Multiple sequence alignment - TraesCS7B01G128600

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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 TraesCS7B01G128600 chr7B 100.000 3398 0 0 1 3398 154143219 154146616 0.000000e+00 6276
1 TraesCS7B01G128600 chr7B 87.518 1418 146 17 1139 2541 153594709 153596110 0.000000e+00 1609
2 TraesCS7B01G128600 chr7B 83.425 362 33 14 1 349 153593066 153593413 9.160000e-81 311
3 TraesCS7B01G128600 chr7B 83.235 340 26 12 674 1012 153594372 153594681 2.000000e-72 283
4 TraesCS7B01G128600 chr7A 93.690 2171 131 5 394 2559 191659691 191661860 0.000000e+00 3245
5 TraesCS7B01G128600 chr7A 88.661 1270 135 5 1139 2402 185982610 185981344 0.000000e+00 1539
6 TraesCS7B01G128600 chr7A 86.972 852 84 8 2573 3398 191661941 191662791 0.000000e+00 933
7 TraesCS7B01G128600 chr7A 90.789 228 13 3 1 225 191659400 191659622 7.130000e-77 298
8 TraesCS7B01G128600 chr7A 82.948 346 38 12 1 337 185983722 185983389 3.320000e-75 292
9 TraesCS7B01G128600 chr7A 89.401 217 17 3 796 1012 185982848 185982638 5.590000e-68 268
10 TraesCS7B01G128600 chr7D 93.701 2175 116 9 394 2559 184559127 184561289 0.000000e+00 3238
11 TraesCS7B01G128600 chr7D 88.147 1392 143 11 1139 2513 184514699 184516085 0.000000e+00 1637
12 TraesCS7B01G128600 chr7D 88.218 331 29 4 2573 2893 184561366 184561696 1.480000e-103 387
13 TraesCS7B01G128600 chr7D 85.664 286 19 9 728 1013 184514409 184514672 7.180000e-72 281
14 TraesCS7B01G128600 chr7D 88.596 228 18 3 1 225 184558836 184559058 1.550000e-68 270
15 TraesCS7B01G128600 chr7D 79.167 168 27 8 2758 2924 174991389 174991229 3.580000e-20 110
16 TraesCS7B01G128600 chr5A 77.708 1108 217 20 1307 2399 275260942 275259850 0.000000e+00 651
17 TraesCS7B01G128600 chr5D 77.527 1108 219 20 1307 2399 212252917 212251825 1.030000e-179 640
18 TraesCS7B01G128600 chr6A 86.154 130 14 4 2801 2929 521992059 521991933 1.640000e-28 137


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 TraesCS7B01G128600 chr7B 154143219 154146616 3397 False 6276.000000 6276 100.000000 1 3398 1 chr7B.!!$F1 3397
1 TraesCS7B01G128600 chr7B 153593066 153596110 3044 False 734.333333 1609 84.726000 1 2541 3 chr7B.!!$F2 2540
2 TraesCS7B01G128600 chr7A 191659400 191662791 3391 False 1492.000000 3245 90.483667 1 3398 3 chr7A.!!$F1 3397
3 TraesCS7B01G128600 chr7A 185981344 185983722 2378 True 699.666667 1539 87.003333 1 2402 3 chr7A.!!$R1 2401
4 TraesCS7B01G128600 chr7D 184558836 184561696 2860 False 1298.333333 3238 90.171667 1 2893 3 chr7D.!!$F2 2892
5 TraesCS7B01G128600 chr7D 184514409 184516085 1676 False 959.000000 1637 86.905500 728 2513 2 chr7D.!!$F1 1785
6 TraesCS7B01G128600 chr5A 275259850 275260942 1092 True 651.000000 651 77.708000 1307 2399 1 chr5A.!!$R1 1092
7 TraesCS7B01G128600 chr5D 212251825 212252917 1092 True 640.000000 640 77.527000 1307 2399 1 chr5D.!!$R1 1092

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
51 53 0.395586 AACCAACCTTGAGCTGTGCA 60.396 50.0 0.00 0.0 0.00 4.57 F
377 431 1.728068 TGCATGCATTCACCATTTGC 58.272 45.0 18.46 0.0 36.91 3.68 F
1695 2404 0.250901 GCAAGTTCTCCAGCTTCCCA 60.251 55.0 0.00 0.0 0.00 4.37 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1056 1762 1.112916 CGGGGCTTGGTGGAAAAACT 61.113 55.0 0.0 0.0 0.00 2.66 R
2353 3074 1.093159 ATCTTCTCGGCTACGACGTT 58.907 50.0 5.5 0.0 45.59 3.99 R
2983 3824 0.107361 AATAACTACCCGCCAGCACC 60.107 55.0 0.0 0.0 0.00 5.01 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
27 28 2.773397 TTCATTCACCGGCGCGAGAA 62.773 55.000 12.10 5.30 0.00 2.87
51 53 0.395586 AACCAACCTTGAGCTGTGCA 60.396 50.000 0.00 0.00 0.00 4.57
151 168 4.592936 CCGACGCGCTACCTCTCG 62.593 72.222 5.73 5.96 0.00 4.04
225 242 2.500098 CCTCCTCGTTTTCAGGTATGGA 59.500 50.000 0.00 0.00 32.20 3.41
227 244 4.344102 CCTCCTCGTTTTCAGGTATGGATA 59.656 45.833 0.00 0.00 32.20 2.59
228 245 5.012148 CCTCCTCGTTTTCAGGTATGGATAT 59.988 44.000 0.00 0.00 32.20 1.63
229 246 6.097915 TCCTCGTTTTCAGGTATGGATATC 57.902 41.667 0.00 0.00 32.20 1.63
230 247 4.923871 CCTCGTTTTCAGGTATGGATATCG 59.076 45.833 0.00 0.00 0.00 2.92
232 249 3.994392 CGTTTTCAGGTATGGATATCGGG 59.006 47.826 0.00 0.00 0.00 5.14
233 250 4.324267 GTTTTCAGGTATGGATATCGGGG 58.676 47.826 0.00 0.00 0.00 5.73
234 251 3.269592 TTCAGGTATGGATATCGGGGT 57.730 47.619 0.00 0.00 0.00 4.95
282 301 5.524646 TCAAAAGAAAAGGTACGGTGTACTG 59.475 40.000 7.02 0.00 0.00 2.74
315 334 2.914695 AAGTACCGTACAAACTGCCA 57.085 45.000 11.26 0.00 0.00 4.92
327 346 2.422276 AACTGCCAATGCTTCGTTTC 57.578 45.000 0.00 0.00 38.71 2.78
345 368 7.367159 TCGTTTCAAAAAGAAGTGTTACTGA 57.633 32.000 0.00 0.00 37.57 3.41
374 428 4.415881 AATCATGCATGCATTCACCATT 57.584 36.364 30.32 18.35 33.90 3.16
377 431 1.728068 TGCATGCATTCACCATTTGC 58.272 45.000 18.46 0.00 36.91 3.68
382 436 2.768698 TGCATTCACCATTTGCCTTTG 58.231 42.857 0.00 0.00 35.51 2.77
400 454 4.365723 CTTTGCTTTGAGATTTGTGCTGT 58.634 39.130 0.00 0.00 0.00 4.40
653 1317 6.150318 AGAAGTTGTATCTTGAGTACGTGTG 58.850 40.000 0.00 0.00 0.00 3.82
824 1524 7.772332 ACCGTTATTACAGAAAGAGCAATAG 57.228 36.000 0.00 0.00 0.00 1.73
825 1525 6.258068 ACCGTTATTACAGAAAGAGCAATAGC 59.742 38.462 0.00 0.00 42.56 2.97
826 1526 6.257849 CCGTTATTACAGAAAGAGCAATAGCA 59.742 38.462 0.00 0.00 45.49 3.49
827 1527 7.201609 CCGTTATTACAGAAAGAGCAATAGCAA 60.202 37.037 0.00 0.00 45.49 3.91
828 1528 8.338259 CGTTATTACAGAAAGAGCAATAGCAAT 58.662 33.333 0.00 0.00 45.49 3.56
831 1531 5.725110 ACAGAAAGAGCAATAGCAATACG 57.275 39.130 0.00 0.00 45.49 3.06
1056 1762 3.081409 GCCGCCTTCCCTCCACTA 61.081 66.667 0.00 0.00 0.00 2.74
1057 1763 3.095347 GCCGCCTTCCCTCCACTAG 62.095 68.421 0.00 0.00 0.00 2.57
1075 1781 1.112916 AGTTTTTCCACCAAGCCCCG 61.113 55.000 0.00 0.00 0.00 5.73
1112 1818 0.394565 GCGAACCTGCCTCCTATCAT 59.605 55.000 0.00 0.00 0.00 2.45
1260 1966 0.767446 CATCAGAGGGGATGCCTCCT 60.767 60.000 8.03 0.00 41.74 3.69
1261 1967 0.870313 ATCAGAGGGGATGCCTCCTA 59.130 55.000 8.03 0.00 41.74 2.94
1293 1999 3.005472 TCGCTTTCCCTCCGATATACTTG 59.995 47.826 0.00 0.00 0.00 3.16
1395 2101 1.440850 CGTCGTCGTCGTTGGCTTA 60.441 57.895 3.67 0.00 38.33 3.09
1410 2116 1.080093 CTTAGGCACGCCGTCTCAA 60.080 57.895 1.61 0.00 41.95 3.02
1412 2118 2.089887 TTAGGCACGCCGTCTCAACA 62.090 55.000 1.61 0.00 41.95 3.33
1505 2214 0.669318 CAGCAAAACGACCCGCTCTA 60.669 55.000 0.00 0.00 30.72 2.43
1695 2404 0.250901 GCAAGTTCTCCAGCTTCCCA 60.251 55.000 0.00 0.00 0.00 4.37
1827 2536 0.980231 CCTTCTCCTACTGCCTGCCT 60.980 60.000 0.00 0.00 0.00 4.75
2157 2872 1.908619 TGCTATGACTTCTCTGGCCAA 59.091 47.619 7.01 0.00 0.00 4.52
2196 2911 2.982488 AGGGATGTCCTTCAAGTTCAGT 59.018 45.455 0.00 0.00 45.47 3.41
2353 3074 2.164422 CGTTCTGCTGAGGTGATCTACA 59.836 50.000 0.00 0.00 0.00 2.74
2419 3147 3.462483 TTCGTGGTAGAAAAGTGAGCA 57.538 42.857 0.00 0.00 0.00 4.26
2447 3185 2.118076 CCACCCAATGTGCCCACT 59.882 61.111 0.00 0.00 44.01 4.00
2474 3222 9.048446 GGTGTCAGTATCTTGTACTTTGTTTTA 57.952 33.333 0.00 0.00 0.00 1.52
2475 3223 9.859692 GTGTCAGTATCTTGTACTTTGTTTTAC 57.140 33.333 0.00 0.00 0.00 2.01
2505 3253 6.663523 CCAACTATGAATAAAGGGGTTGAAGT 59.336 38.462 0.00 0.00 35.90 3.01
2507 3255 7.027874 ACTATGAATAAAGGGGTTGAAGTGA 57.972 36.000 0.00 0.00 0.00 3.41
2517 3265 1.963515 GGTTGAAGTGATGGGTGCTTT 59.036 47.619 0.00 0.00 0.00 3.51
2559 3307 0.179174 CGTAAACCCGGCTGATTTGC 60.179 55.000 0.00 0.00 0.00 3.68
2561 3309 0.606944 TAAACCCGGCTGATTTGCGT 60.607 50.000 0.00 0.00 0.00 5.24
2563 3311 0.606944 AACCCGGCTGATTTGCGTAA 60.607 50.000 0.00 0.00 0.00 3.18
2565 3313 0.179174 CCCGGCTGATTTGCGTAAAC 60.179 55.000 0.00 0.00 0.00 2.01
2566 3314 0.179174 CCGGCTGATTTGCGTAAACC 60.179 55.000 0.00 0.00 0.00 3.27
2567 3315 0.179174 CGGCTGATTTGCGTAAACCC 60.179 55.000 0.00 0.00 0.00 4.11
2568 3316 1.173913 GGCTGATTTGCGTAAACCCT 58.826 50.000 0.00 0.00 0.00 4.34
2569 3317 2.361789 GGCTGATTTGCGTAAACCCTA 58.638 47.619 0.00 0.00 0.00 3.53
2570 3318 2.750712 GGCTGATTTGCGTAAACCCTAA 59.249 45.455 0.00 0.00 0.00 2.69
2571 3319 3.191791 GGCTGATTTGCGTAAACCCTAAA 59.808 43.478 0.00 0.00 0.00 1.85
2576 3391 7.378728 GCTGATTTGCGTAAACCCTAAATATTC 59.621 37.037 0.00 0.00 0.00 1.75
2577 3392 7.708998 TGATTTGCGTAAACCCTAAATATTCC 58.291 34.615 0.00 0.00 0.00 3.01
2586 3401 5.975988 ACCCTAAATATTCCAAGAGCTGA 57.024 39.130 0.00 0.00 0.00 4.26
2591 3406 5.998454 AAATATTCCAAGAGCTGATCGTG 57.002 39.130 1.79 1.79 37.18 4.35
2628 3444 2.414481 GAGCGTGTGTCTACTTCGTCTA 59.586 50.000 0.00 0.00 0.00 2.59
2639 3455 7.219535 GTGTCTACTTCGTCTAATCGCAATTTA 59.780 37.037 0.00 0.00 0.00 1.40
2648 3464 8.971321 TCGTCTAATCGCAATTTAGGTATTTAC 58.029 33.333 0.00 0.00 0.00 2.01
2656 3472 9.221933 TCGCAATTTAGGTATTTACTGAAAAGA 57.778 29.630 0.00 0.00 0.00 2.52
2749 3565 4.318333 CGGAGAGCAATGATTGTACGATTG 60.318 45.833 7.05 0.37 0.00 2.67
2754 3579 4.031028 GCAATGATTGTACGATTGCTCAC 58.969 43.478 17.66 0.00 45.57 3.51
2756 3581 3.224884 TGATTGTACGATTGCTCACGA 57.775 42.857 0.00 0.00 0.00 4.35
2764 3589 1.393539 CGATTGCTCACGAAAACCGAT 59.606 47.619 0.00 0.00 41.76 4.18
2801 3626 0.940126 CAGGCTGACATGGCGAATAC 59.060 55.000 9.42 0.00 37.59 1.89
2806 3631 3.815401 GGCTGACATGGCGAATACTAAAT 59.185 43.478 0.00 0.00 0.00 1.40
2827 3652 3.715628 ACTTTTGACCAACTGATGTGC 57.284 42.857 0.00 0.00 0.00 4.57
2845 3670 0.321653 GCCAAATGAGACGTGACCCT 60.322 55.000 0.00 0.00 0.00 4.34
2856 3681 3.637229 AGACGTGACCCTACCTATCAATG 59.363 47.826 0.00 0.00 0.00 2.82
2893 3718 5.665360 TCCTCTTCACATCTCTCTCTCTCTA 59.335 44.000 0.00 0.00 0.00 2.43
2932 3773 3.439129 ACAACTTTTGGGCGCTAATACTC 59.561 43.478 7.64 0.00 34.12 2.59
2940 3781 2.029739 GGGCGCTAATACTCTTCCTCTC 60.030 54.545 7.64 0.00 0.00 3.20
2947 3788 2.421751 TACTCTTCCTCTCGGTGGAG 57.578 55.000 0.00 0.00 41.89 3.86
2983 3824 4.227134 CGTCCGCCTCTCCATGGG 62.227 72.222 13.02 2.57 0.00 4.00
2987 3828 4.864334 CGCCTCTCCATGGGGTGC 62.864 72.222 12.53 14.71 34.93 5.01
3000 3841 2.662070 GGGTGCTGGCGGGTAGTTA 61.662 63.158 0.00 0.00 0.00 2.24
3012 3853 3.489738 GCGGGTAGTTATTCTCGTAAGCA 60.490 47.826 0.00 0.00 37.18 3.91
3067 3908 2.261671 CACTACCGCGTCTTGCCT 59.738 61.111 4.92 0.00 42.08 4.75
3077 3918 2.044650 TCTTGCCTGCCATGAGCC 60.045 61.111 0.00 0.00 42.71 4.70
3079 3920 1.980232 CTTGCCTGCCATGAGCCAA 60.980 57.895 0.00 0.00 42.71 4.52
3083 3924 1.751927 CCTGCCATGAGCCAACTCC 60.752 63.158 0.00 0.00 42.74 3.85
3085 3926 1.303561 TGCCATGAGCCAACTCCAC 60.304 57.895 0.00 0.00 42.74 4.02
3112 3953 1.153449 CGCTAGGAACGGAATGCCA 60.153 57.895 0.00 0.00 0.00 4.92
3128 3969 1.077169 TGCCAGTAACTCCTCTCTCCA 59.923 52.381 0.00 0.00 0.00 3.86
3133 3974 2.650322 AGTAACTCCTCTCTCCACCTCA 59.350 50.000 0.00 0.00 0.00 3.86
3134 3975 2.938428 AACTCCTCTCTCCACCTCAT 57.062 50.000 0.00 0.00 0.00 2.90
3142 3983 3.002583 TCCACCTCATGCCGCTCA 61.003 61.111 0.00 0.00 0.00 4.26
3178 4019 0.948623 CGTTCCACGCCATGAAGACA 60.949 55.000 0.00 0.00 33.65 3.41
3179 4020 1.453155 GTTCCACGCCATGAAGACAT 58.547 50.000 0.00 0.00 37.19 3.06
3180 4021 1.398390 GTTCCACGCCATGAAGACATC 59.602 52.381 0.00 0.00 34.15 3.06
3195 4036 0.824759 ACATCGGCCTAGTGGAGTTC 59.175 55.000 0.00 0.00 34.57 3.01
3216 4057 0.603707 CTGGCAAGGTTGAGAGCGAA 60.604 55.000 0.00 0.00 0.00 4.70
3218 4059 1.493311 GCAAGGTTGAGAGCGAACG 59.507 57.895 0.00 0.00 0.00 3.95
3220 4061 1.069090 AAGGTTGAGAGCGAACGCA 59.931 52.632 20.66 0.00 44.88 5.24
3227 4068 1.627550 GAGAGCGAACGCAAACTCCC 61.628 60.000 20.66 0.00 44.88 4.30
3228 4069 3.011760 GAGCGAACGCAAACTCCCG 62.012 63.158 20.66 0.00 44.88 5.14
3255 4096 2.979676 CTCTGCGGTGCAAGCCAA 60.980 61.111 12.17 0.92 38.41 4.52
3268 4109 0.969409 AAGCCAATGCCTTCTCCTGC 60.969 55.000 0.00 0.00 38.69 4.85
3274 4115 3.130160 GCCTTCTCCTGCTTGCCG 61.130 66.667 0.00 0.00 0.00 5.69
3279 4120 2.032528 CTCCTGCTTGCCGGTGAA 59.967 61.111 1.90 0.00 0.00 3.18
3289 4130 2.584391 GCCGGTGAAGTGGACCTCT 61.584 63.158 1.90 0.00 0.00 3.69
3297 4138 2.225394 TGAAGTGGACCTCTAGAGCCTT 60.225 50.000 14.73 9.74 0.00 4.35
3299 4140 1.359474 AGTGGACCTCTAGAGCCTTCA 59.641 52.381 14.73 3.49 0.00 3.02
3306 4147 3.205507 ACCTCTAGAGCCTTCATGTCCTA 59.794 47.826 14.73 0.00 0.00 2.94
3310 4151 3.742433 AGAGCCTTCATGTCCTAATCG 57.258 47.619 0.00 0.00 0.00 3.34
3319 4160 3.056536 TCATGTCCTAATCGCAGATAGGC 60.057 47.826 0.00 0.00 45.12 3.93
3337 4178 1.901650 GCGTGACTTCCAAGGCTTCG 61.902 60.000 0.00 0.00 34.24 3.79
3338 4179 0.319555 CGTGACTTCCAAGGCTTCGA 60.320 55.000 0.00 0.00 35.40 3.71
3344 4185 2.005451 CTTCCAAGGCTTCGATGTCTG 58.995 52.381 6.15 1.45 0.00 3.51
3355 4196 0.745486 CGATGTCTGCCATGGCTCAA 60.745 55.000 35.53 19.52 42.51 3.02
3356 4197 1.688772 GATGTCTGCCATGGCTCAAT 58.311 50.000 35.53 23.00 42.51 2.57
3381 4222 3.424703 ACGCCCACTAACTGTCTTACTA 58.575 45.455 0.00 0.00 0.00 1.82
3385 4226 4.222366 GCCCACTAACTGTCTTACTACCTT 59.778 45.833 0.00 0.00 0.00 3.50
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
31 32 0.746659 GCACAGCTCAAGGTTGGTTT 59.253 50.000 0.00 0.00 0.00 3.27
32 33 0.395586 TGCACAGCTCAAGGTTGGTT 60.396 50.000 0.00 0.00 0.00 3.67
33 34 0.178981 ATGCACAGCTCAAGGTTGGT 60.179 50.000 0.00 0.00 0.00 3.67
34 35 0.242825 CATGCACAGCTCAAGGTTGG 59.757 55.000 0.00 0.00 0.00 3.77
35 36 0.388134 GCATGCACAGCTCAAGGTTG 60.388 55.000 14.21 0.00 0.00 3.77
36 37 0.824595 TGCATGCACAGCTCAAGGTT 60.825 50.000 18.46 0.00 0.00 3.50
51 53 2.824041 GGGACGACGCCATTGCAT 60.824 61.111 9.90 0.00 37.32 3.96
253 272 4.885325 ACCGTACCTTTTCTTTTGACATGT 59.115 37.500 0.00 0.00 0.00 3.21
254 273 5.212194 CACCGTACCTTTTCTTTTGACATG 58.788 41.667 0.00 0.00 0.00 3.21
255 274 4.885325 ACACCGTACCTTTTCTTTTGACAT 59.115 37.500 0.00 0.00 0.00 3.06
256 275 4.263435 ACACCGTACCTTTTCTTTTGACA 58.737 39.130 0.00 0.00 0.00 3.58
257 276 4.888038 ACACCGTACCTTTTCTTTTGAC 57.112 40.909 0.00 0.00 0.00 3.18
258 277 5.524646 CAGTACACCGTACCTTTTCTTTTGA 59.475 40.000 0.00 0.00 0.00 2.69
259 278 5.744490 CAGTACACCGTACCTTTTCTTTTG 58.256 41.667 0.00 0.00 0.00 2.44
260 279 4.274214 GCAGTACACCGTACCTTTTCTTTT 59.726 41.667 0.00 0.00 0.00 2.27
282 301 3.887335 TACTTTCACACCCGGCCGC 62.887 63.158 22.85 0.00 0.00 6.53
315 334 6.099341 ACACTTCTTTTTGAAACGAAGCATT 58.901 32.000 17.48 4.87 43.85 3.56
341 364 6.869695 TGCATGCATGATTAGAAAAATCAGT 58.130 32.000 30.64 0.00 39.69 3.41
345 368 7.225931 GGTGAATGCATGCATGATTAGAAAAAT 59.774 33.333 32.79 13.16 36.68 1.82
349 372 4.645588 TGGTGAATGCATGCATGATTAGAA 59.354 37.500 32.79 13.29 36.68 2.10
352 375 5.538849 AATGGTGAATGCATGCATGATTA 57.461 34.783 32.79 18.36 36.68 1.75
353 376 4.415881 AATGGTGAATGCATGCATGATT 57.584 36.364 32.79 23.31 36.68 2.57
374 428 4.121317 CACAAATCTCAAAGCAAAGGCAA 58.879 39.130 0.00 0.00 44.61 4.52
377 431 3.739300 CAGCACAAATCTCAAAGCAAAGG 59.261 43.478 0.00 0.00 0.00 3.11
382 436 3.360249 ACACAGCACAAATCTCAAAGC 57.640 42.857 0.00 0.00 0.00 3.51
457 512 6.377327 AACACCACAATACACTTTGAGAAG 57.623 37.500 0.00 0.00 38.87 2.85
458 513 6.767524 AAACACCACAATACACTTTGAGAA 57.232 33.333 0.00 0.00 0.00 2.87
460 515 8.967218 CAATAAAACACCACAATACACTTTGAG 58.033 33.333 0.00 0.00 0.00 3.02
506 564 3.502211 ACCAATAAGAGTGCCTTGTTTCG 59.498 43.478 0.00 0.00 34.53 3.46
653 1317 7.763528 GGACATATATAGCTGCATAGATATGGC 59.236 40.741 22.61 21.29 41.54 4.40
964 1670 1.001020 TTTGGCGGATGGTGCTCAT 60.001 52.632 0.00 0.00 39.13 2.90
1056 1762 1.112916 CGGGGCTTGGTGGAAAAACT 61.113 55.000 0.00 0.00 0.00 2.66
1057 1763 1.365999 CGGGGCTTGGTGGAAAAAC 59.634 57.895 0.00 0.00 0.00 2.43
1096 1802 2.641815 GGATGATGATAGGAGGCAGGTT 59.358 50.000 0.00 0.00 0.00 3.50
1275 1981 2.036733 CGGCAAGTATATCGGAGGGAAA 59.963 50.000 0.00 0.00 0.00 3.13
1395 2101 2.731691 ATTGTTGAGACGGCGTGCCT 62.732 55.000 21.19 9.66 0.00 4.75
1410 2116 1.204704 TCGAACATCAGAGCGGATTGT 59.795 47.619 0.00 0.00 0.00 2.71
1412 2118 1.204704 TGTCGAACATCAGAGCGGATT 59.795 47.619 0.00 0.00 0.00 3.01
1505 2214 2.203596 AGGACTTGGTCGGGTCGT 60.204 61.111 0.00 0.00 32.65 4.34
1596 2305 6.625081 CGTCACCATAGTTGATGTTGTAGAGA 60.625 42.308 0.00 0.00 30.24 3.10
1695 2404 2.890474 GTCGTGCCGCATCCGAAT 60.890 61.111 7.57 0.00 36.29 3.34
1827 2536 1.608025 GGCCTCGTCATGTTGTGAGAA 60.608 52.381 0.00 0.00 37.56 2.87
1870 2579 3.636231 CTTGCCGGTGTCTGGGGA 61.636 66.667 1.90 0.00 0.00 4.81
2016 2731 3.681835 GTGGTGCCGGAGTCGAGT 61.682 66.667 5.05 0.00 39.00 4.18
2113 2828 2.436824 GAGGTCTTGGAAGGGCGC 60.437 66.667 0.00 0.00 0.00 6.53
2157 2872 1.611673 CCTGGTTGGAAGATCACGCTT 60.612 52.381 0.00 0.00 38.35 4.68
2196 2911 1.107945 TATCGAACACGGCTCCATCA 58.892 50.000 0.00 0.00 0.00 3.07
2280 2998 2.571757 GTGGGATCACTCGACGCA 59.428 61.111 0.00 0.00 40.58 5.24
2353 3074 1.093159 ATCTTCTCGGCTACGACGTT 58.907 50.000 5.50 0.00 45.59 3.99
2447 3185 6.169557 ACAAAGTACAAGATACTGACACCA 57.830 37.500 0.00 0.00 0.00 4.17
2474 3222 7.189087 ACCCCTTTATTCATAGTTGGAAATGT 58.811 34.615 0.00 0.00 0.00 2.71
2475 3223 7.660030 ACCCCTTTATTCATAGTTGGAAATG 57.340 36.000 0.00 0.00 0.00 2.32
2505 3253 1.702182 TGCAAAGAAAGCACCCATCA 58.298 45.000 0.00 0.00 37.02 3.07
2507 3255 3.133362 CCATATGCAAAGAAAGCACCCAT 59.867 43.478 0.00 0.00 45.95 4.00
2517 3265 4.683781 GCAAACGTTTTCCATATGCAAAGA 59.316 37.500 11.66 0.00 32.80 2.52
2543 3291 0.606944 TACGCAAATCAGCCGGGTTT 60.607 50.000 1.64 0.00 0.00 3.27
2544 3292 0.606944 TTACGCAAATCAGCCGGGTT 60.607 50.000 1.64 0.00 0.00 4.11
2559 3307 6.766467 AGCTCTTGGAATATTTAGGGTTTACG 59.234 38.462 0.00 0.00 0.00 3.18
2561 3309 7.867921 TCAGCTCTTGGAATATTTAGGGTTTA 58.132 34.615 0.00 0.00 0.00 2.01
2563 3311 6.327386 TCAGCTCTTGGAATATTTAGGGTT 57.673 37.500 0.00 0.00 0.00 4.11
2565 3313 5.641209 CGATCAGCTCTTGGAATATTTAGGG 59.359 44.000 0.00 0.00 0.00 3.53
2566 3314 6.146837 CACGATCAGCTCTTGGAATATTTAGG 59.853 42.308 0.00 0.00 0.00 2.69
2567 3315 6.703607 ACACGATCAGCTCTTGGAATATTTAG 59.296 38.462 0.00 0.00 0.00 1.85
2568 3316 6.582636 ACACGATCAGCTCTTGGAATATTTA 58.417 36.000 0.00 0.00 0.00 1.40
2569 3317 5.431765 ACACGATCAGCTCTTGGAATATTT 58.568 37.500 0.00 0.00 0.00 1.40
2570 3318 5.028549 ACACGATCAGCTCTTGGAATATT 57.971 39.130 0.00 0.00 0.00 1.28
2571 3319 4.343526 AGACACGATCAGCTCTTGGAATAT 59.656 41.667 0.00 0.00 0.00 1.28
2576 3391 1.203287 TGAGACACGATCAGCTCTTGG 59.797 52.381 0.00 0.00 0.00 3.61
2577 3392 2.257894 GTGAGACACGATCAGCTCTTG 58.742 52.381 0.00 0.00 0.00 3.02
2604 3419 1.914051 CGAAGTAGACACACGCTCATG 59.086 52.381 0.00 0.00 0.00 3.07
2686 3502 1.005450 GGTTCCTCATGCCCTAACCAA 59.995 52.381 11.76 0.00 39.51 3.67
2749 3565 2.005971 ACCTATCGGTTTTCGTGAGC 57.994 50.000 0.00 0.00 42.13 4.26
2750 3566 3.703420 CCTACCTATCGGTTTTCGTGAG 58.297 50.000 0.00 0.00 42.13 3.51
2751 3567 2.159198 GCCTACCTATCGGTTTTCGTGA 60.159 50.000 0.00 0.00 42.13 4.35
2754 3579 1.861971 GGCCTACCTATCGGTTTTCG 58.138 55.000 0.00 0.00 42.13 3.46
2801 3626 7.538678 GCACATCAGTTGGTCAAAAGTATTTAG 59.461 37.037 0.00 0.00 37.28 1.85
2806 3631 3.568007 GGCACATCAGTTGGTCAAAAGTA 59.432 43.478 0.00 0.00 0.00 2.24
2827 3652 2.618053 GTAGGGTCACGTCTCATTTGG 58.382 52.381 0.00 0.00 0.00 3.28
2856 3681 4.646945 TGTGAAGAGGATGACCATCTAGTC 59.353 45.833 9.56 5.16 37.92 2.59
2871 3696 7.219322 TCATAGAGAGAGAGAGATGTGAAGAG 58.781 42.308 0.00 0.00 0.00 2.85
2893 3718 4.012374 AGTTGTTCGATGAAATGCCTCAT 58.988 39.130 0.00 0.00 38.79 2.90
2940 3781 2.584418 CTGCGCATCTCTCCACCG 60.584 66.667 12.24 0.00 0.00 4.94
2970 3811 4.864334 GCACCCCATGGAGAGGCG 62.864 72.222 15.22 0.67 34.81 5.52
2983 3824 0.107361 AATAACTACCCGCCAGCACC 60.107 55.000 0.00 0.00 0.00 5.01
2987 3828 1.407979 ACGAGAATAACTACCCGCCAG 59.592 52.381 0.00 0.00 0.00 4.85
3012 3853 2.034066 CGTGGTGTGGGAAGCCAT 59.966 61.111 0.00 0.00 34.52 4.40
3098 3939 1.628846 AGTTACTGGCATTCCGTTCCT 59.371 47.619 0.00 0.00 34.14 3.36
3104 3945 2.769095 AGAGAGGAGTTACTGGCATTCC 59.231 50.000 0.00 0.00 0.00 3.01
3112 3953 2.650322 TGAGGTGGAGAGAGGAGTTACT 59.350 50.000 0.00 0.00 0.00 2.24
3128 3969 0.322816 ACAATTGAGCGGCATGAGGT 60.323 50.000 13.59 0.00 0.00 3.85
3133 3974 2.114670 CCCGACAATTGAGCGGCAT 61.115 57.895 27.33 1.19 43.52 4.40
3134 3975 2.745884 CCCGACAATTGAGCGGCA 60.746 61.111 27.33 0.00 43.52 5.69
3178 4019 1.063567 AGAGAACTCCACTAGGCCGAT 60.064 52.381 0.00 0.00 33.74 4.18
3179 4020 0.331954 AGAGAACTCCACTAGGCCGA 59.668 55.000 0.00 0.00 33.74 5.54
3180 4021 0.457851 CAGAGAACTCCACTAGGCCG 59.542 60.000 0.00 0.00 33.74 6.13
3195 4036 1.018226 CGCTCTCAACCTTGCCAGAG 61.018 60.000 0.00 0.00 34.21 3.35
3234 4075 3.123620 CTTGCACCGCAGAGCTCC 61.124 66.667 10.93 0.00 40.61 4.70
3255 4096 1.379576 GGCAAGCAGGAGAAGGCAT 60.380 57.895 0.00 0.00 0.00 4.40
3268 4109 1.966451 GGTCCACTTCACCGGCAAG 60.966 63.158 0.00 6.81 0.00 4.01
3274 4115 1.478916 GCTCTAGAGGTCCACTTCACC 59.521 57.143 21.23 0.00 0.00 4.02
3279 4120 1.359474 TGAAGGCTCTAGAGGTCCACT 59.641 52.381 21.23 6.35 0.00 4.00
3289 4130 3.005897 GCGATTAGGACATGAAGGCTCTA 59.994 47.826 0.00 0.00 0.00 2.43
3297 4138 3.056536 GCCTATCTGCGATTAGGACATGA 60.057 47.826 0.00 0.00 37.74 3.07
3299 4140 3.601443 GCCTATCTGCGATTAGGACAT 57.399 47.619 9.22 0.00 37.74 3.06
3310 4151 0.175760 TGGAAGTCACGCCTATCTGC 59.824 55.000 0.00 0.00 0.00 4.26
3319 4160 0.319555 TCGAAGCCTTGGAAGTCACG 60.320 55.000 0.00 0.00 0.00 4.35
3321 4162 1.347707 ACATCGAAGCCTTGGAAGTCA 59.652 47.619 0.00 0.00 0.00 3.41
3337 4178 1.337071 CATTGAGCCATGGCAGACATC 59.663 52.381 37.18 25.18 44.88 3.06
3338 4179 1.399714 CATTGAGCCATGGCAGACAT 58.600 50.000 37.18 20.24 44.88 3.06
3344 4185 1.517694 CGTTGCATTGAGCCATGGC 60.518 57.895 30.12 30.12 44.83 4.40
3355 4196 0.250727 ACAGTTAGTGGGCGTTGCAT 60.251 50.000 0.00 0.00 0.00 3.96
3356 4197 0.882927 GACAGTTAGTGGGCGTTGCA 60.883 55.000 0.00 0.00 0.00 4.08


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

AutoCloner maintained by Alex Coulton.