Multiple sequence alignment - TraesCS2B01G370400

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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 TraesCS2B01G370400 chr2B 100.000 6025 0 0 1 6025 528201422 528207446 0.000000e+00 11127
1 TraesCS2B01G370400 chr2A 91.290 6131 338 87 1 6025 592851110 592857150 0.000000e+00 8183
2 TraesCS2B01G370400 chr2D 92.385 5266 256 53 1 5188 448207267 448212465 0.000000e+00 7369
3 TraesCS2B01G370400 chr2D 96.081 791 30 1 5236 6025 448212468 448213258 0.000000e+00 1288
4 TraesCS2B01G370400 chr2D 80.128 156 22 9 3856 4004 448218979 448219132 2.300000e-19 108
5 TraesCS2B01G370400 chrUn 94.484 417 21 2 4407 4822 477174446 477174031 5.090000e-180 641


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 TraesCS2B01G370400 chr2B 528201422 528207446 6024 False 11127.0 11127 100.000 1 6025 1 chr2B.!!$F1 6024
1 TraesCS2B01G370400 chr2A 592851110 592857150 6040 False 8183.0 8183 91.290 1 6025 1 chr2A.!!$F1 6024
2 TraesCS2B01G370400 chr2D 448207267 448213258 5991 False 4328.5 7369 94.233 1 6025 2 chr2D.!!$F2 6024

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
582 603 0.107654 CTTGGGGAGTAAGCTTCCGG 60.108 60.0 0.00 0.00 41.54 5.14 F
585 606 0.107800 GGGGAGTAAGCTTCCGGAAC 60.108 60.0 14.35 10.64 41.54 3.62 F
586 607 0.107800 GGGAGTAAGCTTCCGGAACC 60.108 60.0 14.35 11.06 29.10 3.62 F
1761 1822 0.603569 ACGTTCGAGGATCACTTGCT 59.396 50.0 0.00 0.00 33.17 3.91 F
2419 2516 0.524862 CAGCAAATCAGAAAGCCGCT 59.475 50.0 0.00 0.00 0.00 5.52 F
3655 3755 0.035439 AATCGGTGTGCTAACCTGGG 60.035 55.0 0.00 0.00 38.14 4.45 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1737 1798 0.167470 GTGATCCTCGAACGTCGTGA 59.833 55.0 0.00 0.00 41.35 4.35 R
1839 1900 0.961019 GGTTGTCCATTTCTGCAGCA 59.039 50.0 9.47 0.00 0.00 4.41 R
1852 1913 1.244019 AAGGCATGGCGAAGGTTGTC 61.244 55.0 14.30 0.00 0.00 3.18 R
2731 2828 0.249398 GGTGTGCGAGTGGGTAATCT 59.751 55.0 0.00 0.00 0.00 2.40 R
3828 3928 0.471022 TGACACACTAGGGTGCAGGA 60.471 55.0 25.20 3.46 46.57 3.86 R
5227 5327 0.320421 ACCTCCATGACACCGTTTCG 60.320 55.0 0.00 0.00 0.00 3.46 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
257 277 2.491621 CTCGTCAGATCTGCGCCA 59.508 61.111 25.14 14.04 32.85 5.69
289 309 1.214589 CCGTCAATCCGTCGTCCTT 59.785 57.895 0.00 0.00 0.00 3.36
295 315 0.672342 AATCCGTCGTCCTTATCCCG 59.328 55.000 0.00 0.00 0.00 5.14
296 316 1.803366 ATCCGTCGTCCTTATCCCGC 61.803 60.000 0.00 0.00 0.00 6.13
346 366 2.926242 TTTCTTCCGTCCGGGGCT 60.926 61.111 0.00 0.00 36.01 5.19
498 519 2.163211 GCTTGAATTGGAGGTTCTGAGC 59.837 50.000 0.00 0.00 32.63 4.26
501 522 4.478206 TGAATTGGAGGTTCTGAGCTAG 57.522 45.455 0.00 0.00 32.79 3.42
570 591 1.602237 GGCGACTGATTCTTGGGGA 59.398 57.895 0.00 0.00 0.00 4.81
571 592 0.462759 GGCGACTGATTCTTGGGGAG 60.463 60.000 0.00 0.00 0.00 4.30
572 593 0.250513 GCGACTGATTCTTGGGGAGT 59.749 55.000 0.00 0.00 0.00 3.85
573 594 1.480954 GCGACTGATTCTTGGGGAGTA 59.519 52.381 0.00 0.00 0.00 2.59
574 595 2.093658 GCGACTGATTCTTGGGGAGTAA 60.094 50.000 0.00 0.00 0.00 2.24
575 596 3.786635 CGACTGATTCTTGGGGAGTAAG 58.213 50.000 0.00 0.00 0.00 2.34
577 598 3.185455 ACTGATTCTTGGGGAGTAAGCT 58.815 45.455 0.00 0.00 0.00 3.74
578 599 3.589288 ACTGATTCTTGGGGAGTAAGCTT 59.411 43.478 3.48 3.48 0.00 3.74
579 600 4.195416 CTGATTCTTGGGGAGTAAGCTTC 58.805 47.826 0.00 0.00 0.00 3.86
580 601 3.054361 TGATTCTTGGGGAGTAAGCTTCC 60.054 47.826 0.00 0.00 39.80 3.46
581 602 0.902531 TCTTGGGGAGTAAGCTTCCG 59.097 55.000 0.00 0.00 41.54 4.30
582 603 0.107654 CTTGGGGAGTAAGCTTCCGG 60.108 60.000 0.00 0.00 41.54 5.14
583 604 0.545787 TTGGGGAGTAAGCTTCCGGA 60.546 55.000 0.00 0.00 41.54 5.14
584 605 0.545787 TGGGGAGTAAGCTTCCGGAA 60.546 55.000 17.73 17.73 41.54 4.30
585 606 0.107800 GGGGAGTAAGCTTCCGGAAC 60.108 60.000 14.35 10.64 41.54 3.62
586 607 0.107800 GGGAGTAAGCTTCCGGAACC 60.108 60.000 14.35 11.06 29.10 3.62
601 625 3.568538 CGGAACCTGCTTCTTTTGATTG 58.431 45.455 0.00 0.00 0.00 2.67
605 629 2.967887 ACCTGCTTCTTTTGATTGCCTT 59.032 40.909 0.00 0.00 0.00 4.35
608 632 2.622942 TGCTTCTTTTGATTGCCTTCGT 59.377 40.909 0.00 0.00 0.00 3.85
614 638 1.603456 TTGATTGCCTTCGTGCTCAA 58.397 45.000 0.00 0.00 0.00 3.02
635 659 8.125448 GCTCAATTTCAGATTATAGAGCGTTTT 58.875 33.333 0.00 0.00 38.00 2.43
643 667 7.439356 TCAGATTATAGAGCGTTTTTGGATGAG 59.561 37.037 0.00 0.00 0.00 2.90
655 679 6.700081 CGTTTTTGGATGAGACGGATAGATTA 59.300 38.462 0.00 0.00 0.00 1.75
681 720 2.869636 GCTTCTGTCTTGTGTGCTAGCT 60.870 50.000 17.23 0.00 0.00 3.32
682 721 3.397482 CTTCTGTCTTGTGTGCTAGCTT 58.603 45.455 17.23 0.00 0.00 3.74
687 727 3.181466 TGTCTTGTGTGCTAGCTTCTTCA 60.181 43.478 17.23 9.69 0.00 3.02
692 732 1.550524 TGTGCTAGCTTCTTCATCCGT 59.449 47.619 17.23 0.00 0.00 4.69
800 854 4.686191 ACTGCTGATCTAGGATTCTTGG 57.314 45.455 0.00 0.00 0.00 3.61
801 855 4.293494 ACTGCTGATCTAGGATTCTTGGA 58.707 43.478 0.00 0.00 0.00 3.53
802 856 4.344679 ACTGCTGATCTAGGATTCTTGGAG 59.655 45.833 0.00 0.00 0.00 3.86
803 857 4.293494 TGCTGATCTAGGATTCTTGGAGT 58.707 43.478 0.00 0.00 0.00 3.85
804 858 4.100653 TGCTGATCTAGGATTCTTGGAGTG 59.899 45.833 0.00 0.00 0.00 3.51
805 859 4.100808 GCTGATCTAGGATTCTTGGAGTGT 59.899 45.833 0.00 0.00 0.00 3.55
806 860 5.599732 CTGATCTAGGATTCTTGGAGTGTG 58.400 45.833 0.00 0.00 0.00 3.82
807 861 3.895232 TCTAGGATTCTTGGAGTGTGC 57.105 47.619 0.00 0.00 0.00 4.57
808 862 3.445008 TCTAGGATTCTTGGAGTGTGCT 58.555 45.455 0.00 0.00 0.00 4.40
809 863 3.840666 TCTAGGATTCTTGGAGTGTGCTT 59.159 43.478 0.00 0.00 0.00 3.91
810 864 5.023452 TCTAGGATTCTTGGAGTGTGCTTA 58.977 41.667 0.00 0.00 0.00 3.09
851 905 2.235650 TCTCCTGTTCAGATTCTGCCTG 59.764 50.000 8.89 6.07 0.00 4.85
878 932 1.526887 CAGTCCTTGTGTTGCACTACG 59.473 52.381 0.00 0.00 35.11 3.51
888 942 3.987868 GTGTTGCACTACGAAGATTCTGA 59.012 43.478 0.00 0.00 0.00 3.27
1012 1073 1.766494 CAAAGCCATGGATGTGCCTA 58.234 50.000 18.40 0.00 37.63 3.93
1032 1093 2.617274 GCCTTCACAGTCCAACCGC 61.617 63.158 0.00 0.00 0.00 5.68
1086 1147 3.616317 CGGATGATCCATATGGCGTTACA 60.616 47.826 17.58 11.68 35.91 2.41
1134 1195 4.399395 CTCTGCGGCAGCCCTTCA 62.399 66.667 24.78 5.88 44.33 3.02
1302 1363 7.831691 TCAAAAGGTTGATTTGGTATCTTCA 57.168 32.000 0.00 0.00 38.88 3.02
1374 1435 1.489649 CTTGGCTCAGATGGTGATCCT 59.510 52.381 0.00 0.00 41.45 3.24
1608 1669 2.238521 TCCAGGCATTTTGTGTTCTCC 58.761 47.619 0.00 0.00 0.00 3.71
1714 1775 3.810310 ACTACAGCAAGCCAGAGTATC 57.190 47.619 0.00 0.00 0.00 2.24
1740 1801 4.040217 AGGATGGAGTATGCTCTTCATCAC 59.960 45.833 22.18 15.20 39.78 3.06
1743 1804 3.181486 TGGAGTATGCTCTTCATCACGAC 60.181 47.826 10.82 0.00 41.38 4.34
1761 1822 0.603569 ACGTTCGAGGATCACTTGCT 59.396 50.000 0.00 0.00 33.17 3.91
1773 1834 4.806247 GGATCACTTGCTATGCCGATATAC 59.194 45.833 0.00 0.00 0.00 1.47
1779 1840 1.202382 GCTATGCCGATATACGACCCC 60.202 57.143 0.00 0.00 45.77 4.95
1852 1913 2.352421 CCTGACTTTGCTGCAGAAATGG 60.352 50.000 20.43 11.91 0.00 3.16
1869 1930 2.700773 GGACAACCTTCGCCATGCC 61.701 63.158 0.00 0.00 0.00 4.40
1902 1963 1.151677 TAACTTGCTCCCCACCCCT 60.152 57.895 0.00 0.00 0.00 4.79
1930 1991 9.403583 CCTTTATTTAGTTATGTTTAGCTGGGA 57.596 33.333 0.00 0.00 0.00 4.37
1959 2022 2.614057 GTGATTTACCCATGAAGGAGCG 59.386 50.000 0.00 0.00 41.22 5.03
1961 2024 2.107950 TTTACCCATGAAGGAGCGTG 57.892 50.000 0.00 0.00 41.22 5.34
1991 2054 5.858381 TCCCACTGCAATGTCTATTATCTC 58.142 41.667 0.00 0.00 0.00 2.75
1992 2055 4.687948 CCCACTGCAATGTCTATTATCTCG 59.312 45.833 0.00 0.00 0.00 4.04
1995 2058 7.093354 CCACTGCAATGTCTATTATCTCGTAT 58.907 38.462 0.00 0.00 0.00 3.06
1999 2062 9.283420 CTGCAATGTCTATTATCTCGTATACTG 57.717 37.037 0.56 0.00 0.00 2.74
2000 2063 7.755373 TGCAATGTCTATTATCTCGTATACTGC 59.245 37.037 0.56 0.00 0.00 4.40
2004 2067 8.617290 TGTCTATTATCTCGTATACTGCTTCA 57.383 34.615 0.56 0.00 0.00 3.02
2015 2078 9.119329 CTCGTATACTGCTTCATTAGTGTATTC 57.881 37.037 0.56 0.00 32.27 1.75
2048 2111 3.213506 TGACAAGGGAACATGAACTGTG 58.786 45.455 0.00 0.00 38.39 3.66
2064 2149 3.966979 ACTGTGATGTGGATGCCATTTA 58.033 40.909 0.00 0.00 35.28 1.40
2084 2169 9.362539 CCATTTATAGATGCCATGAATAAAAGC 57.637 33.333 0.00 0.00 0.00 3.51
2116 2201 9.090692 CTGAAATTTAAATGCTTGTATTCTGGG 57.909 33.333 0.39 0.00 0.00 4.45
2117 2202 8.811017 TGAAATTTAAATGCTTGTATTCTGGGA 58.189 29.630 0.39 0.00 0.00 4.37
2190 2287 6.677431 GCACAATCTGGAATTTCTCTTAGCAG 60.677 42.308 0.00 0.00 0.00 4.24
2249 2346 2.945008 TGTGAACTTGGAGACAGCAAAG 59.055 45.455 0.00 0.00 44.54 2.77
2270 2367 5.378230 AGGATTGCATTGATCAGAAGGTA 57.622 39.130 0.00 0.00 0.00 3.08
2288 2385 6.954684 AGAAGGTACCATTCTTCACTTCTCTA 59.045 38.462 15.94 0.00 38.95 2.43
2290 2387 7.741554 AGGTACCATTCTTCACTTCTCTAAT 57.258 36.000 15.94 0.00 0.00 1.73
2291 2388 7.560368 AGGTACCATTCTTCACTTCTCTAATG 58.440 38.462 15.94 0.00 0.00 1.90
2345 2442 7.305474 ACAAGTTCTCTTTACAGTTTTGTGTG 58.695 34.615 0.00 0.00 38.23 3.82
2419 2516 0.524862 CAGCAAATCAGAAAGCCGCT 59.475 50.000 0.00 0.00 0.00 5.52
2482 2579 2.044946 ATGCTTCCGTTGGCCCTC 60.045 61.111 0.00 0.00 0.00 4.30
2561 2658 5.765182 GTCCTTGATTCTCAGTCAGGAAAAA 59.235 40.000 0.00 0.00 30.32 1.94
2707 2804 0.827368 ATCTGCCGTTCTTCTCTCCC 59.173 55.000 0.00 0.00 0.00 4.30
2713 2810 3.181465 TGCCGTTCTTCTCTCCCAATATC 60.181 47.826 0.00 0.00 0.00 1.63
2731 2828 9.502091 CCCAATATCAGAGAATACGGAATTAAA 57.498 33.333 0.00 0.00 0.00 1.52
2767 2864 1.135689 CACCATGCTCGTAAGTTTGGC 60.136 52.381 0.00 0.00 39.48 4.52
2962 3059 6.240894 TGAAGCAGAGGTTGATAAAGTTGAT 58.759 36.000 0.00 0.00 0.00 2.57
3024 3121 1.895798 CTTGCCTACTGGTCAGTCTGA 59.104 52.381 6.91 0.00 42.54 3.27
3034 3131 2.554462 TGGTCAGTCTGAGAGTTCTTCG 59.446 50.000 1.75 0.00 0.00 3.79
3036 3133 1.197949 TCAGTCTGAGAGTTCTTCGCG 59.802 52.381 0.00 0.00 0.00 5.87
3099 3196 5.828299 TCTTTAATTGATAAGCAACGGGG 57.172 39.130 0.00 0.00 39.78 5.73
3115 3212 2.045926 GGCATGTCCGAGCAGGTT 60.046 61.111 0.00 0.00 41.99 3.50
3130 3227 6.824196 CCGAGCAGGTTCTCTCATACTATATA 59.176 42.308 0.00 0.00 34.51 0.86
3175 3272 1.766494 TGCAAGCATATTGGTCCTGG 58.234 50.000 0.00 0.00 0.00 4.45
3191 3288 9.707957 ATTGGTCCTGGTTTATGAATAATGTTA 57.292 29.630 0.00 0.00 0.00 2.41
3222 3319 5.600696 TGGTTTGAGCTGAAATCTTTTTCC 58.399 37.500 10.35 1.77 40.49 3.13
3230 3327 6.231211 AGCTGAAATCTTTTTCCGAGACTTA 58.769 36.000 0.00 0.00 40.49 2.24
3241 3338 2.362397 TCCGAGACTTATGCTCATCCAC 59.638 50.000 0.00 0.00 32.67 4.02
3248 3345 3.780294 ACTTATGCTCATCCACCTTGGTA 59.220 43.478 0.00 0.00 39.03 3.25
3249 3346 4.413520 ACTTATGCTCATCCACCTTGGTAT 59.586 41.667 0.00 0.00 39.03 2.73
3250 3347 2.715749 TGCTCATCCACCTTGGTATG 57.284 50.000 0.00 0.00 39.03 2.39
3253 3351 3.973305 TGCTCATCCACCTTGGTATGATA 59.027 43.478 5.91 0.00 39.03 2.15
3266 3364 6.039605 CCTTGGTATGATATGTTGAACATGCA 59.960 38.462 20.29 17.18 39.53 3.96
3269 3367 8.688747 TGGTATGATATGTTGAACATGCATAA 57.311 30.769 24.22 14.62 39.53 1.90
3277 3375 5.722263 TGTTGAACATGCATAATTCCTTGG 58.278 37.500 16.39 0.00 0.00 3.61
3278 3376 4.389890 TGAACATGCATAATTCCTTGGC 57.610 40.909 16.39 0.00 0.00 4.52
3281 3379 3.634504 ACATGCATAATTCCTTGGCTCA 58.365 40.909 0.00 0.00 0.00 4.26
3284 3382 5.129815 ACATGCATAATTCCTTGGCTCAAAT 59.870 36.000 0.00 0.00 0.00 2.32
3285 3383 5.266733 TGCATAATTCCTTGGCTCAAATC 57.733 39.130 0.00 0.00 0.00 2.17
3291 3389 3.348647 TCCTTGGCTCAAATCGAATCA 57.651 42.857 0.00 0.00 0.00 2.57
3293 3391 3.879295 TCCTTGGCTCAAATCGAATCATC 59.121 43.478 0.00 0.00 0.00 2.92
3295 3393 4.337555 CCTTGGCTCAAATCGAATCATCTT 59.662 41.667 0.00 0.00 0.00 2.40
3298 3396 4.813161 TGGCTCAAATCGAATCATCTTCTC 59.187 41.667 0.00 0.00 0.00 2.87
3330 3430 7.582435 TTGTTGAAACGCTTAATTTGTTTGA 57.418 28.000 5.03 0.00 36.06 2.69
3336 3436 7.968956 TGAAACGCTTAATTTGTTTGACACTTA 59.031 29.630 5.03 0.00 36.06 2.24
3338 3438 7.673810 ACGCTTAATTTGTTTGACACTTAAC 57.326 32.000 0.00 0.00 0.00 2.01
3373 3473 5.466728 AGTTGTGTGTTATGACTTAGCAGTG 59.533 40.000 0.00 0.00 31.22 3.66
3374 3474 3.745975 TGTGTGTTATGACTTAGCAGTGC 59.254 43.478 7.13 7.13 31.22 4.40
3377 3477 4.245660 GTGTTATGACTTAGCAGTGCTGA 58.754 43.478 27.97 18.86 40.10 4.26
3398 3498 6.562640 GCTGAGCACACACATTTGTAATTTTG 60.563 38.462 0.00 0.00 33.30 2.44
3430 3530 7.458409 AATAATGCCATAGTTCTAATGCCAG 57.542 36.000 0.00 0.00 0.00 4.85
3438 3538 6.322201 CCATAGTTCTAATGCCAGGTTTGATT 59.678 38.462 0.00 0.00 0.00 2.57
3451 3551 5.423886 CAGGTTTGATTAGAGGAGAAGGAC 58.576 45.833 0.00 0.00 0.00 3.85
3473 3573 3.228453 TCCGATAGTTTAGGCTGGTAGG 58.772 50.000 0.00 0.00 0.00 3.18
3478 3578 5.507650 CGATAGTTTAGGCTGGTAGGAACTC 60.508 48.000 0.00 0.00 41.75 3.01
3482 3582 0.044855 AGGCTGGTAGGAACTCCCAT 59.955 55.000 0.00 0.00 45.61 4.00
3525 3625 7.044052 GCACAATAAATCATCTTTCGTAAAGGC 60.044 37.037 7.27 0.00 39.01 4.35
3545 3645 2.224606 CGCATTCTCATGGTTGGCTAT 58.775 47.619 0.00 0.00 0.00 2.97
3547 3647 3.814842 CGCATTCTCATGGTTGGCTATTA 59.185 43.478 0.00 0.00 0.00 0.98
3548 3648 4.319766 CGCATTCTCATGGTTGGCTATTAC 60.320 45.833 0.00 0.00 0.00 1.89
3550 3650 5.049129 GCATTCTCATGGTTGGCTATTACTC 60.049 44.000 0.00 0.00 0.00 2.59
3551 3651 5.692115 TTCTCATGGTTGGCTATTACTCA 57.308 39.130 0.00 0.00 0.00 3.41
3552 3652 5.282055 TCTCATGGTTGGCTATTACTCAG 57.718 43.478 0.00 0.00 0.00 3.35
3553 3653 3.808728 TCATGGTTGGCTATTACTCAGC 58.191 45.455 0.00 0.00 38.35 4.26
3554 3654 3.455910 TCATGGTTGGCTATTACTCAGCT 59.544 43.478 0.00 0.00 39.09 4.24
3555 3655 4.080356 TCATGGTTGGCTATTACTCAGCTT 60.080 41.667 0.00 0.00 39.09 3.74
3556 3656 3.873910 TGGTTGGCTATTACTCAGCTTC 58.126 45.455 0.00 0.00 39.09 3.86
3557 3657 2.866762 GGTTGGCTATTACTCAGCTTCG 59.133 50.000 0.00 0.00 39.09 3.79
3558 3658 3.522553 GTTGGCTATTACTCAGCTTCGT 58.477 45.455 0.00 0.00 39.09 3.85
3559 3659 3.887621 TGGCTATTACTCAGCTTCGTT 57.112 42.857 0.00 0.00 39.09 3.85
3560 3660 4.994907 TGGCTATTACTCAGCTTCGTTA 57.005 40.909 0.00 0.00 39.09 3.18
3561 3661 4.679662 TGGCTATTACTCAGCTTCGTTAC 58.320 43.478 0.00 0.00 39.09 2.50
3562 3662 4.158949 TGGCTATTACTCAGCTTCGTTACA 59.841 41.667 0.00 0.00 39.09 2.41
3563 3663 5.163447 TGGCTATTACTCAGCTTCGTTACAT 60.163 40.000 0.00 0.00 39.09 2.29
3564 3664 5.175856 GGCTATTACTCAGCTTCGTTACATG 59.824 44.000 0.00 0.00 39.09 3.21
3565 3665 5.175856 GCTATTACTCAGCTTCGTTACATGG 59.824 44.000 0.00 0.00 36.07 3.66
3566 3666 4.530710 TTACTCAGCTTCGTTACATGGT 57.469 40.909 0.00 0.00 0.00 3.55
3567 3667 3.402628 ACTCAGCTTCGTTACATGGTT 57.597 42.857 0.00 0.00 0.00 3.67
3568 3668 4.530710 ACTCAGCTTCGTTACATGGTTA 57.469 40.909 0.00 0.00 0.00 2.85
3569 3669 4.890088 ACTCAGCTTCGTTACATGGTTAA 58.110 39.130 0.00 0.00 0.00 2.01
3570 3670 5.488341 ACTCAGCTTCGTTACATGGTTAAT 58.512 37.500 0.00 0.00 0.00 1.40
3571 3671 5.581085 ACTCAGCTTCGTTACATGGTTAATC 59.419 40.000 0.00 0.00 0.00 1.75
3572 3672 5.483811 TCAGCTTCGTTACATGGTTAATCA 58.516 37.500 0.00 0.00 0.00 2.57
3573 3673 6.112734 TCAGCTTCGTTACATGGTTAATCAT 58.887 36.000 0.00 0.00 0.00 2.45
3574 3674 7.269316 TCAGCTTCGTTACATGGTTAATCATA 58.731 34.615 0.00 0.00 0.00 2.15
3575 3675 7.931407 TCAGCTTCGTTACATGGTTAATCATAT 59.069 33.333 0.00 0.00 0.00 1.78
3576 3676 8.559536 CAGCTTCGTTACATGGTTAATCATATT 58.440 33.333 0.00 0.00 0.00 1.28
3577 3677 8.559536 AGCTTCGTTACATGGTTAATCATATTG 58.440 33.333 0.00 0.00 0.00 1.90
3578 3678 8.556194 GCTTCGTTACATGGTTAATCATATTGA 58.444 33.333 0.00 0.00 0.00 2.57
3581 3681 9.607988 TCGTTACATGGTTAATCATATTGAAGT 57.392 29.630 0.00 0.00 0.00 3.01
3582 3682 9.650371 CGTTACATGGTTAATCATATTGAAGTG 57.350 33.333 0.00 0.00 0.00 3.16
3633 3733 6.532302 TCAACATTGATGCATGCATTTAACTC 59.468 34.615 32.60 20.48 36.70 3.01
3646 3746 4.651994 CATTTAACTCTGAATCGGTGTGC 58.348 43.478 0.00 0.00 0.00 4.57
3651 3751 2.271800 CTCTGAATCGGTGTGCTAACC 58.728 52.381 0.00 0.00 36.82 2.85
3655 3755 0.035439 AATCGGTGTGCTAACCTGGG 60.035 55.000 0.00 0.00 38.14 4.45
3686 3786 5.852282 ATCCTCTTGACTAGAAGCTTCTC 57.148 43.478 31.67 18.44 38.70 2.87
3694 3794 3.697045 GACTAGAAGCTTCTCCTGCACTA 59.303 47.826 31.67 11.43 38.70 2.74
3710 3810 2.753452 GCACTACAGGCACAGTCTAGTA 59.247 50.000 0.00 0.00 0.00 1.82
3745 3845 1.801178 GAGAAAAAGCGCAGTACAGCT 59.199 47.619 11.47 6.68 46.97 4.24
3772 3872 6.837568 AGAAGAATATTGGCATGGATGTTCTT 59.162 34.615 17.11 17.11 42.55 2.52
3784 3884 6.237861 GCATGGATGTTCTTCGTAAGTACTTC 60.238 42.308 12.39 3.31 34.43 3.01
3817 3917 0.039326 AGGATGCTGCAAAGAGCCTT 59.961 50.000 6.36 0.00 44.83 4.35
3827 3927 0.846693 AAAGAGCCTTGGTGGTGAGT 59.153 50.000 0.00 0.00 38.35 3.41
3828 3928 0.846693 AAGAGCCTTGGTGGTGAGTT 59.153 50.000 0.00 0.00 38.35 3.01
3859 3959 4.212004 CCTAGTGTGTCACTTTGTCATGTG 59.788 45.833 7.70 0.00 42.59 3.21
3861 3961 4.454678 AGTGTGTCACTTTGTCATGTGAT 58.545 39.130 4.27 0.00 42.59 3.06
3864 3964 5.682862 GTGTGTCACTTTGTCATGTGATTTC 59.317 40.000 4.27 6.87 43.75 2.17
3901 4001 7.201444 CGTTTCTGTGTTGTGATATCTAGGTTC 60.201 40.741 3.98 0.00 0.00 3.62
3921 4021 8.383318 AGGTTCTATAAATGATTTCACGATGG 57.617 34.615 0.00 0.00 0.00 3.51
3922 4022 8.210946 AGGTTCTATAAATGATTTCACGATGGA 58.789 33.333 0.00 0.00 0.00 3.41
3986 4086 2.356382 CGCAGTTTGTCCAACAACCTTA 59.644 45.455 0.00 0.00 37.90 2.69
4016 4116 0.243365 GCCGCACACATGGAATTTCA 59.757 50.000 0.00 0.00 0.00 2.69
4055 4155 4.710324 AGATAAACAAGGTCAACCGTTCA 58.290 39.130 0.00 0.00 42.08 3.18
4088 4188 4.710324 TCCAAACTGTCATTAACTCGGTT 58.290 39.130 0.00 0.00 0.00 4.44
4103 4203 0.321671 CGGTTCATGGAGTGGACAGT 59.678 55.000 0.00 0.00 38.14 3.55
4121 4221 5.171339 ACAGTTCTTTGCAGTATGATCCT 57.829 39.130 0.00 0.00 39.69 3.24
4178 4278 4.180057 CAGAGAAGACTTCATTCCCTTCG 58.820 47.826 17.34 0.00 39.78 3.79
4193 4293 0.792640 CTTCGTGTGATGCTGTGTCC 59.207 55.000 0.00 0.00 0.00 4.02
4202 4302 0.254178 ATGCTGTGTCCAGTCCATCC 59.746 55.000 0.00 0.00 41.02 3.51
4280 4380 2.843113 ACCTGAAGGATGGGAAAGAGAG 59.157 50.000 2.62 0.00 38.94 3.20
4283 4383 3.774216 CTGAAGGATGGGAAAGAGAGAGT 59.226 47.826 0.00 0.00 0.00 3.24
4286 4386 2.238395 AGGATGGGAAAGAGAGAGTTGC 59.762 50.000 0.00 0.00 0.00 4.17
4345 4445 4.791676 CGATGAATTTCACATGCAGACAAG 59.208 41.667 0.15 0.00 0.00 3.16
4383 4483 2.205074 GTGATCACGCCTCTTATGGTG 58.795 52.381 10.69 0.00 42.85 4.17
4405 4505 6.238347 GGTGCGAATGTCACACATCATATTAA 60.238 38.462 0.00 0.00 37.97 1.40
4423 4523 9.958180 TCATATTAATTCTGAAGGAACACAAGA 57.042 29.630 0.00 0.00 36.70 3.02
4430 4530 4.580167 TCTGAAGGAACACAAGAACCATTG 59.420 41.667 0.00 0.00 36.22 2.82
4438 4538 4.934356 ACACAAGAACCATTGTATCCCAT 58.066 39.130 0.00 0.00 41.41 4.00
4475 4575 4.681483 GCTTTACATGACAAAGAAACAGGC 59.319 41.667 21.08 7.43 35.43 4.85
4489 4589 0.674895 ACAGGCTGCATCGAACCTTC 60.675 55.000 15.89 0.00 0.00 3.46
4490 4590 0.392193 CAGGCTGCATCGAACCTTCT 60.392 55.000 0.00 0.00 0.00 2.85
4491 4591 0.392193 AGGCTGCATCGAACCTTCTG 60.392 55.000 0.50 0.00 0.00 3.02
4494 4594 1.372087 CTGCATCGAACCTTCTGCCC 61.372 60.000 4.13 0.00 33.70 5.36
4529 4629 1.938585 TCAAGACTACCAGGGACCAG 58.061 55.000 0.00 0.00 0.00 4.00
4550 4650 1.263356 TAGTGGGAAGGAACTCACCG 58.737 55.000 0.00 0.00 41.65 4.94
4554 4654 2.434359 GAAGGAACTCACCGCCCG 60.434 66.667 0.00 0.00 38.49 6.13
4555 4655 4.699522 AAGGAACTCACCGCCCGC 62.700 66.667 0.00 0.00 38.49 6.13
4583 4683 9.229784 CAACAAGCAGATATTGATATGTTTGAC 57.770 33.333 13.65 0.00 43.97 3.18
4586 4686 7.413475 AGCAGATATTGATATGTTTGACGAC 57.587 36.000 0.00 0.00 0.00 4.34
4589 4689 6.420903 CAGATATTGATATGTTTGACGACCGT 59.579 38.462 0.00 0.00 0.00 4.83
4616 4716 2.038295 CAGGGAGCATACTCATCCTTCC 59.962 54.545 0.00 0.00 45.42 3.46
4643 4743 6.068461 TCTGGTATGACAGACTCTTCTAGT 57.932 41.667 0.00 0.00 42.26 2.57
4664 4764 2.036256 AGTGCATCAAGCCACCCC 59.964 61.111 0.00 0.00 44.83 4.95
4670 4770 1.269012 CATCAAGCCACCCCACATTT 58.731 50.000 0.00 0.00 0.00 2.32
4688 4788 2.922740 TTAAGAAGAACCCAGCACGT 57.077 45.000 0.00 0.00 0.00 4.49
4697 4797 0.470766 ACCCAGCACGTCCACTTAAA 59.529 50.000 0.00 0.00 0.00 1.52
4730 4830 0.602638 CTGCACTTACGGTCAAGGCA 60.603 55.000 0.00 0.00 33.54 4.75
4739 4839 0.233848 CGGTCAAGGCAACGTACAAC 59.766 55.000 0.00 0.00 46.39 3.32
4785 4885 1.829456 CCATCGATGGGCTGGTACA 59.171 57.895 32.99 0.00 44.31 2.90
4825 4925 2.613977 CCAAGAGGTTCAAGCTGTCGAT 60.614 50.000 0.00 0.00 0.00 3.59
4826 4926 2.376808 AGAGGTTCAAGCTGTCGATG 57.623 50.000 0.00 0.00 0.00 3.84
4853 4953 3.067833 GTTCCAGCTCAAGTACAAGGAC 58.932 50.000 0.00 0.00 0.00 3.85
4880 4980 1.221566 CGAGTGGGTCATCATGGCA 59.778 57.895 0.00 0.00 0.00 4.92
4889 4989 2.350522 GTCATCATGGCAAACGACTCT 58.649 47.619 0.00 0.00 0.00 3.24
5023 5123 4.264253 CAGCTGGAAGGACACAATTCATA 58.736 43.478 5.57 0.00 0.00 2.15
5039 5139 4.345859 TTCATAACACGGTGAGGAAGTT 57.654 40.909 16.29 0.00 0.00 2.66
5044 5144 6.425721 TCATAACACGGTGAGGAAGTTTAAAG 59.574 38.462 16.29 0.00 0.00 1.85
5195 5295 1.591504 TAGTGATCGTCGTGCAGGCA 61.592 55.000 0.35 0.00 0.00 4.75
5196 5296 1.811266 GTGATCGTCGTGCAGGCAT 60.811 57.895 0.35 0.00 0.00 4.40
5227 5327 3.463505 CGATGTCGTGCCTGTGAC 58.536 61.111 0.00 0.00 35.67 3.67
5232 5332 1.149361 TGTCGTGCCTGTGACGAAAC 61.149 55.000 0.00 0.00 46.71 2.78
5233 5333 1.947146 TCGTGCCTGTGACGAAACG 60.947 57.895 0.00 0.00 42.63 3.60
5259 5359 0.031716 TGGAGGTCCCTGAGAGGATG 60.032 60.000 0.00 0.00 37.67 3.51
5381 5481 3.154827 TGAATGTTTCTGGACTTCCCC 57.845 47.619 0.00 0.00 34.29 4.81
5447 5547 0.250858 CACATTGGCTGTCAGGGACA 60.251 55.000 1.14 0.00 40.50 4.02
5458 5565 2.371841 TGTCAGGGACACATAAACTGCT 59.628 45.455 0.00 0.00 37.67 4.24
5507 5614 6.074648 TGTAATTTTGGTGAAACTCCTGGAT 58.925 36.000 0.00 0.00 36.74 3.41
5516 5625 5.010617 GGTGAAACTCCTGGATTTTTAAGCA 59.989 40.000 12.58 4.49 36.74 3.91
5614 5729 0.740737 CCGCTCAACCATGGAATTCC 59.259 55.000 21.47 18.17 0.00 3.01
5646 5761 2.477694 CCTATGCTGAGATCGAGATCGC 60.478 54.545 9.40 9.40 42.48 4.58
5668 5783 1.737236 GTGCTTACATGTGGATGCGAA 59.263 47.619 9.11 0.00 32.14 4.70
5756 5872 2.754946 CAGCATGCCATTTTGGACTT 57.245 45.000 15.66 0.00 40.96 3.01
5759 5875 1.608542 GCATGCCATTTTGGACTTGCA 60.609 47.619 6.36 0.00 40.96 4.08
5820 5936 2.063979 ACAGCAGCTGCCGGGTATA 61.064 57.895 34.39 0.00 43.38 1.47
5866 5982 2.929592 GCTACCGTTTGTACTGGACTGG 60.930 54.545 0.00 0.06 0.00 4.00
5871 5987 3.512680 CGTTTGTACTGGACTGGATCTC 58.487 50.000 0.00 0.00 0.00 2.75
5990 6107 0.605319 ATCGGTGGTTGCGTTGTCAT 60.605 50.000 0.00 0.00 0.00 3.06
6015 6132 0.321919 AGCGAAAGAGATGCAGCCAA 60.322 50.000 0.00 0.00 0.00 4.52
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
54 56 0.746563 CGGCCGCCCTCTTTAAATGA 60.747 55.000 14.67 0.00 0.00 2.57
243 263 2.887568 CGGTGGCGCAGATCTGAC 60.888 66.667 27.04 16.37 0.00 3.51
274 294 1.684983 GGGATAAGGACGACGGATTGA 59.315 52.381 0.00 0.00 0.00 2.57
388 408 0.962356 CAGCTCCGGAACCATTTGCT 60.962 55.000 5.23 5.87 0.00 3.91
429 449 0.962356 CCCAATCAGCAGACCACACC 60.962 60.000 0.00 0.00 0.00 4.16
480 501 4.081420 GTCTAGCTCAGAACCTCCAATTCA 60.081 45.833 0.00 0.00 34.17 2.57
498 519 5.404366 TCCGACGAAACAAAATTCAGTCTAG 59.596 40.000 0.00 0.00 34.10 2.43
501 522 4.455124 CTCCGACGAAACAAAATTCAGTC 58.545 43.478 0.00 0.00 33.53 3.51
570 591 0.036294 GCAGGTTCCGGAAGCTTACT 60.036 55.000 39.24 21.17 45.80 2.24
571 592 0.036294 AGCAGGTTCCGGAAGCTTAC 60.036 55.000 39.24 32.63 45.80 2.34
572 593 0.690762 AAGCAGGTTCCGGAAGCTTA 59.309 50.000 39.24 7.52 45.80 3.09
573 594 0.606673 GAAGCAGGTTCCGGAAGCTT 60.607 55.000 39.24 34.88 45.80 3.74
575 596 0.606673 AAGAAGCAGGTTCCGGAAGC 60.607 55.000 33.87 33.87 35.51 3.86
577 598 1.953686 CAAAAGAAGCAGGTTCCGGAA 59.046 47.619 14.35 14.35 35.51 4.30
578 599 1.142060 TCAAAAGAAGCAGGTTCCGGA 59.858 47.619 0.00 0.00 35.51 5.14
579 600 1.604604 TCAAAAGAAGCAGGTTCCGG 58.395 50.000 8.80 0.00 35.51 5.14
580 601 3.568538 CAATCAAAAGAAGCAGGTTCCG 58.431 45.455 8.80 0.00 35.51 4.30
581 602 3.320626 GCAATCAAAAGAAGCAGGTTCC 58.679 45.455 8.80 0.00 35.51 3.62
582 603 3.006217 AGGCAATCAAAAGAAGCAGGTTC 59.994 43.478 4.00 4.00 35.08 3.62
583 604 2.967887 AGGCAATCAAAAGAAGCAGGTT 59.032 40.909 0.00 0.00 0.00 3.50
584 605 2.601905 AGGCAATCAAAAGAAGCAGGT 58.398 42.857 0.00 0.00 0.00 4.00
585 606 3.582780 GAAGGCAATCAAAAGAAGCAGG 58.417 45.455 0.00 0.00 0.00 4.85
586 607 3.240069 CGAAGGCAATCAAAAGAAGCAG 58.760 45.455 0.00 0.00 0.00 4.24
601 625 1.806542 TCTGAAATTGAGCACGAAGGC 59.193 47.619 0.00 0.00 0.00 4.35
605 629 6.422100 GCTCTATAATCTGAAATTGAGCACGA 59.578 38.462 22.44 0.00 44.84 4.35
608 632 6.283694 ACGCTCTATAATCTGAAATTGAGCA 58.716 36.000 24.61 0.00 45.36 4.26
614 638 8.506168 TCCAAAAACGCTCTATAATCTGAAAT 57.494 30.769 0.00 0.00 0.00 2.17
635 659 7.067615 GCTCTATAATCTATCCGTCTCATCCAA 59.932 40.741 0.00 0.00 0.00 3.53
643 667 7.335924 AGACAGAAGCTCTATAATCTATCCGTC 59.664 40.741 0.00 0.00 0.00 4.79
655 679 3.260380 AGCACACAAGACAGAAGCTCTAT 59.740 43.478 0.00 0.00 0.00 1.98
681 720 4.065088 CCTGTTTTCTGACGGATGAAGAA 58.935 43.478 0.00 0.00 0.00 2.52
682 721 3.323691 TCCTGTTTTCTGACGGATGAAGA 59.676 43.478 0.00 0.00 0.00 2.87
687 727 3.325135 AGAAGTCCTGTTTTCTGACGGAT 59.675 43.478 0.00 0.00 32.65 4.18
758 812 4.943705 AGTTCATCATCGGCACAATAACTT 59.056 37.500 0.00 0.00 0.00 2.66
763 817 1.402968 GCAGTTCATCATCGGCACAAT 59.597 47.619 0.00 0.00 0.00 2.71
800 854 5.060662 TGATACAGTGACTAAGCACACTC 57.939 43.478 0.00 0.00 44.07 3.51
801 855 5.468540 TTGATACAGTGACTAAGCACACT 57.531 39.130 0.00 0.00 46.32 3.55
802 856 6.539649 TTTTGATACAGTGACTAAGCACAC 57.460 37.500 0.00 0.00 41.19 3.82
803 857 5.179368 GCTTTTGATACAGTGACTAAGCACA 59.821 40.000 8.63 0.00 41.19 4.57
804 858 5.179368 TGCTTTTGATACAGTGACTAAGCAC 59.821 40.000 11.41 0.00 41.03 4.40
805 859 5.304778 TGCTTTTGATACAGTGACTAAGCA 58.695 37.500 11.41 11.41 42.91 3.91
806 860 5.409826 ACTGCTTTTGATACAGTGACTAAGC 59.590 40.000 6.98 6.98 42.83 3.09
807 861 6.870965 AGACTGCTTTTGATACAGTGACTAAG 59.129 38.462 0.00 0.00 44.40 2.18
808 862 6.759272 AGACTGCTTTTGATACAGTGACTAA 58.241 36.000 0.00 0.00 44.40 2.24
809 863 6.346477 AGACTGCTTTTGATACAGTGACTA 57.654 37.500 0.00 0.00 44.40 2.59
810 864 5.220710 AGACTGCTTTTGATACAGTGACT 57.779 39.130 0.00 0.00 44.40 3.41
851 905 4.976116 GTGCAACACAAGGACTGATTTAAC 59.024 41.667 0.00 0.00 36.32 2.01
878 932 7.080724 GTGTGTCCTTTCAAATCAGAATCTTC 58.919 38.462 0.00 0.00 0.00 2.87
888 942 4.637483 CACAGTGTGTGTCCTTTCAAAT 57.363 40.909 15.43 0.00 43.08 2.32
1012 1073 0.606401 CGGTTGGACTGTGAAGGCAT 60.606 55.000 0.00 0.00 0.00 4.40
1086 1147 3.028850 CCCATCAAAGTTCATCATGGCT 58.971 45.455 0.00 0.00 33.83 4.75
1167 1228 0.756294 ACATCTGGTGTGTGGACGAA 59.244 50.000 0.00 0.00 40.28 3.85
1326 1387 1.004745 GAACTCTTGGCCATTCTCCCA 59.995 52.381 6.09 0.00 0.00 4.37
1374 1435 4.347000 ACCAAACTAGTACTTCCTTGCTCA 59.653 41.667 0.00 0.00 0.00 4.26
1392 1453 1.953311 GCAATAGGCCTCGGAACCAAA 60.953 52.381 9.68 0.00 36.11 3.28
1608 1669 3.121019 CCGGTCTCCTCCTTAGCG 58.879 66.667 0.00 0.00 0.00 4.26
1714 1775 3.640498 TGAAGAGCATACTCCATCCTCAG 59.360 47.826 0.00 0.00 44.65 3.35
1737 1798 0.167470 GTGATCCTCGAACGTCGTGA 59.833 55.000 0.00 0.00 41.35 4.35
1740 1801 1.260206 CAAGTGATCCTCGAACGTCG 58.740 55.000 0.00 0.00 42.10 5.12
1743 1804 2.561733 TAGCAAGTGATCCTCGAACG 57.438 50.000 0.00 0.00 0.00 3.95
1761 1822 2.097036 CTGGGGTCGTATATCGGCATA 58.903 52.381 0.00 0.00 46.87 3.14
1839 1900 0.961019 GGTTGTCCATTTCTGCAGCA 59.039 50.000 9.47 0.00 0.00 4.41
1841 1902 2.095567 CGAAGGTTGTCCATTTCTGCAG 60.096 50.000 7.63 7.63 35.89 4.41
1852 1913 1.244019 AAGGCATGGCGAAGGTTGTC 61.244 55.000 14.30 0.00 0.00 3.18
1932 1993 7.068716 GCTCCTTCATGGGTAAATCACTATTTT 59.931 37.037 0.00 0.00 35.21 1.82
1936 1997 4.442893 CGCTCCTTCATGGGTAAATCACTA 60.443 45.833 0.00 0.00 36.20 2.74
1937 1998 3.682718 CGCTCCTTCATGGGTAAATCACT 60.683 47.826 0.00 0.00 36.20 3.41
1938 1999 2.614057 CGCTCCTTCATGGGTAAATCAC 59.386 50.000 0.00 0.00 36.20 3.06
1939 2000 2.238646 ACGCTCCTTCATGGGTAAATCA 59.761 45.455 0.00 0.00 36.20 2.57
1940 2001 2.614057 CACGCTCCTTCATGGGTAAATC 59.386 50.000 0.00 0.00 36.20 2.17
1959 2022 3.317993 ACATTGCAGTGGGAAGTAAACAC 59.682 43.478 14.25 0.00 35.43 3.32
1961 2024 3.821033 AGACATTGCAGTGGGAAGTAAAC 59.179 43.478 14.25 0.00 0.00 2.01
2015 2078 9.740239 CATGTTCCCTTGTCATGAAATTAATAG 57.260 33.333 0.00 0.00 40.64 1.73
2018 2081 7.773489 TCATGTTCCCTTGTCATGAAATTAA 57.227 32.000 0.00 0.00 42.87 1.40
2034 2097 3.411446 TCCACATCACAGTTCATGTTCC 58.589 45.455 0.00 0.00 41.41 3.62
2035 2098 4.673580 GCATCCACATCACAGTTCATGTTC 60.674 45.833 0.00 0.00 41.41 3.18
2048 2111 5.888105 GCATCTATAAATGGCATCCACATC 58.112 41.667 0.00 0.00 35.80 3.06
2116 2201 6.292381 GGACAGTGCAATATGAATACGAGTTC 60.292 42.308 0.00 0.00 0.00 3.01
2117 2202 5.523916 GGACAGTGCAATATGAATACGAGTT 59.476 40.000 0.00 0.00 0.00 3.01
2152 2237 2.362077 AGATTGTGCAAGAAACACCCAC 59.638 45.455 0.00 0.00 37.22 4.61
2207 2304 5.066117 CACAGCCTACAGAAGAGTTATACGA 59.934 44.000 0.00 0.00 0.00 3.43
2213 2310 3.643792 AGTTCACAGCCTACAGAAGAGTT 59.356 43.478 0.00 0.00 0.00 3.01
2249 2346 4.276926 GGTACCTTCTGATCAATGCAATCC 59.723 45.833 4.06 0.00 0.00 3.01
2255 2352 6.825213 TGAAGAATGGTACCTTCTGATCAATG 59.175 38.462 20.50 0.00 39.47 2.82
2258 2355 5.485353 AGTGAAGAATGGTACCTTCTGATCA 59.515 40.000 20.50 18.29 39.47 2.92
2270 2367 8.160106 AGAAACATTAGAGAAGTGAAGAATGGT 58.840 33.333 0.00 0.00 0.00 3.55
2288 2385 3.368013 CCATGATGCACAGCAGAAACATT 60.368 43.478 0.00 0.00 43.65 2.71
2290 2387 1.542472 CCATGATGCACAGCAGAAACA 59.458 47.619 0.00 0.00 43.65 2.83
2291 2388 1.814394 TCCATGATGCACAGCAGAAAC 59.186 47.619 0.00 0.00 43.65 2.78
2419 2516 8.690203 TTAGAACATCCAAAATCTCAGTGAAA 57.310 30.769 0.00 0.00 0.00 2.69
2482 2579 2.512692 TTGATGAAGGGACCCATGTG 57.487 50.000 14.60 0.00 0.00 3.21
2713 2810 8.989980 GGGTAATCTTTAATTCCGTATTCTCTG 58.010 37.037 0.00 0.00 0.00 3.35
2731 2828 0.249398 GGTGTGCGAGTGGGTAATCT 59.751 55.000 0.00 0.00 0.00 2.40
2809 2906 6.803154 TCTAGTATGTAGTCATCATCACCG 57.197 41.667 0.00 0.00 35.70 4.94
2893 2990 6.707608 TGCATATTCTTTGCATAGTACTGGAG 59.292 38.462 5.39 0.00 44.73 3.86
2926 3023 3.126831 CTCTGCTTCAGAAACTGTTCGT 58.873 45.455 0.00 0.00 40.18 3.85
2962 3059 6.761242 CCTTATACATTACTGCAGTACAAGCA 59.239 38.462 26.02 11.78 40.19 3.91
3024 3121 0.603569 ATCACCACGCGAAGAACTCT 59.396 50.000 15.93 0.00 0.00 3.24
3099 3196 1.078848 AGAACCTGCTCGGACATGC 60.079 57.895 0.00 0.00 36.31 4.06
3145 3242 6.207417 ACCAATATGCTTGCATAGAATACCAC 59.793 38.462 18.35 0.00 26.57 4.16
3149 3246 6.656270 CAGGACCAATATGCTTGCATAGAATA 59.344 38.462 18.35 0.14 0.00 1.75
3161 3258 6.655078 ATTCATAAACCAGGACCAATATGC 57.345 37.500 0.00 0.00 0.00 3.14
3188 3285 4.700213 TCAGCTCAAACCAGGCTAATTAAC 59.300 41.667 0.00 0.00 34.71 2.01
3191 3288 3.439857 TCAGCTCAAACCAGGCTAATT 57.560 42.857 0.00 0.00 34.71 1.40
3198 3295 5.693555 GGAAAAAGATTTCAGCTCAAACCAG 59.306 40.000 0.00 0.00 45.53 4.00
3201 3298 5.519722 TCGGAAAAAGATTTCAGCTCAAAC 58.480 37.500 0.00 0.00 45.53 2.93
3222 3319 2.363680 AGGTGGATGAGCATAAGTCTCG 59.636 50.000 0.00 0.00 33.41 4.04
3230 3327 2.779430 TCATACCAAGGTGGATGAGCAT 59.221 45.455 1.07 0.00 40.96 3.79
3241 3338 6.039605 TGCATGTTCAACATATCATACCAAGG 59.960 38.462 1.72 0.00 36.53 3.61
3248 3345 9.085645 AGGAATTATGCATGTTCAACATATCAT 57.914 29.630 21.05 16.91 36.53 2.45
3249 3346 8.467963 AGGAATTATGCATGTTCAACATATCA 57.532 30.769 21.05 4.97 36.53 2.15
3250 3347 9.188588 CAAGGAATTATGCATGTTCAACATATC 57.811 33.333 21.05 0.00 36.53 1.63
3253 3351 6.342906 CCAAGGAATTATGCATGTTCAACAT 58.657 36.000 21.05 0.00 39.91 2.71
3266 3364 6.547141 TGATTCGATTTGAGCCAAGGAATTAT 59.453 34.615 0.00 0.00 0.00 1.28
3269 3367 4.272489 TGATTCGATTTGAGCCAAGGAAT 58.728 39.130 0.00 0.00 0.00 3.01
3277 3375 5.980698 TGAGAAGATGATTCGATTTGAGC 57.019 39.130 0.00 0.00 0.00 4.26
3278 3376 7.536895 ACTTGAGAAGATGATTCGATTTGAG 57.463 36.000 0.00 0.00 0.00 3.02
3344 3444 9.884636 TGCTAAGTCATAACACACAACTAATAT 57.115 29.630 0.00 0.00 0.00 1.28
3345 3445 9.366216 CTGCTAAGTCATAACACACAACTAATA 57.634 33.333 0.00 0.00 0.00 0.98
3373 3473 3.624326 TTACAAATGTGTGTGCTCAGC 57.376 42.857 0.00 0.00 38.82 4.26
3374 3474 6.476380 ACAAAATTACAAATGTGTGTGCTCAG 59.524 34.615 0.00 0.00 38.82 3.35
3377 3477 6.572519 AGACAAAATTACAAATGTGTGTGCT 58.427 32.000 0.00 0.00 38.82 4.40
3405 3505 7.838079 TGGCATTAGAACTATGGCATTATTT 57.162 32.000 4.78 0.00 44.22 1.40
3413 3513 5.192927 TCAAACCTGGCATTAGAACTATGG 58.807 41.667 0.00 0.00 0.00 2.74
3424 3524 3.782523 TCTCCTCTAATCAAACCTGGCAT 59.217 43.478 0.00 0.00 0.00 4.40
3430 3530 5.666462 GAGTCCTTCTCCTCTAATCAAACC 58.334 45.833 0.00 0.00 37.22 3.27
3451 3551 3.256136 CCTACCAGCCTAAACTATCGGAG 59.744 52.174 0.00 0.00 0.00 4.63
3455 3555 5.221481 GGAGTTCCTACCAGCCTAAACTATC 60.221 48.000 0.00 0.00 0.00 2.08
3457 3557 4.028825 GGAGTTCCTACCAGCCTAAACTA 58.971 47.826 0.00 0.00 0.00 2.24
3473 3573 3.953612 TGGCATGTCAAATATGGGAGTTC 59.046 43.478 0.00 0.00 0.00 3.01
3478 3578 4.813027 GCTAATGGCATGTCAAATATGGG 58.187 43.478 3.01 0.00 41.35 4.00
3506 3606 3.438781 TGCGCCTTTACGAAAGATGATTT 59.561 39.130 4.18 0.00 41.02 2.17
3507 3607 3.006940 TGCGCCTTTACGAAAGATGATT 58.993 40.909 4.18 0.00 41.02 2.57
3525 3625 1.667236 TAGCCAACCATGAGAATGCG 58.333 50.000 0.00 0.00 0.00 4.73
3545 3645 4.530710 ACCATGTAACGAAGCTGAGTAA 57.469 40.909 0.00 0.00 0.00 2.24
3547 3647 3.402628 AACCATGTAACGAAGCTGAGT 57.597 42.857 0.00 0.00 0.00 3.41
3548 3648 5.580691 TGATTAACCATGTAACGAAGCTGAG 59.419 40.000 0.00 0.00 0.00 3.35
3550 3650 5.794687 TGATTAACCATGTAACGAAGCTG 57.205 39.130 0.00 0.00 0.00 4.24
3551 3651 8.559536 CAATATGATTAACCATGTAACGAAGCT 58.440 33.333 0.00 0.00 0.00 3.74
3552 3652 8.556194 TCAATATGATTAACCATGTAACGAAGC 58.444 33.333 0.00 0.00 0.00 3.86
3555 3655 9.607988 ACTTCAATATGATTAACCATGTAACGA 57.392 29.630 0.00 0.00 0.00 3.85
3556 3656 9.650371 CACTTCAATATGATTAACCATGTAACG 57.350 33.333 0.00 0.00 0.00 3.18
3557 3657 9.950680 CCACTTCAATATGATTAACCATGTAAC 57.049 33.333 0.00 0.00 0.00 2.50
3558 3658 9.130661 CCCACTTCAATATGATTAACCATGTAA 57.869 33.333 0.00 0.00 0.00 2.41
3559 3659 8.278639 ACCCACTTCAATATGATTAACCATGTA 58.721 33.333 0.00 0.00 0.00 2.29
3560 3660 7.125391 ACCCACTTCAATATGATTAACCATGT 58.875 34.615 0.00 0.00 0.00 3.21
3561 3661 7.587037 ACCCACTTCAATATGATTAACCATG 57.413 36.000 0.00 0.00 0.00 3.66
3562 3662 9.707957 TTAACCCACTTCAATATGATTAACCAT 57.292 29.630 0.00 0.00 0.00 3.55
3563 3663 9.535170 TTTAACCCACTTCAATATGATTAACCA 57.465 29.630 0.00 0.00 0.00 3.67
3568 3668 8.416329 GCAGATTTAACCCACTTCAATATGATT 58.584 33.333 0.00 0.00 0.00 2.57
3569 3669 7.560991 TGCAGATTTAACCCACTTCAATATGAT 59.439 33.333 0.00 0.00 0.00 2.45
3570 3670 6.889177 TGCAGATTTAACCCACTTCAATATGA 59.111 34.615 0.00 0.00 0.00 2.15
3571 3671 7.067372 TCTGCAGATTTAACCCACTTCAATATG 59.933 37.037 13.74 0.00 0.00 1.78
3572 3672 7.118723 TCTGCAGATTTAACCCACTTCAATAT 58.881 34.615 13.74 0.00 0.00 1.28
3573 3673 6.480763 TCTGCAGATTTAACCCACTTCAATA 58.519 36.000 13.74 0.00 0.00 1.90
3574 3674 5.324409 TCTGCAGATTTAACCCACTTCAAT 58.676 37.500 13.74 0.00 0.00 2.57
3575 3675 4.724399 TCTGCAGATTTAACCCACTTCAA 58.276 39.130 13.74 0.00 0.00 2.69
3576 3676 4.365514 TCTGCAGATTTAACCCACTTCA 57.634 40.909 13.74 0.00 0.00 3.02
3577 3677 4.082733 GGTTCTGCAGATTTAACCCACTTC 60.083 45.833 19.04 0.00 36.24 3.01
3578 3678 3.826729 GGTTCTGCAGATTTAACCCACTT 59.173 43.478 19.04 0.00 36.24 3.16
3579 3679 3.074538 AGGTTCTGCAGATTTAACCCACT 59.925 43.478 25.16 9.85 41.93 4.00
3580 3680 3.421844 AGGTTCTGCAGATTTAACCCAC 58.578 45.455 25.16 14.96 41.93 4.61
3581 3681 3.806949 AGGTTCTGCAGATTTAACCCA 57.193 42.857 25.16 4.21 41.93 4.51
3582 3682 5.099042 TCTAGGTTCTGCAGATTTAACCC 57.901 43.478 25.16 15.08 41.93 4.11
3620 3720 5.163723 ACACCGATTCAGAGTTAAATGCATG 60.164 40.000 0.00 0.00 0.00 4.06
3633 3733 2.002586 CAGGTTAGCACACCGATTCAG 58.997 52.381 0.00 0.00 42.33 3.02
3646 3746 5.604650 AGAGGATATCAAGAACCCAGGTTAG 59.395 44.000 1.09 0.00 38.60 2.34
3651 3751 5.130145 AGTCAAGAGGATATCAAGAACCCAG 59.870 44.000 4.83 0.00 0.00 4.45
3655 3755 7.651704 GCTTCTAGTCAAGAGGATATCAAGAAC 59.348 40.741 4.83 0.00 33.12 3.01
3694 3794 3.617531 GCATTGTACTAGACTGTGCCTGT 60.618 47.826 0.00 0.00 34.83 4.00
3710 3810 0.602638 TTCTCCGCAAGTCGCATTGT 60.603 50.000 2.12 0.00 42.60 2.71
3745 3845 5.698104 ACATCCATGCCAATATTCTTCTCA 58.302 37.500 0.00 0.00 0.00 3.27
3772 3872 3.015327 GCTCCCAGAGAAGTACTTACGA 58.985 50.000 8.42 0.00 0.00 3.43
3784 3884 1.202746 GCATCCTTTAGGCTCCCAGAG 60.203 57.143 0.00 0.00 34.44 3.35
3817 3917 1.148273 GTGCAGGAACTCACCACCA 59.852 57.895 0.00 0.00 34.60 4.17
3827 3927 0.685097 GACACACTAGGGTGCAGGAA 59.315 55.000 25.20 0.00 46.57 3.36
3828 3928 0.471022 TGACACACTAGGGTGCAGGA 60.471 55.000 25.20 3.46 46.57 3.86
3965 4065 3.250220 GGTTGTTGGACAAACTGCG 57.750 52.632 1.77 0.00 42.31 5.18
4016 4116 1.522355 CTTGCGAGATGGCCATCGT 60.522 57.895 34.48 24.48 42.48 3.73
4088 4188 3.743521 CAAAGAACTGTCCACTCCATGA 58.256 45.455 0.00 0.00 0.00 3.07
4121 4221 3.173151 TGGAACAAGAGATCCAGTAGCA 58.827 45.455 0.00 0.00 41.27 3.49
4202 4302 2.226330 TCATCCACAGTTTTCCCAACG 58.774 47.619 0.00 0.00 0.00 4.10
4345 4445 4.730949 TCACCACTGCCACTATAGTTAC 57.269 45.455 1.56 0.00 0.00 2.50
4372 4472 2.609459 GTGACATTCGCACCATAAGAGG 59.391 50.000 0.00 0.00 0.00 3.69
4383 4483 8.285394 AGAATTAATATGATGTGTGACATTCGC 58.715 33.333 0.00 0.00 39.27 4.70
4405 4505 4.792068 TGGTTCTTGTGTTCCTTCAGAAT 58.208 39.130 0.00 0.00 36.69 2.40
4430 4530 3.627577 CACTAACAGCACCAATGGGATAC 59.372 47.826 3.55 0.00 38.05 2.24
4438 4538 3.546724 TGTAAAGCACTAACAGCACCAA 58.453 40.909 0.00 0.00 0.00 3.67
4475 4575 1.372087 GGGCAGAAGGTTCGATGCAG 61.372 60.000 8.54 0.00 40.46 4.41
4489 4589 3.612247 CTTGGGAGGACACGGGCAG 62.612 68.421 0.00 0.00 0.00 4.85
4490 4590 3.636231 CTTGGGAGGACACGGGCA 61.636 66.667 0.00 0.00 0.00 5.36
4494 4594 0.321564 TTGATGCTTGGGAGGACACG 60.322 55.000 0.00 0.00 0.00 4.49
4529 4629 2.159085 CGGTGAGTTCCTTCCCACTATC 60.159 54.545 0.00 0.00 0.00 2.08
4550 4650 1.305219 TATCTGCTTGTTGTGCGGGC 61.305 55.000 0.00 0.00 37.40 6.13
4554 4654 6.732154 ACATATCAATATCTGCTTGTTGTGC 58.268 36.000 0.00 0.00 0.00 4.57
4555 4655 9.016623 CAAACATATCAATATCTGCTTGTTGTG 57.983 33.333 0.00 0.00 0.00 3.33
4556 4656 8.959548 TCAAACATATCAATATCTGCTTGTTGT 58.040 29.630 0.00 0.00 0.00 3.32
4583 4683 3.649277 CTCCCTGCCTTCACGGTCG 62.649 68.421 0.00 0.00 34.25 4.79
4586 4686 1.971505 TATGCTCCCTGCCTTCACGG 61.972 60.000 0.00 0.00 42.00 4.94
4589 4689 0.833287 GAGTATGCTCCCTGCCTTCA 59.167 55.000 0.00 0.00 42.00 3.02
4616 4716 3.360867 AGAGTCTGTCATACCAGAGGTG 58.639 50.000 0.00 0.00 41.93 4.00
4664 4764 4.613622 CGTGCTGGGTTCTTCTTAAATGTG 60.614 45.833 0.00 0.00 0.00 3.21
4670 4770 1.001633 GGACGTGCTGGGTTCTTCTTA 59.998 52.381 0.00 0.00 0.00 2.10
4688 4788 3.403038 GCTGCTCTTGTCTTTAAGTGGA 58.597 45.455 0.00 0.00 0.00 4.02
4730 4830 3.575399 GGTGTCTCCGTTGTACGTT 57.425 52.632 0.00 0.00 40.58 3.99
4785 4885 2.041620 TGGCTATTTCTTCCAGCAGGTT 59.958 45.455 0.00 0.00 37.02 3.50
4825 4925 2.067932 CTTGAGCTGGAACACCCCCA 62.068 60.000 0.00 0.00 0.00 4.96
4826 4926 1.303643 CTTGAGCTGGAACACCCCC 60.304 63.158 0.00 0.00 0.00 5.40
4853 4953 3.036783 GACCCACTCGTCCTCGTCG 62.037 68.421 0.00 0.00 38.33 5.12
4880 4980 2.757868 CTCCTGGAGATCAGAGTCGTTT 59.242 50.000 19.13 0.00 46.18 3.60
4889 4989 1.657751 CGACGCACTCCTGGAGATCA 61.658 60.000 29.71 0.00 33.32 2.92
5023 5123 4.773013 TCTTTAAACTTCCTCACCGTGTT 58.227 39.130 0.00 0.00 0.00 3.32
5044 5144 3.157087 TGAGGGCAACAAAAGATCCTTC 58.843 45.455 0.00 0.00 39.74 3.46
5059 5159 2.350522 CAGTATGACACAGTTGAGGGC 58.649 52.381 0.00 0.00 39.69 5.19
5071 5171 2.686915 ACTACACCTACCGCAGTATGAC 59.313 50.000 0.00 0.00 39.69 3.06
5195 5295 3.315142 ATCGTGCCTGCACCGTCAT 62.315 57.895 16.06 1.49 43.49 3.06
5196 5296 4.002506 ATCGTGCCTGCACCGTCA 62.003 61.111 16.06 0.00 43.49 4.35
5200 5300 3.490759 CGACATCGTGCCTGCACC 61.491 66.667 16.06 1.47 43.49 5.01
5211 5311 0.666274 TTCGTCACAGGCACGACATC 60.666 55.000 0.00 0.00 45.65 3.06
5224 5324 0.389757 TCCATGACACCGTTTCGTCA 59.610 50.000 0.00 0.00 45.62 4.35
5227 5327 0.320421 ACCTCCATGACACCGTTTCG 60.320 55.000 0.00 0.00 0.00 3.46
5232 5332 1.990060 AGGGACCTCCATGACACCG 60.990 63.158 0.00 0.00 38.24 4.94
5233 5333 4.153957 AGGGACCTCCATGACACC 57.846 61.111 0.00 0.00 38.24 4.16
5381 5481 5.520376 ACAAACAGAGAATTTGGAACCAG 57.480 39.130 2.84 0.00 40.64 4.00
5447 5547 6.346096 TCCGATTTAAGCTAGCAGTTTATGT 58.654 36.000 18.83 0.00 0.00 2.29
5458 5565 5.751586 AGGAAAACCATCCGATTTAAGCTA 58.248 37.500 0.00 0.00 44.60 3.32
5507 5614 2.884639 GTCAGCCAGTCCTGCTTAAAAA 59.115 45.455 0.00 0.00 36.81 1.94
5516 5625 4.521146 CAATAAGATTGTCAGCCAGTCCT 58.479 43.478 0.00 0.00 30.39 3.85
5614 5729 6.292757 CGATCTCAGCATAGGAAAAACAGATG 60.293 42.308 0.00 0.00 0.00 2.90
5646 5761 0.378257 GCATCCACATGTAAGCACGG 59.622 55.000 0.00 0.00 31.86 4.94
5756 5872 2.234661 AGTTCCATCTTCTGATCGTGCA 59.765 45.455 0.00 0.00 0.00 4.57
5759 5875 2.499289 AGCAGTTCCATCTTCTGATCGT 59.501 45.455 0.00 0.00 0.00 3.73
5810 5926 0.324923 ACTCCACAGTATACCCGGCA 60.325 55.000 0.00 0.00 0.00 5.69
5820 5936 4.160329 TCCTATCAACAGAACTCCACAGT 58.840 43.478 0.00 0.00 0.00 3.55
5866 5982 4.099573 TCCTATCGGTTGGACTTTGAGATC 59.900 45.833 0.00 0.00 0.00 2.75
5871 5987 2.671396 CGTTCCTATCGGTTGGACTTTG 59.329 50.000 0.00 0.00 31.24 2.77
5990 6107 3.525537 CTGCATCTCTTTCGCTAGGAAA 58.474 45.455 0.00 0.00 42.23 3.13


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

AutoCloner maintained by Alex Coulton.