Multiple sequence alignment - TraesCS2D01G317400

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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 TraesCS2D01G317400 chr2D 100.000 5755 0 0 1 5755 406946311 406940557 0.000000e+00 10628.0
1 TraesCS2D01G317400 chr2D 88.043 92 10 1 2489 2579 170277827 170277736 2.190000e-19 108.0
2 TraesCS2D01G317400 chr2D 87.640 89 11 0 2488 2576 236654247 236654335 2.840000e-18 104.0
3 TraesCS2D01G317400 chr2D 86.441 59 3 1 2973 3031 247818728 247818675 6.230000e-05 60.2
4 TraesCS2D01G317400 chr2A 95.827 2756 80 10 3029 5755 574963789 574961040 0.000000e+00 4420.0
5 TraesCS2D01G317400 chr2A 94.585 2844 102 18 1 2802 574966868 574964035 0.000000e+00 4351.0
6 TraesCS2D01G317400 chr2A 96.552 174 4 2 2802 2974 574963959 574963787 2.620000e-73 287.0
7 TraesCS2D01G317400 chr2A 78.846 208 30 8 5387 5591 672844378 672844574 1.680000e-25 128.0
8 TraesCS2D01G317400 chr2A 94.737 38 0 2 3004 3040 56599362 56599398 2.240000e-04 58.4
9 TraesCS2D01G317400 chr2B 94.163 2827 124 23 1 2802 482723263 482720453 0.000000e+00 4268.0
10 TraesCS2D01G317400 chr2B 96.009 2230 67 8 3527 5755 482719743 482717535 0.000000e+00 3605.0
11 TraesCS2D01G317400 chr2B 98.081 469 8 1 3029 3496 482720207 482719739 0.000000e+00 815.0
12 TraesCS2D01G317400 chr2B 98.266 173 3 0 2802 2974 482720377 482720205 2.610000e-78 303.0
13 TraesCS2D01G317400 chr5A 83.333 168 24 4 5430 5594 691989950 691990116 9.990000e-33 152.0
14 TraesCS2D01G317400 chr5A 79.227 207 29 6 5387 5591 426310303 426310497 1.300000e-26 132.0
15 TraesCS2D01G317400 chr5A 82.692 156 19 8 5229 5378 568001101 568001254 1.300000e-26 132.0
16 TraesCS2D01G317400 chr5A 94.872 39 1 1 3000 3037 689619283 689619321 6.230000e-05 60.2
17 TraesCS2D01G317400 chr7D 80.583 206 30 4 5387 5591 327418215 327418411 3.590000e-32 150.0
18 TraesCS2D01G317400 chr7D 83.529 85 14 0 4486 4570 116986430 116986514 4.780000e-11 80.5
19 TraesCS2D01G317400 chr1A 79.512 205 34 5 5387 5591 496421271 496421075 7.780000e-29 139.0
20 TraesCS2D01G317400 chr4B 79.612 206 31 5 5387 5591 33625953 33626148 2.800000e-28 137.0
21 TraesCS2D01G317400 chr4B 90.698 43 4 0 3000 3042 439317519 439317477 2.240000e-04 58.4
22 TraesCS2D01G317400 chr4B 89.362 47 2 3 2986 3031 262709956 262710000 8.060000e-04 56.5
23 TraesCS2D01G317400 chr7A 77.561 205 36 7 5387 5591 81792801 81792995 1.310000e-21 115.0
24 TraesCS2D01G317400 chr5B 90.805 87 7 1 4486 4572 671127857 671127772 1.310000e-21 115.0
25 TraesCS2D01G317400 chr3B 89.773 88 9 0 4487 4574 740890330 740890243 4.710000e-21 113.0
26 TraesCS2D01G317400 chr3B 90.805 87 4 3 4486 4570 740890246 740890330 4.710000e-21 113.0
27 TraesCS2D01G317400 chr3B 92.308 39 3 0 3002 3040 623657593 623657555 8.060000e-04 56.5
28 TraesCS2D01G317400 chr4A 88.298 94 10 1 4486 4579 544057355 544057447 1.700000e-20 111.0
29 TraesCS2D01G317400 chr3D 87.640 89 11 0 4486 4574 558222107 558222019 2.840000e-18 104.0
30 TraesCS2D01G317400 chr6D 86.957 92 11 1 2489 2579 93317817 93317726 1.020000e-17 102.0
31 TraesCS2D01G317400 chr6D 83.158 95 14 1 4477 4571 413078231 413078323 1.030000e-12 86.1
32 TraesCS2D01G317400 chr4D 86.957 92 11 1 2489 2579 50531449 50531358 1.020000e-17 102.0
33 TraesCS2D01G317400 chr4D 86.957 92 11 1 2489 2579 53611878 53611787 1.020000e-17 102.0
34 TraesCS2D01G317400 chr1D 87.640 89 10 1 2489 2576 472748680 472748768 1.020000e-17 102.0
35 TraesCS2D01G317400 chr1D 94.737 38 1 1 3002 3039 412077000 412077036 2.240000e-04 58.4
36 TraesCS2D01G317400 chr6B 86.207 58 6 1 2973 3028 706747950 706748007 1.730000e-05 62.1
37 TraesCS2D01G317400 chr5D 92.500 40 1 2 2997 3034 66982658 66982697 8.060000e-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 TraesCS2D01G317400 chr2D 406940557 406946311 5754 True 10628.000000 10628 100.000000 1 5755 1 chr2D.!!$R3 5754
1 TraesCS2D01G317400 chr2A 574961040 574966868 5828 True 3019.333333 4420 95.654667 1 5755 3 chr2A.!!$R1 5754
2 TraesCS2D01G317400 chr2B 482717535 482723263 5728 True 2247.750000 4268 96.629750 1 5755 4 chr2B.!!$R1 5754

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
996 1005 0.036306 AACTGGTTGGGAGCTTACGG 59.964 55.000 0.00 0.0 0.00 4.02 F
1023 1032 1.455383 CCAGGTTTTGCTGCTTCGGT 61.455 55.000 0.00 0.0 0.00 4.69 F
2219 2252 1.559682 TGCCAGGTGGGTCTTCTATTC 59.440 52.381 0.00 0.0 39.65 1.75 F
2508 2541 2.056815 GTACTCCCTCCGTCCCACC 61.057 68.421 0.00 0.0 0.00 4.61 F
2986 3118 2.684881 TGACGTATACTCTTTCCGTCCC 59.315 50.000 7.86 0.0 45.29 4.46 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2547 2580 2.158652 TCCGTCCCACGATAGAAGATCT 60.159 50.000 0.00 0.00 46.05 2.75 R
3009 3141 1.887797 TTCCCTCCGTCCCATAATGT 58.112 50.000 0.00 0.00 0.00 2.71 R
4064 4222 1.378250 ATTGCTGAGGCTGGCTCAC 60.378 57.895 27.63 22.78 39.59 3.51 R
4534 4694 6.682746 TCCAAATTAATTGTCGCAGCTTTAA 58.317 32.000 0.39 0.00 37.32 1.52 R
4953 5113 0.606096 TGGACCCACTCACATGTACG 59.394 55.000 0.00 0.00 0.00 3.67 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
51 52 0.508641 CAGAACCGAAGCGTCAACAG 59.491 55.000 0.00 0.00 0.00 3.16
53 54 1.495584 GAACCGAAGCGTCAACAGCA 61.496 55.000 0.00 0.00 37.01 4.41
264 265 2.930562 ACTCCTCCAGGCCCACAC 60.931 66.667 0.00 0.00 34.44 3.82
375 376 0.036952 CGCACACCCAGTCTTCAGAT 60.037 55.000 0.00 0.00 0.00 2.90
417 418 2.753029 GCCTGGAGAGTGTGGCTT 59.247 61.111 0.00 0.00 41.92 4.35
439 440 2.190313 GATCCGGTGCATGAGCCA 59.810 61.111 0.00 0.00 41.13 4.75
657 658 3.154473 TCCCCTGCGAATCTCCGG 61.154 66.667 0.00 0.00 0.00 5.14
695 696 2.833582 ATCGGTGAGGCGATCCGT 60.834 61.111 14.35 3.19 43.94 4.69
711 712 2.231820 CGTTTCGCCGGAGAAAACT 58.768 52.632 31.12 0.00 41.18 2.66
742 747 2.494059 TCCTTCTTCTTTTCTGTGGCG 58.506 47.619 0.00 0.00 0.00 5.69
782 787 2.501128 CACGCCACCGGATCTGAT 59.499 61.111 9.46 0.00 39.22 2.90
787 796 0.811616 GCCACCGGATCTGATGTGAC 60.812 60.000 9.46 0.00 0.00 3.67
795 804 3.491619 CGGATCTGATGTGACCGAATTCT 60.492 47.826 9.23 0.00 45.31 2.40
797 806 4.442052 GGATCTGATGTGACCGAATTCTCA 60.442 45.833 3.52 0.00 0.00 3.27
798 807 4.743057 TCTGATGTGACCGAATTCTCAT 57.257 40.909 3.52 1.08 33.44 2.90
801 810 2.768253 TGTGACCGAATTCTCATGCT 57.232 45.000 3.52 0.00 0.00 3.79
805 814 4.100035 TGTGACCGAATTCTCATGCTATCT 59.900 41.667 3.52 0.00 0.00 1.98
954 963 2.442272 TCCCTCCGGCTGCTCTAC 60.442 66.667 0.00 0.00 0.00 2.59
990 999 1.179174 GGTTGGAACTGGTTGGGAGC 61.179 60.000 0.00 0.00 0.00 4.70
996 1005 0.036306 AACTGGTTGGGAGCTTACGG 59.964 55.000 0.00 0.00 0.00 4.02
1023 1032 1.455383 CCAGGTTTTGCTGCTTCGGT 61.455 55.000 0.00 0.00 0.00 4.69
1060 1069 6.428771 CGAGGTAAGTTTTGTTTCCTTCCATA 59.571 38.462 0.00 0.00 0.00 2.74
1078 1087 7.561356 CCTTCCATATCCCAGTATTTTCTTTGT 59.439 37.037 0.00 0.00 0.00 2.83
1079 1088 8.893563 TTCCATATCCCAGTATTTTCTTTGTT 57.106 30.769 0.00 0.00 0.00 2.83
1080 1089 9.983024 TTCCATATCCCAGTATTTTCTTTGTTA 57.017 29.630 0.00 0.00 0.00 2.41
1128 1144 6.552008 TGGAATAGAATTTTTCCTGTGAGGT 58.448 36.000 13.63 0.00 41.65 3.85
1147 1170 6.699204 GTGAGGTTGTCTGTATCATGTGATAG 59.301 42.308 3.05 0.00 37.67 2.08
1186 1209 8.104566 AGTACTCCTACGATGATATTTAGAGCT 58.895 37.037 0.00 0.00 0.00 4.09
1234 1259 3.627577 ACTTTCTTCACGAATTGCACTGT 59.372 39.130 0.00 0.00 0.00 3.55
1505 1533 8.160765 TCCCAGAAGTAAATTTGTTGATACTCA 58.839 33.333 0.00 0.00 0.00 3.41
1562 1592 5.520376 AATGCATTGGTTGGAAGCTATAC 57.480 39.130 12.09 0.00 0.00 1.47
1611 1641 6.985188 TCTGTTTCAATATAGTTGACAGGC 57.015 37.500 8.71 0.00 0.00 4.85
1671 1701 2.092375 GGGCCAAGTCAAGGTTAGCTAT 60.092 50.000 4.39 0.00 0.00 2.97
1872 1903 8.816144 GCAAGTTTTTGACATCTGTTTCAATAA 58.184 29.630 0.00 0.00 36.36 1.40
2035 2068 2.403132 GACAAGGTGGCTCCACTGCT 62.403 60.000 17.57 5.63 45.52 4.24
2066 2099 4.213482 CCATCCTTATAAACGGCAGTAAGC 59.787 45.833 0.00 0.00 44.65 3.09
2219 2252 1.559682 TGCCAGGTGGGTCTTCTATTC 59.440 52.381 0.00 0.00 39.65 1.75
2226 2259 6.353082 CCAGGTGGGTCTTCTATTCTAACATT 60.353 42.308 0.00 0.00 0.00 2.71
2227 2260 7.147549 CCAGGTGGGTCTTCTATTCTAACATTA 60.148 40.741 0.00 0.00 0.00 1.90
2228 2261 8.432805 CAGGTGGGTCTTCTATTCTAACATTAT 58.567 37.037 0.00 0.00 0.00 1.28
2508 2541 2.056815 GTACTCCCTCCGTCCCACC 61.057 68.421 0.00 0.00 0.00 4.61
2969 3101 4.728882 GCCAACAAAATATCTGCTCTGACG 60.729 45.833 0.00 0.00 0.00 4.35
2971 3103 5.580691 CCAACAAAATATCTGCTCTGACGTA 59.419 40.000 0.00 0.00 0.00 3.57
2972 3104 6.258727 CCAACAAAATATCTGCTCTGACGTAT 59.741 38.462 0.00 0.00 0.00 3.06
2973 3105 7.438160 CCAACAAAATATCTGCTCTGACGTATA 59.562 37.037 0.00 0.00 0.00 1.47
2974 3106 7.932120 ACAAAATATCTGCTCTGACGTATAC 57.068 36.000 0.00 0.00 0.00 1.47
2975 3107 7.717568 ACAAAATATCTGCTCTGACGTATACT 58.282 34.615 0.56 0.00 0.00 2.12
2976 3108 7.863375 ACAAAATATCTGCTCTGACGTATACTC 59.137 37.037 0.56 0.00 0.00 2.59
2977 3109 7.753309 AAATATCTGCTCTGACGTATACTCT 57.247 36.000 0.56 0.00 0.00 3.24
2978 3110 7.753309 AATATCTGCTCTGACGTATACTCTT 57.247 36.000 0.56 0.00 0.00 2.85
2979 3111 7.753309 ATATCTGCTCTGACGTATACTCTTT 57.247 36.000 0.56 0.00 0.00 2.52
2980 3112 5.487153 TCTGCTCTGACGTATACTCTTTC 57.513 43.478 0.56 0.00 0.00 2.62
2981 3113 4.335874 TCTGCTCTGACGTATACTCTTTCC 59.664 45.833 0.56 0.00 0.00 3.13
2982 3114 3.064958 TGCTCTGACGTATACTCTTTCCG 59.935 47.826 0.56 0.00 0.00 4.30
2983 3115 3.065095 GCTCTGACGTATACTCTTTCCGT 59.935 47.826 0.56 0.00 0.00 4.69
2984 3116 4.785975 GCTCTGACGTATACTCTTTCCGTC 60.786 50.000 0.56 0.00 45.88 4.79
2985 3117 3.624861 TCTGACGTATACTCTTTCCGTCC 59.375 47.826 7.86 0.00 45.29 4.79
2986 3118 2.684881 TGACGTATACTCTTTCCGTCCC 59.315 50.000 7.86 0.00 45.29 4.46
2987 3119 2.684881 GACGTATACTCTTTCCGTCCCA 59.315 50.000 0.56 0.00 41.37 4.37
2988 3120 3.294214 ACGTATACTCTTTCCGTCCCAT 58.706 45.455 0.56 0.00 0.00 4.00
2989 3121 4.464008 ACGTATACTCTTTCCGTCCCATA 58.536 43.478 0.56 0.00 0.00 2.74
2990 3122 4.889409 ACGTATACTCTTTCCGTCCCATAA 59.111 41.667 0.56 0.00 0.00 1.90
2991 3123 5.537674 ACGTATACTCTTTCCGTCCCATAAT 59.462 40.000 0.56 0.00 0.00 1.28
2992 3124 5.862323 CGTATACTCTTTCCGTCCCATAATG 59.138 44.000 0.56 0.00 0.00 1.90
2993 3125 5.888982 ATACTCTTTCCGTCCCATAATGT 57.111 39.130 0.00 0.00 0.00 2.71
2994 3126 6.989155 ATACTCTTTCCGTCCCATAATGTA 57.011 37.500 0.00 0.00 0.00 2.29
2995 3127 5.687166 ACTCTTTCCGTCCCATAATGTAA 57.313 39.130 0.00 0.00 0.00 2.41
2996 3128 5.671493 ACTCTTTCCGTCCCATAATGTAAG 58.329 41.667 0.00 0.00 0.00 2.34
2997 3129 5.424252 ACTCTTTCCGTCCCATAATGTAAGA 59.576 40.000 0.00 0.00 0.00 2.10
2998 3130 5.667466 TCTTTCCGTCCCATAATGTAAGAC 58.333 41.667 0.00 0.00 0.00 3.01
2999 3131 5.188163 TCTTTCCGTCCCATAATGTAAGACA 59.812 40.000 0.00 0.00 0.00 3.41
3000 3132 5.623956 TTCCGTCCCATAATGTAAGACAT 57.376 39.130 0.00 0.00 41.31 3.06
3001 3133 6.734502 TTCCGTCCCATAATGTAAGACATA 57.265 37.500 0.00 0.00 37.97 2.29
3002 3134 6.734502 TCCGTCCCATAATGTAAGACATAA 57.265 37.500 0.00 0.00 37.97 1.90
3003 3135 6.518493 TCCGTCCCATAATGTAAGACATAAC 58.482 40.000 0.00 0.00 37.97 1.89
3004 3136 5.404366 CCGTCCCATAATGTAAGACATAACG 59.596 44.000 0.00 0.00 37.97 3.18
3005 3137 5.981315 CGTCCCATAATGTAAGACATAACGT 59.019 40.000 0.00 0.00 37.97 3.99
3006 3138 6.143438 CGTCCCATAATGTAAGACATAACGTC 59.857 42.308 0.00 0.00 45.77 4.34
3020 3152 7.404139 GACATAACGTCTTACATTATGGGAC 57.596 40.000 9.76 1.75 41.81 4.46
3023 3155 3.720949 CGTCTTACATTATGGGACGGA 57.279 47.619 20.50 2.30 43.69 4.69
3024 3156 3.639538 CGTCTTACATTATGGGACGGAG 58.360 50.000 20.50 2.74 43.69 4.63
3025 3157 3.552273 CGTCTTACATTATGGGACGGAGG 60.552 52.174 20.50 5.87 43.69 4.30
3026 3158 2.969950 TCTTACATTATGGGACGGAGGG 59.030 50.000 0.00 0.00 0.00 4.30
3027 3159 2.779429 TACATTATGGGACGGAGGGA 57.221 50.000 0.00 0.00 0.00 4.20
3443 3599 6.782494 GTGGGAATAATTGAAAGGGGATACAT 59.218 38.462 0.00 0.00 39.74 2.29
3504 3660 6.219417 TGGAGATTTCTTTGTTGCTTGAAA 57.781 33.333 0.00 0.00 33.74 2.69
3824 3981 8.196771 AGAAGAGCATAAATGTGTGTTGAAAAA 58.803 29.630 0.00 0.00 0.00 1.94
4010 4168 6.459848 CCACCAATTTTGTTCAAACATTGCAT 60.460 34.615 17.27 10.80 38.95 3.96
4015 4173 9.880064 CAATTTTGTTCAAACATTGCATTGATA 57.120 25.926 15.20 0.00 38.95 2.15
4018 4176 8.828688 TTTGTTCAAACATTGCATTGATATCA 57.171 26.923 15.20 0.00 38.95 2.15
4019 4177 7.815398 TGTTCAAACATTGCATTGATATCAC 57.185 32.000 15.20 4.82 35.63 3.06
4020 4178 6.527372 TGTTCAAACATTGCATTGATATCACG 59.473 34.615 15.20 0.70 35.63 4.35
4021 4179 5.580661 TCAAACATTGCATTGATATCACGG 58.419 37.500 15.20 1.56 30.94 4.94
4022 4180 5.356470 TCAAACATTGCATTGATATCACGGA 59.644 36.000 15.20 0.00 30.94 4.69
4023 4181 5.428496 AACATTGCATTGATATCACGGAG 57.572 39.130 15.20 0.00 0.00 4.63
4024 4182 8.756736 TCAAACATTGCATTGATATCACGGAGT 61.757 37.037 15.20 0.00 33.32 3.85
4025 4183 5.610398 ACATTGCATTGATATCACGGAGTA 58.390 37.500 15.20 0.00 41.61 2.59
4026 4184 5.698089 ACATTGCATTGATATCACGGAGTAG 59.302 40.000 15.20 0.00 41.61 2.57
4534 4694 7.041644 TGTCGCAGCTTTAGTACAAAGTTTTAT 60.042 33.333 14.90 0.00 0.00 1.40
4561 4721 3.725740 GCTGCGACAATTAATTTGGATCG 59.274 43.478 12.95 12.95 39.80 3.69
4816 4976 7.126421 AGAGGAGAGCAGAAGGAATTATAACAA 59.874 37.037 0.00 0.00 0.00 2.83
4831 4991 9.301153 GAATTATAACAACAAAACATAGCCTGG 57.699 33.333 0.00 0.00 0.00 4.45
4871 5031 9.023962 TGGTAATGCAAAAGAATAATTCTCTGT 57.976 29.630 0.00 0.00 39.61 3.41
4944 5104 8.707938 AAATATGCTAGAATTCTTTGTTTGGC 57.292 30.769 14.36 2.35 0.00 4.52
4961 5121 0.810031 GGCGATTCCAGCGTACATGT 60.810 55.000 2.69 2.69 35.00 3.21
5200 5362 8.402472 TGATTTCGGGTATGATAAAATGTGAAC 58.598 33.333 0.00 0.00 0.00 3.18
5324 5486 5.279406 CCACAATATGCCACTCCAAGAAAAA 60.279 40.000 0.00 0.00 0.00 1.94
5410 5572 5.801531 AAGTGGATACCCCTTTGTTTTTC 57.198 39.130 0.00 0.00 35.38 2.29
5434 5596 4.987285 CCCACGACATTCATTCAGATAGAG 59.013 45.833 0.00 0.00 0.00 2.43
5443 5605 8.492782 ACATTCATTCAGATAGAGTCTTTCCAT 58.507 33.333 0.00 0.00 34.00 3.41
5495 5657 7.177392 GCTACCTGGAAGCCAAATATGATAAAT 59.823 37.037 0.00 0.00 33.73 1.40
5519 5681 1.134128 TCTTTGTGGAGCTGCAACTCA 60.134 47.619 18.39 0.24 38.50 3.41
5651 5813 7.723324 AGGCAAAACTATATACATAGACACGT 58.277 34.615 0.00 0.00 38.03 4.49
5663 5825 4.521639 ACATAGACACGTTAGAAGACACCA 59.478 41.667 0.00 0.00 0.00 4.17
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
51 52 4.580044 CGCGTGACGGATGCATGC 62.580 66.667 11.82 11.82 43.13 4.06
359 360 2.030027 TCCATCTGAAGACTGGGTGT 57.970 50.000 8.16 0.00 0.00 4.16
375 376 3.545124 AACGGTGGCGATGCTTCCA 62.545 57.895 0.00 0.00 0.00 3.53
417 418 1.957668 CTCATGCACCGGATCAATCA 58.042 50.000 9.46 0.00 0.00 2.57
439 440 0.905357 GCCCACACTGACATAGACCT 59.095 55.000 0.00 0.00 0.00 3.85
695 696 1.000385 TCGTAGTTTTCTCCGGCGAAA 60.000 47.619 15.48 15.48 30.25 3.46
742 747 3.427638 GCCGGAAGCAGAATTAAAGAACC 60.428 47.826 5.05 0.00 42.97 3.62
782 787 2.768253 AGCATGAGAATTCGGTCACA 57.232 45.000 0.00 0.00 0.00 3.58
818 827 1.064906 CATGGAACTCTGCACCCTGAT 60.065 52.381 0.00 0.00 0.00 2.90
954 963 3.243267 CCAACCCGTGAACTAAAACAAGG 60.243 47.826 0.00 0.00 35.92 3.61
990 999 1.056660 ACCTGGCCATATCCCGTAAG 58.943 55.000 5.51 0.00 0.00 2.34
996 1005 1.410153 CAGCAAAACCTGGCCATATCC 59.590 52.381 5.51 0.00 0.00 2.59
1100 1109 8.208718 TCACAGGAAAAATTCTATTCCATACG 57.791 34.615 15.85 7.24 46.14 3.06
1105 1117 7.039714 ACAACCTCACAGGAAAAATTCTATTCC 60.040 37.037 8.76 8.76 44.45 3.01
1112 1128 4.956075 ACAGACAACCTCACAGGAAAAATT 59.044 37.500 0.00 0.00 37.67 1.82
1128 1144 6.273071 CCGAACTATCACATGATACAGACAA 58.727 40.000 0.00 0.00 36.05 3.18
1147 1170 5.745769 CGTAGGAGTACTTAATTTCCCGAAC 59.254 44.000 0.00 0.00 0.00 3.95
1234 1259 5.302568 AGTGAAATTTGTGCCATCTCAAAGA 59.697 36.000 0.00 0.00 38.55 2.52
1477 1505 9.014297 AGTATCAACAAATTTACTTCTGGGAAG 57.986 33.333 5.83 5.83 0.00 3.46
1525 1555 2.954316 TGCATTCGACGAGCTTCTAAA 58.046 42.857 10.04 0.00 0.00 1.85
1562 1592 6.428159 ACAGTCAGCAAGAGTAAATTAACCAG 59.572 38.462 0.00 0.00 0.00 4.00
1611 1641 1.101635 CAGAGGTGGCTGATGCATGG 61.102 60.000 2.46 0.00 41.91 3.66
1671 1701 3.253220 TCCTCTTACAAGGCTAAACCCA 58.747 45.455 0.00 0.00 40.58 4.51
1872 1903 4.796110 ATACTAGTGAATGGGCCATTGT 57.204 40.909 35.23 26.10 33.90 2.71
1873 1904 6.469782 AAAATACTAGTGAATGGGCCATTG 57.530 37.500 35.23 22.04 33.90 2.82
2035 2068 5.120399 CCGTTTATAAGGATGGCAGTTACA 58.880 41.667 0.00 0.00 0.00 2.41
2066 2099 2.643551 CCCAACATTAGCTACCCACAG 58.356 52.381 0.00 0.00 0.00 3.66
2508 2541 8.443160 TGTAAGCTTGAAAAACGATCTTCTATG 58.557 33.333 9.86 0.00 0.00 2.23
2547 2580 2.158652 TCCGTCCCACGATAGAAGATCT 60.159 50.000 0.00 0.00 46.05 2.75
2720 2775 7.954788 TGCTGCATACGTGTAATAATATTGA 57.045 32.000 0.00 0.00 0.00 2.57
2969 3101 6.756221 ACATTATGGGACGGAAAGAGTATAC 58.244 40.000 0.00 0.00 0.00 1.47
2971 3103 5.888982 ACATTATGGGACGGAAAGAGTAT 57.111 39.130 0.00 0.00 0.00 2.12
2972 3104 6.608405 TCTTACATTATGGGACGGAAAGAGTA 59.392 38.462 0.00 0.00 0.00 2.59
2973 3105 5.424252 TCTTACATTATGGGACGGAAAGAGT 59.576 40.000 0.00 0.00 0.00 3.24
2974 3106 5.753921 GTCTTACATTATGGGACGGAAAGAG 59.246 44.000 0.00 0.00 0.00 2.85
2975 3107 5.188163 TGTCTTACATTATGGGACGGAAAGA 59.812 40.000 0.00 0.00 0.00 2.52
2976 3108 5.424757 TGTCTTACATTATGGGACGGAAAG 58.575 41.667 0.00 0.00 0.00 2.62
2977 3109 5.423704 TGTCTTACATTATGGGACGGAAA 57.576 39.130 0.00 0.00 0.00 3.13
2978 3110 5.623956 ATGTCTTACATTATGGGACGGAA 57.376 39.130 0.00 0.00 34.67 4.30
2979 3111 6.518493 GTTATGTCTTACATTATGGGACGGA 58.482 40.000 0.00 0.00 39.88 4.69
2980 3112 5.404366 CGTTATGTCTTACATTATGGGACGG 59.596 44.000 0.00 0.00 39.88 4.79
2981 3113 5.981315 ACGTTATGTCTTACATTATGGGACG 59.019 40.000 0.00 0.00 39.88 4.79
2982 3114 7.404139 GACGTTATGTCTTACATTATGGGAC 57.596 40.000 0.00 3.17 44.58 4.46
2999 3131 5.302568 TCCGTCCCATAATGTAAGACGTTAT 59.697 40.000 9.63 0.00 46.62 1.89
3000 3132 4.644234 TCCGTCCCATAATGTAAGACGTTA 59.356 41.667 9.63 0.00 46.62 3.18
3001 3133 3.448301 TCCGTCCCATAATGTAAGACGTT 59.552 43.478 9.63 0.00 46.62 3.99
3002 3134 3.025978 TCCGTCCCATAATGTAAGACGT 58.974 45.455 9.63 0.00 46.62 4.34
3004 3136 3.244112 CCCTCCGTCCCATAATGTAAGAC 60.244 52.174 0.00 0.00 0.00 3.01
3005 3137 2.969950 CCCTCCGTCCCATAATGTAAGA 59.030 50.000 0.00 0.00 0.00 2.10
3006 3138 2.969950 TCCCTCCGTCCCATAATGTAAG 59.030 50.000 0.00 0.00 0.00 2.34
3007 3139 3.049108 TCCCTCCGTCCCATAATGTAA 57.951 47.619 0.00 0.00 0.00 2.41
3008 3140 2.779429 TCCCTCCGTCCCATAATGTA 57.221 50.000 0.00 0.00 0.00 2.29
3009 3141 1.887797 TTCCCTCCGTCCCATAATGT 58.112 50.000 0.00 0.00 0.00 2.71
3010 3142 4.844349 ATATTCCCTCCGTCCCATAATG 57.156 45.455 0.00 0.00 0.00 1.90
3011 3143 6.269194 TCTAATATTCCCTCCGTCCCATAAT 58.731 40.000 0.00 0.00 0.00 1.28
3012 3144 5.657446 TCTAATATTCCCTCCGTCCCATAA 58.343 41.667 0.00 0.00 0.00 1.90
3013 3145 5.222484 ACTCTAATATTCCCTCCGTCCCATA 60.222 44.000 0.00 0.00 0.00 2.74
3014 3146 4.097418 CTCTAATATTCCCTCCGTCCCAT 58.903 47.826 0.00 0.00 0.00 4.00
3015 3147 3.116862 ACTCTAATATTCCCTCCGTCCCA 60.117 47.826 0.00 0.00 0.00 4.37
3016 3148 3.508426 ACTCTAATATTCCCTCCGTCCC 58.492 50.000 0.00 0.00 0.00 4.46
3017 3149 5.950549 TGATACTCTAATATTCCCTCCGTCC 59.049 44.000 0.00 0.00 0.00 4.79
3018 3150 6.660094 ACTGATACTCTAATATTCCCTCCGTC 59.340 42.308 0.00 0.00 0.00 4.79
3019 3151 6.553857 ACTGATACTCTAATATTCCCTCCGT 58.446 40.000 0.00 0.00 0.00 4.69
3020 3152 8.625651 CATACTGATACTCTAATATTCCCTCCG 58.374 40.741 0.00 0.00 0.00 4.63
3021 3153 9.482175 ACATACTGATACTCTAATATTCCCTCC 57.518 37.037 0.00 0.00 0.00 4.30
3504 3660 4.307032 AGGATGGCTTGTACTTGACAAT 57.693 40.909 0.00 0.00 46.95 2.71
3537 3694 7.519347 TGTTAGGGGTCTTAAGGTTGATTAT 57.481 36.000 1.85 0.00 0.00 1.28
3824 3981 9.492973 CATCATTACCTTTTCATTCCAAGTTTT 57.507 29.630 0.00 0.00 0.00 2.43
3844 4001 6.971726 ACCATGTTATCATTCTGCATCATT 57.028 33.333 0.00 0.00 31.15 2.57
3846 4003 6.604396 AGAAACCATGTTATCATTCTGCATCA 59.396 34.615 0.00 0.00 31.15 3.07
4010 4168 5.828328 ACACTCATCTACTCCGTGATATCAA 59.172 40.000 7.07 0.00 0.00 2.57
4015 4173 4.783055 ACTACACTCATCTACTCCGTGAT 58.217 43.478 0.00 0.00 0.00 3.06
4016 4174 4.217836 ACTACACTCATCTACTCCGTGA 57.782 45.455 0.00 0.00 0.00 4.35
4017 4175 4.395231 TGAACTACACTCATCTACTCCGTG 59.605 45.833 0.00 0.00 0.00 4.94
4018 4176 4.395542 GTGAACTACACTCATCTACTCCGT 59.604 45.833 0.00 0.00 45.13 4.69
4019 4177 4.911053 GTGAACTACACTCATCTACTCCG 58.089 47.826 0.00 0.00 45.13 4.63
4064 4222 1.378250 ATTGCTGAGGCTGGCTCAC 60.378 57.895 27.63 22.78 39.59 3.51
4534 4694 6.682746 TCCAAATTAATTGTCGCAGCTTTAA 58.317 32.000 0.39 0.00 37.32 1.52
4561 4721 0.912486 ACCAATGTGCTACTCCCTCC 59.088 55.000 0.00 0.00 0.00 4.30
4773 4933 3.515502 TCCTCTCGGTGACAATTCTTCAT 59.484 43.478 0.00 0.00 0.00 2.57
4816 4976 2.162681 GTCAGCCAGGCTATGTTTTGT 58.837 47.619 15.64 0.00 36.40 2.83
4831 4991 3.561725 GCATTACCACTATCCTTGTCAGC 59.438 47.826 0.00 0.00 0.00 4.26
4871 5031 4.949238 ACACATCATTTACAGCCAGCATTA 59.051 37.500 0.00 0.00 0.00 1.90
4944 5104 1.854743 CTCACATGTACGCTGGAATCG 59.145 52.381 0.00 0.00 0.00 3.34
4953 5113 0.606096 TGGACCCACTCACATGTACG 59.394 55.000 0.00 0.00 0.00 3.67
4961 5121 1.668826 AGGCTATTTGGACCCACTCA 58.331 50.000 0.00 0.00 0.00 3.41
5200 5362 6.924111 ACATGCTTATAAAAACTGGGAGTTG 58.076 36.000 0.00 0.00 38.66 3.16
5324 5486 9.884814 AATAGTGAGTTGTACCCTAGATTCTAT 57.115 33.333 0.00 0.00 0.00 1.98
5382 5544 2.083628 AGGGGTATCCACTTACCTCG 57.916 55.000 0.00 0.00 45.83 4.63
5410 5572 2.401583 TCTGAATGAATGTCGTGGGG 57.598 50.000 0.00 0.00 0.00 4.96
5434 5596 9.136952 CAAGAATGAGAAATTTGATGGAAAGAC 57.863 33.333 0.00 0.00 0.00 3.01
5443 5605 6.491062 TCCAGCTTCAAGAATGAGAAATTTGA 59.509 34.615 0.00 0.00 36.78 2.69
5519 5681 4.581824 CCACTTTGGAGCAGTTGCATATAT 59.418 41.667 6.90 0.00 40.96 0.86
5651 5813 3.181455 ACAGTGTGCATGGTGTCTTCTAA 60.181 43.478 0.00 0.00 0.00 2.10
5659 5821 2.988493 GCATAAAACAGTGTGCATGGTG 59.012 45.455 0.00 0.00 37.52 4.17
5663 5825 2.493278 GAGGGCATAAAACAGTGTGCAT 59.507 45.455 0.00 0.00 39.27 3.96


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

AutoCloner maintained by Alex Coulton.