGCGAGA 62.378 66.667 16.62 0.00 0.00 4.04
631 659 2.182030 GAAGGGACGGCGAGACTG 59.818 66.667 16.62 0.00 0.00 3.51
723 883 1.301479 AACGGAACAGAAGGCGTCC 60.301 57.895 0.00 0.00 0.00 4.79
750 910 0.916809 CCCGATTAACCCACTTCCCT 59.083 55.000 0.00 0.00 0.00 4.20
751 911 1.283905 CCCGATTAACCCACTTCCCTT 59.716 52.381 0.00 0.00 0.00 3.95
754 914 2.682858 CGATTAACCCACTTCCCTTCCC 60.683 54.545 0.00 0.00 0.00 3.97
755 915 1.078115 TTAACCCACTTCCCTTCCCC 58.922 55.000 0.00 0.00 0.00 4.81
757 917 4.426313 CCCACTTCCCTTCCCCGC 62.426 72.222 0.00 0.00 0.00 6.13
758 918 4.426313 CCACTTCCCTTCCCCGCC 62.426 72.222 0.00 0.00 0.00 6.13
759 919 4.778143 CACTTCCCTTCCCCGCCG 62.778 72.222 0.00 0.00 0.00 6.46
835 995 8.455682 CAAGTAAAGTAAAGAATTATTGCCCGA 58.544 33.333 0.00 0.00 0.00 5.14
837 998 8.837389 AGTAAAGTAAAGAATTATTGCCCGATC 58.163 33.333 0.00 0.00 0.00 3.69
1028 1212 3.583276 TTGCGACGCCGATGAGGTT 62.583 57.895 18.69 0.00 43.70 3.50
1115 1305 1.779061 GTCGCGCGAATTCAGTTGA 59.221 52.632 36.57 4.96 0.00 3.18
1117 1307 1.575132 CGCGCGAATTCAGTTGACG 60.575 57.895 28.94 0.00 0.00 4.35
1143 1333 0.249868 CGGAGTGTGGCTGACAAGAA 60.250 55.000 0.00 0.00 35.91 2.52
1147 1337 3.319122 GGAGTGTGGCTGACAAGAATTTT 59.681 43.478 0.00 0.00 35.91 1.82
1148 1338 4.540824 GAGTGTGGCTGACAAGAATTTTC 58.459 43.478 0.00 0.00 35.91 2.29
1313 1503 0.108992 GCATCTACGACGTCAACCCA 60.109 55.000 17.16 0.00 0.00 4.51
1733 1923 0.616395 TCTGGATCAACGCCTACCCA 60.616 55.000 0.00 0.00 0.00 4.51
1774 1965 3.344515 ACCCCGCAAAGTAATTCTCTTC 58.655 45.455 0.00 0.00 0.00 2.87
1815 2017 6.826893 ATTAATAAATCAAACATGCCACGC 57.173 33.333 0.00 0.00 0.00 5.34
1833 2035 2.053116 CAGCACACGTGTCGTTGC 60.053 61.111 20.49 19.15 38.32 4.17
1931 2133 1.993948 GGACCCCTACACCCACCTC 60.994 68.421 0.00 0.00 0.00 3.85
2388 2590 7.678837 TCTGCAAATTAATTTTCCATGGAACT 58.321 30.769 27.04 16.05 33.41 3.01
2407 2609 5.510861 GGAACTAGCTGTGAGAAAACTGGTA 60.511 44.000 0.00 0.00 32.81 3.25
2409 2611 3.838244 AGCTGTGAGAAAACTGGTACA 57.162 42.857 0.00 0.00 0.00 2.90
2469 2672 8.577296 CCTTTTTCGGTCAGTCAGAGATATATA 58.423 37.037 0.00 0.00 0.00 0.86
2554 2761 1.401931 GCACATGTGGATCACTGTTGC 60.402 52.381 26.55 4.39 35.11 4.17
2574 2781 0.112995 TCCAAGCTGGACTTTGCCAT 59.887 50.000 0.00 0.00 42.67 4.40
2578 2785 3.084039 CAAGCTGGACTTTGCCATAGAA 58.916 45.455 0.00 0.00 36.04 2.10
2656 2872 3.863424 CCATGCACGTAGTACCAAACTAG 59.137 47.826 0.00 0.00 41.61 2.57
2657 2873 4.491676 CATGCACGTAGTACCAAACTAGT 58.508 43.478 0.00 0.00 41.61 2.57
2658 2874 5.393352 CCATGCACGTAGTACCAAACTAGTA 60.393 44.000 0.00 0.00 41.61 1.82
2671 2887 7.596749 ACCAAACTAGTATTCACTTTCATCG 57.403 36.000 0.00 0.00 36.14 3.84
2708 2928 1.293924 GGTGAGAGATCAACATGGCG 58.706 55.000 0.00 0.00 0.00 5.69
2802 3037 2.012673 GTGACCTAGCTGAATTGCAGG 58.987 52.381 0.00 0.00 45.03 4.85
2856 3091 3.246226 GCTACTAGGTTGCAACGATCATG 59.754 47.826 22.67 12.47 34.70 3.07
3001 3243 2.714530 GAGTTCACGCTCGTGTCTC 58.285 57.895 19.95 21.24 45.55 3.36
3002 3244 1.060726 GAGTTCACGCTCGTGTCTCG 61.061 60.000 19.95 0.00 45.55 4.04
3003 3245 2.081212 GTTCACGCTCGTGTCTCGG 61.081 63.158 19.95 0.00 45.55 4.63
3004 3246 2.255881 TTCACGCTCGTGTCTCGGA 61.256 57.895 19.95 0.00 45.55 4.55
3005 3247 2.183858 TTCACGCTCGTGTCTCGGAG 62.184 60.000 19.95 0.00 45.55 4.63
3007 3249 3.125573 CGCTCGTGTCTCGGAGGA 61.126 66.667 4.96 0.00 40.32 3.71
3008 3250 2.687805 CGCTCGTGTCTCGGAGGAA 61.688 63.158 4.96 0.00 40.32 3.36
3161 3439 5.017490 TCCAAAGTGTTCCTTTTTGGTACA 58.983 37.500 13.17 0.00 46.85 2.90
3172 3452 5.594725 TCCTTTTTGGTACACTTATTGTGCA 59.405 36.000 0.00 0.00 42.37 4.57
3191 3471 2.169978 GCAGTTTAGTATTCCCGAGGGT 59.830 50.000 8.20 0.00 36.47 4.34
3193 3473 3.449737 CAGTTTAGTATTCCCGAGGGTCA 59.550 47.826 8.20 0.00 36.47 4.02
3196 3476 4.476628 TTAGTATTCCCGAGGGTCAAAC 57.523 45.455 8.20 3.28 36.47 2.93
3197 3477 2.547990 AGTATTCCCGAGGGTCAAACT 58.452 47.619 8.20 5.42 36.47 2.66
3200 3480 2.265589 TTCCCGAGGGTCAAACTTTC 57.734 50.000 8.20 0.00 36.47 2.62
3479 3794 1.134521 TGATACGCAGGATGTTGGGAC 60.135 52.381 0.00 0.00 39.31 4.46
3676 3993 3.511610 GGTATGCCATGGCCCCCT 61.512 66.667 33.44 17.47 41.09 4.79
3677 3994 2.116125 GTATGCCATGGCCCCCTC 59.884 66.667 33.44 15.28 41.09 4.30
3695 4013 2.728318 CCTCGCATGTCATCTTATCACG 59.272 50.000 0.00 0.00 0.00 4.35
3857 4196 7.320560 CGTACTTGATACTACATGACACATACG 59.679 40.741 0.00 0.00 0.00 3.06
3961 4302 1.673923 GGAGGCAAAAGGAAAGCATGC 60.674 52.381 10.51 10.51 36.31 4.06
3965 4306 2.419667 GCAAAAGGAAAGCATGCATGT 58.580 42.857 26.79 11.76 37.00 3.21
4135 4485 0.987294 ATATGCGGGGAAGATGGAGG 59.013 55.000 0.00 0.00 0.00 4.30
4313 4675 5.873164 TCTTTTATTTGTTCTAGGCTCGGAC 59.127 40.000 0.00 0.00 0.00 4.79
4464 4827 3.247648 CGGCGAAATTCGGATTAAGATGT 59.752 43.478 17.49 0.00 40.84 3.06
4467 4830 5.435557 GCGAAATTCGGATTAAGATGTCAG 58.564 41.667 17.49 0.00 40.84 3.51
4519 4885 2.936032 ACCACAGAGGAAGGGGCC 60.936 66.667 0.00 0.00 41.22 5.80
4540 4906 3.405831 CCAAGAGAAGTTGATGCACTCA 58.594 45.455 0.00 0.00 0.00 3.41
4552 4918 6.939163 AGTTGATGCACTCAGATTAAACTCTT 59.061 34.615 0.00 0.00 34.68 2.85
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 0.890996 CAGGGTTCAAGTCCTGGTGC 60.891 60.000 0.00 0.00 44.99 5.01
1 2 3.329300 CAGGGTTCAAGTCCTGGTG 57.671 57.895 0.00 0.00 44.99 4.17
5 6 2.155065 CCACCAGGGTTCAAGTCCT 58.845 57.895 0.00 0.00 0.00 3.85
6 7 4.821935 CCACCAGGGTTCAAGTCC 57.178 61.111 0.00 0.00 0.00 3.85
16 17 0.179073 CGTATCTTGAGCCCACCAGG 60.179 60.000 0.00 0.00 39.47 4.45
17 18 0.824109 TCGTATCTTGAGCCCACCAG 59.176 55.000 0.00 0.00 0.00 4.00
18 19 0.535335 GTCGTATCTTGAGCCCACCA 59.465 55.000 0.00 0.00 0.00 4.17
19 20 0.824759 AGTCGTATCTTGAGCCCACC 59.175 55.000 0.00 0.00 0.00 4.61
20 21 1.204941 ACAGTCGTATCTTGAGCCCAC 59.795 52.381 0.00 0.00 0.00 4.61
21 22 1.476891 GACAGTCGTATCTTGAGCCCA 59.523 52.381 0.00 0.00 0.00 5.36
22 23 1.202428 GGACAGTCGTATCTTGAGCCC 60.202 57.143 0.00 0.00 0.00 5.19
23 24 1.202428 GGGACAGTCGTATCTTGAGCC 60.202 57.143 0.00 0.00 0.00 4.70
24 25 1.751924 AGGGACAGTCGTATCTTGAGC 59.248 52.381 0.00 0.00 0.00 4.26
25 26 3.283751 AGAGGGACAGTCGTATCTTGAG 58.716 50.000 0.00 0.00 0.00 3.02
26 27 3.367646 AGAGGGACAGTCGTATCTTGA 57.632 47.619 0.00 0.00 0.00 3.02
27 28 4.202030 GGTTAGAGGGACAGTCGTATCTTG 60.202 50.000 6.22 0.00 0.00 3.02
28 29 3.952967 GGTTAGAGGGACAGTCGTATCTT 59.047 47.826 6.22 0.00 0.00 2.40
29 30 3.053842 TGGTTAGAGGGACAGTCGTATCT 60.054 47.826 0.00 0.65 0.00 1.98
30 31 3.285484 TGGTTAGAGGGACAGTCGTATC 58.715 50.000 0.00 0.00 0.00 2.24
31 32 3.377253 TGGTTAGAGGGACAGTCGTAT 57.623 47.619 0.00 0.00 0.00 3.06
32 33 2.885135 TGGTTAGAGGGACAGTCGTA 57.115 50.000 0.00 0.00 0.00 3.43
33 34 2.233305 ATGGTTAGAGGGACAGTCGT 57.767 50.000 0.00 0.00 0.00 4.34
34 35 3.021695 TGTATGGTTAGAGGGACAGTCG 58.978 50.000 0.00 0.00 0.00 4.18
35 36 4.382793 GGTTGTATGGTTAGAGGGACAGTC 60.383 50.000 0.00 0.00 0.00 3.51
36 37 3.518303 GGTTGTATGGTTAGAGGGACAGT 59.482 47.826 0.00 0.00 0.00 3.55
37 38 3.517901 TGGTTGTATGGTTAGAGGGACAG 59.482 47.826 0.00 0.00 0.00 3.51
38 39 3.262405 GTGGTTGTATGGTTAGAGGGACA 59.738 47.826 0.00 0.00 0.00 4.02
39 40 3.262405 TGTGGTTGTATGGTTAGAGGGAC 59.738 47.826 0.00 0.00 0.00 4.46
40 41 3.517901 CTGTGGTTGTATGGTTAGAGGGA 59.482 47.826 0.00 0.00 0.00 4.20
41 42 3.370527 CCTGTGGTTGTATGGTTAGAGGG 60.371 52.174 0.00 0.00 0.00 4.30
42 43 3.263425 ACCTGTGGTTGTATGGTTAGAGG 59.737 47.826 0.00 0.00 27.29 3.69
43 44 4.553330 ACCTGTGGTTGTATGGTTAGAG 57.447 45.455 0.00 0.00 27.29 2.43
44 45 4.986054 AACCTGTGGTTGTATGGTTAGA 57.014 40.909 0.71 0.00 45.07 2.10
58 59 1.555477 GTTTTGCGAACCAACCTGTG 58.445 50.000 0.00 0.00 31.97 3.66
59 60 0.458260 GGTTTTGCGAACCAACCTGT 59.542 50.000 14.89 0.00 40.03 4.00
60 61 0.457851 TGGTTTTGCGAACCAACCTG 59.542 50.000 18.89 0.00 46.44 4.00
61 62 2.889200 TGGTTTTGCGAACCAACCT 58.111 47.368 18.89 0.00 46.44 3.50
66 67 4.210328 CCAACTATTTTGGTTTTGCGAACC 59.790 41.667 13.35 13.35 40.67 3.62
67 68 5.044558 TCCAACTATTTTGGTTTTGCGAAC 58.955 37.500 3.04 0.00 40.40 3.95
68 69 5.263968 TCCAACTATTTTGGTTTTGCGAA 57.736 34.783 3.04 0.00 40.40 4.70
69 70 4.794655 GCTCCAACTATTTTGGTTTTGCGA 60.795 41.667 3.04 0.00 40.40 5.10
70 71 3.428534 GCTCCAACTATTTTGGTTTTGCG 59.571 43.478 3.04 0.00 40.40 4.85
71 72 3.745975 GGCTCCAACTATTTTGGTTTTGC 59.254 43.478 3.04 4.42 40.40 3.68
72 73 4.749598 GTGGCTCCAACTATTTTGGTTTTG 59.250 41.667 3.04 0.00 40.40 2.44
73 74 4.653801 AGTGGCTCCAACTATTTTGGTTTT 59.346 37.500 3.04 0.00 40.40 2.43
74 75 4.223144 AGTGGCTCCAACTATTTTGGTTT 58.777 39.130 3.04 0.00 40.40 3.27
75 76 3.844640 AGTGGCTCCAACTATTTTGGTT 58.155 40.909 3.04 0.00 40.40 3.67
76 77 3.525800 AGTGGCTCCAACTATTTTGGT 57.474 42.857 3.04 0.00 40.40 3.67
77 78 4.843728 TCTAGTGGCTCCAACTATTTTGG 58.156 43.478 0.00 0.00 40.87 3.28
78 79 6.238211 CGAATCTAGTGGCTCCAACTATTTTG 60.238 42.308 0.00 0.00 0.00 2.44
79 80 5.817816 CGAATCTAGTGGCTCCAACTATTTT 59.182 40.000 0.00 0.00 0.00 1.82
80 81 5.128827 TCGAATCTAGTGGCTCCAACTATTT 59.871 40.000 0.00 0.00 0.00 1.40
81 82 4.649674 TCGAATCTAGTGGCTCCAACTATT 59.350 41.667 0.00 0.00 0.00 1.73
82 83 4.215908 TCGAATCTAGTGGCTCCAACTAT 58.784 43.478 0.00 0.00 0.00 2.12
83 84 3.628008 TCGAATCTAGTGGCTCCAACTA 58.372 45.455 0.00 0.00 0.00 2.24
84 85 2.428890 CTCGAATCTAGTGGCTCCAACT 59.571 50.000 0.00 0.00 0.00 3.16
85 86 2.166664 ACTCGAATCTAGTGGCTCCAAC 59.833 50.000 0.00 0.00 0.00 3.77
86 87 2.166459 CACTCGAATCTAGTGGCTCCAA 59.834 50.000 6.99 0.00 40.56 3.53
87 88 1.751351 CACTCGAATCTAGTGGCTCCA 59.249 52.381 6.99 0.00 40.56 3.86
88 89 2.025155 TCACTCGAATCTAGTGGCTCC 58.975 52.381 13.82 0.00 43.69 4.70
89 90 2.223618 GGTCACTCGAATCTAGTGGCTC 60.224 54.545 17.08 6.02 46.44 4.70
90 91 1.751924 GGTCACTCGAATCTAGTGGCT 59.248 52.381 17.08 0.00 46.44 4.75
91 92 1.476891 TGGTCACTCGAATCTAGTGGC 59.523 52.381 13.82 12.25 46.49 5.01
92 93 3.243569 GGATGGTCACTCGAATCTAGTGG 60.244 52.174 13.82 0.00 43.69 4.00
93 94 3.381590 TGGATGGTCACTCGAATCTAGTG 59.618 47.826 8.44 8.44 44.66 2.74
94 95 3.632333 TGGATGGTCACTCGAATCTAGT 58.368 45.455 0.00 0.00 0.00 2.57
95 96 3.005261 CCTGGATGGTCACTCGAATCTAG 59.995 52.174 0.00 0.32 0.00 2.43
96 97 2.959030 CCTGGATGGTCACTCGAATCTA 59.041 50.000 0.00 0.00 0.00 1.98
97 98 1.759445 CCTGGATGGTCACTCGAATCT 59.241 52.381 0.00 0.00 0.00 2.40
98 99 1.757118 TCCTGGATGGTCACTCGAATC 59.243 52.381 0.00 0.00 37.07 2.52
99 100 1.866015 TCCTGGATGGTCACTCGAAT 58.134 50.000 0.00 0.00 37.07 3.34
100 101 1.482182 CATCCTGGATGGTCACTCGAA 59.518 52.381 25.84 0.00 36.51 3.71
101 102 1.114627 CATCCTGGATGGTCACTCGA 58.885 55.000 25.84 0.00 36.51 4.04
102 103 3.675086 CATCCTGGATGGTCACTCG 57.325 57.895 25.84 0.59 36.51 4.18
131 132 6.661805 GTGGGGAAAACTGTATCCATTTTCTA 59.338 38.462 12.83 0.00 40.56 2.10
200 201 6.818644 GCTGTGAATCTTTGGTATGAAGTAGA 59.181 38.462 0.00 0.00 0.00 2.59
205 206 4.574892 TCGCTGTGAATCTTTGGTATGAA 58.425 39.130 0.00 0.00 0.00 2.57
211 212 1.135972 CCGTTCGCTGTGAATCTTTGG 60.136 52.381 6.95 1.66 39.21 3.28
222 223 2.537792 TTCGACTAGGCCGTTCGCTG 62.538 60.000 16.21 0.00 37.74 5.18
400 420 8.246180 TGTTTATTGTCCGAGGTAGTTAGTTAG 58.754 37.037 0.00 0.00 0.00 2.34
401 421 8.121305 TGTTTATTGTCCGAGGTAGTTAGTTA 57.879 34.615 0.00 0.00 0.00 2.24
402 422 6.996509 TGTTTATTGTCCGAGGTAGTTAGTT 58.003 36.000 0.00 0.00 0.00 2.24
403 423 6.594788 TGTTTATTGTCCGAGGTAGTTAGT 57.405 37.500 0.00 0.00 0.00 2.24
505 525 1.612442 TAGTCGAGCCTGGGCCTTT 60.612 57.895 4.53 0.00 43.17 3.11
528 548 0.671781 GAGCACAGTTCATGCCGACT 60.672 55.000 0.00 0.00 44.53 4.18
548 570 2.861335 GTTTGGGTTAAACTTGTTGGCG 59.139 45.455 0.00 0.00 44.18 5.69
571 593 4.243008 TGTGAAAGCGACCGGGCA 62.243 61.111 8.76 0.00 34.64 5.36
623 651 1.299014 CGATGCTCTCCAGTCTCGC 60.299 63.158 0.00 0.00 0.00 5.03
628 656 1.630126 AATGCCCGATGCTCTCCAGT 61.630 55.000 0.00 0.00 42.00 4.00
631 659 2.028130 CAAATGCCCGATGCTCTCC 58.972 57.895 0.00 0.00 42.00 3.71
750 910 3.243053 TTCTTCACCGGCGGGGAA 61.243 61.111 38.32 38.32 43.57 3.97
751 911 3.702048 CTTCTTCACCGGCGGGGA 61.702 66.667 30.13 30.13 39.97 4.81
757 917 3.330720 AGGGGCCTTCTTCACCGG 61.331 66.667 0.84 0.00 0.00 5.28
758 918 2.245438 GAGAGGGGCCTTCTTCACCG 62.245 65.000 20.22 0.00 0.00 4.94
759 919 1.604915 GAGAGGGGCCTTCTTCACC 59.395 63.158 20.22 2.83 0.00 4.02
760 920 1.604915 GGAGAGGGGCCTTCTTCAC 59.395 63.158 20.22 9.63 0.00 3.18
835 995 1.768077 GGGGTGGAGCTAGGCTGAT 60.768 63.158 0.00 0.00 39.88 2.90
837 998 3.483869 GGGGGTGGAGCTAGGCTG 61.484 72.222 0.00 0.00 39.88 4.85
858 1024 4.373116 CTGTGCGGTAGGTGCGGT 62.373 66.667 0.00 0.00 34.24 5.68
921 1102 2.041265 GGGGAGGGAGAGAGGCAA 59.959 66.667 0.00 0.00 0.00 4.52
1115 1305 3.667282 CACACTCCGACGTCCCGT 61.667 66.667 10.58 1.40 45.10 5.28
1117 1307 4.736896 GCCACACTCCGACGTCCC 62.737 72.222 10.58 0.00 0.00 4.46
1143 1333 2.676076 GCACGCACATTCCAAGAAAAT 58.324 42.857 0.00 0.00 0.00 1.82
1147 1337 1.596752 ACGCACGCACATTCCAAGA 60.597 52.632 0.00 0.00 0.00 3.02
1148 1338 1.440850 CACGCACGCACATTCCAAG 60.441 57.895 0.00 0.00 0.00 3.61
1150 1340 4.024143 GCACGCACGCACATTCCA 62.024 61.111 0.00 0.00 0.00 3.53
1152 1342 4.368808 ACGCACGCACGCACATTC 62.369 61.111 0.00 0.00 36.19 2.67
1430 1620 1.420430 CCGGGAAGTAGGGCTTGATA 58.580 55.000 0.00 0.00 37.59 2.15
1793 1995 5.105752 GGCGTGGCATGTTTGATTTATTAA 58.894 37.500 8.75 0.00 0.00 1.40
1794 1996 4.158579 TGGCGTGGCATGTTTGATTTATTA 59.841 37.500 8.75 0.00 0.00 0.98
1795 1997 3.056250 TGGCGTGGCATGTTTGATTTATT 60.056 39.130 8.75 0.00 0.00 1.40
1802 2004 2.431260 GCTGGCGTGGCATGTTTG 60.431 61.111 8.75 0.01 0.00 2.93
1806 2008 4.409218 GTGTGCTGGCGTGGCATG 62.409 66.667 1.31 1.31 41.86 4.06
1815 2017 2.625906 CAACGACACGTGTGCTGG 59.374 61.111 28.82 14.45 39.99 4.85
1833 2035 1.026718 GGCATCCACGTCAGAAAGGG 61.027 60.000 0.00 0.00 0.00 3.95
1931 2133 0.390340 ACAGCATGCTCGTGTACTGG 60.390 55.000 19.68 5.73 42.53 4.00
2388 2590 4.344102 ACTGTACCAGTTTTCTCACAGCTA 59.656 41.667 0.00 0.00 42.59 3.32
2407 2609 7.175816 CCTGATAGATATGCTGTACTGTACTGT 59.824 40.741 21.03 10.46 0.00 3.55
2409 2611 7.462590 TCCTGATAGATATGCTGTACTGTACT 58.537 38.462 17.98 1.53 0.00 2.73
2413 2616 7.257003 GTGATCCTGATAGATATGCTGTACTG 58.743 42.308 0.00 0.00 0.00 2.74
2469 2672 6.237901 TGCAAATCTTTACCACTGTATGACT 58.762 36.000 0.00 0.00 0.00 3.41
2574 2781 5.457799 GCGACTTTTGCATAGTACGATTCTA 59.542 40.000 17.21 0.00 0.00 2.10
2578 2785 3.782046 AGCGACTTTTGCATAGTACGAT 58.218 40.909 17.21 12.09 33.85 3.73
2656 2872 3.065233 TGCATGCCGATGAAAGTGAATAC 59.935 43.478 16.68 0.00 0.00 1.89
2657 2873 3.277715 TGCATGCCGATGAAAGTGAATA 58.722 40.909 16.68 0.00 0.00 1.75
2658 2874 2.093890 TGCATGCCGATGAAAGTGAAT 58.906 42.857 16.68 0.00 0.00 2.57
2690 2910 0.654683 GCGCCATGTTGATCTCTCAC 59.345 55.000 0.00 0.00 0.00 3.51
2732 2956 4.236416 GCGTGCGTGTGTTGCTGT 62.236 61.111 0.00 0.00 0.00 4.40
2802 3037 3.368427 GCAAGCAAGGGGAAAGAATAACC 60.368 47.826 0.00 0.00 0.00 2.85
2856 3091 6.867662 TTTCTTTCAAAGTGGAGTGATCTC 57.132 37.500 0.00 0.00 39.76 2.75
2991 3233 0.456995 CTTTCCTCCGAGACACGAGC 60.457 60.000 0.00 0.00 45.77 5.03
2996 3238 2.326428 AGTTTCCTTTCCTCCGAGACA 58.674 47.619 0.00 0.00 0.00 3.41
2997 3239 3.244112 TGAAGTTTCCTTTCCTCCGAGAC 60.244 47.826 0.00 0.00 0.00 3.36
2998 3240 2.969950 TGAAGTTTCCTTTCCTCCGAGA 59.030 45.455 0.00 0.00 0.00 4.04
2999 3241 3.067833 GTGAAGTTTCCTTTCCTCCGAG 58.932 50.000 0.00 0.00 0.00 4.63
3001 3243 1.798813 CGTGAAGTTTCCTTTCCTCCG 59.201 52.381 0.00 0.00 0.00 4.63
3002 3244 3.067833 CTCGTGAAGTTTCCTTTCCTCC 58.932 50.000 0.00 0.00 0.00 4.30
3003 3245 3.729966 ACTCGTGAAGTTTCCTTTCCTC 58.270 45.455 0.00 0.00 33.03 3.71
3004 3246 3.134081 TGACTCGTGAAGTTTCCTTTCCT 59.866 43.478 0.00 0.00 38.74 3.36
3005 3247 3.463944 TGACTCGTGAAGTTTCCTTTCC 58.536 45.455 0.00 0.00 38.74 3.13
3007 3249 4.514401 ACTTGACTCGTGAAGTTTCCTTT 58.486 39.130 0.00 0.00 38.74 3.11
3008 3250 4.138487 ACTTGACTCGTGAAGTTTCCTT 57.862 40.909 0.00 0.00 38.74 3.36
3161 3439 6.315393 CGGGAATACTAAACTGCACAATAAGT 59.685 38.462 0.00 0.00 0.00 2.24
3167 3447 3.369052 CCTCGGGAATACTAAACTGCACA 60.369 47.826 0.00 0.00 0.00 4.57
3172 3452 3.716431 TGACCCTCGGGAATACTAAACT 58.284 45.455 9.43 0.00 38.96 2.66
3233 3515 4.469469 TTTGGGTGGAGAAGGAAGAATT 57.531 40.909 0.00 0.00 0.00 2.17
3240 3522 2.584835 TCACATTTGGGTGGAGAAGG 57.415 50.000 0.00 0.00 39.27 3.46
3479 3794 1.669115 CACAGGCTGGTCAAGTCCG 60.669 63.158 20.34 0.00 0.00 4.79
3577 3892 1.470890 GCCATTTTGCTTGCATGCATT 59.529 42.857 25.81 12.51 42.96 3.56
3655 3970 1.898574 GGGCCATGGCATACCTTCG 60.899 63.158 36.56 0.00 44.11 3.79
3676 3993 2.360801 TCCGTGATAAGATGACATGCGA 59.639 45.455 0.00 0.00 0.00 5.10
3677 3994 2.742774 TCCGTGATAAGATGACATGCG 58.257 47.619 0.00 0.00 0.00 4.73
3695 4013 3.756117 AGAAAAGGAGGTTGTGTCATCC 58.244 45.455 0.00 0.00 38.40 3.51
3828 4165 7.466805 TGTGTCATGTAGTATCAAGTACGTAC 58.533 38.462 18.10 18.10 38.38 3.67
3829 4166 7.614124 TGTGTCATGTAGTATCAAGTACGTA 57.386 36.000 0.00 0.00 38.38 3.57
3830 4167 6.505044 TGTGTCATGTAGTATCAAGTACGT 57.495 37.500 0.00 0.00 38.38 3.57
3831 4168 7.320560 CGTATGTGTCATGTAGTATCAAGTACG 59.679 40.741 0.00 0.00 38.38 3.67
3832 4169 8.127327 ACGTATGTGTCATGTAGTATCAAGTAC 58.873 37.037 0.00 0.00 32.89 2.73
3833 4170 8.217131 ACGTATGTGTCATGTAGTATCAAGTA 57.783 34.615 0.00 0.00 0.00 2.24
3834 4171 7.096884 ACGTATGTGTCATGTAGTATCAAGT 57.903 36.000 0.00 0.00 0.00 3.16
3835 4172 8.126700 TGTACGTATGTGTCATGTAGTATCAAG 58.873 37.037 0.00 0.00 0.00 3.02
3836 4173 7.987649 TGTACGTATGTGTCATGTAGTATCAA 58.012 34.615 0.00 0.00 0.00 2.57
3857 4196 0.725117 GCCTTGCGGTGTGTATGTAC 59.275 55.000 0.00 0.00 0.00 2.90
3961 4302 4.616835 GCTTTTTCTCTGGCCTACAACATG 60.617 45.833 3.32 0.00 0.00 3.21
3965 4306 3.508845 AGCTTTTTCTCTGGCCTACAA 57.491 42.857 3.32 0.00 0.00 2.41
4019 4360 4.636435 CCCACCACACCCCACGAC 62.636 72.222 0.00 0.00 0.00 4.34
4135 4485 3.140814 GCATCGGCCACCCTTTCC 61.141 66.667 2.24 0.00 0.00 3.13
4464 4827 1.476085 CAACAACAACAAGGGCACTGA 59.524 47.619 0.00 0.00 0.00 3.41
4467 4830 1.797348 CGACAACAACAACAAGGGCAC 60.797 52.381 0.00 0.00 0.00 5.01
4519 4885 3.405831 TGAGTGCATCAACTTCTCTTGG 58.594 45.455 0.00 0.00 34.02 3.61


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

AutoCloner maintained by Alex Coulton.