Multiple sequence alignment - TraesCS3D01G063700

Loading Multiple Alignment...

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 TraesCS3D01G063700 chr3D 100.000 3251 0 0 1 3251 28125109 28121859 0.000000e+00 6004.0
1 TraesCS3D01G063700 chr3D 76.542 1978 340 73 635 2573 28217967 28216075 0.000000e+00 968.0
2 TraesCS3D01G063700 chr3D 76.372 1676 284 58 857 2496 28224566 28222967 0.000000e+00 798.0
3 TraesCS3D01G063700 chr3D 74.642 1956 394 67 634 2518 28275209 28277133 0.000000e+00 771.0
4 TraesCS3D01G063700 chr3D 100.000 314 0 0 3488 3801 28121622 28121309 7.080000e-162 580.0
5 TraesCS3D01G063700 chr3D 76.710 687 105 26 2607 3251 28277170 28277843 7.870000e-87 331.0
6 TraesCS3D01G063700 chr3D 77.640 322 42 18 3496 3793 28215554 28215239 6.530000e-38 169.0
7 TraesCS3D01G063700 chr3D 79.741 232 30 12 3496 3714 28277883 28278110 6.580000e-33 152.0
8 TraesCS3D01G063700 chr3D 77.113 284 48 13 2735 3013 4651082 4651353 8.510000e-32 148.0
9 TraesCS3D01G063700 chr3D 82.906 117 19 1 1703 1819 9628838 9628723 1.870000e-18 104.0
10 TraesCS3D01G063700 chr3D 81.356 118 16 2 1704 1815 4908911 4909028 1.450000e-14 91.6
11 TraesCS3D01G063700 chr3D 86.885 61 5 3 229 287 550248768 550248709 8.810000e-07 65.8
12 TraesCS3D01G063700 chr3B 91.977 2231 144 10 1022 3251 46328490 46330686 0.000000e+00 3096.0
13 TraesCS3D01G063700 chr3B 91.477 1009 56 16 1334 2342 46305474 46306452 0.000000e+00 1360.0
14 TraesCS3D01G063700 chr3B 92.124 838 59 4 502 1339 46303464 46304294 0.000000e+00 1175.0
15 TraesCS3D01G063700 chr3B 77.328 1976 317 72 644 2573 47222936 47221046 0.000000e+00 1046.0
16 TraesCS3D01G063700 chr3B 91.859 651 41 5 2337 2986 46307410 46308049 0.000000e+00 898.0
17 TraesCS3D01G063700 chr3B 77.164 1467 263 34 635 2058 47211125 47209688 0.000000e+00 787.0
18 TraesCS3D01G063700 chr3B 88.834 609 41 13 362 945 46327896 46328502 0.000000e+00 723.0
19 TraesCS3D01G063700 chr3B 87.654 324 22 5 3495 3801 46308293 46308615 1.000000e-95 361.0
20 TraesCS3D01G063700 chr3B 85.802 324 28 6 3495 3801 46330748 46331070 1.020000e-85 327.0
21 TraesCS3D01G063700 chr3B 79.108 493 80 12 2607 3089 47271818 47272297 6.130000e-83 318.0
22 TraesCS3D01G063700 chr3B 90.213 235 19 4 3017 3251 46308042 46308272 1.720000e-78 303.0
23 TraesCS3D01G063700 chr3B 89.552 134 8 3 362 492 46303290 46303420 8.450000e-37 165.0
24 TraesCS3D01G063700 chr3B 78.049 287 34 17 3496 3762 47272530 47272807 1.830000e-33 154.0
25 TraesCS3D01G063700 chr3B 79.825 228 30 8 3575 3791 47220347 47220125 6.580000e-33 152.0
26 TraesCS3D01G063700 chr3B 73.756 442 89 16 1388 1809 47262981 47263415 8.510000e-32 148.0
27 TraesCS3D01G063700 chr3B 97.531 81 2 0 151 231 46303105 46303185 5.120000e-29 139.0
28 TraesCS3D01G063700 chr3A 91.944 1564 97 7 551 2092 38013676 38012120 0.000000e+00 2163.0
29 TraesCS3D01G063700 chr3A 85.137 1931 246 20 668 2573 37800160 37802074 0.000000e+00 1938.0
30 TraesCS3D01G063700 chr3A 90.672 729 55 5 2453 3178 37996208 37995490 0.000000e+00 957.0
31 TraesCS3D01G063700 chr3A 78.347 1464 248 32 635 2058 38136634 38135200 0.000000e+00 883.0
32 TraesCS3D01G063700 chr3A 92.827 237 7 2 1 227 38014381 38014145 6.080000e-88 335.0
33 TraesCS3D01G063700 chr3A 86.478 318 26 4 3501 3801 37995113 37994796 2.190000e-87 333.0
34 TraesCS3D01G063700 chr3A 91.949 236 13 4 271 502 38014009 38013776 3.660000e-85 326.0
35 TraesCS3D01G063700 chr3A 93.388 121 8 0 2118 2238 37996325 37996205 3.020000e-41 180.0
36 TraesCS3D01G063700 chr3A 82.609 207 31 4 2084 2286 11401823 11402028 1.080000e-40 178.0
37 TraesCS3D01G063700 chr3A 77.329 322 45 16 3496 3793 38134155 38133838 8.450000e-37 165.0
38 TraesCS3D01G063700 chr3A 80.519 231 29 9 3572 3791 38142167 38141942 3.040000e-36 163.0
39 TraesCS3D01G063700 chr3A 79.098 244 36 10 2029 2258 10698601 10698843 1.830000e-33 154.0
40 TraesCS3D01G063700 chr3A 75.254 295 37 17 1774 2058 38157950 38157682 1.440000e-19 108.0
41 TraesCS3D01G063700 chr3A 94.872 39 1 1 80 118 38014337 38014300 4.100000e-05 60.2
42 TraesCS3D01G063700 chr3A 100.000 29 0 0 120 148 38014365 38014337 2.000000e-03 54.7
43 TraesCS3D01G063700 chr1B 81.104 1196 184 27 635 1815 510790820 510791988 0.000000e+00 918.0
44 TraesCS3D01G063700 chr1B 81.466 491 71 15 2607 3092 510792700 510793175 5.960000e-103 385.0
45 TraesCS3D01G063700 chr1B 78.209 335 42 15 1942 2267 510792157 510792469 6.480000e-43 185.0
46 TraesCS3D01G063700 chr1B 85.075 67 10 0 1141 1207 395968022 395968088 6.810000e-08 69.4
47 TraesCS3D01G063700 chr1D 80.785 1197 184 25 635 1815 381004977 381006143 0.000000e+00 894.0
48 TraesCS3D01G063700 chr1D 77.592 1611 245 63 517 2053 456280637 456279069 0.000000e+00 869.0
49 TraesCS3D01G063700 chr1D 77.812 329 40 20 1949 2267 381006254 381006559 5.050000e-39 172.0
50 TraesCS3D01G063700 chr1D 93.506 77 5 0 152 228 456805536 456805460 8.630000e-22 115.0
51 TraesCS3D01G063700 chr2B 76.138 1186 216 27 1147 2281 787786733 787787902 9.220000e-156 560.0
52 TraesCS3D01G063700 chr2B 100.000 38 0 0 249 286 106943393 106943356 1.890000e-08 71.3
53 TraesCS3D01G063700 chr2A 75.603 1037 189 28 1144 2129 771970172 771971195 4.480000e-124 455.0
54 TraesCS3D01G063700 chr2A 94.872 39 0 1 249 287 539588932 539588896 4.100000e-05 60.2
55 TraesCS3D01G063700 chr2A 100.000 31 0 0 249 279 716125826 716125796 1.470000e-04 58.4
56 TraesCS3D01G063700 chr1A 81.837 490 68 16 2607 3092 481629808 481630280 3.560000e-105 392.0
57 TraesCS3D01G063700 chr1A 84.848 66 10 0 1141 1206 367010855 367010920 2.450000e-07 67.6
58 TraesCS3D01G063700 chr2D 74.570 1046 187 39 1133 2129 650597965 650598980 5.960000e-103 385.0
59 TraesCS3D01G063700 chr2D 87.273 55 3 4 249 301 22958451 22958503 4.100000e-05 60.2
60 TraesCS3D01G063700 chr2D 87.273 55 4 3 225 276 316269457 316269403 4.100000e-05 60.2
61 TraesCS3D01G063700 chrUn 75.439 513 90 17 2025 2518 213717962 213718457 2.300000e-52 217.0
62 TraesCS3D01G063700 chrUn 77.352 287 49 12 2735 3017 348472557 348472831 5.080000e-34 156.0
63 TraesCS3D01G063700 chrUn 78.696 230 31 10 2735 2958 35602376 35602159 1.840000e-28 137.0
64 TraesCS3D01G063700 chr6B 78.744 207 34 8 2735 2939 66498756 66498558 3.080000e-26 130.0
65 TraesCS3D01G063700 chr4A 89.474 57 5 1 225 280 417627076 417627132 1.890000e-08 71.3
66 TraesCS3D01G063700 chr7B 87.500 56 3 4 249 302 138261044 138261097 1.140000e-05 62.1
67 TraesCS3D01G063700 chr7B 97.059 34 0 1 249 282 412543702 412543670 5.300000e-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 TraesCS3D01G063700 chr3D 28121309 28125109 3800 True 3292.000000 6004 100.000000 1 3801 2 chr3D.!!$R4 3800
1 TraesCS3D01G063700 chr3D 28222967 28224566 1599 True 798.000000 798 76.372000 857 2496 1 chr3D.!!$R2 1639
2 TraesCS3D01G063700 chr3D 28215239 28217967 2728 True 568.500000 968 77.091000 635 3793 2 chr3D.!!$R5 3158
3 TraesCS3D01G063700 chr3D 28275209 28278110 2901 False 418.000000 771 77.031000 634 3714 3 chr3D.!!$F3 3080
4 TraesCS3D01G063700 chr3B 46327896 46331070 3174 False 1382.000000 3096 88.871000 362 3801 3 chr3B.!!$F3 3439
5 TraesCS3D01G063700 chr3B 47209688 47211125 1437 True 787.000000 787 77.164000 635 2058 1 chr3B.!!$R1 1423
6 TraesCS3D01G063700 chr3B 46303105 46308615 5510 False 628.714286 1360 91.487143 151 3801 7 chr3B.!!$F2 3650
7 TraesCS3D01G063700 chr3B 47220125 47222936 2811 True 599.000000 1046 78.576500 644 3791 2 chr3B.!!$R2 3147
8 TraesCS3D01G063700 chr3B 47271818 47272807 989 False 236.000000 318 78.578500 2607 3762 2 chr3B.!!$F4 1155
9 TraesCS3D01G063700 chr3A 37800160 37802074 1914 False 1938.000000 1938 85.137000 668 2573 1 chr3A.!!$F3 1905
10 TraesCS3D01G063700 chr3A 38012120 38014381 2261 True 587.780000 2163 94.318400 1 2092 5 chr3A.!!$R4 2091
11 TraesCS3D01G063700 chr3A 38133838 38136634 2796 True 524.000000 883 77.838000 635 3793 2 chr3A.!!$R5 3158
12 TraesCS3D01G063700 chr3A 37994796 37996325 1529 True 490.000000 957 90.179333 2118 3801 3 chr3A.!!$R3 1683
13 TraesCS3D01G063700 chr1B 510790820 510793175 2355 False 496.000000 918 80.259667 635 3092 3 chr1B.!!$F2 2457
14 TraesCS3D01G063700 chr1D 456279069 456280637 1568 True 869.000000 869 77.592000 517 2053 1 chr1D.!!$R1 1536
15 TraesCS3D01G063700 chr1D 381004977 381006559 1582 False 533.000000 894 79.298500 635 2267 2 chr1D.!!$F1 1632
16 TraesCS3D01G063700 chr2B 787786733 787787902 1169 False 560.000000 560 76.138000 1147 2281 1 chr2B.!!$F1 1134
17 TraesCS3D01G063700 chr2A 771970172 771971195 1023 False 455.000000 455 75.603000 1144 2129 1 chr2A.!!$F1 985
18 TraesCS3D01G063700 chr2D 650597965 650598980 1015 False 385.000000 385 74.570000 1133 2129 1 chr2D.!!$F2 996

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
966 1220 0.250338 GCTTCAACCTCAACCTCGGT 60.250 55.0 0.0 0.0 34.27 4.69 F
2420 5014 0.039437 TTGACGTGAGAAGGACGAGC 60.039 55.0 0.0 0.0 39.21 5.03 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2433 5028 0.889306 AGCACGACAGGGTCTAGAAC 59.111 55.0 0.00 0.0 0.00 3.01 R
3697 6639 0.532417 AGTCTAGACTACGGCGCGAT 60.532 55.0 24.04 0.0 40.43 4.58 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
80 91 7.097192 TGGTTCATCAGTTCTGTATAGTTCAC 58.903 38.462 0.00 0.00 0.00 3.18
86 97 5.773176 TCAGTTCTGTATAGTTCACCACTGA 59.227 40.000 0.00 0.00 35.97 3.41
119 130 3.743521 TCTTGGTTCATCAGTTCAGTGG 58.256 45.455 0.00 0.00 0.00 4.00
127 138 4.129380 TCATCAGTTCAGTGGTGAAACAG 58.871 43.478 0.00 0.00 44.44 3.16
155 166 9.807649 ACCAATCTGTTAATTTGAAATATCAGC 57.192 29.630 10.07 0.00 36.78 4.26
196 207 6.472686 AACAGCGGTAGAATAGAAGAAGAT 57.527 37.500 0.00 0.00 0.00 2.40
235 246 8.095169 CACCAATCTGTTAGTTAGTACTCCTTT 58.905 37.037 0.00 0.00 35.78 3.11
236 247 8.657712 ACCAATCTGTTAGTTAGTACTCCTTTT 58.342 33.333 0.00 0.00 35.78 2.27
307 419 7.061054 ACTGATCTATGTAGTGTAGCCAGTTA 58.939 38.462 0.00 0.00 33.34 2.24
308 420 7.560262 ACTGATCTATGTAGTGTAGCCAGTTAA 59.440 37.037 0.00 0.00 33.34 2.01
309 421 8.301252 TGATCTATGTAGTGTAGCCAGTTAAA 57.699 34.615 0.00 0.00 0.00 1.52
340 491 3.305064 GGTCTCGAAATGCTCCTAGCTAG 60.305 52.174 14.20 14.20 42.97 3.42
341 492 2.294791 TCTCGAAATGCTCCTAGCTAGC 59.705 50.000 15.74 6.62 42.97 3.42
342 493 2.295909 CTCGAAATGCTCCTAGCTAGCT 59.704 50.000 23.12 23.12 42.97 3.32
343 494 3.487372 TCGAAATGCTCCTAGCTAGCTA 58.513 45.455 22.85 22.85 42.97 3.32
344 495 3.504134 TCGAAATGCTCCTAGCTAGCTAG 59.496 47.826 35.39 35.39 42.97 3.42
486 644 0.893447 GCTACTACAACCACGGGACT 59.107 55.000 0.00 0.00 0.00 3.85
508 666 2.888863 GACTCGCTGGTCCCTCTG 59.111 66.667 0.00 0.00 0.00 3.35
509 667 3.363844 GACTCGCTGGTCCCTCTGC 62.364 68.421 0.00 0.00 0.00 4.26
749 993 1.133606 GGAGATCCTCCTCCGTCTTCT 60.134 57.143 5.78 0.00 46.41 2.85
838 1083 3.934391 AAGTTCCTCCGCCGCTTCG 62.934 63.158 0.00 0.00 0.00 3.79
879 1124 1.192146 CCCTCCTCGGTGTCTTCCAA 61.192 60.000 0.00 0.00 0.00 3.53
960 1208 0.514691 CTCAGCGCTTCAACCTCAAC 59.485 55.000 7.50 0.00 0.00 3.18
966 1220 0.250338 GCTTCAACCTCAACCTCGGT 60.250 55.000 0.00 0.00 34.27 4.69
1000 1254 1.871039 GCACGGAGTTGCAAGTCTTAA 59.129 47.619 28.62 0.00 41.61 1.85
1120 1380 0.591659 GGTTCCGCCAGAGTTCAAAC 59.408 55.000 0.00 0.00 37.17 2.93
1153 1416 2.827129 AACTGGGCTGTGCTCTGCT 61.827 57.895 15.77 0.00 38.34 4.24
1305 1571 2.154854 ATATCATCTCAACGGCCGTG 57.845 50.000 34.95 24.92 0.00 4.94
1361 2812 4.445385 GCTGCTTGTTGGTAATTCACTTTG 59.555 41.667 0.00 0.00 0.00 2.77
1413 2866 7.417116 GGCATACTTGAGTTTGATTTGGATGAT 60.417 37.037 5.88 0.00 0.00 2.45
1449 2902 0.178873 TCAGGGGGCCTCTTGTTACT 60.179 55.000 15.42 0.00 0.00 2.24
1553 3009 2.754552 TGCAATTGTGGCAGAGGAATAC 59.245 45.455 7.40 0.00 36.11 1.89
1640 3096 3.718956 CTCCCTCCCCAGATTGAAGTAAT 59.281 47.826 0.00 0.00 0.00 1.89
1665 3130 4.220724 AGAAAGGTATACTGGGATGCGTA 58.779 43.478 2.25 0.00 0.00 4.42
2001 3584 8.948631 TCTTGACTATTTGTTTGCTAGATAGG 57.051 34.615 0.00 0.00 0.00 2.57
2002 3585 7.495934 TCTTGACTATTTGTTTGCTAGATAGGC 59.504 37.037 0.00 0.00 0.00 3.93
2003 3586 6.649155 TGACTATTTGTTTGCTAGATAGGCA 58.351 36.000 0.00 0.00 36.31 4.75
2004 3587 7.282585 TGACTATTTGTTTGCTAGATAGGCAT 58.717 34.615 0.00 0.00 39.54 4.40
2005 3588 8.428852 TGACTATTTGTTTGCTAGATAGGCATA 58.571 33.333 0.00 0.00 39.54 3.14
2006 3589 8.839310 ACTATTTGTTTGCTAGATAGGCATAG 57.161 34.615 0.00 0.00 39.54 2.23
2020 3607 4.963318 AGGCATAGACAAGCTTATAGCA 57.037 40.909 0.00 0.00 45.56 3.49
2141 3743 0.961019 GCATGTTTGGAACCTCAGCA 59.039 50.000 0.00 0.00 0.00 4.41
2305 3934 8.519799 TCTGTAACAGACCTTTTTCAGATTTT 57.480 30.769 0.00 0.00 35.39 1.82
2330 3959 4.017591 TCTCTCCAATTGGGCTCCATTTAA 60.018 41.667 24.29 0.00 36.21 1.52
2365 4957 6.877611 ACCGAAAATCACTTCTGTTTGTAT 57.122 33.333 0.00 0.00 0.00 2.29
2420 5014 0.039437 TTGACGTGAGAAGGACGAGC 60.039 55.000 0.00 0.00 39.21 5.03
2433 5028 7.389330 TGAGAAGGACGAGCTAGATTAGATAAG 59.611 40.741 0.00 0.00 0.00 1.73
2443 5038 8.873186 AGCTAGATTAGATAAGTTCTAGACCC 57.127 38.462 11.73 0.00 39.92 4.46
2581 5205 6.944290 ACCATTATCAGTAATGATCCCATGTG 59.056 38.462 9.29 7.54 46.59 3.21
2582 5206 6.944290 CCATTATCAGTAATGATCCCATGTGT 59.056 38.462 9.29 0.00 46.59 3.72
2597 5221 5.003160 CCCATGTGTCAACAAGAAGTATCA 58.997 41.667 0.00 0.00 40.46 2.15
2598 5222 5.106555 CCCATGTGTCAACAAGAAGTATCAC 60.107 44.000 0.00 0.00 40.46 3.06
2599 5223 5.702670 CCATGTGTCAACAAGAAGTATCACT 59.297 40.000 0.00 0.00 40.46 3.41
2600 5224 6.873605 CCATGTGTCAACAAGAAGTATCACTA 59.126 38.462 0.00 0.00 40.46 2.74
2601 5225 7.063898 CCATGTGTCAACAAGAAGTATCACTAG 59.936 40.741 0.00 0.00 40.46 2.57
2602 5226 7.050970 TGTGTCAACAAGAAGTATCACTAGT 57.949 36.000 0.00 0.00 31.82 2.57
2603 5227 6.923508 TGTGTCAACAAGAAGTATCACTAGTG 59.076 38.462 17.17 17.17 31.82 2.74
3029 5673 6.515272 AATGGTGGTGATGCTAAGTAAAAG 57.485 37.500 0.00 0.00 0.00 2.27
3089 5735 5.653330 TGCAGATGATCCAAATGTTGTATGT 59.347 36.000 0.00 0.00 0.00 2.29
3210 5915 4.109050 GGCTGAAAATTTTGTTGTCGTCA 58.891 39.130 8.47 0.00 0.00 4.35
3213 5918 5.275881 GCTGAAAATTTTGTTGTCGTCAGTG 60.276 40.000 8.47 0.00 34.95 3.66
3229 5934 5.655090 TCGTCAGTGTTCCAAGGAGATATAA 59.345 40.000 0.00 0.00 0.00 0.98
3239 5944 9.930693 GTTCCAAGGAGATATAACCAGTAATAG 57.069 37.037 0.00 0.00 0.00 1.73
3241 5946 7.678598 TCCAAGGAGATATAACCAGTAATAGGG 59.321 40.741 0.00 0.00 0.00 3.53
3552 6377 3.317149 TGTTACATACGCCTAGGTGCTAG 59.683 47.826 22.51 13.73 34.16 3.42
3558 6383 5.771666 ACATACGCCTAGGTGCTAGTATTAA 59.228 40.000 22.51 0.00 32.62 1.40
3649 6591 1.804151 TGTTGCTGAGTTTGCCGTATC 59.196 47.619 0.00 0.00 0.00 2.24
3663 6605 2.158841 GCCGTATCGTGTCAATGTTGTT 59.841 45.455 0.00 0.00 0.00 2.83
3667 6609 0.665835 TCGTGTCAATGTTGTTGGCC 59.334 50.000 0.00 0.00 0.00 5.36
3678 6620 6.374613 TCAATGTTGTTGGCCGTGTTTATATA 59.625 34.615 0.00 0.00 0.00 0.86
3705 6647 1.138047 AAGAAAGACGTATCGCGCCG 61.138 55.000 0.00 6.13 46.11 6.46
3709 6656 1.709147 AAGACGTATCGCGCCGTAGT 61.709 55.000 16.08 6.10 46.11 2.73
3711 6658 2.098842 GACGTATCGCGCCGTAGTCT 62.099 60.000 16.08 0.00 46.11 3.24
3714 6661 1.143305 GTATCGCGCCGTAGTCTAGA 58.857 55.000 0.00 0.00 0.00 2.43
3719 6670 1.863267 GCGCCGTAGTCTAGACTAGA 58.137 55.000 29.00 11.78 43.84 2.43
3747 6699 8.491152 CAGTAAGATGCTTTTGAATACCTATCG 58.509 37.037 0.00 0.00 0.00 2.92
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
86 97 3.030291 TGAACCAAGAAACAGCACCAAT 58.970 40.909 0.00 0.00 0.00 3.16
127 138 9.585099 TGATATTTCAAATTAACAGATTGGTGC 57.415 29.630 0.00 0.00 0.00 5.01
196 207 3.820467 CAGATTGGTGCTGTTTCTTGGTA 59.180 43.478 0.00 0.00 0.00 3.25
248 259 9.289782 GTACTCCCTCCGTAAACTAATATAAGA 57.710 37.037 0.00 0.00 0.00 2.10
249 260 9.294614 AGTACTCCCTCCGTAAACTAATATAAG 57.705 37.037 0.00 0.00 0.00 1.73
251 262 9.950496 CTAGTACTCCCTCCGTAAACTAATATA 57.050 37.037 0.00 0.00 0.00 0.86
252 263 8.443979 ACTAGTACTCCCTCCGTAAACTAATAT 58.556 37.037 0.00 0.00 0.00 1.28
253 264 7.806180 ACTAGTACTCCCTCCGTAAACTAATA 58.194 38.462 0.00 0.00 0.00 0.98
254 265 6.667661 ACTAGTACTCCCTCCGTAAACTAAT 58.332 40.000 0.00 0.00 0.00 1.73
255 266 6.067217 ACTAGTACTCCCTCCGTAAACTAA 57.933 41.667 0.00 0.00 0.00 2.24
256 267 5.700402 ACTAGTACTCCCTCCGTAAACTA 57.300 43.478 0.00 0.00 0.00 2.24
258 269 5.432645 AGTACTAGTACTCCCTCCGTAAAC 58.567 45.833 26.61 2.35 42.30 2.01
260 271 5.900123 AGTAGTACTAGTACTCCCTCCGTAA 59.100 44.000 33.47 14.20 44.58 3.18
261 272 5.303078 CAGTAGTACTAGTACTCCCTCCGTA 59.697 48.000 33.47 14.86 44.58 4.02
263 274 4.343526 TCAGTAGTACTAGTACTCCCTCCG 59.656 50.000 33.47 19.98 44.58 4.63
315 427 2.682155 AGGAGCATTTCGAGACCTTC 57.318 50.000 0.00 0.00 0.00 3.46
318 430 1.410882 AGCTAGGAGCATTTCGAGACC 59.589 52.381 0.64 0.00 45.56 3.85
345 496 1.470494 TCTCTCTCTGTTGTAGCGCAG 59.530 52.381 11.47 0.00 0.00 5.18
346 497 1.534729 TCTCTCTCTGTTGTAGCGCA 58.465 50.000 11.47 0.00 0.00 6.09
435 591 5.456548 TGACTGATAAAGTGACGGTGTTA 57.543 39.130 0.00 0.00 40.07 2.41
442 598 3.010420 GGGCCTTGACTGATAAAGTGAC 58.990 50.000 0.84 0.00 40.07 3.67
838 1083 2.574018 GCTTTTGGTGGTGGAGGCC 61.574 63.158 0.00 0.00 0.00 5.19
879 1124 3.674410 CGATATCATCATAGGTGCGCTGT 60.674 47.826 9.73 0.00 0.00 4.40
1000 1254 1.647545 CCGTGACGGCAATCAAGCAT 61.648 55.000 12.53 0.00 41.17 3.79
1120 1380 3.750130 GCCCAGTTGACATCATAGCATAG 59.250 47.826 0.00 0.00 0.00 2.23
1153 1416 1.303561 GGTCATGGTTGCTGGCAGA 60.304 57.895 20.86 0.00 0.00 4.26
1305 1571 4.084537 CCAACATAATGAATCTCGTACGGC 60.085 45.833 16.52 1.01 0.00 5.68
1318 1584 4.758674 CAGCCCAGAGATACCAACATAATG 59.241 45.833 0.00 0.00 0.00 1.90
1361 2812 3.406764 CTTATAGGATCCAGCAACCAGC 58.593 50.000 15.82 0.00 46.19 4.85
1413 2866 3.196469 CCCTGATCACAGCTAGACTTTCA 59.804 47.826 0.00 0.00 42.25 2.69
1449 2902 4.883585 GGACTGTCATGGCTGAAATCATTA 59.116 41.667 11.50 0.00 31.85 1.90
1553 3009 0.108520 GGCAGCACCATGACAATTGG 60.109 55.000 10.83 0.00 40.26 3.16
1640 3096 4.442893 CGCATCCCAGTATACCTTTCTTCA 60.443 45.833 0.00 0.00 0.00 3.02
1665 3130 6.497624 AGAAGTATTTCATCTGCATCCTCT 57.502 37.500 0.44 0.00 35.70 3.69
1674 3139 5.456763 GCCCACCCATAGAAGTATTTCATCT 60.457 44.000 0.44 0.00 35.70 2.90
2001 3584 7.917505 ACAAAAATGCTATAAGCTTGTCTATGC 59.082 33.333 9.86 6.37 42.97 3.14
2002 3585 9.793252 AACAAAAATGCTATAAGCTTGTCTATG 57.207 29.630 9.86 0.00 42.97 2.23
2003 3586 9.793252 CAACAAAAATGCTATAAGCTTGTCTAT 57.207 29.630 9.86 0.00 42.97 1.98
2004 3587 8.792633 ACAACAAAAATGCTATAAGCTTGTCTA 58.207 29.630 9.86 0.00 42.97 2.59
2005 3588 7.661040 ACAACAAAAATGCTATAAGCTTGTCT 58.339 30.769 9.86 0.00 42.97 3.41
2006 3589 7.873739 ACAACAAAAATGCTATAAGCTTGTC 57.126 32.000 9.86 0.00 42.97 3.18
2099 3701 5.390613 CCGAATGAGTTAACCATTTGACAC 58.609 41.667 24.36 12.62 37.51 3.67
2199 3821 7.916450 TCAAAAGGTACGGTTTGAACTAAATTG 59.084 33.333 16.14 0.24 41.66 2.32
2201 3823 7.571080 TCAAAAGGTACGGTTTGAACTAAAT 57.429 32.000 16.14 0.00 41.66 1.40
2305 3934 1.710244 TGGAGCCCAATTGGAGAGAAA 59.290 47.619 26.60 3.93 37.39 2.52
2365 4957 7.856145 AAAAACATGCCACAACTCATAAAAA 57.144 28.000 0.00 0.00 0.00 1.94
2377 4970 7.713764 AGAAGACAAAATAAAAACATGCCAC 57.286 32.000 0.00 0.00 0.00 5.01
2406 4999 4.817464 TCTAATCTAGCTCGTCCTTCTCAC 59.183 45.833 0.00 0.00 0.00 3.51
2411 5004 7.722285 AGAACTTATCTAATCTAGCTCGTCCTT 59.278 37.037 0.00 0.00 36.32 3.36
2420 5014 9.802039 ACAGGGTCTAGAACTTATCTAATCTAG 57.198 37.037 7.92 0.00 40.12 2.43
2433 5028 0.889306 AGCACGACAGGGTCTAGAAC 59.111 55.000 0.00 0.00 0.00 3.01
2573 5197 3.576078 ACTTCTTGTTGACACATGGGA 57.424 42.857 0.00 0.00 31.06 4.37
2581 5205 7.371936 AGTCACTAGTGATACTTCTTGTTGAC 58.628 38.462 27.54 10.63 42.18 3.18
2582 5206 7.526142 AGTCACTAGTGATACTTCTTGTTGA 57.474 36.000 27.54 0.00 42.18 3.18
2597 5221 6.264744 TGTTTTACAGCTCACTAGTCACTAGT 59.735 38.462 12.06 12.06 46.75 2.57
2598 5222 6.678878 TGTTTTACAGCTCACTAGTCACTAG 58.321 40.000 10.55 10.55 39.72 2.57
2599 5223 6.489022 TCTGTTTTACAGCTCACTAGTCACTA 59.511 38.462 0.00 0.00 45.54 2.74
2600 5224 5.302059 TCTGTTTTACAGCTCACTAGTCACT 59.698 40.000 0.00 0.00 45.54 3.41
2601 5225 5.529791 TCTGTTTTACAGCTCACTAGTCAC 58.470 41.667 0.00 0.00 45.54 3.67
2602 5226 5.784578 TCTGTTTTACAGCTCACTAGTCA 57.215 39.130 0.00 0.00 45.54 3.41
2603 5227 6.217294 ACTTCTGTTTTACAGCTCACTAGTC 58.783 40.000 0.00 0.00 45.54 2.59
2903 5547 1.880027 CTGGCCGCTACATATTTTCCC 59.120 52.381 0.00 0.00 0.00 3.97
2913 5557 2.652095 TACCCACACTGGCCGCTAC 61.652 63.158 0.00 0.00 35.79 3.58
2989 5633 6.540551 ACCACCATTTTTAATTGTTTGTCCAC 59.459 34.615 0.00 0.00 0.00 4.02
3029 5673 8.511604 TTTTATGATCCAAAAGAGGAGTCATC 57.488 34.615 0.00 0.00 41.90 2.92
3132 5820 9.533253 GATGATGTTTGTAATAAGAAAATGGGG 57.467 33.333 0.00 0.00 0.00 4.96
3161 5849 2.031157 ACACGAATTTGTTAGGTGCAGC 60.031 45.455 8.11 8.11 32.00 5.25
3210 5915 5.726793 ACTGGTTATATCTCCTTGGAACACT 59.273 40.000 0.00 0.00 39.29 3.55
3213 5918 9.930693 CTATTACTGGTTATATCTCCTTGGAAC 57.069 37.037 0.00 0.00 0.00 3.62
3487 6233 5.995282 TGTAAAAACTCATGATCGAACTGGT 59.005 36.000 0.00 0.00 0.00 4.00
3488 6234 6.073276 TGTGTAAAAACTCATGATCGAACTGG 60.073 38.462 0.00 0.00 0.00 4.00
3489 6235 6.887368 TGTGTAAAAACTCATGATCGAACTG 58.113 36.000 0.00 0.00 0.00 3.16
3490 6236 7.361201 CCATGTGTAAAAACTCATGATCGAACT 60.361 37.037 17.55 0.00 0.00 3.01
3491 6237 6.742718 CCATGTGTAAAAACTCATGATCGAAC 59.257 38.462 17.55 0.00 0.00 3.95
3492 6238 6.622679 GCCATGTGTAAAAACTCATGATCGAA 60.623 38.462 17.55 0.00 0.00 3.71
3493 6239 5.163764 GCCATGTGTAAAAACTCATGATCGA 60.164 40.000 17.55 0.00 0.00 3.59
3649 6591 0.660005 CGGCCAACAACATTGACACG 60.660 55.000 2.24 0.00 0.00 4.49
3678 6620 6.087820 GCGCGATACGTCTTTCTTTAGATAAT 59.912 38.462 12.10 0.00 46.11 1.28
3688 6630 0.589729 TACGGCGCGATACGTCTTTC 60.590 55.000 23.12 0.00 46.73 2.62
3697 6639 0.532417 AGTCTAGACTACGGCGCGAT 60.532 55.000 24.04 0.00 40.43 4.58
3705 6647 7.095355 GCATCTTACTGCTCTAGTCTAGACTAC 60.095 44.444 25.58 17.48 40.89 2.73
3747 6699 3.653835 AGGGTAAGCTGAAATTCCCTC 57.346 47.619 0.00 0.00 40.96 4.30


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

AutoCloner maintained by Alex Coulton.