Multiple sequence alignment - TraesCS7D01G490900

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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 TraesCS7D01G490900 chr7D 100.000 3961 0 0 1 3961 600447397 600451357 0.000000e+00 7315.0
1 TraesCS7D01G490900 chr7D 89.099 1321 138 5 1662 2980 599809723 599808407 0.000000e+00 1637.0
2 TraesCS7D01G490900 chr7D 89.002 1273 131 8 1609 2877 599798411 599797144 0.000000e+00 1567.0
3 TraesCS7D01G490900 chr7D 89.482 656 41 16 936 1582 599799115 599798479 0.000000e+00 804.0
4 TraesCS7D01G490900 chr7D 92.195 410 32 0 1117 1526 599810199 599809790 7.380000e-162 580.0
5 TraesCS7D01G490900 chr7D 82.488 217 17 9 867 1077 599810403 599810202 1.890000e-38 171.0
6 TraesCS7D01G490900 chr7A 91.826 2557 127 35 1438 3958 692338127 692340637 0.000000e+00 3489.0
7 TraesCS7D01G490900 chr7A 88.323 1276 141 7 1605 2877 692027318 692026048 0.000000e+00 1524.0
8 TraesCS7D01G490900 chr7A 89.490 647 66 2 2318 2963 692045804 692045159 0.000000e+00 817.0
9 TraesCS7D01G490900 chr7A 88.490 669 45 15 867 1526 692049960 692049315 0.000000e+00 780.0
10 TraesCS7D01G490900 chr7A 86.617 665 85 3 1662 2325 692049248 692048587 0.000000e+00 732.0
11 TraesCS7D01G490900 chr7A 87.649 502 34 16 949 1441 692038852 692038370 3.460000e-155 558.0
12 TraesCS7D01G490900 chr7B 95.806 1979 81 2 428 2405 679788050 679790027 0.000000e+00 3193.0
13 TraesCS7D01G490900 chr7B 89.152 1604 101 44 2401 3961 679793153 679794726 0.000000e+00 1930.0
14 TraesCS7D01G490900 chr7B 88.770 1309 141 5 1662 2968 679672758 679671454 0.000000e+00 1598.0
15 TraesCS7D01G490900 chr7B 88.785 1284 132 11 1598 2877 679634939 679633664 0.000000e+00 1563.0
16 TraesCS7D01G490900 chr7B 91.449 573 37 7 1010 1582 679635553 679634993 0.000000e+00 776.0
17 TraesCS7D01G490900 chr7B 87.316 678 46 17 867 1526 679673480 679672825 0.000000e+00 739.0
18 TraesCS7D01G490900 chr7B 93.451 397 12 1 1 397 679787320 679787702 9.540000e-161 577.0
19 TraesCS7D01G490900 chr6A 78.005 1273 234 36 1723 2964 131229374 131230631 0.000000e+00 758.0
20 TraesCS7D01G490900 chr6A 82.751 458 71 7 1112 1563 129940127 129939672 6.170000e-108 401.0
21 TraesCS7D01G490900 chr6B 83.011 465 71 7 1118 1579 194426044 194425585 7.920000e-112 414.0
22 TraesCS7D01G490900 chr6B 73.790 248 61 4 5 250 658908765 658909010 1.170000e-15 95.3


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 TraesCS7D01G490900 chr7D 600447397 600451357 3960 False 7315.000000 7315 100.000000 1 3961 1 chr7D.!!$F1 3960
1 TraesCS7D01G490900 chr7D 599797144 599799115 1971 True 1185.500000 1567 89.242000 936 2877 2 chr7D.!!$R1 1941
2 TraesCS7D01G490900 chr7D 599808407 599810403 1996 True 796.000000 1637 87.927333 867 2980 3 chr7D.!!$R2 2113
3 TraesCS7D01G490900 chr7A 692338127 692340637 2510 False 3489.000000 3489 91.826000 1438 3958 1 chr7A.!!$F1 2520
4 TraesCS7D01G490900 chr7A 692026048 692027318 1270 True 1524.000000 1524 88.323000 1605 2877 1 chr7A.!!$R1 1272
5 TraesCS7D01G490900 chr7A 692045159 692049960 4801 True 776.333333 817 88.199000 867 2963 3 chr7A.!!$R3 2096
6 TraesCS7D01G490900 chr7B 679787320 679794726 7406 False 1900.000000 3193 92.803000 1 3961 3 chr7B.!!$F1 3960
7 TraesCS7D01G490900 chr7B 679633664 679635553 1889 True 1169.500000 1563 90.117000 1010 2877 2 chr7B.!!$R1 1867
8 TraesCS7D01G490900 chr7B 679671454 679673480 2026 True 1168.500000 1598 88.043000 867 2968 2 chr7B.!!$R2 2101
9 TraesCS7D01G490900 chr6A 131229374 131230631 1257 False 758.000000 758 78.005000 1723 2964 1 chr6A.!!$F1 1241

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
486 804 0.179000 ATCGATGACCCTGAGGCAAC 59.821 55.000 0.00 0.0 36.11 4.17 F
601 919 0.179070 TGCTTACACGCACAGGTCAA 60.179 50.000 0.00 0.0 34.44 3.18 F
763 1081 1.457346 GATCCCCAAGAGCTTGTGTG 58.543 55.000 9.18 0.0 38.85 3.82 F
1005 1340 1.601759 CCATCGATCACCCATGGCC 60.602 63.158 6.09 0.0 30.94 5.36 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1461 1802 0.535797 GGTCCTTGAGGTACCCGAAG 59.464 60.000 8.74 10.72 36.34 3.79 R
1640 2065 0.946221 CCTTGTGCGCTTCTTCTCGT 60.946 55.000 9.73 0.00 0.00 4.18 R
2217 2646 1.432270 GCGATCTTCTTCTTGCCCGG 61.432 60.000 0.00 0.00 0.00 5.73 R
2997 9361 2.108168 TCTGGGAGGACTAATGAACCG 58.892 52.381 0.00 0.00 0.00 4.44 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
34 35 2.093764 TGCCAACACTCAACCCTTTTTG 60.094 45.455 0.00 0.00 0.00 2.44
70 71 1.004918 GAGAAGGGTGTCACGGTGG 60.005 63.158 8.50 0.00 0.00 4.61
88 89 0.535335 GGTTGCTCCACCGATCACTA 59.465 55.000 0.00 0.00 35.97 2.74
161 162 3.329386 CGGCTGATGACAAGAAAGAAGA 58.671 45.455 0.00 0.00 0.00 2.87
195 196 3.790089 ACCTATGGTTTATGGCTAGCC 57.210 47.619 27.71 27.71 27.29 3.93
310 311 1.597027 CCAAAGGAGCGACCAACGT 60.597 57.895 5.84 0.00 44.60 3.99
317 318 1.006102 AGCGACCAACGTTCTCCAG 60.006 57.895 0.00 0.00 44.60 3.86
338 339 2.900106 AAGCTCAGAGGTGGGTGGC 61.900 63.158 1.99 0.00 0.00 5.01
339 340 4.767255 GCTCAGAGGTGGGTGGCG 62.767 72.222 0.00 0.00 0.00 5.69
340 341 4.767255 CTCAGAGGTGGGTGGCGC 62.767 72.222 0.00 0.00 0.00 6.53
379 380 3.981071 TGAACTCTGATGGGGTTGTAG 57.019 47.619 0.00 0.00 0.00 2.74
398 399 1.659794 CCGAGTTTGGTGGCAAAGG 59.340 57.895 0.00 0.00 0.00 3.11
399 400 1.659794 CGAGTTTGGTGGCAAAGGG 59.340 57.895 0.00 0.00 0.00 3.95
400 401 1.805428 CGAGTTTGGTGGCAAAGGGG 61.805 60.000 0.00 0.00 0.00 4.79
401 402 1.459348 AGTTTGGTGGCAAAGGGGG 60.459 57.895 0.00 0.00 0.00 5.40
418 419 3.873812 GGGGGTGCGGTCCTATGG 61.874 72.222 0.00 0.00 0.00 2.74
419 420 3.873812 GGGGTGCGGTCCTATGGG 61.874 72.222 0.00 0.00 0.00 4.00
420 421 2.766651 GGGTGCGGTCCTATGGGA 60.767 66.667 0.00 0.00 39.70 4.37
421 422 2.147387 GGGTGCGGTCCTATGGGAT 61.147 63.158 0.00 0.00 44.33 3.85
422 423 1.371558 GGTGCGGTCCTATGGGATC 59.628 63.158 0.00 0.00 44.33 3.36
423 424 1.407656 GGTGCGGTCCTATGGGATCA 61.408 60.000 9.31 1.69 42.73 2.92
424 425 0.249911 GTGCGGTCCTATGGGATCAC 60.250 60.000 9.31 10.10 42.73 3.06
425 426 0.689412 TGCGGTCCTATGGGATCACA 60.689 55.000 9.31 0.00 42.73 3.58
426 427 0.468226 GCGGTCCTATGGGATCACAA 59.532 55.000 9.31 0.00 42.73 3.33
484 802 2.015456 ATATCGATGACCCTGAGGCA 57.985 50.000 8.54 0.00 36.11 4.75
486 804 0.179000 ATCGATGACCCTGAGGCAAC 59.821 55.000 0.00 0.00 36.11 4.17
562 880 2.211250 AAGTGCATGTTCAGCTGGAT 57.789 45.000 15.13 0.68 0.00 3.41
601 919 0.179070 TGCTTACACGCACAGGTCAA 60.179 50.000 0.00 0.00 34.44 3.18
661 979 2.820197 AGAAGCGATTTCAAGGTTTCCC 59.180 45.455 0.00 0.00 38.31 3.97
710 1028 4.472286 GCGCACAAATTAGCTAAAGTTGA 58.528 39.130 27.37 2.22 44.07 3.18
717 1035 7.750903 CACAAATTAGCTAAAGTTGAAGTAGGC 59.249 37.037 27.37 0.00 44.07 3.93
763 1081 1.457346 GATCCCCAAGAGCTTGTGTG 58.543 55.000 9.18 0.00 38.85 3.82
776 1094 3.440173 AGCTTGTGTGGGATGTAATTTCG 59.560 43.478 0.00 0.00 0.00 3.46
811 1129 5.889425 CGAGCTACGTTTCTTAAATAAAGCG 59.111 40.000 0.00 0.00 34.71 4.68
1005 1340 1.601759 CCATCGATCACCCATGGCC 60.602 63.158 6.09 0.00 30.94 5.36
1656 2081 1.664649 CCACGAGAAGAAGCGCACA 60.665 57.895 11.47 0.00 0.00 4.57
1904 2333 2.671619 AAATGGTGCCCGTCGGTG 60.672 61.111 11.06 2.85 0.00 4.94
2217 2646 3.332493 TACCTCGCCGACGTCAAGC 62.332 63.158 17.16 16.32 41.18 4.01
2486 8850 1.737735 CGTGATCACCTTCAGCGCA 60.738 57.895 20.03 0.00 0.00 6.09
2783 9147 1.133792 CAGGTGGTGTTCTGGAACCTT 60.134 52.381 10.44 0.00 39.24 3.50
2862 9226 1.396301 GCTTCTCCAAGAACATGCTCG 59.604 52.381 0.00 0.00 29.89 5.03
2997 9361 2.595881 GCGTCGTGTGTGTTAAGTGTTC 60.596 50.000 0.00 0.00 0.00 3.18
3009 9373 6.201425 TGTGTTAAGTGTTCGGTTCATTAGTC 59.799 38.462 0.00 0.00 0.00 2.59
3012 9376 4.189639 AGTGTTCGGTTCATTAGTCCTC 57.810 45.455 0.00 0.00 0.00 3.71
3013 9377 3.056035 AGTGTTCGGTTCATTAGTCCTCC 60.056 47.826 0.00 0.00 0.00 4.30
3014 9378 2.235402 TGTTCGGTTCATTAGTCCTCCC 59.765 50.000 0.00 0.00 0.00 4.30
3015 9379 2.235402 GTTCGGTTCATTAGTCCTCCCA 59.765 50.000 0.00 0.00 0.00 4.37
3016 9380 2.108168 TCGGTTCATTAGTCCTCCCAG 58.892 52.381 0.00 0.00 0.00 4.45
3017 9381 2.108168 CGGTTCATTAGTCCTCCCAGA 58.892 52.381 0.00 0.00 0.00 3.86
3072 9436 6.241207 TGATCAGAATTCGTTCAAACTTCC 57.759 37.500 0.00 0.00 0.00 3.46
3074 9438 5.418310 TCAGAATTCGTTCAAACTTCCAC 57.582 39.130 0.00 0.00 0.00 4.02
3075 9439 5.123227 TCAGAATTCGTTCAAACTTCCACT 58.877 37.500 0.00 0.00 0.00 4.00
3077 9441 4.275936 AGAATTCGTTCAAACTTCCACTGG 59.724 41.667 0.00 0.00 0.00 4.00
3079 9443 1.021202 CGTTCAAACTTCCACTGGCA 58.979 50.000 0.00 0.00 0.00 4.92
3082 9446 0.961019 TCAAACTTCCACTGGCATGC 59.039 50.000 9.90 9.90 0.00 4.06
3094 9458 3.753272 CACTGGCATGCTTGTAGTAAAGT 59.247 43.478 18.92 4.94 0.00 2.66
3096 9460 4.455877 ACTGGCATGCTTGTAGTAAAGTTC 59.544 41.667 18.92 0.00 0.00 3.01
3097 9461 4.393834 TGGCATGCTTGTAGTAAAGTTCA 58.606 39.130 18.92 0.00 0.00 3.18
3099 9463 5.300539 TGGCATGCTTGTAGTAAAGTTCAAA 59.699 36.000 18.92 0.00 0.00 2.69
3101 9465 6.438763 GCATGCTTGTAGTAAAGTTCAAACT 58.561 36.000 11.37 0.00 42.04 2.66
3102 9466 7.308348 GGCATGCTTGTAGTAAAGTTCAAACTA 60.308 37.037 18.92 0.00 38.57 2.24
3103 9467 8.237267 GCATGCTTGTAGTAAAGTTCAAACTAT 58.763 33.333 11.37 0.00 38.57 2.12
3120 9484 9.764363 TTCAAACTATATGTACCATCAGACATC 57.236 33.333 0.00 0.00 37.47 3.06
3121 9485 8.367911 TCAAACTATATGTACCATCAGACATCC 58.632 37.037 0.00 0.00 37.47 3.51
3122 9486 6.859112 ACTATATGTACCATCAGACATCCC 57.141 41.667 0.00 0.00 37.47 3.85
3123 9487 6.322931 ACTATATGTACCATCAGACATCCCA 58.677 40.000 0.00 0.00 37.47 4.37
3124 9488 6.962311 ACTATATGTACCATCAGACATCCCAT 59.038 38.462 0.00 0.00 37.47 4.00
3125 9489 3.843893 TGTACCATCAGACATCCCATG 57.156 47.619 0.00 0.00 0.00 3.66
3128 9492 5.154418 TGTACCATCAGACATCCCATGATA 58.846 41.667 0.00 0.00 32.51 2.15
3129 9493 5.606329 TGTACCATCAGACATCCCATGATAA 59.394 40.000 0.00 0.00 32.51 1.75
3131 9495 6.017211 ACCATCAGACATCCCATGATAAAA 57.983 37.500 0.00 0.00 32.51 1.52
3132 9496 5.829924 ACCATCAGACATCCCATGATAAAAC 59.170 40.000 0.00 0.00 32.51 2.43
3133 9497 5.829391 CCATCAGACATCCCATGATAAAACA 59.171 40.000 0.00 0.00 32.51 2.83
3135 9499 7.147863 CCATCAGACATCCCATGATAAAACAAA 60.148 37.037 0.00 0.00 32.51 2.83
3136 9500 7.773489 TCAGACATCCCATGATAAAACAAAA 57.227 32.000 0.00 0.00 0.00 2.44
3138 9502 7.669304 TCAGACATCCCATGATAAAACAAAAGA 59.331 33.333 0.00 0.00 0.00 2.52
3139 9503 8.472413 CAGACATCCCATGATAAAACAAAAGAT 58.528 33.333 0.00 0.00 0.00 2.40
3140 9504 8.689972 AGACATCCCATGATAAAACAAAAGATC 58.310 33.333 0.00 0.00 0.00 2.75
3141 9505 8.365060 ACATCCCATGATAAAACAAAAGATCA 57.635 30.769 0.00 0.00 33.09 2.92
3142 9506 8.472413 ACATCCCATGATAAAACAAAAGATCAG 58.528 33.333 0.00 0.00 32.12 2.90
3143 9507 8.472413 CATCCCATGATAAAACAAAAGATCAGT 58.528 33.333 0.00 0.00 32.12 3.41
3144 9508 7.829725 TCCCATGATAAAACAAAAGATCAGTG 58.170 34.615 0.00 0.00 32.12 3.66
3146 9510 8.306038 CCCATGATAAAACAAAAGATCAGTGAA 58.694 33.333 0.00 0.00 32.12 3.18
3147 9511 9.695526 CCATGATAAAACAAAAGATCAGTGAAA 57.304 29.630 0.00 0.00 32.12 2.69
3163 9554 9.387123 GATCAGTGAAAATAGTCAAGTCAAAAC 57.613 33.333 0.00 0.00 0.00 2.43
3178 9569 8.735315 TCAAGTCAAAACTTTTCTCATGTACAA 58.265 29.630 0.00 0.00 43.28 2.41
3243 9635 0.988832 AGGTTTCTATTCGGTGCCCA 59.011 50.000 0.00 0.00 0.00 5.36
3244 9636 1.353022 AGGTTTCTATTCGGTGCCCAA 59.647 47.619 0.00 0.00 0.00 4.12
3263 9655 8.413229 GTGCCCAAATTCTACACATTATTACAT 58.587 33.333 0.00 0.00 0.00 2.29
3456 9859 4.324254 CCTTCTTGGCCTGAGTAATGGTAA 60.324 45.833 3.32 0.00 0.00 2.85
3485 9888 3.999663 CCTGAACTGAACTTCACATCCTC 59.000 47.826 0.00 0.00 0.00 3.71
3553 9957 0.173481 TCGTTCAGATCAGGCTTCGG 59.827 55.000 0.00 0.00 0.00 4.30
3646 10050 2.512692 TCTATTGCTGGTGTGCCAAT 57.487 45.000 0.00 0.00 45.51 3.16
3801 10207 0.323302 TTCAGCTATCCAACCACGCA 59.677 50.000 0.00 0.00 0.00 5.24
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
8 9 0.598065 GGTTGAGTGTTGGCATGTCC 59.402 55.000 0.00 0.00 0.00 4.02
39 40 2.048222 TTCTCCGAGCGCAACAGG 60.048 61.111 11.47 7.19 0.00 4.00
70 71 2.205074 CATAGTGATCGGTGGAGCAAC 58.795 52.381 0.00 0.00 40.82 4.17
88 89 4.759205 GGCGCCCTGGGTTTCCAT 62.759 66.667 18.11 0.00 43.11 3.41
114 115 1.110442 CAAACCACTCCAGCAACCAA 58.890 50.000 0.00 0.00 0.00 3.67
146 147 7.122353 CCTGGATCATTTCTTCTTTCTTGTCAT 59.878 37.037 0.00 0.00 0.00 3.06
161 162 3.983410 ACCATAGGTAGCCTGGATCATTT 59.017 43.478 15.86 0.00 34.61 2.32
195 196 2.481854 CCATCTCTCGCCTCATTTCTG 58.518 52.381 0.00 0.00 0.00 3.02
310 311 1.898472 CCTCTGAGCTTGTCTGGAGAA 59.102 52.381 0.00 0.00 31.61 2.87
317 318 0.321122 CACCCACCTCTGAGCTTGTC 60.321 60.000 0.00 0.00 0.00 3.18
338 339 2.260088 TTTAATCCACCCCTCCGGCG 62.260 60.000 0.00 0.00 33.26 6.46
339 340 0.185175 ATTTAATCCACCCCTCCGGC 59.815 55.000 0.00 0.00 33.26 6.13
340 341 2.092103 TCAATTTAATCCACCCCTCCGG 60.092 50.000 0.00 0.00 37.81 5.14
341 342 3.290948 TCAATTTAATCCACCCCTCCG 57.709 47.619 0.00 0.00 0.00 4.63
342 343 4.610333 AGTTCAATTTAATCCACCCCTCC 58.390 43.478 0.00 0.00 0.00 4.30
343 344 5.358160 CAGAGTTCAATTTAATCCACCCCTC 59.642 44.000 0.00 0.00 0.00 4.30
344 345 5.015178 TCAGAGTTCAATTTAATCCACCCCT 59.985 40.000 0.00 0.00 0.00 4.79
345 346 5.261216 TCAGAGTTCAATTTAATCCACCCC 58.739 41.667 0.00 0.00 0.00 4.95
346 347 6.183360 CCATCAGAGTTCAATTTAATCCACCC 60.183 42.308 0.00 0.00 0.00 4.61
347 348 6.183360 CCCATCAGAGTTCAATTTAATCCACC 60.183 42.308 0.00 0.00 0.00 4.61
348 349 6.183360 CCCCATCAGAGTTCAATTTAATCCAC 60.183 42.308 0.00 0.00 0.00 4.02
349 350 5.893255 CCCCATCAGAGTTCAATTTAATCCA 59.107 40.000 0.00 0.00 0.00 3.41
350 351 5.893824 ACCCCATCAGAGTTCAATTTAATCC 59.106 40.000 0.00 0.00 0.00 3.01
351 352 7.093771 ACAACCCCATCAGAGTTCAATTTAATC 60.094 37.037 0.00 0.00 0.00 1.75
379 380 1.007387 CTTTGCCACCAAACTCGGC 60.007 57.895 0.00 0.00 46.43 5.54
401 402 3.873812 CCATAGGACCGCACCCCC 61.874 72.222 0.00 0.00 0.00 5.40
402 403 3.873812 CCCATAGGACCGCACCCC 61.874 72.222 0.00 0.00 33.47 4.95
403 404 2.766651 TCCCATAGGACCGCACCC 60.767 66.667 0.00 0.00 37.19 4.61
405 406 2.913631 TGTGATCCCATAGGACCGCAC 61.914 57.143 0.00 0.00 41.60 5.34
406 407 0.689412 TGTGATCCCATAGGACCGCA 60.689 55.000 0.00 0.00 44.47 5.69
412 413 2.787994 GCTCCATTGTGATCCCATAGG 58.212 52.381 0.00 0.00 0.00 2.57
413 414 2.224378 ACGCTCCATTGTGATCCCATAG 60.224 50.000 0.00 0.00 0.00 2.23
414 415 1.768275 ACGCTCCATTGTGATCCCATA 59.232 47.619 0.00 0.00 0.00 2.74
415 416 0.548031 ACGCTCCATTGTGATCCCAT 59.452 50.000 0.00 0.00 0.00 4.00
416 417 0.327924 AACGCTCCATTGTGATCCCA 59.672 50.000 0.00 0.00 0.00 4.37
417 418 1.017387 GAACGCTCCATTGTGATCCC 58.983 55.000 0.00 0.00 0.00 3.85
418 419 1.017387 GGAACGCTCCATTGTGATCC 58.983 55.000 0.00 0.00 41.96 3.36
419 420 2.029838 AGGAACGCTCCATTGTGATC 57.970 50.000 7.76 0.00 45.24 2.92
420 421 2.086869 CAAGGAACGCTCCATTGTGAT 58.913 47.619 7.76 0.00 45.24 3.06
421 422 1.522668 CAAGGAACGCTCCATTGTGA 58.477 50.000 7.76 0.00 45.24 3.58
422 423 0.109597 GCAAGGAACGCTCCATTGTG 60.110 55.000 7.76 0.94 45.24 3.33
423 424 1.577328 CGCAAGGAACGCTCCATTGT 61.577 55.000 7.76 0.00 45.24 2.71
424 425 1.135315 CGCAAGGAACGCTCCATTG 59.865 57.895 7.76 9.62 45.24 2.82
425 426 1.003839 TCGCAAGGAACGCTCCATT 60.004 52.632 7.76 0.00 45.24 3.16
426 427 1.448540 CTCGCAAGGAACGCTCCAT 60.449 57.895 7.76 0.00 45.24 3.41
484 802 1.021390 CGCAAGCCAGAATCTCCGTT 61.021 55.000 0.00 0.00 0.00 4.44
486 804 2.176273 CCGCAAGCCAGAATCTCCG 61.176 63.158 0.00 0.00 0.00 4.63
541 859 2.309613 TCCAGCTGAACATGCACTTTT 58.690 42.857 17.39 0.00 0.00 2.27
543 861 2.211250 ATCCAGCTGAACATGCACTT 57.789 45.000 17.39 0.00 0.00 3.16
562 880 1.340088 TCTGTACCACGGCCAAACTA 58.660 50.000 2.24 0.00 0.00 2.24
601 919 2.328319 GATCTCTCTGATCCAAGGGCT 58.672 52.381 0.00 0.00 44.34 5.19
680 998 0.242286 TAATTTGTGCGCGGCAACAT 59.758 45.000 15.25 10.33 41.47 2.71
686 1004 2.159572 ACTTTAGCTAATTTGTGCGCGG 60.160 45.455 8.83 0.00 0.00 6.46
710 1028 4.929808 CACTACAAAGTTCATCGCCTACTT 59.070 41.667 0.00 0.00 31.97 2.24
717 1035 4.024048 AGCCAAACACTACAAAGTTCATCG 60.024 41.667 0.00 0.00 31.97 3.84
751 1069 3.788227 TTACATCCCACACAAGCTCTT 57.212 42.857 0.00 0.00 0.00 2.85
756 1074 5.621197 TTCGAAATTACATCCCACACAAG 57.379 39.130 0.00 0.00 0.00 3.16
757 1075 5.707764 TCATTCGAAATTACATCCCACACAA 59.292 36.000 0.00 0.00 0.00 3.33
763 1081 6.438763 GGAATGTCATTCGAAATTACATCCC 58.561 40.000 17.37 13.90 40.17 3.85
776 1094 2.810650 ACGTAGCTCGGAATGTCATTC 58.189 47.619 16.00 16.00 44.69 2.67
811 1129 3.439895 TTTTCCAGGTTTAACGTTGCC 57.560 42.857 11.99 10.44 0.00 4.52
843 1161 5.695818 TCGTTTTGCTAATTAAACCTGCTC 58.304 37.500 0.00 0.00 32.05 4.26
846 1164 7.100829 GGTTTCGTTTTGCTAATTAAACCTG 57.899 36.000 17.17 0.00 40.62 4.00
1461 1802 0.535797 GGTCCTTGAGGTACCCGAAG 59.464 60.000 8.74 10.72 36.34 3.79
1564 1911 2.423446 GCGGGCGATGAATCCTCT 59.577 61.111 0.00 0.00 0.00 3.69
1640 2065 0.946221 CCTTGTGCGCTTCTTCTCGT 60.946 55.000 9.73 0.00 0.00 4.18
1865 2291 1.522580 GGCCAGCGAGAGGTTGATC 60.523 63.158 0.00 0.00 41.81 2.92
1904 2333 2.202623 CGGTCGTAGCAGCTGTCC 60.203 66.667 16.64 7.68 0.00 4.02
2217 2646 1.432270 GCGATCTTCTTCTTGCCCGG 61.432 60.000 0.00 0.00 0.00 5.73
2997 9361 2.108168 TCTGGGAGGACTAATGAACCG 58.892 52.381 0.00 0.00 0.00 4.44
3026 9390 3.829886 TTATTTTTGAGCGCCTCACTG 57.170 42.857 2.29 0.00 40.46 3.66
3029 9393 5.384063 TCAAATTATTTTTGAGCGCCTCA 57.616 34.783 2.29 4.38 38.87 3.86
3032 9396 6.035843 TCTGATCAAATTATTTTTGAGCGCC 58.964 36.000 2.29 0.00 44.90 6.53
3033 9397 7.510428 TTCTGATCAAATTATTTTTGAGCGC 57.490 32.000 0.00 0.00 44.90 5.92
3072 9436 3.753272 ACTTTACTACAAGCATGCCAGTG 59.247 43.478 15.66 12.91 0.00 3.66
3074 9438 4.455533 TGAACTTTACTACAAGCATGCCAG 59.544 41.667 15.66 9.93 0.00 4.85
3075 9439 4.393834 TGAACTTTACTACAAGCATGCCA 58.606 39.130 15.66 0.00 0.00 4.92
3077 9441 6.438763 AGTTTGAACTTTACTACAAGCATGC 58.561 36.000 10.51 10.51 35.21 4.06
3101 9465 7.624879 ATCATGGGATGTCTGATGGTACATATA 59.375 37.037 0.00 0.00 36.48 0.86
3102 9466 6.446110 ATCATGGGATGTCTGATGGTACATAT 59.554 38.462 0.00 0.00 36.48 1.78
3103 9467 5.786975 ATCATGGGATGTCTGATGGTACATA 59.213 40.000 0.00 0.00 36.48 2.29
3105 9469 3.975982 ATCATGGGATGTCTGATGGTACA 59.024 43.478 0.00 0.00 35.55 2.90
3106 9470 4.630644 ATCATGGGATGTCTGATGGTAC 57.369 45.455 0.00 0.00 30.86 3.34
3107 9471 6.762077 TTTATCATGGGATGTCTGATGGTA 57.238 37.500 0.00 0.00 34.89 3.25
3108 9472 5.651612 TTTATCATGGGATGTCTGATGGT 57.348 39.130 0.00 0.00 34.89 3.55
3110 9474 6.947644 TGTTTTATCATGGGATGTCTGATG 57.052 37.500 0.00 0.00 34.89 3.07
3112 9476 7.669304 TCTTTTGTTTTATCATGGGATGTCTGA 59.331 33.333 0.00 0.00 34.89 3.27
3113 9477 7.829725 TCTTTTGTTTTATCATGGGATGTCTG 58.170 34.615 0.00 0.00 34.89 3.51
3114 9478 8.599624 ATCTTTTGTTTTATCATGGGATGTCT 57.400 30.769 0.00 0.00 34.89 3.41
3115 9479 8.469200 TGATCTTTTGTTTTATCATGGGATGTC 58.531 33.333 0.00 0.00 34.89 3.06
3120 9484 7.829725 TCACTGATCTTTTGTTTTATCATGGG 58.170 34.615 0.00 0.00 0.00 4.00
3121 9485 9.695526 TTTCACTGATCTTTTGTTTTATCATGG 57.304 29.630 0.00 0.00 0.00 3.66
3131 9495 9.125026 ACTTGACTATTTTCACTGATCTTTTGT 57.875 29.630 0.00 0.00 0.00 2.83
3132 9496 9.604626 GACTTGACTATTTTCACTGATCTTTTG 57.395 33.333 0.00 0.00 0.00 2.44
3133 9497 9.342308 TGACTTGACTATTTTCACTGATCTTTT 57.658 29.630 0.00 0.00 0.00 2.27
3135 9499 8.908786 TTGACTTGACTATTTTCACTGATCTT 57.091 30.769 0.00 0.00 0.00 2.40
3136 9500 8.908786 TTTGACTTGACTATTTTCACTGATCT 57.091 30.769 0.00 0.00 0.00 2.75
3138 9502 9.125026 AGTTTTGACTTGACTATTTTCACTGAT 57.875 29.630 0.00 0.00 0.00 2.90
3139 9503 8.506168 AGTTTTGACTTGACTATTTTCACTGA 57.494 30.769 0.00 0.00 0.00 3.41
3140 9504 9.573133 AAAGTTTTGACTTGACTATTTTCACTG 57.427 29.630 0.00 0.00 0.00 3.66
3147 9511 9.956720 CATGAGAAAAGTTTTGACTTGACTATT 57.043 29.630 5.36 0.00 0.00 1.73
3150 9514 7.396540 ACATGAGAAAAGTTTTGACTTGACT 57.603 32.000 5.36 0.00 0.00 3.41
3151 9515 8.181573 TGTACATGAGAAAAGTTTTGACTTGAC 58.818 33.333 5.36 8.34 0.00 3.18
3152 9516 8.275015 TGTACATGAGAAAAGTTTTGACTTGA 57.725 30.769 5.36 0.00 0.00 3.02
3153 9517 8.909708 TTGTACATGAGAAAAGTTTTGACTTG 57.090 30.769 5.36 9.76 0.00 3.16
3186 9577 9.668497 ATGAGATTCATATAGATGTTGACATGG 57.332 33.333 0.57 0.00 34.88 3.66
3205 9597 9.965902 AGAAACCTGAAAAGTGTATATGAGATT 57.034 29.630 0.00 0.00 0.00 2.40
3223 9615 1.379527 GGGCACCGAATAGAAACCTG 58.620 55.000 0.00 0.00 40.86 4.00
3224 9616 3.875865 GGGCACCGAATAGAAACCT 57.124 52.632 0.00 0.00 40.86 3.50
3263 9655 3.923782 ATGCGCTGCACCATCACCA 62.924 57.895 9.73 0.00 43.04 4.17
3437 9840 3.279434 GGTTACCATTACTCAGGCCAAG 58.721 50.000 5.01 4.23 0.00 3.61
3438 9841 2.645297 TGGTTACCATTACTCAGGCCAA 59.355 45.455 5.01 0.00 0.00 4.52
3439 9842 2.238646 CTGGTTACCATTACTCAGGCCA 59.761 50.000 3.88 0.00 30.82 5.36
3456 9859 1.598130 GTTCAGTTCAGGCGCTGGT 60.598 57.895 7.64 0.00 33.81 4.00
3485 9888 1.990799 TGGTTGACGCAAGATCTACG 58.009 50.000 14.61 14.61 43.62 3.51
3553 9957 1.202452 GGAGCATGCCAAATGGTTAGC 60.202 52.381 15.66 3.05 37.57 3.09
3646 10050 1.176527 GCCATTGCAACTCAGCCTTA 58.823 50.000 0.00 0.00 37.47 2.69
3736 10140 2.100797 CATGATGGTTGTGCGGCG 59.899 61.111 0.51 0.51 0.00 6.46
3751 10155 9.797556 CTGATCATTATTCACAAATCACAACAT 57.202 29.630 0.00 0.00 0.00 2.71
3801 10207 3.876274 ATGTAACATGTCACGAGCTCT 57.124 42.857 12.85 0.00 0.00 4.09


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

AutoCloner maintained by Alex Coulton.