Multiple sequence alignment - TraesCS3B01G404300

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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 TraesCS3B01G404300 chr3B 100.000 3820 0 0 1 3820 639148323 639152142 0.000000e+00 7055.0
1 TraesCS3B01G404300 chr3B 95.020 3534 139 10 310 3820 639552859 639556378 0.000000e+00 5517.0
2 TraesCS3B01G404300 chr3B 92.377 3568 185 34 303 3820 638959697 638963227 0.000000e+00 5001.0
3 TraesCS3B01G404300 chr3B 94.725 2578 103 6 315 2870 639398409 639400975 0.000000e+00 3976.0
4 TraesCS3B01G404300 chr3B 90.992 2531 171 27 266 2788 639753437 639755918 0.000000e+00 3358.0
5 TraesCS3B01G404300 chr3B 95.232 839 37 2 2983 3820 639401150 639401986 0.000000e+00 1325.0
6 TraesCS3B01G404300 chr3B 86.136 1219 130 20 1579 2788 639772243 639773431 0.000000e+00 1279.0
7 TraesCS3B01G404300 chr3B 79.606 1726 259 41 1538 3199 639854829 639856525 0.000000e+00 1151.0
8 TraesCS3B01G404300 chr3B 81.417 1426 210 32 1538 2932 639834835 639836236 0.000000e+00 1114.0
9 TraesCS3B01G404300 chr3B 84.349 1067 110 24 2213 3231 639773556 639774613 0.000000e+00 992.0
10 TraesCS3B01G404300 chr3B 86.424 604 64 7 3232 3819 639774650 639775251 0.000000e+00 645.0
11 TraesCS3B01G404300 chr3B 82.730 608 57 24 3230 3820 639756479 639757055 7.370000e-137 497.0
12 TraesCS3B01G404300 chr3B 98.406 251 3 1 1 250 639552102 639552352 1.260000e-119 440.0
13 TraesCS3B01G404300 chr3B 98.008 251 4 1 1 250 639753202 639753452 5.860000e-118 435.0
14 TraesCS3B01G404300 chr3B 97.233 253 4 3 1 250 638959368 638959620 3.530000e-115 425.0
15 TraesCS3B01G404300 chr3B 98.230 226 3 1 26 250 639397739 639397964 9.950000e-106 394.0
16 TraesCS3B01G404300 chr3B 78.671 572 84 24 3230 3785 639816118 639816667 2.820000e-91 346.0
17 TraesCS3B01G404300 chr3B 79.004 281 41 9 2959 3226 639779431 639779706 3.920000e-40 176.0
18 TraesCS3B01G404300 chr3B 84.932 146 18 3 2652 2796 638997949 638998091 1.110000e-30 145.0
19 TraesCS3B01G404300 chr3B 84.783 138 18 3 2652 2788 639169163 639169298 6.660000e-28 135.0
20 TraesCS3B01G404300 chr3B 100.000 40 0 0 266 305 639397949 639397988 1.470000e-09 75.0
21 TraesCS3B01G404300 chr3B 100.000 40 0 0 266 305 639552337 639552376 1.470000e-09 75.0
22 TraesCS3B01G404300 chr3B 100.000 37 0 0 266 302 638959605 638959641 6.850000e-08 69.4
23 TraesCS3B01G404300 chr3B 83.117 77 2 2 3000 3066 639756240 639756315 4.120000e-05 60.2
24 TraesCS3B01G404300 chr3D 91.999 3037 193 22 234 3231 478737767 478740792 0.000000e+00 4217.0
25 TraesCS3B01G404300 chr3D 84.349 3003 333 67 312 3231 479449720 479452668 0.000000e+00 2815.0
26 TraesCS3B01G404300 chr3D 80.799 1677 245 28 1607 3231 478751505 478753156 0.000000e+00 1242.0
27 TraesCS3B01G404300 chr3D 83.042 1315 172 27 819 2105 479463380 479464671 0.000000e+00 1146.0
28 TraesCS3B01G404300 chr3D 89.621 607 42 4 3232 3820 478740829 478741432 0.000000e+00 752.0
29 TraesCS3B01G404300 chr3D 86.379 580 44 19 312 878 479918918 479918361 5.460000e-168 601.0
30 TraesCS3B01G404300 chr3D 83.609 604 63 15 3230 3820 479214970 479215550 5.620000e-148 534.0
31 TraesCS3B01G404300 chr3D 82.149 605 70 20 3230 3819 479960912 479960331 5.740000e-133 484.0
32 TraesCS3B01G404300 chr3D 81.878 607 67 11 3230 3819 479912452 479911872 4.470000e-129 472.0
33 TraesCS3B01G404300 chr3D 80.723 581 73 19 3230 3793 479123176 479123734 2.120000e-112 416.0
34 TraesCS3B01G404300 chr3D 97.131 244 6 1 8 250 478737571 478737814 9.880000e-111 411.0
35 TraesCS3B01G404300 chr3D 90.090 222 16 2 1 216 479116137 479116358 2.250000e-72 283.0
36 TraesCS3B01G404300 chr3D 80.000 305 47 6 2937 3231 479122840 479123140 2.990000e-51 213.0
37 TraesCS3B01G404300 chr3D 73.494 581 92 29 2689 3229 479895991 479895433 3.050000e-36 163.0
38 TraesCS3B01G404300 chr3A 90.202 2531 157 38 312 2814 622276817 622279284 0.000000e+00 3216.0
39 TraesCS3B01G404300 chr3A 84.286 1400 162 34 312 1680 622817669 622819041 0.000000e+00 1314.0
40 TraesCS3B01G404300 chr3A 83.822 1397 167 33 312 1680 622709269 622710634 0.000000e+00 1273.0
41 TraesCS3B01G404300 chr3A 81.398 1559 210 38 1725 3231 622719359 622720889 0.000000e+00 1199.0
42 TraesCS3B01G404300 chr3A 81.154 1560 216 31 1724 3231 622710636 622712169 0.000000e+00 1181.0
43 TraesCS3B01G404300 chr3A 81.947 565 61 18 3230 3790 622720924 622721451 1.260000e-119 440.0
44 TraesCS3B01G404300 chr3A 90.432 324 28 3 3498 3819 622280024 622280346 1.270000e-114 424.0
45 TraesCS3B01G404300 chr3A 80.135 594 77 17 3230 3820 622820611 622821166 4.600000e-109 405.0
46 TraesCS3B01G404300 chr3A 79.639 609 75 19 3230 3820 622811904 622812481 3.580000e-105 392.0
47 TraesCS3B01G404300 chr3A 90.508 295 28 0 2935 3229 622279387 622279681 1.290000e-104 390.0
48 TraesCS3B01G404300 chr3A 90.984 244 15 2 3234 3477 622279723 622279959 4.760000e-84 322.0
49 TraesCS3B01G404300 chr3A 92.188 192 15 0 1 192 622276562 622276753 4.860000e-69 272.0


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 TraesCS3B01G404300 chr3B 639148323 639152142 3819 False 7055.000000 7055 100.000000 1 3820 1 chr3B.!!$F2 3819
1 TraesCS3B01G404300 chr3B 639552102 639556378 4276 False 2010.666667 5517 97.808667 1 3820 3 chr3B.!!$F10 3819
2 TraesCS3B01G404300 chr3B 638959368 638963227 3859 False 1831.800000 5001 96.536667 1 3820 3 chr3B.!!$F8 3819
3 TraesCS3B01G404300 chr3B 639397739 639401986 4247 False 1442.500000 3976 97.046750 26 3820 4 chr3B.!!$F9 3794
4 TraesCS3B01G404300 chr3B 639854829 639856525 1696 False 1151.000000 1151 79.606000 1538 3199 1 chr3B.!!$F7 1661
5 TraesCS3B01G404300 chr3B 639834835 639836236 1401 False 1114.000000 1114 81.417000 1538 2932 1 chr3B.!!$F6 1394
6 TraesCS3B01G404300 chr3B 639753202 639757055 3853 False 1087.550000 3358 88.711750 1 3820 4 chr3B.!!$F11 3819
7 TraesCS3B01G404300 chr3B 639772243 639775251 3008 False 972.000000 1279 85.636333 1579 3819 3 chr3B.!!$F12 2240
8 TraesCS3B01G404300 chr3B 639816118 639816667 549 False 346.000000 346 78.671000 3230 3785 1 chr3B.!!$F5 555
9 TraesCS3B01G404300 chr3D 479449720 479452668 2948 False 2815.000000 2815 84.349000 312 3231 1 chr3D.!!$F4 2919
10 TraesCS3B01G404300 chr3D 478737571 478741432 3861 False 1793.333333 4217 92.917000 8 3820 3 chr3D.!!$F6 3812
11 TraesCS3B01G404300 chr3D 478751505 478753156 1651 False 1242.000000 1242 80.799000 1607 3231 1 chr3D.!!$F1 1624
12 TraesCS3B01G404300 chr3D 479463380 479464671 1291 False 1146.000000 1146 83.042000 819 2105 1 chr3D.!!$F5 1286
13 TraesCS3B01G404300 chr3D 479918361 479918918 557 True 601.000000 601 86.379000 312 878 1 chr3D.!!$R3 566
14 TraesCS3B01G404300 chr3D 479214970 479215550 580 False 534.000000 534 83.609000 3230 3820 1 chr3D.!!$F3 590
15 TraesCS3B01G404300 chr3D 479960331 479960912 581 True 484.000000 484 82.149000 3230 3819 1 chr3D.!!$R4 589
16 TraesCS3B01G404300 chr3D 479911872 479912452 580 True 472.000000 472 81.878000 3230 3819 1 chr3D.!!$R2 589
17 TraesCS3B01G404300 chr3D 479122840 479123734 894 False 314.500000 416 80.361500 2937 3793 2 chr3D.!!$F7 856
18 TraesCS3B01G404300 chr3A 622709269 622712169 2900 False 1227.000000 1273 82.488000 312 3231 2 chr3A.!!$F3 2919
19 TraesCS3B01G404300 chr3A 622276562 622280346 3784 False 924.800000 3216 90.862800 1 3819 5 chr3A.!!$F2 3818
20 TraesCS3B01G404300 chr3A 622817669 622821166 3497 False 859.500000 1314 82.210500 312 3820 2 chr3A.!!$F5 3508
21 TraesCS3B01G404300 chr3A 622719359 622721451 2092 False 819.500000 1199 81.672500 1725 3790 2 chr3A.!!$F4 2065
22 TraesCS3B01G404300 chr3A 622811904 622812481 577 False 392.000000 392 79.639000 3230 3820 1 chr3A.!!$F1 590

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
142 145 1.820519 GTGCTTTTCCATGCCATCAGA 59.179 47.619 0.0 0.0 0.0 3.27 F
1020 1628 0.891373 CACACACCACAACCCACAAA 59.109 50.000 0.0 0.0 0.0 2.83 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1043 1660 0.035630 ATCTCTCCTTGCCACTGTGC 60.036 55.0 1.29 0.00 0.00 4.57 R
2942 4489 0.110823 GTGCGTCCACGTGATTGAAC 60.111 55.0 19.30 6.68 42.22 3.18 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
122 125 2.566724 GGAGGAGGGCTCTATCTGATTG 59.433 54.545 0.00 0.00 0.00 2.67
142 145 1.820519 GTGCTTTTCCATGCCATCAGA 59.179 47.619 0.00 0.00 0.00 3.27
441 1006 1.913778 TCACATGCATGCCTGACTTT 58.086 45.000 26.94 4.10 0.00 2.66
500 1066 2.889045 TGCGTGTAGACTGACTTTACCT 59.111 45.455 0.00 0.00 0.00 3.08
796 1367 2.094026 GGGTTCGTTTCGTATACCAGGT 60.094 50.000 0.00 0.00 0.00 4.00
811 1382 2.125269 GGTGTAACTCGCGGCCAT 60.125 61.111 6.13 0.00 36.74 4.40
906 1501 9.770097 TCTATAGCTCACCTTTTTCATCAATAG 57.230 33.333 0.00 0.00 0.00 1.73
952 1547 8.152309 AGTGCTTTAATTGATGCTTATCTCTC 57.848 34.615 9.12 0.00 0.00 3.20
982 1577 2.028112 CAGGCTATAAATAGAGGGCGCA 60.028 50.000 10.83 0.00 32.05 6.09
983 1578 2.637872 AGGCTATAAATAGAGGGCGCAA 59.362 45.455 10.83 0.00 32.05 4.85
1020 1628 0.891373 CACACACCACAACCCACAAA 59.109 50.000 0.00 0.00 0.00 2.83
1043 1660 4.393680 ACAAGAGAGTACGTAGAGCAAGAG 59.606 45.833 0.00 0.00 0.00 2.85
1150 1767 1.153667 CTCGAAGGTGAGGAGCAGC 60.154 63.158 0.00 0.00 45.24 5.25
1398 2018 1.900545 GAGGAAGCAACCTAGCCCGT 61.901 60.000 1.73 0.00 40.73 5.28
1413 2033 0.961358 CCCGTCAGGAGTCGTTCTCT 60.961 60.000 9.36 0.00 42.40 3.10
1426 2046 1.537889 TTCTCTTTGCCTCCCCCGA 60.538 57.895 0.00 0.00 0.00 5.14
1457 2077 2.203938 GGTGGAGGAGGTGTGGGA 60.204 66.667 0.00 0.00 0.00 4.37
1546 2184 3.700970 TCCAGCCATCGGTTGCGA 61.701 61.111 0.00 0.00 32.46 5.10
1763 2445 0.462375 CCGGTGATGGGATACGTCAA 59.538 55.000 0.00 0.00 46.16 3.18
1766 2448 1.760613 GGTGATGGGATACGTCAAGGA 59.239 52.381 0.00 0.00 46.16 3.36
2468 3166 9.448438 AGTCTTAAAATAGTCAATGTGTGCATA 57.552 29.630 0.00 0.00 34.39 3.14
2686 4122 9.569167 GTTTATAGCAGTAACATTTTCTTTCCC 57.431 33.333 0.00 0.00 0.00 3.97
2847 4394 5.649395 AGCAATATGTTGATGTGTACTTGCT 59.351 36.000 6.35 5.13 41.23 3.91
2854 4401 6.954944 TGTTGATGTGTACTTGCTCTTTAAC 58.045 36.000 0.00 0.00 0.00 2.01
2869 4416 5.514204 GCTCTTTAACATGATGTGATGCAAC 59.486 40.000 0.00 0.00 0.00 4.17
2870 4417 6.572167 TCTTTAACATGATGTGATGCAACA 57.428 33.333 0.00 0.00 34.37 3.33
2871 4418 6.380995 TCTTTAACATGATGTGATGCAACAC 58.619 36.000 19.32 19.32 40.68 3.32
2885 4432 2.433604 TGCAACACATGTGGTCCATTTT 59.566 40.909 28.64 10.05 34.19 1.82
2898 4445 3.186119 GTCCATTTTTGGTGTGTGTGTG 58.814 45.455 0.00 0.00 0.00 3.82
2899 4446 2.828520 TCCATTTTTGGTGTGTGTGTGT 59.171 40.909 0.00 0.00 0.00 3.72
2900 4447 2.928757 CCATTTTTGGTGTGTGTGTGTG 59.071 45.455 0.00 0.00 0.00 3.82
2901 4448 3.583806 CATTTTTGGTGTGTGTGTGTGT 58.416 40.909 0.00 0.00 0.00 3.72
2902 4449 2.713895 TTTTGGTGTGTGTGTGTGTG 57.286 45.000 0.00 0.00 0.00 3.82
2904 4451 0.877743 TTGGTGTGTGTGTGTGTGTG 59.122 50.000 0.00 0.00 0.00 3.82
2905 4452 0.250510 TGGTGTGTGTGTGTGTGTGT 60.251 50.000 0.00 0.00 0.00 3.72
2935 4482 0.040067 GTCTTTGCCTTTGCTCACGG 60.040 55.000 0.00 0.00 38.71 4.94
2940 4487 0.605319 TGCCTTTGCTCACGGGTTAG 60.605 55.000 0.00 0.00 38.71 2.34
2941 4488 0.321298 GCCTTTGCTCACGGGTTAGA 60.321 55.000 0.00 0.00 33.53 2.10
2942 4489 1.726853 CCTTTGCTCACGGGTTAGAG 58.273 55.000 0.00 0.00 35.01 2.43
2943 4490 1.002087 CCTTTGCTCACGGGTTAGAGT 59.998 52.381 0.00 0.00 34.39 3.24
2945 4492 2.450609 TTGCTCACGGGTTAGAGTTC 57.549 50.000 0.00 0.00 34.39 3.01
2946 4493 1.334160 TGCTCACGGGTTAGAGTTCA 58.666 50.000 0.00 0.00 34.39 3.18
2954 4502 2.666508 CGGGTTAGAGTTCAATCACGTG 59.333 50.000 9.94 9.94 0.00 4.49
2962 4510 1.225376 TTCAATCACGTGGACGCACC 61.225 55.000 17.00 0.00 44.43 5.01
2979 4527 0.606604 ACCTTACTGCGTCGGTGAAT 59.393 50.000 0.00 0.00 0.00 2.57
2985 4533 1.263217 ACTGCGTCGGTGAATTTTGAC 59.737 47.619 0.00 0.00 0.00 3.18
3054 4612 1.596934 GATCCCGTGAGCCTTGACA 59.403 57.895 0.00 0.00 0.00 3.58
3103 4661 0.044244 TCGATTCCCTTTCCCCTCCT 59.956 55.000 0.00 0.00 0.00 3.69
3106 4664 0.123266 ATTCCCTTTCCCCTCCTCCA 59.877 55.000 0.00 0.00 0.00 3.86
3116 4682 2.829003 CTCCTCCACGGCTCGCTA 60.829 66.667 0.00 0.00 0.00 4.26
3130 4696 2.348888 CGCTACTTGAGGGTCCGGT 61.349 63.158 0.00 0.00 33.43 5.28
3135 4701 0.544595 ACTTGAGGGTCCGGTTAGCT 60.545 55.000 0.00 0.00 0.00 3.32
3185 4751 5.065914 CCATGACGGATATCATCAACCTTT 58.934 41.667 11.67 0.00 37.20 3.11
3188 4754 7.148356 CCATGACGGATATCATCAACCTTTATG 60.148 40.741 11.67 5.37 37.20 1.90
3191 4757 8.425703 TGACGGATATCATCAACCTTTATGTTA 58.574 33.333 4.83 0.00 0.00 2.41
3198 4764 8.974060 ATCATCAACCTTTATGTTATTACGGT 57.026 30.769 0.00 0.00 0.00 4.83
3200 4766 8.670135 TCATCAACCTTTATGTTATTACGGTTG 58.330 33.333 11.01 11.01 46.83 3.77
3205 4771 6.711645 ACCTTTATGTTATTACGGTTGTGTGT 59.288 34.615 0.00 0.00 0.00 3.72
3215 4781 1.082117 GGTTGTGTGTATCGGAGGCG 61.082 60.000 0.00 0.00 0.00 5.52
3231 4797 1.144936 GCGAGGGGTGATCCTCTTG 59.855 63.158 8.95 1.79 46.01 3.02
3232 4798 1.144936 CGAGGGGTGATCCTCTTGC 59.855 63.158 8.95 0.00 46.01 4.01
3233 4799 1.529309 GAGGGGTGATCCTCTTGCC 59.471 63.158 3.83 0.00 46.01 4.52
3291 5930 4.006989 ACAGTTAATGTGTGTGTGTGTGT 58.993 39.130 0.00 0.00 41.91 3.72
3292 5931 4.142708 ACAGTTAATGTGTGTGTGTGTGTG 60.143 41.667 0.00 0.00 41.91 3.82
3331 5975 4.577283 CCGGTGGGTCGTGATTATTTTTAT 59.423 41.667 0.00 0.00 0.00 1.40
3427 6071 2.481969 GGTAGCTGCATCTGATGAACGA 60.482 50.000 21.30 3.19 0.00 3.85
3494 6155 3.181487 GGACTGTGTGTTTGATGCAACTT 60.181 43.478 0.00 0.00 0.00 2.66
3731 6425 4.866508 TTGATGTGTACTCCGAAACTCT 57.133 40.909 0.00 0.00 0.00 3.24
3761 6455 8.756927 TCTACTTCTGAGATCAATTGAGTTCAT 58.243 33.333 19.24 10.89 0.00 2.57
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
122 125 1.820519 TCTGATGGCATGGAAAAGCAC 59.179 47.619 3.81 0.00 0.00 4.40
262 265 7.095397 CCGTGTTCTACAAAAATGTCATACAGA 60.095 37.037 0.00 0.00 0.00 3.41
263 266 7.015289 CCGTGTTCTACAAAAATGTCATACAG 58.985 38.462 0.00 0.00 0.00 2.74
264 267 6.706716 TCCGTGTTCTACAAAAATGTCATACA 59.293 34.615 0.00 0.00 0.00 2.29
783 1354 3.181497 GCGAGTTACACCTGGTATACGAA 60.181 47.826 0.00 0.00 0.00 3.85
796 1367 0.604243 AAACATGGCCGCGAGTTACA 60.604 50.000 8.23 0.00 0.00 2.41
811 1382 1.103987 TACTGCCAAAGCGCCAAACA 61.104 50.000 2.29 0.00 44.31 2.83
905 1500 7.519008 GCACTAGATAGCAATTAAATTCACGCT 60.519 37.037 0.00 0.00 0.00 5.07
906 1501 6.575201 GCACTAGATAGCAATTAAATTCACGC 59.425 38.462 0.00 0.00 0.00 5.34
982 1577 0.675633 GTGGTTCAGCCTTGTGCATT 59.324 50.000 0.00 0.00 44.83 3.56
983 1578 0.467844 TGTGGTTCAGCCTTGTGCAT 60.468 50.000 0.00 0.00 44.83 3.96
1020 1628 4.325119 TCTTGCTCTACGTACTCTCTTGT 58.675 43.478 0.00 0.00 0.00 3.16
1043 1660 0.035630 ATCTCTCCTTGCCACTGTGC 60.036 55.000 1.29 0.00 0.00 4.57
1360 1980 2.685017 TGCATCTCCGCCACCTCT 60.685 61.111 0.00 0.00 0.00 3.69
1398 2018 1.000955 GGCAAAGAGAACGACTCCTGA 59.999 52.381 9.80 0.00 45.96 3.86
1413 2033 2.354729 CACATCGGGGGAGGCAAA 59.645 61.111 0.00 0.00 0.00 3.68
1426 2046 0.179004 TCCACCGTCTTTTGGCACAT 60.179 50.000 0.00 0.00 39.30 3.21
1457 2077 0.842635 GGGCTCCCTGTTGATCTCAT 59.157 55.000 0.00 0.00 0.00 2.90
1756 2438 1.829222 GGGGATGAACTCCTTGACGTA 59.171 52.381 0.00 0.00 44.28 3.57
1760 2442 2.025037 CCATTGGGGATGAACTCCTTGA 60.025 50.000 0.00 0.00 44.28 3.02
1789 2471 2.268076 GCGGCACCACAACAATCCT 61.268 57.895 0.00 0.00 0.00 3.24
2468 3166 2.586425 CCACAAGGTGTTTCCATCAGT 58.414 47.619 0.00 0.00 39.02 3.41
2686 4122 1.229428 TTACTATACGACCCCGCTCG 58.771 55.000 0.00 0.00 39.95 5.03
2844 4391 4.701171 TGCATCACATCATGTTAAAGAGCA 59.299 37.500 0.00 0.00 0.00 4.26
2847 4394 6.016443 TGTGTTGCATCACATCATGTTAAAGA 60.016 34.615 23.43 0.00 42.36 2.52
2869 4416 3.181467 ACACCAAAAATGGACCACATGTG 60.181 43.478 19.31 19.31 40.44 3.21
2870 4417 3.037549 ACACCAAAAATGGACCACATGT 58.962 40.909 0.00 0.00 40.44 3.21
2871 4418 3.181467 ACACACCAAAAATGGACCACATG 60.181 43.478 0.00 0.00 40.44 3.21
2885 4432 0.877743 CACACACACACACACACCAA 59.122 50.000 0.00 0.00 0.00 3.67
2913 4460 1.268079 GTGAGCAAAGGCAAAGACTCC 59.732 52.381 0.00 0.00 44.61 3.85
2915 4462 0.947244 CGTGAGCAAAGGCAAAGACT 59.053 50.000 0.00 0.00 44.61 3.24
2917 4464 1.172180 CCCGTGAGCAAAGGCAAAGA 61.172 55.000 0.00 0.00 44.61 2.52
2918 4465 1.286880 CCCGTGAGCAAAGGCAAAG 59.713 57.895 0.00 0.00 44.61 2.77
2919 4466 1.040339 AACCCGTGAGCAAAGGCAAA 61.040 50.000 0.00 0.00 44.61 3.68
2922 4469 0.321298 TCTAACCCGTGAGCAAAGGC 60.321 55.000 0.00 0.00 41.61 4.35
2935 4482 3.678548 GTCCACGTGATTGAACTCTAACC 59.321 47.826 19.30 0.00 0.00 2.85
2940 4487 0.438830 GCGTCCACGTGATTGAACTC 59.561 55.000 19.30 0.00 42.22 3.01
2941 4488 0.249699 TGCGTCCACGTGATTGAACT 60.250 50.000 19.30 0.00 42.22 3.01
2942 4489 0.110823 GTGCGTCCACGTGATTGAAC 60.111 55.000 19.30 6.68 42.22 3.18
2943 4490 1.225376 GGTGCGTCCACGTGATTGAA 61.225 55.000 19.30 0.00 43.00 2.69
2945 4492 1.227999 AAGGTGCGTCCACGTGATTG 61.228 55.000 19.30 6.82 43.00 2.67
2946 4493 0.319083 TAAGGTGCGTCCACGTGATT 59.681 50.000 19.30 1.29 43.00 2.57
2997 4545 9.783081 AGCTCAAATTTCATTGGATTTTAAAGT 57.217 25.926 0.00 0.00 0.00 2.66
3002 4550 9.947433 TGAATAGCTCAAATTTCATTGGATTTT 57.053 25.926 0.00 0.00 0.00 1.82
3070 4628 2.158957 GGAATCGACTACCCAAGCATGA 60.159 50.000 0.00 0.00 0.00 3.07
3071 4629 2.213499 GGAATCGACTACCCAAGCATG 58.787 52.381 0.00 0.00 0.00 4.06
3103 4661 1.934220 CTCAAGTAGCGAGCCGTGGA 61.934 60.000 0.00 0.00 0.00 4.02
3106 4664 2.711922 CCCTCAAGTAGCGAGCCGT 61.712 63.158 0.00 0.00 0.00 5.68
3116 4682 0.544595 AGCTAACCGGACCCTCAAGT 60.545 55.000 9.46 0.00 0.00 3.16
3130 4696 1.156736 GGAGCGCAACTGAAAGCTAA 58.843 50.000 11.47 0.00 40.39 3.09
3135 4701 1.600636 CCAGGGAGCGCAACTGAAA 60.601 57.895 22.26 0.00 34.21 2.69
3185 4751 6.696583 CCGATACACACAACCGTAATAACATA 59.303 38.462 0.00 0.00 0.00 2.29
3188 4754 5.101628 TCCGATACACACAACCGTAATAAC 58.898 41.667 0.00 0.00 0.00 1.89
3191 4757 3.429822 CCTCCGATACACACAACCGTAAT 60.430 47.826 0.00 0.00 0.00 1.89
3198 4764 0.172578 CTCGCCTCCGATACACACAA 59.827 55.000 0.00 0.00 43.47 3.33
3200 4766 1.065928 CCTCGCCTCCGATACACAC 59.934 63.158 0.00 0.00 43.47 3.82
3205 4771 2.367586 ATCACCCCTCGCCTCCGATA 62.368 60.000 0.00 0.00 43.47 2.92
3231 4797 1.150827 GGTTCTTGCAAGCAATTGGC 58.849 50.000 21.99 2.80 45.30 4.52
3232 4798 2.825861 AGGTTCTTGCAAGCAATTGG 57.174 45.000 21.99 0.00 35.20 3.16
3233 4799 5.390145 GCAATTAGGTTCTTGCAAGCAATTG 60.390 40.000 21.99 24.48 45.50 2.32
3291 5930 0.321210 CGGGTGTTACCATCAGCACA 60.321 55.000 0.00 0.00 41.02 4.57
3292 5931 1.024579 CCGGGTGTTACCATCAGCAC 61.025 60.000 0.00 0.00 41.02 4.40
3331 5975 5.188555 ACTGTTCCATCTTCTTCATCAGCTA 59.811 40.000 0.00 0.00 0.00 3.32
3402 6046 2.693074 TCATCAGATGCAGCTACCGTAA 59.307 45.455 3.06 0.00 0.00 3.18
3427 6071 1.463674 GAAGTTGAATGGCGGGTCAT 58.536 50.000 0.00 0.00 0.00 3.06
3494 6155 1.855213 GCCACAATTGTCGCTGCTGA 61.855 55.000 19.38 0.00 0.00 4.26
3702 6396 9.042008 GTTTCGGAGTACACATCAATATATTGT 57.958 33.333 21.89 8.47 38.84 2.71
3709 6403 5.407407 AGAGTTTCGGAGTACACATCAAT 57.593 39.130 0.00 0.00 0.00 2.57
3731 6425 7.398618 ACTCAATTGATCTCAGAAGTAGAAGGA 59.601 37.037 8.96 0.00 0.00 3.36


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

AutoCloner maintained by Alex Coulton.