Multiple sequence alignment - TraesCS7D01G073200

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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 TraesCS7D01G073200 chr7D 100.000 2961 0 0 1 2961 42899945 42902905 0.000000e+00 5469.0
1 TraesCS7D01G073200 chr7D 96.644 149 4 1 1 149 601899108 601899255 2.280000e-61 246.0
2 TraesCS7D01G073200 chr7A 91.986 1959 96 20 428 2351 42536607 42538539 0.000000e+00 2691.0
3 TraesCS7D01G073200 chr7A 95.633 229 6 1 150 378 42535966 42536190 6.030000e-97 364.0
4 TraesCS7D01G073200 chr7A 95.333 150 7 0 1 150 725910628 725910777 3.810000e-59 239.0
5 TraesCS7D01G073200 chr7A 94.444 36 2 0 1443 1478 630695010 630694975 4.120000e-04 56.5
6 TraesCS7D01G073200 chr4A 93.329 1469 59 7 583 2040 650409177 650410617 0.000000e+00 2134.0
7 TraesCS7D01G073200 chr4A 94.653 505 24 3 2038 2540 650410854 650411357 0.000000e+00 780.0
8 TraesCS7D01G073200 chr4A 93.961 414 25 0 2545 2958 650411575 650411988 6.970000e-176 627.0
9 TraesCS7D01G073200 chr4A 85.552 353 23 14 150 502 650408624 650408948 7.860000e-91 344.0
10 TraesCS7D01G073200 chr4D 95.031 161 7 1 1 161 44137888 44138047 4.900000e-63 252.0
11 TraesCS7D01G073200 chr4D 96.644 149 5 0 1 149 121471230 121471378 6.340000e-62 248.0
12 TraesCS7D01G073200 chr4D 88.889 63 7 0 896 958 444886520 444886582 8.800000e-11 78.7
13 TraesCS7D01G073200 chr6D 96.644 149 5 0 1 149 324539083 324539231 6.340000e-62 248.0
14 TraesCS7D01G073200 chr6D 79.091 110 21 2 2349 2457 437429019 437428911 1.140000e-09 75.0
15 TraesCS7D01G073200 chr5D 96.644 149 5 0 1 149 68706304 68706156 6.340000e-62 248.0
16 TraesCS7D01G073200 chr5D 93.252 163 10 1 1 163 26807212 26807051 3.810000e-59 239.0
17 TraesCS7D01G073200 chr3D 95.395 152 7 0 1 152 589001158 589001007 2.950000e-60 243.0
18 TraesCS7D01G073200 chr1D 96.000 150 5 1 1 149 165498 165647 2.950000e-60 243.0
19 TraesCS7D01G073200 chr7B 80.537 149 19 8 2100 2247 64167124 64166985 4.040000e-19 106.0
20 TraesCS7D01G073200 chr7B 96.970 33 1 0 1443 1475 590848031 590848063 4.120000e-04 56.5


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 TraesCS7D01G073200 chr7D 42899945 42902905 2960 False 5469.00 5469 100.00000 1 2961 1 chr7D.!!$F1 2960
1 TraesCS7D01G073200 chr7A 42535966 42538539 2573 False 1527.50 2691 93.80950 150 2351 2 chr7A.!!$F2 2201
2 TraesCS7D01G073200 chr4A 650408624 650411988 3364 False 971.25 2134 91.87375 150 2958 4 chr4A.!!$F1 2808

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
19 20 0.237235 CACACGAACCGGGACAAATG 59.763 55.0 6.32 0.0 32.98 2.32 F
95 96 0.323629 GGTCCCGGTTCATGACTGAA 59.676 55.0 0.00 0.0 39.07 3.02 F
117 118 0.398318 GGGACTAATGGGCTGGCTAG 59.602 60.0 0.00 0.0 0.00 3.42 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1747 2277 0.463116 ACGACAGTTGCGGTTTCCTT 60.463 50.000 0.00 0.00 0.0 3.36 R
1817 2351 1.480219 GCGCGTCGACCCTCAAATAG 61.480 60.000 10.58 0.00 0.0 1.73 R
2045 2818 4.285775 TCCTGGAGAATATGTGACACAACA 59.714 41.667 13.23 3.97 0.0 3.33 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 4.128139 CACACGAACCGGGACAAA 57.872 55.556 6.32 0.00 32.98 2.83
18 19 2.624169 CACACGAACCGGGACAAAT 58.376 52.632 6.32 0.00 32.98 2.32
19 20 0.237235 CACACGAACCGGGACAAATG 59.763 55.000 6.32 0.00 32.98 2.32
20 21 1.209127 CACGAACCGGGACAAATGC 59.791 57.895 6.32 0.00 28.17 3.56
21 22 1.969589 ACGAACCGGGACAAATGCC 60.970 57.895 6.32 0.00 0.00 4.40
22 23 1.674322 CGAACCGGGACAAATGCCT 60.674 57.895 6.32 0.00 33.05 4.75
23 24 1.644786 CGAACCGGGACAAATGCCTC 61.645 60.000 6.32 0.00 33.05 4.70
24 25 1.304134 AACCGGGACAAATGCCTCC 60.304 57.895 6.32 0.00 33.05 4.30
25 26 2.440247 CCGGGACAAATGCCTCCC 60.440 66.667 0.00 0.09 42.73 4.30
27 28 2.674754 GGGACAAATGCCTCCCGA 59.325 61.111 0.00 0.00 36.97 5.14
28 29 1.452108 GGGACAAATGCCTCCCGAG 60.452 63.158 0.00 0.00 36.97 4.63
75 76 2.113139 GGGACGTATGCCCCCATG 59.887 66.667 4.43 0.00 39.81 3.66
76 77 2.113139 GGACGTATGCCCCCATGG 59.887 66.667 4.14 4.14 32.85 3.66
86 87 4.123545 CCCCATGGGTCCCGGTTC 62.124 72.222 29.33 0.00 38.25 3.62
87 88 3.334891 CCCATGGGTCCCGGTTCA 61.335 66.667 23.93 0.00 0.00 3.18
88 89 2.689691 CCCATGGGTCCCGGTTCAT 61.690 63.158 23.93 0.00 0.00 2.57
89 90 1.453745 CCATGGGTCCCGGTTCATG 60.454 63.158 2.85 8.47 37.37 3.07
90 91 1.607071 CATGGGTCCCGGTTCATGA 59.393 57.895 14.43 0.00 39.27 3.07
91 92 0.748005 CATGGGTCCCGGTTCATGAC 60.748 60.000 14.43 8.13 39.27 3.06
92 93 0.914417 ATGGGTCCCGGTTCATGACT 60.914 55.000 2.65 0.00 0.00 3.41
93 94 1.078426 GGGTCCCGGTTCATGACTG 60.078 63.158 0.00 0.00 0.00 3.51
94 95 1.550130 GGGTCCCGGTTCATGACTGA 61.550 60.000 0.00 0.00 36.72 3.41
95 96 0.323629 GGTCCCGGTTCATGACTGAA 59.676 55.000 0.00 0.00 39.07 3.02
102 103 3.927555 TTCATGACTGAACCGGGAC 57.072 52.632 6.32 0.00 36.46 4.46
103 104 1.348064 TTCATGACTGAACCGGGACT 58.652 50.000 6.32 0.00 36.46 3.85
104 105 2.225382 TCATGACTGAACCGGGACTA 57.775 50.000 6.32 0.00 0.00 2.59
105 106 2.531771 TCATGACTGAACCGGGACTAA 58.468 47.619 6.32 0.00 0.00 2.24
106 107 3.104512 TCATGACTGAACCGGGACTAAT 58.895 45.455 6.32 0.00 0.00 1.73
107 108 3.118775 TCATGACTGAACCGGGACTAATG 60.119 47.826 6.32 0.82 0.00 1.90
108 109 1.553248 TGACTGAACCGGGACTAATGG 59.447 52.381 6.32 0.00 0.00 3.16
109 110 0.909623 ACTGAACCGGGACTAATGGG 59.090 55.000 6.32 0.00 0.00 4.00
110 111 0.463833 CTGAACCGGGACTAATGGGC 60.464 60.000 6.32 0.00 0.00 5.36
111 112 0.912487 TGAACCGGGACTAATGGGCT 60.912 55.000 6.32 0.00 0.00 5.19
112 113 0.463833 GAACCGGGACTAATGGGCTG 60.464 60.000 6.32 0.00 0.00 4.85
113 114 1.921869 AACCGGGACTAATGGGCTGG 61.922 60.000 6.32 0.00 0.00 4.85
114 115 2.203209 CGGGACTAATGGGCTGGC 60.203 66.667 0.00 0.00 0.00 4.85
115 116 2.746375 CGGGACTAATGGGCTGGCT 61.746 63.158 0.00 0.00 0.00 4.75
116 117 1.407656 CGGGACTAATGGGCTGGCTA 61.408 60.000 0.00 0.00 0.00 3.93
117 118 0.398318 GGGACTAATGGGCTGGCTAG 59.602 60.000 0.00 0.00 0.00 3.42
118 119 0.398318 GGACTAATGGGCTGGCTAGG 59.602 60.000 0.00 0.00 0.00 3.02
129 130 2.443324 GGCTAGGCCCCAACCAAA 59.557 61.111 4.61 0.00 44.06 3.28
130 131 1.682344 GGCTAGGCCCCAACCAAAG 60.682 63.158 4.61 0.00 44.06 2.77
131 132 2.351244 GCTAGGCCCCAACCAAAGC 61.351 63.158 0.00 0.00 34.90 3.51
132 133 1.682344 CTAGGCCCCAACCAAAGCC 60.682 63.158 0.00 0.00 46.13 4.35
134 135 2.607442 GGCCCCAACCAAAGCCAT 60.607 61.111 0.00 0.00 45.07 4.40
135 136 2.664398 GCCCCAACCAAAGCCATG 59.336 61.111 0.00 0.00 0.00 3.66
136 137 2.216331 GCCCCAACCAAAGCCATGT 61.216 57.895 0.00 0.00 0.00 3.21
137 138 1.767654 GCCCCAACCAAAGCCATGTT 61.768 55.000 0.00 0.00 0.00 2.71
138 139 0.764271 CCCCAACCAAAGCCATGTTT 59.236 50.000 0.00 0.00 0.00 2.83
139 140 1.142667 CCCCAACCAAAGCCATGTTTT 59.857 47.619 0.00 0.00 0.00 2.43
140 141 2.493035 CCCAACCAAAGCCATGTTTTC 58.507 47.619 0.00 0.00 0.00 2.29
141 142 2.104622 CCCAACCAAAGCCATGTTTTCT 59.895 45.455 0.00 0.00 0.00 2.52
142 143 3.323403 CCCAACCAAAGCCATGTTTTCTA 59.677 43.478 0.00 0.00 0.00 2.10
143 144 4.306600 CCAACCAAAGCCATGTTTTCTAC 58.693 43.478 0.00 0.00 0.00 2.59
144 145 4.039124 CCAACCAAAGCCATGTTTTCTACT 59.961 41.667 0.00 0.00 0.00 2.57
145 146 5.242838 CCAACCAAAGCCATGTTTTCTACTA 59.757 40.000 0.00 0.00 0.00 1.82
146 147 6.381801 CAACCAAAGCCATGTTTTCTACTAG 58.618 40.000 0.00 0.00 0.00 2.57
147 148 5.631119 ACCAAAGCCATGTTTTCTACTAGT 58.369 37.500 0.00 0.00 0.00 2.57
148 149 5.473504 ACCAAAGCCATGTTTTCTACTAGTG 59.526 40.000 5.39 0.00 0.00 2.74
159 160 5.811796 TTTCTACTAGTGTAAGGCCAACA 57.188 39.130 5.01 6.11 0.00 3.33
175 176 5.852250 AGGCCAACATTAATATACTCCCTCT 59.148 40.000 5.01 0.00 0.00 3.69
351 352 2.217750 TGTATATTCACCATGTGGCGC 58.782 47.619 0.00 0.00 39.32 6.53
396 404 3.552604 AAAAGACACACACACACACAC 57.447 42.857 0.00 0.00 0.00 3.82
398 406 1.438651 AGACACACACACACACACAC 58.561 50.000 0.00 0.00 0.00 3.82
400 408 0.871722 ACACACACACACACACACAC 59.128 50.000 0.00 0.00 0.00 3.82
402 410 0.871722 ACACACACACACACACACAC 59.128 50.000 0.00 0.00 0.00 3.82
404 412 0.871722 ACACACACACACACACACAC 59.128 50.000 0.00 0.00 0.00 3.82
406 414 0.871722 ACACACACACACACACACAC 59.128 50.000 0.00 0.00 0.00 3.82
408 416 0.871722 ACACACACACACACACACAC 59.128 50.000 0.00 0.00 0.00 3.82
410 418 0.871722 ACACACACACACACACACAC 59.128 50.000 0.00 0.00 0.00 3.82
412 420 0.871722 ACACACACACACACACACAC 59.128 50.000 0.00 0.00 0.00 3.82
414 422 0.871722 ACACACACACACACACACAC 59.128 50.000 0.00 0.00 0.00 3.82
416 424 0.871722 ACACACACACACACACACAC 59.128 50.000 0.00 0.00 0.00 3.82
418 426 0.871722 ACACACACACACACACACAC 59.128 50.000 0.00 0.00 0.00 3.82
420 428 0.871722 ACACACACACACACACACAC 59.128 50.000 0.00 0.00 0.00 3.82
422 430 0.871722 ACACACACACACACACACAC 59.128 50.000 0.00 0.00 0.00 3.82
425 433 2.675348 CACACACACACACACACACATA 59.325 45.455 0.00 0.00 0.00 2.29
513 881 8.445588 CCCTTGTTATATAATCCCTTAGTTGGT 58.554 37.037 0.00 0.00 0.00 3.67
1091 1621 0.450983 GTAGCTACTTGACGCCTCGT 59.549 55.000 16.88 0.00 45.10 4.18
1092 1622 1.135460 GTAGCTACTTGACGCCTCGTT 60.135 52.381 16.88 0.00 41.37 3.85
1093 1623 1.171308 AGCTACTTGACGCCTCGTTA 58.829 50.000 0.00 0.00 41.37 3.18
1094 1624 1.542915 AGCTACTTGACGCCTCGTTAA 59.457 47.619 0.00 0.00 41.37 2.01
1144 1674 5.068723 CCAGACGAGGAGCCTTAATTAGTTA 59.931 44.000 0.00 0.00 0.00 2.24
1291 1821 9.050601 CAATCTTCTGGTTTAGATAAGATGTCC 57.949 37.037 0.00 0.00 34.64 4.02
1299 1829 6.014840 GGTTTAGATAAGATGTCCGACCCATA 60.015 42.308 0.00 0.00 0.00 2.74
1300 1830 6.585695 TTAGATAAGATGTCCGACCCATAC 57.414 41.667 0.00 0.00 0.00 2.39
1384 1914 0.538977 TCTTCTTCGACGTGGAGGGT 60.539 55.000 9.72 0.00 0.00 4.34
1573 2103 2.856346 CGTAAGGTTCGGATGCGCG 61.856 63.158 0.00 0.00 0.00 6.86
1593 2123 4.803426 GCTCGACAGGTCCGGCAG 62.803 72.222 0.00 0.00 0.00 4.85
1594 2124 3.374402 CTCGACAGGTCCGGCAGT 61.374 66.667 0.00 0.00 0.00 4.40
1597 2127 2.997897 GACAGGTCCGGCAGTCCT 60.998 66.667 0.00 0.00 0.00 3.85
1633 2163 2.438795 AGCTCCTCGACCGTCCTC 60.439 66.667 0.00 0.00 0.00 3.71
1657 2187 3.072468 TACGGCGAAGAGTGGGGG 61.072 66.667 16.62 0.00 0.00 5.40
1669 2199 2.041755 AGAGTGGGGGTTTTGGAGATTC 59.958 50.000 0.00 0.00 0.00 2.52
1696 2226 1.141881 CGATGTTCTGGAGGACCCG 59.858 63.158 0.00 0.00 37.93 5.28
1708 2238 1.835531 GAGGACCCGGATTACCTTGAA 59.164 52.381 0.73 0.00 32.53 2.69
1747 2277 2.230025 GAGCTGCACTGTCTCTGTTCTA 59.770 50.000 1.02 0.00 0.00 2.10
1817 2351 4.032900 TCGTCGATCTGCATAAGCTTTTTC 59.967 41.667 3.20 0.00 42.74 2.29
1855 2389 2.223572 CGCATAATCTTTGGGAGCAACC 60.224 50.000 0.00 0.00 38.08 3.77
1942 2476 1.609208 ATGTTTGGTGACTGGTGAGC 58.391 50.000 0.00 0.00 0.00 4.26
1953 2487 4.927425 GTGACTGGTGAGCGTATTTTAAGA 59.073 41.667 0.00 0.00 0.00 2.10
2076 2849 3.852578 ACATATTCTCCAGGACCAAAGGT 59.147 43.478 0.00 0.00 39.44 3.50
2303 3105 4.113815 CCCTGGGGATGCTGCGAA 62.114 66.667 4.27 0.00 37.50 4.70
2366 3168 2.203582 AACCGGGCCAAGGGTTTC 60.204 61.111 19.12 0.00 43.84 2.78
2370 3172 2.526110 GGGCCAAGGGTTTCCACT 59.474 61.111 4.39 0.00 34.83 4.00
2389 3191 1.003233 GGTGCTCCAAGAGGGACAC 60.003 63.158 0.00 0.00 42.15 3.67
2390 3192 1.374758 GTGCTCCAAGAGGGACACG 60.375 63.158 0.00 0.00 42.15 4.49
2474 3276 2.853542 TGGTGAGCCAAGCAGGGA 60.854 61.111 0.00 0.00 42.83 4.20
2489 3291 0.040204 AGGGATTTCACCTTGGCCTG 59.960 55.000 3.32 0.00 33.64 4.85
2509 3311 0.620556 AGTCCGAGCAATCCCATTGT 59.379 50.000 0.00 0.00 42.20 2.71
2540 3342 3.816523 CAGGACCTAGATACGAGGAAGTC 59.183 52.174 0.00 0.00 37.53 3.01
2556 3571 1.227205 GTCCTGATCTGAGCTGCCG 60.227 63.158 0.00 0.00 0.00 5.69
2584 3599 4.873129 CACCGGGATGCCGACGAG 62.873 72.222 28.88 12.82 34.88 4.18
2612 3627 1.070786 GGAGAGGACGCAACAACCA 59.929 57.895 0.00 0.00 0.00 3.67
2656 3671 1.343465 CGACAAAGGACACTGGTAGGT 59.657 52.381 0.00 0.00 0.00 3.08
2657 3672 2.224209 CGACAAAGGACACTGGTAGGTT 60.224 50.000 0.00 0.00 0.00 3.50
2659 3674 2.775384 ACAAAGGACACTGGTAGGTTGA 59.225 45.455 0.00 0.00 0.00 3.18
2753 3768 1.376037 CTCGCCAAGGAAGACCACC 60.376 63.158 0.00 0.00 38.94 4.61
2786 3801 3.365265 GGCCGAAACCAGCACCAG 61.365 66.667 0.00 0.00 0.00 4.00
2796 3811 1.668294 CAGCACCAGAACTCGGAGT 59.332 57.895 4.45 4.45 0.00 3.85
2882 3897 2.998279 GCCCAACCAGCATCAGCAC 61.998 63.158 0.00 0.00 45.49 4.40
2916 3931 0.669318 TGCAACCGAGGTAAGAAGCG 60.669 55.000 0.00 0.00 0.00 4.68
2923 3938 0.802607 GAGGTAAGAAGCGGTCGCAG 60.803 60.000 17.71 0.00 44.88 5.18
2952 3967 3.133767 CTGAAGCCATGCCGCCATG 62.134 63.158 0.00 0.00 46.70 3.66
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 0.237235 CATTTGTCCCGGTTCGTGTG 59.763 55.000 0.00 0.00 0.00 3.82
1 2 1.512156 GCATTTGTCCCGGTTCGTGT 61.512 55.000 0.00 0.00 0.00 4.49
2 3 1.209127 GCATTTGTCCCGGTTCGTG 59.791 57.895 0.00 0.00 0.00 4.35
3 4 1.969589 GGCATTTGTCCCGGTTCGT 60.970 57.895 0.00 0.00 0.00 3.85
4 5 1.644786 GAGGCATTTGTCCCGGTTCG 61.645 60.000 0.00 0.00 0.00 3.95
5 6 1.313091 GGAGGCATTTGTCCCGGTTC 61.313 60.000 0.00 0.00 0.00 3.62
6 7 1.304134 GGAGGCATTTGTCCCGGTT 60.304 57.895 0.00 0.00 0.00 4.44
7 8 2.355115 GGAGGCATTTGTCCCGGT 59.645 61.111 0.00 0.00 0.00 5.28
8 9 2.440247 GGGAGGCATTTGTCCCGG 60.440 66.667 0.00 0.00 43.27 5.73
11 12 1.452108 CCTCGGGAGGCATTTGTCC 60.452 63.158 1.02 0.00 42.44 4.02
12 13 4.225497 CCTCGGGAGGCATTTGTC 57.775 61.111 1.02 0.00 42.44 3.18
48 49 3.688475 ATACGTCCCGGTTCGTGCG 62.688 63.158 24.43 11.66 40.50 5.34
49 50 2.162754 CATACGTCCCGGTTCGTGC 61.163 63.158 24.43 0.00 40.50 5.34
50 51 2.162754 GCATACGTCCCGGTTCGTG 61.163 63.158 24.43 13.76 40.50 4.35
51 52 2.182537 GCATACGTCCCGGTTCGT 59.817 61.111 21.14 21.14 42.82 3.85
52 53 2.584143 GGCATACGTCCCGGTTCG 60.584 66.667 12.74 12.74 0.00 3.95
53 54 2.202974 GGGCATACGTCCCGGTTC 60.203 66.667 0.00 0.00 33.43 3.62
59 60 2.113139 CCATGGGGGCATACGTCC 59.887 66.667 2.85 0.00 35.48 4.79
70 71 2.689691 ATGAACCGGGACCCATGGG 61.690 63.158 30.23 30.23 42.03 4.00
71 72 1.453745 CATGAACCGGGACCCATGG 60.454 63.158 12.15 4.14 34.39 3.66
72 73 0.748005 GTCATGAACCGGGACCCATG 60.748 60.000 12.15 13.18 38.12 3.66
73 74 0.914417 AGTCATGAACCGGGACCCAT 60.914 55.000 12.15 0.00 31.99 4.00
74 75 1.537889 AGTCATGAACCGGGACCCA 60.538 57.895 12.15 0.00 31.99 4.51
75 76 1.078426 CAGTCATGAACCGGGACCC 60.078 63.158 6.32 0.00 31.99 4.46
76 77 0.323629 TTCAGTCATGAACCGGGACC 59.676 55.000 6.32 0.00 40.54 4.46
77 78 3.927555 TTCAGTCATGAACCGGGAC 57.072 52.632 6.32 2.53 40.54 4.46
84 85 1.348064 AGTCCCGGTTCAGTCATGAA 58.652 50.000 0.00 0.00 43.20 2.57
85 86 2.225382 TAGTCCCGGTTCAGTCATGA 57.775 50.000 0.00 0.00 0.00 3.07
86 87 3.198068 CATTAGTCCCGGTTCAGTCATG 58.802 50.000 0.00 0.00 0.00 3.07
87 88 2.170607 CCATTAGTCCCGGTTCAGTCAT 59.829 50.000 0.00 0.00 0.00 3.06
88 89 1.553248 CCATTAGTCCCGGTTCAGTCA 59.447 52.381 0.00 0.00 0.00 3.41
89 90 1.134491 CCCATTAGTCCCGGTTCAGTC 60.134 57.143 0.00 0.00 0.00 3.51
90 91 0.909623 CCCATTAGTCCCGGTTCAGT 59.090 55.000 0.00 0.00 0.00 3.41
91 92 0.463833 GCCCATTAGTCCCGGTTCAG 60.464 60.000 0.00 0.00 0.00 3.02
92 93 0.912487 AGCCCATTAGTCCCGGTTCA 60.912 55.000 0.00 0.00 0.00 3.18
93 94 0.463833 CAGCCCATTAGTCCCGGTTC 60.464 60.000 0.00 0.00 0.00 3.62
94 95 1.607612 CAGCCCATTAGTCCCGGTT 59.392 57.895 0.00 0.00 0.00 4.44
95 96 2.375345 CCAGCCCATTAGTCCCGGT 61.375 63.158 0.00 0.00 0.00 5.28
96 97 2.510906 CCAGCCCATTAGTCCCGG 59.489 66.667 0.00 0.00 0.00 5.73
97 98 1.407656 TAGCCAGCCCATTAGTCCCG 61.408 60.000 0.00 0.00 0.00 5.14
98 99 0.398318 CTAGCCAGCCCATTAGTCCC 59.602 60.000 0.00 0.00 0.00 4.46
99 100 0.398318 CCTAGCCAGCCCATTAGTCC 59.602 60.000 0.00 0.00 0.00 3.85
100 101 0.250510 GCCTAGCCAGCCCATTAGTC 60.251 60.000 0.00 0.00 0.00 2.59
101 102 1.839894 GCCTAGCCAGCCCATTAGT 59.160 57.895 0.00 0.00 0.00 2.24
102 103 4.809070 GCCTAGCCAGCCCATTAG 57.191 61.111 0.00 0.00 0.00 1.73
113 114 2.351244 GCTTTGGTTGGGGCCTAGC 61.351 63.158 0.84 0.00 32.78 3.42
114 115 1.682344 GGCTTTGGTTGGGGCCTAG 60.682 63.158 0.84 0.00 41.20 3.02
115 116 1.809939 ATGGCTTTGGTTGGGGCCTA 61.810 55.000 0.84 0.00 44.36 3.93
116 117 3.178509 ATGGCTTTGGTTGGGGCCT 62.179 57.895 0.84 0.00 44.36 5.19
117 118 2.607442 ATGGCTTTGGTTGGGGCC 60.607 61.111 0.00 0.00 44.31 5.80
118 119 1.767654 AACATGGCTTTGGTTGGGGC 61.768 55.000 0.00 0.00 0.00 5.80
119 120 0.764271 AAACATGGCTTTGGTTGGGG 59.236 50.000 0.00 0.00 0.00 4.96
120 121 2.104622 AGAAAACATGGCTTTGGTTGGG 59.895 45.455 0.00 0.00 0.00 4.12
121 122 3.473923 AGAAAACATGGCTTTGGTTGG 57.526 42.857 0.00 0.00 0.00 3.77
122 123 5.200368 AGTAGAAAACATGGCTTTGGTTG 57.800 39.130 0.00 0.00 0.00 3.77
123 124 6.016276 CACTAGTAGAAAACATGGCTTTGGTT 60.016 38.462 3.59 0.00 0.00 3.67
124 125 5.473504 CACTAGTAGAAAACATGGCTTTGGT 59.526 40.000 3.59 0.00 0.00 3.67
125 126 5.473504 ACACTAGTAGAAAACATGGCTTTGG 59.526 40.000 3.59 0.00 0.00 3.28
126 127 6.560253 ACACTAGTAGAAAACATGGCTTTG 57.440 37.500 3.59 0.00 0.00 2.77
127 128 7.390718 CCTTACACTAGTAGAAAACATGGCTTT 59.609 37.037 3.59 0.00 0.00 3.51
128 129 6.879458 CCTTACACTAGTAGAAAACATGGCTT 59.121 38.462 3.59 0.00 0.00 4.35
129 130 6.407202 CCTTACACTAGTAGAAAACATGGCT 58.593 40.000 3.59 0.00 0.00 4.75
130 131 5.064834 GCCTTACACTAGTAGAAAACATGGC 59.935 44.000 3.59 5.13 0.00 4.40
131 132 5.585047 GGCCTTACACTAGTAGAAAACATGG 59.415 44.000 3.59 0.00 0.00 3.66
132 133 6.170506 TGGCCTTACACTAGTAGAAAACATG 58.829 40.000 3.32 0.00 0.00 3.21
133 134 6.368779 TGGCCTTACACTAGTAGAAAACAT 57.631 37.500 3.32 0.00 0.00 2.71
134 135 5.811796 TGGCCTTACACTAGTAGAAAACA 57.188 39.130 3.32 0.00 0.00 2.83
135 136 5.993441 TGTTGGCCTTACACTAGTAGAAAAC 59.007 40.000 3.32 0.00 0.00 2.43
136 137 6.177310 TGTTGGCCTTACACTAGTAGAAAA 57.823 37.500 3.32 0.00 0.00 2.29
137 138 5.811796 TGTTGGCCTTACACTAGTAGAAA 57.188 39.130 3.32 0.00 0.00 2.52
138 139 6.368779 AATGTTGGCCTTACACTAGTAGAA 57.631 37.500 12.56 0.00 0.00 2.10
139 140 7.484993 TTAATGTTGGCCTTACACTAGTAGA 57.515 36.000 12.56 0.00 0.00 2.59
140 141 9.998106 ATATTAATGTTGGCCTTACACTAGTAG 57.002 33.333 12.56 0.00 0.00 2.57
142 143 9.774413 GTATATTAATGTTGGCCTTACACTAGT 57.226 33.333 12.56 6.81 0.00 2.57
143 144 9.998106 AGTATATTAATGTTGGCCTTACACTAG 57.002 33.333 12.56 0.00 0.00 2.57
144 145 9.991906 GAGTATATTAATGTTGGCCTTACACTA 57.008 33.333 12.56 4.79 0.00 2.74
145 146 7.937394 GGAGTATATTAATGTTGGCCTTACACT 59.063 37.037 12.56 5.71 0.00 3.55
146 147 7.174426 GGGAGTATATTAATGTTGGCCTTACAC 59.826 40.741 12.56 1.26 0.00 2.90
147 148 7.073215 AGGGAGTATATTAATGTTGGCCTTACA 59.927 37.037 12.66 12.66 0.00 2.41
148 149 7.459234 AGGGAGTATATTAATGTTGGCCTTAC 58.541 38.462 3.32 2.54 0.00 2.34
351 352 5.782047 TCATTTTGGATTGCTTACCACTTG 58.218 37.500 0.00 0.00 35.81 3.16
384 392 0.871057 TGTGTGTGTGTGTGTGTGTG 59.129 50.000 0.00 0.00 0.00 3.82
386 394 0.871057 TGTGTGTGTGTGTGTGTGTG 59.129 50.000 0.00 0.00 0.00 3.82
388 396 0.871057 TGTGTGTGTGTGTGTGTGTG 59.129 50.000 0.00 0.00 0.00 3.82
390 398 0.871057 TGTGTGTGTGTGTGTGTGTG 59.129 50.000 0.00 0.00 0.00 3.82
392 400 0.871057 TGTGTGTGTGTGTGTGTGTG 59.129 50.000 0.00 0.00 0.00 3.82
394 402 0.871057 TGTGTGTGTGTGTGTGTGTG 59.129 50.000 0.00 0.00 0.00 3.82
396 404 0.871057 TGTGTGTGTGTGTGTGTGTG 59.129 50.000 0.00 0.00 0.00 3.82
398 406 0.871057 TGTGTGTGTGTGTGTGTGTG 59.129 50.000 0.00 0.00 0.00 3.82
400 408 0.871057 TGTGTGTGTGTGTGTGTGTG 59.129 50.000 0.00 0.00 0.00 3.82
402 410 0.871057 TGTGTGTGTGTGTGTGTGTG 59.129 50.000 0.00 0.00 0.00 3.82
404 412 0.871057 TGTGTGTGTGTGTGTGTGTG 59.129 50.000 0.00 0.00 0.00 3.82
406 414 2.935849 ACTATGTGTGTGTGTGTGTGTG 59.064 45.455 0.00 0.00 0.00 3.82
408 416 3.194062 TGACTATGTGTGTGTGTGTGTG 58.806 45.455 0.00 0.00 0.00 3.82
410 418 5.696270 ACTATTGACTATGTGTGTGTGTGTG 59.304 40.000 0.00 0.00 0.00 3.82
412 420 7.062255 CACTACTATTGACTATGTGTGTGTGTG 59.938 40.741 0.00 0.00 0.00 3.82
414 422 7.312899 TCACTACTATTGACTATGTGTGTGTG 58.687 38.462 0.00 0.00 0.00 3.82
416 424 8.757164 TTTCACTACTATTGACTATGTGTGTG 57.243 34.615 0.00 0.00 0.00 3.82
536 904 6.695292 AGCAAATTTTATCGCTGTTCAAAG 57.305 33.333 0.30 0.00 32.33 2.77
699 1215 7.081976 GCAAACAAGGAAGTAAATTATGTCGT 58.918 34.615 0.00 0.00 0.00 4.34
712 1228 7.973601 ACATTTTACTTTTGCAAACAAGGAAG 58.026 30.769 12.39 8.06 37.04 3.46
1091 1621 7.498900 CACTAAGTGGATGGTGATGCTAATTAA 59.501 37.037 0.00 0.00 32.12 1.40
1092 1622 6.992123 CACTAAGTGGATGGTGATGCTAATTA 59.008 38.462 0.00 0.00 32.12 1.40
1093 1623 5.824624 CACTAAGTGGATGGTGATGCTAATT 59.175 40.000 0.00 0.00 32.12 1.40
1094 1624 5.371526 CACTAAGTGGATGGTGATGCTAAT 58.628 41.667 0.00 0.00 32.12 1.73
1144 1674 4.309099 TGACGGTAAACTCTAAACGCAAT 58.691 39.130 0.00 0.00 0.00 3.56
1291 1821 1.495584 CGCCATTTCGGTATGGGTCG 61.496 60.000 15.51 9.40 44.35 4.79
1299 1829 2.690778 GCTGCTTCGCCATTTCGGT 61.691 57.895 0.00 0.00 36.97 4.69
1300 1830 2.100991 GCTGCTTCGCCATTTCGG 59.899 61.111 0.00 0.00 38.11 4.30
1384 1914 1.142314 GAGTATGGCGGCGGTGTAA 59.858 57.895 9.78 0.00 0.00 2.41
1573 2103 4.436998 CCGGACCTGTCGAGCACC 62.437 72.222 0.00 0.00 0.00 5.01
1579 2109 4.436998 GGACTGCCGGACCTGTCG 62.437 72.222 5.05 0.00 35.34 4.35
1597 2127 4.634703 TGCCAAAGCTCCGCCGAA 62.635 61.111 0.00 0.00 40.80 4.30
1609 2139 2.650116 GGTCGAGGAGCTCTGCCAA 61.650 63.158 14.64 0.00 0.00 4.52
1633 2163 2.520979 CACTCTTCGCCGTAGAAAGAG 58.479 52.381 10.63 10.63 34.56 2.85
1657 2187 1.226018 CGGCGCGAATCTCCAAAAC 60.226 57.895 12.10 0.00 0.00 2.43
1677 2207 1.153349 GGGTCCTCCAGAACATCGC 60.153 63.158 0.00 0.00 31.73 4.58
1696 2226 2.684038 GCAGTCCCCTTCAAGGTAATCC 60.684 54.545 1.78 0.00 31.93 3.01
1708 2238 3.947041 AGGGTGAGGCAGTCCCCT 61.947 66.667 7.16 7.97 41.95 4.79
1747 2277 0.463116 ACGACAGTTGCGGTTTCCTT 60.463 50.000 0.00 0.00 0.00 3.36
1817 2351 1.480219 GCGCGTCGACCCTCAAATAG 61.480 60.000 10.58 0.00 0.00 1.73
1855 2389 6.281405 AGTAAATATCTTAACCACCTGCTCG 58.719 40.000 0.00 0.00 0.00 5.03
1863 2397 9.037737 CGAATTCGGAAGTAAATATCTTAACCA 57.962 33.333 20.16 0.00 35.37 3.67
2045 2818 4.285775 TCCTGGAGAATATGTGACACAACA 59.714 41.667 13.23 3.97 0.00 3.33
2076 2849 5.163237 GGAAATGGTAGTTGGGCACTAGATA 60.163 44.000 0.00 0.00 38.77 1.98
2157 2935 5.435686 TGTGCCCTCTTATGTACTCATTT 57.564 39.130 0.00 0.00 35.70 2.32
2370 3172 1.461268 TGTCCCTCTTGGAGCACCA 60.461 57.895 0.00 0.00 46.38 4.17
2389 3191 1.004080 CTGCCATGGCCTCTATCCG 60.004 63.158 33.44 7.97 41.09 4.18
2390 3192 0.250640 CACTGCCATGGCCTCTATCC 60.251 60.000 33.44 4.41 41.09 2.59
2420 3222 2.034999 TCGTGGGTGCCATTTCCC 59.965 61.111 0.00 0.00 43.67 3.97
2449 3251 3.368822 TGGCTCACCAATGCTTGC 58.631 55.556 0.00 0.00 45.37 4.01
2474 3276 1.272147 GGACTCAGGCCAAGGTGAAAT 60.272 52.381 5.01 0.00 0.00 2.17
2489 3291 1.303309 CAATGGGATTGCTCGGACTC 58.697 55.000 0.00 0.00 32.92 3.36
2509 3311 0.551396 TCTAGGTCCTGATCTGGCGA 59.449 55.000 13.60 2.84 0.00 5.54
2540 3342 2.108566 CCGGCAGCTCAGATCAGG 59.891 66.667 0.00 0.00 0.00 3.86
2542 3344 3.473647 CCCCGGCAGCTCAGATCA 61.474 66.667 0.00 0.00 0.00 2.92
2543 3345 4.247380 CCCCCGGCAGCTCAGATC 62.247 72.222 0.00 0.00 0.00 2.75
2584 3599 3.077556 TCCTCTCCGGCCTTCTGC 61.078 66.667 0.00 0.00 40.16 4.26
2587 3602 4.516195 GCGTCCTCTCCGGCCTTC 62.516 72.222 0.00 0.00 0.00 3.46
2627 3642 0.521735 GTCCTTTGTCGGCATGGTTC 59.478 55.000 9.00 2.07 0.00 3.62
2637 3652 3.139077 CAACCTACCAGTGTCCTTTGTC 58.861 50.000 0.00 0.00 0.00 3.18
2656 3671 0.674581 CATGCTTCCAGCGTCCTCAA 60.675 55.000 0.00 0.00 46.26 3.02
2657 3672 1.078918 CATGCTTCCAGCGTCCTCA 60.079 57.895 0.00 0.00 46.26 3.86
2659 3674 1.078848 GACATGCTTCCAGCGTCCT 60.079 57.895 0.00 0.00 46.26 3.85
2680 3695 2.759973 CTCCAGTCCTAGCGGCCA 60.760 66.667 2.24 0.00 0.00 5.36
2753 3768 1.285641 GCCCATTTGTGTGGTCACG 59.714 57.895 0.00 0.00 46.49 4.35
2786 3801 3.119096 GGCGCCAACTCCGAGTTC 61.119 66.667 24.80 0.64 36.03 3.01
2796 3811 2.813474 CATCTTCGACGGCGCCAA 60.813 61.111 28.98 12.33 37.46 4.52
2818 3833 2.795110 TTGCCCTGTTGCAAGCCAC 61.795 57.895 0.00 0.00 45.77 5.01
2863 3878 3.818787 GCTGATGCTGGTTGGGCG 61.819 66.667 0.00 0.00 36.03 6.13
2882 3897 1.536073 TTGCACGACCTCTCCTCCTG 61.536 60.000 0.00 0.00 0.00 3.86
2916 3931 2.266055 CCTGACCCTTCTGCGACC 59.734 66.667 0.00 0.00 0.00 4.79
2923 3938 4.310288 GCTTCAGCCTGACCCTTC 57.690 61.111 0.00 0.00 34.31 3.46


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

AutoCloner maintained by Alex Coulton.